MRPyCM

A Python implementation of the Polarizable continuum model (PCM) in MRChem. This is implemented using VAMPYR. This is a work in progress.

Installation

Building from source

Important

python 3.11.4+ and pip 23.2.1+ required

You can install add the package to your python/pip/conda environment by cloning the repository and submodules

git clone [email protected]:Gabrielgerez/MRPyCM.git
git submodule update --remote --recursive --init

and then installing it with pip

cd MRPyCM
pip install .

Usage

The code can be used as an import library by:

import MRPycm as mpcm

or you can run the executable computeSolvent.py as:

python computeSolvent.py <dict_str>

where dict_str is a dictionary of input parameters as

{
    'order': int,                           # Polynomial order.
    'box': list of floats,                  # Simulation box size.
    'prec': float,                          # Apply and convergence precision.
    'cav_coords': list of list of floats,   # Coordinate of the center of each sphere.
    'radii': list of floats,                # Radii of each sphere.
    'sigma': float,                         # Width of the boundary of each sphere.
    'eps_out': float,                       # Value of the relative permittivity of the solvent at T=298.15K.
    'perm_type': str,                       # Formulation of the permittivity either "exponential" or "linear".
    'solver_type: str,                      # Which solver to use, avaliable are "standard" (GPESolver), "pb" (PBSolver) and "lpb" (LPBSolver).
    'I': float                              # Ionic strength in mol/L. Can also be interpreted as the electrolyte concentration.
    'max_iter': int,                        # Maximum number of iterations before exiting the solver.
    'kain_hist': int,                       # Number of iterations to keep in the history of the Kain solver.
}