1
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Malpathak S, Ananth N. Semiclassical dynamics in Wigner phase space I: Adiabatic hybrid Wigner dynamics. J Chem Phys 2024; 161:094109. [PMID: 39234962 DOI: 10.1063/5.0223185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Accepted: 08/12/2024] [Indexed: 09/06/2024] Open
Abstract
The Wigner phase space formulation of quantum mechanics is a complete framework for quantum dynamic calculations that elegantly highlights connections with classical dynamics. In this series of two articles, building upon previous efforts, we derive the full hierarchy of approximate semiclassical (SC) dynamic methods for adiabatic and non-adiabatic problems in Wigner phase space. In Paper I, focusing on adiabatic single surface processes, we derive the well-known double Herman-Kluk (DHK) approximation for real-time correlation functions in Wigner phase space and connect it to the linearized SC (LSC) approximation through a stationary phase approximation. We exploit this relationship to introduce a new hybrid SC method, termed Adiabatic Hybrid Wigner Dynamics (AHWD) that allows for a few important "system" degrees of freedom (dofs) to be treated at the DHK level, while treating the rest of the dofs (the "bath") at the LSC level. AHWD is shown to accurately capture quantum interference effects in models of coupled oscillators and the decoherence of vibrational probability density of a model I2 Morse oscillator coupled to an Ohmic thermal bath. We show that AHWD significantly mitigates the sign problem and employs reduced dimensional prefactors bringing calculations of complex system-bath problems within the reach of SC methods. Paper II focuses on extending this hybrid SC dynamics to nonadiabatic processes.
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Affiliation(s)
- Shreyas Malpathak
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, USA
| | - Nandini Ananth
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, USA
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2
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Poulsen JA, Nyman G. Finite-Temperature Correlation Functions Obtained from Combined Real- and Imaginary-Time Propagation of Variational Thawed Gaussian Wavepackets. ENTROPY (BASEL, SWITZERLAND) 2024; 26:412. [PMID: 38785661 PMCID: PMC11120471 DOI: 10.3390/e26050412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 05/02/2024] [Accepted: 05/04/2024] [Indexed: 05/25/2024]
Abstract
We apply the so-called variational Gaussian wavepacket approximation (VGA) for conducting both real- and imaginary-time dynamics to calculate thermal correlation functions. By considering strongly anharmonic systems, such as a quartic potential and a double-well potential at high and low temperatures, it is shown that this method is partially able to account for tunneling. This is contrary to other popular many-body methods, such as ring polymer molecular dynamics and the classical Wigner method, which fail in this respect. It is a historical peculiarity that no one has considered the VGA method for representing both the Boltzmann operator and the real-time propagation. This method should be well suited for molecular systems containing many atoms.
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Affiliation(s)
- Jens Aage Poulsen
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE 413 90 Gothenburg, Sweden
| | - Gunnar Nyman
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE 413 90 Gothenburg, Sweden
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3
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Videla PE, Batista VS. Matsubara dynamics approximation for generalized multi-time correlation functions. J Chem Phys 2023; 158:2889027. [PMID: 37154285 DOI: 10.1063/5.0146654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/21/2023] [Indexed: 05/10/2023] Open
Abstract
We introduce a semi-classical approximation for calculating generalized multi-time correlation functions based on Matsubara dynamics, a classical dynamics approach that conserves the quantum Boltzmann distribution. This method is exact for the zero time and harmonic limits and reduces to classical dynamics when only one Matsubara mode is considered (i.e., the centroid). Generalized multi-time correlation functions can be expressed as canonical phase-space integrals, involving classically evolved observables coupled through Poisson brackets in a smooth Matsubara space. Numerical tests on a simple potential show that the Matsubara approximation exhibits better agreement with exact results than classical dynamics, providing a bridge between the purely quantum and classical descriptions of multi-time correlation functions. Despite the phase problem that prevents practical applications of Matsubara dynamics, the reported work provides a benchmark theory for the future development of quantum-Boltzmann-preserving semi-classical approximations for studies of chemical dynamics in condensed phase systems.
