Sample records for atomic code hullac

  1. Comparisons of laboratory wavelength measurements with theoretical calculations for neon-like through lithium-like argon, sulfur, and silicon

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Lepson, J K; Beiersdorfer, P; Behar, E

    Atomic structure codes have a difficult time accurately calculating the wavelengths of many-electron ions without the benefit of laboratory measurements. This is especially true for wavelengths of lines in the extreme ultraviolet and soft x-ray regions. We are using the low-energy capability of the Livermore electron beam ion traps to compile a comprehensive catalog of astrophysically relevant emission lines in support of satellite x-ray observations. Our database includes wavelength measurements, relative intensities, and line assignments, and is compared to a full set of calculations using the Hebrew University - Lawrence Livermore Atomic Code (HULLAC). Mean deviation of HULLAC calculations frommore » our measured wavelength values is highest for L-shell transitions of neon-like ions and lowest for lithium-like ions, ranging from a mean deviation of over 0.5 {angstrom} for Si V to 12 m{angstrom} in Ar XVI.« less

  2. Measuring the ionization balance of gold in a low-density plasma of importance to ICF

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    May, M; Beiersdorfer, P; Schneider, M

    Charge state distributions (CSDs) have been determined in low density ({approx}10 {sup 12} cm{sup -3}) gold plasmas having either a monoenergetic beam (E{sub Beam} = 2.66, 3.53 and 4.54 keV) or experimentally simulated thermal electron distributions (T{sub e} = 2.0, 2.5 and 3.0 keV). These plasmas were created in the Livermore electron beam ion traps EBIT-I and EBIT-II. Line emission and radiative recombination features of Ni to Kr-like gold ions were recorded in the x-ray region with a crystal spectrometer and a photometrically calibrated microcalorimeter. The CSDs in the experimentally simulated thermal plasmas were inferred by fitting the observed 4f{yields}3dmore » and 5f{yields}3d lines with synthetic spectra from the Hebrew University Lawrence Livermore Atomic Code (HULLAC). Additionally, the CSDs in the beam plasmas were inferred both from fitting the line emission and fitting the radiative recombination emission to calculations from the General Relativistic Atomic Structure Program (GRASP). Despite the relatively simple atomic physics in the low density plasma, differences existed between the experimental CSDs and the simulations from several available codes (e.g. RIGEL). Our experimental CSD relied upon accurate electron impact cross sections provided by HULLAC. To determine their reliability, we have experimentally determined the cross sections for several of the n=3{yields}4 and n=3{yields}5 excitations in Ni to Ga-like Au and compared them to distorted wave calculations. Recent Au spectra recorded during experiments at the HELEN laser facility are presented and compared with those from EBIT-I and EBIT-II.« less

  3. Measuring the Ionization Balance of Gold in a Low-Density Plasma of Importance to ICF

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    May, M.J.; Beiersdorfer, P.; Schneider, M.

    Charge state distributions (CSDs) have been determined in low density ({approx_equal}1012 cm-3) gold plasmas having either a monoenergetic beam (EBeam = 2.66, 3.53 and 4.54 keV) or experimentally simulated thermal electron distributions (Te = 2.0, 2.5 and 3.0 keV). These plasmas were created in the Livermore electron beam ion traps EBIT-I and EBIT-II. Line emission and radiative recombination features of Ni to Kr-like gold ions were recorded in the x-ray region with a crystal spectrometer and a photometrically calibrated microcalorimeter. The CSDs in the experimentally simulated thermal plasmas were inferred by fitting the observed 4f{yields}3d and 5f{yields}3d lines with syntheticmore » spectra from the Hebrew University Lawrence Livermore Atomic Code (HULLAC). Additionally, the CSDs in the beam plasmas were inferred both from fitting the line emission and fitting the radiative recombination emission to calculations from the General Relativistic Atomic Structure Program (GRASP). Despite the relatively simple atomic physics in the low density plasma, differences existed between the experimental CSDs and the simulations from several available codes (e.g. RIGEL). Our experimental CSD relied upon accurate electron impact cross sections provided by HULLAC. To determine their reliability, we have experimentally determined the cross sections for several of the n=3{yields}4 and n=3{yields}5 excitations in Ni to Ga-like Au and compared them to distorted wave calculations. Recent Au spectra recorded during experiments at the HELEN laser facility are presented and compared with those from EBIT-I and EB0011IT-.« less

  4. Wavelengths and energy levels for the Zn I isoelectronic sequence Sn{sup 20+} through U{sup 62+}

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Brown, C.M.; Seely, J.F.; Kania, D.R.

    Calculated and experimentally determined transition energies are presented for the Zn I isoelectronic sequence for the elements with atomic numbers Z = 50-92. The excitation energies were calculated for the 84 levels belonging to the 10 configurations of the type 4l4l{prime} by using the Hebrew University Lawrence Livermore Atomic Code (HULLAC). The analysis of the energy level structure along the isoelectronic sequence accounted for 20 avoided level crossings. The differences between the calculated and experimental transition energies were determined for 16 transitions, and the excitation energies of the levels belonging to the 4s4p, 4p{sup 2}, 4s4d, and 4s4f configurations weremore » derived from the semiempirically corrected transition energies. 16 refs., 3 figs., 1 tab.« less

  5. Accurate Wavelength Measurements and Modeling of Fe XV to Fe XIX Spectra Recorded in High-Density Plasmas between 13.5 and 17 Å

    NASA Astrophysics Data System (ADS)

    May, M. J.; Beiersdorfer, P.; Dunn, J.; Jordan, N.; Hansen, S. B.; Osterheld, A. L.; Faenov, A. Ya.; Pikuz, T. A.; Skobelev, I. Yu.; Flora, F.; Bollanti, S.; Di Lazzaro, P.; Murra, D.; Reale, A.; Reale, L.; Tomassetti, G.; Ritucci, A.; Francucci, M.; Martellucci, S.; Petrocelli, G.

    2005-06-01

    Iron spectra have been recorded from plasmas created at three different laser plasma facilities: the Tor Vergata University laser in Rome (Italy), the Hercules laser at ENEA in Frascati (Italy), and the Compact Multipulse Terawatt (COMET) laser at LLNL in California (USA). The measurements provide a means of identifying dielectronic satellite lines from Fe XVI and Fe XV in the vicinity of the strong 2p-->3d transitions of Fe XVII. About 80 Δn>=1 lines of Fe XV (Mg-like) to Fe XIX (O-like) were recorded between 13.8 and 17.1 Å with a high spectral resolution (λ/Δλ~4000) about 30 of these lines are from Fe XVI and Fe XV. The laser-produced plasmas had electron temperatures between 100 and 500 eV and electron densities between 1020 and 1022 cm-3. The Hebrew University Lawrence Livermore Atomic Code (HULLAC) was used to calculate the atomic structure and atomic rates for Fe XV-XIX. HULLAC was used to calculate synthetic line intensities at Te=200 eV and ne=1021 cm-3 for three different conditions to illustrate the role of opacity: optically thin plasmas with no excitation-autoionization/dielectronic recombination (EA/DR) contributions to the line intensities, optically thin plasmas that included EA/DR contributions to the line intensities, and optically thick plasmas (optical depth ~200 μm) that included EA/DR contributions to the line intensities. The optically thick simulation best reproduced the recorded spectrum from the Hercules laser. However, some discrepancies between the modeling and the recorded spectra remain.

  6. Accurate wavelength measurements and modeling of FeXV to FeXIX spectra recorded in high density plasmas between 13.5 to 17 A.

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    May, M; Beiersdorfer, P; Dunn, J

    Iron spectra have been recorded from plasmas created at three different laser plasma facilities, the Tor Vergata University laser in Rome (Italy), the Hercules laser at ENEA in Frascati (Italy), and the Compact Multipulse Terawatt (COMET) laser at LLNL in California (USA). The measurements provide a means of identifying dielectronic satellite lines from FeXVI and FeXV in the vicinity of the strong 2p {yields} 3d transitions of FeXVII. About 80 {Delta}n {ge} 1 lines of FeXV (Mg-like) to FeXIX (O-like) were recorded between 13.8 to 17.1 {angstrom} with a high spectral resolution ({lambda}/{Delta}{lambda} {approx} 4000), about thirty of these linesmore » are from FeXVI and FeXV. The laser produced plasmas had electron temperatures between 100 to 500 eV and electron densities between 10{sup 20} to 10{sup 22} cm{sup -3}. The Hebrew University Lawrence Livermore Atomic Code (HULLAC) was used to calculate the atomic structure and atomic rates for FeXV to FeXIX. HULLAC was used to calculate synthetic line intensities at T{sub e} = 200 eV and n{sub e} = 10{sup 21}cm{sup -3} for three different conditions to illustrate the role of opacity: optically thin plasmas with no excitation-autoionization/dielectronic recombination (EA/DR) contributions to the line intensities, optically thin plasmas that included EA/DR contributions to the line intensities, and optically thick plasmas (optical depth {approx} 200 {micro}m) that included EA/DR contributions to the line intensities. The optically thick simulation best reproduced the recorded spectrum from the Hercules laser. However some discrepancies between the modeling and the recorded spectra remain.« less

  7. Theoretical Study of Radiation from a Broad Range of Impurity Ions for Magnetic Fusion Diagnostics

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Safronova, Alla

    Spectroscopy of radiation emitted by impurities plays an important role in the study of magnetically confined fusion plasmas. The measurements of these impurities are crucial for the control of the general machine conditions, for the monitoring of the impurity levels, and for the detection of various possible fault conditions. Low-Z impurities, typically present in concentrations of 1%, are lithium, beryllium, boron, carbon, and oxygen. Some of the common medium-Z impurities are metals such as iron, nickel, and copper, and high-Z impurities, such as tungsten, are present in smaller concentrations of 0.1% or less. Despite the relatively small concentration numbers, themore » aforementioned impurities might make a substantial contribution to radiated power, and also influence both plasma conditions and instruments. A detailed theoretical study of line radiation from impurities that covers a very broad spectral range from less than 1 Å to more than 1000 Å has been accomplished and the results were applied to the LLNL Electron Beam Ion Trap (EBIT) and the Sustained Spheromak Physics Experiment (SSPX) and to the National Spherical Torus Experiment (NSTX) at Princeton. Though low- and medium-Z impurities were also studied, the main emphasis was made on the comprehensive theoretical study of radiation from tungsten using different state-of-the-art atomic structure codes such as Relativistic Many-Body Perturbation Theory (RMBPT). The important component of this research was a comparison of the results from the RMBPT code with other codes such as the Multiconfigurational Hartree–Fock developed by Cowan (COWAN code) and the Multiconfiguration Relativistic Hebrew University Lawrence Atomic Code (HULLAC code), and estimation of accuracy of calculations. We also have studied dielectronic recombination, an important recombination process for fusion plasma, for variety of highly and low charged tungsten ions using COWAN and HULLAC codes. Accurate DR rate coefficients are needed for describing the ionization balance of plasmas, which in turn determines the lines contributing to the spectral emission and the radiative power loss. In particular, we have calculated relativistic atomic data and corresponding dielectronic satellite spectra of highly ionized W ions, such as, for example, Li-like W (with the shortest wavelength of x-ray radiation of about 0.2 Å) that might exist in ITER core plasmas at very high temperatures of 30-40 keV. In addition, we have completed relativistic calculations of low ionized W ions from Lu-like (W3+) to Er-like (W6+) and for Sm-like(W12+) and Pm-like (W13+) that cover a spectral range from few hundred to thousand Å and are more relevant to the edge plasma diagnostics in tokamak.« less

  8. Statistical dielectronic recombination rates for multielectron ions in plasma

    NASA Astrophysics Data System (ADS)

    Demura, A. V.; Leont'iev, D. S.; Lisitsa, V. S.; Shurygin, V. A.

    2017-10-01

    We describe the general analytic derivation of the dielectronic recombination (DR) rate coefficient for multielectron ions in a plasma based on the statistical theory of an atom in terms of the spatial distribution of the atomic electron density. The dielectronic recombination rates for complex multielectron tungsten ions are calculated numerically in a wide range of variation of the plasma temperature, which is important for modern nuclear fusion studies. The results of statistical theory are compared with the data obtained using level-by-level codes ADPAK, FAC, HULLAC, and experimental results. We consider different statistical DR models based on the Thomas-Fermi distribution, viz., integral and differential with respect to the orbital angular momenta of the ion core and the trapped electron, as well as the Rost model, which is an analog of the Frank-Condon model as applied to atomic structures. In view of its universality and relative simplicity, the statistical approach can be used for obtaining express estimates of the dielectronic recombination rate coefficients in complex calculations of the parameters of the thermonuclear plasmas. The application of statistical methods also provides information for the dielectronic recombination rates with much smaller computer time expenditures as compared to available level-by-level codes.

  9. Anomalous photo-ionization of 4d shell in medium-Z ionized atoms

    NASA Astrophysics Data System (ADS)

    Klapisch, M.; Busquet, M.

    2013-09-01

    Photoionization (PI) cross sections (PICS) are necessary for the simulation of astrophysical and ICF plasmas. In order to be used in plasma modeling, the PICS are usually fit to simple analytical formulas. We observed an unusual spectral shape of the PICS of the 4d shell of ionized Xe and other elements, computed with different codes: a local minimum occurs around twice the threshold energy. We explain this phenomenon as interference between the bound 4d wavefunction and the free electron wavefunction, which is similar to the Cooper minima for neutral atoms. Consequently, the usual fitting formulas, which consist of a combination of inverse powers of the frequency beyond threshold, may yield rates for PI and radiative recombination (RR) that are incorrect by orders of magnitude. A new fitting algorithm is proposed and is included in the latest version of HULLAC.v9.5.

  10. Extreme Ultraviolet Emission Lines of Iron Fe XI-XIII

    NASA Astrophysics Data System (ADS)

    Lepson, Jaan; Beiersdorfer, P.; Brown, G. V.; Liedahl, D. A.; Brickhouse, N. S.; Dupree, A. K.

    2013-04-01

    The extreme ultraviolet (EUV) spectral region (ca. 20--300 Å) is rich in emission lines from low- to mid-Z ions, particularly from the middle charge states of iron. Many of these emission lines are important diagnostics for astrophysical plasmas, providing information on properties such as elemental abundance, temperature, density, and even magnetic field strength. In recent years, strides have been made to understand the complexity of the atomic levels of the ions that emit the lines that contribute to the richness of the EUV region. Laboratory measurements have been made to verify and benchmark the lines. Here, we present laboratory measurements of Fe XI, Fe XII, and Fe XIII between 40-140 Å. The measurements were made at the Lawrence Livermore electron beam ion trap (EBIT) facility, which has been optimized for laboratory astrophysics, and which allows us to select specific charge states of iron to help line identification. We also present new calculations by the Hebrew University - Lawrence Livermore Atomic Code (HULLAC), which we also utilized for line identification. We found that HULLAC does a creditable job of reproducing the forest of lines we observed in the EBIT spectra, although line positions are in need of adjustment, and line intensities often differed from those observed. We identify or confirm a number of new lines for these charge states. This work was supported by the NASA Solar and Heliospheric Program under Contract NNH10AN31I and the DOE General Plasma Science program. Work was performed in part under the auspices of the Department of Energy by Lawrence Livermore National Laboratory under Contract DEAC52-07NA27344.

  11. Spectroscopic diagnostics of tungsten-doped CH plasmas

    NASA Astrophysics Data System (ADS)

    Klapisch, M.; Colombant, D.; Lehecka, T.

    1998-11-01

    Spectra of CH with different concentrations of W dopant and laser intensities ( 2.5-10 x10^12 W/cm^2 ) were obtained at NRL with the Nike Laser. They were recorded in the 100-500 eV range with an XUV grating spectrometer. The hydrodynamic simulations are performed with the 1D code FAST1D(J. H. Gardner et al., Phys. Plasmas, 5, May (1998).) where non LTE effects are introduced by Busquet's model( M. Busquet, Phys. Fluids B, 5, 4191 (1993); M. Klapisch, A. Bar-Shalom, J. Oreg and D. Colombant, Phys. Plasmas, 5, May (1998).). They are then post-processed with TRANSPEC( O. Peyrusse, J. Quant. Spectrosc. Radiat. Transfer, 51, 281 (1994)), a time dependent collisional radiative code with radiation coupling. The necessary atomic data are obtained from the HULLAC code( M. Klapisch and A. Bar-Shalom, J. Quant. Spectrosc. Radiat. Transfer, 58, 687 (1997).). The post processing and diagnostics were performed on carbon lines and the results are compared with the experimental data.

  12. Benchmarking atomic physics models for magnetically confined fusion plasma physics experiments

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    May, M.J.; Finkenthal, M.; Soukhanovskii, V.

    In present magnetically confined fusion devices, high and intermediate {ital Z} impurities are either puffed into the plasma for divertor radiative cooling experiments or are sputtered from the high {ital Z} plasma facing armor. The beneficial cooling of the edge as well as the detrimental radiative losses from the core of these impurities can be properly understood only if the atomic physics used in the modeling of the cooling curves is very accurate. To this end, a comprehensive experimental and theoretical analysis of some relevant impurities is undertaken. Gases (Ne, Ar, Kr, and Xe) are puffed and nongases are introducedmore » through laser ablation into the FTU tokamak plasma. The charge state distributions and total density of these impurities are determined from spatial scans of several photometrically calibrated vacuum ultraviolet and x-ray spectrographs (3{endash}1600 {Angstrom}), the multiple ionization state transport code transport code (MIST) and a collisional radiative model. The radiative power losses are measured with bolometery, and the emissivity profiles were measured by a visible bremsstrahlung array. The ionization balance, excitation physics, and the radiative cooling curves are computed from the Hebrew University Lawrence Livermore atomic code (HULLAC) and are benchmarked by these experiments. (Supported by U.S. DOE Grant No. DE-FG02-86ER53214 at JHU and Contract No. W-7405-ENG-48 at LLNL.) {copyright} {ital 1999 American Institute of Physics.}« less

  13. Spectroscopics database for warm Xenon and Iron in Astrophysics and Laboratory Astrophysics conditions

    NASA Astrophysics Data System (ADS)

    Busquet, Michel; Klapisch, Marcel; Bar-Shalom, Avi; Oreg, Josse

    2010-11-01

    The main contribution to spectral properties of astrophysics mixtures come often from Iron. On the other hand, in the so-called domain of ``Laboratory Astrophysics,'' where astrophysics phenomena are scaled down to the laboratory, Xenon (and Argon) are commonly used gases. At so called ``warm'' temperatures (T=5-50eV), L-shell Iron and M-shell Xenon present a very large number of spectral lines, originating from billions of levels. More often than not, Local Thermodynamical Equilibrium is assumed, leading to noticeable simplification of the computation. Nevertheless, complex and powerful atomic structure codes are required. We take benefit of powerful statistics and numerics, included in our atomic structure codes, STA[1] and HULLAC[2], to generate the required spectra. Recent improvements in both fields (statistics, numerics and convergence control) allow obtaining large databases (ro x T grid of > 200x200 points, and > 10000 frequencies) for temperature down to a few eV. We plan to port these improvements in the NLTE code SCROLL[3]. [1] A.Bar-Shalom, et al, Phys. Rev. A 40, 3183 (1989) [2] M.Busquet,et al, J.Phys. IV France 133, 973-975 (2006); A.Bar-Shalom, M.Klapisch, J.Oreg, J.Oreg, JQSRT 71, 169, (2001) [3] A.Bar-Shalom, et al, Phys. Rev. E 56, R70 (1997)

  14. Emission line spectra of S VII ? S XIV in the 20 ? 75 ? wavelength region

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Lepson, J K; Beiersdorfer, P; Behar, E

    As part of a larger project to complete a comprehensive catalogue of astrophysically relevant emission lines in support of new-generation X-ray observatories using the Lawrence Livermore electron beam ion traps EBIT-I and EBIT-II, the authors present observations of sulfur lines in the soft X-ray and extreme ultraviolet regions. The database includes wavelength measurements with standard errors, relative intensities, and line assignments for 127 transitions of S VII through S XIV between 20 and 75 {angstrom}. The experimental data are complemented with a full set of calculations using the Hebrew University Lawrence Livermore Atomic Code (HULLAC). A comparison of the laboratorymore » data with Chandra measurements of Procyon allows them to identify S VII-S XI lines.« less

  15. A New Non-LTE Model based on Super Configurations

    NASA Astrophysics Data System (ADS)

    Bar-Shalom, A.; Klapisch, M.

    1996-11-01

    Non-LTE effects are vital for the simulation of radiation in hot plasmas involving even medium Z materials. However, the exceedingly large number of atomic energy levels forbids using a detailed collisional radiative model on-line in the hydrodynamic simulations. For this purpose, greatly simplified models are required. We implemented recently Busquet's model(M. Busquet, Phys. Fluids B, 5, 4191 (1993)) in NRL's RAD2D Hydro code in conservative form (M. Klapisch et al., Bull. Am. Phys. Soc., 40, 1806 (1995), and poster at this meeting.). This model is quick and the results make sense, but in the absence of precisely defined experiments, it is difficult to asses its accuracy. We present here a new collisional radiative model based on superconfigurations( A. Bar-Shalom, J. Oreg, J. F. Seely, U. Feldman, C. M. Brown, B. A. Hammel, R. W. Lee and C. A. Back, Phys. Rev. E, 52, 6686 (1995).), intended to be a benchmark for approximate models used in hydro-codes. It uses accurate rates from the HULLAC Code. Results for various elements will be presented and compared with RADIOM.

  16. Benchmarking statistical averaging of spectra with HULLAC

    NASA Astrophysics Data System (ADS)

    Klapisch, Marcel; Busquet, Michel

    2008-11-01

    Knowledge of radiative properties of hot plasmas is important for ICF, astrophysics, etc When mid-Z or high-Z elements are present, the spectra are so complex that one commonly uses statistically averaged description of atomic systems [1]. In a recent experiment on Fe[2], performed under controlled conditions, high resolution transmission spectra were obtained. The new version of HULLAC [3] allows the use of the same model with different levels of details/averaging. We will take advantage of this feature to check the effect of averaging with comparison with experiment. [1] A Bar-Shalom, J Oreg, and M Klapisch, J. Quant. Spectros. Rad. Transf. 65, 43 (2000). [2] J. E. Bailey, G. A. Rochau, C. A. Iglesias et al., Phys. Rev. Lett. 99, 265002-4 (2007). [3]. M. Klapisch, M. Busquet, and A. Bar-Shalom, AIP Conference Proceedings 926, 206-15 (2007).

  17. A comparison between detailed and configuration-averaged collisional-radiative codes applied to nonlocal thermal equilibrium plasmas

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Poirier, M.; Gaufridy de Dortan, F. de

    A collisional-radiative model describing nonlocal-thermodynamic-equilibrium plasmas is developed. It is based on the HULLAC (Hebrew University Lawrence Livermore Atomic Code) suite for the transitions rates, in the zero-temperature radiation field hypothesis. Two variants of the model are presented: the first one is configuration averaged, while the second one is a detailed level version. Comparisons are made between them in the case of a carbon plasma; they show that the configuration-averaged code gives correct results for an electronic temperature T{sub e}=10 eV (or higher) but fails at lower temperatures such as T{sub e}=1 eV. The validity of the configuration-averaged approximation ismore » discussed: the intuitive criterion requiring that the average configuration-energy dispersion must be less than the electron thermal energy turns out to be a necessary but far from sufficient condition. Another condition based on the resolution of a modified rate-equation system is proposed. Its efficiency is emphasized in the case of low-temperature plasmas. Finally, it is shown that near-threshold autoionization cascade processes may induce a severe failure of the configuration-average formalism.« less

  18. Opacity of iron, nickel, and copper plasmas in the x-ray wavelength range: Theoretical interpretation of 2p-3d absorption spectra

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Blenski, T.; Loisel, G.; Poirier, M.

    2011-09-15

    This paper deals with theoretical studies on the 2p-3d absorption in iron, nickel, and copper plasmas related to LULI2000 (Laboratoire pour l'Utilisation des Lasers Intenses, 2000J facility) measurements in which target temperatures were of the order of 20 eV and plasma densities were in the range 0.004-0.01 g/cm{sup 3}. The radiatively heated targets were close to local thermodynamic equilibrium (LTE). The structure of 2p-3d transitions has been studied with the help of the statistical superconfiguration opacity code sco and with the fine-structure atomic physics codes hullac and fac. A new mixed version of the sco code allowing one to treatmore » part of the configurations by detailed calculation based on the Cowan's code rcg has been also used in these comparisons. Special attention was paid to comparisons between theory and experiment concerning the term features which cannot be reproduced by sco. The differences in the spin-orbit splitting and the statistical (thermal) broadening of the 2p-3d transitions have been investigated as a function of the atomic number Z. It appears that at the conditions of the experiment the role of the term and configuration broadening was different in the three analyzed elements, this broadening being sensitive to the atomic number. Some effects of the temperature gradients and possible non-LTE effects have been studied with the help of the radiative-collisional code scric. The sensitivity of the 2p-3d structures with respect to temperature and density in medium-Z plasmas may be helpful for diagnostics of LTE plasmas especially in future experiments on the {Delta}n=0 absorption in medium-Z plasmas for astrophysical applications.« less

  19. Signature of chaos in the 4 f -core-excited states for highly-charged tungsten ions

    NASA Astrophysics Data System (ADS)

    Safronova, Ulyana; Safronova, Alla

    2014-05-01

    We evaluate radiative and autoionizing transition rates in highly charged W ions in search for the signature of chaos. In particularly, previously published results for Ag-like W27+, Tm-like W5+, and Yb-like W4+ ions as well as newly obtained for I-like W21+, Xe-like W20+, Cs-like W19+, and La-like W17+ ions (with ground configuration [Kr] 4d10 4fk with k = 7, 8, 9, and 11, respectively) are considered that were calculated using the multiconfiguration relativistic Hebrew University Lawrence Livermore Atomic Code (HULLAC code) and the Hartree-Fock-Relativistic method (COWAN code). The main emphasis was on verification of Gaussian statistics of rates as a function of transition energy. There was no evidence of such statistics for above mentioned previously published results as well as for the transitions between the excited and autoionizing states for newly calculated results. However, we did find the Gaussian profile for the transitions between excited states such as the [Kr] 4d10 4fk - [Kr] 4d10 4f k - 1 5 d transitions , for newly calculated W ions. This work is supported in part by DOE under NNSA Cooperative Agreement DE-NA0001984.

  20. Modeling of radiative properties of Sn plasmas for extreme-ultraviolet source

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Sasaki, Akira; Sunahara, Atsushi; Furukawa, Hiroyuki

    Atomic processes in Sn plasmas are investigated for application to extreme-ultraviolet (EUV) light sources used in microlithography. We develop a full collisional radiative (CR) model of Sn plasmas based on calculated atomic data using Hebrew University Lawrence Livermore Atomic Code (HULLAC). Resonance and satellite lines from singly and multiply excited states of Sn ions, which contribute significantly to the EUV emission, are identified and included in the model through a systematic investigation of their effect on the emission spectra. The wavelengths of the 4d-4f+4p-4d transitions of Sn{sup 5+} to Sn{sup 13+} are investigated, because of their importance for determining themore » conversion efficiency of the EUV source, in conjunction with the effect of configuration interaction in the calculation of atomic structure. Calculated emission spectra are compared with those of charge exchange spectroscopy and of laser produced plasma EUV sources. The comparison is also carried out for the opacity of a radiatively heated Sn sample. A reasonable agreement is obtained between calculated and experimental EUV emission spectra observed under the typical condition of EUV sources with the ion density and ionization temperature of the plasma around 10{sup 18} cm{sup -3} and 20 eV, respectively, by applying a wavelength correction to the resonance and satellite lines. Finally, the spectral emissivity and opacity of Sn plasmas are calculated as a function of electron temperature and ion density. The results are useful for radiation hydrodynamics simulations for the optimization of EUV sources.« less

  1. A study of tungsten spectra using large helical device and compact electron beam ion trap in NIFS

    NASA Astrophysics Data System (ADS)

    Morita, S.; Dong, C. F.; Goto, M.; Kato, D.; Murakami, I.; Sakaue, H. A.; Hasuo, M.; Koike, F.; Nakamura, N.; Oishi, T.; Sasaki, A.; Wang, E. H.

    2013-07-01

    Tungsten spectra have been observed from Large Helical Device (LHD) and Compact electron Beam Ion Trap (CoBIT) in wavelength ranges of visible to EUV. The EUV spectra with unresolved transition array (UTA), e.g., 6g-4f, 5g-4f, 5f-4d and 5p-4d transitions for W+24-+33, measured from LHD plasmas are compared with those measured from CoBIT with monoenergetic electron beam (≤2keV). The tungsten spectra from LHD are well analyzed based on the knowledge from CoBIT tungsten spectra. The C-R model code has been developed to explain the UTA spectra in details. Radial profiles of EUV spectra from highly ionized tungsten ions have been measured and analyzed by impurity transport simulation code with ADPAK atomic database code to examine the ionization balance determined by ionization and recombination rate coefficients. As the first trial, analysis of the tungsten density in LHD plasmas is attempted from radial profile of Zn-like WXLV (W44+) 4p-4s transition at 60.9Å based on the emission rate coefficient calculated with HULLAC code. As a result, a total tungsten ion density of 3.5×1010cm-3 at the plasma center is reasonably obtained. In order to observe the spectra from tungsten ions in lower-ionized charge stages, which can give useful information on the tungsten influx in fusion plasmas, the ablation cloud of the impurity pellet is directly measured with visible spectroscopy. A lot of spectra from neutral and singly ionized tungsten are observed and some of them are identified. A magnetic forbidden line from highly ionized tungsten ions has been examined and Cd-like WXXVII (W26+) at 3893.7Å is identified as the ground-term fine-structure transition of 4f23H5-3H4. The possibility of α particle diagnostic in D-T burning plasmas using the magnetic forbidden line is discussed.

  2. A study of tungsten spectra using large helical device and compact electron beam ion trap in NIFS

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Morita, S.; Goto, M.; Murakami, I.

    2013-07-11

    Tungsten spectra have been observed from Large Helical Device (LHD) and Compact electron Beam Ion Trap (CoBIT) in wavelength ranges of visible to EUV. The EUV spectra with unresolved transition array (UTA), e.g., 6g-4f, 5g-4f, 5f-4d and 5p-4d transitions for W{sup +24-+33}, measured from LHD plasmas are compared with those measured from CoBIT with monoenergetic electron beam ({<=}2keV). The tungsten spectra from LHD are well analyzed based on the knowledge from CoBIT tungsten spectra. The C-R model code has been developed to explain the UTA spectra in details. Radial profiles of EUV spectra from highly ionized tungsten ions have beenmore » measured and analyzed by impurity transport simulation code with ADPAK atomic database code to examine the ionization balance determined by ionization and recombination rate coefficients. As the first trial, analysis of the tungsten density in LHD plasmas is attempted from radial profile of Zn-like WXLV (W{sup 44+}) 4p-4s transition at 60.9A based on the emission rate coefficient calculated with HULLAC code. As a result, a total tungsten ion density of 3.5 Multiplication-Sign 10{sup 10}cm{sup -3} at the plasma center is reasonably obtained. In order to observe the spectra from tungsten ions in lower-ionized charge stages, which can give useful information on the tungsten influx in fusion plasmas, the ablation cloud of the impurity pellet is directly measured with visible spectroscopy. A lot of spectra from neutral and singly ionized tungsten are observed and some of them are identified. A magnetic forbidden line from highly ionized tungsten ions has been examined and Cd-like WXXVII (W{sup 26+}) at 3893.7A is identified as the ground-term fine-structure transition of 4f{sup 23}H{sub 5}-{sup 3}H{sub 4}. The possibility of {alpha} particle diagnostic in D-T burning plasmas using the magnetic forbidden line is discussed.« less

  3. Effects of quantum interference between radiative and dielectronic recombination on photorecombination cross-section profiles for the He-like ions Ar{sup 16+} and Fe{sup 24+}

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Behar, Ehud; Jacobs, Verne L.; Oreg, Joseph

    Total cross sections for electron-ion photorecombination (PR) processes are calculated using a projection-operator and resolvent-operator approach. This approach provides a unified quantum-mechanical description of the combined electron-ion PR process, including radiative and dielectronic recombination as coherent, interfering components. An especially adapted version of the Hebrew-University Lawrence-Livermore Atomic Code HULLAC is developed and employed for the calculations. In particular, PR cross sections for He-like argon and iron ions are calculated for incident-electron energies in the vicinity of the 1s2l2l{sup '} and 1s2l3l{sup '} doubly-excited, autoionizing levels of the Li-like ions. Significant effects of quantum interference between radiative and dielectronic recombination, inmore » the form of asymmetric PR cross-section profiles, are predicted, especially for weak transitions. The general behavior of the interference effect, as a function of the ion charge q and as a function of the principal quantum number n{sup '} of the outer electron in the autoionizing state, is investigated using a hydrogenic-scaling analysis. It is found that the degree of asymmetry in the PR cross-section profile can be substantial for close-to-neutral ions and also for very highly-charged ions. In the intermediate-charge regime, on the other hand, the asymmetry is anticipated to be less prominent. The dependence of the quantum-interference effect on n{sup '} is predicted to be much weaker.« less

  4. X-ray Spectral Formation In High-mass X-ray Binaries: The Case Of Vela X-1

    NASA Astrophysics Data System (ADS)

    Akiyama, Shizuka; Mauche, C. W.; Liedahl, D. A.; Plewa, T.

    2007-05-01

    We are working to develop improved models of radiatively-driven mass flows in the presence of an X-ray source -- such as in X-ray binaries, cataclysmic variables, and active galactic nuclei -- in order to infer the physical properties that determine the X-ray spectra of such systems. The models integrate a three-dimensional time-dependent hydrodynamics capability (FLASH); a comprehensive and uniform set of atomic data, improved calculations of the line force multiplier that account for X-ray photoionization and non-LTE population kinetics, and X-ray emission-line models appropriate to X-ray photoionized plasmas (HULLAC); and a Monte Carlo radiation transport code that simulates Compton scattering and recombination cascades following photoionization. As a test bed, we have simulated a high-mass X-ray binary with parameters appropriate to Vela X-1. While the orbital and stellar parameters of this system are well constrained, the physics of X-ray spectral formation is less well understood because the canonical analytical wind velocity profile of OB stars does not account for the dynamical and radiative feedback effects due to the rotation of the system and to the irradiation of the stellar wind by X-rays from the neutron star. We discuss the dynamical wind structure of Vela X-1 as determined by the FLASH simulation, where in the binary the X-ray emission features originate, and how the spatial and spectral properties of the X-ray emission features are modified by Compton scattering, photoabsorption, and fluorescent emission. This work was performed under the auspices of the U.S. Department of Energy by University of California, Lawrence Livermore National Laboratory under Contract W-7405-Eng-48.

  5. The measurement of the intrinsic impurities of molybdenum and carbon in the Alcator C-Mod tokamak plasma using low resolution spectroscopy

    NASA Astrophysics Data System (ADS)

    May, M. J.; Finkenthal, M.; Regan, S. P.; Moos, H. W.; Terry, J. L.; Goetz, J. A.; Graf, M. A.; Rice, J. E.; Marmar, E. S.; Fournier, K. B.; Goldstein, W. H.

    1997-06-01

    The intrinsic impurity content of molybdenum and carbon was measured in the Alcator C-Mod tokamak using low resolution, multilayer mirror (MLM) spectroscopy ( Delta lambda ~1-10 AA). Molybdenum was the dominant high-Z impurity and originated from the molybdenum armour tiles covering all of the plasma facing surfaces (including the inner column, the poloidal divertor plates and the ion cyclotron resonant frequency (ICRF) limiter) at Alcator C-Mod. Despite the all metal first wall, a carbon concentration of 1 to 2% existed in the plasma and was the major low-Z impurity in Alcator C-Mod. Thus, the behaviour of intrinsic molybdenum and carbon penetrating into the main plasma and the effect on the plasma must be measured and characterized during various modes of Alcator C-Mod operation. To this end, soft X-ray extreme ultraviolet (XUV) emission lines of charge states, ranging from hydrogen-like to helium-like lines of carbon (radius/minor radius, r/a~1) at the plasma edge to potassium to chlorine-like (0.4

  6. Hydrodynamical and Spectral Simulations of HMXB Winds

    NASA Astrophysics Data System (ADS)

    Mauche, Christopher W.; Liedahl, D. A.; Plewa, T.

    2006-09-01

    We describe the results of a research program to develop improved models of the X-ray spectra of cosmic sources such as X-ray binaries, CVs, and AGN in which UV line-driven mass flows are photoionized by an X-ray source. Work to date has focused on high-mass X-ray binaries (HMXBs) and on Vela X-1 in particular, for which there are high-quality Chandra HETG spectra in the archive. Our research program combines FLASH hydrodynamic calculations, XSTAR photoionization calculations, HULLAC atomic data, improved calculations of the line force multiplier, X-ray emission models appropriate to X-ray photoionized plasmas, and Monte Carlo radiation transport. We will present movies of the relevant physical quantities (density, temperature, ionization parameter, velocity) from a FLASH two-dimensional time-dependent simulation of Vela X-1, maps showing the emissivity distributions of the X-ray emission lines, and a preliminary comparison of the resulting synthetic spectra to the Chandra HETG spectra. This work was performed under the auspices of the U.S. Department of Energy by University of California, Lawrence Livermore National Laboratory under Contract W-7405-Eng-48.

  7. Optimized atom position and coefficient coding for matching pursuit-based image compression.

    PubMed

    Shoa, Alireza; Shirani, Shahram

    2009-12-01

    In this paper, we propose a new encoding algorithm for matching pursuit image coding. We show that coding performance is improved when correlations between atom positions and atom coefficients are both used in encoding. We find the optimum tradeoff between efficient atom position coding and efficient atom coefficient coding and optimize the encoder parameters. Our proposed algorithm outperforms the existing coding algorithms designed for matching pursuit image coding. Additionally, we show that our algorithm results in better rate distortion performance than JPEG 2000 at low bit rates.

  8. Light element opacities of astrophysical interest from ATOMIC

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Colgan, J.; Kilcrease, D. P.; Magee, N. H. Jr.

    We present new calculations of local-thermodynamic-equilibrium (LTE) light element opacities from the Los Alamos ATOMIC code for systems of astrophysical interest. ATOMIC is a multi-purpose code that can generate LTE or non-LTE quantities of interest at various levels of approximation. Our calculations, which include fine-structure detail, represent a systematic improvement over previous Los Alamos opacity calculations using the LEDCOP legacy code. The ATOMIC code uses ab-initio atomic structure data computed from the CATS code, which is based on Cowan's atomic structure codes, and photoionization cross section data computed from the Los Alamos ionization code GIPPER. ATOMIC also incorporates a newmore » equation-of-state (EOS) model based on the chemical picture. ATOMIC incorporates some physics packages from LEDCOP and also includes additional physical processes, such as improved free-free cross sections and additional scattering mechanisms. Our new calculations are made for elements of astrophysical interest and for a wide range of temperatures and densities.« less

  9. Simulation of Laser Cooling and Trapping in Engineering Applications

    NASA Technical Reports Server (NTRS)

    Ramirez-Serrano, Jaime; Kohel, James; Thompson, Robert; Yu, Nan; Lunblad, Nathan

    2005-01-01

    An advanced computer code is undergoing development for numerically simulating laser cooling and trapping of large numbers of atoms. The code is expected to be useful in practical engineering applications and to contribute to understanding of the roles that light, atomic collisions, background pressure, and numbers of particles play in experiments using laser-cooled and -trapped atoms. The code is based on semiclassical theories of the forces exerted on atoms by magnetic and optical fields. Whereas computer codes developed previously for the same purpose account for only a few physical mechanisms, this code incorporates many more physical mechanisms (including atomic collisions, sub-Doppler cooling mechanisms, Stark and Zeeman energy shifts, gravitation, and evanescent-wave phenomena) that affect laser-matter interactions and the cooling of atoms to submillikelvin temperatures. Moreover, whereas the prior codes can simulate the interactions of at most a few atoms with a resonant light field, the number of atoms that can be included in a simulation by the present code is limited only by computer memory. Hence, the present code represents more nearly completely the complex physics involved when using laser-cooled and -trapped atoms in engineering applications. Another advantage that the code incorporates is the possibility to analyze the interaction between cold atoms of different atomic number. Some properties that cold atoms of different atomic species have, like cross sections and the particular excited states they can occupy when interacting with each other and light fields, play important roles not yet completely understood in the new experiments that are under way in laboratories worldwide to form ultracold molecules. Other research efforts use cold atoms as holders of quantum information, and more recent developments in cavity quantum electrodynamics also use ultracold atoms to explore and expand new information-technology ideas. These experiments give a hint on the wide range of applications and technology developments that can be tackled using cold atoms and light fields. From more precise atomic clocks and gravity sensors to the development of quantum computers, there will be a need to completely understand the whole ensemble of physical mechanisms that play a role in the development of such technologies. The code also permits the study of the dynamic and steady-state operations of technologies that use cold atoms. The physical characteristics of lasers and fields can be time-controlled to give a realistic simulation of the processes involved such that the design process can determine the best control features to use. It is expected that with the features incorporated into the code it will become a tool for the useful application of ultracold atoms in engineering applications. Currently, the software is being used for the analysis and understanding of simple experiments using cold atoms, and for the design of a modular compact source of cold atoms to be used in future research and development projects. The results so far indicate that the code is a useful design instrument that shows good agreement with experimental measurements (see figure), and a Windows-based user-friendly interface is also under development.

  10. ALICE: A non-LTE plasma atomic physics, kinetics and lineshape package

    NASA Astrophysics Data System (ADS)

    Hill, E. G.; Pérez-Callejo, G.; Rose, S. J.

    2018-03-01

    All three parts of an atomic physics, atomic kinetics and lineshape code, ALICE, are described. Examples of the code being used to model the emissivity and opacity of plasmas are discussed and interesting features of the code which build on the existing corpus of models are shown throughout.

  11. Theoretical atomic physics code development I: CATS: Cowan Atomic Structure Code

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Abdallah, J. Jr.; Clark, R.E.H.; Cowan, R.D.

    An adaptation of R.D. Cowan's Atomic Structure program, CATS, has been developed as part of the Theoretical Atomic Physics (TAPS) code development effort at Los Alamos. CATS has been designed to be easy to run and to produce data files that can interface with other programs easily. The CATS produced data files currently include wave functions, energy levels, oscillator strengths, plane-wave-Born electron-ion collision strengths, photoionization cross sections, and a variety of other quantities. This paper describes the use of CATS. 10 refs.

  12. Influence of the plasma environment on atomic structure using an ion-sphere model

    DOE PAGES

    Belkhiri, Madeny Jean; Fontes, Christopher John; Poirier, Michel

    2015-09-03

    Plasma environment effects on atomic structure are analyzed using various atomic structure codes. To monitor the effect of high free-electron density or low temperatures, Fermi-Dirac and Maxwell-Boltzmann statistics are compared. After a discussion of the implementation of the Fermi-Dirac approach within the ion-sphere model, several applications are considered. In order to check the consistency of the modifications brought here to extant codes, calculations have been performed using the Los Alamos Cowan Atomic Structure (cats) code in its Hartree-Fock or Hartree-Fock-Slater form and the parametric potential Flexible Atomic Code (fac). The ground-state energy shifts due to the plasma effects for themore » six most ionized aluminum ions have been calculated using the fac and cats codes and fairly agree. For the intercombination resonance line in Fe 22+, the plasma effect within the uniform electron gas model results in a positive shift that agrees with the MCDF value of B. Saha et al.« less

  13. Influence of the plasma environment on atomic structure using an ion-sphere model

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Belkhiri, Madeny Jean; Fontes, Christopher John; Poirier, Michel

    Plasma environment effects on atomic structure are analyzed using various atomic structure codes. To monitor the effect of high free-electron density or low temperatures, Fermi-Dirac and Maxwell-Boltzmann statistics are compared. After a discussion of the implementation of the Fermi-Dirac approach within the ion-sphere model, several applications are considered. In order to check the consistency of the modifications brought here to extant codes, calculations have been performed using the Los Alamos Cowan Atomic Structure (cats) code in its Hartree-Fock or Hartree-Fock-Slater form and the parametric potential Flexible Atomic Code (fac). The ground-state energy shifts due to the plasma effects for themore » six most ionized aluminum ions have been calculated using the fac and cats codes and fairly agree. For the intercombination resonance line in Fe 22+, the plasma effect within the uniform electron gas model results in a positive shift that agrees with the MCDF value of B. Saha et al.« less

  14. Influence of external radiation on non-LTE opacities of Xe

    NASA Astrophysics Data System (ADS)

    Klapisch, Marcel; Busquet, Michel

    2010-11-01

    In Laboratory Astrophysics, where astrophysics phenomena are scaled down to the laboratory, Xenon is commonly used. In most cases, astrophysical plasmas are not dense enough to warrant LTE. However, they are surrounded by radiation fields. Extensive detailed level computations of non-LTE Xe around Te = 100eV were performed with HULLAC [1], with different radiation temperatures and/or dilution factors. Generally, the effects are very important, even with small dilution factors. [4pt] [1] M. Klapisch and M. Busquet, High Ener. Dens. Phys.5, (2009) 105-9; Bull. Am. Phys. Soc.54, (2009) 210.

  15. GAPD: a GPU-accelerated atom-based polychromatic diffraction simulation code.

    PubMed

    E, J C; Wang, L; Chen, S; Zhang, Y Y; Luo, S N

    2018-03-01

    GAPD, a graphics-processing-unit (GPU)-accelerated atom-based polychromatic diffraction simulation code for direct, kinematics-based, simulations of X-ray/electron diffraction of large-scale atomic systems with mono-/polychromatic beams and arbitrary plane detector geometries, is presented. This code implements GPU parallel computation via both real- and reciprocal-space decompositions. With GAPD, direct simulations are performed of the reciprocal lattice node of ultralarge systems (∼5 billion atoms) and diffraction patterns of single-crystal and polycrystalline configurations with mono- and polychromatic X-ray beams (including synchrotron undulator sources), and validation, benchmark and application cases are presented.

  16. Calculated values of atomic oxygen fluences and solar exposure on selected surfaces of LDEF

    NASA Technical Reports Server (NTRS)

    Gillis, J. R.; Pippin, H. G.; Bourassa, R. J.; Gruenbaum, P. E.

    1995-01-01

    Atomic oxygen (AO) fluences and solar exposure have been modeled for selected hardware from the Long Duration Exposure Facility (LDEF). The atomic oxygen exposure was modeled using the microenvironment modeling code SHADOWV2. The solar exposure was modeled using the microenvironment modeling code SOLSHAD version 1.0.

  17. Influence of the plasma environment on atomic structure using an ion-sphere model

    NASA Astrophysics Data System (ADS)

    Belkhiri, Madeny; Fontes, Christopher J.; Poirier, Michel

    2015-09-01

    Plasma environment effects on atomic structure are analyzed using various atomic structure codes. To monitor the effect of high free-electron density or low temperatures, Fermi-Dirac and Maxwell-Boltzmann statistics are compared. After a discussion of the implementation of the Fermi-Dirac approach within the ion-sphere model, several applications are considered. In order to check the consistency of the modifications brought here to extant codes, calculations have been performed using the Los Alamos Cowan Atomic Structure (cats) code in its Hartree-Fock or Hartree-Fock-Slater form and the parametric potential Flexible Atomic Code (fac). The ground-state energy shifts due to the plasma effects for the six most ionized aluminum ions have been calculated using the fac and cats codes and fairly agree. For the intercombination resonance line in Fe22 +, the plasma effect within the uniform electron gas model results in a positive shift that agrees with the multiconfiguration Dirac-Fock value of B. Saha and S. Fritzsche [J. Phys. B 40, 259 (2007), 10.1088/0953-4075/40/2/002]. Last, the present model is compared to experimental data in titanium measured on the terawatt Astra facility and provides values for electron temperature and density in agreement with the maria code.

  18. Theoretical modeling of laser-induced plasmas using the ATOMIC code

    NASA Astrophysics Data System (ADS)

    Colgan, James; Johns, Heather; Kilcrease, David; Judge, Elizabeth; Barefield, James, II; Clegg, Samuel; Hartig, Kyle

    2014-10-01

    We report on efforts to model the emission spectra generated from laser-induced breakdown spectroscopy (LIBS). LIBS is a popular and powerful method of quickly and accurately characterizing unknown samples in a remote manner. In particular, LIBS is utilized by the ChemCam instrument on the Mars Science Laboratory. We model the LIBS plasma using the Los Alamos suite of atomic physics codes. Since LIBS plasmas generally have temperatures of somewhere between 3000 K and 12000 K, the emission spectra typically result from the neutral and singly ionized stages of the target atoms. We use the Los Alamos atomic structure and collision codes to generate sets of atomic data and use the plasma kinetics code ATOMIC to perform LTE or non-LTE calculations that generate level populations and an emission spectrum for the element of interest. In this presentation we compare the emission spectrum from ATOMIC with an Fe LIBS laboratory-generated plasma as well as spectra from the ChemCam instrument. We also discuss various physics aspects of the modeling of LIBS plasmas that are necessary for accurate characterization of the plasma, such as multi-element target composition effects, radiation transport effects, and accurate line shape treatments. The Los Alamos National Laboratory is operated by Los Alamos National Security, LLC for the National Nuclear Security Administration of the U.S. Department of Energy under Contract No. DE-AC5206NA25396.

  19. MEAM interatomic force calculation subroutine for LAMMPS

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Stukowski, A.

    2010-10-25

    Interatomic force and energy calculation subroutine tobe used with the molecular dynamics simulation code LAMMPS (Ref a.). The code evaluates the total energy and atomic forces (energy gradient) according to cubic spine-based variant (Ref b.) of the Modified Embedded Atom Method (MEAM).

  20. Photoionization and High Density Gas

    NASA Technical Reports Server (NTRS)

    Kallman, T.; Bautista, M.; White, Nicholas E. (Technical Monitor)

    2002-01-01

    We present results of calculations using the XSTAR version 2 computer code. This code is loosely based on the XSTAR v.1 code which has been available for public use for some time. However it represents an improvement and update in several major respects, including atomic data, code structure, user interface, and improved physical description of ionization/excitation. In particular, it now is applicable to high density situations in which significant excited atomic level populations are likely to occur. We describe the computational techniques and assumptions, and present sample runs with particular emphasis on high density situations.

  1. Atomic Physics Effects on Convergent, Child-Langmuir Ion Flow between Nearly Transparent Electrodes

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Santarius, John F.; Emmert, Gilbert A.

    Research during this project at the University of Wisconsin Fusion Technology Institute (UW FTI) on ion and neutral flow through an arbitrary, monotonic potential difference created by nearly transparent electrodes accomplished the following: (1) developed and implemented an integral equation approach for atomic physics effects in helium plasmas; (2) extended the analysis to coupled integral equations that treat atomic and molecular deuterium ions and neutrals; (3) implemented the key deuterium and helium atomic and molecular cross sections; (4) added negative ion production and related cross sections; and (5) benchmarked the code against experimental results. The analysis and codes treat themore » species D0, D20, D+, D2+, D3+, D and, separately at present, He0 and He+. Extensions enhanced the analysis and related computer codes to include He++ ions plus planar and cylindrical geometries.« less

  2. Numerical Studies of Impurities in Fusion Plasmas

    DOE R&D Accomplishments Database

    Hulse, R. A.

    1982-09-01

    The coupled partial differential equations used to describe the behavior of impurity ions in magnetically confined controlled fusion plasmas require numerical solution for cases of practical interest. Computer codes developed for impurity modeling at the Princeton Plasma Physics Laboratory are used as examples of the types of codes employed for this purpose. These codes solve for the impurity ionization state densities and associated radiation rates using atomic physics appropriate for these low-density, high-temperature plasmas. The simpler codes solve local equations in zero spatial dimensions while more complex cases require codes which explicitly include transport of the impurity ions simultaneously with the atomic processes of ionization and recombination. Typical applications are discussed and computational results are presented for selected cases of interest.

  3. Porting LAMMPS to GPUs.

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Brown, William Michael; Plimpton, Steven James; Wang, Peng

    2010-03-01

    LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for soft materials (biomolecules, polymers) and solid-state materials (metals, semiconductors) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality.

  4. MCNP6.1 simulations for low-energy atomic relaxation: Code-to-code comparison with GATEv7.2, PENELOPE2014, and EGSnrc

    NASA Astrophysics Data System (ADS)

    Jung, Seongmoon; Sung, Wonmo; Lee, Jaegi; Ye, Sung-Joon

    2018-01-01

    Emerging radiological applications of gold nanoparticles demand low-energy electron/photon transport calculations including details of an atomic relaxation process. Recently, MCNP® version 6.1 (MCNP6.1) has been released with extended cross-sections for low-energy electron/photon, subshell photoelectric cross-sections, and more detailed atomic relaxation data than the previous versions. With this new feature, the atomic relaxation process of MCNP6.1 has not been fully tested yet with its new physics library (eprdata12) that is based on the Evaluated Atomic Data Library (EADL). In this study, MCNP6.1 was compared with GATEv7.2, PENELOPE2014, and EGSnrc that have been often used to simulate low-energy atomic relaxation processes. The simulations were performed to acquire both photon and electron spectra produced by interactions of 15 keV electrons or photons with a 10-nm-thick gold nano-slab. The photon-induced fluorescence X-rays from MCNP6.1 fairly agreed with those from GATEv7.2 and PENELOPE2014, while the electron-induced fluorescence X-rays of the four codes showed more or less discrepancies. A coincidence was observed in the photon-induced Auger electrons simulated by MCNP6.1 and GATEv7.2. A recent release of MCNP6.1 with eprdata12 can be used to simulate the photon-induced atomic relaxation.

  5. An X-Ray Analysis Database of Photoionization Cross Sections Including Variable Ionization

    NASA Technical Reports Server (NTRS)

    Wang, Ping; Cohen, David H.; MacFarlane, Joseph J.; Cassinelli, Joseph P.

    1997-01-01

    Results of research efforts in the following areas are discussed: review of the major theoretical and experimental data of subshell photoionization cross sections and ionization edges of atomic ions to assess the accuracy of the data, and to compile the most reliable of these data in our own database; detailed atomic physics calculations to complement the database for all ions of 17 cosmically abundant elements; reconciling the data from various sources and our own calculations; and fitting cross sections with functional approximations and incorporating these functions into a compact computer code.Also, efforts included adapting an ionization equilibrium code, tabulating results, and incorporating them into the overall program and testing the code (both ionization equilibrium and opacity codes) with existing observational data. The background and scientific applications of this work are discussed. Atomic physics cross section models and calculations are described. Calculation results are compared with available experimental data and other theoretical data. The functional approximations used for fitting cross sections are outlined and applications of the database are discussed.

  6. Exploring the Ability of a Coarse-grained Potential to Describe the Stress-strain Response of Glassy Polystyrene

    DTIC Science & Technology

    2012-10-01

    using the open-source code Large-scale Atomic/Molecular Massively Parallel Simulator ( LAMMPS ) (http://lammps.sandia.gov) (23). The commercial...parameters are proprietary and cannot be ported to the LAMMPS 4 simulation code. In our molecular dynamics simulations at the atomistic resolution, we...IBI iterative Boltzmann inversion LAMMPS Large-scale Atomic/Molecular Massively Parallel Simulator MAPS Materials Processes and Simulations MS

  7. 77 FR 133 - In the Matter of Connecticut Yankee Atomic Power Company; Northeast Utilities; NSTAR (Haddam Neck...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-03

    ... the Matter of Connecticut Yankee Atomic Power Company; Northeast Utilities; NSTAR (Haddam Neck Plant); Order Approving Application Regarding Proposed Merger I Connecticut Yankee Atomic Power Company..., pursuant to Section 184 of the Atomic Energy Act of 1954, as amended (AEA), and Title 10 of the Code of...

  8. Detailed numerical simulations of laser cooling processes

    NASA Technical Reports Server (NTRS)

    Ramirez-Serrano, J.; Kohel, J.; Thompson, R.; Yu, N.

    2001-01-01

    We developed a detailed semiclassical numerical code of the forces applied on atoms in optical and magnetic fields to increase the understanding of the different roles that light, atomic collisions, background pressure, and number of particles play in experiments with laser cooled and trapped atoms.

  9. Quantum nonlinear optics without photons

    NASA Astrophysics Data System (ADS)

    Stassi, Roberto; Macrı, Vincenzo; Kockum, Anton Frisk; Di Stefano, Omar; Miranowicz, Adam; Savasta, Salvatore; Nori, Franco

    2017-08-01

    Spontaneous parametric down-conversion is a well-known process in quantum nonlinear optics in which a photon incident on a nonlinear crystal spontaneously splits into two photons. Here we propose an analogous physical process where one excited atom directly transfers its excitation to a pair of spatially separated atoms with probability approaching 1. The interaction is mediated by the exchange of virtual rather than real photons. This nonlinear atomic process is coherent and reversible, so the pair of excited atoms can transfer the excitation back to the first one: the atomic analog of sum-frequency generation of light. The parameters used to investigate this process correspond to experimentally demonstrated values in ultrastrong circuit quantum electrodynamics. This approach can be extended to realize other nonlinear interatomic processes, such as four-atom mixing, and is an attractive architecture for the realization of quantum devices on a chip. We show that four-qubit mixing can efficiently implement quantum repetition codes and, thus, can be used for error-correction codes.

  10. K-shell X-ray transition energies of multi-electron ions of silicon and sulfur

    NASA Astrophysics Data System (ADS)

    Beiersdorfer, P.; Brown, G. V.; Hell, N.; Santana, J. A.

    2017-10-01

    Prompted by the detection of K-shell absorption or emission features in the spectra of plasma surrounding high mass X-ray binaries and black holes, recent measurements using the Livermore electron beam ion trap have focused on the energies of the n = 2 to n = 1 K-shell transitions in the L-shell ions of lithiumlike through fluorinelike silicon and sulfur. In parallel, we have made calculations of these transitions using the Flexible Atomic Code and the multi-reference Møller-Plesset (MRMP) atomic physics code. Using this code we have attempted to produce sets of theoretical atomic data with spectroscopic accuracy for all the L-shell ions of silicon and sulfur. We present results of our calculations for oxygenlike and fluorinelike silicon and compare them to the recent electron beam ion trap measurements as well as previous calculations.

  11. Molecular Dynamic Simulations of Interaction of an AFM Probe with the Surface of an SCN Sample

    NASA Technical Reports Server (NTRS)

    Bune, Adris; Kaukler, William; Rose, M. Franklin (Technical Monitor)

    2001-01-01

    Molecular dynamic (MD) simulations is conducted in order to estimate forces of probe-substrate interaction in the Atomic Force Microscope (AFM). First a review of available molecular dynamic techniques is given. Implementation of MD simulation is based on an object-oriented code developed at the University of Delft. Modeling of the sample material - succinonitrile (SCN) - is based on the Lennard-Jones potentials. For the polystyrene probe an atomic interaction potential is used. Due to object-oriented structure of the code modification of an atomic interaction potential is straight forward. Calculation of melting temperature is used for validation of the code and of the interaction potentials. Various fitting parameters of the probe-substrate interaction potentials are considered, as potentials fitted to certain properties and temperature ranges may not be reliable for the others. This research provides theoretical foundation for an interpretation of actual measurements of an interaction forces using AFM.

  12. Tartarus: A relativistic Green's function quantum average atom code

    DOE PAGES

    Gill, Nathanael Matthew; Starrett, Charles Edward

    2017-06-28

    A relativistic Green’s Function quantum average atom model is implemented in the Tartarus code for the calculation of equation of state data in dense plasmas. We first present the relativistic extension of the quantum Green’s Function average atom model described by Starrett [1]. The Green’s Function approach addresses the numerical challenges arising from resonances in the continuum density of states without the need for resonance tracking algorithms or adaptive meshes, though there are still numerical challenges inherent to this algorithm. We discuss how these challenges are addressed in the Tartarus algorithm. The outputs of the calculation are shown in comparisonmore » to PIMC/DFT-MD simulations of the Principal Shock Hugoniot in Silicon. Finally, we also present the calculation of the Hugoniot for Silver coming from both the relativistic and nonrelativistic modes of the Tartarus code.« less

  13. K-shell X-ray transition energies of multi-electron ions of silicon and sulfur

    DOE PAGES

    Beiersdorfer, P.; Brown, G. V.; Hell, N.; ...

    2017-04-20

    Prompted by the detection of K-shell absorption or emission features in the spectra of plasma surrounding high mass X-ray binaries and black holes, recent measurements using the Livermore electron beam ion trap have focused on the energies of the n = 2 to n = 1 K-shell transitions in the L-shell ions of lithiumlike through fluorinelike silicon and sulfur. In parallel, we have made calculations of these transitions using the Flexible Atomic Code and the multi-reference Møller-Plesset (MRMP) atomic physics code. Using this code we have attempted to produce sets of theoretical atomic data with spectroscopic accuracy for all themore » L-shell ions of silicon and sulfur. Here, we present results of our calculations for oxygenlike and fluorinelike silicon and compare them to the recent electron beam ion trap measurements as well as previous calculations.« less

  14. Tartarus: A relativistic Green's function quantum average atom code

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Gill, Nathanael Matthew; Starrett, Charles Edward

    A relativistic Green’s Function quantum average atom model is implemented in the Tartarus code for the calculation of equation of state data in dense plasmas. We first present the relativistic extension of the quantum Green’s Function average atom model described by Starrett [1]. The Green’s Function approach addresses the numerical challenges arising from resonances in the continuum density of states without the need for resonance tracking algorithms or adaptive meshes, though there are still numerical challenges inherent to this algorithm. We discuss how these challenges are addressed in the Tartarus algorithm. The outputs of the calculation are shown in comparisonmore » to PIMC/DFT-MD simulations of the Principal Shock Hugoniot in Silicon. Finally, we also present the calculation of the Hugoniot for Silver coming from both the relativistic and nonrelativistic modes of the Tartarus code.« less

  15. Numeral series hidden in the distribution of atomic mass of amino acids to codon domains in the genetic code.

    PubMed

    Wohlin, Åsa

    2015-03-21

    The distribution of codons in the nearly universal genetic code is a long discussed issue. At the atomic level, the numeral series 2x(2) (x=5-0) lies behind electron shells and orbitals. Numeral series appear in formulas for spectral lines of hydrogen. The question here was if some similar scheme could be found in the genetic code. A table of 24 codons was constructed (synonyms counted as one) for 20 amino acids, four of which have two different codons. An atomic mass analysis was performed, built on common isotopes. It was found that a numeral series 5 to 0 with exponent 2/3 times 10(2) revealed detailed congruency with codon-grouped amino acid side-chains, simultaneously with the division on atom kinds, further with main 3rd base groups, backbone chains and with codon-grouped amino acids in relation to their origin from glycolysis or the citrate cycle. Hence, it is proposed that this series in a dynamic way may have guided the selection of amino acids into codon domains. Series with simpler exponents also showed noteworthy correlations with the atomic mass distribution on main codon domains; especially the 2x(2)-series times a factor 16 appeared as a conceivable underlying level, both for the atomic mass and charge distribution. Furthermore, it was found that atomic mass transformations between numeral systems, possibly interpretable as dimension degree steps, connected the atomic mass of codon bases with codon-grouped amino acids and with the exponent 2/3-series in several astonishing ways. Thus, it is suggested that they may be part of a deeper reference system. Copyright © 2015 The Author. Published by Elsevier Ltd.. All rights reserved.

  16. A computer code for calculations in the algebraic collective model of the atomic nucleus

    NASA Astrophysics Data System (ADS)

    Welsh, T. A.; Rowe, D. J.

    2016-03-01

    A Maple code is presented for algebraic collective model (ACM) calculations. The ACM is an algebraic version of the Bohr model of the atomic nucleus, in which all required matrix elements are derived by exploiting the model's SU(1 , 1) × SO(5) dynamical group. This paper reviews the mathematical formulation of the ACM, and serves as a manual for the code. The code enables a wide range of model Hamiltonians to be analysed. This range includes essentially all Hamiltonians that are rational functions of the model's quadrupole moments qˆM and are at most quadratic in the corresponding conjugate momenta πˆN (- 2 ≤ M , N ≤ 2). The code makes use of expressions for matrix elements derived elsewhere and newly derived matrix elements of the operators [ π ˆ ⊗ q ˆ ⊗ π ˆ ] 0 and [ π ˆ ⊗ π ˆ ] LM. The code is made efficient by use of an analytical expression for the needed SO(5)-reduced matrix elements, and use of SO(5) ⊃ SO(3) Clebsch-Gordan coefficients obtained from precomputed data files provided with the code.

  17. Simulation of non LTE opacity with incoming radiation

    NASA Astrophysics Data System (ADS)

    Klapisch, Marcel; Busquet, Michel

    2009-11-01

    Simulation of radiative properties of hot plasmas is important for ICF, other laboratory plasmas, and astrophysics. When mid-Z or high-Z elements are involved, the spectra are so complex that one commonly uses LTE approximation. This was recently done in interpreting a carefully calibrated experiment on Fe at 160 eV [1]. However some disagreement remains concerning the ion charge distribution. The newest version of HULLAC [2] has the capability to take into account an incoming radiation field in solving the rate equations of the coronal radiative model (CRM). We will show results with different representation of the radiation field.[4pt] [1] J.E. Bailey, G.A. Rochau, C.A. Iglesias, et al., Phys. Rev. Lett. 99, (2007) 265002-4.[0pt] [2] M. Klapisch and M. Busquet, High Ener. Dens. Phys. 5, (2009) 105-9.

  18. Current and anticipated uses of thermal hydraulic codes at the Japan Atomic Energy Research Institute

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Akimoto, Hajime; Kukita; Ohnuki, Akira

    1997-07-01

    The Japan Atomic Energy Research Institute (JAERI) is conducting several research programs related to thermal-hydraulic and neutronic behavior of light water reactors (LWRs). These include LWR safety research projects, which are conducted in accordance with the Nuclear Safety Commission`s research plan, and reactor engineering projects for the development of innovative reactor designs or core/fuel designs. Thermal-hydraulic and neutronic codes are used for various purposes including experimental analysis, nuclear power plant (NPP) safety analysis, and design assessment.

  19. A Nonlinear Model for Fuel Atomization in Spray Combustion

    NASA Technical Reports Server (NTRS)

    Liu, Nan-Suey (Technical Monitor); Ibrahim, Essam A.; Sree, Dave

    2003-01-01

    Most gas turbine combustion codes rely on ad-hoc statistical assumptions regarding the outcome of fuel atomization processes. The modeling effort proposed in this project is aimed at developing a realistic model to produce accurate predictions of fuel atomization parameters. The model involves application of the nonlinear stability theory to analyze the instability and subsequent disintegration of the liquid fuel sheet that is produced by fuel injection nozzles in gas turbine combustors. The fuel sheet is atomized into a multiplicity of small drops of large surface area to volume ratio to enhance the evaporation rate and combustion performance. The proposed model will effect predictions of fuel sheet atomization parameters such as drop size, velocity, and orientation as well as sheet penetration depth, breakup time and thickness. These parameters are essential for combustion simulation codes to perform a controlled and optimized design of gas turbine fuel injectors. Optimizing fuel injection processes is crucial to improving combustion efficiency and hence reducing fuel consumption and pollutants emissions.

  20. The use of the SRIM code for calculation of radiation damage induced by neutrons

    NASA Astrophysics Data System (ADS)

    Mohammadi, A.; Hamidi, S.; Asadabad, Mohsen Asadi

    2017-12-01

    Materials subjected to neutron irradiation will being evolve to structural changes by the displacement cascades initiated by nuclear reaction. This study discusses a methodology to compute primary knock-on atoms or PKAs information that lead to radiation damage. A program AMTRACK has been developed for assessing of the PKAs information. This software determines the specifications of recoil atoms (using PTRAC card of MCNPX code) and also the kinematics of interactions. The deterministic method was used for verification of the results of (MCNPX+AMTRACK). The SRIM (formely TRIM) code is capable to compute neutron radiation damage. The PKAs information was extracted by AMTRACK program, which can be used as an input of SRIM codes for systematic analysis of primary radiation damage. Then the Bushehr Nuclear Power Plant (BNPP) radiation damage on reactor pressure vessel is calculated.

  1. Nuclear Analysis

    NASA Technical Reports Server (NTRS)

    Clement, J. D.; Kirby, K. D.

    1973-01-01

    Exploratory calculations were performed for several gas core breeder reactor configurations. The computational method involved the use of the MACH-1 one dimensional diffusion theory code and the THERMOS integral transport theory code for thermal cross sections. Computations were performed to analyze thermal breeder concepts and nonbreeder concepts. Analysis of breeders was restricted to the (U-233)-Th breeding cycle, and computations were performed to examine a range of parameters. These parameters include U-233 to hydrogen atom ratio in the gaseous cavity, carbon to thorium atom ratio in the breeding blanket, cavity size, and blanket size.

  2. Hybrid MPI-OpenMP Parallelism in the ONETEP Linear-Scaling Electronic Structure Code: Application to the Delamination of Cellulose Nanofibrils.

    PubMed

    Wilkinson, Karl A; Hine, Nicholas D M; Skylaris, Chris-Kriton

    2014-11-11

    We present a hybrid MPI-OpenMP implementation of Linear-Scaling Density Functional Theory within the ONETEP code. We illustrate its performance on a range of high performance computing (HPC) platforms comprising shared-memory nodes with fast interconnect. Our work has focused on applying OpenMP parallelism to the routines which dominate the computational load, attempting where possible to parallelize different loops from those already parallelized within MPI. This includes 3D FFT box operations, sparse matrix algebra operations, calculation of integrals, and Ewald summation. While the underlying numerical methods are unchanged, these developments represent significant changes to the algorithms used within ONETEP to distribute the workload across CPU cores. The new hybrid code exhibits much-improved strong scaling relative to the MPI-only code and permits calculations with a much higher ratio of cores to atoms. These developments result in a significantly shorter time to solution than was possible using MPI alone and facilitate the application of the ONETEP code to systems larger than previously feasible. We illustrate this with benchmark calculations from an amyloid fibril trimer containing 41,907 atoms. We use the code to study the mechanism of delamination of cellulose nanofibrils when undergoing sonification, a process which is controlled by a large number of interactions that collectively determine the structural properties of the fibrils. Many energy evaluations were needed for these simulations, and as these systems comprise up to 21,276 atoms this would not have been feasible without the developments described here.

  3. Ignition and combustion characteristics of metallized propellants

    NASA Technical Reports Server (NTRS)

    Mueller, D. C.; Turns, Stephen R.

    1992-01-01

    During this reporting period, theoretical work on the secondary atomization process was continued and the experimental apparatus was improved. A one-dimensional model of a rocket combustor, incorporating multiple droplet size classes, slurry combustion, secondary atomization, radiation heat transfer, and two-phase slip between slurry droplets and the gas flow was derived and a computer code was written to implement this model. The STANJAN chemical equilibrium solver was coupled with this code to yield gas temperature, density, and composition as functions of axial location. Preliminary results indicate that the model is performing correctly, given current model assumptions. Radiation heat transfer in the combustion chamber is treated as an optically-thick participating media problem requiring a solution of the radiative transfer equation. A cylindrical P sub 1 approximation was employed to yield an analytical expression for chamber-wall heat flux at each axial location. The code exercised to determine the effects of secondary atomization intensity, defined as the number of secondary drops produced per initial drop, on chamber burnout distance and final Al2O3 agglomerate diameter. These results indicate that only weak secondary atomization is required to significantly reduce these two parameters. Stronger atomization intensities were found to yield decreasing marginal benefits. The experimental apparatus was improved to reduce building vibration effects on the optical system alignment. This was accomplished by mounting the burner and the transmitting/receiving optics on a single frame supported by vibration-isolation legs. Calibration and shakedown tests indicate that vibration problems were eliminated and that the system is performing correctly.

