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Jaykhedkar N, Bystrický R, Sýkora M, Bučko T. Investigating the role of dispersion corrections and anharmonic effects on the phase transition in SrZrS3: A systematic analysis from AIMD free energy calculations. J Chem Phys 2024; 160:014710. [PMID: 38180257 DOI: 10.1063/5.0185319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 12/13/2023] [Indexed: 01/06/2024] Open
Abstract
A thermally driven needle-like (NL) to distorted perovskite (DP) phase transition in SrZrS3 was investigated by means of ab initio free energy calculations accelerated by machine learning. As a first step, a systematic screening of the methods to include long-range interactions in semilocal density functional theory Perdew-Burke-Ernzerhof calculations was performed. Out of the ten correction schemes tested, the Tkatchenko-Scheffler method with iterative Hirshfeld partitioning method was found to yield the best match between calculated and experimental lattice geometries, while predicting the correct order of stability of NL and DP phases at zero temperature. This method was then used in free energy calculations, performed using several approaches, so as to determine the effect of various anharmonicity contributions, such as the anisotropic thermal lattice expansion or the thermally induced internal structure changes, on the phase transition temperature (TNP→DP). Accounting for the full anharmonicity by combining the NPT molecular dynamics data with thermodynamic integration with harmonic reference provided our best estimate of TNL→DP = 867 K. Although this result is ∼150 K lower than the experimental value, it still provides an improvement by nearly 300 K compared to the previous theoretical report by Koocher et al. [Inorg. Chem. 62, 11134-11141 (2023)].
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Affiliation(s)
- Namrata Jaykhedkar
- Laboratory of Advanced Materials, Comenius University, Ilkovičova 6, 84104 Bratislava, Slovakia
| | - Roman Bystrický
- Laboratory of Advanced Materials, Comenius University, Ilkovičova 6, 84104 Bratislava, Slovakia
- Institute of Inorganic Chemistry, Slovak Academy of Sciences, Dúbravská Cesta 9, 84236 Bratislava, Slovakia
| | - Milan Sýkora
- Laboratory of Advanced Materials, Comenius University, Ilkovičova 6, 84104 Bratislava, Slovakia
| | - Tomáš Bučko
- Institute of Inorganic Chemistry, Slovak Academy of Sciences, Dúbravská Cesta 9, 84236 Bratislava, Slovakia
- Department of Physical and Theoretical Chemistry, Comenius University, Ilkovičova 6, 84104 Bratislava, Slovakia
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Amsler J, Plessow PN, Studt F, Bučko T. Anharmonic Correction to Adsorption Free Energy from DFT-Based MD Using Thermodynamic Integration. J Chem Theory Comput 2021; 17:1155-1169. [PMID: 33482059 DOI: 10.1021/acs.jctc.0c01022] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Adsorption processes are often governed by weak interactions for which the estimation of entropy contributions by means of the harmonic approximation is prone to be inaccurate. Thermodynamic integration (TI) from the harmonic to the fully interacting system (λ-path integration) can be used to compute anharmonic corrections. Here, we combine TI with (curvilinear) internal coordinates in periodic systems to make the formalism available in computational studies. Our implementation of ab initio molecular dynamics in VASP is independent of the reaction path and can be thus applied to study adsorption processes relative to the gas phase and does hence provide a useful tool for computational catalysis. We discuss the application of the approach on three model systems for which exact semianalytical solutions exist and illustrate and quantify the importance of anharmonic vibrations, hindered rotations, and hindered translations (dissociation). Eventually, we apply the method to study the adsorption of small adsorbates in a zeolite (H-SSZ-13).
