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Title: Dalton Project: A Python platform for molecular- and electronic-structure simulations of complex systems

Abstract

The Dalton Project provides a uniform platform access to the underlying full-fledged quantum chemistry codes Dalton and LSDalton as well as the PyFraME package for automatized fragmentation and parameterization of complex molecular environments. The platform is written in Python and defines a means for library communication and interaction. Intermediate data such as integrals are exposed to the platform and made accessible to the user in the form of NumPy arrays, and the resulting data are extracted, analyzed, and visualized. Complex computational protocols that may, for instance, arise due to a need for environment fragmentation and configuration-space sampling of biochemical systems are readily assisted by the platform. The platform is designed to host additional software libraries and will serve as a hub for future modular software development efforts in the distributed Dalton community.

Authors:
ORCiD logo [1]; ORCiD logo [2]; ORCiD logo [3]; ORCiD logo [4]; ORCiD logo [4]; ORCiD logo [1]; ORCiD logo [3]; ORCiD logo [5];  [6]; ORCiD logo [7]; ORCiD logo [1]; ORCiD logo [8]; ORCiD logo [9]; ORCiD logo [9];  [1]; ORCiD logo [2]; ORCiD logo [10]; ORCiD logo [11]; ORCiD logo [11]; ORCiD logo [4] more »; ORCiD logo [9]; ORCiD logo [1]; ORCiD logo [2]; ORCiD logo [4]; ORCiD logo [3] « less
  1. UiT The Arctic University of Norway, Tromsø, (Norway)
  2. Univ. of Oslo (Norway)
  3. KTH Royal Inst. of Technology, Stockholm (Sweden)
  4. Univ. of Southern Denmark, Odense (Denmark)
  5. Univ. of Warsaw (Poland)
  6. UiT The Arctic University of Norway, Tromsø, (Norway); KTH Royal Inst. of Technology, Stockholm (Sweden)
  7. Lund Univ. (Sweden)
  8. SLAC National Accelerator Lab., Menlo Park, CA (United States)
  9. Technical Univ. of Denmark, Lyngby (Denmark)
  10. KTH Royal Inst. of Technology, Stockholm (Sweden); Kaunas Univ. of Technology (Lithuania)
  11. Univ. of Copenhagen (Denmark)
Publication Date:
Research Org.:
SLAC National Accelerator Lab., Menlo Park, CA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1637901
Grant/Contract Number:  
AC02-76SF00515; 2018-4343; 7014-00050B; 7014-00258B; 250743; 261873; 274918; 262695; 231571; 745967; 765739; 279619
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Journal of Chemical Physics
Additional Journal Information:
Journal Volume: 152; Journal Issue: 21
Publisher:
American Institute of Physics (AIP)
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY

Citation Formats

Olsen, Jógvan Magnus Haugaard, Reine, Simen, Vahtras, Olav, Kjellgren, Erik, Reinholdt, Peter, Hjorth Dundas, Karen Oda, Li, Xin, Cukras, Janusz, Ringholm, Magnus, Hedegård, Erik D., Di Remigio, Roberto, List, Nanna H., Faber, Rasmus, Cabral Tenorio, Bruno Nunes, Bast, Radovan, Pedersen, Thomas Bondo, Rinkevicius, Zilvinas, Sauer, Stephan P. A., Mikkelsen, Kurt V., Kongsted, Jacob, Coriani, Sonia, Ruud, Kenneth, Helgaker, Trygve, Jensen, Hans Jørgen Aa., and Norman, Patrick. Dalton Project: A Python platform for molecular- and electronic-structure simulations of complex systems. United States: N. p., 2020. Web. doi:10.1063/1.5144298.
Olsen, Jógvan Magnus Haugaard, Reine, Simen, Vahtras, Olav, Kjellgren, Erik, Reinholdt, Peter, Hjorth Dundas, Karen Oda, Li, Xin, Cukras, Janusz, Ringholm, Magnus, Hedegård, Erik D., Di Remigio, Roberto, List, Nanna H., Faber, Rasmus, Cabral Tenorio, Bruno Nunes, Bast, Radovan, Pedersen, Thomas Bondo, Rinkevicius, Zilvinas, Sauer, Stephan P. A., Mikkelsen, Kurt V., Kongsted, Jacob, Coriani, Sonia, Ruud, Kenneth, Helgaker, Trygve, Jensen, Hans Jørgen Aa., & Norman, Patrick. Dalton Project: A Python platform for molecular- and electronic-structure simulations of complex systems. United States. doi:10.1063/1.5144298.
Olsen, Jógvan Magnus Haugaard, Reine, Simen, Vahtras, Olav, Kjellgren, Erik, Reinholdt, Peter, Hjorth Dundas, Karen Oda, Li, Xin, Cukras, Janusz, Ringholm, Magnus, Hedegård, Erik D., Di Remigio, Roberto, List, Nanna H., Faber, Rasmus, Cabral Tenorio, Bruno Nunes, Bast, Radovan, Pedersen, Thomas Bondo, Rinkevicius, Zilvinas, Sauer, Stephan P. A., Mikkelsen, Kurt V., Kongsted, Jacob, Coriani, Sonia, Ruud, Kenneth, Helgaker, Trygve, Jensen, Hans Jørgen Aa., and Norman, Patrick. Fri . "Dalton Project: A Python platform for molecular- and electronic-structure simulations of complex systems". United States. doi:10.1063/1.5144298. https://www.osti.gov/servlets/purl/1637901.
@article{osti_1637901,
title = {Dalton Project: A Python platform for molecular- and electronic-structure simulations of complex systems},
author = {Olsen, Jógvan Magnus Haugaard and Reine, Simen and Vahtras, Olav and Kjellgren, Erik and Reinholdt, Peter and Hjorth Dundas, Karen Oda and Li, Xin and Cukras, Janusz and Ringholm, Magnus and Hedegård, Erik D. and Di Remigio, Roberto and List, Nanna H. and Faber, Rasmus and Cabral Tenorio, Bruno Nunes and Bast, Radovan and Pedersen, Thomas Bondo and Rinkevicius, Zilvinas and Sauer, Stephan P. A. and Mikkelsen, Kurt V. and Kongsted, Jacob and Coriani, Sonia and Ruud, Kenneth and Helgaker, Trygve and Jensen, Hans Jørgen Aa. and Norman, Patrick},
abstractNote = {The Dalton Project provides a uniform platform access to the underlying full-fledged quantum chemistry codes Dalton and LSDalton as well as the PyFraME package for automatized fragmentation and parameterization of complex molecular environments. The platform is written in Python and defines a means for library communication and interaction. Intermediate data such as integrals are exposed to the platform and made accessible to the user in the form of NumPy arrays, and the resulting data are extracted, analyzed, and visualized. Complex computational protocols that may, for instance, arise due to a need for environment fragmentation and configuration-space sampling of biochemical systems are readily assisted by the platform. The platform is designed to host additional software libraries and will serve as a hub for future modular software development efforts in the distributed Dalton community.},
doi = {10.1063/1.5144298},
journal = {Journal of Chemical Physics},
number = 21,
volume = 152,
place = {United States},
year = {2020},
month = {6}
}

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  • Kumar, Chandan; Kjærgaard, Thomas; Helgaker, Trygve
  • The Journal of Chemical Physics, Vol. 145, Issue 23
  • DOI: 10.1063/1.4972212

Local electric fields and molecular properties in heterogeneous environments through polarizable embedding
journal, January 2016

  • List, Nanna Holmgaard; Jensen, Hans Jørgen Aagaard; Kongsted, Jacob
  • Physical Chemistry Chemical Physics, Vol. 18, Issue 15
  • DOI: 10.1039/c6cp00669h

Subsystem density-functional theory: Subsystem density-functional theory
journal, July 2014

  • Jacob, Christoph R.; Neugebauer, Johannes
  • Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 4, Issue 4
  • DOI: 10.1002/wcms.1175

Molecular gradient for second-order Møller-Plesset perturbation theory using the divide-expand-consolidate (DEC) scheme
journal, September 2012

  • Kristensen, Kasper; Jørgensen, Poul; Jansík, Branislav
  • The Journal of Chemical Physics, Vol. 137, Issue 11
  • DOI: 10.1063/1.4752432

Structure, Spectroscopy, and Spectral Tuning of the Gas-Phase Retinal Chromophore:  The β-Ionone “Handle” and Alkyl Group Effect
journal, July 2005

