class Strain:
'''
strain
# ---------- args
sigma (float): standard deviation for strain
# ---------- instance methods
gen_child(self, struc)
'''
def __init__(self, atype, mindist, sigma=0.5, maxcnt_ea=100):
# ---------- check args
# ------ atype, nat, mindist
for x in [atype, mindist]:
if not isinstance(x, list):
raise TypeError('{} must be list'.format(x))
if not len(atype) == len(mindist):
raise ValueError('not len(atype) == len(mindist)')
# -- check symmetric
for i in range(len(mindist)):
for j in range(i):
if not mindist[i][j] == mindist[j][i]:
raise ValueError('mindist is not symmetric. '
'({}, {}): {}, ({}, {}): {}'.format(
i, j, mindist[i][j], j, i,
mindist[j][i]))
self.atype = atype
self.mindist = mindist
# ------ sigma
if isinstance(sigma, float):
if sigma <= 0:
raise ValueError('simga must be positive float')
else:
raise TypeError('sigma must be float')
self.sigma = sigma
# ------ maxcnt_ea
if isinstance(maxcnt_ea, int):
if maxcnt_ea <= 0:
raise ValueError('maxcnt_ea must be positive int')
else:
raise TypeError('maxcnt_ea must be int')
self.maxcnt_ea = maxcnt_ea
def gen_child(self, struc):
'''
generate child struture
# ---------- return
(if success) self.child:
(if fail) None:
'''
# ---------- init
cnt = 0
lat_mat = struc.lattice.matrix.T # lattice vector as matrix
# ---------- generate strained structure
while True:
# ------ strain matrix
strain_matrix = np.empty([3, 3])
for i in range(3):
for j in range(3):
if i <= j:
if i == j:
strain_matrix[i][j] = 1.0 + np.random.normal(
loc=0.0, scale=self.sigma)
else:
strain_matrix[i][j] = np.random.normal(
loc=0.0, scale=self.sigma) / 2.0
strain_matrix[j][i] = strain_matrix[i][j]
# ------ strained lattice
strained_lattice = np.dot(strain_matrix, lat_mat).T
# ------ child
self.child = Structure(strained_lattice, struc.species,
struc.frac_coords)
# ------ scale lattice
self.child.scale_lattice(struc.volume)
# ------ check distance
if check_distance(self.child, self.atype, self.mindist):
# -- success
self.child = sort_by_atype(self.child, self.atype)
return self.child
else:
# -- failure
cnt += 1
if cnt >= self.maxcnt_ea:
self.child = None
return None # change parent
