eQE: An open‐source density functional embedding theory code for the condensed phase
Abstract
Abstract In this work, we present the main features and algorithmic details of a novel implementation of the frozen density embedding (FDE) formulation of subsystem density functional theory (DFT) that is specifically designed to enable ab initio molecular dynamics (AIMD) simulations of large‐scale condensed‐phase systems containing 1000s of atoms. This code (available at http://eqe.rutgers.edu ) has been given the moniker of embedded Quantum ESPRESSO (eQE) as it is a generalization of the open‐source Quantum ESPRESSO (QE) suite of programs. The strengths of eQE reside in a hierarchical parallelization scheme that allows for an efficient and fully self‐consistent treatment of the electronic structure (via the addition of an additional DIIS extrapolation layer) while simultaneously exploiting the inherent symmetries and periodicities in the system (via sampling of subsystem‐specific first Brillouin zones and utilization of subsystem‐specific basis sets). While bulk liquids and molecular crystals are two classes of systems that exemplify the utility of the FDE approach (as these systems can be partitioned into weakly interacting subunits), we show that eQE has significantly extended this regime of applicability by outperforming standard semilocal Kohn–Sham DFT (KS‐DFT) for large‐scale heterogeneous catalysts with quite different layer‐specific electronic structure and intrinsic periodicities. eQE features very favorable strongmore »
- Authors:
-
- Department of Chemistry Rutgers University Newark New Jersey 07102
- Department of Chemistry Rutgers University Newark New Jersey 07102, Istituto di Scienze e Tecnologie Molecolari CNR c/o Dipartimento di Chimica, Università degli studi di Milano, via Golgi 19, 20133 Milano Italy
- Theory and Simulations of Materials (THEOS) and National Centre for Computational Design and Discovery of Novel Materials (MARVEL) Institute of Computational Studies, École Polytechnique Fédérale de Lausanne Station 12 Lausanne CH‐1015 Switzerland
- Department of Chemistry and Chemical Biology Cornell University Ithaca New York 14853
- Publication Date:
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1401323
- Resource Type:
- Publisher's Accepted Manuscript
- Journal Name:
- International Journal of Quantum Chemistry
- Additional Journal Information:
- Journal Name: International Journal of Quantum Chemistry Journal Volume: 117 Journal Issue: 16; Journal ID: ISSN 0020-7608
- Publisher:
- Wiley Blackwell (John Wiley & Sons)
- Country of Publication:
- United States
- Language:
- English
Citation Formats
Genova, Alessandro, Ceresoli, Davide, Krishtal, Alisa, Andreussi, Oliviero, DiStasio, Jr, Robert A., and Pavanello, Michele. eQE: An open‐source density functional embedding theory code for the condensed phase. United States: N. p., 2017.
Web. doi:10.1002/qua.25401.
Genova, Alessandro, Ceresoli, Davide, Krishtal, Alisa, Andreussi, Oliviero, DiStasio, Jr, Robert A., & Pavanello, Michele. eQE: An open‐source density functional embedding theory code for the condensed phase. United States. https://doi.org/10.1002/qua.25401
Genova, Alessandro, Ceresoli, Davide, Krishtal, Alisa, Andreussi, Oliviero, DiStasio, Jr, Robert A., and Pavanello, Michele. Fri .
"eQE: An open‐source density functional embedding theory code for the condensed phase". United States. https://doi.org/10.1002/qua.25401.
