Finite-Difference Solution for Laminar or Turbulent Boundary Layer Flow over Axisymmetric Bodies with Ideal Gas, CF4, or Equilibrium Air Chemistry

NASA Technical Reports Server (NTRS)

Hamilton, H. Harris, II; Millman, Daniel R.; Greendyke, Robert B.

1992-01-01

A computer code was developed that uses an implicit finite-difference technique to solve nonsimilar, axisymmetric boundary layer equations for both laminar and turbulent flow. The code can treat ideal gases, air in chemical equilibrium, and carbon tetrafluoride (CF4), which is a useful gas for hypersonic blunt-body simulations. This is the only known boundary layer code that can treat CF4. Comparisons with experimental data have demonstrated that accurate solutions are obtained. The method should prove useful as an analysis tool for comparing calculations with wind tunnel experiments and for making calculations about flight vehicles where equilibrium air chemistry assumptions are valid.

Finite-difference solution for laminar or turbulent boundary layer flow over axisymmetric bodies with ideal gas, CF4, or equilibrium air chemistry

NASA Astrophysics Data System (ADS)

Hamilton, H. Harris, II; Millman, Daniel R.; Greendyke, Robert B.

1992-12-01

A computer code was developed that uses an implicit finite-difference technique to solve nonsimilar, axisymmetric boundary layer equations for both laminar and turbulent flow. The code can treat ideal gases, air in chemical equilibrium, and carbon tetrafluoride (CF4), which is a useful gas for hypersonic blunt-body simulations. This is the only known boundary layer code that can treat CF4. Comparisons with experimental data have demonstrated that accurate solutions are obtained. The method should prove useful as an analysis tool for comparing calculations with wind tunnel experiments and for making calculations about flight vehicles where equilibrium air chemistry assumptions are valid.

Computational models for the viscous/inviscid analysis of jet aircraft exhaust plumes

NASA Astrophysics Data System (ADS)

Dash, S. M.; Pergament, H. S.; Thorpe, R. D.

1980-05-01

Computational models which analyze viscous/inviscid flow processes in jet aircraft exhaust plumes are discussed. These models are component parts of an NASA-LaRC method for the prediction of nozzle afterbody drag. Inviscid/shock processes are analyzed by the SCIPAC code which is a compact version of a generalized shock capturing, inviscid plume code (SCIPPY). The SCIPAC code analyzes underexpanded jet exhaust gas mixtures with a self-contained thermodynamic package for hydrocarbon exhaust products and air. A detailed and automated treatment of the embedded subsonic zones behind Mach discs is provided in this analysis. Mixing processes along the plume interface are analyzed by two upgraded versions of an overlaid, turbulent mixing code (BOAT) developed previously for calculating nearfield jet entrainment. The BOATAC program is a frozen chemistry version of BOAT containing the aircraft thermodynamic package as SCIPAC; BOATAB is an afterburning version with a self-contained aircraft (hydrocarbon/air) finite-rate chemistry package. The coupling of viscous and inviscid flow processes is achieved by an overlaid procedure with interactive effects accounted for by a displacement thickness type correction to the inviscid plume interface.

Computational models for the viscous/inviscid analysis of jet aircraft exhaust plumes. [predicting afterbody drag

NASA Technical Reports Server (NTRS)

Dash, S. M.; Pergament, H. S.; Thorpe, R. D.

1980-01-01

Computational models which analyze viscous/inviscid flow processes in jet aircraft exhaust plumes are discussed. These models are component parts of an NASA-LaRC method for the prediction of nozzle afterbody drag. Inviscid/shock processes are analyzed by the SCIPAC code which is a compact version of a generalized shock capturing, inviscid plume code (SCIPPY). The SCIPAC code analyzes underexpanded jet exhaust gas mixtures with a self-contained thermodynamic package for hydrocarbon exhaust products and air. A detailed and automated treatment of the embedded subsonic zones behind Mach discs is provided in this analysis. Mixing processes along the plume interface are analyzed by two upgraded versions of an overlaid, turbulent mixing code (BOAT) developed previously for calculating nearfield jet entrainment. The BOATAC program is a frozen chemistry version of BOAT containing the aircraft thermodynamic package as SCIPAC; BOATAB is an afterburning version with a self-contained aircraft (hydrocarbon/air) finite-rate chemistry package. The coupling of viscous and inviscid flow processes is achieved by an overlaid procedure with interactive effects accounted for by a displacement thickness type correction to the inviscid plume interface.

Comparison of FDNS liquid rocket engine plume computations with SPF/2

NASA Technical Reports Server (NTRS)

Kumar, G. N.; Griffith, D. O., II; Warsi, S. A.; Seaford, C. M.

1993-01-01

Prediction of a plume's shape and structure is essential to the evaluation of base region environments. The JANNAF standard plume flowfield analysis code SPF/2 predicts plumes well, but cannot analyze base regions. Full Navier-Stokes CFD codes can calculate both zones; however, before they can be used, they must be validated. The CFD code FDNS3D (Finite Difference Navier-Stokes Solver) was used to analyze the single plume of a Space Transportation Main Engine (STME) and comparisons were made with SPF/2 computations. Both frozen and finite rate chemistry models were employed as well as two turbulence models in SPF/2. The results indicate that FDNS3D plume computations agree well with SPF/2 predictions for liquid rocket engine plumes.

Experimental and analytical comparison of flowfields in a 110 N (25 lbf) H2/O2 rocket

NASA Technical Reports Server (NTRS)

Reed, Brian D.; Penko, Paul F.; Schneider, Steven J.; Kim, Suk C.

1991-01-01

A gaseous hydrogen/gaseous oxygen 110 N (25 lbf) rocket was examined through the RPLUS code using the full Navier-Stokes equations with finite rate chemistry. Performance tests were conducted on the rocket in an altitude test facility. Preliminary parametric analyses were performed for a range of mixture ratios and fuel film cooling pcts. It is shown that the computed values of specific impulse and characteristic exhaust velocity follow the trend of the experimental data. Specific impulse computed by the code is lower than the comparable test values by about two to three percent. The computed characteristic exhaust velocity values are lower than the comparable test values by three to four pct. Thrust coefficients computed by the code are found to be within two pct. of the measured values. It is concluded that the discrepancy between computed and experimental performance values could not be attributed to experimental uncertainty.

Computation of Reacting Flows in Combustion Processes

NASA Technical Reports Server (NTRS)

Keith, Theo G., Jr.; Chen, Kuo-Huey

1997-01-01

The main objective of this research was to develop an efficient three-dimensional computer code for chemically reacting flows. The main computer code developed is ALLSPD-3D. The ALLSPD-3D computer program is developed for the calculation of three-dimensional, chemically reacting flows with sprays. The ALL-SPD code employs a coupled, strongly implicit solution procedure for turbulent spray combustion flows. A stochastic droplet model and an efficient method for treatment of the spray source terms in the gas-phase equations are used to calculate the evaporating liquid sprays. The chemistry treatment in the code is general enough that an arbitrary number of reaction and species can be defined by the users. Also, it is written in generalized curvilinear coordinates with both multi-block and flexible internal blockage capabilities to handle complex geometries. In addition, for general industrial combustion applications, the code provides both dilution and transpiration cooling capabilities. The ALLSPD algorithm, which employs the preconditioning and eigenvalue rescaling techniques, is capable of providing efficient solution for flows with a wide range of Mach numbers. Although written for three-dimensional flows in general, the code can be used for two-dimensional and axisymmetric flow computations as well. The code is written in such a way that it can be run in various computer platforms (supercomputers, workstations and parallel processors) and the GUI (Graphical User Interface) should provide a user-friendly tool in setting up and running the code.

Effect of non-equilibrium flow chemistry and surface catalysis on surface heating to AFE

NASA Technical Reports Server (NTRS)

Stewart, David A.; Henline, William D.; Chen, Yih-Kanq

1991-01-01

The effect of nonequilibrium flow chemistry on the surface temperature distribution over the forebody heat shield on the Aeroassisted Flight Experiment (AFE) vehicle was investigated using a reacting boundary-layer code. Computations were performed by using boundary-layer-edge properties determined from global iterations between the boundary-layer code and flow field solutions from a viscous shock layer (VSL) and a full Navier-Stokes solution. Surface temperature distribution over the AFE heat shield was calculated for two flight conditions during a nominal AFE trajectory. This study indicates that the surface temperature distribution is sensitive to the nonequilibrium chemistry in the shock layer. Heating distributions over the AFE forebody calculated using nonequilibrium edge properties were similar to values calculated using the VSL program.

Multi-Zone Liquid Thrust Chamber Performance Code with Domain Decomposition for Parallel Processing

NASA Technical Reports Server (NTRS)

Navaz, Homayun K.

2002-01-01

Computational Fluid Dynamics (CFD) has considerably evolved in the last decade. There are many computer programs that can perform computations on viscous internal or external flows with chemical reactions. CFD has become a commonly used tool in the design and analysis of gas turbines, ramjet combustors, turbo-machinery, inlet ducts, rocket engines, jet interaction, missile, and ramjet nozzles. One of the problems of interest to NASA has always been the performance prediction for rocket and air-breathing engines. Due to the complexity of flow in these engines it is necessary to resolve the flowfield into a fine mesh to capture quantities like turbulence and heat transfer. However, calculation on a high-resolution grid is associated with a prohibitively increasing computational time that can downgrade the value of the CFD for practical engineering calculations. The Liquid Thrust Chamber Performance (LTCP) code was developed for NASA/MSFC (Marshall Space Flight Center) to perform liquid rocket engine performance calculations. This code is a 2D/axisymmetric full Navier-Stokes (NS) solver with fully coupled finite rate chemistry and Eulerian treatment of liquid fuel and/or oxidizer droplets. One of the advantages of this code has been the resemblance of its input file to the JANNAF (Joint Army Navy NASA Air Force Interagency Propulsion Committee) standard TDK code, and its automatic grid generation for JANNAF defined combustion chamber wall geometry. These options minimize the learning effort for TDK users, and make the code a good candidate for performing engineering calculations. Although the LTCP code was developed for liquid rocket engines, it is a general-purpose code and has been used for solving many engineering problems. However, the single zone formulation of the LTCP has limited the code to be applicable to problems with complex geometry. Furthermore, the computational time becomes prohibitively large for high-resolution problems with chemistry, two-equation turbulence model, and two-phase flow. To overcome these limitations, the LTCP code is rewritten to include the multi-zone capability with domain decomposition that makes it suitable for parallel processing, i.e., enabling the code to run every zone or sub-domain on a separate processor. This can reduce the run time by a factor of 6 to 8, depending on the problem.

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.

CAG12 - A CSCM based procedure for flow of an equilibrium chemically reacting gas

NASA Technical Reports Server (NTRS)

Green, M. J.; Davy, W. C.; Lombard, C. K.

1985-01-01

The Conservative Supra Characteristic Method (CSCM), an implicit upwind Navier-Stokes algorithm, is extended to the numerical simulation of flows in chemical equilibrium. The resulting computer code known as Chemistry and Gasdynamics Implicit - Version 2 (CAG12) is described. First-order accurate results are presented for inviscid and viscous Mach 20 flows of air past a hemisphere-cylinder. The solution procedure captures the bow shock in a chemically reacting gas, a technique that is needed for simulating high altitude, rarefied flows. In an initial effort to validate the code, the inviscid results are compared with published gasdynamic and chemistry solutions and satisfactorily agreement is obtained.

Thermodynamic equilibrium-air correlations for flowfield applications

NASA Technical Reports Server (NTRS)

Zoby, E. V.; Moss, J. N.

1981-01-01

Equilibrium-air thermodynamic correlations have been developed for flowfield calculation procedures. A comparison between the postshock results computed by the correlation equations and detailed chemistry calculations is very good. The thermodynamic correlations are incorporated in an approximate inviscid flowfield code with a convective heating capability for the purpose of defining the thermodynamic environment through the shock layer. Comparisons of heating rates computed by the approximate code and a viscous-shock-layer method are good. In addition to presenting the thermodynamic correlations, the impact of several viscosity models on the convective heat transfer is demonstrated.

Containment Sodium Chemistry Models in MELCOR.

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

Louie, David; Humphries, Larry L.; Denman, Matthew R

To meet regulatory needs for sodium fast reactors’ future development, including licensing requirements, Sandia National Laboratories is modernizing MELCOR, a severe accident analysis computer code developed for the U.S. Nuclear Regulatory Commission (NRC). Specifically, Sandia is modernizing MELCOR to include the capability to model sodium reactors. However, Sandia’s modernization effort primarily focuses on the containment response aspects of the sodium reactor accidents. Sandia began modernizing MELCOR in 2013 to allow a sodium coolant, rather than water, for conventional light water reactors. In the past three years, Sandia has been implementing the sodium chemistry containment models in CONTAIN-LMR, a legacy NRCmore » code, into MELCOR. These chemistry models include spray fire, pool fire and atmosphere chemistry models. Only the first two chemistry models have been implemented though it is intended to implement all these models into MELCOR. A new package called “NAC” has been created to manage the sodium chemistry model more efficiently. In 2017 Sandia began validating the implemented models in MELCOR by simulating available experiments. The CONTAIN-LMR sodium models include sodium atmosphere chemistry and sodium-concrete interaction models. This paper presents sodium property models, the implemented models, implementation issues, and a path towards validation against existing experimental data.« less

Optimizing Performance of Combustion Chemistry Solvers on Intel's Many Integrated Core (MIC) Architectures

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

Sitaraman, Hariswaran; Grout, Ray W

This work investigates novel algorithm designs and optimization techniques for restructuring chemistry integrators in zero and multidimensional combustion solvers, which can then be effectively used on the emerging generation of Intel's Many Integrated Core/Xeon Phi processors. These processors offer increased computing performance via large number of lightweight cores at relatively lower clock speeds compared to traditional processors (e.g. Intel Sandybridge/Ivybridge) used in current supercomputers. This style of processor can be productively used for chemistry integrators that form a costly part of computational combustion codes, in spite of their relatively lower clock speeds. Performance commensurate with traditional processors is achieved heremore » through the combination of careful memory layout, exposing multiple levels of fine grain parallelism and through extensive use of vendor supported libraries (Cilk Plus and Math Kernel Libraries). Important optimization techniques for efficient memory usage and vectorization have been identified and quantified. These optimizations resulted in a factor of ~ 3 speed-up using Intel 2013 compiler and ~ 1.5 using Intel 2017 compiler for large chemical mechanisms compared to the unoptimized version on the Intel Xeon Phi. The strategies, especially with respect to memory usage and vectorization, should also be beneficial for general purpose computational fluid dynamics codes.« less

Psi4NumPy: An Interactive Quantum Chemistry Programming Environment for Reference Implementations and Rapid Development.

PubMed

Smith, Daniel G A; Burns, Lori A; Sirianni, Dominic A; Nascimento, Daniel R; Kumar, Ashutosh; James, Andrew M; Schriber, Jeffrey B; Zhang, Tianyuan; Zhang, Boyi; Abbott, Adam S; Berquist, Eric J; Lechner, Marvin H; Cunha, Leonardo A; Heide, Alexander G; Waldrop, Jonathan M; Takeshita, Tyler Y; Alenaizan, Asem; Neuhauser, Daniel; King, Rollin A; Simmonett, Andrew C; Turney, Justin M; Schaefer, Henry F; Evangelista, Francesco A; DePrince, A Eugene; Crawford, T Daniel; Patkowski, Konrad; Sherrill, C David

2018-06-11

Psi4NumPy demonstrates the use of efficient computational kernels from the open-source Psi4 program through the popular NumPy library for linear algebra in Python to facilitate the rapid development of clear, understandable Python computer code for new quantum chemical methods, while maintaining a relatively low execution time. Using these tools, reference implementations have been created for a number of methods, including self-consistent field (SCF), SCF response, many-body perturbation theory, coupled-cluster theory, configuration interaction, and symmetry-adapted perturbation theory. Furthermore, several reference codes have been integrated into Jupyter notebooks, allowing background, underlying theory, and formula information to be associated with the implementation. Psi4NumPy tools and associated reference implementations can lower the barrier for future development of quantum chemistry methods. These implementations also demonstrate the power of the hybrid C++/Python programming approach employed by the Psi4 program.

Investigation of thermal protection systems effects on viscid and inviscid flow fields for manned entry systems

NASA Technical Reports Server (NTRS)

Bartlett, E. P.; Morse, H. L.; Tong, H.

1971-01-01

Procedures and methods for predicting aerothermodynamic heating to delta orbiter shuttle vehicles were reviewed. A number of approximate methods were found to be adequate for large scale parameter studies, but are considered inadequate for final design calculations. It is recommended that final design calculations be based on a computer code which accounts for nonequilibrium chemistry, streamline spreading, entropy swallowing, and turbulence. It is further recommended that this code be developed with the intent that it can be directly coupled with an exact inviscid flow field calculation when the latter becomes available. A nonsimilar, equilibrium chemistry computer code (BLIMP) was used to evaluate the effects of entropy swallowing, turbulence, and various three dimensional approximations. These solutions were compared with available wind tunnel data. It was found study that, for wind tunnel conditions, the effect of entropy swallowing and three dimensionality are small for laminar boundary layers but entropy swallowing causes a significant increase in turbulent heat transfer. However, it is noted that even small effects (say, 10-20%) may be important for the shuttle reusability concept.

A Sequential Fluid-mechanic Chemical-kinetic Model of Propane HCCI Combustion

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

Aceves, S M; Flowers, D L; Martinez-Frias, J

2000-11-29

We have developed a methodology for predicting combustion and emissions in a Homogeneous Charge Compression Ignition (HCCI) Engine. This methodology combines a detailed fluid mechanics code with a detailed chemical kinetics code. Instead of directly linking the two codes, which would require an extremely long computational time, the methodology consists of first running the fluid mechanics code to obtain temperature profiles as a function of time. These temperature profiles are then used as input to a multi-zone chemical kinetics code. The advantage of this procedure is that a small number of zones (10) is enough to obtain accurate results. Thismore » procedure achieves the benefits of linking the fluid mechanics and the chemical kinetics codes with a great reduction in the computational effort, to a level that can be handled with current computers. The success of this procedure is in large part a consequence of the fact that for much of the compression stroke the chemistry is inactive and thus has little influence on fluid mechanics and heat transfer. Then, when chemistry is active, combustion is rather sudden, leaving little time for interaction between chemistry and fluid mixing and heat transfer. This sequential methodology has been capable of explaining the main characteristics of HCCI combustion that have been observed in experiments. In this paper, we use our model to explore an HCCI engine running on propane. The paper compares experimental and numerical pressure traces, heat release rates, and hydrocarbon and carbon monoxide emissions. The results show an excellent agreement, even in parameters that are difficult to predict, such as chemical heat release rates. Carbon monoxide emissions are reasonably well predicted, even though it is intrinsically difficult to make good predictions of CO emissions in HCCI engines. The paper includes a sensitivity study on the effect of the heat transfer correlation on the results of the analysis. Importantly, the paper also shows a numerical study on how parameters such as swirl rate, crevices and ceramic walls could help in reducing HC and CO emissions from HCCI engines.« less

Reacting Chemistry Based Burn Model for Explosive Hydrocodes

NASA Astrophysics Data System (ADS)

Schwaab, Matthew; Greendyke, Robert; Steward, Bryan

2017-06-01

Currently, in hydrocodes designed to simulate explosive material undergoing shock-induced ignition, the state of the art is to use one of numerous reaction burn rate models. These burn models are designed to estimate the bulk chemical reaction rate. Unfortunately, these models are largely based on empirical data and must be recalibrated for every new material being simulated. We propose that the use of an equilibrium Arrhenius rate reacting chemistry model in place of these empirically derived burn models will improve the accuracy for these computational codes. Such models have been successfully used in codes simulating the flow physics around hypersonic vehicles. A reacting chemistry model of this form was developed for the cyclic nitramine RDX by the Naval Research Laboratory (NRL). Initial implementation of this chemistry based burn model has been conducted on the Air Force Research Laboratory's MPEXS multi-phase continuum hydrocode. In its present form, the burn rate is based on the destruction rate of RDX from NRL's chemistry model. Early results using the chemistry based burn model show promise in capturing deflagration to detonation features more accurately in continuum hydrocodes than previously achieved using empirically derived burn models.

A high performance scientific cloud computing environment for materials simulations

NASA Astrophysics Data System (ADS)

Jorissen, K.; Vila, F. D.; Rehr, J. J.

2012-09-01

We describe the development of a scientific cloud computing (SCC) platform that offers high performance computation capability. The platform consists of a scientific virtual machine prototype containing a UNIX operating system and several materials science codes, together with essential interface tools (an SCC toolset) that offers functionality comparable to local compute clusters. In particular, our SCC toolset provides automatic creation of virtual clusters for parallel computing, including tools for execution and monitoring performance, as well as efficient I/O utilities that enable seamless connections to and from the cloud. Our SCC platform is optimized for the Amazon Elastic Compute Cloud (EC2). We present benchmarks for prototypical scientific applications and demonstrate performance comparable to local compute clusters. To facilitate code execution and provide user-friendly access, we have also integrated cloud computing capability in a JAVA-based GUI. Our SCC platform may be an alternative to traditional HPC resources for materials science or quantum chemistry applications.

Hypersonic simulations using open-source CFD and DSMC solvers

NASA Astrophysics Data System (ADS)

Casseau, V.; Scanlon, T. J.; John, B.; Emerson, D. R.; Brown, R. E.

2016-11-01

Hypersonic hybrid hydrodynamic-molecular gas flow solvers are required to satisfy the two essential requirements of any high-speed reacting code, these being physical accuracy and computational efficiency. The James Weir Fluids Laboratory at the University of Strathclyde is currently developing an open-source hybrid code which will eventually reconcile the direct simulation Monte-Carlo method, making use of the OpenFOAM application called dsmcFoam, and the newly coded open-source two-temperature computational fluid dynamics solver named hy2Foam. In conjunction with employing the CVDV chemistry-vibration model in hy2Foam, novel use is made of the QK rates in a CFD solver. In this paper, further testing is performed, in particular with the CFD solver, to ensure its efficacy before considering more advanced test cases. The hy2Foam and dsmcFoam codes have shown to compare reasonably well, thus providing a useful basis for other codes to compare against.

Boost-phase discrimination research activities

NASA Technical Reports Server (NTRS)

Cooper, David M.; Deiwert, George S.

1989-01-01

Theoretical research in two areas was performed. The aerothermodynamics research focused on the hard-body and rocket plume flows. Analytical real gas models to describe finite rate chemistry were developed and incorporated into the three-dimensional flow codes. New numerical algorithms capable of treating multi-species reacting gas equations and treating flows with large gradients were also developed. The computational chemistry research focused on the determination of spectral radiative intensity factors, transport properties and reaction rates. Ab initio solutions to the Schrodinger equation provided potential energy curves transition moments (radiative probabilities and strengths) and potential energy surfaces. These surfaces were then coupled with classical particle reactive trajectories to compute reaction cross-sections and rates.

Modeling, Measurements, and Fundamental Database Development for Nonequilibrium Hypersonic Aerothermodynamics

NASA Technical Reports Server (NTRS)

Bose, Deepak

2012-01-01

The design of entry vehicles requires predictions of aerothermal environment during the hypersonic phase of their flight trajectories. These predictions are made using computational fluid dynamics (CFD) codes that often rely on physics and chemistry models of nonequilibrium processes. The primary processes of interest are gas phase chemistry, internal energy relaxation, electronic excitation, nonequilibrium emission and absorption of radiation, and gas-surface interaction leading to surface recession and catalytic recombination. NASAs Hypersonics Project is advancing the state-of-the-art in modeling of nonequilibrium phenomena by making detailed spectroscopic measurements in shock tube and arcjets, using ab-initio quantum mechanical techniques develop fundamental chemistry and spectroscopic databases, making fundamental measurements of finite-rate gas surface interactions, implementing of detailed mechanisms in the state-of-the-art CFD codes, The development of new models is based on validation with relevant experiments. We will present the latest developments and a roadmap for the technical areas mentioned above

Numerical study of hydrogen-air supersonic combustion by using elliptic and parabolized equations

NASA Technical Reports Server (NTRS)

Chitsomboon, T.; Tiwari, S. N.

1986-01-01

The two-dimensional Navier-Stokes and species continuity equations are used to investigate supersonic chemically reacting flow problems which are related to scramjet-engine configurations. A global two-step finite-rate chemistry model is employed to represent the hydrogen-air combustion in the flow. An algebraic turbulent model is adopted for turbulent flow calculations. The explicit unsplit MacCormack finite-difference algorithm is used to develop a computer program suitable for a vector processing computer. The computer program developed is then used to integrate the system of the governing equations in time until convergence is attained. The chemistry source terms in the species continuity equations are evaluated implicitly to alleviate stiffness associated with fast chemical reactions. The problems solved by the elliptic code are re-investigated by using a set of two-dimensional parabolized Navier-Stokes and species equations. A linearized fully-coupled fully-implicit finite difference algorithm is used to develop a second computer code which solves the governing equations by marching in spce rather than time, resulting in a considerable saving in computer resources. Results obtained by using the parabolized formulation are compared with the results obtained by using the fully-elliptic equations. The comparisons indicate fairly good agreement of the results of the two formulations.

Development and application of GASP 2.0

NASA Technical Reports Server (NTRS)

Mcgrory, W. D.; Huebner, L. D.; Slack, D. C.; Walters, R. W.

1992-01-01

GASP 2.0 represents a major new release of the computational fluid dynamics code in wide use by the aerospace community. The authors have spent the last two years analyzing the strengths and weaknesses of the previous version of the finite-rate chemistry, Navier Stokes solution algorithm. What has resulted is a completely redesigned computer code that offers two to four times the performance of previous versions while requiring as little as one quarter of the memory requirements. In addition to the improvements in efficiency over the original code, Version 2.0 contains many new features. A brief discussion of the improvements made to GASP, and an application using GASP 2.0 which demonstrates some of the new features are presented.

TABULATED EQUIVALENT SDR FLAMELET (TESF) MODEFL

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

KUNDU, PRITHWISH; AMEEN, mUHSIN MOHAMMED; UNNIKRISHNAN, UMESH

The code consists of an implementation of a novel tabulated combustion model for non-premixed flames in CFD solvers. This novel technique/model is used to implement an unsteady flamelet tabulation without using progress variables for non-premixed flames. It also has the capability to include history effects which is unique within tabulated flamelet models. The flamelet table generation code can be run in parallel to generate tables with large chemistry mechanisms in relatively short wall clock times. The combustion model/code reads these tables. This framework can be coupled with any CFD solver with RANS as well as LES turbulence models. This frameworkmore » enables CFD solvers to run large chemistry mechanisms with large number of grids at relatively lower computational costs. Currently it has been coupled with the Converge CFD code and validated against available experimental data. This model can be used to simulate non-premixed combustion in a variety of applications like reciprocating engines, gas turbines and industrial burners operating over a wide range of fuels.« less

Development of the general interpolants method for the CYBER 200 series of supercomputers

NASA Technical Reports Server (NTRS)

Stalnaker, J. F.; Robinson, M. A.; Spradley, L. W.; Kurzius, S. C.; Thoenes, J.

1988-01-01

The General Interpolants Method (GIM) is a 3-D, time-dependent, hybrid procedure for generating numerical analogs of the conservation laws. This study is directed toward the development and application of the GIM computer code for fluid dynamic research applications as implemented for the Cyber 200 series of supercomputers. An elliptic and quasi-parabolic version of the GIM code are discussed. Turbulence models, algebraic and differential equations, were added to the basic viscous code. An equilibrium reacting chemistry model and an implicit finite difference scheme are also included.

A Rocket Engine Design Expert System

NASA Technical Reports Server (NTRS)

Davidian, Kenneth J.

1989-01-01

The overall structure and capabilities of an expert system designed to evaluate rocket engine performance are described. The expert system incorporates a JANNAF standard reference computer code to determine rocket engine performance and a state of the art finite element computer code to calculate the interactions between propellant injection, energy release in the combustion chamber, and regenerative cooling heat transfer. Rule-of-thumb heuristics were incorporated for the H2-O2 coaxial injector design, including a minimum gap size constraint on the total number of injector elements. One dimensional equilibrium chemistry was used in the energy release analysis of the combustion chamber. A 3-D conduction and/or 1-D advection analysis is used to predict heat transfer and coolant channel wall temperature distributions, in addition to coolant temperature and pressure drop. Inputting values to describe the geometry and state properties of the entire system is done directly from the computer keyboard. Graphical display of all output results from the computer code analyses is facilitated by menu selection of up to five dependent variables per plot.

A rocket engine design expert system

NASA Technical Reports Server (NTRS)

Davidian, Kenneth J.

1989-01-01

The overall structure and capabilities of an expert system designed to evaluate rocket engine performance are described. The expert system incorporates a JANNAF standard reference computer code to determine rocket engine performance and a state-of-the-art finite element computer code to calculate the interactions between propellant injection, energy release in the combustion chamber, and regenerative cooling heat transfer. Rule-of-thumb heuristics were incorporated for the hydrogen-oxygen coaxial injector design, including a minimum gap size constraint on the total number of injector elements. One-dimensional equilibrium chemistry was employed in the energy release analysis of the combustion chamber and three-dimensional finite-difference analysis of the regenerative cooling channels was used to calculate the pressure drop along the channels and the coolant temperature as it exits the coolant circuit. Inputting values to describe the geometry and state properties of the entire system is done directly from the computer keyboard. Graphical display of all output results from the computer code analyses is facilitated by menu selection of up to five dependent variables per plot.

Development of a Grid-Independent Geos-Chem Chemical Transport Model (v9-02) as an Atmospheric Chemistry Module for Earth System Models

NASA Technical Reports Server (NTRS)

Long, M. S.; Yantosca, R.; Nielsen, J. E; Keller, C. A.; Da Silva, A.; Sulprizio, M. P.; Pawson, S.; Jacob, D. J.

2015-01-01

The GEOS-Chem global chemical transport model (CTM), used by a large atmospheric chemistry research community, has been re-engineered to also serve as an atmospheric chemistry module for Earth system models (ESMs). This was done using an Earth System Modeling Framework (ESMF) interface that operates independently of the GEOSChem scientific code, permitting the exact same GEOSChem code to be used as an ESM module or as a standalone CTM. In this manner, the continual stream of updates contributed by the CTM user community is automatically passed on to the ESM module, which remains state of science and referenced to the latest version of the standard GEOS-Chem CTM. A major step in this re-engineering was to make GEOS-Chem grid independent, i.e., capable of using any geophysical grid specified at run time. GEOS-Chem data sockets were also created for communication between modules and with external ESM code. The grid-independent, ESMF-compatible GEOS-Chem is now the standard version of the GEOS-Chem CTM. It has been implemented as an atmospheric chemistry module into the NASA GEOS- 5 ESM. The coupled GEOS-5-GEOS-Chem system was tested for scalability and performance with a tropospheric oxidant-aerosol simulation (120 coupled species, 66 transported tracers) using 48-240 cores and message-passing interface (MPI) distributed-memory parallelization. Numerical experiments demonstrate that the GEOS-Chem chemistry module scales efficiently for the number of cores tested, with no degradation as the number of cores increases. Although inclusion of atmospheric chemistry in ESMs is computationally expensive, the excellent scalability of the chemistry module means that the relative cost goes down with increasing number of cores in a massively parallel environment.

Computational models for the analysis of three-dimensional internal and exhaust plume flowfields

NASA Technical Reports Server (NTRS)

Dash, S. M.; Delguidice, P. D.

1977-01-01

This paper describes computational procedures developed for the analysis of three-dimensional supersonic ducted flows and multinozzle exhaust plume flowfields. The models/codes embodying these procedures cater to a broad spectrum of geometric situations via the use of multiple reference plane grid networks in several coordinate systems. Shock capturing techniques are employed to trace the propagation and interaction of multiple shock surfaces while the plume interface, separating the exhaust and external flows, and the plume external shock are discretely analyzed. The computational grid within the reference planes follows the trace of streamlines to facilitate the incorporation of finite-rate chemistry and viscous computational capabilities. Exhaust gas properties consist of combustion products in chemical equilibrium. The computational accuracy of the models/codes is assessed via comparisons with exact solutions, results of other codes and experimental data. Results are presented for the flows in two-dimensional convergent and divergent ducts, expansive and compressive corner flows, flow in a rectangular nozzle and the plume flowfields for exhausts issuing out of single and multiple rectangular nozzles.

CDAC Student Report: Summary of LLNL Internship

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

Herriman, Jane E.

Multiple objectives motivated me to apply for an internship at LLNL: I wanted to experience the work environment at a national lab, to learn about research and job opportunities at LLNL in particular, and to gain greater experience with code development, particularly within the realm of high performance computing (HPC). This summer I was selected to participate in LLNL's Computational Chemistry and Material Science Summer Institute (CCMS). CCMS is a 10 week program hosted by the Quantum Simulations group leader, Dr. Eric Schwegler. CCMS connects graduate students to mentors at LLNL involved in similar re- search and provides weekly seminarsmore » on a broad array of topics from within chemistry and materials science. Dr. Xavier Andrade and Dr. Erik Draeger served as my co-mentors over the summer, and Dr. Andrade continues to mentor me now that CCMS has concluded. Dr. Andrade is a member of the Quantum Simulations group within the Physical and Life Sciences at LLNL, and Dr. Draeger leads the HPC group within the Center for Applied Scientific Computing (CASC). The two have worked together to develop Qb@ll, an open-source first principles molecular dynamics code that was the platform for my summer research project.« less

Developing Chemistry and Kinetic Modeling Tools for Low-Temperature Plasma Simulations

NASA Astrophysics Data System (ADS)

Jenkins, Thomas; Beckwith, Kris; Davidson, Bradley; Kruger, Scott; Pankin, Alexei; Roark, Christine; Stoltz, Peter

2015-09-01

We discuss the use of proper orthogonal decomposition (POD) methods in VSim, a FDTD plasma simulation code capable of both PIC/MCC and fluid modeling. POD methods efficiently generate smooth representations of noisy self-consistent or test-particle PIC data, and are thus advantageous in computing macroscopic fluid quantities from large PIC datasets (e.g. for particle-based closure computations) and in constructing optimal visual representations of the underlying physics. They may also confer performance advantages for massively parallel simulations, due to the significant reduction in dataset sizes conferred by truncated singular-value decompositions of the PIC data. We also demonstrate how complex LTP chemistry scenarios can be modeled in VSim via an interface with MUNCHKIN, a developing standalone python/C++/SQL code that identifies reaction paths for given input species, solves 1D rate equations for the time-dependent chemical evolution of the system, and generates corresponding VSim input blocks with appropriate cross-sections/reaction rates. MUNCHKIN also computes reaction rates from user-specified distribution functions, and conducts principal path analyses to reduce the number of simulated chemical reactions. Supported by U.S. Department of Energy SBIR program, Award DE-SC0009501.

Development of high performance scientific components for interoperability of computing packages

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

Gulabani, Teena Pratap

2008-01-01

Three major high performance quantum chemistry computational packages, NWChem, GAMESS and MPQC have been developed by different research efforts following different design patterns. The goal is to achieve interoperability among these packages by overcoming the challenges caused by the different communication patterns and software design of each of these packages. A chemistry algorithm is hard to develop as well as being a time consuming process; integration of large quantum chemistry packages will allow resource sharing and thus avoid reinvention of the wheel. Creating connections between these incompatible packages is the major motivation of the proposed work. This interoperability is achievedmore » by bringing the benefits of Component Based Software Engineering through a plug-and-play component framework called Common Component Architecture (CCA). In this thesis, I present a strategy and process used for interfacing two widely used and important computational chemistry methodologies: Quantum Mechanics and Molecular Mechanics. To show the feasibility of the proposed approach the Tuning and Analysis Utility (TAU) has been coupled with NWChem code and its CCA components. Results show that the overhead is negligible when compared to the ease and potential of organizing and coping with large-scale software applications.« less

Tabulated Combustion Model Development For Non-Premixed Flames

NASA Astrophysics Data System (ADS)

Kundu, Prithwish

Turbulent non-premixed flames play a very important role in the field of engineering ranging from power generation to propulsion. The coupling of fluid mechanics and complicated combustion chemistry of fuels pose a challenge for the numerical modeling of these type of problems. Combustion modeling in Computational Fluid Dynamics (CFD) is one of the most important tools used for predictive modeling of complex systems and to understand the basic fundamentals of combustion. Traditional combustion models solve a transport equation of each species with a source term. In order to resolve the complex chemistry accurately it is important to include a large number of species. However, the computational cost is generally proportional to the cube of number of species. The presence of a large number of species in a flame makes the use of CFD computationally expensive and beyond reach for some applications or inaccurate when solved with simplified chemistry. For highly turbulent flows, it also becomes important to incorporate the effects of turbulence chemistry interaction (TCI). The aim of this work is to develop high fidelity combustion models based on the flamelet concept and to significantly advance the existing capabilities. A thorough investigation of existing models (Finite-rate chemistry and Representative Interactive Flamelet (RIF)) and comparative study of combustion models was done initially on a constant volume combustion chamber with diesel fuel injection. The CFD modeling was validated with experimental results and was also successfully applied to a single cylinder diesel engine. The effect of number of flamelets on the RIF model and flamelet initialization strategies were studied. The RIF model with multiple flamelets is computationally expensive and a model was proposed on the frame work of RIF. The new model was based on tabulated chemistry and incorporated TCI effects. A multidimensional tabulated chemistry database generation code was developed based on the 1D diffusion flame solver. The proposed model did not use progress variables like the traditional chemistry tabulation methods. The resulting model demonstrated an order of magnitude computational speed up over the RIF model. The results were validated across a wide range of operating conditions for diesel injections and the results were in close agreement to those of the experimental data. History of scalar dissipation rates plays a very important role in non premixed flames. However, tabulated methods have not been able to incorporate this physics in their models. A comparative approach is developed that can quantify these effects and find correlations with flow variables. A new model is proposed to include these effects in tabulated combustion models. The model is initially validated for 1D counterflow diffusion flame problems at engine conditions. The model is further implemented and validated in a 3D RANS code across a range of operating conditions for spray flames.

Creating Semantic Waves: Using Legitimation Code Theory as a Tool to Aid the Teaching of Chemistry

ERIC Educational Resources Information Center

Blackie, Margaret A. L.

2014-01-01

This is a conceptual paper aimed at chemistry educators. The purpose of this paper is to illustrate the use of the semantic code of Legitimation Code Theory in chemistry teaching. Chemistry is an abstract subject which many students struggle to grasp. Legitimation Code Theory provides a way of separating out abstraction from complexity both of…

Assessment of Molecular Modeling & Simulation

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

None

2002-01-03

This report reviews the development and applications of molecular and materials modeling in Europe and Japan in comparison to those in the United States. Topics covered include computational quantum chemistry, molecular simulations by molecular dynamics and Monte Carlo methods, mesoscale modeling of material domains, molecular-structure/macroscale property correlations like QSARs and QSPRs, and related information technologies like informatics and special-purpose molecular-modeling computers. The panel's findings include the following: The United States leads this field in many scientific areas. However, Canada has particular strengths in DFT methods and homogeneous catalysis; Europe in heterogeneous catalysis, mesoscale, and materials modeling; and Japan in materialsmore » modeling and special-purpose computing. Major government-industry initiatives are underway in Europe and Japan, notably in multi-scale materials modeling and in development of chemistry-capable ab-initio molecular dynamics codes.« less

High-speed reacting flow simulation using USA-series codes

NASA Astrophysics Data System (ADS)

Chakravarthy, S. R.; Palaniswamy, S.

In this paper, the finite-rate chemistry (FRC) formulation for the USA-series of codes and three sets of validations are presented. USA-series computational fluid dynamics (CFD) codes are based on Unified Solution Algorithms including explicity and implicit formulations, factorization and relaxation approaches, time marching and space marching methodolgies, etc., in order to be able to solve a very wide class of CDF problems using a single framework. Euler or Navier-Stokes equations are solved using a finite-volume treatment with upwind Total Variation Diminishing discretization for the inviscid terms. Perfect and real gas options are available including equilibrium and nonequilibrium chemistry. This capability has been widely used to study various problems including Space Shuttle exhaust plumes, National Aerospace Plane (NASP) designs, etc. (1) Numerical solutions are presented showing the full range of possible solutions to steady detonation wave problems. (2) Comparison between the solution obtained by the USA code and Generalized Kinetics Analysis Program (GKAP) is shown for supersonic combustion in a duct. (3) Simulation of combustion in a supersonic shear layer is shown to have reasonable agreement with experimental observations.

CARES/LIFE Software Commercialization

NASA Technical Reports Server (NTRS)

1995-01-01

The NASA Lewis Research Center has entered into a letter agreement with BIOSYM Technologies Inc. (now merged with Molecular Simulations Inc. (MSI)). Under this agreement, NASA will provide a developmental copy of the CARES/LIFE computer program to BIOSYM for evaluation. This computer code predicts the time-dependent reliability of a thermomechanically loaded component. BIOSYM will become familiar with CARES/LIFE, provide results of computations useful in validating the code, evaluate it for potential commercialization, and submit suggestions for improvements or extensions to the code or its documentation. If BIOSYM/Molecular Simulations reaches a favorable evaluation of CARES/LIFE, NASA will enter into negotiations for a cooperative agreement with BIOSYM/Molecular Simulations to further develop the code--adding features such as a user-friendly interface and other improvements. This agreement would give BIOSYM intellectual property rights in the modified codes, which they could protect and then commercialize. NASA would provide BIOSYM with the NASA-developed source codes and would agree to cooperate with BIOSYM in further developing the code. In return, NASA would receive certain use rights in the modified CARES/LIFE program. Presently BIOSYM Technologies Inc. has been involved with integration issues concerning its merger with Molecular Simulations Inc., since both companies used to compete in the computational chemistry market, and to some degree, in the materials market. Consequently, evaluation of the CARES/LIFE software is on hold for a month or two while the merger is finalized. Their interest in CARES continues, however, and they expect to get back to the evaluation by early November 1995.

GPU-accelerated atmospheric chemical kinetics in the ECHAM/MESSy (EMAC) Earth system model (version 2.52)

NASA Astrophysics Data System (ADS)

Alvanos, Michail; Christoudias, Theodoros

2017-10-01

This paper presents an application of GPU accelerators in Earth system modeling. We focus on atmospheric chemical kinetics, one of the most computationally intensive tasks in climate-chemistry model simulations. We developed a software package that automatically generates CUDA kernels to numerically integrate atmospheric chemical kinetics in the global climate model ECHAM/MESSy Atmospheric Chemistry (EMAC), used to study climate change and air quality scenarios. A source-to-source compiler outputs a CUDA-compatible kernel by parsing the FORTRAN code generated by the Kinetic PreProcessor (KPP) general analysis tool. All Rosenbrock methods that are available in the KPP numerical library are supported.Performance evaluation, using Fermi and Pascal CUDA-enabled GPU accelerators, shows achieved speed-ups of 4. 5 × and 20. 4 × , respectively, of the kernel execution time. A node-to-node real-world production performance comparison shows a 1. 75 × speed-up over the non-accelerated application using the KPP three-stage Rosenbrock solver. We provide a detailed description of the code optimizations used to improve the performance including memory optimizations, control code simplification, and reduction of idle time. The accuracy and correctness of the accelerated implementation are evaluated by comparing to the CPU-only code of the application. The median relative difference is found to be less than 0.000000001 % when comparing the output of the accelerated kernel the CPU-only code.The approach followed, including the computational workload division, and the developed GPU solver code can potentially be used as the basis for hardware acceleration of numerous geoscientific models that rely on KPP for atmospheric chemical kinetics applications.

Prediction of the Thrust Performance and the Flowfield of Liquid Rocket Engines

NASA Technical Reports Server (NTRS)

Wang, T.-S.

1990-01-01

In an effort to improve the current solutions in the design and analysis of liquid propulsive engines, a computational fluid dynamics (CFD) model capable of calculating the reacting flows from the combustion chamber, through the nozzle to the external plume, was developed. The Space Shuttle Main Engine (SSME) fired at sea level, was investigated as a sample case. The CFD model, FDNS, is a pressure based, non-staggered grid, viscous/inviscid, ideal gas/real gas, reactive code. An adaptive upwinding differencing scheme is employed for the spatial discretization. The upwind scheme is based on fourth order central differencing with fourth order damping for smooth regions, and second order central differencing with second order damping for shock capturing. It is equipped with a CHMQGM equilibrium chemistry algorithm and a PARASOL finite rate chemistry algorithm using the point implicit method. The computed flow results and performance compared well with those of other standard codes and engine hot fire test data. In addition, the transient nozzle flowfield calculation was also performed to demonstrate the ability of FDNS in capturing the flow separation during the startup process.

Acceleration of the chemistry solver for modeling DI engine combustion using dynamic adaptive chemistry (DAC) schemes

NASA Astrophysics Data System (ADS)

Shi, Yu; Liang, Long; Ge, Hai-Wen; Reitz, Rolf D.

2010-03-01

Acceleration of the chemistry solver for engine combustion is of much interest due to the fact that in practical engine simulations extensive computational time is spent solving the fuel oxidation and emission formation chemistry. A dynamic adaptive chemistry (DAC) scheme based on a directed relation graph error propagation (DRGEP) method has been applied to study homogeneous charge compression ignition (HCCI) engine combustion with detailed chemistry (over 500 species) previously using an R-value-based breadth-first search (RBFS) algorithm, which significantly reduced computational times (by as much as 30-fold). The present paper extends the use of this on-the-fly kinetic mechanism reduction scheme to model combustion in direct-injection (DI) engines. It was found that the DAC scheme becomes less efficient when applied to DI engine simulations using a kinetic mechanism of relatively small size and the accuracy of the original DAC scheme decreases for conventional non-premixed combustion engine. The present study also focuses on determination of search-initiating species, involvement of the NOx chemistry, selection of a proper error tolerance, as well as treatment of the interaction of chemical heat release and the fuel spray. Both the DAC schemes were integrated into the ERC KIVA-3v2 code, and simulations were conducted to compare the two schemes. In general, the present DAC scheme has better efficiency and similar accuracy compared to the previous DAC scheme. The efficiency depends on the size of the chemical kinetics mechanism used and the engine operating conditions. For cases using a small n-heptane kinetic mechanism of 34 species, 30% of the computational time is saved, and 50% for a larger n-heptane kinetic mechanism of 61 species. The paper also demonstrates that by combining the present DAC scheme with an adaptive multi-grid chemistry (AMC) solver, it is feasible to simulate a direct-injection engine using a detailed n-heptane mechanism with 543 species with practical computer time.

Overview of the NCC

NASA Technical Reports Server (NTRS)

Liu, Nan-Suey

2001-01-01

A multi-disciplinary design/analysis tool for combustion systems is critical for optimizing the low-emission, high-performance combustor design process. Based on discussions between then NASA Lewis Research Center and the jet engine companies, an industry-government team was formed in early 1995 to develop the National Combustion Code (NCC), which is an integrated system of computer codes for the design and analysis of combustion systems. NCC has advanced features that address the need to meet designer's requirements such as "assured accuracy", "fast turnaround", and "acceptable cost". The NCC development team is comprised of Allison Engine Company (Allison), CFD Research Corporation (CFDRC), GE Aircraft Engines (GEAE), NASA Glenn Research Center (LeRC), and Pratt & Whitney (P&W). The "unstructured mesh" capability and "parallel computing" are fundamental features of NCC from its inception. The NCC system is composed of a set of "elements" which includes grid generator, main flow solver, turbulence module, turbulence and chemistry interaction module, chemistry module, spray module, radiation heat transfer module, data visualization module, and a post-processor for evaluating engine performance parameters. Each element may have contributions from several team members. Such a multi-source multi-element system needs to be integrated in a way that facilitates inter-module data communication, flexibility in module selection, and ease of integration. The development of the NCC beta version was essentially completed in June 1998. Technical details of the NCC elements are given in the Reference List. Elements such as the baseline flow solver, turbulence module, and the chemistry module, have been extensively validated; and their parallel performance on large-scale parallel systems has been evaluated and optimized. However the scalar PDF module and the Spray module, as well as their coupling with the baseline flow solver, were developed in a small-scale distributed computing environment. As a result, the validation of the NCC beta version as a whole was quite limited. Current effort has been focused on the validation of the integrated code and the evaluation/optimization of its overall performance on large-scale parallel systems.

Computations of Axisymmetric Flows in Hypersonic Shock Tubes

NASA Technical Reports Server (NTRS)

Sharma, Surendra P.; Wilson, Gregory J.

1995-01-01

A time-accurate two-dimensional fluid code is used to compute test times in shock tubes operated at supersonic speeds. Unlike previous studies, this investigation resolves the finer temporal details of the shock-tube flow by making use of modern supercomputers and state-of-the-art computational fluid dynamic solution techniques. The code, besides solving the time-dependent fluid equations, also accounts for the finite rate chemistry in the hypersonic environment. The flowfield solutions are used to estimate relevant shock-tube parameters for laminar flow, such as test times, and to predict density and velocity profiles. Boundary-layer parameters such as bar-delta(sub u), bar-delta(sup *), and bar-tau(sub w), and test time parameters such as bar-tau and particle time of flight t(sub f), are computed and compared with those evaluated by using Mirels' correlations. This article then discusses in detail the effects of flow nonuniformities on particle time-of-flight behind the normal shock and, consequently, on the interpretation of shock-tube data. This article concludes that for accurate interpretation of shock-tube data, a detailed analysis of flowfield parameters, using a computer code such as used in this study, must be performed.

Simulation of a hydrocarbon fueled scramjet exhaust

NASA Technical Reports Server (NTRS)

Leng, J.

1982-01-01

Exhaust nozzle flow fields for a fully integrated, hydrocarbon burning scramjet were calculated for flight conditions of M (undisturbed free stream) = 4 at 6.1 km altitude and M (undisturbed free stream) = 6 at 30.5 km altitude. Equilibrium flow, frozen flow, and finite rate chemistry effects are considered. All flow fields were calculated by method of characteristics. Finite rate chemistry results were evaluated by a one dimensional code (Bittker) using streamtube area distributions extracted from the equilibrium flow field, and compared to very slow artificial rate cases for the same streamtube area distribution. Several candidate substitute gas mixtures, designed to simulate the gas dynamics of the real engine exhaust flow, were examined. Two mixtures are found to give excellent simulations of the specified exhaust flow fields when evaluated by the same method of characteristics computer code.

Reacting Multi-Species Gas Capability for USM3D Flow Solver

NASA Technical Reports Server (NTRS)

Frink, Neal T.; Schuster, David M.

2012-01-01

The USM3D Navier-Stokes flow solver contributed heavily to the NASA Constellation Project (CxP) as a highly productive computational tool for generating the aerodynamic databases for the Ares I and V launch vehicles and Orion launch abort vehicle (LAV). USM3D is currently limited to ideal-gas flows, which are not adequate for modeling the chemistry or temperature effects of hot-gas jet flows. This task was initiated to create an efficient implementation of multi-species gas and equilibrium chemistry into the USM3D code to improve its predictive capabilities for hot jet impingement effects. The goal of this NASA Engineering and Safety Center (NESC) assessment was to implement and validate a simulation capability to handle real-gas effects in the USM3D code. This document contains the outcome of the NESC assessment.

The effects of finite rate chemical processes on high enthalpy nozzle performance - A comparison between SPARK and SEAGULL

NASA Technical Reports Server (NTRS)

Carpenter, M. H.

1988-01-01

The generalized chemistry version of the computer code SPARK is extended to include two higher-order numerical schemes, yielding fourth-order spatial accuracy for the inviscid terms. The new and old formulations are used to study the influences of finite rate chemical processes on nozzle performance. A determination is made of the computationally optimum reaction scheme for use in high-enthalpy nozzles. Finite rate calculations are compared with the frozen and equilibrium limits to assess the validity of each formulation. In addition, the finite rate SPARK results are compared with the constant ratio of specific heats (gamma) SEAGULL code, to determine its accuracy in variable gamma flow situations. Finally, the higher-order SPARK code is used to calculate nozzle flows having species stratification. Flame quenching occurs at low nozzle pressures, while for high pressures, significant burning continues in the nozzle.

RADSOURCE. Volume 1, Part 1, A scaling factor prediction computer program technical manual and code validation: Final report

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

Vance, J.N.; Holderness, J.H.; James, D.W.

1992-12-01

Waste stream scaling factors based on sampling programs are vulnerable to one or more of the following factors: sample representativeness, analytic accuracy, and measurement sensitivity. As an alternative to sample analyses or as a verification of the sampling results, this project proposes the use of the RADSOURCE code, which accounts for the release of fuel-source radionuclides. Once the release rates of these nuclides from fuel are known, the code develops scaling factors for waste streams based on easily measured Cobalt-60 (Co-60) and Cesium-137 (Cs-137). The project team developed mathematical models to account for the appearance rate of 10CFR61 radionuclides inmore » reactor coolant. They based these models on the chemistry and nuclear physics of the radionuclides involved. Next, they incorporated the models into a computer code that calculates plant waste stream scaling factors based on reactor coolant gamma- isotopic data. Finally, the team performed special sampling at 17 reactors to validate the models in the RADSOURCE code.« less

Numerical study of supersonic combustors by multi-block grids with mismatched interfaces

NASA Technical Reports Server (NTRS)

Moon, Young J.

1990-01-01

A three dimensional, finite rate chemistry, Navier-Stokes code was extended to a multi-block code with mismatched interface for practical calculations of supersonic combustors. To ensure global conservation, a conservative algorithm was used for the treatment of mismatched interfaces. The extended code was checked against one test case, i.e., a generic supersonic combustor with transverse fuel injection, examining solution accuracy, convergence, and local mass flux error. After testing, the code was used to simulate the chemically reacting flow fields in a scramjet combustor with parallel fuel injectors (unswept and swept ramps). Computational results were compared with experimental shadowgraph and pressure measurements. Fuel-air mixing characteristics of the unswept and swept ramps were compared and investigated.

Development and Implementation of a Scramjet Cycle Analysis Code with a Finite-Rate-Chemistry Combustion Model for Use on a Personal Computer

DTIC Science & Technology

1993-12-01

2 3 9 V List of Fi-ures Figure 1 - Functional...Block Diagram of a Scramjet ........................................ 9 Figure 2 - ’Corrected’ Specific Impulse of Hydrogen-Oxygen Rocket ............. 35...38 Figure 8 - Schematic of Northam/Anderson Mixing Model ............................ 39 Figure 9 - Pressure-Area

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.

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.

Simulation of the vibrational chemistry and the infrared signature induced by a Sprite streamer in the mesosphere

NASA Astrophysics Data System (ADS)

Romand, F.; Payan, S.; Croize, L.

2017-12-01

Since their first observation in 1989, effect of TLEs on the atmospheric composition has become an open and important question. The lack of suitable experimental data is a shortcoming that hampers our understanding of the physics and chemistry induced by these effects. HALESIS (High-Altitude Luminous Events Studied by Infrared Spectro-imagery) is a future experiment dedicated to the measurement of the atmospheric perturbation induced by a TLE in the minutes following its occurrence, from a stratospheric balloon flying at an altitude of 25 km to 40 km. This work aims to quantify the local chemical impact of sprites in the stratosphere and mesosphere. In this paper, we will present the development of a tool which simulates (i) the impact of a sprite on the vibrational chemistry, (ii) the resulting infrared signature and (iii) the propagation of this signature through the atmosphere to an observer. First the Non Local Thermodynamic Equilibrium populations of a background atmosphere were computed using SAMM2 code. The initial thermodynamic and chemical description of atmosphere comes from the Whole Atmosphere community Climate Model (WACCM). Then a perturbation was applied to simulate a sprite. Chemistry due to TLEs was computed using Gordillo-Vazquez kinetic model. Rate coefficients that depend on the electron energy distribution function were calculated from collision cross-section data by solving the electron Boltzmann equation (BE). Time evolutions of the species densities and of vibrational populations in the non-thermal plasma consecutive to sprite discharge were simulated using the computer code ZDPlasKin (S. Pancheshn et al.). Finally, the resulting infrared signatures were propagated from the disturbed area through the atmosphere to an instrument placed in a limb line of sight using a line by line radiative transfer model. We will conclude that sprite could produce a significant infrared signature that last a few tens of seconds after the visible flash.