  4. Atomic-scale Modeling of the Structure and Dynamics of Dislocations in Complex Alloys at High Temperatures

    NASA Technical Reports Server (NTRS)

    Daw, Murray S.; Mills, Michael J.

    2003-01-01

    We report on the progress made during the first year of the project. Most of the progress at this point has been on the theoretical and computational side. Here are the highlights: (1) A new code, tailored for high-end desktop computing, now combines modern Accelerated Dynamics (AD) with the well-tested Embedded Atom Method (EAM); (2) The new Accelerated Dynamics allows the study of relatively slow, thermally-activated processes, such as diffusion, which are much too slow for traditional Molecular Dynamics; (3) We have benchmarked the new AD code on a rather simple and well-known process: vacancy diffusion in copper; and (4) We have begun application of the AD code to the diffusion of vacancies in ordered intermetallics.

  5. X-Ray, EUV, UV and Optical Emissivities of Astrophysical Plasmas

    NASA Technical Reports Server (NTRS)

    Raymond, John C.; West, Donald (Technical Monitor)

    2000-01-01

    This grant primarily covered the development of the thermal X-ray emission model code called APEC, which is meant to replace the Raymond and Smith (1977) code. The new code contains far more spectral lines and a great deal of updated atomic data. The code is now available (http://hea-www.harvard.edu/APEC), though new atomic data is still being added, particularly at longer wavelengths. While initial development of the code was funded by this grant, current work is carried on by N. Brickhouse, R. Smith and D. Liedahl under separate funding. Over the last five years, the grant has provided salary support for N. Brickhouse, R. Smith, a summer student (L. McAllister), an SAO predoctoral fellow (A. Vasquez), and visits by T. Kallman, D. Liedahl, P. Ghavamian, J.M. Laming, J. Li, P. Okeke, and M. Martos. In addition to the code development, the grant supported investigations into X-ray and UV spectral diagnostics as applied to shock waves in the ISM, accreting black holes and white dwarfs, and stellar coronae. Many of these efforts are continuing. Closely related work on the shock waves and coronal mass ejections in the solar corona has grown out of the efforts supported by the grant.

  6. Remote state preparation through hyperentangled atomic states

    NASA Astrophysics Data System (ADS)

    Nawaz, Mehwish; ul-Islam, Rameez-; Ikram, Manzoor

    2018-04-01

    Hyperentangled states have enhanced channel capacity in quantum processing and have yielded` evident increased communication speed in quantum informatics as a consequence of excessively high information content coded over each quantum entity. In the present article, we intend to demonstrate this fact by utilizing atomic states simultaneously entangled both in internal as well as external degrees of freedom, i.e. the de Broglie motion for remote state preparation (RSP). The results clearly demonstrate that we can efficiently communicate two bit information while manipulating only a single quantum subsystem. The states are prepared and manipulated using atomic Bragg diffraction as well as Ramsey interferometry, both of which are now considered as standard, state of the art tools based on cavity quantum electrodynamics. Since atomic Bragg diffraction is a large interaction time regime and produces spatially well separated, decoherence resistant outputs, the schematics presented here for the RSP offer important perspectives on efficient detection as well as unambiguous information coding and readout. The article summarizes the experimental feasibility of the proposal, culminating with a brief discussion.

  7. Development of Spectral and Atomic Models for Diagnosing Energetic Particle Characteristics in Fast Ignition Experiments

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    MacFarlane, Joseph J.; Golovkin, I. E.; Woodruff, P. R.

    2009-08-07

    This Final Report summarizes work performed under DOE STTR Phase II Grant No. DE-FG02-05ER86258 during the project period from August 2006 to August 2009. The project, “Development of Spectral and Atomic Models for Diagnosing Energetic Particle Characteristics in Fast Ignition Experiments,” was led by Prism Computational Sciences (Madison, WI), and involved collaboration with subcontractors University of Nevada-Reno and Voss Scientific (Albuquerque, NM). In this project, we have: Developed and implemented a multi-dimensional, multi-frequency radiation transport model in the LSP hybrid fluid-PIC (particle-in-cell) code [1,2]. Updated the LSP code to support the use of accurate equation-of-state (EOS) tables generated by Prism’smore » PROPACEOS [3] code to compute more accurate temperatures in high energy density physics (HEDP) plasmas. Updated LSP to support the use of Prism’s multi-frequency opacity tables. Generated equation of state and opacity data for LSP simulations for several materials being used in plasma jet experimental studies. Developed and implemented parallel processing techniques for the radiation physics algorithms in LSP. Benchmarked the new radiation transport and radiation physics algorithms in LSP and compared simulation results with analytic solutions and results from numerical radiation-hydrodynamics calculations. Performed simulations using Prism radiation physics codes to address issues related to radiative cooling and ionization dynamics in plasma jet experiments. Performed simulations to study the effects of radiation transport and radiation losses due to electrode contaminants in plasma jet experiments. Updated the LSP code to generate output using NetCDF to provide a better, more flexible interface to SPECT3D [4] in order to post-process LSP output. Updated the SPECT3D code to better support the post-processing of large-scale 2-D and 3-D datasets generated by simulation codes such as LSP. Updated atomic physics modeling to provide for more comprehensive and accurate atomic databases that feed into the radiation physics modeling (spectral simulations and opacity tables). Developed polarization spectroscopy modeling techniques suitable for diagnosing energetic particle characteristics in HEDP experiments. A description of these items is provided in this report. The above efforts lay the groundwork for utilizing the LSP and SPECT3D codes in providing simulation support for DOE-sponsored HEDP experiments, such as plasma jet and fast ignition physics experiments. We believe that taken together, the LSP and SPECT3D codes have unique capabilities for advancing our understanding of the physics of these HEDP plasmas. Based on conversations early in this project with our DOE program manager, Dr. Francis Thio, our efforts emphasized developing radiation physics and atomic modeling capabilities that can be utilized in the LSP PIC code, and performing radiation physics studies for plasma jets. A relatively minor component focused on the development of methods to diagnose energetic particle characteristics in short-pulse laser experiments related to fast ignition physics. The period of performance for the grant was extended by one year to August 2009 with a one-year no-cost extension, at the request of subcontractor University of Nevada-Reno.« less

  8. Stellar and laboratory XUV/EUV line ratios in Fe XVIII and Fe XIX

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Traebert, E.; Beiersdorfer, P.; Clementson, J.

    2012-05-25

    A so-called XUV excess has been suspected with the relative fluxes of Fe XVIII and Fe XIX lines observed in the XUV and EUV ranges of the spectrum of the star Capella as observed by the Chandra spacecraft, even after correction for interstellar absorption. This excess becomes apparent in the comparison of the observations with simulations of stellar spectra obtained using collisional-radiative models that employ, for example, the Atomic Plasma Emission Code (APEC) or the Flexible Atomic Code (FAC). We have addressed this problem by laboratory studies using the Livermore electron beam ion trap (EBIT).

  9. FAC: Flexible Atomic Code

    NASA Astrophysics Data System (ADS)

    Gu, Ming Feng

    2018-02-01

    FAC calculates various atomic radiative and collisional processes, including radiative transition rates, collisional excitation and ionization by electron impact, energy levels, photoionization, and autoionization, and their inverse processes radiative recombination and dielectronic capture. The package also includes a collisional radiative model to construct synthetic spectra for plasmas under different physical conditions.

  10. Multimillion Atom Reactive Simulations of Nanostructured Energetic Materials

    DTIC Science & Technology

    2007-08-01

    code) 2007 Reprint Aug 2006-Aug 2007 Multimillion Atom Reactive Simulations of Nanostructured Energetic Materials W911NF-04-1-0178 sub 2781-USC-DOA...Priya Vashishta 213 821 2663 Reset Multimillion Atom Reactive Simulations of Nanostructured Energetic Materials Priya Vashishta,∗ Rajiv K. Kalia...function of the particle velocity that drives the shock [18]. The MD and experimental data agree very well. Furthermore, the simulation shows a sudden

  11. Coupled-cluster based R-matrix codes (CCRM): Recent developments

    NASA Astrophysics Data System (ADS)

    Sur, Chiranjib; Pradhan, Anil K.

    2008-05-01

    We report the ongoing development of the new coupled-cluster R-matrix codes (CCRM) for treating electron-ion scattering and radiative processes within the framework of the relativistic coupled-cluster method (RCC), interfaced with the standard R-matrix methodology. The RCC method is size consistent and in principle equivalent to an all-order many-body perturbation theory. The RCC method is one of the most accurate many-body theories, and has been applied for several systems. This project should enable the study of electron-interactions with heavy atoms/ions, utilizing not only high speed computing platforms but also improved theoretical description of the relativistic and correlation effects for the target atoms/ions as treated extensively within the RCC method. Here we present a comprehensive outline of the newly developed theoretical method and a schematic representation of the new suite of CCRM codes. We begin with the flowchart and description of various stages involved in this development. We retain the notations and nomenclature of different stages as analogous to the standard R-matrix codes.

  12. Continuum Absorption Coefficient of Atoms and Ions

    NASA Technical Reports Server (NTRS)

    Armaly, B. F.

    1979-01-01

    The rate of heat transfer to the heat shield of a Jupiter probe has been estimated to be one order of magnitude higher than any previously experienced in an outer space exploration program. More than one-third of this heat load is due to an emission of continuum radiation from atoms and ions. The existing computer code for calculating the continuum contribution to the total load utilizes a modified version of Biberman's approximate method. The continuum radiation absorption cross sections of a C - H - O - N ablation system were examined in detail. The present computer code was evaluated and updated by being compared with available exact and approximate calculations and correlations of experimental data. A detailed calculation procedure, which can be applied to other atomic species, is presented. The approximate correlations can be made to agree with the available exact and experimental data.

  13. Quality Scalability Aware Watermarking for Visual Content.

    PubMed

    Bhowmik, Deepayan; Abhayaratne, Charith

    2016-11-01

    Scalable coding-based content adaptation poses serious challenges to traditional watermarking algorithms, which do not consider the scalable coding structure and hence cannot guarantee correct watermark extraction in media consumption chain. In this paper, we propose a novel concept of scalable blind watermarking that ensures more robust watermark extraction at various compression ratios while not effecting the visual quality of host media. The proposed algorithm generates scalable and robust watermarked image code-stream that allows the user to constrain embedding distortion for target content adaptations. The watermarked image code-stream consists of hierarchically nested joint distortion-robustness coding atoms. The code-stream is generated by proposing a new wavelet domain blind watermarking algorithm guided by a quantization based binary tree. The code-stream can be truncated at any distortion-robustness atom to generate the watermarked image with the desired distortion-robustness requirements. A blind extractor is capable of extracting watermark data from the watermarked images. The algorithm is further extended to incorporate a bit-plane discarding-based quantization model used in scalable coding-based content adaptation, e.g., JPEG2000. This improves the robustness against quality scalability of JPEG2000 compression. The simulation results verify the feasibility of the proposed concept, its applications, and its improved robustness against quality scalable content adaptation. Our proposed algorithm also outperforms existing methods showing 35% improvement. In terms of robustness to quality scalable video content adaptation using Motion JPEG2000 and wavelet-based scalable video coding, the proposed method shows major improvement for video watermarking.

  14. Improved Simulations of Astrophysical Plasmas: Computation of New Atomic Data

    NASA Technical Reports Server (NTRS)

    Gorczyca, Thomas W.; Korista, Kirk T.

    2005-01-01

    Our research program is designed to carry out state-of-the-art atomic physics calculations crucial to advancing our understanding of fundamental astrophysical problems. We redress the present inadequacies in the atomic data base along two important areas: dielectronic recombination and inner-shell photoionization and multiple electron ejection/Auger fluorescence therefrom. All of these data are disseminated to the astrophysical community in the proper format for implementation in spectral simulation code.

  15. Computational code in atomic and nuclear quantum optics: Advanced computing multiphoton resonance parameters for atoms in a strong laser field

    NASA Astrophysics Data System (ADS)

    Glushkov, A. V.; Gurskaya, M. Yu; Ignatenko, A. V.; Smirnov, A. V.; Serga, I. N.; Svinarenko, A. A.; Ternovsky, E. V.

    2017-10-01

    The consistent relativistic energy approach to the finite Fermi-systems (atoms and nuclei) in a strong realistic laser field is presented and applied to computing the multiphoton resonances parameters in some atoms and nuclei. The approach is based on the Gell-Mann and Low S-matrix formalism, multiphoton resonance lines moments technique and advanced Ivanov-Ivanova algorithm of calculating the Green’s function of the Dirac equation. The data for multiphoton resonance width and shift for the Cs atom and the 57Fe nucleus in dependence upon the laser intensity are listed.

  16. A New Generation of Los Alamos Opacity Tables

    DOE PAGES

    Colgan, James Patrick; Kilcrease, David Parker; Magee, Jr., Norman H.; ...

    2016-01-26

    We present a new, publicly available, set of Los Alamos OPLIB opacity tables for the elements hydrogen through zinc. Our tables are computed using the Los Alamos ATOMIC opacity and plasma modeling code, and make use of atomic structure calculations that use fine-structure detail for all the elements considered. Our equation-of-state (EOS) model, known as ChemEOS, is based on the minimization of free energy in a chemical picture and appears to be a reasonable and robust approach to determining atomic state populations over a wide range of temperatures and densities. In this paper we discuss in detail the calculations thatmore » we have performed for the 30 elements considered, and present some comparisons of our monochromatic opacities with measurements and other opacity codes. We also use our new opacity tables in solar modeling calculations and compare and contrast such modeling with previous work.« less

  17. GPU implementation of the linear scaling three dimensional fragment method for large scale electronic structure calculations

    NASA Astrophysics Data System (ADS)

    Jia, Weile; Wang, Jue; Chi, Xuebin; Wang, Lin-Wang

    2017-02-01

    LS3DF, namely linear scaling three-dimensional fragment method, is an efficient linear scaling ab initio total energy electronic structure calculation code based on a divide-and-conquer strategy. In this paper, we present our GPU implementation of the LS3DF code. Our test results show that the GPU code can calculate systems with about ten thousand atoms fully self-consistently in the order of 10 min using thousands of computing nodes. This makes the electronic structure calculations of 10,000-atom nanosystems routine work. This speed is 4.5-6 times faster than the CPU calculations using the same number of nodes on the Titan machine in the Oak Ridge leadership computing facility (OLCF). Such speedup is achieved by (a) carefully re-designing of the computationally heavy kernels; (b) redesign of the communication pattern for heterogeneous supercomputers.

  18. Investigation of neutral particle dynamics in Aditya tokamak plasma with DEGAS2 code

    NASA Astrophysics Data System (ADS)

    Dey, Ritu; Ghosh, Joydeep; Chowdhuri, M. B.; Manchanda, R.; Banerjee, S.; Ramaiya, N.; Sharma, Deepti; Srinivasan, R.; Stotler, D. P.; Aditya Team

    2017-08-01

    Neutral particle behavior in Aditya tokamak, which has a circular poloidal ring limiter at one particular toroidal location, has been investigated using DEGAS2 code. The code is based on the calculation using Monte Carlo algorithms and is mainly used in tokamaks with divertor configuration. This code has been successfully implemented in Aditya tokamak with limiter configuration. The penetration of neutral hydrogen atom is studied with various atomic and molecular contributions and it is found that the maximum contribution comes from the dissociation processes. For the same, H α spectrum is also simulated and matched with the experimental one. The dominant contribution around 64% comes from molecular dissociation processes and neutral particle is generated by those processes have energy of ~2.0 eV. Furthermore, the variation of neutral hydrogen density and H α emissivity profile are analysed for various edge temperature profiles and found that there is not much changes in H α emission at the plasma edge with the variation of edge temperature (7-40 eV).

  19. Investigation of neutral particle dynamics in Aditya tokamak plasma with DEGAS2 code

    DOE PAGES

    Dey, Ritu; Ghosh, Joydeep; Chowdhuri, M. B.; ...

    2017-06-09

    Neutral particle behavior in Aditya tokamak, which has a circular poloidal ring limiter at one particular toroidal location, has been investigated using DEGAS2 code. The code is based on the calculation using Monte Carlo algorithms and is mainly used in tokamaks with divertor configuration. This code has been successfully implemented in Aditya tokamak with limiter configuration. The penetration of neutral hydrogen atom is studied with various atomic and molecular contributions and it is found that the maximum contribution comes from the dissociation processes. For the same, H α spectrum is also simulated which was matched with the experimental one. Themore » dominant contribution around 64% comes from molecular dissociation processes and neutral particle is generated by those processes have energy of ~ 2.0 eV. Furthermore, the variation of neutral hydrogen density and H α emissivity profile are analysed for various edge temperature profiles and found that there is not much changes in H α emission at the plasma edge with the variation of edge temperature (7 to 40 eV).« less

  20. Sensitivity Analysis Applied to Atomic Data Used for X-ray Spectrum Synthesis

    NASA Technical Reports Server (NTRS)

    Kallman, Tim

    2006-01-01

    A great deal of work has been devoted to the accumulation of accurate quantities describing atomic processes for use in analysis of astrophysical spectra. But in many situations of interest the interpretation of a quantity which is observed, such as a line flux, depends on the results of a modeling- or spectrum synthesis code. The results of such a code depends in turn 011 many atomic rates or cross sections, and the sensitivity of the observable quantity on the various rates and cross sections may be non-linear and if so cannot easily be derived analytically. In such cases the most practical approach to understanding the sensitivity of observables to atomic cross sections is to perform numerical experiments, by calculating models with various rates perturbed by random (but known) factors. In addition, it is useful to compare the results of such experiments with some sample observations, in order to focus attention on the rates which are of the greatest relevance to real observations. In this paper I will present some attempts to carry out this program, focussing on two sample datasets taken with the Chandra HETG. I will discuss the sensitivity of synthetic spectra to atomic data affecting ionization balance, temperature, and line opacity or emissivity, and discuss the implications for the ultimate goal of inferring astrophysical parameters.

  1. Sensitivity Analysis Applied to Atomic Data Used for X-ray Spectrum Synthesis

    NASA Technical Reports Server (NTRS)

    Kallman, Tim

    2006-01-01

    A great deal of work has been devoted to the accumulation of accurate quantities describing atomic processes for use in analysis of astrophysical spectra. But in many situations of interest the interpretation of a quantity which is observed, such as a line flux, depends on the results of a modeling- or spectrum synthesis code. The results of such a code depends in turn on many atomic rates or cross sections, and the sensitivity of the observable quantity on the various rates and cross sections may be non-linear and if so cannot easily be derived analytically. In such cases the most practical approach to understanding the sensitivity of observables to atomic cross sections is to perform numerical experiments, by calculating models with various rates perturbed by random (but known) factors. In addition, it is useful to compare the results of such experiments with some sample observations, in order to focus attention on the rates which are of the greatest relevance to real observations. In this paper I will present some attempts to carry out this program, focussing on two sample datasets taken with the Chandra HETG. I will discuss the sensitivity of synthetic spectra to atomic data affecting ionization balance, temperature, and line opacity or emissivity, and discuss the implications for the ultimate goal of inferring astrophysical parameters.

  2. Evolution of Xe spectrum and ion charge under sudden incoming radiation

    NASA Astrophysics Data System (ADS)

    Klapisch, Marcel; Busquet, Michel

    2012-06-01

    Experiments [1] and simulations of Xe at high temperature were recently reported, due to the possible scaling of astrophysical radiative shocks [2]. We used the newest version of HULLAC [3] to compute energy levels, radiative and collisional transition rates and level populations in a Coronal Radiative Model for the ions Xe9+ to Xe44+ (36263 configurations), at electron temperature of 100 eV and electron density of 10^19 -- 10^21 e/cm^3, in the presence of an external Planckian radiation field. Static and time dependent influence of the radiation on ion charge and spectrum is described. We show an effect of shell structure on relaxation of ion charge when the radiation field is suddenly turn on.[4pt] [1] Busquet, M., Thais, F., Gonzalez, M., et al., J. App. Phys. 107, 083302 (2010).[0pt] [2] Ryutov, D., Drake, R. P., Kane, J., et al., Astrophys. J. 518, 821 (1999).[0pt] [3] Klapisch, M. and Busquet, M., High Ener. Dens. Phys. 7, 98 (2011).

  3. Stretching of short monatomic gold chains-some model calculations

    NASA Astrophysics Data System (ADS)

    Sumali, Priyanka, Verma, Veena; Dharamvir, Keya

    2012-06-01

    The Mechanical properties of zig-zag monatomic gold chains containing 5 and 7 atoms were studied using the Siesta Code (SC), which works within the framework of DFT formalism and Gupta Potential (GP), which is an effective atom-atom potential. The zig-zag chains were stretched by keeping the end atoms fixed while rest of the atoms were relaxed till minimum energy is obtained. Energy, Force and Young's Modulus found using GP and SC were plotted as functions of total length. It is found that the breaking force in case of GP is of order of 1.6nN while for SIESTA is of the order of 2.9nN for both the chains.

  4. Low-energy Scattering of Positronium by Atoms

    NASA Technical Reports Server (NTRS)

    Ray, Hasi

    2007-01-01

    The survey reports theoretical studies involving positronium (Ps) - atom scattering. Investigations carried out in last few decades have been briefly reviewed in this article. A brief description of close-coupling approximation (CCA), the first-Born approximation (FBA) and the Born-Oppenheimer approximation (BOA) for Ps-Atom systems are made. The CCA codes of Ray et a1 [1-6] are reinvestigated using very fine mesh-points to search for resonances. The article advocates the need for an extended basis set & a systematic study using CCAs.

  5. From deep TLS validation to ensembles of atomic models built from elemental motions. Addenda and corrigendum

    DOE PAGES

    Urzhumtsev, Alexandre; Afonine, Pavel V.; Van Benschoten, Andrew H.; ...

    2016-08-31

    Researcher feedback has indicated that in Urzhumtsevet al.[(2015)Acta Cryst.D71, 1668–1683] clarification of key parts of the algorithm for interpretation of TLS matrices in terms of elemental atomic motions and corresponding ensembles of atomic models is required. Also, it has been brought to the attention of the authors that the incorrect PDB code was reported for one of test models. Lastly, these issues are addressed in this article.

  6. Index to the Understanding the Atom Series.

    ERIC Educational Resources Information Center

    Atomic Energy Commission, Oak Ridge, TN. Div. of Technical Information.

    The topics covered by 47 booklets in the series are indexed. Page references are not given, but the booklet covering each topic is indicated by a code explained in the first two pages of the index. A brief account of the educational services program of the Atomic Energy Commission describing the booklets, films, and other services provided for…

  7. Time-resolved x-ray spectra from laser-generated high-density plasmas

    NASA Astrophysics Data System (ADS)

    Andiel, U.; Eidmann, Klaus; Witte, Klaus-Juergen

    2001-04-01

    We focused frequency doubled ultra short laser pulses on solid C, F, Na and Al targets, K-shell emission was systematically investigated by time resolved spectroscopy using a sub-ps streak camera. A large number of laser shots can be accumulated when triggering the camera with an Auston switch system at very high temporal precision. The system provides an outstanding time resolution of 1.7ps accumulating thousands of laser shots. The time duration of the He-(alpha) K-shell resonance lines was observed in the range of (2-4)ps and shows a decrease with the atomic number. The experimental results are well reproduced by hydro code simulations post processed with an atomic kinetics code.

  8. Mass-invariance of the iron enrichment in the hot haloes of massive ellipticals, groups, and clusters of galaxies

    NASA Astrophysics Data System (ADS)

    Mernier, F.; de Plaa, J.; Werner, N.; Kaastra, J. S.; Raassen, A. J. J.; Gu, L.; Mao, J.; Urdampilleta, I.; Truong, N.; Simionescu, A.

    2018-05-01

    X-ray measurements find systematically lower Fe abundances in the X-ray emitting haloes pervading groups (kT ≲ 1.7 keV) than in clusters of galaxies. These results have been difficult to reconcile with theoretical predictions. However, models using incomplete atomic data or the assumption of isothermal plasmas may have biased the best fit Fe abundance in groups and giant elliptical galaxies low. In this work, we take advantage of a major update of the atomic code in the spectral fitting package SPEX to re-evaluate the Fe abundance in 43 clusters, groups, and elliptical galaxies (the CHEERS sample) in a self-consistent analysis and within a common radius of 0.1r500. For the first time, we report a remarkably similar average Fe enrichment in all these systems. Unlike previous results, this strongly suggests that metals are synthesised and transported in these haloes with the same average efficiency across two orders of magnitude in total mass. We show that the previous metallicity measurements in low temperature systems were biased low due to incomplete atomic data in the spectral fitting codes. The reasons for such a code-related Fe bias, also implying previously unconsidered biases in the emission measure and temperature structure, are discussed.

  9. Algorithms and physical parameters involved in the calculation of model stellar atmospheres

    NASA Astrophysics Data System (ADS)

    Merlo, D. C.

    This contribution summarizes the Doctoral Thesis presented at Facultad de Matemática, Astronomía y Física, Universidad Nacional de Córdoba for the degree of PhD in Astronomy. We analyze some algorithms and physical parameters involved in the calculation of model stellar atmospheres, such as atomic partition functions, functional relations connecting gaseous and electronic pressure, molecular formation, temperature distribution, chemical compositions, Gaunt factors, atomic cross-sections and scattering sources, as well as computational codes for calculating models. Special attention is paid to the integration of hydrostatic equation. We compare our results with those obtained by other authors, finding reasonable agreement. We make efforts on the implementation of methods that modify the originally adopted temperature distribution in the atmosphere, in order to obtain constant energy flux throughout. We find limitations and we correct numerical instabilities. We integrate the transfer equation solving directly the integral equation involving the source function. As a by-product, we calculate updated atomic partition functions of the light elements. Also, we discuss and enumerate carefully selected formulae for the monochromatic absorption and dispersion of some atomic and molecular species. Finally, we obtain a flexible code to calculate model stellar atmospheres.

  10. Theoretical study of Ag doping-induced vacancies defects in armchair graphene

    NASA Astrophysics Data System (ADS)

    Benchallal, L.; Haffad, S.; Lamiri, L.; Boubenider, F.; Zitoune, H.; Kahouadji, B.; Samah, M.

    2018-06-01

    We have performed a density functional theory (DFT) study of the absorption of silver atoms (Ag,Ag2 and Ag3) in graphene using SIESTA code, in the generalized gradient approximation (GGA). The absorption energy, geometry, magnetic moments and charge transfer of Ag clusters-graphene system are calculated. The minimum energy configuration demonstrates that all structures remain planar and silver atoms fit into this plane. The charge transfer between the silver clusters and carbon atoms constituting the graphene surface is an indicative of a strong bond. The structure doped with a single silver atom has a magnetic moment and the two other are nonmagnetic.

  11. Liquid rocket combustor computer code development

    NASA Technical Reports Server (NTRS)

    Liang, P. Y.

    1985-01-01

    The Advanced Rocket Injector/Combustor Code (ARICC) that has been developed to model the complete chemical/fluid/thermal processes occurring inside rocket combustion chambers are highlighted. The code, derived from the CONCHAS-SPRAY code originally developed at Los Alamos National Laboratory incorporates powerful features such as the ability to model complex injector combustion chamber geometries, Lagrangian tracking of droplets, full chemical equilibrium and kinetic reactions for multiple species, a fractional volume of fluid (VOF) description of liquid jet injection in addition to the gaseous phase fluid dynamics, and turbulent mass, energy, and momentum transport. Atomization and droplet dynamic models from earlier generation codes are transplated into the present code. Currently, ARICC is specialized for liquid oxygen/hydrogen propellants, although other fuel/oxidizer pairs can be easily substituted.

  12. A Model for Atomic and Molecular Interstellar Gas: The Meudon PDR Code

    NASA Astrophysics Data System (ADS)

    Le Petit, Franck; Nehmé, Cyrine; Le Bourlot, Jacques; Roueff, Evelyne

    2006-06-01

    We present the revised ``Meudon'' model of photon-dominated region (PDR) code, available on the Web under the GNU Public License. General organization of the code is described down to a level that should allow most observers to use it as an interpretation tool with minimal help from our part. Two grids of models, one for low-excitation diffuse clouds and one for dense highly illuminated clouds, are discussed, and some new results on PDR modelization highlighted.

  13. Estimations of Mo X-pinch plasma parameters on QiangGuang-1 facility by L-shell spectral analyses

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Wu, Jian; Qiu, Aici; State Key Laboratory of Intense Pulsed Radiation Simulation and Effect, Northwest Institute of Nuclear Technology, Xi'an 710024

    2013-08-15

    Plasma parameters of molybdenum (Mo) X-pinches on the 1-MA QiangGuang-1 facility were estimated by L-shell spectral analysis. X-ray radiation from X-pinches had a pulsed width of 1 ns, and its spectra in 2–3 keV were measured with a time-integrated X-ray spectrometer. Relative intensities of spectral features were derived by correcting for the spectral sensitivity of the spectrometer. With an open source, atomic code FAC (flexible atomic code), ion structures, and various atomic radiative-collisional rates for O-, F-, Ne-, Na-, Mg-, and Al-like ionization stages were calculated, and synthetic spectra were constructed at given plasma parameters. By fitting the measured spectramore » with the modeled, Mo X-pinch plasmas on the QiangGuang-1 facility had an electron density of about 10{sup 21} cm{sup −3} and the electron temperature of about 1.2 keV.« less

  14. PCTDSE: A parallel Cartesian-grid-based TDSE solver for modeling laser-atom interactions

    NASA Astrophysics Data System (ADS)

    Fu, Yongsheng; Zeng, Jiaolong; Yuan, Jianmin

    2017-01-01

    We present a parallel Cartesian-grid-based time-dependent Schrödinger equation (TDSE) solver for modeling laser-atom interactions. It can simulate the single-electron dynamics of atoms in arbitrary time-dependent vector potentials. We use a split-operator method combined with fast Fourier transforms (FFT), on a three-dimensional (3D) Cartesian grid. Parallelization is realized using a 2D decomposition strategy based on the Message Passing Interface (MPI) library, which results in a good parallel scaling on modern supercomputers. We give simple applications for the hydrogen atom using the benchmark problems coming from the references and obtain repeatable results. The extensions to other laser-atom systems are straightforward with minimal modifications of the source code.

  15. PyNeb: a new tool for analyzing emission lines. I. Code description and validation of results

    NASA Astrophysics Data System (ADS)

    Luridiana, V.; Morisset, C.; Shaw, R. A.

    2015-01-01

    Analysis of emission lines in gaseous nebulae yields direct measures of physical conditions and chemical abundances and is the cornerstone of nebular astrophysics. Although the physical problem is conceptually simple, its practical complexity can be overwhelming since the amount of data to be analyzed steadily increases; furthermore, results depend crucially on the input atomic data, whose determination also improves each year. To address these challenges we created PyNeb, an innovative code for analyzing emission lines. PyNeb computes physical conditions and ionic and elemental abundances and produces both theoretical and observational diagnostic plots. It is designed to be portable, modular, and largely customizable in aspects such as the atomic data used, the format of the observational data to be analyzed, and the graphical output. It gives full access to the intermediate quantities of the calculation, making it possible to write scripts tailored to the specific type of analysis one wants to carry out. In the case of collisionally excited lines, PyNeb works by solving the equilibrium equations for an n-level atom; in the case of recombination lines, it works by interpolation in emissivity tables. The code offers a choice of extinction laws and ionization correction factors, which can be complemented by user-provided recipes. It is entirely written in the python programming language and uses standard python libraries. It is fully vectorized, making it apt for analyzing huge amounts of data. The code is stable and has been benchmarked against IRAF/NEBULAR. It is public, fully documented, and has already been satisfactorily used in a number of published papers.

  16. PDB file parser and structure class implemented in Python.

    PubMed

    Hamelryck, Thomas; Manderick, Bernard

    2003-11-22

    The biopython project provides a set of bioinformatics tools implemented in Python. Recently, biopython was extended with a set of modules that deal with macromolecular structure. Biopython now contains a parser for PDB files that makes the atomic information available in an easy-to-use but powerful data structure. The parser and data structure deal with features that are often left out or handled inadequately by other packages, e.g. atom and residue disorder (if point mutants are present in the crystal), anisotropic B factors, multiple models and insertion codes. In addition, the parser performs some sanity checking to detect obvious errors. The Biopython distribution (including source code and documentation) is freely available (under the Biopython license) from http://www.biopython.org

  17. Analysis of soft x-ray emission spectra of laser-produced dysprosium, erbium and thulium plasmas

    NASA Astrophysics Data System (ADS)

    Sheil, John; Dunne, Padraig; Higashiguchi, Takeshi; Kos, Domagoj; Long, Elaine; Miyazaki, Takanori; O'Reilly, Fergal; O'Sullivan, Gerard; Sheridan, Paul; Suzuki, Chihiro; Sokell, Emma; White, Elgiva; Kilbane, Deirdre

    2017-03-01

    Soft x-ray emission spectra of dysprosium, erbium and thulium ions created in laser-produced plasmas were recorded with a flat-field grazing-incidence spectrometer in the 2.5-8 nm spectral range. The ions were produced using an Nd:YAG laser of 7 ns pulse duration and the spectra were recorded at various power densities. The experimental spectra were interpreted with the aid of the Cowan suite of atomic structure codes and the flexible atomic code. At wavelengths above 5.5 nm the spectra are dominated by overlapping n = 4 - n = 4 unresolved transition arrays from adjacent ion stages. Below 6 nm, n = 4 - n = 5 transitions also give rise to a series of interesting overlapping spectral features.

  18. MC3, Version 1

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Cawkwell, Marc Jon

    2016-09-09

    The MC3 code is used to perform Monte Carlo simulations in the isothermal-isobaric ensemble (constant number of particles, temperature, and pressure) on molecular crystals. The molecules within the periodic simulation cell are treated as rigid bodies, alleviating the requirement for a complex interatomic potential. Intermolecular interactions are described using generic, atom-centered pair potentials whose parameterization is taken from the literature [D. E. Williams, J. Comput. Chem., 22, 1154 (2001)] and electrostatic interactions arising from atom-centered, fixed, point partial charges. The primary uses of the MC3 code are the computation of i) the temperature and pressure dependence of lattice parameters andmore » thermal expansion coefficients, ii) tensors of elastic constants and compliances via the Parrinello and Rahman’s fluctuation formula [M. Parrinello and A. Rahman, J. Chem. Phys., 76, 2662 (1982)], and iii) the investigation of polymorphic phase transformations. The MC3 code is written in Fortran90 and requires LAPACK and BLAS linear algebra libraries to be linked during compilation. Computationally expensive loops are accelerated using OpenMP.« less

  19. DOE Office of Scientific and Technical Information (OSTI.GOV)

    Dey, Ritu; Ghosh, Joydeep; Chowdhuri, M. B.

    Neutral particle behavior in Aditya tokamak, which has a circular poloidal ring limiter at one particular toroidal location, has been investigated using DEGAS2 code. The code is based on the calculation using Monte Carlo algorithms and is mainly used in tokamaks with divertor configuration. This code has been successfully implemented in Aditya tokamak with limiter configuration. The penetration of neutral hydrogen atom is studied with various atomic and molecular contributions and it is found that the maximum contribution comes from the dissociation processes. For the same, H α spectrum is also simulated which was matched with the experimental one. Themore » dominant contribution around 64% comes from molecular dissociation processes and neutral particle is generated by those processes have energy of ~ 2.0 eV. Furthermore, the variation of neutral hydrogen density and H α emissivity profile are analysed for various edge temperature profiles and found that there is not much changes in H α emission at the plasma edge with the variation of edge temperature (7 to 40 eV).« less

  20. NLTE opacity calculations: C-Si and C-Ge mixtures

    NASA Astrophysics Data System (ADS)

    Jarrah, W.; Benredjem, D.; Pain, J.-C.; Dubau, J.

    2017-09-01

    The opacity is an important issue in the knowledge of the radiative properties of ICF and astrophysical plasmas. We present the opacity of dopants (silicon, germanium) embedded in the ablator of some ICF capsules. In recent works, Hill and Rose calculated the opacity of silicon in LTE and non-LTE plasmas, while Minguez and co-workers focused on the opacity of carbon. We have used the Cowan code to calculate the atomic structure of carbon, silicon and germanium in various ionic stages. The cross-sections of atomic processes (collisional excitation, collisional ionization) are obtained by fitting the values given by the code FAC to the Van Regemorter-like formulas of Sampson and Zhang. A corrected Gaunt factor is then obtained. A collisional-radiative code was developed in order to obtain the ionic populations, the level populations and the opacity. Line broadening and line shift are taken into account. The ionization potential depression is included in our calculations. The effect of a radiation field on the opacity is examined.

  1. Handling of Atomic Data

    NASA Astrophysics Data System (ADS)

    Rauch, T.; Deetjen, J. L.

    2003-01-01

    State-of-the-art NLTE model atmosphere codes have arrived at a high level of ``numerical'' sophistication and are an adequate tool to analyze the available high-quality spectra from the infrared to the X-ray wavelength range. The computational capacities allow the calculation which include all elements from hydrogen up to the iron group and the lack of reliable atomic data has become a crucial problem for further progress. We summarize briefly the available sources of atomic data and how these are implemented in the Tübingen Model Atmosphere Package (TMAP).

  2. Atomization and Mixing Study

    NASA Technical Reports Server (NTRS)

    Ferrenberg, A.; Hunt, K.; Duesberg, J.

    1985-01-01

    The primary objective was the obtainment of atomization and mixing performance data for a variety of typical liquid oxygen/hydrocarbon injector element designs. Such data are required to establish injector design criteria and to provide critical inputs to liquid rocket engine combustor performance and stability analysis, and computational codes and methods. Deficiencies and problems with the atomization test equipment were identified, and action initiated to resolve them. Test results of the gas/liquid mixing tests indicated that an assessment of test methods was required. A series of 71 liquid/liquid tests were performed.

  3. Observing heliospheric neutral atoms at 1 AU

    NASA Astrophysics Data System (ADS)

    Heerikhuisen, Jacob; Pogorelov, Nikolai; Florinski, Vladimir; Zank, Gary

    2006-09-01

    Although in situ observations of distant heliospheric plasma by the Voyagers has proven to be extremely enlightening, such point observations need to be complemented with global measurements taken remotely to obtain a complete picture of the heliosphere and local interstellar environment. Neutral atoms, with their contempt for magnetic fields, provide useful probes of the plasma that generated them. However, there will be a number of ambiguities in neutral atom readings that require a deeper understanding of the plasma processes generating neutral atoms, as well as the loss mechanisms on their flight to the observation point. We introduce a procedure for generating all-sky maps of energetic H-atoms, calculated directly in our Monte-Carlo neutral atom code. Results obtained for a self-consistent axisymmetric MHD-Boltzmann calculation, as well as several non-selfconsistent 3D sky maps, will be presented.

  4. VizieR Online Data Catalog: Energy levels & transition rates for F-like ions (Si+, 2016)

    NASA Astrophysics Data System (ADS)

    Si, R.; Li, S.; Guo, X. L.; Chen, Z. B.; Brage, T.; Jonsson, P.; Wang, K.; Yan, J.; Chen, C. Y.; Zou, Y. M.

    2017-01-01

    For the multiconfiguration Dirac-Hartree-Fock (MCDHF) calculation we use the latest version of the GRASP2K code (Jonsson+ 2013CoPhC.184.2197J), while the many-body perturbation theory (MBPT) calculation is performed using the Flexible Atomic Code (FAC; Gu 2008CaJPh..86..675G). (2 data files).

  5. Ignition and combustion characteristics of metallized propellants, phase 2

    NASA Technical Reports Server (NTRS)

    Mueller, D. C.; Turns, S. R.

    1994-01-01

    Experimental and analytical investigations focusing on aluminum/hydrocarbon gel droplet secondary atomization and its effects on gel-fueled rocket engine performance are being conducted. A single laser sheet sizing/velocimetry diagnostic technique, which should eliminate sizing bias in the data collection process, has been designed and constructed to overcome limitations of the two-color forward-scatter technique used in previous work. Calibration of this system is in progress and the data acquisition/validation code is being written. Narrow-band measurements of radiant emission, discussed in previous reports, will be used to determine if aluminum ignition has occurred in a gel droplet. A one-dimensional model of a gel-fueled rocket combustion chamber, described in earlier reports, has been exercised in conjunction with a two-dimensional, two-phase nozzle code to predict the performance of an aluminum/hydrocarbon fueled engine. Estimated secondary atomization effects on propellant burnout distance, condensed particle radiation losses to the chamber walls, and nozzle two phase flow losses are also investigated. Calculations indicate that only modest secondary atomization is required to significantly reduce propellant burnout distances, aluminum oxide residual size, and radiation heat losses. Radiation losses equal to approximately 2-13 percent of the energy released during combustion were estimated, depending on secondary atomization intensity. A two-dimensional, two-phase nozzle code was employed to estimate radiation and nozzle two phase flow effects on overall engine performance. Radiation losses yielded a one percent decrease in engine Isp. Results also indicate that secondary atomization may have less effect on two-phase losses than it does on propellant burnout distance and no effect if oxide particle coagulation and shear induced droplet breakup govern oxide particle size. Engine Isp was found to decrease from 337.4 to 293.7 seconds as gel aluminum mass loading was varied from 0-70 wt percent. Engine Isp efficiencies, accounting for radiation and two phase flow effects, on the order of 0.946 were calculated for a 60 wt percent gel, assuming a fragmentation ratio of five.

  6. Study of premixing phase of steam explosion with JASMINE code in ALPHA program

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Moriyama, Kiyofumi; Yamano, Norihiro; Maruyama, Yu

    Premixing phase of steam explosion has been studied in ALPHA Program at Japan Atomic Energy Research Institute (JAERI). An analytical model to simulate the premixing phase, JASMINE (JAERI Simulator for Multiphase Interaction and Explosion), has been developed based on a multi-dimensional multi-phase thermal hydraulics code MISTRAL (by Fuji Research Institute Co.). The original code was extended to simulate the physics in the premixing phenomena. The first stage of the code validation was performed by analyzing two mixing experiments with solid particles and water: the isothermal experiment by Gilbertson et al. (1992) and the hot particle experiment by Angelini et al.more » (1993) (MAGICO). The code predicted reasonably well the experiments. Effectiveness of the TVD scheme employed in the code was also demonstrated.« less

  7. The displacement effect of a fluorine atom in CaF2 on the band structure

    NASA Astrophysics Data System (ADS)

    Mir, A.; Zaoui, A.; Bensaid, D.

    2018-05-01

    We obtained the results for each configuration [100], [110] and [111] and each configuration contains two atoms of calcium and four fluorine atoms with lattice type B. This study was made by a code that is based on the DFT called wien2k. The results obtained are in good agreement with the experiment. For CaF2, an important variation of the fluoride ions concentration in CaF2 after displacement has been observed on the map of e-Density. The interpretation of the results is based on the existence of an important number of defects which are created by changing the atomic positions inside of sub lattice.

  8. Neutron displacement cross-sections for tantalum and tungsten at energies up to 1 GeV

    NASA Astrophysics Data System (ADS)

    Broeders, C. H. M.; Konobeyev, A. Yu.; Villagrasa, C.

    2005-06-01

    The neutron displacement cross-section has been evaluated for tantalum and tungsten at energies from 10 -5 eV up to 1 GeV. The nuclear optical model, the intranuclear cascade model combined with the pre-equilibrium and evaporation models were used for the calculations. The number of defects produced by recoil atoms nuclei in materials was calculated by the Norgett, Robinson, Torrens model and by the approach combining calculations using the binary collision approximation model and the results of the molecular dynamics simulation. The numerical calculations were done using the NJOY code, the ECIS96 code, the MCNPX code and the IOTA code.

  9. Energy levels, radiative rates and electron impact excitation rates for transitions in He-like Ga XXX, Ge XXXI, As XXXII, Se XXXIII and Br XXXIV

    NASA Astrophysics Data System (ADS)

    Aggarwal, Kanti M.; Keenan, Francis P.

    2013-04-01

    We report calculations of energy levels, radiative rates and electron impact excitation cross sections and rates for transitions in He-like Ga XXX, Ge XXXI, As XXXII, Se XXXIII and Br XXXIV. The grasp (general-purpose relativistic atomic structure package) is adopted for calculating energy levels and radiative rates. For determining the collision strengths, and subsequently the excitation rates, the Dirac atomic R-matrix code (darc) is used. Oscillator strengths, radiative rates and line strengths are reported for all E1, E2, M1 and M2 transitions among the lowest 49 levels of each ion. Additionally, theoretical lifetimes are provided for all 49 levels of the above five ions. Collision strengths are averaged over a Maxwellian velocity distribution and the effective collision strengths obtained listed over a wide temperature range up to 108 K. Comparisons are made with similar data obtained using the flexible atomic code (fac) to highlight the importance of resonances, included in calculations with darc, in the determination of effective collision strengths. Discrepancies between the collision strengths from darc and fac, particularly for some forbidden transitions, are also discussed. Finally, discrepancies between the present results for effective collision strengths with the darc code and earlier semi-relativistic R-matrix data are noted over a wide range of electron temperatures for many transitions in all ions.

  10. Scalable and portable visualization of large atomistic datasets

    NASA Astrophysics Data System (ADS)

    Sharma, Ashish; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya

    2004-10-01

    A scalable and portable code named Atomsviewer has been developed to interactively visualize a large atomistic dataset consisting of up to a billion atoms. The code uses a hierarchical view frustum-culling algorithm based on the octree data structure to efficiently remove atoms outside of the user's field-of-view. Probabilistic and depth-based occlusion-culling algorithms then select atoms, which have a high probability of being visible. Finally a multiresolution algorithm is used to render the selected subset of visible atoms at varying levels of detail. Atomsviewer is written in C++ and OpenGL, and it has been tested on a number of architectures including Windows, Macintosh, and SGI. Atomsviewer has been used to visualize tens of millions of atoms on a standard desktop computer and, in its parallel version, up to a billion atoms. Program summaryTitle of program: Atomsviewer Catalogue identifier: ADUM Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADUM Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Computer for which the program is designed and others on which it has been tested: 2.4 GHz Pentium 4/Xeon processor, professional graphics card; Apple G4 (867 MHz)/G5, professional graphics card Operating systems under which the program has been tested: Windows 2000/XP, Mac OS 10.2/10.3, SGI IRIX 6.5 Programming languages used: C++, C and OpenGL Memory required to execute with typical data: 1 gigabyte of RAM High speed storage required: 60 gigabytes No. of lines in the distributed program including test data, etc.: 550 241 No. of bytes in the distributed program including test data, etc.: 6 258 245 Number of bits in a word: Arbitrary Number of processors used: 1 Has the code been vectorized or parallelized: No Distribution format: tar gzip file Nature of physical problem: Scientific visualization of atomic systems Method of solution: Rendering of atoms using computer graphic techniques, culling algorithms for data minimization, and levels-of-detail for minimal rendering Restrictions on the complexity of the problem: None Typical running time: The program is interactive in its execution Unusual features of the program: None References: The conceptual foundation and subsequent implementation of the algorithms are found in [A. Sharma, A. Nakano, R.K. Kalia, P. Vashishta, S. Kodiyalam, P. Miller, W. Zhao, X.L. Liu, T.J. Campbell, A. Haas, Presence—Teleoperators and Virtual Environments 12 (1) (2003)].

  11. An analytical benchmark and a Mathematica program for MD codes: Testing LAMMPS on the 2nd generation Brenner potential

    NASA Astrophysics Data System (ADS)

    Favata, Antonino; Micheletti, Andrea; Ryu, Seunghwa; Pugno, Nicola M.

    2016-10-01

    An analytical benchmark and a simple consistent Mathematica program are proposed for graphene and carbon nanotubes, that may serve to test any molecular dynamics code implemented with REBO potentials. By exploiting the benchmark, we checked results produced by LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) when adopting the second generation Brenner potential, we made evident that this code in its current implementation produces results which are offset from those of the benchmark by a significant amount, and provide evidence of the reason.

  12. Science & Technology Review November 2007

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Chinn, D J

    2007-10-16

    This month's issue has the following articles: (1) Simulating the Electromagnetic World--Commentary by Steven R. Patterson; (2) A Code to Model Electromagnetic Phenomena--EMSolve, a Livermore supercomputer code that simulates electromagnetic fields, is helping advance a wide range of research efforts; (3) Characterizing Virulent Pathogens--Livermore researchers are developing multiplexed assays for rapid detection of pathogens; (4) Imaging at the Atomic Level--A powerful new electron microscope at the Laboratory is resolving materials at the atomic level for the first time; (5) Scientists without Borders--Livermore scientists lend their expertise on peaceful nuclear applications to their counterparts in other countries; and (6) Probing Deepmore » into the Nucleus--Edward Teller's contributions to the fast-growing fields of nuclear and particle physics were part of a physics golden age.« less

  13. AtomDB Progress Report: Atomic data and new models for X-ray spectroscopy.

    NASA Astrophysics Data System (ADS)

    Smith, Randall K.; Foster, Adam; Brickhouse, Nancy S.; Stancil, Phillip C.; Cumbee, Renata; Mullen, Patrick Dean; AtomDB Team

    2018-06-01

    The AtomDB project collects atomic data from both theoretical and observational/experimental sources, providing both a convenient interface (http://www.atomdb.org/Webguide/webguide.php) as well as providing input to spectral models for many types of astrophysical X-ray plasmas. We have released several updates to AtomDB in response to the Hitomi data, including new data for the Fe K complex, and have expanded the range of models available in AtomDB to include the Kronos charge exchange models from Mullen at al. (2016, ApJS, 224, 2). Combined with the previous AtomDB charge exchange model (http://www.atomdb.org/CX/), these data enable a velocity-dependent model for X-ray and EUV charge exchange spectra. We also present a new Kappa-distribution spectral model, enabling plasmas with non-Maxwellian electron distributions to be modeled with AtomDB. Tools are provided within pyAtomDB to explore and exploit these new plasma models. This presentation will review these enhancements and describe plans for the new few years of database and code development in preparation for XARM, Athena, and (hopefully) Arcus.

  14. Testing Photoionization Calculations Using Chandra X-ray Spectra

    NASA Technical Reports Server (NTRS)

    Kallman, Tim

    2008-01-01

    A great deal of work has been devoted to the accumulation of accurate quantities describing atomic processes for use in analysis of astrophysical spectra. But in many situations of interest the interpretation of a quantity which is observed, such as a line flux, depends on the results of a modeling- or spectrum synthesis code. The results of such a code depends in turn on many atomic rates or cross sections, and the sensitivity of the observable quantity on the various rates and cross sections may be non-linear and if so cannot easily be derived analytically. In such cases the most practical approach to understanding the sensitivity of observables to atomic cross sections is to perform numerical experiments, by calculating models with various rates perturbed by random (but known) factors. In addition, it is useful to compare the results of such experiments with some sample observations, in order to focus attention on the rates which are of the greatest relevance to real observations. In this paper I will present some attempts to carry out this program, focussing on two sample datasets taken with the Chandra HETG. I will discuss the sensitivity of synthetic spectra to atomic data affecting ionization balance, temperature, and line opacity or emissivity, and discuss the implications for the ultimate goal of inferring astrophysical parameters.

  15. Polarization-dependent atomic dipole traps behind a circular aperture for neutral-atom quantum computing

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Gillen-Christandl, Katharina; Copsey, Bert D.

    2011-02-15

    The neutral-atom quantum computing community has successfully implemented almost all necessary steps for constructing a neutral-atom quantum computer. We present computational results of a study aimed at solving the remaining problem of creating a quantum memory with individually addressable sites for quantum computing. The basis of this quantum memory is the diffraction pattern formed by laser light incident on a circular aperture. Very close to the aperture, the diffraction pattern has localized bright and dark spots that can serve as red-detuned or blue-detuned atomic dipole traps. These traps are suitable for quantum computing even for moderate laser powers. In particular,more » for moderate laser intensities ({approx}100 W/cm{sup 2}) and comparatively small detunings ({approx}1000-10 000 linewidths), trap depths of {approx}1 mK and trap frequencies of several to tens of kilohertz are achieved. Our results indicate that these dipole traps can be moved by tilting the incident laser beams without significantly changing the trap properties. We also explored the polarization dependence of these dipole traps. We developed a code that calculates the trapping potential energy for any magnetic substate of any hyperfine ground state of any alkali-metal atom for any laser detuning much smaller than the fine-structure splitting for any given electric field distribution. We describe details of our calculations and include a summary of different notations and conventions for the reduced matrix element and how to convert it to SI units. We applied this code to these traps and found a method for bringing two traps together and apart controllably without expelling the atoms from the trap and without significant tunneling probability between the traps. This approach can be scaled up to a two-dimensional array of many pinholes, forming a quantum memory with single-site addressability, in which pairs of atoms can be brought together and apart for two-qubit gates for quantum computing.« less

  16. Effect on magnetic properties of germanium encapsulated C60 fullerene

    NASA Astrophysics Data System (ADS)

    Umran, Nibras Mossa; Kumar, Ranjan

    2013-02-01

    Structural and electronic properties of Gen(n = 1-4) doped C60 fullerene are investigated with ab initio density functional theory calculations by using an efficient computer code, known as SIESTA. The pseudopotentials are constructed using a Trouiller-Martins scheme, to describe the interaction of valence electrons with the atomic cores. In endohedral doped embedding of more germanium atoms complexes we have seen that complexes are stable and thereafter cage break down. We have also investigated that binding energy, electronic affinity increases and magnetic moment oscillating behavior as the number of semiconductor atoms in C60 fullerene goes on increasing.

  17. Comparison of stochastic optimization methods for all-atom folding of the Trp-Cage protein.

    PubMed

    Schug, Alexander; Herges, Thomas; Verma, Abhinav; Lee, Kyu Hwan; Wenzel, Wolfgang

    2005-12-09

    The performances of three different stochastic optimization methods for all-atom protein structure prediction are investigated and compared. We use the recently developed all-atom free-energy force field (PFF01), which was demonstrated to correctly predict the native conformation of several proteins as the global optimum of the free energy surface. The trp-cage protein (PDB-code 1L2Y) is folded with the stochastic tunneling method, a modified parallel tempering method, and the basin-hopping technique. All the methods correctly identify the native conformation, and their relative efficiency is discussed.

  18. ELSEPA—Dirac partial-wave calculation of elastic scattering of electrons and positrons by atoms, positive ions and molecules

    NASA Astrophysics Data System (ADS)

    Salvat, Francesc; Jablonski, Aleksander; Powell, Cedric J.

    2005-01-01

    The FORTRAN 77 code system ELSEPA for the calculation of elastic scattering of electrons and positrons by atoms, positive ions and molecules is presented. These codes perform relativistic (Dirac) partial-wave calculations for scattering by a local central interaction potential V(r). For atoms and ions, the static-field approximation is adopted, with the potential set equal to the electrostatic interaction energy between the projectile and the target, plus an approximate local exchange interaction when the projectile is an electron. For projectiles with kinetic energies up to 10 keV, the potential may optionally include a semiempirical correlation-polarization potential to describe the effect of the target charge polarizability. Also, for projectiles with energies less than 1 MeV, an imaginary absorptive potential can be introduced to account for the depletion of the projectile wave function caused by open inelastic channels. Molecular cross sections are calculated by means of a single-scattering independent-atom approximation in which the electron density of a bound atom is approximated by that of the free neutral atom. Elastic scattering by individual atoms in solids is described by means of a muffin-tin model potential. Partial-wave calculations are feasible on modest personal computers for energies up to about 5 MeV. The ELSEPA code also implements approximate factorization methods that allow the fast calculation of elastic cross sections for much higher energies. The interaction model adopted in the calculations is defined by the user by combining the different options offered by the code. The nuclear charge distribution can be selected among four analytical models (point nucleus, uniformly charged sphere, Fermi's distribution and Helm's uniform-uniform distribution). The atomic electron density is handled in numerical form. The distribution package includes data files with electronic densities of neutral atoms of the elements hydrogen to lawrencium ( Z=1-103) obtained from multiconfiguration Dirac-Fock self-consistent calculations. For comparison purposes, three simple analytical approximations to the electron density of neutral atoms (corresponding to the Thomas-Fermi, the Thomas-Fermi-Dirac and the Dirac-Hartree-Fock-Slater models) are also included. For calculations of elastic scattering by ions, the electron density should be provided by the user. The exchange potential for electron scattering can be selected among three different analytical approximations (Thomas-Fermi, Furness-McCarthy, Riley-Truhlar). The offered options for the correlation-polarization potential are based on the empirical Buckingham potential. The imaginary absorption potential is calculated from the local-density approximation proposed by Salvat [Phys. Rev. A 68 (2003) 012708]. Program summaryTitle of program:ELSEPA Catalogue identifier: ADUS Program summary URL:http://cpc.cs.qub.ac.uk/cpc/summaries/ADUS Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland License provisions: none Computer for which the program is designed and others in which it is operable: Any computer with a FORTRAN 77 compiler Operating systems under which the program has been tested: Windows XP, Windows 2000, Debian GNU/Linux 3.0r0 (sarge) Compilers:Compaq Visual Fortran v6.5 (Windows); GNU FORTRAN, g77 (Windows and Linux) Programming language used: FORTRAN 77 No. of bits in a word: 32 Memory required to execute with typical data: 0.6 Mb No. of lines in distributed program, including test data, etc.:135 489 No. of bytes in distributed program, including test data, etc.: 1 280 006 Distribution format: tar.gz Keywords: Dirac partial-wave analysis, electron elastic scattering, positron elastic scattering, differential cross sections, momentum transfer cross sections, transport cross sections, scattering amplitudes, spin polarization, scattering by complex potentials, high-energy atomic screening functions Nature of the physical problem: The code calculates differential cross sections, total cross sections and transport cross sections for single elastic scattering of electrons and positrons by neutral atoms, positive ions and randomly oriented molecules. For projectiles with kinetic energies less than about 5 MeV, the programs can also compute scattering amplitudes and spin polarization functions. Method of solution: The effective interaction between the projectile and a target atom is represented by a local central potential that can optionally include an imaginary (absorptive) part to account approximately for the coupling with inelastic channels. For projectiles with kinetic energy less that about 5 MeV, the code performs a conventional relativistic Dirac partial-wave analysis. For higher kinetic energies, where the convergence of the partial-wave series is too slow, approximate factorization methods are used. Restrictions on the complexity of the program: The calculations are based on the static-field approximation. The optional correlation-polarization and inelastic absorption corrections are obtained from approximate, semiempirical models. Calculations for molecules are based on a single-scattering independent-atom approximation. To ensure accuracy of the results for scattering by ions, the electron density of the ion must be supplied by the user. Typical running time: on a 2.8 GHz Pentium 4, the calculation of elastic scattering by atoms and ions takes between a few seconds and about two minutes, depending on the atomic number of the target, the adopted potential model and the kinetic energy of the projectile. Unusual features of the program: The program calculates elastic cross sections for electrons and positrons with kinetic energies in a wide range, from a few tens of eV up to about 1 GeV. Calculations can be performed for neutral atoms of all elements, from hydrogen to lawrencium ( Z=1-103), ions and simple molecules. Commercial products are identified to specify the calculational procedures. Such identification does not imply recommendation or endorsement by the National Institute of Standards and Technology, the University of Barcelona or the Polish Academy of Sciences, nor does it imply that the products are necessarily the best available for the purpose.

  19. Next-generation acceleration and code optimization for light transport in turbid media using GPUs

    PubMed Central

    Alerstam, Erik; Lo, William Chun Yip; Han, Tianyi David; Rose, Jonathan; Andersson-Engels, Stefan; Lilge, Lothar

    2010-01-01

    A highly optimized Monte Carlo (MC) code package for simulating light transport is developed on the latest graphics processing unit (GPU) built for general-purpose computing from NVIDIA - the Fermi GPU. In biomedical optics, the MC method is the gold standard approach for simulating light transport in biological tissue, both due to its accuracy and its flexibility in modelling realistic, heterogeneous tissue geometry in 3-D. However, the widespread use of MC simulations in inverse problems, such as treatment planning for PDT, is limited by their long computation time. Despite its parallel nature, optimizing MC code on the GPU has been shown to be a challenge, particularly when the sharing of simulation result matrices among many parallel threads demands the frequent use of atomic instructions to access the slow GPU global memory. This paper proposes an optimization scheme that utilizes the fast shared memory to resolve the performance bottleneck caused by atomic access, and discusses numerous other optimization techniques needed to harness the full potential of the GPU. Using these techniques, a widely accepted MC code package in biophotonics, called MCML, was successfully accelerated on a Fermi GPU by approximately 600x compared to a state-of-the-art Intel Core i7 CPU. A skin model consisting of 7 layers was used as the standard simulation geometry. To demonstrate the possibility of GPU cluster computing, the same GPU code was executed on four GPUs, showing a linear improvement in performance with an increasing number of GPUs. The GPU-based MCML code package, named GPU-MCML, is compatible with a wide range of graphics cards and is released as an open-source software in two versions: an optimized version tuned for high performance and a simplified version for beginners (http://code.google.com/p/gpumcml). PMID:21258498

  20. Implementation of a 3D halo neutral model in the TRANSP code and application to projected NSTX-U plasmas

    NASA Astrophysics Data System (ADS)

    Medley, S. S.; Liu, D.; Gorelenkova, M. V.; Heidbrink, W. W.; Stagner, L.

    2016-02-01

    A 3D halo neutral code developed at the Princeton Plasma Physics Laboratory and implemented for analysis using the TRANSP code is applied to projected National Spherical Torus eXperiment-Upgrade (NSTX-U plasmas). The legacy TRANSP code did not handle halo neutrals properly since they were distributed over the plasma volume rather than remaining in the vicinity of the neutral beam footprint as is actually the case. The 3D halo neutral code uses a ‘beam-in-a-box’ model that encompasses both injected beam neutrals and resulting halo neutrals. Upon deposition by charge exchange, a subset of the full, one-half and one-third beam energy components produce first generation halo neutrals that are tracked through successive generations until an ionization event occurs or the descendant halos exit the box. The 3D halo neutral model and neutral particle analyzer (NPA) simulator in the TRANSP code have been benchmarked with the Fast-Ion D-Alpha simulation (FIDAsim) code, which provides Monte Carlo simulations of beam neutral injection, attenuation, halo generation, halo spatial diffusion, and photoemission processes. When using the same atomic physics database, TRANSP and FIDAsim simulations achieve excellent agreement on the spatial profile and magnitude of beam and halo neutral densities and the NPA energy spectrum. The simulations show that the halo neutral density can be comparable to the beam neutral density. These halo neutrals can double the NPA flux, but they have minor effects on the NPA energy spectrum shape. The TRANSP and FIDAsim simulations also suggest that the magnitudes of beam and halo neutral densities are relatively sensitive to the choice of the atomic physics databases.

  1. Implementation of a 3D halo neutral model in the TRANSP code and application to projected NSTX-U plasmas

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Medley, S. S.; Liu, D.; Gorelenkova, M. V.

    2016-01-12

    A 3D halo neutral code developed at the Princeton Plasma Physics Laboratory and implemented for analysis using the TRANSP code is applied to projected National Spherical Torus eXperiment-Upgrade (NSTX-U plasmas). The legacy TRANSP code did not handle halo neutrals properly since they were distributed over the plasma volume rather than remaining in the vicinity of the neutral beam footprint as is actually the case. The 3D halo neutral code uses a 'beam-in-a-box' model that encompasses both injected beam neutrals and resulting halo neutrals. Upon deposition by charge exchange, a subset of the full, one-half and one-third beam energy components producemore » first generation halo neutrals that are tracked through successive generations until an ionization event occurs or the descendant halos exit the box. The 3D halo neutral model and neutral particle analyzer (NPA) simulator in the TRANSP code have been benchmarked with the Fast-Ion D-Alpha simulation (FIDAsim) code, which provides Monte Carlo simulations of beam neutral injection, attenuation, halo generation, halo spatial diffusion, and photoemission processes. When using the same atomic physics database, TRANSP and FIDAsim simulations achieve excellent agreement on the spatial profile and magnitude of beam and halo neutral densities and the NPA energy spectrum. The simulations show that the halo neutral density can be comparable to the beam neutral density. These halo neutrals can double the NPA flux, but they have minor effects on the NPA energy spectrum shape. The TRANSP and FIDAsim simulations also suggest that the magnitudes of beam and halo neutral densities are relatively sensitive to the choice of the atomic physics databases.« less

  2. Statistical study of defects caused by primary knock-on atoms in fcc Cu and bcc W using molecular dynamics

    NASA Astrophysics Data System (ADS)

    Warrier, M.; Bhardwaj, U.; Hemani, H.; Schneider, R.; Mutzke, A.; Valsakumar, M. C.

    2015-12-01

    We report on molecular Dynamics (MD) simulations carried out in fcc Cu and bcc W using the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) code to study (i) the statistical variations in the number of interstitials and vacancies produced by energetic primary knock-on atoms (PKA) (0.1-5 keV) directed in random directions and (ii) the in-cascade cluster size distributions. It is seen that around 60-80 random directions have to be explored for the average number of displaced atoms to become steady in the case of fcc Cu, whereas for bcc W around 50-60 random directions need to be explored. The number of Frenkel pairs produced in the MD simulations are compared with that from the Binary Collision Approximation Monte Carlo (BCA-MC) code SDTRIM-SP and the results from the NRT model. It is seen that a proper choice of the damage energy, i.e. the energy required to create a stable interstitial, is essential for the BCA-MC results to match the MD results. On the computational front it is seen that in-situ processing saves the need to input/output (I/O) atomic position data of several tera-bytes when exploring a large number of random directions and there is no difference in run-time because the extra run-time in processing data is offset by the time saved in I/O.

  3. The Los Alamos suite of relativistic atomic physics codes

    DOE PAGES

    Fontes, C. J.; Zhang, H. L.; Jr, J. Abdallah; ...

    2015-05-28

    The Los Alamos SuitE of Relativistic (LASER) atomic physics codes is a robust, mature platform that has been used to model highly charged ions in a variety of ways. The suite includes capabilities for calculating data related to fundamental atomic structure, as well as the processes of photoexcitation, electron-impact excitation and ionization, photoionization and autoionization within a consistent framework. These data can be of a basic nature, such as cross sections and collision strengths, which are useful in making predictions that can be compared with experiments to test fundamental theories of highly charged ions, such as quantum electrodynamics. The suitemore » can also be used to generate detailed models of energy levels and rate coefficients, and to apply them in the collisional-radiative modeling of plasmas over a wide range of conditions. Such modeling is useful, for example, in the interpretation of spectra generated by a variety of plasmas. In this work, we provide a brief overview of the capabilities within the Los Alamos relativistic suite along with some examples of its application to the modeling of highly charged ions.« less

  4. The MOLDY short-range molecular dynamics package

    NASA Astrophysics Data System (ADS)

    Ackland, G. J.; D'Mellow, K.; Daraszewicz, S. L.; Hepburn, D. J.; Uhrin, M.; Stratford, K.

    2011-12-01

    We describe a parallelised version of the MOLDY molecular dynamics program. This Fortran code is aimed at systems which may be described by short-range potentials and specifically those which may be addressed with the embedded atom method. This includes a wide range of transition metals and alloys. MOLDY provides a range of options in terms of the molecular dynamics ensemble used and the boundary conditions which may be applied. A number of standard potentials are provided, and the modular structure of the code allows new potentials to be added easily. The code is parallelised using OpenMP and can therefore be run on shared memory systems, including modern multicore processors. Particular attention is paid to the updates required in the main force loop, where synchronisation is often required in OpenMP implementations of molecular dynamics. We examine the performance of the parallel code in detail and give some examples of applications to realistic problems, including the dynamic compression of copper and carbon migration in an iron-carbon alloy. Program summaryProgram title: MOLDY Catalogue identifier: AEJU_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEJU_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License version 2 No. of lines in distributed program, including test data, etc.: 382 881 No. of bytes in distributed program, including test data, etc.: 6 705 242 Distribution format: tar.gz Programming language: Fortran 95/OpenMP Computer: Any Operating system: Any Has the code been vectorised or parallelized?: Yes. OpenMP is required for parallel execution RAM: 100 MB or more Classification: 7.7 Nature of problem: Moldy addresses the problem of many atoms (of order 10 6) interacting via a classical interatomic potential on a timescale of microseconds. It is designed for problems where statistics must be gathered over a number of equivalent runs, such as measuring thermodynamic properities, diffusion, radiation damage, fracture, twinning deformation, nucleation and growth of phase transitions, sputtering etc. In the vast majority of materials, the interactions are non-pairwise, and the code must be able to deal with many-body forces. Solution method: Molecular dynamics involves integrating Newton's equations of motion. MOLDY uses verlet (for good energy conservation) or predictor-corrector (for accurate trajectories) algorithms. It is parallelised using open MP. It also includes a static minimisation routine to find the lowest energy structure. Boundary conditions for surfaces, clusters, grain boundaries, thermostat (Nose), barostat (Parrinello-Rahman), and externally applied strain are provided. The initial configuration can be either a repeated unit cell or have all atoms given explictly. Initial velocities are generated internally, but it is also possible to specify the velocity of a particular atom. A wide range of interatomic force models are implemented, including embedded atom, Morse or Lennard-Jones. Thus the program is especially well suited to calculations of metals. Restrictions: The code is designed for short-ranged potentials, and there is no Ewald sum. Thus for long range interactions where all particles interact with all others, the order- N scaling will fail. Different interatomic potential forms require recompilation of the code. Additional comments: There is a set of associated open-source analysis software for postprocessing and visualisation. This includes local crystal structure recognition and identification of topological defects. Running time: A set of test modules for running time are provided. The code scales as order N. The parallelisation shows near-linear scaling with number of processors in a shared memory environment. A typical run of a few tens of nanometers for a few nanoseconds will run on a timescale of days on a multiprocessor desktop.

  5. The Challenges of Plasma Modeling: Current Status and Future Plans

    NASA Astrophysics Data System (ADS)

    Foster, A. R.; Smith, R. K.; Brickhouse, N. S.; Kallman, T. R.; Witthoeft, M. C.

    2010-12-01

    Successfully modeling X-ray emission from astrophysical plasmas requires a wide range of atomic data to be rapidly accessible by modeling codes, enabling calculation of synthetic spectra for fitting with observations. Over many years the astrophysical databases have roughly kept pace with the advances in detector and spectrometer technology. We outline here the basic atomic processes contributing to the emission from different types of plasmas and briefly touch on the difference between the methods used to calculate this data. We then discuss in more detail the different issues addressed by atomic databases in regards to what data to store and how to make it accessible. Finally, the question of the effect of uncertainties in atomic data is explored, as a reminder to observers that atomic data is not known to infinite precision, and should not be treated as such.

  6. Thermal-hydraulic interfacing code modules for CANDU reactors

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Liu, W.S.; Gold, M.; Sills, H.

    1997-07-01

    The approach for CANDU reactor safety analysis in Ontario Hydro Nuclear (OHN) and Atomic Energy of Canada Limited (AECL) is presented. Reflecting the unique characteristics of CANDU reactors, the procedure of coupling the thermal-hydraulics, reactor physics and fuel channel/element codes in the safety analysis is described. The experience generated in the Canadian nuclear industry may be useful to other types of reactors in the areas of reactor safety analysis.