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Affiliation(s)
- Jonas Amsler
- Institute of Catalysis Research and Technology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Philipp N Plessow
- Institute of Catalysis Research and Technology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Felix Studt
- Institute of Catalysis Research and Technology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.,Institute for Chemical Technology and Polymer Chemistry, Karlsruhe Institute of Technology, Kaiserstr. 12, 76131 Karlsruhe, Germany
| | - Tomáš Bučko
- Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, SK-84215 Bratislava, Slovakia.,Institute of Inorganic Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, SK-84236 Bratislava, Slovakia
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3
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Purohit A, Schultz AJ, Kofke DA. Implementation of harmonically mapped averaging in LAMMPS, and effect of potential truncation on anharmonic properties. J Chem Phys 2020; 152:014107. [PMID: 31914768 DOI: 10.1063/1.5129942] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Implementation of the harmonically mapped averaging (HMA) framework in the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is presented for on-the-fly computations of the energy, pressure, and heat capacity of crystalline systems during canonical molecular dynamics simulations. HMA has a low central processing unit and storage requirements and is straightforward to use. As a case study, the properties of the Lennard-Jones and embedded-atom model (parameterized for nickel) crystals are computed. The results demonstrate the higher efficiency of the new class compared to the inbuilt LAMMPS classes for calculating these properties. However, HMA loses its effectiveness in systems where diffusion occurs in the crystal, and an example is presented to allow this behavior to be recognized. In addition to its improved precision, HMA is less affected by small errors introduced by having a larger time step in molecular dynamics simulations. We also present an analysis of the effect of potential truncation on anharmonic properties, and show that artifacts of truncation on the HMA averages can be eliminated simply by shifting the potential energy to zero at the truncation radius. Full properties can be obtained by adding easily computed values for the lattice and harmonic properties using the untruncated potential.
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Affiliation(s)
- Apoorva Purohit
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, New York 14260-4200, USA
| | - Andrew J Schultz
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, New York 14260-4200, USA
| | - David A Kofke
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, New York 14260-4200, USA
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Zhuang L, Wang R, Lindberg GE, Hu H, Li XZ, Wang F. From a Liquid to a Crystal without Going through a First-Order Phase Transition: Determining the Free Energy of Melting with Glassy Intermediates. J Phys Chem B 2019; 123:7740-7747. [DOI: 10.1021/acs.jpcb.9b06840] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lin Zhuang
- State Key Laboratory for Artificial Microstructure and Mesoscopic Physics, and School of Physics, Peking University, Beijing 100871, People’s Republic of China
| | - Rui Wang
- International Center for Quantum Materials, School of Physics, Peking University, Beijing 100871, People’s Republic of China
| | - Gerrick E. Lindberg
- Department of Chemistry and Biochemistry, and Department of Applied Physics and Materials Science, Northern Arizona University, 700 South Osborne Drive, Flagstaff, Arizona 86011, United States
| | - Hongyi Hu
- Department of Chemistry and Biochemistry, University of Arkansas, 119 Chemistry Building, Fayetteville, Arkansas 72701, United States
| | - Xin-Zheng Li
- State Key Laboratory for Artificial Microstructure and Mesoscopic Physics, and School of Physics, Peking University, Beijing 100871, People’s Republic of China
- Collaborative Innovation Center of Quantum Matter, Peking University, Beijing 100871, People’s Republic of China
| | - Feng Wang
- Department of Chemistry and Biochemistry, University of Arkansas, 119 Chemistry Building, Fayetteville, Arkansas 72701, United States
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Purohit A, Schultz AJ, Kofke DA. Force-sampling methods for density distributions as instances of mapped averaging. Mol Phys 2019. [DOI: 10.1080/00268976.2019.1572243] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Apoorva Purohit
- Department of Chemical and Biological Engineering, The State University of New York, Buffalo, NY, USA
| | - Andrew J. Schultz
- Department of Chemical and Biological Engineering, The State University of New York, Buffalo, NY, USA
| | - David A. Kofke
- Department of Chemical and Biological Engineering, The State University of New York, Buffalo, NY, USA
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Kolafa J. Free Energy of Classical Molecular Crystals by Thermodynamic Integration from a Harmonic Reference. J Chem Theory Comput 2019; 15:68-77. [PMID: 30461278 DOI: 10.1021/acs.jctc.8b00674] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We develop an algorithm for calculating the normal modes of vibration of mechanical systems with constraints, particularly of molecules with rigid bonds and models of rigid molecules, and use it to obtain the harmonic free energy of a crystal. The anharmonic correction is then calculated by the conventional thermodynamic integration over temperature in the NVT ensemble. Attention is paid to finite-size errors, tail corrections, thermostat choice, ergodicity, and other sources of inaccuracies. The calculated free energy of ice XIV modeled by the TIP4P/2005 potential agrees with the previously reported value and is by one order more accurate.