Development and Performance of the Modularized, High-performance Computing and Hybrid-architecture Capable GEOS-Chem Chemical Transport Model

NASA Astrophysics Data System (ADS)

Long, M. S.; Yantosca, R.; Nielsen, J.; Linford, J. C.; Keller, C. A.; Payer Sulprizio, M.; Jacob, D. J.

2014-12-01

The GEOS-Chem global chemical transport model (CTM), used by a large atmospheric chemistry research community, has been reengineered to serve as a platform for a range of computational atmospheric chemistry science foci and applications. Development included modularization for coupling to general circulation and Earth system models (ESMs) and the adoption of co-processor capable atmospheric chemistry solvers. This was done using an Earth System Modeling Framework (ESMF) interface that operates independently of GEOS-Chem scientific code to permit seamless transition from the GEOS-Chem stand-alone serial CTM to deployment as a coupled ESM module. In this manner, the continual stream of updates contributed by the CTM user community is automatically available for broader applications, which remain state-of-science and directly referenceable to the latest version of the standard GEOS-Chem CTM. These developments are now available as part of the standard version of the GEOS-Chem CTM. The system has been implemented as an atmospheric chemistry module within the NASA GEOS-5 ESM. The coupled GEOS-5/GEOS-Chem system was tested for weak and strong scalability and performance with a tropospheric oxidant-aerosol simulation. Results confirm that the GEOS-Chem chemical operator scales efficiently for any number of processes. Although inclusion of atmospheric chemistry in ESMs is computationally expensive, the excellent scalability of the chemical operator means that the relative cost goes down with increasing number of processes, making fine-scale resolution simulations possible.

Mathematical Description of Complex Chemical Kinetics and Application to CFD Modeling Codes

NASA Technical Reports Server (NTRS)

Bittker, D. A.

1993-01-01

A major effort in combustion research at the present time is devoted to the theoretical modeling of practical combustion systems. These include turbojet and ramjet air-breathing engines as well as ground-based gas-turbine power generating systems. The ability to use computational modeling extensively in designing these products not only saves time and money, but also helps designers meet the quite rigorous environmental standards that have been imposed on all combustion devices. The goal is to combine the very complex solution of the Navier-Stokes flow equations with realistic turbulence and heat-release models into a single computer code. Such a computational fluid-dynamic (CFD) code simulates the coupling of fluid mechanics with the chemistry of combustion to describe the practical devices. This paper will focus on the task of developing a simplified chemical model which can predict realistic heat-release rates as well as species composition profiles, and is also computationally rapid. We first discuss the mathematical techniques used to describe a complex, multistep fuel oxidation chemical reaction and develop a detailed mechanism for the process. We then show how this mechanism may be reduced and simplified to give an approximate model which adequately predicts heat release rates and a limited number of species composition profiles, but is computationally much faster than the original one. Only such a model can be incorporated into a CFD code without adding significantly to long computation times. Finally, we present some of the recent advances in the development of these simplified chemical mechanisms.

Mathematical description of complex chemical kinetics and application to CFD modeling codes

NASA Technical Reports Server (NTRS)

Bittker, D. A.

1993-01-01

A major effort in combustion research at the present time is devoted to the theoretical modeling of practical combustion systems. These include turbojet and ramjet air-breathing engines as well as ground-based gas-turbine power generating systems. The ability to use computational modeling extensively in designing these products not only saves time and money, but also helps designers meet the quite rigorous environmental standards that have been imposed on all combustion devices. The goal is to combine the very complex solution of the Navier-Stokes flow equations with realistic turbulence and heat-release models into a single computer code. Such a computational fluid-dynamic (CFD) code simulates the coupling of fluid mechanics with the chemistry of combustion to describe the practical devices. This paper will focus on the task of developing a simplified chemical model which can predict realistic heat-release rates as well as species composition profiles, and is also computationally rapid. We first discuss the mathematical techniques used to describe a complex, multistep fuel oxidation chemical reaction and develop a detailed mechanism for the process. We then show how this mechanism may be reduced and simplified to give an approximate model which adequately predicts heat release rates and a limited number of species composition profiles, but is computationally much faster than the original one. Only such a model can be incorporated into a CFD code without adding significantly to long computation times. Finally, we present some of the recent advances in the development of these simplified chemical mechanisms.

Coupling geodynamic with thermodynamic modelling for reconstructions of magmatic systems

NASA Astrophysics Data System (ADS)

Rummel, Lisa; Kaus, Boris J. P.; White, Richard

2016-04-01

Coupling geodynamic with petrological models is fundamental for understanding magmatic systems from the melting source in the mantle to the point of magma crystallisation in the upper crust. Most geodynamic codes use very simplified petrological models consisting of a single, fixed, chemistry. Here, we develop a method to better track the petrological evolution of the source rock and corresponding volcanic and plutonic rocks by combining a geodynamic code with a thermodynamic model for magma generation and evolution. For the geodynamic modelling a finite element code (MVEP2) solves the conservation of mass, momentum and energy equations. The thermodynamic modelling of phase equilibria in magmatic systems is performed with pMELTS for mantle-like bulk compositions. The thermodynamic dependent properties calculated by pMELTS are density, melt fraction and the composition of the liquid and solid phase in the chemical system: SiO2-TiO2-Al2O3-Fe2O3-Cr2O3-FeO-MgO-CaO-Na2O-K2O-P2O5-H2O. In order to take into account the chemical depletion of the source rock with increasing melt extraction events, calculation of phase diagrams is performed in two steps: 1) With an initial rock composition density, melt fraction as well as liquid and solid composition are computed over the full upper mantle P-T range. 2) Once the residual rock composition (equivalent to the solid composition after melt extraction) is significantly different from the initial rock composition and the melt fraction is lower than a critical value, the residual composition is used for next calculations with pMELTS. The implementation of several melt extraction events take the change in chemistry into account until the solidus is shifted to such high temperatures that the rock cannot be molten anymore under upper mantle conditions. An advantage of this approach is that we can track the change of melt chemistry with time, which can be compared with natural constraints. In the thermo-mechanical code the thermodynamic dependent properties from pre-computed phase diagrams are carried by each particle using marker-in-cell method . Thus the physical and chemical properties can change locally as a function of previous melt extraction events, pressure and temperature conditions. After each melt extraction event, the residual rock composition is compared with the bulk composition of previous computed phase diagrams, so that the used phase diagram is replaced by the phase diagram with the closest bulk chemistry. In the thermo-mechanical code, the melt is extracted directly to the surface as volcanites and within the crust as plutonites. The density of the crust and new generated crust is calculated with the thermodynamic modelling tool Perple_X. We have investigated the influence of several input parameters on the magma composition to compare it with real rock samples from Eifel (West-Germany). In order to take the very inhomogeneous chemistry of European mantle into account, we include not only primitive mantle but also metasomatised mantle fragments in the melting source of a plume (Eifel plume).

SPRAI: coupling of radiative feedback and primordial chemistry in moving mesh hydrodynamics

NASA Astrophysics Data System (ADS)

Jaura, O.; Glover, S. C. O.; Klessen, R. S.; Paardekooper, J.-P.

2018-04-01

In this paper, we introduce a new radiative transfer code SPRAI (Simplex Photon Radiation in the Arepo Implementation) based on the SIMPLEX radiation transfer method. This method, originally used only for post-processing, is now directly integrated into the AREPO code and takes advantage of its adaptive unstructured mesh. Radiated photons are transferred from the sources through the series of Voronoi gas cells within a specific solid angle. From the photon attenuation, we derive corresponding photon fluxes and ionization rates and feed them to a primordial chemistry module. This gives us a self-consistent method for studying dynamical and chemical processes caused by ionizing sources in primordial gas. Since the computational cost of the SIMPLEX method does not scale directly with the number of sources, it is convenient for studying systems such as primordial star-forming haloes that may form multiple ionizing sources.

Optimizing Tensor Contraction Expressions for Hybrid CPU-GPU Execution

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

Ma, Wenjing; Krishnamoorthy, Sriram; Villa, Oreste

2013-03-01

Tensor contractions are generalized multidimensional matrix multiplication operations that widely occur in quantum chemistry. Efficient execution of tensor contractions on Graphics Processing Units (GPUs) requires several challenges to be addressed, including index permutation and small dimension-sizes reducing thread block utilization. Moreover, to apply the same optimizations to various expressions, we need a code generation tool. In this paper, we present our approach to automatically generate CUDA code to execute tensor contractions on GPUs, including management of data movement between CPU and GPU. To evaluate our tool, GPU-enabled code is generated for the most expensive contractions in CCSD(T), a key coupledmore » cluster method, and incorporated into NWChem, a popular computational chemistry suite. For this method, we demonstrate speedup over a factor of 8.4 using one GPU (instead of one core per node) and over 2.6 when utilizing the entire system using hybrid CPU+GPU solution with 2 GPUs and 5 cores (instead of 7 cores per node). Finally, we analyze the implementation behavior on future GPU systems.« less

CHMWTR: A Plasma Chemistry Code for Water Vapor

DTIC Science & Technology

2012-02-01

Naval Research Laboratory Washington, DC 20375-5320 NRL/MR/6790--12-9383 CHMWTR: A Plasma Chemistry Code for Water Vapor Daniel F. GorDon Michael...NUMBER OF PAGES 17. LIMITATION OF ABSTRACT CHMWTR: A Plasma Chemistry Code for Water Vapor Daniel F. Gordon, Michael H. Helle, Theodore G. Jones, and K...October 2011 NRL *Directed Energy Scholar, Directed Energy Professional Society Plasma chemistry Breakdown field Conductivity 67-4270-02 CHMWTR: a Plasma

Partial Overhaul and Initial Parallel Optimization of KINETICS, a Coupled Dynamics and Chemistry Atmosphere Model

NASA Technical Reports Server (NTRS)

Nguyen, Howard; Willacy, Karen; Allen, Mark

2012-01-01

KINETICS is a coupled dynamics and chemistry atmosphere model that is data intensive and computationally demanding. The potential performance gain from using a supercomputer motivates the adaptation from a serial version to a parallelized one. Although the initial parallelization had been done, bottlenecks caused by an abundance of communication calls between processors led to an unfavorable drop in performance. Before starting on the parallel optimization process, a partial overhaul was required because a large emphasis was placed on streamlining the code for user convenience and revising the program to accommodate the new supercomputers at Caltech and JPL. After the first round of optimizations, the partial runtime was reduced by a factor of 23; however, performance gains are dependent on the size of the data, the number of processors requested, and the computer used.

plasmaFoam: An OpenFOAM framework for computational plasma physics and chemistry

NASA Astrophysics Data System (ADS)

Venkattraman, Ayyaswamy; Verma, Abhishek Kumar

2016-09-01

As emphasized in the 2012 Roadmap for low temperature plasmas (LTP), scientific computing has emerged as an essential tool for the investigation and prediction of the fundamental physical and chemical processes associated with these systems. While several in-house and commercial codes exist, with each having its own advantages and disadvantages, a common framework that can be developed by researchers from all over the world will likely accelerate the impact of computational studies on advances in low-temperature plasma physics and chemistry. In this regard, we present a finite volume computational toolbox to perform high-fidelity simulations of LTP systems. This framework, primarily based on the OpenFOAM solver suite, allows us to enhance our understanding of multiscale plasma phenomenon by performing massively parallel, three-dimensional simulations on unstructured meshes using well-established high performance computing tools that are widely used in the computational fluid dynamics community. In this talk, we will present preliminary results obtained using the OpenFOAM-based solver suite with benchmark three-dimensional simulations of microplasma devices including both dielectric and plasma regions. We will also discuss the future outlook for the solver suite.

Comparison of numerical techniques for integration of stiff ordinary differential equations arising in combustion chemistry

NASA Technical Reports Server (NTRS)

Radhakrishnan, K.

1984-01-01

The efficiency and accuracy of several algorithms recently developed for the efficient numerical integration of stiff ordinary differential equations are compared. The methods examined include two general-purpose codes, EPISODE and LSODE, and three codes (CHEMEQ, CREK1D, and GCKP84) developed specifically to integrate chemical kinetic rate equations. The codes are applied to two test problems drawn from combustion kinetics. The comparisons show that LSODE is the fastest code currently available for the integration of combustion kinetic rate equations. An important finding is that an interactive solution of the algebraic energy conservation equation to compute the temperature does not result in significant errors. In addition, this method is more efficient than evaluating the temperature by integrating its time derivative. Significant reductions in computational work are realized by updating the rate constants (k = at(supra N) N exp(-E/RT) only when the temperature change exceeds an amount delta T that is problem dependent. An approximate expression for the automatic evaluation of delta T is derived and is shown to result in increased efficiency.

An efficient solver for large structured eigenvalue problems in relativistic quantum chemistry

NASA Astrophysics Data System (ADS)

Shiozaki, Toru

2017-01-01

We report an efficient program for computing the eigenvalues and symmetry-adapted eigenvectors of very large quaternionic (or Hermitian skew-Hamiltonian) matrices, using which structure-preserving diagonalisation of matrices of dimension N > 10, 000 is now routine on a single computer node. Such matrices appear frequently in relativistic quantum chemistry owing to the time-reversal symmetry. The implementation is based on a blocked version of the Paige-Van Loan algorithm, which allows us to use the Level 3 BLAS subroutines for most of the computations. Taking advantage of the symmetry, the program is faster by up to a factor of 2 than state-of-the-art implementations of complex Hermitian diagonalisation; diagonalising a 12, 800 × 12, 800 matrix took 42.8 (9.5) and 85.6 (12.6) minutes with 1 CPU core (16 CPU cores) using our symmetry-adapted solver and Intel Math Kernel Library's ZHEEV that is not structure-preserving, respectively. The source code is publicly available under the FreeBSD licence.

CFD Based Design of a Filming Injector for N+3 Combustors

NASA Technical Reports Server (NTRS)

Ajmani, Kumud; Mongia, Hukam; Lee, Phil

2016-01-01

An effort was undertaken to perform CFD analysis of fluid flow in Lean-Direct Injection (LDI) combustors with axial swirl-venturi elements for next-generation LDI-3 combustor design. The National Combustion Code (NCC) was used to perform non-reacting and two-phase reacting flow computations for a newly-designed pre-filming type fuel injector LDI-3 injector, in a single-injector and a five-injector array configuration. All computations were performed with a consistent approach of mesh-optimization, spray-modeling, ignition and kinetics-modeling. Computational predictions of the aerodynamics of the single-injector were used to arrive at an optimized main-injector design that meets effective area and fuel-air mixing criteria. Emissions (EINOx) characteristics were predicted for a medium-power engine cycle condition, and will be compared with data when it is made available from experimental measurements. The use of a PDF-like turbulence-chemistry interaction model with NCC's Time-Filtered Navier-Stokes (TFNS) solver is shown to produce a significant impact on the CFD results, when compared with a laminar-chemistry TFNS approach for the five-injector computations.

Addition of equilibrium air to an upwind Navier-Stokes code and other first steps toward a more generalized flow solver

NASA Technical Reports Server (NTRS)

Rosen, Bruce S.

1991-01-01

An upwind three-dimensional volume Navier-Stokes code is modified to facilitate modeling of complex geometries and flow fields represented by proposed National Aerospace Plane concepts. Code enhancements include an equilibrium air model, a generalized equilibrium gas model and several schemes to simplify treatment of complex geometric configurations. The code is also restructured for inclusion of an arbitrary number of independent and dependent variables. This latter capability is intended for eventual use to incorporate nonequilibrium/chemistry gas models, more sophisticated turbulence and transition models, or other physical phenomena which will require inclusion of additional variables and/or governing equations. Comparisons of computed results with experimental data and results obtained using other methods are presented for code validation purposes. Good correlation is obtained for all of the test cases considered, indicating the success of the current effort.

A new algorithm to handle finite nuclear mass effects in electronic calculations: the ISOTOPE program.

PubMed

Gonçalves, Cristina P; Mohallem, José R

2004-11-15

We report the development of a simple algorithm to modify quantum chemistry codes based on the LCAO procedure, to account for the isotope problem in electronic structure calculations. No extra computations are required compared to standard Born-Oppenheimer calculations. An upgrade of the Gamess package called ISOTOPE is presented, and its applicability is demonstrated in some examples.

Simulation of Aerosols and Chemistry with a Unified Global Model

NASA Technical Reports Server (NTRS)

Chin, Mian

2004-01-01

This project is to continue the development of the global simulation capabilities of tropospheric and stratospheric chemistry and aerosols in a unified global model. This is a part of our overall investigation of aerosol-chemistry-climate interaction. In the past year, we have enabled the tropospheric chemistry simulations based on the GEOS-CHEM model, and added stratospheric chemical reactions into the GEOS-CHEM such that a globally unified troposphere-stratosphere chemistry and transport can be simulated consistently without any simplifications. The tropospheric chemical mechanism in the GEOS-CHEM includes 80 species and 150 reactions. 24 tracers are transported, including O3, NOx, total nitrogen (NOy), H2O2, CO, and several types of hydrocarbon. The chemical solver used in the GEOS-CHEM model is a highly accurate sparse-matrix vectorized Gear solver (SMVGEAR). The stratospheric chemical mechanism includes an additional approximately 100 reactions and photolysis processes. Because of the large number of total chemical reactions and photolysis processes and very different photochemical regimes involved in the unified simulation, the model demands significant computer resources that are currently not practical. Therefore, several improvements will be taken, such as massive parallelization, code optimization, or selecting a faster solver. We have also continued aerosol simulation (including sulfate, dust, black carbon, organic carbon, and sea-salt) in the global model to cover most of year 2002. These results have been made available to many groups worldwide and accessible from the website http://code916.gsfc.nasa.gov/People/Chin/aot.html.

Chemical application of diffusion quantum Monte Carlo

NASA Technical Reports Server (NTRS)

Reynolds, P. J.; Lester, W. A., Jr.

1984-01-01

The diffusion quantum Monte Carlo (QMC) method gives a stochastic solution to the Schroedinger equation. This approach is receiving increasing attention in chemical applications as a result of its high accuracy. However, reducing statistical uncertainty remains a priority because chemical effects are often obtained as small differences of large numbers. As an example, the single-triplet splitting of the energy of the methylene molecule CH sub 2 is given. The QMC algorithm was implemented on the CYBER 205, first as a direct transcription of the algorithm running on the VAX 11/780, and second by explicitly writing vector code for all loops longer than a crossover length C. The speed of the codes relative to one another as a function of C, and relative to the VAX, are discussed. The computational time dependence obtained versus the number of basis functions is discussed and this is compared with that obtained from traditional quantum chemistry codes and that obtained from traditional computer architectures.

Development of an upwind, finite-volume code with finite-rate chemistry

NASA Technical Reports Server (NTRS)

Molvik, Gregory A.

1994-01-01

Under this grant, two numerical algorithms were developed to predict the flow of viscous, hypersonic, chemically reacting gases over three-dimensional bodies. Both algorithms take advantage of the benefits of upwind differencing, total variation diminishing techniques, and a finite-volume framework, but obtain their solution in two separate manners. The first algorithm is a zonal, time-marching scheme, and is generally used to obtain solutions in the subsonic portions of the flow field. The second algorithm is a much less expensive, space-marching scheme and can be used for the computation of the larger, supersonic portion of the flow field. Both codes compute their interface fluxes with a temporal Riemann solver and the resulting schemes are made fully implicit including the chemical source terms and boundary conditions. Strong coupling is used between the fluid dynamic, chemical, and turbulence equations. These codes have been validated on numerous hypersonic test cases and have provided excellent comparison with existing data.

Earth system modelling on system-level heterogeneous architectures: EMAC (version 2.42) on the Dynamical Exascale Entry Platform (DEEP)

NASA Astrophysics Data System (ADS)

Christou, Michalis; Christoudias, Theodoros; Morillo, Julián; Alvarez, Damian; Merx, Hendrik

2016-09-01

We examine an alternative approach to heterogeneous cluster-computing in the many-core era for Earth system models, using the European Centre for Medium-Range Weather Forecasts Hamburg (ECHAM)/Modular Earth Submodel System (MESSy) Atmospheric Chemistry (EMAC) model as a pilot application on the Dynamical Exascale Entry Platform (DEEP). A set of autonomous coprocessors interconnected together, called Booster, complements a conventional HPC Cluster and increases its computing performance, offering extra flexibility to expose multiple levels of parallelism and achieve better scalability. The EMAC model atmospheric chemistry code (Module Efficiently Calculating the Chemistry of the Atmosphere (MECCA)) was taskified with an offload mechanism implemented using OmpSs directives. The model was ported to the MareNostrum 3 supercomputer to allow testing with Intel Xeon Phi accelerators on a production-size machine. The changes proposed in this paper are expected to contribute to the eventual adoption of Cluster-Booster division and Many Integrated Core (MIC) accelerated architectures in presently available implementations of Earth system models, towards exploiting the potential of a fully Exascale-capable platform.

Flame-Vortex Studies to Quantify Markstein Numbers Needed to Model Flame Extinction Limits

NASA Technical Reports Server (NTRS)

Driscoll, James F.; Feikema, Douglas A.

2003-01-01

This has quantified a database of Markstein numbers for unsteady flames; future work will quantify a database of flame extinction limits for unsteady conditions. Unsteady extinction limits have not been documented previously; both a stretch rate and a residence time must be measured, since extinction requires that the stretch rate be sufficiently large for a sufficiently long residence time. Ma was measured for an inwardly-propagating flame (IPF) that is negatively-stretched under microgravity conditions. Computations also were performed using RUN-1DL to explain the measurements. The Markstein number of an inwardly-propagating flame, for both the microgravity experiment and the computations, is significantly larger than that of an outwardy-propagating flame. The computed profiles of the various species within the flame suggest reasons. Computed hydrogen concentrations build up ahead of the IPF but not the OPF. Understanding was gained by running the computations for both simplified and full-chemistry conditions. Numerical Simulations. To explain the experimental findings, numerical simulations of both inwardly and outwardly propagating spherical flames (with complex chemistry) were generated using the RUN-1DL code, which includes 16 species and 46 reactions.

Quantum chemical study of methane oxidation species

NASA Technical Reports Server (NTRS)

Jackels, Charles F.

1993-01-01

The research funded by this project has focused on quantum chemical investigations of molecular species thought to be important in the chemistry of the earth's upper and lower atmospheres. The body of this report contains brief discussions of the results of the several phases of this investigation. In many instances these results have been presented at scientific meetings and/or published in refereed journals. Those bibliographic references are given. In addition to the study of specific chemical systems, there were several phases during the course of this investigation where much of the effort went into the development and modification of computer codes necessary to carry out these calculations on the wide range of computer equipment used during this study. This type of code maintenance and development work did not generally result in publications and presentations, but a brief review is given.

Incorporation of coupled nonequilibrium chemistry into a two-dimensional nozzle code (SEAGULL)

NASA Technical Reports Server (NTRS)

Ratliff, A. W.

1979-01-01

A two-dimensional multiple shock nozzle code (SEAGULL) was extended to include the effects of finite rate chemistry. The basic code that treats multiple shocks and contact surfaces was fully coupled with a generalized finite rate chemistry and vibrational energy exchange package. The modified code retains all of the original SEAGULL features plus the capability to treat chemical and vibrational nonequilibrium reactions. Any chemical and/or vibrational energy exchange mechanism can be handled as long as thermodynamic data and rate constants are available for all participating species.

Assessment of chemistry models for compressible reacting flows

NASA Astrophysics Data System (ADS)

Lapointe, Simon; Blanquart, Guillaume

2014-11-01

Recent technological advances in propulsion and power devices and renewed interest in the development of next generation supersonic and hypersonic vehicles have increased the need for detailed understanding of turbulence-combustion interactions in compressible reacting flows. In numerical simulations of such flows, accurate modeling of the fuel chemistry is a critical component of capturing the relevant physics. Various chemical models are currently being used in reacting flow simulations. However, the differences between these models and their impacts on the fluid dynamics in the context of compressible flows are not well understood. In the present work, a numerical code is developed to solve the fully coupled compressible conservation equations for reacting flows. The finite volume code is based on the theoretical and numerical framework developed by Oefelein (Prog. Aero. Sci. 42 (2006) 2-37) and employs an all-Mach-number formulation with dual time-stepping and preconditioning. The numerical approach is tested on turbulent premixed flames at high Karlovitz numbers. Different chemical models of varying complexity and computational cost are used and their effects are compared.

Development of a MELCOR Sodium Chemistry (NAC) Package - FY17 Progress.

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

Louie, David; Humphries, Larry L.

This report describes the status of the development of MELCOR Sodium Chemistry (NAC) package. This development is based on the CONTAIN-LMR sodium physics and chemistry models to be implemented in MELCOR. In the past three years, the sodium equation of state as a working fluid from the nuclear fusion safety research and from the SIMMER code has been implemented into MELCOR. The chemistry models from the CONTAIN-LMR code, such as the spray and pool fire mode ls, have also been implemented into MELCOR. This report describes the implemented models and the issues encountered. Model descriptions and input descriptions are provided.more » Development testing of the spray and pool fire models is described, including the code-to-code comparison with CONTAIN-LMR. The report ends with an expected timeline for the remaining models to be implemented, such as the atmosphere chemistry, sodium-concrete interactions, and experimental validation tests .« less

Automatic Differentiation in Quantum Chemistry with Applications to Fully Variational Hartree-Fock.

PubMed

Tamayo-Mendoza, Teresa; Kreisbeck, Christoph; Lindh, Roland; Aspuru-Guzik, Alán

2018-05-23

Automatic differentiation (AD) is a powerful tool that allows calculating derivatives of implemented algorithms with respect to all of their parameters up to machine precision, without the need to explicitly add any additional functions. Thus, AD has great potential in quantum chemistry, where gradients are omnipresent but also difficult to obtain, and researchers typically spend a considerable amount of time finding suitable analytical forms when implementing derivatives. Here, we demonstrate that AD can be used to compute gradients with respect to any parameter throughout a complete quantum chemistry method. We present DiffiQult , a Hartree-Fock implementation, entirely differentiated with the use of AD tools. DiffiQult is a software package written in plain Python with minimal deviation from standard code which illustrates the capability of AD to save human effort and time in implementations of exact gradients in quantum chemistry. We leverage the obtained gradients to optimize the parameters of one-particle basis sets in the context of the floating Gaussian framework.

Component-based integration of chemistry and optimization software.

PubMed

Kenny, Joseph P; Benson, Steven J; Alexeev, Yuri; Sarich, Jason; Janssen, Curtis L; McInnes, Lois Curfman; Krishnan, Manojkumar; Nieplocha, Jarek; Jurrus, Elizabeth; Fahlstrom, Carl; Windus, Theresa L

2004-11-15

Typical scientific software designs make rigid assumptions regarding programming language and data structures, frustrating software interoperability and scientific collaboration. Component-based software engineering is an emerging approach to managing the increasing complexity of scientific software. Component technology facilitates code interoperability and reuse. Through the adoption of methodology and tools developed by the Common Component Architecture Forum, we have developed a component architecture for molecular structure optimization. Using the NWChem and Massively Parallel Quantum Chemistry packages, we have produced chemistry components that provide capacity for energy and energy derivative evaluation. We have constructed geometry optimization applications by integrating the Toolkit for Advanced Optimization, Portable Extensible Toolkit for Scientific Computation, and Global Arrays packages, which provide optimization and linear algebra capabilities. We present a brief overview of the component development process and a description of abstract interfaces for chemical optimizations. The components conforming to these abstract interfaces allow the construction of applications using different chemistry and mathematics packages interchangeably. Initial numerical results for the component software demonstrate good performance, and highlight potential research enabled by this platform.

Automatic Differentiation in Quantum Chemistry with Applications to Fully Variational Hartree–Fock

PubMed Central

2018-01-01

Automatic differentiation (AD) is a powerful tool that allows calculating derivatives of implemented algorithms with respect to all of their parameters up to machine precision, without the need to explicitly add any additional functions. Thus, AD has great potential in quantum chemistry, where gradients are omnipresent but also difficult to obtain, and researchers typically spend a considerable amount of time finding suitable analytical forms when implementing derivatives. Here, we demonstrate that AD can be used to compute gradients with respect to any parameter throughout a complete quantum chemistry method. We present DiffiQult, a Hartree–Fock implementation, entirely differentiated with the use of AD tools. DiffiQult is a software package written in plain Python with minimal deviation from standard code which illustrates the capability of AD to save human effort and time in implementations of exact gradients in quantum chemistry. We leverage the obtained gradients to optimize the parameters of one-particle basis sets in the context of the floating Gaussian framework.

Pharmacophore screening of the protein data bank for specific binding site chemistry.

PubMed

Campagna-Slater, Valérie; Arrowsmith, Andrew G; Zhao, Yong; Schapira, Matthieu

2010-03-22

A simple computational approach was developed to screen the Protein Data Bank (PDB) for putative pockets possessing a specific binding site chemistry and geometry. The method employs two commonly used 3D screening technologies, namely identification of cavities in protein structures and pharmacophore screening of chemical libraries. For each protein structure, a pocket finding algorithm is used to extract potential binding sites containing the correct types of residues, which are then stored in a large SDF-formatted virtual library; pharmacophore filters describing the desired binding site chemistry and geometry are then applied to screen this virtual library and identify pockets matching the specified structural chemistry. As an example, this approach was used to screen all human protein structures in the PDB and identify sites having chemistry similar to that of known methyl-lysine binding domains that recognize chromatin methylation marks. The selected genes include known readers of the histone code as well as novel binding pockets that may be involved in epigenetic signaling. Putative allosteric sites were identified on the structures of TP53BP1, L3MBTL3, CHEK1, KDM4A, and CREBBP.

CFD Code Development for Combustor Flows

NASA Technical Reports Server (NTRS)

Norris, Andrew

2003-01-01

During the lifetime of this grant, work has been performed in the areas of model development, code development, code validation and code application. For model development, this has included the PDF combustion module, chemical kinetics based on thermodynamics, neural network storage of chemical kinetics, ILDM chemical kinetics and assumed PDF work. Many of these models were then implemented in the code, and in addition many improvements were made to the code, including the addition of new chemistry integrators, property evaluation schemes, new chemistry models and turbulence-chemistry interaction methodology. Validation of all new models and code improvements were also performed, while application of the code to the ZCET program and also the NPSS GEW combustor program were also performed. Several important items remain under development, including the NOx post processing, assumed PDF model development and chemical kinetic development. It is expected that this work will continue under the new grant.

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.

SOPHAEROS code development and its application to falcon tests

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

Lajtha, G.; Missirlian, M.; Kissane, M.

1996-12-31

One of the key issues in source-term evaluation in nuclear reactor severe accidents is determination of the transport behavior of fission products released from the degrading core. The SOPHAEROS computer code is being developed to predict fission product transport in a mechanistic way in light water reactor circuits. These applications of the SOPHAEROS code to the Falcon experiments, among others not presented here, indicate that the numerical scheme of the code is robust, and no convergence problems are encountered. The calculation is also very fast being three times longer on a Sun SPARC 5 workstation than real time and typicallymore » {approx} 10 times faster than an identical calculation with the VICTORIA code. The study demonstrates that the SOPHAEROS 1.3 code is a suitable tool for prediction of the vapor chemistry and fission product transport with a reasonable level of accuracy. Furthermore, the fexibility of the code material data bank allows improvement of understanding of fission product transport and deposition in the circuit. Performing sensitivity studies with different chemical species or with different properties (saturation pressure, chemical equilibrium constants) is very straightforward.« less

Final Report: Ionization chemistry of high temperature molecular fluids

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

Fried, L E

2007-02-26

With the advent of coupled chemical/hydrodynamic reactive flow models for high explosives, understanding detonation chemistry is of increasing importance to DNT. The accuracy of first principles detonation codes, such as CHEETAH, are dependent on an accurate representation of the species present under detonation conditions. Ionic species and non-molecular phases are not currently included coupled chemistry/hydrodynamic simulations. This LDRD will determine the prevalence of such species during high explosive detonations, by carrying out experimental and computational investigation of common detonation products under extreme conditions. We are studying the phase diagram of detonation products such as H{sub 2}O, or NH{sub 3} andmore » mixtures under conditions of extreme pressure (P > 1 GPa) and temperature (T > 1000K). Under these conditions, the neutral molecular form of matter transforms to a phase dominated by ions. The phase boundaries of such a region are unknown.« less

Numerical study of shock-wave/boundary layer interactions in premixed hydrogen-air hypersonic flows

NASA Technical Reports Server (NTRS)

Yungster, Shaye

1991-01-01

A computational study of shock wave/boundary layer interactions involving premixed combustible gases, and the resulting combustion processes is presented. The analysis is carried out using a new fully implicit, total variation diminishing (TVD) code developed for solving the fully coupled Reynolds-averaged Navier-Stokes equations and species continuity equations in an efficient manner. To accelerate the convergence of the basic iterative procedure, this code is combined with vector extrapolation methods. The chemical nonequilibrium processes are simulated by means of a finite-rate chemistry model for hydrogen-air combustion. Several validation test cases are presented and the results compared with experimental data or with other computational results. The code is then applied to study shock wave/boundary layer interactions in a ram accelerator configuration. Results indicate a new combustion mechanism in which a shock wave induces combustion in the boundary layer, which then propagates outwards and downstream. At higher Mach numbers, spontaneous ignition in part of the boundary layer is observed, which eventually extends along the entire boundary layer at still higher values of the Mach number.

An efficient MPI/OpenMP parallelization of the Hartree–Fock–Roothaan method for the first generation of Intel® Xeon Phi™ processor architecture

DOE PAGES

Mironov, Vladimir; Moskovsky, Alexander; D’Mello, Michael; ...

2017-10-04

The Hartree-Fock (HF) method in the quantum chemistry package GAMESS represents one of the most irregular algorithms in computation today. Major steps in the calculation are the irregular computation of electron repulsion integrals (ERIs) and the building of the Fock matrix. These are the central components of the main Self Consistent Field (SCF) loop, the key hotspot in Electronic Structure (ES) codes. By threading the MPI ranks in the official release of the GAMESS code, we not only speed up the main SCF loop (4x to 6x for large systems), but also achieve a significant (>2x) reduction in the overallmore » memory footprint. These improvements are a direct consequence of memory access optimizations within the MPI ranks. We benchmark our implementation against the official release of the GAMESS code on the Intel R Xeon PhiTM supercomputer. Here, scaling numbers are reported on up to 7,680 cores on Intel Xeon Phi coprocessors.« less

Development of an upwind, finite-volume code with finite-rate chemistry

NASA Technical Reports Server (NTRS)

Molvik, Gregory A.

1995-01-01

Under this grant, two numerical algorithms were developed to predict the flow of viscous, hypersonic, chemically reacting gases over three-dimensional bodies. Both algorithms take advantage of the benefits of upwind differencing, total variation diminishing techniques and of a finite-volume framework, but obtain their solution in two separate manners. The first algorithm is a zonal, time-marching scheme, and is generally used to obtain solutions in the subsonic portions of the flow field. The second algorithm is a much less expensive, space-marching scheme and can be used for the computation of the larger, supersonic portion of the flow field. Both codes compute their interface fluxes with a temporal Riemann solver and the resulting schemes are made fully implicit including the chemical source terms and boundary conditions. Strong coupling is used between the fluid dynamic, chemical and turbulence equations. These codes have been validated on numerous hypersonic test cases and have provided excellent comparison with existing data. This report summarizes the research that took place from August 1,1994 to January 1, 1995.

The NATA code: Theory and analysis, volume 1. [user manuals (computer programming) - gas dynamics, wind tunnels

NASA Technical Reports Server (NTRS)

Bade, W. L.; Yos, J. M.

1975-01-01

A computer program for calculating quasi-one-dimensional gas flow in axisymmetric and two-dimensional nozzles and rectangular channels is presented. Flow is assumed to start from a state of thermochemical equilibrium at a high temperature in an upstream reservoir. The program provides solutions based on frozen chemistry, chemical equilibrium, and nonequilibrium flow with finite reaction rates. Electronic nonequilibrium effects can be included using a two-temperature model. An approximate laminar boundary layer calculation is given for the shear and heat flux on the nozzle wall. Boundary layer displacement effects on the inviscid flow are considered also. Chemical equilibrium and transport property calculations are provided by subroutines. The code contains precoded thermochemical, chemical kinetic, and transport cross section data for high-temperature air, CO2-N2-Ar mixtures, helium, and argon. It provides calculations of the stagnation conditions on axisymmetric or two-dimensional models, and of the conditions on the flat surface of a blunt wedge. The primary purpose of the code is to describe the flow conditions and test conditions in electric arc heated wind tunnels.

Numerical study of shock-wave/boundary layer interactions in premixed hydrogen-air hypersonic flows

NASA Technical Reports Server (NTRS)

Yungster, Shaye

1990-01-01

A computational study of shock wave/boundary layer interactions involving premixed combustible gases, and the resulting combustion processes is presented. The analysis is carried out using a new fully implicit, total variation diminishing (TVD) code developed for solving the fully coupled Reynolds-averaged Navier-Stokes equations and species continuity equations in an efficient manner. To accelerate the convergence of the basic iterative procedure, this code is combined with vector extrapolation methods. The chemical nonequilibrium processes are simulated by means of a finite-rate chemistry model for hydrogen-air combustion. Several validation test cases are presented and the results compared with experimental data or with other computational results. The code is then applied to study shock wave/boundary layer interactions in a ram accelerator configuration. Results indicate a new combustion mechanism in which a shock wave induces combustion in the boundary layer, which then propagates outwards and downstream. At higher Mach numbers, spontaneous ignition in part of the boundary layer is observed, which eventually extends along the entire boundary layer at still higher values of the Mach number.

Combinatorial computational chemistry approach for materials design: applications in deNOx catalysis, Fischer-Tropsch synthesis, lanthanoid complex, and lithium ion secondary battery.

PubMed

Koyama, Michihisa; Tsuboi, Hideyuki; Endou, Akira; Takaba, Hiromitsu; Kubo, Momoji; Del Carpio, Carlos A; Miyamoto, Akira

2007-02-01

Computational chemistry can provide fundamental knowledge regarding various aspects of materials. While its impact in scientific research is greatly increasing, its contributions to industrially important issues are far from satisfactory. In order to realize industrial innovation by computational chemistry, a new concept "combinatorial computational chemistry" has been proposed by introducing the concept of combinatorial chemistry to computational chemistry. This combinatorial computational chemistry approach enables theoretical high-throughput screening for materials design. In this manuscript, we review the successful applications of combinatorial computational chemistry to deNO(x) catalysts, Fischer-Tropsch catalysts, lanthanoid complex catalysts, and cathodes of the lithium ion secondary battery.

Strategies for vectorizing the sparse matrix vector product on the CRAY XMP, CRAY 2, and CYBER 205

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.; Partridge, Harry

1987-01-01

Large, randomly sparse matrix vector products are important in a number of applications in computational chemistry, such as matrix diagonalization and the solution of simultaneous equations. Vectorization of this process is considered for the CRAY XMP, CRAY 2, and CYBER 205, using a matrix of dimension of 20,000 with from 1 percent to 6 percent nonzeros. Efficient scatter/gather capabilities add coding flexibility and yield significant improvements in performance. For the CYBER 205, it is shown that minor changes in the IO can reduce the CPU time by a factor of 50. Similar changes in the CRAY codes make a far smaller improvement.

Application of computational fluid dynamics to the design of the Space Transportation Main Engine subscale nozzle

NASA Technical Reports Server (NTRS)

Garrett, J. L.; Syed, S. A.

1992-01-01

CFD analyses of the Space Transportation Main Engine film/dump cooled subscale nozzle are presented, with an emphasis on the timely impact of CFD in the design of the subscale nozzle secondary coolant system. Calculations were performed with the Generalized Aerodynamic Simulation Program (GASP), using a Baldwin-Lomas Turbulence model, and finite rate hydrogen-oxygen chemistry. Design iterations for both the secondary coolant cavity passage and the secondary coolant lip are presented. In addition, validation of the GASP chemistry and turbulence models by comparison with data and other CFD codes are presented for a hypersonic laminar separation corner, a backward facing step, and a 2D scramjet nozzle with hydrogen-oxygen kinetics.

BLT-EC (Breach, Leach and Transport-Equilibrium Chemistry) data input guide. A computer model for simulating release and coupled geochemical transport of contaminants from a subsurface disposal facility

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

MacKinnon, R.J.; Sullivan, T.M.; Kinsey, R.R.

1997-05-01

The BLT-EC computer code has been developed, implemented, and tested. BLT-EC is a two-dimensional finite element computer code capable of simulating the time-dependent release and reactive transport of aqueous phase species in a subsurface soil system. BLT-EC contains models to simulate the processes (container degradation, waste-form performance, transport, chemical reactions, and radioactive production and decay) most relevant to estimating the release and transport of contaminants from a subsurface disposal system. Water flow is provided through tabular input or auxiliary files. Container degradation considers localized failure due to pitting corrosion and general failure due to uniform surface degradation processes. Waste-form performancemore » considers release to be limited by one of four mechanisms: rinse with partitioning, diffusion, uniform surface degradation, and solubility. Transport considers the processes of advection, dispersion, diffusion, chemical reaction, radioactive production and decay, and sources (waste form releases). Chemical reactions accounted for include complexation, sorption, dissolution-precipitation, oxidation-reduction, and ion exchange. Radioactive production and decay in the waste form is simulated. To improve the usefulness of BLT-EC, a pre-processor, ECIN, which assists in the creation of chemistry input files, and a post-processor, BLTPLOT, which provides a visual display of the data have been developed. BLT-EC also includes an extensive database of thermodynamic data that is also accessible to ECIN. This document reviews the models implemented in BLT-EC and serves as a guide to creating input files and applying BLT-EC.« less

A NIST Kinetic Data Base for PAH Reaction and Soot Particle Inception During Combusion

DTIC Science & Technology

2007-12-01

in Computational Fluid Dynamics (CFD) codes hat have lead to the capability of describing complex reactive flow problems and thus simulating... parameters . However in the absence of data estimates must be made. Since the chemistry of combustion is extremely complex and for proper description...118:381-389 9. Babushok, V. and Tsang, W., J. Prop. and Pwr . 20 (2004) 403-414. 10. . Fournet, R., Warth, V., Glaude, P.A., Battin-Leclerc, F

NCC: A Multidisciplinary Design/Analysis Tool for Combustion Systems

NASA Technical Reports Server (NTRS)

Liu, Nan-Suey; Quealy, Angela

1999-01-01

A multi-disciplinary design/analysis tool for combustion systems is critical for optimizing the low-emission, high-performance combustor design process. Based on discussions between NASA Lewis Research Center and the jet engine companies, an industry-government team was formed in early 1995 to develop the National Combustion Code (NCC), which is an integrated system of computer codes for the design and analysis of combustion systems. NCC has advanced features that address the need to meet designer's requirements such as "assured accuracy", "fast turnaround", and "acceptable cost". The NCC development team is comprised of Allison Engine Company (Allison), CFD Research Corporation (CFDRC), GE Aircraft Engines (GEAE), NASA Lewis Research Center (LeRC), and Pratt & Whitney (P&W). This development team operates under the guidance of the NCC steering committee. The "unstructured mesh" capability and "parallel computing" are fundamental features of NCC from its inception. The NCC system is composed of a set of "elements" which includes grid generator, main flow solver, turbulence module, turbulence and chemistry interaction module, chemistry module, spray module, radiation heat transfer module, data visualization module, and a post-processor for evaluating engine performance parameters. Each element may have contributions from several team members. Such a multi-source multi-element system needs to be integrated in a way that facilitates inter-module data communication, flexibility in module selection, and ease of integration.

The production of nitric oxide in the troposphere as a result of solid-rocket-motor afterburning

NASA Technical Reports Server (NTRS)

Stewart, R. B.; Gomberg, R. I.

1976-01-01

As part of an ongoing assessment of the environmental effects of solid-rocket-motor operations in the troposphere, estimates were made of the nitric oxide produced in the troposphere by the space shuttle and Titan 3-C boosters. Calculations were made with the low-altitude plume computer program and included the effects of coupled finite-rate chemistry and turbulent mixing. A recent measurement of nitric oxide taken in the effluent cloud of a Titan 3-C booster is compared with calculations made with this computer code. The various chemical reactions of the exhaust gases are listed in tabular form.

Computation of Thermodynamic Equilibria Pertinent to Nuclear Materials in Multi-Physics Codes

NASA Astrophysics Data System (ADS)

Piro, Markus Hans Alexander

Nuclear energy plays a vital role in supporting electrical needs and fulfilling commitments to reduce greenhouse gas emissions. Research is a continuing necessity to improve the predictive capabilities of fuel behaviour in order to reduce costs and to meet increasingly stringent safety requirements by the regulator. Moreover, a renewed interest in nuclear energy has given rise to a "nuclear renaissance" and the necessity to design the next generation of reactors. In support of this goal, significant research efforts have been dedicated to the advancement of numerical modelling and computational tools in simulating various physical and chemical phenomena associated with nuclear fuel behaviour. This undertaking in effect is collecting the experience and observations of a past generation of nuclear engineers and scientists in a meaningful way for future design purposes. There is an increasing desire to integrate thermodynamic computations directly into multi-physics nuclear fuel performance and safety codes. A new equilibrium thermodynamic solver is being developed with this matter as a primary objective. This solver is intended to provide thermodynamic material properties and boundary conditions for continuum transport calculations. There are several concerns with the use of existing commercial thermodynamic codes: computational performance; limited capabilities in handling large multi-component systems of interest to the nuclear industry; convenient incorporation into other codes with quality assurance considerations; and, licensing entanglements associated with code distribution. The development of this software in this research is aimed at addressing all of these concerns. The approach taken in this work exploits fundamental principles of equilibrium thermodynamics to simplify the numerical optimization equations. In brief, the chemical potentials of all species and phases in the system are constrained by estimates of the chemical potentials of the system components at each iterative step, and the objective is to minimize the residuals of the mass balance equations. Several numerical advantages are achieved through this simplification. In particular, computational expense is reduced and the rate of convergence is enhanced. Furthermore, the software has demonstrated the ability to solve systems involving as many as 118 component elements. An early version of the code has already been integrated into the Advanced Multi-Physics (AMP) code under development by the Oak Ridge National Laboratory, Los Alamos National Laboratory, Idaho National Laboratory and Argonne National Laboratory. Keywords: Engineering, Nuclear -- 0552, Engineering, Material Science -- 0794, Chemistry, Mathematics -- 0405, Computer Science -- 0984

Modeling of the Very Low Frequency (VLF) radio wave signal profile due to solar flares using the GEANT4 Monte Carlo simulation coupled with ionospheric chemistry

NASA Astrophysics Data System (ADS)

Palit, S.; Basak, T.; Mondal, S. K.; Pal, S.; Chakrabarti, S. K.

2013-03-01

X-ray photons emitted during solar flares cause ionization in the lower ionosphere (~ 60 to 100 km) in excess of what is expected from a quiet sun. Very Low Frequency (VLF) radio wave signals reflected from the D region are affected by this excess ionization. In this paper, we reproduce the deviation in VLF signal strength during solar flares by numerical modeling. We use GEANT4 Monte Carlo simulation code to compute the rate of ionization due to a M-class and a X-class flare. The output of the simulation is then used in a simplified ionospheric chemistry model to calculate the time variation of electron density at different altitudes in the lower ionosphere. The resulting electron density variation profile is then self-consistently used in the LWPC code to obtain the time variation of the VLF signal change. We did the modeling of the VLF signal along the NWC (Australia) to IERC/ICSP (India) propagation path and compared the results with observations. The agreement is found to be very satisfactory.

Evolution of computational chemistry, the "launch pad" to scientific computational models: The early days from a personal account, the present status from the TACC-2012 congress, and eventual future applications from the global simulation approach

NASA Astrophysics Data System (ADS)

Clementi, Enrico

2012-06-01

This is the introductory chapter to the AIP Proceedings volume "Theory and Applications of Computational Chemistry: The First Decade of the Second Millennium" where we discuss the evolution of "computational chemistry". Very early variational computational chemistry developments are reported in Sections 1 to 7, and 11, 12 by recalling some of the computational chemistry contributions by the author and his collaborators (from late 1950 to mid 1990); perturbation techniques are not considered in this already extended work. Present day's computational chemistry is partly considered in Sections 8 to 10 where more recent studies by the author and his collaborators are discussed, including the Hartree-Fock-Heitler-London method; a more general discussion on present day computational chemistry is presented in Section 14. The following chapters of this AIP volume provide a view of modern computational chemistry. Future computational chemistry developments can be extrapolated from the chapters of this AIP volume; further, in Sections 13 and 15 present an overall analysis on computational chemistry, obtained from the Global Simulation approach, by considering the evolution of scientific knowledge confronted with the opportunities offered by modern computers.

Dilution physics modeling: Dissolution/precipitation chemistry

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

Onishi, Y.; Reid, H.C.; Trent, D.S.

This report documents progress made to date on integrating dilution/precipitation chemistry and new physical models into the TEMPEST thermal-hydraulics computer code. Implementation of dissolution/precipitation chemistry models is necessary for predicting nonhomogeneous, time-dependent, physical/chemical behavior of tank wastes with and without a variety of possible engineered remediation and mitigation activities. Such behavior includes chemical reactions, gas retention, solids resuspension, solids dissolution and generation, solids settling/rising, and convective motion of physical and chemical species. Thus this model development is important from the standpoint of predicting the consequences of various engineered activities, such as mitigation by dilution, retrieval, or pretreatment, that can affectmore » safe operations. The integration of a dissolution/precipitation chemistry module allows the various phase species concentrations to enter into the physical calculations that affect the TEMPEST hydrodynamic flow calculations. The yield strength model of non-Newtonian sludge correlates yield to a power function of solids concentration. Likewise, shear stress is concentration-dependent, and the dissolution/precipitation chemistry calculations develop the species concentration evolution that produces fluid flow resistance changes. Dilution of waste with pure water, molar concentrations of sodium hydroxide, and other chemical streams can be analyzed for the reactive species changes and hydrodynamic flow characteristics.« less

Virtually going green: The role of quantum computational chemistry in reducing pollution and toxicity in chemistry

NASA Astrophysics Data System (ADS)

Stevens, Jonathan

2017-07-01

Continuing advances in computational chemistry has permitted quantum mechanical calculation to assist in research in green chemistry and to contribute to the greening of chemical practice. Presented here are recent examples illustrating the contribution of computational quantum chemistry to green chemistry, including the possibility of using computation as a green alternative to experiments, but also illustrating contributions to greener catalysis and the search for greener solvents. Examples of applications of computation to ambitious projects for green synthetic chemistry using carbon dioxide are also presented.

Software Integration in Multi-scale Simulations: the PUPIL System

NASA Astrophysics Data System (ADS)

Torras, J.; Deumens, E.; Trickey, S. B.

2006-10-01

The state of the art for computational tools in both computational chemistry and computational materials physics includes many algorithms and functionalities which are implemented again and again. Several projects aim to reduce, eliminate, or avoid this problem. Most such efforts seem to be focused within a particular specialty, either quantum chemistry or materials physics. Multi-scale simulations, by their very nature however, cannot respect that specialization. In simulation of fracture, for example, the energy gradients that drive the molecular dynamics (MD) come from a quantum mechanical treatment that most often derives from quantum chemistry. That “QM” region is linked to a surrounding “CM” region in which potentials yield the forces. The approach therefore requires the integration or at least inter-operation of quantum chemistry and materials physics algorithms. The same problem occurs in “QM/MM” simulations in computational biology. The challenge grows if pattern recognition or other analysis codes of some kind must be used as well. The most common mode of inter-operation is user intervention: codes are modified as needed and data files are managed “by hand” by the user (interactively and via shell scripts). User intervention is however inefficient by nature, difficult to transfer to the community, and prone to error. Some progress (e.g Sethna’s work at Cornell [C.R. Myers et al., Mat. Res. Soc. Symp. Proc., 538(1999) 509, C.-S. Chen et al., Poster presented at the Material Research Society Meeting (2000)]) has been made on using Python scripts to achieve a more efficient level of interoperation. In this communication we present an alternative approach to merging current working packages without the necessity of major recoding and with only a relatively light wrapper interface. The scheme supports communication among the different components required for a given multi-scale calculation and access to the functionalities of those components for the potential user. A general main program allows the management of every package with a special communication protocol between their interfaces following the directives introduced by the user which are stored in an XML structured file. The initial prototype of the PUPIL (Program for User Packages Interfacing and Linking) system has been done using Java as a fast, easy prototyping object oriented (OO) language. In order to test it, we have applied this prototype to a previously studied problem, the fracture of a silica nanorod. We did so joining two different packages to do a QM/MD calculation. The results show the potential for this software system to do different kind of simulations and its simplicity of maintenance.

Theoretical Hammett Plot for the Gas-Phase Ionization of Benzoic Acid versus Phenol: A Computational Chemistry Lab Exercise

ERIC Educational Resources Information Center

Ziegler, Blake E.

2013-01-01

Computational chemistry undergraduate laboratory courses are now part of the chemistry curriculum at many universities. However, there remains a lack of computational chemistry exercises available to instructors. This exercise is presented for students to develop skills using computational chemistry software while supplementing their knowledge of…

chemf: A purely functional chemistry toolkit.

PubMed

Höck, Stefan; Riedl, Rainer

2012-12-20

Although programming in a type-safe and referentially transparent style offers several advantages over working with mutable data structures and side effects, this style of programming has not seen much use in chemistry-related software. Since functional programming languages were designed with referential transparency in mind, these languages offer a lot of support when writing immutable data structures and side-effects free code. We therefore started implementing our own toolkit based on the above programming paradigms in a modern, versatile programming language. We present our initial results with functional programming in chemistry by first describing an immutable data structure for molecular graphs together with a couple of simple algorithms to calculate basic molecular properties before writing a complete SMILES parser in accordance with the OpenSMILES specification. Along the way we show how to deal with input validation, error handling, bulk operations, and parallelization in a purely functional way. At the end we also analyze and improve our algorithms and data structures in terms of performance and compare it to existing toolkits both object-oriented and purely functional. All code was written in Scala, a modern multi-paradigm programming language with a strong support for functional programming and a highly sophisticated type system. We have successfully made the first important steps towards a purely functional chemistry toolkit. The data structures and algorithms presented in this article perform well while at the same time they can be safely used in parallelized applications, such as computer aided drug design experiments, without further adjustments. This stands in contrast to existing object-oriented toolkits where thread safety of data structures and algorithms is a deliberate design decision that can be hard to implement. Finally, the level of type-safety achieved by Scala highly increased the reliability of our code as well as the productivity of the programmers involved in this project.

chemf: A purely functional chemistry toolkit

PubMed Central

2012-01-01

Background Although programming in a type-safe and referentially transparent style offers several advantages over working with mutable data structures and side effects, this style of programming has not seen much use in chemistry-related software. Since functional programming languages were designed with referential transparency in mind, these languages offer a lot of support when writing immutable data structures and side-effects free code. We therefore started implementing our own toolkit based on the above programming paradigms in a modern, versatile programming language. Results We present our initial results with functional programming in chemistry by first describing an immutable data structure for molecular graphs together with a couple of simple algorithms to calculate basic molecular properties before writing a complete SMILES parser in accordance with the OpenSMILES specification. Along the way we show how to deal with input validation, error handling, bulk operations, and parallelization in a purely functional way. At the end we also analyze and improve our algorithms and data structures in terms of performance and compare it to existing toolkits both object-oriented and purely functional. All code was written in Scala, a modern multi-paradigm programming language with a strong support for functional programming and a highly sophisticated type system. Conclusions We have successfully made the first important steps towards a purely functional chemistry toolkit. The data structures and algorithms presented in this article perform well while at the same time they can be safely used in parallelized applications, such as computer aided drug design experiments, without further adjustments. This stands in contrast to existing object-oriented toolkits where thread safety of data structures and algorithms is a deliberate design decision that can be hard to implement. Finally, the level of type-safety achieved by Scala highly increased the reliability of our code as well as the productivity of the programmers involved in this project. PMID:23253942

Nonequilibrium radiation and chemistry models for aerocapture vehicle flowfields

NASA Technical Reports Server (NTRS)

Carlson, Leland A.