@article{osti_1401323,
title = {eQE: An open‐source density functional embedding theory code for the condensed phase},
author = {Genova, Alessandro and Ceresoli, Davide and Krishtal, Alisa and Andreussi, Oliviero and DiStasio, Jr, Robert A. and Pavanello, Michele},
abstractNote = {Abstract In this work, we present the main features and algorithmic details of a novel implementation of the frozen density embedding (FDE) formulation of subsystem density functional theory (DFT) that is specifically designed to enable ab initio molecular dynamics (AIMD) simulations of large‐scale condensed‐phase systems containing 1000s of atoms. This code (available at http://eqe.rutgers.edu ) has been given the moniker of embedded Quantum ESPRESSO (eQE) as it is a generalization of the open‐source Quantum ESPRESSO (QE) suite of programs. The strengths of eQE reside in a hierarchical parallelization scheme that allows for an efficient and fully self‐consistent treatment of the electronic structure (via the addition of an additional DIIS extrapolation layer) while simultaneously exploiting the inherent symmetries and periodicities in the system (via sampling of subsystem‐specific first Brillouin zones and utilization of subsystem‐specific basis sets). While bulk liquids and molecular crystals are two classes of systems that exemplify the utility of the FDE approach (as these systems can be partitioned into weakly interacting subunits), we show that eQE has significantly extended this regime of applicability by outperforming standard semilocal Kohn–Sham DFT (KS‐DFT) for large‐scale heterogeneous catalysts with quite different layer‐specific electronic structure and intrinsic periodicities. eQE features very favorable strong parallel scaling for a model system of bulk liquid water composed of 256 water molecules, which allows for a significant decrease in the overall time to solution when compared to KS‐DFT. We show that eQE achieves speedups greater than one order of magnitude ( ) when performing AIMD simulations of such large‐scale condensed‐phase systems as: (1) molecular liquids via bulk liquid water represented by 1024 independent water molecules (3072 atoms with a 25.3× speedup over KS‐DFT), (2) polypeptide/biomolecule solvation via ( gly ) 6 solvated in (H 2 O) 395 (1230 atoms with a 38.6× speedup over KS‐DFT), and (3) molecular crystals via a 3 × 3 × 3 periodic supercell of pentacene (1940 atoms with a 12.0× speedup over KS‐DFT). These results represent a significant improvement over the current state‐of‐the‐art and now enable subsystem DFT‐based AIMD simulations of realistically sized condensed‐phase systems of interest throughout chemistry, physics, and materials science.},
doi = {10.1002/qua.25401},
journal = {International Journal of Quantum Chemistry},
number = 16,
volume = 117,
place = {United States},
year = {Fri May 26 00:00:00 EDT 2017},
month = {Fri May 26 00:00:00 EDT 2017}
}
https://doi.org/10.1002/qua.25401
Web of Science
Works referenced in this record:
Orbital-free density functional theory: Kinetic potentials and ab initio local pseudopotentials
journal, May 2007
- Chai, Jeng-Da; Weeks, John D.
- Physical Review B, Vol. 75, Issue 20
An atomic orbital-based formulation of the complete active space self-consistent field method on graphical processing units
journal, June 2015
- Hohenstein, Edward G.; Luehr, Nathan; Ufimtsev, Ivan S.
- The Journal of Chemical Physics, Vol. 142, Issue 22
Bond energy decomposition analysis for subsystem density functional theory
journal, March 2013
- Beyhan, S. Maya; Götz, Andreas W.; Visscher, Lucas
- The Journal of Chemical Physics, Vol. 138, Issue 9
Obtaining a gradient-corrected kinetic-energy functional from the Perdew-Wang exchange functional
journal, December 1994
- Lembarki, A.; Chermette, H.
- Physical Review A, Vol. 50, Issue 6
Comparison of frozen-density embedding and discrete reaction field solvent models for molecular properties
journal, January 2006
- Jacob, Christoph R.; Neugebauer, Johannes; Jensen, Lasse
- Physical Chemistry Chemical Physics, Vol. 8, Issue 20
Self-consistent embedding theory for locally correlated configuration interaction wave functions in condensed matter
journal, August 2006
- Huang, Patrick; Carter, Emily A.
- The Journal of Chemical Physics, Vol. 125, Issue 8
Density functional theory embedding for correlated wavefunctions: Improved methods for open-shell systems and transition metal complexes
journal, December 2012
- Goodpaster, Jason D.; Barnes, Taylor A.; Manby, Frederick R.
- The Journal of Chemical Physics, Vol. 137, Issue 22
QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials
journal, September 2009
- Giannozzi, Paolo; Baroni, Stefano; Bonini, Nicola
- Journal of Physics: Condensed Matter, Vol. 21, Issue 39, Article No. 395502
Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs
journal, January 2006
- Jurečka, Petr; Šponer, Jiří; Černý, Jiří
- Physical Chemistry Chemical Physics, Vol. 8, Issue 17, p. 1985-1993
Periodic subsystem density-functional theory
journal, November 2014
- Genova, Alessandro; Ceresoli, Davide; Pavanello, Michele
- The Journal of Chemical Physics, Vol. 141, Issue 17
Design of a Next Generation Force Field: The X-POL Potential
journal, August 2007
- Xie, Wangshen; Gao, Jiali
- Journal of Chemical Theory and Computation, Vol. 3, Issue 6
Linear Scaling Constrained Density Functional Theory in CONQUEST
journal, March 2011
- Sena, Alex M. P.; Miyazaki, Tsuyoshi; Bowler, David R.
