from molecular_builder import create_bulk_crystal, carve_geometry, fetch_prepared_system
from molecular_builder.geometry import BerkovichGeometry, CylinderGeometry
slab = fetch_prepared_system("vashishta_1990_like_amorphous_silica/quench_950K")
slab.cell[2,2] = 80 # Expand cell in z direction to fit indenter
indenter = create_bulk_crystal("diamond", (144, 144, 80), round="down")
carve_geometry(indenter, BerkovichGeometry((75, 75, 40)), side="out")
carve_geometry(indenter, CylinderGeometry((75, 75, 50), 60, 200, orientation=(0,0,1)), side="out")
atoms = slab+indenter
atoms.write("indenter_and_glass.data", format="lammps-data")
import numpy as np
from molecular_builder import fetch_prepared_system, carve_geometry
from molecular_builder.geometry import SphereGeometry
from pack_water import PackWater
from pack_water.geometry import BoxGeometry, Fixed
import ase
# Fetch amorphous silica
silica = fetch_prepared_system("amorphous_silica_1")
num_spheres = 20
for sphere in range(num_spheres):
i, j, k, l = np.random.uniform(size=4)
x, y, z, r = i * 357, j * 143, k * 143, l * 30
geometry = SphereGeometry([x, y, z],
r,
periodic_boundary_condition=(True, True, True))
tmp_carved = carve_geometry(silica, geometry, side="in")
print(f"tmp carved: {tmp_carved}")
# Write amorphous silica with voids to pdb-filetype
silica.write("amorphous_void.pdb", format="proteindatabank")
# Fill voids with water
packer = PackWater(filetype="pdb")
packer.append(Fixed("amorphous_void.pdb", 0, 0, 0, number=1))
packer.append(BoxGeometry(0, 0, 0, 358, 143.2, 143.2, density=0.998))
packer(outfile="water.data")
from molecular_builder import create_bulk_crystal, carve_geometry, fetch_prepared_system, write
from molecular_builder.geometry import BerkovichGeometry, CylinderGeometry
slab = fetch_prepared_system(
"vashishta_1990_like_amorphous_silica/quench_950K",
type_mapping=[(1, 14), (2, 8)])
print(slab.numbers)
slab.cell[2, 2] = 80 # Expand cell in z direction to fit indenter
indenter = create_bulk_crystal("diamond", (144, 144, 80), round="down")
carve_geometry(indenter, BerkovichGeometry((75, 75, 40)), side="out")
carve_geometry(indenter,
CylinderGeometry((75, 75, 50), 60, 200, orientation=(0, 0, 1)),
side="out")
atoms = slab + indenter
write(atoms,
"indenter_over_silica.png",
bond_specs=[("Si", "O", 1.9)],
camera_dir=(2, 1.5, -0.4),
atom_radii=[("Si", 0.2), ("O", 0.2)],
size=(1280, 960))
from molecular_builder import fetch_prepared_system, write
atoms = fetch_prepared_system(
"vashishta_1990_like_amorphous_silica_quench_300K",
type_mapping=[[1, 14], [2, 8]])
write(atoms, "amorphous_silica.png")