evenmn / pack-water

Pack water for molecular dynamics simulations. Relies on the packmol library.

Pack water

pack-water a package for water packing, which relies on the Packmol package. It is ment to be used as input to LAMMPS for molecular dynamics simulations. The inputs include number of molecules, length of box/density of water and whether or not the packed water should support periodic boundary conditions. However, the package supports cubic shapes only.

NB: This package will no longer be updated. Instead, the functionality is included in the molecular builder, which is a more general python package for preparing systems for molecular dynamics simulations.

Installation

First download the contents:

$ git clone https://github.com/evenmn/pack-water.git

and then install pack-water:

$ cd pack-water
$ pip install .

Prerequisites

• Packmol

Example usage

The package is very straightforward to use:

from pack_water import PackWater
from pack_water.geometry import SphereGeometry, BoxGeometry
    
packer = PackWater()
packer.append(BoxGeometry(0, 0, 0, 40, 40, 20, density=0.998,  side='in'))
packer.append(SphereGeometry(70, 20, 20, 20, number=2000,  side='in'))
packer(pbc=3.0, outfile="data.out")

This Python script gives the following output: