DL_POLY Quantum 2.0, a vastly expanded software based on DL_POLY Classic 1.10, is a highly parallelized computational suite written in FORTRAN77 with a modular structure for incorporating nuclear quantum effects into large-scale/long-time molecular dynamics simulations. This is achieved by presenting users with a wide selection of state-of-the-art dynamics methods that utilize the isomorphism between a classical ring polymer and Feynman’s path integral formalism of quantum mechanics. The flexible and user-friendly input/output handling system allows the control of methodology, integration schemes, and thermostatting. DL_POLY Quantum is equipped with a module specifically assigned for calculating correlation functions and printing out the values for sought-after quantities, such as dipole moments and center-of-mass velocities, with packaged tools for calculating infrared absorption spectra and diffusion coefficients.
REFERENCES
1.
B. J.
Alder
and T. E.
Wainwright
, “Studies in molecular dynamics. I. General method
,” J. Chem. Phys.
31
, 459
–466
(1959
).2.
D.
Chandler
, “From 50 years ago, the birth of modern liquid-state science
,” Annu. Rev. Phys. Chem.
68
, 19
–38
(2017
).3.
M. P.
Allen
and D. J.
Tildesley
, Computer Simulation of Liquids
, 2nd ed. (Oxford University Press
, 2017
).4.
M. E.
Tuckerman
, Statistical Mechanics: Theory and Molecular Simulation
, 2nd ed. (Oxford University Press
, 2023
).5.
A.
Rimola
, D.
Costa
, M.
Sodupe
, J.-F.
Lambert
, and P.
Ugliengo
, “Silica surface features and their role in the adsorption of biomolecules: Computational modeling and experiments
,” Chem. Rev.
113
, 4216
–4313
(2013
).6.
P.
Li
and K. M.
Merz
, Jr., “Metal ion modeling using classical mechanics
,” Chem. Rev.
117
, 1564
–1686
(2017
).7.
B. B.
Hansen
, S.
Spittle
, B.
Chen
, D.
Poe
, Y.
Zhang
, J. M.
Klein
, A.
Horton
, L.
Adhikari
, T.
Zelovich
, B. W.
Doherty
, B.
Gurkan
, E. J.
Maginn
, A.
Ragauskas
, M.
Dadmun
, T. A.
Zawodzinski
, G. A.
Baker
, M. E.
Tuckerman
, R. F.
Savinell
, and J. R.
Sangoro
, “Deep eutectic solvents: A review of fundamentals and applications
,” Chem. Rev.
121
, 1232
–1285
(2021
).8.
A.
Vidal-Limon
, J. E.
Aguilar-Toala
, and A. M.
Liceaga
, “Integration of molecular docking analysis and molecular dynamics simulations for studying food proteins and bioactive peptides
,” J. Agric. Food Chem.
70
, 934
–943
(2022
).9.
M.
Born
and R.
Oppenheimer
, “Zur quantentheorie der molekeln
,” Ann. Phys.
389
, 457
–484
(1927
).10.
T.
Markland
and M.
Ceriotti
, “Nuclear quantum effects enter the mainstream
,” Nat. Rev. Chem
2
, 0109
(2018
).11.
L. D.
Fosdick
, “Numerical estimation of the partition function in quantum statistics
,” J. Math. Phys.
3
, 1251
–1264
(1962
).12.
L. D.
Fosdick
and H. F.
Jordan
, “Path-integral calculation of the two-particle slater sum for He4
,” Phys. Rev.
143
, 58
–66
(1966
).13.
J. A.
Barker
, “A quantum-statistical Monte Carlo method; path integrals with boundary conditions
,” J. Chem. Phys.
70
, 2914
–2918
(1979
).14.
D.
Chandler
and P. G.
Wolynes
, “Exploiting the isomorphism between quantum theory and classical statistical mechanics of polyatomic fluids
,” J. Chem. Phys.
74
, 4078
–4095
(1981
).15.
R. P.
Feynman
and A. R.
Hibbs
, Quantum Mechanics and Path Integrals
, Emended ed. (Dover Publications
, 2005
).16.
G. A.
Voth
, “Path-integral centroid methods in quantum statistical mechanics and dynamics
,” in Advances in Chemical Physics
(John Wiley & Sons Ltd
, 1996
), pp. 135
–218
.17.
S.
Habershon
, D. E.
Manolopoulos
, T. E.
Markland
, and T. F.
Miller
, “Ring-polymer molecular dynamics: Quantum effects in chemical dynamics from Classical Trajectories in an extended phase space
,” Annu. Rev. Phys. Chem.
64
, 387
–413
(2013
).18.
B.
Hirshberg
, V.
Rizzi
, and M.
Parrinello
, “Path integral molecular dynamics for bosons
,” Proc. Natl. Acad. Sci. U. S. A.
116
, 21445
–21449
(2019
).19.
M.
Parrinello
and A.
Rahman
, “Study of an F center in molten kcl
,” J. Chem. Phys.
80
, 860
–867
(1984
).20.
J.
Cao
and G. A.
Voth
, “The formulation of quantum statistical mechanics based on the Feynman path centroid density. IV. Algorithms for centroid molecular dynamics
,” J. Chem. Phys.
101
, 6168
–6183
(1994
).21.
S.
Jang
and G. A.
Voth
, “Path integral centroid variables and the formulation of their exact real time dynamics
,” J. Chem. Phys.
111
, 2357
–2370
(1999
).22.
S.
Jang
and G. A.
Voth
, “A derivation of centroid molecular dynamics and other approximate time evolution methods for path integral centroid variables
,” J. Chem. Phys.
111
, 2371
–2384
(1999
).23.
I. R.
Craig
and D. E.
Manolopoulos
, “Quantum statistics and classical mechanics: Real time correlation functions from ring polymer molecular dynamics
,” J. Chem. Phys.
121
, 3368
–3373
(2004
).24.
I. R.
Craig
and D. E.
Manolopoulos
, “Chemical reaction rates from ring polymer molecular dynamics
,” J. Chem. Phys.
122
, 084106
(2005
).25.
I. R.
Craig
and D. E.
Manolopoulos
, “A refined ring polymer molecular dynamics theory of chemical reaction rates
,” J. Chem. Phys.
123
, 034102
(2005
).26.
P.
Shushkov
, R.
Li
, and J. C.
Tully
, “Ring polymer molecular dynamics with surface hopping
,” J. Chem. Phys.
137
, 22A549
(2012
).27.
J. O.
Richardson
and M.
Thoss
, “Communication: Nonadiabatic ring-polymer molecular dynamics
,” J. Chem. Phys.
139
, 031102
(2013
).28.
N.
Ananth
, “Mapping variable ring polymer molecular dynamics: A path-integral based method for nonadiabatic processes
,” J. Chem. Phys.
139
, 124102
(2013
).29.
S. N.
Chowdhury
and P.
Huo
, “Coherent state mapping ring polymer molecular dynamics for non-adiabatic quantum propagations
,” J. Chem. Phys.
147
, 214109
(2017
).30.
F. A.
Shakib
and P.
Huo
, “Ring polymer surface hopping: Incorporating nuclear quantum effects into nonadiabatic molecular dynamics simulations
,” J. Phys. Chem. Lett.
8
, 3073
–3080
(2017
).31.
D. K.
Limbu
and F. A.
Shakib
, “Real-time dynamics and detailed balance in ring polymer surface hopping: The impact of frustrated hops
,” J. Phys. Chem. Lett.
14
, 8658
–8666
(2023
).32.
D. K.
Limbu
and F. A.
Shakib
, “SHARP pack: A modular software for incorporating nuclear quantum effects into non-adiabatic dynamics simulations
,” Software Impacts
19
, 100604
(2024
).33.
S.
Habershon
, G. S.
Fanourgakis
, and D. E.
