Sample records for allikmets triin parik

  1. Genetics Home Reference: age-related macular degeneration


    ... Shahid H, Sigurdsson H, Silvestri G, Sivakumaran TA, Smith RT, Sobrin L, Souied EH, Stambolian DE, Stefansson ... AY, Zack DJ, Campochiaro B, Campochiaro P, Ripke S, Smith RT, Barile GR, Katsanis N, Allikmets R, Daly ...

  2. Comparison of Three Efficient Approximate Exact-Exchange Algorithms: The Chain-of-Spheres Algorithm, Pair-Atomic Resolution-of-the-Identity Method, and Auxiliary Density Matrix Method.


    Rebolini, Elisa; Izsák, Róbert; Reine, Simen Sommerfelt; Helgaker, Trygve; Pedersen, Thomas Bondo


    We compare the performance of three approximate methods for speeding up evaluation of the exchange contribution in Hartree-Fock and hybrid Kohn-Sham calculations: the chain-of-spheres algorithm (COSX; Neese , F. Chem. Phys. 2008 , 356 , 98 - 109 ), the pair-atomic resolution-of-identity method (PARI-K; Merlot , P. J. Comput. Chem. 2013 , 34 , 1486 - 1496 ), and the auxiliary density matrix method (ADMM; Guidon , M. J. Chem. Theory Comput. 2010 , 6 , 2348 - 2364 ). Both the efficiency relative to that of a conventional linear-scaling algorithm and the accuracy of total, atomization, and orbital energies are compared for a subset containing 25 of the 200 molecules in the Rx200 set using double-, triple-, and quadruple-ζ basis sets. The accuracy of relative energies is further compared for small alkane conformers (ACONF test set) and Diels-Alder reactions (DARC test set). Overall, we find that the COSX method provides good accuracy for orbital energies as well as total and relative energies, and the method delivers a satisfactory speedup. The PARI-K and in particular ADMM algorithms require further development and optimization to fully exploit their indisputable potential.

  3. Efficient Implementation of the Pair Atomic Resolution of the Identity Approximation for Exact Exchange for Hybrid and Range-Separated Density Functionals

    PubMed Central


    An efficient new molecular orbital (MO) basis algorithm is reported implementing the pair atomic resolution of the identity approximation (PARI) to evaluate the exact exchange contribution (K) to self-consistent field methods, such as hybrid and range-separated hybrid density functionals. The PARI approximation, in which atomic orbital (AO) basis function pairs are expanded using auxiliary basis functions centered only on their two respective atoms, was recently investigated by Merlot et al. [J. Comput. Chem.2013, 34, 1486]. Our algorithm is significantly faster than quartic scaling RI-K, with an asymptotic exchange speedup for hybrid functionals of (1 + X/N), where N and X are the AO and auxiliary basis dimensions. The asymptotic speedup is 2 + 2X/N for range separated hybrids such as CAM-B3LYP, ωB97X-D, and ωB97X-V which include short- and long-range exact exchange. The observed speedup for exchange in ωB97X-V for a C68 graphene fragment in the cc-pVTZ basis is 3.4 relative to RI-K. Like conventional RI-K, our method greatly outperforms conventional integral evaluation in large basis sets; a speedup of 19 is obtained in the cc-pVQZ basis on a C54 graphene fragment. Negligible loss of accuracy relative to exact integral evaluation is demonstrated on databases of bonded and nonbonded interactions. We also demonstrate both analytically and numerically that the PARI-K approximation is variationally stable. PMID:25691831