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PySurf: A Framework for Database Accelerated Direct Dynamics
[Image: see text] The greatest restriction to the theoretical study of the dynamics of photoinduced processes is computationally expensive electronic structure calculations. Machine learning algorithms have the potential to reduce the number of these computations significantly. Here, PySurf is intro...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American
Chemical Society
2020
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7726901/ https://www.ncbi.nlm.nih.gov/pubmed/33231447 http://dx.doi.org/10.1021/acs.jctc.0c00825 |
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author | Menger, Maximilian F. S. J. Ehrmaier, Johannes Faraji, Shirin |
author_facet | Menger, Maximilian F. S. J. Ehrmaier, Johannes Faraji, Shirin |
author_sort | Menger, Maximilian F. S. J. |
collection | PubMed |
description | [Image: see text] The greatest restriction to the theoretical study of the dynamics of photoinduced processes is computationally expensive electronic structure calculations. Machine learning algorithms have the potential to reduce the number of these computations significantly. Here, PySurf is introduced as an innovative code framework, which is specifically designed for rapid prototyping and development tasks for data science applications in computational chemistry. It comes with powerful Plugin and Workflow engines, which allows intuitive customization for individual tasks. Data is automatically stored through the database framework, which enables additional interpolation of properties in previously evaluated regions of the conformational space. To illustrate the potential of the framework, a code for nonadiabatic surface hopping simulations based on the Landau–Zener algorithm is presented here. Deriving gradients from the interpolated potential energy surfaces allows for full-dimensional nonadiabatic surface hopping simulations using only adiabatic energies (energy only). Simulations of a pyrazine model and ab initio-based calculations of the SO(2) molecule show that energy-only calculations with PySurf are able to correctly predict the nonadiabatic dynamics of these prototype systems. The results reveal the degree of sophistication, which can be achieved by the database accelerated energy-only surface hopping simulations being competitive to commonly used semiclassical approaches. |
format | Online Article Text |
id | pubmed-7726901 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | American
Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-77269012020-12-14 PySurf: A Framework for Database Accelerated Direct Dynamics Menger, Maximilian F. S. J. Ehrmaier, Johannes Faraji, Shirin J Chem Theory Comput [Image: see text] The greatest restriction to the theoretical study of the dynamics of photoinduced processes is computationally expensive electronic structure calculations. Machine learning algorithms have the potential to reduce the number of these computations significantly. Here, PySurf is introduced as an innovative code framework, which is specifically designed for rapid prototyping and development tasks for data science applications in computational chemistry. It comes with powerful Plugin and Workflow engines, which allows intuitive customization for individual tasks. Data is automatically stored through the database framework, which enables additional interpolation of properties in previously evaluated regions of the conformational space. To illustrate the potential of the framework, a code for nonadiabatic surface hopping simulations based on the Landau–Zener algorithm is presented here. Deriving gradients from the interpolated potential energy surfaces allows for full-dimensional nonadiabatic surface hopping simulations using only adiabatic energies (energy only). Simulations of a pyrazine model and ab initio-based calculations of the SO(2) molecule show that energy-only calculations with PySurf are able to correctly predict the nonadiabatic dynamics of these prototype systems. The results reveal the degree of sophistication, which can be achieved by the database accelerated energy-only surface hopping simulations being competitive to commonly used semiclassical approaches. American Chemical Society 2020-11-24 2020-12-08 /pmc/articles/PMC7726901/ /pubmed/33231447 http://dx.doi.org/10.1021/acs.jctc.0c00825 Text en © 2020 American Chemical Society This is an open access article published under a Creative Commons Non-Commercial No Derivative Works (CC-BY-NC-ND) Attribution License (http://pubs.acs.org/page/policy/authorchoice_ccbyncnd_termsofuse.html) , which permits copying and redistribution of the article, and creation of adaptations, all for non-commercial purposes. |
spellingShingle | Menger, Maximilian F. S. J. Ehrmaier, Johannes Faraji, Shirin PySurf: A Framework for Database Accelerated Direct Dynamics |
title | PySurf: A Framework for Database Accelerated Direct
Dynamics |
title_full | PySurf: A Framework for Database Accelerated Direct
Dynamics |
title_fullStr | PySurf: A Framework for Database Accelerated Direct
Dynamics |
title_full_unstemmed | PySurf: A Framework for Database Accelerated Direct
Dynamics |
title_short | PySurf: A Framework for Database Accelerated Direct
Dynamics |
title_sort | pysurf: a framework for database accelerated direct
dynamics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7726901/ https://www.ncbi.nlm.nih.gov/pubmed/33231447 http://dx.doi.org/10.1021/acs.jctc.0c00825 |
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