Manolopoulos
, “Comparison of path integral molecular dynamics methods for the infrared absorption spectrum of liquid water
,” J. Chem. Phys.
129
, 074501
(2008
).34.
A.
Witt
, S. D.
Ivanov
, M.
Shiga
, H.
Forbert
, and D.
Marx
, “On the applicability of centroid and ring polymer path integral molecular dynamics for vibrational spectroscopy
,” J. Chem. Phys.
130
, 194510
(2009
).35.
V.
Kapil
, M.
Rossi
, O.
Marsalek
, R.
Petraglia
, Y.
Litman
, T.
Spura
, B.
Cheng
, A.
Cuzzocrea
, R. H.
Meißner
, D. M.
Wilkins
, B. A.
Helfrecht
, P.
Juda
, S. P.
Bienvenue
, W.
Fang
, J.
Kessler
, I.
Poltavsky
, S.
Vandenbrande
, J.
Wieme
, C.
Corminboeuf
, T. D.
Kühne
, D. E.
Manolopoulos
, T. E.
Markland
, J. O.
Richardson
, A.
Tkatchenko
, G. A.
Tribello
, V.
Van Speybroeck
, and M.
Ceriotti
, “I-PI 2.0: A universal force engine for advanced molecular simulations
,” Comput. Phys. Commun.
236
, 214
–223
(2019
).36.
T. E.
Markland
and D. E.
Manolopoulos
, “An efficient ring polymer contraction scheme for imaginary time path integral simulations
,” J. Chem. Phys.
129
, 024105
(2008
).37.
V.
Kapil
, J.
VandeVondele
, and M.
Ceriotti
, “Accurate molecular dynamics and nuclear quantum effects at low cost by multiple steps in real and imaginary time: Using density functional theory to accelerate wavefunction methods
,” J. Chem. Phys.
144
, 054111
(2016
).38.
M.
Tuckerman
, B. J.
Berne
, and G. J.
Martyna
, “Reversible multiple time scale molecular dynamics
,” J. Chem. Phys.
97
, 1990
–2001
(1992
).39.
A. P.
Thompson
, H. M.
Aktulga
, R.
Berger
, D. S.
Bolintineanu
, W. M.
Brown
, P. S.
Crozier
, P. J.
in ’t Veld
, A.
Kohlmeyer
, S. G.
Moore
, T. D.
Nguyen
, R.
Shan
, M. J.
Stevens
, J.
Tranchida
, C.
Trott
, and S. J.
Plimpton
, “LAMMPS—A flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales
,” Comput. Phys. Commun.
271
, 108171
(2022
).40.
M. R.
Momeni
and F. A.
Shakib
, “DL_POLY Quantum molecular simulation package
,” available from https://github.com/fashakib/DL_POLY–Quantum–v1.0.41.
W.
Smith
, T. R.
Forester
, and I. T.
Todorov
, “DL_POLY Classic molecular simulation package
,” STFC Daresbury Laboratory, available from https://gitlab.com/DL_POLY_Classic.42.
R. P.
Feynman
, A. R.
Hibbs
, and D. F.
Styer
, “Quantum mechanics and path integrals
,” Courier Corporation, 2010
.43.
H. F.
Trotter
, “On the product of semi-groups of operators
,” Proc. Am. Math. Soc.
10
, 545
–551
(1959
).44.
R.
Collepardo-Guevara
, I. R.
Craig
, and D. E.
Manolopoulos
, “Proton transfer in a polar solvent from ring polymer reaction rate theory
,” J. Chem. Phys.
128
, 144502
(2008
).45.
R. L.
Kenion
and N.
Ananth
, “Direct simulation of electron transfer in the cobalt hexammine(II/III) self-exchange reaction
,” Phys. Chem. Chem. Phys.
18
, 26117
–26124
(2016
).46.
J. S.
Kretchmer
and T. F. I.
Miller
, “Tipping the balance between concerted versus sequential proton-coupled electron transfer
,” Inorg. Chem.
