def primitive(inp):
"""
Replicates a primitive unit cell in all directions
"""
logger.info("\tConstructing lattice from primitive unit cell...")
const = inp.bead_radius*2
cells_per_side = int((((2*inp.char_radius)//const)+1)//2*2+1)
cells_range = list(range(cells_per_side))
triplets = np.array(list(itertools.product(cells_range, repeat=3)))
xyz = triplets*const
xyz = center(xyz)
return xyz
def hcp(inp):
"""
Replicates a hexagonal closely packed unit cell in all directions
"""
logger.info("\tConstructing lattice from HCP unit cell...")
const = inp.bead_radius * 2
cells_per_side = int(((2 * inp.char_radius) // const) // 2 * 2) + 3
xyz = np.array([])
for i in range(cells_per_side):
for j in range(cells_per_side):
for k in range(cells_per_side):
xyz = np.append(xyz, [
2 * i + (j + k) % 2,
np.sqrt(3) * (j + k % 2 / 3), 2 * np.sqrt(6) / 3 * k
])
#The following loops fix the edges of the hcp cube
i = cells_per_side
for j in range(cells_per_side // 2 + 1):
for k in range(cells_per_side // 2 + 1):
xyz = np.append(
xyz, [i * 2, j * 2 * np.sqrt(3), k * 2 * 2 * np.sqrt(6) / 3])
for j in range(cells_per_side // 2):
for k in range(cells_per_side // 2):
xyz = np.append(xyz, [
i * 2, j * 2 * np.sqrt(3) + 4 * np.sqrt(3) / 3,
(2 * k + 1) * 2 * np.sqrt(6) / 3
])
j = cells_per_side
for i in range(cells_per_side):
for k in range(cells_per_side // 2 + 1):
xyz = np.append(
xyz, [i * 2, j * np.sqrt(3), k * 2 * 2 * np.sqrt(6) / 3])
k = cells_per_side
for i in range(cells_per_side):
for j in range(cells_per_side // 2):
xyz = np.append(
xyz, [i * 2, j * 2 * np.sqrt(3), k * 2 * np.sqrt(6) / 3])
xyz = np.append(
xyz,
[2 * i + 1, (2 * j + 1) * np.sqrt(3), k * 2 * np.sqrt(6) / 3])
xyz = xyz * const / 2
xyz = xyz.reshape((len(xyz) // 3, 3))
xyz = np.unique(xyz, axis=0)
xyz = center(xyz)
ndx_near = np.argmin(np.linalg.norm(xyz, axis=1))
xyz = xyz - xyz[ndx_near, :]
return xyz
def bcc(inp):
"""
Replicates a body-centered cubic unit cell in all directions
"""
logger.info("\tConstructing lattice from BCC unit cell...")
const = inp.bead_radius*4/np.sqrt(3)
cells_per_side = int((((2*inp.char_radius)//const)+1)//2*2+1)
cells_per_side = cells_per_side*2+1
cells_range = list(range(cells_per_side))
triplets = np.array(list(itertools.product(cells_range, repeat=3)))
xyz = []
for trip in triplets:
if np.all(trip%2==0):
xyz.append(trip)
elif np.all(trip[:2]%2==1) and trip[2]%2==1:
xyz.append(trip)
xyz = np.array(xyz)*const/2
xyz = center(xyz)
return xyz
def fcc(inp):
"""
Replicates a face-centered cubic unit cell in all directions
"""
logger.info("\tConstructing lattice from FCC unit cell...")
const = inp.bead_radius * np.sqrt(8)
cells_per_side = int((((2 * inp.char_radius) // const) + 1) // 2 * 2 + 1)
cells_per_side = cells_per_side * 2 + 1
cells_range = list(range(cells_per_side))
triplets = np.array(list(itertools.product(cells_range, repeat=3)))
xyz = []
for trip in triplets:
if trip[2] % 2 == 0:
if np.all(trip[:2] % 2 == 0) or np.all(trip[:2] % 2 != 0):
xyz.append(trip)
elif trip[0] % 2 != trip[1] % 2:
xyz.append(trip)
xyz = np.array(xyz) * const / 2
xyz = center(xyz)
#print_xyz(xyz, "fcc.xyz")
return xyz