Literature DB >> 32414239

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

Daniel G A Smith1, Lori A Burns2, Andrew C Simmonett3, Robert M Parrish2, Matthew C Schieber2, Raimondas Galvelis4, Peter Kraus5, Holger Kruse6, Roberto Di Remigio7, Asem Alenaizan2, Andrew M James8, Susi Lehtola9, Jonathon P Misiewicz10, Maximilian Scheurer11, Robert A Shaw12, Jeffrey B Schriber2, Yi Xie2, Zachary L Glick2, Dominic A Sirianni2, Joseph Senan O'Brien2, Jonathan M Waldrop13, Ashutosh Kumar8, Edward G Hohenstein14, Benjamin P Pritchard1, Bernard R Brooks3, Henry F Schaefer10, Alexander Yu Sokolov15, Konrad Patkowski13, A Eugene DePrince16, Uğur Bozkaya17, Rollin A King18, Francesco A Evangelista19, Justin M Turney10, T Daniel Crawford1, C David Sherrill2.   

Abstract

PSI4 is a free and open-source ab initio electronic structure program providing implementations of Hartree-Fock, density functional theory, many-body perturbation theory, configuration interaction, density cumulant theory, symmetry-adapted perturbation theory, and coupled-cluster theory. Most of the methods are quite efficient, thanks to density fitting and multi-core parallelism. The program is a hybrid of C++ and Python, and calculations may be run with very simple text files or using the Python API, facilitating post-processing and complex workflows; method developers also have access to most of PSI4's core functionalities via Python. Job specification may be passed using The Molecular Sciences Software Institute (MolSSI) QCSCHEMA data format, facilitating interoperability. A rewrite of our top-level computation driver, and concomitant adoption of the MolSSI QCARCHIVE INFRASTRUCTURE project, makes the latest version of PSI4 well suited to distributed computation of large numbers of independent tasks. The project has fostered the development of independent software components that may be reused in other quantum chemistry programs.

Year:  2020        PMID: 32414239      PMCID: PMC7228781          DOI: 10.1063/5.0006002

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  126 in total

1.  Orbital-optimized third-order Møller-Plesset perturbation theory and its spin-component and spin-opposite scaled variants: application to symmetry breaking problems.

Authors:  Uğur Bozkaya
Journal:  J Chem Phys       Date:  2011-12-14       Impact factor: 3.488

2.  Communication: Practical intramolecular symmetry adapted perturbation theory via Hartree-Fock embedding.

Authors:  Robert M Parrish; Jérôme F Gonthier; Clémence Corminbœuf; C David Sherrill
Journal:  J Chem Phys       Date:  2015-08-07       Impact factor: 3.488

3.  Tractability gains in symmetry-adapted perturbation theory including coupled double excitations: CCD+ST(CCD) dispersion with natural orbital truncations.

Authors:  Robert M Parrish; Edward G Hohenstein; C David Sherrill
Journal:  J Chem Phys       Date:  2013-11-07       Impact factor: 3.488

4.  Analytic Energy Gradients for Variational Two-Electron Reduced-Density-Matrix-Driven Complete Active Space Self-Consistent Field Theory.

Authors:  Elvis Maradzike; Gergely Gidofalvi; Justin M Turney; Henry F Schaefer; A Eugene DePrince
Journal:  J Chem Theory Comput       Date:  2017-08-11       Impact factor: 6.006

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

Authors:  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
Journal:  J Phys Condens Matter       Date:  2017-03-21       Impact factor: 2.333

6.  Psi4NumPy: An Interactive Quantum Chemistry Programming Environment for Reference Implementations and Rapid Development.

Authors:  Daniel G A Smith; Lori A Burns; Dominic A Sirianni; Daniel R Nascimento; Ashutosh Kumar; Andrew M James; Jeffrey B Schriber; Tianyuan Zhang; Boyi Zhang; Adam S Abbott; Eric J Berquist; Marvin H Lechner; Leonardo A Cunha; Alexander G Heide; Jonathan M Waldrop; Tyler Y Takeshita; Asem Alenaizan; Daniel Neuhauser; Rollin A King; Andrew C Simmonett; Justin M Turney; Henry F Schaefer; Francesco A Evangelista; A Eugene DePrince; T Daniel Crawford; Konrad Patkowski; C David Sherrill
Journal:  J Chem Theory Comput       Date:  2018-06-11       Impact factor: 6.006

7.  ωB97M-V: A combinatorially optimized, range-separated hybrid, meta-GGA density functional with VV10 nonlocal correlation.

