def choose_structures( _howmany, _min = 2, _max = 9 ):
import random
import numpy as np
from pylada import crystal, enumeration
lattice, str_list = list_all_structures( _min, _max )
for i in xrange(_howmany):
nsupercell = random.randint(0, len(str_list)-1)
while len(str_list[nsupercell][3]) == 0:
nsupercell = random.randint(0, len(str_list)-1)
nstr = 0
if len(str_list[nsupercell][3]) > 1:
nstr = random.randint(0, len(str_list[nsupercell][3])-1)
supercell, flavorbase, smith = str_list[nsupercell][:3]
x = str_list[nsupercell][3].pop(nstr)
# creates structure
structure = crystal.sStructure()
structure.cell = np.dot(lattice.cell, supercell.hermite)
crystal.fill_structure(structure)
structure.scale = lattice.scale
enumeration.as_structure(structure, x, flavorbase)
yield crystal.Structure(structure)
def read_database(filename, withperms=True):
from numpy import array as np_array, dot as np_dot, zeros as np_zeros
from pylada import crystal, enumeration
lattice = crystal.Lattice()
with open(filename, "r") as file:
# reads lattice
for line in file:
data = line.split()
if len(data) == 0: continue
if data[0] == "cell:":
lattice.cell = np_array(data[1:], dtype="float64").reshape(3,3)
elif data[0] == "scale:":
lattice.scale = float(line.split()[1])
elif data[0] == "site:":
data = line.split()
data.pop(0)
site = crystal.Site()
for i in range(3): site.pos[i] = float(data.pop(0))
while len(data): site.type.append( data.pop(0) )
lattice.sites.append(site)
elif data[0] == "endlattice": break
lattice.set_as_crystal_lattice()
transforms = enumeration.create_transforms(lattice)
specialized = []
nsites = len([0 for i in lattice.sites if len(i.type) > 1])
hermite = None
flavorbase = None
transform = None
structure = crystal.Structure()
structure.scale = lattice.scale
for line in file:
data = line.split()
if len(data) == 0: continue
if data[0] == "n:": continue
if data[0] == "hermite:":
hermite = np_array(data[1:], dtype="float64").reshape(3,3)
specialized = []
elif data[0] == "transform:":
transform = np_array(data[1:], dtype="float64").reshape(3,3)
elif data[0] == "smith:":
smith = np_array( data[1:], dtype = "int64" )
translations = enumeration.Translation(smith, nsites)
cell = np_dot(lattice.cell, hermite)
structure = crystal.fill_structure(cell)
for transformation in transforms:
if not transformation.invariant(cell): continue
transformation.init(transform, smith)
if not transformation.is_trivial:
specialized.append( transformation )
elif data[0] == "flavorbase:":
card, nflavors = int(data[1]), int(data[2])
flavorbase = enumeration.create_flavorbase(card, nflavors)
label_exchange=enumeration.LabelExchange(card, nflavors)
elif len(data) > 0:
assert flavorbase is not None
assert hermite is not None
for x in data:
# adds label permutations that are not equivalent by affine transforms.
x = int(x)
others = set([x])
if withperms:
for labelperm in label_exchange:
u = labelperm(x, flavorbase)
if u in others: continue
dont = False
for transform in specialized:
t = transform(u, flavorbase)
if t in others:
dont = True
break
for translation in translations:
v = translation(t, flavorbase)
if v in others:
dont = True
break
if not dont: others.add(u)
for u in others:
enumeration.as_structure(structure, u, flavorbase)
yield structure