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Journal Articles

ModelHamiltonian: A Python-scriptable library for generating 0-, 1-, and 2-electron integrals

Valerii Chuiko, Addison D. S. Richards, Gabriela Sánchez-Díaz, Marco Martínez-González, Wesley Sanchez, Giovanni B. Da Rosa, Michelle Richer, Yilin Zhao, William Adams, Paul A. Johnson, Farnaz Heidar-Zadeh, Paul W. Ayers
Journal: The Journal of Chemical Physics
J. Chem. Phys. 161, 132503 (2024)
https://doi.org/10.1063/5.0219015
Published: October 2024
View article titled, ModelHamiltonian: A Python-scriptable library for generating 0-, 1-, and 2-electron integrals
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Journal Articles

PyCI: A Python-scriptable library for arbitrary determinant CI

Michelle Richer, Gabriela Sánchez-Díaz, Marco Martínez-González, Valerii Chuiko, Taewon David Kim, Alireza Tehrani, Shuoyang Wang, Pratiksha B. Gaikwad, Carlos E. V. de Moura, Cassandra Masschelein, Ramón Alain Miranda-Quintana, Augusto Gerolin, Farnaz Heidar-Zadeh, Paul W. Ayers
Journal: The Journal of Chemical Physics
J. Chem. Phys. 161, 132502 (2024)
https://doi.org/10.1063/5.0219010
Published: October 2024
View article titled, PyCI: A Python-scriptable library for arbitrary determinant CI
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Journal Articles

mpsqd: A matrix product state based Python package to simulate closed and open system quantum dynamics

Editor’s Pick
Weizhong Guan, Peng Bao, Jiawei Peng, Zhenggang Lan, Qiang Shi
Journal: The Journal of Chemical Physics
J. Chem. Phys. 161, 122501 (2024)
https://doi.org/10.1063/5.0226214
Published: September 2024
View article titled, mpsqd: A matrix product state based Python package to simulate closed and open system quantum dynamics
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Journal Articles

OQuPy: A Python package to efficiently simulate non-Markovian open quantum systems with process tensors

Gerald E. Fux, Piper Fowler-Wright, Joel Beckles, Eoin P. Butler, Paul R. Eastham, Dominic Gribben, Jonathan Keeling, Dainius Kilda, Peter Kirton, Ewen D. C. Lawrence, Brendon W. Lovett, Eoin O’Neill, Aidan Strathearn, Roosmarijn de Wit
Journal: The Journal of Chemical Physics
J. Chem. Phys. 161, 124108 (2024)
https://doi.org/10.1063/5.0225367
Published: September 2024
View article titled, OQuPy: A Python package to efficiently simulate non-Markovian open quantum systems with process tensors
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Journal Articles

Markov-chain sampling for long-range systems without evaluating the energy

Gabriele Tartero, Werner Krauth
Journal: The Journal of Chemical Physics
J. Chem. Phys. 161, 094106 (2024)
https://doi.org/10.1063/5.0225561
Published: September 2024
View article titled, Markov-chain sampling for long-range systems without evaluating the energy
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Journal Articles

Guest editorial: Special Topic on software for atomistic machine learning

Matthias Rupp, Emine Küçükbenli, Gábor Csányi
Journal: The Journal of Chemical Physics
J. Chem. Phys. 161, 060401 (2024)
https://doi.org/10.1063/5.0228461
Published: August 2024
View article titled, Guest editorial: Special Topic on software for atomistic machine learning
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Journal Articles

PyCTRAMER: A Python package for charge transfer rate constant of condensed-phase systems from Marcus theory to Fermi’s golden rule

Zengkui Liu, Dominikus Brian, Xiang Sun
Journal: The Journal of Chemical Physics
J. Chem. Phys. 161, 064101 (2024)
https://doi.org/10.1063/5.0224524
Published: August 2024
View article titled, PyCTRAMER: A Python package for charge transfer rate constant of condensed-phase systems from Marcus theory to Fermi’s golden rule
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Journal Articles

pyMBE: The Python-based molecule builder for ESPResSo

David Beyer, Paola B. Torres, Sebastian P. Pineda, Claudio F. Narambuena, Jean-Noël Grad, Peter Košovan, Pablo M. Blanco
Journal: The Journal of Chemical Physics
J. Chem. Phys. 161, 022502 (2024)
https://doi.org/10.1063/5.0216389
Published: July 2024
View article titled, pyMBE: The Python-based molecule builder for ESPResSo
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Journal Articles

MolSym: A Python package for handling symmetry in molecular quantum chemistry

Stephen M. Goodlett, Nathaniel L. Kitzmiller, Justin M. Turney, Henry F. Schaefer, III
Journal: The Journal of Chemical Physics
J. Chem. Phys. 161, 024107 (2024)
https://doi.org/10.1063/5.0216738
Published: July 2024
View article titled, <sc>MolSym</sc>: A Python package for handling symmetry in molecular quantum chemistry
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Journal Articles

Force Field X: A computational microscope to study genetic variation and organic crystals using theory and experiment

