IOData: A python library for reading, writing, and converting computational chemistry file formats and generating input files.

作者: Toon Verstraelen , William Adams , Leila Pujal , Alireza Tehrani , Braden D. Kelly

DOI: 10.1002/JCC.26468

关键词:

摘要: IOData is a free and open-source Python library for parsing, storing, converting various file formats commonly used by quantum chemistry, molecular dynamics, plane-wave density-functional-theory software programs. In addition, supports flexible framework generating input files packages. While designed released stand-alone use, its original purpose was to facilitate the interoperability of modules in HORTON ChemTools packages with external (third-party) chemistry solid-state be easy maintain, extend; this why we wrote adopted many principles modern development, including comprehensive documentation, extensive testing, continuous integration/delivery protocols, package management. This article official release note library.

参考文章(15)
Yihan Shao, Zhengting Gan, Evgeny Epifanovsky, Andrew TB Gilbert, Michael Wormit, Joerg Kussmann, Adrian W Lange, Andrew Behn, Jia Deng, Xintian Feng, Debashree Ghosh, Matthew Goldey, Paul R Horn, Leif D Jacobson, Ilya Kaliman, Rustam Z Khaliullin, Tomasz Kuś, Arie Landau, Jie Liu, Emil I Proynov, Young Min Rhee, Ryan M Richard, Mary A Rohrdanz, Ryan P Steele, Eric J Sundstrom, H Lee Woodcock III, Paul M Zimmerman, Dmitry Zuev, Ben Albrecht, Ethan Alguire, Brian Austin, Gregory JO Beran, Yves A Bernard, Eric Berquist, Kai Brandhorst, Ksenia B Bravaya, Shawn T Brown, David Casanova, Chun-Min Chang, Yunqing Chen, Siu Hung Chien, Kristina D Closser, Deborah L Crittenden, Michael Diedenhofen, Robert A DiStasio Jr, Hainam Do, Anthony D Dutoi, Richard G Edgar, Shervin Fatehi, Laszlo Fusti-Molnar, An Ghysels, Anna Golubeva-Zadorozhnaya, Joseph Gomes, Magnus WD Hanson-Heine, Philipp HP Harbach, Andreas W Hauser, Edward G Hohenstein, Zachary C Holden, Thomas-C Jagau, Hyunjun Ji, Benjamin Kaduk, Kirill Khistyaev, Jaehoon Kim, Jihan Kim, Rollin A King, Phil Klunzinger, Dmytro Kosenkov, Tim Kowalczyk, Caroline M Krauter, Ka Un Lao, Adèle D Laurent, Keith V Lawler, Sergey V Levchenko, Ching Yeh Lin, Fenglai Liu, Ester Livshits, Rohini C Lochan, Arne Luenser, Prashant Manohar, Samuel F Manzer, Shan-Ping Mao, Narbe Mardirossian, Aleksandr V Marenich, Simon A Maurer, Nicholas J Mayhall, Eric Neuscamman, C Melania Oana, Roberto Olivares-Amaya, Darragh P O’Neill, John A Parkhill, Trilisa M Perrine, Roberto Peverati, Alexander Prociuk, Dirk R Rehn, Edina Rosta, Nicholas J Russ, Shaama M Sharada, Sandeep Sharma, David W Small, Alexander Sodt, Tamar Stein, David Stück, Yu-Chuan Su, Alex JW Thom, Takashi Tsuchimochi, Vitalii Vanovschi, Leslie Vogt, Oleg Vydrov, Tao Wang, Mark A Watson, Jan Wenzel, Alec White, Christopher F Williams, Jun Yang, Sina Yeganeh, Shane R Yost, Zhi-Qiang You, Igor Ying Zhang, Xing Zhang, Yan Zhao, Bernard R Brooks, Garnet KL Chan, Daniel M Chipman, Christopher J Cramer, William A Goddard III, Mark S Gordon, Warren J Hehre, Andreas Klamt, Henry F Schaefer III, Michael W Schmidt, C David Sherrill, Donald G Truhlar, Arieh Warshel, Xin Xu, Alán Aspuru-Guzik, Roi Baer, Alexis T Bell, Nicholas A Besley, Jeng-Da Chai, Andreas Dreuw, Barry D Dunietz, Thomas R Furlani, Steven R Gwaltney, Chao-Ping Hsu, Yousung Jung, Jing Kong, Daniel S Lambrecht, WanZhen Liang, Christian Ochsenfeld, Vitaly A Rassolov, None, Advances in molecular quantum chemistry contained in the Q-Chem 4 program package Molecular Physics. ,vol. 113, pp. 184- 215 ,(2015) , 10.1080/00268976.2014.952696