  7. NASA Radiation Protection Research for Exploration Missions

    NASA Technical Reports Server (NTRS)

    Wilson, John W.; Cucinotta, Francis A.; Tripathi, Ram K.; Heinbockel, John H.; Tweed, John; Mertens, Christopher J.; Walker, Steve A.; Blattnig, Steven R.; Zeitlin, Cary J.

    2006-01-01

    The HZETRN code was used in recent trade studies for renewed lunar exploration and currently used in engineering development of the next generation of space vehicles, habitats, and EVA equipment. A new version of the HZETRN code capable of simulating high charge and energy (HZE) ions, light-ions and neutrons with either laboratory or space boundary conditions with enhanced neutron and light-ion propagation is under development. Atomic and nuclear model requirements to support that development will be discussed. Such engineering design codes require establishing validation processes using laboratory ion beams and space flight measurements in realistic geometries. We discuss limitations of code validation due to the currently available data and recommend priorities for new data sets.

  8. Development of a New System for Transport Simulation and Analysis at General Atomics

    NASA Astrophysics Data System (ADS)

    St. John, H. E.; Peng, Q.; Freeman, J.; Crotinger, J.

    1997-11-01

    General Atomics has begun a long term program to improve all aspects of experimental data analysis related to DIII--D. The object is to make local and visiting physicists as productive as possible, with only a small investment in training, by developing intuitive, sophisticated interfaces to existing and newly created computer programs. Here we describe our initial work and results of a pilot project in this program. The pilot project is a collaboratory effort between LLNL and GA which will ultimately result in the merger of Corsica and ONETWO (and selected modules from other codes) into a new advanced transport code system. The initial goal is to produce a graphical user interface to the transport code ONETWO which will couple to a programmable (steerable) front end designed for the transport system. This will be an object oriented scheme written primarily in python. The programmable application will integrate existing C, C^++, and Fortran methods in a single computational paradigm. Its most important feature is the use of plug in physics modules which will allow a high degree of customization.

  9. SOLAR OPACITY CALCULATIONS USING THE SUPER-TRANSITION-ARRAY METHOD

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Krief, M.; Feigel, A.; Gazit, D., E-mail: menahem.krief@mail.huji.ac.il

    A new opacity model has been developed based on the Super-Transition-Array (STA) method for the calculation of monochromatic opacities of plasmas in local thermodynamic equilibrium. The atomic code, named STAR (STA-Revised), is described and used to calculate spectral opacities for a solar model implementing the recent AGSS09 composition. Calculations are carried out throughout the solar radiative zone. The relative contributions of different chemical elements and atomic processes to the total Rosseland mean opacity are analyzed in detail. Monochromatic opacities and charge-state distributions are compared with the widely used Opacity Project (OP) code, for several elements near the radiation–convection interface. STARmore » Rosseland opacities for the solar mixture show a very good agreement with OP and the OPAL opacity code throughout the radiation zone. Finally, an explicit STA calculation was performed of the full AGSS09 photospheric mixture, including all heavy metals. It was shown that, due to their extremely low abundance, and despite being very good photon absorbers, the heavy elements do not affect the Rosseland opacity.« less

  10. molgw 1: Many-body perturbation theory software for atoms, molecules, and clusters

    DOE PAGES

    Bruneval, Fabien; Rangel, Tonatiuh; Hamed, Samia M.; ...

    2016-07-12

    Here, we summarize the MOLGW code that implements density-functional theory and many-body perturbation theory in a Gaussian basis set. The code is dedicated to the calculation of the many-body self-energy within the GW approximation and the solution of the Bethe–Salpeter equation. These two types of calculations allow the user to evaluate physical quantities that can be compared to spectroscopic experiments. Quasiparticle energies, obtained through the calculation of the GW self-energy, can be compared to photoemission or transport experiments, and neutral excitation energies and oscillator strengths, obtained via solution of the Bethe–Salpeter equation, are measurable by optical absorption. The implementation choicesmore » outlined here have aimed at the accuracy and robustness of calculated quantities with respect to measurements. Furthermore, the algorithms implemented in MOLGW allow users to consider molecules or clusters containing up to 100 atoms with rather accurate basis sets, and to choose whether or not to apply the resolution-of-the-identity approximation. Finally, we demonstrate the parallelization efficacy of the MOLGW code over several hundreds of processors.« less

  11. Investigation of the impact of high liquid viscosity on jet atomization in crossflow via high-fidelity simulations

    NASA Astrophysics Data System (ADS)

    Li, Xiaoyi; Gao, Hui; Soteriou, Marios C.

    2017-08-01

    Atomization of extremely high viscosity liquid can be of interest for many applications in aerospace, automotive, pharmaceutical, and food industries. While detailed atomization measurements usually face grand challenges, high-fidelity numerical simulations offer the advantage to comprehensively explore the atomization details. In this work, a previously validated high-fidelity first-principle simulation code HiMIST is utilized to simulate high-viscosity liquid jet atomization in crossflow. The code is used to perform a parametric study of the atomization process in a wide range of Ohnesorge numbers (Oh = 0.004-2) and Weber numbers (We = 10-160). Direct comparisons between the present study and previously published low-viscosity jet in crossflow results are performed. The effects of viscous damping and slowing on jet penetration, liquid surface instabilities, ligament formation/breakup, and subsequent droplet formation are investigated. Complex variations in near-field and far-field jet penetrations with increasing Oh at different We are observed and linked with the underlying jet deformation and breakup physics. Transition in breakup regimes and increase in droplet size with increasing Oh are observed, mostly consistent with the literature reports. The detailed simulations elucidate a distinctive edge-ligament-breakup dominated process with long surviving ligaments for the higher Oh cases, as opposed to a two-stage edge-stripping/column-fracture process for the lower Oh counterparts. The trend of decreasing column deflection with increasing We is reversed as Oh increases. A predominantly unimodal droplet size distribution is predicted at higher Oh, in contrast to the bimodal distribution at lower Oh. It has been found that both Rayleigh-Taylor and Kelvin-Helmholtz linear stability theories cannot be easily applied to interpret the distinct edge breakup process and further study of the underlying physics is needed.

  12. High performance computing in biology: multimillion atom simulations of nanoscale systems

    PubMed Central

    Sanbonmatsu, K. Y.; Tung, C.-S.

    2007-01-01

    Computational methods have been used in biology for sequence analysis (bioinformatics), all-atom simulation (molecular dynamics and quantum calculations), and more recently for modeling biological networks (systems biology). Of these three techniques, all-atom simulation is currently the most computationally demanding, in terms of compute load, communication speed, and memory load. Breakthroughs in electrostatic force calculation and dynamic load balancing have enabled molecular dynamics simulations of large biomolecular complexes. Here, we report simulation results for the ribosome, using approximately 2.64 million atoms, the largest all-atom biomolecular simulation published to date. Several other nanoscale systems with different numbers of atoms were studied to measure the performance of the NAMD molecular dynamics simulation program on the Los Alamos National Laboratory Q Machine. We demonstrate that multimillion atom systems represent a 'sweet spot' for the NAMD code on large supercomputers. NAMD displays an unprecedented 85% parallel scaling efficiency for the ribosome system on 1024 CPUs. We also review recent targeted molecular dynamics simulations of the ribosome that prove useful for studying conformational changes of this large biomolecular complex in atomic detail. PMID:17187988

  13. Measurement of neutron spectra in the AWE workplace using a Bonner sphere spectrometer.

    PubMed

    Danyluk, Peter

    2010-12-01

    A Bonner sphere spectrometer has been used to measure the neutron spectra in eight different workplace areas at AWE (Atomic Weapons Establishment). The spectra were analysed by the National Physical Laboratory using their principal unfolding code STAY'SL and the results were also analysed by AWE using a bespoke parametrised unfolding code. The bespoke code was designed specifically for the AWE workplace and is very simple to use. Both codes gave results, in good agreement. It was found that the measured fluence rate varied from 2 to 70 neutrons cm⁻² s⁻¹ (± 10%) and the ambient dose equivalent H*(10) varied from 0.5 to 57 µSv h⁻¹ (± 20%). A detailed description of the development and use of the bespoke code is presented.

  14. TORUS: Radiation transport and hydrodynamics code

    NASA Astrophysics Data System (ADS)

    Harries, Tim

    2014-04-01

    TORUS is a flexible radiation transfer and radiation-hydrodynamics code. The code has a basic infrastructure that includes the AMR mesh scheme that is used by several physics modules including atomic line transfer in a moving medium, molecular line transfer, photoionization, radiation hydrodynamics and radiative equilibrium. TORUS is useful for a variety of problems, including magnetospheric accretion onto T Tauri stars, spiral nebulae around Wolf-Rayet stars, discs around Herbig AeBe stars, structured winds of O supergiants and Raman-scattered line formation in symbiotic binaries, and dust emission and molecular line formation in star forming clusters. The code is written in Fortran 2003 and is compiled using a standard Gnu makefile. The code is parallelized using both MPI and OMP, and can use these parallel sections either separately or in a hybrid mode.

  15. Energy levels and radiative rates for transitions in Cr-like Co IV and Ni V

    NASA Astrophysics Data System (ADS)

    Aggarwal, K. M.; Bogdanovich, P.; Karpuškienė, R.; Keenan, F. P.; Kisielius, R.; Stancalie, V.

    2016-01-01

    We report calculations of energy levels and radiative rates (A-values) for transitions in Cr-like Co IV and Ni V. The quasi-relativistic Hartree-Fock (QRHF) code is adopted for calculating the data although GRASP (general-purpose relativistic atomic structure package) and flexible atomic code (FAC) have also been employed for comparison purposes. No radiative rates are available in the literature to compare with our results, but our calculated energies are in close agreement with those compiled by NIST for a majority of the levels. However, there are discrepancies for a few levels of up to 3%. The A-values are listed for all significantly contributing E1, E2 and M1 transitions, and the corresponding lifetimes reported, although unfortunately no previous theoretical or experimental results exist to compare with our data.

  16. Lightweight computational steering of very large scale molecular dynamics simulations

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Beazley, D.M.; Lomdahl, P.S.

    1996-09-01

    We present a computational steering approach for controlling, analyzing, and visualizing very large scale molecular dynamics simulations involving tens to hundreds of millions of atoms. Our approach relies on extensible scripting languages and an easy to use tool for building extensions and modules. The system is extremely easy to modify, works with existing C code, is memory efficient, and can be used from inexpensive workstations and networks. We demonstrate how we have used this system to manipulate data from production MD simulations involving as many as 104 million atoms running on the CM-5 and Cray T3D. We also show howmore » this approach can be used to build systems that integrate common scripting languages (including Tcl/Tk, Perl, and Python), simulation code, user extensions, and commercial data analysis packages.« less

  17. Neutron radiation damage studies in the structural materials of a 500 MWe fast breeder reactor using DPA cross-sections from ENDF / B-VII.1

    NASA Astrophysics Data System (ADS)

    Saha, Uttiyoarnab; Devan, K.; Bachchan, Abhitab; Pandikumar, G.; Ganesan, S.

    2018-04-01

    The radiation damage in the structural materials of a 500 MWe Indian prototype fast breeder reactor (PFBR) is re-assessed by computing the neutron displacement per atom (dpa) cross-sections from the recent nuclear data library evaluated by the USA, ENDF / B-VII.1, wherein revisions were taken place in the new evaluations of basic nuclear data because of using the state-of-the-art neutron cross-section experiments, nuclear model-based predictions and modern data evaluation techniques. An indigenous computer code, computation of radiation damage (CRaD), is developed at our centre to compute primary-knock-on atom (PKA) spectra and displacement cross-sections of materials both in point-wise and any chosen group structure from the evaluated nuclear data libraries. The new radiation damage model, athermal recombination-corrected displacement per atom (arc-dpa), developed based on molecular dynamics simulations is also incorporated in our study. This work is the result of our earlier initiatives to overcome some of the limitations experienced while using codes like RECOIL, SPECTER and NJOY 2016, to estimate radiation damage. Agreement of CRaD results with other codes and ASTM standard for Fe dpa cross-section is found good. The present estimate of total dpa in D-9 steel of PFBR necessitates renormalisation of experimental correlations of dpa and radiation damage to ensure consistency of damage prediction with ENDF / B-VII.1 library.

  18. Extreme ultraviolet emission spectra of Gd and Tb ions

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kilbane, D.; O'Sullivan, G.

    2010-11-15

    Theoretical extreme ultraviolet emission spectra of gadolinium and terbium ions calculated with the Cowan suite of codes and the flexible atomic code (FAC) relativistic code are presented. 4d-4f and 4p-4d transitions give rise to unresolved transition arrays in a range of ions. The effects of configuration interaction are investigated for transitions between singly excited configurations. Optimization of emission at 6.775 nm and 6.515 nm is achieved for Gd and Tb ions, respectively, by consideration of plasma effects. The resulting synthetic spectra are compared with experimental spectra recorded using the laser produced plasma technique.

  19. How to differentiate collective variables in free energy codes: Computer-algebra code generation and automatic differentiation

    NASA Astrophysics Data System (ADS)

    Giorgino, Toni

    2018-07-01

    The proper choice of collective variables (CVs) is central to biased-sampling free energy reconstruction methods in molecular dynamics simulations. The PLUMED 2 library, for instance, provides several sophisticated CV choices, implemented in a C++ framework; however, developing new CVs is still time consuming due to the need to provide code for the analytical derivatives of all functions with respect to atomic coordinates. We present two solutions to this problem, namely (a) symbolic differentiation and code generation, and (b) automatic code differentiation, in both cases leveraging open-source libraries (SymPy and Stan Math, respectively). The two approaches are demonstrated and discussed in detail implementing a realistic example CV, the local radius of curvature of a polymer. Users may use the code as a template to streamline the implementation of their own CVs using high-level constructs and automatic gradient computation.

  20. Ab-initio atomic level stress and role of d-orbitals in CuZr, CuZn and CuY

    NASA Astrophysics Data System (ADS)

    Ojha, Madhusudan; Nicholson, Don M.; Egami, Takeshi

    2015-03-01

    Atomic level stress offers a new tool to characterize materials within the local approximation to density functional theory (DFT). Ab-initio atomic level stresses in B2 structures of CuZr, CuZn and CuY are calculated and results are explained on the basis of d-orbital contributions to Density of States (DOS). The overlap of d-orbital DOS plays an important role in the relative magnitude of atomic level stresses in these structures. The trends in atomic level stresses that we observed in these simple B2 structures are also seen in complex structures such as liquids, glasses and solid solutions. The stresses are however modified by the different coordination and relaxed separation distances in these complex structures. We used the Locally Self-Consistent Multiple Scattering (LSMS) code and Vienna Ab-initio Simulation Package (VASP) for ab-initio calculations.

  1. Advancing Efficient All-Electron Electronic Structure Methods Based on Numeric Atom-Centered Orbitals for Energy Related Materials

    NASA Astrophysics Data System (ADS)

    Blum, Volker

    This talk describes recent advances of a general, efficient, accurate all-electron electronic theory approach based on numeric atom-centered orbitals; emphasis is placed on developments related to materials for energy conversion and their discovery. For total energies and electron band structures, we show that the overall accuracy is on par with the best benchmark quality codes for materials, but scalable to large system sizes (1,000s of atoms) and amenable to both periodic and non-periodic simulations. A recent localized resolution-of-identity approach for the Coulomb operator enables O (N) hybrid functional based descriptions of the electronic structure of non-periodic and periodic systems, shown for supercell sizes up to 1,000 atoms; the same approach yields accurate results for many-body perturbation theory as well. For molecular systems, we also show how many-body perturbation theory for charged and neutral quasiparticle excitation energies can be efficiently yet accurately applied using basis sets of computationally manageable size. Finally, the talk highlights applications to the electronic structure of hybrid organic-inorganic perovskite materials, as well as to graphene-based substrates for possible future transition metal compound based electrocatalyst materials. All methods described here are part of the FHI-aims code. VB gratefully acknowledges contributions by numerous collaborators at Duke University, Fritz Haber Institute Berlin, TU Munich, USTC Hefei, Aalto University, and many others around the globe.

  2. Photoneutron Reaction Data for Nuclear Physics and Astrophysics

    NASA Astrophysics Data System (ADS)

    Utsunomiya, Hiroaki; Renstrøm, Therese; Tveten, Gry Merete; Gheorghe, Ioana; Filipescu, Dan Mihai; Belyshev, Sergey; Stopani, Konstantin; Wang, Hongwei; Fan, Gongtao; Lui, Yiu-Wing; Symochko, Dmytro; Goriely, Stephane; Larsen, Ann-Cecilie; Siem, Sunniva; Varlamov, Vladimir; Ishkhanov, Boris; Glodariu, Tudor; Krzysiek, Mateusz; Takenaka, Daiki; Ari-izumi, Takashi; Amano, Sho; Miyamoto, Shuji

    2018-05-01

    We discuss the role of photoneutron reaction data in nuclear physics and astrophysics in conjunction with the Coordinated Research Project of the International Atomic Energy Agency with the code F41032 (IAEA-CRP F41032).

  3. Multigrid based First-Principles Molecular Dynamics

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Fattebert, Jean-Luc; Osei-Kuffuor, Daniel; Dunn, Ian

    2017-06-01

    MGmol ls a First-Principles Molecular Dynamics code. It relies on the Born-Oppenheimer approximation and models the electronic structure using Density Functional Theory, either LDA or PBE. Norm-conserving pseudopotentials are used to model atomic cores.

  4. Population kinetics on K alpha lines of partially ionized Cl atoms.

    PubMed

    Kawamura, Tohru; Nishimura, Hiroaki; Koike, Fumihiro; Ochi, Yoshihiro; Matsui, Ryoji; Miao, Wen Yong; Okihara, Shinichiro; Sakabe, Shuji; Uschmann, Ingo; Förster, Eckhart; Mima, Kunioki

    2002-07-01

    A population kinetics code was developed to analyze K alpha emission from partially ionized chlorine atoms in hydrocarbon plasmas. Atomic processes are solved under collisional-radiative equilibrium for two-temperature plasmas. It is shown that the fast electrons dominantly contribute to ionize the K-shell bound electrons (i.e., inner-shell ionization) and the cold electrons to the outer-shell bound ones. Ratios of K alpha lines of partially ionized atoms are presented as a function of cold-electron temperature. The model was validated by observation of the K alpha lines from a chlorinated plastic target irradiated with 1 TW Ti:sapphire laser pulses at 1.5 x 10(17) W/cm(2), inferring a plasma temperature of about 100 eV on the target surface.

  5. Influence of spray nozzle shape upon atomization process

    NASA Astrophysics Data System (ADS)

    Beniuga, Marius; Mihai, Ioan

    2016-12-01

    The atomization process is affected by a number of operating parameters (pressure, viscosity, temperature, etc.) [1-6] and the adopted constructive solution. In this article are compared parameters of atomized liquid jet with two nozzles that have different lifespan, one being new and the other one out. The last statement shows that the second nozzle was monitored as time of operation on the one hand and on the other hand, two dimensional nozzles have been analyzed using laser profilometry. To compare the experimental parameters was carried an experimental stand to change the period and pulse width in injecting liquid through two nozzles. Atomized liquid jets were photographed and filmed quickly. Images obtained were analyzed using a Matlab code that allowed to determine a number of parameters that characterize an atomized jet. Knowing the conditions and operating parameters of atomized jet, will establish a new wastewater nozzle block of parameter values that can be implemented in controller that provides dosing of the liquid injected. Experimental measurements to observe the myriad forms of atomized droplets to a wide range of operating conditions, realized using the electronic control module.

  6. Las Palmeras Molecular Dynamics: A flexible and modular molecular dynamics code

    NASA Astrophysics Data System (ADS)

    Davis, Sergio; Loyola, Claudia; González, Felipe; Peralta, Joaquín

    2010-12-01

    Las Palmeras Molecular Dynamics (LPMD) is a highly modular and extensible molecular dynamics (MD) code using interatomic potential functions. LPMD is able to perform equilibrium MD simulations of bulk crystalline solids, amorphous solids and liquids, as well as non-equilibrium MD (NEMD) simulations such as shock wave propagation, projectile impacts, cluster collisions, shearing, deformation under load, heat conduction, heterogeneous melting, among others, which involve unusual MD features like non-moving atoms and walls, unstoppable atoms with constant-velocity, and external forces like electric fields. LPMD is written in C++ as a compromise between efficiency and clarity of design, and its architecture is based on separate components or plug-ins, implemented as modules which are loaded on demand at runtime. The advantage of this architecture is the ability to completely link together the desired components involved in the simulation in different ways at runtime, using a user-friendly control file language which describes the simulation work-flow. As an added bonus, the plug-in API (Application Programming Interface) makes it possible to use the LPMD components to analyze data coming from other simulation packages, convert between input file formats, apply different transformations to saved MD atomic trajectories, and visualize dynamical processes either in real-time or as a post-processing step. Individual components, such as a new potential function, a new integrator, a new file format, new properties to calculate, new real-time visualizers, and even a new algorithm for handling neighbor lists can be easily coded, compiled and tested within LPMD by virtue of its object-oriented API, without the need to modify the rest of the code. LPMD includes already several pair potential functions such as Lennard-Jones, Morse, Buckingham, MCY and the harmonic potential, as well as embedded-atom model (EAM) functions such as the Sutton-Chen and Gupta potentials. Integrators to choose include Euler (if only for demonstration purposes), Verlet and Velocity Verlet, Leapfrog and Beeman, among others. Electrostatic forces are treated as another potential function, by default using the plug-in implementing the Ewald summation method. Program summaryProgram title: LPMD Catalogue identifier: AEHG_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHG_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License version 3 No. of lines in distributed program, including test data, etc.: 509 490 No. of bytes in distributed program, including test data, etc.: 6 814 754 Distribution format: tar.gz Programming language: C++ Computer: 32-bit and 64-bit workstation Operating system: UNIX RAM: Minimum 1024 bytes Classification: 7.7 External routines: zlib, OpenGL Nature of problem: Study of Statistical Mechanics and Thermodynamics of condensed matter systems, as well as kinetics of non-equilibrium processes in the same systems. Solution method: Equilibrium and non-equilibrium molecular dynamics method, Monte Carlo methods. Restrictions: Rigid molecules are not supported. Polarizable atoms and chemical bonds (proteins) either. Unusual features: The program is able to change the temperature of the simulation cell, the pressure, cut regions of the cell, color the atoms by properties, even during the simulation. It is also possible to fix the positions and/or velocity of groups of atoms. Visualization of atoms and some physical properties during the simulation. Additional comments: The program does not only perform molecular dynamics and Monte Carlo simulations, it is also able to filter and manipulate atomic configurations, read and write different file formats, convert between them, evaluate different structural and dynamical properties. Running time: 50 seconds on a 1000-step simulation of 4000 argon atoms, running on a single 2.67 GHz Intel processor.

  7. A computer model for liquid jet atomization in rocket thrust chambers

    NASA Astrophysics Data System (ADS)

    Giridharan, M. G.; Lee, J. G.; Krishnan, A.; Yang, H. Q.; Ibrahim, E.; Chuech, S.; Przekwas, A. J.

    1991-12-01

    The process of atomization has been used as an efficient means of burning liquid fuels in rocket engines, gas turbine engines, internal combustion engines, and industrial furnaces. Despite its widespread application, this complex hydrodynamic phenomenon has not been well understood, and predictive models for this process are still in their infancy. The difficulty in simulating the atomization process arises from the relatively large number of parameters that influence it, including the details of the injector geometry, liquid and gas turbulence, and the operating conditions. In this study, numerical models are developed from first principles, to quantify factors influencing atomization. For example, the surface wave dynamics theory is used for modeling the primary atomization and the droplet energy conservation principle is applied for modeling the secondary atomization. The use of empirical correlations has been minimized by shifting the analyses to fundamental levels. During applications of these models, parametric studies are performed to understand and correlate the influence of relevant parameters on the atomization process. The predictions of these models are compared with existing experimental data. The main tasks of this study were the following: development of a primary atomization model; development of a secondary atomization model; development of a model for impinging jets; development of a model for swirling jets; and coupling of the primary atomization model with a CFD code.

  8. Efficient molecular dynamics simulations with many-body potentials on graphics processing units

    NASA Astrophysics Data System (ADS)

    Fan, Zheyong; Chen, Wei; Vierimaa, Ville; Harju, Ari

    2017-09-01

    Graphics processing units have been extensively used to accelerate classical molecular dynamics simulations. However, there is much less progress on the acceleration of force evaluations for many-body potentials compared to pairwise ones. In the conventional force evaluation algorithm for many-body potentials, the force, virial stress, and heat current for a given atom are accumulated within different loops, which could result in write conflict between different threads in a CUDA kernel. In this work, we provide a new force evaluation algorithm, which is based on an explicit pairwise force expression for many-body potentials derived recently (Fan et al., 2015). In our algorithm, the force, virial stress, and heat current for a given atom can be accumulated within a single thread and is free of write conflicts. We discuss the formulations and algorithms and evaluate their performance. A new open-source code, GPUMD, is developed based on the proposed formulations. For the Tersoff many-body potential, the double precision performance of GPUMD using a Tesla K40 card is equivalent to that of the LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) molecular dynamics code running with about 100 CPU cores (Intel Xeon CPU X5670 @ 2.93 GHz).

  9. Spectral and Atomic Physics Analysis of Xenon L-Shell Emission From High Energy Laser Produced Plasmas

    NASA Astrophysics Data System (ADS)

    Thorn, Daniel; Kemp, G. E.; Widmann, K.; Benjamin, R. D.; May, M. J.; Colvin, J. D.; Barrios, M. A.; Fournier, K. B.; Liedahl, D.; Moore, A. S.; Blue, B. E.

    2016-10-01

    The spectrum of the L-shell (n =2) radiation in mid to high-Z ions is useful for probing plasma conditions in the multi-keV temperature range. Xenon in particular with its L-shell radiation centered around 4.5 keV is copiously produced from plasmas with electron temperatures in the 5-10 keV range. We report on a series of time-resolved L-shell Xe spectra measured with the NIF X-ray Spectrometer (NXS) in high-energy long-pulse (>10 ns) laser produced plasmas at the National Ignition Facility. The resolving power of the NXS is sufficiently high (E/ ∂E >100) in the 4-5 keV spectral band that the emission from different charge states is observed. An analysis of the time resolved L-shell spectrum of Xe is presented along with spectral modeling by detailed radiation transport and atomic physics from the SCRAM code and comparison with predictions from HYDRA a radiation-hydrodynamics code with inline atomic-physics from CRETIN. This work was performed under the auspices of the U.S. Department of Energy by LLNL under Contract DE-AC52-07NA27344.

  10. JavaGenes Molecular Evolution

    NASA Technical Reports Server (NTRS)

    Lohn, Jason; Smith, David; Frank, Jeremy; Globus, Al; Crawford, James

    2007-01-01

    JavaGenes is a general-purpose, evolutionary software system written in Java. It implements several versions of a genetic algorithm, simulated annealing, stochastic hill climbing, and other search techniques. This software has been used to evolve molecules, atomic force field parameters, digital circuits, Earth Observing Satellite schedules, and antennas. This version differs from version 0.7.28 in that it includes the molecule evolution code and other improvements. Except for the antenna code, JaveGenes is available for NASA Open Source distribution.

  11. Update and evaluation of decay data for spent nuclear fuel analyses

    NASA Astrophysics Data System (ADS)

    Simeonov, Teodosi; Wemple, Charles

    2017-09-01

    Studsvik's approach to spent nuclear fuel analyses combines isotopic concentrations and multi-group cross-sections, calculated by the CASMO5 or HELIOS2 lattice transport codes, with core irradiation history data from the SIMULATE5 reactor core simulator and tabulated isotopic decay data. These data sources are used and processed by the code SNF to predict spent nuclear fuel characteristics. Recent advances in the generation procedure for the SNF decay data are presented. The SNF decay data includes basic data, such as decay constants, atomic masses and nuclide transmutation chains; radiation emission spectra for photons from radioactive decay, alpha-n reactions, bremsstrahlung, and spontaneous fission, electrons and alpha particles from radioactive decay, and neutrons from radioactive decay, spontaneous fission, and alpha-n reactions; decay heat production; and electro-atomic interaction data for bremsstrahlung production. These data are compiled from fundamental (ENDF, ENSDF, TENDL) and processed (ESTAR) sources for nearly 3700 nuclides. A rigorous evaluation procedure of internal consistency checks and comparisons to measurements and benchmarks, and code-to-code verifications is performed at the individual isotope level and using integral characteristics on a fuel assembly level (e.g., decay heat, radioactivity, neutron and gamma sources). Significant challenges are presented by the scope and complexity of the data processing, a dearth of relevant detailed measurements, and reliance on theoretical models for some data.

  12. GPU Linear Algebra Libraries and GPGPU Programming for Accelerating MOPAC Semiempirical Quantum Chemistry Calculations.

    PubMed

    Maia, Julio Daniel Carvalho; Urquiza Carvalho, Gabriel Aires; Mangueira, Carlos Peixoto; Santana, Sidney Ramos; Cabral, Lucidio Anjos Formiga; Rocha, Gerd B

    2012-09-11

    In this study, we present some modifications in the semiempirical quantum chemistry MOPAC2009 code that accelerate single-point energy calculations (1SCF) of medium-size (up to 2500 atoms) molecular systems using GPU coprocessors and multithreaded shared-memory CPUs. Our modifications consisted of using a combination of highly optimized linear algebra libraries for both CPU (LAPACK and BLAS from Intel MKL) and GPU (MAGMA and CUBLAS) to hasten time-consuming parts of MOPAC such as the pseudodiagonalization, full diagonalization, and density matrix assembling. We have shown that it is possible to obtain large speedups just by using CPU serial linear algebra libraries in the MOPAC code. As a special case, we show a speedup of up to 14 times for a methanol simulation box containing 2400 atoms and 4800 basis functions, with even greater gains in performance when using multithreaded CPUs (2.1 times in relation to the single-threaded CPU code using linear algebra libraries) and GPUs (3.8 times). This degree of acceleration opens new perspectives for modeling larger structures which appear in inorganic chemistry (such as zeolites and MOFs), biochemistry (such as polysaccharides, small proteins, and DNA fragments), and materials science (such as nanotubes and fullerenes). In addition, we believe that this parallel (GPU-GPU) MOPAC code will make it feasible to use semiempirical methods in lengthy molecular simulations using both hybrid QM/MM and QM/QM potentials.

  13. Thermally activated decomposition of (Ga,Mn)As thin layer at medium temperature post growth annealing

    NASA Astrophysics Data System (ADS)

    Melikhov, Y.; Konstantynov, P.; Domagala, J.; Sadowski, J.; Chernyshova, M.; Wojciechowski, T.; Syryanyy, Y.; Demchenko, I. N.

    2016-05-01

    The redistribution of Mn atoms in Ga1-xMnxAs layer during medium-temperature annealing, 250-450 oC, by Mn K-edge X-ray absorption fine structure (XAFS) recorded at ALBA facility, was studied. For this purpose Ga1-xMnxAs thin layer with x=0.01 was grown on AlAs buffer layer deposited on GaAs(100) substrate by molecular beam epitaxy (MBE) followed by annealing. The examined layer was detached from the substrate using a “lift-off” procedure in order to eliminate elastic scattering in XAFS spectra. Fourier transform analysis of experimentally obtained EXAFS spectra allowed to propose a model which describes a redistribution/diffusion of Mn atoms in the host matrix. Theoretical XANES spectra, simulated using multiple scattering formalism (FEFF code) with the support of density functional theory (WIEN2k code), qualitatively describe the features observed in the experimental fine structure.

  14. Roothaan's approach to solve the Hartree-Fock equations for atoms confined by soft walls: Basis set with correct asymptotic behavior.

    PubMed

    Rodriguez-Bautista, Mariano; Díaz-García, Cecilia; Navarrete-López, Alejandra M; Vargas, Rubicelia; Garza, Jorge

    2015-07-21

    In this report, we use a new basis set for Hartree-Fock calculations related to many-electron atoms confined by soft walls. One- and two-electron integrals were programmed in a code based in parallel programming techniques. The results obtained with this proposal for hydrogen and helium atoms were contrasted with other proposals to study just one and two electron confined atoms, where we have reproduced or improved the results previously reported. Usually, an atom enclosed by hard walls has been used as a model to study confinement effects on orbital energies, the main conclusion reached by this model is that orbital energies always go up when the confinement radius is reduced. However, such an observation is not necessarily valid for atoms confined by penetrable walls. The main reason behind this result is that for atoms with large polarizability, like beryllium or potassium, external orbitals are delocalized when the confinement is imposed and consequently, the internal orbitals behave as if they were in an ionized atom. Naturally, the shell structure of these atoms is modified drastically when they are confined. The delocalization was an argument proposed for atoms confined by hard walls, but it was never verified. In this work, the confinement imposed by soft walls allows to analyze the delocalization concept in many-electron atoms.

  15. Roothaan’s approach to solve the Hartree-Fock equations for atoms confined by soft walls: Basis set with correct asymptotic behavior

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Rodriguez-Bautista, Mariano; Díaz-García, Cecilia; Navarrete-López, Alejandra M.

    2015-07-21

    In this report, we use a new basis set for Hartree-Fock calculations related to many-electron atoms confined by soft walls. One- and two-electron integrals were programmed in a code based in parallel programming techniques. The results obtained with this proposal for hydrogen and helium atoms were contrasted with other proposals to study just one and two electron confined atoms, where we have reproduced or improved the results previously reported. Usually, an atom enclosed by hard walls has been used as a model to study confinement effects on orbital energies, the main conclusion reached by this model is that orbital energiesmore » always go up when the confinement radius is reduced. However, such an observation is not necessarily valid for atoms confined by penetrable walls. The main reason behind this result is that for atoms with large polarizability, like beryllium or potassium, external orbitals are delocalized when the confinement is imposed and consequently, the internal orbitals behave as if they were in an ionized atom. Naturally, the shell structure of these atoms is modified drastically when they are confined. The delocalization was an argument proposed for atoms confined by hard walls, but it was never verified. In this work, the confinement imposed by soft walls allows to analyze the delocalization concept in many-electron atoms.« less

  16. Methodology trends on gamma and electron radiation damage simulation studies in solids under high fluency irradiation environments

    NASA Astrophysics Data System (ADS)

    Cruz Inclán, Carlos M.; González Lazo, Eduardo; Rodríguez Rodríguez, Arturo; Guzmán Martínez, Fernando; Abreu Alfonso, Yamiel; Piñera Hernández, Ibrahin; Leyva Fabelo, Antonio

    2017-09-01

    The present work deals with the numerical simulation of gamma and electron radiation damage processes under high brightness and radiation particle fluency on regard to two new radiation induced atom displacement processes, which concern with both, the Monte Carlo Method based numerical simulation of the occurrence of atom displacement process as a result of gamma and electron interactions and transport in a solid matrix and the atom displacement threshold energies calculated by Molecular Dynamic methodologies. The two new radiation damage processes here considered in the framework of high brightness and particle fluency irradiation conditions are: 1) The radiation induced atom displacement processes due to a single primary knockout atom excitation in a defective target crystal matrix increasing its defect concentrations (vacancies, interstitials and Frenkel pairs) as a result of a severe and progressive material radiation damage and 2) The occurrence of atom displacements related to multiple primary knockout atom excitations for the same or different atomic species in an perfect target crystal matrix due to subsequent electron elastic atomic scattering in the same atomic neighborhood during a crystal lattice relaxation time. In the present work a review numeral simulation attempts of these two new radiation damage processes are presented, starting from the former developed algorithms and codes for Monte Carlo simulation of atom displacements induced by electron and gamma in

  17. Configuration interaction in charge exchange spectra of tin and xenon

    NASA Astrophysics Data System (ADS)

    D'Arcy, R.; Morris, O.; Ohashi, H.; Suda, S.; Tanuma, H.; Fujioka, S.; Nishimura, H.; Nishihara, K.; Suzuki, C.; Kato, T.; Koike, F.; O'Sullivan, G.

    2011-06-01

    Charge-state-specific extreme ultraviolet spectra from both tin ions and xenon ions have been recorded at Tokyo Metropolitan University. The electron cyclotron resonance source spectra were produced from charge exchange collisions between the ions and rare gas target atoms. To identify unknown spectral lines of tin and xenon, atomic structure calculations were performed for Sn14+-Sn17+ and Xe16+-Xe20+ using the Hartree-Fock configuration interaction code of Cowan (1981 The Theory of Atomic Structure and Spectra (Berkeley, CA: University of California Press)). The energies of the capture states involved in the single-electron process that occurs in these slow collisions were estimated using the classical over-barrier model.

  18. Band structures of TiO2 doped with N, C and B*

    PubMed Central

    Xu, Tian-Hua; Song, Chen-Lu; Liu, Yong; Han, Gao-Rong

    2006-01-01

    This study on the band structures and charge densities of nitrogen (N)-, carbon (C)- and boron (B)-doped titanium dioxide (TiO2) by first-principles simulation with the CASTEP code (Segall et al., 2002) showed that the three 2p bands of impurity atom are located above the valence-band maximum and below the Ti 3d bands, and that along with the decreasing of impurity atomic number, the fluctuations become more intensive. We cannot observe obvious band-gap narrowing in our result. Therefore, the cause of absorption in visible light might be the isolated impurity atom 2p states in band-gap rather than the band-gap narrowing. PMID:16532532

  19. Coding considerations for standalone molecular dynamics simulations of atomistic structures

    NASA Astrophysics Data System (ADS)

    Ocaya, R. O.; Terblans, J. J.

    2017-10-01

    The laws of Newtonian mechanics allow ab-initio molecular dynamics to model and simulate particle trajectories in material science by defining a differentiable potential function. This paper discusses some considerations for the coding of ab-initio programs for simulation on a standalone computer and illustrates the approach by C language codes in the context of embedded metallic atoms in the face-centred cubic structure. The algorithms use velocity-time integration to determine particle parameter evolution for up to several thousands of particles in a thermodynamical ensemble. Such functions are reusable and can be placed in a redistributable header library file. While there are both commercial and free packages available, their heuristic nature prevents dissection. In addition, developing own codes has the obvious advantage of teaching techniques applicable to new problems.

  20. Parallel Grand Canonical Monte Carlo (ParaGrandMC) Simulation Code

    NASA Technical Reports Server (NTRS)

    Yamakov, Vesselin I.

    2016-01-01

    This report provides an overview of the Parallel Grand Canonical Monte Carlo (ParaGrandMC) simulation code. This is a highly scalable parallel FORTRAN code for simulating the thermodynamic evolution of metal alloy systems at the atomic level, and predicting the thermodynamic state, phase diagram, chemical composition and mechanical properties. The code is designed to simulate multi-component alloy systems, predict solid-state phase transformations such as austenite-martensite transformations, precipitate formation, recrystallization, capillary effects at interfaces, surface absorption, etc., which can aid the design of novel metallic alloys. While the software is mainly tailored for modeling metal alloys, it can also be used for other types of solid-state systems, and to some degree for liquid or gaseous systems, including multiphase systems forming solid-liquid-gas interfaces.

  1. Atomistic Simulations of Surface Cross-Slip Nucleation in Face-Centered Cubic Nickel and Copper (Postprint)

    DTIC Science & Technology

    2013-02-15

    molecular dynamics code, LAMMPS [9], developed at Sandia National Laboratory. The simulation cell is a rectangular parallelepiped, with the z-axis...with assigned energies within LAMMPs of greater than 4.42 eV (Ni) or 3.52 eV (Cu) (the energy of atoms in the stacking fault region), the partial...molecular dynamics code LAMMPS , which was developed at Sandia National Laboratory by Dr. Steve Plimpton and co-workers. This work was supported by the

  2. Multibillion-atom Molecular Dynamics Simulations of Plasticity, Spall, and Ejecta

    NASA Astrophysics Data System (ADS)

    Germann, Timothy C.

    2007-06-01

    Modern supercomputing platforms, such as the IBM BlueGene/L at Lawrence Livermore National Laboratory and the Roadrunner hybrid supercomputer being built at Los Alamos National Laboratory, are enabling large-scale classical molecular dynamics simulations of phenomena that were unthinkable just a few years ago. Using either the embedded atom method (EAM) description of simple (close-packed) metals, or modified EAM (MEAM) models of more complex solids and alloys with mixed covalent and metallic character, simulations containing billions to trillions of atoms are now practical, reaching volumes in excess of a cubic micron. In order to obtain any new physical insights, however, it is equally important that the analysis of such systems be tractable. This is in fact possible, in large part due to our highly efficient parallel visualization code, which enables the rendering of atomic spheres, Eulerian cells, and other geometric objects in a matter of minutes, even for tens of thousands of processors and billions of atoms. After briefly describing the BlueGene/L and Roadrunner architectures, and the code optimization strategies that were employed, results obtained thus far on BlueGene/L will be reviewed, including: (1) shock compression and release of a defective EAM Cu sample, illustrating the plastic deformation accompanying void collapse as well as the subsequent void growth and linkup upon release; (2) solid-solid martensitic phase transition in shock-compressed MEAM Ga; and (3) Rayleigh-Taylor fluid instability modeled using large-scale direct simulation Monte Carlo (DSMC) simulations. I will also describe our initial experiences utilizing Cell Broadband Engine processors (developed for the Sony PlayStation 3), and planned simulation studies of ejecta and spall failure in polycrystalline metals that will be carried out when the full Petaflop Opteron/Cell Roadrunner supercomputer is assembled in mid-2008.

  3. Charge exchange cross sections in slow collisions of Si3+ with Hydrogen atom

    NASA Astrophysics Data System (ADS)

    Joseph, Dwayne; Quashie, Edwin; Saha, Bidhan

    2011-05-01

    In recent years both the experimental and theoretical studies of electron transfer in ion-atom collisions have progressed considerably. Accurate determination of the cross sections and an understanding of the dynamics of the electron-capture process by multiply charged ions from atomic hydrogen over a wide range of projectile velocities are important in various field ranging from fusion plasma to astrophysics. The soft X-ray emission from comets has been explained by charge transfer of solar wind ions, among them Si3+, with neutrals in the cometary gas vapor. The cross sections are evaluated using the (a) full quantum and (b) semi-classical molecular orbital close coupling (MOCC) methods. Adiabatic potentials and wave functions for relavent singlet and triplet states are generated using the MRDCI structure codes. Details will be presented at the conference. In recent years both the experimental and theoretical studies of electron transfer in ion-atom collisions have progressed considerably. Accurate determination of the cross sections and an understanding of the dynamics of the electron-capture process by multiply charged ions from atomic hydrogen over a wide range of projectile velocities are important in various field ranging from fusion plasma to astrophysics. The soft X-ray emission from comets has been explained by charge transfer of solar wind ions, among them Si3+, with neutrals in the cometary gas vapor. The cross sections are evaluated using the (a) full quantum and (b) semi-classical molecular orbital close coupling (MOCC) methods. Adiabatic potentials and wave functions for relavent singlet and triplet states are generated using the MRDCI structure codes. Details will be presented at the conference. Work supported by NSF CREST project (grant #0630370).

  4. Abstract ID: 176 Geant4 implementation of inter-atomic interference effect in small-angle coherent X-ray scattering for materials of medical interest.

    PubMed

    Paternò, Gianfranco; Cardarelli, Paolo; Contillo, Adriano; Gambaccini, Mauro; Taibi, Angelo

    2018-01-01

    Advanced applications of digital mammography such as dual-energy and tomosynthesis require multiple exposures and thus deliver higher dose compared to standard mammograms. A straightforward manner to reduce patient dose without affecting image quality would be removal of the anti-scatter grid, provided that the involved reconstruction algorithms are able to take the scatter figure into account [1]. Monte Carlo simulations are very well suited for the calculation of X-ray scatter distribution and can be used to integrate such information within the reconstruction software. Geant4 is an open source C++ particle tracking code widely used in several physical fields, including medical physics [2,3]. However, the coherent scattering cross section used by the standard Geant4 code does not take into account the influence of molecular interference. According to the independent atomic scattering approximation (the so-called free-atom model), coherent radiation is indistinguishable from primary radiation because its angular distribution is peaked in the forward direction. Since interference effects occur between x-rays scattered by neighbouring atoms in matter, it was shown experimentally that the scatter distribution is affected by the molecular structure of the target, even in amorphous materials. The most important consequence is that the coherent scatter distribution is not peaked in the forward direction, and the position of the maximum is strongly material-dependent [4]. In this contribution, we present the implementation of a method to take into account inter-atomic interference in small-angle coherent scattering in Geant4, including a dedicated data set of suitable molecular form factor values for several materials of clinical interest. Furthermore, we present scatter images of simple geometric phantoms in which the Rayleigh contribution is rigorously evaluated. Copyright © 2017.

  5. Synthetic NPA diagnostic for energetic particles in JET plasmas

    NASA Astrophysics Data System (ADS)

    Varje, J.; Sirén, P.; Weisen, H.; Kurki-Suonio, T.; Äkäslompolo, S.; contributors, JET

    2017-11-01

    Neutral particle analysis (NPA) is one of the few methods for diagnosing fast ions inside a plasma by measuring neutral atom fluxes emitted due to charge exchange reactions. The JET tokamak features an NPA diagnostic which measures neutral atom fluxes and energy spectra simultaneously for hydrogen, deuterium and tritium species. A synthetic NPA diagnostic has been developed and used to interpret these measurements to diagnose energetic particles in JET plasmas with neutral beam injection (NBI) heating. The synthetic NPA diagnostic performs a Monte Carlo calculation of the neutral atom fluxes in a realistic geometry. The 4D fast ion distributions, representing NBI ions, were simulated using the Monte Carlo orbit-following code ASCOT. Neutral atom density profiles were calculated using the FRANTIC neutral code in the JINTRAC modelling suite. Additionally, for rapid analysis, a scan of neutral profiles was precalculated with FRANTIC for a range of typical plasma parameters. These were taken from the JETPEAK database, which includes a comprehensive set of data from the flat-top phases of nearly all discharges in recent JET campaigns. The synthetic diagnostic was applied to various JET plasmas in the recent hydrogen campaign where different hydrogen/deuterium mixtures and NBI configurations were used. The simulated neutral fluxes from the fast ion distributions were found to agree with the measured fluxes, reproducing the slowing-down profiles for different beam isotopes and energies and quantitatively estimating the fraction of hydrogen and deuterium fast ions.

  6. Recent Progress in the Development of a Multi-Layer Green's Function Code for Ion Beam Transport

    NASA Technical Reports Server (NTRS)

    Tweed, John; Walker, Steven A.; Wilson, John W.; Tripathi, Ram K.

    2008-01-01

    To meet the challenge of future deep space programs, an accurate and efficient engineering code for analyzing the shielding requirements against high-energy galactic heavy radiation is needed. To address this need, a new Green's function code capable of simulating high charge and energy ions with either laboratory or space boundary conditions is currently under development. The computational model consists of combinations of physical perturbation expansions based on the scales of atomic interaction, multiple scattering, and nuclear reactive processes with use of the Neumann-asymptotic expansions with non-perturbative corrections. The code contains energy loss due to straggling, nuclear attenuation, nuclear fragmentation with energy dispersion and downshifts. Previous reports show that the new code accurately models the transport of ion beams through a single slab of material. Current research efforts are focused on enabling the code to handle multiple layers of material and the present paper reports on progress made towards that end.

  7. Code-Phase Clock Bias and Frequency Offset in PPP Clock Solutions.

    PubMed

    Defraigne, Pascale; Sleewaegen, Jean-Marie

    2016-07-01

    Precise point positioning (PPP) is a zero-difference single-station technique that has proved to be very effective for time and frequency transfer, enabling the comparison of atomic clocks with a precision of a hundred picoseconds and a one-day stability below the 1e-15 level. It was, however, noted that for some receivers, a frequency difference is observed between the clock solution based on the code measurements and the clock solution based on the carrier-phase measurements. These observations reveal some inconsistency either between the code and carrier phases measured by the receiver or between the data analysis strategy of codes and carrier phases. One explanation for this discrepancy is the time offset that can exist for some receivers between the code and the carrier-phase latching. This paper explains how a code-phase bias in the receiver hardware can induce a frequency difference between the code and the carrier-phase clock solutions. The impact on PPP is then quantified. Finally, the possibility to determine this code-phase bias in the PPP modeling is investigated, and the first results are shown to be inappropriate due to the high level of code noise.

  8. 38 CFR 3.903 - Subversive activities.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Uniform Code of Military Justice, Articles 94, 104 and 106 (10 U.S.C. 894, 904, and 906); (4) In the following sections of the Atomic Energy Act of 1954: Sections 222 through 226 (42 U.S.C. 2272-2276); and (5...

  9. 38 CFR 3.903 - Subversive activities.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Uniform Code of Military Justice, Articles 94, 104 and 106 (10 U.S.C. 894, 904, and 906); (4) In the following sections of the Atomic Energy Act of 1954: Sections 222 through 226 (42 U.S.C. 2272-2276); and (5...

  10. A Comprehensive review on the open source hackable text editor-ATOM

    NASA Astrophysics Data System (ADS)

    Sumangali, K.; Borra, Lokesh; Suraj Mishra, Amol

    2017-11-01

    This document represents a comprehensive study of “Atom”, one of the best open-source code editors available with many features built-in to support multitude of programming environments and to provide a more productive toolset for developers.

  11. 77 FR 64435 - Branch Technical Position on the Import of Non-U.S. Origin Radioactive Sources

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-10-22

    ... exclusion, initially adopted in a 1995 rule.\\3\\ In accordance with International Atomic Energy Agency (IAEA) Code of Conduct on the Safety and Security of Radioactive Sources and the IAEA supplemental Guidance on...

  12. Advanced Kr Atomic Structure and Ionization Kinetics for Pinches on ZR

    NASA Astrophysics Data System (ADS)

    Dasgupta, Arati; Clark, Robert; Giuliani, John; Ouart, Nick; Davis, Jack; Jones, Brent; Ampleford, Dave; Hansen, Stephanie

    2011-10-01

    High fluence photon sources above 10 keV are a challenge for HED plasmas. This motivates Kr atomic modeling as its K-shell radiation starts at 13 keV. We have developed atomic structure and collisional-radiatve data for the full K-and L-shell and much of the M-shell using the the state-of-the-art Flexible Atomic Code. All relevant atomic collisional and radiative processes that affect ionization balance and are necessary to accurately model the pinch dynamics and the spectroscopic details of the emitted radiation are included in constructing the model. This non-LTE CRE model will be used to generate synthetic spectra for fixed densities and temperatures relevant for Kr gas-puff simulations in ZR. Work supported by DOE/NNSA. Sandia is a multi-program laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

  13. CRITIC2: A program for real-space analysis of quantum chemical interactions in solids

    NASA Astrophysics Data System (ADS)

    Otero-de-la-Roza, A.; Johnson, Erin R.; Luaña, Víctor

    2014-03-01

    We present CRITIC2, a program for the analysis of quantum-mechanical atomic and molecular interactions in periodic solids. This code, a greatly improved version of the previous CRITIC program (Otero-de-la Roza et al., 2009), can: (i) find critical points of the electron density and related scalar fields such as the electron localization function (ELF), Laplacian, … (ii) integrate atomic properties in the framework of Bader’s Atoms-in-Molecules theory (QTAIM), (iii) visualize non-covalent interactions in crystals using the non-covalent interactions (NCI) index, (iv) generate relevant graphical representations including lines, planes, gradient paths, contour plots, atomic basins, … and (v) perform transformations between file formats describing scalar fields and crystal structures. CRITIC2 can interface with the output produced by a variety of electronic structure programs including WIEN2k, elk, PI, abinit, Quantum ESPRESSO, VASP, Gaussian, and, in general, any other code capable of writing the scalar field under study to a three-dimensional grid. CRITIC2 is parallelized, completely documented (including illustrative test cases) and publicly available under the GNU General Public License. Catalogue identifier: AECB_v2_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AECB_v2_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: yes No. of lines in distributed program, including test data, etc.: 11686949 No. of bytes in distributed program, including test data, etc.: 337020731 Distribution format: tar.gz Programming language: Fortran 77 and 90. Computer: Workstations. Operating system: Unix, GNU/Linux. Has the code been vectorized or parallelized?: Shared-memory parallelization can be used for most tasks. Classification: 7.3. Catalogue identifier of previous version: AECB_v1_0 Journal reference of previous version: Comput. Phys. Comm. 180 (2009) 157 Nature of problem: Analysis of quantum-chemical interactions in periodic solids by means of atoms-in-molecules and related formalisms. Solution method: Critical point search using Newton’s algorithm, atomic basin integration using bisection, qtree and grid-based algorithms, diverse graphical representations and computation of the non-covalent interactions index on a three-dimensional grid. Additional comments: !!!!! The distribution file for this program is over 330 Mbytes and therefore is not delivered directly when download or Email is requested. Instead a html file giving details of how the program can be obtained is sent. !!!!! Running time: Variable, depending on the crystal and the source of the underlying scalar field.

  14. MARS15

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Mokhov, Nikolai

    MARS is a Monte Carlo code for inclusive and exclusive simulation of three-dimensional hadronic and electromagnetic cascades, muon, heavy-ion and low-energy neutron transport in accelerator, detector, spacecraft and shielding components in the energy range from a fraction of an electronvolt up to 100 TeV. Recent developments in the MARS15 physical models of hadron, heavy-ion and lepton interactions with nuclei and atoms include a new nuclear cross section library, a model for soft pion production, the cascade-exciton model, the quark gluon string models, deuteron-nucleus and neutrino-nucleus interaction models, detailed description of negative hadron and muon absorption and a unified treatment ofmore » muon, charged hadron and heavy-ion electromagnetic interactions with matter. New algorithms are implemented into the code and thoroughly benchmarked against experimental data. The code capabilities to simulate cascades and generate a variety of results in complex media have been also enhanced. Other changes in the current version concern the improved photo- and electro-production of hadrons and muons, improved algorithms for the 3-body decays, particle tracking in magnetic fields, synchrotron radiation by electrons and muons, significantly extended histograming capabilities and material description, and improved computational performance. In addition to direct energy deposition calculations, a new set of fluence-to-dose conversion factors for all particles including neutrino are built into the code. The code includes new modules for calculation of Displacement-per-Atom and nuclide inventory. The powerful ROOT geometry and visualization model implemented in MARS15 provides a large set of geometrical elements with a possibility of producing composite shapes and assemblies and their 3D visualization along with a possible import/export of geometry descriptions created by other codes (via the GDML format) and CAD systems (via the STEP format). The built-in MARS-MAD Beamline Builder (MMBLB) was redesigned for use with the ROOT geometry package that allows a very efficient and highly-accurate description, modeling and visualization of beam loss induced effects in arbitrary beamlines and accelerator lattices. The MARS15 code includes links to the MCNP-family codes for neutron and photon production and transport below 20 MeV, to the ANSYS code for thermal and stress analyses and to the STRUCT code for multi-turn particle tracking in large synchrotrons and collider rings.« less

  15. Measurement of electron impact collisional excitation cross sections of Ni to Ge-like gold

    DOE PAGES

    May, M. J.; Beiersdorfer, P.; Jordan, N.; ...

    2017-03-01

    We have measured the collisional excitation cross sections for the 3d→4f and 3d→5f excitations in Au ions near the Ni-like charge state by using beam plasmas created in the Livermore electron beam ion trap EBIT-I. The cross sections have been experimentally determined at approximately 1, 2 and 3 keV above the threshold energy, ET, for the 3d→4f excitations (ET ~2.5 keV) and at approximately 0.1, 1 and 2 keV above the threshold energy for the 3d→5f excitations (ET ~3.3 keV). The cross section measurements were made possible by using the GSFC x-ray microcalorimeter at the Livermore EBIT facility. The absolutemore » cross sections are determined from the ratio of the intensity of the collisionally excited bound-bound transitions to the intensity of the radiative recombination lines produced in EBIT-I plasmas. The effects of polarization and Auger decay channels are accounted for in the cross section determination. Measured cross sections are compared with those from HULLAC, DWS and FAC calculations. Finally, the measurements demonstrate that some errors exist in the calculated excitation cross sections.« less

  16. Measurement of electron impact collisional excitation cross sections of Ni to Ge-like gold

    NASA Astrophysics Data System (ADS)

    May, M. J.; Beiersdorfer, P.; Jordan, N.; Scofield, J. H.; Reed, K. J.; Brown, G. V.; Hansen, S. B.; Porter, F. S.; Kelley, R.; Kilbourne, C. A.; Boyce, K. R.

    2017-03-01

    We have measured the collisional excitation cross sections for the 3d→4f and 3d→5f excitations in Au ions near the Ni-like charge state by using beam plasmas created in the Livermore electron beam ion trap EBIT-I. The cross sections have been experimentally determined at approximately 1, 2 and 3 keV above the threshold energy, ET, for the 3d→4f excitations (ET ˜ 2.5 keV) and at approximately 0.1, 1 and 2 keV above the threshold energy for the 3d→5f excitations (ET ˜ 3.3 keV). The cross section measurements were made possible by using the GSFC x-ray microcalorimeter at the Livermore EBIT facility. The absolute cross sections are determined from the ratio of the intensity of the collisionally excited bound-bound transitions to the intensity of the radiative recombination lines produced in EBIT-I plasmas. The effects of polarization and Auger decay channels are accounted for in the cross section determination. Measured cross sections are compared with those from HULLAC, DWS and FAC calculations. The measurements demonstrate that some errors exist in the calculated excitation cross sections.

  17. Application of low energy ion blocking for adsorption site determination of Na Atoms on a Cu(111) surface

    NASA Astrophysics Data System (ADS)

    Zhang, R.; Makarenko, B.; Bahrim, B.; Rabalais, J. W.

    2010-07-01

    Ion blocking in the low keV energy range is demonstrated to be a sensitive method for probing surface adsorption sites by means of the technique of time-of-flight scattering and recoiling spectroscopy (TOF-SARS). Adsorbed atoms can block the nearly isotropic backscattering of primary ions from surface atoms in the outmost layers of a crystal. The relative adsorption site position can be derived unambiguously by simple geometrical constructs between the adsorbed atom site and the surface atom sites. Classical ion trajectory simulations using the scattering and recoiling imaging code (SARIC) and molecular dynamics (MD) simulations provide the detailed ion trajectories. Herein we present a quantitative analysis of the blocking effects produced by sub-monolayer Na adsorbed on a Cu(111) surface at room temperature. The results show that the Na adsorption site preferences are different at different Na coverages. At a coverage θ = 0.25 monolayer, Na atoms preferentially populate the fcc threefold surface sites with a height of 2.7 ± 0.1 Å above the 1st layer Cu atoms. At a lower coverage of θ = 0.10 monolayer, there is no adsorption site preference for the Na atoms on the Cu(111) surface.

  18. The Development of a Nonequilibrium Radiative Heat Transfer Computational Model for High Altitude Entry Vehicle Flowfield Methods

    NASA Technical Reports Server (NTRS)

    Carlson, Leland A.

    1995-01-01

    This final report will attempt to concisely summarize the activities and accomplishments associated with NASA Grant and to include pertinent documents in an appendix. The project initially had one primary and several secondary objectives. The original primary objective was to couple into the NASA Johnson Space Center (JSC) nonequilibrium chemistry Euler equation entry vehicle flowfield code, INEQ3D, the Texas A&M University (TAMU) local thermodynamic nonequilibrium (LTNE) radiation model. This model had previously been developed and verified under NASA Langley and NASA Johnson sponsorship as part of a viscous shock layer entry vehicle flowfield code. The secondary objectives were: (1) to investigate the necessity of including the radiative flux term in the vibrational-electron-electronic (VEE) energy equation as well as in the global energy equation, (2) to determine the importance of including the small net change in electronic energy between products and reactants which occurs during a chemical reaction, and (3) to study the effect of atom-atom impact ionization reactions on entry vehicle nonequilibrium flowfield chemistry and radiation. For each, of these objectives, it was assumed that the code would be applicable to lunar return entry conditions, i.e. altitude above 75 km, velocity greater, than 11 km/sec, where nonequilibrium chemistry and radiative heating phenomena would be significant. In addition, it was tacitly assumed that as part of the project the code would be applied to a variety of flight conditions and geometries.

  19. A theoretical evaluation of aluminum gel propellant two-phase flow losses on vehicle performance

    NASA Technical Reports Server (NTRS)

    Mueller, Donn C.; Turns, Stephen R.

    1993-01-01

    A one-dimensional model of a hydrocarbon/Al/O2(gaseous) fueled rocket combustion chamber was developed to study secondary atomization effects on propellant combustion. This chamber model was coupled with a two dimensional, two-phase flow nozzle code to estimate the two-phase flow losses associated with solid combustion products. Results indicate that moderate secondary atomization significantly reduces propellant burnout distance and Al2O3 particle size; however, secondary atomization provides only moderate decreases in two-phase flow induced I(sub sp) losses. Despite these two-phase flow losses, a simple mission study indicates that aluminum gel propellants may permit a greater maximum payload than the hydrocarbon/O2 bi-propellant combination for a vehicle of fixed propellant volume. Secondary atomization was also found to reduce radiation losses from the solid combustion products to the chamber walls, primarily through reductions in propellant burnout distance.

  20. THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures.

    PubMed

    Theobald, Douglas L; Wuttke, Deborah S

    2006-09-01

    THESEUS is a command line program for performing maximum likelihood (ML) superpositions and analysis of macromolecular structures. While conventional superpositioning methods use ordinary least-squares (LS) as the optimization criterion, ML superpositions provide substantially improved accuracy by down-weighting variable structural regions and by correcting for correlations among atoms. ML superpositioning is robust and insensitive to the specific atoms included in the analysis, and thus it does not require subjective pruning of selected variable atomic coordinates. Output includes both likelihood-based and frequentist statistics for accurate evaluation of the adequacy of a superposition and for reliable analysis of structural similarities and differences. THESEUS performs principal components analysis for analyzing the complex correlations found among atoms within a structural ensemble. ANSI C source code and selected binaries for various computing platforms are available under the GNU open source license from http://monkshood.colorado.edu/theseus/ or http://www.theseus3d.org.

  1. Hα line shape in front of the limiter in the HT-6M tokamak

    NASA Astrophysics Data System (ADS)

    Wan, Baonian; Li, Jiangang; Luo, Jiarong; Xie, Jikang; Wu, Zhenwei; Zhang, Xianmei; HT-6M Group

    1999-11-01

    The Hα line shape in front of the limiter in the HT-6M tokamak is analysed by multi-Gaussian fitting. The energy distribution of neutral hydrogen atoms reveals that Hα radiation is contributed by Franck-Condon atoms, atoms reflected at the limiter surface and charge exchange. Multi-Gaussian fitting of the Hα spectral profile indicates contributions of 60% from reflection particles and 40% from molecule dissociation to recycling. Ion temperatures in central regions are obtained from the spectral width of charge exchange components. Dissociation of hydrogen molecules and reflection of particles at the limiter surface are dominant in edge recycling. Reduction of particle reflection at the limiter surface is important for controlling edge recycling. The measured profiles of neutral hydrogen atom density are reproduced by a particle continuity equation and a simplified one dimensional Monte Carlo simulation code.

  2. Cretin Memory Flow on Sierra

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Langer, S. H.; Scott, H. A.

    2016-08-05

    The Cretin iCOE project has a goal of enabling the efficient generation of Non-LTE opacities for use in radiation-hydrodynamic simulation codes using the Nvidia boards on LLNL’s upcoming Sierra system. Achieving the desired level of accuracy for some simulations require the use of a vary large number of atomic configurations (a configuration includes the atomic level for all electrons and how they are coupled together). The NLTE rate matrix needs to be solved separately in each zone. Calculating NLTE opacities can consume more time than all other physics packages used in a simulation.

  3. Development of an analytical-numerical model to predict radiant emission or absorption

    NASA Technical Reports Server (NTRS)

    Wallace, Tim L.

    1994-01-01

    The development of an analytical-numerical model to predict radiant emission or absorption is discussed. A voigt profile is assumed to predict the spectral qualities of a singlet atomic transition line for atomic species of interest to the OPAD program. The present state of this model is described in each progress report required under contract. Model and code development is guided by experimental data where available. When completed, the model will be used to provide estimates of specie erosion rates from spectral data collected from rocket exhaust plumes or other sources.

  4. Analysis of Crystallographic Structure of a Japanese Sword by the Pulsed Neutron Transmission Method

    NASA Astrophysics Data System (ADS)

    Kino, K.; Ayukawa, N.; Kiyanagi, Y.; Uchida, T.; Uno, S.; Grazzi, F.; Scherillo, A.

    We measured two-dimensional transmission spectra of pulsed neutron beams for a Japanese sword sample. Atom density, crystalline size, and preferred orientation of crystals were obtained using the RITS code. The position dependence of the atomic density is consistent with the shape of the sample. The crystalline size is very small and shows position dependence, which is understood by the unique structure of Japanese swords. The preferred orientation has strong position dependence. Our study shows the usefulness of the pulsed neutron transmission method for cultural metal artifacts.

  5. Final technical report for DE-SC00012633 AToM (Advanced Tokamak Modeling)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Holland, Christopher; Orlov, Dmitri; Izzo, Valerie

    This final report for the AToM project documents contributions from University of California, San Diego researchers over the period of 9/1/2014 – 8/31/2017. The primary focus of these efforts was on performing validation studies of core tokamak transport models using the OMFIT framework, including development of OMFIT workflow scripts. Additional work was performed to develop tools for use of the nonlinear magnetohydrodynamics code NIMROD in OMFIT, and its use in the study of runaway electron dynamics in tokamak disruptions.

  6. A Simple X-Y Scanner.

    ERIC Educational Resources Information Center

    Halse, M. R.; Hudson, W. J.

    1986-01-01

    Describes an X-Y scanner used to create acoustic holograms. Scanner is computer controlled and can be adapted to digitize pictures. Scanner geometry is discussed. An appendix gives equipment details. The control program in ATOM BASIC and 6502 machine code is available from the authors. (JM)

  7. Differential dpa calculations with SPECTRA-PKA

    NASA Astrophysics Data System (ADS)

    Gilbert, M. R.; Sublet, J.-Ch.

    2018-06-01

    The processing code SPECTRA-PKA produces energy spectra of primary atomic recoil events (or primary knock-on atoms, PKAs) for any material composition exposed to an irradiation spectrum. Such evaluations are vital inputs for simulations aimed at understanding the evolution of damage in irradiated material, which is generated in cascade displacement events initiated by PKAs. These PKA spectra present the full complexity of the input (to SPECTRA-PKA) nuclear data-library evaluations of recoil events. However, the commonly used displacements per atom (dpa) measure, which is an integral measure over all possible recoil events of the displacement damage dose, is still widely used and has many useful applications - as both a comparative and correlative quantity. This paper describes the methodology employed that allows the SPECTRA-PKA code to evaluate dpa rates using the energy-dependent recoil (PKA) cross section data used for the PKA distributions. This avoids the need for integral displacement kerma cross sections and also provides new insight into the relative importance of different reaction channels (and associated different daughter residual and emitted particles) to the total integrated dpa damage dose. Results are presented for Fe, Ni, W, and SS316. Fusion dpa rates are compared to those in fission, highlighting the increased contribution to damage creation in the former from high-energy threshold reactions.

  8. Electron impact excitation of N IV: calculations with the DARC code and a comparison with ICFT results

    NASA Astrophysics Data System (ADS)

    Aggarwal, K. M.; Keenan, F. P.; Lawson, K. D.

    2016-10-01

    There have been discussions in the recent literature regarding the accuracy of the available electron impact excitation rates (equivalently effective collision strengths Υ) for transitions in Be-like ions. In the present paper we demonstrate, once again, that earlier results for Υ are indeed overestimated (by up to four orders of magnitude), for over 40 per cent of transitions and over a wide range of temperatures. To do this we have performed two sets of calculations for N IV, with two different model sizes consisting of 166 and 238 fine-structure energy levels. As in our previous work, for the determination of atomic structure the GRASP (General-purpose Relativistic Atomic Structure Package) is adopted and for the scattering calculations (the standard and parallelised versions of) the Dirac Atomic R-matrix Code (DARC) are employed. Calculations for collision strengths and effective collision strengths have been performed over a wide range of energy (up to 45 Ryd) and temperature (up to 2.0 × 106 K), useful for applications in a variety of plasmas. Corresponding results for energy levels, lifetimes and A-values for all E1, E2, M1 and M2 transitions among 238 levels of N IV are also reported.

  9. Dirac R-matrix calculations of photoionization cross sections of Ni XII and atomic structure data of Ni XIII

    NASA Astrophysics Data System (ADS)

    Nazir, R. T.; Bari, M. A.; Bilal, M.; Sardar, S.; Nasim, M. H.; Salahuddin, M.

    2017-02-01

    We performed R-matrix calculations for photoionization cross sections of the two ground state configuration 3s23p5 (^2P^o3/2,1/2) levels and 12 excited states of Ni XII using relativistic Dirac Atomic R-matrix Codes (DARC) across the photon energy range between the ionizations thresholds of the corresponding states and well above the thresholds of the last level of the Ni XIII target ion. Generally, a good agreement is obtained between our results and the earlier theoretical photoionization cross sections. Moreover, we have used two independent fully relativistic GRASP and FAC codes to calculate fine-structure energy levels, wavelengths, oscillator strengths, transitions rates among the lowest 48 levels belonging to the configuration (3s23p4, 3s3p5, 3p6, 3s23p33d) in Ni XIII. Additionally, radiative lifetimes of all the excited states of Ni XIII are presented. Our results of the atomic structure of Ni XIII show good agreement with other theoretical and experimental results available in the literature. A good agreement is found between our calculated lifetimes and the experimental ones. Our present results are useful for plasma diagnostic of fusion and astrophysical plasmas.

  10. Supervised dictionary learning for inferring concurrent brain networks.

    PubMed

    Zhao, Shijie; Han, Junwei; Lv, Jinglei; Jiang, Xi; Hu, Xintao; Zhao, Yu; Ge, Bao; Guo, Lei; Liu, Tianming

    2015-10-01

    Task-based fMRI (tfMRI) has been widely used to explore functional brain networks via predefined stimulus paradigm in the fMRI scan. Traditionally, the general linear model (GLM) has been a dominant approach to detect task-evoked networks. However, GLM focuses on task-evoked or event-evoked brain responses and possibly ignores the intrinsic brain functions. In comparison, dictionary learning and sparse coding methods have attracted much attention recently, and these methods have shown the promise of automatically and systematically decomposing fMRI signals into meaningful task-evoked and intrinsic concurrent networks. Nevertheless, two notable limitations of current data-driven dictionary learning method are that the prior knowledge of task paradigm is not sufficiently utilized and that the establishment of correspondences among dictionary atoms in different brains have been challenging. In this paper, we propose a novel supervised dictionary learning and sparse coding method for inferring functional networks from tfMRI data, which takes both of the advantages of model-driven method and data-driven method. The basic idea is to fix the task stimulus curves as predefined model-driven dictionary atoms and only optimize the other portion of data-driven dictionary atoms. Application of this novel methodology on the publicly available human connectome project (HCP) tfMRI datasets has achieved promising results.

  11. Development of probabilistic design method for annular fuels

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Ozawa, Takayuki

    2007-07-01

    The increase of linear power and burn-up during the reactor operation is considered as one measure to ensure the utility of fast reactors in the future; for this the application of annular oxide fuels is under consideration. The annular fuel design code CEPTAR was developed in the Japan Atomic Energy Agency (JAEA) and verified by using many irradiation experiences with oxide fuels. In addition, the probabilistic fuel design code BORNFREE was also developed to provide a safe and reasonable fuel design and to evaluate the design margins quantitatively. This study aimed at the development of a probabilistic design method formore » annular oxide fuels; this was implemented in the developed BORNFREE-CEPTAR code, and the code was used to make a probabilistic evaluation with regard to the permissive linear power. (author)« less

  12. C2x: A tool for visualisation and input preparation for CASTEP and other electronic structure codes

    NASA Astrophysics Data System (ADS)

    Rutter, M. J.