1990-01-01

The continued development and improvement of the viscous shock layer (VSL) nonequilibrium chemistry blunt body engineering code, the incorporation in a coupled manner of radiation models into the VSL code, and the initial development of appropriate precursor models are presented.

24th Current Trends in Computational Chemistry

DTIC Science & Technology

2017-05-17

Standard Form 298 (Rev 8/98) Prescribed by ANSI Std. Z39.18 Final Report W911NF-16-1-0470 69708-CH-CF.1 601-979-3723 a. REPORT 14. ABSTRACT 16...5d. PROJECT NUMBER 5e. TASK NUMBER 5f. WORK UNIT NUMBER 5c. PROGRAM ELEMENT NUMBER 5b. GRANT NUMBER 5a. CONTRACT NUMBER Form Approved OMB NO...number. PLEASE DO NOT RETURN YOUR FORM TO THE ABOVE ADDRESS. Jackson State University 1400 John R. Lynch Street Jackson, MS 39217 -0002 Agency Code

A Computational Chemistry Database for Semiconductor Processing

NASA Technical Reports Server (NTRS)

Jaffe, R.; Meyyappan, M.; Arnold, J. O. (Technical Monitor)

1998-01-01

The concept of 'virtual reactor' or 'virtual prototyping' has received much attention recently in the semiconductor industry. Commercial codes to simulate thermal CVD and plasma processes have become available to aid in equipment and process design efforts, The virtual prototyping effort would go nowhere if codes do not come with a reliable database of chemical and physical properties of gases involved in semiconductor processing. Commercial code vendors have no capabilities to generate such a database, rather leave the task to the user of finding whatever is needed. While individual investigations of interesting chemical systems continue at Universities, there has not been any large scale effort to create a database. In this presentation, we outline our efforts in this area. Our effort focuses on the following five areas: 1. Thermal CVD reaction mechanism and rate constants. 2. Thermochemical properties. 3. Transport properties.4. Electron-molecule collision cross sections. and 5. Gas-surface interactions.

Avogadro: an advanced semantic chemical editor, visualization, and analysis platform

PubMed Central

2012-01-01

Background The Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible, high quality rendering, and a powerful plugin architecture. Typical uses include building molecular structures, formatting input files, and analyzing output of a wide variety of computational chemistry packages. By using the CML file format as its native document type, Avogadro seeks to enhance the semantic accessibility of chemical data types. Results The work presented here details the Avogadro library, which is a framework providing a code library and application programming interface (API) with three-dimensional visualization capabilities; and has direct applications to research and education in the fields of chemistry, physics, materials science, and biology. The Avogadro application provides a rich graphical interface using dynamically loaded plugins through the library itself. The application and library can each be extended by implementing a plugin module in C++ or Python to explore different visualization techniques, build/manipulate molecular structures, and interact with other programs. We describe some example extensions, one which uses a genetic algorithm to find stable crystal structures, and one which interfaces with the PackMol program to create packed, solvated structures for molecular dynamics simulations. The 1.0 release series of Avogadro is the main focus of the results discussed here. Conclusions Avogadro offers a semantic chemical builder and platform for visualization and analysis. For users, it offers an easy-to-use builder, integrated support for downloading from common databases such as PubChem and the Protein Data Bank, extracting chemical data from a wide variety of formats, including computational chemistry output, and native, semantic support for the CML file format. For developers, it can be easily extended via a powerful plugin mechanism to support new features in organic chemistry, inorganic complexes, drug design, materials, biomolecules, and simulations. Avogadro is freely available under an open-source license from http://avogadro.openmolecules.net. PMID:22889332

Avogadro: an advanced semantic chemical editor, visualization, and analysis platform.

PubMed

Hanwell, Marcus D; Curtis, Donald E; Lonie, David C; Vandermeersch, Tim; Zurek, Eva; Hutchison, Geoffrey R

2012-08-13

The Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible, high quality rendering, and a powerful plugin architecture. Typical uses include building molecular structures, formatting input files, and analyzing output of a wide variety of computational chemistry packages. By using the CML file format as its native document type, Avogadro seeks to enhance the semantic accessibility of chemical data types. The work presented here details the Avogadro library, which is a framework providing a code library and application programming interface (API) with three-dimensional visualization capabilities; and has direct applications to research and education in the fields of chemistry, physics, materials science, and biology. The Avogadro application provides a rich graphical interface using dynamically loaded plugins through the library itself. The application and library can each be extended by implementing a plugin module in C++ or Python to explore different visualization techniques, build/manipulate molecular structures, and interact with other programs. We describe some example extensions, one which uses a genetic algorithm to find stable crystal structures, and one which interfaces with the PackMol program to create packed, solvated structures for molecular dynamics simulations. The 1.0 release series of Avogadro is the main focus of the results discussed here. Avogadro offers a semantic chemical builder and platform for visualization and analysis. For users, it offers an easy-to-use builder, integrated support for downloading from common databases such as PubChem and the Protein Data Bank, extracting chemical data from a wide variety of formats, including computational chemistry output, and native, semantic support for the CML file format. For developers, it can be easily extended via a powerful plugin mechanism to support new features in organic chemistry, inorganic complexes, drug design, materials, biomolecules, and simulations. Avogadro is freely available under an open-source license from http://avogadro.openmolecules.net.

Algebraic Turbulence-Chemistry Interaction Model

NASA Technical Reports Server (NTRS)

Norris, Andrew T.

2012-01-01

The results of a series of Perfectly Stirred Reactor (PSR) and Partially Stirred Reactor (PaSR) simulations are compared to each other over a wide range of operating conditions. It is found that the PaSR results can be simulated by a PSR solution with just an adjusted chemical reaction rate. A simple expression has been developed that gives the required change in reaction rate for a PSR solution to simulate the PaSR results. This expression is the basis of a simple turbulence-chemistry interaction model. The interaction model that has been developed is intended for use with simple one-step global reaction mechanisms and for steady-state flow simulations. Due to the simplicity of the model there is very little additional computational cost in adding it to existing CFD codes.

Assessment of Reduced-Kinetics Mechanisms for Combustion of Jet Fuel in CFD Applications

NASA Technical Reports Server (NTRS)

Ajmani, Kumud; Kundu, Krihna P.; Yungster, Shaye J.

2014-01-01

A computational effort was undertaken to analyze the details of fluid flow in Lean-Direct Injection (LDI) combustors for next-generation LDI design. The National Combustor Code (NCC) was used to perform reacting flow computations on single-element LDI injector configurations. The feasibility of using a reduced chemical-kinetics approach, which optimizes the reaction rates and species to model the emissions characteristics typical of lean-burning gas-turbine combustors, was assessed. The assessments were performed with Reynolds- Averaged Navier-Stokes (RANS) and Time-Filtered Navier Stokes (TFNS) time-integration, with a Lagrangian spray model with the NCC code. The NCC predictions for EINOx and combustor exit temperature were compared with experimental data for two different single-element LDI injector configurations, with 60deg and 45deg axially swept swirler vanes. The effects of turbulence-chemistry interaction on the predicted flow in a typical LDI combustor were studied with detailed comparisons of NCC TFNS with experimental data.

Air Quality Modeling and Forecasting over the United States Using WRF-Chem

NASA Astrophysics Data System (ADS)

Boxe, C.; Hafsa, U.; Blue, S.; Emmanuel, S.; Griffith, E.; Moore, J.; Tam, J.; Khan, I.; Cai, Z.; Bocolod, B.; Zhao, J.; Ahsan, S.; Gurung, D.; Tang, N.; Bartholomew, J.; Rafi, R.; Caltenco, K.; Rivas, M.; Ditta, H.; Alawlaqi, H.; Rowley, N.; Khatim, F.; Ketema, N.; Strothers, J.; Diallo, I.; Owens, C.; Radosavljevic, J.; Austin, S. A.; Johnson, L. P.; Zavala-Gutierrez, R.; Breary, N.; Saint-Hilaire, D.; Skeete, D.; Stock, J.; Salako, O.

2016-12-01

WRF-Chem is the Weather Research and Forecasting (WRF) model coupled with Chemistry. The model simulates the emission, transport, mixing, and chemical transformation of trace gases and aerosols simultaneously with the meteorology. The model is used for investigation of regional-scale air quality, field program analysis, and cloud-scale interactions between clouds and chemistry. The development of WRF-Chem is a collaborative effort among the community led by NOAA/ESRL scientists. The Official WRF-Chem web page is located at the NOAA web site. Our model development is closely linked with both NOAA/ESRL and DOE/PNNL efforts. Description of PNNL WRF-Chem model development is located at the PNNL web site as well as the PNNL Aerosol Modeling Testbed. High school and undergraduate students, representative of academic institutions throughout USA's Tri-State Area (New York, New Jersey, Connecticut), set up WRF-Chem on CUNY CSI's High Performance Computing Center. Students learned the back-end coding that governs WRF-Chems structure and the front-end coding that displays visually specified weather simulations and forecasts. Students also investigated the impact, to select baseline simulations/forecasts, due to the reaction, NO2 + OH + M → HOONO + M (k = 9.2 × 10-12 cm3 molecule-1 s-1, Mollner et al. 2010). The reaction of OH and NO2 to form gaseous nitric acid (HONO2) is among the most influential and in atmospheric chemistry. Till a few years prior, its rate coefficient remained poorly determined under tropospheric conditions because of difficulties in making laboratory measurements at 760 torr. These activities fosters student coding competencies and deep insights into weather forecast and air quality.

Sudoku Puzzles for First-Year Organic Chemistry Students

ERIC Educational Resources Information Center

Perez, Alice L.; Lamoureux, G.

2007-01-01

Sudoku puzzle was designed to teach about amino acids and functional groups to the students of undergraduate organic chemistry students. The puzzles focus on helping the student learn the name, 3-letter code and 1-letter code of common amino acids and functional groups.

Computational study of 3-D hot-spot initiation in shocked insensitive high-explosive

NASA Astrophysics Data System (ADS)

Najjar, F. M.; Howard, W. M.; Fried, L. E.; Manaa, M. R.; Nichols, A., III; Levesque, G.

2012-03-01

High-explosive (HE) material consists of large-sized grains with micron-sized embedded impurities and pores. Under various mechanical/thermal insults, these pores collapse generating hightemperature regions leading to ignition. A hydrodynamic study has been performed to investigate the mechanisms of pore collapse and hot spot initiation in TATB crystals, employing a multiphysics code, ALE3D, coupled to the chemistry module, Cheetah. This computational study includes reactive dynamics. Two-dimensional high-resolution large-scale meso-scale simulations have been performed. The parameter space is systematically studied by considering various shock strengths, pore diameters and multiple pore configurations. Preliminary 3-D simulations are undertaken to quantify the 3-D dynamics.

Extension of a Kinetic Approach to Chemical Reactions to Electronic Energy Levels and Reactions Involving Charged Species with Application to DSMC Simulations

NASA Technical Reports Server (NTRS)

Liechty, Derek S.

2014-01-01

The ability to compute rarefied, ionized hypersonic flows is becoming more important as missions such as Earth reentry, landing high mass payloads on Mars, and the exploration of the outer planets and their satellites are being considered. Recently introduced molecular-level chemistry models that predict equilibrium and nonequilibrium reaction rates using only kinetic theory and fundamental molecular properties are extended in the current work to include electronic energy level transitions and reactions involving charged particles. These extensions are shown to agree favorably with reported transition and reaction rates from the literature for near-equilibrium conditions. Also, the extensions are applied to the second flight of the Project FIRE flight experiment at 1634 seconds with a Knudsen number of 0.001 at an altitude of 76.4 km. In order to accomplish this, NASA's direct simulation Monte Carlo code DAC was rewritten to include the ability to simulate charge-neutral ionized flows, take advantage of the recently introduced chemistry model, and to include the extensions presented in this work. The 1634 second data point was chosen for comparisons to be made in order to include a CFD solution. The Knudsen number at this point in time is such that the DSMC simulations are still tractable and the CFD computations are at the edge of what is considered valid because, although near-transitional, the flow is still considered to be continuum. It is shown that the inclusion of electronic energy levels in the DSMC simulation is necessary for flows of this nature and is required for comparison to the CFD solution. The flow field solutions are also post-processed by the nonequilibrium radiation code HARA to compute the radiative portion.

Axisymmetric Plume Simulations with NASA's DSMC Analysis Code

NASA Technical Reports Server (NTRS)

Stewart, B. D.; Lumpkin, F. E., III

2012-01-01

A comparison of axisymmetric Direct Simulation Monte Carlo (DSMC) Analysis Code (DAC) results to analytic and Computational Fluid Dynamics (CFD) solutions in the near continuum regime and to 3D DAC solutions in the rarefied regime for expansion plumes into a vacuum is performed to investigate the validity of the newest DAC axisymmetric implementation. This new implementation, based on the standard DSMC axisymmetric approach where the representative molecules are allowed to move in all three dimensions but are rotated back to the plane of symmetry by the end of the move step, has been fully integrated into the 3D-based DAC code and therefore retains all of DAC s features, such as being able to compute flow over complex geometries and to model chemistry. Axisymmetric DAC results for a spherically symmetric isentropic expansion are in very good agreement with a source flow analytic solution in the continuum regime and show departure from equilibrium downstream of the estimated breakdown location. Axisymmetric density contours also compare favorably against CFD results for the R1E thruster while temperature contours depart from equilibrium very rapidly away from the estimated breakdown surface. Finally, axisymmetric and 3D DAC results are in very good agreement over the entire plume region and, as expected, this new axisymmetric implementation shows a significant reduction in computer resources required to achieve accurate simulations for this problem over the 3D simulations.

FY06 L2C2 HE program report Zaug et al.

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

Zaug, J M; Crowhurst, J C; Howard, W M

2008-08-01

The purpose of this project is to advance the improvement of LLNL thermochemical computational models that form the underlying basis or input for laboratory hydrodynamic simulations. Our general work approach utilizes, by design, tight experimental-theoretical research interactions that allow us to not empirically, but rather more scientifically improve LLNL computational results. The ultimate goal here is to confidently predict through computer models, the performance and safety parameters of currently maintained, modified, and newly designed stockpile systems. To attain our goal we make relevant experimental measurements on candidate detonation products constrained under static high-pressure and temperature conditions. The reduced information frommore » these measurements is then used to construct analytical forms that describe the potential surface (repulsive energy as a function of interatomic separation distance) of single and mixed fluid or detonation product species. These potential surface shapes are also constructed using input from well-trusted shock wave physics and assorted thermodynamic data available in the open literature. Our potential surfaces permit one to determine the equations of state (P,V,T), the equilibrium chemistry, phase, and chemical interactions of detonation products under a very wide range of extreme pressure temperature conditions. Using our foundation of experimentally refined potential surfaces we are in a position to calculate, with confidence, the energetic output and chemical speciation occurring from a specific combustion and/or detonation reaction. The thermochemical model we developed and use for calculating the equilibrium chemistry, kinetics, and energy from ultrafast processes is named 'Cheetah'. Computational results from our Cheetah code are coupled to laboratory ALE3D hydrodynamic simulation codes where the complete response behavior of an existing or proposed system is ultimately predicted. The Cheetah thermochemical code is also used by well over 500 U.S. government DoD and DOE community users who calculate the chemical properties of detonated high explosives, propellants, and pyrotechnics. To satisfy the growing needs of LLNL and the general user community we continue to improve the robustness of our Cheetah code. The P-T range of current speed of sound experiments will soon be extended by a factor of four and our recently developed technological advancements permit us to, for the first time, study any chemical specie or fluid mixture. New experiments will focus on determining the miscibility or coexistence curves of detonation product mixtures. Our newly constructed ultrafast laser diagnostics will permit us to determine what chemical species exist under conditions approaching Chapman-Jouguet (CJ) detonation states. Furthermore we will measure the time evolution of candidate species and use our chemical kinetics data to develop new and validate existing rate laws employed in future versions of our Cheetah thermochemical code.« less

The Application of SERS (Surface Enhanced Raman Scattering) to Study Surface Oxidation Reactions of Phosphonates.

DTIC Science & Technology

1988-02-15

Center Attn: Dr. Ron Atkins Code 50C Chemistry Division Crane, Indiana 47522-5050 China Lake, California 93555 Scientific Advisor INaval Civil...Superintendent Marine Sciences Division Chemistry Division, Code 6100 San Diego, California 91232 Naval Research Laboratory Washington, D.C. 20375-5000 ,! .1

On the Green's function of the partially diffusion-controlled reversible ABCD reaction for radiation chemistry codes

NASA Astrophysics Data System (ADS)

Plante, Ianik; Devroye, Luc

2015-09-01

Several computer codes simulating chemical reactions in particles systems are based on the Green's functions of the diffusion equation (GFDE). Indeed, many types of chemical systems have been simulated using the exact GFDE, which has also become the gold standard for validating other theoretical models. In this work, a simulation algorithm is presented to sample the interparticle distance for partially diffusion-controlled reversible ABCD reaction. This algorithm is considered exact for 2-particles systems, is faster than conventional look-up tables and uses only a few kilobytes of memory. The simulation results obtained with this method are compared with those obtained with the independent reaction times (IRT) method. This work is part of our effort in developing models to understand the role of chemical reactions in the radiation effects on cells and tissues and may eventually be included in event-based models of space radiation risks. However, as many reactions are of this type in biological systems, this algorithm might play a pivotal role in future simulation programs not only in radiation chemistry, but also in the simulation of biochemical networks in time and space as well.

Modeling of very low frequency (VLF) radio wave signal profile due to solar flares using the GEANT4 Monte Carlo simulation coupled with ionospheric chemistry

NASA Astrophysics Data System (ADS)

Palit, S.; Basak, T.; Mondal, S. K.; Pal, S.; Chakrabarti, S. K.

2013-09-01

X-ray photons emitted during solar flares cause ionization in the lower ionosphere (~60 to 100 km) in excess of what is expected to occur due to a quiet sun. Very low frequency (VLF) radio wave signals reflected from the D-region of the ionosphere are affected by this excess ionization. In this paper, we reproduce the deviation in VLF signal strength during solar flares by numerical modeling. We use GEANT4 Monte Carlo simulation code to compute the rate of ionization due to a M-class flare and a X-class flare. The output of the simulation is then used in a simplified ionospheric chemistry model to calculate the time variation of electron density at different altitudes in the D-region of the ionosphere. The resulting electron density variation profile is then self-consistently used in the LWPC code to obtain the time variation of the change in VLF signal. We did the modeling of the VLF signal along the NWC (Australia) to IERC/ICSP (India) propagation path and compared the results with observations. The agreement is found to be very satisfactory.

An Approximate Axisymmetric Viscous Shock Layer Aeroheating Method for Three-Dimensional Bodies

NASA Technical Reports Server (NTRS)

Brykina, Irina G.; Scott, Carl D.

1998-01-01

A technique is implemented for computing hypersonic aeroheating, shear stress, and other flow properties on the windward side of a three-dimensional (3D) blunt body. The technique uses a 2D/axisymmetric flow solver modified by scale factors for a, corresponding equivalent axisymmetric body. Examples are given in which a 2D solver is used to calculate the flow at selected meridional planes on elliptic paraboloids in reentry flight. The report describes the equations and the codes used to convert the body surface parameters into input used to scale the 2D viscous shock layer equations in the axisymmetric viscous shock layer code. Very good agreement is obtained with solutions to finite rate chemistry 3D thin viscous shock layer equations for a finite rate catalytic body.

Propel: A Discontinuous-Galerkin Finite Element Code for Solving the Reacting Navier-Stokes Equations

NASA Astrophysics Data System (ADS)

Johnson, Ryan; Kercher, Andrew; Schwer, Douglas; Corrigan, Andrew; Kailasanath, Kazhikathra

2017-11-01

This presentation focuses on the development of a Discontinuous Galerkin (DG) method for application to chemically reacting flows. The in-house code, called Propel, was developed by the Laboratory of Computational Physics and Fluid Dynamics at the Naval Research Laboratory. It was designed specifically for developing advanced multi-dimensional algorithms to run efficiently on new and innovative architectures such as GPUs. For these results, Propel solves for convection and diffusion simultaneously with detailed transport and thermodynamics. Chemistry is currently solved in a time-split approach using Strang-splitting with finite element DG time integration of chemical source terms. Results presented here show canonical unsteady reacting flow cases, such as co-flow and splitter plate, and we report performance for higher order DG on CPU and GPUs.

Integrating Computational Chemistry into a Course in Classical Thermodynamics

ERIC Educational Resources Information Center

Martini, Sheridan R.; Hartzell, Cynthia J.

2015-01-01

Computational chemistry is commonly addressed in the quantum mechanics course of undergraduate physical chemistry curricula. Since quantum mechanics traditionally follows the thermodynamics course, there is a lack of curricula relating computational chemistry to thermodynamics. A method integrating molecular modeling software into a semester long…

Influence of Natural Convection and Thermal Radiation Multi-Component Transport in MOCVD Reactors

NASA Technical Reports Server (NTRS)

Lowry, S.; Krishnan, A.; Clark, I.

1999-01-01

The influence of Grashof and Reynolds number in Metal Organic Chemical Vapor (MOCVD) reactors is being investigated under a combined empirical/numerical study. As part of that research, the deposition of Indium Phosphide in an MOCVD reactor is modeled using the computational code CFD-ACE. The model includes the effects of convection, conduction, and radiation as well as multi-component diffusion and multi-step surface/gas phase chemistry. The results of the prediction are compared with experimental data for a commercial reactor and analyzed with respect to the model accuracy.

Gordon Research Conference on Computational Chemistry Held in Plymouth, New Hampshire on 4-8 July 1988

DTIC Science & Technology

1988-07-01

NUMBER(S) S. MONITORING ORGANIZATION REPORT NUMBER(S) _ R.TR- 90 - 0 4 70 6a. NAME OF PERFORMING ORGANIZATION 6b. OFFICE SYMBOL 7a. NAME OF MONITORING...University of Rhode Island Building 410 Kingston, RI 18195 Boiling AFB, DC 20332-6448 . Sa. NAME OF FUNDING / SPONSORING Sb. OFFICE SYMBOL 9, PROCUREMENT...AS RPT. 3 OTIC USERS UNCLASSIFIED 22a- NAME OF RESPONSIBLE INDIVIDUAL 22b. TELEPHONE (Include Area Code) 22c OFFICE SYMBOL Dr Anthony J. Matuszko (202

Measurement of Atmospheric Pressure Air Plasma via Pulsed Electron Beam and Sustaining Electric Field

DTIC Science & Technology

2007-08-29

cell plasma code ( MAGIC ) and an air-chemistry code are used to quantify beam propagation through an electron-beam transmission window into air and the...to generate and maintain plasma in air on the timescale of 1 ms. 15. SUBJECT TERMS Air Chemistry, Air Plasma, MAGIC Modeling, Plasma, Power, Test-Cell...Microwave diagnostics quantify electron number density and optical diagnostics quantify ozone production. A particle in cell plasma code ( MAGIC ) and an

Outlook Bright for Computers in Chemistry.

ERIC Educational Resources Information Center

Baum, Rudy M.

1981-01-01

Discusses the recent decision to close down the National Resource for Computation in Chemistry (NRCC), implications of that decision, and various alternatives in the field of computational chemistry. (CS)

Ethics in Science: The Unique Consequences of Chemistry.

PubMed

Kovac, Jeffrey

2015-01-01

This article discusses the ethical issues unique to the science and practice of chemistry. These issues arise from chemistry's position in the middle between the theoretical and the practical, a science concerned with molecules that are of the right size to directly affect human life. Many of the issues are raised by the central activity of chemistry--synthesis. Chemists make thousands of new substances each year. Many are beneficial, but others are threats. Since the development of the chemical industry in the nineteenth century, chemistry has contributed to the deterioration of the environment but has also helped to reduce pollution. Finally, we discuss the role of codes of ethics and whether the current codes of conduct for chemists are adequate for the challenges of today's world.

Open chemistry: RESTful web APIs, JSON, NWChem and the modern web application.

PubMed

Hanwell, Marcus D; de Jong, Wibe A; Harris, Christopher J

2017-10-30

An end-to-end platform for chemical science research has been developed that integrates data from computational and experimental approaches through a modern web-based interface. The platform offers an interactive visualization and analytics environment that functions well on mobile, laptop and desktop devices. It offers pragmatic solutions to ensure that large and complex data sets are more accessible. Existing desktop applications/frameworks were extended to integrate with high-performance computing resources, and offer command-line tools to automate interaction-connecting distributed teams to this software platform on their own terms. The platform was developed openly, and all source code hosted on the GitHub platform with automated deployment possible using Ansible coupled with standard Ubuntu-based machine images deployed to cloud machines. The platform is designed to enable teams to reap the benefits of the connected web-going beyond what conventional search and analytics platforms offer in this area. It also has the goal of offering federated instances, that can be customized to the sites/research performed. Data gets stored using JSON, extending upon previous approaches using XML, building structures that support computational chemistry calculations. These structures were developed to make it easy to process data across different languages, and send data to a JavaScript-based web client.

Open chemistry: RESTful web APIs, JSON, NWChem and the modern web application

DOE PAGES

Hanwell, Marcus D.; de Jong, Wibe A.; Harris, Christopher J.

2017-10-30

An end-to-end platform for chemical science research has been developed that integrates data from computational and experimental approaches through a modern web-based interface. The platform offers an interactive visualization and analytics environment that functions well on mobile, laptop and desktop devices. It offers pragmatic solutions to ensure that large and complex data sets are more accessible. Existing desktop applications/frameworks were extended to integrate with high-performance computing resources, and offer command-line tools to automate interaction - connecting distributed teams to this software platform on their own terms. The platform was developed openly, and all source code hosted on the GitHub platformmore » with automated deployment possible using Ansible coupled with standard Ubuntu-based machine images deployed to cloud machines. The platform is designed to enable teams to reap the benefits of the connected web - going beyond what conventional search and analytics platforms offer in this area. It also has the goal of offering federated instances, that can be customized to the sites/research performed. Data gets stored using JSON, extending upon previous approaches using XML, building structures that support computational chemistry calculations. These structures were developed to make it easy to process data across different languages, and send data to a JavaScript-based web client.« less

Open chemistry: RESTful web APIs, JSON, NWChem and the modern web application

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

Hanwell, Marcus D.; de Jong, Wibe A.; Harris, Christopher J.

An end-to-end platform for chemical science research has been developed that integrates data from computational and experimental approaches through a modern web-based interface. The platform offers an interactive visualization and analytics environment that functions well on mobile, laptop and desktop devices. It offers pragmatic solutions to ensure that large and complex data sets are more accessible. Existing desktop applications/frameworks were extended to integrate with high-performance computing resources, and offer command-line tools to automate interaction - connecting distributed teams to this software platform on their own terms. The platform was developed openly, and all source code hosted on the GitHub platformmore » with automated deployment possible using Ansible coupled with standard Ubuntu-based machine images deployed to cloud machines. The platform is designed to enable teams to reap the benefits of the connected web - going beyond what conventional search and analytics platforms offer in this area. It also has the goal of offering federated instances, that can be customized to the sites/research performed. Data gets stored using JSON, extending upon previous approaches using XML, building structures that support computational chemistry calculations. These structures were developed to make it easy to process data across different languages, and send data to a JavaScript-based web client.« less

Development of a model and computer code to describe solar grade silicon production processes. [phase changes in chemical reactors

NASA Technical Reports Server (NTRS)

Gould, R. K.

1978-01-01

Mechanisms for the SiCl4/Na and SiF4/Na reaction systems were examined. Reaction schemes which include 25 elementary reactions were formulated for each system and run to test the sensitivity of the computed concentration and temperature profiles to the values given estimated rate coefficients. It was found that, for SiCl4/Na, the rate of production of free Si is largely mixing-limited for reasonable rate coefficient estimates. For the SiF4/Na system the results indicate that the endothermicities of many of the reactions involved in producing Si from SiF4/Na cause this system to be chemistry-limited rather than mixing-limited.

Disciplines, models, and computers: the path to computational quantum chemistry.

PubMed

Lenhard, Johannes

2014-12-01

Many disciplines and scientific fields have undergone a computational turn in the past several decades. This paper analyzes this sort of turn by investigating the case of computational quantum chemistry. The main claim is that the transformation from quantum to computational quantum chemistry involved changes in three dimensions. First, on the side of instrumentation, small computers and a networked infrastructure took over the lead from centralized mainframe architecture. Second, a new conception of computational modeling became feasible and assumed a crucial role. And third, the field of computa- tional quantum chemistry became organized in a market-like fashion and this market is much bigger than the number of quantum theory experts. These claims will be substantiated by an investigation of the so-called density functional theory (DFT), the arguably pivotal theory in the turn to computational quantum chemistry around 1990.

A generalized chemistry version of SPARK

NASA Technical Reports Server (NTRS)

Carpenter, Mark H.

1988-01-01

An extension of the reacting H2-air computer code SPARK is presented, which enables the code to be used on any reacting flow problem. Routines are developed calculating in a general fashion, the reaction rates, and chemical Jacobians of any reacting system. In addition, an equilibrium routine is added so that the code will have frozen, finite rate, and equilibrium capabilities. The reaction rate for the species is determined from the law of mass action using Arrhenius expressions for the rate constants. The Jacobian routines are determined by numerically or analytically differentiating the law of mass action for each species. The equilibrium routine is based on a Gibbs free energy minimization routine. The routines are written in FORTRAN 77, with special consideration given to vectorization. Run times for the generalized routines are generally 20 percent slower than reaction specific routines. The numerical efficiency of the generalized analytical Jacobian, however, is nearly 300 percent better than the reaction specific numerical Jacobian used in SPARK.

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

The NATA code; theory and analysis. Volume 2: User's manual

NASA Technical Reports Server (NTRS)

Bade, W. L.; Yos, J. M.

1975-01-01

The NATA code is a computer program for calculating quasi-one-dimensional gas flow in axisymmetric nozzles and rectangular channels, primarily to describe conditions in electric archeated wind tunnels. The program provides solutions based on frozen chemistry, chemical equilibrium, and nonequilibrium flow with finite reaction rates. The shear and heat flux on the nozzle wall are calculated and boundary layer displacement effects on the inviscid flow are taken into account. The program contains compiled-in thermochemical, chemical kinetic and transport cross section data for high-temperature air, CO2-N2-Ar mixtures, helium, and argon. It calculates stagnation conditions on axisymmetric or two-dimensional models and conditions on the flat surface of a blunt wedge. Included in the report are: definitions of the inputs and outputs; precoded data on gas models, reactions, thermodynamic and transport properties of species, and nozzle geometries; explanations of diagnostic outputs and code abort conditions; test problems; and a user's manual for an auxiliary program (NOZFIT) used to set up analytical curvefits to nozzle profiles.

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

Stagnation-point heat-transfer rate predictions at aeroassist flight conditions

NASA Technical Reports Server (NTRS)

Gupta, Roop N.; Jones, Jim J.; Rochelle, William C.

1992-01-01

The results are presented for the stagnation-point heat-transfer rates used in the design process of the Aeroassist Flight Experiment (AFE) vehicle over its entire aeropass trajectory. The prediction methods used in this investigation demonstrate the application of computational fluid dynamics (CFD) techniques to a wide range of flight conditions and their usefulness in a design process. The heating rates were computed by a viscous-shock-layer (VSL) code at the lower altitudes and by a Navier-Stokes (N-S) code for the higher altitude cases. For both methods, finite-rate chemically reacting gas was considered, and a temperature-dependent wall-catalysis model was used. The wall temperature for each case was assumed to be radiative equilibrium temperature, based on total heating. The radiative heating was estimated by using a correlation equation. Wall slip was included in the N-S calculation method, and this method implicitly accounts for shock slip. The N-S/VSL combination of projection methods was established by comparison with the published benchmark flow-field code LAURA results at lower altitudes, and the direct simulation Monte Carlo results at higher altitude cases. To obtain the design heating rate over the entire forward face of the vehicle, a boundary-layer method (BLIMP code) that employs reacting chemistry and surface catalysis was used. The ratio of the VSL or N-S method prediction to that obtained from the boundary-layer method code at the stagnation point is used to define an adjustment factor, which accounts for the errors involved in using the boundary-layer method.

A Hartree-Fock Application Using UPC++ and the New DArray Library

DOE PAGES

Ozog, David; Kamil, Amir; Zheng, Yili; ...

2016-07-21

The Hartree-Fock (HF) method is the fundamental first step for incorporating quantum mechanics into many-electron simulations of atoms and molecules, and it is an important component of computational chemistry toolkits like NWChem. The GTFock code is an HF implementation that, while it does not have all the features in NWChem, represents crucial algorithmic advances that reduce communication and improve load balance by doing an up-front static partitioning of tasks, followed by work stealing whenever necessary. To enable innovations in algorithms and exploit next generation exascale systems, it is crucial to support quantum chemistry codes using expressive and convenient programming modelsmore » and runtime systems that are also efficient and scalable. Here, this paper presents an HF implementation similar to GTFock using UPC++, a partitioned global address space model that includes flexible communication, asynchronous remote computation, and a powerful multidimensional array library. UPC++ offers runtime features that are useful for HF such as active messages, a rich calculus for array operations, hardware-supported fetch-and-add, and functions for ensuring asynchronous runtime progress. We present a new distributed array abstraction, DArray, that is convenient for the kinds of random-access array updates and linear algebra operations on block-distributed arrays with irregular data ownership. Finally, we analyze the performance of atomic fetch-and-add operations (relevant for load balancing) and runtime attentiveness, then compare various techniques and optimizations for each. Our optimized implementation of HF using UPC++ and the DArrays library shows up to 20% improvement over GTFock with Global Arrays at scales up to 24,000 cores.« less

A Hartree-Fock Application Using UPC++ and the New DArray Library

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

Ozog, David; Kamil, Amir; Zheng, Yili

The Hartree-Fock (HF) method is the fundamental first step for incorporating quantum mechanics into many-electron simulations of atoms and molecules, and it is an important component of computational chemistry toolkits like NWChem. The GTFock code is an HF implementation that, while it does not have all the features in NWChem, represents crucial algorithmic advances that reduce communication and improve load balance by doing an up-front static partitioning of tasks, followed by work stealing whenever necessary. To enable innovations in algorithms and exploit next generation exascale systems, it is crucial to support quantum chemistry codes using expressive and convenient programming modelsmore » and runtime systems that are also efficient and scalable. Here, this paper presents an HF implementation similar to GTFock using UPC++, a partitioned global address space model that includes flexible communication, asynchronous remote computation, and a powerful multidimensional array library. UPC++ offers runtime features that are useful for HF such as active messages, a rich calculus for array operations, hardware-supported fetch-and-add, and functions for ensuring asynchronous runtime progress. We present a new distributed array abstraction, DArray, that is convenient for the kinds of random-access array updates and linear algebra operations on block-distributed arrays with irregular data ownership. Finally, we analyze the performance of atomic fetch-and-add operations (relevant for load balancing) and runtime attentiveness, then compare various techniques and optimizations for each. Our optimized implementation of HF using UPC++ and the DArrays library shows up to 20% improvement over GTFock with Global Arrays at scales up to 24,000 cores.« less

The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching.

PubMed

Willighagen, Egon L; Mayfield, John W; Alvarsson, Jonathan; Berg, Arvid; Carlsson, Lars; Jeliazkova, Nina; Kuhn, Stefan; Pluskal, Tomáš; Rojas-Chertó, Miquel; Spjuth, Ola; Torrance, Gilleain; Evelo, Chris T; Guha, Rajarshi; Steinbeck, Christoph

2017-06-06

The Chemistry Development Kit (CDK) is a widely used open source cheminformatics toolkit, providing data structures to represent chemical concepts along with methods to manipulate such structures and perform computations on them. The library implements a wide variety of cheminformatics algorithms ranging from chemical structure canonicalization to molecular descriptor calculations and pharmacophore perception. It is used in drug discovery, metabolomics, and toxicology. Over the last 10 years, the code base has grown significantly, however, resulting in many complex interdependencies among components and poor performance of many algorithms. We report improvements to the CDK v2.0 since the v1.2 release series, specifically addressing the increased functional complexity and poor performance. We first summarize the addition of new functionality, such atom typing and molecular formula handling, and improvement to existing functionality that has led to significantly better performance for substructure searching, molecular fingerprints, and rendering of molecules. Second, we outline how the CDK has evolved with respect to quality control and the approaches we have adopted to ensure stability, including a code review mechanism. This paper highlights our continued efforts to provide a community driven, open source cheminformatics library, and shows that such collaborative projects can thrive over extended periods of time, resulting in a high-quality and performant library. By taking advantage of community support and contributions, we show that an open source cheminformatics project can act as a peer reviewed publishing platform for scientific computing software. Graphical abstract CDK 2.0 provides new features and improved performance.

HELIOS: A new open-source radiative transfer code

NASA Astrophysics Data System (ADS)

Malik, Matej; Grosheintz, Luc; Lukas Grimm, Simon; Mendonça, João; Kitzmann, Daniel; Heng, Kevin

2015-12-01

I present the new open-source code HELIOS, developed to accurately describe radiative transfer in a wide variety of irradiated atmospheres. We employ a one-dimensional multi-wavelength two-stream approach with scattering. Written in Cuda C++, HELIOS uses the GPU’s potential of massive parallelization and is able to compute the TP-profile of an atmosphere in radiative equilibrium and the subsequent emission spectrum in a few minutes on a single computer (for 60 layers and 1000 wavelength bins).The required molecular opacities are obtained with the recently published code HELIOS-K [1], which calculates the line shapes from an input line list and resamples the numerous line-by-line data into a manageable k-distribution format. Based on simple equilibrium chemistry theory [2] we combine the k-distribution functions of the molecules H2O, CO2, CO & CH4 to generate a k-table, which we then employ in HELIOS.I present our results of the following: (i) Various numerical tests, e.g. isothermal vs. non-isothermal treatment of layers. (ii) Comparison of iteratively determined TP-profiles with their analytical parametric prescriptions [3] and of the corresponding spectra. (iii) Benchmarks of TP-profiles & spectra for various elemental abundances. (iv) Benchmarks of averaged TP-profiles & spectra for the exoplanets GJ1214b, HD189733b & HD209458b. (v) Comparison with secondary eclipse data for HD189733b, XO-1b & Corot-2b.HELIOS is being developed, together with the dynamical core THOR and the chemistry solver VULCAN, in the group of Kevin Heng at the University of Bern as part of the Exoclimes Simulation Platform (ESP) [4], which is an open-source project aimed to provide community tools to model exoplanetary atmospheres.-----------------------------[1] Grimm & Heng 2015, ArXiv, 1503.03806[2] Heng, Lyons & Tsai, Arxiv, 1506.05501Heng & Lyons, ArXiv, 1507.01944[3] e.g. Heng, Mendonca & Lee, 2014, ApJS, 215, 4H[4] exoclime.net

Automatic computer procedure for generating exact and analytical kinetic energy operators based on the polyspherical approach: General formulation and removal of singularities

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

Ndong, Mamadou; Lauvergnat, David; Nauts, André

2013-11-28

We present new techniques for an automatic computation of the kinetic energy operator in analytical form. These techniques are based on the use of the polyspherical approach and are extended to take into account Cartesian coordinates as well. An automatic procedure is developed where analytical expressions are obtained by symbolic calculations. This procedure is a full generalization of the one presented in Ndong et al., [J. Chem. Phys. 136, 034107 (2012)]. The correctness of the new implementation is analyzed by comparison with results obtained from the TNUM program. We give several illustrations that could be useful for users of themore » code. In particular, we discuss some cyclic compounds which are important in photochemistry. Among others, we show that choosing a well-adapted parameterization and decomposition into subsystems can allow one to avoid singularities in the kinetic energy operator. We also discuss a relation between polyspherical and Z-matrix coordinates: this comparison could be helpful for building an interface between the new code and a quantum chemistry package.« less

Towards a generalized computational fluid dynamics technique for all Mach numbers

NASA Technical Reports Server (NTRS)

Walters, R. W.; Slack, D. C.; Godfrey, A. G.

1993-01-01

Currently there exists no single unified approach for efficiently and accurately solving computational fluid dynamics (CFD) problems across the Mach number regime, from truly low speed incompressible flows to hypersonic speeds. There are several CFD codes that have evolved into sophisticated prediction tools with a wide variety of features including multiblock capabilities, generalized chemistry and thermodynamics models among other features. However, as these codes evolve, the demand placed on the end user also increases simply because of the myriad of features that are incorporated into these codes. In order for a user to be able to solve a wide range of problems, several codes may be needed requiring the user to be familiar with the intricacies of each code and their rather complicated input files. Moreover, the cost of training users and maintaining several codes becomes prohibitive. The objective of the current work is to extend the compressible, characteristic-based, thermochemical nonequilibrium Navier-Stokes code GASP to very low speed flows and simultaneously improve convergence at all speeds. Before this work began, the practical speed range of GASP was Mach numbers on the order of 0.1 and higher. In addition, a number of new techniques have been developed for more accurate physical and numerical modeling. The primary focus has been on the development of optimal preconditioning techniques for the Euler and the Navier-Stokes equations with general finite-rate chemistry models and both equilibrium and nonequilibrium thermodynamics models. We began with the work of Van Leer, Lee, and Roe for inviscid, one-dimensional perfect gases and extended their approach to include three-dimensional reacting flows. The basic steps required to accomplish this task were a transformation to stream-aligned coordinates, the formulation of the preconditioning matrix, incorporation into both explicit and implicit temporal integration schemes, and modification of the numerical flux formulae. In addition, we improved the convergence rate of the implicit time integration schemes in GASP through the use of inner iteration strategies and the use of the GMRES (General Minimized Resisual) which belongs to the class of algorithms referred to as Krylov subspace iteration. Finally, we significantly improved the practical utility of GASP through the addition of mesh sequencing, a technique in which computations begin on a coarse grid and get interpolated onto successively finer grids. The fluid dynamic problems of interest to the propulsion community involve complex flow physics spanning different velocity regimes and possibly involving chemical reactions. This class of problems results in widely disparate time scales causing numerical stiffness. Even in the absence of chemical reactions, eigenvalue stiffness manifests itself at transonic and very low speed flows which can be quantified by the large condition number of the system and evidenced by slow convergence rates. This results in the need for thorough numerical analysis and subsequent implementation of sophisticated numerical techniques for these difficult yet practical problems. As a result of this work, we have been able to extend the range of applicability of compressible codes to very low speed inviscid flows (M = .001) and reacting flows.

Computer Series, 101: Accurate Equations of State in Computational Chemistry Projects.

ERIC Educational Resources Information Center

Albee, David; Jones, Edward

1989-01-01

Discusses the use of computers in chemistry courses at the United States Military Academy. Provides two examples of computer projects: (1) equations of state, and (2) solving for molar volume. Presents BASIC and PASCAL listings for the second project. Lists 10 applications for physical chemistry. (MVL)

Development and Assessment of a Chemistry-Based Computer Video Game as a Learning Tool

ERIC Educational Resources Information Center

Martinez-Hernandez, Kermin Joel

2010-01-01

The chemistry-based computer video game is a multidisciplinary collaboration between chemistry and computer graphics and technology fields developed to explore the use of video games as a possible learning tool. This innovative approach aims to integrate elements of commercial video game and authentic chemistry context environments into a learning…

Publication and Retrieval of Computational Chemical-Physical Data Via the Semantic Web. Final Technical Report

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

Ostlund, Neil

This research showed the feasibility of applying the concepts of the Semantic Web to Computation Chemistry. We have created the first web portal (www.chemsem.com) that allows data created in the calculations of quantum chemistry, and other such chemistry calculations to be placed on the web in a way that makes the data accessible to scientists in a semantic form never before possible. The semantic web nature of the portal allows data to be searched, found, and used as an advance over the usual approach of a relational database. The semantic data on our portal has the nature of a Giantmore » Global Graph (GGG) that can be easily merged with related data and searched globally via a SPARQL Protocol and RDF Query Language (SPARQL) that makes global searches for data easier than with traditional methods. Our Semantic Web Portal requires that the data be understood by a computer and hence defined by an ontology (vocabulary). This ontology is used by the computer in understanding the data. We have created such an ontology for computational chemistry (purl.org/gc) that encapsulates a broad knowledge of the field of computational chemistry. We refer to this ontology as the Gainesville Core. While it is perhaps the first ontology for computational chemistry and is used by our portal, it is only a start of what must be a long multi-partner effort to define computational chemistry. In conjunction with the above efforts we have defined a new potential file standard (Common Standard for eXchange – CSX for computational chemistry data). This CSX file is the precursor of data in the Resource Description Framework (RDF) form that the semantic web requires. Our portal translates CSX files (as well as other computational chemistry data files) into RDF files that are part of the graph database that the semantic web employs. We propose a CSX file as a convenient way to encapsulate computational chemistry data.« less

Computational Chemistry in the Pharmaceutical Industry: From Childhood to Adolescence.

PubMed

Hillisch, Alexander; Heinrich, Nikolaus; Wild, Hanno

2015-12-01

Computational chemistry within the pharmaceutical industry has grown into a field that proactively contributes to many aspects of drug design, including target selection and lead identification and optimization. While methodological advancements have been key to this development, organizational developments have been crucial to our success as well. In particular, the interaction between computational and medicinal chemistry and the integration of computational chemistry into the entire drug discovery process have been invaluable. Over the past ten years we have shaped and developed a highly efficient computational chemistry group for small-molecule drug discovery at Bayer HealthCare that has significantly impacted the clinical development pipeline. In this article we describe the setup and tasks of the computational group and discuss external collaborations. We explain what we have found to be the most valuable and productive methods and discuss future directions for computational chemistry method development. We share this information with the hope of igniting interesting discussions around this topic. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The chemical basis for the origin of the genetic code and the process of protein synthesis

NASA Technical Reports Server (NTRS)

1982-01-01

The major thrust is to understand just how the process of protein synthesis, including that very important aspect, genetic coding, came to be. Two aspects of the problem: the chemistry of active aminoacyl species; and affinities between amino acids and nucleotides, and specifically, how these affinities might affect the chemistry between the two are stressed.

Performance of Versions 1,2 and 3 of the Goddard Earth Observing System (GEOS) Chemistry-Climate Model (CCM)

NASA Technical Reports Server (NTRS)

Pawson, Steven; Stolarski, Richard S.; Nielsen, J. Eric; Duncan, Bryan N.

2008-01-01

Version 1 of the Goddard Earth Observing System Chemistry-Climate Model (GEOS CCM) was used in the first CCMVa1 model evaluation and forms the basis for several studies of links between ozone and the circulation. That version of the CCM was based on the GEOS-4 GCM. Versions 2 and 3 of the GEOS CCM are based on the GEOS-5 GCM, which retains the "Lin-Rood" dynamical core but has a totally different set of physical parameterizatiOns to GEOS-4. In Version 2 of the GEOS CCM the Goddard stratospheric chemistry module is retained. Difference between Versions 1 and 2 thus reflect the physics changes of the underlying GCMs. Several comparisons between these two models are made, several of which reveal improvements in Version 2 (including a more realistic representation of the interannual variability of the Antarctic vortex). In Version 3 of the GEOS CCM, the stratospheric chemistry mechanism is replaced by the "GMI COMBO" code that includes tropospheric chemistry and different computational approaches. An advantage of this model version. is the reduction of high ozone biases that prevail at low chlorine loadings in Versions 1 and 2. This poster will compare and contrast various aspects of the three model versions that are relevant for understanding interactions between ozone and climate.

Transuranic Computational Chemistry.

PubMed

Kaltsoyannis, Nikolas

2018-02-26

Recent developments in the chemistry of the transuranic elements are surveyed, with particular emphasis on computational contributions. Examples are drawn from molecular coordination and organometallic chemistry, and from the study of extended solid systems. The role of the metal valence orbitals in covalent bonding is a particular focus, especially the consequences of the stabilization of the 5f orbitals as the actinide series is traversed. The fledgling chemistry of transuranic elements in the +II oxidation state is highlighted. Throughout, the symbiotic interplay of experimental and computational studies is emphasized; the extraordinary challenges of experimental transuranic chemistry afford computational chemistry a particularly valuable role at the frontier of the periodic table. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

European scientific notes. Volume 38. Number 1. Monthly publication

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

Shaffer, L.E.

1984-01-01

Topics include: Gender-mixed Crews on Dutch Combat Ships; Max-Planck-Institute for Psycholinguistics; Cancer Therapy with Magnetism; 9th European Underwater Biomedical Society Convention; International Center for Genetic Engineering and Biotechnology; Biotechnological Route to Polyphenylene; 2nd Romania-US Seminar on Polymer Chemistry; Statistical Climatology; A Code for Generating Dynamic Models of Robots; Fifth Generation Computing Systems; New Data Logger; Erosion by Liquid and Solid Impact, ELSI VI; Physical Chemistry of the Solid State -- Metals and alloys; NATO Buys a New Oceanographic Research Vessel; Oceanexpo/Oceantropigues 1984; Progress in Development of Wave Energy to Generate Electricity; IAPSO Symposia and Oceanography at the 18th IUGG; Newmore » Decision Support System; High Energy Channeling Research in Switzerland; Muon-Catalyzed Fusion; 2nd International Symposium on Acoustic Remote Sensing of the Atmosphere and Ocean; and Support of Science Research by the British Military.« less

Exploiting Locality in Quantum Computation for Quantum Chemistry.

PubMed

McClean, Jarrod R; Babbush, Ryan; Love, Peter J; Aspuru-Guzik, Alán

2014-12-18

Accurate prediction of chemical and material properties from first-principles quantum chemistry is a challenging task on traditional computers. Recent developments in quantum computation offer a route toward highly accurate solutions with polynomial cost; however, this solution still carries a large overhead. In this Perspective, we aim to bring together known results about the locality of physical interactions from quantum chemistry with ideas from quantum computation. We show that the utilization of spatial locality combined with the Bravyi-Kitaev transformation offers an improvement in the scaling of known quantum algorithms for quantum chemistry and provides numerical examples to help illustrate this point. We combine these developments to improve the outlook for the future of quantum chemistry on quantum computers.

Effect of Surface Nonequilibrium Thermochemistry in Simulation of Carbon Based Ablators

NASA Technical Reports Server (NTRS)

Chen, Yih-Kang; Gokcen, Tahir

2012-01-01

This study demonstrates that coupling of a material thermal response code and a flow solver using finite-rate gas/surface interaction model provides time-accurate solutions for multidimensional ablation of carbon based charring ablators. The material thermal response code used in this study is the Two-dimensional Implicit Thermal Response and Ablation Program (TITAN), which predicts charring material thermal response and shape change on hypersonic space vehicles. Its governing equations include total energy balance, pyrolysis gas momentum conservation, and a three-component decomposition model. The flow code solves the reacting Navier-Stokes equations using Data Parallel Line Relaxation (DPLR) method. Loose coupling between material response and flow codes is performed by solving the surface mass balance in DPLR and the surface energy balance in TITAN. Thus, the material surface recession is predicted by finite-rate gas/surface interaction boundary conditions implemented in DPLR, and the surface temperature and pyrolysis gas injection rate are computed in TITAN. Two sets of gas/surface interaction chemistry between air and carbon surface developed by Park and Zhluktov, respectively, are studied. Coupled fluid-material response analyses of stagnation tests conducted in NASA Ames Research Center arc-jet facilities are considered. The ablating material used in these arc-jet tests was a Phenolic Impregnated Carbon Ablator (PICA). Computational predictions of in-depth material thermal response and surface recession are compared with the experimental measurements for stagnation cold wall heat flux ranging from 107 to 1100 Watts per square centimeter.

Effect of Non-Equilibrium Surface Thermochemistry in Simulation of Carbon Based Ablators

NASA Technical Reports Server (NTRS)

Chen, Yih-Kanq; Gokcen, Tahir

2012-01-01

This study demonstrates that coupling of a material thermal response code and a flow solver using non-equilibrium gas/surface interaction model provides time-accurate solutions for the multidimensional ablation of carbon based charring ablators. The material thermal response code used in this study is the Two-dimensional Implicit Thermal-response and AblatioN Program (TITAN), which predicts charring material thermal response and shape change on hypersonic space vehicles. Its governing equations include total energy balance, pyrolysis gas mass conservation, and a three-component decomposition model. The flow code solves the reacting Navier-Stokes equations using Data Parallel Line Relaxation (DPLR) method. Loose coupling between the material response and flow codes is performed by solving the surface mass balance in DPLR and the surface energy balance in TITAN. Thus, the material surface recession is predicted by finite-rate gas/surface interaction boundary conditions implemented in DPLR, and the surface temperature and pyrolysis gas injection rate are computed in TITAN. Two sets of nonequilibrium gas/surface interaction chemistry between air and the carbon surface developed by Park and Zhluktov, respectively, are studied. Coupled fluid-material response analyses of stagnation tests conducted in NASA Ames Research Center arc-jet facilities are considered. The ablating material used in these arc-jet tests was Phenolic Impregnated Carbon Ablator (PICA). Computational predictions of in-depth material thermal response and surface recession are compared with the experimental measurements for stagnation cold wall heat flux ranging from 107 to 1100 Watts per square centimeter.

In-Service Chemistry Teachers Training: The Impact of Introducing Computer Technology on Teachers' Attitudes.

ERIC Educational Resources Information Center

Dori, Y. J.; Barnea, N.

A computer-assisted instruction (CAI) module on polymers was used to introduce chemistry teachers (n=64) to the variety of possibilities and benefits of using courseware in the current chemistry curriculum in Israel. From an analysis of a pre-and post-attitude questionnaire regarding the use of computers in chemistry teaching, it was concluded…

Study and modeling of finite rate chemistry effects in turbulent non-premixed flames

NASA Technical Reports Server (NTRS)

Vervisch, Luc

1993-01-01

The development of numerical models that reflect some of the most important features of turbulent reacting flows requires information about the behavior of key quantities in well defined combustion regimes. In turbulent flames, the coupling between turbulent and chemical processes is so strong that it is extremely difficult to isolate the role played by one individual physical phenomenon. Direct numerical simulation (hereafter DNS) allows us to study in detail the turbulence-chemistry interaction in some restricted but completely defined situations. Globally, non-premixed flames are controlled by two limiting regimes: the fast chemistry case, where the turbulent flame can be pictured as a random distribution of local chemical equilibrium problems; and the slow chemistry case, where the chemistry integrates in time the turbulent fluctuations. The Damkoehler number, ratio of a mechanical time scale to chemical time scale, is used to distinguish between these regimes. Today most of the industrial computer codes are able to perform predictions in the hypothesis of local equilibrium chemistry using a presumed shape for the probability density function (pdt) of the conserved scalar. However, the finite rate chemistry situation is of great interest because industrial burners usually generate regimes in which, at some points, the flame is undergoing local extinction or at least non-equilibrium situations. Moreover, this variety of situations strongly influences the production of pollutants. To quantify finite rate chemistry effect, the interaction between a non-premixed flame and a free decaying turbulence is studied using DNS. The attention is focused on the dynamic of extinction, and an attempt is made to quantify the effect of the reaction on the small scale mixing process. The unequal diffusivity effect is also addressed. Finally, a simple turbulent combustion model based on the DNS observations and tractable in real flow configurations is proposed.

An interactive computer lab of the galvanic cell for students in biochemistry.

PubMed

Ahlstrand, Emma; Buetti-Dinh, Antoine; Friedman, Ran

2018-01-01

We describe an interactive module that can be used to teach basic concepts in electrochemistry and thermodynamics to first year natural science students. The module is used together with an experimental laboratory and improves the students' understanding of thermodynamic quantities such as Δ r G, Δ r H, and Δ r S that are calculated but not directly measured in the lab. We also discuss how new technologies can substitute some parts of experimental chemistry courses, and improve accessibility to course material. Cloud computing platforms such as CoCalc facilitate the distribution of computer codes and allow students to access and apply interactive course tools beyond the course's scope. Despite some limitations imposed by cloud computing, the students appreciated the approach and the enhanced opportunities to discuss study questions with their classmates and instructor as facilitated by the interactive tools. © 2017 by The International Union of Biochemistry and Molecular Biology, 46(1):58-65, 2018. © 2017 The International Union of Biochemistry and Molecular Biology.

