DL_MONTE: a general purpose program for parallel Monte Carlo simulation

Purton, John A.; Crabtree, Jenny C; Parker, Stephen C.

doi:10.1080/08927022.2013.839871

Cited by 78 publications

(54 citation statements)

References 55 publications

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“…Generalpurpose MC programs that provide access to a wide range of techniques -including advanced techniques for complex systems -have been lacking. As far as we are aware there are only a handful of general-purpose MC programs available to the community [30][31][32][33][34], and of these, only Casandra [30] and DL MONTE [34] are under active development. However, the development of such programs is essential if the unique capabilities of MC are to be fully exploited by the scientific community.…”

Section: Introductionmentioning

confidence: 99%

“…In this work we present DL MONTE (version 2), with particular emphasis on the extensive functionality which has been added to the program since the release of version 1 in 2013 [34]. The most important additions include the lattice-switch MC method; and the widely-used methods for calculating free energy profiles -hereafter collectively referred to as free energy difference (FED) methods -which can be used in conjunction with replica-exchange parallel tempering.…”

Section: Introductionmentioning

confidence: 99%

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DL_MONTE: a multipurpose code for Monte Carlo simulation

Brukhno

Grant

Underwood

et al. 2019

Molecular Simulation

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DL MONTE is an open source, general-purpose software package for performing Monte Carlo simulations. It includes a wide variety of force fields and MC techniques, and thus is applicable to a broad range of problems in molecular simulation. Here we provide an overview of DL MONTE, focusing on key features recently added to the package. These include the ability to treat systems confined to a planar pore (i.e. 'slit' or 'slab' boundary conditions); the lattice-switch Monte Carlo (LSMC) method for evaluating precise free energy differences between competing polymorphs; various commonly-used methods for evaluating free energy profiles along transition pathways (including umbrella sampling, Wang-Landau and transition matrix); and a supplementary Python toolkit for simulation management and application of the histogram reweighting analysis method. We provide two 'real world' examples to elucidate the use of these methods in DL MONTE. In particular, we apply umbrella sampling to calculate the free energy profile associated with the translocation of a lipid through a bilayer. Moreover we employ LSMC to examine the thermodynamic stability of two plastic crystal phases of water at high pressure. Beyond this, we provide instructions on how to access DL MONTE, and point to additional information valuable to existing and prospective users.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

DL_MONTE: a multipurpose code for Monte Carlo simulation

Brukhno

Grant

Underwood

et al. 2019

Molecular Simulation

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“…Moreover, it has been shown that mixing rules applied to CO 2 ‐zeolite interactions yielded overestimated isotherms at low pressures and underestimated isotherms at high pressure. Crossing of the isotherm resulting from MD simulations with the one resulting from experiment demonstrates a qualitatively correct behavior from using mixing rules . The qualitatively correct behavior may originate from the general nature of the force zeolite force field and its transferability to other surfaces and interfaces.…”

Section: Computational Detailsmentioning

confidence: 77%

“…The CLAYFF‐based zeolite force field used was constructed by primarily fitting to structural experimental data of zeolite . Hence, there was no focus on reproducing the dynamics of the surface.…”

Section: Computational Detailsmentioning

confidence: 99%

Effects of glycol on adsorption dynamics of idealized water droplets on LTA‐3A zeolite surfaces

Olsen

Kvamme

2019

AIChE Journal

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During production of natural gas, glycol may follow the gas stream due to hydrate prevention or glycol dehumidification. Further dehumidification can be achieved by Linde Type A‐3A zeolite. Local glycol concentrations can form through adsorption to surrounding clay material or zeolite, thus blocking zeolite windows or contaminating condensed water droplets close to the surface. Idealized nanoscale water droplets and their adsorption dynamics onto zeolite structures were simulated, with and without glycol contamination. Blockage of the zeolite windows was also investigated. Water from contaminated droplets adsorbed slower than uncontaminated droplets due to hindrance caused by glycols adsorbed to the zeolite surfaces, thus decreasing initial water loading rates. The adsorption free energy barrier of water was higher for D4R‐terminated zeolite than for alpha cavity‐terminated zeolite. Adsorbed glycols blocked zeolite cavities. However, temperature increase resulted in partial desorption of the glycols, while water desorbed at a lower temperature than for glycol.

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“…4 We describe how LSMC can be used to evaluate interfacial free energies in Section 8. 5 Specifically, LSMC is earmarked for inclusion in the general-purpose Monte Carlo code DL MONTE [26]. 6 Of course, in doing this the user's module is free to interface with 'external' modules, or even external programs.…”

Section: Introductionmentioning

confidence: 99%

monteswitch : A package for evaluating solid–solid free energy differences via lattice-switch Monte Carlo

Underwood

Ackland

2017

Computer Physics Communications

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Lattice-switch Monte Carlo (LSMC) is a method for evaluating the free energy between two given solid phases. LSMC is a general method, being applicable to a wide range of problems and interatomic potentials. Furthermore it is extremely efficient, ostensibly more efficient than other existing general methods. Here we introduce a package, monteswitch, which can be used to perform LSMC simulations. The package can be used to evaluate the free energy differences between pairs of solid phases, including multicomponent phases, via LSMC for atomic (i.e., non-molecular) systems in the NVT and NPT ensembles. It could also be used to evaluate the free energy cost associated with interfaces and defects. Regarding interatomic potentials, monteswitch currently supports various commonly-used pair potentials, including the hard-sphere, Lennard-Jones, and Morse potentials, as well as the embedded atom model. However the main strength of the package is its versatility: it is designed so that users can easily implement their own potentials. the free energy difference between two solid phases. The package presented here allows LSMC simulations to be performed for a variety of interatomic potentials, including commonly-used pair potentials and the embedded atom model. Furthermore the package is designed so that users can easily implement their own potentials. The package supports LSMC simulations in the NVT and NPT ensembles, and can treat multicomponent systems. A version of the main program is included which is parallelised using MPI. This program parallelises the LSMC calculation by simulating multiple replicas of the system in parallel. KeywordsRestrictions: monteswitch cannot treat molecular systems, i.e., systems in which the particles exhibit rotational degrees of freedom, and is restricted to systems which can be represented within an orthorhombic supercell. Furthermore, the interatomic potential is 'hard-coded' in the sense that implementing a different potential requires that the package be recompiled. Additional comments: monteswitch includes programs to assist with the creation of input files and the post-processing of output files created by the main Monte Carlo programs. A user manual, a suite of test cases, a worked example, and a collection of plug-ins to implement various commonly-used interatomic potentials are also included with the package. Running time: Depends on the nature of the problem and the underlying computing platform. For the Zr EAM example in the manuscript one iteration (i.e., one 160,000-sweep weight-function-generation simulation and one 700,000-sweep production simulation) took a wall-clock time of approximately 1.9 hours on a desktop machine (an iMac14,2 with a 3.2GHz Intel Core i5-4570 processor) exploiting 4 cores for the 384-atom system, and 17.7 hours for the 1296-atom system. For each ensemble in the hard-sphere example the 18,000,000-sweep weight-function-generation simulation and two 125,000,000-sweep production simulations took a total of approximately 11 hours exploiting 16 core...

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DL_MONTE: a general purpose program for parallel Monte Carlo simulation

Cited by 78 publications

References 55 publications

DL_MONTE: a multipurpose code for Monte Carlo simulation

DL_MONTE: a multipurpose code for Monte Carlo simulation

Effects of glycol on adsorption dynamics of idealized water droplets on LTA‐3A zeolite surfaces

monteswitch : A package for evaluating solid–solid free energy differences via lattice-switch Monte Carlo

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