    2018-04-01

    The c2x code fills two distinct roles. Its first role is in acting as a converter between the binary format .check files from the widely-used CASTEP [1] electronic structure code and various visualisation programs. Its second role is to manipulate and analyse the input and output files from a variety of electronic structure codes, including CASTEP, ONETEP and VASP, as well as the widely-used 'Gaussian cube' file format. Analysis includes symmetry analysis, and manipulation arbitrary cell transformations. It continues to be under development, with growing functionality, and is written in a form which would make it easy to extend it to working directly with files from other electronic structure codes. Data which c2x is capable of extracting from CASTEP's binary checkpoint files include charge densities, spin densities, wavefunctions, relaxed atomic positions, forces, the Fermi level, the total energy, and symmetry operations. It can recreate .cell input files from checkpoint files. Volumetric data can be output in formats useable by many common visualisation programs, and c2x will itself calculate integrals, expand data into supercells, and interpolate data via combinations of Fourier and trilinear interpolation. It can extract data along arbitrary lines (such as lines between atoms) as 1D output. C2x is able to convert between several common formats for describing molecules and crystals, including the .cell format of CASTEP. It can construct supercells, reduce cells to their primitive form, and add specified k-point meshes. It uses the spglib library [2] to report symmetry information, which it can add to .cell files. C2x is a command-line utility, so is readily included in scripts. It is available under the GPL and can be obtained from http://www.c2x.org.uk. It is believed to be the only open-source code which can read CASTEP's .check files, so it will have utility in other projects.

  13. Aluminum/hydrocarbon gel propellants: An experimental and theoretical investigation of secondary atomization and predicted rocket engine performance

    NASA Astrophysics Data System (ADS)

    Mueller, Donn Christopher

    1997-12-01

    Experimental and theoretical investigations of aluminum/hydrocarbon gel propellant secondary atomization and its potential effects on rocket engine performance were conducted. In the experimental efforts, a dilute, polydisperse, gel droplet spray was injected into the postflame region of a burner and droplet size distributions was measured as a function of position above the burner using a laser-based sizing/velocimetry technique. The sizing/velocimetry technique was developed to measure droplets in the 10-125 mum size range and avoids size-biased detection through the use of a uniformly illuminated probe volume. The technique was used to determine particle size distributions and velocities at various axial locations above the burner for JP-10, and 50 and 60 wt% aluminum gels. Droplet shell formation models were applied to aluminum/hydrocarbon gels to examine particle size and mass loading effects on the minimum droplet diameter that will permit secondary atomization. This diameter was predicted to be 38.1 and 34.7 mum for the 50 and 60 wt% gels, which is somewhat greater than the experimentally measured 30 and 25 mum diameters. In the theoretical efforts, three models were developed and an existing rocket code was exercised to gain insights into secondary atomization. The first model was designed to predict gel droplet properties and shell stresses after rigid shell formation, while the second, a one-dimensional gel spray combustion model was created to quantify the secondary atomization process. Experimental and numerical comparisons verify that secondary atomization occurs in 10-125 mum diameter particles although an exact model could not be derived. The third model, a one-dimensional gel-fueled rocket combustion chamber, was developed to evaluate secondary atomization effects on various engine performance parameters. Results show that only modest secondary atomization may be required to reduce propellant burnout distance and radiation losses. A solid propellant engine code was employed to estimate nozzle two-phase flow losses and engine performance for upper-stage and booster missions (3-6% and 2-3%, respectively). Given these losses and other difficulties, metallized gel propellants may be impractical in high-expansion ratio engines. Although uncertainties remain, it appears that performance gains will be minimal in gross-weight limited missions, but that significant gains may arise in volume-limited missions.

  14. Theoretical Kinetics Analysis for Ḣ Atom Addition to 1,3-Butadiene and Related Reactions on the Ċ4H7 Potential Energy Surface.

    PubMed

    Li, Yang; Klippenstein, Stephen J; Zhou, Chong-Wen; Curran, Henry J

    2017-10-12

    The oxidation chemistry of the simplest conjugated hydrocarbon, 1,3-butadiene, can provide a first step in understanding the role of polyunsaturated hydrocarbons in combustion and, in particular, an understanding of their contribution toward soot formation. On the basis of our previous work on propene and the butene isomers (1-, 2-, and isobutene), it was found that the reaction kinetics of Ḣ-atom addition to the C═C double bond plays a significant role in fuel consumption kinetics and influences the predictions of high-temperature ignition delay times, product species concentrations, and flame speed measurements. In this study, the rate constants and thermodynamic properties for Ḣ-atom addition to 1,3-butadiene and related reactions on the Ċ 4 H 7 potential energy surface have been calculated using two different series of quantum chemical methods and two different kinetic codes. Excellent agreement is obtained between the two different kinetics codes. The calculated results including zero-point energies, single-point energies, rate constants, barrier heights, and thermochemistry are systematically compared among the two quantum chemical methods. 1-Methylallyl (Ċ 4 H 7 1-3) and 3-buten-1-yl (Ċ 4 H 7 1-4) radicals and C 2 H 4 + Ċ 2 H 3 are found to be the most important channels and reactivity-promoting products, respectively. We calculated that terminal addition is dominant (>80%) compared to internal Ḣ-atom addition at all temperatures in the range 298-2000 K. However, this dominance decreases with increasing temperature. The calculated rate constants for the bimolecular reaction C 4 H 6 + Ḣ → products and C 2 H 4 + Ċ 2 H 3 → products are in excellent agreement with both experimental and theoretical results from the literature. For selected C 4 species, the calculated thermochemical values are also in good agreement with literature data. In addition, the rate constants for H atom abstraction by Ḣ atoms have also been calculated, and it is found that abstraction from the central carbon atoms is the dominant channel (>70%) at temperatures in the range of 298-2000 K. Finally, by incorporating our calculated rate constants for both Ḣ atom addition and abstraction into our recently developed 1,3-butadiene model, we show that laminar flame speed predictions are significantly improved, emphasizing the value of this study.

  15. Molybdenum and carbon atom and carbon cluster sputtering under low-energy noble gas plasma bombardment

    NASA Astrophysics Data System (ADS)

    Oyarzabal, Eider

    Exit-angle resolved Mo atom sputtering yield under Xe ion bombardment and carbon atom and cluster (C2 and C3) sputtering yields under Xe, Kr, Ar, Ne and He ion bombardment from a plasma are measured for low incident energies (75--225 eV). An energy-resolved quadrupole mass spectrometer (QMS) is used to detect the fraction of un-scattered sputtered neutrals that become ionized in the plasma; the angular distribution is obtained by changing the angle between the target and the QMS aperture. A one-dimensional Monte Carlo code is used to simulate the interaction of the plasma and the sputtered particles between the sample and the QMS. The elastic scattering cross-sections of C, C2 and C3 with the different bombarding gas neutrals is obtained by varying the distance between the sample and the QMS and by performing a best fit of the simulation results to the experimental results. Because the results obtained with the QMS are relative, the Mo atom sputtering results are normalized to the existing data in the literature and the total sputtering yield for carbon (C+C 2+C3) for each bombarding gas is obtained from weight loss measurements. The absolute sputtering yield for C, C2 and C 3 is then calculated from the integration of the measured angular distribution, taking into account the scattering and ionization of the sputtered particles between the sample and the QMS. The angular sputtering distribution for Mo has a maximum at theta=60°, and this maximum becomes less pronounced as the incident ion energy increases. The results of the Monte Carlo TRIDYN code simulation for the angular distribution of Mo atoms sputtered by Xe bombardment are in agreement with the experiments. For carbon sputtering under-cosine angular distributions of the sputtered atoms and clusters for all the studied bombarding gases are also observed. The C, C2 and C3 sputtering yield data shows a clear decrease of the atom to cluster (C/C2 and C/C3) sputtering ratio as the incident ion mass increases, changing from a carbon atom preferential erosion for the lower incident ion masses (He, Ne and Ar) to a cluster preferential erosion for the higher incident ion masses (Kr and Xe).

  16. Neutron production by cosmic-ray muons in various materials

    NASA Astrophysics Data System (ADS)

    Manukovsky, K. V.; Ryazhskaya, O. G.; Sobolevsky, N. M.; Yudin, A. V.

    2016-07-01

    The results obtained by studying the background of neutrons produced by cosmic-raymuons in underground experimental facilities intended for rare-event searches and in surrounding rock are presented. The types of this rock may include granite, sedimentary rock, gypsum, and rock salt. Neutron production and transfer were simulated using the Geant4 and SHIELD transport codes. These codes were tuned via a comparison of the results of calculations with experimental data—in particular, with data of the Artemovsk research station of the Institute for Nuclear Research (INR, Moscow, Russia)—as well as via an intercomparison of results of calculations with the Geant4 and SHIELD codes. It turns out that the atomic-number dependence of the production and yield of neutrons has an irregular character and does not allow a description in terms of a universal function of the atomic number. The parameters of this dependence are different for two groups of nuclei—nuclei consisting of alpha particles and all of the remaining nuclei. Moreover, there are manifest exceptions from a power-law dependence—for example, argon. This may entail important consequences both for the existing underground experimental facilities and for those under construction. Investigation of cosmic-ray-induced neutron production in various materials is of paramount importance for the interpretation of experiments conducted at large depths under the Earth's surface.

  17. A simple model for molecular hydrogen chemistry coupled to radiation hydrodynamics

    NASA Astrophysics Data System (ADS)

    Nickerson, Sarah; Teyssier, Romain; Rosdahl, Joakim

    2018-06-01

    We introduce non-equilibrium molecular hydrogen chemistry into the radiation-hydrodynamics code RAMSES-RT. This is an adaptive mesh refinement grid code with radiation hydrodynamics that couples the thermal chemistry of hydrogen and helium to moment-based radiative transfer with the Eddington tensor closure model. The H2 physics that we include are formation on dust grains, gas phase formation, formation by three-body collisions, collisional destruction, photodissociation, photoionisation, cosmic ray ionisation and self-shielding. In particular, we implement the first model for H2 self-shielding that is tied locally to moment-based radiative transfer by enhancing photo-destruction. This self-shielding from Lyman-Werner line overlap is critical to H2 formation and gas cooling. We can now track the non-equilibrium evolution of molecular, atomic, and ionised hydrogen species with their corresponding dissociating and ionising photon groups. Over a series of tests we show that our model works well compared to specialised photodissociation region codes. We successfully reproduce the transition depth between molecular and atomic hydrogen, molecular cooling of the gas, and a realistic Strömgren sphere embedded in a molecular medium. In this paper we focus on test cases to demonstrate the validity of our model on small scales. Our ultimate goal is to implement this in large-scale galactic simulations.

  18. Using NJOY to Create MCNP ACE Files and Visualize Nuclear Data

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kahler, Albert Comstock

    We provide lecture materials that describe the input requirements to create various MCNP ACE files (Fast, Thermal, Dosimetry, Photo-nuclear and Photo-atomic) with the NJOY Nuclear Data Processing code system. Input instructions to visualize nuclear data with NJOY are also provided.

  19. Recent Livermore Excitation and Dielectronic Recombination Measurements for Laboratory and Astrophysical Spectral Modeling

    NASA Technical Reports Server (NTRS)

    Beiersdorfer, P.; Brown, G. V.; Gu, M.-F.; Harris, C. L.; Kahn, S. M.; Kim, S.-H.; Neill, P. A.; Savin, D. W.; Smith, A. J.; Utter, S. B.

    2000-01-01

    Using the EBIT facility in Livermore we produce definitive atomic data for input into spectral synthesis codes. Recent measurements of line excitation and dielectronic recombination of highly charged K-shell and L-shell ions are presented to illustrate this point.

  20. 77 FR 2924 - Notice of Public Meeting and Request for Comment on the Branch Technical Position on the Import...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-20

    ... exclusion, initially adopted in a 1995 rule.\\3\\ In accordance with International Atomic Energy Agency (IAEA) Code of Conduct on the Safety and Security of Radioactive Sources and the IAEA supplemental Guidance on...

  1. Modeling Solar Wind Flow with the Multi-Scale Fluid-Kinetic Simulation Suite

    DOE PAGES

    Pogorelov, N.V.; Borovikov, S. N.; Bedford, M. C.; ...

    2013-04-01

    Multi-Scale Fluid-Kinetic Simulation Suite (MS-FLUKSS) is a package of numerical codes capable of performing adaptive mesh refinement simulations of complex plasma flows in the presence of discontinuities and charge exchange between ions and neutral atoms. The flow of the ionized component is described with the ideal MHD equations, while the transport of atoms is governed either by the Boltzmann equation or multiple Euler gas dynamics equations. We have enhanced the code with additional physical treatments for the transport of turbulence and acceleration of pickup ions in the interplanetary space and at the termination shock. In this article, we present themore » results of our numerical simulation of the solar wind (SW) interaction with the local interstellar medium (LISM) in different time-dependent and stationary formulations. Numerical results are compared with the Ulysses, Voyager, and OMNI observations. Finally, the SW boundary conditions are derived from in-situ spacecraft measurements and remote observations.« less

  2. A MATLAB-based finite-element visualization of quantum reactive scattering. I. Collinear atom-diatom reactions

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Warehime, Mick; Alexander, Millard H., E-mail: mha@umd.edu

    We restate the application of the finite element method to collinear triatomic reactive scattering dynamics with a novel treatment of the scattering boundary conditions. The method provides directly the reactive scattering wave function and, subsequently, the probability current density field. Visualizing these quantities provides additional insight into the quantum dynamics of simple chemical reactions beyond simplistic one-dimensional models. Application is made here to a symmetric reaction (H+H{sub 2}), a heavy-light-light reaction (F+H{sub 2}), and a heavy-light-heavy reaction (F+HCl). To accompany this article, we have written a MATLAB code which is fast, simple enough to be accessible to a wide audience,more » as well as generally applicable to any problem that can be mapped onto a collinear atom-diatom reaction. The code and user's manual are available for download from http://www2.chem.umd.edu/groups/alexander/FEM.« less

  3. Energy Levels and Oscillator Strengths for Ne-like Iron Ions

    NASA Astrophysics Data System (ADS)

    Zhong, J. Y.; Zhang, J.; Zhao, G.; Lu, X..

    2004-02-01

    Energy levels and oscillator strengths among the 27 fine-structure levels belonging to the (1s22s2)2p6, 2p53s, 2p53p and 2p53d configurations of neon-like iron ion have been calculated by using three atomic structure codes, RCN/RCG, AUTOSTRUCTURE (AS) and GRASP. The relativistic corrections of the wave functions are taken into account in RCN/RCG calculations. The results well agree with experimental and theoretical data wherever available. Finally the accuracy of three codes was analyzed.

  4. Non LTE Effects in Laser Plasmas

    NASA Astrophysics Data System (ADS)

    Klapisch, Marcel

    1997-11-01

    Laser produced plasmas are not in Local Thermodynamical Equilibrium(LTE) because of the strong gradients and the escaping radiation. Departure from LTE changes the average charge state Z^*, and through it the electron temperature and other thermodynamical variables. Hydrodynamic simulations using LTE and non LTE modes show that in some cases the temperatures can change by an order of magnitude. Several rad/hydro models have solved the approximate atomic rate equations in-line within the average atom model(W. A. Lokke and W. H. Grasburger, LLNL, Report UCRL-52276 (1977),G. Pollack, LANL, Report LA-UR-90-2423 (1990)), or with global rates(M. Busquet, J. P. Raucourt and J. C. Gauthier, J. Quant. Spectrosc. Radiat. Transfer, 54, 81 (1995)). A new technique developed by Busquet, the Radiation Dependent Ionization Model (RADIOM)(M. Busquet, Phys. Fluids B, 5, 4191 (1993)) has been implemented in the NRL hydro-code. It uses an ionization temperature Tz to obtain the opacities and EOS in table look-ups. A very elaborate LTE atomic physics such as the STA code( A. Bar-Shalom and J. Oreg, Phys. Rev. E, 54, 1850 (1996), and ref. therein), or OPAL, can then be used off-line for generating the tables. The algorithm for Tz is very simple and quick. RADIOM has recently been benchmarked with a new detailed collisional radiative model SCROLL(A. Bar-Shalom, J. Oreg and M. Klapisch, Phys. Rev. E, to appear in July (1997)) on a range of temperatures, densities and atomic numbers. RADIOM has been surprisingly successful in calculations of non-LTE opacities.

  5. Quantum-capacity-approaching codes for the detected-jump channel

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Grassl, Markus; Wei Zhaohui; Ji Zhengfeng

    2010-12-15

    The quantum-channel capacity gives the ultimate limit for the rate at which quantum data can be reliably transmitted through a noisy quantum channel. Degradable quantum channels are among the few channels whose quantum capacities are known. Given the quantum capacity of a degradable channel, it remains challenging to find a practical coding scheme which approaches capacity. Here we discuss code designs for the detected-jump channel, a degradable channel with practical relevance describing the physics of spontaneous decay of atoms with detected photon emission. We show that this channel can be used to simulate a binary classical channel with both erasuresmore » and bit flips. The capacity of the simulated classical channel gives a lower bound on the quantum capacity of the detected-jump channel. When the jump probability is small, it almost equals the quantum capacity. Hence using a classical capacity-approaching code for the simulated classical channel yields a quantum code which approaches the quantum capacity of the detected-jump channel.« less

  6. GOES satellite time code dissemination

    NASA Technical Reports Server (NTRS)

    Beehler, R. E.

    1983-01-01

    The GOES time code system, the performance achieved to date, and some potential improvements in the future are discussed. The disseminated time code is originated from a triply redundant set of atomic standards, time code generators and related equipment maintained by NBS at NOAA's Wallops Island, VA satellite control facility. It is relayed by two GOES satellites located at 75 W and 135 W longitude on a continuous basis to users within North and South America (with overlapping coverage) and well out into the Atlantic and Pacific ocean areas. Downlink frequencies are near 468 MHz. The signals from both satellites are monitored and controlled from the NBS labs at Boulder, CO with additional monitoring input from geographically separated receivers in Washington, D.C. and Hawaii. Performance experience with the received time codes for periods ranging from several years to one day is discussed. Results are also presented for simultaneous, common-view reception by co-located receivers and by receivers separated by several thousand kilometers.

  7. A test of the IAEA code of practice for absorbed dose determination in photon and electron beams

    NASA Astrophysics Data System (ADS)

    Leitner, Arnold; Tiefenboeck, Wilhelm; Witzani, Josef; Strachotinsky, Christian

    1990-12-01

    The IAEA (International Atomic Energy Agency) code of practice TRS 277 gives recommendations for absorbed dose determination in high energy photon and electron beams based on the use of ionization chambers calibrated in terms of exposure of air kerma. The scope of the work was to test the code for cobalt 60 gamma radiation and for several radiation qualities at four different types of electron accelerators and to compare the ionization chamber dosimetry with ferrous sulphate dosimetry. The results show agreement between the two methods within about one per cent for all the investigated qualities. In addition the response of the TLD capsules of the IAEA/WHO TL dosimetry service was determined.

  8. A Monte Carlo calculation model of electronic portal imaging device for transit dosimetry through heterogeneous media

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Yoon, Jihyung; Jung, Jae Won, E-mail: jungj@ecu.edu; Kim, Jong Oh

    2016-05-15

    Purpose: To develop and evaluate a fast Monte Carlo (MC) dose calculation model of electronic portal imaging device (EPID) based on its effective atomic number modeling in the XVMC code. Methods: A previously developed EPID model, based on the XVMC code by density scaling of EPID structures, was modified by additionally considering effective atomic number (Z{sub eff}) of each structure and adopting a phase space file from the EGSnrc code. The model was tested under various homogeneous and heterogeneous phantoms and field sizes by comparing the calculations in the model with measurements in EPID. In order to better evaluate themore » model, the performance of the XVMC code was separately tested by comparing calculated dose to water with ion chamber (IC) array measurement in the plane of EPID. Results: In the EPID plane, calculated dose to water by the code showed agreement with IC measurements within 1.8%. The difference was averaged across the in-field regions of the acquired profiles for all field sizes and phantoms. The maximum point difference was 2.8%, affected by proximity of the maximum points to penumbra and MC noise. The EPID model showed agreement with measured EPID images within 1.3%. The maximum point difference was 1.9%. The difference dropped from the higher value of the code by employing the calibration that is dependent on field sizes and thicknesses for the conversion of calculated images to measured images. Thanks to the Z{sub eff} correction, the EPID model showed a linear trend of the calibration factors unlike those of the density-only-scaled model. The phase space file from the EGSnrc code sharpened penumbra profiles significantly, improving agreement of calculated profiles with measured profiles. Conclusions: Demonstrating high accuracy, the EPID model with the associated calibration system may be used for in vivo dosimetry of radiation therapy. Through this study, a MC model of EPID has been developed, and their performance has been rigorously investigated for transit dosimetry.« less

  9. Addressing the challenges of standalone multi-core simulations in molecular dynamics

    NASA Astrophysics Data System (ADS)

    Ocaya, R. O.; Terblans, J. J.

    2017-07-01

    Computational modelling in material science involves mathematical abstractions of force fields between particles with the aim to postulate, develop and understand materials by simulation. The aggregated pairwise interactions of the material's particles lead to a deduction of its macroscopic behaviours. For practically meaningful macroscopic scales, a large amount of data are generated, leading to vast execution times. Simulation times of hours, days or weeks for moderately sized problems are not uncommon. The reduction of simulation times, improved result accuracy and the associated software and hardware engineering challenges are the main motivations for many of the ongoing researches in the computational sciences. This contribution is concerned mainly with simulations that can be done on a "standalone" computer based on Message Passing Interfaces (MPI), parallel code running on hardware platforms with wide specifications, such as single/multi- processor, multi-core machines with minimal reconfiguration for upward scaling of computational power. The widely available, documented and standardized MPI library provides this functionality through the MPI_Comm_size (), MPI_Comm_rank () and MPI_Reduce () functions. A survey of the literature shows that relatively little is written with respect to the efficient extraction of the inherent computational power in a cluster. In this work, we discuss the main avenues available to tap into this extra power without compromising computational accuracy. We also present methods to overcome the high inertia encountered in single-node-based computational molecular dynamics. We begin by surveying the current state of the art and discuss what it takes to achieve parallelism, efficiency and enhanced computational accuracy through program threads and message passing interfaces. Several code illustrations are given. The pros and cons of writing raw code as opposed to using heuristic, third-party code are also discussed. The growing trend towards graphical processor units and virtual computing clouds for high-performance computing is also discussed. Finally, we present the comparative results of vacancy formation energy calculations using our own parallelized standalone code called Verlet-Stormer velocity (VSV) operating on 30,000 copper atoms. The code is based on the Sutton-Chen implementation of the Finnis-Sinclair pairwise embedded atom potential. A link to the code is also given.

  10. Numerical simulation of physicochemical interactions between oxygen atom and phosphatidylcholine due to direct irradiation of atmospheric pressure nonequilibrium plasma to biological membrane with quantum mechanical molecular dynamics

    NASA Astrophysics Data System (ADS)

    Uchida, Satoshi; Yoshida, Taketo; Tochikubo, Fumiyoshi

    2017-10-01

    Plasma medicine is one of the most attractive applications using atmospheric pressure nonequilibrium plasma. With respect to direct contact of the discharge plasma with a biological membrane, reactive oxygen species play an important role in induction of medical effects. However, complicated interactions between the plasma radicals and membrane have not been understood well. In the present work, we simulated elemental processes at the first stage of physicochemical interactions between oxygen atom and phosphatidylcholine using the quantum mechanical molecular dynamics code in a general software AMBER. The change in the above processes was classified according to the incident energy of oxygen atom. At an energy of 1 eV, the abstraction of a hydrogen atom and recombination to phosphatidylcholine were simultaneously occurred in chemical attachment of incident oxygen atom. The exothermal energy of the reaction was about 80% of estimated one based on the bond energies of ethane. An oxygen atom over 10 eV separated phosphatidylcholine partially. The behaviour became increasingly similar to physical sputtering. The reaction probability of oxygen atom was remarkably high in comparison with that of hydrogen peroxide. These results suggest that we can uniformly estimate various physicochemical dynamics of reactive oxygen species against membrane lipids.

  11. A universal preconditioner for simulating condensed phase materials.

    PubMed

    Packwood, David; Kermode, James; Mones, Letif; Bernstein, Noam; Woolley, John; Gould, Nicholas; Ortner, Christoph; Csányi, Gábor

    2016-04-28

    We introduce a universal sparse preconditioner that accelerates geometry optimisation and saddle point search tasks that are common in the atomic scale simulation of materials. Our preconditioner is based on the neighbourhood structure and we demonstrate the gain in computational efficiency in a wide range of materials that include metals, insulators, and molecular solids. The simple structure of the preconditioner means that the gains can be realised in practice not only when using expensive electronic structure models but also for fast empirical potentials. Even for relatively small systems of a few hundred atoms, we observe speedups of a factor of two or more, and the gain grows with system size. An open source Python implementation within the Atomic Simulation Environment is available, offering interfaces to a wide range of atomistic codes.

  12. The atomic simulation environment-a Python library for working with atoms.

    PubMed

    Hjorth Larsen, Ask; Jørgen Mortensen, Jens; Blomqvist, Jakob; Castelli, Ivano E; Christensen, Rune; Dułak, Marcin; Friis, Jesper; Groves, Michael N; Hammer, Bjørk; Hargus, Cory; Hermes, Eric D; Jennings, Paul C; Bjerre Jensen, Peter; Kermode, James; Kitchin, John R; Leonhard Kolsbjerg, Esben; Kubal, Joseph; Kaasbjerg, Kristen; Lysgaard, Steen; Bergmann Maronsson, Jón; Maxson, Tristan; Olsen, Thomas; Pastewka, Lars; Peterson, Andrew; Rostgaard, Carsten; Schiøtz, Jakob; Schütt, Ole; Strange, Mikkel; Thygesen, Kristian S; Vegge, Tejs; Vilhelmsen, Lasse; Walter, Michael; Zeng, Zhenhua; Jacobsen, Karsten W

    2017-07-12

    The atomic simulation environment (ASE) is a software package written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations. In ASE, tasks are fully scripted in Python. The powerful syntax of Python combined with the NumPy array library make it possible to perform very complex simulation tasks. For example, a sequence of calculations may be performed with the use of a simple 'for-loop' construction. Calculations of energy, forces, stresses and other quantities are performed through interfaces to many external electronic structure codes or force fields using a uniform interface. On top of this calculator interface, ASE provides modules for performing many standard simulation tasks such as structure optimization, molecular dynamics, handling of constraints and performing nudged elastic band calculations.

  13. Atomicrex—a general purpose tool for the construction of atomic interaction models

    NASA Astrophysics Data System (ADS)

    Stukowski, Alexander; Fransson, Erik; Mock, Markus; Erhart, Paul

    2017-07-01

    We introduce atomicrex, an open-source code for constructing interatomic potentials as well as more general types of atomic-scale models. Such effective models are required to simulate extended materials structures comprising many thousands of atoms or more, because electronic structure methods become computationally too expensive at this scale. atomicrex covers a wide range of interatomic potential types and fulfills many needs in atomistic model development. As inputs, it supports experimental property values as well as ab initio energies and forces, to which models can be fitted using various optimization algorithms. The open architecture of atomicrex allows it to be used in custom model development scenarios beyond classical interatomic potentials while thanks to its Python interface it can be readily integrated e.g., with electronic structure calculations or machine learning algorithms.

  14. A universal preconditioner for simulating condensed phase materials

    NASA Astrophysics Data System (ADS)

    Packwood, David; Kermode, James; Mones, Letif; Bernstein, Noam; Woolley, John; Gould, Nicholas; Ortner, Christoph; Csányi, Gábor

    2016-04-01

    We introduce a universal sparse preconditioner that accelerates geometry optimisation and saddle point search tasks that are common in the atomic scale simulation of materials. Our preconditioner is based on the neighbourhood structure and we demonstrate the gain in computational efficiency in a wide range of materials that include metals, insulators, and molecular solids. The simple structure of the preconditioner means that the gains can be realised in practice not only when using expensive electronic structure models but also for fast empirical potentials. Even for relatively small systems of a few hundred atoms, we observe speedups of a factor of two or more, and the gain grows with system size. An open source Python implementation within the Atomic Simulation Environment is available, offering interfaces to a wide range of atomistic codes.

  15. The atomic simulation environment—a Python library for working with atoms

    NASA Astrophysics Data System (ADS)

    Hjorth Larsen, Ask; Jørgen Mortensen, Jens; Blomqvist, Jakob; Castelli, Ivano E.; Christensen, Rune; Dułak, Marcin; Friis, Jesper; Groves, Michael N.; Hammer, Bjørk; Hargus, Cory; Hermes, Eric D.; Jennings, Paul C.; Bjerre Jensen, Peter; Kermode, James; Kitchin, John R.; Leonhard Kolsbjerg, Esben; Kubal, Joseph; Kaasbjerg, Kristen; Lysgaard, Steen; Bergmann Maronsson, Jón; Maxson, Tristan; Olsen, Thomas; Pastewka, Lars; Peterson, Andrew; Rostgaard, Carsten; Schiøtz, Jakob; Schütt, Ole; Strange, Mikkel; Thygesen, Kristian S.; Vegge, Tejs; Vilhelmsen, Lasse; Walter, Michael; Zeng, Zhenhua; Jacobsen, Karsten W.

    2017-07-01

    The atomic simulation environment (ASE) is a software package written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations. In ASE, tasks are fully scripted in Python. The powerful syntax of Python combined with the NumPy array library make it possible to perform very complex simulation tasks. For example, a sequence of calculations may be performed with the use of a simple ‘for-loop’ construction. Calculations of energy, forces, stresses and other quantities are performed through interfaces to many external electronic structure codes or force fields using a uniform interface. On top of this calculator interface, ASE provides modules for performing many standard simulation tasks such as structure optimization, molecular dynamics, handling of constraints and performing nudged elastic band calculations.

  16. GPU acceleration of the Locally Selfconsistent Multiple Scattering code for first principles calculation of the ground state and statistical physics of materials

    NASA Astrophysics Data System (ADS)

    Eisenbach, Markus; Larkin, Jeff; Lutjens, Justin; Rennich, Steven; Rogers, James H.

    2017-02-01

    The Locally Self-consistent Multiple Scattering (LSMS) code solves the first principles Density Functional theory Kohn-Sham equation for a wide range of materials with a special focus on metals, alloys and metallic nano-structures. It has traditionally exhibited near perfect scalability on massively parallel high performance computer architectures. We present our efforts to exploit GPUs to accelerate the LSMS code to enable first principles calculations of O(100,000) atoms and statistical physics sampling of finite temperature properties. We reimplement the scattering matrix calculation for GPUs with a block matrix inversion algorithm that only uses accelerator memory. Using the Cray XK7 system Titan at the Oak Ridge Leadership Computing Facility we achieve a sustained performance of 14.5PFlop/s and a speedup of 8.6 compared to the CPU only code.

  17. A Radiation Shielding Code for Spacecraft and Its Validation

    NASA Technical Reports Server (NTRS)

    Shinn, J. L.; Cucinotta, F. A.; Singleterry, R. C.; Wilson, J. W.; Badavi, F. F.; Badhwar, G. D.; Miller, J.; Zeitlin, C.; Heilbronn, L.; Tripathi, R. K.

    2000-01-01

    The HZETRN code, which uses a deterministic approach pioneered at NASA Langley Research Center, has been developed over the past decade to evaluate the local radiation fields within sensitive materials (electronic devices and human tissue) on spacecraft in the space environment. The code describes the interactions of shield materials with the incident galactic cosmic rays, trapped protons, or energetic protons from solar particle events in free space and low Earth orbit. The content of incident radiations is modified by atomic and nuclear reactions with the spacecraft and radiation shield materials. High-energy heavy ions are fragmented into less massive reaction products, and reaction products are produced by direct knockout of shield constituents or from de-excitation products. An overview of the computational procedures and database which describe these interactions is given. Validation of the code with recent Monte Carlo benchmarks, and laboratory and flight measurement is also included.

  18. Improvements on non-equilibrium and transport Green function techniques: The next-generation TRANSIESTA

    NASA Astrophysics Data System (ADS)

    Papior, Nick; Lorente, Nicolás; Frederiksen, Thomas; García, Alberto; Brandbyge, Mads

    2017-03-01

    We present novel methods implemented within the non-equilibrium Green function code (NEGF) TRANSIESTA based on density functional theory (DFT). Our flexible, next-generation DFT-NEGF code handles devices with one or multiple electrodes (Ne ≥ 1) with individual chemical potentials and electronic temperatures. We describe its novel methods for electrostatic gating, contour optimizations, and assertion of charge conservation, as well as the newly implemented algorithms for optimized and scalable matrix inversion, performance-critical pivoting, and hybrid parallelization. Additionally, a generic NEGF "post-processing" code (TBTRANS/PHTRANS) for electron and phonon transport is presented with several novelties such as Hamiltonian interpolations, Ne ≥ 1 electrode capability, bond-currents, generalized interface for user-defined tight-binding transport, transmission projection using eigenstates of a projected Hamiltonian, and fast inversion algorithms for large-scale simulations easily exceeding 106 atoms on workstation computers. The new features of both codes are demonstrated and bench-marked for relevant test systems.

  19. GPU acceleration of the Locally Selfconsistent Multiple Scattering code for first principles calculation of the ground state and statistical physics of materials

    DOE PAGES

    Eisenbach, Markus; Larkin, Jeff; Lutjens, Justin; ...

    2016-07-12

    The Locally Self-consistent Multiple Scattering (LSMS) code solves the first principles Density Functional theory Kohn–Sham equation for a wide range of materials with a special focus on metals, alloys and metallic nano-structures. It has traditionally exhibited near perfect scalability on massively parallel high performance computer architectures. In this paper, we present our efforts to exploit GPUs to accelerate the LSMS code to enable first principles calculations of O(100,000) atoms and statistical physics sampling of finite temperature properties. We reimplement the scattering matrix calculation for GPUs with a block matrix inversion algorithm that only uses accelerator memory. Finally, using the Craymore » XK7 system Titan at the Oak Ridge Leadership Computing Facility we achieve a sustained performance of 14.5PFlop/s and a speedup of 8.6 compared to the CPU only code.« less

  20. Multi-scale modeling of irradiation effects in spallation neutron source materials

    NASA Astrophysics Data System (ADS)

    Yoshiie, T.; Ito, T.; Iwase, H.; Kaneko, Y.; Kawai, M.; Kishida, I.; Kunieda, S.; Sato, K.; Shimakawa, S.; Shimizu, F.; Hashimoto, S.; Hashimoto, N.; Fukahori, T.; Watanabe, Y.; Xu, Q.; Ishino, S.

    2011-07-01

    Changes in mechanical property of Ni under irradiation by 3 GeV protons were estimated by multi-scale modeling. The code consisted of four parts. The first part was based on the Particle and Heavy-Ion Transport code System (PHITS) code for nuclear reactions, and modeled the interactions between high energy protons and nuclei in the target. The second part covered atomic collisions by particles without nuclear reactions. Because the energy of the particles was high, subcascade analysis was employed. The direct formation of clusters and the number of mobile defects were estimated using molecular dynamics (MD) and kinetic Monte-Carlo (kMC) methods in each subcascade. The third part considered damage structural evolutions estimated by reaction kinetic analysis. The fourth part involved the estimation of mechanical property change using three-dimensional discrete dislocation dynamics (DDD). Using the above four part code, stress-strain curves for high energy proton irradiated Ni were obtained.

  1. DOUBLE code simulations of emissivities of fast neutrals for different plasma observation view-lines of neutral particle analyzers on the COMPASS tokamak

    NASA Astrophysics Data System (ADS)

    Mitosinkova, K.; Tomes, M.; Stockel, J.; Varju, J.; Stano, M.

    2018-03-01

    Neutral particle analyzers (NPA) measure line-integrated energy spectra of fast neutral atoms escaping the tokamak plasma, which are a product of charge-exchange (CX) collisions of plasma ions with background neutrals. They can observe variations in the ion temperature T i of non-thermal fast ions created by additional plasma heating. However, the plasma column which a fast atom has to pass through must be sufficiently short in comparison with the fast atom’s mean-free-path. Tokamak COMPASS is currently equipped with one NPA installed at a tangential mid-plane port. This orientation is optimal for observing non-thermal fast ions. However, in this configuration the signal at energies useful for T i derivation is lost in noise due to the too long fast atoms’ trajectories. Thus, a second NPA is planned to be connected for the purpose of measuring T i. We analyzed different possible view-lines (perpendicular mid-plane, tangential mid-plane, and top view) for the second NPA using the DOUBLE Monte-Carlo code and compared the results with the performance of the present NPA with tangential orientation. The DOUBLE code provides fast-atoms’ emissivity functions along the NPA view-line. The position of the median of these emissivity functions is related to the location from where the measured signal originates. Further, we compared the difference between the real central T i used as a DOUBLE code input and the T iCX derived from the exponential decay of simulated energy spectra. The advantages and disadvantages of each NPA location are discussed.

  2. Electronic stopping in oxides beyond Bragg additivity

    NASA Astrophysics Data System (ADS)

    Sigmund, P.; Schinner, A.

    2018-01-01

    We present stopping cross sections calculated by our PASS code for several ions in metal oxides and SiO2 over a wide energy range. Input takes into account changes in the valence structure by assigning two additional electrons to the 2p shell of oxygen and removing the appropriate number of electrons from the outer shells of the metal atom. Results are compared with tabulated experimental values and with two versions of Bragg's additivity rule. Calculated stopping cross sections are applied in testing a recently-proposed scaling rule, which relates the stopping cross section to the number of oxygen atoms per molecule.

  3. Neutral recycling effects on ITG turbulence

    DOE PAGES

    Stotler, D. P.; Lang, J.; Chang, C. S.; ...

    2017-07-04

    Here, the effects of recycled neutral atoms on tokamak ion temperature gradient (ITG) driven turbulence have been investigated in a steep edge pedestal, magnetic separatrix configuration, with the full-f edge gryokinetic code XGC1. An adiabatic electron model has been used; hence, the impacts of neutral particles and turbulence on the density gradient are not considered, nor are electromagnetic turbulence effects. The neutral atoms enhance the ITG turbulence, first, by increasing the ion temperature gradient in the pedestal via the cooling effects of charge exchange and, second, by a relative reduction in themore » $$E\\times B$$ shearing rate.« less

  4. Neutral recycling effects on ITG turbulence

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Stotler, D. P.; Lang, J.; Chang, C. S.

    Here, the effects of recycled neutral atoms on tokamak ion temperature gradient (ITG) driven turbulence have been investigated in a steep edge pedestal, magnetic separatrix configuration, with the full-f edge gryokinetic code XGC1. An adiabatic electron model has been used; hence, the impacts of neutral particles and turbulence on the density gradient are not considered, nor are electromagnetic turbulence effects. The neutral atoms enhance the ITG turbulence, first, by increasing the ion temperature gradient in the pedestal via the cooling effects of charge exchange and, second, by a relative reduction in themore » $$E\\times B$$ shearing rate.« less

  5. Lasers in Synthesis, Characterization and Processing of Diamond, International Center, Tashkent, Uzbekistan, 6-9 October 1997

    DTIC Science & Technology

    1997-01-01

    Chemistry Division, Code 6174 Materiaux Leninsky prospekt, 53 Gas/Surface Dinamics Section et des Hautes Pressions Moscow 117924, Russia Washington, D.C...reactor for diamond CVD. Strengths and limitations of this and the various alternative H atom detection methods will be summarised, before

  6. Hanford Site Groundwater Monitoring for Fiscal Year 2002

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Hartman, Mary J.; Morasch, Launa F.; Webber, William D.

    2003-02-28

    This report presents the results of groundwater and vadose zone monitoring and remediation for fiscal year 2002 on the U.S. Department of Energy's Hanford Site in Washington State. This report is written to meet the requirements in CERCLA, RCRA, the Atomic Energy Act of 1954, and Washington State Administrative Code.

  7. BSR: B-spline atomic R-matrix codes

    NASA Astrophysics Data System (ADS)

    Zatsarinny, Oleg

    2006-02-01

    BSR is a general program to calculate atomic continuum processes using the B-spline R-matrix method, including electron-atom and electron-ion scattering, and radiative processes such as bound-bound transitions, photoionization and polarizabilities. The calculations can be performed in LS-coupling or in an intermediate-coupling scheme by including terms of the Breit-Pauli Hamiltonian. New version program summaryTitle of program: BSR Catalogue identifier: ADWY Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADWY Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Computers on which the program has been tested: Microway Beowulf cluster; Compaq Beowulf cluster; DEC Alpha workstation; DELL PC Operating systems under which the new version has been tested: UNIX, Windows XP Programming language used: FORTRAN 95 Memory required to execute with typical data: Typically 256-512 Mwords. Since all the principal dimensions are allocatable, the available memory defines the maximum complexity of the problem No. of bits in a word: 8 No. of processors used: 1 Has the code been vectorized or parallelized?: no No. of lines in distributed program, including test data, etc.: 69 943 No. of bytes in distributed program, including test data, etc.: 746 450 Peripherals used: scratch disk store; permanent disk store Distribution format: tar.gz Nature of physical problem: This program uses the R-matrix method to calculate electron-atom and electron-ion collision processes, with options to calculate radiative data, photoionization, etc. The calculations can be performed in LS-coupling or in an intermediate-coupling scheme, with options to include Breit-Pauli terms in the Hamiltonian. Method of solution: The R-matrix method is used [P.G. Burke, K.A. Berrington, Atomic and Molecular Processes: An R-Matrix Approach, IOP Publishing, Bristol, 1993; P.G. Burke, W.D. Robb, Adv. At. Mol. Phys. 11 (1975) 143; K.A. Berrington, W.B. Eissner, P.H. Norrington, Comput. Phys. Comm. 92 (1995) 290].

  8. Parallel algorithm for multiscale atomistic/continuum simulations using LAMMPS

    NASA Astrophysics Data System (ADS)

    Pavia, F.; Curtin, W. A.

    2015-07-01

    Deformation and fracture processes in engineering materials often require simultaneous descriptions over a range of length and time scales, with each scale using a different computational technique. Here we present a high-performance parallel 3D computing framework for executing large multiscale studies that couple an atomic domain, modeled using molecular dynamics and a continuum domain, modeled using explicit finite elements. We use the robust Coupled Atomistic/Discrete-Dislocation (CADD) displacement-coupling method, but without the transfer of dislocations between atoms and continuum. The main purpose of the work is to provide a multiscale implementation within an existing large-scale parallel molecular dynamics code (LAMMPS) that enables use of all the tools associated with this popular open-source code, while extending CADD-type coupling to 3D. Validation of the implementation includes the demonstration of (i) stability in finite-temperature dynamics using Langevin dynamics, (ii) elimination of wave reflections due to large dynamic events occurring in the MD region and (iii) the absence of spurious forces acting on dislocations due to the MD/FE coupling, for dislocations further than 10 Å from the coupling boundary. A first non-trivial example application of dislocation glide and bowing around obstacles is shown, for dislocation lengths of ∼50 nm using fewer than 1 000 000 atoms but reproducing results of extremely large atomistic simulations at much lower computational cost.

  9. Emission spectra of photoionized plasmas induced by intense EUV pulses: Experimental and theoretical investigations

    NASA Astrophysics Data System (ADS)

    Saber, Ismail; Bartnik, Andrzej; Skrzeczanowski, Wojciech; Wachulak, Przemysław; Jarocki, Roman; Fiedorowicz, Henryk

    2017-03-01

    Experimental measurements and numerical modeling of emission spectra in photoionized plasma in the ultraviolet and visible light (UV/Vis) range for noble gases have been investigated. The photoionized plasmas were created using laser-produced plasma (LPP) extreme ultraviolet (EUV) source. The source was based on a gas puff target; irradiated with 10ns/10J/10Hz Nd:YAG laser. The EUV radiation pulses were collected and focused using grazing incidence multifoil EUV collector. The laser pulses were focused on a gas stream, injected into a vacuum chamber synchronously with the EUV pulses. Irradiation of gases resulted in a formation of low temperature photoionized plasmas emitting radiation in the UV/Vis spectral range. Atomic photoionized plasmas produced this way consisted of atomic and ionic with various ionization states. The most dominated observed spectral lines originated from radiative transitions in singly charged ions. To assist in a theoretical interpretation of the measured spectra, an atomic code based on Cowan's programs and a collisional-radiative PrismSPECT code have been used to calculate the theoretical spectra. A comparison of the calculated spectral lines with experimentally obtained results is presented. Electron temperature in plasma is estimated using the Boltzmann plot method, by an assumption that a local thermodynamic equilibrium (LTE) condition in the plasma is validated in the first few ionization states. A brief discussion for the measured and computed spectra is given.

  10. Atomic Oxygen Density Retrievals using FUV Observations by the Imaging Ultraviolet Spectrograph on MAVEN

    NASA Astrophysics Data System (ADS)

    Evans, J. Scott; Stevens, Michael H.; Schneider, Nicholas M.; Stewart, Ian; Deighan, Justin; Jain, Sonal Kumar; Eparvier, Francis; Thiemann, E. M.; Bougher, Stephen W.; Jakosky, Bruce

    2016-10-01

    We present the first direct retrievals of neutral atomic oxygen in Mars's upper atmosphere using daytime FUV periapse limb scan observations from 130 - 200 km tangent altitude. Atmospheric composition is inferred using the Atmospheric Ultraviolet Radiance Integrated Code [Strickland et al., 1999] adapted to the Martian atmosphere [Evans et al., 2015]. For our retrievals we use O I 135.6 nm emission observed by IUVS on MAVEN under daytime conditions (solar zenith angle < 60 degrees) over both northern and southern hemispheres (latitudes between -65 and +35 degrees) from October 2014 to August 2016. We investigate the sensitivity of atomic oxygen density retrievals to variability in solar irradiance, solar longitude, and local time. We compare our retrievals to predictions from the Mars Global Ionosphere-Thermosphere Model [MGITM, Bougher et al., 2015] and the Mars Climate Database [MCD, Forget et al., 1999] and quantify the differences throughout the altitude region of interest. The retrieved densities are used to characterize global transport of atomic oxygen in the Martian thermosphere.

  11. Atomic Data for the CHIANTI Database

    NASA Technical Reports Server (NTRS)

    Bhatia, Anand K.; Landi, E.

    2012-01-01

    The CHIANTI spectral code consists of an atomic database and a suite of computer programs to calculate the optically thin spectrum of astrophysical objects and to carry out spectroscopic plasma diagnostics. The database includes atomic energy levels, wavelengths, radiative transition rates, collisional excitation, ionization and recombination rate coefficients, as well as data to calculate free-free, free-bound and two-photon continuum emission. In recent years, we have been pursuing a program to calculate atomic data for ions whose lines have been observed in astrophysical spectra but have been neglected in the literature, and to provide CHIANTI with all the data necessary to predict line intensities. There are two types of such ions: those for which calculations are available for low-energy configurations but not for high-energy configurations (i.e., C-like, N-like, O-like systems), and ions that have never or only seldom been studied. This poster will summarize the current status of this project and indicate the future activities .

  12. An atomic and molecular fluid model for efficient edge-plasma transport simulations at high densities

    NASA Astrophysics Data System (ADS)

    Rognlien, Thomas; Rensink, Marvin

    2016-10-01

    Transport simulations for the edge plasma of tokamaks and other magnetic fusion devices requires the coupling of plasma and recycling or injected neutral gas. There are various neutral models used for this purpose, e.g., atomic fluid model, a Monte Carlo particle models, transition/escape probability methods, and semi-analytic models. While the Monte Carlo method is generally viewed as the most accurate, it is time consuming, which becomes even more demanding for device simulations of high densities and size typical of fusion power plants because the neutral collisional mean-free path becomes very small. Here we examine the behavior of an extended fluid neutral model for hydrogen that includes both atoms and molecules, which easily includes nonlinear neutral-neutral collision effects. In addition to the strong charge-exchange between hydrogen atoms and ions, elastic scattering is included among all species. Comparisons are made with the DEGAS 2 Monte Carlo code. Work performed for U.S. DoE by LLNL under Contract DE-AC52-07NA27344.

  13. Modeling the heating and atomic kinetics of a photoionized neon plasma experiment

    NASA Astrophysics Data System (ADS)

    Lockard, Tom E.

    Motivated by gas cell photoionized plasma experiments performed by our group at the Z facility of Sandia National Laboratories, we discuss in this dissertation a modeling study of the heating and ionization of the plasma for conditions characteristic of these experiments. Photoionized plasmas are non-equilibrium systems driven by a broadband x-ray radiation flux. They are commonly found in astrophysics but rarely seen in the laboratory. Several modeling tools have been employed: (1) a view-factor computer code constrained with side x-ray power and gated monochromatic image measurements of the z-pinch radiation, to model the time-history of the photon-energy resolved x-ray flux driving the photoionized plasma, (2) a Boltzmann self-consistent electron and atomic kinetics model to simulate the electron distribution function and configuration-averaged atomic kinetics, (3) a radiation-hydrodynamics code with inline non-equilibrium atomic kinetics to perform a comprehensive numerical simulation of the experiment and plasma heating, and (4) steady-state and time-dependent collisional-radiative atomic kinetics calculations with fine-structure energy level description to assess transient effects in the ionization and charge state distribution of the plasma. The results indicate that the photon-energy resolved x-ray flux impinging on the front window of the gas cell is very well approximated by a linear combination of three geometrically-diluted Planckian distributions. Knowledge of the spectral details of the x-ray drive turned out to be important for the heating and ionization of the plasma. The free electrons in the plasma thermalize quickly relative to the timescales associated with the time-history of the x-ray drive and the plasma atomic kinetics. Hence, electrons are well described by a Maxwellian energy distribution of a single temperature. This finding is important to support the application of a radiation-hydrodynamic model to simulate the experiment. It is found that the computed plasma heating compares well with experimental observation when the effects of the windows, hydrodynamics, and non-equilbirium neon emissivity and opacity are employed. The atomic kinetics shows significant time-dependent effects because the timescale of the x-ray drive is too short compared to that of the photoionization process. These modeling and simulation results are important to test theory and modeling assumptions and approximations, and also to provide guidance on data interpretation and analysis.

  14. Calculations of the energy levels and oscillator strengths of the Ne-like Fe Ion (Fe XVII)

    NASA Astrophysics Data System (ADS)

    Zhong, Jia-yong; Zhang, Jie; Zhao, Gang; Lu, Xin

    Energy levels and oscillator strengths among the 27 fine-structure levels belonging to the (ls 22s 2)2p 6, 2p 53s, 2p 53p and 2p 53d configurations of the neon-like iron ion have been calculated using three atomic structure codes RCN/RCG, AUTOSTRUCTURE (AS) and GRASP. Relativistic corrections of the wave functions are taken into account in the RCN/RCG calculation. The results agree well with the available experimental and theoretical data. The accuracy of the three codes is analysed.

  15. NEBULAR: Spectrum synthesis for mixed hydrogen-helium gas in ionization equilibrium

    NASA Astrophysics Data System (ADS)

    Schirmer, Mischa

    2016-08-01

    NEBULAR synthesizes the spectrum of a mixed hydrogen helium gas in collisional ionization equilibrium. It is not a spectral fitting code, but it can be used to resample a model spectrum onto the wavelength grid of a real observation. It supports a wide range of temperatures and densities. NEBULAR includes free-free, free-bound, two-photon and line emission from HI, HeI and HeII. The code will either return the composite model spectrum, or, if desired, the unrescaled atomic emission coefficients. It is written in C++ and depends on the GNU Scientific Library (GSL).

  16. Scalability improvements to NRLMOL for DFT calculations of large molecules

    NASA Astrophysics Data System (ADS)

    Diaz, Carlos Manuel

    Advances in high performance computing (HPC) have provided a way to treat large, computationally demanding tasks using thousands of processors. With the development of more powerful HPC architectures, the need to create efficient and scalable code has grown more important. Electronic structure calculations are valuable in understanding experimental observations and are routinely used for new materials predictions. For the electronic structure calculations, the memory and computation time are proportional to the number of atoms. Memory requirements for these calculations scale as N2, where N is the number of atoms. While the recent advances in HPC offer platforms with large numbers of cores, the limited amount of memory available on a given node and poor scalability of the electronic structure code hinder their efficient usage of these platforms. This thesis will present some developments to overcome these bottlenecks in order to study large systems. These developments, which are implemented in the NRLMOL electronic structure code, involve the use of sparse matrix storage formats and the use of linear algebra using sparse and distributed matrices. These developments along with other related development now allow ground state density functional calculations using up to 25,000 basis functions and the excited state calculations using up to 17,000 basis functions while utilizing all cores on a node. An example on a light-harvesting triad molecule is described. Finally, future plans to further improve the scalability will be presented.

  17. Neutron production by cosmic-ray muons in various materials

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Manukovsky, K. V.; Ryazhskaya, O. G.; Sobolevsky, N. M.

    The results obtained by studying the background of neutrons produced by cosmic-raymuons in underground experimental facilities intended for rare-event searches and in surrounding rock are presented. The types of this rock may include granite, sedimentary rock, gypsum, and rock salt. Neutron production and transfer were simulated using the Geant4 and SHIELD transport codes. These codes were tuned via a comparison of the results of calculations with experimental data—in particular, with data of the Artemovsk research station of the Institute for Nuclear Research (INR, Moscow, Russia)—as well as via an intercomparison of results of calculations with the Geant4 and SHIELD codes.more » It turns out that the atomic-number dependence of the production and yield of neutrons has an irregular character and does not allow a description in terms of a universal function of the atomic number. The parameters of this dependence are different for two groups of nuclei—nuclei consisting of alpha particles and all of the remaining nuclei. Moreover, there are manifest exceptions from a power-law dependence—for example, argon. This may entail important consequences both for the existing underground experimental facilities and for those under construction. Investigation of cosmic-ray-induced neutron production in various materials is of paramount importance for the interpretation of experiments conducted at large depths under the Earth’s surface.« less

  18. Simplified Thermo-Chemical Modelling For Hypersonic Flow

    NASA Astrophysics Data System (ADS)

    Sancho, Jorge; Alvarez, Paula; Gonzalez, Ezequiel; Rodriguez, Manuel

    2011-05-01

    Hypersonic flows are connected with high temperatures, generally associated with strong shock waves that appear in such flows. At high temperatures vibrational degrees of freedom of the molecules may become excited, the molecules may dissociate into atoms, the molecules or free atoms may ionize, and molecular or ionic species, unimportant at lower temperatures, may be formed. In order to take into account these effects, a chemical model is needed, but this model should be simplified in order to be handled by a CFD code, but with a sufficient precision to take into account the physics more important. This work is related to a chemical non-equilibrium model validation, implemented into a commercial CFD code, in order to obtain the flow field around bodies in hypersonic flow. The selected non-equilibrium model is composed of seven species and six direct reactions together with their inverse. The commercial CFD code where the non- equilibrium model has been implemented is FLUENT. For the validation, the X38/Sphynx Mach 20 case is rebuilt on a reduced geometry, including the 1/3 Lref forebody. This case has been run in laminar regime, non catalytic wall and with radiative equilibrium wall temperature. The validated non-equilibrium model is applied to the EXPERT (European Experimental Re-entry Test-bed) vehicle at a specified trajectory point (Mach number 14). This case has been run also in laminar regime, non catalytic wall and with radiative equilibrium wall temperature.

  19. DYNECHARM++: a toolkit to simulate coherent interactions of high-energy charged particles in complex structures

    NASA Astrophysics Data System (ADS)

    Bagli, Enrico; Guidi, Vincenzo

    2013-08-01

    A toolkit for the simulation of coherent interactions between high-energy charged particles and complex crystal structures, called DYNECHARM++ has been developed. The code has been written in C++ language taking advantage of this object-oriented programing method. The code is capable to evaluating the electrical characteristics of complex atomic structures and to simulate and track the particle trajectory within them. Calculation method of electrical characteristics based on their expansion in Fourier series has been adopted. Two different approaches to simulate the interaction have been adopted, relying on the full integration of particle trajectories under the continuum potential approximation and on the definition of cross-sections of coherent processes. Finally, the code has proved to reproduce experimental results and to simulate interaction of charged particles with complex structures.

  20. Using Histories to Implement Atomic Objects

    NASA Technical Reports Server (NTRS)

    Ng, Pui

    1987-01-01

    In this paper we describe an approach of implementing atomicity. Atomicity requires that computations appear to be all-or-nothing and executed in a serialization order. The approach we describe has three characteristics. First, it utilizes the semantics of an application to improve concurrency. Second, it reduces the complexity of application-dependent synchronization code by analyzing the process of writing it. In fact, the process can be automated with logic programming. Third, our approach hides the protocol used to arrive at a serialization order from the applications. As a result, different protocols can be used without affecting the applications. Our approach uses a history tree abstraction. The history tree captures the ordering relationship among concurrent computations. By determining what types of computations exist in the history tree and their parameters, a computation can determine whether it can proceed.

  1. A universal preconditioner for simulating condensed phase materials

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Packwood, David; Ortner, Christoph, E-mail: c.ortner@warwick.ac.uk; Kermode, James, E-mail: j.r.kermode@warwick.ac.uk

    2016-04-28

    We introduce a universal sparse preconditioner that accelerates geometry optimisation and saddle point search tasks that are common in the atomic scale simulation of materials. Our preconditioner is based on the neighbourhood structure and we demonstrate the gain in computational efficiency in a wide range of materials that include metals, insulators, and molecular solids. The simple structure of the preconditioner means that the gains can be realised in practice not only when using expensive electronic structure models but also for fast empirical potentials. Even for relatively small systems of a few hundred atoms, we observe speedups of a factor ofmore » two or more, and the gain grows with system size. An open source Python implementation within the Atomic Simulation Environment is available, offering interfaces to a wide range of atomistic codes.« less

  2. Theoretical Kinetics Analysis for $$\\dot{H}$$ Atom Addition to 1,3-Butadiene and Related Reactions on the $$\\dot{C}$$ 4H 7 Potential Energy Surface

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Li, Yang; Klippenstein, Stephen J.; Zhou, Chong-Wen

    The oxidation chemistry of the simplest conjugated hydrocarbon, 1,3-butadiene, can provide a first step in understanding the role of poly-unsaturated hydrocarbons in combustion and, in particular, an understanding of their contribution towards soot formation. Based on our previous work on propene and the butene isomers (1-, 2- and isobutene), it was found that the reaction kinetics of H-atom addition to the C=C double bond plays a significant role in fuel consumption kinetics and influences the predictions of high-temperature ignition delay times, product species concentrations and flame speed measurements. In this study, the rate constants and thermodynamic properties formore » $$\\dot{H}$$-atom addition to 1,3-butadiene and related reactions on the $$\\dot{C}$$ 4H 7 potential energy surface have been calculated using two different series of quantum chemical methods and two different kinetic codes. Excellent agreement is obtained between the two different kinetics codes. The calculated results including zero point energies, single point energies, rate constants, barrier heights and thermochemistry are systematically compared among the two quantum chemical methods. 1-methylallyl ($$\\dot{C}$$ 4H 71-3) and 3-buten-1- yl ($$\\dot{C}$$ 4H 71-4) radicals and C 2H 4 + $$\\dot{C}$$2H3 are found to be the most important channels and reactivity promoting products, respectively. We calculated that terminal addition is dominant (> 80%) compared to internal $$\\dot{H}$$-atom addition at all temperatures in the range 298 – 2000 K. However, this dominance decreases with increasing temperature. The calculated rate constants for the bimolecular reaction C 4H 6 + $$\\dot{H}$$ → products and C 2H 4 + $$\\dot{C}$$ 2H 3 → products are in excellent agreement with both experimental and theoretical results from the literature. For selected C 4 species the calculated thermochemical values are also in good agreement with literature data. In addition, the rate constants for H-atom abstraction by $$\\dot{H}$$ atoms have also been calculated, and it is found that abstraction from the central carbon atoms is the dominant channel (> 70%) at temperatures in the range 298 – 2000 K. Lastly, by incorporating our calculated rate constants for both H-atom addition and abstraction into our recently developed 1,3-butadiene model, we show that laminar flame speed predictions are significantly improved, emphasizing the value of this study.« less

  3. 76 FR 14699 - Southern Nuclear Operating Company; Notice of Availability of Application for a Combined License

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-03-17

    ... NUCLEAR REGULATORY COMMISSION [Docket Nos. 52-025 and 52-026; NRC-2008-0252] Southern Nuclear... Atomic Energy Act and Title 10 of the Code of Federal Regulations (10 CFR) Part 52, ``Licenses... of 10 CFR Part 52. The information submitted by the applicant includes certain administrative...

  4. 76 FR 16645 - Southern Nuclear Operating Company; Notice of Availability of Application for a Combined License

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-03-24

    ... NUCLEAR REGULATORY COMMISSION [Docket Nos. 52-025 and 52-026; NRC-2008-0252] Southern Nuclear... Atomic Energy Act and Title 10 of the Code of Federal Regulations (10 CFR) Part 52, ``Licenses... of 10 CFR Part 52. The information submitted by the applicant includes certain administrative...

  5. 78 FR 16921 - Physical Protection of Byproduct Material

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-03-19

    ... 1 and category 2 thresholds are based on the quantities established by the International Atomic... orders that were issued to licensees using a graded approach based on the relative risk and quantity of... 5,400 Ytterbium-169 300 8,100 3 81.0 These materials and thresholds are based on the IAEA Code of...

  6. Polarization entanglement purification for concatenated Greenberger-Horne-Zeilinger state

    NASA Astrophysics Data System (ADS)

    Zhou, Lan; Sheng, Yu-Bo

    2017-10-01

    Entanglement purification plays a fundamental role in long-distance quantum communication. In the paper, we put forward the first polarization entanglement purification protocol (EPP) for one type of nonlocal logic-qubit entanglement, i.e., concatenated Greenberger-Horne-Zeilinger (C-GHZ) state, resorting to the photon-atom interaction in low-quality (Q) cavity. In contrast to existing EPPs, this protocol can purify the bit-flip error and phase-flip error in both physic and logic level. Instead of measuring the photons directly, this protocol only requires to measure the atom states to judge whether the protocol is successful. In this way, the purified logic entangled states can be preserved for further application. Moreover, it makes this EPP repeatable so as to obtain a higher fidelity of logic entangled states. As the logic-qubit entanglement utilizes the quantum error correction (QEC) codes, which has an inherent stability against noise and decoherence, this EPP combined with the QEC codes may provide a double protection for the entanglement from the channel noise and may have potential applications in long-distance quantum communication.

  7. Collisional-radiative modeling of tungsten at temperatures of 1200–2400 eV

    DOE PAGES

    Colgan, James; Fontes, Christopher; Zhang, Honglin; ...

    2015-04-30

    We discuss new collisional-radiative modeling calculations of tungsten at moderate temperatures of 1200 to 2400 eV. Such plasma conditions are relevant to ongoing experimental work at ASDEX Upgrade and are expected to be relevant for ITER. Our calculations are made using the Los Alamos National Laboratory (LANL) collisional-radiative modeling ATOMIC code. These calculations formed part of a submission to the recent NLTE-8 workshop that was held in November 2013. This series of workshops provides a forum for detailed comparison of plasma and spectral quantities from NLTE collisional-radiative modeling codes. We focus on the LANL ATOMIC calculations for tungsten that weremore » submitted to the NLTE-8 workshop and discuss different models that were constructed to predict the tungsten emission. In particular, we discuss comparisons between semi-relativistic configuration-average and fully relativistic configuration-average calculations. As a result, we also present semi-relativistic calculations that include fine-structure detail, and discuss the difficult problem of ensuring completeness with respect to the number of configurations included in a CR calculation.« less

  8. The linearly scaling 3D fragment method for large scale electronic structure calculations

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Zhao, Zhengji; Meza, Juan; Lee, Byounghak

    2009-07-28

    The Linearly Scaling three-dimensional fragment (LS3DF) method is an O(N) ab initio electronic structure method for large-scale nano material simulations. It is a divide-and-conquer approach with a novel patching scheme that effectively cancels out the artificial boundary effects, which exist in all divide-and-conquer schemes. This method has made ab initio simulations of thousand-atom nanosystems feasible in a couple of hours, while retaining essentially the same accuracy as the direct calculation methods. The LS3DF method won the 2008 ACM Gordon Bell Prize for algorithm innovation. Our code has reached 442 Tflop/s running on 147,456 processors on the Cray XT5 (Jaguar) atmore » OLCF, and has been run on 163,840 processors on the Blue Gene/P (Intrepid) at ALCF, and has been applied to a system containing 36,000 atoms. In this paper, we will present the recent parallel performance results of this code, and will apply the method to asymmetric CdSe/CdS core/shell nanorods, which have potential applications in electronic devices and solar cells.« less

  9. The Linearly Scaling 3D Fragment Method for Large Scale Electronic Structure Calculations

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Zhao, Zhengji; Meza, Juan; Lee, Byounghak

    2009-06-26

    The Linearly Scaling three-dimensional fragment (LS3DF) method is an O(N) ab initio electronic structure method for large-scale nano material simulations. It is a divide-and-conquer approach with a novel patching scheme that effectively cancels out the artificial boundary effects, which exist in all divide-and-conquer schemes. This method has made ab initio simulations of thousand-atom nanosystems feasible in a couple of hours, while retaining essentially the same accuracy as the direct calculation methods. The LS3DF method won the 2008 ACM Gordon Bell Prize for algorithm innovation. Our code has reached 442 Tflop/s running on 147,456 processors on the Cray XT5 (Jaguar) atmore » OLCF, and has been run on 163,840 processors on the Blue Gene/P (Intrepid) at ALCF, and has been applied to a system containing 36,000 atoms. In this paper, we will present the recent parallel performance results of this code, and will apply the method to asymmetric CdSe/CdS core/shell nanorods, which have potential applications in electronic devices and solar cells.« less

  10. Neutral helium beam probe

    NASA Astrophysics Data System (ADS)

    Karim, Rezwanul

    1999-10-01

    This article discusses the development of a code where diagnostic neutral helium beam can be used as a probe. The code solves numerically the evolution of the population densities of helium atoms at their several different energy levels as the beam propagates through the plasma. The collisional radiative model has been utilized in this numerical calculation. The spatial dependence of the metastable states of neutral helium atom, as obtained in this numerical analysis, offers a possible diagnostic tool for tokamak plasma. The spatial evolution for several hypothetical plasma conditions was tested. Simulation routines were also run with the plasma parameters (density and temperature profiles) similar to a shot in the Princeton beta experiment modified (PBX-M) tokamak and a shot in Tokamak Fusion Test Reactor tokamak. A comparison between the simulation result and the experimentally obtained data (for each of these two shots) is presented. A good correlation in such comparisons for a number of such shots can establish the accurateness and usefulness of this probe. The result can possibly be extended for other plasma machines and for various plasma conditions in those machines.

  11. INTRIGOSS: A new Library of High Resolution Synthetic Spectra

    NASA Astrophysics Data System (ADS)

    Franchini, Mariagrazia; Morossi, Carlo; Di Marcancantonio, Paolo; Chavez, Miguel; GES-Builders

    2018-01-01

    INTRIGOSS (INaf Trieste Grid Of Synthetic Spectra) is a new High Resolution (HiRes) synthetic spectral library designed for studying F, G, and K stars. The library is based on atmosphere models computed with specified individual element abundances via ATLAS12 code. Normalized SPectra (NSP) and surface Flux SPectra (FSP), in the 4800-5400 Å wavelength range, were computed by means of the SPECTRUM code. The synthetic spectra are computed with an atomic and bi-atomic molecular line list including "bona fide" Predicted Lines (PLs) built by tuning loggf to reproduce very high SNR Solar spectrum and the UVES-U580 spectra of five cool giants extracted from the Gaia-ESO survey (GES). The astrophysical gf-values were then assessed by using more than 2000 stars with homogenous and accurate atmosphere parameters and detailed chemical composition from GES. The validity and greater accuracy of INTRIGOSS NSPs and FSPs with respect to other available spectral libraries is discussed. INTRIGOSS will be available on the web and will be a valuable tool for both stellar atmospheric parameters and stellar population studies.

  12. Determining the mass attenuation coefficient, effective atomic number, and electron density of raw wood and binderless particleboards of Rhizophora spp. by using Monte Carlo simulation

    NASA Astrophysics Data System (ADS)

    Marashdeh, Mohammad W.; Al-Hamarneh, Ibrahim F.; Abdel Munem, Eid M.; Tajuddin, A. A.; Ariffin, Alawiah; Al-Omari, Saleh

    Rhizophora spp. wood has the potential to serve as a solid water or tissue equivalent phantom for photon and electron beam dosimetry. In this study, the effective atomic number (Zeff) and effective electron density (Neff) of raw wood and binderless Rhizophora spp. particleboards in four different particle sizes were determined in the 10-60 keV energy region. The mass attenuation coefficients used in the calculations were obtained using the Monte Carlo N-Particle (MCNP5) simulation code. The MCNP5 calculations of the attenuation parameters for the Rhizophora spp. samples were plotted graphically against photon energy and discussed in terms of their relative differences compared with those of water and breast tissue. Moreover, the validity of the MCNP5 code was examined by comparing the calculated attenuation parameters with the theoretical values obtained by the XCOM program based on the mixture rule. The results indicated that the MCNP5 process can be followed to determine the attenuation of gamma rays with several photon energies in other materials.

  13. Relativistic opacities for astrophysical applications

    DOE PAGES

    Fontes, Christopher John; Fryer, Christopher Lee; Hungerford, Aimee L.; ...

    2015-06-29

    Here, we report on the use of the Los Alamos suite of relativistic atomic physics codes to generate radiative opacities for the modeling of astrophysically relevant plasmas under local thermodynamic equilibrium (LTE) conditions. The atomic structure calculations are carried out in fine-structure detail, including full configuration interaction. Three example applications are considered: iron opacities at conditions relevant to the base of the solar convection zone, nickel opacities for the modeling of stellar envelopes, and samarium opacities for the modeling of light curves produced by neutron star mergers. In the first two examples, comparisons are made between opacities that are generatedmore » with the fully and semi-relativistic capabilities in the Los Alamos suite of codes. As expected for these highly charged, iron-peak ions, the two methods produce reasonably similar results, providing confidence that the numerical methods have been correctly implemented. However, discrepancies greater than 10% are observed for nickel and investigated in detail. In the final application, the relativistic capability is used in a preliminary investigation of the complicated absorption spectrum associated with cold lanthanide elements.« less

  14. Numerical simulations of primary and secondary hydrogen ENA fluxes at 1 AU

    DOE PAGES

    Zirnstein, Eric; Heerikhuisen, Jacob; Pogorelov, Nikolai

    2012-11-20

    The interaction between the solar wind (SW) and the local interstellar medium (LISM) creates energetic neutral atoms (ENAs), mainly Hydrogen (H), at energies similar to ions in the SW. H ENAs are born from charge exchanges between SW protons and LISM H atoms. A large portion of measurable primary ENAs are born in the inner heliosheath (IHS), where the heated and condensed SW plasma has a large thermal component to direct ENAs back toward 1 AU. Secondary ENAs, however, require secondary charge exchanges before being detected at 1 AU. Primary ENAs born in the supersonic and subsonic SW may exitmore » the HP, charge exchange into pick-up ions (PUIs), and charge exchange again to become secondary ENAs. Recent IBEX observations show a ribbon of flux dominating the entire sky. It is possible that the IBEX ribbon is created through secondary charge exchange processes. In this article we present a numerical code that calculates primary and secondary H ENA fluxes by integrating along ENA trajectories. Here we will provide descriptions of the code and preliminary results.« less

  15. Electron impact excitation of Kr XXXII

    NASA Astrophysics Data System (ADS)

    Aggarwal, K. M.; Keenan, F. P.; Lawson, K. D.

