1
|
Liu J, Lan J, He X. Toward High-level Machine Learning Potential for Water Based on Quantum Fragmentation and Neural Networks. J Phys Chem A 2022; 126:3926-3936. [PMID: 35679610 DOI: 10.1021/acs.jpca.2c00601] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Accurate and efficient simulation of liquids, such as water and salt solutions, using high-level wave function theories is still a formidable task for computational chemists owing to the high computational costs. In this study, we develop a deep machine learning potential based on fragment-based second-order Møller-Plesset perturbation theory (DP-MP2) for water through neural networks. We show that the DP-MP2 potential predicts the structural, dynamical, and thermodynamic properties of liquid water in better agreement with the experimental data than previous studies based on density functional theory (DFT). The nuclear quantum effects (NQEs) on the properties of liquid water are also examined, which are noticeable in affecting the structural and dynamical properties of liquid water under ambient conditions. This work provides a general framework for quantitative predictions of the properties of condensed-phase systems with the accuracy of high-level wave function theory while achieving significant computational savings compared to ab initio simulations.
Collapse
Affiliation(s)
- Jinfeng Liu
- Department of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China.,Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Jinggang Lan
- Chaire de Simulation à l'Echelle Atomique (CSEA), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.,New York University-East China Normal University Center for Computational Chemistry, NYU Shanghai, Shanghai 200062, China
| |
Collapse
|
2
|
Christlmaier EM, Kats D, Alavi A, Usvyat D. Full Configuration Interaction Quantum Monte Carlo treatment of fragments embedded in a periodic mean field. J Chem Phys 2022; 156:154107. [DOI: 10.1063/5.0084040] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present an embedded fragment approach for high-level quantum chemical calculations on local features in periodic systems. The fragment is defined as a set of localized orbitals (occupied and virtual) corresponding to a converged periodic Hartree-Fock solution. These orbitals serve as the basis for the in-fragment post-Hartree Fock treatment. The embedding field for the fragment, consisting of the Coulomb and exchange potential from the rest of the crystal, is included in the fragment's one-electron Hamiltonian. As an application of the embedded fragment approach we investigate the performanceof full configuration interaction quantum Monte Carlo (FCIQMC) with the adaptive shift. As the orbital choice we use the natural orbitals from the distinguishable cluster method with singles and doubles. FCIQMC is a stochastic approximation to the full CI method and can be routinely applied to much larger active spaces than the latter. This makes this method especially attractive in the context of open shell defects in crystals, where fragments of adequate size can be ratherlarge. As a test case we consider dissociation of a fluorine atom from a fluorographane surface. This process poses a challenge for high-level electronic structure models as both the static and dynamic correlations are essential here. Furthermore the active space for an adequate fragment (32 electrons in 173 orbitals) is already quite large even for FCIQMC. Despite this, FCIQMC delivers accurate dissociation and total energies.
Collapse
Affiliation(s)
| | - Daniel Kats
- Max-Planck-Institute for Solid State Research, Germany
| | - Ali Alavi
- Max-Planck-Institute for Solid State Research, Germany
| | - Denis Usvyat
- Institute of Chemistry, Humboldt University of Berlin, Germany
| |
Collapse
|
3
|
Stein F, Hutter J. Double-hybrid density functionals for the condensed phase: Gradients, stress tensor, and auxiliary-density matrix method acceleration. J Chem Phys 2022; 156:074107. [DOI: 10.1063/5.0082327] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Frederick Stein
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Jürg Hutter
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| |
Collapse
|
4
|
Lan J, Yamamoto YI, Suzuki T, Rybkin VV. Shallow and deep trap states of solvated electrons in methanol and their formation, electronic excitation, and relaxation dynamics. Chem Sci 2022; 13:3837-3844. [PMID: 35432888 PMCID: PMC8966712 DOI: 10.1039/d1sc06666h] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 02/24/2022] [Indexed: 11/30/2022] Open