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Affiliation(s)
- Jiří Kolafa
- Department of Physical Chemistry , University of Chemistry and Technology , Technická 5 , 166 28 Praha 6 , Czech Republic
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Schultz AJ, Kofke DA. Comprehensive high-precision high-accuracy equation of state and coexistence properties for classical Lennard-Jones crystals and low-temperature fluid phases. J Chem Phys 2018; 149:204508. [DOI: 10.1063/1.5053714] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Andrew J. Schultz
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, New York 14260-4200, USA
| | - David A. Kofke
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, New York 14260-4200, USA
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Moustafa SG, Schultz AJ, Kofke DA. Effects of thermostatting in molecular dynamics on anharmonic properties of crystals: Application to fcc Al at high pressure and temperature. J Chem Phys 2018; 149:124109. [PMID: 30278666 DOI: 10.1063/1.5043614] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The precision and accuracy of the anharmonic energy calculated in the canonical (NVT) ensemble using three different thermostats (viz., Andersen, Langevin, and Nosé-Hoover) along with no thermostat (i.e., microcanonical, NVE) are compared via application to aluminum crystals at ≈100 GPa for temperatures up to melting (4000 K) using ab initio molecular dynamics (AIMD) simulation. In addition to the role of the thermostat, the effect of using either conventional or the recently introduced harmonically mapped averaging (HMA) method is considered. The effect of AIMD time-step size Δt on the ensemble averages gauges accuracy, while for a given Δt, the stochastic uncertainty (computed using block averaging) provides the metric for precision. We identify the rate of convergence of block averages (with respect to block size) as an important issue in this context, as it imposes a minimum simulation length required to achieve reliable statistics, and it differs considerably among the methods. We observe that HMA with a Langevin thermostat in an NVT simulation shows the best performance, from the point of view of accuracy, precision, and simulation length. In addition, we introduce a novel HMA-based ensemble average for the temperature. In application to NVE simulations, the new formulation exhibits much smaller fluctuations compared to the conventional kinetic-energy approach; however, it provides only marginal improvement in uncertainty due to strong negative correlations exhibited by the conventional form (which acts to reduce its uncertainty but also slows convergence of the block averages).
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Affiliation(s)
- Sabry G Moustafa
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, New York 14260-4200, USA
| | - Andrew J Schultz
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, New York 14260-4200, USA
| | - David A Kofke
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, New York 14260-4200, USA
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Moučka F, Kolafa J, Lísal M, Smith WR. Chemical potentials of alkaline earth metal halide aqueous electrolytes and solubility of their hydrates by molecular simulation: Application to CaCl2, antarcticite, and sinjarite. J Chem Phys 2018; 148:222832. [DOI: 10.1063/1.5024212] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- Filip Moučka
- Department of Molecular and Mesoscopic Modelling, Institute of Chemical Process Fundamentals of the CAS, v. v. i., 165 02 Prague 6-Suchdol, Czech Republic
- Department of Physics, Faculty of Science, J. E. Purkinje University, 400 96 Ústí nad Labem, Czech Republic
| | - Jiří Kolafa
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, 166 28 Praha 6, Czech Republic
| | - Martin Lísal
- Department of Molecular and Mesoscopic Modelling, Institute of Chemical Process Fundamentals of the CAS, v. v. i., 165 02 Prague 6-Suchdol, Czech Republic
- Department of Physics, Faculty of Science, J. E. Purkinje University, 400 96 Ústí nad Labem, Czech Republic
| | - William R. Smith
- Department of Mathematics and Statistics, University of Guelph, Guelph, Ontario N1G 2W1, Canada
- Department of Chemistry, University of Guelph, Guelph, Ontario N1G 2W1, Canada
- Department of Chemical Engineering, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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Schultz AJ, Moustafa SG, Kofke DA. No system-size anomalies in entropy of bcc iron at Earth's inner-core conditions. Sci Rep 2018; 8:7295. [PMID: 29740025 PMCID: PMC5940814 DOI: 10.1038/s41598-018-25419-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 04/19/2018] [Indexed: 11/09/2022] Open
Abstract
New molecular modeling data show that the entropy of bcc iron exhibits no system-size anomalies, implying that it should be feasible to compute accurate free energies of this system using first-principles methods without requiring a prohibitively large number of atoms. Conclusions are based on rigorous calculations of size-dependent free energies for a Sutton-Chen model of iron previously fit to ab initio calculations, and refute statements recently appearing in the literature indicating that the size of the simulation cell is critical for stabilization of the bcc phase.