The semantics of Chemical Markup Language (CML) for computational chemistry : CompChem.

PubMed

Phadungsukanan, Weerapong; Kraft, Markus; Townsend, Joe A; Murray-Rust, Peter

2012-08-07

: This paper introduces a subdomain chemistry format for storing computational chemistry data called CompChem. It has been developed based on the design, concepts and methodologies of Chemical Markup Language (CML) by adding computational chemistry semantics on top of the CML Schema. The format allows a wide range of ab initio quantum chemistry calculations of individual molecules to be stored. These calculations include, for example, single point energy calculation, molecular geometry optimization, and vibrational frequency analysis. The paper also describes the supporting infrastructure, such as processing software, dictionaries, validation tools and database repositories. In addition, some of the challenges and difficulties in developing common computational chemistry dictionaries are discussed. The uses of CompChem are illustrated by two practical applications.

The semantics of Chemical Markup Language (CML) for computational chemistry : CompChem

PubMed Central

2012-01-01

This paper introduces a subdomain chemistry format for storing computational chemistry data called CompChem. It has been developed based on the design, concepts and methodologies of Chemical Markup Language (CML) by adding computational chemistry semantics on top of the CML Schema. The format allows a wide range of ab initio quantum chemistry calculations of individual molecules to be stored. These calculations include, for example, single point energy calculation, molecular geometry optimization, and vibrational frequency analysis. The paper also describes the supporting infrastructure, such as processing software, dictionaries, validation tools and database repositories. In addition, some of the challenges and difficulties in developing common computational chemistry dictionaries are discussed. The uses of CompChem are illustrated by two practical applications. PMID:22870956

Computer model predictions of the local effects of large, solid-fuel rocket motors on stratospheric ozone. Technical report

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

Zittel, P.F.

1994-09-10

The solid-fuel rocket motors of large space launch vehicles release gases and particles that may significantly affect stratospheric ozone densities along the vehicle's path. In this study, standard rocket nozzle and flowfield computer codes have been used to characterize the exhaust gases and particles through the afterburning region of the solid-fuel motors of the Titan IV launch vehicle. The models predict that a large fraction of the HCl gas exhausted by the motors is converted to Cl and Cl2 in the plume afterburning region. Estimates of the subsequent chemistry suggest that on expansion into the ambient daytime stratosphere, the highlymore » reactive chlorine may significantly deplete ozone in a cylinder around the vehicle track that ranges from 1 to 5 km in diameter over the altitude range of 15 to 40 km. The initial ozone depletion is estimated to occur on a time scale of less than 1 hour. After the initial effects, the dominant chemistry of the problem changes, and new models are needed to follow the further expansion, or closure, of the ozone hole on a longer time scale.« less

NASA aerospace database subject scope: An overview

NASA Technical Reports Server (NTRS)

1993-01-01

Outlined here is the subject scope of the NASA Aerospace Database, a publicly available subset of the NASA Scientific and Technical (STI) Database. Topics of interest to NASA are outlined and placed within the framework of the following broad aerospace subject categories: aeronautics, astronautics, chemistry and materials, engineering, geosciences, life sciences, mathematical and computer sciences, physics, social sciences, space sciences, and general. A brief discussion of the subject scope is given for each broad area, followed by a similar explanation of each of the narrower subject fields that follow. The subject category code is listed for each entry.

Automated Transition State Search and Its Application to Diverse Types of Organic Reactions.

PubMed

Jacobson, Leif D; Bochevarov, Art D; Watson, Mark A; Hughes, Thomas F; Rinaldo, David; Ehrlich, Stephan; Steinbrecher, Thomas B; Vaitheeswaran, S; Philipp, Dean M; Halls, Mathew D; Friesner, Richard A

2017-11-14

Transition state search is at the center of multiple types of computational chemical predictions related to mechanistic investigations, reactivity and regioselectivity predictions, and catalyst design. The process of finding transition states in practice is, however, a laborious multistep operation that requires significant user involvement. Here, we report a highly automated workflow designed to locate transition states for a given elementary reaction with minimal setup overhead. The only essential inputs required from the user are the structures of the separated reactants and products. The seamless workflow combining computational technologies from the fields of cheminformatics, molecular mechanics, and quantum chemistry automatically finds the most probable correspondence between the atoms in the reactants and the products, generates a transition state guess, launches a transition state search through a combined approach involving the relaxing string method and the quadratic synchronous transit, and finally validates the transition state via the analysis of the reactive chemical bonds and imaginary vibrational frequencies as well as by the intrinsic reaction coordinate method. Our approach does not target any specific reaction type, nor does it depend on training data; instead, it is meant to be of general applicability for a wide variety of reaction types. The workflow is highly flexible, permitting modifications such as a choice of accuracy, level of theory, basis set, or solvation treatment. Successfully located transition states can be used for setting up transition state guesses in related reactions, saving computational time and increasing the probability of success. The utility and performance of the method are demonstrated in applications to transition state searches in reactions typical for organic chemistry, medicinal chemistry, and homogeneous catalysis research. In particular, applications of our code to Michael additions, hydrogen abstractions, Diels-Alder cycloadditions, carbene insertions, and an enzyme reaction model involving a molybdenum complex are shown and discussed.

Construction of a robust, large-scale, collaborative database for raw data in computational chemistry: the Collaborative Chemistry Database Tool (CCDBT).

PubMed

Chen, Mingyang; Stott, Amanda C; Li, Shenggang; Dixon, David A

2012-04-01

A robust metadata database called the Collaborative Chemistry Database Tool (CCDBT) for massive amounts of computational chemistry raw data has been designed and implemented. It performs data synchronization and simultaneously extracts the metadata. Computational chemistry data in various formats from different computing sources, software packages, and users can be parsed into uniform metadata for storage in a MySQL database. Parsing is performed by a parsing pyramid, including parsers written for different levels of data types and sets created by the parser loader after loading parser engines and configurations. Copyright © 2011 Elsevier Inc. All rights reserved.

From data to analysis: linking NWChem and Avogadro with the syntax and semantics of Chemical Markup Language

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

De Jong, Wibe A.; Walker, Andrew M.; Hanwell, Marcus D.

Background Multidisciplinary integrated research requires the ability to couple the diverse sets of data obtained from a range of complex experiments and computer simulations. Integrating data requires semantically rich information. In this paper the generation of semantically rich data from the NWChem computational chemistry software is discussed within the Chemical Markup Language (CML) framework. Results The NWChem computational chemistry software has been modified and coupled to the FoX library to write CML compliant XML data files. The FoX library was expanded to represent the lexical input files used by the computational chemistry software. Conclusions The production of CML compliant XMLmore » files for the computational chemistry software NWChem can be relatively easily accomplished using the FoX library. A unified computational chemistry or CompChem convention and dictionary needs to be developed through a community-based effort. The long-term goal is to enable a researcher to do Google-style chemistry and physics searches.« less

A Simple and Accurate Network for Hydrogen and Carbon Chemistry in the Interstellar Medium

NASA Astrophysics Data System (ADS)

Gong, Munan; Ostriker, Eve C.; Wolfire, Mark G.

2017-07-01

Chemistry plays an important role in the interstellar medium (ISM), regulating the heating and cooling of the gas and determining abundances of molecular species that trace gas properties in observations. Although solving the time-dependent equations is necessary for accurate abundances and temperature in the dynamic ISM, a full chemical network is too computationally expensive to incorporate into numerical simulations. In this paper, we propose a new simplified chemical network for hydrogen and carbon chemistry in the atomic and molecular ISM. We compare results from our chemical network in detail with results from a full photodissociation region (PDR) code, and also with the Nelson & Langer (NL99) network previously adopted in the simulation literature. We show that our chemical network gives similar results to the PDR code in the equilibrium abundances of all species over a wide range of densities, temperature, and metallicities, whereas the NL99 network shows significant disagreement. Applying our network to 1D models, we find that the CO-dominated regime delimits the coldest gas and that the corresponding temperature tracks the cosmic-ray ionization rate in molecular clouds. We provide a simple fit for the locus of CO-dominated regions as a function of gas density and column. We also compare with observations of diffuse and translucent clouds. We find that the CO, {{CH}}x, and {{OH}}x abundances are consistent with equilibrium predictions for densities n=100{--}1000 {{cm}}-3, but the predicted equilibrium C abundance is higher than that seen in observations, signaling the potential importance of non-equilibrium/dynamical effects.

Computational Chemistry Comparison and Benchmark Database

National Institute of Standards and Technology Data Gateway

SRD 101 NIST Computational Chemistry Comparison and Benchmark Database (Web, free access)   The NIST Computational Chemistry Comparison and Benchmark Database is a collection of experimental and ab initio thermochemical properties for a selected set of molecules. The goals are to provide a benchmark set of molecules for the evaluation of ab initio computational methods and allow the comparison between different ab initio computational methods for the prediction of thermochemical properties.

Extension of a Kinetic Approach to Chemical Reactions to Electronic Energy Levels and Reactions Involving Charged Species With Application to DSMC Simulations

NASA Technical Reports Server (NTRS)

Liechty, Derek S.

2013-01-01

The ability to compute rarefied, ionized hypersonic flows is becoming more important as missions such as Earth reentry, landing high mass payloads on Mars, and the exploration of the outer planets and their satellites are being considered. Recently introduced molecular-level chemistry models that predict equilibrium and nonequilibrium reaction rates using only kinetic theory and fundamental molecular properties are extended in the current work to include electronic energy level transitions and reactions involving charged particles. These extensions are shown to agree favorably with reported transition and reaction rates from the literature for nearequilibrium conditions. Also, the extensions are applied to the second flight of the Project FIRE flight experiment at 1634 seconds with a Knudsen number of 0.001 at an altitude of 76.4 km. In order to accomplish this, NASA's direct simulation Monte Carlo code DAC was rewritten to include the ability to simulate charge-neutral ionized flows, take advantage of the recently introduced chemistry model, and to include the extensions presented in this work. The 1634 second data point was chosen for comparisons to be made in order to include a CFD solution. The Knudsen number at this point in time is such that the DSMC simulations are still tractable and the CFD computations are at the edge of what is considered valid because, although near-transitional, the flow is still considered to be continuum. It is shown that the inclusion of electronic energy levels in the DSMC simulation is necessary for flows of this nature and is required for comparison to the CFD solution. The flow field solutions are also post-processed by the nonequilibrium radiation code HARA to compute the radiative portion of the heating and is then compared to the total heating measured in flight.

Web-Based Job Submission Interface for the GAMESS Computational Chemistry Program

ERIC Educational Resources Information Center

Perri, M. J.; Weber, S. H.

2014-01-01

A Web site is described that facilitates use of the free computational chemistry software: General Atomic and Molecular Electronic Structure System (GAMESS). Its goal is to provide an opportunity for undergraduate students to perform computational chemistry experiments without the need to purchase expensive software.

THE INTEGRATED USE OF COMPUTATIONAL CHEMISTRY, SCANNING PROBE MICROSCOPY, AND VIRTUAL REALITY TO PREDICT THE CHEMICAL REACTIVITY OF ENVIRONMENTAL SURFACES

EPA Science Inventory

In the last decade three new techniques scanning probe microscopy (SPM), virtual reality (YR) and computational chemistry ave emerged with the combined capability of a priori predicting the chemically reactivity of environmental surfaces. Computational chemistry provides the cap...

Comptox Chemistry Dashboard: Web-Based Data Integration Hub for Environmental Chemistry and Toxicology Data (ACS Fall meeting 4 of 12)

EPA Science Inventory

The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program integrate advances in biology, chemistry, exposure and computer science to help prioritize chemicals for further research based on potential human health risks. This work involves computational and da...

Modeling of high speed chemically reacting flow-fields

NASA Technical Reports Server (NTRS)

Drummond, J. P.; Carpenter, Mark H.; Kamath, H.

1989-01-01

The SPARK3D and SPARK3D-PNS computer programs were developed to model 3-D supersonic, chemically reacting flow-fields. The SPARK3D code is a full Navier-Stokes solver, and is suitable for use in scramjet combustors and other regions where recirculation may be present. The SPARK3D-PNS is a parabolized Navier-Stokes solver and provides an efficient means of calculating steady-state combustor far-fields and nozzles. Each code has a generalized chemistry package, making modeling of any chemically reacting flow possible. Research activities by the Langley group range from addressing fundamental theoretical issues to simulating problems of practical importance. Algorithmic development includes work on higher order and upwind spatial difference schemes. Direct numerical simulations employ these algorithms to address the fundamental issues of flow stability and transition, and the chemical reaction of supersonic mixing layers and jets. It is believed that this work will lend greater insight into phenomenological model development for simulating supersonic chemically reacting flows in practical combustors. Currently, the SPARK3D and SPARK3D-PNS codes are used to study problems of engineering interest, including various injector designs and 3-D combustor-nozzle configurations. Examples, which demonstrate the capabilities of each code are presented.

Computational Aerothermodynamic Simulation Issues on Unstructured Grids

NASA Technical Reports Server (NTRS)

Gnoffo, Peter A.; White, Jeffery A.

2004-01-01

The synthesis of physical models for gas chemistry and turbulence from the structured grid codes LAURA and VULCAN into the unstructured grid code FUN3D is described. A directionally Symmetric, Total Variation Diminishing (STVD) algorithm and an entropy fix (eigenvalue limiter) keyed to local cell Reynolds number are introduced to improve solution quality for hypersonic aeroheating applications. A simple grid-adaptation procedure is incorporated within the flow solver. Simulations of flow over an ellipsoid (perfect gas, inviscid), Shuttle Orbiter (viscous, chemical nonequilibrium) and comparisons to the structured grid solvers LAURA (cylinder, Shuttle Orbiter) and VULCAN (flat plate) are presented to show current capabilities. The quality of heating in 3D stagnation regions is very sensitive to algorithm options in general, high aspect ratio tetrahedral elements complicate the simulation of high Reynolds number, viscous flow as compared to locally structured meshes aligned with the flow.

NCC: A Physics-Based Design and Analysis Tool for Combustion Systems

NASA Technical Reports Server (NTRS)

Liu, Nan-Suey; Quealy, Angela

2000-01-01

The National Combustion Code (NCC) is an integrated system of computer codes for physics-based design and analysis of combustion systems. It uses unstructured meshes and runs on parallel computing platforms. The NCC is composed of a set of distinct yet closely related modules. They are: (1) a gaseous flow module solving 3-D Navier-Stokes equations; (2) a turbulence module containing the non-linear k-epsilon models; (3) a chemistry module using either the conventional reduced kinetics approach of solving species equations or the Intrinsic Low Dimensional Manifold (ILDM) kinetics approach of table looking up in conjunction with solving the equations of the progressive variables; (4) a turbulence-chemistry interaction module including the option of solving the joint probability density function (PDF) for species and enthalpy; and (5) a spray module for solving the liquid phase equations. In early 1995, an industry-government team was formed to develop the NCC. In July 1998, the baseline beta version was completed and presented in two NCC sessions at the 34th AIAA/ASME/SAE/ASEE Joint Propulsion Conference & Exhibit, July 1998. An overview of this baseline beta version was presented at the NASA HPCCP/CAS Workshop 98, August 1998. Since then, the effort has been focused on the streamlining, validation, and enhancement of the th baseline beta version. The progress is presented in two NCC sessions at the AIAA 38 Aerospace Sciences Meeting & Exhibit, January 2000. At this NASA HPCCP/CAS Workshop 2000, an overview of the NCC papers presented at the AIAA 38 th Aerospace Sciences Meeting & Exhibit is presented, with emphasis on the reduction of analysis time of simulating the (gaseous) reacting flows in full combustors. In addition, results of NCC simulation of a modern turbofan combustor will also be reported.

Information processing in the CNS: a supramolecular chemistry?

PubMed

Tozzi, Arturo

2015-10-01

How does central nervous system process information? Current theories are based on two tenets: (a) information is transmitted by action potentials, the language by which neurons communicate with each other-and (b) homogeneous neuronal assemblies of cortical circuits operate on these neuronal messages where the operations are characterized by the intrinsic connectivity among neuronal populations. In this view, the size and time course of any spike is stereotypic and the information is restricted to the temporal sequence of the spikes; namely, the "neural code". However, an increasing amount of novel data point towards an alternative hypothesis: (a) the role of neural code in information processing is overemphasized. Instead of simply passing messages, action potentials play a role in dynamic coordination at multiple spatial and temporal scales, establishing network interactions across several levels of a hierarchical modular architecture, modulating and regulating the propagation of neuronal messages. (b) Information is processed at all levels of neuronal infrastructure from macromolecules to population dynamics. For example, intra-neuronal (changes in protein conformation, concentration and synthesis) and extra-neuronal factors (extracellular proteolysis, substrate patterning, myelin plasticity, microbes, metabolic status) can have a profound effect on neuronal computations. This means molecular message passing may have cognitive connotations. This essay introduces the concept of "supramolecular chemistry", involving the storage of information at the molecular level and its retrieval, transfer and processing at the supramolecular level, through transitory non-covalent molecular processes that are self-organized, self-assembled and dynamic. Finally, we note that the cortex comprises extremely heterogeneous cells, with distinct regional variations, macromolecular assembly, receptor repertoire and intrinsic microcircuitry. This suggests that every neuron (or group of neurons) embodies different molecular information that hands an operational effect on neuronal computation.

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.

Assessment of Turbulence-Chemistry Interaction Models in the National Combustion Code (NCC) - Part I

NASA Technical Reports Server (NTRS)

Wey, Thomas Changju; Liu, Nan-suey

2011-01-01

This paper describes the implementations of the linear-eddy model (LEM) and an Eulerian FDF/PDF model in the National Combustion Code (NCC) for the simulation of turbulent combustion. The impacts of these two models, along with the so called laminar chemistry model, are then illustrated via the preliminary results from two combustion systems: a nine-element gas fueled combustor and a single-element liquid fueled combustor.

Life is physics and chemistry and communication.

PubMed

Witzany, Guenther

2015-04-01

Manfred Eigen extended Erwin Schroedinger's concept of "life is physics and chemistry" through the introduction of information theory and cybernetic systems theory into "life is physics and chemistry and information." Based on this assumption, Eigen developed the concepts of quasispecies and hypercycles, which have been dominant in molecular biology and virology ever since. He insisted that the genetic code is not just used metaphorically: it represents a real natural language. However, the basics of scientific knowledge changed dramatically within the second half of the 20th century. Unfortunately, Eigen ignored the results of the philosophy of science discourse on essential features of natural languages and codes: a natural language or code emerges from populations of living agents that communicate. This contribution will look at some of the highlights of this historical development and the results relevant for biological theories about life. © 2014 New York Academy of Sciences.

Incorporation of a Chemical Equilibrium Equation of State into LOCI-Chem

NASA Technical Reports Server (NTRS)

Cox, Carey F.

2005-01-01

Renewed interest in development of advanced high-speed transport, reentry vehicles and propulsion systems has led to a resurgence of research into high speed aerodynamics. As this flow regime is typically dominated by hot reacting gaseous flow, efficient models for the characteristic chemical activity are necessary for accurate and cost effective analysis and design of aerodynamic vehicles that transit this regime. The LOCI-Chem code recently developed by Ed Luke at Mississippi State University for NASA/MSFC and used by NASA/MSFC and SSC represents an important step in providing an accurate, efficient computational tool for the simulation of reacting flows through the use of finite-rate kinetics [3]. Finite rate chemistry however, requires the solution of an additional N-1 species mass conservation equations with source terms involving reaction kinetics that are not fully understood. In the equilibrium limit, where the reaction rates approach infinity, these equations become very stiff. Through the use of the assumption of local chemical equilibrium the set of governing equations is reduced back to the usual gas dynamic equations, and thus requires less computation, while still allowing for the inclusion of reacting flow phenomenology. The incorporation of a chemical equilibrium equation of state module into the LOCI-Chem code was the primary objective of the current research. The major goals of the project were: (1) the development of a chemical equilibrium composition solver, and (2) the incorporation of chemical equilibrium solver into LOCI-Chem. Due to time and resource constraints, code optimization was not considered unless it was important to the proper functioning of the code.

Biomarkers of Renal Tumor Burden and Progression in TSC

DTIC Science & Technology

2012-09-01

code) Standard Form 298 (Rev. 8-98) Prescribed by ANSI Std. Z39.18 Biomarkers of Renal Tumor Burden and Progression in TSC Dr. Elahna Paul 1...appearance and growth rates) and renal function parameters (e.g. blood pressure, serum chemistries, urinalysis and urine chemistries). (2) Measure...and renal function parameters (e.g. blood pressure, serum chemistries, urinalysis and urine chemistries). (2) Measure soluble growth factors

The ChemViz Project: Using a Supercomputer To Illustrate Abstract Concepts in Chemistry.

ERIC Educational Resources Information Center

Beckwith, E. Kenneth; Nelson, Christopher

1998-01-01

Describes the Chemistry Visualization (ChemViz) Project, a Web venture maintained by the University of Illinois National Center for Supercomputing Applications (NCSA) that enables high school students to use computational chemistry as a technique for understanding abstract concepts. Discusses the evolution of computational chemistry and provides a…

Axisymmetric computational fluid dynamics analysis of a film/dump-cooled rocket nozzle plume

NASA Technical Reports Server (NTRS)

Tucker, P. K.; Warsi, S. A.

1993-01-01

Prediction of convective base heating rates for a new launch vehicle presents significant challenges to analysts concerned with base environments. The present effort seeks to augment classical base heating scaling techniques via a detailed investigation of the exhaust plume shear layer of a single H2/O2 Space Transportation Main Engine (STME). Use of fuel-rich turbine exhaust to cool the STME nozzle presented concerns regarding potential recirculation of these gases to the base region with attendant increase in the base heating rate. A pressure-based full Navier-Stokes computational fluid dynamics (CFD) code with finite rate chemistry is used to predict plumes for vehicle altitudes of 10 kft and 50 kft. Levels of combustible species within the plume shear layers are calculated in order to assess assumptions made in the base heating analysis.

Boost-phase discrimination research

NASA Technical Reports Server (NTRS)

Langhoff, Stephen R.; Feiereisen, William J.

1993-01-01

The final report describes the combined work of the Computational Chemistry and Aerothermodynamics branches within the Thermosciences Division at NASA Ames Research Center directed at understanding the signatures of shock-heated air. Considerable progress was made in determining accurate transition probabilities for the important band systems of NO that account for much of the emission in the ultraviolet region. Research carried out under this project showed that in order to reproduce the observed radiation from the bow shock region of missiles in their boost phase it is necessary to include the Burnett terms in the constituent equation, account for the non-Boltzmann energy distribution, correctly model the NO formation and rotational excitation process, and use accurate transition probabilities for the NO band systems. This work resulted in significant improvements in the computer code NEQAIR that models both the radiation and fluid dynamics in the shock region.

Effects of Combined Hands-on Laboratory and Computer Modeling on Student Learning of Gas Laws: A Quasi-Experimental Study

ERIC Educational Resources Information Center

Liu, Xiufeng

2006-01-01

Based on current theories of chemistry learning, this study intends to test a hypothesis that computer modeling enhanced hands-on chemistry laboratories are more effective than hands-on laboratories or computer modeling laboratories alone in facilitating high school students' understanding of chemistry concepts. Thirty-three high school chemistry…

Improving Students' Understanding of Molecular Structure through Broad-Based Use of Computer Models in the Undergraduate Organic Chemistry Lecture

ERIC Educational Resources Information Center

Springer, Michael T.

2014-01-01

Several articles suggest how to incorporate computer models into the organic chemistry laboratory, but relatively few papers discuss how to incorporate these models broadly into the organic chemistry lecture. Previous research has suggested that "manipulating" physical or computer models enhances student understanding; this study…

Computations and interpretations: The growth of quantum chemistry, 1927-1967

NASA Astrophysics Data System (ADS)

Park, Buhm Soon

1999-10-01

This dissertation is a contribution to the historical study of scientific disciplines in the twentieth century. It seeks to examine the development of quantum chemistry during the four decades after its inception in 1927. This development was manifest in theories, tools, scientists, and institutions, all of which constituted the disciplinary identity of quantum chemistry. To characterize its identity, I deal with the origins of key ideas and concepts; the change of computational tools from desk calculators to digital computers; the formation of a network among research groups and individuals; and the institutionalization of annual meetings. The dissertation's thesis is three-fold. First, in the pre- World War II years, there were individual contributions to the development of theories in quantum chemistry, but the founding fathers worked in their disciplinary contexts of physics or chemistry with little interest in building a quantum chemistry community. Second, the introduction of electronic digital computers in the postwar years affected the resurgence of the ab initio approach-the attempt to solve the Schrödinger equation without recourse to empirical data-and also the emergence of a community of quantum chemists. But the use of computers did not give rise to a consensus over the aims, methods, or content of the discipline. Third, quantum chemistry exerted a significant influence upon the transformation of chemical education and research in general, thanks to ``chemical translators,'' who sought to explain the gist of quantum chemistry in a language that chemists could understand. In sum, quantum chemistry has been a discipline characterized by diverse traditions, and the whole of chemistry has been under the influence of computations and interpretations made by quantum chemists.

A fully coupled petrological geodynamical model to investigate the evolution of crustal magma chambers

NASA Astrophysics Data System (ADS)

Rummel, Lisa; Kaus, Boris J. P.; White, Richard W.

2017-04-01

The evolution of crustal magma chambers can be considered from a range of different physical and chemical perspectives. Most previous studies focus either on the petrological side (assuming only thermal effects and ignoring mechanics), or on the mechanical evolution (assuming a fixed melt chemistry). Here, we develop a method that fully couples petrological with geodynamic modelling, by combining a finite element code, MVEP2, with a thermodynamic modelling approach (Perple_X) that takes the evolving chemistry into account. The evolution of melt chemistry in a crustal magma chamber is analyzed by focusing on the effects of depth and temperature as well as size and shape of the magma chamber(s). The models show that each of these factors influences the melting behavior of rocks, the magma composition and their effects on the mechanics in the upper lithosphere. Interactions with country rocks (assimilation), ongoing rock depletion (fractional melting) and a possible open system behavior (fractional crystallization) and their effects on magma chemistry are taken into account. The chemical and mineralogical evolution of the melt source, composition (10 oxide component system) of intrusive and extrusive rocks as well as melt fraction and density are tracked on particles using a marker-in-cell-method in the geodynamic code. After each melt extraction event, the employed phase diagram is updated or recalculated based on the residuum chemistry that shifts the solidus to higher temperatures with sequential melt extraction. The resulting wide range in chemical compositions and the volume of intrusive and extrusive rocks are tracked in time and space over the melting region. The newly generated crust employs phase diagrams which are directly computed from the chemistry of extracted melts. Plutons are able to melt again as long as the local temperature is higher in the model than the solidus temperature in the employed phase diagram. As a result, our models make testable predictions on types of erupted lavas. We show an application to the plume-related intracontinental West Eifel volcanism (Germany), where our models explain a sudden change in K2O/Na2O-ratios in the volcanic rocks by a transition between melting a metasomatized and a pyrolitic mantle. We also show initial results from crustal melt extraction in an arc system.

Sfg

NASA Astrophysics Data System (ADS)

Fischer, R. X.; Baur, W. H.

This document is part of Subvolume E `Zeolite-Type Crystal Structures and their Chemistry. Framework Type Codes RON to STI' of Volume 14 `Microporous and other Framework Materials with Zeolite-Type Structures' of Landolt-Börnstein Group IV `Physical Chemistry'.

Vet

NASA Astrophysics Data System (ADS)

Fischer, R. X.; Baur, W. H.

This document is part of Subvolume F 'Zeolite-Type Crystal Structures and their Chemistry. Framework Type Codes STO to ZON' of Volume 14 'Microporous and other Framework Materials with Zeolite-Type Structures' of Landolt-Börnstein Group IV 'Physical Chemistry'.

Multiscale Simulations of ALD in Cross Flow Reactors

DOE PAGES

Yanguas-Gil, Angel; Libera, Joseph A.; Elam, Jeffrey W.

2014-08-13

In this study, we have developed a multiscale simulation code that allows us to study the impact of surface chemistry on the coating of large area substrates with high surface area/high aspect-ratio features. Our code, based on open-source libraries, takes advantage of the ALD surface chemistry to achieve an extremely efficient two-way coupling between reactor and feature length scales, and it can provide simulated quartz crystal microbalance and mass spectrometry data at any point of the reactor. By combining experimental surface characterization with simple analysis of growth profiles in a tubular cross flow reactor, we are able to extract amore » minimal set of reactions to effectively model the surface chemistry, including the presence of spurious CVD, to evaluate the impact of surface chemistry on the coating of large, high surface area substrates.« less

The equation of state of predominant detonation products

NASA Astrophysics Data System (ADS)

Zaug, Joseph; Crowhurst, Jonathan; Bastea, Sorin; Fried, Laurence

2009-06-01

The equation of state of detonation products, when incorporated into an experimentally grounded thermochemical reaction algorithm can be used to predict the performance of explosives. Here we report laser based Impulsive Stimulated Light Scattering measurements of the speed of sound from a variety of polar and nonpolar detonation product supercritical fluids and mixtures. The speed of sound data are used to improve the exponential-six potentials employed within the Cheetah thermochemical code. We will discuss the improvements made to Cheetah in terms of predictions vs. measured performance data for common polymer blended explosives. Accurately computing the chemistry that occurs from reacted binder materials is one important step forward in our efforts.

The Effect of Spray Initial Conditions on Heat Release and Emissions in LDI CFD Calculations

NASA Technical Reports Server (NTRS)

Iannetti, Anthony C.; Liu, Nan-Suey; Davoudzadeh, Farhad

2008-01-01

The mass and velocity distribution of liquid spray has a primary effect on the combustion heat release process. This heat release process then affects emissions like nitrogen oxides (NOx) and carbon monoxide (CO). Computational Fluid Dynamics gives the engineer insight into these processes, but various setup options exist (number of droplet groups, and initial droplet temperature) for spray initial conditions. This paper studies these spray initial condition options using the National Combustion Code (NCC) on a single swirler lean direct injection (LDI) flame tube. Using laminar finite rate chemistry, comparisons are made against experimental data for velocity measurements, temperature, and emissions (NOx, CO).

Turbulent Mixing Chemistry in Disks

NASA Astrophysics Data System (ADS)

Semenov, D.; Wiebe, D.

2006-11-01

A gas-grain chemical model with surface reaction and 1D/2D turbulent mixing is available for protoplanetary disks and molecular clouds. Current version is based on the updated UMIST'95 database with gas-grain interactions (accretion, desorption, photoevaporation, etc.) and modified rate equation approach to surface chemistry (see also abstract for the static chemistry code).

Nonequilibrium chemistry boundary layer integral matrix procedure

NASA Technical Reports Server (NTRS)

Tong, H.; Buckingham, A. C.; Morse, H. L.

1973-01-01

The development of an analytic procedure for the calculation of nonequilibrium boundary layer flows over surfaces of arbitrary catalycities is described. An existing equilibrium boundary layer integral matrix code was extended to include nonequilibrium chemistry while retaining all of the general boundary condition features built into the original code. For particular application to the pitch-plane of shuttle type vehicles, an approximate procedure was developed to estimate the nonequilibrium and nonisentropic state at the edge of the boundary layer.

Current Status of Post-combustor Trace Chemistry Modeling and Simulation at NASA Glenn Research Center

NASA Technical Reports Server (NTRS)

Wey, Thomas; Liu, Nan-Suey

2003-01-01

The overall objective of the current effort at NASA GRC is to evaluate, develop, and apply methodologies suitable for modeling intra-engine trace chemical changes over post combustor flow path relevant to the pollutant emissions from aircraft engines. At the present time, the focus is the high pressure turbine environment. At first, the trace chemistry model of CNEWT were implemented into GLENN-HT as well as NCC. Then, CNEWT, CGLENN-HT, and NCC were applied to the trace species evolution in a cascade of Cambridge University's No. 2 rotor and in a turbine vane passage. In general, the results from these different codes provide similar features. However, the details of some of the quantities of interest can be sensitive to the differences of these codes. This report summaries the implementation effort and presents the comparison of the No. 2 rotor results obtained from these different codes. The comparison of the turbine vane passage results is reported elsewhere. In addition to the implementation of trace chemistry model into existing CFD codes, several pre/post-processing tools that can handle the manipulations of the geometry, the unstructured and structured grids as well as the CFD solutions also have been enhanced and seamlessly tied with NCC, CGLENN-HT, and CNEWT. Thus, a complete CFD package consisting of pre/post-processing tools and flow solvers suitable for post-combustor intra-engine trace chemistry study is assembled.

APOLLO: A computer program for the calculation of chemical equilibrium and reaction kinetics of chemical systems

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

Nguyen, H.D.

1991-11-01

Several of the technologies being evaluated for the treatment of waste material involve chemical reactions. Our example is the in situ vitrification (ISV) process where electrical energy is used to melt soil and waste into a ``glass like`` material that immobilizes and encapsulates any residual waste. During the ISV process, various chemical reactions may occur that produce significant amounts of products which must be contained and treated. The APOLLO program was developed to assist in predicting the composition of the gases that are formed. Although the development of this program was directed toward ISV applications, it should be applicable tomore » other technologies where chemical reactions are of interest. This document presents the mathematical methodology of the APOLLO computer code. APOLLO is a computer code that calculates the products of both equilibrium and kinetic chemical reactions. The current version, written in FORTRAN, is readily adaptable to existing transport programs designed for the analysis of chemically reacting flow systems. Separate subroutines EQREACT and KIREACT for equilibrium ad kinetic chemistry respectively have been developed. A full detailed description of the numerical techniques used, which include both Lagrange multiplies and a third-order integrating scheme is presented. Sample test problems are presented and the results are in excellent agreement with those reported in the literature.« less

APOLLO: A computer program for the calculation of chemical equilibrium and reaction kinetics of chemical systems

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

Nguyen, H.D.

1991-11-01

Several of the technologies being evaluated for the treatment of waste material involve chemical reactions. Our example is the in situ vitrification (ISV) process where electrical energy is used to melt soil and waste into a glass like'' material that immobilizes and encapsulates any residual waste. During the ISV process, various chemical reactions may occur that produce significant amounts of products which must be contained and treated. The APOLLO program was developed to assist in predicting the composition of the gases that are formed. Although the development of this program was directed toward ISV applications, it should be applicable tomore » other technologies where chemical reactions are of interest. This document presents the mathematical methodology of the APOLLO computer code. APOLLO is a computer code that calculates the products of both equilibrium and kinetic chemical reactions. The current version, written in FORTRAN, is readily adaptable to existing transport programs designed for the analysis of chemically reacting flow systems. Separate subroutines EQREACT and KIREACT for equilibrium ad kinetic chemistry respectively have been developed. A full detailed description of the numerical techniques used, which include both Lagrange multiplies and a third-order integrating scheme is presented. Sample test problems are presented and the results are in excellent agreement with those reported in the literature.« less

Promoting Intrinsic and Extrinsic Motivation among Chemistry Students Using Computer-Assisted Instruction

ERIC Educational Resources Information Center

Gambari, Isiaka A.; Gbodi, Bimpe E.; Olakanmi, Eyitao U.; Abalaka, Eneojo N.

2016-01-01

The role of computer-assisted instruction in promoting intrinsic and extrinsic motivation among Nigerian secondary school chemistry students was investigated in this study. The study employed two modes of computer-assisted instruction (computer simulation instruction and computer tutorial instructional packages) and two levels of gender (male and…

Issues and approach to develop validated analysis tools for hypersonic flows: One perspective

NASA Technical Reports Server (NTRS)

Deiwert, George S.

1993-01-01

Critical issues concerning the modeling of low density hypervelocity flows where thermochemical nonequilibrium effects are pronounced are discussed. Emphasis is on the development of validated analysis tools, and the activity in the NASA Ames Research Center's Aerothermodynamics Branch is described. Inherent in the process is a strong synergism between ground test and real gas computational fluid dynamics (CFD). Approaches to develop and/or enhance phenomenological models and incorporate them into computational flowfield simulation codes are discussed. These models were partially validated with experimental data for flows where the gas temperature is raised (compressive flows). Expanding flows, where temperatures drop, however, exhibit somewhat different behavior. Experimental data for these expanding flow conditions is sparse and reliance must be made on intuition and guidance from computational chemistry to model transport processes under these conditions. Ground based experimental studies used to provide necessary data for model development and validation are described. Included are the performance characteristics of high enthalpy flow facilities, such as shock tubes and ballistic ranges.

The winding road to being a code monkey

NASA Astrophysics Data System (ADS)

Sarahan, Michael

2017-09-01

I am now a software engineer at a company that provides data analytics services, and helps support the open source data science community. I have been a computer nerd for a very long time, but it was my CEU experience at Texas A&M with Sherry Yennello (2003-2005) that helped me put my nerd skills to productive use. My project then was simulation of pulse shape discrimination electronics, and it was an excellent introduction to core computational concerns, such as digitization: when you see a line on the screen, that's not really how the computer sees it. I wandered in graduate school through a chemistry program into using electron microscopes. My programming interest got me into image and signal processing, which led naturally to jobs in analyzing data, and also in acquiring data. Throughout, it was always difficult just to make software work. I got pretty good at making it work. That's what I do for a living now - package software so that it is easy for other people to do great science with.

Issues and approach to develop validated analysis tools for hypersonic flows: One perspective

NASA Technical Reports Server (NTRS)

Deiwert, George S.

1992-01-01

Critical issues concerning the modeling of low-density hypervelocity flows where thermochemical nonequilibrium effects are pronounced are discussed. Emphasis is on the development of validated analysis tools. A description of the activity in the Ames Research Center's Aerothermodynamics Branch is also given. Inherent in the process is a strong synergism between ground test and real-gas computational fluid dynamics (CFD). Approaches to develop and/or enhance phenomenological models and incorporate them into computational flow-field simulation codes are discussed. These models have been partially validated with experimental data for flows where the gas temperature is raised (compressive flows). Expanding flows, where temperatures drop, however, exhibit somewhat different behavior. Experimental data for these expanding flow conditions are sparse; reliance must be made on intuition and guidance from computational chemistry to model transport processes under these conditions. Ground-based experimental studies used to provide necessary data for model development and validation are described. Included are the performance characteristics of high-enthalpy flow facilities, such as shock tubes and ballistic ranges.

ChemoPy: freely available python package for computational biology and chemoinformatics.

PubMed

Cao, Dong-Sheng; Xu, Qing-Song; Hu, Qian-Nan; Liang, Yi-Zeng

2013-04-15

Molecular representation for small molecules has been routinely used in QSAR/SAR, virtual screening, database search, ranking, drug ADME/T prediction and other drug discovery processes. To facilitate extensive studies of drug molecules, we developed a freely available, open-source python package called chemoinformatics in python (ChemoPy) for calculating the commonly used structural and physicochemical features. It computes 16 drug feature groups composed of 19 descriptors that include 1135 descriptor values. In addition, it provides seven types of molecular fingerprint systems for drug molecules, including topological fingerprints, electro-topological state (E-state) fingerprints, MACCS keys, FP4 keys, atom pairs fingerprints, topological torsion fingerprints and Morgan/circular fingerprints. By applying a semi-empirical quantum chemistry program MOPAC, ChemoPy can also compute a large number of 3D molecular descriptors conveniently. The python package, ChemoPy, is freely available via http://code.google.com/p/pychem/downloads/list, and it runs on Linux and MS-Windows. Supplementary data are available at Bioinformatics online.

Numerical investigation of combustion field of hypervelocity scramjet engine

NASA Astrophysics Data System (ADS)

Zhang, Shikong; Li, Jiang; Qin, Fei; Huang, Zhiwei; Xue, Rui

2016-12-01

A numerical study of the ground testing of a hydrogen-fueled scramjet engine was undertaken using the commercial computational-fluid-dynamics code CFD++. The simulated Mach number was 12. A 7-species, 9-reaction-step hydrogen-air chemistry kinetics system was adopted for the Reynolds-averaged Navier-Stokes simulation. The two-equation SST turbulence model, which takes into account the wall functions, was used to handle the turbulence-chemistry interactions. The results were validated by experimentally measuring the wall pressure distribution, and the values obtained proved to be in good agreement. The flow pattern at non-reaction/reaction is presented, as are the results of analyzing the supersonic premix/non-premix flame structure, the reaction heat release distribution in different modes, and the change in the equivalence ratio. In this study, we realize the working mode of a hypervelocity engine and provide some suggestions for the combustion organization of the engine as well as offer insight into the potential for exploiting the processes of combustion and flow.

The EDIT-COMGEOM Code

DTIC Science & Technology

1975-09-01

This report assumes a familiarity with the GIFT and MAGIC computer codes. The EDIT-COMGEOM code is a FORTRAN computer code. The EDIT-COMGEOM code...converts the target description data which was used in the MAGIC computer code to the target description data which can be used in the GIFT computer code

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.

Performance Evaluation of NWChem Ab-Initio Molecular Dynamics (AIMD) Simulations on the Intel® Xeon Phi™ Processor

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

Bylaska, Eric J.; Jacquelin, Mathias; De Jong, Wibe A.

2017-10-20

Ab-initio Molecular Dynamics (AIMD) methods are an important class of algorithms, as they enable scientists to understand the chemistry and dynamics of molecular and condensed phase systems while retaining a first-principles-based description of their interactions. Many-core architectures such as the Intel® Xeon Phi™ processor are an interesting and promising target for these algorithms, as they can provide the computational power that is needed to solve interesting problems in chemistry. In this paper, we describe the efforts of refactoring the existing AIMD plane-wave method of NWChem from an MPI-only implementation to a scalable, hybrid code that employs MPI and OpenMP tomore » exploit the capabilities of current and future many-core architectures. We describe the optimizations required to get close to optimal performance for the multiplication of the tall-and-skinny matrices that form the core of the computational algorithm. We present strong scaling results on the complete AIMD simulation for a test case that simulates 256 water molecules and that strong-scales well on a cluster of 1024 nodes of Intel Xeon Phi processors. We compare the performance obtained with a cluster of dual-socket Intel® Xeon® E5–2698v3 processors.« less

A computer program for performance prediction of tripropellant rocket engines with tangential slot injection

NASA Technical Reports Server (NTRS)

Dang, Anthony; Nickerson, Gary R.

1987-01-01

For the development of a Heavy Lift Launch Vehicle (HLLV) several engines with different operating cycles and using LOX/Hydrocarbon propellants are presently being examined. Some concepts utilize hydrogen for thrust chamber wall cooling followed by a gas generator turbine drive cycle with subsequent dumping of H2/O2 combustion products into the nozzle downstream of the throat. In the Space Transportation Booster Engine (STBE) selection process the specific impulse will be one of the optimization criteria; however, the current performance prediction programs do not have the capability to include a third propellant in this process, nor to account for the effect of dumping the gas-generator product tangentially inside the nozzle. The purpose is to describe a computer program for accurately predicting the performance of such an engine. The code consists of two modules; one for the inviscid performance, and the other for the viscous loss. For the first module, the two-dimensional kinetics program (TDK) was modified to account for tripropellant chemistry, and for the effect of tangential slot injection. For the viscous loss, the Mass Addition Boundary Layer program (MABL) was modified to include the effects of the boundary layer-shear layer interaction, and tripropellant chemistry. Calculations were made for a real engine and compared with available data.

A Study of Cavitation-Ignition Bubble Combustion

NASA Technical Reports Server (NTRS)

Nguyen, Quang-Viet; Jacqmin, David A.

2005-01-01

We present the results of an experimental and computational study of the physics and chemistry of cavitation-ignition bubble combustion (CIBC), a process that occurs when combustible gaseous mixtures are ignited by the high temperatures found inside a rapidly collapsing bubble. The CIBC process was modeled using a time-dependent compressible fluid-dynamics code that includes finite-rate chemistry. The model predicts that gas-phase reactions within the bubble produce CO and other gaseous by-products of combustion. In addition, heat and mechanical energy release through a bubble volume-expansion phase are also predicted by the model. We experimentally demonstrate the CIBC process using an ultrasonically excited cavitation flow reactor with various hydrocarbon-air mixtures in liquid water. Low concentrations (< 160 ppm) of carbon monoxide (CO) emissions from the ultrasonic reactor were measured, and found to be proportional to the acoustic excitation power. The results of the model were consistent with the measured experimental results. Based on the experimental findings, the computational model, and previous reports of the "micro-diesel effect" in industrial hydraulic systems, we conclude that CIBC is indeed possible and exists in ultrasonically- and hydrodynamically-induced cavitation. Finally, estimates of the utility of CIBC process as a means of powering an idealized heat engine are also presented.

MELCOR/CONTAIN LMR Implementation Report - FY16 Progress.

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

Louie, David; Humphries, Larry L.

2016-11-01

This report describes the progress of the CONTAIN - LMR sodium physics and chemistry models to be implemented in MELCOR 2.1. In the past three years , the implementation included the addition of sodium equations of state and sodium properties from two different sources. The first source is based on the previous work done by Idaho National Laboratory by modifying MELCOR to include liquid lithium equation of state as a working fluid to model the nuclear fusion safety research. The second source uses properties generated for the SIMMER code. The implemented modeling has been tested and results are reported inmore » this document. In addition, the CONTAIN - LMR code was derived from an early version of the CONTAIN code, and many physical models that were developed since this early version of CONTAIN are not available in this early code version. Therefore, CONTAIN 2 has been updated with the sodium models in CONTAIN - LMR as CONTAIN2 - LMR, which may be used to provide code-to-code comparison with CONTAIN - LMR and MELCOR when the sodium chemistry models from CONTAIN - LMR have been completed. Both the spray fire and pool fire chemistry routines from CONTAIN - LMR have been integrated into MELCOR 2.1, and debugging and testing are in progress. Because MELCOR only models the equation of state for liquid and gas phases of the coolant, a modeling gap still exists when dealing with experiments or accident conditions that take place when the ambient temperature is below the freezing point of sodium. An alternative method is under investigation to overcome this gap . We are no longer working on the separate branch from the main branch of MELCOR 2.1 since the major modeling of MELCOR 2.1 has been completed. At the current stage, the newly implemented sodium chemistry models will be a part of the main MELCOR release version (MELCOR 2.2). This report will discuss the accomplishments and issues relating to the implementation. Also, we will report on the planned completion of all remaining tasks in the upcoming FY2017, including the atmospheric chemistry model and sodium - concrete interaction model implementation .« less

Alternative modeling methods for plasma-based Rf ion sources

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

Veitzer, Seth A., E-mail: veitzer@txcorp.com; Kundrapu, Madhusudhan, E-mail: madhusnk@txcorp.com; Stoltz, Peter H., E-mail: phstoltz@txcorp.com

Rf-driven ion sources for accelerators and many industrial applications benefit from detailed numerical modeling and simulation of plasma characteristics. For instance, modeling of the Spallation Neutron Source (SNS) internal antenna H{sup −} source has indicated that a large plasma velocity is induced near bends in the antenna where structural failures are often observed. This could lead to improved designs and ion source performance based on simulation and modeling. However, there are significant separations of time and spatial scales inherent to Rf-driven plasma ion sources, which makes it difficult to model ion sources with explicit, kinetic Particle-In-Cell (PIC) simulation codes. Inmore » particular, if both electron and ion motions are to be explicitly modeled, then the simulation time step must be very small, and total simulation times must be large enough to capture the evolution of the plasma ions, as well as extending over many Rf periods. Additional physics processes such as plasma chemistry and surface effects such as secondary electron emission increase the computational requirements in such a way that even fully parallel explicit PIC models cannot be used. One alternative method is to develop fluid-based codes coupled with electromagnetics in order to model ion sources. Time-domain fluid models can simulate plasma evolution, plasma chemistry, and surface physics models with reasonable computational resources by not explicitly resolving electron motions, which thereby leads to an increase in the time step. This is achieved by solving fluid motions coupled with electromagnetics using reduced-physics models, such as single-temperature magnetohydrodynamics (MHD), extended, gas dynamic, and Hall MHD, and two-fluid MHD models. We show recent results on modeling the internal antenna H{sup −} ion source for the SNS at Oak Ridge National Laboratory using the fluid plasma modeling code USim. We compare demonstrate plasma temperature equilibration in two-temperature MHD models for the SNS source and present simulation results demonstrating plasma evolution over many Rf periods for different plasma temperatures. We perform the calculations in parallel, on unstructured meshes, using finite-volume solvers in order to obtain results in reasonable time.« less

Alternative modeling methods for plasma-based Rf ion sources.

PubMed

Veitzer, Seth A; Kundrapu, Madhusudhan; Stoltz, Peter H; Beckwith, Kristian R C

2016-02-01

Rf-driven ion sources for accelerators and many industrial applications benefit from detailed numerical modeling and simulation of plasma characteristics. For instance, modeling of the Spallation Neutron Source (SNS) internal antenna H(-) source has indicated that a large plasma velocity is induced near bends in the antenna where structural failures are often observed. This could lead to improved designs and ion source performance based on simulation and modeling. However, there are significant separations of time and spatial scales inherent to Rf-driven plasma ion sources, which makes it difficult to model ion sources with explicit, kinetic Particle-In-Cell (PIC) simulation codes. In particular, if both electron and ion motions are to be explicitly modeled, then the simulation time step must be very small, and total simulation times must be large enough to capture the evolution of the plasma ions, as well as extending over many Rf periods. Additional physics processes such as plasma chemistry and surface effects such as secondary electron emission increase the computational requirements in such a way that even fully parallel explicit PIC models cannot be used. One alternative method is to develop fluid-based codes coupled with electromagnetics in order to model ion sources. Time-domain fluid models can simulate plasma evolution, plasma chemistry, and surface physics models with reasonable computational resources by not explicitly resolving electron motions, which thereby leads to an increase in the time step. This is achieved by solving fluid motions coupled with electromagnetics using reduced-physics models, such as single-temperature magnetohydrodynamics (MHD), extended, gas dynamic, and Hall MHD, and two-fluid MHD models. We show recent results on modeling the internal antenna H(-) ion source for the SNS at Oak Ridge National Laboratory using the fluid plasma modeling code USim. We compare demonstrate plasma temperature equilibration in two-temperature MHD models for the SNS source and present simulation results demonstrating plasma evolution over many Rf periods for different plasma temperatures. We perform the calculations in parallel, on unstructured meshes, using finite-volume solvers in order to obtain results in reasonable time.

Comparisons of a Three-Dimensional, Full Navier Stokes Computer Model with High Mach Number Combuster Test Data

NASA Technical Reports Server (NTRS)

Watkins, William B.

1990-01-01

Comparisons between scramjet combustor data and a three-dimensional full Navier-Stokes calculation have been made to verify and substantiate computational fluid dynamics (CFD) codes and application procedures. High Mach number scramjet combustor development will rely heavily on CFD applications to provide wind tunnel-equivalent data of quality sufficient to design, build and fly hypersonic aircraft. Therefore. detailed comparisons between CFD results and test data are imperative. An experimental case is presented, for which combustor wall static pressures were measured and flow-fieid interferograms were obtained. A computer model was done of the experiment, and counterpart parameters are compared with experiment. The experiment involved a subscale combustor designed and fabricated for the National Aero-Space Plane Program, and tested in the Calspan Corporation 96" hypersonic shock tunnel. The combustor inlet ramp was inclined at a 20 angle to the shock tunnel nozzle axis, and resulting combustor entrance flow conditions simulated freestream M=10. The combustor body and cowl walls were instrumented with static pressure transducers, and the combustor lateral walls contained windows through which flowfield holographic interferograms were obtained. The CFD calculation involved a three-dimensional time-averaged full Navier-Stokes code applied to the axial flow segment containing fuel injection and combustion. The full Navier-Stokes approach allowed for mixed supersonic and subsonic flow, downstream-upstream communication in subsonic flow regions, and effects of adverse pressure gradients. The code included hydrogen-air chemistry in the combustor segment which begins near fuel injection and continues through combustor exhaust. Combustor ramp and inlet segments on the combustor lateral centerline were modelled as two dimensional. Comparisons to be shown include calculated versus measured wall static pressures as functions of axial flow coordinate, and calculated path-averaged density contours versus an holographic Interferogram.

Naval Weapons Center Plume Radar Frequency Interference Code

DTIC Science & Technology

1982-10-01

ppm sodium. Both equilibrium and finite rate chemistry during the expansion from the chamber were tried as initial conditions for the plume. In...was too large. The difference between the.e two sets of initial conditions diminished downstream as the chemistry in the plume mixing region began to...Rerkirre Arvliral I Comirlnrnde!- ir.C h ic 1. tVS. Pacific Hice ((Code 3251 1 Corimu tinde r. ’n, r-d I leer. Pearl I atar I Coimniaide r. Sevent

Effect of Turbulent Fluctuations on Infrared Radiation from a Tactical Missile Plume

DTIC Science & Technology

1982-02-01

Reacting Flows ...... 21 Reacting Flow Calculations ..................................... 21 Turbulence- Chemistry Interaction...a two-equation, turbulence kinetic energy model. The code is capable of handling multi-species, multi-step chemistry . However, it does not calculate...that are expected to be important in turbulence- chemistry and turbulence-radiation interactions. The program calculates only two turbulence guantities

ON UPGRADING THE NUMERICS IN COMBUSTION CHEMISTRY CODES. (R824970)

EPA Science Inventory

A method of updating and reusing legacy FORTRAN codes for combustion simulations is presented using the DAEPACK software package. The procedure is demonstrated on two codes that come with the CHEMKIN-II package, CONP and SENKIN, for the constant-pressure batch reactor simulati...

Integrating Computational Chemistry into the Physical Chemistry Curriculum

ERIC Educational Resources Information Center

Johnson, Lewis E.; Engel, Thomas

2011-01-01

Relatively few undergraduate physical chemistry programs integrate molecular modeling into their quantum mechanics curriculum owing to concerns about limited access to computational facilities, the cost of software, and concerns about increasing the course material. However, modeling exercises can be integrated into an undergraduate course at a…

Comparison of Coupled Radiative Flow Solutions with Project Fire 2 Flight Data

NASA Technical Reports Server (NTRS)

Olynick, David R.; Henline, W. D.; Chambers, Lin Hartung; Candler, G. V.

1995-01-01

A nonequilibrium, axisymmetric, Navier-Stokes flow solver with coupled radiation has been developed for use in the design or thermal protection systems for vehicles where radiation effects are important. The present method has been compared with an existing now and radiation solver and with the Project Fire 2 experimental data. Good agreement has been obtained over the entire Fire 2 trajectory with the experimentally determined values of the stagnation radiation intensity in the 0.2-6.2 eV range and with the total stagnation heating. The effects of a number of flow models are examined to determine which combination of physical models produces the best agreement with the experimental data. These models include radiation coupling, multitemperature thermal models, and finite rate chemistry. Finally, the computational efficiency of the present model is evaluated. The radiation properties model developed for this study is shown to offer significant computational savings compared to existing codes.

Comparison of DSMC and CFD Solutions of Fire II Including Radiative Heating

NASA Technical Reports Server (NTRS)

Liechty, Derek S.; Johnston, Christopher O.; Lewis, Mark J.