55
, 1022
–1031
(2016
).47.
T. D.
Hone
, P. J.
Rossky
, and G. A.
Voth
, “A comparative study of imaginary time path integral based methods for quantum dynamics
,” J. Chem. Phys.
124
, 154103
(2006
).48.
S.
Habershon
, T. E.
Markland
, and D. E.
Manolopoulos
, “Competing quantum effects in the dynamics of a flexible water model
,” J. Chem. Phys.
131
, 024501
(2009
).49.
M.
Suzuki
, “General theory of fractal path integrals with applications to many-body theories and statistical physics
,” J. Math. Phys.
32
, 400
–407
(1991
).50.
H.
Yoshida
, “Construction of higher order symplectic integrators
,” Phys. Lett. A
150
, 262
–268
(1990
).51.
G. J.
Martyna
, M. E.
Tuckerman
, and M. L.
Klein
, “Explicit reversible integrators for extended systems dynamics
,” Mol. Phys.
87
, 1117
–1157
(1996
).52.
G. J.
Martyna
, D. J.
Tobias
, and M. L.
Klein
, “Constant pressure molecular dynamics algorithms
,” J. Chem. Phys.
101
, 4177
–4189
(1994
).53.
M. E.
Tuckerman
, B. J.
Berne
, G. J.
Martyna
, and M. L.
Klein
, “Efficient molecular dynamics and hybrid Monte Carlo algorithms for path integrals
,” J. Chem. Phys.
99
, 2796
–2808
(1993
).54.
B.
Leimkuhler
, E.
Noorizadeh
, and F.
Theil
, “A gentle stochastic thermostat for molecular dynamics
,” J. Stat. Phys.
135
, 261
–277
(2009
).55.
G. J.
Martyna
, M. L.
Klein
, and M.
Tuckerman
, “Nosé–Hoover chains: The canonical ensemble via continuous dynamics
,” J. Chem. Phys.
97
, 2635
–2643
(1992
).56.
M.
Ceriotti
, M.
Parrinello
, T. E.
Markland
, and D. E.
Manolopoulos
, “Efficient stochastic thermostatting of path integral molecular dynamics
,” J. Chem. Phys.
133
, 124104
(2010
).57.
M.
Ceriotti
, D. E.
Manolopoulos
, and M.
Parrinello
, “Accelerating the convergence of path integral dynamics with a generalized Langevin equation
,” J. Chem. Phys.
134
, 084104
(2011
).58.
M.
Rossi
, M.
Ceriotti
, and D. E.
Manolopoulos
, “How to remove the spurious resonances from ring polymer molecular dynamics
,” J. Chem. Phys.
140
, 234116
(2014
).59.
W.
Smith
, “Molecular dynamics on hypercube parallel computers
,” Comput. Phys. Commun.
62
, 229
–248
(1991
).60.
W.
Smith
, “Molecular dynamics on distributed memory (MIMD) parallel computers
,” Theor. Chim. Acta
84
, 385
–398
(1993
).61.
W.
Xia
, A.
Mahmood
, R.
Zou
, and Q.
Xu
, “Metal–organic frameworks and their derived nanostructures for electrochemical energy storage and conversion
,” Energy Environ. Sci.
8
, 1837
–1866
(2015
).62.
A. E.
Baumann
, D. A.
Burns
, B.
Liu
, and V. S.
Thoi
, “Metal-organic framework functionalization and design strategies for advanced electrochemical energy storage devices
,” Commun. Chem.
2
, 86
(2019
).63.
T.
Qiu
, Z.
Liang
, W.
Guo
, H.
Tabassum
, S.
Gao
, and R.
Zou
, “Metal–organic framework-based materials for energy conversion and storage
,” ACS Energy Lett.
5
, 520
–532
(2020
).64.
D.
Farrusseng
, S.
Aguado
, and C.
Pinel
, “Metal–organic frameworks: Opportunities for catalysis
,” Angew. Chem., Int. Ed.