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Affiliation(s)
- Pablo E Videla
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520-8107, USA
| | - Victor S Batista
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520-8107, USA
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4
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He X, Wu B, Shang Y, Li B, Cheng X, Liu J. New phase space formulations and quantum dynamics approaches. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1619] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Xin He
- Beijing National Laboratory for Molecular Sciences Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University Beijing China
| | - Baihua Wu
- Beijing National Laboratory for Molecular Sciences Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University Beijing China
| | - Youhao Shang
- Beijing National Laboratory for Molecular Sciences Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University Beijing China
| | - Bingqi Li
- Beijing National Laboratory for Molecular Sciences Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University Beijing China
| | - Xiangsong Cheng
- Beijing National Laboratory for Molecular Sciences Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University Beijing China
| | - Jian Liu
- Beijing National Laboratory for Molecular Sciences Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University Beijing China
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5
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Poulsen JA, Nyman G. A Divergence-Free Wigner Transform of the Boltzmann Operator Based on an Effective Frequency Theory. J Phys Chem A 2021; 125:9209-9225. [PMID: 34636560 PMCID: PMC8543443 DOI: 10.1021/acs.jpca.1c05860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
![]()
The centroid effective
frequency representation of path integrals
as developed by Feynman and Kleinert was originally aimed at calculating
partition functions and related quantities in the canonical ensemble.
In its path integral formulation, only closed paths
were relevant. This formulation has been used by the present authors
in order to calculate the many-body Wigner function of the Boltzmann
operator, which includes also open paths. This usage of the theory
outside of the original intention can lead to mathematical divergence
issues for potentials with barriers, particularly at low temperature.
In the present paper, we modify the effective frequency theory of
Feynman and Kleinert by also including open paths in its variational
equations. In this way, a divergence-free approximation to the Boltzmann
operator matrix elements is derived. This generalized version of Feynman
and Kleinert’s formulation is thus more robust and can be applied
to all types of barriers at all temperatures. This new version is
used to calculate the Wigner functions of the Boltzmann operator for
a quartic oscillator and for a double well potential and both static
and dynamic properties are studied at several temperatures. The new
theory is found to be essentially as precise as the original one.
Its advantage is that it will always deliver a well-defined, even
if approximate, Wigner function, which can, for instance, be used
for sampling initial conditions for molecular dynamics simulations.
As will be discussed, the theory can be systematically improved by
including higher-order Fourier modes into the nonquadratic part of
the trial action.
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Affiliation(s)
- Jens Aage Poulsen
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE 405 30 Gothenburg, Sweden
| | - Gunnar Nyman
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE 405 30 Gothenburg, Sweden
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6
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Plé T, Huppert S, Finocchi F, Depondt P, Bonella S. Anharmonic spectral features via trajectory-based quantum dynamics: A perturbative analysis of the interplay between dynamics and sampling. J Chem Phys 2021; 155:104108. [PMID: 34525824 DOI: 10.1063/5.0056824] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The performance of different approximate algorithms for computing anharmonic features in vibrational spectra is analyzed and compared on model and more realistic systems that present relevant nuclear quantum effects. The methods considered combine approximate sampling of the quantum thermal distribution with classical time propagation and include Matsubara dynamics, path integral dynamics approaches, linearized initial value representation, and the recently introduced adaptive quantum thermal bath. A perturbative analysis of these different methods enables us to account for the observed numerical performance on prototypes for overtones and combination bands and to draw qualitatively correct trends for the numerical results obtained for Fermi resonances. Our results prove that the unequal performances of these approaches often derive from the method employed to sample initial conditions and not, as usually assumed, from the lack of coherence in the time propagation. Furthermore, as confirmed by the analysis reported in Benson and Althorpe, J. Chem. Phys. 130, 194510 (2021), we demonstrate, both via the perturbative approach and numerically, that path integral dynamics methods fail to reproduce the intensities of these anharmonic features and follow purely classical trends with respect to their temperature behavior. Finally, the remarkably accurate performance of the adaptive quantum thermal bath approach is documented and motivated.
