Molecular Dynamics With Constraints (mdwc3) - Python 3 version

This is the Python 3 version of the original mdwc code

The molecular dynamics with constraints (mdwc3) package is a command line open source Python program for molecular dynamics simulations. It does constraint molecular dynamics with either NPT (keeping pressure constant with the Parrinello Rahman lagrangian, and keeping the temperature constant with the Nose thermostat) or NVT (keeping the temperature constant with the Nose thermostat). mdwc3 performs constraint dynamics following the SHAKE algorithm and allows constraints for bond distances, angles, atomic positions, lattice parameters (a, b, c), angles between lattice vectors, and volume of the unit cell.

Mdwc has the mdwc3 script to interface the mdwc code with an external first principles code for the calculations of energies and forces, so far, the only supported DFT code is Abinit. You can use the mdwc functions to carry on constrained molecular dynamics with other first principals codes (for more details look at the jupyter notebook section)

mdwc requirements

For its correct functioning mlmd needs the following codes:

1. Python = 3.7

2. Numpy >= 1.17.2

• Abinit to use the mdwc3 script

mdwc user manual

This is for the Python 2 version, but it is applicable to the Python 3 version as well.

mdwc

installation

First, download or clone the repository.

git clone https://github.com/romerogroup/mdwc3.git

Then run the setup.

python setup.py install

Or simply install it with pip.

pip install mdwc3

Running mdwc3

mdwc3 -name c_8 -mpirun True -np 32 -NVT False    

Contributors

• Prof. Aldo H. Romero [West Virginia University]

• Arturo Hernandez [West Virginia University] (Developer)

• Uthpala Herath [West Virginia University] (Simulation and testing)

• Pedram Tavazohi [West Virginia University] (Simulation and testing)