Programs in Physics & Physical Chemistry
|[Licence| Download | New Version Template] aenz_v1_2.tar.gz(1363 Kbytes)|
|Manuscript Title: MCMC2 (version 1.1.1): A Monte Carlo code for multiply charged clusters|
|Authors: David A. Bonhommeau|
|Program title: MCMC2|
|Catalogue identifier: AENZ_v1_2|
Distribution format: tar.gz
|Journal reference: Comput. Phys. Commun. 196(2015)614|
|Programming language: Fortran 90 with MPI extensions for parallelization.|
|Computer: x86 and IBM platforms.|
|Has the code been vectorised or parallelized?: Yes, parallelized using MPI extensions. Number of CPUs used: Up to 999|
|RAM: (per CPU core) 10-20 MB. The physical memory needed for the simulation depends on the cluster size, the values indicated are typical for small or medium-sized clusters (N ≤ 300 - 400). The size of An+N clusters (N = number of particles, n = number of charged particles with n≤N ) should not exceed 1.6 x 104 (respectively 2.0 x 104) particles on servers with 2 GB (respectively 3 GB) of RAM per CPU core if n = 0 (neutral clusters) or n = N ("fully-charged" clusters). For charged clusters composed of neutral and charged particles (eg, n = N/2), the maximum cluster size can drop to 1.4 x 104 and 1.8 x 104 on servers with 2 GB and 3 GB of RAM, respectively (see the figure given in Supplementary Material).|
|Supplementary material: A figure showing the amount of RAM required per replica as a function of the size of An+N clusters can be downloaded.|
|Keywords: Monte Carlo simulations, Coarse-grained models, Charged clusters, Charged droplets, Electrospray ionisation, Parallel Tempering, Parallel Charging.|
|PACS: 05.10.Ln, 36.40.Wa, 36.40.Ei, 36.40.Qv.|
Does the new version supersede the previous version?: Yes
Nature of problem:
We provide a general parallel code to investigate structural and thermodynamic properties of multiply charged clusters.
Parallel Monte Carlo methods are implemented for the exploration of the configuration space of multiply charged clusters. Two parallel Monte Carlo methods were found appropriate to achieve such a goal: the Parallel Tempering method, where replicas of the same cluster at different temperatures are distributed among different CPUs, and Parallel Charging where replicas (at the same temperature) having different particle charges or numbers of charged particles are distributed on different CPUs.
Reasons for new version:
This new version of the MCMC2 program for modeling the thermodynamic and structural properties of multiply-charged clusters fixes some minor bugs present in earlier versions. A figure representing the required RAM per replica as a function of the cluster size (N ≤ 20000) is also provided as benchmark.
Summary of revisions:
The current version of the code uses Lennard-Jones interactions, as the main cohesive interaction between spherical particles, and electrostatic interactions (charge-charge, charge-induced dipole, induced dipole-induced dipole, polarisation). Furthermore, the Monte Carlo simulations can only be performed in the N V T ensemble and the size of charged clusters should not exceed 2.0x104 particles on CPU cores with less than 3GB of RAM each. It is worth noting that the latter restriction is not significantly crippling since MCMC2 should be mainly devoted to the investigation of medium-sized cluster properties due to the difficulty to converge Monte Carlo simulations on large systems (N ≥ 103) .
The Parallel Charging methods, based on the same philosophy as Parallel Tempering but with particle charges and number of charged particles as parameters instead of temperature, is an interesting new approach to explore energy landscapes. Splitting of the simulations is allowed and averages are accordingly updated.
The running time depends on the number of Monte Carlo steps, cluster size, and the type of interactions selected (eg, polarisation turned on or off, and method used for calculating the induced dipoles). Typically a complete simulation can last from a few tens of minutes or a few hours for small clusters (N ≤ 100, not including polarisation interactions), to one week for large clusters (N ≥ 1000 not including polarisation interactions), and several weeks for large clusters (N ≥ 1000) when including polarisation interactions. A restart procedure has been implemented that enables a splitting of the simulation accumulation phase.
|||E. Pahl, F. Calvo, L. Koci, P. Schwerdtfeger, Accurate Melting Temperatures for Neon and Argon from Ab Initio Monte Carlo Simulations, Angew. Chem. Int. Ed. 47 (2008) 8207.|
|||D. A. Bonhommeau, M.-P. Gaigeot, MCMC2: A Monte Carlo code for multiply-charged clusters, Comput. Phys. Commun. 184 (2013) 873-884.|
|||D. A. Bonhommeau, M. Lewerenz, M.-P. Gaigeot, MCMC2 (version 1.1): A Monte Carlo code for multiply-charged clusters, Comput. Phys. Commun. 185 (2014) 1188-1191.|
|||M. A. Miller, D. A. Bonhommeau, C. J. Heard, Y. Shin, R. Spezia, M.-P. Gaigeot, Structure and stability of charged clusters, J. Phys.: Condens. Matter. 24 (2012) 284130.|
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