Literature DB >> 18500853

Parallel implementation of electronic structure energy, gradient, and Hessian calculations.

V Lotrich1, N Flocke, M Ponton, A D Yau, A Perera, E Deumens, R J Bartlett.   

Abstract

ACES III is a newly written program in which the computationally demanding components of the computational chemistry code ACES II [J. F. Stanton et al., Int. J. Quantum Chem. 526, 879 (1992); [ACES II program system, University of Florida, 1994] have been redesigned and implemented in parallel. The high-level algorithms include Hartree-Fock (HF) self-consistent field (SCF), second-order many-body perturbation theory [MBPT(2)] energy, gradient, and Hessian, and coupled cluster singles, doubles, and perturbative triples [CCSD(T)] energy and gradient. For SCF, MBPT(2), and CCSD(T), both restricted HF and unrestricted HF reference wave functions are available. For MBPT(2) gradients and Hessians, a restricted open-shell HF reference is also supported. The methods are programed in a special language designed for the parallelization project. The language is called super instruction assembly language (SIAL). The design uses an extreme form of object-oriented programing. All compute intensive operations, such as tensor contractions and diagonalizations, all communication operations, and all input-output operations are handled by a parallel program written in C and FORTRAN 77. This parallel program, called the super instruction processor (SIP), interprets and executes the SIAL program. By separating the algorithmic complexity (in SIAL) from the complexities of execution on computer hardware (in SIP), a software system is created that allows for very effective optimization and tuning on different hardware architectures with quite manageable effort.

Year:  2008        PMID: 18500853     DOI: 10.1063/1.2920482

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  7 in total

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Journal:  J Mol Graph Model       Date:  2016-07-30       Impact factor: 2.518

2.  Pragmatic ab initio prediction of enthalpies of formation for large molecules: accuracy of MP2 geometries and frequencies using CCSD(T) correlation energies.

Authors:  Robert W Molt; Alexandre Bazanté; Thomas Watson; Rodney J Bartlett
Journal:  J Mol Model       Date:  2012-11-20       Impact factor: 1.810

3.  Structure and Biophysics for a Six Letter DNA Alphabet that Includes Imidazo[1,2-a]-1,3,5-triazine-2(8H)-4(3H)-dione (X) and 2,4-Diaminopyrimidine (K).

Authors:  Isha Singh; Myong-Jung Kim; Robert W Molt; Shuichi Hoshika; Steven A Benner; Millie M Georgiadis
Journal:  ACS Synth Biol       Date:  2017-08-15       Impact factor: 5.110

4.  Signature properties of water: Their molecular electronic origins.

Authors:  Vlad P Sokhan; Andrew P Jones; Flaviu S Cipcigan; Jason Crain; Glenn J Martyna
Journal:  Proc Natl Acad Sci U S A       Date:  2015-05-04       Impact factor: 11.205

5.  Accurate benchmark calculations on the gas-phase basicities of small molecules.

Authors:  Xiao He; Laszlo Fusti-Molnar; Kenneth M Merz
Journal:  J Phys Chem A       Date:  2009-09-17       Impact factor: 2.781

6.  Exploring water radiolysis in proton cancer therapy: Time-dependent, non-adiabatic simulations of H+ + (H2O)1-6.

Authors:  Austin J Privett; Erico S Teixeira; Christopher Stopera; Jorge A Morales
Journal:  PLoS One       Date:  2017-04-04       Impact factor: 3.240

7.  Electron Nuclear Dynamics Simulations of Proton Cancer Therapy Reactions: Water Radiolysis and Proton- and Electron-Induced DNA Damage in Computational Prototypes.

Authors:  Erico S Teixeira; Karthik Uppulury; Austin J Privett; Christopher Stopera; Patrick M McLaurin; Jorge A Morales
Journal:  Cancers (Basel)       Date:  2018-05-06       Impact factor: 6.639

  7 in total

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