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Journal Articles

Adaptive accelerated reactive molecular dynamics driven by parallel collective variables overcoming dimensionality explosion

Rui Zhou, Luyao Bao, Weifeng Bu, Feng Zhou
Journal: The Journal of Chemical Physics
J. Chem. Phys. 161, 054103 (2024)
https://doi.org/10.1063/5.0222514
Published: August 2024
View article titled, Adaptive accelerated reactive molecular dynamics driven by parallel collective variables overcoming dimensionality explosion
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Journal Articles

STORMM: Structure and topology replica molecular mechanics for chemical simulations

David S. Cerutti, Rafal Wiewiora, Simon Boothroyd, Woody Sherman
Journal: The Journal of Chemical Physics
J. Chem. Phys. 161, 032501 (2024)
https://doi.org/10.1063/5.0211032
Published: July 2024
View article titled, STORMM: Structure and topology replica molecular mechanics for chemical simulations
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Journal Articles

Efficient all-electron hybrid density functionals for atomistic simulations beyond 10 000 atoms

Sebastian Kokott, Florian Merz, Yi Yao, Christian Carbogno, Mariana Rossi, Ville Havu, Markus Rampp, Matthias Scheffler, Volker Blum
Journal: The Journal of Chemical Physics
J. Chem. Phys. 161, 024112 (2024)
https://doi.org/10.1063/5.0208103
Published: July 2024
View article titled, Efficient all-electron hybrid density functionals for atomistic simulations beyond 10 000 atoms
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Journal Articles

Measuring friction from simulations of folded graphene sheets

Charlie M. Rawlins, Gareth A. Tribello
Journal: The Journal of Chemical Physics
J. Chem. Phys. 160, 174112 (2024)
https://doi.org/10.1063/5.0203397
Published: May 2024
View article titled, Measuring friction from simulations of folded graphene sheets
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Journal Articles

Hybrid programming-model strategies for GPU offloading of electronic structure calculation kernels

Jean-Luc Fattebert, Christian F. A. Negre, Joshua Finkelstein, Jamaludin Mohd-Yusof, Daniel Osei-Kuffuor, Michael E. Wall, Yu Zhang, Nicolas Bock, Susan M. Mniszewski
Journal: The Journal of Chemical Physics
J. Chem. Phys. 160, 122501 (2024)
https://doi.org/10.1063/5.0198797
Published: March 2024
View article titled, Hybrid programming-model strategies for GPU offloading of electronic structure calculation kernels
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Journal Articles

Pseudo-marginal approximation to the free energy in a micro–macro Markov chain Monte Carlo method

Hannes Vandecasteele, Giovanni Samaey
Journal: The Journal of Chemical Physics
J. Chem. Phys. 160, 104702 (2024)
https://doi.org/10.1063/5.0199562
Published: March 2024
View article titled, Pseudo-marginal approximation to the free energy in a micro–macro Markov chain Monte Carlo method
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Journal Articles

A fast, dense Chebyshev solver for electronic structure on GPUs

Editor’s Pick
Joshua Finkelstein, Christian F. A. Negre, Jean-Luc Fattebert
Journal: The Journal of Chemical Physics
J. Chem. Phys. 159, 101101 (2023)
https://doi.org/10.1063/5.0164255
Published: September 2023
View article titled, A fast, dense Chebyshev solver for electronic structure on GPUs
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Journal Articles

A hybrid CPU/GPU method for Hartree–Fock self-consistent-field calculation

Ji Qi, Yingfeng Zhang, Minghui Yang
Journal: The Journal of Chemical Physics
J. Chem. Phys. 159, 104101 (2023)
https://doi.org/10.1063/5.0156934
Published: September 2023
View article titled, A hybrid CPU/GPU method for Hartree–Fock self-consistent-field calculation
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Journal Articles

Combining fragmentation method and high-performance computing: Geometry optimization and vibrational spectra of proteins

Nityananda Sahu, Subodh S. Khire, Shridhar R. Gadre
Journal: The Journal of Chemical Physics
J. Chem. Phys. 159, 044309 (2023)
https://doi.org/10.1063/5.0149572
Published: July 2023
View article titled, Combining fragmentation method and high-performance computing: Geometry optimization and vibrational spectra of proteins
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Includes: Supplementary data
Journal Articles

Toward an extreme-scale electronic structure system

Jorge L. Galvez Vallejo, Calum Snowdon, Ryan Stocks, Fazeleh Kazemian, Fiona Chuo Yan Yu, Christopher Seidl, Zoe Seeger, Melisa Alkan, David Poole, Bryce M. Westheimer, Mehaboob Basha, Marco De La Pierre, Alistair Rendell, Ekaterina I. Izgorodina, Mark S. Gordon, Giuseppe M. J. Barca
Journal: The Journal of Chemical Physics
J. Chem. Phys. 159, 044112 (2023)
https://doi.org/10.1063/5.0156399
Published: July 2023
View article titled, Toward an extreme-scale electronic structure system
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Journal Articles