Abstract
We present condensed-phase first-principles molecular dynamics simulations to elucidate the presence of different electron trapping sites in liquid methanol and their roles in the formation, electronic transitions, and relaxation of solvated electrons (emet−) in methanol. Excess electrons injected into liquid methanol are most likely trapped by methyl groups, but rapidly diffuse to more stable trapping sites with dangling OH bonds. After localization at the sites with one free OH bond (1OH trapping sites), reorientation of other methanol molecules increases the OH coordination number and the trap depth, and ultimately four OH bonds become coordinated with the excess electrons under thermal conditions. The simulation identified four distinct trapping states with different OH coordination numbers. The simulation results also revealed that electronic transitions of emet− are primarily due to charge transfer between electron trapping sites (cavities) formed by OH and methyl groups, and that these transitions differ from hydrogenic electronic transitions involving aqueous solvated electrons (eaq−). Such charge transfer also explains the alkyl-chain-length dependence of the photoabsorption peak wavelength and the excited-state lifetime of solvated electrons in primary alcohols. Condensed-phase first-principles molecular dynamics simulations elucidate the presence of different electron trapping sites in liquid methanol and their roles in the formation, electronic transitions, and relaxation of solvated electrons.![]()
Collapse
Affiliation(s)
- Jinggang Lan
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Yo-ichi Yamamoto
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Toshinori Suzuki
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Vladimir V. Rybkin
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| |
Collapse
|
5
|
Kathmann SM. Electric fields and potentials in condensed phases. Phys Chem Chem Phys 2021; 23:23836-23849. [PMID: 34647950 DOI: 10.1039/d1cp03571a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The electric fields and potentials inside and at the interface of matter are relevant to many branches of physics, chemistry, and biology. Accurate quantification of these fields and/or potentials is essential to control and exploit chemical and physical transformations. Before we understand the response of matter to external fields, it is first important to understand the intrinsic interior and interfacial fields and potentials, both classically and quantum mechanically, as well as how they are probed experimentally. Here we compare and contrast, beginning with the hydrogen atom in vacuum and ending with concentrated aqueous NaCl electrolyte, both classical and quantum mechanical electric potentials and fields. We make contact with experimental vibrational Stark, electrochemical, X-ray, and electron spectroscopic probes of these potentials and fields, outline relevant conceptual difficulties, and underscore the advantage of electron holography as a basis to better understand electrostatics in matter.
Collapse
Affiliation(s)
- Shawn M Kathmann
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA.
| |
Collapse
|
6
|
Rybkin VV. Formulation and Implementation of Density Functional Embedding Theory Using Products of Basis Functions. J Chem Theory Comput 2021; 17:3995-4005. [PMID: 34048247 DOI: 10.1021/acs.jctc.1c00175] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The representation of embedding potential using products of atomic orbital basis functions has been developed in the context of density functional embedding theory. The formalism allows to treat pseudopotential and all-electron calculations on the same footing and enables simple transfer of the embedding potential in a compact matrix form. In addition, a cost-reduction procedure for the basis set and potential reduction based on population analysis has been proposed. Implemented for the condensed-phase and molecular systems within Gaussian and plane-waves and Gaussian and augmented plane-waves formalisms, the scheme has been tested for proton-transfer reactions in the cluster and the condensed phase and projected density of states of carbon monoxide adsorbed on platinum surface. With the computational scaling of the embedding potential optimization similar to that of hybrid density functional theory with a significantly reduced prefactor, the method allows for large-scale applications to extended systems.