  • Cembran, Alessandro; González-Luque, Remedios; Altoè, Piero
  • The Journal of Physical Chemistry A, Vol. 109, Issue 29
  • DOI: 10.1021/jp052068c

The explicitly correlated same number of optimized parameters (SNOOP-F12) scheme for calculating intermolecular interaction energies
journal, May 2016

  • Rasmussen, Troels Hels; Wang, Yang Min; Kjærgaard, Thomas
  • The Journal of Chemical Physics, Vol. 144, Issue 20
  • DOI: 10.1063/1.4950846

PCMSolver: An open-source library for solvation modeling: DI REMIGIO et al.
journal, October 2018

  • Di Remigio, Roberto; Steindal, Arnfinn Hykkerud; Mozgawa, Krzysztof
  • International Journal of Quantum Chemistry, Vol. 119, Issue 1
  • DOI: 10.1002/qua.25685

Trust Region Minimization of Orbital Localization Functions
journal, August 2012

  • Høyvik, Ida-Marie; Jansik, Branislav; Jørgensen, Poul
  • Journal of Chemical Theory and Computation, Vol. 8, Issue 9
  • DOI: 10.1021/ct300473g

Restricted density functional theory of linear time-dependent properties in open-shell molecules
journal, July 2003

  • Rinkevicius, Zilvinas; Tunell, Ingvar; Sałek, Paweł
  • The Journal of Chemical Physics, Vol. 119, Issue 1
  • DOI: 10.1063/1.1577329

Zero-point vibrational corrections to isotropic hyperfine coupling constants in polyatomic molecules
journal, January 2011

  • Chen, Xing; Rinkevicius, Zilvinas; Cao, Zexing
  • Phys. Chem. Chem. Phys., Vol. 13, Issue 2
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The Second-Order Polarization Propagator Approximation (SOPPA) method coupled to the polarizable continuum model
journal, July 2014

  • Eriksen, Janus J.; Solanko, Lukasz M.; Nåbo, Lina J.
  • Computational and Theoretical Chemistry, Vol. 1040-1041
  • DOI: 10.1016/j.comptc.2014.02.034

Density-functional theory calculations of optical rotatory dispersion in the nonresonant and resonant frequency regions
journal, March 2004

  • Norman, Patrick; Ruud, Kenneth; Helgaker, Trygve
  • The Journal of Chemical Physics, Vol. 120, Issue 11
  • DOI: 10.1063/1.1647515

On the importance of excited state dynamic response electron correlation in polarizable embedding methods
journal, June 2012

  • Eriksen, Janus J.; Sauer, Stephan P. A.; Mikkelsen, Kurt V.
  • Journal of Computational Chemistry, Vol. 33, Issue 25
  • DOI: 10.1002/jcc.23032

Theory of Separability of Many‐Electron Systems
journal, December 1971

  • Huzinaga, S.; Cantu, A. A.
  • The Journal of Chemical Physics, Vol. 55, Issue 12
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Density functional theory for hyperfine coupling constants with the restricted-unrestricted approach
journal, January 2004

  • Rinkevicius, Zilvinas; Telyatnyk, Lyudmyla; Vahtras, Olav
  • The Journal of Chemical Physics, Vol. 121, Issue 16
  • DOI: 10.1063/1.1799013

Spin adapted implementation of EOM-CCSD for triplet excited states: Probing intersystem crossings of acetylacetone at the carbon and oxygen K-edges
journal, October 2019

  • Faber, Rasmus; Kjønstad, Eirik F.; Koch, Henrik
  • The Journal of Chemical Physics, Vol. 151, Issue 14
  • DOI: 10.1063/1.5112164

On the criteria to be used in decomposing systems into modules
journal, December 1972


Arbitrary-Order Density Functional Response Theory from Automatic Differentiation
journal, May 2010

  • Ekström, Ulf; Visscher, Lucas; Bast, Radovan
  • Journal of Chemical Theory and Computation, Vol. 6, Issue 7
  • DOI: 10.1021/ct100117s

Nuclear Magnetic Shielding Constants from Quantum Mechanical/Molecular Mechanical Calculations Using Polarizable Embedding: Role of the Embedding Potential
journal, February 2014

