Monte Carlo code, input files, and simulation outputs for contact-based collective move simulations of MOF formations (cobalt succinate)

A C++ implementation of a molecular Monte Carlo simulation with a contact-based collective move algorithm (CCMC: Contact Cluster Monte Carlo). This simulation features periodic boundary conditions. Interaction energies are defined by two-body distance/energy potentials of mean force, suitable for implicit-solvent simulations.

Input files are provided for simulations of assembly in the cobalt succinate system.

Inputs and outputs of production runs are provided, as these are the full datasets underlying our paper reporting the CCMC method and initial results.

Keywords:
Monte Carlo, collective move, cluster formation, MOF, Metal-organic framework, Formation and assembly

Cite this dataset as:
Wells, S., Düren, T., 2019. Monte Carlo code, input files, and simulation outputs for contact-based collective move simulations of MOF formations (cobalt succinate). Bath: University of Bath Research Data Archive. Available from: https://doi.org/10.15125/BATH-00517.

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Data

CMMC-InputsAndConfigExamples.zip
application/zip (79kB)
Creative Commons: Attribution 4.0

This folder contains some examples of inputs for the Contact Cluster Monte Carlo (CMMC) code. The included CIF file, containing 400 cobalt-oxygen octahedra and 80 succinate ligand units, is an example of structure input. The associated .bond file defines the bonding topology of the structure in the CIF file. The gen.mcfg and run.mcfg files are config files controlling execution. The .txt file contains potentials of mean force for cobalt succinates. See README for details.

CMMC-Production.zip
application/zip (1GB)
Creative Commons: Attribution 4.0

The subfolders contain the actual production inputs and outputs corresponding to simulations at ligand-poor compositions (labelled as A1F) which experimentally generate phase F, and ligand-rich compositions (labelled as A6F) which experimentally generate phase A. Each folder is numerically labelled according to the collective move probability (00, 05 or 09 for P=0, 0.5, 0.9) and the link probability (0.5 in all cases for these runs) with two independently seeded runs being labelled as -a and -b.

Code

CMMC-code.zip
application/zip (259kB)
Software: GNU GPL 3.0

This folder contains all the source code and header files to compile our implementation of Contact Cluster Monte Carlo (CCMC). makeMC.sh is a bash script which will compile the executables. The associated phaseA/phaseF files identify specific geometric motifs in cobalt succinate MOF structures. The main code, however, is fully general. Further details are provided in the included README-code file.

Creators

Stephen Wells
University of Bath

Tina Düren
University of Bath

Documentation

Data collection method:

The code was written in standard C++ on a Linux system. The data were produced by running the code with inputs provided on a Linux system. The outputs are provided as plain-text simulation output files: molecular structures in CIF format, and statistical reports of the number and size of molecular clusters.

Data processing and preparation activities:

The simulation outputs were processed in plain text in order to extract data for input to spreadsheets.

Technical details and requirements:

All work was conducted on a multiprocessor Linux desktop workstation.

Funders

European Research Council (ERC)
https://doi.org/10.13039/501100000781

Tina Duren - GROWMOF Modelling of MOF Self-Assembley, Crustal Growth and Thin Film Formation
648283

Publication details

Publication date: 8 May 2019
by: University of Bath

Version: 1

DOI: https://doi.org/10.15125/BATH-00517

URL for this record: https://researchdata.bath.ac.uk/id/eprint/517

Related articles

Wells, S. A., Cessford, N. F., Seaton, N. A. and Düren, T., 2019. Early stages of phase selection in MOF formation observed in molecular Monte Carlo simulations. RSC Advances, 9(25), pp.14382-14390. Available from: https://doi.org/10.1039/C9RA01504C.

Contact information

Please contact the Research Data Service in the first instance for all matters concerning this item.

Contact person: Tina Düren

Departments:

Faculty of Engineering & Design
Chemical Engineering