Collapse
Affiliation(s)
- Vladimir V Rybkin
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, Zürich 8057, Switzerland
| |
Collapse
|
7
|
Piras A, Ehlert C, Gryn'ova G. Sensing and sensitivity: Computational chemistry of
graphene‐based
sensors. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1526] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Anna Piras
- Heidelberg Institute for Theoretical Studies (HITS gGmbH) and Interdisciplinary Center for Scientific Computing (IWR) Heidelberg University Heidelberg Germany
| | - Christopher Ehlert
- Heidelberg Institute for Theoretical Studies (HITS gGmbH) and Interdisciplinary Center for Scientific Computing (IWR) Heidelberg University Heidelberg Germany
| | - Ganna Gryn'ova
- Heidelberg Institute for Theoretical Studies (HITS gGmbH) and Interdisciplinary Center for Scientific Computing (IWR) Heidelberg University Heidelberg Germany
| |
Collapse
|
8
|
Wilhelm J, Seewald P, Golze D. Low-Scaling GW with Benchmark Accuracy and Application to Phosphorene Nanosheets. J Chem Theory Comput 2021; 17:1662-1677. [DOI: 10.1021/acs.jctc.0c01282] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Jan Wilhelm
- Institute of Theoretical Physics, University of Regensburg, D-93053 Regensburg, Germany
| | - Patrick Seewald
- Department of Chemistry, University of Zurich, CH-8057 Zurich, Switzerland
| | - Dorothea Golze
- Department of Applied Physics, Aalto University, FI-00076 Aalto, Finland
| |
Collapse
|
9
|
Lan J, Kapil V, Gasparotto P, Ceriotti M, Iannuzzi M, Rybkin VV. Simulating the ghost: quantum dynamics of the solvated electron. Nat Commun 2021; 12:766. [PMID: 33536410 PMCID: PMC7859219 DOI: 10.1038/s41467-021-20914-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 01/04/2021] [Indexed: 01/13/2023] Open
Abstract
The nature of the bulk hydrated electron has been a challenge for both experiment and theory due to its short lifetime and high reactivity, and the need for a high-level of electronic structure theory to achieve predictive accuracy. The lack of a classical atomistic structural formula makes it exceedingly difficult to model the solvated electron using conventional empirical force fields, which describe the system in terms of interactions between point particles associated with atomic nuclei. Here we overcome this problem using a machine-learning model, that is sufficiently flexible to describe the effect of the excess electron on the structure of the surrounding water, without including the electron in the model explicitly. The resulting potential is not only able to reproduce the stable cavity structure but also recovers the correct localization dynamics that follow the injection of an electron in neat water. The machine learning model achieves the accuracy of the state-of-the-art correlated wave function method it is trained on. It is sufficiently inexpensive to afford a full quantum statistical and dynamical description and allows us to achieve accurate determination of the structure, diffusion mechanisms, and vibrational spectroscopy of the solvated electron.
Collapse
Affiliation(s)
- Jinggang Lan
- Department of Chemistry, University of Zurich, Zürich, Switzerland.
| | - Venkat Kapil
- Laboratory of Computational Science and Modelling, Institute of Materials, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Piero Gasparotto
- Empa, Swiss Federal Laboratories for Materials Science and Technology, Dübendorf, Switzerland
| | - Michele Ceriotti
- Laboratory of Computational Science and Modelling, Institute of Materials, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | | | | |
Collapse
|
10
|
Rybkin VV. Mechanism of Aqueous Carbon Dioxide Reduction by the Solvated Electron. J Phys Chem B 2020; 124:10435-10441. [PMID: 33170009 DOI: 10.1021/acs.jpcb.0c07859] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aqueous solvated electron (eaq-), a key species in radiation and plasma chemistry, can efficiently reduce CO2 in a potential green chemistry application. Here, the mechanism of this reaction is unravelled by condensed-phase molecular dynamics based on the correlated wave function and an accurate density functional theory (DFT) approximation. Here, we design and apply the holistic protocol for solvated electron's reactions encompassing all relevant reaction stages starting from diffusion. The carbon dioxide reduction proceeds via a cavity intermediate, which is separated from the product (CO2-) by an energy barrier due to the bending of CO2 and the corresponding solvent reorganization energy. The formation of the intermediate is caused by solvated electron's diffusion, whereas the intermediate transformation to CO2- is triggered by hydrogen bond breaking in the second solvation shell of the solvated electron. This picture of an activation-controlled eaq- reaction is very different from both rapid barrierless electron transfer and proton-coupled electron transfer, where key transformations are caused by proton migration.