    2009-09-01

    Collision strengths (Ω) have been calculated for all 7750 transitions among the lowest 125 levels belonging to the 2s2p,2s2p,2p,2s3ℓ,2s2p3ℓ, and 2p3ℓ configurations of boron-like krypton, Kr XXXII, for which the Dirac Atomic R-matrix Code has been adopted. All partial waves with angular momentum J⩽40 have been included, sufficient for the convergence of Ω for forbidden transitions. For allowed transitions, a top-up has been included in order to obtain converged values of Ω up to an energy of 500 Ryd. Resonances in the thresholds region have been resolved in a narrow energy mesh, and results for effective collision strengths (ϒ) have been obtained after averaging the values of Ω over a Maxwellian distribution of electron velocities. Values of ϒ are reported over a wide temperature range below 107.3K, and the accuracy of the results is assessed. Values of ϒ are also listed in the temperature range 7.3⩽logTe(K)⩽9.0, obtained from the nonresonant collision strengths from the Flexible Atomic Code.

  16. Simulation of beam-induced plasma in gas-filled rf cavities

    DOE PAGES

    Yu, Kwangmin; Samulyak, Roman; Yonehara, Katsuya; ...

    2017-03-07

    Processes occurring in a radio-frequency (rf) cavity, filled with high pressure gas and interacting with proton beams, have been studied via advanced numerical simulations. Simulations support the experimental program on the hydrogen gas-filled rf cavity in the Mucool Test Area (MTA) at Fermilab, and broader research on the design of muon cooling devices. space, a 3D electromagnetic particle-in-cell (EM-PIC) code with atomic physics support, was used in simulation studies. Plasma dynamics in the rf cavity, including the process of neutral gas ionization by proton beams, plasma loading of the rf cavity, and atomic processes in plasma such as electron-ion andmore » ion-ion recombination and electron attachment to dopant molecules, have been studied. Here, through comparison with experiments in the MTA, simulations quantified several uncertain values of plasma properties such as effective recombination rates and the attachment time of electrons to dopant molecules. Simulations have achieved very good agreement with experiments on plasma loading and related processes. Lastly, the experimentally validated code space is capable of predictive simulations of muon cooling devices.« less

  17. Characterizing RNA Dynamics at Atomic Resolution Using Solution-state NMR Spectroscopy

    PubMed Central

    Bothe, Jameson R.; Nikolova, Evgenia N.; Eichhorn, Catherine D.; Chugh, Jeetender; Hansen, Alexandar L.; Al-Hashimi, Hashim M.

    2012-01-01

    Many recently discovered non-coding RNAs do not fold into a single native conformation, but rather, sample many different conformations along their free energy landscape to carry out their biological function. Unprecedented insights into the RNA dynamic structure landscape are provided by solution-state NMR techniques that measure the structural, kinetic, and thermodynamic characteristics of motions spanning picosecond to second timescales at atomic resolution. From these studies a basic description of the RNA dynamic structure landscape is emerging, bringing new insights into how RNA structures change to carry out their function as well as applications in RNA-targeted drug discovery and RNA bioengineering. PMID:22036746

  18. Energy Levels and Radiative Rates for Transitions in F-like Sc XIII and Ne-like Sc XII and Y XXX

    NASA Astrophysics Data System (ADS)

    Aggarwal, Kanti

    2018-05-01

    Energy levels, radiative rates and lifetimes are reported for F-like Sc~XIII and Ne-like Sc~XII and Y~XXX for which the general-purpose relativistic atomic structure package ({\\sc grasp}) has been adopted. For all three ions limited data exist in the literature but comparisons have been made wherever possible to assess the accuracy of the calculations. In the present work the lowest 102, 125 and 139 levels have been considered for the respective ions. Additionally, calculations have also been performed with the flexible atomic code ({\\sc fac}) to (particularly) confirm the accuracy of energy levels.

  19. Numerical study on the variation of pressure on India Bhabha Atomic Research Center (BARC) and Imperial College plasma focus machines

    NASA Astrophysics Data System (ADS)

    Singh, Arwinder; Heoh, Saw Sor; Sing, Lee

    2017-03-01

    In this paper, we use Lee's 5 phase model code to configure both the India Bhabha Atomic Research Center (BARC) Plasma focus machine operating in the pressure (P0) range from 1 Torr to 14 Torr as well as the Imperial College Plasma Focus Machine operating in the pressure (P0) range from 0.5 Torr to 6 Torr to compare the computational neutron yield to the experimental neutron yield as well as to obtain the relationship between axial speed va, radial shock speed vs, piston speed vp and pinch temperature with P0 for these machines.

  20. The First Non-Dispersive High-Resolution Spectroscopy of an X-ray-bright Galaxy Cluster

    NASA Astrophysics Data System (ADS)

    Yamaguchi, Hiroya; Hitomi Collaboration

    2018-06-01

    The Hitomi X-ray Observatory was equipped with the Soft X-ray Spectrometer (SXS), an X-ray microcalorimeter that achieved an energy resolution of 5 eV (@0.5-10 keV) for extended objects. This offered an unprecedented benchmark of atomic modeling and database for hot collisional plasmas, revealing both successes and challenges in the current atomic codes that are widely used by the X-ray astronomy community. I will review the Hitomi observations of the brightest part of the Perseus Cluster, whose X-ray spectrum is dominated by thermal emission from the intra-cluster medium (ICM). The SXS successfully measured the turbulent velocities and metal abundances of the ICM, which radically altered our understanding of the dynamics and chemical enrichment in this object. At the same time, the high-resolution X-ray data led to significant improvement in the atomic models, such as AtomDB and SPEX -- I will briefly overview how this improvement was made. Nevertheless, there are still significant discrepancies among the public atomic models, causing systematic uncertainties in measurements of the temperature, abundance, and degree of the resonance scattering. Requirements for future improvements will be summarized in this context.

  1. First principles study of hydrogen adsorption on carbon nanowires.

    NASA Astrophysics Data System (ADS)

    Tapia, Alejandro; Aguilera, Luis; Murrieta, Gabriel; de Coss, Romeo

    2007-03-01

    Recently has been reported a new type of one-dimensional carbon structures. Carbon nanowires formed by a linear carbon-atom chain inside an armchair (5,5) carbon nanotube has been observed using high-resolution transmission electron microscopy. In the present work we have studied the changes in the electronic structure of a carbon nanowires and (5,5) single-walled carbon nanotubes (SWCN) when a hydrogen atom is adsorbed. We used the Density Functional Theory and the calculations where performed by the pseudopotentials LCAO method (SIESTA code) and the Generalized Gradient Approximation (GGA) for the exchange-correlation potential. We have analyzed the changes in the atomic structure, density of states (LDOS), and the local orbital population. We found charge transfer from the nanotube to the linear chain and the hydrogen atom, the electronic character of the chain and nanotube sub-systems in chain@SWCN is the same that in the corresponding isolated systems, chain or SWCN. But the hydrogen adsorption produced changes in the atomic estructure and the electronic properties. This research was supported by PRIORI-UADY under Grant No. FING-05-004 and Consejo Nacional de Ciencia y Tecnolog'ia (Conacyt) under Grants No. 43830-F and 49985-J.

  2. A study to compute integrated dpa for neutron and ion irradiation environments using SRIM-2013

    NASA Astrophysics Data System (ADS)

    Saha, Uttiyoarnab; Devan, K.; Ganesan, S.

    2018-05-01

    Displacements per atom (dpa), estimated based on the standard Norgett-Robinson-Torrens (NRT) model, is used for assessing radiation damage effects in fast reactor materials. A computer code CRaD has been indigenously developed towards establishing the infrastructure to perform improved radiation damage studies in Indian fast reactors. We propose a method for computing multigroup neutron NRT dpa cross sections based on SRIM-2013 simulations. In this method, for each neutron group, the recoil or primary knock-on atom (PKA) spectrum and its average energy are first estimated with CRaD code from ENDF/B-VII.1. This average PKA energy forms the input for SRIM simulation, wherein the recoil atom is taken as the incoming ion on the target. The NRT-dpa cross section of iron computed with "Quick" Kinchin-Pease (K-P) option of SRIM-2013 is found to agree within 10% with the standard NRT-dpa values, if damage energy from SRIM simulation is used. SRIM-2013 NRT-dpa cross sections applied to estimate the integrated dpa for Fe, Cr and Ni are in good agreement with established computer codes and data. A similar study carried out for polyatomic material, SiC, shows encouraging results. In this case, it is observed that the NRT approach with average lattice displacement energy of 25 eV coupled with the damage energies from the K-P option of SRIM-2013 gives reliable displacement cross sections and integrated dpa for various reactor spectra. The source term of neutron damage can be equivalently determined in the units of dpa by simulating self-ion bombardment. This shows that the information of primary recoils obtained from CRaD can be reliably applied to estimate the integrated dpa and damage assessment studies in accelerator-based self-ion irradiation experiments of structural materials. This study would help to advance the investigation of possible correlations between the damages induced by ions and reactor neutrons.

  3. The GBS code for tokamak scrape-off layer simulations

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Halpern, F.D., E-mail: federico.halpern@epfl.ch; Ricci, P.; Jolliet, S.

    2016-06-15

    We describe a new version of GBS, a 3D global, flux-driven plasma turbulence code to simulate the turbulent dynamics in the tokamak scrape-off layer (SOL), superseding the code presented by Ricci et al. (2012) [14]. The present work is driven by the objective of studying SOL turbulent dynamics in medium size tokamaks and beyond with a high-fidelity physics model. We emphasize an intertwining framework of improved physics models and the computational improvements that allow them. The model extensions include neutral atom physics, finite ion temperature, the addition of a closed field line region, and a non-Boussinesq treatment of the polarizationmore » drift. GBS has been completely refactored with the introduction of a 3-D Cartesian communicator and a scalable parallel multigrid solver. We report dramatically enhanced parallel scalability, with the possibility of treating electromagnetic fluctuations very efficiently. The method of manufactured solutions as a verification process has been carried out for this new code version, demonstrating the correct implementation of the physical model.« less

  4. CoMD Implementation Suite in Emerging Programming Models

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Haque, Riyaz; Reeve, Sam; Juallmes, Luc

    CoMD-Em is a software implementation suite of the CoMD [4] proxy app using different emerging programming models. It is intended to analyze the features and capabilities of novel programming models that could help ensure code and performance portability and scalability across heterogeneous platforms while improving programmer productivity. Another goal is to provide the authors and venders with some meaningful feedback regarding the capabilities and limitations of their models. The actual application is a classical molecular dynamics (MD) simulation using either the Lennard-Jones method (LJ) or the embedded atom method (EAM) for primary particle interaction. The code can be extended tomore » support alternate interaction models. The code is expected ro run on a wide class of heterogeneous hardware configurations like shard/distributed/hybrid memory, GPU's and any other platform supported by the underlying programming model.« less

  5. Benchmark test of neutron transport calculations: indium, nickel, gold, europium, and cobalt activation with and without energy moderated fission neutrons by iron simulating the Hiroshima atomic bomb casing.

    PubMed

    Iwatani, K; Hoshi, M; Shizuma, K; Hiraoka, M; Hayakawa, N; Oka, T; Hasai, H

    1994-10-01

    A benchmark test of the Monte Carlo neutron and photon transport code system (MCNP) was performed using a bare- and energy-moderated 252Cf fission neutron source which was obtained by transmission through 10-cm-thick iron. An iron plate was used to simulate the effect of the Hiroshima atomic bomb casing. This test includes the activation of indium and nickel for fast neutrons and gold, europium, and cobalt for thermal and epithermal neutrons, which were inserted in the moderators. The latter two activations are also to validate 152Eu and 60Co activity data obtained from the atomic bomb-exposed specimens collected at Hiroshima and Nagasaki, Japan. The neutron moderators used were Lucite and Nylon 6 and the total thickness of each moderator was 60 cm or 65 cm. Measured activity data (reaction yield) of the neutron-irradiated detectors in these moderators decreased to about 1/1,000th or 1/10,000th, which corresponds to about 1,500 m ground distance from the hypocenter in Hiroshima. For all of the indium, nickel, and gold activity data, the measured and calculated values agreed within 25%, and the corresponding values for europium and cobalt were within 40%. From this study, the MCNP code was found to be accurate enough for the bare- and energy-moderated 252Cf neutron activation calculations of these elements using moderators containing hydrogen, carbon, nitrogen, and oxygen.

  6. DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kaurov, Alexander A., E-mail: kaurov@uchicago.edu

    We explore a time-dependent energy dissipation of the energetic electrons in the inhomogeneous intergalactic medium (IGM) during the epoch of cosmic reionization. In addition to the atomic processes, we take into account the inverse Compton (IC) scattering of the electrons on the cosmic microwave background photons, which is the dominant channel of energy loss for electrons with energies above a few MeV. We show that: (1) the effect on the IGM has both local (atomic processes) and non-local (IC radiation) components; (2) the energy distribution between hydrogen and helium ionizations depends on the initial energy of an electron; (3) themore » local baryon overdensity significantly affects the fractions of energy distributed in each channel; and (4) the relativistic effect of the atomic cross-section becomes important during the epoch of cosmic reionization. We release our code as open source for further modification by the community.« less

  7. DFT study of Al doped armchair SWCNTs

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Dhiman, Shobhna, E-mail: s-dhiman@hotmail.com; Rani, Anita; Kumar, Ranjan

    2016-05-23

    Electronic properties of endohedrally doped armchair single-walled carbon nanotubes (SWCNTs) with a chain of six Al atoms have been studied using ab-initio density functional theory. We investigate the binding energy/atom, ionization potential, electron Affinity and Homo-Lumo gap of doped armchair SWNTs from (4,4) to (6,6) with two ends open. BE/dopant atom and ionization potential is maximum for (6, 6) doped armchair carbon nanotube; suggest that it is more stable than (4, 4) and (5, 5) doped tubes. HOMO - LUMO gap of Al doped arm chair carbon nanotubes decreases linearly with the increase in diameter of the tube. This showsmore » that confinement induce a strong effect on electronic properties of doped tubes. These combined systems can be used for future nano electronics. The ab–initio calculations were performed with SIESTA code using generalized gradient approximation (GGA).« less

  8. Parallelization of the FLAPW method

    NASA Astrophysics Data System (ADS)

    Canning, A.; Mannstadt, W.; Freeman, A. J.

    2000-08-01

    The FLAPW (full-potential linearized-augmented plane-wave) method is one of the most accurate first-principles methods for determining structural, electronic and magnetic properties of crystals and surfaces. Until the present work, the FLAPW method has been limited to systems of less than about a hundred atoms due to the lack of an efficient parallel implementation to exploit the power and memory of parallel computers. In this work, we present an efficient parallelization of the method by division among the processors of the plane-wave components for each state. The code is also optimized for RISC (reduced instruction set computer) architectures, such as those found on most parallel computers, making full use of BLAS (basic linear algebra subprograms) wherever possible. Scaling results are presented for systems of up to 686 silicon atoms and 343 palladium atoms per unit cell, running on up to 512 processors on a CRAY T3E parallel supercomputer.

  9. Direct Numerical Simulation of Liquid Nozzle Spray with Comparison to Shadowgraphy and X-Ray Computed Tomography Experimental Results

    NASA Astrophysics Data System (ADS)

    van Poppel, Bret; Owkes, Mark; Nelson, Thomas; Lee, Zachary; Sowell, Tyler; Benson, Michael; Vasquez Guzman, Pablo; Fahrig, Rebecca; Eaton, John; Kurman, Matthew; Kweon, Chol-Bum; Bravo, Luis

    2014-11-01

    In this work, we present high-fidelity Computational Fluid Dynamics (CFD) results of liquid fuel injection from a pressure-swirl atomizer and compare the simulations to experimental results obtained using both shadowgraphy and phase-averaged X-ray computed tomography (CT) scans. The CFD and experimental results focus on the dense near-nozzle region to identify the dominant mechanisms of breakup during primary atomization. Simulations are performed using the NGA code of Desjardins et al (JCP 227 (2008)) and employ the volume of fluid (VOF) method proposed by Owkes and Desjardins (JCP 270 (2013)), a second order accurate, un-split, conservative, three-dimensional VOF scheme providing second order density fluxes and capable of robust and accurate high density ratio simulations. Qualitative features and quantitative statistics are assessed and compared for the simulation and experimental results, including the onset of atomization, spray cone angle, and drop size and distribution.

  10. Outer satellite atmospheres: Their nature and planetary interactions

    NASA Technical Reports Server (NTRS)

    Smyth, W. H.; Combi, M. R.

    1982-01-01

    Significant progress is reported in early modeling analysis of observed sodium cloud images with our new model which includes the oscillating Io plasma torus ionization sink. Both the general w-D morphology of the region B cloud as well as the large spatial gradient seen between the region A and B clouds are found to be consistent with an isotropic flux of sodium atoms from Io. Model analysis of the spatially extended high velocity directional features provided substantial evidence for a magnetospheric wind driven gas escape mechanism from Io. In our efforts to define the source(s) of hydrogen atoms in the Saturn system, major steps were taken in order to understand the role of Titan. We have completed the comparison of the Voyager UVS data with previous Titan model results, as well as the update of the old model computer code to handle the spatially varying ionization sink for H atoms.

  11. Development of a model and computer code to describe solar grade silicon production processes

    NASA Technical Reports Server (NTRS)

    Srivastava, R.; Gould, R. K.

    1979-01-01

    Mathematical models, and computer codes based on these models were developed which allow prediction of the product distribution in chemical reactors in which gaseous silicon compounds are converted to condensed phase silicon. The reactors to be modeled are flow reactors in which silane or one of the halogenated silanes is thermally decomposed or reacted with an alkali metal, H2 or H atoms. Because the product of interest is particulate silicon, processes which must be modeled, in addition to mixing and reaction of gas-phase reactants, include the nucleation and growth of condensed Si via coagulation, condensation, and heterogeneous reaction.

  12. Atomic-scale to Meso-scale Simulation Studies of Thermal Ageing and Irradiation Effects in Fe- Cr Alloys

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Stanley, Eugene; Liu, Li

    In this project, we target at three primary objectives: (1) Molecular Dynamics (MD) code development for Fe-Cr alloys, which can be utilized to provide thermodynamic and kinetic properties as inputs in mesoscale Phase Field (PF) simulations; (2) validation and implementation of the MD code to explain thermal ageing and radiation damage; and (3) an integrated modeling platform for MD and PF simulations. These two simulation tools, MD and PF, will ultimately be merged to understand and quantify the kinetics and mechanisms of microstructure and property evolution of Fe-Cr alloys under various thermal and irradiation environments

  13. Making Ordered DNA and Protein Structures from Computer-Printed Transparency Film Cut-Outs

    ERIC Educational Resources Information Center

    Jittivadhna, Karnyupha; Ruenwongsa, Pintip; Panijpan, Bhinyo

    2009-01-01

    Instructions are given for building physical scale models of ordered structures of B-form DNA, protein [alpha]-helix, and parallel and antiparallel protein [beta]-pleated sheets made from colored computer printouts designed for transparency film sheets. Cut-outs from these sheets are easily assembled. Conventional color coding for atoms are used…

  14. Android Protection Mechanism: A Signed Code Security Mechanism for Smartphone Applications

    DTIC Science & Technology

    2011-03-01

    status registers, exceptions, endian support, unaligned access support, synchronization primitives , the Jazelle Extension, and saturated integer...supports comprehensive non-blocking shared-memory synchronization primitives that scale for multiple-processor system designs. This is an improvement... synchronization . Memory semaphores can be loaded and altered without interruption because the load and store operations are atomic. Processor

  15. Surface Electrochemistry of Metals

    DTIC Science & Technology

    1993-04-30

    maxima along the 12 directions of open channels .vhich are also the interatomic directions). Elastic scattering angular distributions always contain... scatterer geometric relationships for such samples. Distributions from ordered atomic bilayers reveal that the Auger signal from the underlayer is attenuated...are developing a theoretical model and computational code which include both elastic scattering and inhomogeneous inelastic scattering . We seek

  16. 10 CFR 725.23 - Terms and conditions of access.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... enrichment of special nuclear material any U.S. patent or any U.S. patent application (otherwise in condition... application and all claims for just compensation under section 173 of the Atomic Energy Act of 1954, with... 35 U.S. Code by reason of the imposition of any secrecy order on any patent application, and all...

  17. 10 CFR 725.23 - Terms and conditions of access.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... enrichment of special nuclear material any U.S. patent or any U.S. patent application (otherwise in condition... application and all claims for just compensation under section 173 of the Atomic Energy Act of 1954, with... 35 U.S. Code by reason of the imposition of any secrecy order on any patent application, and all...

  18. Nonequilibrium radiation and chemistry models for aerocapture vehicle flowfields, volume 1

    NASA Technical Reports Server (NTRS)

    Carlson, Leland A.

    1991-01-01

    The following subject areas are covered: the development of detailed nonequilibrium radiation models for molecules along with appropriate models for atoms; the inclusion of nongray radiation gasdynamic coupling in the VSL (Viscous Shock Layer) code; the development and evaluation of various electron-electronic energy models; and an examination of the effects of shock slip.

  19. Sparse Coding and Dictionary Learning Based on the MDL Principle

    DTIC Science & Technology

    2010-10-01

    average bits per pixel obtained was 4.08 bits per pixel ( bpp ), with p = 250 atoms in the final dictionary. We repeated this using `2 instead of Huber...loss, obtaining 4.12 bpp and p = 245. We now show example results obtained with our framework in two very different applications. In both cases we

  20. A Real-Time All-Atom Structural Search Engine for Proteins

    PubMed Central

    Gonzalez, Gabriel; Hannigan, Brett; DeGrado, William F.

    2014-01-01

    Protein designers use a wide variety of software tools for de novo design, yet their repertoire still lacks a fast and interactive all-atom search engine. To solve this, we have built the Suns program: a real-time, atomic search engine integrated into the PyMOL molecular visualization system. Users build atomic-level structural search queries within PyMOL and receive a stream of search results aligned to their query within a few seconds. This instant feedback cycle enables a new “designability”-inspired approach to protein design where the designer searches for and interactively incorporates native-like fragments from proven protein structures. We demonstrate the use of Suns to interactively build protein motifs, tertiary interactions, and to identify scaffolds compatible with hot-spot residues. The official web site and installer are located at http://www.degradolab.org/suns/ and the source code is hosted at https://github.com/godotgildor/Suns (PyMOL plugin, BSD license), https://github.com/Gabriel439/suns-cmd (command line client, BSD license), and https://github.com/Gabriel439/suns-search (search engine server, GPLv2 license). PMID:25079944

  1. REU in Physics at Kansas State University--- an Evolving Program

    NASA Astrophysics Data System (ADS)

    Corwin, Kristan; Glymour, Bruce; Lara, Amy; Weaver, Larry; Zollman, Dean

    2009-03-01

    The REU site in the Physics Department at Kansas State University, funded by NSF for 13 years between 1992 and 2007, originally focused on atomic collision physics. Now the theme has broadened to include laser-matter interactions on atomic and nanoscales, and an ethics component is incorporated. Students study how atoms and molecules interact with ultra-fast optical and x-ray pulses, reveal the structure of nanoparticle crystallization and gel formation with scattered laser light, and develop computer codes for atomic interactions in Bose-Einstein condensates and nanoparticle self-assembly from lattices to gels; some have traveled to Japan for neutrino experiments. The students we select come primarily from smaller colleges and universities in the Midwest where research opportunities are limited. Prof. Weaver, who has served as PI since 1992, facilitates their transition from a teaching to research environment through lectures and individual interactions. Our program is in a period of transition. While Prof. Weaver continues to be the ``impedance match'' between students and mentors, other leadership roles are gradually being assumed by a team of faculty members who strive to preserve the intimacy and excellence of the program.

  2. Atomic structure calculations for F-like tungsten

    NASA Astrophysics Data System (ADS)

    Sunny, Aggarwal

    2014-09-01

    Energy levels, wavefunction compositions and lifetimes have been computed for all levels of 1s22s22p5, 1s22s2p6, 1s22s22p43s, 1s22s22p43p, and 1s22s22p43d configurations in highly charged F-like tungsten ion. The multiconfigurational Dirac—Fock method (MCDF) is adopted to generate the wavefunctions. We have also presented the transition wavelengths, oscillator strengths, transition probabilities, and line strengths for the electric dipole (E1) and magnetic quadrupole (M2) transition from the 1s22s22p5 ground configuration. We have performed parallel calculations with the flexible atomic code (FAC) for comparing the atomic data. The reliability of present data is assessed by comparison with other theoretical and experimental data available in the literature. Good agreement is found between our results and those obtained using different approaches confirm the quality of our results. Additionally, we have predicted some new atomic data for F-like W that were not available so far and may be important for plasma diagnostic analysis in fusion plasma.

  3. A real-time all-atom structural search engine for proteins.

    PubMed

    Gonzalez, Gabriel; Hannigan, Brett; DeGrado, William F

    2014-07-01

    Protein designers use a wide variety of software tools for de novo design, yet their repertoire still lacks a fast and interactive all-atom search engine. To solve this, we have built the Suns program: a real-time, atomic search engine integrated into the PyMOL molecular visualization system. Users build atomic-level structural search queries within PyMOL and receive a stream of search results aligned to their query within a few seconds. This instant feedback cycle enables a new "designability"-inspired approach to protein design where the designer searches for and interactively incorporates native-like fragments from proven protein structures. We demonstrate the use of Suns to interactively build protein motifs, tertiary interactions, and to identify scaffolds compatible with hot-spot residues. The official web site and installer are located at http://www.degradolab.org/suns/ and the source code is hosted at https://github.com/godotgildor/Suns (PyMOL plugin, BSD license), https://github.com/Gabriel439/suns-cmd (command line client, BSD license), and https://github.com/Gabriel439/suns-search (search engine server, GPLv2 license).

  4. A numerical study on liquid charging inside electrostatic atomizers

    NASA Astrophysics Data System (ADS)

    Kashir, Babak; Perri, Anthony; Sankaran, Abhilash; Staszel, Christopher; Yarin, Alexander; Mashayek, Farzad

    2016-11-01

    The charging of the dielectric liquid inside an electrostatic atomizer is studied numerically by developing codes based on the OpenFOAM platform. Electrostatic atomization is an appealing technology in painting, fuel injection and oil coating systems due to improved particle-size distribution, enhanced controlability of droplets' trajectories and lower power consumption. The numerical study is conducted concurrently to an experimental investigation to facilitate the validation and deliver feedback for further development. The atomizer includes a pin electrode that is placed at the center of a converging chamber. The chamber orifice is located at a known distance from the electrode tip. The pin electrode is connected to a high voltage that leads to the charging of the liquid. In the present work, the theoretical foundations of separated treatment of the polarized layer and the electronuetral bulk flow are set by describing the governing equations, relevant boundary conditions and the matching condition between these two domains. The resulting split domains are solved numerically to find the distribution of velocity and electrostatic fields over the specified regions. National Science Foundation Award Number: 1505276.

  5. Performance of the density matrix functional theory in the quantum theory of atoms in molecules.

    PubMed

    García-Revilla, Marco; Francisco, E; Costales, A; Martín Pendás, A

    2012-02-02

    The generalization to arbitrary molecular geometries of the energetic partitioning provided by the atomic virial theorem of the quantum theory of atoms in molecules (QTAIM) leads to an exact and chemically intuitive energy partitioning scheme, the interacting quantum atoms (IQA) approach, that depends on the availability of second-order reduced density matrices (2-RDMs). This work explores the performance of this approach in particular and of the QTAIM in general with approximate 2-RDMs obtained from the density matrix functional theory (DMFT), which rests on the natural expansion (natural orbitals and their corresponding occupation numbers) of the first-order reduced density matrix (1-RDM). A number of these functionals have been implemented in the promolden code and used to perform QTAIM and IQA analyses on several representative molecules and model chemical reactions. Total energies, covalent intra- and interbasin exchange-correlation interactions, as well as localization and delocalization indices have been determined with these functionals from 1-RDMs obtained at different levels of theory. Results are compared to the values computed from the exact 2-RDMs, whenever possible.

  6. Monte Carlo calculations of thermal neutron capture in gadolinium: a comparison of GEANT4 and MCNP with measurements.

    PubMed

    Enger, Shirin A; Munck af Rosenschöld, Per; Rezaei, Arash; Lundqvist, Hans

    2006-02-01

    GEANT4 is a Monte Carlo code originally implemented for high-energy physics applications and is well known for particle transport at high energies. The capacity of GEANT4 to simulate neutron transport in the thermal energy region is not equally well known. The aim of this article is to compare MCNP, a code commonly used in low energy neutron transport calculations and GEANT4 with experimental results and select the suitable code for gadolinium neutron capture applications. To account for the thermal neutron scattering from chemically bound atoms [S(alpha,beta)] in biological materials a comparison of thermal neutron fluence in tissue-like poly(methylmethacrylate) phantom is made with MCNP4B, GEANT4 6.0 patch1, and measurements from the neutron capture therapy (NCT) facility at the Studsvik, Sweden. The fluence measurements agreed with MCNP calculated results considering S(alpha,beta). The location of the thermal neutron peak calculated with MCNP without S(alpha,beta) and GEANT4 is shifted by about 0.5 cm towards a shallower depth and is 25%-30% lower in amplitude. Dose distribution from the gadolinium neutron capture reaction is then simulated by MCNP and compared with measured data. The simulations made by MCNP agree well with experimental results. As long as thermal neutron scattering from chemically bound atoms are not included in GEANT4 it is not suitable for NCT applications.

  7. Master equation theory applied to the redistribution of polarized radiation in the weak radiation field limit. V. The two-term atom

    NASA Astrophysics Data System (ADS)

    Bommier, Véronique

    2017-11-01

    Context. In previous papers of this series, we presented a formalism able to account for both statistical equilibrium of a multilevel atom and coherent and incoherent scatterings (partial redistribution). Aims: This paper provides theoretical expressions of the redistribution function for the two-term atom. This redistribution function includes both coherent (RII) and incoherent (RIII) scattering contributions with their branching ratios. Methods: The expressions were derived by applying the formalism outlined above. The statistical equilibrium equation for the atomic density matrix is first formally solved in the case of the two-term atom with unpolarized and infinitely sharp lower levels. Then the redistribution function is derived by substituting this solution for the expression of the emissivity. Results: Expressions are provided for both magnetic and non-magnetic cases. Atomic fine structure is taken into account. Expressions are also separately provided under zero and non-zero hyperfine structure. Conclusions: Redistribution functions are widely used in radiative transfer codes. In our formulation, collisional transitions between Zeeman sublevels within an atomic level (depolarizing collisions effect) are taken into account when possible (I.e., in the non-magnetic case). However, the need for a formal solution of the statistical equilibrium as a preliminary step prevents us from taking into account collisional transfers between the levels of the upper term. Accounting for these collisional transfers could be done via a numerical solution of the statistical equilibrium equation system.

  8. Modeling Solar Atmospheric Phenomena with AtomDB and PyAtomDB

    NASA Astrophysics Data System (ADS)

    Dupont, Marcus; Foster, Adam

    2018-01-01

    Taking advantage of the modeling tools made available by PyAtomDB (Foster 2015), we evaluated the impact of changing atomic data on solar phenomena, in particular their effects on models of coronal mass ejections (CME). Intitially, we perform modifications to the canonical SunNEI code (Murphy et al. 2011) in order to include non-equilibrium ionization (NEI) processes that occur in the CME modeled in SunNEI. The methods used involve the consideration of radiaitive cooling as well as ion balance calculations. These calculations were subsequently implemented within the SunNEI simulation. The insertion of aforementioned processes and parameter customizaton produced quite similar results of the original except for the case of iron. These differences were traced to inconsistencies in the recombination rates for Argon-like iron ions between the CHIANTI and AtomDB databases, even though they in theory use the same data. The key finding was that theoretical models are greatly impacted by the relative atomic database update cycles.Following the SunNEI comparison, we then use the AtomDB database to model the time depedencies of intensity flux spikes produced by a coronal shock wave (Ma et al. 2011). We produced a theretical representation for an ionizing plasma that interpolated over the intensity in four Astronomical Imaging Assembly (AIA) filters. Specifically, the 171 A (Fe IX) ,193 A (Fe XII, FeXXIV),211 A (Fe XIV),and 335 A (Fe XVI) wavelengths in order to assess the comparative spectral emissions between AtomDB and the observed data. The results of the theoretical model, in principle, shine light on both the equilibrium conditions before the shock and the non-equilibrium response to the shock front, as well as discrepancies introduced by changing the atomic data.

  9. Atomic and Molecular Systems in Intense Ultrashort Laser Pulses

    NASA Astrophysics Data System (ADS)

    Saenz, A.

    2008-07-01

    The full quantum mechanical treatment of atomic and molecular systems exposed to intense laser pulses is a so far unsolved challenge, even for systems as small as molecular hydrogen. Therefore, a number of simplified qualitative and quantitative models have been introduced in order to provide at least some interpretational tools for experimental data. The assessment of these models describing the molecular response is complicated, since a comparison to experiment requires often a number of averages to be performed. This includes in many cases averaging of different orientations of the molecule with respect to the laser field, focal volume effects, etc. Furthermore, the pulse shape and even the peak intensity is experimentally not known with very high precision; considering, e.g., the exponential intensity dependence of the ionization signal. Finally, experiments usually provide only relative yields. As a consequence of all these averagings and uncertainties, it is possible that different models may successfully explain some experimental results or features, although these models disagree substantially, if their predictions are compared before averaging. Therefore, fully quantum-mechanical approaches at least for small atomic and molecular systems are highly desirable and have been developed in our group. This includes efficient codes for solving the time-dependent Schrodinger equation of atomic hydrogen, helium or other effective one- or two-electron atoms as well as for the electronic motion in linear (effective) one-and two-electron diatomic molecules like H_2.Very recently, a code for larger molecular systems that adopts the so-called single-active electron approximation was also successfully implemented and applied. In the first part of this talk popular models describing intense laser-field ionization of atoms and their extensions to molecules are described. Then their validity is discussed on the basis of quantum-mechanical calculations. Finally, some peculiar molecular strong-field effects and the possibility of strong-field control mechanisms will be demonstrated. This includes phenomena like enhanced ionization and bond softening as well as the creation of vibrational wavepacket in the non-ionized electronic ground state of H_2 by creating a Schrodinger-cat state between the ionized and the non-ionized molecules. The latter, theoretically predicted phenomenon was very recently experimentally observed and lead to the real-time observation of the so far fastest molecular motion.

  10. Theoretical investigation on the soft X-ray spectrum of the highly-charged W54+ ions

    NASA Astrophysics Data System (ADS)

    Ding, Xiaobin; Yang, Jiaoxia; Koike, Fumihiro; Murakami, Izumi; Kato, Daiji; Sakaue, Hiroyuki A.; Nakamura, Nobuyuki; Dong, Chenzhong

    2018-01-01

    A detailed level collisional-radiative model of the E1 transition spectrum of Ca-like W54+ ion has been constructed. All the necessary atomic data has been calculated by relativistic configuration interaction (RCI) method with the implementation of Flexible Atomic Code (FAC). The results are in reasonable agreement with the available experimental and previous theoretical data. The synthetic spectrum has explained the EBIT spectrum in 29.5-32.5 Å , while several new strong transitions has been predicted to be observed in 18.5-19.6 Å for the future EBIT experiment with electron density ne = 1012 cm-3 and electron beam energy Ee = 18.2 keV.

  11. OBJECT KINETIC MONTE CARLO SIMULATIONS OF RADIATION DAMAGE IN BULK TUNGSTEN

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Nandipati, Giridhar; Setyawan, Wahyu; Heinisch, Howard L.

    2015-09-22

    We used our recently developed lattice based OKMC code; KSOME [1] to carryout simulations of radiation damage in bulk W. We study the effect of dimensionality of self interstitial atom (SIA) diffusion i.e. 1D versus 3D on the defect accumulation during irradiation with a primary knock-on atom (PKA) energy of 100 keV at 300 K for the dose rates of 10-5 and 10-6 dpa/s. As expected 3D SIA diffusion significantly reduces damage accumulation due to increased probability of recombination events. In addition, dose rate, over the limited range examined here, appears to have no effect in both cases of SIAmore » diffusion.« less

  12. Quaternionic representation of the genetic code.

    PubMed

    Carlevaro, C Manuel; Irastorza, Ramiro M; Vericat, Fernando

    2016-03-01

    A heuristic diagram of the evolution of the standard genetic code is presented. It incorporates, in a way that resembles the energy levels of an atom, the physical notion of broken symmetry and it is consistent with original ideas by Crick on the origin and evolution of the code as well as with the chronological order of appearance of the amino acids along the evolution as inferred from work that mixtures known experimental results with theoretical speculations. Suggested by the diagram we propose a Hamilton quaternions based mathematical representation of the code as it stands now-a-days. The central object in the description is a codon function that assigns to each amino acid an integer quaternion in such a way that the observed code degeneration is preserved. We emphasize the advantages of a quaternionic representation of amino acids taking as an example the folding of proteins. With this aim we propose an algorithm to go from the quaternions sequence to the protein three dimensional structure which can be compared with the corresponding experimental one stored at the Protein Data Bank. In our criterion the mathematical representation of the genetic code in terms of quaternions merits to be taken into account because it describes not only most of the known properties of the genetic code but also opens new perspectives that are mainly derived from the close relationship between quaternions and rotations. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  13. Auto Code Generation for Simulink-Based Attitude Determination Control System

    NASA Technical Reports Server (NTRS)

    MolinaFraticelli, Jose Carlos

    2012-01-01

    This paper details the work done to auto generate C code from a Simulink-Based Attitude Determination Control System (ADCS) to be used in target platforms. NASA Marshall Engineers have developed an ADCS Simulink simulation to be used as a component for the flight software of a satellite. This generated code can be used for carrying out Hardware in the loop testing of components for a satellite in a convenient manner with easily tunable parameters. Due to the nature of the embedded hardware components such as microcontrollers, this simulation code cannot be used directly, as it is, on the target platform and must first be converted into C code; this process is known as auto code generation. In order to generate C code from this simulation; it must be modified to follow specific standards set in place by the auto code generation process. Some of these modifications include changing certain simulation models into their atomic representations which can bring new complications into the simulation. The execution order of these models can change based on these modifications. Great care must be taken in order to maintain a working simulation that can also be used for auto code generation. After modifying the ADCS simulation for the auto code generation process, it is shown that the difference between the output data of the former and that of the latter is between acceptable bounds. Thus, it can be said that the process is a success since all the output requirements are met. Based on these results, it can be argued that this generated C code can be effectively used by any desired platform as long as it follows the specific memory requirements established in the Simulink Model.

  14. Development of Safety Analysis Code System of Beam Transport and Core for Accelerator Driven System

    NASA Astrophysics Data System (ADS)

    Aizawa, Naoto; Iwasaki, Tomohiko

    2014-06-01

    Safety analysis code system of beam transport and core for accelerator driven system (ADS) is developed for the analyses of beam transients such as the change of the shape and position of incident beam. The code system consists of the beam transport analysis part and the core analysis part. TRACE 3-D is employed in the beam transport analysis part, and the shape and incident position of beam at the target are calculated. In the core analysis part, the neutronics, thermo-hydraulics and cladding failure analyses are performed by the use of ADS dynamic calculation code ADSE on the basis of the external source database calculated by PHITS and the cross section database calculated by SRAC, and the programs of the cladding failure analysis for thermoelastic and creep. By the use of the code system, beam transient analyses are performed for the ADS proposed by Japan Atomic Energy Agency. As a result, the rapid increase of the cladding temperature happens and the plastic deformation is caused in several seconds. In addition, the cladding is evaluated to be failed by creep within a hundred seconds. These results have shown that the beam transients have caused a cladding failure.

  15. A project based on multi-configuration Dirac-Fock calculations for plasma spectroscopy

    NASA Astrophysics Data System (ADS)

    Comet, M.; Pain, J.-C.; Gilleron, F.; Piron, R.

    2017-09-01

    We present a project dedicated to hot plasma spectroscopy based on a Multi-Configuration Dirac-Fock (MCDF) code, initially developed by J. Bruneau. The code is briefly described and the use of the transition state method for plasma spectroscopy is detailed. Then an opacity code for local-thermodynamic-equilibrium plasmas using MCDF data, named OPAMCDF, is presented. Transition arrays for which the number of lines is too large to be handled in a Detailed Line Accounting (DLA) calculation can be modeled within the Partially Resolved Transition Array method or using the Unresolved Transition Arrays formalism in jj-coupling. An improvement of the original Partially Resolved Transition Array method is presented which gives a better agreement with DLA computations. Comparisons with some absorption and emission experimental spectra are shown. Finally, the capability of the MCDF code to compute atomic data required for collisional-radiative modeling of plasma at non local thermodynamic equilibrium is illustrated. In addition to photoexcitation, this code can be used to calculate photoionization, electron impact excitation and ionization cross-sections as well as autoionization rates in the Distorted-Wave or Close Coupling approximations. Comparisons with cross-sections and rates available in the literature are discussed.

  16. Dynamical beam manipulation based on 2-bit digitally-controlled coding metasurface.

    PubMed

    Huang, Cheng; Sun, Bo; Pan, Wenbo; Cui, Jianhua; Wu, Xiaoyu; Luo, Xiangang

    2017-02-08

    Recently, a concept of digital metamaterials has been proposed to manipulate field distribution through proper spatial mixtures of digital metamaterial bits. Here, we present a design of 2-bit digitally-controlled coding metasurface that can effectively modulate the scattered electromagnetic wave and realize different far-field beams. Each meta-atom of this metasurface integrates two pin diodes, and by tuning their operating states, the metasurface has four phase responses of 0, π/2, π, and 3π/2, corresponding to four basic digital elements "00", "01", "10", and "11", respectively. By designing the coding sequence of the above digital element array, the reflected beam can be arbitrarily controlled. The proposed 2-bit digital metasurface has been demonstrated to possess capability of achieving beam deflection, multi-beam and beam diffusion, and the dynamical switching of these different scattering patterns is completed by a programmable electric source.

  17. The 2017 Release Cloudy

    NASA Astrophysics Data System (ADS)

    Ferland, G. J.; Chatzikos, M.; Guzmán, F.; Lykins, M. L.; van Hoof, P. A. M.; Williams, R. J. R.; Abel, N. P.; Badnell, N. R.; Keenan, F. P.; Porter, R. L.; Stancil, P. C.

    2017-10-01

    We describe the 2017 release of the spectral synthesis code Cloudy, summarizing the many improvements to the scope and accuracy of the physics which have been made since the previous release. Exporting the atomic data into external data files has enabled many new large datasets to be incorporated into the code. The use of the complete datasets is not realistic for most calculations, so we describe the limited subset of data used by default, which predicts significantly more lines than the previous release of Cloudy. This version is nevertheless faster than the previous release, as a result of code optimizations. We give examples of the accuracy limits using small models, and the performance requirements of large complete models. We summarize several advances in the H- and He-like iso-electronic sequences and use our complete collisional-radiative models to establish the densities where the coronal and local thermodynamic equilibrium approximations work.

  18. Dynamical beam manipulation based on 2-bit digitally-controlled coding metasurface

    PubMed Central

    Huang, Cheng; Sun, Bo; Pan, Wenbo; Cui, Jianhua; Wu, Xiaoyu; Luo, Xiangang

    2017-01-01

    Recently, a concept of digital metamaterials has been proposed to manipulate field distribution through proper spatial mixtures of digital metamaterial bits. Here, we present a design of 2-bit digitally-controlled coding metasurface that can effectively modulate the scattered electromagnetic wave and realize different far-field beams. Each meta-atom of this metasurface integrates two pin diodes, and by tuning their operating states, the metasurface has four phase responses of 0, π/2, π, and 3π/2, corresponding to four basic digital elements “00”, “01”, “10”, and “11”, respectively. By designing the coding sequence of the above digital element array, the reflected beam can be arbitrarily controlled. The proposed 2-bit digital metasurface has been demonstrated to possess capability of achieving beam deflection, multi-beam and beam diffusion, and the dynamical switching of these different scattering patterns is completed by a programmable electric source. PMID:28176870

  19. Molecular dynamics and dynamic Monte-Carlo simulation of irradiation damage with focused ion beams

    NASA Astrophysics Data System (ADS)

    Ohya, Kaoru

    2017-03-01

    The focused ion beam (FIB) has become an important tool for micro- and nanostructuring of samples such as milling, deposition and imaging. However, this leads to damage of the surface on the nanometer scale from implanted projectile ions and recoiled material atoms. It is therefore important to investigate each kind of damage quantitatively. We present a dynamic Monte-Carlo (MC) simulation code to simulate the morphological and compositional changes of a multilayered sample under ion irradiation and a molecular dynamics (MD) simulation code to simulate dose-dependent changes in the backscattering-ion (BSI)/secondary-electron (SE) yields of a crystalline sample. Recent progress in the codes for research to simulate the surface morphology and Mo/Si layers intermixing in an EUV lithography mask irradiated with FIBs, and the crystalline orientation effect on BSI and SE yields relating to the channeling contrast in scanning ion microscopes, is also presented.

  20. Validation of fast-ion D-alpha spectrum measurements during EAST neutral-beam heated plasmas

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Huang, J., E-mail: juan.huang@ipp.ac.cn; Wu, C. R.; Hou, Y. M.

    2016-11-15

    To investigate the fast ion behavior, a fast ion D-alpha (FIDA) diagnostic system has been installed on EAST. Fast ion features can be inferred from the Doppler shifted spectrum of Balmer-alpha light from energetic hydrogenic atoms. This paper will focus on the validation of FIDA measurements performed using MHD-quiescent discharges in 2015 campaign. Two codes have been applied to calculate the D{sub α} spectrum: one is a Monte Carlo code, Fortran 90 version FIDASIM, and the other is an analytical code, Simulation of Spectra (SOS). The predicted SOS fast-ion spectrum agrees well with the measurement; however, the level of fast-ionmore » part from FIDASIM is lower. The discrepancy is possibly due to the difference between FIDASIM and SOS velocity distribution function. The details will be presented in the paper to primarily address comparisons of predicted and observed spectrum shapes/amplitudes.« less

  1. Density functional study of structural and electronic properties of Al{sub n}@C{sub 60}

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Dhiman, Shobhna, E-mail: s-dhiman@hotmail.com; Kumar, Ranjan; Dharamvir, Keya

    2014-04-24

    Fullerene derivatives have been shown to make contributions in many types of applications. Ab initio investigation of structural and electronic properties of aluminum doped endohedral fullerene has been performed using numerical atomic orbital density functional theory. We have obtained ground state structures for Al{sub n}@C{sub 60} (n=1–10). Which shows that C{sub 60} molecule can accommodate maximum of nine aluminum atoms, for n > 9 the cage eventually break. Encapsulated large number of aluminum atoms leads to deformation of cage with diameter varies from 7.16Å to 7.95Å. Binding energy/Al atom is found to increase till n = 4 and after thatmore » it decreases with the number of Al atoms with a sudden increase for n=10 due to breakage of C{sub 60} cage and electronic affinity first increases till n=4 then it decreases up to n=9 with a sharp increase for n=10. Ionization potential also first increases and then decreases. Homo-Lumo gap decreases till n=3 with a sharp increase for n=4, after that it shows an oscillatory nature. The results obtained are consistent with available theoretical and experimental results. The ab-initio calculations were performed using SIESTA code with generalized gradient approximation (GGA)« less

  2. Laser program annual report, 1979

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Coleman, L.W.; Strack, J.R.

    1980-03-01

    This volume contains four sections that covers the areas of target design, target fabrication, diagnostics, and experiments. Section 3 reports on target design activities, plasma theory and simulation, code development, and atomic theory. Section 4 presents the accomplishments of the target fabrication group, and Section 5 presents results of diagnostic developments and applications for the year. The results of laser-target experiments are presented. (MOW)

  3. Atomic scale simulations for improved CRUD and fuel performance modeling

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Andersson, Anders David Ragnar; Cooper, Michael William Donald

    2017-01-06

    A more mechanistic description of fuel performance codes can be achieved by deriving models and parameters from atomistic scale simulations rather than fitting models empirically to experimental data. The same argument applies to modeling deposition of corrosion products on fuel rods (CRUD). Here are some results from publications in 2016 carried out using the CASL allocation at LANL.

  4. Operation Greenhouse: Communications

    DTIC Science & Technology

    1951-01-01

    jottication •__ By,. , Dtsl•-bution1 TECHNICAL REPORT mailability Code’s Avait and -or Dist Special COMMUNICATIONS OPERATION GREENHOUSE 1951 COMMANDED BY...stem GREENHOUSE to include technical informa- therefrom. tion and operational experience not desirable Details of operation, such as call sign, fre- for...Atomic planning, organization, and engineering for Weapons Proving Ground. Where, in this re- Operation GREENHOUSE , since the solution port, reference is

  5. Mixing of the Interstellar and Solar Plasmas at the Heliospheric Interface

    DOE PAGES

    Pogorelov, N. V.; Borovikov, S. N.

    2015-10-12

    From the ideal MHD perspective, the heliopause is a tangential discontinuity that separates the solar wind plasma from the local interstellar medium plasma. There are physical processes, however, that make the heliopause permeable. They can be subdivided into kinetic and MHD categories. Kinetic processes occur on small length and time scales, and cannot be resolved with MHD equations. On the other hand, MHD instabilities of the heliopause have much larger scales and can be easily observed by spacecraft. The heliopause may also be a subject of magnetic reconnection. In this paper, we discuss mechanisms of plasma mixing at the heliopausemore » in the context of Voyager 1 observations. Numerical results are obtained with a Multi-Scale Fluid-Kinetic Simulation Suite (MS-FLUKSS), which is a package of numerical codes capable of performing adaptive mesh refinement simulations of complex plasma flows in the presence of discontinuities and charge exchange between ions and neutral atoms. The flow of the ionized component is described with the ideal MHD equations, while the transport of atoms is governed either by the Boltzmann equation or multiple Euler gas dynamics equations. The code can also treat nonthermal ions and turbulence produced by them.« less

  6. An efficient dictionary learning algorithm and its application to 3-D medical image denoising.

    PubMed

    Li, Shutao; Fang, Leyuan; Yin, Haitao

    2012-02-01

    In this paper, we propose an efficient dictionary learning algorithm for sparse representation of given data and suggest a way to apply this algorithm to 3-D medical image denoising. Our learning approach is composed of two main parts: sparse coding and dictionary updating. On the sparse coding stage, an efficient algorithm named multiple clusters pursuit (MCP) is proposed. The MCP first applies a dictionary structuring strategy to cluster the atoms with high coherence together, and then employs a multiple-selection strategy to select several competitive atoms at each iteration. These two strategies can greatly reduce the computation complexity of the MCP and assist it to obtain better sparse solution. On the dictionary updating stage, the alternating optimization that efficiently approximates the singular value decomposition is introduced. Furthermore, in the 3-D medical image denoising application, a joint 3-D operation is proposed for taking the learning capabilities of the presented algorithm to simultaneously capture the correlations within each slice and correlations across the nearby slices, thereby obtaining better denoising results. The experiments on both synthetically generated data and real 3-D medical images demonstrate that the proposed approach has superior performance compared to some well-known methods. © 2011 IEEE

  7. OPserver: opacities and radiative accelerations on demand

    NASA Astrophysics Data System (ADS)

    Mendoza, C.; González, J.; Seaton, M. J.; Buerger, P.; Bellorín, A.; Meléndez, M.; Rodríguez, L. S.; Delahaye, F.; Zeippen, C. J.; Palacios, E.; Pradhan, A. K.

    2009-05-01

    We report on developments carried out within the Opacity Project (OP) to upgrade atomic database services to comply with e-infrastructure requirements. We give a detailed description of an interactive, online server for astrophysical opacities, referred to as OPserver, to be used in sophisticated stellar modelling where Rosseland mean opacities and radiative accelerations are computed at every depth point and each evolution cycle. This is crucial, for instance, in chemically peculiar stars and in the exploitation of the new asteroseismological data. OPserver, downloadable with the new OPCD_3.0 release from the Centre de Données Astronomiques de Strasbourg, France, computes mean opacities and radiative data for arbitrary chemical mixtures from the OP monochromatic opacities. It is essentially a client-server network restructuring and optimization of the suite of codes included in the earlier OPCD_2.0 release. The server can be installed locally or, alternatively, accessed remotely from the Ohio Supercomputer Center, Columbus, Ohio, USA. The client is an interactive web page or a subroutine library that can be linked to the user code. The suitability of this scheme in grid computing environments is emphasized, and its extension to other atomic database services for astrophysical purposes is discussed.

  8. Monte Carlo simulations of ionization potential depression in dense plasmas

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Stransky, M., E-mail: stransky@fzu.cz

    A particle-particle grand canonical Monte Carlo model with Coulomb pair potential interaction was used to simulate modification of ionization potentials by electrostatic microfields. The Barnes-Hut tree algorithm [J. Barnes and P. Hut, Nature 324, 446 (1986)] was used to speed up calculations of electric potential. Atomic levels were approximated to be independent of the microfields as was assumed in the original paper by Ecker and Kröll [Phys. Fluids 6, 62 (1963)]; however, the available levels were limited by the corresponding mean inter-particle distance. The code was tested on hydrogen and dense aluminum plasmas. The amount of depression was up tomore » 50% higher in the Debye-Hückel regime for hydrogen plasmas, in the high density limit, reasonable agreement was found with the Ecker-Kröll model for hydrogen plasmas and with the Stewart-Pyatt model [J. Stewart and K. Pyatt, Jr., Astrophys. J. 144, 1203 (1966)] for aluminum plasmas. Our 3D code is an improvement over the spherically symmetric simplifications of the Ecker-Kröll and Stewart-Pyatt models and is also not limited to high atomic numbers as is the underlying Thomas-Fermi model used in the Stewart-Pyatt model.« less

  9. Density Functional O(N) Calculations

    NASA Astrophysics Data System (ADS)

    Ordejón, Pablo

    1998-03-01

    We have developed a scheme for performing Density Functional Theory calculations with O(N) scaling.(P. Ordejón, E. Artacho and J. M. Soler, Phys. Rev. B, 53), 10441 (1996) The method uses arbitrarily flexible and complete Atomic Orbitals (AO) basis sets. This gives a wide range of choice, from extremely fast calculations with minimal basis sets, to greatly accurate calculations with complete sets. The size-efficiency of AO bases, together with the O(N) scaling of the algorithm, allow the application of the method to systems with many hundreds of atoms, in single processor workstations. I will present the SIESTA code,(D. Sanchez-Portal, P. Ordejón, E. Artacho and J. M. Soler, Int. J. Quantum Chem., 65), 453 (1997) in which the method is implemented, with several LDA, LSD and GGA functionals available, and using norm-conserving, non-local pseudopotentials (in the Kleinman-Bylander form) to eliminate the core electrons. The calculation of static properties such as energies, forces, pressure, stress and magnetic moments, as well as molecular dynamics (MD) simulations capabilities (including variable cell shape, constant temperature and constant pressure MD) are fully implemented. I will also show examples of the accuracy of the method, and applications to large-scale materials and biomolecular systems.

  10. Analysis of unresolved transition arrays in XUV spectral region from highly charged lead ions produced by subnanosecond laser pulse

    NASA Astrophysics Data System (ADS)

    Wu, Tao; Higashiguchi, Takeshi; Li, Bowen; Arai, Goki; Hara, Hiroyuki; Kondo, Yoshiki; Miyazaki, Takanori; Dinh, Thanh-Hung; O'Reilly, Fergal; Sokell, Emma; O'Sullivan, Gerry

    2017-02-01

    Soft x-ray and extreme ultraviolet (XUV) spectra from lead (Pb, Z=82) laser-produced plasmas (LPPs) were measured in the 1.0-7.0 nm wavelength region employing a 150-ps, 1064-nm Nd:YAG laser with focused power densities in the range from 3.1×1013 W/cm2 to 1.4×1014 W/cm2. The flexible atomic code (FAC) and the Cowan's suite of atomic structure codes were applied to compute and explain the radiation properties of the lead spectra observed. The most prominent structure in the spectra is a broad double peak, which is produced by Δn=0, n=4-4 and Δn=1, n=4-5 transition arrays emitted from highly charged lead ions. The emission characteristics of Δn=1, n=4-5 transitions were investigated by the use of the unresolved transition arrays (UTAs) model. Numerous new spectral features generated by Δn=1, n=4-5 transitions in ions from Pb21+ to Pb45+ are discerned with the aid of the results from present computations as well as consideration of previous theoretical predictions and experimental data.

  11. The Electronic Structure of Transition Metal Coated Fullerenes

    NASA Astrophysics Data System (ADS)

    Patton, David C.; Pederson, Mark R.; Kaxiras, Efthimios

    1998-03-01

    Clusters composed of fullerene molecules with an outer shell of transition metal atoms in the composition C_60M_62 (M being a transition metal) have been produced with laser vaporisation techniques(F. Tast, N. Malinowski, S. Frank, M. Heinebrodt, I.M.L. Billas, and T. P. Martin, Z. Phys D 40), 351 (1997).. We have studied several of these very large systems with a parallel version of the all-electron NRLMOL cluster code. Optimized geometries of the metal encased fullerenes C_60Ti_62 and C_60V_62 are presented along with their HOMO-LUMO gaps, electron affinities, ionization energies, and cohesive energies. We compare the stability of these clusters to relaxed met-car structures (e.g. Ti_8C_12) and to relaxed rocksalt metal-carbide fragments (TiC)n with n=8 and 32. In addition to metal-coated fullerenes we consider the possibility of a trilayered structure consisting of a small shell of metal atoms enclosed by a metal coated fullerene. The nature of bonding in these systems is analyzed by studying the electronic charge distributions.

  12. Simulation study of 3-5 keV x-ray conversion efficiency from Ar K-shell vs. Ag L-shell targets on the National Ignition Facility laser

    NASA Astrophysics Data System (ADS)

    Kemp, G. E.; Colvin, J. D.; Fournier, K. B.; May, M. J.; Barrios, M. A.; Patel, M. V.; Scott, H. A.; Marinak, M. M.

    2015-05-01

    Tailored, high-flux, multi-keV x-ray sources are desirable for studying x-ray interactions with matter for various civilian, space and military applications. For this study, we focus on designing an efficient laser-driven non-local thermodynamic equilibrium 3-5 keV x-ray source from photon-energy-matched Ar K-shell and Ag L-shell targets at sub-critical densities (˜nc/10) to ensure supersonic, volumetric laser heating with minimal losses to kinetic energy, thermal x rays and laser-plasma instabilities. Using Hydra, a multi-dimensional, arbitrary Lagrangian-Eulerian, radiation-hydrodynamics code, we performed a parameter study by varying initial target density and laser parameters for each material using conditions readily achievable on the National Ignition Facility (NIF) laser. We employ a model, benchmarked against Kr data collected on the NIF, that uses flux-limited Lee-More thermal conductivity and multi-group implicit Monte-Carlo photonics with non-local thermodynamic equilibrium, detailed super-configuration accounting opacities from Cretin, an atomic-kinetics code. While the highest power laser configurations produced the largest x-ray yields, we report that the peak simulated laser to 3-5 keV x-ray conversion efficiencies of 17.7% and 36.4% for Ar and Ag, respectively, occurred at lower powers between ˜100-150 TW. For identical initial target densities and laser illumination, the Ag L-shell is observed to have ≳10× higher emissivity per ion per deposited laser energy than the Ar K-shell. Although such low-density Ag targets have not yet been demonstrated, simulations of targets fabricated using atomic layer deposition of Ag on silica aerogels (˜20% by atomic fraction) suggest similar performance to atomically pure metal foams and that either fabrication technique may be worth pursuing for an efficient 3-5 keV x-ray source on NIF.

  13. Critic: a new program for the topological analysis of solid-state electron densities

    NASA Astrophysics Data System (ADS)

    Otero-de-la-Roza, A.; Blanco, M. A.; Pendás, A. Martín; Luaña, Víctor

    2009-01-01

    In this paper we introduce CRITIC, a new program for the topological analysis of the electron densities of crystalline solids. Two different versions of the code are provided, one adapted to the LAPW (Linear Augmented Plane Wave) density calculated by the WIEN2K package and the other to the ab initio Perturbed Ion ( aiPI) density calculated with the PI7 code. Using the converged ground state densities, CRITIC can locate their critical points, determine atomic basins and integrate properties within them, and generate several graphical representations which include topological atomic basins and primary bundles, contour maps of ρ and ∇ρ, vector maps of ∇ρ, chemical graphs, etc. Program summaryProgram title: CRITIC Catalogue identifier: AECB_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AECB_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GPL, version 3 No. of lines in distributed program, including test data, etc.: 1 206 843 No. of bytes in distributed program, including test data, etc.: 12 648 065 Distribution format: tar.gz Programming language: FORTRAN 77 and 90 Computer: Any computer capable of compiling Fortran Operating system: Unix, GNU/Linux Classification: 7.3 Nature of problem: Topological analysis of the electron density in periodic solids. Solution method: The automatic localization of the electron density critical points is based on a recursive partitioning of the Wigner-Seitz cell into tetrahedra followed by a Newton search from significant points on each tetrahedra. Plotting of and integration on the atomic basins is currently based on a new implementation of Keith's promega algorithm. Running time: Variable, depending on the task. From seconds to a few minutes for the localization of critical points. Hours to days for the determination of the atomic basins shape and properties. Times correspond to a typical 2007 PC.

  14. libvdwxc: a library for exchange-correlation functionals in the vdW-DF family

    NASA Astrophysics Data System (ADS)

    Hjorth Larsen, Ask; Kuisma, Mikael; Löfgren, Joakim; Pouillon, Yann; Erhart, Paul; Hyldgaard, Per

    2017-09-01

    We present libvdwxc, a general library for evaluating the energy and potential for the family of vdW-DF exchange-correlation functionals. libvdwxc is written in C and provides an efficient implementation of the vdW-DF method and can be interfaced with various general-purpose DFT codes. Currently, the Gpaw and Octopus codes implement interfaces to libvdwxc. The present implementation emphasizes scalability and parallel performance, and thereby enables ab initio calculations of nanometer-scale complexes. The numerical accuracy is benchmarked on the S22 test set whereas parallel performance is benchmarked on ligand-protected gold nanoparticles ({{Au}}144{({{SC}}11{{NH}}25)}60) up to 9696 atoms.

  15. Study of helium emissions from active solar regions

    NASA Technical Reports Server (NTRS)

    Kulander, J. L.

    1973-01-01

    A theoretical study is made of the visible and UV line radiation of He I atoms and He II ions from a plane-parallel model flare layer. Codes were developed for the solution of the statistically steady state equation for a 30 level He I - II - III model, and the line and continuum transport equations. These codes are described and documented in the report along with sample solutions. Optical depths and some line intensities are presented for a 1000 km thick layer. Solutions of the steady state equations are presented for electron temperatures 10,000 to 50,000 K and electron densities 10 to the 10th power to 10 to the 14th power/cu cm.

  16. Determination of the delta(2H/1H)of Water: RSIL Lab Code 1574

    USGS Publications Warehouse

    Revesz, Kinga; Coplen, Tyler B.

    2008-01-01

    Reston Stable Isotope Laboratory (RSIL) lab code 1574 describes a method used to determine the relative hydrogen isotope-ratio delta(2H,1H), abbreviated hereafter as d2H of water. The d2H measurement of water also is a component of the National Water Quality Laboratory (NWQL) schedules 1142 and 1172. The water is collected unfiltered in a 60-mL glass bottle and capped with a Polyseal cap. In the laboratory, the water sample is equilibrated with gaseous hydrogen using a platinum catalyst (Horita, 1988; Horita and others, 1989; Coplen and others, 1991). The reaction for the exchange of one hydrogen atom is shown in equation 1.

  17. "The only feasible means." The Pentagon's ambivalent relationship with the Nuremberg Code.

    PubMed

    Moreno, J D

    1996-01-01

    Convinced that armed conflict with the Soviet Union was all but inevitable, that such conflict would involve unconventional atomic, biological, and chemical warfare, and that research with human subjects was essential to respond to the threat, in the early 1950s the U.S. Department of Defense promulgated a policy governing human experimentation based on the Nuremberg Code. Yet the policymaking process focused on the abstract issue of whether human experiments should go forward at all, ignoring the reality of humans subjects research already under way and leaving unanswered ethical questions about how to conduct such research. Documents newly released to the Advisory Committee on Human Radiation Experiments tell the story of the Pentagon policy.

  18. GenLocDip: A Generalized Program to Calculate and Visualize Local Electric Dipole Moments.

    PubMed

    Groß, Lynn; Herrmann, Carmen

    2016-09-30

    Local dipole moments (i.e., dipole moments of atomic or molecular subsystems) are essential for understanding various phenomena in nanoscience, such as solvent effects on the conductance of single molecules in break junctions or the interaction between the tip and the adsorbate in atomic force microscopy. We introduce GenLocDip, a program for calculating and visualizing local dipole moments of molecular subsystems. GenLocDip currently uses the Atoms-In-Molecules (AIM) partitioning scheme and is interfaced to various AIM programs. This enables postprocessing of a variety of electronic structure output formats including cube and wavefunction files, and, in general, output from any other code capable of writing the electron density on a three-dimensional grid. It uses a modified version of Bader's and Laidig's approach for achieving origin-independence of local dipoles by referring to internal reference points which can (but do not need to be) bond critical points (BCPs). Furthermore, the code allows the export of critical points and local dipole moments into a POVray readable input format. It is particularly designed for fragments of large systems, for which no BCPs have been calculated for computational efficiency reasons, because large interfragment distances prevent their identification, or because a local partitioning scheme different from AIM was used. The program requires only minimal user input and is written in the Fortran90 programming language. To demonstrate the capabilities of the program, examples are given for covalently and non-covalently bound systems, in particular molecular adsorbates. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  19. The fully relativistic implementation of the convergent close-coupling method

    NASA Astrophysics Data System (ADS)

    Bostock, Christopher James

    2011-04-01

    The calculation of accurate excitation and ionization cross sections for electron collisions with atoms and ions plays a fundamental role in atomic and molecular physics, laser physics, x-ray spectroscopy, plasma physics and chemistry. Within the veil of plasma physics lie important research areas affiliated with the lighting industry, nuclear fusion and astrophysics. For high energy projectiles or targets with a large atomic number it is presently understood that a scattering formalism based on the Dirac equation is required to incorporate relativistic effects. This tutorial outlines the development of the relativistic convergent close-coupling (RCCC) method and highlights the following three main accomplishments. (i) The inclusion of the Breit interaction, a relativistic correction to the Coulomb potential, in the RCCC method. This led to calculations that resolved a discrepancy between theory and experiment for the polarization of x-rays emitted by highly charged hydrogen-like ions excited by electron impact (Bostock et al 2009 Phys. Rev. A 80 052708). (ii) The extension of the RCCC method to accommodate two-electron and quasi-two-electron targets. The method was applied to electron scattering from mercury. Accurate plasma physics modelling of mercury-based fluorescent lamps requires detailed information on a large number of electron impact excitation cross sections involving transitions between various states (Bostock et al 2010 Phys. Rev. A 82 022713). (iii) The third accomplishment outlined in this tutorial is the restructuring of the RCCC computer code to utilize a hybrid OpenMP-MPI parallelization scheme which now enables the RCCC code to run on the latest high performance supercomputer architectures.

  20. SIGACE Code for Generating High-Temperature ACE Files; Validation and Benchmarking

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Sharma, Amit R.; Ganesan, S.; Trkov, A.

    2005-05-24

    A code named SIGACE has been developed as a tool for MCNP users within the scope of a research contract awarded by the Nuclear Data Section of the International Atomic Energy Agency (IAEA) (Ref: 302-F4-IND-11566 B5-IND-29641). A new recipe has been evolved for generating high-temperature ACE files for use with the MCNP code. Under this scheme the low-temperature ACE file is first converted to an ENDF formatted file using the ACELST code and then Doppler broadened, essentially limited to the data in the resolved resonance region, to any desired higher temperature using SIGMA1. The SIGACE code then generates a high-temperaturemore » ACE file for use with the MCNP code. A thinning routine has also been introduced in the SIGACE code for reducing the size of the ACE files. The SIGACE code and the recipe for generating ACE files at higher temperatures has been applied to the SEFOR fast reactor benchmark problem (sodium-cooled fast reactor benchmark described in ENDF-202/BNL-19302, 1974 document). The calculated Doppler coefficient is in good agreement with the experimental value. A similar calculation using ACE files generated directly with the NJOY system also agrees with our SIGACE computed results. The SIGACE code and the recipe is further applied to study the numerical benchmark configuration of selected idealized PWR pin cell configurations with five different fuel enrichments as reported by Mosteller and Eisenhart. The SIGACE code that has been tested with several FENDL/MC files will be available, free of cost, upon request, from the Nuclear Data Section of the IAEA.« less

  1. Nondestructive imaging of atomically thin nanostructures buried in silicon

    PubMed Central

    Gramse, Georg; Kölker, Alexander; Lim, Tingbin; Stock, Taylor J. Z.; Solanki, Hari; Schofield, Steven R.; Brinciotti, Enrico; Aeppli, Gabriel; Kienberger, Ferry; Curson, Neil J.

    2017-01-01

    It is now possible to create atomically thin regions of dopant atoms in silicon patterned with lateral dimensions ranging from the atomic scale (angstroms) to micrometers. These structures are building blocks of quantum devices for physics research and they are likely also to serve as key components of devices for next-generation classical and quantum information processing. Until now, the characteristics of buried dopant nanostructures could only be inferred from destructive techniques and/or the performance of the final electronic device; this severely limits engineering and manufacture of real-world devices based on atomic-scale lithography. Here, we use scanning microwave microscopy (SMM) to image and electronically characterize three-dimensional phosphorus nanostructures fabricated via scanning tunneling microscope–based lithography. The SMM measurements, which are completely nondestructive and sensitive to as few as 1900 to 4200 densely packed P atoms 4 to 15 nm below a silicon surface, yield electrical and geometric properties in agreement with those obtained from electrical transport and secondary ion mass spectroscopy for unpatterned phosphorus δ layers containing ~1013 P atoms. The imaging resolution was 37 ± 1 nm in lateral and 4 ± 1 nm in vertical directions, both values depending on SMM tip size and depth of dopant layers. In addition, finite element modeling indicates that resolution can be substantially improved using further optimized tips and microwave gradient detection. Our results on three-dimensional dopant structures reveal reduced carrier mobility for shallow dopant layers and suggest that SMM could aid the development of fabrication processes for surface code quantum computers. PMID:28782006

  2. PlasmaPy: initial development of a Python package for plasma physics

    NASA Astrophysics Data System (ADS)

    Murphy, Nicholas; Leonard, Andrew J.; Stańczak, Dominik; Haggerty, Colby C.; Parashar, Tulasi N.; Huang, Yu-Min; PlasmaPy Community

    2017-10-01

    We report on initial development of PlasmaPy: an open source community-driven Python package for plasma physics. PlasmaPy seeks to provide core functionality that is needed for the formation of a fully open source Python ecosystem for plasma physics. PlasmaPy prioritizes code readability, consistency, and maintainability while using best practices for scientific computing such as version control, continuous integration testing, embedding documentation in code, and code review. We discuss our current and planned capabilities, including features presently under development. The development roadmap includes features such as fluid and particle simulation capabilities, a Grad-Shafranov solver, a dispersion relation solver, atomic data retrieval methods, and tools to analyze simulations and experiments. We describe several ways to contribute to PlasmaPy. PlasmaPy has a code of conduct and is being developed under a BSD license, with a version 0.1 release planned for 2018. The success of PlasmaPy depends on active community involvement, so anyone interested in contributing to this project should contact the authors. This work was partially supported by the U.S. Department of Energy.