2011-01-01

The ability to compute rarefied, ionized hypersonic flows is becoming more important as missions such as Earth reentry, landing high mass payloads on Mars, and the exploration of the outer planets and their satellites are being considered. These flows may also contain significant radiative heating. To prepare for these missions, NASA is developing the capability to simulate rarefied, ionized flows and to then calculate the resulting radiative heating to the vehicle's surface. In this study, the DSMC codes DAC and DS2V are used to obtain charge-neutral ionization solutions. NASA s direct simulation Monte Carlo code DAC is currently being updated to include the ability to simulate charge-neutral ionized flows, take advantage of the recently introduced Quantum-Kinetic chemistry model, and to include electronic energy levels as an additional internal energy mode. The Fire II flight test is used in this study to assess these new capabilities. The 1634 second data point was chosen for comparisons to be made in order to include comparisons to computational fluid dynamics solutions. The Knudsen number at this point in time is such that the DSMC simulations are still tractable and the CFD computations are at the edge of what is considered valid. It is shown that there can be quite a bit of variability in the vibrational temperature inferred from DSMC solutions and that, from how radiative heating is computed, the electronic temperature is much better suited for radiative calculations. To include the radiative portion of heating, the flow-field solutions are post-processed by the non-equilibrium radiation code HARA. Acceptable agreement between CFD and DSMC flow field solutions is demonstrated and the progress of the updates to DAC, along with an appropriate radiative heating solution, are discussed. In addition, future plans to generate more high fidelity radiative heat transfer solutions are discussed.

The performance of low-cost commercial cloud computing as an alternative in computational chemistry.

PubMed

Thackston, Russell; Fortenberry, Ryan C

2015-05-05

The growth of commercial cloud computing (CCC) as a viable means of computational infrastructure is largely unexplored for the purposes of quantum chemistry. In this work, the PSI4 suite of computational chemistry programs is installed on five different types of Amazon World Services CCC platforms. The performance for a set of electronically excited state single-point energies is compared between these CCC platforms and typical, "in-house" physical machines. Further considerations are made for the number of cores or virtual CPUs (vCPUs, for the CCC platforms), but no considerations are made for full parallelization of the program (even though parallelization of the BLAS library is implemented), complete high-performance computing cluster utilization, or steal time. Even with this most pessimistic view of the computations, CCC resources are shown to be more cost effective for significant numbers of typical quantum chemistry computations. Large numbers of large computations are still best utilized by more traditional means, but smaller-scale research may be more effectively undertaken through CCC services. © 2015 Wiley Periodicals, Inc.

What Chemists (or Chemistry Students) Need to Know about Computing.

ERIC Educational Resources Information Center

Swift, Mary L.; Zielinski, Theresa Julia

1995-01-01

Presents key points of an on-line conference discussion and integrates them with information from the literature. Key points included: computer as a tool for learning, study, research, and communication; hardware, software, computing concepts, and other teaching concerns; and the appropriate place for chemistry computer-usage instruction. (45…

An Educational Approach to Computationally Modeling Dynamical Systems

ERIC Educational Resources Information Center

Chodroff, Leah; O'Neal, Tim M.; Long, David A.; Hemkin, Sheryl

2009-01-01

Chemists have used computational science methodologies for a number of decades and their utility continues to be unabated. For this reason we developed an advanced lab in computational chemistry in which students gain understanding of general strengths and weaknesses of computation-based chemistry by working through a specific research problem.…

Propellant Chemistry for CFD Applications

NASA Technical Reports Server (NTRS)

Farmer, R. C.; Anderson, P. G.; Cheng, Gary C.

1996-01-01

Current concepts for reusable launch vehicle design have created renewed interest in the use of RP-1 fuels for high pressure and tri-propellant propulsion systems. Such designs require the use of an analytical technology that accurately accounts for the effects of real fluid properties, combustion of large hydrocarbon fuel modules, and the possibility of soot formation. These effects are inadequately treated in current computational fluid dynamic (CFD) codes used for propulsion system analyses. The objective of this investigation is to provide an accurate analytical description of hydrocarbon combustion thermodynamics and kinetics that is sufficiently computationally efficient to be a practical design tool when used with CFD codes such as the FDNS code. A rigorous description of real fluid properties for RP-1 and its combustion products will be derived from the literature and from experiments conducted in this investigation. Upon the establishment of such a description, the fluid description will be simplified by using the minimum of empiricism necessary to maintain accurate combustion analyses and including such empirical models into an appropriate CFD code. An additional benefit of this approach is that the real fluid properties analysis simplifies the introduction of the effects of droplet sprays into the combustion model. Typical species compositions of RP-1 have been identified, surrogate fuels have been established for analyses, and combustion and sooting reaction kinetics models have been developed. Methods for predicting the necessary real fluid properties have been developed and essential experiments have been designed. Verification studies are in progress, and preliminary results from these studies will be presented. The approach has been determined to be feasible, and upon its completion the required methodology for accurate performance and heat transfer CFD analyses for high pressure, tri-propellant propulsion systems will be available.

Molecular Modeling and Computational Chemistry at Humboldt State University.

ERIC Educational Resources Information Center

Paselk, Richard A.; Zoellner, Robert W.

2002-01-01

Describes a molecular modeling and computational chemistry (MM&CC) facility for undergraduate instruction and research at Humboldt State University. This facility complex allows the introduction of MM&CC throughout the chemistry curriculum with tailored experiments in general, organic, and inorganic courses as well as a new molecular modeling…

Integration of Computational Chemistry into the Undergraduate Organic Chemistry Laboratory Curriculum

ERIC Educational Resources Information Center

Esselman, Brian J.; Hill, Nicholas J.

2016-01-01

Advances in software and hardware have promoted the use of computational chemistry in all branches of chemical research to probe important chemical concepts and to support experimentation. Consequently, it has become imperative that students in the modern undergraduate curriculum become adept at performing simple calculations using computational…

Conformational Analysis of Drug Molecules: A Practical Exercise in the Medicinal Chemistry Course

ERIC Educational Resources Information Center

Yuriev, Elizabeth; Chalmers, David; Capuano, Ben

2009-01-01

Medicinal chemistry is a specialized, scientific discipline. Computational chemistry and structure-based drug design constitute important themes in the education of medicinal chemists. This problem-based task is associated with structure-based drug design lectures. It requires students to use computational techniques to investigate conformational…

Chemistry by Computer.

ERIC Educational Resources Information Center

Garmon, Linda

1981-01-01

Describes the features of various computer chemistry programs. Utilization of computer graphics, color, digital imaging, and other innovations are discussed in programs including those which aid in the identification of unknowns, predict whether chemical reactions are feasible, and predict the biological activity of xenobiotic compounds. (CS)

FastChem: An ultra-fast equilibrium chemistry

NASA Astrophysics Data System (ADS)

Kitzmann, Daniel; Stock, Joachim

2018-04-01

FastChem is an equilibrium chemistry code that calculates the chemical composition of the gas phase for given temperatures and pressures. Written in C++, it is based on a semi-analytic approach, and is optimized for extremely fast and accurate calculations.

ASSESSING THE IMPACT OF LANDUSE/LANDCOVER ON STREAM CHEMISTRY IN MARYLAND

EPA Science Inventory

Spatial and statistical analyses were conducted to investigate the relationships between stream chemistry (nitrate, sulfate, dissolved organic carbon, etc.), habitat and satellite-derived landuse maps for the state of Maryland. Hydrologic Unit Code (HUC) watershed boundaries (8-...

Chemical vapor deposition fluid flow simulation modelling tool

NASA Technical Reports Server (NTRS)

Bullister, Edward T.

1992-01-01

Accurate numerical simulation of chemical vapor deposition (CVD) processes requires a general purpose computational fluid dynamics package combined with specialized capabilities for high temperature chemistry. In this report, we describe the implementation of these specialized capabilities in the spectral element code NEKTON. The thermal expansion of the gases involved is shown to be accurately approximated by the low Mach number perturbation expansion of the incompressible Navier-Stokes equations. The radiative heat transfer between multiple interacting radiating surfaces is shown to be tractable using the method of Gebhart. The disparate rates of reaction and diffusion in CVD processes are calculated via a point-implicit time integration scheme. We demonstrate the use above capabilities on prototypical CVD applications.

An improved flux-split algorithm applied to hypersonic flows in chemical equilibrium

NASA Technical Reports Server (NTRS)

Palmer, Grant

1988-01-01

An explicit, finite-difference, shock-capturing numerical algorithm is presented and applied to hypersonic flows assumed to be in thermochemical equilibrium. Real-gas chemistry is either loosely coupled to the gasdynamics by way of a Gibbs free energy minimization package or fully coupled using species mass conservation equations with finite-rate chemical reactions. A scheme is developed that maintains stability in the explicit, finite-rate formulation while allowing relatively high time steps. The codes use flux vector splitting to difference the inviscid fluxes and employ real-gas corrections to viscosity and thermal conductivity. Numerical results are compared against existing ballistic range and flight data. Flows about complex geometries are also computed.

Solution strategies and heat transfer calculations for three-dimensional configurations at hypersonic speeds

NASA Technical Reports Server (NTRS)

Weilmuenster, K. J.; Gnoffo, Peter A.

1992-01-01

A procedure which reduces the memory requirements for computing the viscous flow over a modified Orbiter geometry at a hypersonic flight condition is presented. The Langley Aerothermodynamic Upwind Relaxation Algorithm (LAURA) code which incorporates a thermochemical nonequilibrium chemistry model, a finite rate catalytic wall boundary condition and wall temperature distribution based on radiation equilibrium is used in this study. In addition, the effect of choice of 'min mod' function, eigenvalue limiter and grid density on surface heating is investigated. The surface heating from a flowfield calculation at Mach number 22, altitude of 230,000 ft and 40 deg angle of attack is compared with flight data from three Orbiter flights.

Computer-aided drug discovery research at a global contract research organization

NASA Astrophysics Data System (ADS)

Kitchen, Douglas B.

2017-03-01

Computer-aided drug discovery started at Albany Molecular Research, Inc in 1997. Over nearly 20 years the role of cheminformatics and computational chemistry has grown throughout the pharmaceutical industry and at AMRI. This paper will describe the infrastructure and roles of CADD throughout drug discovery and some of the lessons learned regarding the success of several methods. Various contributions provided by computational chemistry and cheminformatics in chemical library design, hit triage, hit-to-lead and lead optimization are discussed. Some frequently used computational chemistry techniques are described. The ways in which they may contribute to discovery projects are presented based on a few examples from recent publications.

Computer-aided drug discovery research at a global contract research organization.

PubMed

Kitchen, Douglas B

2017-03-01

Computer-aided drug discovery started at Albany Molecular Research, Inc in 1997. Over nearly 20 years the role of cheminformatics and computational chemistry has grown throughout the pharmaceutical industry and at AMRI. This paper will describe the infrastructure and roles of CADD throughout drug discovery and some of the lessons learned regarding the success of several methods. Various contributions provided by computational chemistry and cheminformatics in chemical library design, hit triage, hit-to-lead and lead optimization are discussed. Some frequently used computational chemistry techniques are described. The ways in which they may contribute to discovery projects are presented based on a few examples from recent publications.

Chemical nonequilibrium Navier-Stokes solutions for hypersonic flow over an ablating graphite nosetip

NASA Technical Reports Server (NTRS)

Chen, Y. K.; Henline, W. D.

1993-01-01

The general boundary conditions including mass and energy balances of chemically equilibrated or nonequilibrated gas adjacent to ablating surfaces have been derived. A computer procedure based on these conditions was developed and interfaced with the Navier-Stokes solver for predictions of the flow field, surface temperature, and surface ablation rates over re-entry space vehicles with ablating Thermal Protection Systems (TPS). The Navier-Stokes solver with general surface thermochemistry boundary conditions can predict more realistic solutions and provide useful information for the design of TPS. A test case with a proposed hypersonic test vehicle configuration and associated free stream conditions was developed. Solutions with various surface boundary conditions were obtained, and the effect of nonequilibrium gas as well as surface chemistry on surface heating and ablation rate were examined. The solutions of the GASP code with complete ablating surface conditions were compared with those of the ASC code. The direction of future work is also discussed.

Cars Thermometry in a Supersonic Combustor for CFD Code Validation

NASA Technical Reports Server (NTRS)

Cutler, A. D.; Danehy, P. M.; Springer, R. R.; DeLoach, R.; Capriotti, D. P.

2002-01-01

An experiment has been conducted to acquire data for the validation of computational fluid dynamics (CFD) codes used in the design of supersonic combustors. The primary measurement technique is coherent anti-Stokes Raman spectroscopy (CARS), although surface pressures and temperatures have also been acquired. Modern- design- of-experiment techniques have been used to maximize the quality of the data set (for the given level of effort) and minimize systematic errors. The combustor consists of a diverging duct with single downstream- angled wall injector. Nominal entrance Mach number is 2 and enthalpy nominally corresponds to Mach 7 flight. Temperature maps are obtained at several planes in the flow for two cases: in one case the combustor is piloted by injecting fuel upstream of the main injector, the second is not. Boundary conditions and uncertainties are adequately characterized. Accurate CFD calculation of the flow will ultimately require accurate modeling of the chemical kinetics and turbulence-chemistry interactions as well as accurate modeling of the turbulent mixing

A DSMC Study of Low Pressure Argon Discharge

NASA Astrophysics Data System (ADS)

Hash, David; Meyyappan, M.

1997-10-01

Work toward a self-consistent plasma simulation using the DSMC method for examination of the flowfields of low-pressure high density plasma reactors is presented. Presently, DSMC simulations for these applications involve either treating the electrons as a fluid or imposing experimentally determined values for the electron number density profile. In either approach, the electrons themselves are not physically simulated. Self-consistent plasma DSMC simulations have been conducted for aerospace applications but at a severe computational cost due in part to the scalar architectures on which the codes were employed. The present work attempts to conduct such simulations at a more reasonable cost using a plasma version of the object-oriented parallel Cornell DSMC code, MONACO, on an IBM SP-2. Due the availability of experimental data, the GEC reference cell is chosen to conduct preliminary investigations. An argon discharge is examined thus affording a simple chemistry set with eight gas-phase reactions and five species: Ar, Ar^+, Ar^*, Ar_2, and e where Ar^* is a metastable.

Investigation of the transient fuel preburner manifold and combustor

NASA Technical Reports Server (NTRS)

Wang, Ten-See; Chen, Yen-Sen; Farmer, Richard C.

1989-01-01

A computational fluid dynamics (CFD) model with finite rate reactions, FDNS, was developed to study the start transient of the Space Shuttle Main Engine (SSME) fuel preburner (FPB). FDNS is a time accurate, pressure based CFD code. An upwind scheme was employed for spatial discretization. The upwind scheme was based on second and fourth order central differencing with adaptive artificial dissipation. A state of the art two-equation k-epsilon (T) turbulence model was employed for the turbulence calculation. A Pade' Rational Solution (PARASOL) chemistry algorithm was coupled with the point implicit procedure. FDNS was benchmarked with three well documented experiments: a confined swirling coaxial jet, a non-reactive ramjet dump combustor, and a reactive ramjet dump combustor. Excellent comparisons were obtained for the benchmark cases. The code was then used to study the start transient of an axisymmetric SSME fuel preburner. Predicted transient operation of the preburner agrees well with experiment. Furthermore, it was also found that an appreciable amount of unburned oxygen entered the turbine stages.

Efficient 3D kinetic Monte Carlo method for modeling of molecular structure and dynamics.

PubMed

Panshenskov, Mikhail; Solov'yov, Ilia A; Solov'yov, Andrey V

2014-06-30

Self-assembly of molecular systems is an important and general problem that intertwines physics, chemistry, biology, and material sciences. Through understanding of the physical principles of self-organization, it often becomes feasible to control the process and to obtain complex structures with tailored properties, for example, bacteria colonies of cells or nanodevices with desired properties. Theoretical studies and simulations provide an important tool for unraveling the principles of self-organization and, therefore, have recently gained an increasing interest. The present article features an extension of a popular code MBN EXPLORER (MesoBioNano Explorer) aiming to provide a universal approach to study self-assembly phenomena in biology and nanoscience. In particular, this extension involves a highly parallelized module of MBN EXPLORER that allows simulating stochastic processes using the kinetic Monte Carlo approach in a three-dimensional space. We describe the computational side of the developed code, discuss its efficiency, and apply it for studying an exemplary system. Copyright © 2014 Wiley Periodicals, Inc.

Using Computer Visualization Models in High School Chemistry: The Role of Teacher Beliefs.

ERIC Educational Resources Information Center

Robblee, Karen M.; Garik, Peter; Abegg, Gerald L.; Faux, Russell; Horwitz, Paul

This paper discusses the role of high school chemistry teachers' beliefs in implementing computer visualization software to teach atomic and molecular structure from a quantum mechanical perspective. The informants in this study were four high school chemistry teachers with comparable academic and professional backgrounds. These teachers received…

Integrating Free Computer Software in Chemistry and Biochemistry Instruction: An International Collaboration

ERIC Educational Resources Information Center

Cedeno, David L.; Jones, Marjorie A.; Friesen, Jon A.; Wirtz, Mark W.; Rios, Luz Amalia; Ocampo, Gonzalo Taborda

2010-01-01

At the Universidad de Caldas, Manizales, Colombia, we used their new computer facilities to introduce chemistry graduate students to biochemical database mining and quantum chemistry calculations using freeware. These hands-on workshops allowed the students a strong introduction to easily accessible software and how to use this software to begin…

MELCOR/CONTAIN LMR Implementation Report-Progress FY15

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

Humphries, Larry L.; Louie, David L.Y.

2016-01-01

This report describes the progress of the CONTAIN-LMR sodium physics and chemistry models to be implemented in to MELCOR 2.1. It also describes the progress to implement these models into CONT AIN 2 as well. In the past two years, the implementation included the addition of sodium equations of state and sodium properties from two different sources. The first source is based on the previous work done by Idaho National Laborat ory by modifying MELCOR to include liquid lithium equation of state as a working fluid to mode l the nuclear fusion safety research. The second source uses properties generatedmore » for the SIMMER code. Testing and results from this implementation of sodium pr operties are given. In addition, the CONTAIN-LMR code was derived from an early version of C ONTAIN code. Many physical models that were developed sin ce this early version of CONTAIN are not captured by this early code version. Therefore, CONTAIN 2 is being updated with the sodium models in CONTAIN-LMR in or der to facilitate verification of these models with the MELCOR code. Although CONTAIN 2, which represents the latest development of CONTAIN, now contains ma ny of the sodium specific models, this work is not complete due to challenges from the lower cell architecture in CONTAIN 2, which is different from CONTAIN- LMR. This implementation should be completed in the coming year, while sodi um models from C ONTAIN-LMR are being integrated into MELCOR. For testing, CONTAIN decks have been developed for verification and validation use. In terms of implementing the sodium m odels into MELCOR, a separate sodium model branch was created for this document . Because of massive development in the main stream MELCOR 2.1 code and the require ment to merge the latest code version into this branch, the integration of the s odium models were re-directed to implement the sodium chemistry models first. This change led to delays of the actual implementation. For aid in the future implementation of sodium models, a new sodium chemistry package was created. Thus reporting for the implementation of the sodium chemistry is discussed in this report.« less

SDA 7: A modular and parallel implementation of the simulation of diffusional association software

PubMed Central

Martinez, Michael; Romanowska, Julia; Kokh, Daria B.; Ozboyaci, Musa; Yu, Xiaofeng; Öztürk, Mehmet Ali; Richter, Stefan

2015-01-01

The simulation of diffusional association (SDA) Brownian dynamics software package has been widely used in the study of biomacromolecular association. Initially developed to calculate bimolecular protein–protein association rate constants, it has since been extended to study electron transfer rates, to predict the structures of biomacromolecular complexes, to investigate the adsorption of proteins to inorganic surfaces, and to simulate the dynamics of large systems containing many biomacromolecular solutes, allowing the study of concentration‐dependent effects. These extensions have led to a number of divergent versions of the software. In this article, we report the development of the latest version of the software (SDA 7). This release was developed to consolidate the existing codes into a single framework, while improving the parallelization of the code to better exploit modern multicore shared memory computer architectures. It is built using a modular object‐oriented programming scheme, to allow for easy maintenance and extension of the software, and includes new features, such as adding flexible solute representations. We discuss a number of application examples, which describe some of the methods available in the release, and provide benchmarking data to demonstrate the parallel performance. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:26123630

Additional support for the TDK/MABL computer program

NASA Technical Reports Server (NTRS)

Nickerson, G. R.; Dunn, Stuart S.

1993-01-01

An advanced version of the Two-Dimensional Kinetics (TDK) computer program was developed under contract and released to the propulsion community in early 1989. Exposure of the code to this community indicated a need for improvements in certain areas. In particular, the TDK code needed to be adapted to the special requirements imposed by the Space Transportation Main Engine (STME) development program. This engine utilizes injection of the gas generator exhaust into the primary nozzle by means of a set of slots. The subsequent mixing of this secondary stream with the primary stream with finite rate chemical reaction can have a major impact on the engine performance and the thermal protection of the nozzle wall. In attempting to calculate this reacting boundary layer problem, the Mass Addition Boundary Layer (MABL) module of TDK was found to be deficient in several respects. For example, when finite rate chemistry was used to determine gas properties, (MABL-K option) the program run times became excessive because extremely small step sizes were required to maintain numerical stability. A robust solution algorithm was required so that the MABL-K option could be viable as a rocket propulsion industry design tool. Solving this problem was a primary goal of the phase 1 work effort.

21 CFR 314.440 - Addresses for applications and abbreviated applications.

Code of Federal Regulations, 2011 CFR

2011-04-01

... mail code for the Office of Generic Drugs is HFD-600, the mail codes for the Divisions of Chemistry I... leukapheresis; (3) Blood component processing solutions and shelf life extenders; and (4) Oxygen carriers. [50...

21 CFR 314.440 - Addresses for applications and abbreviated applications.

Code of Federal Regulations, 2013 CFR

2013-04-01

... mail code for the Office of Generic Drugs is HFD-600, the mail codes for the Divisions of Chemistry I... leukapheresis; (3) Blood component processing solutions and shelf life extenders; and (4) Oxygen carriers. [50...

21 CFR 314.440 - Addresses for applications and abbreviated applications.

Code of Federal Regulations, 2014 CFR

2014-04-01

... mail code for the Office of Generic Drugs is HFD-600, the mail codes for the Divisions of Chemistry I... leukapheresis; (3) Blood component processing solutions and shelf life extenders; and (4) Oxygen carriers. [50...

21 CFR 314.440 - Addresses for applications and abbreviated applications.

Code of Federal Regulations, 2012 CFR

2012-04-01

... mail code for the Office of Generic Drugs is HFD-600, the mail codes for the Divisions of Chemistry I... leukapheresis; (3) Blood component processing solutions and shelf life extenders; and (4) Oxygen carriers. [50...

Hypersonic and Unsteady Flow Science Issues for Explosively Formed Penetrators

DTIC Science & Technology

2006-08-01

under going real- time dynamic deformation. ACCOMPLISHMENTS/RESULTS • Completed initial assessment of flow chemistry • Completed initial stability... flow chemistry during rapid deformation •Cannot use static boundary conditions in CFD codes •Interfaces one approach to coupling with hydrocodes

Development and assessment of a chemistry-based computer video game as a learning tool

NASA Astrophysics Data System (ADS)

Martinez-Hernandez, Kermin Joel

The chemistry-based computer video game is a multidisciplinary collaboration between chemistry and computer graphics and technology fields developed to explore the use of video games as a possible learning tool. This innovative approach aims to integrate elements of commercial video game and authentic chemistry context environments into a learning experience through gameplay. The project consists of three areas: development, assessment, and implementation. However, the foci of this study were the development and assessment of the computer video game including possible learning outcomes and game design elements. A chemistry-based game using a mixed genre of a single player first-person game embedded with action-adventure and puzzle components was developed to determine if students' level of understanding of chemistry concepts change after gameplay intervention. Three phases have been completed to assess students' understanding of chemistry concepts prior and after gameplay intervention. Two main assessment instruments (pre/post open-ended content survey and individual semi-structured interviews) were used to assess student understanding of concepts. In addition, game design elements were evaluated for future development phases. Preliminary analyses of the interview data suggest that students were able to understand most of the chemistry challenges presented in the game and the game served as a review for previously learned concepts as well as a way to apply such previous knowledge. To guarantee a better understanding of the chemistry concepts, additions such as debriefing and feedback about the content presented in the game seem to be needed. The use of visuals in the game to represent chemical processes, game genre, and game idea appear to be the game design elements that students like the most about the current computer video game.

From transistor to trapped-ion computers for quantum chemistry.

PubMed

Yung, M-H; Casanova, J; Mezzacapo, A; McClean, J; Lamata, L; Aspuru-Guzik, A; Solano, E

2014-01-07

Over the last few decades, quantum chemistry has progressed through the development of computational methods based on modern digital computers. However, these methods can hardly fulfill the exponentially-growing resource requirements when applied to large quantum systems. As pointed out by Feynman, this restriction is intrinsic to all computational models based on classical physics. Recently, the rapid advancement of trapped-ion technologies has opened new possibilities for quantum control and quantum simulations. Here, we present an efficient toolkit that exploits both the internal and motional degrees of freedom of trapped ions for solving problems in quantum chemistry, including molecular electronic structure, molecular dynamics, and vibronic coupling. We focus on applications that go beyond the capacity of classical computers, but may be realizable on state-of-the-art trapped-ion systems. These results allow us to envision a new paradigm of quantum chemistry that shifts from the current transistor to a near-future trapped-ion-based technology.

From transistor to trapped-ion computers for quantum chemistry

PubMed Central

Yung, M.-H.; Casanova, J.; Mezzacapo, A.; McClean, J.; Lamata, L.; Aspuru-Guzik, A.; Solano, E.

2014-01-01

Over the last few decades, quantum chemistry has progressed through the development of computational methods based on modern digital computers. However, these methods can hardly fulfill the exponentially-growing resource requirements when applied to large quantum systems. As pointed out by Feynman, this restriction is intrinsic to all computational models based on classical physics. Recently, the rapid advancement of trapped-ion technologies has opened new possibilities for quantum control and quantum simulations. Here, we present an efficient toolkit that exploits both the internal and motional degrees of freedom of trapped ions for solving problems in quantum chemistry, including molecular electronic structure, molecular dynamics, and vibronic coupling. We focus on applications that go beyond the capacity of classical computers, but may be realizable on state-of-the-art trapped-ion systems. These results allow us to envision a new paradigm of quantum chemistry that shifts from the current transistor to a near-future trapped-ion-based technology. PMID:24395054

The EPA CompTox Chemistry Dashboard - an online resource for environmental chemists (ACS Spring Meeting)

EPA Science Inventory

The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program integrates advances in biology, chemistry, and computer science to help prioritize chemicals for further research based on potential human health risks. This work involves computational and data drive...

The EPA Comptox Chemistry Dashboard: A Web-Based Data Integration Hub for Toxicology Data (SOT)

EPA Science Inventory

The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program integrates advances in biology, chemistry, and computer science to help prioritize chemicals for further research based on potential human health risks. This work involves computational and data drive...

Computational Chemistry Using Modern Electronic Structure Methods

ERIC Educational Resources Information Center

Bell, Stephen; Dines, Trevor J.; Chowdhry, Babur Z.; Withnall, Robert

2007-01-01

Various modern electronic structure methods are now days used to teach computational chemistry to undergraduate students. Such quantum calculations can now be easily used even for large size molecules.

Ethics in Science: The Unique Consequences of Chemistry

PubMed Central

Kovac, Jeffrey

2015-01-01

This article discusses the ethical issues unique to the science and practice of chemistry. These issues arise from chemistry’s position in the middle between the theoretical and the practical, a science concerned with molecules that are of the right size to directly affect human life. Many of the issues are raised by the central activity of chemistry––synthesis. Chemists make thousands of new substances each year. Many are beneficial, but others are threats. Since the development of the chemical industry in the nineteenth century, chemistry has contributed to the deterioration of the environment but has also helped to reduce pollution. Finally, we discuss the role of codes of ethics and whether the current codes of conduct for chemists are adequate for the challenges of today’s world. PMID:26155729

Computer Simulations of Quantum Theory of Hydrogen Atom for Natural Science Education Students in a Virtual Lab

ERIC Educational Resources Information Center

Singh, Gurmukh

2012-01-01

The present article is primarily targeted for the advanced college/university undergraduate students of chemistry/physics education, computational physics/chemistry, and computer science. The most recent software system such as MS Visual Studio .NET version 2010 is employed to perform computer simulations for modeling Bohr's quantum theory of…

Computer-based, Jeopardy™-like game in general chemistry for engineering majors

NASA Astrophysics Data System (ADS)

Ling, S. S.; Saffre, F.; Kadadha, M.; Gater, D. L.; Isakovic, A. F.

2013-03-01

We report on the design of Jeopardy™-like computer game for enhancement of learning of general chemistry for engineering majors. While we examine several parameters of student achievement and attitude, our primary concern is addressing the motivation of students, which tends to be low in a traditionally run chemistry lectures. The effect of the game-playing is tested by comparing paper-based game quiz, which constitutes a control group, and computer-based game quiz, constituting a treatment group. Computer-based game quizzes are Java™-based applications that students run once a week in the second part of the last lecture of the week. Overall effectiveness of the semester-long program is measured through pretest-postest conceptual testing of general chemistry. The objective of this research is to determine to what extent this ``gamification'' of the course delivery and course evaluation processes may be beneficial to the undergraduates' learning of science in general, and chemistry in particular. We present data addressing gender-specific difference in performance, as well as background (pre-college) level of general science and chemistry preparation. We outline the plan how to extend such approach to general physics courses and to modern science driven electives, and we offer live, in-lectures examples of our computer gaming experience. We acknowledge support from Khalifa University, Abu Dhabi

Ambarish Nag | NREL

Science.gov Websites

|Mathematical biology Education Ph.D., Computational Chemistry, University of Chicago M.S., Chemistry , University of Chicago M.S., (2-Year) Chemistry, Indian Institute of Technology, Kanpur, India B.S., Chemistry

Introduction of Digital Computer Technology Into the Undergraduate Chemistry Laboratory. Final Technical Report.

ERIC Educational Resources Information Center

Perone, Sam P.

The objective of this project has been the development of a successful approach for the incorporation of on-line computer technology into the undergraduate chemistry laboratory. This approach assumes no prior programing, electronics or instrumental analysis experience on the part of the student; it does not displace the chemistry content with…

Computational Chemistry in the Undergraduate Laboratory: A Mechanistic Study of the Wittig Reaction

ERIC Educational Resources Information Center

Albrecht, Birgit

2014-01-01

The Wittig reaction is one of the most useful reactions in organic chemistry. Despite its prominence early in the organic chemistry curriculum, the exact mechanism of this reaction is still under debate, and this controversy is often neglected in the classroom. Introducing a simple computational study of the Wittig reaction illustrates the…

Quantum chemistry simulation on quantum computers: theories and experiments.

PubMed

Lu, Dawei; Xu, Boruo; Xu, Nanyang; Li, Zhaokai; Chen, Hongwei; Peng, Xinhua; Xu, Ruixue; Du, Jiangfeng

2012-07-14

It has been claimed that quantum computers can mimic quantum systems efficiently in the polynomial scale. Traditionally, those simulations are carried out numerically on classical computers, which are inevitably confronted with the exponential growth of required resources, with the increasing size of quantum systems. Quantum computers avoid this problem, and thus provide a possible solution for large quantum systems. In this paper, we first discuss the ideas of quantum simulation, the background of quantum simulators, their categories, and the development in both theories and experiments. We then present a brief introduction to quantum chemistry evaluated via classical computers followed by typical procedures of quantum simulation towards quantum chemistry. Reviewed are not only theoretical proposals but also proof-of-principle experimental implementations, via a small quantum computer, which include the evaluation of the static molecular eigenenergy and the simulation of chemical reaction dynamics. Although the experimental development is still behind the theory, we give prospects and suggestions for future experiments. We anticipate that in the near future quantum simulation will become a powerful tool for quantum chemistry over classical computations.

Computational chemistry at Janssen

NASA Astrophysics Data System (ADS)

van Vlijmen, Herman; Desjarlais, Renee L.; Mirzadegan, Tara

2017-03-01

Computer-aided drug discovery activities at Janssen are carried out by scientists in the Computational Chemistry group of the Discovery Sciences organization. This perspective gives an overview of the organizational and operational structure, the science, internal and external collaborations, and the impact of the group on Drug Discovery at Janssen.

Results of comparative RBMK neutron computation using VNIIEF codes (cell computation, 3D statics, 3D kinetics). Final report

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

Grebennikov, A.N.; Zhitnik, A.K.; Zvenigorodskaya, O.A.

1995-12-31

In conformity with the protocol of the Workshop under Contract {open_quotes}Assessment of RBMK reactor safety using modern Western Codes{close_quotes} VNIIEF performed a neutronics computation series to compare western and VNIIEF codes and assess whether VNIIEF codes are suitable for RBMK type reactor safety assessment computation. The work was carried out in close collaboration with M.I. Rozhdestvensky and L.M. Podlazov, NIKIET employees. The effort involved: (1) cell computations with the WIMS, EKRAN codes (improved modification of the LOMA code) and the S-90 code (VNIIEF Monte Carlo). Cell, polycell, burnup computation; (2) 3D computation of static states with the KORAT-3D and NEUmore » codes and comparison with results of computation with the NESTLE code (USA). The computations were performed in the geometry and using the neutron constants presented by the American party; (3) 3D computation of neutron kinetics with the KORAT-3D and NEU codes. These computations were performed in two formulations, both being developed in collaboration with NIKIET. Formulation of the first problem maximally possibly agrees with one of NESTLE problems and imitates gas bubble travel through a core. The second problem is a model of the RBMK as a whole with imitation of control and protection system controls (CPS) movement in a core.« less

Using Games To Teach Chemistry: An Annotated Bibliography

NASA Astrophysics Data System (ADS)

Russell, Jeanne V.

1999-04-01

A list of published or marketed games based on a chemistry motif is presented. Each game is listed according to its level, subject matter, and title. A bibliographic notation and a short description are given for each game. For Introductory/High School/General Chemistry, 45 games are listed under the subjects General Knowledge; Elements & Atomic Structure (not Symbols); Nomenclature, Formulas, & Equation Writing; Chemical Reactions: Solutions & Solubilities; and Other Subjects. Seventeen games are listed under Organic Chemistry and 4 games under Other Chemistry Games. Computer games designed for outdated computers (PDP-11, TRS-80, and Apple II) are not included.

Report of Workshop on Repetitive Opening Switches

DTIC Science & Technology

1981-06-01

needed. This work must also pay close attention to the poorly understood plasma chemistry in these switches and develop models for discharges and dis...circuit model. Inclusion of plasma chemistry . 2. Compile and measure (when need- ed) fundamental data such as rate coefficients, cross-sec- tions, etc...Include plasma chemistry effects in the code. Conduct literature search. Carry out basic measurements for gas- es and gas mixtures under con

Computers in Science: Thinking Outside the Discipline.

ERIC Educational Resources Information Center

Hamilton, Todd M.

2003-01-01

Describes the Computers in Science course which integrates computer-related techniques into the science disciplines of chemistry, physics, biology, and Earth science. Uses a team teaching approach and teaches students how to solve chemistry problems with spreadsheets, identify minerals with X-rays, and chemical and force analysis. (Contains 14…

Computer-Based Molecular Modelling: Finnish School Teachers' Experiences and Views

ERIC Educational Resources Information Center

Aksela, Maija; Lundell, Jan

2008-01-01

Modern computer-based molecular modelling opens up new possibilities for chemistry teaching at different levels. This article presents a case study seeking insight into Finnish school teachers' use of computer-based molecular modelling in teaching chemistry, into the different working and teaching methods used, and their opinions about necessary…

Transient Macroscopic Chemistry in the DSMC Method

NASA Astrophysics Data System (ADS)

Goldsworthy, M. J.; Macrossan, M. N.; Abdel-Jawad, M.

2008-12-01

In the Direct Simulation Monte Carlo method, a combination of statistical and deterministic procedures applied to a finite number of `simulator' particles are used to model rarefied gas-kinetic processes. Traditionally, chemical reactions are modelled using information from specific colliding particle pairs. In the Macroscopic Chemistry Method (MCM), the reactions are decoupled from the specific particle pairs selected for collisions. Information from all of the particles within a cell is used to determine a reaction rate coefficient for that cell. MCM has previously been applied to steady flow DSMC simulations. Here we show how MCM can be used to model chemical kinetics in DSMC simulations of unsteady flow. Results are compared with a collision-based chemistry procedure for two binary reactions in a 1-D unsteady shock-expansion tube simulation and during the unsteady development of 2-D flow through a cavity. For the shock tube simulation, close agreement is demonstrated between the two methods for instantaneous, ensemble-averaged profiles of temperature and species mole fractions. For the cavity flow, a high degree of thermal non-equilibrium is present and non-equilibrium reaction rate correction factors are employed in MCM. Very close agreement is demonstrated for ensemble averaged mole fraction contours predicted by the particle and macroscopic methods at three different flow-times. A comparison of the accumulated number of net reactions per cell shows that both methods compute identical numbers of reaction events. For the 2-D flow, MCM required similar CPU and memory resources to the particle chemistry method. The Macroscopic Chemistry Method is applicable to any general DSMC code using any viscosity or non-reacting collision models and any non-reacting energy exchange models. MCM can be used to implement any reaction rate formulations, whether these be from experimental or theoretical studies.

Report of work done for technical assistance agreement 1269 between Sandia National Laboratories and the Watkins-Johnson Company: Chemical reaction mechanisms for computational models of SiO{sub 2} CVD

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

Ho, P.; Johannes, J.; Kudriavtsev, V.

The use of computational modeling to improve equipment and process designs for chemical vapor deposition (CVD) reactors is becoming increasingly common. Commercial codes are available that facilitate the modeling of chemically-reacting flows, but chemical reaction mechanisms must be separately developed for each system of interest. One f the products of the Watkins-Johnson Company (WJ) is a reactor marketed to semiconductor manufacturers for the atmospheric-pressure chemical vapor deposition (APCVD) of silicon oxide films. In this process, TEOS (tetraethoxysilane, Si(OC{sub 2}H{sub 5}){sub 4}) and ozone (O{sub 3}) are injected (in nitrogen and oxygen carrier gases) over hot silicon wafers that are beingmore » carried through the system on a moving belt. As part of their equipment improvement process, WJ is developing computational models of this tool. In this effort, they are collaborating with Sandia National Laboratories (SNL) to draw on Sandia`s experience base in understanding and modeling the chemistry of CVD processes.« less

Current and Future Critical Issues in Rocket Propulsion Systems

NASA Technical Reports Server (NTRS)

Navaz, Homayun K.; Dix, Jeff C.

1998-01-01

The objective of this research was to tackle several problems that are currently of great importance to NASA. In a liquid rocket engine several complex processes take place that are not thoroughly understood. Droplet evaporation, turbulence, finite rate chemistry, instability, and injection/atomization phenomena are some of the critical issues being encountered in a liquid rocket engine environment. Pulse Detonation Engines (PDE) performance, combustion chamber instability analysis, 60K motor flowfield pattern from hydrocarbon fuel combustion, and 3D flowfield analysis for the Combined Cycle engine were of special interest to NASA. During the summer of 1997, we made an attempt to generate computational results for all of the above problems and shed some light on understanding some of the complex physical phenomena. For this purpose, the Liquid Thrust Chamber Performance (LTCP) code, mainly designed for liquid rocket engine applications, was utilized. The following test cases were considered: (1) Characterization of a detonation wave in a Pulse Detonation Tube; (2) 60K Motor wall temperature studies; (3) Propagation of a pressure pulse in a combustion chamber (under single and two-phase flow conditions); (4) Transonic region flowfield analysis affected by viscous effects; (5) Exploring the viscous differences between a smooth and a corrugated wall; and (6) 3D thrust chamber flowfield analysis of the Combined Cycle engine. It was shown that the LTCP-2D and LTCP-3D codes are capable of solving complex and stiff conservation equations for gaseous and droplet phases in a very robust and efficient manner. These codes can be run on a workstation and personal computers (PC's).

Case Studies in Systems Chemistry. Final Report. [Includes Complete Case Study, Carboxylic Acid Equilibria

ERIC Educational Resources Information Center

Fleck, George

This publication was produced as a teaching tool for college chemistry. The book is a text for a computer-based unit on the chemistry of acid-base titrations, and is designed for use with FORTRAN or BASIC computer systems, and with a programmable electronic calculator, in a variety of educational settings. The text attempts to present computer…

Introduction to Computational Chemistry: Teaching Hu¨ckel Molecular Orbital Theory Using an Excel Workbook for Matrix Diagonalization

ERIC Educational Resources Information Center

Litofsky, Joshua; Viswanathan, Rama

2015-01-01

Matrix diagonalization, the key technique at the heart of modern computational chemistry for the numerical solution of the Schrödinger equation, can be easily introduced in the physical chemistry curriculum in a pedagogical context using simple Hückel molecular orbital theory for p bonding in molecules. We present details and results of…

Effects of Computer Based Learning on Students' Attitudes and Achievements towards Analytical Chemistry

ERIC Educational Resources Information Center

Akcay, Hüsamettin; Durmaz, Asli; Tüysüz, Cengiz; Feyzioglu, Burak

2006-01-01

The aim of this study was to compare the effects of computer-based learning and traditional method on students' attitudes and achievement towards analytical chemistry. Students from Chemistry Education Department at Dokuz Eylul University (D.E.U) were selected randomly and divided into three groups; two experimental (Eg-1 and Eg-2) and a control…

Reaction of formaldehyde at the ortho- and para-positions of phenol: exploration of mechanisms using computational chemistry.

Treesearch

Anthony H. Conner; Melissa S. Reeves

2001-01-01

Computational chemistry methods can be used to explore the theoretical chemistry behind reactive systems, to compare the relative chemical reactivity of different systems, and, by extension, to predict the reactivity of new systems. Ongoing research has focused on the reactivity of a wide variety of phenolic compounds with formaldehyde using semi-empirical and ab...

Workshop report on large-scale matrix diagonalization methods in chemistry theory institute

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

Bischof, C.H.; Shepard, R.L.; Huss-Lederman, S.

The Large-Scale Matrix Diagonalization Methods in Chemistry theory institute brought together 41 computational chemists and numerical analysts. The goal was to understand the needs of the computational chemistry community in problems that utilize matrix diagonalization techniques. This was accomplished by reviewing the current state of the art and looking toward future directions in matrix diagonalization techniques. This institute occurred about 20 years after a related meeting of similar size. During those 20 years the Davidson method continued to dominate the problem of finding a few extremal eigenvalues for many computational chemistry problems. Work on non-diagonally dominant and non-Hermitian problems asmore » well as parallel computing has also brought new methods to bear. The changes and similarities in problems and methods over the past two decades offered an interesting viewpoint for the success in this area. One important area covered by the talks was overviews of the source and nature of the chemistry problems. The numerical analysts were uniformly grateful for the efforts to convey a better understanding of the problems and issues faced in computational chemistry. An important outcome was an understanding of the wide range of eigenproblems encountered in computational chemistry. The workshop covered problems involving self- consistent-field (SCF), configuration interaction (CI), intramolecular vibrational relaxation (IVR), and scattering problems. In atomic structure calculations using the Hartree-Fock method (SCF), the symmetric matrices can range from order hundreds to thousands. These matrices often include large clusters of eigenvalues which can be as much as 25% of the spectrum. However, if Cl methods are also used, the matrix size can be between 10{sup 4} and 10{sup 9} where only one or a few extremal eigenvalues and eigenvectors are needed. Working with very large matrices has lead to the development of« less

Novel 3D/VR interactive environment for MD simulations, visualization and analysis.

PubMed

Doblack, Benjamin N; Allis, Tim; Dávila, Lilian P

2014-12-18

The increasing development of computing (hardware and software) in the last decades has impacted scientific research in many fields including materials science, biology, chemistry and physics among many others. A new computational system for the accurate and fast simulation and 3D/VR visualization of nanostructures is presented here, using the open-source molecular dynamics (MD) computer program LAMMPS. This alternative computational method uses modern graphics processors, NVIDIA CUDA technology and specialized scientific codes to overcome processing speed barriers common to traditional computing methods. In conjunction with a virtual reality system used to model materials, this enhancement allows the addition of accelerated MD simulation capability. The motivation is to provide a novel research environment which simultaneously allows visualization, simulation, modeling and analysis. The research goal is to investigate the structure and properties of inorganic nanostructures (e.g., silica glass nanosprings) under different conditions using this innovative computational system. The work presented outlines a description of the 3D/VR Visualization System and basic components, an overview of important considerations such as the physical environment, details on the setup and use of the novel system, a general procedure for the accelerated MD enhancement, technical information, and relevant remarks. The impact of this work is the creation of a unique computational system combining nanoscale materials simulation, visualization and interactivity in a virtual environment, which is both a research and teaching instrument at UC Merced.

Novel 3D/VR Interactive Environment for MD Simulations, Visualization and Analysis

PubMed Central

Doblack, Benjamin N.; Allis, Tim; Dávila, Lilian P.

2014-01-01

The increasing development of computing (hardware and software) in the last decades has impacted scientific research in many fields including materials science, biology, chemistry and physics among many others. A new computational system for the accurate and fast simulation and 3D/VR visualization of nanostructures is presented here, using the open-source molecular dynamics (MD) computer program LAMMPS. This alternative computational method uses modern graphics processors, NVIDIA CUDA technology and specialized scientific codes to overcome processing speed barriers common to traditional computing methods. In conjunction with a virtual reality system used to model materials, this enhancement allows the addition of accelerated MD simulation capability. The motivation is to provide a novel research environment which simultaneously allows visualization, simulation, modeling and analysis. The research goal is to investigate the structure and properties of inorganic nanostructures (e.g., silica glass nanosprings) under different conditions using this innovative computational system. The work presented outlines a description of the 3D/VR Visualization System and basic components, an overview of important considerations such as the physical environment, details on the setup and use of the novel system, a general procedure for the accelerated MD enhancement, technical information, and relevant remarks. The impact of this work is the creation of a unique computational system combining nanoscale materials simulation, visualization and interactivity in a virtual environment, which is both a research and teaching instrument at UC Merced. PMID:25549300

Using quantum chemistry muscle to flex massive systems: How to respond to something perturbing

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

Bertoni, Colleen

Computational chemistry uses the theoretical advances of quantum mechanics and the algorithmic and hardware advances of computer science to give insight into chemical problems. It is currently possible to do highly accurate quantum chemistry calculations, but the most accurate methods are very computationally expensive. Thus it is only feasible to do highly accurate calculations on small molecules, since typically more computationally efficient methods are also less accurate. The overall goal of my dissertation work has been to try to decrease the computational expense of calculations without decreasing the accuracy. In particular, my dissertation work focuses on fragmentation methods, intermolecular interactionsmore » methods, analytic gradients, and taking advantage of new hardware.« less

The role of computational chemistry in the science and measurements of the atmosphere

NASA Technical Reports Server (NTRS)

Phillips, D. H.

1978-01-01

The role of computational chemistry in determining the stability, photochemistry, spectroscopic parameters, and parameters for estimating reaction rates of atmospheric constituents is discussed. Examples dealing with the photolysis cross sections of HOCl and (1 Delta g) O2 and with the stability of gaseous NH4Cl and asymmetric ClO3 are presented. It is concluded that computational chemistry can play an important role in the study of atmospheric constituents, particularly reactive and short-lived species which are difficult to investigate experimentally.

Computational chemistry and aeroassisted orbital transfer vehicles

NASA Technical Reports Server (NTRS)

Cooper, D. M.; Jaffe, R. L.; Arnold, J. O.

1985-01-01

An analysis of the radiative heating phenomena encountered during a typical aeroassisted orbital transfer vehicle (AOTV) trajectory was made to determine the potential impact of computational chemistry on AOTV design technology. Both equilibrium and nonequilibrium radiation mechanisms were considered. This analysis showed that computational chemistry can be used to predict (1) radiative intensity factors and spectroscopic data; (2) the excitation rates of both atoms and molecules; (3) high-temperature reaction rate constants for metathesis and charge exchange reactions; (4) particle ionization and neutralization rates and cross sections; and (5) spectral line widths.

The Development of Computational Thinking in a High School Chemistry Course

ERIC Educational Resources Information Center

Matsumoto, Paul S.; Cao, Jiankang

2017-01-01

Computational thinking is a component of the Science and Engineering Practices in the Next Generation Science Standards, which were adopted by some states. We describe the activities in a high school chemistry course that may develop students' computational thinking skills by primarily using Excel, a widely available spreadsheet software. These…

Proceedings: Conference on Computers in Chemical Education and Research, Dekalb, Illinois, 19-23 July 1971.

ERIC Educational Resources Information Center

1971

Computers have effected a comprehensive transformation of chemistry. Computers have greatly enhanced the chemist's ability to do model building, simulations, data refinement and reduction, analysis of data in terms of models, on-line data logging, automated control of experiments, quantum chemistry and statistical and mechanical calculations, and…

Molecular Orbitals of NO, NO[superscript+], and NO[superscript-]: A Computational Quantum Chemistry Experiment

ERIC Educational Resources Information Center

Orenha, Renato P.; Galembeck, Sérgio E.

2014-01-01

This computational experiment presents qualitative molecular orbital (QMO) and computational quantum chemistry exercises of NO, NO[superscript+], and NO[superscript-]. Initially students explore several properties of the target molecules by Lewis diagrams and the QMO theory. Then, they compare qualitative conclusions with EHT and DFT calculations…

Development of Comprehensive Reduced Kinetic Models for Supersonic Reacting Shear Layer Simulations

NASA Technical Reports Server (NTRS)

Zambon, A. C.; Chelliah, H. K.; Drummond, J. P.

2006-01-01

Large-scale simulations of multi-dimensional unsteady turbulent reacting flows with detailed chemistry and transport can be computationally extremely intensive even on distributed computing architectures. With the development of suitable reduced chemical kinetic models, the number of scalar variables to be integrated can be decreased, leading to a significant reduction in the computational time required for the simulation with limited loss of accuracy in the results. A general MATLAB-based automated mechanism reduction procedure is presented to reduce any complex starting mechanism (detailed or skeletal) with minimal human intervention. Based on the application of the quasi steady-state (QSS) approximation for certain chemical species and on the elimination of the fast reaction rates in the mechanism, several comprehensive reduced models, capable of handling different fuels such as C2H4, CH4 and H2, have been developed and thoroughly tested for several combustion problems (ignition, propagation and extinction) and physical conditions (reactant compositions, temperatures, and pressures). A key feature of the present reduction procedure is the explicit solution of the concentrations of the QSS species, needed for the evaluation of the elementary reaction rates. In contrast, previous approaches relied on an implicit solution due to the strong coupling between QSS species, requiring computationally expensive inner iterations. A novel algorithm, based on the definition of a QSS species coupling matrix, is presented to (i) introduce appropriate truncations to the QSS algebraic relations and (ii) identify the optimal sequence for the explicit solution of the concentration of the QSS species. With the automatic generation of the relevant source code, the resulting reduced models can be readily implemented into numerical codes.

National resource for computation in chemistry, phase I: evaluation and recommendations

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

Not Available

1980-05-01

The National Resource for Computation in Chemistry (NRCC) was inaugurated at the Lawrence Berkeley Laboratory (LBL) in October 1977, with joint funding by the Department of Energy (DOE) and the National Science Foundation (NSF). The chief activities of the NRCC include: assembling a staff of eight postdoctoral computational chemists, establishing an office complex at LBL, purchasing a midi-computer and graphics display system, administering grants of computer time, conducting nine workshops in selected areas of computational chemistry, compiling a library of computer programs with adaptations and improvements, initiating a software distribution system, providing user assistance and consultation on request. This reportmore » presents assessments and recommendations of an Ad Hoc Review Committee appointed by the DOE and NSF in January 1980. The recommendations are that NRCC should: (1) not fund grants for computing time or research but leave that to the relevant agencies, (2) continue the Workshop Program in a mode similar to Phase I, (3) abandon in-house program development and establish instead a competitive external postdoctoral program in chemistry software development administered by the Policy Board and Director, and (4) not attempt a software distribution system (leaving that function to the QCPE). Furthermore, (5) DOE should continue to make its computational facilities available to outside users (at normal cost rates) and should find some way to allow the chemical community to gain occasional access to a CRAY-level computer.« less

Implementation of a 3D mixing layer code on parallel computers

NASA Technical Reports Server (NTRS)

Roe, K.; Thakur, R.; Dang, T.; Bogucz, E.

1995-01-01

This paper summarizes our progress and experience in the development of a Computational-Fluid-Dynamics code on parallel computers to simulate three-dimensional spatially-developing mixing layers. In this initial study, the three-dimensional time-dependent Euler equations are solved using a finite-volume explicit time-marching algorithm. The code was first programmed in Fortran 77 for sequential computers. The code was then converted for use on parallel computers using the conventional message-passing technique, while we have not been able to compile the code with the present version of HPF compilers.

Development and Formative Evaluation of Computer Simulated College Chemistry Experiments.

ERIC Educational Resources Information Center

Cavin, Claudia S.; Cavin, E. D.

1978-01-01

This article describes the design, preparation, and initial evaluation of a set of computer-simulated chemistry experiments. The experiments entailed the use of an atomic emission spectroscope and a single-beam visible absorption spectrophometer. (Author/IRT)

Research and Teaching: Computational Methods in General Chemistry--Perceptions of Programming, Prior Experience, and Student Outcomes

ERIC Educational Resources Information Center

Wheeler, Lindsay B.; Chiu, Jennie L.; Grisham, Charles M.

2016-01-01

This article explores how integrating computational tools into a general chemistry laboratory course can influence student perceptions of programming and investigates relationships among student perceptions, prior experience, and student outcomes.

The Computer Bulletin Board.

ERIC Educational Resources Information Center

Batt, Russell H., Ed.

1989-01-01

Describes two chemistry computer programs: (1) "Eureka: A Chemistry Problem Solver" (problem files may be written by the instructor, MS-DOS 2.0, IBM with 384K); and (2) "PC-File+" (database management, IBM with 416K and two floppy drives). (MVL)

Integrative Biological Chemistry Program Includes The Use Of Informatics Tools, GIS And SAS Software Applications

PubMed Central

D’Souza, Malcolm J.; Kashmar, Richard J.; Hurst, Kent; Fiedler, Frank; Gross, Catherine E.; Deol, Jasbir K.; Wilson, Alora

2015-01-01

Wesley College is a private, primarily undergraduate minority-serving institution located in the historic district of Dover, Delaware (DE). The College recently revised its baccalaureate biological chemistry program requirements to include a one-semester Physical Chemistry for the Life Sciences course and project-based experiential learning courses using instrumentation, data-collection, data-storage, statistical-modeling analysis, visualization, and computational techniques. In this revised curriculum, students begin with a traditional set of biology, chemistry, physics, and mathematics major core-requirements, a geographic information systems (GIS) course, a choice of an instrumental analysis course or a statistical analysis systems (SAS) programming course, and then, students can add major-electives that further add depth and value to their future post-graduate specialty areas. Open-sourced georeferenced census, health and health disparity data were coupled with GIS and SAS tools, in a public health surveillance system project, based on US county zip-codes, to develop use-cases for chronic adult obesity where income, poverty status, health insurance coverage, education, and age were categorical variables. Across the 48 contiguous states, obesity rates are found to be directly proportional to high poverty and inversely proportional to median income and educational achievement. For the State of Delaware, age and educational attainment were found to be limiting obesity risk-factors in its adult population. Furthermore, the 2004–2010 obesity trends showed that for two of the less densely populated Delaware counties; Sussex and Kent, the rates of adult obesity were found to be progressing at much higher proportions when compared to the national average. PMID:26191337

Integrative Biological Chemistry Program Includes The Use Of Informatics Tools, GIS And SAS Software Applications.

PubMed

D'Souza, Malcolm J; Kashmar, Richard J; Hurst, Kent; Fiedler, Frank; Gross, Catherine E; Deol, Jasbir K; Wilson, Alora

Wesley College is a private, primarily undergraduate minority-serving institution located in the historic district of Dover, Delaware (DE). The College recently revised its baccalaureate biological chemistry program requirements to include a one-semester Physical Chemistry for the Life Sciences course and project-based experiential learning courses using instrumentation, data-collection, data-storage, statistical-modeling analysis, visualization, and computational techniques. In this revised curriculum, students begin with a traditional set of biology, chemistry, physics, and mathematics major core-requirements, a geographic information systems (GIS) course, a choice of an instrumental analysis course or a statistical analysis systems (SAS) programming course, and then, students can add major-electives that further add depth and value to their future post-graduate specialty areas. Open-sourced georeferenced census, health and health disparity data were coupled with GIS and SAS tools, in a public health surveillance system project, based on US county zip-codes, to develop use-cases for chronic adult obesity where income, poverty status, health insurance coverage, education, and age were categorical variables. Across the 48 contiguous states, obesity rates are found to be directly proportional to high poverty and inversely proportional to median income and educational achievement. For the State of Delaware, age and educational attainment were found to be limiting obesity risk-factors in its adult population. Furthermore, the 2004-2010 obesity trends showed that for two of the less densely populated Delaware counties; Sussex and Kent, the rates of adult obesity were found to be progressing at much higher proportions when compared to the national average.

