""" In this example, we pack 10,000 water molecules in a sphere of
radius 50 Å and center (50, 50, 50).
"""
from molecular_builder import pack_water
from molecular_builder.geometry import SphereGeometry
water = pack_water(nummol=10000, geometry=SphereGeometry((50, 50, 50), 50))
water.write("water_sphere.data", format="lammps-data")
from molecular_builder import pack_water, write from molecular_builder.geometry import BoxGeometry geometry = BoxGeometry((50, 25, 25), (100, 50, 50)) atoms = pack_water(nummol=2000, geometry=geometry) write(atoms, "box.data") write(atoms, "box.png", camera_dir=[1, 2, -1])
import numpy as np
L = np.array([80, 60, 80])
atoms = create_bulk_crystal("brucite", L)
L = atoms.cell.lengths()
geometry = BoxGeometry(center=L / 2,
length=[L[0], L[1] / 2 - 3, 4 * L[2] / 5 + 2],
periodic_boundary_condition=(True, True, True))
carve_geometry(atoms, geometry, side="out")
volume = atoms.cell.volume
water_volume = volume - geometry.volume()
pack_water(atoms=atoms, volume=water_volume, pbc=2.0, tolerance=1.8)
write(atoms, "brucite_in_water.data", bond_specs=("O", "H", 1.02))
write(atoms,
"brucite_in_water_perspective.png",
bond_specs=("O", "H", 1.02),
camera_dir=[1, 0, 0],
viewport_type="perspective",
size=(480, 640))
write(atoms,
"brucite_in_water_orthogonal.png",
bond_specs=("O", "H", 1.02),
camera_dir=[1, 0, 0],
viewport_type="orthogonal",
size=(480, 640))
from molecular_builder import create_bulk_crystal, carve_geometry, fetch_prepared_system, write, pack_water
from molecular_builder.geometry import BoxGeometry
blob = fetch_prepared_system("ch_blob/10nm", type_mapping=[(1, 6), (2, 1)])
blob.positions[:, 2] += 37
slab = fetch_prepared_system(
"vashishta_1990_like_amorphous_silica/quench_950K",
type_mapping=[(1, 14), (2, 8)])
slab.cell[2, 2] += 105
sodium_chlorate = create_bulk_crystal("sodium_chlorate",
size=(slab.cell[0, 0], slab.cell[1,
1], 25),
round="down")
carve_geometry(sodium_chlorate,
BoxGeometry([slab.cell[0, 0] * 3 / 4, slab.cell[1, 1] / 2, 0],
[slab.cell[0, 0] / 2, slab.cell[1, 1] + 100, 5]),
side="in")
sodium_chlorate.translate((0, 0, 118))
atoms = (slab + blob) + sodium_chlorate
pack_water(atoms, 10000, pbc=2.0, tolerance=2.0)
write(atoms,
"sodium_chlorate_hydrocarbon_blob_water.png",
camera_dir=(0, 1, 0),
viewport_type="orthogonal",
bond_specs=[("O", "H", 0.95), ("Si", "O", 1.9)],
atom_radii=[("Si", 0.2), ("O", 0.6)])
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])
""" In this example, we pack 10,000 water molecules in a box with center
(50, 25, 25) and length (100Å, 50Å, 50Å).
"""
from molecular_builder import pack_water
from molecular_builder.geometry import BoxGeometry
water = pack_water(nummol=10000,
geometry=BoxGeometry((50, 25, 25), (100, 50, 50)))
water.write("water_box.data", format="lammps-data")
import numpy as np
from molecular_builder import fetch_prepared_system, carve_geometry, pack_water
from molecular_builder.geometry import SphereGeometry, CubeGeometry
# Amorphous silica of size (357, 143, 143)
amorph = fetch_prepared_system("amorphous_silica_1")
num_spheres = 5
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 + 5
geometry = SphereGeometry([x, y, z],
r,
periodic_boundary_condition=(True, True, True))
tmp_carved = carve_geometry(amorph, geometry, side="in")
print(f"tmp carved: {tmp_carved}")
water = pack_water(2000,
atoms=amorph) #, geometry=CubeGeometry([60,60,60], 130))
system = water + amorph
amorph.write("amorph.data", format="lammps-data")
water.write("water.data", format="lammps-data")
system.write("system.data", format="lammps-data")
""" In this example, we first fetch a block of amorphous silica of size (357Å, 143Å, 143Å). We then carve spheres of random sizes at random locations, and finally pack 10,000 water molecules into the voids.
"""
from molecular_builder import fetch_prepared_system, carve_geometry, pack_water
from molecular_builder.geometry import SphereGeometry
import numpy as np
# Amorphous silica of size (357, 143, 143)
amorph = 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 * 50
geometry = SphereGeometry((x, y, z),
r,
periodic_boundary_condition=(1, 1, 1))
tmp_carved = carve_geometry(amorph, geometry, side="in")
print(f"tmp carved: {tmp_carved}")
amorph.write("amorph.data", format="lammps-data")
# Pack water into voids
water = pack_water(nummol=10000, atoms=amorph)
system = water + amorph
water.write("water.data", format="lammps-data")
system.write("system.data", format="lammps-data")