  • Steinmann, Casper; Olsen, Jógvan Magnus Haugaard; Kongsted, Jacob
  • Journal of Chemical Theory and Computation, Vol. 10, Issue 3
  • DOI: 10.1021/ct400880n

Linear scaling coupled cluster method with correlation energy based error control
journal, July 2010

  • Ziółkowski, Marcin; Jansík, Branislav; Kjærgaard, Thomas
  • The Journal of Chemical Physics, Vol. 133, Issue 1
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Efficient linear-scaling second-order Møller-Plesset perturbation theory: The divide–expand–consolidate RI-MP2 model
journal, February 2016

  • Baudin, Pablo; Ettenhuber, Patrick; Reine, Simen
  • The Journal of Chemical Physics, Vol. 144, Issue 5
  • DOI: 10.1063/1.4940732

VeloxChem: A Python‐driven density‐functional theory program for spectroscopy simulations in high‐performance computing environments
journal, December 2019

  • Rinkevicius, Zilvinas; Li, Xin; Vahtras, Olav
  • WIREs Computational Molecular Science
  • DOI: 10.1002/wcms.1457

SciPy 1.0: fundamental algorithms for scientific computing in Python
journal, February 2020


Note: FixSol solvation model and FIXPVA2 tessellation scheme
journal, December 2012

  • Thellamurege, Nandun M.; Li, Hui
  • The Journal of Chemical Physics, Vol. 137, Issue 24
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A density matrix-based quasienergy formulation of the Kohn–Sham density functional response theory using perturbation- and time-dependent basis sets
journal, December 2008

  • Thorvaldsen, Andreas J.; Ruud, Kenneth; Kristensen, Kasper
  • The Journal of Chemical Physics, Vol. 129, Issue 21
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Polarizable Density Embedding: A New QM/QM/MM-Based Computational Strategy
journal, December 2014

  • Olsen, Jógvan Magnus Haugaard; Steinmann, Casper; Ruud, Kenneth
  • The Journal of Physical Chemistry A, Vol. 119, Issue 21
  • DOI: 10.1021/jp510138k

Charge-constrained auxiliary-density-matrix methods for the Hartree–Fock exchange contribution
journal, September 2014

  • Merlot, Patrick; Izsák, Róbert; Borgoo, Alex
  • The Journal of Chemical Physics, Vol. 141, Issue 9
  • DOI: 10.1063/1.4894267

Investigation of Multiconfigurational Short-Range Density Functional Theory for Electronic Excitations in Organic Molecules
journal, April 2016

  • Hubert, Mickaël; Hedegård, Erik D.; Jensen, Hans Jørgen Aa.
  • Journal of Chemical Theory and Computation, Vol. 12, Issue 5
  • DOI: 10.1021/acs.jctc.5b01141

On the universality of the long-/short-range separation in multiconfigurational density-functional theory. II. Investigating f[sup 0] actinide species
journal, January 2009

  • Fromager, Emmanuel; Réal, Florent; Wåhlin, Pernilla
  • The Journal of Chemical Physics, Vol. 131, Issue 5
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CC2 oscillator strengths within the local framework for calculating excitation energies (LoFEx)
journal, April 2017

  • Baudin, Pablo; Kjærgaard, Thomas; Kristensen, Kasper
  • The Journal of Chemical Physics, Vol. 146, Issue 14
  • DOI: 10.1063/1.4979713

Performance of SOPPA-based methods in the calculation of vertical excitation energies and oscillator strengths
journal, March 2015


Nonlinear response theory with relaxation: The first-order hyperpolarizability
journal, November 2005

  • Norman, Patrick; Bishop, David M.; Jensen, Hans Jørgen Aa.
  • The Journal of Chemical Physics, Vol. 123, Issue 19
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Computational Approach for Studying Optical Properties of DNA Systems in Solution
journal, September 2016

  • Nørby, Morten Steen; Steinmann, Casper; Olsen, Jógvan Magnus Haugaard
  • Journal of Chemical Theory and Computation, Vol. 12, Issue 10
  • DOI: 10.1021/acs.jctc.6b00706

Merging multireference perturbation and density-functional theories by means of range separation: Potential curves for Be 2 , Mg 2 , and Ca 2
journal, February 2010