  3. A soft X-ray source based on a low divergence, high repetition rate ultraviolet laser

    NASA Astrophysics Data System (ADS)

    Crawford, E. A.; Hoffman, A. L.; Milroy, R. D.; Quimby, D. C.; Albrecht, G. F.

    The CORK code is utilized to evaluate the applicability of low divergence ultraviolet lasers for efficient production of soft X-rays. The use of the axial hydrodynamic code wih one ozone radial expansion to estimate radial motion and laser energy is examined. The calculation of ionization levels of the plasma and radiation rates by employing the atomic physics and radiation model included in the CORK code is described. Computations using the hydrodynamic code to determine the effect of laser intensity, spot size, and wavelength on plasma electron temperature are provided. The X-ray conversion efficiencies of the lasers are analyzed. It is observed that for a 1 GW laser power the X-ray conversion efficiency is a function of spot size, only weakly dependent on pulse length for time scales exceeding 100 psec, and better conversion efficiencies are obtained at shorter wavelengths. It is concluded that these small lasers focused to 30 micron spot sizes and 10 to the 14th W/sq cm intensities are useful sources of 1-2 keV radiation.

  4. On fully three-dimensional resistive wall mode and feedback stabilization computationsa)

    NASA Astrophysics Data System (ADS)

    Strumberger, E.; Merkel, P.; Sempf, M.; Günter, S.

    2008-05-01

    Resistive walls, located close to the plasma boundary, reduce the growth rates of external kink modes to resistive time scales. For such slowly growing resistive wall modes, the stabilization by an active feedback system becomes feasible. The fully three-dimensional stability code STARWALL, and the feedback optimization code OPTIM have been developed [P. Merkel and M. Sempf, 21st IAEA Fusion Energy Conference 2006, Chengdu, China (International Atomic Energy Agency, Vienna, 2006, paper TH/P3-8] to compute the growth rates of resistive wall modes in the presence of nonaxisymmetric, multiply connected wall structures and to model the active feedback stabilization of these modes. In order to demonstrate the capabilities of the codes and to study the effect of the toroidal mode coupling caused by multiply connected wall structures, the codes are applied to test equilibria using the resistive wall structures currently under debate for ITER [M. Shimada et al., Nucl. Fusion 47, S1 (2007)] and ASDEX Upgrade [W. Köppendörfer et al., Proceedings of the 16th Symposium on Fusion Technology, London, 1990 (Elsevier, Amsterdam, 1991), Vol. 1, p. 208].

  5. On fully three-dimensional resistive wall mode and feedback stabilization computations

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Strumberger, E.; Merkel, P.; Sempf, M.

    2008-05-15

    Resistive walls, located close to the plasma boundary, reduce the growth rates of external kink modes to resistive time scales. For such slowly growing resistive wall modes, the stabilization by an active feedback system becomes feasible. The fully three-dimensional stability code STARWALL, and the feedback optimization code OPTIM have been developed [P. Merkel and M. Sempf, 21st IAEA Fusion Energy Conference 2006, Chengdu, China (International Atomic Energy Agency, Vienna, 2006, paper TH/P3-8] to compute the growth rates of resistive wall modes in the presence of nonaxisymmetric, multiply connected wall structures and to model the active feedback stabilization of these modes.more » In order to demonstrate the capabilities of the codes and to study the effect of the toroidal mode coupling caused by multiply connected wall structures, the codes are applied to test equilibria using the resistive wall structures currently under debate for ITER [M. Shimada et al., Nucl. Fusion 47, S1 (2007)] and ASDEX Upgrade [W. Koeppendoerfer et al., Proceedings of the 16th Symposium on Fusion Technology, London, 1990 (Elsevier, Amsterdam, 1991), Vol. 1, p. 208].« less

  6. ALCBEAM - Neutral beam formation and propagation code for beam-based plasma diagnostics

    NASA Astrophysics Data System (ADS)

    Bespamyatnov, I. O.; Rowan, W. L.; Liao, K. T.

    2012-03-01

    ALCBEAM is a new three-dimensional neutral beam formation and propagation code. It was developed to support the beam-based diagnostics installed on the Alcator C-Mod tokamak. The purpose of the code is to provide reliable estimates of the local beam equilibrium parameters: such as beam energy fractions, density profiles and excitation populations. The code effectively unifies the ion beam formation, extraction and neutralization processes with beam attenuation and excitation in plasma and neutral gas and beam stopping by the beam apertures. This paper describes the physical processes interpreted and utilized by the code, along with exploited computational methods. The description is concluded by an example simulation of beam penetration into plasma of Alcator C-Mod. The code is successfully being used in Alcator C-Mod tokamak and expected to be valuable in the support of beam-based diagnostics in most other tokamak environments. Program summaryProgram title: ALCBEAM Catalogue identifier: AEKU_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEKU_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 66 459 No. of bytes in distributed program, including test data, etc.: 7 841 051 Distribution format: tar.gz Programming language: IDL Computer: Workstation, PC Operating system: Linux RAM: 1 GB Classification: 19.2 Nature of problem: Neutral beams are commonly used to heat and/or diagnose high-temperature magnetically-confined laboratory plasmas. An accurate neutral beam characterization is required for beam-based measurements of plasma properties. Beam parameters such as density distribution, energy composition, and atomic excited populations of the beam atoms need to be known. Solution method: A neutral beam is initially formed as an ion beam which is extracted from the ion source by high voltage applied to the extraction and accelerating grids. The current distribution of a single beamlet emitted from a single pore of IOS depends on the shape of the plasma boundary in the emission region. Total beam extracted by IOS is calculated at every point of 3D mesh as sum of all contributions from each grid pore. The code effectively unifies the ion beam formation, extraction and neutralization processes with neutral beam attenuation and excitation in plasma and neutral gas and beam stopping by the beam apertures. Running time: 10 min for a standard run.

  7. Resonant scattering as a sensitive diagnostic of current collisional plasma models

    NASA Astrophysics Data System (ADS)

    Ogorzalek, Anna; Zhuravleva, Irina; Allen, Steven W.; Pinto, Ciro; Werner, Norbert; Mantz, Adam; Canning, Rebecca; Fabian, Andrew C.; Kaastra, Jelle S.; de Plaa, Jelle

    2017-08-01

    Resonant scattering is a subtle process that suppresses fluxes of some of the brightest optically thick X-ray emission lines produced by collisional plasmas in galaxy clusters and massive early-type galaxies. The amplitude of the effect depends on the turbulent structure of the hot gas, making it a sensitive velocity probe. It is therefore crucial to properly model this effect in order to correctly interpret high resolution X-ray spectra. Our measurements of resonant scattering with XMM-Newton Reflection Grating Spectrometer in giant elliptical galaxies and with Hitomi in the center of Perseus Cluster show that the potentially rich inference from this effect is limited by the uncertainties in the atomic data underlying plasma codes such as APEC and SPEX. Typically, the effect is of the order of 10-20%, while the discrepancy between the two codes is of similar order or even higher. Precise knowledge of the emissivity and oscillator strengths of lines emitted by Fe XVII and Fe XXV, as well as their respective uncertainties propagated through plasma codes are key to understanding gas dynamics and microphysics in giant galaxies and cluster ICM, respectively. This is especially crucial for massive ellipticals, where sub-eV resolution would be needed to measure line broadening precisely, making resonant scattering an important velocity diagnostic in these systems for the foreseeable future. In this poster, I will summarize current status of resonant scattering measurements and show how they depend on the assumed atomic data. I will also discuss which improvements are essential to maximize scientific inference from future high resolution X-ray spectra.

  8. Deceleration processes of secondary electrons produced by a high-energy Auger electron in a biological context.

    PubMed

    Kai, Takeshi; Yokoya, Akinari; Ukai, Masatoshi; Fujii, Kentaro; Watanabe, Ritsuko

    2016-11-01

    To simulate the deceleration processes of secondary electrons produced by a high-energy Auger electron in water, and particularly to focus on the spatial and temporal distributions of the secondary electron and the collision events (e.g. ionization, electronic excitation, and dissociative electron attachment) that are involved in the multiplication of lesions at sites of DNA damage. We developed a dynamic Monte Carlo code that considers the Coulombic force between an ejected electron and its parent cation produced by the Auger electron in water. Thus our code can simulate some return electrons to the parent cations. Using the code, we calculated to within the order of femtoseconds the temporal evolution of collision events, the mean energy, and the mean traveling distance (including its spatial probability distribution) of the electron at an ejected energy of 20 eV. Some of the decelerating electrons in water in the Coulombic field were attracted to the ionized atoms (cations) by the Coulombic force within hundreds of femtoseconds, although the force did not significantly enhance the number of ionization, electronic excitation, and dissociative electron attachment collision events leading to water radiolysis. The secondary electrons are decelerated in water by the Coulombic force and recombined to the ionized atoms (cations). Furthermore, the some return electrons might be prehydrated in water layer near the parent cation in DNA if the electrons might be emitted from the DNA. The prehydrated electron originated from the return electron might play a significant role in inducing DNA damage.

  9. On the Numerical Analysis of Decay Rate Enhancement in Metallic Environment

    NASA Astrophysics Data System (ADS)

    Mehedinteanu, S.

    2007-10-01

    Motivated on the very recent experiments to determine the acceleration of the alpha decay of meta-stable radionuclides in metallic environment some work has been done to strengthten the importance in the process of electrons screening in metals. Thus, by combining the Gamow decay theory with electrostatic screening in Debye-Hückel approximation (jellium model) a formula for ``the shift'' in screening energy which enters in the decay enhancement factor expression that copes well with these experiments has been derived. It was established that to simulate the poly-atoms system containing decaying isotopes in QM&MD codes calculations, and to include ``the screening energy shift'' of protons, decay alpha, beta+ particles due to all surrounding interacting effects, it is sufficiently only to substitute the code ruly pseudo-potential input for hydrogen-like atoms (including alpha) by a screened Coulomb potential as from the well-known Gamow alpha decay theory. For demonstration is used the QM&MD code package which usually performs density-functional theory (DFT) total-energy calculations for materials ranging from insulators to transition metals. This package employs first-principles pseudo-potentials and a plane-wave basis-set, and it was used to do a special calculus for some metal environments (Pd) where protons-deuterons are implanted or when it is alloyed with a radionuclide-like isotopes (174Hf72), the results compare well with the existing experiments on the decay enhancement. These works give further arguments for a cheap solution to remove the transuranic waste (involving all alpha-decay) of used-up rods of fission reactors in a time period of a few years.

  10. Classification of melanoma lesions using sparse coded features and random forests

    NASA Astrophysics Data System (ADS)

    Rastgoo, Mojdeh; Lemaître, Guillaume; Morel, Olivier; Massich, Joan; Garcia, Rafael; Meriaudeau, Fabrice; Marzani, Franck; Sidibé, Désiré

    2016-03-01

    Malignant melanoma is the most dangerous type of skin cancer, yet it is the most treatable kind of cancer, conditioned by its early diagnosis which is a challenging task for clinicians and dermatologists. In this regard, CAD systems based on machine learning and image processing techniques are developed to differentiate melanoma lesions from benign and dysplastic nevi using dermoscopic images. Generally, these frameworks are composed of sequential processes: pre-processing, segmentation, and classification. This architecture faces mainly two challenges: (i) each process is complex with the need to tune a set of parameters, and is specific to a given dataset; (ii) the performance of each process depends on the previous one, and the errors are accumulated throughout the framework. In this paper, we propose a framework for melanoma classification based on sparse coding which does not rely on any pre-processing or lesion segmentation. Our framework uses Random Forests classifier and sparse representation of three features: SIFT, Hue and Opponent angle histograms, and RGB intensities. The experiments are carried out on the public PH2 dataset using a 10-fold cross-validation. The results show that SIFT sparse-coded feature achieves the highest performance with sensitivity and specificity of 100% and 90.3% respectively, with a dictionary size of 800 atoms and a sparsity level of 2. Furthermore, the descriptor based on RGB intensities achieves similar results with sensitivity and specificity of 100% and 71.3%, respectively for a smaller dictionary size of 100 atoms. In conclusion, dictionary learning techniques encode strong structures of dermoscopic images and provide discriminant descriptors.

  11. Determination of recombination radius in Si for binary collision approximation codes

    DOE PAGES

    Vizkelethy, Gyorgy; Foiles, Stephen M.

    2015-09-11

    Displacement damage caused by ions or neutrons in microelectronic devices can have significant effect on the performance of these devices. Therefore, it is important to predict not only the displacement damage profile, but also its magnitude precisely. Analytical methods and binary collision approximation codes working with amorphous targets use the concept of displacement energy, the energy that a lattice atom has to receive to create a permanent replacement. It was found that this “displacement energy” is direction dependent; it can range from 12 to 32 eV in silicon. Obviously, this model fails in BCA codes that work with crystalline targets,more » such as Marlowe. Marlowe does not use displacement energy; instead, it uses lattice binding energy only and then pairs the interstitial atoms with vacancies. Then based on the configuration of the Frenkel pairs it classifies them as close, near, or distant pairs, and considers the distant pairs the permanent replacements. Unfortunately, this separation is an ad hoc assumption, and the results do not agree with molecular dynamics calculations. After irradiation, there is a prompt recombination of interstitials and vacancies if they are nearby, within a recombination radius. In order to implement this recombination radius in Marlowe, we used the comparison of MD and Marlowe calculation in a range of ion energies in single crystal silicon target. As a result, the calculations showed that a single recombination radius of ~7.4 Å in Marlowe for a range of ion energies gives an excellent agreement with MD.« less

  12. A discriminatory function for prediction of protein-DNA interactions based on alpha shape modeling.

    PubMed

    Zhou, Weiqiang; Yan, Hong

    2010-10-15

    Protein-DNA interaction has significant importance in many biological processes. However, the underlying principle of the molecular recognition process is still largely unknown. As more high-resolution 3D structures of protein-DNA complex are becoming available, the surface characteristics of the complex become an important research topic. In our work, we apply an alpha shape model to represent the surface structure of the protein-DNA complex and developed an interface-atom curvature-dependent conditional probability discriminatory function for the prediction of protein-DNA interaction. The interface-atom curvature-dependent formalism captures atomic interaction details better than the atomic distance-based method. The proposed method provides good performance in discriminating the native structures from the docking decoy sets, and outperforms the distance-dependent formalism in terms of the z-score. Computer experiment results show that the curvature-dependent formalism with the optimal parameters can achieve a native z-score of -8.17 in discriminating the native structure from the highest surface-complementarity scored decoy set and a native z-score of -7.38 in discriminating the native structure from the lowest RMSD decoy set. The interface-atom curvature-dependent formalism can also be used to predict apo version of DNA-binding proteins. These results suggest that the interface-atom curvature-dependent formalism has a good prediction capability for protein-DNA interactions. The code and data sets are available for download on http://www.hy8.com/bioinformatics.htm kenandzhou@hotmail.com.

  13. Atomic spectral-product representations of molecular electronic structure: metric matrices and atomic-product composition of molecular eigenfunctions.

    PubMed

    Ben-Nun, M; Mills, J D; Hinde, R J; Winstead, C L; Boatz, J A; Gallup, G A; Langhoff, P W

    2009-07-02

    Recent progress is reported in development of ab initio computational methods for the electronic structures of molecules employing the many-electron eigenstates of constituent atoms in spectral-product forms. The approach provides a universal atomic-product description of the electronic structure of matter as an alternative to more commonly employed valence-bond- or molecular-orbital-based representations. The Hamiltonian matrix in this representation is seen to comprise a sum over atomic energies and a pairwise sum over Coulombic interaction terms that depend only on the separations of the individual atomic pairs. Overall electron antisymmetry can be enforced by unitary transformation when appropriate, rather than as a possibly encumbering or unnecessary global constraint. The matrix representative of the antisymmetrizer in the spectral-product basis, which is equivalent to the metric matrix of the corresponding explicitly antisymmetric basis, provides the required transformation to antisymmetric or linearly independent states after Hamiltonian evaluation. Particular attention is focused in the present report on properties of the metric matrix and on the atomic-product compositions of molecular eigenstates as described in the spectral-product representations. Illustrative calculations are reported for simple but prototypically important diatomic (H(2), CH) and triatomic (H(3), CH(2)) molecules employing algorithms and computer codes devised recently for this purpose. This particular implementation of the approach combines Slater-orbital-based one- and two-electron integral evaluations, valence-bond constructions of standard tableau functions and matrices, and transformations to atomic eigenstate-product representations. The calculated metric matrices and corresponding potential energy surfaces obtained in this way elucidate a number of aspects of the spectral-product development, including the nature of closure in the representation, the general redundancy or linear dependence of its explicitly antisymmetrized form, the convergence of the apparently disparate atomic-product and explicitly antisymmetrized atomic-product forms to a common invariant subspace, and the nature of a chemical bonding descriptor provided by the atomic-product compositions of molecular eigenstates. Concluding remarks indicate additional studies in progress and the prognosis for performing atomic spectral-product calculations more generally and efficiently.

  14. A Qualitative Report of the Ways High School Chemistry Students Attempt to Represent a Chemical Reaction at the Atomic/Molecular Level

    ERIC Educational Resources Information Center

    Kern, Anne L.; Wood, Nathan B.; Roehrig, Gillian H.; Nyachwaya, James

    2010-01-01

    We report the findings of a large-scale (n = 1,337) qualitative descriptive analysis of U.S. high schools students' particulate representations of a chemical reaction, specifically, the combustion of methane. Data were collected as part of an end of course exam. Student representations were coded into 17 distinct subcategories under one of five…

  15. Naval Research Laboratory Major Facilities 2008

    DTIC Science & Technology

    2008-10-01

    Development Laboratory • Secure Supercomputing Facility • CBD/Tilghman Island IR Field Evaluation Facility • Ultra-Short-Pulse Laser Effects Research...EMI Test Facility • Proximity Operations Testbed GENERAL INFORMATION • Maps EX EC U TI V E D IR EC TO RA TE Code 1100 – Institute for Nanoscience...facility: atomic force microscope (AFM); benchtop transmission electron microscope (TEM); cascade probe station; critical point dryer ; dual beam focused

  16. The Emergence of Atomic-Level Structural Information for Ordered Metal-Solution Interfaces: Some Recent Contributions from In-Situ Infrared Spectroscopy and Scanning Tunneling Microscopy

    DTIC Science & Technology

    1992-02-28

    Distribution/ Availabilit Codes jAval’ an~d/or Dist Speoial (19. cont.) reconstruction at gold-aqueous interfaces. All three low-index gold surfaces are...uncharged (vide supra). This difference may well be due to the influence of the interfacial water , or conceivably to adsorbed perchlorate anions. Both Au

  17. Spray combustion model improvement study, 1

    NASA Technical Reports Server (NTRS)

    Chen, C. P.; Kim, Y. M.; Shang, H. M.

    1993-01-01

    This study involves the development of numerical and physical modeling in spray combustion. These modeling efforts are mainly motivated to improve the physical submodels of turbulence, combustion, atomization, dense spray effects, and group vaporization. The present mathematical formulation can be easily implemented in any time-marching multiple pressure correction methodologies such as MAST code. A sequence of validation cases includes the nonevaporating, evaporating and_burnin dense_sprays.

  18. Numerical optimization of a picosecond pulse driven Ni-like Nb x-ray laser at 20.3 nm

    NASA Astrophysics Data System (ADS)

    Lu, X.; Zhong, J. Y.; Li, Y. J.; Zhang, J.

    2003-07-01

    Detailed simulations of a Ni-like Nb x-ray laser pumped by a nanosecond prepulse followed by a picosecond main pulse are presented. The atomic physics data are obtained using the Cowan code [R. D. Cowan, The Theory of Atomic Structure and Spectra (University of California Press, Berkeley, CA, 1981)]. The optimization calculations are performed in terms of the intensity of prepulse and the time delay between the prepulse and the main pulse. A high gain over 150 cm-1 is obtained for the optimized drive pulse configuration. The ray-tracing calculations suggest that the total pump energy for a saturated x-ray laser can be reduced to less than 1 J.

  19. Configuration-interaction relativistic-many-body-perturbation-theory calculations of photoionization cross sections from quasicontinuum oscillator strengths

    DOE PAGES

    Savukov, I. M.; Filin, D. V.

    2014-12-29

    Many applications are in need of accurate photoionization cross sections, especially in the case of complex atoms. Configuration-interaction relativistic-many-body-perturbation theory (CI-RMBPT) has been successful in predicting atomic energies, matrix elements between discrete states, and other properties, which is quite promising, but it has not been applied to photoionization problems owing to extra complications arising from continuum states. In this paper a method that will allow the conversion of discrete CI-(R)MPBT oscillator strengths (OS) to photoionization cross sections with minimal modifications of the codes is introduced and CI-RMBPT cross sections of Ne, Ar, Kr, and Xe are calculated. A consistent agreementmore » with experiment is found. RMBPT corrections are particularly significant for Ar, Kr, and Xe and improve agreement with experimental results compared to the particle-hole CI method. As a result, the demonstrated conversion method can be applied to CI-RMBPT photoionization calculations for a large number of multivalence atoms and ions.« less

  20. Numerical analysis of the spatial nonuniformity in a Cs-seeded H{sup -} ion source

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Takado, N.; Hanatani, J.; Mizuno, T.

    The H{sup -} ion production and transport processes are numerically simulated to clarify the origin of H{sup -} beam nonuniformity. The three-dimensional transport code using the Monte Carlo method has been applied to H{sup 0} atoms and H{sup -} ions in the large 'JAERI 10A negative ion source' under the Cs-seeded condition, in which negative ions are dominantly produced by the surface production process. The results show that a large fraction of hydrogen atoms is produced in the region with high electron temperature. This leads to a spatial nonuniformity of H{sup 0} atom flux to the plasma grid and themore » resultant H{sup -} ion surface production. In addition, most surface-produced H{sup -} ions are extracted even through the high T{sub e} region without destruction. These results indicate a correlation between the production process of the H{sup -} ion and the spatial nonuniformity of the H{sup -} ion beam.« less

  1. Atomic Processes in X-ray Photoioinzed Gas

    NASA Technical Reports Server (NTRS)

    Kallman, Timothy

    2005-01-01

    It has long been known that photoionization and photoabsorption play a dominant role in determining the state of gas in nebulae surrounding hot stars and in active galaxies. Recent observations of X-ray spectra demonstrate that these processes are also dominant in highly ionized gas near compact objects, and also affect the transmission of X-rays from the majority of astronomical sources. This has led to new insights into the understanding of what is going on in these sources. It has also pointed out the need for accurate atomic cross sections for photoionization and absorption, notably for processes involving inner shells. The xstar code can be used for calculating the heating, ionization and reprocessing of X-rays by gas in a range of ionization states and temperatures. It has recently been updated to include an improved treatment of inner shell transitions in iron. I will review the capabilities of xstar, the atomic data, and illustrate some applications to recent X-ray spectral observations.

  2. Safe transport of radioactive materials in Egypt

    NASA Astrophysics Data System (ADS)

    El-Shinawy, Rifaat M. K.

    1994-07-01

    In Egypt the national regulations for safe transport of radioactive materials (RAM) are based on the International Atomic Energy Agency (IAEA) regulations. In addition, regulations for the safe transport of these materials through the Suez Canal (SC) were laid down by the Egyptian Atomic Energy Authority (EAEA) and the Suez Canal Authority (SCA). They are continuously updated to meet the increased knowledge and the gained experience. The technical and protective measures taken during transport of RAM through SC are mentioned. Assessment of the impact of transporting radioactive materials through the Suez Canal using the INTERTRAN computer code was carried out in cooperation with IAEA. The transported activities and empty containers, the number of vessels carrying RAM through the canal from 1963 to 1991 and their nationalities are also discussed. The protective measures are mentioned.A review of the present situation of the radioactive wastes storage facilities at the Atomic Energy site at Inshas is given along with the regulation for safe transportation and disposal of radioactive wastes

  3. Prediction of another semimetallic silicene allotrope with Dirac fermions

    NASA Astrophysics Data System (ADS)

    Wu, Haiping; Qian, Yan; Du, Zhengwei; Zhu, Renzhu; Kan, Erjun; Deng, Kaiming

    2017-11-01

    Materials with Dirac point are so amazing since the charge carriers are massless and have an effective speed of light. However, among the predicted two-dimensional silicon allotropes with Dirac point, no one has been directly proved by experiment. This fact motivates us to search for other two-dimensional silicon allotropes. As a result, another stable single atomic layer thin silicon allotrope is found with the help of CALYPSO code in this work. This silicene allotrope is composed of eight-membered rings linked by Si-Si bonds with buckling formation. The electronic calculation reveals that it behaves as a nodal line semimetal with the linear energy dispersion relation near the Fermi surface. Notably, the ab initio molecular dynamics simulations display that the original atomic configuration can be remained even at an extremely high temperature of 1000 K. Additionally, hydrogenation could induce a semimetal-semiconductor transition in this silicene allotrope. We hope this work can expand the family of single atomic layer thin silicon allotropes with special applications.

  4. Effect of aluminum on the local structure of silicon in zeolites as studied by Si K edge X-ray absorption near-edge fine structure: spectra simulation with a non-muffin tin atomic background.

    PubMed

    Bugaev, Lusegen A; Bokhoven, Jeroen A van; Khrapko, Valerii V

    2009-04-09

    Experimental Si K edge X-ray absorption near-edge fine structure (XANES) of zeolite faujasite, mordenite, and beta are interpreted by means of the FEFF8 code, replacing the theoretical atomic background mu(0) by a background that was extracted from an experimental spectrum. To some extent, this diminished the effect of the inaccuracy introduced by the MT potential and accounted for the intrinsic loss of photoelectrons. The agreement of the theoretical and experimental spectra at energies above the white lines enabled us to identify structural distortion around silicon, which occurs with increasing aluminum content. The Si K edge XANES spectra are very sensitive to slight distortions in the silicon coordination. Placing an aluminum atom on a nearest neighboring T site causes a distortion in the silicon tetrahedron, shortening one of the silicon-oxygen bonds relative to the other three.

  5. Parallelization of the FLAPW method and comparison with the PPW method

    NASA Astrophysics Data System (ADS)

    Canning, Andrew; Mannstadt, Wolfgang; Freeman, Arthur

    2000-03-01

    The FLAPW (full-potential linearized-augmented plane-wave) method is one of the most accurate first-principles methods for determining electronic and magnetic properties of crystals and surfaces. In the past the FLAPW method has been limited to systems of about a hundred atoms due to the lack of an efficient parallel implementation to exploit the power and memory of parallel computers. In this work we present an efficient parallelization of the method by division among the processors of the plane-wave components for each state. The code is also optimized for RISC (reduced instruction set computer) architectures, such as those found on most parallel computers, making full use of BLAS (basic linear algebra subprograms) wherever possible. Scaling results are presented for systems of up to 686 silicon atoms and 343 palladium atoms per unit cell running on up to 512 processors on a Cray T3E parallel supercomputer. Some results will also be presented on a comparison of the plane-wave pseudopotential method and the FLAPW method on large systems.

  6. Predicting activity approach based on new atoms similarity kernel function.

    PubMed

    Abu El-Atta, Ahmed H; Moussa, M I; Hassanien, Aboul Ella

    2015-07-01

    Drug design is a high cost and long term process. To reduce time and costs for drugs discoveries, new techniques are needed. Chemoinformatics field implements the informational techniques and computer science like machine learning and graph theory to discover the chemical compounds properties, such as toxicity or biological activity. This is done through analyzing their molecular structure (molecular graph). To overcome this problem there is an increasing need for algorithms to analyze and classify graph data to predict the activity of molecules. Kernels methods provide a powerful framework which combines machine learning with graph theory techniques. These kernels methods have led to impressive performance results in many several chemoinformatics problems like biological activity prediction. This paper presents a new approach based on kernel functions to solve activity prediction problem for chemical compounds. First we encode all atoms depending on their neighbors then we use these codes to find a relationship between those atoms each other. Then we use relation between different atoms to find similarity between chemical compounds. The proposed approach was compared with many other classification methods and the results show competitive accuracy with these methods. Copyright © 2015 Elsevier Inc. All rights reserved.

  7. TIPTOPbase: the Iron Project and the Opacity Project Atomic Database

    NASA Astrophysics Data System (ADS)

    Mendoza, Claudio; Nahar, Sultana; Pradhan, Anil; Seaton, Micheal; Zeippen, Claude

    2001-05-01

    The Opacity Project, the IRON Project, and the RmaX Network (The Opacity Project Team, Vol.1,2), IOPP, Bristol (1995,1996); Hummer et al., Astron. Astrophys. 279, 298 (1993) are international computational efforts concerned with the production of high quality atomic data for astrophysical applications. Research groups from Canada, France, Germany, UK, USA and Venezuela are involved. Extensive data sets containing accurate energy levels, f-values, A-values, photoionisation cross sections, collision strengths, recombination rates, and opacitites have been computed for cosmically abundant elements using state-of-the-art atomic physics codes. Their volume, completeness and overall accuracy are presently unmatched in the field of laboratory astrophysics. Some of the data sets have been available since 1993 from a public on-line database service referred to as TOPbase (Cunto et al Astron. Astrophys. 275), L5 (1993), ( http://cdsweb.u-strasbg.fr/OP.html at CDS France, and http://heasarc.gsfc.nasa.gov/topbase, at NSAS USA). We are currently involved in a major effort to scale the existing database services to develop a robust platform for the high-profile dissemination of atomic data to the scientific community within the next 12 months. (Partial support from the NSF and NASA is acknowledged.)

  8. Bayesian data analysis tools for atomic physics

    NASA Astrophysics Data System (ADS)

    Trassinelli, Martino

    2017-10-01

    We present an introduction to some concepts of Bayesian data analysis in the context of atomic physics. Starting from basic rules of probability, we present the Bayes' theorem and its applications. In particular we discuss about how to calculate simple and joint probability distributions and the Bayesian evidence, a model dependent quantity that allows to assign probabilities to different hypotheses from the analysis of a same data set. To give some practical examples, these methods are applied to two concrete cases. In the first example, the presence or not of a satellite line in an atomic spectrum is investigated. In the second example, we determine the most probable model among a set of possible profiles from the analysis of a statistically poor spectrum. We show also how to calculate the probability distribution of the main spectral component without having to determine uniquely the spectrum modeling. For these two studies, we implement the program Nested_fit to calculate the different probability distributions and other related quantities. Nested_fit is a Fortran90/Python code developed during the last years for analysis of atomic spectra. As indicated by the name, it is based on the nested algorithm, which is presented in details together with the program itself.

  9. Atomic structure calculations and identification of EUV and SXR spectral lines in Sr XXX

    NASA Astrophysics Data System (ADS)

    Goyal, Arun; Khatri, Indu; Aggarwal, Sunny; Singh, A. K.; Mohan, Man

    2015-08-01

    We report an extensive theoretical study of atomic data for Sr XXX in a wide range with L-shell electron excitations to the M-shell. We have calculated energy levels, wave-function compositions and lifetimes for lowest 113 fine structure levels and wavelengths of an extreme Ultraviolet (EUV) and soft X-ray (SXR) transitions. We have employed multi-configuration Dirac Fock method (MCDF) approach within the framework of Dirac-Coulomb Hamiltonian including quantum electrodynamics (QED) and Breit corrections. We have also presented the radiative data for electric and magnetic dipole (E1, M1) and quadrupole (E2, M2) transitions from the ground state. We have made comparisons with available energy levels compiled by NIST and achieve good agreement. But due to inadequate data in the literature, analogous relativistic distorted wave calculations have also been performed using flexible atomic code (FAC) to assess the reliability and accuracy of our results. Additionally, we have provided new atomic data for Sr XXX which is not published elsewhere in the literature and we believe that our results may be beneficial in fusion plasma research and astrophysical investigations and applications.

  10. Modeling of crack growth under mixed-mode loading by a molecular dynamics method and a linear fracture mechanics approach

    NASA Astrophysics Data System (ADS)

    Stepanova, L. V.

    2017-12-01

    Atomistic simulations of the central crack growth process in an infinite plane medium under mixed-mode loading using Large-Scale Atomic/Molecular Massively Parallel Simulator (LAMMPS), a classical molecular dynamics code, are performed. The inter-atomic potential used in this investigation is the Embedded Atom Method (EAM) potential. Plane specimens with an initial central crack are subjected to mixed-mode loadings. The simulation cell contains 400,000 atoms. The crack propagation direction angles under different values of the mixity parameter in a wide range of values from pure tensile loading to pure shear loading in a wide range of temperatures (from 0.1 K to 800 K) are obtained and analyzed. It is shown that the crack propagation direction angles obtained by molecular dynamics coincide with the crack propagation direction angles given by the multi-parameter fracture criteria based on the strain energy density and the multi-parameter description of the crack-tip fields. The multi-parameter fracture criteria are based on the multi-parameter stress field description taking into account the higher order terms of the Williams series expansion of the crack tip fields.

  11. Assessment of radiological protection systems among diagnostic radiology facilities in North East India.

    PubMed

    Singh, Thokchom Dewan; Jayaraman, T; Arunkumar Sharma, B

    2017-03-01

    This study aims to assess the adequacy level of radiological protection systems available in the diagnostic radiology facilities located in three capital cities of North East (NE) India. It further attempts to understand, using a multi-disciplinary approach, how the safety codes/standards in diagnostic radiology framed by the Atomic Energy Regulatory Board (AERB) and the International Atomic Energy Agency (IAEA) to achieve adequate radiological protection in facilities, have been perceived, conceptualized, and applied accordingly in these facilities. About 30 diagnostic radiology facilities were randomly selected from three capitals of states in NE India; namely Imphal (Manipur), Shillong (Meghalaya) and Guwahati (Assam). A semi-structured questionnaire developed based on a multi-disciplinary approach was used for this study. It was observed that radiological practices undertaken in these facilities were not exactly in line with safety codes/standards in diagnostic radiology of the AERB and the IAEA. About 50% of the facilities had registered/licensed x-ray equipment with the AERB. More than 80% of the workers did not use radiation protective devices, although these devices were available in the facilities. About 85% of facilities had no institutional risk management system. About 70% of the facilities did not carry out periodic quality assurance testing of their x-ray equipment or surveys of radiation leakage around the x-ray room, and did not display radiation safety indicators in the x-ray rooms. Workers in these facilities exhibited low risk perception about the risks associated with these practices. The majority of diagnostic radiology facilities in NE India did not comply with the radiological safety codes/standards framed by the AERB and IAEA. The study found inadequate levels of radiological protection systems in the majority of facilities. This study suggests a need to establish firm measures that comply with the radiological safety codes/standards of the AERB and IAEA to protect patients, workers and the public of this region.

  12. Molecular Dynamics of Hot Dense Plasmas: New Horizons

    NASA Astrophysics Data System (ADS)

    Graziani, Frank

    2011-10-01

    We describe the status of a new time-dependent simulation capability for hot dense plasmas. The backbone of this multi-institutional computational and experimental effort--the Cimarron Project--is the massively parallel molecular dynamics (MD) code ``ddcMD''. The project's focus is material conditions such as exist in inertial confinement fusion experiments, and in many stellar interiors: high temperatures, high densities, significant electromagnetic fields, mixtures of high- and low- Zelements, and non-Maxwellian particle distributions. Of particular importance is our ability to incorporate into this classical MD code key atomic, radiative, and nuclear processes, so that their interacting effects under non-ideal plasma conditions can be investigated. This talk summarizes progress in computational methodology, discusses strengths and weaknesses of quantum statistical potentials as effective interactions for MD, explains the model used for quantum events possibly occurring in a collision and highlights some significant results obtained to date. We describe the status of a new time-dependent simulation capability for hot dense plasmas. The backbone of this multi-institutional computational and experimental effort--the Cimarron Project--is the massively parallel molecular dynamics (MD) code ``ddcMD''. The project's focus is material conditions such as exist in inertial confinement fusion experiments, and in many stellar interiors: high temperatures, high densities, significant electromagnetic fields, mixtures of high- and low- Zelements, and non-Maxwellian particle distributions. Of particular importance is our ability to incorporate into this classical MD code key atomic, radiative, and nuclear processes, so that their interacting effects under non-ideal plasma conditions can be investigated. This talk summarizes progress in computational methodology, discusses strengths and weaknesses of quantum statistical potentials as effective interactions for MD, explains the model used for quantum events possibly occurring in a collision and highlights some significant results obtained to date. This work is performed under the auspices of the U. S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

  13. A domain specific language for performance portable molecular dynamics algorithms

    NASA Astrophysics Data System (ADS)

    Saunders, William Robert; Grant, James; Müller, Eike Hermann

    2018-03-01

    Developers of Molecular Dynamics (MD) codes face significant challenges when adapting existing simulation packages to new hardware. In a continuously diversifying hardware landscape it becomes increasingly difficult for scientists to be experts both in their own domain (physics/chemistry/biology) and specialists in the low level parallelisation and optimisation of their codes. To address this challenge, we describe a "Separation of Concerns" approach for the development of parallel and optimised MD codes: the science specialist writes code at a high abstraction level in a domain specific language (DSL), which is then translated into efficient computer code by a scientific programmer. In a related context, an abstraction for the solution of partial differential equations with grid based methods has recently been implemented in the (Py)OP2 library. Inspired by this approach, we develop a Python code generation system for molecular dynamics simulations on different parallel architectures, including massively parallel distributed memory systems and GPUs. We demonstrate the efficiency of the auto-generated code by studying its performance and scalability on different hardware and compare it to other state-of-the-art simulation packages. With growing data volumes the extraction of physically meaningful information from the simulation becomes increasingly challenging and requires equally efficient implementations. A particular advantage of our approach is the easy expression of such analysis algorithms. We consider two popular methods for deducing the crystalline structure of a material from the local environment of each atom, show how they can be expressed in our abstraction and implement them in the code generation framework.

  14. Towards efficient data exchange and sharing for big-data driven materials science: metadata and data formats

    NASA Astrophysics Data System (ADS)

    Ghiringhelli, Luca M.; Carbogno, Christian; Levchenko, Sergey; Mohamed, Fawzi; Huhs, Georg; Lüders, Martin; Oliveira, Micael; Scheffler, Matthias

    2017-11-01

    With big-data driven materials research, the new paradigm of materials science, sharing and wide accessibility of data are becoming crucial aspects. Obviously, a prerequisite for data exchange and big-data analytics is standardization, which means using consistent and unique conventions for, e.g., units, zero base lines, and file formats. There are two main strategies to achieve this goal. One accepts the heterogeneous nature of the community, which comprises scientists from physics, chemistry, bio-physics, and materials science, by complying with the diverse ecosystem of computer codes and thus develops "converters" for the input and output files of all important codes. These converters then translate the data of each code into a standardized, code-independent format. The other strategy is to provide standardized open libraries that code developers can adopt for shaping their inputs, outputs, and restart files, directly into the same code-independent format. In this perspective paper, we present both strategies and argue that they can and should be regarded as complementary, if not even synergetic. The represented appropriate format and conventions were agreed upon by two teams, the Electronic Structure Library (ESL) of the European Center for Atomic and Molecular Computations (CECAM) and the NOvel MAterials Discovery (NOMAD) Laboratory, a European Centre of Excellence (CoE). A key element of this work is the definition of hierarchical metadata describing state-of-the-art electronic-structure calculations.

  15. Ab initio MD simulations of Mg2SiO4 liquid at high pressures and temperatures relevant to the Earth's mantle

    NASA Astrophysics Data System (ADS)

    Martin, G. B.; Kirtman, B.; Spera, F. J.

    2010-12-01

    Computational studies implementing Density Functional Theory (DFT) methods have become very popular in the Materials Sciences in recent years. DFT codes are now used routinely to simulate properties of geomaterials—mainly silicates and geochemically important metals such as Fe. These materials are ubiquitous in the Earth’s mantle and core and in terrestrial exoplanets. Because of computational limitations, most First Principles Molecular Dynamics (FPMD) calculations are done on systems of only 100 atoms for a few picoseconds. While this approach can be useful for calculating physical quantities related to crystal structure, vibrational frequency, and other lattice-scale properties (especially in crystals), it would be useful to be able to compute larger systems especially for extracting transport properties and coordination statistics. Previous studies have used codes such as VASP where CPU time increases as N2, making calculations on systems of more than 100 atoms computationally very taxing. SIESTA (Soler, et al. 2002) is a an order-N (linear-scaling) DFT code that enables electronic structure and MD computations on larger systems (N 1000) by making approximations such as localized numerical orbitals. Here we test the applicability of SIESTA to simulate geosilicates in the liquid and glass state. We have used SIESTA for MD simulations of liquid Mg2SiO4 at various state points pertinent to the Earth’s mantle and congruous with those calculated in a previous DFT study using the VASP code (DeKoker, et al. 2008). The core electronic wave functions of Mg, Si, and O were approximated using pseudopotentials with a core cutoff radius of 1.38, 1.0, and 0.61 Angstroms respectively. The Ceperly-Alder parameterization of the Local Density Approximation (LDA) was used as the exchange-correlation functional. Known systematic overbinding of LDA was corrected with the addition of a pressure term, P 1.6 GPa, which is the pressure calculated by SIESTA at the experimental zero-pressure volume of forsterite under static conditions (Stixrude and Lithgow-Bertollini 2005). Results are reported here that show SIESTA calculations of T and P on densities in the range of 2.7 - 5.0 g/cc of liquid Mg2SiO4 are similar to the VASP calculations of DeKoker et al. (2008), which used the same functional. This opens the possibility of conducting fast /emph{ab initio} MD simulations of geomaterials with a hundreds of atoms.

  16. Implementation of the Regulatory Authority Information System in Egypt

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Carson, S.D.; Schetnan, R.; Hasan, A.

    2006-07-01

    As part of the implementation of a bar-code-based system to track radioactive sealed sources (RSS) in Egypt, the Regulatory Authority Information System Personal Digital Assistant (RAIS PDA) Application was developed to extend the functionality of the International Atomic Energy Agency's (IAEA's) RAIS database by allowing users to download RSS data from the database to a portable PDA equipped with a bar-code scanner. [1, 4] The system allows users in the field to verify radioactive sealed source data, gather radioactive sealed source audit information, and upload that data to the RAIS database. This paper describes the development of the RAIS PDAmore » Application, its features, and how it will be implemented in Egypt. (authors)« less

  17. Solution of the neutronics code dynamic benchmark by finite element method

    NASA Astrophysics Data System (ADS)

    Avvakumov, A. V.; Vabishchevich, P. N.; Vasilev, A. O.; Strizhov, V. F.

    2016-10-01

    The objective is to analyze the dynamic benchmark developed by Atomic Energy Research for the verification of best-estimate neutronics codes. The benchmark scenario includes asymmetrical ejection of a control rod in a water-type hexagonal reactor at hot zero power. A simple Doppler feedback mechanism assuming adiabatic fuel temperature heating is proposed. The finite element method on triangular calculation grids is used to solve the three-dimensional neutron kinetics problem. The software has been developed using the engineering and scientific calculation library FEniCS. The matrix spectral problem is solved using the scalable and flexible toolkit SLEPc. The solution accuracy of the dynamic benchmark is analyzed by condensing calculation grid and varying degree of finite elements.

  18. Numerical simulation of ion charge breeding in electron beam ion source

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Zhao, L., E-mail: zhao@far-tech.com; Kim, Jin-Soo

    2014-02-15

    The Electron Beam Ion Source particle-in-cell code (EBIS-PIC) tracks ions in an EBIS electron beam while updating electric potential self-consistently and atomic processes by the Monte Carlo method. Recent improvements to the code are reported in this paper. The ionization module has been improved by using experimental ionization energies and shell effects. The acceptance of injected ions and the emittance of extracted ion beam are calculated by extending EBIS-PIC to the beam line transport region. An EBIS-PIC simulation is performed for a Cs charge-breeding experiment at BNL. The charge state distribution agrees well with experiments, and additional simulation results ofmore » radial profiles and velocity space distributions of the trapped ions are presented.« less

  19. Simultaneous dense coding affected by fluctuating massless scalar field

    NASA Astrophysics Data System (ADS)

    Huang, Zhiming; Ye, Yiyong; Luo, Darong

    2018-04-01

    In this paper, we investigate the simultaneous dense coding (SDC) protocol affected by fluctuating massless scalar field. The noisy model of SDC protocol is constructed and the master equation that governs the SDC evolution is deduced. The success probabilities of SDC protocol are discussed for different locking operators under the influence of vacuum fluctuations. We find that the joint success probability is independent of the locking operators, but other success probabilities are not. For quantum Fourier transform and double controlled-NOT operators, the success probabilities drop with increasing two-atom distance, but SWAP operator is not. Unlike the SWAP operator, the success probabilities of Bob and Charlie are different. For different noisy interval values, different locking operators have different robustness to noise.

  20. EBR-II Static Neutronic Calculations by PHISICS / MCNP6 codes

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Paolo Balestra; Carlo Parisi; Andrea Alfonsi

    2016-02-01

    The International Atomic Energy Agency (IAEA) launched a Coordinated Research Project (CRP) on the Shutdown Heat Removal Tests (SHRT) performed in the '80s at the Experimental fast Breeder Reactor EBR-II, USA. The scope of the CRP is to improve and validate the simulation tools for the study and the design of the liquid metal cooled fast reactors. Moreover, training of the next generation of fast reactor analysts is being also considered the other scope of the CRP. In this framework, a static neutronic model was developed, using state-of-the art neutron transport codes like SCALE/PHISICS (deterministic solution) and MCNP6 (stochastic solution).more » Comparison between both solutions is briefly illustrated in this summary.« less

  1. Numerical study of the Columbia high-beta device: Torus-II

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Izzo, R.

    1981-01-01

    The ionization, heating and subsequent long-time-scale behavior of the helium plasma in the Columbia fusion device, Torus-II, is studied. The purpose of this work is to perform numerical simulations while maintaining a high level of interaction with experimentalists. The device is operated as a toroidal z-pinch to prepare the gas for heating. This ionization of helium is studied using a zero-dimensional, two-fluid code. It is essentially an energy balance calculation that follows the development of the various charge states of the helium and any impurities (primarily silicon and oxygen) that are present. The code is an atomic physics model ofmore » Torus-II. In addition to ionization, we include three-body and radiative recombination processes.« less

  2. A neutron spectrum unfolding computer code based on artificial neural networks

    NASA Astrophysics Data System (ADS)

    Ortiz-Rodríguez, J. M.; Reyes Alfaro, A.; Reyes Haro, A.; Cervantes Viramontes, J. M.; Vega-Carrillo, H. R.

    2014-02-01

    The Bonner Spheres Spectrometer consists of a thermal neutron sensor placed at the center of a number of moderating polyethylene spheres of different diameters. From the measured readings, information can be derived about the spectrum of the neutron field where measurements were made. Disadvantages of the Bonner system are the weight associated with each sphere and the need to sequentially irradiate the spheres, requiring long exposure periods. Provided a well-established response matrix and adequate irradiation conditions, the most delicate part of neutron spectrometry, is the unfolding process. The derivation of the spectral information is not simple because the unknown is not given directly as a result of the measurements. The drawbacks associated with traditional unfolding procedures have motivated the need of complementary approaches. Novel methods based on Artificial Intelligence, mainly Artificial Neural Networks, have been widely investigated. In this work, a neutron spectrum unfolding code based on neural nets technology is presented. This code is called Neutron Spectrometry and Dosimetry with Artificial Neural networks unfolding code that was designed in a graphical interface. The core of the code is an embedded neural network architecture previously optimized using the robust design of artificial neural networks methodology. The main features of the code are: easy to use, friendly and intuitive to the user. This code was designed for a Bonner Sphere System based on a 6LiI(Eu) neutron detector and a response matrix expressed in 60 energy bins taken from an International Atomic Energy Agency compilation. The main feature of the code is that as entrance data, for unfolding the neutron spectrum, only seven rate counts measured with seven Bonner spheres are required; simultaneously the code calculates 15 dosimetric quantities as well as the total flux for radiation protection purposes. This code generates a full report with all information of the unfolding in the HTML format. NSDann unfolding code is freely available, upon request to the authors.

  3. Compressive Hyperspectral Imaging and Anomaly Detection

    DTIC Science & Technology

    2010-02-01

    Level Set Systems 1058 Embury Street Pacific Palisades , CA 90272 8. PERFORMING ORGANIZATION REPORT NUMBER 1A-2010 9. SPONSORING/MONITORING...were obtained from a simple algorithm, namely, the atoms in the trained image were very similar to the simple cell receptive fields in early vision...Field, "Emergence of simple- cell receptive field properties by learning a sparse code for natural images,’" Nature 381(6583), pp. 607-609, 1996. M

  4. Energy distributions and radiation transport in uranium plasmas

    NASA Technical Reports Server (NTRS)

    Miley, G. H.; Bathke, C.; Maceda, E.; Choi, C.

    1976-01-01

    An approximate analytic model, based on continuous electron slowing, has been used for survey calculations. Where more accuracy is required, a Monte Carlo technique is used which combines an analytic representation of Coulombic collisions with a random walk treatment of inelastic collisions. The calculated electron distributions have been incorporated into another code that evaluates both the excited atomic state densities within the plasma and the radiative flux emitted from the plasma.

  5. OBJECT KINETIC MONTE CARLO SIMULATIONS OF MICROSTRUCTURE EVOLUTION

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Nandipati, Giridhar; Setyawan, Wahyu; Heinisch, Howard L.

    2013-09-30

    The objective is to report the development of the flexible object kinetic Monte Carlo (OKMC) simulation code KSOME (kinetic simulation of microstructure evolution) which can be used to simulate microstructure evolution of complex systems under irradiation. In this report we briefly describe the capabilities of KSOME and present preliminary results for short term annealing of single cascades in tungsten at various primary-knock-on atom (PKA) energies and temperatures.

  6. New cross sections for H on H2 collisional transitions

    NASA Astrophysics Data System (ADS)

    Zou, Qianxia

    2011-12-01

    The cross section for H on H2 collisions is important for astrophysics as well as our understanding of the simple chemical systems. This is the simplest atom-molecule cross section. With a new H3 potential surface by Mielke et al., we have modified the ABC code by Skouteris, Castillo and Manolopoulos to calculate new cross sections. These cross sections are compared to previous cross section calculations.

  7. Group-sparse representation with dictionary learning for medical image denoising and fusion.

    PubMed

    Li, Shutao; Yin, Haitao; Fang, Leyuan

    2012-12-01

    Recently, sparse representation has attracted a lot of interest in various areas. However, the standard sparse representation does not consider the intrinsic structure, i.e., the nonzero elements occur in clusters, called group sparsity. Furthermore, there is no dictionary learning method for group sparse representation considering the geometrical structure of space spanned by atoms. In this paper, we propose a novel dictionary learning method, called Dictionary Learning with Group Sparsity and Graph Regularization (DL-GSGR). First, the geometrical structure of atoms is modeled as the graph regularization. Then, combining group sparsity and graph regularization, the DL-GSGR is presented, which is solved by alternating the group sparse coding and dictionary updating. In this way, the group coherence of learned dictionary can be enforced small enough such that any signal can be group sparse coded effectively. Finally, group sparse representation with DL-GSGR is applied to 3-D medical image denoising and image fusion. Specifically, in 3-D medical image denoising, a 3-D processing mechanism (using the similarity among nearby slices) and temporal regularization (to perverse the correlations across nearby slices) are exploited. The experimental results on 3-D image denoising and image fusion demonstrate the superiority of our proposed denoising and fusion approaches.

  8. Calculation of Free-Atom Fractions in Hydrocarbon-Fueled Rocket Engine Plume

    NASA Technical Reports Server (NTRS)

    Verma, Satyajit

    2006-01-01

    Free atom fractions (Beta) of nine elements are calculated in the exhaust plume of CH4- oxygen and RP-1-oxygen fueled rocket engines using free energy minimization method. The Chemical Equilibrium and Applications (CEA) computer program developed by the Glenn Research Center, NASA is used for this purpose. Data on variation of Beta in both fuels as a function of temperature (1600 K - 3100 K) and oxygen to fuel ratios (1.75 to 2.25 by weight) is presented in both tabular and graphical forms. Recommendation is made for the Beta value for a tenth element, Palladium. The CEA computer code was also run to compare with experimentally determined Beta values reported in literature for some of these elements. A reasonable agreement, within a factor of three, between the calculated and reported values is observed. Values reported in this work will be used as a first approximation for pilot rocket engine testing studies at the Stennis Space Center for at least six elements Al, Ca, Cr, Cu, Fe and Ni - until experimental values are generated. The current estimates will be improved when more complete thermodynamic data on the remaining four elements Ag, Co, Mn and Pd are added to the database. A critique of the CEA code is also included.

  9. Protein and gene structure of a blue laccase from Pleurotus ostreatus1.

    PubMed Central

    Giardina, P; Palmieri, G; Scaloni, A; Fontanella, B; Faraco, V; Cennamo, G; Sannia, G

    1999-01-01

    A new laccase isoenzyme (POXA1b, where POX is phenol oxidase), produced by Pleurotus ostreatus in cultures supplemented with copper sulphate, has been purified and fully characterized. The main characteristics of this protein (molecular mass in native and denaturing conditions, pI and catalytic properties) are almost identical to the previously studied laccase POXA1w. However, POXA1b contains four copper atoms per molecule instead of one copper, two zinc and one iron atom per molecule of POXA1w. Furthermore, POXA1b shows an unusually high stability at alkaline pH. The gene and cDNA coding for POXA1b have been cloned and sequenced. The gene coding sequence contains 1599 bp, interrupted by 15 introns. Comparison of the structure of the poxa1b gene with the two previously studied P. ostreatus laccase genes (pox1 and poxc) suggests that these genes belong to two different subfamilies. The amino acid sequence of POXA1b deduced from the cDNA sequence has been almost completely verified by means of matrix-assisted laser desorption ionization MS. It has been demonstrated that three out of six putative glycosylation sites are post-translationally modified and the structure of the bound glycosidic moieties has been determined, whereas two other putative glycosylation sites are unmodified. PMID:10417329

  10. Quantitative analysis of vacuum-ultraviolet radiation from nanosecond laser-zinc interaction

    NASA Astrophysics Data System (ADS)

    Parchamy, Homaira; Szilagyi, John; Masnavi, Majid; Richardson, Martin

    2018-07-01

    The paper reports measurements of the vacuum-ultraviolet spectral irradiances of a flat zinc target over a wavelength region of 124-164 nm generated by 10 and 60 ns duration low-intensities, 5 ×109 - 3 ×1010 W cm-2, 1.06 μm wavelength laser pulses. Maximum radiation conversion efficiencies of 2.5%/2πsr and 0.8%/2πsr were measured for 60 and 10 ns laser pulses at the intensities of 5 ×109 and 1.4 ×1010 W cm-2, respectively. Atomic structure calculations using a relativistic configuration-interaction, flexible atomic code and a developed non-local thermodynamic equilibrium population kinetics model in comparison to the experimental spectra detected by the Seya-Namioka type monochromator reveal the strong broadband experimental emission originates mainly from 3d94p-3d94s, 3d94d-3d94p and 3d84p-3d84s, 3d84d-3d84p unresolved-transition arrays of double and triple ionized zinc, respectively. Two-dimensional radiation-hydrodynamics code is used to investigate time-space plasma evolution and spectral radiation of a 10 ns full-width-at-half-maximum Gaussian laser pulse-zinc interaction.

  11. Silicon Nitride Equation of State

    NASA Astrophysics Data System (ADS)

    Swaminathan, Pazhayannur; Brown, Robert

    2015-06-01

    This report presents the development a global, multi-phase equation of state (EOS) for the ceramic silicon nitride (Si3N4) . Structural forms include amorphous silicon nitride normally used as a thin film and three crystalline polymorphs. Crystalline phases include hexagonal α-Si3N4, hexagonalβ-Si3N4, and the cubic spinel c-Si3N4. Decomposition at about 1900 °C results in a liquid silicon phase and gas phase products such as molecular nitrogen, atomic nitrogen, and atomic silicon. The silicon nitride EOS was developed using EOSPro which is a new and extended version of the PANDA II code. Both codes are valuable tools and have been used successfully for a variety of material classes. Both PANDA II and EOSPro can generate a tabular EOS that can be used in conjunction with hydrocodes. The paper describes the development efforts for the component solid phases and presents results obtained using the EOSPro phase transition model to investigate the solid-solid phase transitions in relation to the available shock data. Furthermore, the EOSPro mixture model is used to develop a model for the decomposition products and then combined with the single component solid models to study the global phase diagram. Sponsored by the NASA Goddard Space Flight Center Living With a Star program office.

  12. GPU accelerated cell-based adaptive mesh refinement on unstructured quadrilateral grid

    NASA Astrophysics Data System (ADS)

    Luo, Xisheng; Wang, Luying; Ran, Wei; Qin, Fenghua

    2016-10-01

    A GPU accelerated inviscid flow solver is developed on an unstructured quadrilateral grid in the present work. For the first time, the cell-based adaptive mesh refinement (AMR) is fully implemented on GPU for the unstructured quadrilateral grid, which greatly reduces the frequency of data exchange between GPU and CPU. Specifically, the AMR is processed with atomic operations to parallelize list operations, and null memory recycling is realized to improve the efficiency of memory utilization. It is found that results obtained by GPUs agree very well with the exact or experimental results in literature. An acceleration ratio of 4 is obtained between the parallel code running on the old GPU GT9800 and the serial code running on E3-1230 V2. With the optimization of configuring a larger L1 cache and adopting Shared Memory based atomic operations on the newer GPU C2050, an acceleration ratio of 20 is achieved. The parallelized cell-based AMR processes have achieved 2x speedup on GT9800 and 18x on Tesla C2050, which demonstrates that parallel running of the cell-based AMR method on GPU is feasible and efficient. Our results also indicate that the new development of GPU architecture benefits the fluid dynamics computing significantly.

  13. Use of Hilbert Curves in Parallelized CUDA code: Interaction of Interstellar Atoms with the Heliosphere

    NASA Astrophysics Data System (ADS)

    Destefano, Anthony; Heerikhuisen, Jacob

    2015-04-01

    Fully 3D particle simulations can be a computationally and memory expensive task, especially when high resolution grid cells are required. The problem becomes further complicated when parallelization is needed. In this work we focus on computational methods to solve these difficulties. Hilbert curves are used to map the 3D particle space to the 1D contiguous memory space. This method of organization allows for minimized cache misses on the GPU as well as a sorted structure that is equivalent to an octal tree data structure. This type of sorted structure is attractive for uses in adaptive mesh implementations due to the logarithm search time. Implementations using the Message Passing Interface (MPI) library and NVIDIA's parallel computing platform CUDA will be compared, as MPI is commonly used on server nodes with many CPU's. We will also compare static grid structures with those of adaptive mesh structures. The physical test bed will be simulating heavy interstellar atoms interacting with a background plasma, the heliosphere, simulated from fully consistent coupled MHD/kinetic particle code. It is known that charge exchange is an important factor in space plasmas, specifically it modifies the structure of the heliosphere itself. We would like to thank the Alabama Supercomputer Authority for the use of their computational resources.

  14. Atomistic Simulations of High-intensity XFEL Pulses on Diffractive Imaging of Nano-sized System Dynamics

    NASA Astrophysics Data System (ADS)

    Ho, Phay; Knight, Christopher; Bostedt, Christoph; Young, Linda; Tegze, Miklos; Faigel, Gyula

    2016-05-01

    We have developed a large-scale atomistic computational method based on a combined Monte Carlo and Molecular Dynamics (MC/MD) method to simulate XFEL-induced radiation damage dynamics of complex materials. The MD algorithm is used to propagate the trajectories of electrons, ions and atoms forward in time and the quantum nature of interactions with an XFEL pulse is accounted for by a MC method to calculate probabilities of electronic transitions. Our code has good scalability with MPI/OpenMP parallelization, and it has been run on Mira, a petascale system at the Argonne Leardership Computing Facility, with particle number >50 million. Using this code, we have examined the impact of high-intensity 8-keV XFEL pulses on the x-ray diffraction patterns of argon clusters. The obtained patterns show strong pulse parameter dependence, providing evidence of significant lattice rearrangement and diffuse scattering. Real-space electronic reconstruction was performed using phase retrieval methods. We found that the structure of the argon cluster can be recovered with atomic resolution even in the presence of considerable radiation damage. This work was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Chemical Sciences, Geosciences, and Biosciences Division.

  15. A program to compute the two-step excitation of mesospheric sodium atoms for the Polychromatic Laser Guide Star Project

    NASA Astrophysics Data System (ADS)

    Bellanger, Véronique; Courcelle, Arnaud; Petit, Alain

    2004-09-01

    A program to compute the two-step excitation of sodium atoms ( 3S→3P→4D) using the density-matrix formalism is presented. The BEACON program calculates population evolution and the number of photons emitted by fluorescence from the 3P, 4D, 4P, 4S levels. Program summaryTitle of program: BEACON Catalogue identifier:ADSX Program Summary URL:http://cpc.cs.qub.ac.uk/cpc/summaries/ADSX Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Licensing provisions: none Operating systems under which the program has been tested: Win; Unix Programming language used: FORTRAN 77 Memory required to execute with typical data: 1 Mw Number of bits in a word: 32 Number of processors used: 1 (a parallel version of this code is also available and can be obtained on request) Number of lines in distributed program, including test data, etc.: 29 287 Number of bytes in distributed program, including test data, etc.: 830 331 Distribution format: tar.gz CPC Program Library subprograms used: none Nature of physical problem: Resolution of the Bloch equations in the case of the two-step laser excitation of sodium atoms. Method of solution: The program BEACON calculates the evolution of level population versus time using the density-matrix formalism. The number of photons emitted from the 3P, 4D and 4P levels is calculated using the branching ratios and the level lifetimes. Restriction on the complexity of the problem: Since the backscatter emission is calculated after the excitation process, excitation with laser pulse duration longer than the 4D level lifetime cannot be rigorously treated. Particularly, cw laser excitation cannot be calculated with this code. Typical running time:12 h

  16. Atomic Data for Nebular Abundance Determinations: Photoionization and Recombination Properties of Xenon Ions

    NASA Astrophysics Data System (ADS)

    Sterling, Nicholas C.; Kerlin, Austin B.

    2016-01-01

    We present preliminary results of a study of the photoionization (PI) and recombination properties of low-charge Xe ions. The abundances of neutron(n)-capture elements (atomic number Z > 30) are of interest in planetary nebulae (PNe) since they can be enriched by slow n-capture nucleosynthesis (the ``s-process'') in the progenitor asymptotic giant branch (AGB) stars. Xe is particularly valuable, because it is the most widely-observed ``heavy-s'' species (Z > 40) in PNe. Its abundance relative to lighter n-capture elements can be used to determine s-process neutron exposures, and constrain s-process enrichment patterns as a function of progenitor metallicity. Using the atomic structure code AUTOSTRUCTURE (Badnell 2011, Comp. Phys. Comm., 182, 1528), we have computed multi-configuration Breit-Pauli distorted-wave PI cross sections and radiative recombination (RR) and dielectronic recombination (DR) rate coefficients for neutral through six-times ionized Xe, data which are critically needed for accurate Xe abundance determinations in ionized nebulae. We find good agreement between our computed direct PI cross sections and experimental measurements. Internal uncertainties are estimated for our calculations by using three different configuration interaction expansions for each ion, and by testing the sensitivity of our results to the radial orbital scaling parameters. As found for other n-capture elements (Sterling & Witthoeft 2011, A&A, 529, A147; Sterling 2011, A&A, 533, A62), DR is the dominant recombination mechanism for Xe ions at nebular temperatures (~104 K). Following Sterling et al. (2015, ApJS, 218, 25), these data will be added to nebular modeling codes to compute ionization correction factors for unobserved Xe ions in PNe, which will enable elemental Xe abundances to be determined with much higher accuracy than is currently possible. This work is supported by NSF award AST-1412928.

  17. Expanding the capability of reaction-diffusion codes using pseudo traps and temperature partitioning: Applied to hydrogen uptake and release from tungsten

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Simmonds, M. J.; Yu, J. H.; Wang, Y. Q.

    Simulating the implantation and thermal desorption evolution in a reaction-diffusion model requires solving a set of coupled differential equations that describe the trapping and release of atomic species in Plasma Facing Materials (PFMs). These fundamental equations are well outlined by the Tritium Migration Analysis Program (TMAP) which can model systems with no more than three active traps per atomic species. To overcome this limitation, we have developed a Pseudo Trap and Temperature Partition (PTTP) scheme allowing us to lump multiple inactive traps into one pseudo trap, simplifying the system of equations to be solved. For all temperatures, we show themore » trapping of atoms from solute is exactly accounted for when using a pseudo trap. However, a single effective pseudo trap energy can not well replicate the release from multiple traps, each with its own detrapping energy. However, atoms held in a high energy trap will remain trapped at relatively low temperatures, and thus there is a temperature range in which release from high energy traps is effectively inactive. By partitioning the temperature range into segments, a pseudo trap can be defined for each segment to account for multiple high energy traps that are actively trapping but are effectively not releasing atoms. With increasing temperature, as in controlled thermal desorption, the lowest energy trap is nearly emptied and can be removed from the set of coupled equations, while the next higher energy trap becomes an actively releasing trap. Each segment is thus calculated sequentially, with the last time step of a given segment solution being used as an initial input for the next segment as only the pseudo and actively releasing traps are modeled. This PTTP scheme is then applied to experimental thermal desorption data for tungsten (W) samples damaged with heavy ions, which display six distinct release peaks during thermal desorption. Without modifying the TMAP7 source code the PTTP scheme is shown to successfully model the D retention in all six traps. In conclusion, we demonstrate the full reconstruction from the plasma implantation phase through the controlled thermal desorption phase with detrapping energies near 0.9, 1.1, 1.4, 1.7, 1.9 and 2.1 eV for a W sample damaged at room temperature.« less

  18. Expanding the capability of reaction-diffusion codes using pseudo traps and temperature partitioning: Applied to hydrogen uptake and release from tungsten

    DOE PAGES

    Simmonds, M. J.; Yu, J. H.; Wang, Y. Q.; ...

    2018-06-04

    Simulating the implantation and thermal desorption evolution in a reaction-diffusion model requires solving a set of coupled differential equations that describe the trapping and release of atomic species in Plasma Facing Materials (PFMs). These fundamental equations are well outlined by the Tritium Migration Analysis Program (TMAP) which can model systems with no more than three active traps per atomic species. To overcome this limitation, we have developed a Pseudo Trap and Temperature Partition (PTTP) scheme allowing us to lump multiple inactive traps into one pseudo trap, simplifying the system of equations to be solved. For all temperatures, we show themore » trapping of atoms from solute is exactly accounted for when using a pseudo trap. However, a single effective pseudo trap energy can not well replicate the release from multiple traps, each with its own detrapping energy. However, atoms held in a high energy trap will remain trapped at relatively low temperatures, and thus there is a temperature range in which release from high energy traps is effectively inactive. By partitioning the temperature range into segments, a pseudo trap can be defined for each segment to account for multiple high energy traps that are actively trapping but are effectively not releasing atoms. With increasing temperature, as in controlled thermal desorption, the lowest energy trap is nearly emptied and can be removed from the set of coupled equations, while the next higher energy trap becomes an actively releasing trap. Each segment is thus calculated sequentially, with the last time step of a given segment solution being used as an initial input for the next segment as only the pseudo and actively releasing traps are modeled. This PTTP scheme is then applied to experimental thermal desorption data for tungsten (W) samples damaged with heavy ions, which display six distinct release peaks during thermal desorption. Without modifying the TMAP7 source code the PTTP scheme is shown to successfully model the D retention in all six traps. In conclusion, we demonstrate the full reconstruction from the plasma implantation phase through the controlled thermal desorption phase with detrapping energies near 0.9, 1.1, 1.4, 1.7, 1.9 and 2.1 eV for a W sample damaged at room temperature.« less

  19. JDFTx: Software for joint density-functional theory

    DOE PAGES

    Sundararaman, Ravishankar; Letchworth-Weaver, Kendra; Schwarz, Kathleen A.; ...

    2017-11-14

    Density-functional theory (DFT) has revolutionized computational prediction of atomic-scale properties from first principles in physics, chemistry and materials science. Continuing development of new methods is necessary for accurate predictions of new classes of materials and properties, and for connecting to nano- and mesoscale properties using coarse-grained theories. JDFTx is a fully-featured open-source electronic DFT software designed specifically to facilitate rapid development of new theories, models and algorithms. Using an algebraic formulation as an abstraction layer, compact C++11 code automatically performs well on diverse hardware including GPUs (Graphics Processing Units). This code hosts the development of joint density-functional theory (JDFT) thatmore » combines electronic DFT with classical DFT and continuum models of liquids for first-principles calculations of solvated and electrochemical systems. In addition, the modular nature of the code makes it easy to extend and interface with, facilitating the development of multi-scale toolkits that connect to ab initio calculations, e.g. photo-excited carrier dynamics combining electron and phonon calculations with electromagnetic simulations.« less

  20. JDFTx: Software for joint density-functional theory

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Sundararaman, Ravishankar; Letchworth-Weaver, Kendra; Schwarz, Kathleen A.

    Density-functional theory (DFT) has revolutionized computational prediction of atomic-scale properties from first principles in physics, chemistry and materials science. Continuing development of new methods is necessary for accurate predictions of new classes of materials and properties, and for connecting to nano- and mesoscale properties using coarse-grained theories. JDFTx is a fully-featured open-source electronic DFT software designed specifically to facilitate rapid development of new theories, models and algorithms. Using an algebraic formulation as an abstraction layer, compact C++11 code automatically performs well on diverse hardware including GPUs (Graphics Processing Units). This code hosts the development of joint density-functional theory (JDFT) thatmore » combines electronic DFT with classical DFT and continuum models of liquids for first-principles calculations of solvated and electrochemical systems. In addition, the modular nature of the code makes it easy to extend and interface with, facilitating the development of multi-scale toolkits that connect to ab initio calculations, e.g. photo-excited carrier dynamics combining electron and phonon calculations with electromagnetic simulations.« less

  1. High-Throughput Characterization of Porous Materials Using Graphics Processing Units

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kim, Jihan; Martin, Richard L.; Rübel, Oliver

    We have developed a high-throughput graphics processing units (GPU) code that can characterize a large database of crystalline porous materials. In our algorithm, the GPU is utilized to accelerate energy grid calculations where the grid values represent interactions (i.e., Lennard-Jones + Coulomb potentials) between gas molecules (i.e., CHmore » $$_{4}$$ and CO$$_{2}$$) and material's framework atoms. Using a parallel flood fill CPU algorithm, inaccessible regions inside the framework structures are identified and blocked based on their energy profiles. Finally, we compute the Henry coefficients and heats of adsorption through statistical Widom insertion Monte Carlo moves in the domain restricted to the accessible space. The code offers significant speedup over a single core CPU code and allows us to characterize a set of porous materials at least an order of magnitude larger than ones considered in earlier studies. For structures selected from such a prescreening algorithm, full adsorption isotherms can be calculated by conducting multiple grand canonical Monte Carlo simulations concurrently within the GPU.« less

  2. Verification of combined thermal-hydraulic and heat conduction analysis code FLOWNET/TRUMP

    NASA Astrophysics Data System (ADS)

    Maruyama, Soh; Fujimoto, Nozomu; Kiso, Yoshihiro; Murakami, Tomoyuki; Sudo, Yukio

    1988-09-01

    This report presents the verification results of the combined thermal-hydraulic and heat conduction analysis code, FLOWNET/TRUMP which has been utilized for the core thermal hydraulic design, especially for the analysis of flow distribution among fuel block coolant channels, the determination of thermal boundary conditions for fuel block stress analysis and the estimation of fuel temperature in the case of fuel block coolant channel blockage accident in the design of the High Temperature Engineering Test Reactor(HTTR), which the Japan Atomic Energy Research Institute has been planning to construct in order to establish basic technologies for future advanced very high temperature gas-cooled reactors and to be served as an irradiation test reactor for promotion of innovative high temperature new frontier technologies. The verification of the code was done through the comparison between the analytical results and experimental results of the Helium Engineering Demonstration Loop Multi-channel Test Section(HENDEL T(sub 1-M)) with simulated fuel rods and fuel blocks.

