MPMC and MCMD: Free High‐Performance Simulation Software for Atomistic Systems

Abstract

Advancements in parallel computing and hardware have allowed computational exploration of chemical systems of interest with unprecendented accuracy and efficiency. The typical development of molecular simulation software is initially inspired by a particular scientific inquiry. The softwares presented herein, MPMC (Massively Parallel Monte Carlo) and MCMD (Monte Carlo/Molecular Dynamics) were born out of a pursuit to simulate condensed phase physical and chemical interactions in porous materials. MPMC first began in 2005 and has been used for dozens of published results in the literature but has not yet been introduced in a standalone paper. MCMD is a more recent expansion and re‐write with some published work, focused on adding molecular dynamics algorithms for transport and other time‐dependent properties of chemical systems. Each software functions as a standalone with some unique and other overlapping features. A driving aim of this work is to consider periodic, long‐range polarization effects in classical simulation, and both codes are optimized to perform such calculations. Sample results will be presented which highlight methodically that inclusion of explicit polarization produces simulation results with predictive power which in general are in greater agreement with experiment than non‐polarizable analogous simulations.

Molecular Sieving of Acetylene from Ethylene in a Rigid Ultra‐microporous Metal Organic Framework.

“…These were calculated using the Lennard‐Jones 12‐6 potential, [26] partial charges with Ewald summation, [30] and a Thole‐Applequist type model, [31] respectively. All MC simulations were performed using the Massively Parallel Monte Carlo (MPMC) code [32] …”

“…All MC simulations were performed using the Massively Parallel Monte Carlo (MPMC) code. [32] Simulations of C 2 H 2 adsorption were carried out in FÀ PYMOÀ Cu using grand canonical Monte Carlo (GCMC) methods [33] at 195 K and 1.0 atm in order to the obtain the modeled structure at saturation. For the state point considered, the simulations consisted of 2.5 × 10 6 MC steps to guarantee equilibration, followed by an additional 2.5 × 10 6 steps to ensure reasonable ensemble averages for the particle number.…”

Simulations of H2 Sorption in an Anthracene-Functionalized rht-Metal–Organic Framework

“…Grand canonical Monte Carlo simulations (GCMC) of H 2 sorption in MFM-132 were carried out using the massively parallel Monte Carlo code, which was developed and maintained by our group and is currently available for download on GitHub. , The simulations were performed on a single rigid unit cell of the MOF. Periodic boundary conditions were used to approximate the behavior of an infinitely extended crystalline environment.…”

Tuning the Selectivity between C2H2 and CO2 in Molecular Porous Materials

“…All simulations were performed using the Massively Parallel Monte Carlo (MPMC) code, an open-source that is currently available for download on GitHub. 28,29…”

“…Using the Monte Carlo -Molecular Dynamics (MCMD) code, 29,33 periodic molecular dynamics (MD) simulations in the canonical (N V T ) ensemble were performed on a single molecule of C 2 H 2 and CO 2 , individually, localized at the primary binding site in MPM-1-TIFSIX. This was done in order to estimate the diffusion barrier for each adsorbate to escape the confined region between two large channels in the structure.…”