Polymer system initialization workflow that utilizes a random walk and dissipative particle dynamics as a soft push potential.
Build a software environment using the environment.yml file and the command conda env create -f environment.yml
1 - Run a dpd simulation and check the bond lengths and inter-particle distances. 2 - Run a dpd simulation with an energy stabilization cutoff. Write out simulation to trajectory file. 3 - Run a dpd simulation with option for angles and dihedrals. Write out to trajectory file. Start a Lennard-Jones WCA simulation with optional angles and dihedrals. 4 - Replace the random walk in the DPD workflow with mbuild self-avoiding random walk. 5 - Run DPD on a rigid body model used for anisotropic coarse-graining. Based on flowerMD classes.
First, clone the PhantomWalk repository:
git clone git@github.com:cmelab/PhantomWalk
cd PhantomWalkSet up & activate the conda environment shipped with PhantomWalk:
conda env create -f ./environment.yml
conda activate phantomwalkInstall PhantomWalk into the environment with pip:
python -m pip install -e .If PhantomWalk is being installed for development purposes, the dev environment should be used instead, which provides packages necessary for testing.
conda env create -f ./environment-dev.yml
conda activateBefore running tests, ensure you have activated the PhantomWalk dev environment.
PhantomWalk tests can be run by invoking pytest in the PhantomWalk repo:
pytestSee the pytest documentation
for more details on how pytest works and how to use it.