from ase.io import read
from molecular_builder import carve_geometry, write
from molecular_builder.geometry import ProceduralSurfaceGeometry
atoms = read("block.data", format="lammps-data", style="molecular")
# Define function to add
def f(x, y):
if x < 100:
return x / 100
else:
return 1 - (x - 100) / 100
# Carve out geometry from beta-cristobalite
geometry = ProceduralSurfaceGeometry(point=(100, 100, 40),
normal=(0, 0, 1),
thickness=20,
method='simplex',
scale=3,
octaves=2,
seed=16591,
threshold=0,
repeat=True,
f=f)
num_carved = carve_geometry(atoms, geometry, side="out")
write(atoms, "add_function.data")
write(atoms, "add_function.png", camera_dir=[0, 1, -1])
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 ase.io import read
from molecular_builder import carve_geometry, write
from molecular_builder.geometry import ProceduralSurfaceGeometry
atoms = read("block.data", format="lammps-data", style="molecular")
# Carve out geometry from beta-cristobalite
geometry = ProceduralSurfaceGeometry(point=(100, 100, 40),
normal=(0, 0, 1),
thickness=20,
seed=97455)
num_carved = carve_geometry(atoms, geometry, side="out")
write(atoms, "basic.data")
write(atoms, "basic.png", camera_dir=[2, 1, -1])
from ase.io import read
from molecular_builder import carve_geometry, write
from molecular_builder.geometry import ProceduralSurfaceGeometry
atoms = read("block.data", format="lammps-data", style="molecular")
# Carve out geometry from beta-cristobalite
geometry = ProceduralSurfaceGeometry(point=(100, 100, 40),
normal=(0, 0, 1),
thickness=20,
method='simplex',
scale=3,
octaves=2,
seed=16591)
num_carved = carve_geometry(atoms, geometry, side="out")
write(atoms, "parameters.data")
write(atoms, "parameters.png", camera_dir=[2, 1, -1])
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")