About

Molecular builder is a python package for creating input structures for molecular dynamics simulations.

It is focused on creating bulk structures and carving out geometries. Therefore, molecular-builder comes with a database of crystal structures and a collection og geometries that can be used to create various structures in various shapes.

A main goal of this package is to make the whole process of setting up an initial geometry for a molecular dynamics simulation programmable, and thus reliable.

For example, creating an \(\alpha\)-quartz block with a cylidrical hole in it can be done as follows:

from molecular_builder import create_bulk_crystal, carve_geometry, write
from molecular_builder.geometry import CylinderGeometry

atoms = create_bulk_crystal("alpha_quartz", [60, 60, 60])

geometry = CylinderGeometry([30,30,30], 20, 100, orientation=[1,0,0])

carve_geometry(atoms, geometry, side="in")

write(atoms, "alpha_quartz_cylinder_hole.data")
write(atoms, "alpha_quartz_cylinder_hole.png", camera_dir=[3, 1, -1])

This simple script produces a lammps data file and an image of the created system:

We can make a similar system with water packed in the newly created hole:

from molecular_builder import create_bulk_crystal, carve_geometry, write, pack_water
from molecular_builder.geometry import CylinderGeometry
import numpy as np

atoms = create_bulk_crystal("alpha_quartz", [60, 60, 60])

r = 25
l = atoms.cell[0][0]

geometry = CylinderGeometry([30,30,30], r, 100, orientation=[1,0,0])

water_volume = np.pi*r**2*l

carve_geometry(atoms, geometry, side="in")

pack_water(atoms, volume=water_volume, pbc=4.0, tolerance=1.5, density=0.8)

write(atoms, "alpha_quartz_cylinder_hole_water.data")
write(atoms, "alpha_quartz_cylinder_hole_water.png", camera_dir=[3, 1, -1])