  3. Coupling molecular dynamics with lattice Boltzmann method based on the immersed boundary method

    NASA Astrophysics Data System (ADS)

    Tan, Jifu; Sinno, Talid; Diamond, Scott

    2017-11-01

    The study of viscous fluid flow coupled with rigid or deformable solids has many applications in biological and engineering problems, e.g., blood cell transport, drug delivery, and particulate flow. We developed a partitioned approach to solve this coupled Multiphysics problem. The fluid motion was solved by Palabos (Parallel Lattice Boltzmann Solver), while the solid displacement and deformation was simulated by LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator). The coupling was achieved through the immersed boundary method (IBM). The code modeled both rigid and deformable solids exposed to flow. The code was validated with the classic problem of rigid ellipsoid particle orbit in shear flow, blood cell stretching test and effective blood viscosity, and demonstrated essentially linear scaling over 16 cores. An example of the fluid-solid coupling was given for flexible filaments (drug carriers) transport in a flowing blood cell suspensions, highlighting the advantages and capabilities of the developed code. NIH 1U01HL131053-01A1.

  4. Measurement of the intensity ratio of Auger and conversion electrons for the electron capture decay of 125I.

    PubMed

    Alotiby, M; Greguric, I; Kibédi, T; Lee, B Q; Roberts, M; Stuchbery, A E; Tee, Pi; Tornyi, T; Vos, M

    2018-03-21

    Auger electrons emitted after nuclear decay have potential application in targeted cancer therapy. For this purpose it is important to know the Auger electron yield per nuclear decay. In this work we describe a measurement of the ratio of the number of conversion electrons (emitted as part of the nuclear decay process) to the number of Auger electrons (emitted as part of the atomic relaxation process after the nuclear decay) for the case of 125 I. Results are compared with Monte-Carlo type simulations of the relaxation cascade using the BrIccEmis code. Our results indicate that for 125 I the calculations based on rates from the Evaluated Atomic Data Library underestimate the K Auger yields by 20%.

  5. Application of the R-matrix method to photoionization of molecules.

    PubMed

    Tashiro, Motomichi

    2010-04-07

    The R-matrix method has been used for theoretical calculation of electron collision with atoms and molecules for long years. The method was also formulated to treat photoionization process, however, its application has been mostly limited to photoionization of atoms. In this work, we implement the R-matrix method to treat molecular photoionization problem based on the UK R-matrix codes. This method can be used for diatomic as well as polyatomic molecules, with multiconfigurational description for electronic states of both target neutral molecule and product molecular ion. Test calculations were performed for valence electron photoionization of nitrogen (N(2)) as well as nitric oxide (NO) molecules. Calculated photoionization cross sections and asymmetry parameters agree reasonably well with the available experimental results, suggesting usefulness of the method for molecular photoionization.

  6. Measurement of the intensity ratio of Auger and conversion electrons for the electron capture decay of 125I

    NASA Astrophysics Data System (ADS)

    Alotiby, M.; Greguric, I.; Kibédi, T.; Lee, B. Q.; Roberts, M.; Stuchbery, A. E.; Tee, Pi; Tornyi, T.; Vos, M.

    2018-03-01

    Auger electrons emitted after nuclear decay have potential application in targeted cancer therapy. For this purpose it is important to know the Auger electron yield per nuclear decay. In this work we describe a measurement of the ratio of the number of conversion electrons (emitted as part of the nuclear decay process) to the number of Auger electrons (emitted as part of the atomic relaxation process after the nuclear decay) for the case of 125I. Results are compared with Monte-Carlo type simulations of the relaxation cascade using the BrIccEmis code. Our results indicate that for 125I the calculations based on rates from the Evaluated Atomic Data Library underestimate the K Auger yields by 20%.

  7. Systematic Comparison of Photoionized Plasma Codes with Application to Spectroscopic Studies of AGN in X-Rays

    NASA Technical Reports Server (NTRS)

    Mehdipour, M.; Kaastra, J. S.; Kallman, T.

    2016-01-01

    Atomic data and plasma models play a crucial role in the diagnosis and interpretation of astrophysical spectra, thus influencing our understanding of the Universe. In this investigation we present a systematic comparison of the leading photoionization codes to determine how much their intrinsic differences impact X-ray spectroscopic studies of hot plasmas in photoionization equilibrium. We carry out our computations using the Cloudy, SPEX, and XSTAR photoionization codes, and compare their derived thermal and ionization states for various ionizing spectral energy distributions. We examine the resulting absorption-line spectra from these codes for the case of ionized outflows in active galactic nuclei. By comparing the ionic abundances as a function of ionization parameter, we find that on average there is about 30 deviation between the codes in where ionic abundances peak. For H-like to B-like sequence ions alone, this deviation in is smaller at about 10 on average. The comparison of the absorption-line spectra in the X-ray band shows that there is on average about 30 deviation between the codes in the optical depth of the lines produced at log 1 to 2, reducing to about 20 deviation at log 3. We also simulate spectra of the ionized outflows with the current and upcoming high-resolution X-ray spectrometers, on board XMM-Newton, Chandra, Hitomi, and Athena. From these simulations we obtain the deviation on the best-fit model parameters, arising from the use of different photoionization codes, which is about 10 to40. We compare the modeling uncertainties with the observational uncertainties from the simulations. The results highlight the importance of continuous development and enhancement of photoionization codes for the upcoming era of X-ray astronomy with Athena.

  8. Modeling of Flow Blockage in a Liquid Metal-Cooled Reactor Subassembly with a Subchannel Analysis Code

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Jeong, Hae-Yong; Ha, Kwi-Seok; Chang, Won-Pyo

    The local blockage in a subassembly of a liquid metal-cooled reactor (LMR) is of importance to the plant safety because of the compact design and the high power density of the core. To analyze the thermal-hydraulic parameters in a subassembly of a liquid metal-cooled reactor with a flow blockage, the Korea Atomic Energy Research Institute has developed the MATRA-LMR-FB code. This code uses the distributed resistance model to describe the sweeping flow formed by the wire wrap around the fuel rods and to model the recirculation flow after a blockage. The hybrid difference scheme is also adopted for the descriptionmore » of the convective terms in the recirculating wake region of low velocity. Some state-of-the-art turbulent mixing models were implemented in the code, and the models suggested by Rehme and by Zhukov are analyzed and found to be appropriate for the description of the flow blockage in an LMR subassembly. The MATRA-LMR-FB code predicts accurately the experimental data of the Oak Ridge National Laboratory 19-pin bundle with a blockage for both the high-flow and low-flow conditions. The influences of the distributed resistance model, the hybrid difference method, and the turbulent mixing models are evaluated step by step with the experimental data. The appropriateness of the models also has been evaluated through a comparison with the results from the COMMIX code calculation. The flow blockage for the KALIMER design has been analyzed with the MATRA-LMR-FB code and is compared with the SABRE code to guarantee the design safety for the flow blockage.« less

  9. A first principles study of the electronic structure, elastic and thermal properties of UB2

    NASA Astrophysics Data System (ADS)

    Jossou, Ericmoore; Malakkal, Linu; Szpunar, Barbara; Oladimeji, Dotun; Szpunar, Jerzy A.

    2017-07-01

    Uranium diboride (UB2) has been widely deployed for refractory use and is a proposed material for Accident Tolerant Fuel (ATF) due to its high thermal conductivity. However, the applicability of UB2 towards high temperature usage in a nuclear reactor requires the need to investigate the thermomechanical properties, and recent studies have failed in highlighting applicable properties. In this work, we present an in-depth theoretical outlook of the structural and thermophysical properties of UB2, including but not limited to elastic, electronic and thermal transport properties. These calculations were performed within the framework of Density Functional Theory (DFT) + U approach, using Quantum ESPRESSO (QE) code considering the addition of Coulomb correlations on the uranium atom. The phonon spectra and elastic constant analysis show the dynamic and mechanical stability of UB2 structure respectively. The electronic structure of UB2 was investigated using full potential linear augmented plane waves plus local orbitals method (FP-LAPW+lo) as implemented in WIEN2k code. The absence of a band gap in the total and partial density of states confirms the metallic nature while the valence electron density plot reveals the presence of covalent bond between adjacent B-B atoms. We predicted the lattice thermal conductivity (kL) by solving Boltzmann Transport Equation (BTE) using ShengBTE. The second order harmonic and third-order anharmonic interatomic force constants required as input to ShengBTE was calculated using the Density-functional perturbation theory (DFPT). However, we predicted the electronic thermal conductivity (kel) using Wiedemann-Franz law as implemented in Boltztrap code. We also show that the sound velocity along 'a' and 'c' axes exhibit high anisotropy, which accounts for the anisotropic thermal conductivity of UB2.

  10. GPU Acceleration of the Locally Selfconsistent Multiple Scattering Code for First Principles Calculation of the Ground State and Statistical Physics of Materials

    NASA Astrophysics Data System (ADS)

    Eisenbach, Markus

    The Locally Self-consistent Multiple Scattering (LSMS) code solves the first principles Density Functional theory Kohn-Sham equation for a wide range of materials with a special focus on metals, alloys and metallic nano-structures. It has traditionally exhibited near perfect scalability on massively parallel high performance computer architectures. We present our efforts to exploit GPUs to accelerate the LSMS code to enable first principles calculations of O(100,000) atoms and statistical physics sampling of finite temperature properties. Using the Cray XK7 system Titan at the Oak Ridge Leadership Computing Facility we achieve a sustained performance of 14.5PFlop/s and a speedup of 8.6 compared to the CPU only code. This work has been sponsored by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, Material Sciences and Engineering Division and by the Office of Advanced Scientific Computing. This work used resources of the Oak Ridge Leadership Computing Facility, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC05-00OR22725.

  11. Simulated Raman Spectral Analysis of Organic Molecules

    NASA Astrophysics Data System (ADS)

    Lu, Lu

    The advent of the laser technology in the 1960s solved the main difficulty of Raman spectroscopy, resulted in simplified Raman spectroscopy instruments and also boosted the sensitivity of the technique. Up till now, Raman spectroscopy is commonly used in chemistry and biology. As vibrational information is specific to the chemical bonds, Raman spectroscopy provides fingerprints to identify the type of molecules in the sample. In this thesis, we simulate the Raman Spectrum of organic and inorganic materials by General Atomic and Molecular Electronic Structure System (GAMESS) and Gaussian, two computational codes that perform several general chemistry calculations. We run these codes on our CPU-based high-performance cluster (HPC). Through the message passing interface (MPI), a standardized and portable message-passing system which can make the codes run in parallel, we are able to decrease the amount of time for computation and increase the sizes and capacities of systems simulated by the codes. From our simulations, we will set up a database that allows search algorithm to quickly identify N-H and O-H bonds in different materials. Our ultimate goal is to analyze and identify the spectra of organic matter compositions from meteorites and compared these spectra with terrestrial biologically-produced amino acids and residues.

  12. NEQAIR96,Nonequilibrium and Equilibrium Radiative Transport and Spectra Program: User's Manual

    NASA Technical Reports Server (NTRS)

    Whiting, Ellis E.; Park, Chul; Liu, Yen; Arnold, James O.; Paterson, John A.

    1996-01-01

    This document is the User's Manual for a new version of the NEQAIR computer program, NEQAIR96. The program is a line-by-line and a line-of-sight code. It calculates the emission and absorption spectra for atomic and diatomic molecules and the transport of radiation through a nonuniform gas mixture to a surface. The program has been rewritten to make it easy to use, run faster, and include many run-time options that tailor a calculation to the user's requirements. The accuracy and capability have also been improved by including the rotational Hamiltonian matrix formalism for calculating rotational energy levels and Hoenl-London factors for dipole and spin-allowed singlet, doublet, triplet, and quartet transitions. Three sample cases are also included to help the user become familiar with the steps taken to produce a spectrum. A new user interface is included that uses check location, to select run-time options and to enter selected run data, making NEQAIR96 easier to use than the older versions of the code. The ease of its use and the speed of its algorithms make NEQAIR96 a valuable educational code as well as a practical spectroscopic prediction and diagnostic code.

  13. Fundamental approaches for analysis thermal hydraulic parameter for Puspati Research Reactor

    NASA Astrophysics Data System (ADS)

    Hashim, Zaredah; Lanyau, Tonny Anak; Farid, Mohamad Fairus Abdul; Kassim, Mohammad Suhaimi; Azhar, Noraishah Syahirah

    2016-01-01

    The 1-MW PUSPATI Research Reactor (RTP) is the one and only nuclear pool type research reactor developed by General Atomic (GA) in Malaysia. It was installed at Malaysian Nuclear Agency and has reached the first criticality on 8 June 1982. Based on the initial core which comprised of 80 standard TRIGA fuel elements, the very fundamental thermal hydraulic model was investigated during steady state operation using the PARET-code. The main objective of this paper is to determine the variation of temperature profiles and Departure of Nucleate Boiling Ratio (DNBR) of RTP at full power operation. The second objective is to confirm that the values obtained from PARET-code are in agreement with Safety Analysis Report (SAR) for RTP. The code was employed for the hot and average channels in the core in order to calculate of fuel's center and surface, cladding, coolant temperatures as well as DNBR's values. In this study, it was found that the results obtained from the PARET-code showed that the thermal hydraulic parameters related to safety for initial core which was cooled by natural convection was in agreement with the designed values and safety limit in SAR.

  14. Comparison of computational results of the SABRE LMFBR pin bundle blockage code with data from well-instrumented out-of-pile test bundles (THORS bundles 3A and 5A)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Dearing, J.F.

    The Subchannel Analysis of Blockages in Reactor Elements (SABRE) computer code, developed by the United Kingdom Atomic Energy Authority, is currently the only practical tool available for performing detailed analyses of velocity and temperature fields in the recirculating flow regions downstream of blockages in liquid-metal fast breeder reactor (LMFBR) pin bundles. SABRE is a subchannel analysis code; that is, it accurately represents the complex geometry of nuclear fuel pins arranged on a triangular lattice. The results of SABRE computational models are compared here with temperature data from two out-of-pile 19-pin test bundles from the Thermal-Hydraulic Out-of-Reactor Safety (THORS) Facility atmore » Oak Ridge National Laboratory. One of these bundles has a small central flow blockage (bundle 3A), while the other has a large edge blockage (bundle 5A). Values that give best agreement with experiment for the empirical thermal mixing correlation factor, FMIX, in SABRE are suggested. These values of FMIX are Reynolds-number dependent, however, indicating that the coded turbulent mixing correlation is not appropriate for wire-wrap pin bundles.« less

  15. DOE Office of Scientific and Technical Information (OSTI.GOV)

    Arnold H. Kritz

    PTRANSP, which is the predictive version of the TRANSP code, was developed in a collaborative effort involving the Princeton Plasma Physics Laboratory, General Atomics Corporation, Lawrence Livermore National Laboratory, and Lehigh University. The PTRANSP/TRANSP suite of codes is the premier integrated tokamak modeling software in the United States. A production service for PTRANSP/TRANSP simulations is maintained at the Princeton Plasma Physics Laboratory; the server has a simple command line client interface and is subscribed to by about 100 researchers from tokamak projects in the US, Europe, and Asia. This service produced nearly 13000 PTRANSP/TRANSP simulations in the four year periodmore » FY 2005 through FY 2008. Major archives of TRANSP results are maintained at PPPL, MIT, General Atomics, and JET. Recent utilization, counting experimental analysis simulations as well as predictive simulations, more than doubled from slightly over 2000 simulations per year in FY 2005 and FY 2006 to over 4300 simulations per year in FY 2007 and FY 2008. PTRANSP predictive simulations applied to ITER increased eight fold from 30 simulations per year in FY 2005 and FY 2006 to 240 simulations per year in FY 2007 and FY 2008, accounting for more than half of combined PTRANSP/TRANSP service CPU resource utilization in FY 2008. PTRANSP studies focused on ITER played a key role in journal articles. Examples of validation studies carried out for momentum transport in PTRANSP simulations were presented at the 2008 IAEA conference. The increase in number of PTRANSP simulations has continued (more than 7000 TRANSP/PTRANSP simulations in 2010) and results of PTRANSP simulations appear in conference proceedings, for example the 2010 IAEA conference, and in peer reviewed papers. PTRANSP provides a bridge to the Fusion Simulation Program (FSP) and to the future of integrated modeling. Through years of widespread usage, each of the many parts of the PTRANSP suite of codes has been thoroughly validated against experimental data and benchmarked against other codes. At the same time, architectural modernizations are improving the modularity of the PTRANSP code base. The NUBEAM neutral beam and fusion products fast ion model, the Plasma State data repository (developed originally in the SWIM SciDAC project and adapted for use in PTRANSP), and other components are already shared with the SWIM, FACETS, and CPES SciDAC FSP prototype projects. Thus, the PTRANSP code is already serving as a bridge between our present integrated modeling capability and future capability. As the Fusion Simulation Program builds toward the facility currently available in the PTRANSP suite of codes, early versions of the FSP core plasma model will need to be benchmarked against the PTRANSP simulations. This will be necessary to build user confidence in FSP, but this benchmarking can only be done if PTRANSP itself is maintained and developed.« less

  16. Classical theory of atomic collisions - The first hundred years

    NASA Astrophysics Data System (ADS)

    Grujić, Petar V.

    2012-05-01

    Classical calculations of the atomic processes started in 1911 with famous Rutherford's evaluation of the differential cross section for α particles scattered on foil atoms [1]. The success of these calculations was soon overshadowed by the rise of Quantum Mechanics in 1925 and its triumphal success in describing processes at the atomic and subatomic levels. It was generally recognized that the classical approach should be inadequate and it was neglected until 1953, when the famous paper by Gregory Wannier appeared, in which the threshold law for the single ionization cross section behaviour by electron impact was derived. All later calculations and experimental studies confirmed the law derived by purely classical theory. The next step was taken by Ian Percival and collaborators in 60s, who developed a general classical three-body computer code, which was used by many researchers in evaluating various atomic processes like ionization, excitation, detachment, dissociation, etc. Another approach was pursued by Michal Gryzinski from Warsaw, who started a far reaching programme for treating atomic particles and processes as purely classical objects [2]. Though often criticized for overestimating the domain of the classical theory, results of his group were able to match many experimental data. Belgrade group was pursuing the classical approach using both analytical and numerical calculations, studying a number of atomic collisions, in particular near-threshold processes. Riga group, lead by Modris Gailitis [3], contributed considerably to the field, as it was done by Valentin Ostrovsky and coworkers from Sanct Petersbourg, who developed powerful analytical methods within purely classical mechanics [4]. We shall make an overview of these approaches and show some of the remarkable results, which were subsequently confirmed by semiclassical and quantum mechanical calculations, as well as by the experimental evidence. Finally we discuss the theoretical and epistemological background of the classical calculations and explain why these turned out so successful, despite the essentially quantum nature of the atomic and subatomic systems.

  17. On the importance of local orbitals using second energy derivatives for d and f electrons

    NASA Astrophysics Data System (ADS)

    Karsai, Ferenc; Tran, Fabien; Blaha, Peter

    2017-11-01

    The all-electron linearized augmented plane wave (LAPW) methods are among the most accurate to solve the Kohn-Sham equations of density functional theory for periodic solids. In the LAPW methods, the unit cell is partitioned into spheres surrounding the atoms, inside which the wave functions are expanded into spherical harmonics, and the interstitial region, where the wave functions are expanded in Fourier series. Recently, Michalicek et al. (2013) reported an analysis of the so-called linearization error, which is inherent to the basis functions inside the spheres, and advocated the use of local orbital basis functions involving the second energy derivative of the radial part (HDLO). In the present work, we report the implementation of such basis functions into the WIEN2k code, and discuss in detail the improvement in terms of accuracy. From our tests, which involve atoms from the whole periodic table, it is concluded that for ground-state properties (e.g., equilibrium volume) the use of HDLO is necessary only for atoms with d or f electrons in the valence and large atomic spheres. For unoccupied states which are not too high above the Fermi energy, HDLO systematically improve the band structure, which may be of importance for the calculation of optical properties.

  18. IAEA activities on atomic, molecular and plasma-material interaction data for fusion

    NASA Astrophysics Data System (ADS)

    Braams, Bastiaan J.; Chung, Hyun-Kyung

    2013-09-01

    The IAEA Atomic and Molecular Data Unit (http://www-amdis.iaea.org/) aims to provide internationally evaluated and recommended data for atomic, molecular and plasma-material interaction (A+M+PMI) processes in fusion research. The Unit organizes technical meetings and coordinates an A+M Data Centre Network (DCN) and a Code Centre Network (CCN). In addition the Unit organizes Coordinated Research Projects (CRPs), for which the objectives are mixed between development of new data and evaluation and recommendation of existing data. In the area of A+M data we are placing new emphasis in our meeting schedule on data evaluation and especially on uncertainties in calculated cross section data and the propagation of uncertainties through structure data and fundamental cross sections to effective rate coefficients. Following a recent meeting of the CCN it is intended to use electron scattering on Be, Ne and N2 as exemplars for study of uncertainties and uncertainty propagation in calculated data; this will be discussed further at the presentation. Please see http://www-amdis.iaea.org/CRP/ for more on our active and planned CRPs, which are concerned with atomic processes in core and edge plasma and with plasma interaction with beryllium-based surfaces and with irradiated tungsten.

  19. How localized is ``local?'' Efficiency vs. accuracy of O(N) domain decomposition in local orbital based all-electron electronic structure theory

    NASA Astrophysics Data System (ADS)

    Havu, Vile; Blum, Volker; Scheffler, Matthias

    2007-03-01

    Numeric atom-centered local orbitals (NAO) are efficient basis sets for all-electron electronic structure theory. The locality of NAO's can be exploited to render (in principle) all operations of the self-consistency cycle O(N). This is straightforward for 3D integrals using domain decomposition into spatially close subsets of integration points, enabling critical computational savings that are effective from ˜tens of atoms (no significant overhead for smaller systems) and make large systems (100s of atoms) computationally feasible. Using a new all-electron NAO-based code,^1 we investigate the quantitative impact of exploiting this locality on two distinct classes of systems: Large light-element molecules [Alanine-based polypeptide chains (Ala)n], and compact transition metal clusters. Strict NAO locality is achieved by imposing a cutoff potential with an onset radius rc, and exploited by appropriately shaped integration domains (subsets of integration points). Conventional tight rc<= 3å have no measurable accuracy impact in (Ala)n, but introduce inaccuracies of 20-30 meV/atom in Cun. The domain shape impacts the computational effort by only 10-20 % for reasonable rc. ^1 V. Blum, R. Gehrke, P. Havu, V. Havu, M. Scheffler, The FHI Ab Initio Molecular Simulations (aims) Project, Fritz-Haber-Institut, Berlin (2006).

  20. Statistical radii associated with amino acids to determine the contact map: fixing the structure of a type I cohesin domain in the Clostridium thermocellum cellulosome

    NASA Astrophysics Data System (ADS)

    Chwastyk, Mateusz; Poma Bernaola, Adolfo; Cieplak, Marek

    2015-07-01

    We propose to improve and simplify protein refinement procedures through consideration of which pairs of amino acid residues should form native contacts. We first consider 11 330 proteins from the CATH database to determine statistical distributions of contacts associated with a given type of amino acid. The distributions are set across the distances between the α-C atoms that are in contact. Based on this data, we determine typical radii of effective spheres that can be placed on the α-C atoms in order to reconstruct the distribution of the contact lengths. This is done by checking for overlaps with enlarged van der Waals spheres associated with heavy atoms on other amino acids. The resulting contacts can be used to identify non-native contacts that may arise during the time evolution of structure-based models. Here, the radii are used to guide reconstruction of nine missing side chains in a type I cohesin domain with the Protein Data Bank code 1AOH. We first identify the likely missing contacts and then sculpt the corresponding side chains by standard refinement tools to achieve consistency with the expected contact map. One ambiguity in refinement is resolved by determining all-atom conformational energies.

  1. Geophysical Plasmas and Atmospheric Modeling.

    DTIC Science & Technology

    1982-01-01

    analysis of structuring observed in the STARFISH event and early time structure formation in the LWIR predicted for a standard event, (2) IR structure...for the LWIR problem, the SCORPIO code was coupled to a numerical module which describes the behavior of the Rayleigh-Taylor insta- bility, as discussed...the LWIR C1-14p) induced by sunlight and earthshine. Of the constituents in nuclear debris the uranium atom is of particular interest because it

  2. Investigation of Electron Impact Processes Relevant to Visible Lasers

    DTIC Science & Technology

    1976-04-01

    Projecta Agency, 1400 Wilson Boulevard. Arlington, Virginia. Attn: Program Management (2 copies) Director, Naval Reaearch Laboratory, Washin...M *•’ , — ■■ FOREWORD Contract No. : N00014-75-C-0064 ARPA Order No, : 1806 Program Code No. : 5E20 Short Title of Work: Lead Atom...Bo„eSs, (617)389-3000. Ext. 451 Scientlftc Officer: Dlreetor, Phy.lc. Program , Phy5leal Selenees Division 01 Office of Naval Research

  3. The Potential of Micro Electro Mechanical Systems and Nanotechnology for the U.S. Army

    DTIC Science & Technology

    2001-05-01

    Quantitative Structure Activity Relationship ( QSAR ) model . The QSAR model calculates the proper composition of the polymer-carbon black matrix...example, the BEI Gyrochip Model QRS11 from Systron Donner Inertial Division has a startup time of less than 1 second, a Mean Time Between Failure (MTBF... modeling from many equations per atom to a few lines of code. This approach is amenable to parallel processing. Nevertheless, their programs require

  4. Simulation of plasma loading of high-pressure RF cavities

    NASA Astrophysics Data System (ADS)

    Yu, K.; Samulyak, R.; Yonehara, K.; Freemire, B.

    2018-01-01

    Muon beam-induced plasma loading of radio-frequency (RF) cavities filled with high pressure hydrogen gas with 1% dry air dopant has been studied via numerical simulations. The electromagnetic code SPACE, that resolves relevant atomic physics processes, including ionization by the muon beam, electron attachment to dopant molecules, and electron-ion and ion-ion recombination, has been used. Simulations studies have been performed in the range of parameters typical for practical muon cooling channels.

  5. CFD Simulation of Liquid Rocket Engine Injectors

    NASA Technical Reports Server (NTRS)

    Farmer, Richard; Cheng, Gary; Chen, Yen-Sen; Garcia, Roberto (Technical Monitor)

    2001-01-01

    Detailed design issues associated with liquid rocket engine injectors and combustion chamber operation require CFD methodology which simulates highly three-dimensional, turbulent, vaporizing, and combusting flows. The primary utility of such simulations involves predicting multi-dimensional effects caused by specific injector configurations. SECA, Inc. and Engineering Sciences, Inc. have been developing appropriate computational methodology for NASA/MSFC for the past decade. CFD tools and computers have improved dramatically during this time period; however, the physical submodels used in these analyses must still remain relatively simple in order to produce useful results. Simulations of clustered coaxial and impinger injector elements for hydrogen and hydrocarbon fuels, which account for real fluid properties, is the immediate goal of this research. The spray combustion codes are based on the FDNS CFD code' and are structured to represent homogeneous and heterogeneous spray combustion. The homogeneous spray model treats the flow as a continuum of multi-phase, multicomponent fluids which move without thermal or velocity lags between the phases. Two heterogeneous models were developed: (1) a volume-of-fluid (VOF) model which represents the liquid core of coaxial or impinger jets and their atomization and vaporization, and (2) a Blob model which represents the injected streams as a cloud of droplets the size of the injector orifice which subsequently exhibit particle interaction, vaporization, and combustion. All of these spray models are computationally intensive, but this is unavoidable to accurately account for the complex physics and combustion which is to be predicted, Work is currently in progress to parallelize these codes to improve their computational efficiency. These spray combustion codes were used to simulate the three test cases which are the subject of the 2nd International Workshop on-Rocket Combustion Modeling. Such test cases are considered by these investigators to be very valuable for code validation because combustion kinetics, turbulence models and atomization models based on low pressure experiments of hydrogen air combustion do not adequately verify analytical or CFD submodels which are necessary to simulate rocket engine combustion. We wish to emphasize that the simulations which we prepared for this meeting are meant to test the accuracy of the approximations used in our general purpose spray combustion models, rather than represent a definitive analysis of each of the experiments which were conducted. Our goal is to accurately predict local temperatures and mixture ratios in rocket engines; hence predicting individual experiments is used only for code validation. To replace the conventional JANNAF standard axisymmetric finite-rate (TDK) computer code 2 for performance prediction with CFD cases, such codes must posses two features. Firstly, they must be as easy to use and of comparable run times for conventional performance predictions. Secondly, they must provide more detailed predictions of the flowfields near the injector face. Specifically, they must accurately predict the convective mixing of injected liquid propellants in terms of the injector element configurations.

  6. SPECT3D - A multi-dimensional collisional-radiative code for generating diagnostic signatures based on hydrodynamics and PIC simulation output

    NASA Astrophysics Data System (ADS)

    MacFarlane, J. J.; Golovkin, I. E.; Wang, P.; Woodruff, P. R.; Pereyra, N. A.

    2007-05-01

    SPECT3D is a multi-dimensional collisional-radiative code used to post-process the output from radiation-hydrodynamics (RH) and particle-in-cell (PIC) codes to generate diagnostic signatures (e.g. images, spectra) that can be compared directly with experimental measurements. This ability to post-process simulation code output plays a pivotal role in assessing the reliability of RH and PIC simulation codes and their physics models. SPECT3D has the capability to operate on plasmas in 1D, 2D, and 3D geometries. It computes a variety of diagnostic signatures that can be compared with experimental measurements, including: time-resolved and time-integrated spectra, space-resolved spectra and streaked spectra; filtered and monochromatic images; and X-ray diode signals. Simulated images and spectra can include the effects of backlighters, as well as the effects of instrumental broadening and time-gating. SPECT3D also includes a drilldown capability that shows where frequency-dependent radiation is emitted and absorbed as it propagates through the plasma towards the detector, thereby providing insights on where the radiation seen by a detector originates within the plasma. SPECT3D has the capability to model a variety of complex atomic and radiative processes that affect the radiation seen by imaging and spectral detectors in high energy density physics (HEDP) experiments. LTE (local thermodynamic equilibrium) or non-LTE atomic level populations can be computed for plasmas. Photoabsorption rates can be computed using either escape probability models or, for selected 1D and 2D geometries, multi-angle radiative transfer models. The effects of non-thermal (i.e. non-Maxwellian) electron distributions can also be included. To study the influence of energetic particles on spectra and images recorded in intense short-pulse laser experiments, the effects of both relativistic electrons and energetic proton beams can be simulated. SPECT3D is a user-friendly software package that runs on Windows, Linux, and Mac platforms. A parallel version of SPECT3D is supported for Linux clusters for large-scale calculations. We will discuss the major features of SPECT3D, and present example results from simulations and comparisons with experimental data.

  7. Atomic Processes for XUV Lasers: Alkali Atoms and Ions

    NASA Astrophysics Data System (ADS)

    Dimiduk, David Paul

    The development of extreme ultraviolet (XUV) lasers is dependent upon knowledge of processes in highly excited atoms. Described here are spectroscopy experiments which have identified and characterized certain autoionizing energy levels in core-excited alkali atoms and ions. Such levels, termed quasi-metastable, have desirable characteristics as upper levels for efficient, powerful XUV lasers. Quasi -metastable levels are among the most intense emission lines in the XUV spectra of core-excited alkalis. Laser experiments utilizing these levels have proved to be useful in characterizing other core-excited levels. Three experiments to study quasi-metastable levels are reported. The first experiment is vacuum ultraviolet (VUV) absorption spectroscopy on the Cs 109 nm transitions using high-resolution laser techniques. This experiment confirms the identification of transitions to a quasi-metastable level, estimates transition oscillator strengths, and estimates the hyperfine splitting of the quasi-metastable level. The second experiment, XUV emission spectroscopy of Ca II and Sr II in a microwave-heated plasma, identifies transitions from quasi-metastable levels in these ions, and provides confirming evidence of their radiative, rather than autoionizing, character. In the third experiment, core-excited Ca II ions are produced by inner-shell photoionization of Ca with soft x-rays from a laser-produced plasma. This preliminary experiment demonstrated a method of creating large numbers of these highly-excited ions for future spectroscopic experiments. Experimental and theoretical evidence suggests the CA II 3{ rm p}^5 3d4s ^4 {rm F}^circ_{3/2 } quasi-metastable level may be directly pumped via a dipole ionization process from the Ca I ground state. The direct process is permitted by J conservation, and occurs due to configuration mixing in the final state and possibly the initial state as well. The experiments identifying and characterizing quasi-metastable levels are compared to calculations using the Hartree-Fock code RCN/RCG. Calculated parameters include energy levels, wavefunctions, and transition rates. Based on an extension of this code, earlier unexplained experiments showing strong two-electron radiative transitions from quasi-metastable levels are now understood.

  8. SPECIES - EVALUATING THERMODYNAMIC PROPERTIES, TRANSPORT PROPERTIES & EQUILIBRIUM CONSTANTS OF AN 11-SPECIES AIR MODEL

    NASA Technical Reports Server (NTRS)

    Thompson, R. A.

    1994-01-01

    Accurate numerical prediction of high-temperature, chemically reacting flowfields requires a knowledge of the physical properties and reaction kinetics for the species involved in the reacting gas mixture. Assuming an 11-species air model at temperatures below 30,000 degrees Kelvin, SPECIES (Computer Codes for the Evaluation of Thermodynamic Properties, Transport Properties, and Equilibrium Constants of an 11-Species Air Model) computes values for the species thermodynamic and transport properties, diffusion coefficients and collision cross sections for any combination of the eleven species, and reaction rates for the twenty reactions normally occurring. The species represented in the model are diatomic nitrogen, diatomic oxygen, atomic nitrogen, atomic oxygen, nitric oxide, ionized nitric oxide, the free electron, ionized atomic nitrogen, ionized atomic oxygen, ionized diatomic nitrogen, and ionized diatomic oxygen. Sixteen subroutines compute the following properties for both a single species, interaction pair, or reaction, and an array of all species, pairs, or reactions: species specific heat and static enthalpy, species viscosity, species frozen thermal conductivity, diffusion coefficient, collision cross section (OMEGA 1,1), collision cross section (OMEGA 2,2), collision cross section ratio, and equilibrium constant. The program uses least squares polynomial curve-fits of the most accurate data believed available to provide the requested values more quickly than is possible with table look-up methods. The subroutines for computing transport coefficients and collision cross sections use additional code to correct for any electron pressure when working with ionic species. SPECIES was developed on a SUN 3/280 computer running the SunOS 3.5 operating system. It is written in standard FORTRAN 77 for use on any machine, and requires roughly 92K memory. The standard distribution medium for SPECIES is a 5.25 inch 360K MS-DOS format diskette. The contents of the diskettes are compressed using the PKWARE archiving tools. The utility to unarchive the files, PKUNZIP.EXE, is included. This program was last updated in 1991. SUN and SunOS are registered trademarks of Sun Microsystems, Inc.

  9. Simulation study of 3–5 keV x-ray conversion efficiency from Ar K-shell vs. Ag L-shell targets on the National Ignition Facility laser

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kemp, G. E., E-mail: kemp10@llnl.gov; Colvin, J. D.; Fournier, K. B.

    2015-05-15

    Tailored, high-flux, multi-keV x-ray sources are desirable for studying x-ray interactions with matter for various civilian, space and military applications. For this study, we focus on designing an efficient laser-driven non-local thermodynamic equilibrium 3–5 keV x-ray source from photon-energy-matched Ar K-shell and Ag L-shell targets at sub-critical densities (∼n{sub c}/10) to ensure supersonic, volumetric laser heating with minimal losses to kinetic energy, thermal x rays and laser-plasma instabilities. Using HYDRA, a multi-dimensional, arbitrary Lagrangian-Eulerian, radiation-hydrodynamics code, we performed a parameter study by varying initial target density and laser parameters for each material using conditions readily achievable on the National Ignition Facilitymore » (NIF) laser. We employ a model, benchmarked against Kr data collected on the NIF, that uses flux-limited Lee-More thermal conductivity and multi-group implicit Monte-Carlo photonics with non-local thermodynamic equilibrium, detailed super-configuration accounting opacities from CRETIN, an atomic-kinetics code. While the highest power laser configurations produced the largest x-ray yields, we report that the peak simulated laser to 3–5 keV x-ray conversion efficiencies of 17.7% and 36.4% for Ar and Ag, respectively, occurred at lower powers between ∼100–150 TW. For identical initial target densities and laser illumination, the Ag L-shell is observed to have ≳10× higher emissivity per ion per deposited laser energy than the Ar K-shell. Although such low-density Ag targets have not yet been demonstrated, simulations of targets fabricated using atomic layer deposition of Ag on silica aerogels (∼20% by atomic fraction) suggest similar performance to atomically pure metal foams and that either fabrication technique may be worth pursuing for an efficient 3–5 keV x-ray source on NIF.« less

  10. The role of configuration interaction in the LTE opacity of Fe

    NASA Astrophysics Data System (ADS)

    Colgan, James; Kilcrease, David; Magee, Norm; Armstrong, Gregory; Abdallah, Joe; Sherrill, Manolo; Fontes, Christopher; Zhang, Honglin; Hakel, Peter

    2013-05-01

    The Los Alamos National Laboratory code ATOMIC has been recently used to generate a series of local-thermodynamic-equilibrium (LTE) light element opacities for the elements H through Ne. Our calculations, which include fine-structure detail, represent a systematic improvement over previous Los Alamos opacity calculations using the LEDCOP legacy code. Recent efforts have resulted in comprehensive new calculations of the opacity of Fe. In this presentation we explore the role of configuration interaction (CI) in the Fe opacity, and show where CI influences the monochromatic opacity. We present such comparisons for conditions of astrophysical interest. The Los Alamos National Laboratory is operated by Los Alamos National Security, LLC for the National Nuclear Security Administration of the U.S. Department of Energy under Contract No. DE-AC5206NA25396.

  11. DOE Office of Scientific and Technical Information (OSTI.GOV)

    Antonelli, Perry Edward

    A low-level model-to-model interface is presented that will enable independent models to be linked into an integrated system of models. The interface is based on a standard set of functions that contain appropriate export and import schemas that enable models to be linked with no changes to the models themselves. These ideas are presented in the context of a specific multiscale material problem that couples atomistic-based molecular dynamics calculations to continuum calculations of fluid ow. These simulations will be used to examine the influence of interactions of the fluid with an adjacent solid on the fluid ow. The interface willmore » also be examined by adding it to an already existing modeling code, Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) and comparing it with our own molecular dynamics code.« less

  12. DAGON: a 3D Maxwell-Bloch code

    NASA Astrophysics Data System (ADS)

    Oliva, Eduardo; Cotelo, Manuel; Escudero, Juan Carlos; González-Fernández, Agustín.; Sanchís, Alberto; Vera, Javier; Vicéns, Sergio; Velarde, Pedro

    2017-05-01

    The amplification of UV radiation and high order harmonics (HOH) in plasmas is a subject of raising interest due to its different potential applications in several fields like environment and security (detection at distance), biology, materials science and industry (3D imaging) and atomic and plasma physics (pump-probe experiments). In order to develop these sources, it is necessary to properly understand the amplification process. Being the plasma an inhomogeneous medium which changes with time, it is desirable to have a full time-dependent 3D description of the interaction of UV and XUV radiation with plasmas. For these reasons, at the Instituto de Fusíon Nuclear we have developed DAGON, a 3D Maxwell-Bloch code capable of studying the full spationtemporal structure of the amplification process abovementioned.

  13. Determination of performance of non-ideal aluminized explosives.

    PubMed

    Keshavarz, Mohammad Hossein; Mofrad, Reza Teimuri; Poor, Karim Esmail; Shokrollahi, Arash; Zali, Abbas; Yousefi, Mohammad Hassan

    2006-09-01

    Non-ideal explosives can have Chapman-Jouguet (C-J) detonation pressure significantly different from those expected from existing thermodynamic computer codes, which usually allows finding the parameters of ideal detonation of individual high explosives with good accuracy. A simple method is introduced by which detonation pressure of non-ideal aluminized explosives with general formula C(a)H(b)N(c)O(d)Al(e) can be predicted only from a, b, c, d and e at any loading density without using any assumed detonation products and experimental data. Calculated detonation pressures show good agreement with experimental values with respect to computed results obtained by complicated computer code. It is shown here how loading density and atomic composition can be integrated into an empirical formula for predicting detonation pressure of proposed aluminized explosives.

  14. Monte Carlo event generators in atomic collisions: A new tool to tackle the few-body dynamics

    NASA Astrophysics Data System (ADS)

    Ciappina, M. F.; Kirchner, T.; Schulz, M.

    2010-04-01

    We present a set of routines to produce theoretical event files, for both single and double ionization of atoms by ion impact, based on a Monte Carlo event generator (MCEG) scheme. Such event files are the theoretical counterpart of the data obtained from a kinematically complete experiment; i.e. they contain the momentum components of all collision fragments for a large number of ionization events. Among the advantages of working with theoretical event files is the possibility to incorporate the conditions present in a real experiment, such as the uncertainties in the measured quantities. Additionally, by manipulating them it is possible to generate any type of cross sections, specially those that are usually too complicated to compute with conventional methods due to a lack of symmetry. Consequently, the numerical effort of such calculations is dramatically reduced. We show examples for both single and double ionization, with special emphasis on a new data analysis tool, called four-body Dalitz plots, developed very recently. Program summaryProgram title: MCEG Catalogue identifier: AEFV_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEFV_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 2695 No. of bytes in distributed program, including test data, etc.: 18 501 Distribution format: tar.gz Programming language: FORTRAN 77 with parallelization directives using scripting Computer: Single machines using Linux and Linux servers/clusters (with cores with any clock speed, cache memory and bits in a word) Operating system: Linux (any version and flavor) and FORTRAN 77 compilers Has the code been vectorised or parallelized?: Yes RAM: 64-128 kBytes (the codes are very cpu intensive) Classification: 2.6 Nature of problem: The code deals with single and double ionization of atoms by ion impact. Conventional theoretical approaches aim at a direct calculation of the corresponding cross sections. This has the important shortcoming that it is difficult to account for the experimental conditions when comparing results to measured data. In contrast, the present code generates theoretical event files of the same type as are obtained in a real experiment. From these event files any type of cross sections can be easily extracted. The theoretical schemes are based on distorted wave formalisms for both processes of interest. Solution method: The codes employ a Monte Carlo Event Generator based on theoretical formalisms to generate event files for both single and double ionization. One of the main advantages of having access to theoretical event files is the possibility of adding the conditions present in real experiments (parameter uncertainties, environmental conditions, etc.) and to incorporate additional physics in the resulting event files (e.g. elastic scattering or other interactions absent in the underlying calculations). Additional comments: The computational time can be dramatically reduced if a large number of processors is used. Since the codes has no communication between processes it is possible to achieve an efficiency of a 100% (this number certainly will be penalized by the queuing waiting time). Running time: Times vary according to the process, single or double ionization, to be simulated, the number of processors and the type of theoretical model. The typical running time is between several hours and up to a few weeks.

  15. On the use of symmetry in the ab initio quantum mechanical simulation of nanotubes and related materials.

    PubMed

    Noel, Yves; D'arco, Philippe; Demichelis, Raffaella; Zicovich-Wilson, Claudio M; Dovesi, Roberto

    2010-03-01

    Nanotubes can be characterized by a very high point symmetry, comparable or even larger than the one of the most symmetric crystalline systems (cubic, 48 point symmetry operators). For example, N = 2n rototranslation symmetry operators connect the atoms of the (n,0) nanotubes. This symmetry is fully exploited in the CRYSTAL code. As a result, ab initio quantum mechanical large basis set calculations of carbon nanotubes containing more than 150 atoms in the unit cell become very cheap, because the irreducible part of the unit cell reduces to two atoms only. The nanotube symmetry is exploited at three levels in the present implementation. First, for the automatic generation of the nanotube structure (and then of the input file for the SCF calculation) starting from a two-dimensional structure (in the specific case, graphene). Second, the nanotube symmetry is used for the calculation of the mono- and bi-electronic integrals that enter into the Fock (Kohn-Sham) matrix definition. Only the irreducible wedge of the Fock matrix is computed, with a saving factor close to N. Finally, the symmetry is exploited for the diagonalization, where each irreducible representation is separately treated. When M atomic orbitals per carbon atom are used, the diagonalization computing time is close to Nt, where t is the time required for the diagonalization of each 2M x 2M matrix. The efficiency and accuracy of the computational scheme is documented. (c) 2009 Wiley Periodicals, Inc.

  16. Detonation of Meta-stable Clusters

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kuhl, Allen; Kuhl, Allen L.; Fried, Laurence E.

    2008-05-31

    We consider the energy accumulation in meta-stable clusters. This energy can be much larger than the typical chemical bond energy (~;;1 ev/atom). For example, polymeric nitrogen can accumulate 4 ev/atom in the N8 (fcc) structure, while helium can accumulate 9 ev/atom in the excited triplet state He2* . They release their energy by cluster fission: N8 -> 4N2 and He2* -> 2He. We study the locus of states in thermodynamic state space for the detonation of such meta-stable clusters. In particular, the equilibrium isentrope, starting at the Chapman-Jouguet state, and expanding down to 1 atmosphere was calculated with the Cheetahmore » code. Large detonation pressures (3 and 16 Mbar), temperatures (12 and 34 kilo-K) and velocities (20 and 43 km/s) are a consequence of the large heats of detonation (6.6 and 50 kilo-cal/g) for nitrogen and helium clusters respectively. If such meta-stable clusters could be synthesized, they offer the potential for large increases in the energy density of materials.« less

  17. The Russian effort in establishing large atomic and molecular databases

    NASA Astrophysics Data System (ADS)

    Presnyakov, Leonid P.

    1998-07-01

    The database activities in Russia have been developed in connection with UV and soft X-ray spectroscopic studies of extraterrestrial and laboratory (magnetically confined and laser-produced) plasmas. Two forms of database production are used: i) a set of computer programs to calculate radiative and collisional data for the general atom or ion, and ii) development of numeric database systems with the data stored in the computer. The first form is preferable for collisional data. At the Lebedev Physical Institute, an appropriate set of the codes has been developed. It includes all electronic processes at collision energies from the threshold up to the relativistic limit. The ion -atom (and -ion) collisional data are calculated with the methods developed recently. The program for the calculations of the level populations and line intensities is used for spectrical diagnostics of transparent plasmas. The second form of database production is widely used at the Institute of Physico-Technical Measurements (VNIIFTRI), and the Troitsk Center: the Institute of Spectroscopy and TRINITI. The main results obtained at the centers above are reviewed. Plans for future developments jointly with international collaborations are discussed.

  18. Calculation of low-Z impurity pellet induced fluxes of charge exchange neutral particles escaping from magnetically confined toroidal plasmas.

    PubMed

    Goncharov, P R; Ozaki, T; Sudo, S; Tamura, N; Tolstikhina, I Yu; Sergeev, V Yu

    2008-10-01

    Measurements of energy- and time-resolved neutral hydrogen and helium fluxes from an impurity pellet ablation cloud, referred to as pellet charge exchange or PCX experiments, can be used to study local fast ion energy distributions in fusion plasmas. The estimation of the local distribution function f(i)(E) of fast ions entering the cloud requires knowledge of both the fraction F(0)(E) of incident ions exiting the cloud as neutral atoms and the attenuation factor A(E,rho) describing the loss of fast atoms in the plasma. Determination of A(E,rho), in turn, requires the total stopping cross section sigma(loss) of neutral atoms in the plasma and the Jacobian reflecting the measurement geometry and the magnetic surface shape. The obtained functions F(0)(E) and A(E,rho) enter multiplicatively into the probability density for escaping neutral particle kinetic energy. A general calculation scheme has been developed and realized as a FORTRAN code, which is to be applied for the calculation of f(i)(E) from PCX experimental results obtained with low-Z impurity pellets.

  19. Protein-protein interaction specificity is captured by contact preferences and interface composition.

    PubMed

    Nadalin, Francesca; Carbone, Alessandra

    2018-02-01

    Large-scale computational docking will be increasingly used in future years to discriminate protein-protein interactions at the residue resolution. Complete cross-docking experiments make in silico reconstruction of protein-protein interaction networks a feasible goal. They ask for efficient and accurate screening of the millions structural conformations issued by the calculations. We propose CIPS (Combined Interface Propensity for decoy Scoring), a new pair potential combining interface composition with residue-residue contact preference. CIPS outperforms several other methods on screening docking solutions obtained either with all-atom or with coarse-grain rigid docking. Further testing on 28 CAPRI targets corroborates CIPS predictive power over existing methods. By combining CIPS with atomic potentials, discrimination of correct conformations in all-atom structures reaches optimal accuracy. The drastic reduction of candidate solutions produced by thousands of proteins docked against each other makes large-scale docking accessible to analysis. CIPS source code is freely available at http://www.lcqb.upmc.fr/CIPS. alessandra.carbone@lip6.fr. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

  20. Logical synchronization: how evidence and hypotheses steer atomic clocks

    NASA Astrophysics Data System (ADS)

    Myers, John M.; Madjid, F. Hadi

    2014-05-01

    A clock steps a computer through a cycle of phases. For the propagation of logical symbols from one computer to another, each computer must mesh its phases with arrivals of symbols from other computers. Even the best atomic clocks drift unforeseeably in frequency and phase; feedback steers them toward aiming points that depend on a chosen wave function and on hypotheses about signal propagation. A wave function, always under-determined by evidence, requires a guess. Guessed wave functions are coded into computers that steer atomic clocks in frequency and position—clocks that step computers through their phases of computations, as well as clocks, some on space vehicles, that supply evidence of the propagation of signals. Recognizing the dependence of the phasing of symbol arrivals on guesses about signal propagation elevates `logical synchronization.' from its practice in computer engineering to a dicipline essential to physics. Within this discipline we begin to explore questions invisible under any concept of time that fails to acknowledge the unforeseeable. In particular, variation of spacetime curvature is shown to limit the bit rate of logical communication.

  1. Atomic structure of unligated laccase from Cerrena maxima at 1.76 A with molecular oxygen and hydrogen peroxide

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Zhukova, Yu. N., E-mail: amm@ns.crys.ras.ru; Lyashenko, A. V.; Lashkov, A. A.

    2010-05-15

    The three-dimensional structure of unligated laccase from Cerrena maxima was established by X-ray diffraction at 1.76-A resolution; R{sub work} = 18.07%, R{sub free} = 21.71%, rmsd of bond lengths, bond angles, and chiral angles are 0.008 A, 1.19{sup o}, and 0.077{sup o}, respectively. The coordinate error for the refined structure estimated from the Luzzati plot is 0.195 A. The maximum average error in the atomic coordinates is 0.047 A. A total of 99.4% of amino-acid residues of the polypeptide chain are in the most favorable, allowable, and accessible regions of the Ramachandran plot. The three-dimensional structures of the complexes ofmore » laccase from C. maxima with molecular oxygen and hydrogen peroxide were determined by the molecular simulation. These data provide insight into the structural aspect of the mechanism of the enzymatic cycle. The structure factors and the refined atomic coordinates were deposited in the Protein Data Bank (PDB-ID code is 3DIV).« less

  2. Discriminative Bayesian Dictionary Learning for Classification.

    PubMed

    Akhtar, Naveed; Shafait, Faisal; Mian, Ajmal

    2016-12-01

    We propose a Bayesian approach to learn discriminative dictionaries for sparse representation of data. The proposed approach infers probability distributions over the atoms of a discriminative dictionary using a finite approximation of Beta Process. It also computes sets of Bernoulli distributions that associate class labels to the learned dictionary atoms. This association signifies the selection probabilities of the dictionary atoms in the expansion of class-specific data. Furthermore, the non-parametric character of the proposed approach allows it to infer the correct size of the dictionary. We exploit the aforementioned Bernoulli distributions in separately learning a linear classifier. The classifier uses the same hierarchical Bayesian model as the dictionary, which we present along the analytical inference solution for Gibbs sampling. For classification, a test instance is first sparsely encoded over the learned dictionary and the codes are fed to the classifier. We performed experiments for face and action recognition; and object and scene-category classification using five public datasets and compared the results with state-of-the-art discriminative sparse representation approaches. Experiments show that the proposed Bayesian approach consistently outperforms the existing approaches.

  3. First principles study of NH3 adsorption on carbon nanowires

    NASA Astrophysics Data System (ADS)

    Tapia, Jorge-Alejandro; Sanchez, Alvaro-Daniel; Acosta, Cesar; Canto, Gabriel

    2009-03-01

    Recently has been reported a new type of one-dimensional carbon structures. Carbon nanowires formed by a linear carbon-atom chain inside an armchair (5,5) carbon nanotube has been observed using high-resolution transmission electron microscopy. Theoretical and experimental studies of the NH3 adsorption in the carbon nanotubes report changes in the electronic properties of the carbon nanotubes. In the present work we have studied the electronic and structure properties of carbon nanowires (chain@SWCNT) when NH3 atoms are adsorbed. We used the Density Functional Theory and the calculations where performed by the pseudopotentials LCAO method (SIESTA code) and the Generalized Gradient Approximation (GGA) for the exchange-correlation potential. We have analyzed the changes in the atomic structure and density of states (DOS). We found that the electronic character of the carbon chain of the chain@SWCNT system, can be modulate by NH3 adsorption. This research was supported by SEP under Grant No. PROMEP/103.5/07/2595 and the Consejo Nacional de Ciencia y Tecnolog'ia (Conacyt) under Grants No. 82497 and 60534.

  4. An Information Theory-Inspired Strategy for Design of Re-programmable Encrypted Graphene-based Coding Metasurfaces at Terahertz Frequencies.

    PubMed

    Momeni, Ali; Rouhi, Kasra; Rajabalipanah, Hamid; Abdolali, Ali

    2018-04-18

    Inspired by the information theory, a new concept of re-programmable encrypted graphene-based coding metasurfaces was investigated at terahertz frequencies. A channel-coding function was proposed to convolutionally record an arbitrary information message onto unrecognizable but recoverable parity beams generated by a phase-encrypted coding metasurface. A single graphene-based reflective cell with dual-mode biasing voltages was designed to act as "0" and "1" meta-atoms, providing broadband opposite reflection phases. By exploiting graphene tunability, the proposed scheme enabled an unprecedented degree of freedom in the real-time mapping of information messages onto multiple parity beams which could not be damaged, altered, and reverse-engineered. Various encryption types such as mirroring, anomalous reflection, multi-beam generation, and scattering diffusion can be dynamically attained via our multifunctional metasurface. Besides, contrary to conventional time-consuming and optimization-based methods, this paper convincingly offers a fast, straightforward, and efficient design of diffusion metasurfaces of arbitrarily large size. Rigorous full-wave simulations corroborated the results where the phase-encrypted metasurfaces exhibited a polarization-insensitive reflectivity less than -10 dB over a broadband frequency range from 1 THz to 1.7 THz. This work reveals new opportunities for the extension of re-programmable THz-coding metasurfaces and may be of interest for reflection-type security systems, computational imaging, and camouflage technology.

  5. Lowest-energy structures and electronic properties of Na-Si binary clusters from ab initio global search.

    PubMed

    Sai, Linwei; Tang, Lingli; Zhao, Jijun; Wang, Jun; Kumar, Vijay

    2011-11-14

    The ground state structures of neutral and anionic clusters of Na(n)Si(m) (1 ≤ n ≤ 3, 1 ≤ m ≤ 11) have been determined using genetic algorithm incorporated in first principles total energy code. The size dependence of the structural and electronic properties is discussed in detail. It is found that the lowest-energy structures of Na(n)Si(m) clusters resemble those of the pure Si clusters. Interestingly, Na atoms in neutral Na(n)Si(m) clusters are usually well separated by the Si(m) skeleton, whereas Na atoms can form Na-Na bonds in some anionic clusters. The ionization potentials, adiabatic electron affinities, and photoelectron spectra are also calculated and the results compare well with the experimental data. © 2011 American Institute of Physics

  6. Photoionization of Se+ and Se2+ Ions: Experiment and Theory

    NASA Astrophysics Data System (ADS)

    Esteves, D. A.; Sterling, N. C.; Alna'Washi, Ghassan; Aguilar, A.; Kilcoyne, A. L. D.; Balance, C. P.; Norrington, P. H.; McLaughlin, B. M.

    2007-06-01

    The determination of elemental abundances in astrophysical nebulae are highly dependent on the accuracy of the available atomic data. Numerical simulations show that derived Se abundances in ionized nebulae can be uncertain by factors of two or more from atomic data uncertainties alone. Of these uncertainties, photoionization cross section data are the most important, particularly in the near threshold region of the valence shell. Absolute photoionization cross sections for Se^+ and Se^2+ ions near their thresholds have been measured at the Advanced Light Source in Berkeley, using the merged beams photo-ion technique. Theoretical photoionization cross sections calculations were performed for both of these Se ions using the state-of-the-art fully relativistic Dirac R-matrix code (DARC). The calculations show encouraging agreement with the experimental measurements. A more comprehensive set of results will be presented at the meeting.

  7. Simulations of Neon Pellets for Plasma Disruption Mitigation in Tokamaks

    NASA Astrophysics Data System (ADS)

    Bosviel, Nicolas; Samulyak, Roman; Parks, Paul

    2017-10-01

    Numerical studies of the ablation of neon pellets in tokamaks in the plasma disruption mitigation parameter space have been performed using a time-dependent pellet ablation model based on the front tracking code FronTier-MHD. The main features of the model include the explicit tracking of the solid pellet/ablated gas interface, a self-consistent evolving potential distribution in the ablation cloud, JxB forces, atomic processes, and an improved electrical conductivity model. The equation of state model accounts for atomic processes in the ablation cloud as well as deviations from the ideal gas law in the dense, cold layers of neon gas near the pellet surface. Simulations predict processes in the ablation cloud and pellet ablation rates and address the sensitivity of pellet ablation processes to details of physics models, in particular the equation of state.

  8. Analysis of spectra of 3s-3p and 3p-3d transitions of highly-charged copper ions

    NASA Astrophysics Data System (ADS)

    Su, M. G.; Min, Q.; He, S. Q.; Wu, L.; Sun, R.; Ding, X. B.; Sun, D. X.

    2017-08-01

    Beam-foil excited spectra in the range of 160-360 Å from highly charged copper ions were identified with the aid of the National Institute of Standards and Technology Atomic Spectra Database and theoretical calculations with Cowan and Flexible Atomic Code (FAC) calculations. Spectra arising from 3s-3p and 3p-3d transitions of Cu13+-Cu22+ ions were considered. The ion fraction at an ion beam energy of 110 MeV was estimated from the equilibrium charge distribution of the fast ion beams after passing through the solid. The corresponding simulated spectra were in good agreement with the experimental result. Our Cowan and FAC calculation results should be useful for further spectral identification and lifetime measurements of highly charged copper ions.

  9. Energy levels and radiative rates for Ne-like ions from Cu to Ga

    NASA Astrophysics Data System (ADS)

    Singh, Narendra; Aggarwal, Sunny

    2017-11-01

    Energy levels, lifetimes and wave function compositions are computed for 127 fine structural levels in Ne-like ions (Z=29{-}31). Configuration interaction has been included among 51 configurations (generating 1016 levels) and multiconfigurational Dirac-Fock method is used to generate the wave functions. Similar calculations have also been performed using the fully relativistic flexible atomic code (FAC). Transition wavelength, oscillator strength, transition probabilities and line strength are reported for electric dipole (E1), electric quadrupole (E2), magnetic dipole (M1) and magnetic quadrupole (M2) transitions from the ground level. We compared our calculated results with the available data in the literature. The calculated results are found to be in close agreement with the previous results. Further, we predict some new atomic data which may be important for plasma diagnostics.

  10. Full-dimensional quantum calculations of ground-state tunneling splitting of malonaldehyde using an accurate ab initio potential energy surface

    NASA Astrophysics Data System (ADS)

    Wang, Yimin; Braams, Bastiaan J.; Bowman, Joel M.; Carter, Stuart; Tew, David P.

    2008-06-01

    Quantum calculations of the ground vibrational state tunneling splitting of H-atom and D-atom transfer in malonaldehyde are performed on a full-dimensional ab initio potential energy surface (PES). The PES is a fit to 11 147 near basis-set-limit frozen-core CCSD(T) electronic energies. This surface properly describes the invariance of the potential with respect to all permutations of identical atoms. The saddle-point barrier for the H-atom transfer on the PES is 4.1 kcal/mol, in excellent agreement with the reported ab initio value. Model one-dimensional and ``exact'' full-dimensional calculations of the splitting for H- and D-atom transfer are done using this PES. The tunneling splittings in full dimensionality are calculated using the unbiased ``fixed-node'' diffusion Monte Carlo (DMC) method in Cartesian and saddle-point normal coordinates. The ground-state tunneling splitting is found to be 21.6 cm-1 in Cartesian coordinates and 22.6 cm-1 in normal coordinates, with an uncertainty of 2-3 cm-1. This splitting is also calculated based on a model which makes use of the exact single-well zero-point energy (ZPE) obtained with the MULTIMODE code and DMC ZPE and this calculation gives a tunneling splitting of 21-22 cm-1. The corresponding computed splittings for the D-atom transfer are 3.0, 3.1, and 2-3 cm-1. These calculated tunneling splittings agree with each other to within less than the standard uncertainties obtained with the DMC method used, which are between 2 and 3 cm-1, and agree well with the experimental values of 21.6 and 2.9 cm-1 for the H and D transfer, respectively.

  11. Full-dimensional quantum calculations of ground-state tunneling splitting of malonaldehyde using an accurate ab initio potential energy surface.

    PubMed

    Wang, Yimin; Braams, Bastiaan J; Bowman, Joel M; Carter, Stuart; Tew, David P

    2008-06-14

    Quantum calculations of the ground vibrational state tunneling splitting of H-atom and D-atom transfer in malonaldehyde are performed on a full-dimensional ab initio potential energy surface (PES). The PES is a fit to 11 147 near basis-set-limit frozen-core CCSD(T) electronic energies. This surface properly describes the invariance of the potential with respect to all permutations of identical atoms. The saddle-point barrier for the H-atom transfer on the PES is 4.1 kcalmol, in excellent agreement with the reported ab initio value. Model one-dimensional and "exact" full-dimensional calculations of the splitting for H- and D-atom transfer are done using this PES. The tunneling splittings in full dimensionality are calculated using the unbiased "fixed-node" diffusion Monte Carlo (DMC) method in Cartesian and saddle-point normal coordinates. The ground-state tunneling splitting is found to be 21.6 cm(-1) in Cartesian coordinates and 22.6 cm(-1) in normal coordinates, with an uncertainty of 2-3 cm(-1). This splitting is also calculated based on a model which makes use of the exact single-well zero-point energy (ZPE) obtained with the MULTIMODE code and DMC ZPE and this calculation gives a tunneling splitting of 21-22 cm(-1). The corresponding computed splittings for the D-atom transfer are 3.0, 3.1, and 2-3 cm(-1). These calculated tunneling splittings agree with each other to within less than the standard uncertainties obtained with the DMC method used, which are between 2 and 3 cm(-1), and agree well with the experimental values of 21.6 and 2.9 cm(-1) for the H and D transfer, respectively.

  12. DensToolKit: A comprehensive open-source package for analyzing the electron density and its derivative scalar and vector fields

    NASA Astrophysics Data System (ADS)

    Solano-Altamirano, J. M.; Hernández-Pérez, Julio M.

    2015-11-01

    DensToolKit is a suite of cross-platform, optionally parallelized, programs for analyzing the molecular electron density (ρ) and several fields derived from it. Scalar and vector fields, such as the gradient of the electron density (∇ρ), electron localization function (ELF) and its gradient, localized orbital locator (LOL), region of slow electrons (RoSE), reduced density gradient, localized electrons detector (LED), information entropy, molecular electrostatic potential, kinetic energy densities K and G, among others, can be evaluated on zero, one, two, and three dimensional grids. The suite includes a program for searching critical points and bond paths of the electron density, under the framework of Quantum Theory of Atoms in Molecules. DensToolKit also evaluates the momentum space electron density on spatial grids, and the reduced density matrix of order one along lines joining two arbitrary atoms of a molecule. The source code is distributed under the GNU-GPLv3 license, and we release the code with the intent of establishing an open-source collaborative project. The style of DensToolKit's code follows some of the guidelines of an object-oriented program. This allows us to supply the user with a simple manner for easily implement new scalar or vector fields, provided they are derived from any of the fields already implemented in the code. In this paper, we present some of the most salient features of the programs contained in the suite, some examples of how to run them, and the mathematical definitions of the implemented fields along with hints of how we optimized their evaluation. We benchmarked our suite against both a freely-available program and a commercial package. Speed-ups of ˜2×, and up to 12× were obtained using a non-parallel compilation of DensToolKit for the evaluation of fields. DensToolKit takes similar times for finding critical points, compared to a commercial package. Finally, we present some perspectives for the future development and growth of the suite.

  13. ab initio MD simulations of geomaterials with ~1000 atoms

    NASA Astrophysics Data System (ADS)

    Martin, G. B.; Kirtman, B.; Spera, F. J.

    2009-12-01

    In the last two decades, ab initio studies of materials using Density Functional Theory (DFT) have increased exponentially in popularity. DFT codes are now used routinely to simulate properties of geomaterials--mainly silicates and geochemically important metals such as Fe. These materials are ubiquitous in the Earth’s mantle and core and in terrestrial exoplanets. Because of computational limitations, most First Principles Molecular Dynamics (FPMD) calculations are done on systems of only ~100 atoms for a few picoseconds. While this approach can be useful for calculating physical quantities related to crystal structure, vibrational frequency, and other lattice-scale properties (especially in crystals), it is statistically marginal for duplicating physical properties of the liquid state like transport and structure. In MD simulations in the NEV ensemble, temperature (T), and pressure (P) fluctuations scale as N-1/2; small particle number (N) systems are therefore characterized by greater statistical state point location uncertainty than large N systems. Previous studies have used codes such as VASP where CPU time increases with N2, making calculations with N much greater than 100 impractical. SIESTA (Soler, et al. 2002) is a DFT code that enables electronic structure and MD computations on larger systems (N~103) by making some approximations, such as localized numerical orbitals, that would be useful in modeling some properties of geomaterials. Here we test the applicability of SIESTA to simulate geosilicates, both hydrous and anhydrous, in the solid and liquid state. We have used SIESTA for lattice calculations of brucite, Mg(OH)2, that compare very well to experiment and calculations using CRYSTAL, another DFT code. Good agreement between more classical DFT calculations and SIESTA is needed to justify study of geosilicates using SIESTA across a range of pressures and temperatures relevant to the Earth’s interior. Thus, it is useful to adjust parameters in SIESTA in accordance with calculations from CRYSTAL as a check on feasibility. Results are reported here that suggest SIESTA may indeed be useful to model silicate liquids at very high T and P.

  14. Preliminary Three-Dimensional Simulation of Sediment and Cesium Transport in the Ogi Dam Reservoir using FLESCOT – Task 6, Subtask 2

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Onishi, Yasuo; Kurikami, Hiroshi; Yokuda, Satoru T.

    2014-03-28

    After the accident at the Fukushima Daiichi Nuclear Power Plant in March 2011, the Japan Atomic Energy Agency and the Pacific Northwest National Laboratory initiated a collaborative project on environmental restoration. In October 2013, the collaborative team started a task of three-dimensional modeling of sediment and cesium transport in the Fukushima environment using the FLESCOT (Flow, Energy, Salinity, Sediment Contaminant Transport) code. As the first trial, we applied it to the Ogi Dam Reservoir that is one of the reservoirs in the Japan Atomic Energy Agency’s (JAEA’s) investigation project. Three simulation cases under the following different temperature conditions were studied:more » • incoming rivers and the Ogi Dam Reservoir have the same water temperature • incoming rivers have lower water temperature than that of the reservoir • incoming rivers have higher water temperature than that of the reservoir. The preliminary simulations suggest that seasonal temperature changes influence the sediment and cesium transport. The preliminary results showed the following: • Suspended sand, and cesium adsorbed by sand, coming into the reservoirs from upstream rivers is deposited near the reservoir entrance. • Suspended silt, and cesium adsorbed by silt, is deposited farther in the reservoir. • Suspended clay, and cesium adsorbed by clay, travels the farthest into the reservoir. With sufficient time, the dissolved cesium reaches the downstream end of the reservoir. This preliminary modeling also suggests the possibility of a suitable dam operation to control the cesium migration farther downstream from the dam. JAEA has been sampling in the Ogi Dam Reservoir, but these data were not yet available for the current model calibration and validation for this reservoir. Nonetheless these preliminary FLESCOT modeling results were qualitatively valid and confirmed the applicability of the FLESCOT code to the Ogi Dam Reservoir, and in general to other reservoirs in the Fukushima environment. The issues to be addressed in future are the following: • Validate the simulation results by comparison with the investigation data. • Confirm the applicability of the FLESCOT code to Fukushima coastal areas. • Increase computation speed by parallelizing the FLESCOT code.« less

  15. Simulation of plasma loading of high-pressure RF cavities

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Yu, K.; Samulyak, R.; Yonehara, K.

    2018-01-11

    Muon beam-induced plasma loading of radio-frequency (RF) cavities filled with high pressure hydrogen gas with 1% dry air dopant has been studied via numerical simulations. The electromagnetic code SPACE, that resolves relevant atomic physics processes, including ionization by the muon beam, electron attachment to dopant molecules, and electron-ion and ion-ion recombination, has been used. Simulations studies have also been performed in the range of parameters typical for practical muon cooling channels.

  16. A step in time: Changes in standard-frequency and time-signal broadcasts, 1 January 1972

    NASA Technical Reports Server (NTRS)

    Chi, A. R.; Fosque, H. S.

    1973-01-01

    An improved coordinated universal time (UTC) system has been adopted by the International Radio Consultative Committee. It was implemented internationally by the standard-frequency and time-broadcast stations on 1 Jan. 1972. The new UTC system eliminates the frequency offset of 300 parts in 10 to the 10th power between the old UTC and atomic time, thus making the broadcast time interval (the UTC second) constant and defined by the resonant frequency of cesium atoms. The new time scale is kept in synchronism with the rotation of the Earth within plus or minus 0.7 s by step-time adjustments of exactly 1 s, when needed. A time code has been added to the disseminated time signals to permit universal time to be obtained from the broadcasts to the nearest 0.1 s for users requiring such precision. The texts of the International Radio Consultative Committee recommendation and report to implement the new UTC system are given. The coding formats used by various standard time broadcast services to transmit the difference between the universal time (UT1) and the UTC are also given. For users' convenience, worldwide primary VLF and HF transmissions stations, frequencies, and schedules of time emissions are also included. Actual time-step adjustments made by various stations on 1 Jan. 1972, are provided for future reference.

