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New scaling relations to compute atom-in-material polarizabilities and dispersion coefficients: part 2. Linear-scaling computational algorithms and parallelization
We present two algorithms to compute system-specific polarizabilities and dispersion coefficients such that required memory and computational time scale linearly with increasing number of atoms in the unit cell for large systems. The first algorithm computes the atom-in-material (AIM) static polariz...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
The Royal Society of Chemistry
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9073276/ https://www.ncbi.nlm.nih.gov/pubmed/35529131 http://dx.doi.org/10.1039/c9ra01983a |
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author | Manz, Thomas A. Chen, Taoyi |
author_facet | Manz, Thomas A. Chen, Taoyi |
author_sort | Manz, Thomas A. |
collection | PubMed |
description | We present two algorithms to compute system-specific polarizabilities and dispersion coefficients such that required memory and computational time scale linearly with increasing number of atoms in the unit cell for large systems. The first algorithm computes the atom-in-material (AIM) static polarizability tensors, force-field polarizabilities, and C(6), C(8), C(9), C(10) dispersion coefficients using the MCLF method. The second algorithm computes the AIM polarizability tensors and C(6) coefficients using the TS-SCS method. Linear-scaling computational cost is achieved using a dipole interaction cutoff length function combined with iterative methods that avoid large dense matrix multiplies and large matrix inversions. For MCLF, Richardson extrapolation of the screening increments is used. For TS-SCS, a failproof conjugate residual (FCR) algorithm is introduced that solves any linear equation system having Hermitian coefficients matrix. These algorithms have mathematically provable stable convergence that resists round-off errors. We parallelized these methods to provide rapid computation on multi-core computers. Excellent parallelization efficiencies were obtained, and adding parallel processors does not significantly increase memory requirements. This enables system-specific polarizabilities and dispersion coefficients to be readily computed for materials containing millions of atoms in the unit cell. The largest example studied herein is an ice crystal containing >2 million atoms in the unit cell. For this material, the FCR algorithm solved a linear equation system containing >6 million rows, 7.57 billion interacting atom pairs, 45.4 billion stored non-negligible matrix components used in each large matrix-vector multiplication, and ∼19 million unknowns per frequency point (>300 million total unknowns). |
format | Online Article Text |
id | pubmed-9073276 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | The Royal Society of Chemistry |
record_format | MEDLINE/PubMed |
spelling | pubmed-90732762022-05-06 New scaling relations to compute atom-in-material polarizabilities and dispersion coefficients: part 2. Linear-scaling computational algorithms and parallelization Manz, Thomas A. Chen, Taoyi RSC Adv Chemistry We present two algorithms to compute system-specific polarizabilities and dispersion coefficients such that required memory and computational time scale linearly with increasing number of atoms in the unit cell for large systems. The first algorithm computes the atom-in-material (AIM) static polarizability tensors, force-field polarizabilities, and C(6), C(8), C(9), C(10) dispersion coefficients using the MCLF method. The second algorithm computes the AIM polarizability tensors and C(6) coefficients using the TS-SCS method. Linear-scaling computational cost is achieved using a dipole interaction cutoff length function combined with iterative methods that avoid large dense matrix multiplies and large matrix inversions. For MCLF, Richardson extrapolation of the screening increments is used. For TS-SCS, a failproof conjugate residual (FCR) algorithm is introduced that solves any linear equation system having Hermitian coefficients matrix. These algorithms have mathematically provable stable convergence that resists round-off errors. We parallelized these methods to provide rapid computation on multi-core computers. Excellent parallelization efficiencies were obtained, and adding parallel processors does not significantly increase memory requirements. This enables system-specific polarizabilities and dispersion coefficients to be readily computed for materials containing millions of atoms in the unit cell. The largest example studied herein is an ice crystal containing >2 million atoms in the unit cell. For this material, the FCR algorithm solved a linear equation system containing >6 million rows, 7.57 billion interacting atom pairs, 45.4 billion stored non-negligible matrix components used in each large matrix-vector multiplication, and ∼19 million unknowns per frequency point (>300 million total unknowns). The Royal Society of Chemistry 2019-10-17 /pmc/articles/PMC9073276/ /pubmed/35529131 http://dx.doi.org/10.1039/c9ra01983a Text en This journal is © The Royal Society of Chemistry https://creativecommons.org/licenses/by/3.0/ |
spellingShingle | Chemistry Manz, Thomas A. Chen, Taoyi New scaling relations to compute atom-in-material polarizabilities and dispersion coefficients: part 2. Linear-scaling computational algorithms and parallelization |
title | New scaling relations to compute atom-in-material polarizabilities and dispersion coefficients: part 2. Linear-scaling computational algorithms and parallelization |
title_full | New scaling relations to compute atom-in-material polarizabilities and dispersion coefficients: part 2. Linear-scaling computational algorithms and parallelization |
title_fullStr | New scaling relations to compute atom-in-material polarizabilities and dispersion coefficients: part 2. Linear-scaling computational algorithms and parallelization |
title_full_unstemmed | New scaling relations to compute atom-in-material polarizabilities and dispersion coefficients: part 2. Linear-scaling computational algorithms and parallelization |
title_short | New scaling relations to compute atom-in-material polarizabilities and dispersion coefficients: part 2. Linear-scaling computational algorithms and parallelization |
title_sort | new scaling relations to compute atom-in-material polarizabilities and dispersion coefficients: part 2. linear-scaling computational algorithms and parallelization |
topic | Chemistry |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9073276/ https://www.ncbi.nlm.nih.gov/pubmed/35529131 http://dx.doi.org/10.1039/c9ra01983a |
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