Authors:  Narbe Mardirossian; Martin Head-Gordon
Journal:  J Chem Phys       Date:  2016-06-07       Impact factor: 3.488

8.  Assessment of Density Functional Methods for Geometry Optimization of Bimolecular van der Waals Complexes.

Authors:  Dominic A Sirianni; Asem Alenaizan; Daniel L Cheney; C David Sherrill
Journal:  J Chem Theory Comput       Date:  2018-05-29       Impact factor: 6.006

9.  Automation of AMOEBA polarizable force field parameterization for small molecules.

Authors:  Johnny C Wu; Gaurav Chattree; Pengyu Ren
Journal:  Theor Chem Acc       Date:  2012-02-26       Impact factor: 1.702

10.  Orbital-optimized coupled-electron pair theory and its analytic gradients: accurate equilibrium geometries, harmonic vibrational frequencies, and hydrogen transfer reactions.

Authors:  Uğur Bozkaya; C David Sherrill
Journal:  J Chem Phys       Date:  2013-08-07       Impact factor: 3.488

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  26 in total

1.  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

2.  Deep Neural Network Model to Predict the Electrostatic Parameters in the Polarizable Classical Drude Oscillator Force Field.

Authors:  Anmol Kumar; Poonam Pandey; Payal Chatterjee; Alexander D MacKerell
Journal:  J Chem Theory Comput       Date:  2022-02-11       Impact factor: 6.006

3.  Quantum Chemistry Common Driver and Databases (QCDB) and Quantum Chemistry Engine (QCEngine): Automation and interoperability among computational chemistry programs.

Authors:  Daniel G A Smith; Annabelle T Lolinco; Zachary L Glick; Jiyoung Lee; Asem Alenaizan; Taylor A Barnes; Carlos H Borca; Roberto Di Remigio; David L Dotson; Sebastian Ehlert; Alexander G Heide; Michael F Herbst; Jan Hermann; Colton B Hicks; Joshua T Horton; Adrian G Hurtado; Peter Kraus; Holger Kruse; Sebastian J R Lee; Jonathon P Misiewicz; Levi N Naden; Farhad Ramezanghorbani; Maximilian Scheurer; Jeffrey B Schriber; Andrew C Simmonett; Johannes Steinmetzer; Jeffrey R Wagner; Logan Ward; Matthew Welborn; Doaa Altarawy; Jamshed Anwar; John D Chodera; Andreas Dreuw; Heather J Kulik; Fang Liu; Todd J Martínez; Devin A Matthews; Henry F Schaefer; Jiří Šponer; Justin M Turney; Lee-Ping Wang; Nuwan De Silva; Rollin A King; John F Stanton; Mark S Gordon; Theresa L Windus; C David Sherrill; Lori A Burns
Journal:  J Chem Phys       Date:  2021-11-28       Impact factor: 3.488

Review 4.  Constructing and interpreting volcano plots and activity maps to navigate homogeneous catalyst landscapes.

Authors:  Rubén Laplaza; Shubhajit Das; Matthew D Wodrich; Clémence Corminboeuf
Journal:  Nat Protoc       Date:  2022-08-17       Impact factor: 17.021

5.  Development and Benchmarking of Open Force Field v1.0.0-the Parsley Small-Molecule Force Field.

Authors:  Yudong Qiu; Daniel G A Smith; Simon Boothroyd; Hyesu Jang; David F Hahn; Jeffrey Wagner; Caitlin C Bannan; Trevor Gokey; Victoria T Lim; Chaya D Stern; Andrea Rizzi; Bryon Tjanaka; Gary Tresadern; Xavier Lucas; Michael R Shirts; Michael K Gilson; John D Chodera; Christopher I Bayly; David L Mobley; Lee-Ping Wang
Journal:  J Chem Theory Comput       Date:  2021-09-22       Impact factor: 6.578

6.  AMOEBA binding free energies for the SAMPL7 TrimerTrip host-guest challenge.

Authors:  Yuanjun Shi; Marie L Laury; Zhi Wang; Jay W Ponder
Journal:  J Comput Aided Mol Des       Date:  2020-11-03       Impact factor: 3.686

7.  Effects of Magnesium, Calcium, and Aluminum Chelation on Fluoroquinolone Absorption Rate and Bioavailability: A Computational Study.

Authors:  Daniel M Walden; Maksim Khotimchenko; Hypatia Hou; Kaushik Chakravarty; Jyotika Varshney
Journal:  Pharmaceutics       Date:  2021-04-21       Impact factor: 6.321

8.  Multi-photon above threshold ionization of multi-electron atoms and molecules using the R-matrix approach.

Authors:  Jakub Benda; Zdeněk Mašín
Journal:  Sci Rep       Date:  2021-06-03       Impact factor: 4.379

9.  Advanced Electrostatic Model for Monovalent Ions Based on Ab Initio Energy Decomposition.

Authors:  Zhifeng Jing; Chengwen Liu; Pengyu Ren
Journal:  J Chem Inf Model       Date:  2021-06-07       Impact factor: 6.162

10.  Computational Resources for Bioscience Education.

Authors:  Rajiv K Kar
Journal:  Appl Biochem Biotechnol       Date:  2021-06-08       Impact factor: 2.926

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