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Affiliation(s)
- Andrew J Schultz
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, New York, 14260-4200, USA
| | - Sabry G Moustafa
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, New York, 14260-4200, USA
| | - David A Kofke
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, New York, 14260-4200, USA.
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12
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Shtukenberg AG, Zhu Q, Carter DJ, Vogt L, Hoja J, Schneider E, Song H, Pokroy B, Polishchuk I, Tkatchenko A, Oganov AR, Rohl AL, Tuckerman ME, Kahr B. Powder diffraction and crystal structure prediction identify four new coumarin polymorphs. Chem Sci 2017; 8:4926-4940. [PMID: 28959416 PMCID: PMC5607859 DOI: 10.1039/c7sc00168a] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 04/30/2017] [Indexed: 11/21/2022] Open
Abstract
Coumarin, a simple, commodity chemical isolated from beans in 1820, has, to date, only yielded one solid state structure. Here, we report a rich polymorphism of coumarin grown from the melt. Four new metastable forms were identified and their crystal structures were solved using a combination of computational crystal structure prediction algorithms and X-ray powder diffraction. With five crystal structures, coumarin has become one of the few rigid molecules showing extensive polymorphism at ambient conditions. We demonstrate the crucial role of advanced electronic structure calculations including many-body dispersion effects for accurate ranking of the stability of coumarin polymorphs and the need to account for anharmonic vibrational contributions to their free energy. As such, coumarin is a model system for studying weak intermolecular interactions, crystallization mechanisms, and kinetic effects.
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Affiliation(s)
- Alexander G Shtukenberg
- Department of Chemistry , Molecular Design Institute , New York University , New York City , NY 10003 , USA .
| | - Qiang Zhu
- Department of Physics and Astronomy , High Pressure Science and Engineering Center , University of Nevada Las Vegas , Nevada 89154 , USA .
- Department of Geosciences , Stony Brook University , Stony Brook , NY 11794 , USA
| | - Damien J Carter
- Curtin Institute for Computation and Department of Chemistry , Curtin University , P.O. Box U1987 , Perth , 6845 , Western Australia , Australia
| | - Leslie Vogt
- Department of Chemistry , New York University , New York City , NY 10003 , USA
| | - Johannes Hoja
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6 , Berlin , 14195 , Germany
- Physics and Materials Science Research Unit , University of Luxembourg , 1511 Luxembourg , Luxembourg
| | - Elia Schneider
- Department of Chemistry , New York University , New York City , NY 10003 , USA
| | - Hongxing Song
- Department of Chemistry , New York University , New York City , NY 10003 , USA
| | - Boaz Pokroy
- Department of Materials Science and Engineering , Russell Berrie Nanotechnology Institute , Technion Israel Institute of Technology , Haifa 32000 , Israel
| | - Iryna Polishchuk
- Department of Materials Science and Engineering , Russell Berrie Nanotechnology Institute , Technion Israel Institute of Technology , Haifa 32000 , Israel
| | - Alexandre Tkatchenko
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6 , Berlin , 14195 , Germany
- Physics and Materials Science Research Unit , University of Luxembourg , 1511 Luxembourg , Luxembourg
| | - Artem R Oganov
- Skolkovo Institute of Science and Technology , Skolkovo Innovation Center , 3 Nobel St. , Moscow 143026 , Russia
- Department of Geosciences , Stony Brook University , Stony Brook , NY 11794 , USA
| | - Andrew L Rohl
- Curtin Institute for Computation and Department of Chemistry , Curtin University , P.O. Box U1987 , Perth , 6845 , Western Australia , Australia
| | - Mark E Tuckerman
- Department of Chemistry , New York University , New York City , NY 10003 , USA
- Courant Institute of Mathematical Sciences , New York University , New York City , NY 10003 , USA
- New York University-East China Normal University Center for Computational Chemistry at NYU Shanghai , 3663 Zhongshan Road North , Shanghai 200062 , China
| | - Bart Kahr
- Department of Chemistry , Molecular Design Institute , New York University , New York City , NY 10003 , USA .
- Department of Advanced Science and Engineering (TWIns) , Waseda University , Wakamatsucho, 3-2 , Shinjuku , 162-0056 Tokyo , Japan
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