from molecular_builder import create_bulk_crystal, carve_geometry, write from molecular_builder.geometry import BoxGeometry atoms = create_bulk_crystal("silicon_carbide_3c", [100, 100, 100]) geometry = BoxGeometry([50, 50, 50], [70, 70, 70]) carve_geometry(atoms, geometry, side="out") write(atoms, "box.data") write(atoms, "box.png", camera_dir=[3, 2, -1])
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")
from molecular_builder import create_bulk_crystal, write atoms = create_bulk_crystal("beta_cristobalite", size=[20, 20, 20]) write(atoms, "beta_cristobalite.data") write(atoms, "beta_cristobalite.png", viewport_type="orthogonal")
from molecular_builder import create_bulk_crystal, carve_geometry, write, pack_water from molecular_builder.geometry import BoxGeometry 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",
c = 5.51891759 # length of triclinic unit cell in c-dir (and z-dir) angle = 60 h = b * np.sin(np.deg2rad(angle)) # length of triclinic unit cell in y-dir numcellsx = -(-xlen // a) # number of cells in x-dir, rounded up numcellsy = -(-ylen // h) # number of cells in y-dir, rounded up numcellsz = -(-zlen // c) # number of cells in z-dir, rounded up lengthx = numcellsx * a # actual length in x-dir lengthy = numcellsy * h # actual length in y-dir lengthz = numcellsz * c # actual length in z-dir lengthnoise = np.asarray((lengthx, lengthy, lengthz)) scalenoise = lengthnoise / scale # Create bulk of alpha-quartz quartz = create_bulk_crystal("alpha_quartz", (xlen, ylen, zlen)) # Carve out geometry from alpha-quartz surface_geometry = ProceduralSurfaceGeometry(point=(xlen/2, ylen/2, zlen/2), normal=(0, 0, 1), thickness=noise_thickness, octaves=octaves, scale=scalenoise, pbc=lengthnoise, angle=angle, method='perlin', threshold=0) carve_geometry(quartz, surface_geometry, side="in") quartz.write("quartz.data", format="lammps-data")
from molecular_builder import create_bulk_crystal, carve_geometry from molecular_builder.geometry import PlaneGeometry atoms = create_bulk_crystal("alpha_quartz", [120, 120, 120]) geometry = PlaneGeometry([60, 60, 60], [1, 0, 0], periodic_boundary_condition=(True, True, True)) num_carved, carved = carve_geometry(atoms, geometry, side="in", return_carved=True) atoms.write("block_inside_plane.data", format="lammps-data") carved.write("block_outside_plane.data", format="lammps-data")
from molecular_builder import create_bulk_crystal, write atoms = create_bulk_crystal("alpha_quartz", size=[20, 20, 20]) write(atoms, "alpha_quartz.data") write(atoms, "alpha_quartz.png", viewport_type="orthogonal")
from molecular_builder import create_bulk_crystal, carve_geometry, write from molecular_builder.geometry import ProceduralSurfaceGeometry # Create bulk of beta-cristobalite atoms = create_bulk_crystal("beta_cristobalite", [200, 200, 50]) write(atoms, "block.png") # Carve out geometry from beta-cristobalite geometry = ProceduralSurfaceGeometry(point=(100, 100, 40), normal=(0, 0, 1), thickness=20, octaves=1, method='simplex', ) num_carved, carved = carve_geometry(atoms, geometry, side="out", return_carved=True) write(atoms, "block_with_procedural_surface.png")
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])
from molecular_builder import create_bulk_crystal, write atoms = create_bulk_crystal("alpha_quartz", [50, 100, 50]) write(atoms, "alpha_quartz_mb.data", bond_specs=[("Si", "O", 2.8)]) write(atoms, "alpha_quartz_mb.png", bond_specs=[("Si", "O", 2.8)])
"""Here, we demonstrate how the PlaneGeometry can be used to carve polygons of an arbitrary number of corners and a certain height, named polygonal cylinders. The slope of the unit circle at point (sin(θ), cos(θ)) is (cos(θ), sin(θ)). """ from molecular_builder import create_bulk_crystal, carve_geometry from molecular_builder.geometry import PlaneGeometry # Declare polygon parameters num_sides = 5 scaling = 30 center = (60, 60, 0) # Create bulk of beta-cristobalite atoms = create_bulk_crystal("beta_cristobalite", [120, 120, 120]) # Define the various planes (normal vector and point in plane) import numpy as np thetas = np.linspace(0, 2 * np.pi, num_sides + 1)[:-1] normals = [np.sin(thetas), np.cos(thetas), np.zeros(num_sides)] normals = np.asarray(normals).T points = scaling * normals + center # Carve out geometry from beta-cristobalite geometry = PlaneGeometry(points, normals) num_carved, carved = carve_geometry(atoms, geometry, side="in", return_carved=True)