Rose A. Gogal, Aaron J. Nessler, Andrew C. Thiel, Hernan V. Bernabe, Rae A. Corrigan Grove, Leah M. Cousineau, Jacob M. Litman, Jacob M. Miller, Guowei Qi, Matthew J. Speranza, Mallory R. Tollefson, Timothy D. Fenn, Jacob J. Michaelson, Okimasa Okada, Jean-Philip Piquemal, Jay W. Ponder, Jana Shen, Richard J. H. Smith, Wei Yang, Pengyu Ren, Michael J. Schnieders
Journal: The Journal of Chemical Physics
J. Chem. Phys. 161, 012501 (2024)
https://doi.org/10.1063/5.0214652
Published: July 2024
View article titled, Force Field X: A computational microscope to study genetic variation and organic crystals using theory and experiment
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Journal Articles

Plugin-based interoperability and ecosystem management for the MolSSI Driver Interface Project

T. A. Barnes, S. Ellis, J. Chen, S. J. Plimpton, J. A. Nash
Journal: The Journal of Chemical Physics
J. Chem. Phys. 160, 214114 (2024)
https://doi.org/10.1063/5.0214279
Published: June 2024
View article titled, Plugin-based interoperability and ecosystem management for the MolSSI Driver Interface Project
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Journal Articles

Working with benchmark datasets in the Cuby framework

Jan Řezáč, Outi Vilhelmiina Kontkanen, Martin Nováček
Journal: The Journal of Chemical Physics
J. Chem. Phys. 160, 202501 (2024)
https://doi.org/10.1063/5.0203372
Published: May 2024
View article titled, Working with benchmark datasets in the Cuby framework
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Includes: Supplementary data
Journal Articles

Grid : A Python library for molecular integration, interpolation, differentiation, and more

Alireza Tehrani, Xiaotian Derrick Yang, Marco Martínez-González, Leila Pujal, Raymundo Hernández-Esparza, Matthew Chan, Esteban Vöhringer-Martinez, Toon Verstraelen, Paul W. Ayers, Farnaz Heidar-Zadeh
Journal: The Journal of Chemical Physics
J. Chem. Phys. 160, 172503 (2024)
https://doi.org/10.1063/5.0202240
Published: May 2024
View article titled, Grid : A Python library for molecular integration, interpolation, differentiation, and more
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Journal Articles

Interoperable workflows by exchanging grid-based data between quantum-chemical program packages

Kevin Focke, Matteo De Santis, Mario Wolter, Jessica A. Martinez B, Valérie Vallet, André Severo Pereira Gomes, Małgorzata Olejniczak, Christoph R. Jacob
Journal: The Journal of Chemical Physics
J. Chem. Phys. 160, 162503 (2024)
https://doi.org/10.1063/5.0201701
Published: April 2024
View article titled, Interoperable workflows by exchanging grid-based data between quantum-chemical program packages
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Journal Articles

Massively scalable workflows for quantum chemistry: BigChem and ChemCloud

Colton B. Hicks, Todd J. Martinez
Journal: The Journal of Chemical Physics
J. Chem. Phys. 160, 142501 (2024)
https://doi.org/10.1063/5.0190834
Published: April 2024
View article titled, Massively scalable workflows for quantum chemistry: <sc>BigChem</sc> and <sc>ChemCloud</sc>
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Includes: Supplementary data
Journal Articles

Rapid simulation of two-dimensional spectra with correlated anisotropic dimensions

Deepansh J. Srivastava, Jay H. Baltisberger, Philip J. Grandinetti
Journal: The Journal of Chemical Physics
J. Chem. Phys. 160, 134104 (2024)
https://doi.org/10.1063/5.0200042
Published: April 2024
View article titled, Rapid simulation of two-dimensional spectra with correlated anisotropic dimensions
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Includes: Supplementary data
Journal Articles

Application of density matrix Wigner transforms for ultrafast macromolecular and chemical x-ray crystallography

Featured
Samuel Perrett, Viktoria Chatrchyan, Tiago Buckup, Jasper J. van Thor
Journal: The Journal of Chemical Physics
J. Chem. Phys. 160, 100901 (2024)
https://doi.org/10.1063/5.0188888
Published: March 2024
View article titled, Application of density matrix Wigner transforms for ultrafast macromolecular and chemical x-ray crystallography
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Includes: Supplementary data
Journal Articles

Determining internal coordinate sets for optimal representation of molecular vibration

Kemal Oenen, Dennis F. Dinu, Klaus R. Liedl
Journal: The Journal of Chemical Physics
J. Chem. Phys. 160, 014104 (2024)
https://doi.org/10.1063/5.0180657
Published: January 2024
View article titled, Determining internal coordinate sets for optimal representation of molecular vibration
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Includes: Supplementary data
Journal Articles

Special Topic on High Performance Computing in Chemical Physics

Tjerk P. Straatsma, Theresa L. Windus, Takahito Nakajima
Journal: The Journal of Chemical Physics
J. Chem. Phys. 159, 210401 (2023)
https://doi.org/10.1063/5.0185894
Published: December 2023
View article titled, Special Topic on High Performance Computing in Chemical Physics
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Journal Articles

Reproducibility of density functional approximations: How new functionals should be reported

Susi Lehtola, Miguel A. L. Marques
Journal: The Journal of Chemical Physics
J. Chem. Phys. 159, 114116 (2023)
https://doi.org/10.1063/5.0167763
Published: September 2023
View article titled, Reproducibility of density functional approximations: How new functionals should be reported
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Includes: Supplementary data