Literature DB >> 21541961

PyADF--a scripting framework for multiscale quantum chemistry.

Christoph R Jacob1, S Maya Beyhan, Rosa E Bulo, André Severo Pereira Gomes, Andreas W Götz, Karin Kiewisch, Jetze Sikkema, Lucas Visscher.   

Abstract

Applications of quantum chemistry have evolved from single or a few calculations to more complicated workflows, in which a series of interrelated computational tasks is performed. In particular multiscale simulations, which combine different levels of accuracy, typically require a large number of individual calculations that depend on each other. Consequently, there is a need to automate such workflows. For this purpose we have developed PYADF, a scripting framework for quantum chemistry. PYADF handles all steps necessary in a typical workflow in quantum chemistry and is easily extensible due to its object-oriented implementation in the Python programming language. We give an overview of the capabilities of PYADF and illustrate its usefulness in quantum-chemical multiscale simulations with a number of examples taken from recent applications.
Copyright © 2011 Wiley Periodicals, Inc.

Entities:  

Keywords:  embedding; multiscale; scripting; workflow

Year:  2011        PMID: 21541961     DOI: 10.1002/jcc.21810

Source DB:  PubMed          Journal:  J Comput Chem        ISSN: 0192-8651            Impact factor:   3.376


  10 in total

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Authors:  Jalal Z A Laloo; Nassirah Laloo; Lydia Rhyman; Ponnadurai Ramasami
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2.  JACOB: an enterprise framework for computational chemistry.

Authors:  Mark P Waller; Thomas Dresselhaus; Jack Yang
Journal:  J Comput Chem       Date:  2013-04-03       Impact factor: 3.376

3.  Open Babel: An open chemical toolbox.

Authors:  Noel M O'Boyle; Michael Banck; Craig A James; Chris Morley; Tim Vandermeersch; Geoffrey R Hutchison
Journal:  J Cheminform       Date:  2011-10-07       Impact factor: 5.514

4.  Multi-level meta-workflows: new concept for regularly occurring tasks in quantum chemistry.

Authors:  Junaid Arshad; Alexander Hoffmann; Sandra Gesing; Richard Grunzke; Jens Krüger; Tamas Kiss; Sonja Herres-Pawlis; Gabor Terstyanszky
Journal:  J Cheminform       Date:  2016-10-20       Impact factor: 5.514

5.  QMflows: A Tool Kit for Interoperable Parallel Workflows in Quantum Chemistry.

Authors:  Felipe Zapata; Lars Ridder; Johan Hidding; Christoph R Jacob; Ivan Infante; Lucas Visscher
Journal:  J Chem Inf Model       Date:  2019-07-01       Impact factor: 4.956

6.  Computer-assisted catalyst development via automated modelling of conformationally complex molecules: application to diphosphinoamine ligands.

Authors:  Sibo Lin; Jenna C Fromer; Yagnaseni Ghosh; Brian Hanna; Mohamed Elanany; Wei Xu
Journal:  Sci Rep       Date:  2021-02-25       Impact factor: 4.379

7.  Environment Effects on X-Ray Absorption Spectra With Quantum Embedded Real-Time Time-Dependent Density Functional Theory Approaches.

Authors:  Matteo De Santis; Valérie Vallet; André Severo Pereira Gomes
Journal:  Front Chem       Date:  2022-02-28       Impact factor: 5.221

8.  Frozen-Density Embedding for Including Environmental Effects in the Dirac-Kohn-Sham Theory: An Implementation Based on Density Fitting and Prototyping Techniques.

Authors:  Matteo De Santis; Diego Sorbelli; Valérie Vallet; André Severo Pereira Gomes; Loriano Storchi; Leonardo Belpassi
Journal:  J Chem Theory Comput       Date:  2022-09-29       Impact factor: 6.578

9.  Towards theoretical spectroscopy with error bars: systematic quantification of the structural sensitivity of calculated spectra.

Authors:  Tobias G Bergmann; Michael O Welzel; Christoph R Jacob
Journal:  Chem Sci       Date:  2019-12-27       Impact factor: 9.825

10.  Environmental Effects with Frozen-Density Embedding in Real-Time Time-Dependent Density Functional Theory Using Localized Basis Functions.

Authors:  Matteo De Santis; Leonardo Belpassi; Christoph R Jacob; André Severo Pereira Gomes; Francesco Tarantelli; Lucas Visscher; Loriano Storchi
Journal:  J Chem Theory Comput       Date:  2020-08-15       Impact factor: 6.006

  10 in total

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