Development of an Undergraduate Course in the Use of Digital Computers With Chemistry Instrumentation.

ERIC Educational Resources Information Center

Wilkins, Charles L.

Computer-assisted instruction (CAI) has proven useful in teaching chemistry instrumentation techniques to undergraduate students. The work completed at the time of this interim report has clearly shown that a general purpose laboratory computer system, equipped with suitable devices to allow direct data input from experiments, can be an effective…

Chemical Equilibrium, Unit 2: Le Chatelier's Principle. A Computer-Enriched Module for Introductory Chemistry. Student's Guide and Teacher's Guide.

ERIC Educational Resources Information Center

Jameson, A. Keith

Presented are the teacher's guide and student materials for one of a series of self-instructional, computer-based learning modules for an introductory, undergraduate chemistry course. The student manual for this unit on Le Chatelier's principle includes objectives, prerequisites, pretest, instructions for executing the computer program, and…

Using Free Computational Resources to Illustrate the Drug Design Process in an Undergraduate Medicinal Chemistry Course

ERIC Educational Resources Information Center

Rodrigues, Ricardo P.; Andrade, Saulo F.; Mantoani, Susimaire P.; Eifler-Lima, Vera L.; Silva, Vinicius B.; Kawano, Daniel F.

2015-01-01

Advances in, and dissemination of, computer technologies in the field of drug research now enable the use of molecular modeling tools to teach important concepts of drug design to chemistry and pharmacy students. A series of computer laboratories is described to introduce undergraduate students to commonly adopted "in silico" drug design…

The Use of Modular Computer-Based Lessons in a Modification of the Classical Introductory Course in Organic Chemistry.

ERIC Educational Resources Information Center

Stotter, Philip L.; Culp, George H.

An experimental course in organic chemistry utilized computer-assisted instructional (CAI) techniques. The CAI lessons provided tutorial drill and practice and simulated experiments and reactions. The Conversational Language for Instruction and Computing was used, along with a CDC 6400-6600 system; students scheduled and completed the lessons at…

CHEMEX; Understanding and Solving Problems in Chemistry. A Computer-Assisted Instruction Program for General Chemistry.

ERIC Educational Resources Information Center

Lower, Stephen K.

A brief overview of CHEMEX--a problem-solving, tutorial style computer-assisted instructional course--is provided and sample problems are offered. In CHEMEX, students receive problems in advance and attempt to solve them before moving through the computer program, which assists them in overcoming difficulties and serves as a review mechanism.…

The Impact of Learner's Prior Knowledge on Their Use of Chemistry Computer Simulations: A Case Study

ERIC Educational Resources Information Center

Liu, Han-Chin; Andre, Thomas; Greenbowe, Thomas

2008-01-01

It is complicated to design a computer simulation that adapts to students with different characteristics. This study documented cases that show how college students' prior chemistry knowledge level affected their interaction with peers and their approach to solving problems with the use of computer simulations that were designed to learn…

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.

Numerical simulation of weakly ionized hypersonic flow over reentry capsules

NASA Astrophysics Data System (ADS)

Scalabrin, Leonardo C.

The mathematical and numerical formulation employed in the development of a new multi-dimensional Computational Fluid Dynamics (CFD) code for the simulation of weakly ionized hypersonic flows in thermo-chemical non-equilibrium over reentry configurations is presented. The flow is modeled using the Navier-Stokes equations modified to include finite-rate chemistry and relaxation rates to compute the energy transfer between different energy modes. The set of equations is solved numerically by discretizing the flowfield using unstructured grids made of any mixture of quadrilaterals and triangles in two-dimensions or hexahedra, tetrahedra, prisms and pyramids in three-dimensions. The partial differential equations are integrated on such grids using the finite volume approach. The fluxes across grid faces are calculated using a modified form of the Steger-Warming Flux Vector Splitting scheme that has low numerical dissipation inside boundary layers. The higher order extension of inviscid fluxes in structured grids is generalized in this work to be used in unstructured grids. Steady state solutions are obtained by integrating the solution over time implicitly. The resulting sparse linear system is solved by using a point implicit or by a line implicit method in which a tridiagonal matrix is assembled by using lines of cells that are formed starting at the wall. An algorithm that assembles these lines using completely general unstructured grids is developed. The code is parallelized to allow simulation of computationally demanding problems. The numerical code is successfully employed in the simulation of several hypersonic entry flows over space capsules as part of its validation process. Important quantities for the aerothermodynamics design of capsules such as aerodynamic coefficients and heat transfer rates are compared to available experimental and flight test data and other numerical results yielding very good agreement. A sensitivity analysis of predicted radiative heating of a space capsule to several thermo-chemical non-equilibrium models is also performed.

Supercomputing with TOUGH2 family codes for coupled multi-physics simulations of geologic carbon sequestration

NASA Astrophysics Data System (ADS)

Yamamoto, H.; Nakajima, K.; Zhang, K.; Nanai, S.

2015-12-01

Powerful numerical codes that are capable of modeling complex coupled processes of physics and chemistry have been developed for predicting the fate of CO2 in reservoirs as well as its potential impacts on groundwater and subsurface environments. However, they are often computationally demanding for solving highly non-linear models in sufficient spatial and temporal resolutions. Geological heterogeneity and uncertainties further increase the challenges in modeling works. Two-phase flow simulations in heterogeneous media usually require much longer computational time than that in homogeneous media. Uncertainties in reservoir properties may necessitate stochastic simulations with multiple realizations. Recently, massively parallel supercomputers with more than thousands of processors become available in scientific and engineering communities. Such supercomputers may attract attentions from geoscientist and reservoir engineers for solving the large and non-linear models in higher resolutions within a reasonable time. However, for making it a useful tool, it is essential to tackle several practical obstacles to utilize large number of processors effectively for general-purpose reservoir simulators. We have implemented massively-parallel versions of two TOUGH2 family codes (a multi-phase flow simulator TOUGH2 and a chemically reactive transport simulator TOUGHREACT) on two different types (vector- and scalar-type) of supercomputers with a thousand to tens of thousands of processors. After completing implementation and extensive tune-up on the supercomputers, the computational performance was measured for three simulations with multi-million grid models, including a simulation of the dissolution-diffusion-convection process that requires high spatial and temporal resolutions to simulate the growth of small convective fingers of CO2-dissolved water to larger ones in a reservoir scale. The performance measurement confirmed that the both simulators exhibit excellent scalabilities showing almost linear speedup against number of processors up to over ten thousand cores. Generally this allows us to perform coupled multi-physics (THC) simulations on high resolution geologic models with multi-million grid in a practical time (e.g., less than a second per time step).

40 CFR 194.23 - Models and computer codes.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 26 2013-07-01 2013-07-01 false Models and computer codes. 194.23... General Requirements § 194.23 Models and computer codes. (a) Any compliance application shall include: (1... obtain stable solutions; (iv) Computer models accurately implement the numerical models; i.e., computer...

40 CFR 194.23 - Models and computer codes.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 26 2012-07-01 2011-07-01 true Models and computer codes. 194.23... General Requirements § 194.23 Models and computer codes. (a) Any compliance application shall include: (1... obtain stable solutions; (iv) Computer models accurately implement the numerical models; i.e., computer...

40 CFR 194.23 - Models and computer codes.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 25 2014-07-01 2014-07-01 false Models and computer codes. 194.23... General Requirements § 194.23 Models and computer codes. (a) Any compliance application shall include: (1... obtain stable solutions; (iv) Computer models accurately implement the numerical models; i.e., computer...

40 CFR 194.23 - Models and computer codes.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 24 2010-07-01 2010-07-01 false Models and computer codes. 194.23... General Requirements § 194.23 Models and computer codes. (a) Any compliance application shall include: (1... obtain stable solutions; (iv) Computer models accurately implement the numerical models; i.e., computer...

40 CFR 194.23 - Models and computer codes.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 25 2011-07-01 2011-07-01 false Models and computer codes. 194.23... General Requirements § 194.23 Models and computer codes. (a) Any compliance application shall include: (1... obtain stable solutions; (iv) Computer models accurately implement the numerical models; i.e., computer...

Text Analysis of Chemistry Thesis and Dissertation Titles

ERIC Educational Resources Information Center

Scalfani, Vincent F.

2017-01-01

Programmatic text analysis can be used to understand patterns and reveal trends in data that would otherwise be difficult or impossible to uncover with manual coding methods. This work uses programmatic text analysis, specifically term frequency counts, to study nearly 10,000 chemistry thesis and dissertation titles from 1911-2015. The thesis and…

Building "My First NMRviewer": A Project Incorporating Coding and Programming Tasks in the Undergraduate Chemistry Curricula

ERIC Educational Resources Information Center

Arrabal-Campos, Francisco M.; Cortés-Villena, Alejandro; Fernández, Ignacio

2017-01-01

This paper presents a programming project named NMRviewer that allows students to visualize transformed and processed 1 H NMR data in an accessible, interactive format while allowing instructors to incorporate programming content into the chemistry curricula. Using the MATLAB graphical user interface development environment (GUIDE), students can…

Argumentation and Participation Patterns in General Chemistry Peer-Led Sessions

ERIC Educational Resources Information Center

Kulatunga, Ushiri; Moog, Richard S.; Lewis, Jennifer E.

2013-01-01

This article focuses on the use of Toulmin's argumentation scheme to investigate the characteristics of student group argumentation in Peer-Led Guided Inquiry sessions for a General Chemistry I course. A coding scheme based on Toulmin's [Toulmin [1958] "The uses of argument." Cambridge: Cambridge University Press] argumentation…

Collaboration and critical thinking in an online chemistry environment

NASA Astrophysics Data System (ADS)

Kershisnik, Elizabeth Irene

The purpose of this dissertation was to examine collaboration and student's critical thinking and cognitive achievement within online chemistry courses. This quantitative study focused on the apparent lack of research relating collaboration and critical thinking in online science courses. Collaboration was determined using the small group collaboration model coding scheme, which examined student postings in asynchronous discussion forums for quantity, equality, and shareness. Critical thinking was measured using the chemistry concept reasoning test, the online self-diagnostic test, and also asynchronous student homework discussion postings that were coded using the community of inquiry cognitive presence indicators. Finally cognitive achievement was determined using quiz scores and the student's final grade. Even though no significant findings were revealed in this exploratory quasi-experimental study, this research did add to the educational technology knowledge base since very few studies have investigated the chemistry discipline in an online environment. Continued research in this area is vital to understanding how critical thinking progresses, how it can be assessed, and what factors in the classroom, be it virtual or face-to-face, have the greatest effect on critical thinking.

Programs for Fundamentals of Chemistry.

ERIC Educational Resources Information Center

Gallardo, Julio; Delgado, Steven

This document provides computer programs, written in BASIC PLUS, for presenting fundamental or remedial college chemistry students with chemical problems in a computer assisted instructional program. Programs include instructions, a sample run, and 14 separate practice sessions covering: mathematical operations, using decimals, solving…

Laboratory manual: mineral X-ray diffraction data retrieval/plot computer program

USGS Publications Warehouse

Hauff, Phoebe L.; VanTrump, George

1976-01-01

The Mineral X-Ray Diffraction Data Retrieval/Plot Computer Program--XRDPLT (VanTrump and Hauff, 1976a) is used to retrieve and plot mineral X-ray diffraction data. The program operates on a file of mineral powder diffraction data (VanTrump and Hauff, 1976b) which contains two-theta or 'd' values, and intensities, chemical formula, mineral name, identification number, and mineral group code. XRDPLT is a machine-independent Fortran program which operates in time-sharing mode on a DEC System i0 computer and the Gerber plotter (Evenden, 1974). The program prompts the user to respond from a time-sharing terminal in a conversational format with the required input information. The program offers two major options: retrieval only; retrieval and plot. The first option retrieves mineral names, formulas, and groups from the file by identification number, by the mineral group code (a classification by chemistry or structure), or by searches based on the formula components. For example, it enables the user to search for minerals by major groups (i.e., feldspars, micas, amphiboles, oxides, phosphates, carbonates) by elemental composition (i.e., Fe, Cu, AI, Zn), or by a combination of these (i.e., all copper-bearing arsenates). The second option retrieves as the first, but also plots the retrieved 2-theta and intensity values as diagrammatic X-ray powder patterns on mylar sheets or overlays. These plots can be made using scale combinations compatible with chart recorder diffractograms and 114.59 mm powder camera films. The overlays are then used to separate or sieve out unrelated minerals until unknowns are matched and identified.

[Advancements of computer chemistry in separation of Chinese medicine].

PubMed

Li, Lingjuan; Hong, Hong; Xu, Xuesong; Guo, Liwei

2011-12-01

Separating technique of Chinese medicine is not only a key technique in the field of Chinese medicine' s research and development, but also a significant step in the modernization of Chinese medicinal preparation. Computer chemistry can build model and look for the regulations from Chinese medicine system which is full of complicated data. This paper analyzed the applicability, key technology, basic mode and common algorithm of computer chemistry applied in the separation of Chinese medicine, introduced the mathematic mode and the setting methods of Extraction kinetics, investigated several problems which based on traditional Chinese medicine membrane procession, and forecasted the application prospect.

Fermion-to-qubit mappings with varying resource requirements for quantum simulation

NASA Astrophysics Data System (ADS)

Steudtner, Mark; Wehner, Stephanie

2018-06-01

The mapping of fermionic states onto qubit states, as well as the mapping of fermionic Hamiltonian into quantum gates enables us to simulate electronic systems with a quantum computer. Benefiting the understanding of many-body systems in chemistry and physics, quantum simulation is one of the great promises of the coming age of quantum computers. Interestingly, the minimal requirement of qubits for simulating Fermions seems to be agnostic of the actual number of particles as well as other symmetries. This leads to qubit requirements that are well above the minimal requirements as suggested by combinatorial considerations. In this work, we develop methods that allow us to trade-off qubit requirements against the complexity of the resulting quantum circuit. We first show that any classical code used to map the state of a fermionic Fock space to qubits gives rise to a mapping of fermionic models to quantum gates. As an illustrative example, we present a mapping based on a nonlinear classical error correcting code, which leads to significant qubit savings albeit at the expense of additional quantum gates. We proceed to use this framework to present a number of simpler mappings that lead to qubit savings with a more modest increase in gate difficulty. We discuss the role of symmetries such as particle conservation, and savings that could be obtained if an experimental platform could easily realize multi-controlled gates.

New algorithm for tensor contractions on multi-core CPUs, GPUs, and accelerators enables CCSD and EOM-CCSD calculations with over 1000 basis functions on a single compute node.

PubMed

Kaliman, Ilya A; Krylov, Anna I

2017-04-30

A new hardware-agnostic contraction algorithm for tensors of arbitrary symmetry and sparsity is presented. The algorithm is implemented as a stand-alone open-source code libxm. This code is also integrated with general tensor library libtensor and with the Q-Chem quantum-chemistry package. An overview of the algorithm, its implementation, and benchmarks are presented. Similarly to other tensor software, the algorithm exploits efficient matrix multiplication libraries and assumes that tensors are stored in a block-tensor form. The distinguishing features of the algorithm are: (i) efficient repackaging of the individual blocks into large matrices and back, which affords efficient graphics processing unit (GPU)-enabled calculations without modifications of higher-level codes; (ii) fully asynchronous data transfer between disk storage and fast memory. The algorithm enables canonical all-electron coupled-cluster and equation-of-motion coupled-cluster calculations with single and double substitutions (CCSD and EOM-CCSD) with over 1000 basis functions on a single quad-GPU machine. We show that the algorithm exhibits predicted theoretical scaling for canonical CCSD calculations, O(N 6 ), irrespective of the data size on disk. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Protein Engineering: Development of a Metal Ion Dependent Switch

DTIC Science & Technology

2017-05-22

Society of Chemistry Royal Society of Chemistry Biochemistry PNAS Escherichia coli Journal of Biotechnology Biochemistry Nature Protocols Journal of...Molecular Biology Biochemistry Royal Society of Chemistry Proteins: Structure, Function, and Bioinformatics Journal of Molecular Biology Biophysical...Biophysical Journal Protein Science Journal of Computational Chemistry Current Opinion in Chemical Biology Royal Society of Chemistry

Computational chemistry for NH 3 synthesis, hydrotreating, and NO x reduction: Three topics of special interest to Haldor Topsøe

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

Elnabawy, Ahmed O.; Rangarajan, Srinivas; Mavrikakis, Manos

Computational chemistry, especially density functional theory, has experienced a remarkable growth in terms of application over the last few decades. This is attributed to the improvements in theory and computing infrastructure that enable the analysis of systems of unprecedented size and detail at an affordable computational expense. In this perspective, we discuss recent progress and current challenges facing electronic structure theory in the context of heterogeneous catalysis. We specifically focus on the impact of computational chemistry in elucidating and designing catalytic systems in three topics of interest to Haldor Topsøe – ammonia, synthesis, hydrotreating, and NO x reduction. Furthermore, wemore » then discuss the common tools and concepts in computational catalysis that underline these topics and provide a perspective on the challenges and future directions of research in this area of catalysis research.« less

Computational chemistry for NH 3 synthesis, hydrotreating, and NO x reduction: Three topics of special interest to Haldor Topsøe

DOE PAGES

Elnabawy, Ahmed O.; Rangarajan, Srinivas; Mavrikakis, Manos

2015-06-05

Computational chemistry, especially density functional theory, has experienced a remarkable growth in terms of application over the last few decades. This is attributed to the improvements in theory and computing infrastructure that enable the analysis of systems of unprecedented size and detail at an affordable computational expense. In this perspective, we discuss recent progress and current challenges facing electronic structure theory in the context of heterogeneous catalysis. We specifically focus on the impact of computational chemistry in elucidating and designing catalytic systems in three topics of interest to Haldor Topsøe – ammonia, synthesis, hydrotreating, and NO x reduction. Furthermore, wemore » then discuss the common tools and concepts in computational catalysis that underline these topics and provide a perspective on the challenges and future directions of research in this area of catalysis research.« less

Computer Based Instructional Techniques in Undergraduate Introductory Organic Chemistry: Rationale, Developmental Techniques, Programming Strategies and Evaluation.

ERIC Educational Resources Information Center

Culp, G. H.; And Others

Over 100 interactive computer programs for use in general and organic chemistry at the University of Texas at Austin have been prepared. The rationale for the programs is based upon the belief that computer-assisted instruction (CAI) can improve education by, among other things, freeing teachers from routine tasks, measuring entry skills,…

Non-adiabatic Excited State Molecule Dynamics Modeling of Photochemistry and Photophysics of Materials

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

Nelson, Tammie Renee; Tretiak, Sergei

2017-01-06

Understanding and controlling excited state dynamics lies at the heart of all our efforts to design photoactive materials with desired functionality. This tailor-design approach has become the standard for many technological applications (e.g., solar energy harvesting) including the design of organic conjugated electronic materials with applications in photovoltaic and light-emitting devices. Over the years, our team has developed efficient LANL-based codes to model the relevant photophysical processes following photoexcitation (spatial energy transfer, excitation localization/delocalization, and/or charge separation). The developed approach allows the non-radiative relaxation to be followed on up to ~10 ps timescales for large realistic molecules (hundreds of atomsmore » in size) in the realistic solvent dielectric environment. The Collective Electronic Oscillator (CEO) code is used to compute electronic excited states, and the Non-adiabatic Excited State Molecular Dynamics (NA-ESMD) code is used to follow the non-adiabatic dynamics on multiple coupled Born-Oppenheimer potential energy surfaces. Our preliminary NA-ESMD simulations have revealed key photoinduced mechanisms controlling competing interactions and relaxation pathways in complex materials, including organic conjugated polymer materials, and have provided a detailed understanding of photochemical products and intermediates and the internal conversion process during the initiation of energetic materials. This project will be using LANL-based CEO and NA-ESMD codes to model nonradiative relaxation in organic and energetic materials. The NA-ESMD and CEO codes belong to a class of electronic structure/quantum chemistry codes that require large memory, “long-queue-few-core” distribution of resources in order to make useful progress. The NA-ESMD simulations are trivially parallelizable requiring ~300 processors for up to one week runtime to reach a meaningful restart point.« less

Atomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS)

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

Perkins, Stephen J.; Wright, David W.; Zhang, Hailiang

2016-10-14

The capabilities of current computer simulations provide a unique opportunity to model small-angle scattering (SAS) data at the atomistic level, and to include other structural constraints ranging from molecular and atomistic energetics to crystallography, electron microscopy and NMR. This extends the capabilities of solution scattering and provides deeper insights into the physics and chemistry of the systems studied. Realizing this potential, however, requires integrating the experimental data with a new generation of modelling software. To achieve this, the CCP-SAS collaboration (http://www.ccpsas.org/) is developing open-source, high-throughput and user-friendly software for the atomistic and coarse-grained molecular modelling of scattering data. Robust state-of-the-artmore » molecular simulation engines and molecular dynamics and Monte Carlo force fields provide constraints to the solution structure inferred from the small-angle scattering data, which incorporates the known physical chemistry of the system. The implementation of this software suite involves a tiered approach in whichGenAppprovides the deployment infrastructure for running applications on both standard and high-performance computing hardware, andSASSIEprovides a workflow framework into which modules can be plugged to prepare structures, carry out simulations, calculate theoretical scattering data and compare results with experimental data.GenAppproduces the accessible web-based front end termedSASSIE-web, andGenAppandSASSIEalso make community SAS codes available. Applications are illustrated by case studies: (i) inter-domain flexibility in two- to six-domain proteins as exemplified by HIV-1 Gag, MASP and ubiquitin; (ii) the hinge conformation in human IgG2 and IgA1 antibodies; (iii) the complex formed between a hexameric protein Hfq and mRNA; and (iv) synthetic `bottlebrush' polymers.« less

Atomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS).

PubMed

Perkins, Stephen J; Wright, David W; Zhang, Hailiang; Brookes, Emre H; Chen, Jianhan; Irving, Thomas C; Krueger, Susan; Barlow, David J; Edler, Karen J; Scott, David J; Terrill, Nicholas J; King, Stephen M; Butler, Paul D; Curtis, Joseph E

2016-12-01

The capabilities of current computer simulations provide a unique opportunity to model small-angle scattering (SAS) data at the atomistic level, and to include other structural constraints ranging from molecular and atomistic energetics to crystallography, electron microscopy and NMR. This extends the capabilities of solution scattering and provides deeper insights into the physics and chemistry of the systems studied. Realizing this potential, however, requires integrating the experimental data with a new generation of modelling software. To achieve this, the CCP-SAS collaboration (http://www.ccpsas.org/) is developing open-source, high-throughput and user-friendly software for the atomistic and coarse-grained molecular modelling of scattering data. Robust state-of-the-art molecular simulation engines and molecular dynamics and Monte Carlo force fields provide constraints to the solution structure inferred from the small-angle scattering data, which incorporates the known physical chemistry of the system. The implementation of this software suite involves a tiered approach in which GenApp provides the deployment infrastructure for running applications on both standard and high-performance computing hardware, and SASSIE provides a workflow framework into which modules can be plugged to prepare structures, carry out simulations, calculate theoretical scattering data and compare results with experimental data. GenApp produces the accessible web-based front end termed SASSIE-web , and GenApp and SASSIE also make community SAS codes available. Applications are illustrated by case studies: (i) inter-domain flexibility in two- to six-domain proteins as exemplified by HIV-1 Gag, MASP and ubiquitin; (ii) the hinge conformation in human IgG2 and IgA1 antibodies; (iii) the complex formed between a hexameric protein Hfq and mRNA; and (iv) synthetic 'bottlebrush' polymers.

Computer Description of Black Hawk Helicopter

DTIC Science & Technology

1979-06-01

Model Combinatorial Geometry Models Black Hawk Helicopter Helicopter GIFT Computer Code Geometric Description of Targets 20. ABSTRACT...description was made using the technique of combinatorial geometry (COM-GEOM) and will be used as input to the GIFT computer code which generates Tliic...rnHp The data used bv the COVART comtmter code was eenerated bv the Geometric Information for Targets ( GIFT )Z computer code. This report documents

[Computational chemistry in structure-based drug design].

PubMed

Cao, Ran; Li, Wei; Sun, Han-Zi; Zhou, Yu; Huang, Niu

2013-07-01

Today, the understanding of the sequence and structure of biologically relevant targets is growing rapidly and researchers from many disciplines, physics and computational science in particular, are making significant contributions to modern biology and drug discovery. However, it remains challenging to rationally design small molecular ligands with desired biological characteristics based on the structural information of the drug targets, which demands more accurate calculation of ligand binding free-energy. With the rapid advances in computer power and extensive efforts in algorithm development, physics-based computational chemistry approaches have played more important roles in structure-based drug design. Here we reviewed the newly developed computational chemistry methods in structure-based drug design as well as the elegant applications, including binding-site druggability assessment, large scale virtual screening of chemical database, and lead compound optimization. Importantly, here we address the current bottlenecks and propose practical solutions.

Impact of 3-D orographic gravity wave parameterisation on stratosphere dynamics

NASA Astrophysics Data System (ADS)

Eichinger, Roland; Garny, Hella; Cai, Duy; Jöckel, Patrick

2017-04-01

Stratosphere dynamics are strongly influenced by gravity waves (GWs) propagating upwards from the troposphere. Some of these GWs are generated through flow over small-scale orography and can not be resolved by common general circulation models (GCMs). Due to computational model designs, their parameterisation usually follows a one dimensional columnar approach that, among other simplifications, neglects the horizontal propagation of GWs on their way up into the Middle Atmosphere. This causes contradictions between models and observations in location and strength of GW drag force through their dissipation and as a consequence, also in stratospheric mean flow. In the EMAC (ECHAM MESSy Atmospheric Chemistry) model, we have found this deficiency to cause a too weak Antarctic polar vortex, which directly impacts stratospheric temperatures and thereby the chemical reactions that determine ozone depletion. For this reason, we adapt a three dimensional parameterisation for orographic GWs, that had been implemented and tested in the MIROC GCM, to the MESSy coding standard. This computationally light scheme can then be used in a modular and flexible way in a cascade of model setups from an idealised version for conceptional process analyses to full climate chemistry simulations for quantitative investigations. This model enhancement can help to reconcile models and observations in wave drag forcing itself, but in consequence, also in Brewer-Dobson Circulation trends across the recent decades. Furthermore, uncertainties in weather and climate predictions as well as in future ozone projections can be reduced.

User manual for semi-circular compact range reflector code: Version 2

NASA Technical Reports Server (NTRS)

Gupta, Inder J.; Burnside, Walter D.

1987-01-01

A computer code has been developed at the Ohio State University ElectroScience Laboratory to analyze a semi-circular paraboloidal reflector with or without a rolled edge at the top and a skirt at the bottom. The code can be used to compute the total near field of the reflector or its individual components at a given distance from the center of the paraboloid. The code computes the fields along a radial, horizontal, vertical or axial cut at that distance. Thus, it is very effective in computing the size of the sweet spot for a semi-circular compact range reflector. This report describes the operation of the code. Various input and output statements are explained. Some results obtained using the computer code are presented to illustrate the code's capability as well as being samples of input/output sets.

Development of the Orion Crew Module Static Aerodynamic Database. Part 1; Hypersonic

NASA Technical Reports Server (NTRS)

Bibb, Karen L.; Walker, Eric L.; Robinson, Philip E.

2011-01-01

The Orion aerodynamic database provides force and moment coefficients given the velocity, attitude, configuration, etc. of the Crew Exploration Vehicle (CEV). The database is developed and maintained by the NASA CEV Aerosciences Project team from computational and experimental aerodynamic simulations. The database is used primarily by the Guidance, Navigation, and Control (GNC) team to design vehicle trajectories and assess flight performance. The initial hypersonic re-entry portion of the Crew Module (CM) database was developed in 2006. Updates incorporating additional data and improvements to the database formulation and uncertainty methodologies have been made since then. This paper details the process used to develop the CM database, including nominal values and uncertainties, for Mach numbers greater than 8 and angles of attack between 140deg and 180deg. The primary available data are more than 1000 viscous, reacting gas chemistry computational simulations using both the Laura and Dplr codes, over a range of Mach numbers from 2 to 37 and a range of angles of attack from 147deg to 172deg. Uncertainties were based on grid convergence, laminar-turbulent solution variations, combined altitude and code-to-code variations, and expected heatshield asymmetry. A radial basis function response surface tool, NEAR-RS, was used to fit the coefficient data smoothly in a velocity-angle-of-attack space. The resulting database is presented and includes some data comparisons and a discussion of the predicted variation of trim angle of attack and lift-to-drag ratio. The database provides a variation in trim angle of attack on the order of +/-2deg, and a range in lift-to-drag ratio of +/-0.035 for typical vehicle flight conditions.

LABORATORY AND COMPUTATIONAL INVESTIGATIONS OF THE ATMOSPHERIC CHEMISTRY OF KEY OXIDATION PRODUCTS CONTROLLING TROPOSPHERIC OZONE FORMATION

EPA Science Inventory

Major uncertainties remain in our ability to identify the key reactions and primary oxidation products of volatile hydrocarbons that contribute to ozone formation in the troposphere. To reduce these uncertainties, computational chemistry, mechanistic and process analysis techniqu...

Chemical calculations on Cray computers

NASA Technical Reports Server (NTRS)

Taylor, Peter R.; Bauschlicher, Charles W., Jr.; Schwenke, David W.

1989-01-01

The influence of recent developments in supercomputing on computational chemistry is discussed with particular reference to Cray computers and their pipelined vector/limited parallel architectures. After reviewing Cray hardware and software the performance of different elementary program structures are examined, and effective methods for improving program performance are outlined. The computational strategies appropriate for obtaining optimum performance in applications to quantum chemistry and dynamics are discussed. Finally, some discussion is given of new developments and future hardware and software improvements.

Hanford meteorological station computer codes: Volume 9, The quality assurance computer codes

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

Burk, K.W.; Andrews, G.L.

1989-02-01

The Hanford Meteorological Station (HMS) was established in 1944 on the Hanford Site to collect and archive meteorological data and provide weather forecasts and related services for Hanford Site approximately 1/2 mile east of the 200 West Area and is operated by PNL for the US Department of Energy. Meteorological data are collected from various sensors and equipment located on and off the Hanford Site. These data are stored in data bases on the Digital Equipment Corporation (DEC) VAX 11/750 at the HMS (hereafter referred to as the HMS computer). Files from those data bases are routinely transferred to themore » Emergency Management System (EMS) computer at the Unified Dose Assessment Center (UDAC). To ensure the quality and integrity of the HMS data, a set of Quality Assurance (QA) computer codes has been written. The codes will be routinely used by the HMS system manager or the data base custodian. The QA codes provide detailed output files that will be used in correcting erroneous data. The following sections in this volume describe the implementation and operation of QA computer codes. The appendices contain detailed descriptions, flow charts, and source code listings of each computer code. 2 refs.« less

Supercomputing in Aerospace

NASA Technical Reports Server (NTRS)

Kutler, Paul; Yee, Helen

1987-01-01

Topics addressed include: numerical aerodynamic simulation; computational mechanics; supercomputers; aerospace propulsion systems; computational modeling in ballistics; turbulence modeling; computational chemistry; computational fluid dynamics; and computational astrophysics.

Chemistry Notes.

ERIC Educational Resources Information Center

School Science Review, 1983

1983-01-01

Presents background information, laboratory procedures, classroom materials/activities, and chemistry experiments. Topics include sublimation, electronegativity, electrolysis, experimental aspects of strontianite, halide test, evaluation of present and future computer programs in chemistry, formula building, care of glass/saturated calomel…

Effect of Material Ion Exchanges on the Mechanical Stiffness Properties and Shear Deformation of Hydrated Cement Material Chemistry Structure C-S-H Jennit - A Computational Modeling Study

DTIC Science & Technology

2014-01-01

Study Material properties and performance are governed by material molecular chemistry structures and molecular level interactions. Methods to...understand relationships between the material properties and performance and their correlation to the molecular level chemistry and morphology, and thus...find ways of manipulating and adjusting matters at the atomistic level in order to improve material performance are required. A computational material

User's manual for semi-circular compact range reflector code

NASA Technical Reports Server (NTRS)

Gupta, Inder J.; Burnside, Walter D.

1986-01-01

A computer code was developed to analyze a semi-circular paraboloidal reflector antenna with a rolled edge at the top and a skirt at the bottom. The code can be used to compute the total near field of the antenna or its individual components at a given distance from the center of the paraboloid. Thus, it is very effective in computing the size of the sweet spot for RCS or antenna measurement. The operation of the code is described. Various input and output statements are explained. Some results obtained using the computer code are presented to illustrate the code's capability as well as being samples of input/output sets.

Highly fault-tolerant parallel computation

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

Spielman, D.A.

We re-introduce the coded model of fault-tolerant computation in which the input and output of a computational device are treated as words in an error-correcting code. A computational device correctly computes a function in the coded model if its input and output, once decoded, are a valid input and output of the function. In the coded model, it is reasonable to hope to simulate all computational devices by devices whose size is greater by a constant factor but which are exponentially reliable even if each of their components can fail with some constant probability. We consider fine-grained parallel computations inmore » which each processor has a constant probability of producing the wrong output at each time step. We show that any parallel computation that runs for time t on w processors can be performed reliably on a faulty machine in the coded model using w log{sup O(l)} w processors and time t log{sup O(l)} w. The failure probability of the computation will be at most t {center_dot} exp(-w{sup 1/4}). The codes used to communicate with our fault-tolerant machines are generalized Reed-Solomon codes and can thus be encoded and decoded in O(n log{sup O(1)} n) sequential time and are independent of the machine they are used to communicate with. We also show how coded computation can be used to self-correct many linear functions in parallel with arbitrarily small overhead.« less

An emulator for minimizing computer resources for finite element analysis

NASA Technical Reports Server (NTRS)

Melosh, R.; Utku, S.; Islam, M.; Salama, M.

1984-01-01

A computer code, SCOPE, has been developed for predicting the computer resources required for a given analysis code, computer hardware, and structural problem. The cost of running the code is a small fraction (about 3 percent) of the cost of performing the actual analysis. However, its accuracy in predicting the CPU and I/O resources depends intrinsically on the accuracy of calibration data that must be developed once for the computer hardware and the finite element analysis code of interest. Testing of the SCOPE code on the AMDAHL 470 V/8 computer and the ELAS finite element analysis program indicated small I/O errors (3.2 percent), larger CPU errors (17.8 percent), and negligible total errors (1.5 percent).

Development of Pflotran Code for Waste Isolation Pilot Plant Performance Assessment

NASA Astrophysics Data System (ADS)

Zeitler, T.; Day, B. A.; Frederick, J.; Hammond, G. E.; Kim, S.; Sarathi, R.; Stein, E.

2017-12-01

The Waste Isolation Pilot Plant (WIPP) has been developed by the U.S. Department of Energy (DOE) for the geologic (deep underground) disposal of transuranic (TRU) waste. Containment of TRU waste at the WIPP is regulated by the U.S. Environmental Protection Agency (EPA). The DOE demonstrates compliance with the containment requirements by means of performance assessment (PA) calculations. WIPP PA calculations estimate the probability and consequence of potential radionuclide releases from the repository to the accessible environment for a regulatory period of 10,000 years after facility closure. The long-term performance of the repository is assessed using a suite of sophisticated computational codes. There is a current effort to enhance WIPP PA capabilities through the further development of the PFLOTRAN software, a state-of-the-art massively parallel subsurface flow and reactive transport code. Benchmark testing of the individual WIPP-specific process models implemented in PFLOTRAN (e.g., gas generation, chemistry, creep closure, actinide transport, and waste form) has been performed, including results comparisons for PFLOTRAN and existing WIPP PA codes. Additionally, enhancements to the subsurface hydrologic flow mode have been made. Repository-scale testing has also been performed for the modified PFLTORAN code and detailed results will be presented. Ultimately, improvements to the current computational environment will result in greater detail and flexibility in the repository model due to a move from a two-dimensional calculation grid to a three-dimensional representation. The result of the effort will be a state-of-the-art subsurface flow and transport capability that will serve WIPP PA into the future for use in compliance recertification applications (CRAs) submitted to the EPA. Sandia National Laboratories is a multi-mission laboratory managed and operated by National Technology and Engineering Solutions of Sandia, LLC., a wholly owned subsidiary of Honeywell International, Inc., for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-NA0003525. This research is funded by WIPP programs administered by the Office of Environmental Management (EM) of the U.S. Department of Energy.SAND2017-8198A.

NSR&D FY17 Report: CartaBlanca Capability Enhancements

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

Long, Christopher Curtis; Dhakal, Tilak Raj; Zhang, Duan Zhong

Over the last several years, particle technology in the CartaBlanca code has been matured and has been successfully applied to a wide variety of physical problems. It has been shown that the particle methods, especially Los Alamos's dual domain material point method, is capable of computing many problems involves complex physics, chemistries accompanied by large material deformations, where the traditional finite element or Eulerian method encounter significant difficulties. In FY17, the CartaBlanca code has been enhanced with physical models and numerical algorithms. We started out to compute penetration and HE safety problems. Most of the year we focused on themore » TEPLA model improvement testing against the sweeping wave experiment by Gray et al., because it was found that pore growth and material failure are essentially important for our tasks and needed to be understood for modeling the penetration and the can experiments efficiently. We extended the TEPLA mode from the point view of ensemble phase average to include the effects of nite deformation. It is shown that the assumed pore growth model in TEPLA is actually an exact result from the theory. Alone this line, we then generalized the model to include finite deformations to consider nonlinear dynamics of large deformation. The interaction between the HE product gas and the solid metal is based on the multi-velocity formation. Our preliminary numerical results suggest good agreement between the experiment and the numerical results, pending further verification. To improve the parallel processing capabilities of the CartaBlanca code, we are actively working with the Next Generation Code (NGC) project to rewrite selected packages using C++. This work is expected to continue in the following years. This effort also makes the particle technology developed with CartaBlanca project available to other part of the laboratory. Working with the NGC project and rewriting some parts of the code also given us an opportunity to improve our numerical implementations of the method and to take advantage of recently advances in the numerical methods, such as multiscale algorithms.« less

A generalized one-dimensional computer code for turbomachinery cooling passage flow calculations

NASA Technical Reports Server (NTRS)

Kumar, Ganesh N.; Roelke, Richard J.; Meitner, Peter L.

1989-01-01

A generalized one-dimensional computer code for analyzing the flow and heat transfer in the turbomachinery cooling passages was developed. This code is capable of handling rotating cooling passages with turbulators, 180 degree turns, pin fins, finned passages, by-pass flows, tip cap impingement flows, and flow branching. The code is an extension of a one-dimensional code developed by P. Meitner. In the subject code, correlations for both heat transfer coefficient and pressure loss computations were developed to model each of the above mentioned type of coolant passages. The code has the capability of independently computing the friction factor and heat transfer coefficient on each side of a rectangular passage. Either the mass flow at the inlet to the channel or the exit plane pressure can be specified. For a specified inlet total temperature, inlet total pressure, and exit static pressure, the code computers the flow rates through the main branch and the subbranches, flow through tip cap for impingement cooling, in addition to computing the coolant pressure, temperature, and heat transfer coefficient distribution in each coolant flow branch. Predictions from the subject code for both nonrotating and rotating passages agree well with experimental data. The code was used to analyze the cooling passage of a research cooled radial rotor.

U.S. EPA’s Computational Toxicology Program: Innovation Powered by Chemistry (Dalton State College presentation)

EPA Science Inventory

Invited presentation at Dalton College, Dalton, GA to the Alliance for Innovation & Sustainability, April 20, 2017. U.S. EPA’s Computational Toxicology Program: Innovation Powered by Chemistry It is estimated that tens of thousands of commercial and industrial chemicals are ...

Applied Computational Chemistry for the Blind and Visually Impaired

ERIC Educational Resources Information Center

Wedler, Henry B.; Cohen, Sarah R.; Davis, Rebecca L.; Harrison, Jason G.; Siebert, Matthew R.; Willenbring, Dan; Hamann, Christian S.; Shaw, Jared T.; Tantillo, Dean J.

2012-01-01

We describe accommodations that we have made to our applied computational-theoretical chemistry laboratory to provide access for blind and visually impaired students interested in independent investigation of structure-function relationships. Our approach utilizes tactile drawings, molecular model kits, existing software, Bash and Perl scripts…

From data to analysis: linking NWChem and Avogadro with the syntax and semantics of Chemical Markup Language.

PubMed

de Jong, Wibe A; Walker, Andrew M; Hanwell, Marcus D

2013-05-24

Multidisciplinary integrated research requires the ability to couple the diverse sets of data obtained from a range of complex experiments and computer simulations. Integrating data requires semantically rich information. In this paper an end-to-end use of semantically rich data in computational chemistry is demonstrated utilizing the Chemical Markup Language (CML) framework. Semantically rich data is generated by the NWChem computational chemistry software with the FoX library and utilized by the Avogadro molecular editor for analysis and visualization. The NWChem computational chemistry software has been modified and coupled to the FoX library to write CML compliant XML data files. The FoX library was expanded to represent the lexical input files and molecular orbitals used by the computational chemistry software. Draft dictionary entries and a format for molecular orbitals within CML CompChem were developed. The Avogadro application was extended to read in CML data, and display molecular geometry and electronic structure in the GUI allowing for an end-to-end solution where Avogadro can create input structures, generate input files, NWChem can run the calculation and Avogadro can then read in and analyse the CML output produced. The developments outlined in this paper will be made available in future releases of NWChem, FoX, and Avogadro. The production of CML compliant XML files for computational chemistry software such as NWChem can be accomplished relatively easily using the FoX library. The CML data can be read in by a newly developed reader in Avogadro and analysed or visualized in various ways. A community-based effort is needed to further develop the CML CompChem convention and dictionary. This will enable the long-term goal of allowing a researcher to run simple "Google-style" searches of chemistry and physics and have the results of computational calculations returned in a comprehensible form alongside articles from the published literature.

From data to analysis: linking NWChem and Avogadro with the syntax and semantics of Chemical Markup Language

PubMed Central

2013-01-01

Background Multidisciplinary integrated research requires the ability to couple the diverse sets of data obtained from a range of complex experiments and computer simulations. Integrating data requires semantically rich information. In this paper an end-to-end use of semantically rich data in computational chemistry is demonstrated utilizing the Chemical Markup Language (CML) framework. Semantically rich data is generated by the NWChem computational chemistry software with the FoX library and utilized by the Avogadro molecular editor for analysis and visualization. Results The NWChem computational chemistry software has been modified and coupled to the FoX library to write CML compliant XML data files. The FoX library was expanded to represent the lexical input files and molecular orbitals used by the computational chemistry software. Draft dictionary entries and a format for molecular orbitals within CML CompChem were developed. The Avogadro application was extended to read in CML data, and display molecular geometry and electronic structure in the GUI allowing for an end-to-end solution where Avogadro can create input structures, generate input files, NWChem can run the calculation and Avogadro can then read in and analyse the CML output produced. The developments outlined in this paper will be made available in future releases of NWChem, FoX, and Avogadro. Conclusions The production of CML compliant XML files for computational chemistry software such as NWChem can be accomplished relatively easily using the FoX library. The CML data can be read in by a newly developed reader in Avogadro and analysed or visualized in various ways. A community-based effort is needed to further develop the CML CompChem convention and dictionary. This will enable the long-term goal of allowing a researcher to run simple “Google-style” searches of chemistry and physics and have the results of computational calculations returned in a comprehensible form alongside articles from the published literature. PMID:23705910

Markstein Numbers of Negatively-Stretched Premixed Flames: Microgravity Measurements and Computations

NASA Technical Reports Server (NTRS)

Ibarreta, Alfonso F.; Driscoll, James F.; Feikema, Douglas A.; Salzman, Jack (Technical Monitor)

2001-01-01

The effect of flame stretch, composed of strain and curvature, plays a major role in the propagation of turbulent premixed flames. Although all forms of stretch (positive and negative) are present in turbulent conditions, little research has been focused on the stretch due to curvature. The present study quantifies the Markstein number (which characterizes the sensitivity of the flame propagation speed to the imposed stretch rate) for an inwardly-propagating flame (IPF). This flame is of interest because it is negatively stretched, and is subjected to curvature effects alone, without the competing effects of strain. In an extension of our previous work, microgravity experiments were run using a vortex-flame interaction to create a pocket of reactants surrounded by an IPF. Computations using the RUN-1DL code of Rogg were also performed in order to explain the measurements. It was found that the Markstein number of an inwardly-propagating flame, for both the microgravity experiment and the computations, is significantly larger than that of an outwardly-propagating flame. Further insight was gained by running the computations for the simplified (hypothetical) cases of one step chemistry, unity Lewis number, and negligible heat release. Results provide additional evidence that the Markstein numbers associated with strain and curvature have different values.

LOSCAR: Long-term Ocean-atmosphere-Sediment CArbon cycle Reservoir Model

NASA Astrophysics Data System (ADS)

Zeebe, R. E.

2011-06-01

The LOSCAR model is designed to efficiently compute the partitioning of carbon between ocean, atmosphere, and sediments on time scales ranging from centuries to millions of years. While a variety of computationally inexpensive carbon cycle models are already available, many are missing a critical sediment component, which is indispensable for long-term integrations. One of LOSCAR's strengths is the coupling of ocean-atmosphere routines to a computationally efficient sediment module. This allows, for instance, adequate computation of CaCO3 dissolution, calcite compensation, and long-term carbon cycle fluxes, including weathering of carbonate and silicate rocks. The ocean component includes various biogeochemical tracers such as total carbon, alkalinity, phosphate, oxygen, and stable carbon isotopes. We have previously published applications of the model tackling future projections of ocean chemistry and weathering, pCO2 sensitivity to carbon cycle perturbations throughout the Cenozoic, and carbon/calcium cycling during the Paleocene-Eocene Thermal Maximum. The focus of the present contribution is the detailed description of the model including numerical architecture, processes and parameterizations, tuning, and examples of input and output. Typical CPU integration times of LOSCAR are of order seconds for several thousand model years on current standard desktop machines. The LOSCAR source code in C can be obtained from the author by sending a request to loscar.model@gmail.com.

Comparisons of Lagrangian and Eulerian PDF methods in simulations of non-premixed turbulent jet flames with moderate-to-strong turbulence-chemistry interactions

NASA Astrophysics Data System (ADS)

Jaishree, J.; Haworth, D. C.

2012-06-01

Transported probability density function (PDF) methods have been applied widely and effectively for modelling turbulent reacting flows. In most applications of PDF methods to date, Lagrangian particle Monte Carlo algorithms have been used to solve a modelled PDF transport equation. However, Lagrangian particle PDF methods are computationally intensive and are not readily integrated into conventional Eulerian computational fluid dynamics (CFD) codes. Eulerian field PDF methods have been proposed as an alternative. Here a systematic comparison is performed among three methods for solving the same underlying modelled composition PDF transport equation: a consistent hybrid Lagrangian particle/Eulerian mesh (LPEM) method, a stochastic Eulerian field (SEF) method and a deterministic Eulerian field method with a direct-quadrature-method-of-moments closure (a multi-environment PDF-MEPDF method). The comparisons have been made in simulations of a series of three non-premixed, piloted methane-air turbulent jet flames that exhibit progressively increasing levels of local extinction and turbulence-chemistry interactions: Sandia/TUD flames D, E and F. The three PDF methods have been implemented using the same underlying CFD solver, and results obtained using the three methods have been compared using (to the extent possible) equivalent physical models and numerical parameters. Reasonably converged mean and rms scalar profiles are obtained using 40 particles per cell for the LPEM method or 40 Eulerian fields for the SEF method. Results from these stochastic methods are compared with results obtained using two- and three-environment MEPDF methods. The relative advantages and disadvantages of each method in terms of accuracy and computational requirements are explored and identified. In general, the results obtained from the two stochastic methods (LPEM and SEF) are very similar, and are in closer agreement with experimental measurements than those obtained using the MEPDF method, while MEPDF is the most computationally efficient of the three methods. These and other findings are discussed in detail.

Efficient Proximity Computation Techniques Using ZIP Code Data for Smart Cities †

PubMed Central

Murdani, Muhammad Harist; Hong, Bonghee

2018-01-01

In this paper, we are interested in computing ZIP code proximity from two perspectives, proximity between two ZIP codes (Ad-Hoc) and neighborhood proximity (Top-K). Such a computation can be used for ZIP code-based target marketing as one of the smart city applications. A naïve approach to this computation is the usage of the distance between ZIP codes. We redefine a distance metric combining the centroid distance with the intersecting road network between ZIP codes by using a weighted sum method. Furthermore, we prove that the results of our combined approach conform to the characteristics of distance measurement. We have proposed a general and heuristic approach for computing Ad-Hoc proximity, while for computing Top-K proximity, we have proposed a general approach only. Our experimental results indicate that our approaches are verifiable and effective in reducing the execution time and search space. PMID:29587366

Efficient Proximity Computation Techniques Using ZIP Code Data for Smart Cities †.

PubMed

Murdani, Muhammad Harist; Kwon, Joonho; Choi, Yoon-Ho; Hong, Bonghee

2018-03-24

In this paper, we are interested in computing ZIP code proximity from two perspectives, proximity between two ZIP codes ( Ad-Hoc ) and neighborhood proximity ( Top-K ). Such a computation can be used for ZIP code-based target marketing as one of the smart city applications. A naïve approach to this computation is the usage of the distance between ZIP codes. We redefine a distance metric combining the centroid distance with the intersecting road network between ZIP codes by using a weighted sum method. Furthermore, we prove that the results of our combined approach conform to the characteristics of distance measurement. We have proposed a general and heuristic approach for computing Ad-Hoc proximity, while for computing Top-K proximity, we have proposed a general approach only. Our experimental results indicate that our approaches are verifiable and effective in reducing the execution time and search space.

Chemistry Division: Annual progress report for period ending March 31, 1987

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

Not Available

1987-08-01

This report is divided into the following sections: coal chemistry; aqueous chemistry at high temperatures and pressures; geochemistry of crustal processes to high temperatures and pressures; chemistry of advanced inorganic materials; structure and dynamics of advanced polymeric materials; chemistry of transuranium elements and compounds; separations chemistry; reactions and catalysis in molten salts; surface science related to heterogeneous catalysis; electron spectroscopy; chemistry related to nuclear waste disposal; computational modeling of security document printing; and special topics. (DLC)

Development of the Connected Chemistry as Formative Assessment Pedagogy for High School Chemistry Teaching

ERIC Educational Resources Information Center

Park, Mihwa; Liu, Xiufeng; Waight, Noemi

2017-01-01

This paper describes the development of Connected Chemistry as Formative Assessment (CCFA) pedagogy, which integrates three promising teaching and learning approaches, computer models, formative assessments, and learning progressions, to promote student understanding in chemistry. CCFA supports student learning in making connections among the…

A Computational Investigation of Sooting Limits of Spherical Diffusion Flames

NASA Technical Reports Server (NTRS)

Lecoustre, V. R.; Chao, B. H.; Sunderland, P. B.; Urban, D. L.; Stocker, D. P.; Axelbaum, R. L.

2007-01-01

Limiting conditions for soot particle inception in spherical diffusion flames were investigated numerically. The flames were modeled using a one-dimensional, time accurate diffusion flame code with detailed chemistry and transport and an optically thick radiation model. Seventeen normal and inverse flames were considered, covering a wide range of stoichiometric mixture fraction, adiabatic flame temperature, and residence time. These flames were previously observed to reach their sooting limits after 2 s of microgravity. Sooting-limit diffusion flames with residence times longer than 200 ms were found to have temperatures near 1190 K where C/O = 0.6, whereas flames with shorter residence times required increased temperatures. Acetylene was found to be a reasonable surrogate for soot precursor species in these flames, having peak mole fractions of about 0.01.

Development of a Charge-Implicit ReaxFF Potential for Hydrocarbon Systems.

PubMed

Kański, Michał; Maciążek, Dawid; Postawa, Zbigniew; Ashraf, Chowdhury M; van Duin, Adri C T; Garrison, Barbara J

2018-01-18

Molecular dynamics (MD) simulations continue to make important contributions to understanding chemical and physical processes. Concomitant with the growth of MD simulations is the need to have interaction potentials that both represent the chemistry of the system and are computationally efficient. We propose a modification to the ReaxFF potential for carbon and hydrogen that eliminates the time-consuming charge equilibration, eliminates the acknowledged flaws of the electronegativity equalization method, includes an expanded training set for condensed phases, has a repulsive wall for simulations of energetic particle bombardment, and is compatible with the LAMMPS code. This charge-implicit ReaxFF potential is five times faster than the conventional ReaxFF potential for a simulation of keV particle bombardment with a sample size of over 800 000 atoms.

FUEL-FLEXIBLE GASIFICATION-COMBUSTION TECHNOLOGY FOR PRODUCTION OF H2 AND SEQUESTRATION-READY CO2

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

George Rizeq; Janice West; Arnaldo Frydman

Further development of a combustion Large Eddy Simulation (LES) code for the design of advanced gaseous combustion systems is described in this sixth quarterly report. CFD Research Corporation (CFDRC) is developing the LES module within the parallel, unstructured solver included in the commercial CFD-ACE+ software. In this quarter, in-situ adaptive tabulation (ISAT) for efficient chemical rate storage and retrieval was implemented and tested within the Linear Eddy Model (LEM). ISAT type 3 is being tested so that extrapolation can be performed and further improve the retrieval rate. Further testing of the LEM for subgrid chemistry was performed for parallel applicationsmore » and for multi-step chemistry. Validation of the software on backstep and bluff-body reacting cases were performed. Initial calculations of the SimVal experiment at Georgia Tech using their LES code were performed. Georgia Tech continues the effort to parameterize the LEM over composition space so that a neural net can be used efficiently in the combustion LES code. A new and improved Artificial Neural Network (ANN), with log-transformed output, for the 1-step chemistry was implemented in CFDRC's LES code and gave reasonable results. This quarter, the 2nd consortium meeting was held at CFDRC. Next quarter, LES software development and testing will continue. Alpha testing of the code will continue to be performed on cases of interest to the industrial consortium. Optimization of subgrid models will be pursued, particularly with the ISAT approach. Also next quarter, the demonstration of the neural net approach, for multi-step chemical kinetics speed-up in CFD-ACE+, will be accomplished.« less

Static Chemistry in Disks or Clouds

NASA Astrophysics Data System (ADS)

Semenov, D.; Wiebe, D.

2006-11-01

This FORTRAN77 code can be used to model static, time-dependent chemistry in ISM and circumstellar disks. Current version is based on the OSU'06 gas-grain astrochemical network with all updates to the reaction rates, and includes surface chemistry from Hasegawa & Herbst (1993) and Hasegawa, Herbst, and Leung (1992). Surface chemistry can be modeled either with the standard rate equation approach or modified rate equation approach (useful in disks). Gas-grain interactions include sticking of neutral molecules to grains, dissociative recombination of ions on grains as well as thermal, UV, X-ray, and CRP-induced desorption of frozen species. An advanced X-ray chemistry and 3 grain sizes with power-law size distribution are also included. An deuterium extension to this chemical model is available.

Density functional theory in the solid state

PubMed Central

Hasnip, Philip J.; Refson, Keith; Probert, Matt I. J.; Yates, Jonathan R.; Clark, Stewart J.; Pickard, Chris J.