Hans-Joachim Werner, Peter J. Knowles, Gerald Knizia, Frederick R. Manby, Martin Schütz, Molpro: a general-purpose quantum chemistry program package Wiley Interdisciplinary Reviews: Computational Molecular Science. ,vol. 2, pp. 242- 253 ,(2012) , 10.1002/WCMS.82
Noel M. O'boyle, Adam L. Tenderholt, Karol M. Langner, cclib: A library for package-independent computational chemistry algorithms Journal of Computational Chemistry. ,vol. 29, pp. 839- 845 ,(2008) , 10.1002/JCC.20823
Tian Lu, Feiwu Chen, Multiwfn: a multifunctional wavefunction analyzer. Journal of Computational Chemistry. ,vol. 33, pp. 580- 592 ,(2012) , 10.1002/JCC.22885
Robert T. McGibbon, Kyle A. Beauchamp, Matthew P. Harrigan, Christoph Klein, Jason M. Swails, Carlos X. Hernández, Christian R. Schwantes, Lee-Ping Wang, Thomas J. Lane, Vijay S. Pande, MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories Biophysical Journal. ,vol. 109, pp. 1528- 1532 ,(2015) , 10.1016/J.BPJ.2015.08.015
Noel M O'Boyle, Michael Banck, Craig A James, Chris Morley, Tim Vandermeersch, Geoffrey R Hutchison, Open Babel: An open chemical toolbox Journal of Cheminformatics. ,vol. 3, pp. 33- 33 ,(2011) , 10.1186/1758-2946-3-33
Naveen Michaud-Agrawal, Elizabeth J. Denning, Thomas B. Woolf, Oliver Beckstein, MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations Journal of Computational Chemistry. ,vol. 32, pp. 2319- 2327 ,(2011) , 10.1002/JCC.21787
Farnaz Heidar-Zadeh, Michael Richer, Stijn Fias, Ramón Alain Miranda-Quintana, Matthew Chan, Marco Franco-Pérez, Cristina E. González-Espinoza, Taewon David Kim, Caitlin Lanssens, Anand H.G. Patel, Xiaotian Derrick Yang, Esteban Vöhringer-Martinez, Carlos Cárdenas, Toon Verstraelen, Paul W. Ayers, An explicit approach to conceptual density functional theory descriptors of arbitrary order Chemical Physics Letters. ,vol. 660, pp. 307- 312 ,(2016) , 10.1016/J.CPLETT.2016.07.039
Ask Hjorth Larsen, 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, None, The Atomic Simulation Environment - A Python library for working with atoms Journal of Physics: Condensed Matter. ,vol. 29, pp. 273002- ,(2017) , 10.1088/1361-648X/AA680E
Robert M. Parrish, Lori A. Burns, Daniel G. A. Smith, Andrew C. Simmonett, A. Eugene DePrince, Edward G. Hohenstein, Uğur Bozkaya, Alexander Yu. Sokolov, Roberto Di Remigio, Ryan M. Richard, Jérôme F. Gonthier, Andrew M. James, Harley R. McAlexander, Ashutosh Kumar, Masaaki Saitow, Xiao Wang, Benjamin P. Pritchard, Prakash Verma, Henry F. Schaefer, Konrad Patkowski, Rollin A. King, Edward F. Valeev, Francesco A. Evangelista, Justin M. Turney, T. Daniel Crawford, C. David Sherrill, Psi4 1.1: An Open-Source Electronic Structure Program Emphasizing Automation, Advanced Libraries, and Interoperability Journal of Chemical Theory and Computation. ,vol. 13, pp. 3185- 3197 ,(2017) , 10.1021/ACS.JCTC.7B00174