  • Fromager, Emmanuel; Cimiraglia, Renzo; Jensen, Hans Jørgen Aa.
  • Physical Review A, Vol. 81, Issue 2
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Auxiliary Density Matrix Methods for Hartree−Fock Exchange Calculations
journal, July 2010

  • Guidon, Manuel; Hutter, Jürg; VandeVondele, Joost
  • Journal of Chemical Theory and Computation, Vol. 6, Issue 8
  • DOI: 10.1021/ct1002225

The same number of optimized parameters scheme for determining intermolecular interaction energies
journal, March 2015

  • Kristensen, Kasper; Ettenhuber, Patrick; Eriksen, Janus Juul
  • The Journal of Chemical Physics, Vol. 142, Issue 11
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Spin-component-scaled electron correlation methods: SCS electron correlation methods
journal, June 2012

  • Grimme, Stefan; Goerigk, Lars; Fink, Reinhold F.
  • Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 2, Issue 6
  • DOI: 10.1002/wcms.1110

Matplotlib: A 2D Graphics Environment
journal, January 2007


Complex polarization propagator calculations of magnetic circular dichroism spectra
journal, March 2008

  • Solheim, Harald; Ruud, Kenneth; Coriani, Sonia
  • The Journal of Chemical Physics, Vol. 128, Issue 9
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Asymmetric-Lanczos-Chain-Driven Implementation of Electronic Resonance Convergent Coupled-Cluster Linear Response Theory
journal, April 2012

  • Coriani, Sonia; Fransson, Thomas; Christiansen, Ove
  • Journal of Chemical Theory and Computation, Vol. 8, Issue 5
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Internal-to-Cartesian back transformation of molecular geometry steps using high-order geometric derivatives
journal, May 2013

  • Rybkin, Vladimir V.; Ekström, Ulf; Helgaker, Trygve
  • Journal of Computational Chemistry, Vol. 34, Issue 21
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The NumPy Array: A Structure for Efficient Numerical Computation
journal, March 2011

  • van der Walt, Stéfan; Colbert, S. Chris; Varoquaux, Gaël
  • Computing in Science & Engineering, Vol. 13, Issue 2
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The structure of the “THE”-multiprogramming system
journal, May 1968


Local orbitals by minimizing powers of the orbital variance
journal, May 2011

  • Jansík, Branislav; Høst, Stinne; Kristensen, Kasper
  • The Journal of Chemical Physics, Vol. 134, Issue 19
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The molecular gradient using the divide-expand-consolidate resolution of the identity second-order Møller-Plesset perturbation theory: The DEC-RI-MP2 gradient
journal, July 2016

  • Bykov, Dmytro; Kristensen, Kasper; Kjærgaard, Thomas
  • The Journal of Chemical Physics, Vol. 145, Issue 2
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A local framework for calculating coupled cluster singles and doubles excitation energies (LoFEx-CCSD)
journal, December 2016


Photoionization cross section by Stieltjes imaging applied to coupled cluster Lanczos pseudo-spectra
journal, September 2013

  • Cukras, Janusz; Coriani, Sonia; Decleva, Piero
  • The Journal of Chemical Physics, Vol. 139, Issue 9
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Excitation Spectra of Nucleobases with Multiconfigurational Density Functional Theory
journal, December 2015

  • Hubert, Mickaël; Jensen, Hans Jørgen Aa.; Hedegård, Erik D.
  • The Journal of Physical Chemistry A, Vol. 120, Issue 1
  • DOI: 10.1021/acs.jpca.5b09662

On the universality of the long-/short-range separation in multiconfigurational density-functional theory
journal, February 2007

  • Fromager, Emmanuel; Toulouse, Julien; Jensen, Hans Jørgen Aa.
  • The Journal of Chemical Physics, Vol. 126, Issue 7
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Molecular inner-shell photoabsorption/photoionization cross sections at core-valence-separated coupled cluster level: Theory and examples
journal, June 2019

  • Tenorio, Bruno Nunes Cabral; Moitra, Torsha; Nascimento, Marco Antonio Chaer
  • The Journal of Chemical Physics, Vol. 150, Issue 22
  • DOI: 10.1063/1.5096777