2014-01-01

Density functional theory (DFT) has been used in many fields of the physical sciences, but none so successfully as in the solid state. From its origins in condensed matter physics, it has expanded into materials science, high-pressure physics and mineralogy, solid-state chemistry and more, powering entire computational subdisciplines. Modern DFT simulation codes can calculate a vast range of structural, chemical, optical, spectroscopic, elastic, vibrational and thermodynamic phenomena. The ability to predict structure–property relationships has revolutionized experimental fields, such as vibrational and solid-state NMR spectroscopy, where it is the primary method to analyse and interpret experimental spectra. In semiconductor physics, great progress has been made in the electronic structure of bulk and defect states despite the severe challenges presented by the description of excited states. Studies are no longer restricted to known crystallographic structures. DFT is increasingly used as an exploratory tool for materials discovery and computational experiments, culminating in ex nihilo crystal structure prediction, which addresses the long-standing difficult problem of how to predict crystal structure polymorphs from nothing but a specified chemical composition. We present an overview of the capabilities of solid-state DFT simulations in all of these topics, illustrated with recent examples using the CASTEP computer program. PMID:24516184

Volume accumulator design analysis computer codes

NASA Technical Reports Server (NTRS)

Whitaker, W. D.; Shimazaki, T. T.

1973-01-01

The computer codes, VANEP and VANES, were written and used to aid in the design and performance calculation of the volume accumulator units (VAU) for the 5-kwe reactor thermoelectric system. VANEP computes the VAU design which meets the primary coolant loop VAU volume and pressure performance requirements. VANES computes the performance of the VAU design, determined from the VANEP code, at the conditions of the secondary coolant loop. The codes can also compute the performance characteristics of the VAU's under conditions of possible modes of failure which still permit continued system operation.

Xenobiology: State-of-the-Art, Ethics, and Philosophy of New-to-Nature Organisms.

PubMed

Schmidt, Markus; Pei, Lei; Budisa, Nediljko

The basic chemical constitution of all living organisms in the context of carbon-based chemistry consists of a limited number of small molecules and polymers. Until the twenty-first century, biology was mainly an analytical science and has now reached a point where it merges with engineering science, paving the way for synthetic biology. One of the objectives of synthetic biology is to try to change the chemical compositions of living cells, that is, to create an artificial biological diversity, which in turn fosters a new sub-field of synthetic biology, xenobiology. In particular, the genetic code in living systems is based on highly standardized chemistry composed of the same "letters" or nucleotides as informational polymers (DNA, RNA) and the 20 amino acids which serve as basic building blocks for proteins. The universality of the genetic code enables not only vertical gene transfer within the same species but also horizontal gene transfer across biological taxa, which require a high degree of standardization and interconnectivity. Although some minor alterations of the standard genetic code are found in nature (e.g., proteins containing non-conical amino acids exist in nature, and some organisms use alternated coding systems), all structurally deep chemistry changes within living systems are generally lethal, making the creation of artificial biological system an extremely difficult challenge.In this context, one of the great challenges for bioscience is the development of a strategy for expanding the standard basic chemical repertoire of living cells. Attempts to alter the meaning of the genetic information stored in DNA as an informational polymer by changing the chemistry of the polymer (i.e., xeno-nucleic acids) or by changes in the genetic code have already yielded successful results. In the future this should enable the partial or full redirection of the biological information flow to generate "new" version(s) of the genetic code derived from the "old" biological world.In addition to the scientific challenges, the attempt to increase biochemical diversity also raises important ethical and philosophical issues. Although promotors of this branch of synthetic biology highlight the many potential applications to come (e.g., novel tools for diagnostics and fighting infection diseases), such developments could also bring risks affecting social, political, and other structures of nearly all societies.

"Hour of Code": Can It Change Students' Attitudes toward Programming?

ERIC Educational Resources Information Center

Du, Jie; Wimmer, Hayden; Rada, Roy

2016-01-01

The Hour of Code is a one-hour introduction to computer science organized by Code.org, a non-profit dedicated to expanding participation in computer science. This study investigated the impact of the Hour of Code on students' attitudes towards computer programming and their knowledge of programming. A sample of undergraduate students from two…

Writing and Computing across the USM Chemistry Curriculum

NASA Astrophysics Data System (ADS)

Gordon, Nancy R.; Newton, Thomas A.; Rhodes, Gale; Ricci, John S.; Stebbins, Richard G.; Tracy, Henry J.

2001-01-01

The faculty of the University of Southern Maine believes the ability to communicate effectively is one of the most important skills required of successful chemists. To help students achieve that goal, the faculty has developed a Writing and Computer Program consisting of writing and computer assignments of gradually increasing sophistication for all our laboratory courses. The assignments build in complexity until, at the junior level, students are writing full journal-quality laboratory reports. Computer assignments also increase in difficulty as students attack more complicated subjects. We have found the program easy to initiate and our part-time faculty concurs as well. The Writing and Computing across the Curriculum Program also serves to unite the entire chemistry curriculum. We believe the program is helping to reverse what the USM chemistry faculty and other educators have found to be a steady deterioration in the writing skills of many of today's students.

Talking about Code: Integrating Pedagogical Code Reviews into Early Computing Courses

ERIC Educational Resources Information Center

Hundhausen, Christopher D.; Agrawal, Anukrati; Agarwal, Pawan

2013-01-01

Given the increasing importance of soft skills in the computing profession, there is good reason to provide students withmore opportunities to learn and practice those skills in undergraduate computing courses. Toward that end, we have developed an active learning approach for computing education called the "Pedagogical Code Review"…

Biennial Conference on Chemical Education: Abstracts of Papers (9th, Bozeman, Montana, July 27-August 2, 1986).

ERIC Educational Resources Information Center

1986

This document includes summaries of conference presentations dealing with a wide variety of topics, including chemistry units for the elementary classroom, science experimentation in the secondary school, computer simulations, computer interfaces, videodisc technology, correspondence teaching of general chemistry, interdisciplinary energy courses,…

Using Computer Simulations in Chemistry Problem Solving

ERIC Educational Resources Information Center

Avramiotis, Spyridon; Tsaparlis, Georgios

2013-01-01

This study is concerned with the effects of computer simulations of two novel chemistry problems on the problem solving ability of students. A control-experimental group, equalized by pair groups (n[subscript Exp] = n[subscript Ctrl] = 78), research design was used. The students had no previous experience of chemical practical work. Student…

RESEARCH STRATEGIES FOR THE APPLICATION OF THE TECHNIQUES OF COMPUTATIONAL BIOLOGICAL CHEMISTRY TO ENVIRONMENTAL PROBLEMS

EPA Science Inventory

On October 25 and 26, 1984, the U.S. EPA sponsored a workshop to consider the potential applications of the techniques of computational biological chemistry to problems in environmental health. Eleven extramural scientists from the various related disciplines and a similar number...

PREDICTING CHEMICAL REACTIVITY OF HUMIC SUBSTANCES FOR MINERALS AND XENOBIOTICS: USE OF COMPUTATIONAL CHEMISTRY, SCANNING PROBE MICROSCOPY AND VIRTUAL REALITY

EPA Science Inventory

In this chapter we review the literature on scanning probe microscopy (SPM), virtual reality (VR), and computational chemistry and our earlier work dealing with modeling lignin, lignin-carbohydrate complexes (LCC), humic substances (HSs) and non-bonded organo-mineral interactions...

Computational Chemistry Studies on the Carbene Hydroxymethylene

ERIC Educational Resources Information Center

Marzzacco, Charles J.; Baum, J. Clayton

2011-01-01

A density functional theory computational chemistry exercise on the structure and vibrational spectrum of the carbene hydroxymethylene is presented. The potential energy curve for the decomposition reaction of the carbene to formaldehyde and the geometry of the transition state are explored. The results are in good agreement with recent…

Dissociation of the Ethyl Radical: An Exercise in Computational Chemistry

ERIC Educational Resources Information Center

Nassabeh, Nahal; Tran, Mark; Fleming, Patrick E.

2014-01-01

A set of exercises for use in a typical physical chemistry laboratory course are described, modeling the unimolecular dissociation of the ethyl radical to form ethylene and atomic hydrogen. Students analyze the computational results both qualitatively and quantitatively. Qualitative structural changes are compared to approximate predicted values…

Modelling of soot formation in laminar diffusion flames using a comprehensive CFD-PBE model with detailed gas-phase chemistry

NASA Astrophysics Data System (ADS)

Akridis, Petros; Rigopoulos, Stelios

2017-01-01

A discretised population balance equation (PBE) is coupled with an in-house computational fluid dynamics (CFD) code in order to model soot formation in laminar diffusion flames. The unsteady Navier-Stokes, species and enthalpy transport equations and the spatially-distributed discretised PBE for the soot particles are solved in a coupled manner, together with comprehensive gas-phase chemistry and an optically thin radiation model, thus yielding the complete particle size distribution of the soot particles. Nucleation, surface growth and oxidation are incorporated into the PBE using an acetylene-based soot model. The potential of the proposed methodology is investigated by comparing with experimental results from the Santoro jet burner [Santoro, Semerjian and Dobbins, Soot particle measurements in diffusion flames, Combustion and Flame, Vol. 51 (1983), pp. 203-218; Santoro, Yeh, Horvath and Semerjian, The transport and growth of soot particles in laminar diffusion flames, Combustion Science and Technology, Vol. 53 (1987), pp. 89-115] for three laminar axisymmetric non-premixed ethylene flames: a non-smoking, an incipient smoking and a smoking flame. Overall, good agreement is observed between the numerical and the experimental results.

Guidelines for developing vectorizable computer programs

NASA Technical Reports Server (NTRS)

Miner, E. W.

1982-01-01

Some fundamental principles for developing computer programs which are compatible with array-oriented computers are presented. The emphasis is on basic techniques for structuring computer codes which are applicable in FORTRAN and do not require a special programming language or exact a significant penalty on a scalar computer. Researchers who are using numerical techniques to solve problems in engineering can apply these basic principles and thus develop transportable computer programs (in FORTRAN) which contain much vectorizable code. The vector architecture of the ASC is discussed so that the requirements of array processing can be better appreciated. The "vectorization" of a finite-difference viscous shock-layer code is used as an example to illustrate the benefits and some of the difficulties involved. Increases in computing speed with vectorization are illustrated with results from the viscous shock-layer code and from a finite-element shock tube code. The applicability of these principles was substantiated through running programs on other computers with array-associated computing characteristics, such as the Hewlett-Packard (H-P) 1000-F.

The Helicopter Antenna Radiation Prediction Code (HARP)

NASA Technical Reports Server (NTRS)

Klevenow, F. T.; Lynch, B. G.; Newman, E. H.; Rojas, R. G.; Scheick, J. T.; Shamansky, H. T.; Sze, K. Y.

1990-01-01

The first nine months effort in the development of a user oriented computer code, referred to as the HARP code, for analyzing the radiation from helicopter antennas is described. The HARP code uses modern computer graphics to aid in the description and display of the helicopter geometry. At low frequencies the helicopter is modeled by polygonal plates, and the method of moments is used to compute the desired patterns. At high frequencies the helicopter is modeled by a composite ellipsoid and flat plates, and computations are made using the geometrical theory of diffraction. The HARP code will provide a user friendly interface, employing modern computer graphics, to aid the user to describe the helicopter geometry, select the method of computation, construct the desired high or low frequency model, and display the results.

Enhanced fault-tolerant quantum computing in d-level systems.

PubMed

Campbell, Earl T

2014-12-05

Error-correcting codes protect quantum information and form the basis of fault-tolerant quantum computing. Leading proposals for fault-tolerant quantum computation require codes with an exceedingly rare property, a transversal non-Clifford gate. Codes with the desired property are presented for d-level qudit systems with prime d. The codes use n=d-1 qudits and can detect up to ∼d/3 errors. We quantify the performance of these codes for one approach to quantum computation known as magic-state distillation. Unlike prior work, we find performance is always enhanced by increasing d.

Convergence acceleration of the Proteus computer code with multigrid methods

NASA Technical Reports Server (NTRS)

Demuren, A. O.; Ibraheem, S. O.

1992-01-01

Presented here is the first part of a study to implement convergence acceleration techniques based on the multigrid concept in the Proteus computer code. A review is given of previous studies on the implementation of multigrid methods in computer codes for compressible flow analysis. Also presented is a detailed stability analysis of upwind and central-difference based numerical schemes for solving the Euler and Navier-Stokes equations. Results are given of a convergence study of the Proteus code on computational grids of different sizes. The results presented here form the foundation for the implementation of multigrid methods in the Proteus code.

Implementation of radiation shielding calculation methods. Volume 1: Synopsis of methods and summary of results

NASA Technical Reports Server (NTRS)

Capo, M. A.; Disney, R. K.

1971-01-01

The work performed in the following areas is summarized: (1) Analysis of Realistic nuclear-propelled vehicle was analyzed using the Marshall Space Flight Center computer code package. This code package includes one and two dimensional discrete ordinate transport, point kernel, and single scatter techniques, as well as cross section preparation and data processing codes, (2) Techniques were developed to improve the automated data transfer in the coupled computation method of the computer code package and improve the utilization of this code package on the Univac-1108 computer system. (3) The MSFC master data libraries were updated.

Nonuniform code concatenation for universal fault-tolerant quantum computing

NASA Astrophysics Data System (ADS)

Nikahd, Eesa; Sedighi, Mehdi; Saheb Zamani, Morteza

2017-09-01

Using transversal gates is a straightforward and efficient technique for fault-tolerant quantum computing. Since transversal gates alone cannot be computationally universal, they must be combined with other approaches such as magic state distillation, code switching, or code concatenation to achieve universality. In this paper we propose an alternative approach for universal fault-tolerant quantum computing, mainly based on the code concatenation approach proposed in [T. Jochym-O'Connor and R. Laflamme, Phys. Rev. Lett. 112, 010505 (2014), 10.1103/PhysRevLett.112.010505], but in a nonuniform fashion. The proposed approach is described based on nonuniform concatenation of the 7-qubit Steane code with the 15-qubit Reed-Muller code, as well as the 5-qubit code with the 15-qubit Reed-Muller code, which lead to two 49-qubit and 47-qubit codes, respectively. These codes can correct any arbitrary single physical error with the ability to perform a universal set of fault-tolerant gates, without using magic state distillation.

Reviews and syntheses: Revisiting the boron systematics of aragonite and their application to coral calcification

NASA Astrophysics Data System (ADS)

DeCarlo, Thomas M.; Holcomb, Michael; McCulloch, Malcolm T.

2018-05-01

The isotopic and elemental systematics of boron in aragonitic coral skeletons have recently been developed as a proxy for the carbonate chemistry of the coral extracellular calcifying fluid. With knowledge of the boron isotopic fractionation in seawater and the B/Ca partition coefficient (KD) between aragonite and seawater, measurements of coral skeleton δ11B and B/Ca can potentially constrain the full carbonate system. Two sets of abiogenic aragonite precipitation experiments designed to quantify KD have recently made possible the application of this proxy system. However, while different KD formulations have been proposed, there has not yet been a comprehensive analysis that considers both experimental datasets and explores the implications for interpreting coral skeletons. Here, we evaluate four potential KD formulations: three previously presented in the literature and one newly developed. We assess how well each formulation reconstructs the known fluid carbonate chemistry from the abiogenic experiments, and we evaluate the implications for deriving the carbonate chemistry of coral calcifying fluid. Three of the KD formulations performed similarly when applied to abiogenic aragonites precipitated from seawater and to coral skeletons. Critically, we find that some uncertainty remains in understanding the mechanism of boron elemental partitioning between aragonite and seawater, and addressing this question should be a target of additional abiogenic precipitation experiments. Despite this, boron systematics can already be applied to quantify the coral calcifying fluid carbonate system, although uncertainties associated with the proxy system should be carefully considered for each application. Finally, we present a user-friendly computer code that calculates coral calcifying fluid carbonate chemistry, including propagation of uncertainties, given inputs of boron systematics measured in coral skeleton.

Manifestations of metacognitive activity during the collaborative planning of chemistry practical investigations

NASA Astrophysics Data System (ADS)

Mathabathe, Kgadi Clarrie; Potgieter, Marietjie

2017-07-01

This paper elaborates a process followed to characterise manifestations of cognitive regulation during the collaborative planning of chemistry practical investigations. Metacognitive activity was defined as the demonstration of planning, monitoring, control and evaluation of cognitive activities by students while carrying out the chemistry task. Inherent in collaborative learning is the social aspect of metacognition, which in this study was evidenced in social cognitive regulation (notably of intra- and interpersonal metacognitive regulations) as groups of students went about planning their practical investigations. Discussions of two of the learning groups (n = 4; n = 3) as they planned the extended practical investigation were recorded, transcribed and analysed for indicators of any inherent metacognitive activity. The process of characterising the manifestations of metacognition resulted in the development of a coding system which specifies not only the regulatory strategies at play but the type of regulation (self or other), the area of regulation (cognition, task performance or behaviour) as well as the depth of regulatory contributions (high or low). The fine-grained coding system allowed for a finer theoretical elucidation of the social nature of metacognition. The implications of this study for metacognition and chemistry education research are highlighted.

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.

Green's function methods in heavy ion shielding

NASA Technical Reports Server (NTRS)

Wilson, John W.; Costen, Robert C.; Shinn, Judy L.; Badavi, Francis F.

1993-01-01

An analytic solution to the heavy ion transport in terms of Green's function is used to generate a highly efficient computer code for space applications. The efficiency of the computer code is accomplished by a nonperturbative technique extending Green's function over the solution domain. The computer code can also be applied to accelerator boundary conditions to allow code validation in laboratory experiments.

Quantitatively probing water and its isotopomers: from theory to experiments; the contribution of a chemical and astrophysical European network 'Our Astrochemical History'

NASA Astrophysics Data System (ADS)

Wiesenfeld, Laurent

2015-08-01

In order to retrieve actual molecular abundances from astrophysical observations of molecular spectral lines, knowledge of the rotational levels excitation schemes is essential to go beyond Local Thermodynamical Equilibrium. These rates are almost always obtained from theoretical investigations, by computing classical or quantum dynamics of the interaction of molecules with these colliders (roueff2013).Our laboratories have recently calculated a set of collision coefficients characterizing the efficiency of energy transfer between molecular hydrogen of helium and a large variety of interstellar molecules. One of the main goal has been water and its isotopomers, computingrates for H2O, HDO and D2O in collision with H2 (valiron2008,faure2012,daniel2011).We felt it necessary to have a multidisciplinary approach: theoretical on the one hand, experimental on the second. Indeed, excitation coefficient computation is a process involving many codes and approximations. Hence we compared our theoretical results to several experiments: spectroscopy of the H2O-H2 van der Waals complex (vanderavoird 2012), differential cross sections (yang 2010, 2011), pressure broadening (drouin 2012).Thanks to these precise determinations, many water abundances could be quantitatively measured, like the HDO/H2O ratio (coutens 2012).While the excitation of water is by now well understood, much remains to be done for heavier molecules, paving the way to quantitative measures of complex organic molecules . A multi disciplinary approach is necessary, that keeps in mind the necessities of actual astrophysical observations. To do so, we describe the European COST network ‘Our Astrochemical History’ (http://prague2015astrohistory.vscht.cz/) , which brings together specialists of many areas of chemistry together with astronomy, in order to address this kind of problem. It focussses on the molecular evolution towards higher complexity and aim sat delivering new schemes for physical chemistry at large, like chemistry of transient species and photochemistry, in gas or on surfaces.

Analytical modeling of operating characteristics of premixing-prevaporizing fuel-air mixing passages. Volume 2: User's manual

NASA Technical Reports Server (NTRS)

Anderson, O. L.; Chiappetta, L. M.; Edwards, D. E.; Mcvey, J. B.

1982-01-01

A user's manual describing the operation of three computer codes (ADD code, PTRAK code, and VAPDIF code) is presented. The general features of the computer codes, the input/output formats, run streams, and sample input cases are described.

Automated apparatus and method of generating native code for a stitching machine

NASA Technical Reports Server (NTRS)

Miller, Jeffrey L. (Inventor)

2000-01-01

A computer system automatically generates CNC code for a stitching machine. The computer determines the locations of a present stitching point and a next stitching point. If a constraint is not found between the present stitching point and the next stitching point, the computer generates code for making a stitch at the next stitching point. If a constraint is found, the computer generates code for changing a condition (e.g., direction) of the stitching machine's stitching head.

Computer codes developed and under development at Lewis

NASA Technical Reports Server (NTRS)

Chamis, Christos C.

1992-01-01

The objective of this summary is to provide a brief description of: (1) codes developed or under development at LeRC; and (2) the development status of IPACS with some typical early results. The computer codes that have been developed and/or are under development at LeRC are listed in the accompanying charts. This list includes: (1) the code acronym; (2) select physics descriptors; (3) current enhancements; and (4) present (9/91) code status with respect to its availability and documentation. The computer codes list is grouped by related functions such as: (1) composite mechanics; (2) composite structures; (3) integrated and 3-D analysis; (4) structural tailoring; and (5) probabilistic structural analysis. These codes provide a broad computational simulation infrastructure (technology base-readiness) for assessing the structural integrity/durability/reliability of propulsion systems. These codes serve two other very important functions: they provide an effective means of technology transfer; and they constitute a depository of corporate memory.

Evaluation of the Community Multiscale Air Quality (CMAQ) ...

EPA Pesticide Factsheets

The Community Multiscale Air Quality (CMAQ) model is a state-of-the-science air quality model that simulates the emission, transport and fate of numerous air pollutants, including ozone and particulate matter. The Computational Exposure Division (CED) of the U.S. Environmental Protection Agency develops the CMAQ model and periodically releases new versions of the model that include bug fixes and various other improvements to the modeling system. In the fall of 2016, CMAQ version 5.1.1 will be released. This new version of CMAQ will contain important bug fixes to several issues that were identified in CMAQv5.1 (the current public release version of the CMAQ model), and additionally include updates to other portions of the code. Some specific model updates include a new implementation of the wind-blown dust calculation in CMAQv5.1.1 which fixes several bugs that were identified in the current implementation of wind-blown dust in CMAQv5.1. Several other major updates to the model include an update to the calculation of aerosols; implementation of full halogen chemistry (CMAQv5.1 contains a partial implementation of halogen chemistry), which is particularly important for hemispheric applications of the CMAQ model, as halogen chemistry is need to accurately simulation the destruction of ozone over the ocean; and the new carbon bond 6 (CB6) chemical mechanism. Several annual, and numerous episodic, CMAQv5.1.1 simulations will be performed to assess the impact of these

Services for Emodnet-Chemistry Data Products

NASA Astrophysics Data System (ADS)

Santinelli, Giorgio; Hendriksen, Gerrit; Barth, Alexander

2016-04-01

In the framework of Emodnet Chemistry lot, data products from regional leaders were made available in order to transform information into a database. This has been done by using functions and scripts, reading so-called enriched ODV files and inserting data directly into a cloud relational geodatabase. The main table is the one of observations which contains the main data and meta-data associated with the enriched ODV files. A particular implementation in data loading is used in order to improve on-the-fly computational speed. Data from Baltic Sea, North Sea, Mediterrean, Black Sea and part of the Atlantic region has been entered into the geodatabase, and consequently being instantly available from the OceanBrowser Emodnet portal. Furthermore, Deltares has developed an application that provides additional visualisation services for the aggregated and validated data collections. The visualisations are produced by making use of part of the OpenEarthTool stack (http://www.openearth.eu), by the integration of Web Feature Services and by the implementation of Web Processing Services. The goal is the generation of server-side plots of timeseries, profiles, timeprofiles and maps of selected parameters from data sets of selected stations. Regional data collections are retrieved using Emodnet Chemistry cloud relational geo-database. The spatial resolution in time and the intensity of data availability for selected parameters is shown using Web Service requests via the OceanBrowser Emodnet Web portal. OceanBrowser also shows station reference codes, which are used to establish a link for additional metadata, further data shopping and download.

Incorporating Computational Chemistry into the Chemical Engineering Curriculum

ERIC Educational Resources Information Center

Wilcox, Jennifer

2006-01-01

A graduate-level computational chemistry course was designed and developed and carried out in the Department of Chemical Engineering at Worcester Polytechnic Institute in the Fall of 2005. The thrust of the course was a reaction assignment that led students through a series of steps, beginning with energetic predictions based upon fundamental…

Students' Cognitive Focus during a Chemistry Laboratory Exercise: Effects of a Computer-Simulated Prelab

ERIC Educational Resources Information Center

Winberg, T. Mikael; Berg, C. Anders R.

2007-01-01

To enhance the learning outcomes achieved by students, learners undertook a computer-simulated activity based on an acid-base titration prior to a university-level chemistry laboratory activity. Students were categorized with respect to their attitudes toward learning. During the laboratory exercise, questions that students asked their assistant…

Probing Student Teachers' Subject Content Knowledge in Chemistry: Case Studies Using Dynamic Computer Models

ERIC Educational Resources Information Center

Toplis, Rob

2008-01-01

This paper reports case study research into the knowledge and understanding of chemistry for six secondary science student teachers. It combines innovative student-generated computer animations, using "ChemSense" software, with interviews to probe understanding of four common chemical processes used in the secondary school curriculum. Findings…

Investigating the Effectiveness of Computer Simulations for Chemistry Learning

ERIC Educational Resources Information Center

Plass, Jan L.; Milne, Catherine; Homer, Bruce D.; Schwartz, Ruth N.; Hayward, Elizabeth O.; Jordan, Trace; Verkuilen, Jay; Ng, Florrie; Wang, Yan; Barrientos, Juan

2012-01-01

Are well-designed computer simulations an effective tool to support student understanding of complex concepts in chemistry when integrated into high school science classrooms? We investigated scaling up the use of a sequence of simulations of kinetic molecular theory and associated topics of diffusion, gas laws, and phase change, which we designed…

A Computer Algebra Approach to Solving Chemical Equilibria in General Chemistry

ERIC Educational Resources Information Center

Kalainoff, Melinda; Lachance, Russ; Riegner, Dawn; Biaglow, Andrew

2012-01-01

In this article, we report on a semester-long study of the incorporation into our general chemistry course, of advanced algebraic and computer algebra techniques for solving chemical equilibrium problems. The method presented here is an alternative to the commonly used concentration table method for describing chemical equilibria in general…

Using the tabulated diffusion flamelet model ADF-PCM to simulate a lifted methane-air jet flame

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

Michel, Jean-Baptiste; Colin, Olivier; Angelberger, Christian

2009-07-15

Two formulations of a turbulent combustion model based on the approximated diffusion flame presumed conditional moment (ADF-PCM) approach [J.-B. Michel, O. Colin, D. Veynante, Combust. Flame 152 (2008) 80-99] are presented. The aim is to describe autoignition and combustion in nonpremixed and partially premixed turbulent flames, while accounting for complex chemistry effects at a low computational cost. The starting point is the computation of approximate diffusion flames by solving the flamelet equation for the progress variable only, reading all chemical terms such as reaction rates or mass fractions from an FPI-type look-up table built from autoigniting PSR calculations using complexmore » chemistry. These flamelets are then used to generate a turbulent look-up table where mean values are estimated by integration over presumed probability density functions. Two different versions of ADF-PCM are presented, differing by the probability density functions used to describe the evolution of the stoichiometric scalar dissipation rate: a Dirac function centered on the mean value for the basic ADF-PCM formulation, and a lognormal function for the improved formulation referenced ADF-PCM{chi}. The turbulent look-up table is read in the CFD code in the same manner as for PCM models. The developed models have been implemented into the compressible RANS CFD code IFP-C3D and applied to the simulation of the Cabra et al. experiment of a lifted methane jet flame [R. Cabra, J. Chen, R. Dibble, A. Karpetis, R. Barlow, Combust. Flame 143 (2005) 491-506]. The ADF-PCM{chi} model accurately reproduces the experimental lift-off height, while it is underpredicted by the basic ADF-PCM model. The ADF-PCM{chi} model shows a very satisfactory reproduction of the experimental mean and fluctuating values of major species mass fractions and temperature, while ADF-PCM yields noticeable deviations. Finally, a comparison of the experimental conditional probability densities of the progress variable for a given mixture fraction with model predictions is performed, showing that ADF-PCM{chi} reproduces the experimentally observed bimodal shape and its dependency on the mixture fraction, whereas ADF-PCM cannot retrieve this shape. (author)« less

Reactivity effects in VVER-1000 of the third unit of the kalinin nuclear power plant at physical start-up. Computations in ShIPR intellectual code system with library of two-group cross sections generated by UNK code

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

Zizin, M. N.; Zimin, V. G.; Zizina, S. N., E-mail: zizin@adis.vver.kiae.ru

2010-12-15

The ShIPR intellectual code system for mathematical simulation of nuclear reactors includes a set of computing modules implementing the preparation of macro cross sections on the basis of the two-group library of neutron-physics cross sections obtained for the SKETCH-N nodal code. This library is created by using the UNK code for 3D diffusion computation of first VVER-1000 fuel loadings. Computation of neutron fields in the ShIPR system is performed using the DP3 code in the two-group diffusion approximation in 3D triangular geometry. The efficiency of all groups of control rods for the first fuel loading of the third unit ofmore » the Kalinin Nuclear Power Plant is computed. The temperature, barometric, and density effects of reactivity as well as the reactivity coefficient due to the concentration of boric acid in the reactor were computed additionally. Results of computations are compared with the experiment.« less

Reactivity effects in VVER-1000 of the third unit of the kalinin nuclear power plant at physical start-up. Computations in ShIPR intellectual code system with library of two-group cross sections generated by UNK code

NASA Astrophysics Data System (ADS)

Zizin, M. N.; Zimin, V. G.; Zizina, S. N.; Kryakvin, L. V.; Pitilimov, V. A.; Tereshonok, V. A.

2010-12-01

The ShIPR intellectual code system for mathematical simulation of nuclear reactors includes a set of computing modules implementing the preparation of macro cross sections on the basis of the two-group library of neutron-physics cross sections obtained for the SKETCH-N nodal code. This library is created by using the UNK code for 3D diffusion computation of first VVER-1000 fuel loadings. Computation of neutron fields in the ShIPR system is performed using the DP3 code in the two-group diffusion approximation in 3D triangular geometry. The efficiency of all groups of control rods for the first fuel loading of the third unit of the Kalinin Nuclear Power Plant is computed. The temperature, barometric, and density effects of reactivity as well as the reactivity coefficient due to the concentration of boric acid in the reactor were computed additionally. Results of computations are compared with the experiment.

Users manual and modeling improvements for axial turbine design and performance computer code TD2-2

NASA Technical Reports Server (NTRS)

Glassman, Arthur J.

1992-01-01

Computer code TD2 computes design point velocity diagrams and performance for multistage, multishaft, cooled or uncooled, axial flow turbines. This streamline analysis code was recently modified to upgrade modeling related to turbine cooling and to the internal loss correlation. These modifications are presented in this report along with descriptions of the code's expanded input and output. This report serves as the users manual for the upgraded code, which is named TD2-2.

An Object-Oriented Approach to Writing Computational Electromagnetics Codes

NASA Technical Reports Server (NTRS)

Zimmerman, Martin; Mallasch, Paul G.

1996-01-01

Presently, most computer software development in the Computational Electromagnetics (CEM) community employs the structured programming paradigm, particularly using the Fortran language. Other segments of the software community began switching to an Object-Oriented Programming (OOP) paradigm in recent years to help ease design and development of highly complex codes. This paper examines design of a time-domain numerical analysis CEM code using the OOP paradigm, comparing OOP code and structured programming code in terms of software maintenance, portability, flexibility, and speed.

Mass spectrometry. [in organic chemistry

NASA Technical Reports Server (NTRS)

Burlingame, A. L.; Shackleton, C. H. L.; Howe, I.; Chizhov, O. S.

1978-01-01

A review of mass spectrometry in organic chemistry is given, dealing with advances in instrumentation and computer techniques, selected topics in gas-phase ion chemistry, and applications in such fields as biomedicine, natural-product studies, and environmental pollution analysis. Innovative techniques and instrumentation are discussed, along with chromatographic-mass spectrometric on-line computer techniques, mass spectral interpretation and management techniques, and such topics in gas-phase ion chemistry as electron-impact ionization and decomposition, photoionization, field ionization and desorption, high-pressure mass spectrometry, ion cyclotron resonance, and isomerization reactions of organic ions. Applications of mass spectrometry are examined with respect to bio-oligomers and their constituents, biomedically important substances, microbiology, environmental organic analysis, and organic geochemistry.

Computer Description of the Field Artillery Ammunition Supply Vehicle

DTIC Science & Technology

1983-04-01

Combinatorial Geometry (COM-GEOM) GIFT Computer Code Computer Target Description 2& AfTNACT (Cmne M feerve shb N ,neemssalyan ify by block number) A...input to the GIFT computer code to generate target vulnerability data. F.a- 4 ono OF I NOV 5S OLETE UNCLASSIFIED SECUOITY CLASSIFICATION OF THIS PAGE...Combinatorial Geometry (COM-GEOM) desrription. The "Geometric Information for Tarqets" ( GIFT ) computer code accepts the CO!-GEOM description and

48 CFR 252.227-7013 - Rights in technical data-Noncommercial items.

Code of Federal Regulations, 2011 CFR

2011-10-01

... causing a computer to perform a specific operation or series of operations. (3) Computer software means computer programs, source code, source code listings, object code listings, design details, algorithms... or will be developed exclusively with Government funds; (ii) Studies, analyses, test data, or similar...

48 CFR 252.227-7013 - Rights in technical data-Noncommercial items.

Code of Federal Regulations, 2012 CFR

2012-10-01

... causing a computer to perform a specific operation or series of operations. (3) Computer software means computer programs, source code, source code listings, object code listings, design details, algorithms... or will be developed exclusively with Government funds; (ii) Studies, analyses, test data, or similar...

48 CFR 252.227-7013 - Rights in technical data-Noncommercial items.

Code of Federal Regulations, 2014 CFR

2014-10-01

... causing a computer to perform a specific operation or series of operations. (3) Computer software means computer programs, source code, source code listings, object code listings, design details, algorithms... or will be developed exclusively with Government funds; (ii) Studies, analyses, test data, or similar...

48 CFR 252.227-7013 - Rights in technical data-Noncommercial items.

Code of Federal Regulations, 2010 CFR

2010-10-01

... causing a computer to perform a specific operation or series of operations. (3) Computer software means computer programs, source code, source code listings, object code listings, design details, algorithms... developed exclusively with Government funds; (ii) Studies, analyses, test data, or similar data produced for...

Calibration of Axisymmetric and Quasi-1D Solvers for High Enthalpy Nozzles

NASA Technical Reports Server (NTRS)

Papadopoulos, P. E.; Gochberg, L. A.; Tokarcik-Polsky, S.; Venkatapathy, E.; Deiwert, G. S.; Edwards, Thomas A. (Technical Monitor)

1994-01-01

The proposed paper will present a numerical investigation of the flow characteristics and boundary layer development in the nozzles of high enthalpy shock tunnel facilities used for hypersonic propulsion testing. The computed flow will be validated against existing experimental data. Pitot pressure data obtained at the entrance of the test cabin will be used to validate the numerical simulations. It is necessary to accurately model the facility nozzles in order to characterize the test article flow conditions. Initially the axisymmetric nozzle flow will be computed using a Navier Stokes solver for a range of reservoir conditions. The calculated solutions will be compared and calibrated against available experimental data from the DLR HEG piston-driven shock tunnel and the 16-inch shock tunnel at NASA Ames Research Center. The Reynolds number is assumed to be high enough at the throat that the boundary layer flow is assumed turbulent at this point downstream. The real gas affects will be examined. In high Mach number facilities the boundary layer is thick. Attempts will be made to correlate the boundary layer displacement thickness. The displacement thickness correlation will be used to calibrate the quasi-1D codes NENZF and LSENS in order to provide fast and efficient tools of characterizing the facility nozzles. The calibrated quasi-1D codes will be implemented to study the effects of chemistry and the flow condition variations at the test section due to small variations in the driver gas conditions.

Using Computational Chemistry Activities to Promote Learning and Retention in a Secondary School General Chemistry Setting

ERIC Educational Resources Information Center

Ochterski, Joseph W.

2014-01-01

This article describes the results of using state-of-the-art, research-quality software as a learning tool in a general chemistry secondary school classroom setting. I present three activities designed to introduce fundamental chemical concepts regarding molecular shape and atomic orbitals to students with little background in chemistry, such as…

Symbolic Mathematics Engines in Teaching Chemistry: A Symposium Report

ERIC Educational Resources Information Center

Ellison, Mark

2004-01-01

The use of Symbolic Mathematics Engines (SMEs) in chemical education as a part of the Division of Computers in Chemistry was discussed by a panel of educators at the Symbolic Calculation in Chemistry symposium in Philadelphia in 2004. The panelists agreed that many more topics in chemistry are amenable to SME's exploration and that symbolic…

Antenna pattern study, task 2

NASA Technical Reports Server (NTRS)

Harper, Warren

1989-01-01

Two electromagnetic scattering codes, NEC-BSC and ESP3, were delivered and installed on a NASA VAX computer for use by Marshall Space Flight Center antenna design personnel. The existing codes and certain supplementary software were updated, the codes installed on a computer that will be delivered to the customer, to provide capability for graphic display of the data to be computed by the use of the codes and to assist the customer in the solution of specific problems that demonstrate the use of the codes. With the exception of one code revision, all of these tasks were performed.

Recent plant studies using Victoria 2.0

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

BIXLER,NATHAN E.; GASSER,RONALD D.

2000-03-08

VICTORIA 2.0 is a mechanistic computer code designed to analyze fission product behavior within the reactor coolant system (RCS) during a severe nuclear reactor accident. It provides detailed predictions of the release of radioactive and nonradioactive materials from the reactor core and transport and deposition of these materials within the RCS and secondary circuits. These predictions account for the chemical and aerosol processes that affect radionuclide behavior. VICTORIA 2.0 was released in early 1999; a new version VICTORIA 2.1, is now under development. The largest improvements in VICTORIA 2.1 are connected with the thermochemical database, which is being revised andmore » expanded following the recommendations of a peer review. Three risk-significant severe accident sequences have recently been investigated using the VICTORIA 2.0 code. The focus here is on how various chemistry options affect the predictions. Additionally, the VICTORIA predictions are compared with ones made using the MELCOR code. The three sequences are a station blackout in a GE BWR and steam generator tube rupture (SGTR) and pump-seal LOCA sequences in a 3-loop Westinghouse PWR. These sequences cover a range of system pressures, from fully depressurized to full system pressure. The chief results of this study are the fission product fractions that are retained in the core, RCS, secondary, and containment and the fractions that are released into the environment.« less

Development of the Code RITRACKS

NASA Technical Reports Server (NTRS)

Plante, Ianik; Cucinotta, Francis A.

2013-01-01

A document discusses the code RITRACKS (Relativistic Ion Tracks), which was developed to simulate heavy ion track structure at the microscopic and nanoscopic scales. It is a Monte-Carlo code that simulates the production of radiolytic species in water, event-by-event, and which may be used to simulate tracks and also to calculate dose in targets and voxels of different sizes. The dose deposited by the radiation can be calculated in nanovolumes (voxels). RITRACKS allows simulation of radiation tracks without the need of extensive knowledge of computer programming or Monte-Carlo simulations. It is installed as a regular application on Windows systems. The main input parameters entered by the user are the type and energy of the ion, the length and size of the irradiated volume, the number of ions impacting the volume, and the number of histories. The simulation can be started after the input parameters are entered in the GUI. The number of each kind of interactions for each track is shown in the result details window. The tracks can be visualized in 3D after the simulation is complete. It is also possible to see the time evolution of the tracks and zoom on specific parts of the tracks. The software RITRACKS can be very useful for radiation scientists to investigate various problems in the fields of radiation physics, radiation chemistry, and radiation biology. For example, it can be used to simulate electron ejection experiments (radiation physics).

48 CFR 252.227-7013 - Rights in technical data-Noncommercial items.

Code of Federal Regulations, 2013 CFR

2013-10-01

... causing a computer to perform a specific operation or series of operations. (3) Computer software means computer programs, source code, source code listings, object code listings, design details, algorithms... funds; (ii) Studies, analyses, test data, or similar data produced for this contract, when the study...

COMPUTATIONAL CHEMISTRY: AN EMERGING TECHNOLOGY FOR SOLVING PROBLEMS IN ATMOSPHERIC CHEMISTRY

EPA Science Inventory

Over the past three decades, atmospheric chemistry has served as an important component in developing strategies for reducing ambient concentrations of air pollutants. Laboratory studies are carried out to investigate the key chemical reactions that determine the fates and lif...

Parallel Computation of the Jacobian Matrix for Nonlinear Equation Solvers Using MATLAB

NASA Technical Reports Server (NTRS)

Rose, Geoffrey K.; Nguyen, Duc T.; Newman, Brett A.

2017-01-01

Demonstrating speedup for parallel code on a multicore shared memory PC can be challenging in MATLAB due to underlying parallel operations that are often opaque to the user. This can limit potential for improvement of serial code even for the so-called embarrassingly parallel applications. One such application is the computation of the Jacobian matrix inherent to most nonlinear equation solvers. Computation of this matrix represents the primary bottleneck in nonlinear solver speed such that commercial finite element (FE) and multi-body-dynamic (MBD) codes attempt to minimize computations. A timing study using MATLAB's Parallel Computing Toolbox was performed for numerical computation of the Jacobian. Several approaches for implementing parallel code were investigated while only the single program multiple data (spmd) method using composite objects provided positive results. Parallel code speedup is demonstrated but the goal of linear speedup through the addition of processors was not achieved due to PC architecture.

User Instructions for the Systems Assessment Capability, Rev. 1, Computer Codes Volume 3: Utility Codes

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

Eslinger, Paul W.; Aaberg, Rosanne L.; Lopresti, Charles A.

2004-09-14

This document contains detailed user instructions for a suite of utility codes developed for Rev. 1 of the Systems Assessment Capability. The suite of computer codes for Rev. 1 of Systems Assessment Capability performs many functions.

Preconditioning for the Navier-Stokes equations with finite-rate chemistry

NASA Technical Reports Server (NTRS)

Godfrey, Andrew G.

1993-01-01

The extension of Van Leer's preconditioning procedure to generalized finite-rate chemistry is discussed. Application to viscous flow is begun with the proper preconditioning matrix for the one-dimensional Navier-Stokes equations. Eigenvalue stiffness is resolved and convergence-rate acceleration is demonstrated over the entire Mach-number range from nearly stagnant flow to hypersonic. Specific benefits are realized at the low and transonic flow speeds typical of complete propulsion-system simulations. The extended preconditioning matrix necessarily accounts for both thermal and chemical nonequilibrium. Numerical analysis reveals the possible theoretical improvements from using a preconditioner for all Mach number regimes. Numerical results confirm the expectations from the numerical analysis. Representative test cases include flows with previously troublesome embedded high-condition-number areas. Van Leer, Lee, and Roe recently developed an optimal, analytic preconditioning technique to reduce eigenvalue stiffness over the full Mach-number range. By multiplying the flux-balance residual with the preconditioning matrix, the acoustic wave speeds are scaled so that all waves propagate at the same rate, an essential property to eliminate inherent eigenvalue stiffness. This session discusses a synthesis of the thermochemical nonequilibrium flux-splitting developed by Grossman and Cinnella and the characteristic wave preconditioning of Van Leer into a powerful tool for implicitly solving two and three-dimensional flows with generalized finite-rate chemistry. For finite-rate chemistry, the state vector of unknowns is variable in length. Therefore, the preconditioning matrix extended to generalized finite-rate chemistry must accommodate a flexible system of moving waves. Fortunately, no new kind of wave appears in the system. The only existing waves are entropy and vorticity waves, which move with the fluid, and acoustic waves, which propagate in Mach number dependent directions. The nonequilibrium vibrational energies and species densities in the unknown state vector act strictly as convective waves. The essential concept for extending the preconditioning to generalized chemistry models is determining the differential variables which symmetrize the flux Jacobians. The extension is then straight-forward. This algorithm research effort will be released in a future version of the production level computational code coined the General Aerodynamic Simulation Program (GASP), developed by Walters, Slack, and McGrory.

Development and Application of Computational/In Vitro Toxicological Methods for Chemical Hazard Risk Reduction of New Materials for Advanced Weapon Systems

NASA Technical Reports Server (NTRS)

Frazier, John M.; Mattie, D. R.; Hussain, Saber; Pachter, Ruth; Boatz, Jerry; Hawkins, T. W.

2000-01-01

The development of quantitative structure-activity relationship (QSAR) is essential for reducing the chemical hazards of new weapon systems. The current collaboration between HEST (toxicology research and testing), MLPJ (computational chemistry) and PRS (computational chemistry, new propellant synthesis) is focusing R&D efforts on basic research goals that will rapidly transition to useful products for propellant development. Computational methods are being investigated that will assist in forecasting cellular toxicological end-points. Models developed from these chemical structure-toxicity relationships are useful for the prediction of the toxicological endpoints of new related compounds. Research is focusing on the evaluation tools to be used for the discovery of such relationships and the development of models of the mechanisms of action. Combinations of computational chemistry techniques, in vitro toxicity methods, and statistical correlations, will be employed to develop and explore potential predictive relationships; results for series of molecular systems that demonstrate the viability of this approach are reported. A number of hydrazine salts have been synthesized for evaluation. Computational chemistry methods are being used to elucidate the mechanism of action of these salts. Toxicity endpoints such as viability (LDH) and changes in enzyme activity (glutahoione peroxidase and catalase) are being experimentally measured as indicators of cellular damage. Extrapolation from computational/in vitro studies to human toxicity, is the ultimate goal. The product of this program will be a predictive tool to assist in the development of new, less toxic propellants.

Chemistry for Kids: Generating Carbon Dioxide in Elementary School Chemistry and Using a Computer To Write about It.

ERIC Educational Resources Information Center

Schlenker, Richard M.; Yoshida, Sarah

This material describes an activity using vinegar and baking soda to generate carbon dioxide, and writing a report using the Appleworks word processing program for grades 3 to 8 students. Time requirement, relevant process skills, vocabulary, mathematics skills, computer skills, and materials are listed. Activity procedures including class…

Characterization of High Explosives and Other Energetic Compounds by Computational Chemistry and Molecular Modeling: Experiments for Undergraduate Curriculum

ERIC Educational Resources Information Center

Bumpus, John A.; Lewis, Anne; Stotts, Corey; Cramer, Christopher J.

2007-01-01

Experiments suited for the undergraduate instructional laboratory in which the heats of formation of several aliphatic and aromatic compounds are calculated, are described. The experiments could be used to introduce students to commercially available computational chemistry and its thermodynamics, while assess and compare the energy content of…

Introductory Molecular Orbital Theory: An Honors General Chemistry Computational Lab as Implemented Using Three-Dimensional Modeling Software

ERIC Educational Resources Information Center

Ruddick, Kristie R.; Parrill, Abby L.; Petersen, Richard L.

2012-01-01

In this study, a computational molecular orbital theory experiment was implemented in a first-semester honors general chemistry course. Students used the GAMESS (General Atomic and Molecular Electronic Structure System) quantum mechanical software (as implemented in ChemBio3D) to optimize the geometry for various small molecules. Extended Huckel…

Software platform virtualization in chemistry research and university teaching

PubMed Central

2009-01-01

Background Modern chemistry laboratories operate with a wide range of software applications under different operating systems, such as Windows, LINUX or Mac OS X. Instead of installing software on different computers it is possible to install those applications on a single computer using Virtual Machine software. Software platform virtualization allows a single guest operating system to execute multiple other operating systems on the same computer. We apply and discuss the use of virtual machines in chemistry research and teaching laboratories. Results Virtual machines are commonly used for cheminformatics software development and testing. Benchmarking multiple chemistry software packages we have confirmed that the computational speed penalty for using virtual machines is low and around 5% to 10%. Software virtualization in a teaching environment allows faster deployment and easy use of commercial and open source software in hands-on computer teaching labs. Conclusion Software virtualization in chemistry, mass spectrometry and cheminformatics is needed for software testing and development of software for different operating systems. In order to obtain maximum performance the virtualization software should be multi-core enabled and allow the use of multiprocessor configurations in the virtual machine environment. Server consolidation, by running multiple tasks and operating systems on a single physical machine, can lead to lower maintenance and hardware costs especially in small research labs. The use of virtual machines can prevent software virus infections and security breaches when used as a sandbox system for internet access and software testing. Complex software setups can be created with virtual machines and are easily deployed later to multiple computers for hands-on teaching classes. We discuss the popularity of bioinformatics compared to cheminformatics as well as the missing cheminformatics education at universities worldwide. PMID:20150997

Software platform virtualization in chemistry research and university teaching.

PubMed

Kind, Tobias; Leamy, Tim; Leary, Julie A; Fiehn, Oliver

2009-11-16

Modern chemistry laboratories operate with a wide range of software applications under different operating systems, such as Windows, LINUX or Mac OS X. Instead of installing software on different computers it is possible to install those applications on a single computer using Virtual Machine software. Software platform virtualization allows a single guest operating system to execute multiple other operating systems on the same computer. We apply and discuss the use of virtual machines in chemistry research and teaching laboratories. Virtual machines are commonly used for cheminformatics software development and testing. Benchmarking multiple chemistry software packages we have confirmed that the computational speed penalty for using virtual machines is low and around 5% to 10%. Software virtualization in a teaching environment allows faster deployment and easy use of commercial and open source software in hands-on computer teaching labs. Software virtualization in chemistry, mass spectrometry and cheminformatics is needed for software testing and development of software for different operating systems. In order to obtain maximum performance the virtualization software should be multi-core enabled and allow the use of multiprocessor configurations in the virtual machine environment. Server consolidation, by running multiple tasks and operating systems on a single physical machine, can lead to lower maintenance and hardware costs especially in small research labs. The use of virtual machines can prevent software virus infections and security breaches when used as a sandbox system for internet access and software testing. Complex software setups can be created with virtual machines and are easily deployed later to multiple computers for hands-on teaching classes. We discuss the popularity of bioinformatics compared to cheminformatics as well as the missing cheminformatics education at universities worldwide.

Scientific Ethics in Chemical Education

NASA Astrophysics Data System (ADS)

Kovac, Jeffrey

1996-10-01

Scientific ethics is a subset of professional ethics, the special rules of conduct adhered to by people engaged in those pursuits called professions. It is distinct from, but consistent with, both ordinary morality and moral theory. The codes of professional ethics derive from the two bargains that define a profession: the internal code of practice and the external bargain between the profession and society. While the informal code of professional conduct is well understood by working scientists, it is rarely explicitly included in the chemistry curriculum. Instead, we have relied on informal methods to teach students scientific ethics, a strategy that is haphazard at best. In this paper I argue that scientific ethics can and must be taught as part of the chemistry curriculum and that this is the best done through the case-study method. Many decisions made by working scientists have both a technical and an ethical component. Students need to learn how to make good decisions in professional ethics. The alternative is, at best, sloppy science and, at worst, scientific misconduct.

Highly parallel implementation of non-adiabatic Ehrenfest molecular dynamics

NASA Astrophysics Data System (ADS)

Kanai, Yosuke; Schleife, Andre; Draeger, Erik; Anisimov, Victor; Correa, Alfredo

2014-03-01

While the adiabatic Born-Oppenheimer approximation tremendously lowers computational effort, many questions in modern physics, chemistry, and materials science require an explicit description of coupled non-adiabatic electron-ion dynamics. Electronic stopping, i.e. the energy transfer of a fast projectile atom to the electronic system of the target material, is a notorious example. We recently implemented real-time time-dependent density functional theory based on the plane-wave pseudopotential formalism in the Qbox/qb@ll codes. We demonstrate that explicit integration using a fourth-order Runge-Kutta scheme is very suitable for modern highly parallelized supercomputers. Applying the new implementation to systems with hundreds of atoms and thousands of electrons, we achieved excellent performance and scalability on a large number of nodes both on the BlueGene based ``Sequoia'' system at LLNL as well as the Cray architecture of ``Blue Waters'' at NCSA. As an example, we discuss our work on computing the electronic stopping power of aluminum and gold for hydrogen projectiles, showing an excellent agreement with experiment. These first-principles calculations allow us to gain important insight into the the fundamental physics of electronic stopping.

Computational thermochemistry: Automated generation of scale factors for vibrational frequencies calculated by electronic structure model chemistries

NASA Astrophysics Data System (ADS)

Yu, Haoyu S.; Fiedler, Lucas J.; Alecu, I. M.; Truhlar, Donald G.

2017-01-01

We present a Python program, FREQ, for calculating the optimal scale factors for calculating harmonic vibrational frequencies, fundamental vibrational frequencies, and zero-point vibrational energies from electronic structure calculations. The program utilizes a previously published scale factor optimization model (Alecu et al., 2010) to efficiently obtain all three scale factors from a set of computed vibrational harmonic frequencies. In order to obtain the three scale factors, the user only needs to provide zero-point energies of 15 or 6 selected molecules. If the user has access to the Gaussian 09 or Gaussian 03 program, we provide the option for the user to run the program by entering the keywords for a certain method and basis set in the Gaussian 09 or Gaussian 03 program. Four other Python programs, input.py, input6, pbs.py, and pbs6.py, are also provided for generating Gaussian 09 or Gaussian 03 input and PBS files. The program can also be used with data from any other electronic structure package. A manual of how to use this program is included in the code package.

Comparisons of Calculations with PARTRAC and NOREC: Transport of Electrons in Liquid Water

PubMed Central

Dingfelder, M.; Ritchie, R. H.; Turner, J. E.; Friedland, W.; Paretzke, H. G.; Hamm, R. N.

2013-01-01

Monte Carlo computer models that simulate the detailed, event-by-event transport of electrons in liquid water are valuable for the interpretation and understanding of findings in radiation chemistry and radiation biology. Because of the paucity of experimental data, such efforts must rely on theoretical principles and considerable judgment in their development. Experimental verification of numerical input is possible to only a limited extent. Indirect support for model validity can be gained from a comparison of details between two independently developed computer codes as well as the observable results calculated with them. In this study, we compare the transport properties of electrons in liquid water using two such models, PARTRAC and NOREC. Both use interaction cross sections based on plane-wave Born approximations and a numerical parameterization of the complex dielectric response function for the liquid. The models are described and compared, and their similarities and differences are highlighted. Recent developments in the field are discussed and taken into account. The calculated stopping powers, W values, and slab penetration characteristics are in good agreement with one another and with other independent sources. PMID:18439039

Numerical simulation of electromagnetic wave attenuation in a nonequilibrium chemically reacting hypervelocity flow

NASA Astrophysics Data System (ADS)

Nusca, Michael Joseph, Jr.

The effects of various gasdynamic phenomena on the attenuation of an electromagnetic wave propagating through the nonequilibrium chemically reacting air flow field generated by an aerodynamic body travelling at high velocity is investigated. The nonequilibrium flow field is assumed to consist of seven species including nitric oxide ions and free electrons. The ionization of oxygen and nitrogen atoms is ignored. The aerodynamic body considered is a blunt wedge. The nonequilibrium chemically reacting flow field around this body is numerically simulated using a computer code based on computational fluid dynamics. The computer code solves the Navier-Stokes equations including mass diffusion and heat transfer, using a time-marching, explicit Runge-Kutta scheme. A nonequilibrium air kinetics model consisting of seven species and twenty-eight reactions as well as an equilibrium air model consisting of the same seven species are used. The body surface boundaries are considered as adiabatic or isothermal walls, as well as fully-catalytic and non-catalytic surfaces. Both laminar and turbulent flows are considered; wall generated flow turbulence is simulated using an algebraic mixing length model. An electromagnetic wave is considered as originating from an antenna within the body and is effected by the free electrons in the chemically reacting flow. Analysis of the electromagnetics is performed separately from the fluid dynamic analysis using a series solution of Maxwell's equations valid for the propagation of a long-wavelength plane electromagnetic wave through a thin (i.e., in comparison to wavelength) inhomogeneous plasma layer. The plasma layer is the chemically reacting shock layer around the body. The Navier-Stokes equations are uncoupled from Maxwell's equations. The results of this computational study demonstrate for the first time and in a systematic fashion, the importance of several parameters including equilibrium chemistry, nonequilibrium chemical kinetics, the reaction mechanism, flow viscosity, mass diffusion, and wall boundary conditions on modeling wave attenuation resulting from the interaction of an electromagnetic wave with an aerodynamic plasma. Comparison is made with experimental data.

