dlmonte_docker

Mirror of the docker hub image https://hub.docker.com/repository/docker/jrhmanning/dl_monte

DL_MONTE Docker

This container houses the executable code for DL_MONTE 2.07, a general-purpose Monte Carlo simulation program for a range of molecular simulations. Further information on DL_MONTE can be found here.

Getting Started

These instructions will cover usage information and for the docker container

Prerequisites

In order to run this container you'll need docker installed.

• Windows
• OS X
• Linux

Usage

The container has several pre-formatted template simulation files and runscripts contained within /scripts/, which can be run directly when calling a script with the container:

docker run -v $PWD/interface/:/run/interface/ jrhmanning/dl_monte:latest python isotherm_runner.py --InputFolder=/run/interface --OutputFolder=/run/interface --Framework=Cu_BTC

Simulation templates

Currently, the repository contains a single template control object:

• AdsorptionExample, within the isotherm_control_generator.py file.
  • This describes a simple GCMC isotherm with no advanced sampling, which can be modified to suit most standard adsorption simulation workflows.

Simulation scripts

The repository contains the following simulation run scripts, which uses dlmontepython.simtask to automate GCMC tasks:

• isotherm_runner.py
  • Runs an isotherm on a fixed-atom framework found in a .cif file. Runs through different pressure values to perform GCMC, and return a .csv and .png file summarising the results.

Simulation Parameters

Simulation parameters can be controlled using argument parsing inside the various python scripts to control or amend parameters. These should be uniform across all simulation scripts included.

• InputFolder
  • The input directory containing your input .cif file
• OutputFolder
  • The output directory whee your simulation outputs will be located.
• FrameworkName
  • The name of your .cif file (without the file type, e.g. Cu_BTC, not Cu_BTC.cif)
• GasComposition
  • The name and relative frequency of each proble molecule (N.B. only single gas molecules is currently supported)
• Temperature
  • The single temperature of your isotherm (in K)
• Pressures
  • The pressure values if your isotherm, as a comma-separated string (e.g. '1,2,5,1000')
• Charges
  • A boolean to turn off the Ewald summation, if you want to run a much faster simulation

Roadmap

• Integration with IBM's ST4SD framework and definition of a flowIR package
• Incorporation of Lennard-Jones potentials for educational systems
• Incorporation of template control files from tutorials and test cases from DL_MONTE repository
• Changing free_energy_sweep.py to use Converge objects instead of Measurement

Built With

• DL_MONTE 2.07
• dlmontepython
• ase

Find Us

• Gitlab

License

This project is licensed under the BSD 3-clause License - see the LICENSE.md file for details.