48
, 7502
–7513
(2009
).65.
L.
Zhu
, X.-Q.
Liu
, H.-L.
Jiang
, and L.-B.
Sun
, “Metal–organic frameworks for heterogeneous basic catalysis
,” Chem. Rev.
117
, 8129
–8176
(2017
).66.
V.
Bernales
, M. A.
Ortuño
, D. G.
Truhlar
, C. J.
Cramer
, and L.
Gagliardi
, “Computational design of functionalized metal–organic framework nodes for catalysis
,” ACS Cent. Sci.
4
, 5
–19
(2018
).67.
M. R.
Momeni
and F. A.
Shakib
, “Deterministic role of structural flexibility on catalytic activity of conductive 2D layered metal–organic frameworks
,” Chem. Commun.
57
, 315
–318
(2021
).68.
Z.
Meng
, R. M.
Stolz
, L.
Mendecki
, and K. A.
Mirica
, “Electrically-transduced chemical sensors based on two-dimensional nanomaterials
,” Chem. Rev.
119
, 478
–598
(2019
).69.
L. S.
Xie
, G.
Skorupskii
, and M.
Dincă
, “Electrically conductive metal–organic frameworks
,” Chem. Rev.
120
, 8536
–8580
(2020
).70.
M. R.
Momeni
, Z.
Zhang
, D.
Dell’Angelo
, and F. A.
Shakib
, “Tuning electronic properties of conductive 2D layered metal–organic frameworks via host–guest interactions: Dioxygen as an electroactive chemical stimuli
,” APL Mater.
9
, 051109
(2021
).71.
Z.
Zhang
, D.
Dell’Angelo
, M. R.
Momeni
, Y.
Shi
, and F. A.
Shakib
, “Metal-to-semiconductor transition in two-dimensional metal–organic frameworks: An ab initio dynamics perspective
,” ACS Appl. Mater. Interfaces
13
, 25270
–25279
(2021
).72.
Z.
Zhang
, D. S.
Valente
, Y.
Shi
, D. K.
Limbu
, M. R.
Momeni
, and F. A.
Shakib
, “In silico high-throughput design and prediction of structural and electronic properties of low-dimensional metal–organic frameworks
,” ACS Appl. Mater. Interfaces
15
, 9494
–9507
(2023
).73.
H.
Kim
, S.
Yang
, S. R.
Rao
, S.
Narayanan
, E. A.
Kapustin
, H.
Furukawa
, A. S.
Umans
, O. M.
Yaghi
, and E. N.
Wang
, “Water harvesting from air with metal-organic frameworks powered by natural sunlight
,” Science
356
, 430
–434
(2017
).74.
W.
Xu
and O. M.
Yaghi
, “Metal–organic frameworks for water harvesting from air, anywhere, anytime
,” ACS Cent. Sci.
6
, 1348
–1354
(2020
).75.
W.
Song
, Z.
Zheng
, A. H.
Alawadhi
, and O. M.
Yaghi
, “Mof water harvester produces water from death valley desert air in ambient sunlight
,” Nat. Water
1
, 626
–634
(2023
).76.
M. A.
Addicoat
, N.
Vankova
, I. F.
Akter
, and T.
Heine
, “Extension of the universal force field to metal–organic frameworks
,” J. Chem. Theory Comput.
10
, 880
–891
(2014
).77.
S.
Bureekaew
, S.
Amirjalayer
, M.
Tafipolsky
, C.
Spickermann
, T. K.
Roy
, and R.
Schmid
, “MOF-FF—A flexible first-principles derived force field for metal-organic frameworks
,” Phys. Status Solidi B
250
, 1128
–1141
(2013
).78.
J. K.
Bristow
, D.
Tiana
, and A.
Walsh
, “Transferable force field for metal–organic frameworks from first-principles: BTW-FF
,” J. Chem. Theory Comput.
10
, 4644
–4652
(2014
).79.