- Journal of Chemical Theory and Computation, Vol. 7, Issue 4
Chemistry with ADF
journal, January 2001
- te Velde, G.; Bickelhaupt, F. M.; Baerends, E. J.
- Journal of Computational Chemistry, Vol. 22, Issue 9, p. 931-967
Generalized Gradient Approximations of the Noninteracting Kinetic Energy from the Semiclassical Atom Theory: Rationalization of the Accuracy of the Frozen Density Embedding Theory for Nonbonded Interactions
journal, July 2011
- Laricchia, S.; Fabiano, E.; Constantin, L. A.
- Journal of Chemical Theory and Computation, Vol. 7, Issue 8
The Dalton quantum chemistry program system: The Dalton program
journal, September 2013
- Aidas, Kestutis; Angeli, Celestino; Bak, Keld L.
- Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 4, Issue 3
Electronic structure calculations on workstation computers: The program system turbomole
journal, October 1989
- Ahlrichs, Reinhart; Bär, Michael; Häser, Marco
- Chemical Physics Letters, Vol. 162, Issue 3
\mathcal{O}(N) methods in electronic structure calculations
journal, February 2012
- Bowler, D. R.; Miyazaki, T.
- Reports on Progress in Physics, Vol. 75, Issue 3
Subsystem real-time time dependent density functional theory
journal, April 2015
- Krishtal, Alisa; Ceresoli, Davide; Pavanello, Michele
- The Journal of Chemical Physics, Vol. 142, Issue 15
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
An accurate and linear-scaling method for calculating charge-transfer excitation energies and diabatic couplings
journal, February 2013
- Pavanello, Michele; Van Voorhis, Troy; Visscher, Lucas
- The Journal of Chemical Physics, Vol. 138, Issue 5
Laplacian-Level Kinetic Energy Approximations Based on the Fourth-Order Gradient Expansion: Global Assessment and Application to the Subsystem Formulation of Density Functional Theory
journal, November 2013
- Laricchia, Savio; Constantin, Lucian A.; Fabiano, Eduardo
- Journal of Chemical Theory and Computation, Vol. 10, Issue 1
Calculation of nuclear magnetic resonance shieldings using frozen-density embedding
journal, November 2006
- Jacob, Christoph R.; Visscher, Lucas
- The Journal of Chemical Physics, Vol. 125, Issue 19
Periodic density functional embedding theory for complete active space self-consistent field and configuration interaction calculations: Ground and excited states
journal, January 2002
- Klüner, Thorsten; Govind, Niranjan; Wang, Yan Alexander
- The Journal of Chemical Physics, Vol. 116, Issue 1
On the accuracy of frozen density embedding calculations with hybrid and orbital-dependent functionals for non-bonded interaction energies
journal, July 2012
- Laricchia, S.; Fabiano, E.; Sala, F. Della
- The Journal of Chemical Physics, Vol. 137, Issue 1
Subsystem density-functional theory as an effective tool for modeling ground and excited states, their dynamics and many-body interactions
journal, April 2015
- Krishtal, Alisa; Sinha, Debalina; Genova, Alessandro
- Journal of Physics: Condensed Matter, Vol. 27, Issue 18
Introducing ONETEP : Linear-scaling density functional simulations on parallel computers
journal, February 2005
- Skylaris, Chris-Kriton; Haynes, Peter D.; Mostofi, Arash A.