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Affiliation(s)
- Thomas Plé
- Sorbonne Université, CNRS, Institut des NanoSciences de Paris, INSP, 4 Place Jussieu, F-75005 Paris, France
| | - Simon Huppert
- Sorbonne Université, CNRS, Institut des NanoSciences de Paris, INSP, 4 Place Jussieu, F-75005 Paris, France
| | - Fabio Finocchi
- Sorbonne Université, CNRS, Institut des NanoSciences de Paris, INSP, 4 Place Jussieu, F-75005 Paris, France
| | - Philippe Depondt
- Sorbonne Université, CNRS, Institut des NanoSciences de Paris, INSP, 4 Place Jussieu, F-75005 Paris, France
| | - Sara Bonella
- CECAM Centre Européen de Calcul Atomique et Moléculaire, École Polytechnique Fédérale de Lausanne, Batochimie, Avenue Forel 2, 1015 Lausanne, Switzerland
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7
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He X, Wu B, Gong Z, Liu J. Commutator Matrix in Phase Space Mapping Models for Nonadiabatic Quantum Dynamics. J Phys Chem A 2021; 125:6845-6863. [PMID: 34339600 DOI: 10.1021/acs.jpca.1c04429] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
We show that a novel, general phase space mapping Hamiltonian for nonadiabatic systems, which is reminiscent of the renowned Meyer-Miller mapping Hamiltonian, involves a commutator variable matrix rather than the conventional zero-point-energy parameter. In the exact mapping formulation on constraint space for phase space approaches for nonadiabatic dynamics, the general mapping Hamiltonian with commutator variables can be employed to generate approximate trajectory-based dynamics. Various benchmark model tests, which range from gas phase to condensed phase systems, suggest that the overall performance of the general mapping Hamiltonian is better than that of the conventional Meyer-Miller Hamiltonian.
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Affiliation(s)
- Xin He
- Beijing National Laboratory for Molecular Sciences, Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Baihua Wu
- Beijing National Laboratory for Molecular Sciences, Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Zhihao Gong
- Beijing National Laboratory for Molecular Sciences, Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jian Liu
- Beijing National Laboratory for Molecular Sciences, Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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8
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Liu X, Zhang L, Liu J. Machine learning phase space quantum dynamics approaches. J Chem Phys 2021; 154:184104. [PMID: 34241027 DOI: 10.1063/5.0046689] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Derived from phase space expressions of the quantum Liouville theorem, equilibrium continuity dynamics is a category of trajectory-based phase space dynamics methods, which satisfies the two critical fundamental criteria: conservation of the quantum Boltzmann distribution for the thermal equilibrium system and being exact for any thermal correlation functions (even of nonlinear operators) in the classical and harmonic limits. The effective force and effective mass matrix are important elements in the equations of motion of equilibrium continuity dynamics, where only the zeroth term of an exact series expansion of the phase space propagator is involved. We introduce a machine learning approach for fitting these elements in quantum phase space, leading to a much more efficient integration of the equations of motion. Proof-of-concept applications to realistic molecules demonstrate that machine learning phase space dynamics approaches are possible as well as competent in producing reasonably accurate results with a modest computation effort.
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Affiliation(s)
- Xinzijian Liu
- Beijing National Laboratory for Molecular Sciences, Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Linfeng Zhang
- Beijing Institute of Big Data Research, Beijing 100871, China
| | - Jian Liu
- Beijing National Laboratory for Molecular Sciences, Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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9
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Zhang ZJ, Chen ZF, Liu J. Path integral Liouville dynamics simulations of vibrational spectra of formaldehyde and hydrogen peroxide. CHINESE J CHEM PHYS 2020. [DOI: 10.1063/1674-0068/cjcp2006099] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Zhi-jun Zhang
- Beijing National Laboratory for Molecular Sciences, Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Zi-fei Chen
- Beijing National Laboratory for Molecular Sciences, Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jian Liu
- Beijing National Laboratory for Molecular Sciences, Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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10
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Plé T, Huppert S, Finocchi F, Depondt P, Bonella S. Sampling the thermal Wigner density via a generalized Langevin dynamics. J Chem Phys 2019; 151:114114. [PMID: 31542021 DOI: 10.1063/1.5099246] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The Wigner thermal density is a function of considerable interest in the area of approximate (linearized or semiclassical) quantum dynamics where it is employed to generate initial conditions for the propagation of appropriate sets of classical trajectories. In this paper, we propose an original approach to compute the Wigner density based on a generalized Langevin equation. The stochastic dynamics is nontrivial in that it contains a coordinate-dependent friction coefficient and a generalized force that couples momenta and coordinates. These quantities are, in general, not known analytically and have to be estimated via auxiliary calculations. The performance of the new sampling scheme is tested on standard model systems with highly nonclassical features such as relevant zero point energy effects, correlation between momenta and coordinates, and negative parts of the Wigner density. In its current brute force implementation, the algorithm, whose convergence can be systematically checked, is accurate and has only limited overhead compared to schemes with similar characteristics. We briefly discuss potential ways to further improve its numerical efficiency.