A. J.
Rieth
, K. M.
Hunter
, M.
Dincă
, and F.
Paesani
, “Hydrogen bonding structure of confined water templated by a metal-organic framework with open metal sites
,” Nat. Commun.
10
, 4771
(2019
).80.
Y.
Shi
, M. R.
Momeni
, Y.-J.
Chen
, D. K.
Limbu
, Z.
Zhang
, and F. A.
Shakib
, “Water induced structural transformations in flexible two-dimensional layered conductive metal–organic frameworks
,” Chem. Mater.
34
, 7730
–7740
(2022
).81.
Y.
Wu
, A.
Kobayashi
, G. J.
Halder
, V. K.
Peterson
, K. W.
Chapman
, N.
Lock
, P. D.
Southon
, and C. J.
Kepert
, “Negative thermal expansion in the metal–organic framework material Cu3(1,3,5-benzenetricarboxylate)2
,” Angew. Chem., Int. Ed.
47
, 8929
–8932
(2008
).82.
M.
Ceriotti
and D. E.
Manolopoulos
, “Efficient first-principles calculation of the quantum kinetic energy and momentum distribution of nuclei
,” Phys. Rev. Lett.
109
, 100604
(2012
).83.
J. E.
Bertie
and Z.
Lan
, “Infrared intensities of liquids XX: The intensity of the OH stretching band of liquid water revisited, and the best current values of the optical constants of H2O(l) at 25°C between 15,000 and 1 cm−1
,” Appl. Spectrosc.
50
, 1047
–1057
(1996
).84.
A. E. I.
DePrince
and J. R.
Hammond
, “Coupled cluster theory on graphics processing units I. The coupled cluster doubles method
,” J. Chem. Theory Comput.
7
, 1287
–1295
(2011
).85.
I. S.
Ufimtsev
and T. J.
Martínez
, “Graphical processing units for quantum chemistry
,” Comput. Sci. Eng.
10
, 26
–34
(2008
).86.
I. S.
Ufimtsev
and T. J.
Martinez
, “Quantum chemistry on graphical processing units. 3. Analytical energy gradients, geometry optimization, and first principles molecular dynamics
,” J. Chem. Theory Comput.
5
, 2619
–2628
(2009
).87.
T. J.
Boerner
, S.
Deems
, T. R.
Furlani
, S. L.
Knuth
, and J.
Towns
, “Access: Advancing innovation: NSF’s advanced cyberinfrastructure coordination ecosystem: Services & support
,” in Practice and Experience in Advanced Research Computing, PEARC’23
(Association for Computing Machinery
, New York
, 2023
), pp. 173
–176
.88.
A.
Pérez
, M. E.
Tuckerman
, and M. H.
Müser
, “A comparative study of the centroid and ring-polymer molecular dynamics methods for approximating quantum time correlation functions from path integrals
,” J. Chem. Phys.
130
, 184105
(2009
).89.
L.
Verlet
, “‘Computer experiments’ on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules
,” Phys. Rev.
159
, 98
–103
(1967
).90.
M.
Ceriotti
, G.
Bussi
, and M.
Parrinello
, “Colored-noise thermostats à la carte
,” J. Chem. Theory Comput.
6
, 1170
–1180
(2010
).91.
F.
Uhl
, D.
Marx
, and M.
Ceriotti
, “Accelerated path integral methods for atomistic simulations at ultra-low temperatures
,” J. Chem. Phys.
145
, 054101
(2016
).92.
93.
N. L.
Allinger
, Y. H.
Yuh
, and J. H.
Lii
, “Molecular mechanics. The MM3 force field for hydrocarbons. 1
,” J. Am. Chem. Soc.
111
, 8551
–8566
(1989
).94.
T.-C.
Lim
, “Alignment of buckingham parameters to generalized Lennard-Jones potential functions
,” Z. Naturforsch. A
64
, 200
–204
(2009
).© 2024 Author(s). Published under an exclusive license by AIP Publishing.
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