Literature DB >> 28323250

The atomic simulation environment-a Python library for working with atoms.

Ask Hjorth Larsen1, Jens Jørgen Mortensen, Jakob Blomqvist, Ivano E Castelli, Rune Christensen, Marcin Dułak, Jesper Friis, Michael N Groves, Bjørk Hammer, Cory Hargus, Eric D Hermes, Paul C Jennings, Peter Bjerre Jensen, James Kermode, John R Kitchin, Esben Leonhard Kolsbjerg, Joseph Kubal, Kristen Kaasbjerg, Steen Lysgaard, Jón Bergmann Maronsson, Tristan Maxson, Thomas Olsen, Lars Pastewka, Andrew Peterson, Carsten Rostgaard, Jakob Schiøtz, Ole Schütt, Mikkel Strange, Kristian S Thygesen, Tejs Vegge, Lasse Vilhelmsen, Michael Walter, Zhenhua Zeng, Karsten W Jacobsen.   

Abstract

The atomic simulation environment (ASE) is a software package written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations. In ASE, tasks are fully scripted in Python. The powerful syntax of Python combined with the NumPy array library make it possible to perform very complex simulation tasks. For example, a sequence of calculations may be performed with the use of a simple 'for-loop' construction. Calculations of energy, forces, stresses and other quantities are performed through interfaces to many external electronic structure codes or force fields using a uniform interface. On top of this calculator interface, ASE provides modules for performing many standard simulation tasks such as structure optimization, molecular dynamics, handling of constraints and performing nudged elastic band calculations.

Year:  2017        PMID: 28323250     DOI: 10.1088/1361-648X/aa680e

Source DB:  PubMed          Journal:  J Phys Condens Matter        ISSN: 0953-8984            Impact factor:   2.333


  153 in total

1.  Adsorption and diffusion of sulfur on the (111), (100), (110), and (211) surfaces of FCC metals: Density functional theory calculations.

Authors:  Christopher R Bernard Rodríguez; Juan A Santana
Journal:  J Chem Phys       Date:  2018-11-28       Impact factor: 3.488

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3.  Driving torsion scans with wavefront propagation.

Authors:  Yudong Qiu; Daniel G A Smith; Chaya D Stern; Mudong Feng; Hyesu Jang; Lee-Ping Wang
Journal:  J Chem Phys       Date:  2020-06-28       Impact factor: 3.488

4.  NGLview-interactive molecular graphics for Jupyter notebooks.

Authors:  Hai Nguyen; David A Case; Alexander S Rose
Journal:  Bioinformatics       Date:  2018-04-01       Impact factor: 6.937

5.  Atom-by-Atom Construction of a Cyclic Artificial Molecule in Silicon.

Authors:  Jonathan Wyrick; Xiqiao Wang; Pradeep Namboodiri; Scott W Schmucker; Ranjit V Kashid; Richard M Silver
Journal:  Nano Lett       Date:  2018-11-20       Impact factor: 11.189

6.  Large H2O solubility in dense silica and its implications for the interiors of water-rich planets.

Authors:  Carole Nisr; Huawei Chen; Kurt Leinenweber; Andrew Chizmeshya; Vitali B Prakapenka; Clemens Prescher; Sergey N Tkachev; Yue Meng; Zhenxian Liu; Sang-Heon Shim
Journal:  Proc Natl Acad Sci U S A       Date:  2020-04-20       Impact factor: 11.205

7.  Psi4 1.4: Open-source software for high-throughput quantum chemistry.

Authors:  Daniel G A Smith; Lori A Burns; Andrew C Simmonett; Robert M Parrish; Matthew C Schieber; Raimondas Galvelis; Peter Kraus; Holger Kruse; Roberto Di Remigio; Asem Alenaizan; Andrew M James; Susi Lehtola; Jonathon P Misiewicz; Maximilian Scheurer; Robert A Shaw; Jeffrey B Schriber; Yi Xie; Zachary L Glick; Dominic A Sirianni; Joseph Senan O'Brien; Jonathan M Waldrop; Ashutosh Kumar; Edward G Hohenstein; Benjamin P Pritchard; Bernard R Brooks; Henry F Schaefer; Alexander Yu Sokolov; Konrad Patkowski; A Eugene DePrince; Uğur Bozkaya; Rollin A King; Francesco A Evangelista; Justin M Turney; T Daniel Crawford; C David Sherrill
Journal:  J Chem Phys       Date:  2020-05-14       Impact factor: 3.488

8.  TeraChem: Accelerating electronic structure and ab initio molecular dynamics with graphical processing units.

Authors:  Stefan Seritan; Christoph Bannwarth; B Scott Fales; Edward G Hohenstein; Sara I L Kokkila-Schumacher; Nathan Luehr; James W Snyder; Chenchen Song; Alexey V Titov; Ivan S Ufimtsev; Todd J Martínez
Journal:  J Chem Phys       Date:  2020-06-14       Impact factor: 3.488

9.  Revealing the structure of a catalytic combustion active-site ensemble combining uniform nanocrystal catalysts and theory insights.

Authors:  An-Chih Yang; Tej Choksi; Verena Streibel; Hassan Aljama; Cody J Wrasman; Luke T Roling; Emmett D Goodman; Dionne Thomas; Simon R Bare; Roel S Sánchez-Carrera; Ansgar Schäfer; Yuejin Li; Frank Abild-Pedersen; Matteo Cargnello
Journal:  Proc Natl Acad Sci U S A       Date:  2020-06-17       Impact factor: 11.205

10.  Supported Catalyst Deactivation by Decomposition into Single Atoms Is Suppressed by Increasing Metal Loading.

Authors:  Emmett D Goodman; Aaron C Johnston-Peck; Elisabeth M Dietze; Cody J Wrasman; Adam S Hoffman; Frank Abild-Pedersen; Simon R Bare; Philipp N Plessow; Matteo Cargnello
Journal:  Nat Catal       Date:  2019
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