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Affiliation(s)
- Thomas Plé
- Sorbonne Université, CNRS, Institut des NanoSciences de Paris, INSP, 4 Place Jussieu, F-75005 Paris, France
| | - Simon Huppert
- Sorbonne Université, CNRS, Institut des NanoSciences de Paris, INSP, 4 Place Jussieu, F-75005 Paris, France
| | - Fabio Finocchi
- Sorbonne Université, CNRS, Institut des NanoSciences de Paris, INSP, 4 Place Jussieu, F-75005 Paris, France
| | - Philippe Depondt
- Sorbonne Université, CNRS, Institut des NanoSciences de Paris, INSP, 4 Place Jussieu, F-75005 Paris, France
| | - Sara Bonella
- CECAM Centre Européen de Calcul Atomique et Moléculaire, École Polytechnique Fédérale de Lausanne, Batochimie, Avenue Forel 2, 1015 Lausanne, Switzerland
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11
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Morzan UN, Alonso de Armiño DJ, Foglia NO, Ramírez F, González Lebrero MC, Scherlis DA, Estrin DA. Spectroscopy in Complex Environments from QM–MM Simulations. Chem Rev 2018; 118:4071-4113. [DOI: 10.1021/acs.chemrev.8b00026] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Uriel N. Morzan
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Diego J. Alonso de Armiño
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Nicolás O. Foglia
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Francisco Ramírez
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Mariano C. González Lebrero
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Damián A. Scherlis
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Darío A. Estrin
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
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12
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Affiliation(s)
- Xinzijian Liu
- Beijing National Laboratory For Molecular Sciences, Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Jian Liu
- Beijing National Laboratory For Molecular Sciences, Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
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13
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Orr L, Hernández de la Peña L, Roy PN. Formulation of state projected centroid molecular dynamics: Microcanonical ensemble and connection to the Wigner distribution. J Chem Phys 2017; 146:214116. [PMID: 28595402 PMCID: PMC5462618 DOI: 10.1063/1.4984229] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Accepted: 05/15/2017] [Indexed: 11/14/2022] Open
Abstract
A derivation of quantum statistical mechanics based on the concept of a Feynman path centroid is presented for the case of generalized density operators using the projected density operator formalism of Blinov and Roy [J. Chem. Phys. 115, 7822-7831 (2001)]. The resulting centroid densities, centroid symbols, and centroid correlation functions are formulated and analyzed in the context of the canonical equilibrium picture of Jang and Voth [J. Chem. Phys. 111, 2357-2370 (1999)]. The case where the density operator projects onto a particular energy eigenstate of the system is discussed, and it is shown that one can extract microcanonical dynamical information from double Kubo transformed correlation functions. It is also shown that the proposed projection operator approach can be used to formally connect the centroid and Wigner phase-space distributions in the zero reciprocal temperature β limit. A Centroid Molecular Dynamics (CMD) approximation to the state-projected exact quantum dynamics is proposed and proven to be exact in the harmonic limit. The state projected CMD method is also tested numerically for a quartic oscillator and a double-well potential and found to be more accurate than canonical CMD. In the case of a ground state projection, this method can resolve tunnelling splittings of the double well problem in the higher barrier regime where canonical CMD fails. Finally, the state-projected CMD framework is cast in a path integral form.
