This repository contains a collection of examples for the MoSDeF Cassandra Monte Carlo package. With the exception of the final slit pore example, all of the examples can be performed on a modern desktop or laptop in a reasonable period of time (< $\sim$1 hour).
- MoSDeF Cassandra: Docs, GitHub
- Cassandra: Docs, GitHub
- MoSDeF tools
- TRUE simulations
- Installing Docker
- Installing Miniconda
There are two options for installing the packages required to run the simulations in this repository: (1) via conda, or (2) via docker. If you are working in an HPC environment, you may need to use singularity rather than docker. Installation instructions for miniconda and docker can be found in the "helpful links" section above.
Make sure you have conda installed. Then, clone the repository to your machine:
git clone https://github.com/rsdefever/mc_examples.git
Create a new conda environment (mc-ex) and install the required packages:
conda create --name mc-ex --file mc_examples/requirements.txt
Finally, install the mc_examples via pip:
cd mc_examples/
pip install .
This final step is only strictly necessary if you plan on running the slit pore example.
Make sure you have docker installed. Get the docker image from dockerhub with the following:
docker pull rsdefever/mc_examples:latest
You may run the examples directly within the repository or in another location on your machine. If the mc_examples is installed at PATH_TO_MC_EXAMPLES, and you want to run the NpT example under PATH_TO_WORKSPACE/npt, you would do the following
conda activate mc-ex
cd PATH_TO_WORKSPACE
mkdir npt
cd npt/
python PATH_TO_MC_EXAMPLES/mc_examples/simple_examples/npt_methane/npt.py
python PATH_TO_MC_EXAMPLES/mc_examples/simple_examples/npt_methane/analyze.py
To run the GEMC example:
conda activate mc-ex
cd PATH_TO_WORKSPACE
mkdir gemc
cd gemc/
python PATH_TO_MC_EXAMPLES/mc_examples/simple_examples/gemc_ethane/gemc.py
python PATH_TO_MC_EXAMPLES/mc_examples/simple_examples/gemc_ethane/analyze.py
First, change to the directory on your local machine where you want to store the simulation output. This is notated below as PATH_TO_WORKSPACE. Then, we call the appropriate script from within the docker container.
To run the NpT example:
cd PATH_TO_WORKSPACE/
mdkir npt
cd npt/
docker run -t --mount type=bind,source=$(pwd),target=/workspace rsdefever/mc_examples:latest "python /software/mc_examples/mc_examples/simple_examples/npt_methane/npt.py"
docker run -t --mount type=bind,source=$(pwd),target=/workspace rsdefever/mc_examples:latest "python /software/mc_examples/mc_examples/simple_examples/npt_methane/analyze.py"
To run the NpT example:
cd PATH_TO_WORKSPACE/
mdkir gemc
cd gemc/
docker run -t --mount type=bind,source=$(pwd),target=/workspace rsdefever/mc_examples:latest "python /software/mc_examples/mc_examples/simple_examples/gemc_ethane/npt.py"
docker run -t --mount type=bind,source=$(pwd),target=/workspace rsdefever/mc_examples:latest "python /software/mc_examples/mc_examples/simple_examples/gemc_ethane/analyze.py"
Once again, we assume mc_examples is installed at PATH_TO_MC_EXAMPLES, and you want to run the examples under PATH_TO_WORKSPACE/.
conda activate mc-ex
cd PATH_TO_WORKSPACE
mkdir zeolite
cd zeolite
cp -r PATH_TO_MC_EXAMPLES/mc_examples/realistic_workflows/zeolite_adsorption/resources .
python PATH_TO_MC_EXAMPLES/mc_examples/realistic_workflows/zeolite_adsorption/run_fluid.py
python PATH_TO_MC_EXAMPLES/mc_examples/realistic_workflows/zeolite_adsorption/analyze_fluid.py
python PATH_TO_MC_EXAMPLES/mc_examples/realistic_workflows/zeolite_adsorption/run_adsorption.py
python PATH_TO_MC_EXAMPLES/mc_examples/realistic_workflows/zeolite_adsorption/analyze_adsorption.py
The output from the analysis scripts will be located in a directory named plots/.
cd PATH_TO_WORKSPACE/
mdkir zeolite
cd zeolite/
docker run -t --mount type=bind,source=$(pwd),target=/workspace rsdefever/mc_examples:latest "python /software/mc_examples/mc_examples/realistic_workflows/zeolite_adsorption/run_fluid.py"
docker run -t --mount type=bind,source=$(pwd),target=/workspace rsdefever/mc_examples:latest "python /software/mc_examples/mc_examples/realistic_workflows/zeolite_adsorption/analyze_fluid.py"
docker run -t --mount type=bind,source=$(pwd),target=/workspace rsdefever/mc_examples:latest "python /software/mc_examples/mc_examples/realistic_workflows/zeolite_adsorption/run_adsorption.py"
docker run -t --mount type=bind,source=$(pwd),target=/workspace rsdefever/mc_examples:latest "python /software/mc_examples/mc_examples/realistic_workflows/zeolite_adsorption/analyze_adsorption.py"