Collapse
Affiliation(s)
- Vladimir V Rybkin
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| |
Collapse
|
11
|
Kühne TD, Iannuzzi M, Del Ben M, Rybkin VV, Seewald P, Stein F, Laino T, Khaliullin RZ, Schütt O, Schiffmann F, Golze D, Wilhelm J, Chulkov S, Bani-Hashemian MH, Weber V, Borštnik U, Taillefumier M, Jakobovits AS, Lazzaro A, Pabst H, Müller T, Schade R, Guidon M, Andermatt S, Holmberg N, Schenter GK, Hehn A, Bussy A, Belleflamme F, Tabacchi G, Glöß A, Lass M, Bethune I, Mundy CJ, Plessl C, Watkins M, VandeVondele J, Krack M, Hutter J. CP2K: An electronic structure and molecular dynamics software package - Quickstep: Efficient and accurate electronic structure calculations. J Chem Phys 2020; 152:194103. [PMID: 33687235 DOI: 10.1063/5.0007045] [Citation(s) in RCA: 924] [Impact Index Per Article: 231.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
CP2K is an open source electronic structure and molecular dynamics software package to perform atomistic simulations of solid-state, liquid, molecular, and biological systems. It is especially aimed at massively parallel and linear-scaling electronic structure methods and state-of-the-art ab initio molecular dynamics simulations. Excellent performance for electronic structure calculations is achieved using novel algorithms implemented for modern high-performance computing systems. This review revisits the main capabilities of CP2K to perform efficient and accurate electronic structure simulations. The emphasis is put on density functional theory and multiple post-Hartree-Fock methods using the Gaussian and plane wave approach and its augmented all-electron extension.
Collapse
Affiliation(s)
- Thomas D Kühne
- Dynamics of Condensed Matter and Center for Sustainable Systems Design, Chair of Theoretical Chemistry, Paderborn University, Warburger Str. 100, D-33098 Paderborn, Germany
| | - Marcella Iannuzzi
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Mauro Del Ben
- Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Vladimir V Rybkin
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Patrick Seewald
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Frederick Stein
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Teodoro Laino
- IBM Research Europe, CH-8803 Rüschlikon, Switzerland
| | - Rustam Z Khaliullin
- Department of Chemistry, McGill University, CH-801 Sherbrooke St. West, Montreal, Quebec H3A 0B8, Canada
| | - Ole Schütt
- Department of Materials, ETH Zürich, CH-8092 Zürich, Switzerland
| | | | - Dorothea Golze
- Department of Applied Physics, Aalto University, Otakaari 1, FI-02150 Espoo, Finland
| | - Jan Wilhelm
- Institute of Theoretical Physics, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Sergey Chulkov
- School of Mathematics and Physics, University of Lincoln, Brayford Pool, Lincoln, United Kingdom
| | | | - Valéry Weber
- IBM Research Europe, CH-8803 Rüschlikon, Switzerland
| | | | | | | | | | - Hans Pabst
- Intel Extreme Computing, Software and Systems, Zürich, Switzerland
| | - Tiziano Müller
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Robert Schade
- Department of Computer Science and Paderborn Center for Parallel Computing, Paderborn University, Warburger Str. 100, D-33098 Paderborn, Germany
| | - Manuel Guidon
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Samuel Andermatt
- Integrated Systems Laboratory, ETH Zürich, CH-8092 Zürich, Switzerland
| | - Nico Holmberg
- Department of Chemistry and Materials Science, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
| | - Gregory K Schenter
- Physical Science Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, USA
| | - Anna Hehn
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Augustin Bussy
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Fabian Belleflamme
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Gloria Tabacchi
- Department of Science and High Technology, University of Insubria and INSTM, via Valleggio 9, I-22100 Como, Italy
| | - Andreas Glöß
- BASF SE, Carl-Bosch-Straße 38, D-67056 Ludwigshafen am Rhein, Germany
| | - Michael Lass
- Department of Computer Science and Paderborn Center for Parallel Computing, Paderborn University, Warburger Str. 100, D-33098 Paderborn, Germany
| | - Iain Bethune
- Hartree Centre, Science and Technology Facilities Council, Sci-Tech Daresbury, Warrington WA4 4AD, United Kingdom
| | - Christopher J Mundy
- Physical Science Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, USA
| | - Christian Plessl
- Department of Computer Science and Paderborn Center for Parallel Computing, Paderborn University, Warburger Str. 100, D-33098 Paderborn, Germany
| | - Matt Watkins
- School of Mathematics and Physics, University of Lincoln, Brayford Pool, Lincoln, United Kingdom
| | - Joost VandeVondele
- Swiss National Supercomputing Centre (CSCS), ETH Zürich, Zürich, Switzerland
| | - Matthias Krack
- Laboratory for Scientific Computing and Modelling, Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland
| | - Jürg Hutter
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| |
Collapse
|
12
|
Rybkin VV. Sampling Potential Energy Surfaces in the Condensed Phase with Many‐Body Electronic Structure Methods. Chemistry 2019; 26:362-368. [DOI: 10.1002/chem.201904012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Indexed: 11/10/2022]
Affiliation(s)
- Vladimir V. Rybkin
- Department of ChemistryUniversity of Zurich Winterthurerstrasse 190 CH-8057 Zurich Switzerland
| |
Collapse
|
13
|
Bruneval F. Assessment of the Linearized GW Density Matrix for Molecules. J Chem Theory Comput 2019; 15:4069-4078. [DOI: 10.1021/acs.jctc.9b00333] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Fabien Bruneval
- DEN, Service de Recherches de Métallurgie Physique, CEA, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
| |
Collapse
|
14
|
Wilhelm J, VandeVondele J, Rybkin VV. Dynamics of the Bulk Hydrated Electron from Many-Body Wave-Function Theory. Angew Chem Int Ed Engl 2019; 58:3890-3893. [PMID: 30776181 PMCID: PMC6594240 DOI: 10.1002/anie.201814053] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Indexed: 11/10/2022]
Abstract
The structure of the hydrated electron is a matter of debate as it evades direct experimental observation owing to the short life time and low concentrations of the species. Herein, the first molecular dynamics simulation of the bulk hydrated electron based on correlated wave‐function theory provides conclusive evidence in favor of a persistent tetrahedral cavity made up by four water molecules, and against the existence of stable non‐cavity structures. Such a cavity is formed within less than a picosecond after the addition of an excess electron to neat liquid water, with less regular cavities appearing as intermediates. The cavities are bound together by weak H−H bonds, the number of which correlates well with the number of coordinated water molecules, each type of cavity leaving a distinct spectroscopic signature. Simulations predict regions of negative spin density and a gyration radius that are both in agreement with experimental data.
Collapse
Affiliation(s)
- Jan Wilhelm
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland.,Current address: BASF SE, Ludwigshafen, Germany
| | - Joost VandeVondele
- Scientific Software & Libraries unit, CSCS, ETH Zurich, Wolfgang-Pauli-Strasse 27, CH-8093, Zurich, Switzerland
| | - Vladimir V Rybkin
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| |
Collapse
|
15
|
Wilhelm J, VandeVondele J, Rybkin VV. Dynamics of the Bulk Hydrated Electron from Many‐Body Wave‐Function Theory. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201814053] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Jan Wilhelm
- Department of ChemistryUniversity of Zurich Winterthurerstrasse 190 CH-8057 Zurich Switzerland
- Current address: BASF SE Ludwigshafen Germany
| | - Joost VandeVondele
- Scientific Software & Libraries unit, CSCSETH Zurich Wolfgang-Pauli-Strasse 27 CH-8093 Zurich Switzerland
| | - Vladimir V. Rybkin
- Department of ChemistryUniversity of Zurich Winterthurerstrasse 190 CH-8057 Zurich Switzerland
| |
Collapse
|
16
|
Hofer TS, Hünenberger PH. Absolute proton hydration free energy, surface potential of water, and redox potential of the hydrogen electrode from first principles: QM/MM MD free-energy simulations of sodium and potassium hydration. J Chem Phys 2018; 148:222814. [DOI: 10.1063/1.5000799] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Thomas S. Hofer
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, Centre for Chemistry and Biomedicine, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
| | | |
Collapse
|
17
|
Wilhelm J, Golze D, Talirz L, Hutter J, Pignedoli CA. Toward GW Calculations on Thousands of Atoms. J Phys Chem Lett 2018; 9:306-312. [PMID: 29280376 DOI: 10.1021/acs.jpclett.7b02740] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The GW approximation of many-body perturbation theory is an accurate method for computing electron addition and removal energies of molecules and solids. In a canonical implementation, however, its computational cost is [Formula: see text] in the system size N, which prohibits its application to many systems of interest. We present a full-frequency GW algorithm in a Gaussian-type basis, whose computational cost scales with N2 to N3. The implementation is optimized for massively parallel execution on state-of-the-art supercomputers and is suitable for nanostructures and molecules in the gas, liquid or condensed phase, using either pseudopotentials or all electrons. We validate the accuracy of the algorithm on the GW100 molecular test set, finding mean absolute deviations of 35 meV for ionization potentials and 27 meV for electron affinities. Furthermore, we study the length-dependence of quasiparticle energies in armchair graphene nanoribbons of up to 1734 atoms in size, and compute the local density of states across a nanoscale heterojunction.