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Affiliation(s)
- Lindsay Orr
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | | | - Pierre-Nicholas Roy
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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14
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Teh HH, Cheng YC. On the accuracy of the LSC-IVR approach for excitation energy transfer in molecular aggregates. J Chem Phys 2017; 146:144105. [DOI: 10.1063/1.4979894] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Hung-Hsuan Teh
- Department of Chemistry and Center for Quantum Science and Engineering, National Taiwan University, Taipei City 106, Taiwan
| | - Yuan-Chung Cheng
- Department of Chemistry and Center for Quantum Science and Engineering, National Taiwan University, Taipei City 106, Taiwan
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15
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Liu J, Zhang Z. Path integral Liouville dynamics: Applications to infrared spectra of OH, water, ammonia, and methane. J Chem Phys 2016; 144:034307. [DOI: 10.1063/1.4939953] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jian Liu
- Beijing National Laboratory for Molecular Sciences, Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Zhijun Zhang
- Beijing National Laboratory for Molecular Sciences, Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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16
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Coughtrie DJ, Tew DP. A Gaussian wave packet phase-space representation of quantum canonical statistics. J Chem Phys 2015; 143:044102. [DOI: 10.1063/1.4927235] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- David J. Coughtrie
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - David P. Tew
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
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17
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Smith KKG, Poulsen JA, Nyman G, Cunsolo A, Rossky PJ. Application of a new ensemble conserving quantum dynamics simulation algorithm to liquid para-hydrogen and ortho-deuterium. J Chem Phys 2015; 142:244113. [DOI: 10.1063/1.4922888] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Kyle K. G. Smith
- Institute for Computational Engineering and Sciences and Department of Chemistry,University of Texas at Austin, Austin, Texas 78712, USA
| | - Jens Aage Poulsen
- Physical Chemistry, Department of Chemistry and Molecular Biology, University of Gothenburg, SE 41296 Gothenburg, Sweden
| | - Gunnar Nyman
- Physical Chemistry, Department of Chemistry and Molecular Biology, University of Gothenburg, SE 41296 Gothenburg, Sweden
| | - Alessandro Cunsolo
- Photon Sciences Directorate, Brookhaven National Laboratory, P.O. Box 5000, Upton, New York 11973, USA
| | - Peter J. Rossky
- Department of Chemistry, Rice University, Houston, Texas 77251, USA
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18
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Smith KKG, Poulsen JA, Nyman G, Rossky PJ. A new class of ensemble conserving algorithms for approximate quantum dynamics: Theoretical formulation and model problems. J Chem Phys 2015; 142:244112. [DOI: 10.1063/1.4922887] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Kyle K. G. Smith
- Institute for Computational Engineering and Sciences and Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, USA
| | - Jens Aage Poulsen
- Physical Chemistry, Department of Chemistry and Molecular Biology, University of Gothenburg, SE 41296 Gothenburg, Sweden
| | - Gunnar Nyman
- Physical Chemistry, Department of Chemistry and Molecular Biology, University of Gothenburg, SE 41296 Gothenburg, Sweden
| | - Peter J. Rossky
- Department of Chemistry, Rice University, Houston, Texas 77251, USA
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Abstract
We show a new imaginary time path integral based method--path integral Liouville dynamics (PILD), which can be derived from the equilibrium Liouville dynamics [J. Liu and W. H. Miller, J. Chem. Phys. 134, 104101 (2011)] in the Wigner phase space. Numerical tests of PILD with the simple (white noise) Langevin thermostat have been made for two strongly anharmonic model problems. Since implementation of PILD does not request any specific form of the potential energy surface, the results suggest that PILD offers a potentially useful approach for general condensed phase molecular systems to have the two important properties: conserves the quantum canonical distribution and recovers exact thermal correlation functions (of even nonlinear operators, i.e., nonlinear functions of position or momentum operators) in the classical, high temperature, and harmonic limits.
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Affiliation(s)
- Jian Liu
- Beijing National Laboratory for Molecular Sciences, Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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Hele TJH, Willatt MJ, Muolo A, Althorpe SC. Boltzmann-conserving classical dynamics in quantum time-correlation functions: “Matsubara dynamics”. J Chem Phys 2015; 142:134103. [DOI: 10.1063/1.4916311] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Timothy J. H. Hele
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Michael J. Willatt
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Andrea Muolo
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Stuart C. Althorpe
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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21
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Coughtrie DJ, Tew DP. The Nosé-Hoover looped chain thermostat for low temperature thawed Gaussian wave-packet dynamics. J Chem Phys 2014; 140:194106. [PMID: 24852529 DOI: 10.1063/1.4875517] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We have used a generalised coherent state resolution of the identity to map the quantum canonical statistical average for a general system onto a phase-space average over the centre and width parameters of a thawed Gaussian wave packet. We also propose an artificial phase-space density that has the same behaviour as the canonical phase-space density in the low-temperature limit, and have constructed a novel Nosé-Hoover looped chain thermostat that generates this density in conjunction with variational thawed Gaussian wave-packet dynamics. This forms a new platform for evaluating statistical properties of quantum condensed-phase systems that has an explicit connection to the time-dependent Schrödinger equation, whilst retaining many of the appealing features of path-integral molecular dynamics.