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

NASA Technical Reports Server (NTRS)

Gould, R. K.; Srivastava, R.

1979-01-01

Two computer codes were developed for describing flow reactors in which high purity, solar grade silicon is produced via reduction of gaseous silicon halides. The first is the CHEMPART code, an axisymmetric, marching code which treats two phase flows with models describing detailed gas-phase chemical kinetics, particle formation, and particle growth. It can be used to described flow reactors in which reactants, mix, react, and form a particulate phase. Detailed radial gas-phase composition, temperature, velocity, and particle size distribution profiles are computed. Also, deposition of heat, momentum, and mass (either particulate or vapor) on reactor walls is described. The second code is a modified version of the GENMIX boundary layer code which is used to compute rates of heat, momentum, and mass transfer to the reactor walls. This code lacks the detailed chemical kinetics and particle handling features of the CHEMPART code but has the virtue of running much more rapidly than CHEMPART, while treating the phenomena occurring in the boundary layer in more detail.

Mobilizing EPA's Comptox Chemistry Dashboard Data on Mobile Devices (ACS Spring Meeting)

EPA Science Inventory

The EPA’s National Center of Computational Toxicology (NCCT) Chemistry Dashboard provides access to chemistry data for about 720,000 chemical substances. The application is used to source, for example: physicochemical property data, bioassay screening data and functional use, and...

Software Applications on the Peregrine System | High-Performance Computing

Science.gov Websites

programming and optimization. Gaussian Chemistry Program for calculating molecular electronic structure and Materials Science Open-source classical molecular dynamics program designed for massively parallel systems framework Q-Chem Chemistry ab initio quantum chemistry package for predictin molecular structures

Students' Learning with the Connected Chemistry (CC1) Curriculum: Navigating the Complexities of the Particulate World

ERIC Educational Resources Information Center

Levy, Sharona T.; Wilensky, Uri

2009-01-01

The focus of this study is students' learning with a Connected Chemistry unit, CC1 (denotes Connected Chemistry, chapter 1), a computer-based environment for learning the topics of gas laws and kinetic molecular theory in chemistry (Levy and Wilensky 2009). An investigation was conducted into high-school students' learning with Connected…

Comparison of two computer codes for crack growth analysis: NASCRAC Versus NASA/FLAGRO

NASA Technical Reports Server (NTRS)

Stallworth, R.; Meyers, C. A.; Stinson, H. C.

1989-01-01

Results are presented from the comparison study of two computer codes for crack growth analysis - NASCRAC and NASA/FLAGRO. The two computer codes gave compatible conservative results when the part through crack analysis solutions were analyzed versus experimental test data. Results showed good correlation between the codes for the through crack at a lug solution. For the through crack at a lug solution, NASA/FLAGRO gave the most conservative results.

Parallelization of the Physical-Space Statistical Analysis System (PSAS)

NASA Technical Reports Server (NTRS)

Larson, J. W.; Guo, J.; Lyster, P. M.

1999-01-01

Atmospheric data assimilation is a method of combining observations with model forecasts to produce a more accurate description of the atmosphere than the observations or forecast alone can provide. Data assimilation plays an increasingly important role in the study of climate and atmospheric chemistry. The NASA Data Assimilation Office (DAO) has developed the Goddard Earth Observing System Data Assimilation System (GEOS DAS) to create assimilated datasets. The core computational components of the GEOS DAS include the GEOS General Circulation Model (GCM) and the Physical-space Statistical Analysis System (PSAS). The need for timely validation of scientific enhancements to the data assimilation system poses computational demands that are best met by distributed parallel software. PSAS is implemented in Fortran 90 using object-based design principles. The analysis portions of the code solve two equations. The first of these is the "innovation" equation, which is solved on the unstructured observation grid using a preconditioned conjugate gradient (CG) method. The "analysis" equation is a transformation from the observation grid back to a structured grid, and is solved by a direct matrix-vector multiplication. Use of a factored-operator formulation reduces the computational complexity of both the CG solver and the matrix-vector multiplication, rendering the matrix-vector multiplications as a successive product of operators on a vector. Sparsity is introduced to these operators by partitioning the observations using an icosahedral decomposition scheme. PSAS builds a large (approx. 128MB) run-time database of parameters used in the calculation of these operators. Implementing a message passing parallel computing paradigm into an existing yet developing computational system as complex as PSAS is nontrivial. One of the technical challenges is balancing the requirements for computational reproducibility with the need for high performance. The problem of computational reproducibility is well known in the parallel computing community. It is a requirement that the parallel code perform calculations in a fashion that will yield identical results on different configurations of processing elements on the same platform. In some cases this problem can be solved by sacrificing performance. Meeting this requirement and still achieving high performance is very difficult. Topics to be discussed include: current PSAS design and parallelization strategy; reproducibility issues; load balance vs. database memory demands, possible solutions to these problems.

Computational Predictions of the Performance Wright 'Bent End' Propellers

NASA Technical Reports Server (NTRS)

Wang, Xiang-Yu; Ash, Robert L.; Bobbitt, Percy J.; Prior, Edwin (Technical Monitor)

2002-01-01

Computational analysis of two 1911 Wright brothers 'Bent End' wooden propeller reproductions have been performed and compared with experimental test results from the Langley Full Scale Wind Tunnel. The purpose of the analysis was to check the consistency of the experimental results and to validate the reliability of the tests. This report is one part of the project on the propeller performance research of the Wright 'Bent End' propellers, intend to document the Wright brothers' pioneering propeller design contributions. Two computer codes were used in the computational predictions. The FLO-MG Navier-Stokes code is a CFD (Computational Fluid Dynamics) code based on the Navier-Stokes Equations. It is mainly used to compute the lift coefficient and the drag coefficient at specified angles of attack at different radii. Those calculated data are the intermediate results of the computation and a part of the necessary input for the Propeller Design Analysis Code (based on Adkins and Libeck method), which is a propeller design code used to compute the propeller thrust coefficient, the propeller power coefficient and the propeller propulsive efficiency.

Proceduracy: Computer Code Writing in the Continuum of Literacy

ERIC Educational Resources Information Center

Vee, Annette

2010-01-01

This dissertation looks at computer programming through the lens of literacy studies, building from the concept of code as a written text with expressive and rhetorical power. I focus on the intersecting technological and social factors of computer code writing as a literacy--a practice I call "proceduracy". Like literacy, proceduracy is a human…

Computer Code Aids Design Of Wings

NASA Technical Reports Server (NTRS)

Carlson, Harry W.; Darden, Christine M.

1993-01-01

AERO2S computer code developed to aid design engineers in selection and evaluation of aerodynamically efficient wing/canard and wing/horizontal-tail configurations that includes simple hinged-flap systems. Code rapidly estimates longitudinal aerodynamic characteristics of conceptual airplane lifting-surface arrangements. Developed in FORTRAN V on CDC 6000 computer system, and ported to MS-DOS environment.

Cloud Computing for Complex Performance Codes.

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

Appel, Gordon John; Hadgu, Teklu; Klein, Brandon Thorin

This report describes the use of cloud computing services for running complex public domain performance assessment problems. The work consisted of two phases: Phase 1 was to demonstrate complex codes, on several differently configured servers, could run and compute trivial small scale problems in a commercial cloud infrastructure. Phase 2 focused on proving non-trivial large scale problems could be computed in the commercial cloud environment. The cloud computing effort was successfully applied using codes of interest to the geohydrology and nuclear waste disposal modeling community.

APC: A New Code for Atmospheric Polarization Computations

NASA Technical Reports Server (NTRS)

Korkin, Sergey V.; Lyapustin, Alexei I.; Rozanov, Vladimir V.

2014-01-01

A new polarized radiative transfer code Atmospheric Polarization Computations (APC) is described. The code is based on separation of the diffuse light field into anisotropic and smooth (regular) parts. The anisotropic part is computed analytically. The smooth regular part is computed numerically using the discrete ordinates method. Vertical stratification of the atmosphere, common types of bidirectional surface reflection and scattering by spherical particles or spheroids are included. A particular consideration is given to computation of the bidirectional polarization distribution function (BPDF) of the waved ocean surface.

Pairing Heterocyclic Cations with closo-dodecafluorododecaborate (2-) Synthesis of Binary Heterocyclium (1+) Salts and a Ag4(heterocycle)8(4+) Salt of B12F12(2-)

DTIC Science & Technology

2011-01-01

10989). 13. SUPPLEMENTARY NOTES Journal article published in the Journal of Fluorine Chemistry, Vol. 132, Nov 2011. PA Case Number: 10989...TELEPHONE NUMBER (include area code) N/A Standard Form 298 (Rev. 8-98) Prescribed by ANSI Std. 239.18 Journal of Fluorine Chemistry 132 (2011... Fluorine Chemistry jo ur n al h o mep ag e: www .e lsev ier . c om / loc ate / f luo r1. Introduction Eight new binary salts that pair the icosahedral

Tracing footprints of environmental events in tree ring chemistry using neutron activation analysis

NASA Astrophysics Data System (ADS)

Sahin, Dagistan

The aim of this study is to identify environmental effects on tree-ring chemistry. It is known that industrial pollution, volcanic eruptions, dust storms, acid rain and similar events can cause substantial changes in soil chemistry. Establishing whether a particular group of trees is sensitive to these changes in soil environment and registers them in the elemental chemistry of contemporary growth rings is the over-riding goal of any Dendrochemistry research. In this study, elemental concentrations were measured in tree-ring samples of absolutely dated eleven modern forest trees, grown in the Mediterranean region, Turkey, collected and dated by the Malcolm and Carolyn Wiener Laboratory for Aegean and Near Eastern Dendrochronology laboratory at Cornell University. Correlations between measured elemental concentrations in the tree-ring samples were analyzed using statistical tests to answer two questions. Does the current concentration of a particular element depend on any other element within the tree? And, are there any elements showing correlated abnormal concentration changes across the majority of the trees? Based on the detailed analysis results, the low mobility of sodium and bromine, positive correlations between calcium, zinc and manganese, positive correlations between trace elements lanthanum, samarium, antimony, and gold within tree-rings were recognized. Moreover, zinc, lanthanum, samarium and bromine showed strong, positive correlations among the trees and were identified as possible environmental signature elements. New Dendrochemistry information found in this study would be also useful in explaining tree physiology and elemental chemistry in Pinus nigra species grown in Turkey. Elemental concentrations in tree-ring samples were measured using Neutron Activation Analysis (NAA) at the Pennsylvania State University Radiation Science and Engineering Center (RSEC). Through this study, advanced methodologies for methodological, computational and experimental NAA were developed to ensure an acceptable accuracy and certainty in the elemental concentration measurements in tree-ring samples. Two independent analysis methods of NAA were used; the well known k-zero method and a novel method developed in this study, called the Multi-isotope Iterative Westcott (MIW) method. The MIW method uses reaction rate probabilities for a group of isotopes, which can be calculated by a neutronic simulation or measured by experimentation, and determines the representative values for the neutron flux and neutron flux characterization parameters based on Westcott convention. Elemental concentration calculations for standard reference material and tree-ring samples were then performed using the MIW and k-zero analysis methods of the NAA and the results were cross verified. In the computational part of this study, a detailed burnup coupled neutronic simulation was developed to analyze real-time neutronic changes in a TRIGA Mark III reactor core, in this study, the Penn State Breazeale Reactor (PSBR) core. To the best of the author`s knowledge, this is the first burnup coupled neutronic simulation with realistic time steps and full fuel temperature profile for a TRIGA reactor using Monte Carlo Utility for Reactor Evolutions (MURE) code and Monte Carlo Neutral-Particle Code (MCNP) coupling. High fidelity and flexibility in the simulation was aimed to replicate the real core operation through the day. This approach resulted in an enhanced accuracy in neutronic representation of the PSBR core with respect to previous neutronic simulation models for the PSBR core. An important contribution was made in the NAA experimentation practices employed in Dendrochemistry studies at the RSEC. Automated laboratory control and analysis software for NAA measurements in the RSEC Radionuclide Applications Laboratory was developed. Detailed laboratory procedures were written in this study comprising preparation, handling and measurements of tree-ring samples in the Radionuclide Applications Laboratory.

DI Diesel Performance and Emissions Models

DTIC Science & Technology

2003-06-11

Skeletal mechanism for NOx chemistry in diesel engines ,” SAE Paper 981450, 1998 SAE Transactions, Vol. 107, Sect. 4, J. Fuels and... mechanism for NOx chemistry proposed by Mellor et al. (1998a) is incorporated in an engine simulation code. The two-zone model, also proposed by Mellor et...34Dynamic Application of a Skeletal Mechanism for DI Diesel NOx Emissions," SAE Paper 2001-01-1984, SAE Trans., J. Fuels & Lubricants,

Oceanic Chemistry and Biology Group (ONR Code 422CB) Program Science Report, FY 81,

DTIC Science & Technology

1982-03-01

instruments to provide the tools needed by the marine chemical conmunity to address small scale length features and rapidly f evolving phenomena. Underway...Through a combined application of field and laboratory studies an attempt is being made to identify the marine abiotic processes which are potentially...Biodeterioration Dissolved Organics Particulate Matter Bioluminescence HEBBLE Sediment Traps Bioturbation Marine Biology STIE Boring Organisms Marine Chemistry

A survey of upwind methods for flows with equilibrium and non-equilibrium chemistry and thermodynamics

NASA Technical Reports Server (NTRS)

Grossman, B.; Garrett, J.; Cinnella, P.

1989-01-01

Several versions of flux-vector split and flux-difference split algorithms were compared with regard to general applicability and complexity. Test computations were performed using curve-fit equilibrium air chemistry for an M = 5 high-temperature inviscid flow over a wedge, and an M = 24.5 inviscid flow over a blunt cylinder for test computations; for these cases, little difference in accuracy was found among the versions of the same flux-split algorithm. For flows with nonequilibrium chemistry, the effects of the thermodynamic model on the development of flux-vector split and flux-difference split algorithms were investigated using an equilibrium model, a general nonequilibrium model, and a simplified model based on vibrational relaxation. Several numerical examples are presented, including nonequilibrium air chemistry in a high-temperature shock tube and nonequilibrium hydrogen-air chemistry in a supersonic diffuser.

Chemistry on the Go: Review of Chemistry Apps on Smartphones

ERIC Educational Resources Information Center

Libman, Diana; Huang, Ling

2013-01-01

touch-controlled computers such as smartphones and iPods are seeing dramatic growth with increasing adoption rates. This review covers about 30 popular and mostly free apps that can be used to learn chemistry and to serve as reference or research tools. The target…

Richard J. French, Ph.D. | NREL

Science.gov Websites

J. French, Ph.D. Photo of Richard J. French Rick French Researcher IV-Chemistry Richard.French Laboratory equipment design and construction Computer-aided design (CAD) Education Ph.D., Chemistry, Oregon State University B.S., Chemistry, Wheaton College Professional Experience Research Scientist, National

Hypercube matrix computation task

NASA Technical Reports Server (NTRS)

Calalo, Ruel H.; Imbriale, William A.; Jacobi, Nathan; Liewer, Paulett C.; Lockhart, Thomas G.; Lyzenga, Gregory A.; Lyons, James R.; Manshadi, Farzin; Patterson, Jean E.

1988-01-01

A major objective of the Hypercube Matrix Computation effort at the Jet Propulsion Laboratory (JPL) is to investigate the applicability of a parallel computing architecture to the solution of large-scale electromagnetic scattering problems. Three scattering analysis codes are being implemented and assessed on a JPL/California Institute of Technology (Caltech) Mark 3 Hypercube. The codes, which utilize different underlying algorithms, give a means of evaluating the general applicability of this parallel architecture. The three analysis codes being implemented are a frequency domain method of moments code, a time domain finite difference code, and a frequency domain finite elements code. These analysis capabilities are being integrated into an electromagnetics interactive analysis workstation which can serve as a design tool for the construction of antennas and other radiating or scattering structures. The first two years of work on the Hypercube Matrix Computation effort is summarized. It includes both new developments and results as well as work previously reported in the Hypercube Matrix Computation Task: Final Report for 1986 to 1987 (JPL Publication 87-18).

Effectiveness of Using Computer-Assisted Supplementary Instruction for Teaching the Mole Concept

NASA Astrophysics Data System (ADS)

Yalçinalp, Serpil; Geban, Ömer; Özkan, Ilker

This study examined the effect of computer-assisted instruction (CAI), used as a problem-solving supplement to classroom instruction, on students' understanding of chemical formulas and mole concept, their attitudes toward chemistry subjects, and CAI. The objective was to assess the effectiveness of CAI over recitation hours when both teaching methods were used as a supplement to the traditional chemistry instruction. We randomly selected two classes in a secondary school. Each teaching strategy was randomly assigned to one class. The experimental group received supplementary instruction delivered via CAI, while the control group received similar instruction through recitation hours. The data were analyzed using two-way analysis of variance and t-test. It was found that the students who used the CAI accompanied with lectures scored significantly higher than those who attended recitation hours, in terms of school subject achievement in chemistry and attitudes toward chemistry subjects. In addition, there was a significant improvement in the attitudes of students in the experimental group toward the use of computers in a chemistry course. There was no significant difference between the performances of females versus males in each treatment group.Received: 26 April 1994; Revised: 6 April 1995;

Calculation of Water Drop Trajectories to and About Arbitrary Three-Dimensional Bodies in Potential Airflow

NASA Technical Reports Server (NTRS)

Norment, H. G.

1980-01-01

Calculations can be performed for any atmospheric conditions and for all water drop sizes, from the smallest cloud droplet to large raindrops. Any subsonic, external, non-lifting flow can be accommodated; flow into, but not through, inlets also can be simulated. Experimental water drop drag relations are used in the water drop equations of motion and effects of gravity settling are included. Seven codes are described: (1) a code used to debug and plot body surface description data; (2) a code that processes the body surface data to yield the potential flow field; (3) a code that computes flow velocities at arrays of points in space; (4) a code that computes water drop trajectories from an array of points in space; (5) a code that computes water drop trajectories and fluxes to arbitrary target points; (6) a code that computes water drop trajectories tangent to the body; and (7) a code that produces stereo pair plots which include both the body and trajectories. Code descriptions include operating instructions, card inputs and printouts for example problems, and listing of the FORTRAN codes. Accuracy of the calculations is discussed, and trajectory calculation results are compared with prior calculations and with experimental data.

Utilizing GPUs to Accelerate Turbomachinery CFD Codes

NASA Technical Reports Server (NTRS)

MacCalla, Weylin; Kulkarni, Sameer

2016-01-01

GPU computing has established itself as a way to accelerate parallel codes in the high performance computing world. This work focuses on speeding up APNASA, a legacy CFD code used at NASA Glenn Research Center, while also drawing conclusions about the nature of GPU computing and the requirements to make GPGPU worthwhile on legacy codes. Rewriting and restructuring of the source code was avoided to limit the introduction of new bugs. The code was profiled and investigated for parallelization potential, then OpenACC directives were used to indicate parallel parts of the code. The use of OpenACC directives was not able to reduce the runtime of APNASA on either the NVIDIA Tesla discrete graphics card, or the AMD accelerated processing unit. Additionally, it was found that in order to justify the use of GPGPU, the amount of parallel work being done within a kernel would have to greatly exceed the work being done by any one portion of the APNASA code. It was determined that in order for an application like APNASA to be accelerated on the GPU, it should not be modular in nature, and the parallel portions of the code must contain a large portion of the code's computation time.

Open Source Molecular Modeling

PubMed Central

Pirhadi, Somayeh; Sunseri, Jocelyn; Koes, David Ryan

2016-01-01

The success of molecular modeling and computational chemistry efforts are, by definition, dependent on quality software applications. Open source software development provides many advantages to users of modeling applications, not the least of which is that the software is free and completely extendable. In this review we categorize, enumerate, and describe available open source software packages for molecular modeling and computational chemistry. PMID:27631126

Using an Advanced Computational Laboratory Experiment to Extend and Deepen Physical Chemistry Students' Understanding of Atomic Structure

ERIC Educational Resources Information Center

Hoffman, Gary G.

2015-01-01

A computational laboratory experiment is described, which involves the advanced study of an atomic system. The students use concepts and techniques typically covered in a physical chemistry course but extend those concepts and techniques to more complex situations. The students get a chance to explore the study of atomic states and perform…

Using a Tablet PC to Enhance Student Engagement and Learning in an Introductory Organic Chemistry Course

ERIC Educational Resources Information Center

Derting, Terry L.; Cox, James R.

2008-01-01

Over the past three decades, computer-based technologies have influenced all aspects of chemistry, including chemical education. Pen-based computing applications, such as the tablet PC, have reemerged in the past few years and are providing new ways for educators to deliver content and engage students inside and outside the classroom and…

Implementing a Computer Program that Captures Students' Work on Customizable, Periodic-System Data Assignments

ERIC Educational Resources Information Center

Wiediger, Susan D.

2009-01-01

The periodic table and the periodic system are central to chemistry and thus to many introductory chemistry courses. A number of existing activities use various data sets to model the development process for the periodic table. This paper describes an image arrangement computer program developed to mimic a paper-based card sorting periodic table…

Computational Modeling of the Optical Rotation of Amino Acids: An "in Silico" Experiment for Physical Chemistry

ERIC Educational Resources Information Center

Simpson, Scott; Autschbach, Jochen; Zurek, Eva

2013-01-01

A computational experiment that investigates the optical activity of the amino acid valine has been developed for an upper-level undergraduate physical chemistry laboratory course. Hybrid density functional theory calculations were carried out for valine to confirm the rule that adding a strong acid to a solution of an amino acid in the l…

A Compilation of Postgraduate Theses Written in Turkey on Computer Assisted Instruction in Chemistry Education

ERIC Educational Resources Information Center

Bozdogan, Aykut Emre; Demirbas, Murat

2014-01-01

The purpose of the study conducted is to present in-depth information about the postgraduate theses written within the context of Computer Assisted Instruction in Chemistry Education in Turkey. The theses collected in National Thesis Centre of Turkish Council of Higher Education were examined. As a result of an examination, it was found that about…

Factors Affecting Energy Barriers for Pyramidal Inversion in Amines and Phosphines: A Computational Chemistry Lab Exercise

ERIC Educational Resources Information Center

Montgomery, Craig D.

2013-01-01

An undergraduate exercise in computational chemistry that investigates the energy barrier for pyramidal inversion of amines and phosphines is presented. Semiempirical calculations (PM3) of the ground-state and transition-state energies for NR[superscript 1]R[superscript 2]R[superscript 3] and PR[superscript 1]R[superscript 2]R[superscript 3] allow…

Solutions, Unit 5: Colligative Properties of Solutions. A Computer-Enriched Module for Introductory Chemistry. Student's Guide and Teacher's Guide.

ERIC Educational Resources Information Center

Bader, Morris

Presented are the teacher's guide and student manual for one of a series of self-instructional, computer-based learning modules for an introductory, undergraduate chemistry course. The student manual for this unit on the colligative properties of solutions includes objectives, prerequisites, pretest, discussion, and 20 problem sets. Included in…

PASCO: Structural panel analysis and sizing code: Users manual - Revised

NASA Technical Reports Server (NTRS)

Anderson, M. S.; Stroud, W. J.; Durling, B. J.; Hennessy, K. W.

1981-01-01

A computer code denoted PASCO is described for analyzing and sizing uniaxially stiffened composite panels. Buckling and vibration analyses are carried out with a linked plate analysis computer code denoted VIPASA, which is included in PASCO. Sizing is based on nonlinear mathematical programming techniques and employs a computer code denoted CONMIN, also included in PASCO. Design requirements considered are initial buckling, material strength, stiffness and vibration frequency. A user's manual for PASCO is presented.

Networked Instructional Chemistry: Using Technology To Teach Chemistry

NASA Astrophysics Data System (ADS)

Smith, Stanley; Stovall, Iris

1996-10-01

Networked multimedia microcomputers provide new ways to help students learn chemistry and to help instructors manage the learning environment. This technology is used to replace some traditional laboratory work, collect on-line experimental data, enhance lectures and quiz sections with multimedia presentations, provide prelaboratory training for beginning nonchemistry- major organic laboratory, provide electronic homework for organic chemistry students, give graduate students access to real NMR data for analysis, and provide access to molecular modeling tools. The integration of all of these activities into an active learning environment is made possible by a client-server network of hundreds of computers. This requires not only instructional software but also classroom and course management software, computers, networking, and room management. Combining computer-based work with traditional course material is made possible with software management tools that allow the instructor to monitor the progress of each student and make available an on-line gradebook so students can see their grades and class standing. This client-server based system extends the capabilities of the earlier mainframe-based PLATO system, which was used for instructional computing. This paper outlines the components of a technology center used to support over 5,000 students per semester.

Nanoinformatics: an emerging area of information technology at the intersection of bioinformatics, computational chemistry and nanobiotechnology.

PubMed

González-Nilo, Fernando; Pérez-Acle, Tomás; Guínez-Molinos, Sergio; Geraldo, Daniela A; Sandoval, Claudia; Yévenes, Alejandro; Santos, Leonardo S; Laurie, V Felipe; Mendoza, Hegaly; Cachau, Raúl E

2011-01-01

After the progress made during the genomics era, bioinformatics was tasked with supporting the flow of information generated by nanobiotechnology efforts. This challenge requires adapting classical bioinformatic and computational chemistry tools to store, standardize, analyze, and visualize nanobiotechnological information. Thus, old and new bioinformatic and computational chemistry tools have been merged into a new sub-discipline: nanoinformatics. This review takes a second look at the development of this new and exciting area as seen from the perspective of the evolution of nanobiotechnology applied to the life sciences. The knowledge obtained at the nano-scale level implies answers to new questions and the development of new concepts in different fields. The rapid convergence of technologies around nanobiotechnologies has spun off collaborative networks and web platforms created for sharing and discussing the knowledge generated in nanobiotechnology. The implementation of new database schemes suitable for storage, processing and integrating physical, chemical, and biological properties of nanoparticles will be a key element in achieving the promises in this convergent field. In this work, we will review some applications of nanobiotechnology to life sciences in generating new requirements for diverse scientific fields, such as bioinformatics and computational chemistry.

SCELib3.0: The new revision of SCELib, the parallel computational library of molecular properties in the Single Center Approach

NASA Astrophysics Data System (ADS)

Sanna, N.; Baccarelli, I.; Morelli, G.

2009-12-01

SCELib is a computer program which implements the Single Center Expansion (SCE) method to describe molecular electronic densities and the interaction potentials between a charged projectile (electron or positron) and a target molecular system. The first version (CPC Catalog identifier ADMG_v1_0) was submitted to the CPC Program Library in 2000, and version 2.0 (ADMG_v2_0) was submitted in 2004. We here announce the new release 3.0 which presents additional features with respect to the previous versions aiming at a significative enhance of its capabilities to deal with larger molecular systems. SCELib 3.0 allows for ab initio effective core potential (ECP) calculations of the molecular wavefunctions to be used in the SCE method in addition to the standard all-electron description of the molecule. The list of supported architectures has been updated and the code has been ported to platforms based on accelerating coprocessors, such as the NVIDIA GPGPU and the new parallel model adopted is able to efficiently run on a mixed many-core computing system. Program summaryProgram title: SCELib3.0 Catalogue identifier: ADMG_v3_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADMG_v3_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.: 2 018 862 No. of bytes in distributed program, including test data, etc.: 4 955 014 Distribution format: tar.gz Programming language: C Compilers used: xlc V8.x, Intel C V10.x, Portland Group V7.x, nvcc V2.x Computer: All SMP platforms based on AIX, Linux and SUNOS operating systems over SPARC, POWER, Intel Itanium2, X86, em64t and Opteron processors Operating system: SUNOS, IBM AIX, Linux RedHat (Enterprise), Linux SuSE (SLES) Has the code been vectorized or parallelized?: Yes. 1 to 32 (CPU or GPU) used RAM: Up to 32 GB depending on the molecular system and runtime parameters Classification: 16.5 Catalogue identifier of previous version: ADMG_v2_0 Journal reference of previous version: Comput. Phys. Comm. 162 (2004) 51 External routines: CUDA libraries (SDK V2.x). Does the new version supersede the previous version?: Yes Nature of problem: In this set of codes an efficient procedure is implemented to describe the wavefunction and related molecular properties of a polyatomic molecular system within the Single Center of Expansion (SCE) approximation. The resulting SCE wavefunction, electron density, electrostatic and correlation/polarization potentials can then be used in a wide variety of applications, such as electron-molecule scattering calculations, quantum chemistry studies, biomodelling and drug design. Solution method: The polycentre Hartree-Fock solution for a molecule of arbitrary geometry, based on linear combination of Gaussian-Type Orbital (GTO), is expanded over a single center, typically the Center Of Mass (C.O.M.), by means of a Gauss Legendre/Chebyschev quadrature over the θ,φ angular coordinates. The resulting SCE numerical wavefunction is then used to calculate the one-particle electron density, the electrostatic potential and two different models for the correlation/polarization potentials induced by the impinging electron, which have the correct asymptotic behavior for the leading dipole molecular polarizabilities. Reasons for new version: The present release of SCELib allows the study of larger molecular systems with respect to the previous versions by means of theoretical and technological advances, with the first implementation of the code over a many-core computing system. Summary of revisions: The major features added with respect to SCELib Version 2.0 are molecular wavefunctions obtained via the Los Alamos (Hay and Wadt) LAN ECP plus DZ description of the inner-shell electrons (on Na-La, Hf-Bi elements) [1] can now be single-center-expanded; the addition required modifications of: (i) the filtering code readgau, (ii) the main reading function setinp, (iii) the sphint code (including changes to the CalcMO code), (iv) the densty code, (v) the vst code; the classes of platforms supported now include two more architectures based on accelerated coprocessors (Nvidia GSeries GPGPU and ClearSpeed e720 (ClearSpeed version, experimental; initial preliminary porting of the sphint() function not for production runs - see the code documentation for additional detail). A single-precision representation for real numbers in the SCE mapping of the GTOs ( sphint code), has been implemented into the new code; the I h symmetry point group for the molecular systems has been added to those already allowed in the SCE procedure; the orientation of the molecular axis system for the Cs (planar) symmetry has been changed in accord with the standard orientation adopted by the latest version of the quantum chemistry code (Gaussian C03 [2]), which is used to generate the input multi-centre molecular wavefunctions ( z-axis perpendicular to the symmetry plane); the abelian subgroup for the Cs point group has been changed from C 1 to Cs; atomic basis functions including g-type GTOs can now be single-center-expanded. Restrictions: Depending on the molecular system under study and on the operating conditions the program may or may not fit into available RAM memory. In this case a feature of the program is to memory map a disk file in order to efficiently access the memory data through a disk device. The parallel GP-GPU implementation limits the number of CPU threads to the number of GPU cores present. Running time: The execution time strongly depends on the molecular target description and on the hardware/OS chosen, it is directly proportional to the ( r,θ,φ) grid size and to the number of angular basis functions used. Thus, from the program printout of the main arrays memory occupancy, the user can approximately derive the expected computer time needed for a given calculation executed in serial mode. For parallel executions the overall efficiency must be further taken into account, and this depends on the no. of processors used as well as on the parallel architecture chosen, so a simple general law is at present not determinable. References:[1] P.J. Hay, W.R. Wadt, J. Chem. Phys. 82 (1985) 270; W.R. Wadt, P.J. Hay, J. Chem. Phys. 284 (1985);P.J. Hay, W.R. Wadt, J. Chem. Phys. 299 (1985). [2] M.J. Frisch et al., Gaussian 03, revision C.02, Gaussian, Inc., Wallingford, CT, 2004.

What is information?

PubMed

Barbieri, Marcello

2016-03-13

Molecular biology is based on two great discoveries: the first is that genes carry hereditary information in the form of linear sequences of nucleotides; the second is that in protein synthesis a sequence of nucleotides is translated into a sequence of amino acids, a process that amounts to a transfer of information from genes to proteins. These discoveries have shown that the information of genes and proteins is the specific linear order of their sequences. This is a clear definition of information and there is no doubt that it reflects an experimental reality. What is not clear, however, is the ontological status of information, and the result is that today we have two conflicting paradigms in biology. One is the 'chemical paradigm', the idea that 'life is chemistry', or, more precisely, that 'life is an extremely complex form of chemistry'. The other is the 'information paradigm', the view that chemistry is not enough, that 'life is chemistry plus information'. This implies that there is an ontological difference between information and chemistry, a difference which is often expressed by saying that information-based processes like heredity and natural selection simply do not exist in the world of chemistry. Against this conclusion, the supporters of the chemical paradigm have argued that the concept of information is only a linguistic metaphor, a word that summarizes the result of countless underlying chemical reactions. The supporters of the information paradigm insist that information is a real and fundamental component of the living world, but have not been able to prove this point. As a result, the chemical view has not been abandoned and the two paradigms both coexist today. Here, it is shown that a solution to the ontological problem of information does exist. It comes from the idea that life is artefact-making, that genes and proteins are molecular artefacts manufactured by molecular machines and that artefacts necessarily require sequences and coding rules in addition to the quantities of physics and chemistry. More precisely, it is shown that the production of artefacts requires new observables that are referred to as nominable entities because they can be described only by naming their components in their natural order. From an ontological point of view, in conclusion, information is a nominable entity, a fundamental but not-computable observable. © 2016 The Author(s).

NASA Rotor 37 CFD Code Validation: Glenn-HT Code

NASA Technical Reports Server (NTRS)

Ameri, Ali A.

2010-01-01

In order to advance the goals of NASA aeronautics programs, it is necessary to continuously evaluate and improve the computational tools used for research and design at NASA. One such code is the Glenn-HT code which is used at NASA Glenn Research Center (GRC) for turbomachinery computations. Although the code has been thoroughly validated for turbine heat transfer computations, it has not been utilized for compressors. In this work, Glenn-HT was used to compute the flow in a transonic compressor and comparisons were made to experimental data. The results presented here are in good agreement with this data. Most of the measures of performance are well within the measurement uncertainties and the exit profiles of interest agree with the experimental measurements.

Final report for the Tera Computer TTI CRADA

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

Davidson, G.S.; Pavlakos, C.; Silva, C.

1997-01-01

Tera Computer and Sandia National Laboratories have completed a CRADA, which examined the Tera Multi-Threaded Architecture (MTA) for use with large codes of importance to industry and DOE. The MTA is an innovative architecture that uses parallelism to mask latency between memories and processors. The physical implementation is a parallel computer with high cross-section bandwidth and GaAs processors designed by Tera, which support many small computation threads and fast, lightweight context switches between them. When any thread blocks while waiting for memory accesses to complete, another thread immediately begins execution so that high CPU utilization is maintained. The Tera MTAmore » parallel computer has a single, global address space, which is appealing when porting existing applications to a parallel computer. This ease of porting is further enabled by compiler technology that helps break computations into parallel threads. DOE and Sandia National Laboratories were interested in working with Tera to further develop this computing concept. While Tera Computer would continue the hardware development and compiler research, Sandia National Laboratories would work with Tera to ensure that their compilers worked well with important Sandia codes, most particularly CTH, a shock physics code used for weapon safety computations. In addition to that important code, Sandia National Laboratories would complete research on a robotic path planning code, SANDROS, which is important in manufacturing applications, and would evaluate the MTA performance on this code. Finally, Sandia would work directly with Tera to develop 3D visualization codes, which would be appropriate for use with the MTA. Each of these tasks has been completed to the extent possible, given that Tera has just completed the MTA hardware. All of the CRADA work had to be done on simulators.« less

Operations analysis (study 2.1). Program listing for the LOVES computer code

NASA Technical Reports Server (NTRS)

Wray, S. T., Jr.

1974-01-01

A listing of the LOVES computer program is presented. The program is coded partially in SIMSCRIPT and FORTRAN. This version of LOVES is compatible with both the CDC 7600 and the UNIVAC 1108 computers. The code has been compiled, loaded, and executed successfully on the EXEC 8 system for the UNIVAC 1108.

ADVANCED COMPUTATIONAL METHODS IN DOSE MODELING: APPLICATION OF COMPUTATIONAL BIOPHYSICAL TRANSPORT, COMPUTATIONAL CHEMISTRY, AND COMPUTATIONAL BIOLOGY

EPA Science Inventory

Computational toxicology (CompTox) leverages the significant gains in computing power and computational techniques (e.g., numerical approaches, structure-activity relationships, bioinformatics) realized over the last few years, thereby reducing costs and increasing efficiency i...

Analysis of the Length of Braille Texts in English Braille American Edition, the Nemeth Code, and Computer Braille Code versus the Unified English Braille Code

ERIC Educational Resources Information Center

Knowlton, Marie; Wetzel, Robin

2006-01-01

This study compared the length of text in English Braille American Edition, the Nemeth code, and the computer braille code with the Unified English Braille Code (UEBC)--also known as Unified English Braille (UEB). The findings indicate that differences in the length of text are dependent on the type of material that is transcribed and the grade…

A MATLAB based 3D modeling and inversion code for MT data

NASA Astrophysics Data System (ADS)

Singh, Arun; Dehiya, Rahul; Gupta, Pravin K.; Israil, M.

2017-07-01

The development of a MATLAB based computer code, AP3DMT, for modeling and inversion of 3D Magnetotelluric (MT) data is presented. The code comprises two independent components: grid generator code and modeling/inversion code. The grid generator code performs model discretization and acts as an interface by generating various I/O files. The inversion code performs core computations in modular form - forward modeling, data functionals, sensitivity computations and regularization. These modules can be readily extended to other similar inverse problems like Controlled-Source EM (CSEM). The modular structure of the code provides a framework useful for implementation of new applications and inversion algorithms. The use of MATLAB and its libraries makes it more compact and user friendly. The code has been validated on several published models. To demonstrate its versatility and capabilities the results of inversion for two complex models are presented.

Laboratory Sequence in Computational Methods for Introductory Chemistry

NASA Astrophysics Data System (ADS)

Cody, Jason A.; Wiser, Dawn C.

2003-07-01

A four-exercise laboratory sequence for introductory chemistry integrating hands-on, student-centered experience with computer modeling has been designed and implemented. The progression builds from exploration of molecular shapes to intermolecular forces and the impact of those forces on chemical separations made with gas chromatography and distillation. The sequence ends with an exploration of molecular orbitals. The students use the computers as a tool; they build the molecules, submit the calculations, and interpret the results. Because of the construction of the sequence and its placement spanning the semester break, good laboratory notebook practices are reinforced and the continuity of course content and methods between semesters is emphasized. The inclusion of these techniques in the first year of chemistry has had a positive impact on student perceptions and student learning.

77 FR 5852 - Proposal Review Panel for Chemistry; Notice of Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-06

... NATIONAL SCIENCE FOUNDATION Proposal Review Panel for Chemistry; Notice of Meeting In accordance with the Federal Advisory Committee Act (Pub. L. 92- 463, as amended), the National Science Foundation... and Computation for Chemistry Presentations. 11:45 a.m.-1 p.m. Closed--Executive Session, review and...

Public Access to Environmental Chemistry Data via the CompTox Chemistry Dashboard (ACS Fall Meeting 6 of 12)

EPA Science Inventory

The National Center for Computational Toxicology (NCCT) has assembled and delivered an enormous quantity and diversity of data for the environmental sciences through the CompTox Chemistry Dashboard. These data include high-throughput in vitro screening data, in vivo and functiona...

Applications of automatic differentiation in computational fluid dynamics

NASA Technical Reports Server (NTRS)

Green, Lawrence L.; Carle, A.; Bischof, C.; Haigler, Kara J.; Newman, Perry A.

1994-01-01

Automatic differentiation (AD) is a powerful computational method that provides for computing exact sensitivity derivatives (SD) from existing computer programs for multidisciplinary design optimization (MDO) or in sensitivity analysis. A pre-compiler AD tool for FORTRAN programs called ADIFOR has been developed. The ADIFOR tool has been easily and quickly applied by NASA Langley researchers to assess the feasibility and computational impact of AD in MDO with several different FORTRAN programs. These include a state-of-the-art three dimensional multigrid Navier-Stokes flow solver for wings or aircraft configurations in transonic turbulent flow. With ADIFOR the user specifies sets of independent and dependent variables with an existing computer code. ADIFOR then traces the dependency path throughout the code, applies the chain rule to formulate derivative expressions, and generates new code to compute the required SD matrix. The resulting codes have been verified to compute exact non-geometric and geometric SD for a variety of cases. in less time than is required to compute the SD matrix using centered divided differences.

Fundamentals, current state of the development of, and prospects for further improvement of the new-generation thermal-hydraulic computational HYDRA-IBRAE/LM code for simulation of fast reactor systems

NASA Astrophysics Data System (ADS)

Alipchenkov, V. M.; Anfimov, A. M.; Afremov, D. A.; Gorbunov, V. S.; Zeigarnik, Yu. A.; Kudryavtsev, A. V.; Osipov, S. L.; Mosunova, N. A.; Strizhov, V. F.; Usov, E. V.

2016-02-01

The conceptual fundamentals of the development of the new-generation system thermal-hydraulic computational HYDRA-IBRAE/LM code are presented. The code is intended to simulate the thermalhydraulic processes that take place in the loops and the heat-exchange equipment of liquid-metal cooled fast reactor systems under normal operation and anticipated operational occurrences and during accidents. The paper provides a brief overview of Russian and foreign system thermal-hydraulic codes for modeling liquid-metal coolants and gives grounds for the necessity of development of a new-generation HYDRA-IBRAE/LM code. Considering the specific engineering features of the nuclear power plants (NPPs) equipped with the BN-1200 and the BREST-OD-300 reactors, the processes and the phenomena are singled out that require a detailed analysis and development of the models to be correctly described by the system thermal-hydraulic code in question. Information on the functionality of the computational code is provided, viz., the thermalhydraulic two-phase model, the properties of the sodium and the lead coolants, the closing equations for simulation of the heat-mass exchange processes, the models to describe the processes that take place during the steam-generator tube rupture, etc. The article gives a brief overview of the usability of the computational code, including a description of the support documentation and the supply package, as well as possibilities of taking advantages of the modern computer technologies, such as parallel computations. The paper shows the current state of verification and validation of the computational code; it also presents information on the principles of constructing of and populating the verification matrices for the BREST-OD-300 and the BN-1200 reactor systems. The prospects are outlined for further development of the HYDRA-IBRAE/LM code, introduction of new models into it, and enhancement of its usability. It is shown that the program of development and practical application of the code will allow carrying out in the nearest future the computations to analyze the safety of potential NPP projects at a qualitatively higher level.

Performance assessment of KORAT-3D on the ANL IBM-SP computer

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

Alexeyev, A.V.; Zvenigorodskaya, O.A.; Shagaliev, R.M.

1999-09-01

The TENAR code is currently being developed at the Russian Federal Nuclear Center (VNIIEF) as a coupled dynamics code for the simulation of transients in VVER and RBMK systems and other nuclear systems. The neutronic module in this code system is KORAT-3D. This module is also one of the most computationally intensive components of the code system. A parallel version of KORAT-3D has been implemented to achieve the goal of obtaining transient solutions in reasonable computational time, particularly for RBMK calculations that involve the application of >100,000 nodes. An evaluation of the KORAT-3D code performance was recently undertaken on themore » Argonne National Laboratory (ANL) IBM ScalablePower (SP) parallel computer located in the Mathematics and Computer Science Division of ANL. At the time of the study, the ANL IBM-SP computer had 80 processors. This study was conducted under the auspices of a technical staff exchange program sponsored by the International Nuclear Safety Center (INSC).« less

Profugus

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

Evans, Thomas; Hamilton, Steven; Slattery, Stuart

Profugus is an open-source mini-application (mini-app) for radiation transport and reactor applications. It contains the fundamental computational kernels used in the Exnihilo code suite from Oak Ridge National Laboratory. However, Exnihilo is production code with a substantial user base. Furthermore, Exnihilo is export controlled. This makes collaboration with computer scientists and computer engineers difficult. Profugus is designed to bridge that gap. By encapsulating the core numerical algorithms in an abbreviated code base that is open-source, computer scientists can analyze the algorithms and easily make code-architectural changes to test performance without compromising the production code values of Exnihilo. Profugus is notmore » meant to be production software with respect to problem analysis. The computational kernels in Profugus are designed to analyze performance, not correctness. Nonetheless, users of Profugus can setup and run problems with enough real-world features to be useful as proof-of-concept for actual production work.« less

NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations

NASA Astrophysics Data System (ADS)

Valiev, M.; Bylaska, E. J.; Govind, N.; Kowalski, K.; Straatsma, T. P.; Van Dam, H. J. J.; Wang, D.; Nieplocha, J.; Apra, E.; Windus, T. L.; de Jong, W. A.

2010-09-01

The latest release of NWChem delivers an open-source computational chemistry package with extensive capabilities for large scale simulations of chemical and biological systems. Utilizing a common computational framework, diverse theoretical descriptions can be used to provide the best solution for a given scientific problem. Scalable parallel implementations and modular software design enable efficient utilization of current computational architectures. This paper provides an overview of NWChem focusing primarily on the core theoretical modules provided by the code and their parallel performance. Program summaryProgram title: NWChem Catalogue identifier: AEGI_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGI_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Open Source Educational Community License No. of lines in distributed program, including test data, etc.: 11 709 543 No. of bytes in distributed program, including test data, etc.: 680 696 106 Distribution format: tar.gz Programming language: Fortran 77, C Computer: all Linux based workstations and parallel supercomputers, Windows and Apple machines Operating system: Linux, OS X, Windows Has the code been vectorised or parallelized?: Code is parallelized Classification: 2.1, 2.2, 3, 7.3, 7.7, 16.1, 16.2, 16.3, 16.10, 16.13 Nature of problem: Large-scale atomistic simulations of chemical and biological systems require efficient and reliable methods for ground and excited solutions of many-electron Hamiltonian, analysis of the potential energy surface, and dynamics. Solution method: Ground and excited solutions of many-electron Hamiltonian are obtained utilizing density-functional theory, many-body perturbation approach, and coupled cluster expansion. These solutions or a combination thereof with classical descriptions are then used to analyze potential energy surface and perform dynamical simulations. Additional comments: Full documentation is provided in the distribution file. This includes an INSTALL file giving details of how to build the package. A set of test runs is provided in the examples directory. The distribution file for this program is over 90 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: Running time depends on the size of the chemical system, complexity of the method, number of cpu's and the computational task. It ranges from several seconds for serial DFT energy calculations on a few atoms to several hours for parallel coupled cluster energy calculations on tens of atoms or ab-initio molecular dynamics simulation on hundreds of atoms.

Investigation of Navier-Stokes Code Verification and Design Optimization

NASA Technical Reports Server (NTRS)

Vaidyanathan, Rajkumar

2004-01-01

With rapid progress made in employing computational techniques for various complex Navier-Stokes fluid flow problems, design optimization problems traditionally based on empirical formulations and experiments are now being addressed with the aid of computational fluid dynamics (CFD). To be able to carry out an effective CFD-based optimization study, it is essential that the uncertainty and appropriate confidence limits of the CFD solutions be quantified over the chosen design space. The present dissertation investigates the issues related to code verification, surrogate model-based optimization and sensitivity evaluation. For Navier-Stokes (NS) CFD code verification a least square extrapolation (LSE) method is assessed. This method projects numerically computed NS solutions from multiple, coarser base grids onto a freer grid and improves solution accuracy by minimizing the residual of the discretized NS equations over the projected grid. In this dissertation, the finite volume (FV) formulation is focused on. The interplay between the xi concepts and the outcome of LSE, and the effects of solution gradients and singularities, nonlinear physics, and coupling of flow variables on the effectiveness of LSE are investigated. A CFD-based design optimization of a single element liquid rocket injector is conducted with surrogate models developed using response surface methodology (RSM) based on CFD solutions. The computational model consists of the NS equations, finite rate chemistry, and the k-6 turbulence closure. With the aid of these surrogate models, sensitivity and trade-off analyses are carried out for the injector design whose geometry (hydrogen flow angle, hydrogen and oxygen flow areas and oxygen post tip thickness) is optimized to attain desirable goals in performance (combustion length) and life/survivability (the maximum temperatures on the oxidizer post tip and injector face and a combustion chamber wall temperature). A preliminary multi-objective optimization study is carried out using a geometric mean approach. Following this, sensitivity analyses with the aid of variance-based non-parametric approach and partial correlation coefficients are conducted using data available from surrogate models of the objectives and the multi-objective optima to identify the contribution of the design variables to the objective variability and to analyze the variability of the design variables and the objectives. In summary the present dissertation offers insight into an improved coarse to fine grid extrapolation technique for Navier-Stokes computations and also suggests tools for a designer to conduct design optimization study and related sensitivity analyses for a given design problem.

Astrochem: Abundances of chemical species in the interstellar medium

NASA Astrophysics Data System (ADS)

Maret, Sébastien; Bergin, Edwin A.

2015-07-01

Astrochem computes the abundances of chemical species in the interstellar medium, as function of time. It studies the chemistry in a variety of astronomical objects, including diffuse clouds, dense clouds, photodissociation regions, prestellar cores, protostars, and protostellar disks. Astrochem reads a network of chemical reactions from a text file, builds up a system of kinetic rates equations, and solves it using a state-of-the-art stiff ordinary differential equation (ODE) solver. The Jacobian matrix of the system is computed implicitly, so the resolution of the system is extremely fast: large networks containing several thousands of reactions are usually solved in a few seconds. A variety of gas phase process are considered, as well as simple gas-grain interactions, such as the freeze-out and the desorption via several mechanisms (thermal desorption, cosmic-ray desorption and photo-desorption). The computed abundances are written in a HDF5 file, and can be plotted in different ways with the tools provided with Astrochem. Chemical reactions and their rates are written in a format which is meant to be easy to read and to edit. A tool to convert the chemical networks from the OSU and KIDA databases into this format is also provided. Astrochem is written in C, and its source code is distributed under the terms of the GNU General Public License (GPL).

Fast H.264/AVC FRExt intra coding using belief propagation.

PubMed

Milani, Simone

2011-01-01

In the H.264/AVC FRExt coder, the coding performance of Intra coding significantly overcomes the previous still image coding standards, like JPEG2000, thanks to a massive use of spatial prediction. Unfortunately, the adoption of an extensive set of predictors induces a significant increase of the computational complexity required by the rate-distortion optimization routine. The paper presents a complexity reduction strategy that aims at reducing the computational load of the Intra coding with a small loss in the compression performance. The proposed algorithm relies on selecting a reduced set of prediction modes according to their probabilities, which are estimated adopting a belief-propagation procedure. Experimental results show that the proposed method permits saving up to 60 % of the coding time required by an exhaustive rate-distortion optimization method with a negligible loss in performance. Moreover, it permits an accurate control of the computational complexity unlike other methods where the computational complexity depends upon the coded sequence.

2,445 Hours of Code: What I Learned from Facilitating Hour of Code Events in High School Libraries

ERIC Educational Resources Information Center

Colby, Jennifer

2015-01-01

This article describes a school librarian's experience with initiating an Hour of Code event for her school's student body. Hadi Partovi of Code.org conceived the Hour of Code "to get ten million students to try one hour of computer science" (Partovi, 2013a), which is implemented during Computer Science Education Week with a goal of…

Numerical algorithm comparison for the accurate and efficient computation of high-incidence vortical flow

NASA Technical Reports Server (NTRS)

Chaderjian, Neal M.

1991-01-01

Computations from two Navier-Stokes codes, NSS and F3D, are presented for a tangent-ogive-cylinder body at high angle of attack. Features of this steady flow include a pair of primary vortices on the leeward side of the body as well as secondary vortices. The topological and physical plausibility of this vortical structure is discussed. The accuracy of these codes are assessed by comparison of the numerical solutions with experimental data. The effects of turbulence model, numerical dissipation, and grid refinement are presented. The overall efficiency of these codes are also assessed by examining their convergence rates, computational time per time step, and maximum allowable time step for time-accurate computations. Overall, the numerical results from both codes compared equally well with experimental data, however, the NSS code was found to be significantly more efficient than the F3D code.

User's Manual for FEMOM3DR. Version 1.0

NASA Technical Reports Server (NTRS)

Reddy, C. J.

1998-01-01

FEMoM3DR is a computer code written in FORTRAN 77 to compute radiation characteristics of antennas on 3D body using combined Finite Element Method (FEM)/Method of Moments (MoM) technique. The code is written to handle different feeding structures like coaxial line, rectangular waveguide, and circular waveguide. This code uses the tetrahedral elements, with vector edge basis functions for FEM and triangular elements with roof-top basis functions for MoM. By virtue of FEM, this code can handle any arbitrary shaped three dimensional bodies with inhomogeneous lossy materials; and due to MoM the computational domain can be terminated in any arbitrary shape. The User's Manual is written to make the user acquainted with the operation of the code. The user is assumed to be familiar with the FORTRAN 77 language and the operating environment of the computers on which the code is intended to run.

Selection of a computer code for Hanford low-level waste engineered-system performance assessment

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

McGrail, B.P.; Mahoney, L.A.

Planned performance assessments for the proposed disposal of low-level waste (LLW) glass produced from remediation of wastes stored in underground tanks at Hanford, Washington will require calculations of radionuclide release rates from the subsurface disposal facility. These calculations will be done with the aid of computer codes. Currently available computer codes were ranked in terms of the feature sets implemented in the code that match a set of physical, chemical, numerical, and functional capabilities needed to assess release rates from the engineered system. The needed capabilities were identified from an analysis of the important physical and chemical process expected tomore » affect LLW glass corrosion and the mobility of radionuclides. The highest ranked computer code was found to be the ARES-CT code developed at PNL for the US Department of Energy for evaluation of and land disposal sites.« less

User's manual for a material transport code on the Octopus Computer Network

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

Naymik, T.G.; Mendez, G.D.

1978-09-15

A code to simulate material transport through porous media was developed at Oak Ridge National Laboratory. This code has been modified and adapted for use at Lawrence Livermore Laboratory. This manual, in conjunction with report ORNL-4928, explains the input, output, and execution of the code on the Octopus Computer Network.

Performance analysis of three dimensional integral equation computations on a massively parallel computer. M.S. Thesis

NASA Technical Reports Server (NTRS)

Logan, Terry G.

1994-01-01

The purpose of this study is to investigate the performance of the integral equation computations using numerical source field-panel method in a massively parallel processing (MPP) environment. A comparative study of computational performance of the MPP CM-5 computer and conventional Cray-YMP supercomputer for a three-dimensional flow problem is made. A serial FORTRAN code is converted into a parallel CM-FORTRAN code. Some performance results are obtained on CM-5 with 32, 62, 128 nodes along with those on Cray-YMP with a single processor. The comparison of the performance indicates that the parallel CM-FORTRAN code near or out-performs the equivalent serial FORTRAN code for some cases.

The numerical modelling of MHD astrophysical flows with chemistry

NASA Astrophysics Data System (ADS)

Kulikov, I.; Chernykh, I.; Protasov, V.

2017-10-01

The new code for numerical simulation of magnetic hydrodynamical astrophysical flows with consideration of chemical reactions is given in the paper. At the heart of the code - the new original low-dissipation numerical method based on a combination of operator splitting approach and piecewise-parabolic method on the local stencil. The chemodynamics of the hydrogen while the turbulent formation of molecular clouds is modeled.

Computer Description of the M561 Utility Truck

DTIC Science & Technology

1984-10-01

GIFT Computer Code Sustainabi1ity Predictions for Army Spare Components Requirements for Combat (SPARC) 20. ABSTRACT (Caotfmia «a NWM eitim ft...used as input to the GIFT computer code to generate target vulnerability data. DO FORM V JAM 73 1473 EDITION OF I NOV 65 IS OBSOLETE Unclass i f ied...anaLyiis requires input from the Geometric Information for Targets ( GIFT ) ’ computer code. This report documents the combina- torial geometry (Com-Geom