- The Journal of Chemical Physics, Vol. 122, Issue 8
Prediction of Electronic Excited States of Adsorbates on Metal Surfaces from First Principles
journal, June 2001
- Klüner, Thorsten; Govind, Niranjan; Wang, Yan
- Physical Review Letters, Vol. 86, Issue 26
Avoiding fractional electrons in subsystem DFT based ab-initio molecular dynamics yields accurate models for liquid water and solvated OH radical
journal, June 2016
- Genova, Alessandro; Ceresoli, Davide; Pavanello, Michele
- The Journal of Chemical Physics, Vol. 144, Issue 23
Kinetic-energy density functional: Atoms and shell structure
journal, September 1996
- García-González, P.; Alvarellos, J. E.; Chacón, E.
- Physical Review A, Vol. 54, Issue 3
Frozen density embedding with non-integer subsystems’ particle numbers
journal, March 2014
- Fabiano, Eduardo; Laricchia, Savio; Sala, Fabio Della
- The Journal of Chemical Physics, Vol. 140, Issue 11
Frozen density embedding with hybrid functionals
journal, October 2010
- Laricchia, S.; Fabiano, E.; Della Sala, F.
- The Journal of Chemical Physics, Vol. 133, Issue 16
Self-Consistent Equations Including Exchange and Correlation Effects
journal, November 1965
- Kohn, W.; Sham, L. J.
- Physical Review, Vol. 140, Issue 4A, p. A1133-A1138
On the calculation of general response properties in subsystem density functional theory
journal, August 2009
- Neugebauer, Johannes
- The Journal of Chemical Physics, Vol. 131, Issue 8
Convergence acceleration of iterative sequences. the case of scf iteration
journal, July 1980
- Pulay, Péter
- Chemical Physics Letters, Vol. 73, Issue 2
Accurate and efficient linear scaling DFT calculations with universal applicability
journal, January 2015
- Mohr, Stephan; Ratcliff, Laura E.; Genovese, Luigi
- Physical Chemistry Chemical Physics, Vol. 17, Issue 47
Linear scaling density functional calculations via the continuous fast multipole method
journal, May 1996
- White, Christopher A.; Johnson, Benny G.; Gill, Peter M. W.
- Chemical Physics Letters, Vol. 253, Issue 3-4
The individual and collective effects of exact exchange and dispersion interactions on the ab initio structure of liquid water
journal, August 2014
- DiStasio, Robert A.; Santra, Biswajit; Li, Zhaofeng
- The Journal of Chemical Physics, Vol. 141, Issue 8
Frozen Density Embedding with External Orthogonality in Delocalized Covalent Systems
journal, June 2015
- Chulhai, Dhabih V.; Jensen, Lasse
- Journal of Chemical Theory and Computation, Vol. 11, Issue 7
Local electric dipole moments for periodic systems via density functional theory embedding
journal, December 2014
- Luber, Sandra
- The Journal of Chemical Physics, Vol. 141, Issue 23
A flexible implementation of frozen-density embedding for use in multilevel simulations
journal, January 2008
- Jacob, Christoph R.; Neugebauer, Johannes; Visscher, Lucas
- Journal of Computational Chemistry, Vol. 29, Issue 6
Exploiting the locality of periodic subsystem density-functional theory: efficient sampling of the Brillouin zone
journal, November 2015
- Genova, Alessandro; Pavanello, Michele
- Journal of Physics: Condensed Matter, Vol. 27, Issue 49
A class of methods for solving nonlinear simultaneous equations
journal, January 1965
- Broyden, C. G.
- Mathematics of Computation, Vol. 19, Issue 92
Exact kinetic energy enables accurate evaluation of weak interactions by the FDE-vdW method
journal, August 2015
- Sinha, Debalina; Pavanello, Michele
- The Journal of Chemical Physics, Vol. 143, Issue 8
Comparative Study of Selected Wave Function and Density Functional Methods for Noncovalent Interaction Energy Calculations Using the Extended S22 Data Set
journal, July 2010
- Gráfová, Lucie; Pitoňák, Michal; Řezáč, Jan
- Journal of Chemical Theory and Computation, Vol. 6, Issue 8
First-principles simulation: ideas, illustrations and the CASTEP code
journal, March 2002
- Segall, M. D.; Lindan, Philip J. D.; Probert, M. J.