  17. Post-irradiation examination of uranium 7 wt% molybdenum atomized dispersion fuel

    NASA Astrophysics Data System (ADS)

    Leenaers, A.; Van den Berghe, S.; Koonen, E.; Jarousse, C.; Huet, F.; Trotabas, M.; Boyard, M.; Guillot, S.; Sannen, L.; Verwerft, M.

    2004-10-01

    Two low-enriched uranium fuel plates consisting of U-7wt%Mo atomized powder dispersed in an aluminum matrix, have been irradiated in the FUTURE irradiation rig of the BR2 reactor at SCK•CEN. The plates were submitted to a heat flux of maximum 353 W/cm 2 while the surface cladding temperature is kept below 130 °C. After 40 full power days, visual examination and profilometry of the fuel plates revealed an increase of the plate thickness. In view of this observation, the irradiation campaign was prematurely stopped and the fuel plates were retrieved from the reactor, having at their end-of-life a maximum burn-up of 32.8% 235U (6.5% FIMA). The microstructure of one of the fuel plates has been characterized in an extensive post-irradiation campaign. The U(Mo) fuel particles have been found to interact with the Al matrix, resulting in an interaction layer which can be identified as (U,Mo)Al 3 and (U,Mo)Al 4. Based on the composition of the interaction layer it is shown that the observed physical parameters like thickness of the interaction layer between the Al matrix and the U(Mo) fuel particles compare well to the values calculated by the MAIA code, an U(Mo) behavior modeling code developed by the Commissariat à l'énergie atomique (CEA).

  18. Atomic Data and Spectral Line Intensities for NI XVII

    NASA Technical Reports Server (NTRS)

    Bhatia, A. K.; Landi, E.

    2011-01-01

    Electron impact collision strengths, energy levels, oscillator strengths, and spontaneous radiative decay rates are calculated for Ni XVII. We include in the calculations the 23 lowest configurations, corresponding to 159 fine-structure levels: 3l3l', 3l4l0'' , and 3s5l0''' , with l,l' = s,p,d, l'' = s,p,d, f, and l''' = s,p,d. Collision strengths are calculated at five incident energies for all transitions at varying energies above the threshold of each transition. One additional energy, very close to the threshold of each transition, has also been included. Calculations have been carried out using the Flexible Atomic Code in the distorted wave approximation. Additional calculations have been performed with the University College London suite of codes for comparison. Excitation rate coefficients are calculated as a function of electron temperature by assuming a Maxwellian electron velocity distribution. Using the excitation rate coefficients and the radiative transition rates of the present work, statistical equilibrium equations for level populations are solved at electron densities covering the range of 10(exp 8) - 10(exp 14) / cubic cm and at an electron temperature of logT(sub e)e(K) = 6.5, corresponding to the maximum abundance of Ni XVII. Spectral line intensities are calculated, and their diagnostic relevance is discussed. This dataset will be made available in the next version of the CHIANTI database

  19. Ab initio density-functional calculations in materials science: from quasicrystals over microporous catalysts to spintronics.

    PubMed

    Hafner, Jürgen

    2010-09-29

    During the last 20 years computer simulations based on a quantum-mechanical description of the interactions between electrons and atomic nuclei have developed an increasingly important impact on materials science, not only in promoting a deeper understanding of the fundamental physical phenomena, but also enabling the computer-assisted design of materials for future technologies. The backbone of atomic-scale computational materials science is density-functional theory (DFT) which allows us to cast the intractable complexity of electron-electron interactions into the form of an effective single-particle equation determined by the exchange-correlation functional. Progress in DFT-based calculations of the properties of materials and of simulations of processes in materials depends on: (1) the development of improved exchange-correlation functionals and advanced post-DFT methods and their implementation in highly efficient computer codes, (2) the development of methods allowing us to bridge the gaps in the temperature, pressure, time and length scales between the ab initio calculations and real-world experiments and (3) the extension of the functionality of these codes, permitting us to treat additional properties and new processes. In this paper we discuss the current status of techniques for performing quantum-based simulations on materials and present some illustrative examples of applications to complex quasiperiodic alloys, cluster-support interactions in microporous acid catalysts and magnetic nanostructures.

  20. Silicon nitride equation of state

    NASA Astrophysics Data System (ADS)

    Brown, Robert C.; Swaminathan, Pazhayannur K.

    2017-01-01

    This report presents the development of a global, multi-phase equation of state (EOS) for the ceramic silicon nitride (Si3N4).1 Structural forms include amorphous silicon nitride normally used as a thin film and three crystalline polymorphs. Crystalline phases include hexagonal α-Si3N4, hexagonal β-Si3N4, and the cubic spinel c-Si3N4. Decomposition at about 1900 °C results in a liquid silicon phase and gas phase products such as molecular nitrogen, atomic nitrogen, and atomic silicon. The silicon nitride EOS was developed using EOSPro which is a new and extended version of the PANDA II code. Both codes are valuable tools and have been used successfully for a variety of material classes. Both PANDA II and EOSPro can generate a tabular EOS that can be used in conjunction with hydrocodes. The paper describes the development efforts for the component solid phases and presents results obtained using the EOSPro phase transition model to investigate the solid-solid phase transitions in relation to the available shock data that have indicated a complex and slow time dependent phase change to the c-Si3N4 phase. Furthermore, the EOSPro mixture model is used to develop a model for the decomposition products; however, the need for a kinetic approach is suggested to combine with the single component solid models to simulate and further investigate the global phase coexistences.

  1. Vfold: a web server for RNA structure and folding thermodynamics prediction.

    PubMed

    Xu, Xiaojun; Zhao, Peinan; Chen, Shi-Jie

    2014-01-01

    The ever increasing discovery of non-coding RNAs leads to unprecedented demand for the accurate modeling of RNA folding, including the predictions of two-dimensional (base pair) and three-dimensional all-atom structures and folding stabilities. Accurate modeling of RNA structure and stability has far-reaching impact on our understanding of RNA functions in human health and our ability to design RNA-based therapeutic strategies. The Vfold server offers a web interface to predict (a) RNA two-dimensional structure from the nucleotide sequence, (b) three-dimensional structure from the two-dimensional structure and the sequence, and (c) folding thermodynamics (heat capacity melting curve) from the sequence. To predict the two-dimensional structure (base pairs), the server generates an ensemble of structures, including loop structures with the different intra-loop mismatches, and evaluates the free energies using the experimental parameters for the base stacks and the loop entropy parameters given by a coarse-grained RNA folding model (the Vfold model) for the loops. To predict the three-dimensional structure, the server assembles the motif scaffolds using structure templates extracted from the known PDB structures and refines the structure using all-atom energy minimization. The Vfold-based web server provides a user friendly tool for the prediction of RNA structure and stability. The web server and the source codes are freely accessible for public use at "http://rna.physics.missouri.edu".

  2. Towards robust algorithms for current deposition and dynamic load-balancing in a GPU particle in cell code

    NASA Astrophysics Data System (ADS)

    Rossi, Francesco; Londrillo, Pasquale; Sgattoni, Andrea; Sinigardi, Stefano; Turchetti, Giorgio

    2012-12-01

    We present `jasmine', an implementation of a fully relativistic, 3D, electromagnetic Particle-In-Cell (PIC) code, capable of running simulations in various laser plasma acceleration regimes on Graphics-Processing-Units (GPUs) HPC clusters. Standard energy/charge preserving FDTD-based algorithms have been implemented using double precision and quadratic (or arbitrary sized) shape functions for the particle weighting. When porting a PIC scheme to the GPU architecture (or, in general, a shared memory environment), the particle-to-grid operations (e.g. the evaluation of the current density) require special care to avoid memory inconsistencies and conflicts. Here we present a robust implementation of this operation that is efficient for any number of particles per cell and particle shape function order. Our algorithm exploits the exposed GPU memory hierarchy and avoids the use of atomic operations, which can hurt performance especially when many particles lay on the same cell. We show the code multi-GPU scalability results and present a dynamic load-balancing algorithm. The code is written using a python-based C++ meta-programming technique which translates in a high level of modularity and allows for easy performance tuning and simple extension of the core algorithms to various simulation schemes.

  3. CERES: An ab initio code dedicated to the calculation of the electronic structure and magnetic properties of lanthanide complexes.

    PubMed

    Calvello, Simone; Piccardo, Matteo; Rao, Shashank Vittal; Soncini, Alessandro

    2018-03-05

    We have developed and implemented a new ab initio code, Ceres (Computational Emulator of Rare Earth Systems), completely written in C++11, which is dedicated to the efficient calculation of the electronic structure and magnetic properties of the crystal field states arising from the splitting of the ground state spin-orbit multiplet in lanthanide complexes. The new code gains efficiency via an optimized implementation of a direct configurational averaged Hartree-Fock (CAHF) algorithm for the determination of 4f quasi-atomic active orbitals common to all multi-electron spin manifolds contributing to the ground spin-orbit multiplet of the lanthanide ion. The new CAHF implementation is based on quasi-Newton convergence acceleration techniques coupled to an efficient library for the direct evaluation of molecular integrals, and problem-specific density matrix guess strategies. After describing the main features of the new code, we compare its efficiency with the current state-of-the-art ab initio strategy to determine crystal field levels and properties, and show that our methodology, as implemented in Ceres, represents a more time-efficient computational strategy for the evaluation of the magnetic properties of lanthanide complexes, also allowing a full representation of non-perturbative spin-orbit coupling effects. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  4. Entangled cloning of stabilizer codes and free fermions

    NASA Astrophysics Data System (ADS)

    Hsieh, Timothy H.

    2016-10-01

    Though the no-cloning theorem [Wooters and Zurek, Nature (London) 299, 802 (1982), 10.1038/299802a0] prohibits exact replication of arbitrary quantum states, there are many instances in quantum information processing and entanglement measurement in which a weaker form of cloning may be useful. Here, I provide a construction for generating an "entangled clone" for a particular but rather expansive and rich class of states. Given a stabilizer code or free fermion Hamiltonian, this construction generates an exact entangled clone of the original ground state, in the sense that the entanglement between the original and the exact copy can be tuned to be arbitrarily small but finite, or large, and the relation between the original and the copy can also be modified to some extent. For example, this Rapid Communication focuses on generating time-reversed copies of stabilizer codes and particle-hole transformed ground states of free fermion systems, although untransformed clones can also be generated. The protocol leverages entanglement to simulate a transformed copy of the Hamiltonian without having to physically implement it and can potentially be realized in superconducting qubits or ultracold atomic systems.

  5. Development of Safety Assessment Code for Decommissioning of Nuclear Facilities

    NASA Astrophysics Data System (ADS)

    Shimada, Taro; Ohshima, Soichiro; Sukegawa, Takenori

    A safety assessment code, DecDose, for decommissioning of nuclear facilities has been developed, based on the experiences of the decommissioning project of Japan Power Demonstration Reactor (JPDR) at Japan Atomic Energy Research Institute (currently JAEA). DecDose evaluates the annual exposure dose of the public and workers according to the progress of decommissioning, and also evaluates the public dose at accidental situations including fire and explosion. As for the public, both the internal and the external doses are calculated by considering inhalation, ingestion, direct radiation from radioactive aerosols and radioactive depositions, and skyshine radiation from waste containers. For external dose for workers, the dose rate from contaminated components and structures to be dismantled is calculated. Internal dose for workers is calculated by considering dismantling conditions, e.g. cutting speed, cutting length of the components and exhaust velocity. Estimation models for dose rate and staying time were verified by comparison with the actual external dose of workers which were acquired during JPDR decommissioning project. DecDose code is expected to contribute the safety assessment for decommissioning of nuclear facilities.

  6. GW/Bethe-Salpeter calculations for charged and model systems from real-space DFT

    NASA Astrophysics Data System (ADS)

    Strubbe, David A.

    GW and Bethe-Salpeter (GW/BSE) calculations use mean-field input from density-functional theory (DFT) calculations to compute excited states of a condensed-matter system. Many parts of a GW/BSE calculation are efficiently performed in a plane-wave basis, and extensive effort has gone into optimizing and parallelizing plane-wave GW/BSE codes for large-scale computations. Most straightforwardly, plane-wave DFT can be used as a starting point, but real-space DFT is also an attractive starting point: it is systematically convergeable like plane waves, can take advantage of efficient domain parallelization for large systems, and is well suited physically for finite and especially charged systems. The flexibility of a real-space grid also allows convenient calculations on non-atomic model systems. I will discuss the interfacing of a real-space (TD)DFT code (Octopus, www.tddft.org/programs/octopus) with a plane-wave GW/BSE code (BerkeleyGW, www.berkeleygw.org), consider performance issues and accuracy, and present some applications to simple and paradigmatic systems that illuminate fundamental properties of these approximations in many-body perturbation theory.

  7. Interatomic Coulombic Decay Effects in Theoretical DNA Recombination Systems Involving Protein Interaction Sites

    NASA Astrophysics Data System (ADS)

    Vargas, E. L.; Rivas, D. A.; Duot, A. C.; Hovey, R. T.; Andrianarijaona, V. M.

    2015-03-01

    DNA replication is the basis for all biological reproduction. A strand of DNA will ``unzip'' and bind with a complimentary strand, creating two identical strands. In this study, we are considering how this process is affected by Interatomic Coulombic Decay (ICD), specifically how ICD affects the individual coding proteins' ability to hold together. ICD mainly deals with how the electron returns to its original state after excitation and how this affects its immediate atomic environment, sometimes affecting the connectivity between interaction sites on proteins involved in the DNA coding process. Biological heredity is fundamentally controlled by DNA and its replication therefore it affects every living thing. The small nature of the proteins (within the range of nanometers) makes it a good candidate for research of this scale. Understanding how ICD affects DNA molecules can give us invaluable insight into the human genetic code and the processes behind cell mutations that can lead to cancer. Authors wish to give special thanks to Pacific Union College Student Senate in Angwin, California, for their financial support.

  8. A Monte Carlo simulation code for calculating damage and particle transport in solids: The case for electron-bombarded solids for electron energies up to 900 MeV

    NASA Astrophysics Data System (ADS)

    Yan, Qiang; Shao, Lin

    2017-03-01

    Current popular Monte Carlo simulation codes for simulating electron bombardment in solids focus primarily on electron trajectories, instead of electron-induced displacements. Here we report a Monte Carol simulation code, DEEPER (damage creation and particle transport in matter), developed for calculating 3-D distributions of displacements produced by electrons of incident energies up to 900 MeV. Electron elastic scattering is calculated by using full-Mott cross sections for high accuracy, and primary-knock-on-atoms (PKAs)-induced damage cascades are modeled using ZBL potential. We compare and show large differences in 3-D distributions of displacements and electrons in electron-irradiated Fe. The distributions of total displacements are similar to that of PKAs at low electron energies. But they are substantially different for higher energy electrons due to the shifting of PKA energy spectra towards higher energies. The study is important to evaluate electron-induced radiation damage, for the applications using high flux electron beams to intentionally introduce defects and using an electron analysis beam for microstructural characterization of nuclear materials.

  9. U. S. statutes of general interest to safeguards and security officers

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Cadwell, J.J.

    1988-01-01

    A handbook of enforcement provisions of Federal law and regulations was prepared for use by U.S. DOE Security Inspectors. This handbook provides security inspectors for the U.S. Department of Energy, security officers at Nuclear Regulatory Licensee facilities, and others with a single document containing most of the Federal law provisions available to assist them in enforcing agency regulations. The handbook contains selected enforcement provisions of Titles 18, 42 and 50 of the United States Code (USC). Topical coverage of Title 18 includes Espionage and Misrepresentation or Impersonation; Theft and Embezzlement; Malicious Mischief; Conspiracy; Search and Seizure. A miscellaneous section dealsmore » with explosives, blackmail, firearms, and other subjects. Certain enforcement sections of Title 42 of the USC (The Atomic Energy Act) and of the Internal Security Act of the United States Code (Title 50) are also provided. Finally, relevant parts of the Federal Property Management Regulations of Title 50, Chapter 101 of the Code of Federal Regulations are presented. A comprehensive index is provided based on key words.« less

  10. Plasma viscosity with mass transport in spherical inertial confinement fusion implosion simulations

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Vold, E. L.; Molvig, K.; Joglekar, A. S.

    2015-11-15

    The effects of viscosity and small-scale atomic-level mixing on plasmas in inertial confinement fusion (ICF) currently represent challenges in ICF research. Many current ICF hydrodynamic codes ignore the effects of viscosity though recent research indicates viscosity and mixing by classical transport processes may have a substantial impact on implosion dynamics. We have implemented a Lagrangian hydrodynamic code in one-dimensional spherical geometry with plasma viscosity and mass transport and including a three temperature model for ions, electrons, and radiation treated in a gray radiation diffusion approximation. The code is used to study ICF implosion differences with and without plasma viscosity andmore » to determine the impacts of viscosity on temperature histories and neutron yield. It was found that plasma viscosity has substantial impacts on ICF shock dynamics characterized by shock burn timing, maximum burn temperatures, convergence ratio, and time history of neutron production rates. Plasma viscosity reduces the need for artificial viscosity to maintain numerical stability in the Lagrangian formulation and also modifies the flux-limiting needed for electron thermal conduction.« less

  11. Investigation of plasma behavior during noble gas injection in the end-cell of GAMMA 10/PDX by using the multi-fluid code ‘LINDA’

    NASA Astrophysics Data System (ADS)

    Islam, M. S.; Nakashima, Y.; Hatayama, A.

    2017-12-01

    The linear divertor analysis with fluid model (LINDA) code has been developed in order to simulate plasma behavior in the end-cell of linear fusion device GAMMA 10/PDX. This paper presents the basic structure and simulated results of the LINDA code. The atomic processes of hydrogen and impurities have been included in the present model in order to investigate energy loss processes and mechanism of plasma detachment. A comparison among Ar, Kr and Xe shows that Xe is the most effective gas on the reduction of electron and ion temperature. Xe injection leads to strong reduction in the temperature of electron and ion. The energy loss terms for both the electron and the ion are enhanced significantly during Xe injection. It is shown that the major energy loss channels for ion and electron are charge-exchange loss and radiative power loss of the radiator gas, respectively. These outcomes indicate that Xe injection in the plasma edge region is effective for reducing plasma energy and generating detached plasma in linear device GAMMA 10/PDX.

  12. Plasma viscosity with mass transport in spherical inertial confinement fusion implosion simulations

    DOE PAGES

    Vold, Erik Lehman; Joglekar, Archis S.; Ortega, Mario I.; ...

    2015-11-20

    The effects of viscosity and small-scale atomic-level mixing on plasmas in inertial confinement fusion(ICF) currently represent challenges in ICF research. Many current ICF hydrodynamic codes ignore the effects of viscosity though recent research indicates viscosity and mixing by classical transport processes may have a substantial impact on implosion dynamics. In this paper, we have implemented a Lagrangian hydrodynamic code in one-dimensional spherical geometry with plasmaviscosity and mass transport and including a three temperature model for ions, electrons, and radiation treated in a gray radiation diffusion approximation. The code is used to study ICF implosion differences with and without plasmaviscosity andmore » to determine the impacts of viscosity on temperature histories and neutron yield. It was found that plasmaviscosity has substantial impacts on ICF shock dynamics characterized by shock burn timing, maximum burn temperatures, convergence ratio, and time history of neutron production rates. Finally, plasmaviscosity reduces the need for artificial viscosity to maintain numerical stability in the Lagrangian formulation and also modifies the flux-limiting needed for electron thermal conduction.« less

  13. Tensor Dictionary Learning for Positive Definite Matrices.

    PubMed

    Sivalingam, Ravishankar; Boley, Daniel; Morellas, Vassilios; Papanikolopoulos, Nikolaos

    2015-11-01

    Sparse models have proven to be extremely successful in image processing and computer vision. However, a majority of the effort has been focused on sparse representation of vectors and low-rank models for general matrices. The success of sparse modeling, along with popularity of region covariances, has inspired the development of sparse coding approaches for these positive definite descriptors. While in earlier work, the dictionary was formed from all, or a random subset of, the training signals, it is clearly advantageous to learn a concise dictionary from the entire training set. In this paper, we propose a novel approach for dictionary learning over positive definite matrices. The dictionary is learned by alternating minimization between sparse coding and dictionary update stages, and different atom update methods are described. A discriminative version of the dictionary learning approach is also proposed, which simultaneously learns dictionaries for different classes in classification or clustering. Experimental results demonstrate the advantage of learning dictionaries from data both from reconstruction and classification viewpoints. Finally, a software library is presented comprising C++ binaries for all the positive definite sparse coding and dictionary learning approaches presented here.

  14. SKIRT: Hybrid parallelization of radiative transfer simulations

    NASA Astrophysics Data System (ADS)

    Verstocken, S.; Van De Putte, D.; Camps, P.; Baes, M.

    2017-07-01

    We describe the design, implementation and performance of the new hybrid parallelization scheme in our Monte Carlo radiative transfer code SKIRT, which has been used extensively for modelling the continuum radiation of dusty astrophysical systems including late-type galaxies and dusty tori. The hybrid scheme combines distributed memory parallelization, using the standard Message Passing Interface (MPI) to communicate between processes, and shared memory parallelization, providing multiple execution threads within each process to avoid duplication of data structures. The synchronization between multiple threads is accomplished through atomic operations without high-level locking (also called lock-free programming). This improves the scaling behaviour of the code and substantially simplifies the implementation of the hybrid scheme. The result is an extremely flexible solution that adjusts to the number of available nodes, processors and memory, and consequently performs well on a wide variety of computing architectures.

  15. A Web 2.0 Interface to Ion Stopping Power and Other Physics Routines for High Energy Density Physics Applications

    NASA Astrophysics Data System (ADS)

    Stoltz, Peter; Veitzer, Seth

    2008-04-01

    We present a new Web 2.0-based interface to physics routines for High Energy Density Physics applications. These routines include models for ion stopping power, sputtering, secondary electron yields and energies, impact ionization cross sections, and atomic radiated power. The Web 2.0 interface allows users to easily explore the results of the models before using the routines within other codes or to analyze experimental results. We discuss how we used various Web 2.0 tools, including the Python 2.5, Django, and the Yahoo User Interface library. Finally, we demonstrate the interface by showing as an example the stopping power algorithms researchers are currently using within the Hydra code to analyze warm, dense matter experiments underway at the Neutralized Drift Compression Experiment facility at Lawrence Berkeley National Laboratory.

  16. Coupling LAMMPS with Lattice Boltzmann fluid solver: theory, implementation, and applications

    NASA Astrophysics Data System (ADS)

    Tan, Jifu; Sinno, Talid; Diamond, Scott

    2016-11-01

    Studying of fluid flow coupled with solid has many applications in biological and engineering problems, e.g., blood cell transport, particulate flow, drug delivery. We present a partitioned approach to solve the coupled Multiphysics problem. The fluid motion is solved by the Lattice Boltzmann method, while the solid displacement and deformation is simulated by Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS). The coupling is achieved through the immersed boundary method so that the expensive remeshing step is eliminated. The code can model both rigid and deformable solids. The code also shows very good scaling results. It was validated with classic problems such as migration of rigid particles, ellipsoid particle's orbit in shear flow. Examples of the applications in blood flow, drug delivery, platelet adhesion and rupture are also given in the paper. NIH.

  17. LAMMPS Project Report for the Trinity KNL Open Science Period.

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Moore, Stan Gerald; Thompson, Aidan P.; Wood, Mitchell

    LAMMPS is a classical molecular dynamics code (lammps.sandia.gov) used to model materials science problems at Sandia National Laboratories and around the world. LAMMPS was one of three Sandia codes selected to participate in the Trinity KNL (TR2) Open Science period. During this period, three different problems of interest were investigated using LAMMPS. The first was benchmarking KNL performance using different force field models. The second was simulating void collapse in shocked HNS energetic material using an all-atom model. The third was simulating shock propagation through poly-crystalline RDX energetic material using a coarse-grain model, the results of which were used inmore » an ACM Gordon Bell Prize submission. This report describes the results of these simulations, lessons learned, and some hardware issues found on Trinity KNL as part of this work.« less

  18. A Theoretical Evaluation of Secondary Atomization Effects on Engine Performance for Aluminum Gel Propellants

    NASA Technical Reports Server (NTRS)

    Mueller, D. C.; Turns, S. R.

    1994-01-01

    A one-dimensional model of a gel-fueled rocket combustion chamber has been developed. This model includes the processes of liquid hydrocarbon burnout, secondary atomization. aluminum ignition, and aluminum combustion. Also included is a model of radiative heat transfer from the solid combustion products to the chamber walls. Calculations indicate that only modest secondary atomization is required to significantly reduce propellant burnout distances, aluminum oxide residual size and radiation heat wall losses. Radiation losses equal to approximately 2-13 percent of the energy released during combustion were estimated. A two-dimensional, two-phase nozzle code was employed to estimate radiation and nozzle two-phase flow effects on overall engine performance. Radiation losses yielded a 1 percent decrease in engine I(sub sp). Results also indicate that secondary atomization may have less effect on two-phase losses than it does on propellant burnout distance and no effect if oxide particle coagulation and shear induced droplet breakup govern oxide particle size. Engine I(sub sp) was found to decrease from 337.4 to 293.7 seconds as gel aluminum mass loading was varied from 0-70 wt percent. Engine I(sub sp) efficiencies, accounting for radiation and two-phase flow effects, on the order of 0.946 were calculated for a 60 wt percent gel, assuming a fragmentation ratio of 5.

  19. SGO: A fast engine for ab initio atomic structure global optimization by differential evolution

    NASA Astrophysics Data System (ADS)

    Chen, Zhanghui; Jia, Weile; Jiang, Xiangwei; Li, Shu-Shen; Wang, Lin-Wang

    2017-10-01

    As the high throughout calculations and material genome approaches become more and more popular in material science, the search for optimal ways to predict atomic global minimum structure is a high research priority. This paper presents a fast method for global search of atomic structures at ab initio level. The structures global optimization (SGO) engine consists of a high-efficiency differential evolution algorithm, accelerated local relaxation methods and a plane-wave density functional theory code running on GPU machines. The purpose is to show what can be achieved by combining the superior algorithms at the different levels of the searching scheme. SGO can search the global-minimum configurations of crystals, two-dimensional materials and quantum clusters without prior symmetry restriction in a relatively short time (half or several hours for systems with less than 25 atoms), thus making such a task a routine calculation. Comparisons with other existing methods such as minima hopping and genetic algorithm are provided. One motivation of our study is to investigate the properties of magnetic systems in different phases. The SGO engine is capable of surveying the local minima surrounding the global minimum, which provides the information for the overall energy landscape of a given system. Using this capability we have found several new configurations for testing systems, explored their energy landscape, and demonstrated that the magnetic moment of metal clusters fluctuates strongly in different local minima.

  20. Evaluation of interatomic potentials for rainbow scattering under axial channeling at KCl(0 0 1) surface by three-dimensional computer simulations based on binary collision approximation

    NASA Astrophysics Data System (ADS)

    Takeuchi, Wataru

    2017-05-01

    The rainbow angles corresponding to prominent peaks in the angular distributions of scattered projectiles with small angle, attributed to rainbow scattering (RS), under axial surface channeling conditions are strongly influenced by the interatomic potentials between projectiles and target atoms. The dependence of rainbow angles on normal energy of projectile energy to the target surface, being experimentally obtained by Specht et al. for RS of He, N, Ne and Ar atoms under <1 0 0> and <1 1 0> axial channeling conditions at a KCl(0 0 1) surface with projectile energies of 1-60 keV, was evaluated by the three-dimensional computer simulations using the ACOCT code based on the binary collision approximation with interatomic pair potentials. Good agreement between the ACOCT results using the ZBL pair potential and the individual pair potentials calculated from Hartree-Fock (HF) wave functions and the experimental ones was found for RS of He, N and Ne atoms from the atomic rows along <1 0 0> direction. For <1 1 0> direction, the ACOCT results employing the Moliere pair potential with adjustable screening length of O'Connor-Biersack (OB) formula, the ZBL pair potential and the individual HF pair potentials except for Ar → KCl using the OB pair potential are nearly in agreement with the experimental ones.

  1. Fast, clash-free RNA conformational morphing using molecular junctions

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Heliou, Amelie; Budday, Dominik; Fonseca, Rasmus

    Non-coding ribonucleic acids (ncRNA) are functional RNA molecules that are not translated into protein. They are extremely dynamic, adopting diverse conformational substates, which enables them to modulate their interaction with a large number of other molecules. The flexibility of ncRNA provides a challenge for probing their complex 3D conformational landscape, both experimentally and computationally. As a result, despite their conformational diversity, ncRNAs mostly preserve their secondary structure throughout the dynamic ensemble. Here we present a kinematics-based procedure to morph an RNA molecule between conformational substates, while avoiding inter-atomic clashes. We represent an RNA as a kinematic linkage, with fixed groupsmore » of atoms as rigid bodies and rotatable bonds as degrees of freedom. Our procedure maintains RNA secondary structure by treating hydrogen bonds between base pairs as constraints. The constraints define a lower-dimensional, secondary-structure constraint manifold in conformation space, where motions are largely governed by molecular junctions of unpaired nucleotides. On a large benchmark set, we show that our morphing procedure compares favorably to peer algorithms, and can approach goal conformations to within a low all-atom RMSD by directing fewer than 1% of its atoms. Furthermore, our results suggest that molecular junctions can modulate 3D structural rearrangements, while secondary structure elements guide large parts of the molecule along the transition to the correct final conformation.« less

  2. An equation of state for partially ionized plasmas: The Coulomb contribution to the free energy

    NASA Astrophysics Data System (ADS)

    Kilcrease, D. P.; Colgan, J.; Hakel, P.; Fontes, C. J.; Sherrill, M. E.

    2015-09-01

    We have previously developed an equation of state (EOS) model called ChemEOS (Hakel and Kilcrease, Atomic Processes in Plasmas, Eds., J. Cohen et al., AIP, 2004) for a plasma of interacting ions, atoms and electrons. It is based on a chemical picture of the plasma and is derived from an expression for the Helmholtz free energy of the interacting species. All other equilibrium thermodynamic quantities are then obtained by minimizing this free energy subject to constraints, thus leading to a thermodynamically consistent EOS. The contribution to this free energy from the Coulomb interactions among the particles is treated using the method of Chabrier and Potekhin (Phys. Rev. E 58, 4941 (1998)) which we have adapted for partially ionized plasmas. This treatment is further examined and is found to give rise to unphysical behavior for various elements at certain values of the density and temperature where the Coulomb coupling begins to become significant and the atoms are partially ionized. We examine the source of this unphysical behavior and suggest corrections that produce acceptable results. The sensitivity of the thermodynamic properties and frequency-dependent opacity of iron is examined with and without these corrections. The corrected EOS is used to determine the fractional ion populations and level populations for a new generation of OPLIB low-Z opacity tables currently being prepared at Los Alamos National Laboratory with the ATOMIC code.

  3. Fast, clash-free RNA conformational morphing using molecular junctions

    DOE PAGES

    Heliou, Amelie; Budday, Dominik; Fonseca, Rasmus; ...

    2017-03-13

    Non-coding ribonucleic acids (ncRNA) are functional RNA molecules that are not translated into protein. They are extremely dynamic, adopting diverse conformational substates, which enables them to modulate their interaction with a large number of other molecules. The flexibility of ncRNA provides a challenge for probing their complex 3D conformational landscape, both experimentally and computationally. As a result, despite their conformational diversity, ncRNAs mostly preserve their secondary structure throughout the dynamic ensemble. Here we present a kinematics-based procedure to morph an RNA molecule between conformational substates, while avoiding inter-atomic clashes. We represent an RNA as a kinematic linkage, with fixed groupsmore » of atoms as rigid bodies and rotatable bonds as degrees of freedom. Our procedure maintains RNA secondary structure by treating hydrogen bonds between base pairs as constraints. The constraints define a lower-dimensional, secondary-structure constraint manifold in conformation space, where motions are largely governed by molecular junctions of unpaired nucleotides. On a large benchmark set, we show that our morphing procedure compares favorably to peer algorithms, and can approach goal conformations to within a low all-atom RMSD by directing fewer than 1% of its atoms. Furthermore, our results suggest that molecular junctions can modulate 3D structural rearrangements, while secondary structure elements guide large parts of the molecule along the transition to the correct final conformation.« less

  4. Fast analysis of molecular dynamics trajectories with graphics processing units-Radial distribution function histogramming

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Levine, Benjamin G., E-mail: ben.levine@temple.ed; Stone, John E., E-mail: johns@ks.uiuc.ed; Kohlmeyer, Axel, E-mail: akohlmey@temple.ed

    2011-05-01

    The calculation of radial distribution functions (RDFs) from molecular dynamics trajectory data is a common and computationally expensive analysis task. The rate limiting step in the calculation of the RDF is building a histogram of the distance between atom pairs in each trajectory frame. Here we present an implementation of this histogramming scheme for multiple graphics processing units (GPUs). The algorithm features a tiling scheme to maximize the reuse of data at the fastest levels of the GPU's memory hierarchy and dynamic load balancing to allow high performance on heterogeneous configurations of GPUs. Several versions of the RDF algorithm aremore » presented, utilizing the specific hardware features found on different generations of GPUs. We take advantage of larger shared memory and atomic memory operations available on state-of-the-art GPUs to accelerate the code significantly. The use of atomic memory operations allows the fast, limited-capacity on-chip memory to be used much more efficiently, resulting in a fivefold increase in performance compared to the version of the algorithm without atomic operations. The ultimate version of the algorithm running in parallel on four NVIDIA GeForce GTX 480 (Fermi) GPUs was found to be 92 times faster than a multithreaded implementation running on an Intel Xeon 5550 CPU. On this multi-GPU hardware, the RDF between two selections of 1,000,000 atoms each can be calculated in 26.9 s per frame. The multi-GPU RDF algorithms described here are implemented in VMD, a widely used and freely available software package for molecular dynamics visualization and analysis.« less

  5. Fast Analysis of Molecular Dynamics Trajectories with Graphics Processing Units—Radial Distribution Function Histogramming

    PubMed Central

    Stone, John E.; Kohlmeyer, Axel

    2011-01-01

    The calculation of radial distribution functions (RDFs) from molecular dynamics trajectory data is a common and computationally expensive analysis task. The rate limiting step in the calculation of the RDF is building a histogram of the distance between atom pairs in each trajectory frame. Here we present an implementation of this histogramming scheme for multiple graphics processing units (GPUs). The algorithm features a tiling scheme to maximize the reuse of data at the fastest levels of the GPU’s memory hierarchy and dynamic load balancing to allow high performance on heterogeneous configurations of GPUs. Several versions of the RDF algorithm are presented, utilizing the specific hardware features found on different generations of GPUs. We take advantage of larger shared memory and atomic memory operations available on state-of-the-art GPUs to accelerate the code significantly. The use of atomic memory operations allows the fast, limited-capacity on-chip memory to be used much more efficiently, resulting in a fivefold increase in performance compared to the version of the algorithm without atomic operations. The ultimate version of the algorithm running in parallel on four NVIDIA GeForce GTX 480 (Fermi) GPUs was found to be 92 times faster than a multithreaded implementation running on an Intel Xeon 5550 CPU. On this multi-GPU hardware, the RDF between two selections of 1,000,000 atoms each can be calculated in 26.9 seconds per frame. The multi-GPU RDF algorithms described here are implemented in VMD, a widely used and freely available software package for molecular dynamics visualization and analysis. PMID:21547007

  6. Laser program annual report, 1980

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Coleman, L.W.; Krupke, W.F.; Strack, J.R.

    1981-06-01

    Volume 2 contains five sections that cover the areas of target design, target fabrication, diagnostics, and fusion experiments. Section 3 reports on target design activities, plasma theory and simulation, code development, and atomic theory. Section 4 presents the accomplishments of the Target Fabrication Group, Section 5 contains the results of our diagnostics development, and Section 6 describes advances made in the management and analysis of experimental data. Finally, Section 7 in Volume 2 reports the results of laser target experiments conducted during the year.

  7. Hydrocarbon-Fueled Rocket Engine Plume Diagnostics: Analytical Developments and Experimental Results

    NASA Technical Reports Server (NTRS)

    Tejwani, Gopal D.; McVay, Gregory P.; Langford, Lester A.; St. Cyr, William W.

    2006-01-01

    A viewgraph presentation describing experimental results and analytical developments about plume diagnostics for hydrocarbon-fueled rocket engines is shown. The topics include: 1) SSC Plume Diagnostics Background; 2) Engine Health Monitoring Approach; 3) Rocket Plume Spectroscopy Simulation Code; 4) Spectral Simulation for 10 Atomic Species and for 11 Diatomic Molecular Electronic Bands; 5) "Best" Lines for Plume Diagnostics for Hydrocarbon-Fueled Rocket Engines; 6) Experimental Set Up for the Methane Thruster Test Program and Experimental Results; and 7) Summary and Recommendations.

  8. Neutronics Assessments for a RIA Fragmentation Line Beam Dump Concept

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Boles, J L; Reyes, S; Ahle, L E

    Heavy ion and radiation transport calculations are in progress for conceptual beam dump designs for the fragmentation line of the proposed Rare Isotope Accelerator (RIA). Using the computer code PHITS, a preliminary design of a motor-driven rotating wheel beam dump and adjacent downstream multipole has been modeled. Selected results of these calculations are given, including neutron and proton flux in the wheel, absorbed dose and displacements per atom in the hub materials, and heating from prompt radiation and from decay heat in the multipole.

  9. An Essential Protein Repair Enzyme: Investigation of the Molecular Recognition Mechanism of Methionine Sulfoxide Reductase A

    DTIC Science & Technology

    2008-05-01

    4 ). The three-dimensional spatial orientation of the atoms for these resolved solution structures (Protein Data Bank accession codes: 2gt3...Crystal structure of the Escherichia coli peptide methionine sulphoxide reductase at 1.9 Å resolution . Struct. Fold. Des. 8: 1167 – 1178. 2 . Brot...sources (8). There is a 67% sequence identity between the E.coli and human MsrA ( 2 ). N-terminus C-terminus Figure 2 . Three-dimensional structure

  10. Efficient hybrid-symbolic methods for quantum mechanical calculations

    NASA Astrophysics Data System (ADS)

    Scott, T. C.; Zhang, Wenxing

    2015-06-01

    We present hybrid symbolic-numerical tools to generate optimized numerical code for rapid prototyping and fast numerical computation starting from a computer algebra system (CAS) and tailored to any given quantum mechanical problem. Although a major focus concerns the quantum chemistry methods of H. Nakatsuji which has yielded successful and very accurate eigensolutions for small atoms and molecules, the tools are general and may be applied to any basis set calculation with a variational principle applied to its linear and non-linear parameters.

  11. Swedish Defence Research Abstracts 1980/81-3 (Froe Forsvars Forsknings Referat 1980/81-3).

    DTIC Science & Technology

    1981-11-01

    computes the refractive index or the thickness of thin mono- or multi -layer films. The program is written in Fortran and is adapted to the ellipsometer at...Unmnnounced EtN8PECT: Justlflotl Distribution/ Availability Codes Avail and/or Dist Special 2 Index to FRO 80/81-3 A PROTECTION - ATOMIC Al The nuclear...aberrations in PHA-stimulated human lymphocytes in the GI stage (in English) B PROTECTION - BIOLOGICAL BI Threat scenario (119) Epidemiological aspects

  12. Theoretical Investigation Leading to Energy Storage in Atomic and Molecular Systems

    DTIC Science & Technology

    1990-12-01

    can be calculated in a single run. 21 j) Non-gradient optimization of basis function exponents is possible. The source code can be modified to carry...basis. The 10s3p/5s3p basis consists of the 9s/4s contraction of Siegbahn and Liu (Reference 91) augmented by a diffuse s-type function ( exponent ...vibrational modes. Introduction of diffuse basis functions and optimization of the d-orbital exponents have a small but important effect on the

  13. Quantum Turbulence ---Another da Vinci Code---

    NASA Astrophysics Data System (ADS)

    Tsubota, M.

    Quantum turbulence comprises a tangle of quantized vorticeswhich are stable topological defects created by Bose-Einstein condensation, being realized in superfluid helium and atomic Bose-Einstein condensates. In recent years there has been a growing interest in quantum turbulence. One of the important motivations is to understand the relation between quantum and classical turbulence. Quantum turbulence is expected to be much simpler than usual classical turbulence and give a prototype of turbulence. This article reviews shortly the recent research developments on quantum turbulence.

  14. Radiative transfer in molecular lines

    NASA Astrophysics Data System (ADS)

    Asensio Ramos, A.; Trujillo Bueno, J.; Cernicharo, J.

    2001-07-01

    The highly convergent iterative methods developed by Trujillo Bueno and Fabiani Bendicho (1995) for radiative transfer (RT) applications are generalized to spherical symmetry with velocity fields. These RT methods are based on Jacobi, Gauss-Seidel (GS), and SOR iteration and they form the basis of a new NLTE multilevel transfer code for atomic and molecular lines. The benchmark tests carried out so far are presented and discussed. The main aim is to develop a number of powerful RT tools for the theoretical interpretation of molecular spectra.

  15. Poem: A Fast Monte Carlo Code for the Calculation of X-Ray Transition Zone Dose and Current

    DTIC Science & Technology

    1975-01-15

    stored on the photon interaction data tape. Following the photoelectric ionization the atom will relax emitting either a fluorescent photon or an Auger 50...shell fluorescence yield CL have been obtained from the Storm and Israel1 9 and 25 Bambynek, et al. compilations, with preference given to the...Bambynek compilation, and stored on the photon inter- action data tape. The mean M fluorescence yield wM is approximated by zero. The total electron source

  16. SC'11 Poster: A Highly Efficient MGPT Implementation for LAMMPS; with Strong Scaling

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Oppelstrup, T; Stukowski, A; Marian, J

    2011-12-07

    The MGPT potential has been implemented as a drop in package to the general molecular dynamics code LAMMPS. We implement an improved communication scheme that shrinks the communication layer thickness, and increases the load balancing. This results in unprecedented strong scaling, and speedup continuing beyond 1/8 atom/core. In addition, we have optimized the small matrix linear algebra with generic blocking (for all processors) and specific SIMD intrinsics for vectorization on Intel, AMD, and BlueGene CPUs.

  17. Localized basis sets for unbound electrons in nanoelectronics.

    PubMed

    Soriano, D; Jacob, D; Palacios, J J

    2008-02-21

    It is shown how unbound electron wave functions can be expanded in a suitably chosen localized basis sets for any desired range of energies. In particular, we focus on the use of Gaussian basis sets, commonly used in first-principles codes. The possible usefulness of these basis sets in a first-principles description of field emission or scanning tunneling microscopy at large bias is illustrated by studying a simpler related phenomenon: The lifetime of an electron in a H atom subjected to a strong electric field.

  18. Multivariate temporal dictionary learning for EEG.

    PubMed

    Barthélemy, Q; Gouy-Pailler, C; Isaac, Y; Souloumiac, A; Larue, A; Mars, J I

    2013-04-30

    This article addresses the issue of representing electroencephalographic (EEG) signals in an efficient way. While classical approaches use a fixed Gabor dictionary to analyze EEG signals, this article proposes a data-driven method to obtain an adapted dictionary. To reach an efficient dictionary learning, appropriate spatial and temporal modeling is required. Inter-channels links are taken into account in the spatial multivariate model, and shift-invariance is used for the temporal model. Multivariate learned kernels are informative (a few atoms code plentiful energy) and interpretable (the atoms can have a physiological meaning). Using real EEG data, the proposed method is shown to outperform the classical multichannel matching pursuit used with a Gabor dictionary, as measured by the representative power of the learned dictionary and its spatial flexibility. Moreover, dictionary learning can capture interpretable patterns: this ability is illustrated on real data, learning a P300 evoked potential. Copyright © 2013 Elsevier B.V. All rights reserved.

  19. Embedded-cluster calculations in a numeric atomic orbital density-functional theory framework.

    PubMed

    Berger, Daniel; Logsdail, Andrew J; Oberhofer, Harald; Farrow, Matthew R; Catlow, C Richard A; Sherwood, Paul; Sokol, Alexey A; Blum, Volker; Reuter, Karsten

    2014-07-14

    We integrate the all-electron electronic structure code FHI-aims into the general ChemShell package for solid-state embedding quantum and molecular mechanical (QM/MM) calculations. A major undertaking in this integration is the implementation of pseudopotential functionality into FHI-aims to describe cations at the QM/MM boundary through effective core potentials and therewith prevent spurious overpolarization of the electronic density. Based on numeric atomic orbital basis sets, FHI-aims offers particularly efficient access to exact exchange and second order perturbation theory, rendering the established QM/MM setup an ideal tool for hybrid and double-hybrid level density functional theory calculations of solid systems. We illustrate this capability by calculating the reduction potential of Fe in the Fe-substituted ZSM-5 zeolitic framework and the reaction energy profile for (photo-)catalytic water oxidation at TiO2(110).

  20. Embedded-cluster calculations in a numeric atomic orbital density-functional theory framework

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Berger, Daniel, E-mail: daniel.berger@ch.tum.de; Oberhofer, Harald; Reuter, Karsten

    2014-07-14

    We integrate the all-electron electronic structure code FHI-aims into the general ChemShell package for solid-state embedding quantum and molecular mechanical (QM/MM) calculations. A major undertaking in this integration is the implementation of pseudopotential functionality into FHI-aims to describe cations at the QM/MM boundary through effective core potentials and therewith prevent spurious overpolarization of the electronic density. Based on numeric atomic orbital basis sets, FHI-aims offers particularly efficient access to exact exchange and second order perturbation theory, rendering the established QM/MM setup an ideal tool for hybrid and double-hybrid level density functional theory calculations of solid systems. We illustrate this capabilitymore » by calculating the reduction potential of Fe in the Fe-substituted ZSM-5 zeolitic framework and the reaction energy profile for (photo-)catalytic water oxidation at TiO{sub 2}(110)« less

  1. Sheet, ligament and droplet formation in swirling primary atomization

    NASA Astrophysics Data System (ADS)

    Shao, Changxiao; Luo, Kun; Chai, Min; Fan, Jianren

    2018-04-01

    We report direct numerical simulations of swirling liquid atomization to understand the physical mechanism underlying the sheet breakup of a non-turbulent liquid swirling jet which lacks in-depth investigation. The volume-of-fluid (VOF) method coupled with adapted mesh refinement (AMR) technique in GERRIS code is employed in the present simulation. The mechanisms of sheet, ligament and droplet formation are investigated. It is observed that the olive-shape sheet structure is similar to the experimental result qualitatively. The numerical results show that surface tension, pressure difference and swirling effect contribute to the contraction and extension of liquid sheet. The ligament formation is partially at the sheet rim or attributed to the extension of liquid hole. Especially, the movement of hairpin vortex exerts by an anti-radial direction force to the sheet surface and leads to the sheet thinness. In addition, droplet formation is attributed to breakup of ligament and central sheet.

  2. Kinetic Simulation and Energetic Neutral Atom Imaging of the Magnetosphere

    NASA Technical Reports Server (NTRS)

    Fok, Mei-Ching H.

    2011-01-01

    Advanced simulation tools and measurement techniques have been developed to study the dynamic magnetosphere and its response to drivers in the solar wind. The Comprehensive Ring Current Model (CRCM) is a kinetic code that solves the 3D distribution in space, energy and pitch-angle information of energetic ions and electrons. Energetic Neutral Atom (ENA) imagers have been carried in past and current satellite missions. Global morphology of energetic ions were revealed by the observed ENA images. We have combined simulation and ENA analysis techniques to study the development of ring current ions during magnetic storms and substorms. We identify the timing and location of particle injection and loss. We examine the evolution of ion energy and pitch-angle distribution during different phases of a storm. In this talk we will discuss the findings from our ring current studies and how our simulation and ENA analysis tools can be applied to the upcoming TRIO-CINAMA mission.

  3. Wavelengths and energy levels for the Zn I isoelectronic sequence Ga[sup 1+] through Xe[sup 24+

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Seely, J.F.; Bar-Shalom, A.

    Calculated and experimentally determined transition energies were compared for the Zn I isoelectronic sequence for the elements with atomic numbers Z = 31-54. Using the Hebrew Univ. Lawrence Livermore Atomic Code, the excitation energies were calculated for the 109 levels belonging to the lowest 16 configurations of the types 4/4/[prime] and 4/5/[prime]. The analysis of the energy-level structure along the isoelectronic sequence accounted for a number of avoided level crossings. The differences between the calculated and experimental transition energies were determined for 24 transitions among the 4s[sup 2], 4s4p, 4p[sup 2], 4s4d, and 4s4f configurations. Wavelengths were predicted for previouslymore » unobserved transitions in the highly charged ions. 15 refs., 4 figs., 3 tabs.« less

  4. Droplet breakup in accelerating gas flows. Part 2: Secondary atomization

    NASA Technical Reports Server (NTRS)

    Zajac, L. J.

    1973-01-01

    An experimental investigation to determine the effects of an accelerating gas flow on the atomization characteristics of liquid sprays was conducted. The sprays were produced by impinging two liquid jets. The liquid was molten wax and the gas was nitrogen. The use of molten wax allowed for a quantitative measure of the resulting dropsize distribution. The results of this study, indicate that a significant amount of droplet breakup will occur as a result of the action of the gas on the liquid droplets. Empirical correlations are presented in terms of parameters that were found to affect the mass median dropsize most significantly, the orifice diameter, the liquid injection velocity, and the maximum gas velocity. An empirical correlation for the normalized dropsize distribution is also presented. These correlations are in a form that may be incorporated readily into existing combustion model computer codes for the purpose of calculating rocket engine combustion performance.

  5. Analysis of neutron spectrum effects on primary damage in tritium breeding blankets

    NASA Astrophysics Data System (ADS)

    Choi, Yong Hee; Joo, Han Gyu

    2012-07-01

    The effect of neutron spectrum on primary damages in a structural material of a tritium breeding blanket is investigated with a newly established recoil spectrum estimation system. First, a recoil spectrum generation code is developed to obtain the energy spectrum of primary knock-on atoms (PKAs) for a given neutron spectrum utilizing the latest ENDF/B data. Secondly, a method for approximating the high energy tail of the recoil spectrum is introduced to avoid expensive molecular dynamics calculations for high energy PKAs using the concept of recoil energy of the secondary knock-on atoms originated by the INtegration of CAScades (INCAS) model. Thirdly, the modified spectrum is combined with a set of molecular dynamics calculation results to estimate the primary damage parameters such as the number of surviving point defects. Finally, the neutron spectrum is varied by changing the material of the spectral shifter and the result in primary damage parameters is examined.

  6. Lanthanide/Actinide Opacities

    NASA Astrophysics Data System (ADS)

    Hungerford, Aimee; Fontes, Christopher J.

    2018-06-01

    Gravitational wave observations benefit from accompanying electromagnetic signals in order to accurately determine the sky positions of the sources. The ejecta of neutron star mergers are expected to produce such electromagnetic transients, called macronovae (e.g. the recent and unprecedented observation of GW170817). Characteristics of the ejecta include large velocity gradients and the presence of heavy r-process elements, which pose significant challenges to the accurate calculation of radiative opacities and radiation transport. Opacities include a dense forest of bound-bound features arising from near-neutral lanthanide and actinide elements. Here we present an overview of current theoretical opacity determinations that are used by neutron star merger light curve modelers. We will touch on atomic physics and plasma modeling codes that are used to generate these opacities, as well as the limited body of laboratory experiments that may serve as points of validation for these complex atomic physics calculations.

  7. QMCPACK: an open source ab initio quantum Monte Carlo package for the electronic structure of atoms, molecules and solids

    NASA Astrophysics Data System (ADS)

    Kim, Jeongnim; Baczewski, Andrew D.; Beaudet, Todd D.; Benali, Anouar; Chandler Bennett, M.; Berrill, Mark A.; Blunt, Nick S.; Josué Landinez Borda, Edgar; Casula, Michele; Ceperley, David M.; Chiesa, Simone; Clark, Bryan K.; Clay, Raymond C., III; Delaney, Kris T.; Dewing, Mark; Esler, Kenneth P.; Hao, Hongxia; Heinonen, Olle; Kent, Paul R. C.; Krogel, Jaron T.; Kylänpää, Ilkka; Li, Ying Wai; Lopez, M. Graham; Luo, Ye; Malone, Fionn D.; Martin, Richard M.; Mathuriya, Amrita; McMinis, Jeremy; Melton, Cody A.; Mitas, Lubos; Morales, Miguel A.; Neuscamman, Eric; Parker, William D.; Pineda Flores, Sergio D.; Romero, Nichols A.; Rubenstein, Brenda M.; Shea, Jacqueline A. R.; Shin, Hyeondeok; Shulenburger, Luke; Tillack, Andreas F.; Townsend, Joshua P.; Tubman, Norm M.; Van Der Goetz, Brett; Vincent, Jordan E.; ChangMo Yang, D.; Yang, Yubo; Zhang, Shuai; Zhao, Luning

    2018-05-01

    QMCPACK is an open source quantum Monte Carlo package for ab initio electronic structure calculations. It supports calculations of metallic and insulating solids, molecules, atoms, and some model Hamiltonians. Implemented real space quantum Monte Carlo algorithms include variational, diffusion, and reptation Monte Carlo. QMCPACK uses Slater–Jastrow type trial wavefunctions in conjunction with a sophisticated optimizer capable of optimizing tens of thousands of parameters. The orbital space auxiliary-field quantum Monte Carlo method is also implemented, enabling cross validation between different highly accurate methods. The code is specifically optimized for calculations with large numbers of electrons on the latest high performance computing architectures, including multicore central processing unit and graphical processing unit systems. We detail the program’s capabilities, outline its structure, and give examples of its use in current research calculations. The package is available at http://qmcpack.org.

  8. Simultaneous estimation of plasma parameters from spectroscopic data of neutral helium using least square fitting of CR-model

    NASA Astrophysics Data System (ADS)

    Jain, Jalaj; Prakash, Ram; Vyas, Gheesa Lal; Pal, Udit Narayan; Chowdhuri, Malay Bikas; Manchanda, Ranjana; Halder, Nilanjan; Choyal, Yaduvendra

    2015-12-01

    In the present work an effort has been made to estimate the plasma parameters simultaneously like—electron density, electron temperature, ground state atom density, ground state ion density and metastable state density from the observed visible spectra of penning plasma discharge (PPD) source using least square fitting. The analysis is performed for the prominently observed neutral helium lines. The atomic data and analysis structure (ADAS) database is used to provide the required collisional-radiative (CR) photon emissivity coefficients (PECs) values under the optical thin plasma condition in the analysis. With this condition the estimated plasma temperature from the PPD is found rather high. It is seen that the inclusion of opacity in the observed spectral lines through PECs and addition of diffusion of neutrals and metastable state species in the CR-model code analysis improves the electron temperature estimation in the simultaneous measurement.

  9. Computational Investigation of Graphene-Carbon Nanotube-Polymer Composite

    NASA Astrophysics Data System (ADS)

    Jha, Sanjiv; Roth, Michael; Todde, Guido; Subramanian, Gopinath; Shukla, Manoj; Univ of Southern Mississippi Collaboration; US Army Engineer Research; Development Center 3909 Halls Ferry Road Vicksburg, MS 39180, USA Collaboration

    Graphene is a single atom thick two dimensional carbon sheet where sp2 -hybridized carbon atoms are arranged in a honeycomb structure. The functionalization of graphene and carbon nanotubes (CNTs) with polymer is a route for developing high performance nanocomposite materials. We study the interfacial interactions among graphene, CNT, and Nylon 6 polymer using computational methods based on density functional theory (DFT) and empirical force-field. Our DFT calculations are carried out using Quantum-ESPRESSO electronic structure code with van der Waals functional (vdW-DF2), whereas the empirical calculations are performed using LAMMPS with the COMPASS force-field. Our results demonstrated that the interactions between (8,8) CNT and graphene, and between CNT/graphene and Nylon 6 consist mostly of van der Waals type. The computed Young's moduli indicated that the mechanical properties of carbon nanostructures are enhanced by their interactions with polymer. The presence of Stone-Wales (SW) defects lowered the Young's moduli of carbon nanostructures.

  10. Relaxation of Actinide Surfaces: An All Electron Study

    NASA Astrophysics Data System (ADS)

    Atta-Fynn, Raymond; Dholabhai, Pratik; Ray, Asok

    2006-10-01

    Fully relativistic full potential density functional calculations with a linearized augmented plane wave plus local orbitals basis (LAPW + lo) have been performed to investigate the relaxations of heavy actinide surfaces, namely the (111) surface of fcc δ-Pu and the (0001) surface of dhcp Am using WIEN2k. This code uses the LAPW + lo method with the unit cell divided into non-overlapping atom-centered spheres and an interstitial region. The APW+lo basis is used to describe all s, p, d, and f states and LAPW basis to describe all higher angular momentum states. Each surface was modeled by a three-layer periodic slab separated by 60 Bohr vacuum with four atoms per surface unit cell. In general, we have found a contraction of the interlayer separations for both Pu and Am. We will report, in detail, the electronic and geometric structures of the relaxed surfaces and comparisons with the respective non-relaxed surfaces.

  11. Incoherent dictionary learning for reducing crosstalk noise in least-squares reverse time migration

    NASA Astrophysics Data System (ADS)

    Wu, Juan; Bai, Min

    2018-05-01

    We propose to apply a novel incoherent dictionary learning (IDL) algorithm for regularizing the least-squares inversion in seismic imaging. The IDL is proposed to overcome the drawback of traditional dictionary learning algorithm in losing partial texture information. Firstly, the noisy image is divided into overlapped image patches, and some random patches are extracted for dictionary learning. Then, we apply the IDL technology to minimize the coherency between atoms during dictionary learning. Finally, the sparse representation problem is solved by a sparse coding algorithm, and image is restored by those sparse coefficients. By reducing the correlation among atoms, it is possible to preserve most of the small-scale features in the image while removing much of the long-wavelength noise. The application of the IDL method to regularization of seismic images from least-squares reverse time migration shows successful performance.

  12. QMCPACK: an open source ab initio quantum Monte Carlo package for the electronic structure of atoms, molecules and solids.

    PubMed

    Kim, Jeongnim; Baczewski, Andrew T; Beaudet, Todd D; Benali, Anouar; Bennett, M Chandler; Berrill, Mark A; Blunt, Nick S; Borda, Edgar Josué Landinez; Casula, Michele; Ceperley, David M; Chiesa, Simone; Clark, Bryan K; Clay, Raymond C; Delaney, Kris T; Dewing, Mark; Esler, Kenneth P; Hao, Hongxia; Heinonen, Olle; Kent, Paul R C; Krogel, Jaron T; Kylänpää, Ilkka; Li, Ying Wai; Lopez, M Graham; Luo, Ye; Malone, Fionn D; Martin, Richard M; Mathuriya, Amrita; McMinis, Jeremy; Melton, Cody A; Mitas, Lubos; Morales, Miguel A; Neuscamman, Eric; Parker, William D; Pineda Flores, Sergio D; Romero, Nichols A; Rubenstein, Brenda M; Shea, Jacqueline A R; Shin, Hyeondeok; Shulenburger, Luke; Tillack, Andreas F; Townsend, Joshua P; Tubman, Norm M; Van Der Goetz, Brett; Vincent, Jordan E; Yang, D ChangMo; Yang, Yubo; Zhang, Shuai; Zhao, Luning

    2018-05-16

    QMCPACK is an open source quantum Monte Carlo package for ab initio electronic structure calculations. It supports calculations of metallic and insulating solids, molecules, atoms, and some model Hamiltonians. Implemented real space quantum Monte Carlo algorithms include variational, diffusion, and reptation Monte Carlo. QMCPACK uses Slater-Jastrow type trial wavefunctions in conjunction with a sophisticated optimizer capable of optimizing tens of thousands of parameters. The orbital space auxiliary-field quantum Monte Carlo method is also implemented, enabling cross validation between different highly accurate methods. The code is specifically optimized for calculations with large numbers of electrons on the latest high performance computing architectures, including multicore central processing unit and graphical processing unit systems. We detail the program's capabilities, outline its structure, and give examples of its use in current research calculations. The package is available at http://qmcpack.org.

  13. An investigation into the role of metastable states on excited populations of weakly ionized argon plasmas, with applications for optical diagnostics

    NASA Astrophysics Data System (ADS)

    Arnold, Nicholas; Loch, Stuart; Ballance, Connor; Thomas, Ed

    2017-10-01

    Low temperature plasmas (Te < 10 eV) are ubiquitous in the medical, industrial, basic, and dusty plasma communities, and offer an opportunity for researchers to gain a better understanding of atomic processes in plasmas. Here, we report on a new atomic dataset for neutral and low charge states of argon, from which rate coefficients and cross-sections for the electron-impact excitation of neutral argon are determined. We benchmark by comparing with electron impact excitation cross-sections available in the literature, with very good agreement. We have used the Atomic Data and Analysis Structure (ADAS) code suite to calculate a level-resolved, generalized collisional-radiative (GCR) model for line emission in low temperature argon plasmas. By combining our theoretical model with experimental electron temperature, density, and spectral measurements from the Auburn Linear eXperiment for Instability Studies (ALEXIS), we have developed diagnostic techniques to measure metastable fraction, electron temperature, and electron density. In the future we hope to refine our methods, and extend our model to plasmas other than ALEXIS. Supported by the U.S. Department of Energy. Grant Number: DE-FG02-00ER54476.

  14. Large-scale quantum transport calculations for electronic devices with over ten thousand atoms

    NASA Astrophysics Data System (ADS)

    Lu, Wenchang; Lu, Yan; Xiao, Zhongcan; Hodak, Miro; Briggs, Emil; Bernholc, Jerry

    The non-equilibrium Green's function method (NEGF) has been implemented in our massively parallel DFT software, the real space multigrid (RMG) code suite. Our implementation employs multi-level parallelization strategies and fully utilizes both multi-core CPUs and GPU accelerators. Since the cost of the calculations increases dramatically with the number of orbitals, an optimal basis set is crucial for including a large number of atoms in the ``active device'' part of the simulations. In our implementation, the localized orbitals are separately optimized for each principal layer of the device region, in order to obtain an accurate and optimal basis set. As a large example, we calculated the transmission characteristics of a Si nanowire p-n junction. The nanowire is along (110) direction in order to minimize the number dangling bonds that are saturated by H atoms. Its diameter is 3 nm. The length of 24 nm is necessary because of the long-range screening length in Si. Our calculations clearly show the I-V characteristics of a diode, i.e., the current increases exponentially with forward bias and is near zero with backward bias. Other examples will also be presented, including three-terminal transistors and large sensor structures.

  15. Atom Resonance Lines for Modeling Atmosphere: Studies of Pressure-Broadening of Alkali Atom Resonance Lines for Modeling Atmospheres of Extrasolar Giant Planets and Brown Dwarfs

    NASA Technical Reports Server (NTRS)

    Hasan, Hashima (Technical Monitor); Kirby, K.; Babb, J.; Yoshino, K.

    2005-01-01

    We report on progress made in a joint program of theoretical and experimental research to study the line-broadening of alkali atom resonance lines due to collisions with species such as helium and molecular hydrogen. Accurate knowledge of the line profiles of Na and K as a function of temperature and pressure will allow such lines to serve as valuable diagnostics of the atmospheres of brown dwarfs and extra-solar giant planets. A new experimental apparatus has been designed, built and tested over the past year, and we are poised to begin collecting data on the first system of interest, the potassium resonance lines perturbed by collisions with helium. On the theoretical front, calculations of line-broadening due to sodium collisions with helium are nearly complete, using accurate molecular potential energy curves and transition moments just recently computed for this system. In addition we have completed calculations of the three relevant potential energy curves and associated transition moments for K - He, using the MOLPRO quantum chemistry codes. Currently, calculations of the potential surfaces describing K-H2 are in progress.

  16. Inelastic transport theory from first principles: Methodology and application to nanoscale devices

    NASA Astrophysics Data System (ADS)

    Frederiksen, Thomas; Paulsson, Magnus; Brandbyge, Mads; Jauho, Antti-Pekka

    2007-05-01

    We describe a first-principles method for calculating electronic structure, vibrational modes and frequencies, electron-phonon couplings, and inelastic electron transport properties of an atomic-scale device bridging two metallic contacts under nonequilibrium conditions. The method extends the density-functional codes SIESTA and TRANSIESTA that use atomic basis sets. The inelastic conductance characteristics are calculated using the nonequilibrium Green’s function formalism, and the electron-phonon interaction is addressed with perturbation theory up to the level of the self-consistent Born approximation. While these calculations often are computationally demanding, we show how they can be approximated by a simple and efficient lowest order expansion. Our method also addresses effects of energy dissipation and local heating of the junction via detailed calculations of the power flow. We demonstrate the developed procedures by considering inelastic transport through atomic gold wires of various lengths, thereby extending the results presented in Frederiksen [Phys. Rev. Lett. 93, 256601 (2004)]. To illustrate that the method applies more generally to molecular devices, we also calculate the inelastic current through different hydrocarbon molecules between gold electrodes. Both for the wires and the molecules our theory is in quantitative agreement with experiments, and characterizes the system-specific mode selectivity and local heating.

  17. Monte Carlo simulation of electrothermal atomization on a desktop personal computer

    NASA Astrophysics Data System (ADS)

    Histen, Timothy E.; Güell, Oscar A.; Chavez, Iris A.; Holcombea, James A.

    1996-07-01

    Monte Carlo simulations have been applied to electrothermal atomization (ETA) using a tubular atomizer (e.g. graphite furnace) because of the complexity in the geometry, heating, molecular interactions, etc. The intense computational time needed to accurately model ETA often limited its effective implementation to the use of supercomputers. However, with the advent of more powerful desktop processors, this is no longer the case. A C-based program has been developed and can be used under Windows TM or DOS. With this program, basic parameters such as furnace dimensions, sample placement, furnace heating and kinetic parameters such as activation energies for desorption and adsorption can be varied to show the absorbance profile dependence on these parameters. Even data such as time-dependent spatial distribution of analyte inside the furnace can be collected. The DOS version also permits input of external temperaturetime data to permit comparison of simulated profiles with experimentally obtained absorbance data. The run-time versions are provided along with the source code. This article is an electronic publication in Spectrochimica Acta Electronica (SAE), the electronic section of Spectrochimica Acta Part B (SAB). The hardcopy text is accompanied by a diskette with a program (PC format), data files and text files.

  18. Vanadium fine-structure K-shell electron impact ionization cross sections for fast-electron diagnostic in laser–solid experiments

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Palmeri, P., E-mail: patrick.palmeri@umons.ac.be; Quinet, P., E-mail: pascal.quinet@umons.ac.be; IPNAS, Université de Liège, B-4000 Liège

    2015-09-15

    The K-shell electron impact ionization (EII) cross section, along with the K-shell fluorescence yield, is one of the key atomic parameters for fast-electron diagnostic in laser–solid experiments through the K-shell emission cross section. In addition, in a campaign dedicated to the modeling of the K lines of astrophysical interest (Palmeri et al. (2012)), the K-shell fluorescence yields for the K-vacancy fine-structure atomic levels of all the vanadium isonuclear ions have been calculated. In this study, the K-shell EII cross sections connecting the ground and the metastable levels of the parent vanadium ions to the daughter ions K-vacancy levels considered in Palmerimore » et al. (2012) have been determined. The relativistic distorted-wave (DW) approximation implemented in the FAC atomic code has been used for the incident electron kinetic energies up to 20 times the K-shell threshold energies. Moreover, the resulting DW cross sections have been extrapolated at higher energies using the asymptotic behavior of the modified relativistic binary encounter Bethe model (MRBEB) of Guerra et al. (2012) with the density-effect correction proposed by Davies et al. (2013)« less

  19. Molybdoenzyme That Catalyzes the Anaerobic Hydroxylation of a Tertiary Carbon Atom in the Side Chain of Cholesterol*

    PubMed Central

    Dermer, Juri; Fuchs, Georg

    2012-01-01

    Cholesterol is a ubiquitous hydrocarbon compound that can serve as substrate for microbial growth. This steroid and related cyclic compounds are recalcitrant due to their low solubility in water, complex ring structure, the presence of quaternary carbon atoms, and the low number of functional groups. Aerobic metabolism therefore makes use of reactive molecular oxygen as co-substrate of oxygenases to hydroxylate and cleave the sterane ring system. Consequently, anaerobic metabolism must substitute oxygenase-catalyzed steps by O2-independent hydroxylases. Here we show that one of the initial reactions of anaerobic cholesterol metabolism in the β-proteobacterium Sterolibacterium denitrificans is catalyzed by an unprecedented enzyme that hydroxylates the tertiary C25 atom of the side chain without molecular oxygen forming a tertiary alcohol. This steroid C25 dehydrogenase belongs to the dimethyl sulfoxide dehydrogenase molybdoenzyme family, the closest relative being ethylbenzene dehydrogenase. It is a heterotrimer, which is probably located at the periplasmic side of the membrane and contains one molybdenum cofactor, five [Fe-S] clusters, and one heme b. The draft genome of the organism contains several genes coding for related enzymes that probably replace oxygenases in steroid metabolism. PMID:22942275

  20. Semantic Interoperability for Computational Mineralogy: Experiences of the eMinerals Consortium

    NASA Astrophysics Data System (ADS)

    Walker, A. M.; White, T. O.; Dove, M. T.; Bruin, R. P.; Couch, P. A.; Tyer, R. P.

    2006-12-01

    The use of atomic scale computer simulation of minerals to obtain information for geophysics and environmental science has grown enormously over the past couple of decades. It is now routine to probe mineral behavior in the Earth's deep interior and in the surface environment by borrowing methods and simulation codes from computational chemistry and physics. It is becoming increasingly important to use methods embodied in more than one of these codes to solve any single scientific problem. However, scientific codes are rarely designed for easy interoperability and data exchange; data formats are often code-specific, poorly documented and fragile, liable to frequent change between software versions, and even compiler versions. This means that the scientist's simple desire to use the methodological approaches offered by multiple codes is frustrated, and even the sharing of data between collaborators becomes fraught with difficulties. The eMinerals consortium was formed in the early stages of the UK eScience program with the aim of developing the tools needed to apply atomic scale simulation to environmental problems in a grid-enabled world, and to harness the computational power offered by grid technologies to address some outstanding mineralogical problems. One example of the kind of problem we can tackle is the origin of the compressibility anomaly in silica glass. By passing data directly between simulation and analysis tools we were able to probe this effect in more detail than has previously been possible and have shown how the anomaly is related to the details of the amorphous structure. In order to approach this kind of problem we have constructed a mini-grid, a small scale and extensible combined compute- and data-grid that allows the execution of many calculations in parallel, and the transparent storage of semantically-rich marked-up result data. Importantly, we automatically capture multiple kinds of metadata and key results from each calculation. We believe that the lessons learned and tools developed will be useful in many areas of science beyond the computational mineralogy. Key tools that will be described include: a pure Fortran XML library (FoX) that presents XPath, SAX and DOM interfaces as well as permitting the easy production of valid XML from legacy Fortran programs; a job submission framework that automatically schedules calculations to remote grid resources, handles data staging and metadata capture; and a tool (AgentX) that map concepts from an ontology onto locations in documents of various formats that we use to enable data exchange.

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