Subspace recursive Fermi-operator expansion strategies for large-scale DFT eigenvalue problems on HPC architectures

Sameer Khadatkar, Phani Motamarri
Journal: The Journal of Chemical Physics
J. Chem. Phys. 159, 031102 (2023)
https://doi.org/10.1063/5.0150287
Published: July 2023
View article titled, Subspace recursive Fermi-operator expansion strategies for large-scale DFT eigenvalue problems on HPC architectures
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Journal Articles

Gaussian functions with odd power of r produced by the free complement theory

Yusaku I. Kurokawa, Hiroshi Nakatsuji
Journal: The Journal of Chemical Physics
J. Chem. Phys. 159, 024103 (2023)
https://doi.org/10.1063/5.0155105
Published: July 2023
View article titled, Gaussian functions with odd power of <em>r</em> produced by the free complement theory
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Journal Articles

Distributed memory, GPU accelerated Fock construction for hybrid, Gaussian basis density functional theory

David B. Williams-Young, Andrey Asadchev, Doru Thom Popovici, David Clark, Jonathan Waldrop, Theresa L. Windus, Edward F. Valeev, Wibe A. de Jong
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 234104 (2023)
https://doi.org/10.1063/5.0151070
Published: June 2023
View article titled, Distributed memory, GPU accelerated Fock construction for hybrid, Gaussian basis density functional theory
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Includes: Supplementary data
Journal Articles

Protein–ligand interactions from a quantum fragmentation perspective: The case of the SARS-CoV-2 main protease interacting with α-ketoamide inhibitors

Luigi Genovese, William Dawson, Takahito Nakajima, Viviana Cristiglio, Valérie Vallet, Michel Masella
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 214121 (2023)
https://doi.org/10.1063/5.0148064
Published: June 2023
View article titled, Protein–ligand interactions from a quantum fragmentation perspective: The case of the SARS-CoV-2 main protease interacting with <em>α</em>-ketoamide inhibitors
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Includes: Supplementary data
Journal Articles

Sparse tensor based nuclear gradients for periodic Hartree–Fock and low-scaling correlated wave function methods in the CP2K software package: A massively parallel and GPU accelerated implementation

Augustin Bussy, Ole Schütt, Jürg Hutter
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 164109 (2023)
https://doi.org/10.1063/5.0144493
Published: April 2023
View article titled, Sparse tensor based nuclear gradients for periodic Hartree–Fock and low-scaling correlated wave function methods in the CP2K software package: A massively parallel and GPU accelerated implementation
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Includes: Supplementary data
Journal Articles

Densest packing of flexible polymers in 2D films

Clara Pedrosa, Daniel Martínez-Fernández, Miguel Herranz, Katerina Foteinopoulou, Nikos Ch. Karayiannis, Manuel Laso
Journal: The Journal of Chemical Physics
J. Chem. Phys. 158, 164502 (2023)
https://doi.org/10.1063/5.0137115
Published: April 2023
View article titled, Densest packing of flexible polymers in 2D films
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Journal Articles

A comparison between the one- and two-step spin–orbit coupling approaches based on the ab initio density matrix renormalization group

Huanchen Zhai, Garnet Kin-Lic Chan
Journal: The Journal of Chemical Physics
J. Chem. Phys. 157, 164108 (2022)
https://doi.org/10.1063/5.0107805
Published: October 2022
View article titled, A comparison between the one- and two-step spin–orbit coupling approaches based on the <em>ab initio</em> density matrix renormalization group
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Includes: Supplementary data
Journal Articles

Assessing the effect of a liquid water layer on the adsorption of hydrate anti-agglomerants using molecular simulations

Stephan Mohr, Rémi Pétuya, Juan Sarria, Nirupam Purkayastha, Scot Bodnar, Jonathan Wylde, Ioannis N. Tsimpanogiannis
Journal: The Journal of Chemical Physics
J. Chem. Phys. 157, 094703 (2022)
https://doi.org/10.1063/5.0100260
Published: September 2022
View article titled, Assessing the effect of a liquid water layer on the adsorption of hydrate anti-agglomerants using molecular simulations
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Includes: Supplementary data
Journal Articles

Computational discovery of stable and metastable ternary oxynitrides

Abhishek Sharan, Stephan Lany
Journal: The Journal of Chemical Physics
J. Chem. Phys. 154, 234706 (2021)
https://doi.org/10.1063/5.0050356
Published: June 2021
View article titled, Computational discovery of stable and metastable ternary oxynitrides
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Includes: Supplementary data
Journal Articles

Low communication high performance ab initio density matrix renormalization group algorithms

Editor’s Pick
Huanchen Zhai, Garnet Kin-Lic Chan
Journal: The Journal of Chemical Physics
J. Chem. Phys. 154, 224116 (2021)
https://doi.org/10.1063/5.0050902
Published: June 2021
View article titled, Low communication high performance <em>ab initio</em> density matrix renormalization group algorithms
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