- Journal of Physics: Condensed Matter, Vol. 14, Issue 11
Revealing electronic open quantum systems with subsystem TDDFT
journal, March 2016
- Krishtal, Alisa; Pavanello, Michele
- The Journal of Chemical Physics, Vol. 144, Issue 12
Accurate basis set truncation for wavefunction embedding
journal, July 2013
- Barnes, Taylor A.; Goodpaster, Jason D.; Manby, Frederick R.
- The Journal of Chemical Physics, Vol. 139, Issue 2
Exact nonadditive kinetic potentials for embedded density functional theory
journal, August 2010
- Goodpaster, Jason D.; Ananth, Nandini; Manby, Frederick R.
- The Journal of Chemical Physics, Vol. 133, Issue 8
A Simple, Exact Density-Functional-Theory Embedding Scheme
journal, July 2012
- Manby, Frederick R.; Stella, Martina; Goodpaster, Jason D.
- Journal of Chemical Theory and Computation, Vol. 8, Issue 8
Density-decomposed orbital-free density functional theory for covalently bonded molecules and materials
journal, December 2012
- Xia, Junchao; Carter, Emily A.
- Physical Review B, Vol. 86, Issue 23
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
Frozen density functional approach for ab initio calculations of solvated molecules
journal, July 1993
- Wesolowski, Tomasz Adam; Warshel, Arieh
- The Journal of Physical Chemistry, Vol. 97, Issue 30
Molecular binding energies from partition density functional theory
journal, December 2011
- Nafziger, Jonathan; Wu, Qin; Wasserman, Adam
- The Journal of Chemical Physics, Vol. 135, Issue 23
Density functional embedding for molecular systems
journal, April 2006
- Iannuzzi, Marcella; Kirchner, Barbara; Hutter, Jürg
- Chemical Physics Letters, Vol. 421, Issue 1-3
Embedded density functional theory for covalently bonded and strongly interacting subsystems
journal, April 2011
- Goodpaster, Jason D.; Barnes, Taylor A.; Miller, Thomas F.
- The Journal of Chemical Physics, Vol. 134, Issue 16
Linear Scaling Self-Consistent Field Calculations with Millions of Atoms in the Condensed Phase
journal, March 2012
- VandeVondele, Joost; Borštnik, Urban; Hutter, Jürg
- Journal of Chemical Theory and Computation, Vol. 8, Issue 10
Advances in electronic structure theory
book, January 2005
- Gordon, Mark S.; Schmidt, Michael W.
- Theory and Applications of Computational Chemistry
Optimization algorithm for the generation of ONCV pseudopotentials
journal, November 2015
- Schlipf, Martin; Gygi, François
- Computer Physics Communications, Vol. 196
Combining Linear-Scaling DFT with Subsystem DFT in Born–Oppenheimer and Ehrenfest Molecular Dynamics Simulations: From Molecules to a Virus in Solution
journal, June 2016
- Andermatt, Samuel; Cha, Jinwoong; Schiffmann, Florian
- Journal of Chemical Theory and Computation, Vol. 12, Issue 7
An efficient, fragment-based electronic structure method for molecular systems: Self-consistent polarization with perturbative two-body exchange and dispersion
journal, March 2011
- Jacobson, Leif D.; Herbert, John M.
- The Journal of Chemical Physics, Vol. 134, Issue 9
Electronic-structure calculations by first-principles density-based embedding of explicitly correlated systems
journal, April 1999
- Govind, Niranjan; Wang, Yan Alexander; Carter, Emily A.
- The Journal of Chemical Physics, Vol. 110, Issue 16
FDE-vdW: A van der Waals inclusive subsystem density-functional theory
journal, July 2014
- Kevorkyants, Ruslan; Eshuis, Henk; Pavanello, Michele
- The Journal of Chemical Physics, Vol. 141, Issue 4
Perspective on density functional theory
journal, April 2012
- Burke, Kieron
- The Journal of Chemical Physics, Vol. 136, Issue 15
Frozen-Density Embedding Strategy for Multilevel Simulations of Electronic Structure
journal, April 2015
- Wesolowski, Tomasz A.; Shedge, Sapana; Zhou, Xiuwen
- Chemical Reviews, Vol. 115, Issue 12
Couplings between electronic transitions in a subsystem formulation of time-dependent density functional theory
journal, April 2007
- Neugebauer, Johannes
- The Journal of Chemical Physics, Vol. 126, Issue 13