solvis-tools 0.1.5

A module for analyzing and visualizing solvation shells in LAMMPS output files, but would work with most files that can be handled by ASE.

solvis

About

Various ways to analyze and visualize solvation shell structures, which wraps PyVista. Meant primarily for analyzing the outputs produced by LAMMPS, but anything that ASE can handle should work.

Installation

From PyPI

You can install solvis from PyPI like so:

pip install solvis-tools

From source

We use micromamba as the package manager, but feel free to use your own poison. Create and activate the environment.

micromamba create -f environment.yml
micromamba activate solvisenv

In order to install the code, run the following in the top-level directory:

pip install -e .

Examples

Each example is self-contained. Mostly, they show how to handle interactive plotting. To close the interactive window, press q.

Tests

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

pytest -v

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.

Note that test_hydrogen_bond.py and test_plot_octahedral_shell.py actually compare the results of images created for a single hydrogen bond and for an octahedral shell showing hydrogen bonds formed by the acceptor seventh molecule, respectively. The images compared against are present in the top-level image_cache_dir directory. The package pytest-pyvista is used for image verification.

To view a coverage report, run the following from the top-level directory:

pytest --cov=solvis tests/

Image Gallery