Collapse
Affiliation(s)
- Jan Wilhelm
- Department of Chemistry, University of Zurich , Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Dorothea Golze
- COMP/Department of Applied Physics, Aalto University , P.O. Box 11100, FI-00076 Aalto, Finland
| | - Leopold Talirz
- Laboratory of Molecular Simulation, École Polytechnique Fédérale de Lausanne , Rue de l'Industrie 17, CH-1951 Sion, Switzerland
- Theory and Simulation of Materials, École Polytechnique Fédérale de Lausanne , Station 9, CH-1015 Lausanne, Switzerland
| | - Jürg Hutter
- Department of Chemistry, University of Zurich , Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Carlo A Pignedoli
- Swiss Federal Laboratories for Materials Science and Technology (Empa) , Überlandstrasse 129, CH-8600 Dübendorf, Switzerland
| |
Collapse
|
18
|
Usvyat D, Maschio L, Schütz M. Periodic and fragment models based on the local correlation approach. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018. [DOI: 10.1002/wcms.1357] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Denis Usvyat
- Institut für ChemieHumboldt‐Universität zu BerlinBerlinGermany
| | - Lorenzo Maschio
- Dipartimento di Chimica and NIS (Nanostructured Interfaces and Surfaces) CentreUniversità di TorinoTorinoItaly
| | - Martin Schütz
- Institut für ChemieHumboldt‐Universität zu BerlinBerlinGermany
| |
Collapse
|
19
|
Katouda M, Nakajima T. MPI/OpenMP hybrid parallel algorithm for resolution of identity second-order Møller-Plesset perturbation calculation of analytical energy gradient for massively parallel multicore supercomputers. J Comput Chem 2017; 38:489-507. [PMID: 28133838 DOI: 10.1002/jcc.24701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 11/16/2016] [Accepted: 11/16/2016] [Indexed: 11/09/2022]
Abstract
A massively parallel algorithm of the analytical energy gradient calculations based the resolution of identity Møller-Plesset perturbation (RI-MP2) method from the restricted Hartree-Fock reference is presented for geometry optimization calculations and one-electron property calculations of large molecules. This algorithm is designed for massively parallel computation on multicore supercomputers applying the Message Passing Interface (MPI) and Open Multi-Processing (OpenMP) hybrid parallel programming model. In this algorithm, the two-dimensional hierarchical MP2 parallelization scheme is applied using a huge number of MPI processes (more than 1000 MPI processes) for acceleration of the computationally demanding O(N5 ) step such as calculations of occupied-occupied and virtual-virtual blocks of MP2 one-particle density matrix and MP2 two-particle density matrices. The new parallel algorithm performance is assessed using test calculations of several large molecules such as buckycatcher C60 @C60 H28 (144 atoms, 1820 atomic orbitals (AOs) for def2-SVP basis set, and 3888 AOs for def2-TZVP), nanographene dimer (C96 H24 )2 (240 atoms, 2928 AOs for def2-SVP, and 6432 AOs for cc-pVTZ), and trp-cage protein 1L2Y (304 atoms and 2906 AOs for def2-SVP) using up to 32,768 nodes and 262,144 central processing unit (CPU) cores of the K computer. The results of geometry optimization calculations of trp-cage protein 1L2Y at the RI-MP2/def2-SVP level using the 3072 nodes and 24,576 cores of the K computer are presented and discussed to assess the efficiency of the proposed algorithm. © 2017 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Michio Katouda
- Computational Molecular Science Research Team, RIKEN Advanced Institute for Computational Science, 7-1-26 Minatojima-minami-machi, Chuo-ku, Kobe, 650-0047, Japan
| | - Takahito Nakajima
- Computational Molecular Science Research Team, RIKEN Advanced Institute for Computational Science, 7-1-26 Minatojima-minami-machi, Chuo-ku, Kobe, 650-0047, Japan
| |
Collapse
|