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Affiliation(s)
- David J Coughtrie
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - David P Tew
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
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Shen T, Su NQ, Wu A, Xu X. Perturbative treatment of anharmonic vibrational effects on bond distances: An extended langevin dynamics method. J Comput Chem 2013; 35:467-78. [DOI: 10.1002/jcc.23516] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 12/06/2013] [Indexed: 11/10/2022]
Affiliation(s)
- Tonghao Shen
- Department of chemistry, State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering; Xiamen University; Xiamen 361005 People's Republic of China
| | - Neil Qiang Su
- Department of Chemistry, Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, MOE Laboratory for Computational Physical Science; Fudan University; Shanghai 200433 People's Republic of China
| | - Anan Wu
- Department of chemistry, State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering; Xiamen University; Xiamen 361005 People's Republic of China
| | - Xin Xu
- Department of chemistry, State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering; Xiamen University; Xiamen 361005 People's Republic of China
- Department of Chemistry, Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, MOE Laboratory for Computational Physical Science; Fudan University; Shanghai 200433 People's Republic of China
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Isborn CM, Götz AW, Clark MA, Walker RC, Martínez TJ. Electronic Absorption Spectra from MM and ab initio QM/MM Molecular Dynamics: Environmental Effects on the Absorption Spectrum of Photoactive Yellow Protein. J Chem Theory Comput 2012; 8:5092-5106. [PMID: 23476156 PMCID: PMC3590007 DOI: 10.1021/ct3006826] [Citation(s) in RCA: 145] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We describe a new interface of the GPU parallelized TeraChem electronic structure package and the Amber molecular dynamics package for quantum mechanical (QM) and mixed QM and molecular mechanical (MM) molecular dynamics simulations. This QM/MM interface is used for computation of the absorption spectra of the photoactive yellow protein (PYP) chromophore in vacuum, aqueous solution, and protein environments. The computed excitation energies of PYP require a very large QM region (hundreds of atoms) covalently bonded to the chromophore in order to achieve agreement with calculations that treat the entire protein quantum mechanically. We also show that 40 or more surrounding water molecules must be included in the QM region in order to obtain converged excitation energies of the solvated PYP chromophore. These results indicate that large QM regions (with hundreds of atoms) are a necessity in QM/MM calculations.
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Affiliation(s)
- Christine M. Isborn
- PULSE Institute and Department of Chemistry, Stanford University, Stanford, CA 94305
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025
| | - Andreas W. Götz
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093
| | - Matthew A. Clark
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093
| | - Ross C. Walker
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Todd J. Martínez
- PULSE Institute and Department of Chemistry, Stanford University, Stanford, CA 94305
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025
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Liu J, Miller WH, Fanourgakis GS, Xantheas SS, Imoto S, Saito S. Insights in quantum dynamical effects in the infrared spectroscopy of liquid water from a semiclassical study with an ab initio-based flexible and polarizable force field. J Chem Phys 2012; 135:244503. [PMID: 22225165 DOI: 10.1063/1.3670960] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The dynamical properties of liquid water play an important role in many processes in nature. In this paper, we focus on the infrared (IR) absorption spectrum of liquid water based on the linearized semiclassical initial value representation (LSC-IVR) with the local Gaussian approximation (LGA) [J. Liu and W. H. Miller, J. Chem. Phys. 131, 074113 (2009)] and an ab initio based, flexible, polarizable Thole-type model (TTM3-F) [G. S. Fanourgakis and S. S. Xantheas, J. Chem. Phys. 128, 074506 (2008)]. Although the LSC-IVR (LGA) gives the exact result for the isolated three-dimensional shifted harmonic stretching model, it yields a blueshifted peak position for the more realistic anharmonic stretching potential. By using the short-time information of the LSC-IVR correlation function; however, it is shown how one can obtain more accurate results for the position of the stretching peak. Due to the physical decay in the condensed phase system, the LSC-IVR (LGA) is a good and practical approximate quantum approach for the IR spectrum of liquid water. The present results offer valuable insight into future attempts to improve the accuracy of the TTM3-F potential or other ab initio-based models in reproducing the IR spectrum of liquid water.
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Affiliation(s)
- Jian Liu
- Department of Chemistry, University of California, Berkeley, California 94720-1460, USA
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Georgescu I, Mandelshtam VA. A fast variational Gaussian wavepacket method: Size-induced structural transitions in large neon clusters. J Chem Phys 2011; 135:154106. [DOI: 10.1063/1.3651473] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Liu J, Alder BJ, Miller WH. A semiclassical study of the thermal conductivity of low temperature liquids. J Chem Phys 2011; 135:114105. [DOI: 10.1063/1.3639107] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Liu J. Two more approaches for generating trajectory-based dynamics which conserves the canonical distribution in the phase space formulation of quantum mechanics. J Chem Phys 2011; 134:194110. [DOI: 10.1063/1.3589406] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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