Transport Property Calculations

This repository is meant to enable calculations of transport properties from equilibrium dynamics simulations. Presently, the source code is mostly in Python.

Installation

We assume the existence of a reasonable build tool-chain. This means on an HPC you might need something like (on elja) ml load GCC.

With micromamba or conda

To install into a micromamba (or conda) environment, please follow the following steps. The Python dependencies are inside environment.yml. Create the environment using the following command, inside the top-level directory:

micromamba create -f environment.yml

In order to activate the environment, use:

micromamba activate trnsprtProp

where trnsprtProp is the name of the environment, specified in the environment.yml file. Henceforth, in order to activate the environment, just use the micromamba activate trnsprtProp command. If using conda, the equivalent commands are:

conda env create -f environment.yml
conda activate trnsprtProp

To deactivate the environment, just use micromamba deactivate.

Although this started out as a purely Python module (we started out using flit), we now use pybind11. Now we use invoke and meson.

In order to install the code, run the following:

inv build # flit build
inv build --install

Tests

To run tests (which are inside the tests directory), written with pytest, run the following command from the top-level directory:

pytest

In order to debug tests using pdb, you can write the command breakpoint() inside the Python files (in tests) wherever you want to set a breakpoint. Then, run pytest --pdb. This will stop the code at the line where you put the breakpoint() command.

To see more verbose output from pytest, including tests that pass, you can run pytest -rA.

Running the code

This program can be run from the command-line using the following:

transportProp

Help options can be accessed using:

transportProp --help 

Options for subcommands can be run, for instance:

transportProp msd --help

Validation

Using the VMD Diffusion Coefficient Tool, the MSD (mean-squared displacement) was calculated for a trajectory of mW water. In a Jupyter Notebook, the diffusion coefficient is calculated using linear regression. Please see the validation directory for more details.