Literature DB >> 26593003

Linear Scaling Self-Consistent Field Calculations with Millions of Atoms in the Condensed Phase.

Joost VandeVondele1, Urban Borštnik2, Jürg Hutter2.   

Abstract

In this work, the applicability and performance of a linear scaling algorithm is investigated for three-dimensional condensed phase systems. A simple but robust approach based on the matrix sign function is employed together with a thresholding matrix multiplication that does not require a prescribed sparsity pattern. Semiempirical methods and density functional theory have been tested. We demonstrate that self-consistent calculations with 1 million atoms are feasible for simple systems. With this approach, the computational cost of the calculation depends strongly on basis set quality. In the current implementation, high quality calculations for dense systems are limited to a few hundred thousand atoms. We report on the sparsities of the involved matrices as obtained at convergence and for intermediate iterations. We investigate how determining the chemical potential impacts the computational cost for very large systems.

Year:  2012        PMID: 26593003     DOI: 10.1021/ct200897x

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  10 in total

1.  EMPIRE: a highly parallel semiempirical molecular orbital program: 1: self-consistent field calculations.

Authors:  Matthias Hennemann; Timothy Clark
Journal:  J Mol Model       Date:  2014-06-20       Impact factor: 1.810

2.  Large-scale QM/MM free energy simulations of enzyme catalysis reveal the influence of charge transfer.

Authors:  Heather J Kulik
Journal:  Phys Chem Chem Phys       Date:  2018-08-08       Impact factor: 3.676

3.  Quantum crystallographic charge density of urea.

Authors:  Michael E Wall
Journal:  IUCrJ       Date:  2016-06-08       Impact factor: 4.769

4.  How Large Should the QM Region Be in QM/MM Calculations? The Case of Catechol O-Methyltransferase.

Authors:  Heather J Kulik; Jianyu Zhang; Judith P Klinman; Todd J Martínez
Journal:  J Phys Chem B       Date:  2016-10-28       Impact factor: 2.991

5.  Machine Learning Adaptive Basis Sets for Efficient Large Scale Density Functional Theory Simulation.

Authors:  Ole Schütt; Joost VandeVondele
Journal:  J Chem Theory Comput       Date:  2018-07-28       Impact factor: 6.006

6.  Parallel Implementation of Large-Scale Linear Scaling Density Functional Theory Calculations With Numerical Atomic Orbitals in HONPAS.

Authors:  Zhaolong Luo; Xinming Qin; Lingyun Wan; Wei Hu; Jinlong Yang
Journal:  Front Chem       Date:  2020-11-26       Impact factor: 5.221

Review 7.  Recent advances in QM/MM free energy calculations using reference potentials.

Authors:  Fernanda Duarte; Beat A Amrein; David Blaha-Nelson; Shina C L Kamerlin
Journal:  Biochim Biophys Acta       Date:  2014-07-16

8.  Performance analysis of electronic structure codes on HPC systems: a case study of SIESTA.

Authors:  Fabiano Corsetti
Journal:  PLoS One       Date:  2014-04-18       Impact factor: 3.240

9.  Parametrization of an Orbital-Based Linear-Scaling Quantum Force Field for Noncovalent Interactions.

Authors:  Timothy J Giese; Haoyuan Chen; Ming Huang; Darrin M York
Journal:  J Chem Theory Comput       Date:  2014-02-11       Impact factor: 6.006

10.  Elucidating the fundamental forces in protein crystal formation: the case of crambin.

Authors:  Massimo Delle Piane; Marta Corno; Roberto Orlando; Roberto Dovesi; Piero Ugliengo
Journal:  Chem Sci       Date:  2015-11-24       Impact factor: 9.825

  10 in total

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