def expand(self, ratio):
if self.celldm:
for i in range(3):
self.celldm[i] = self.celldm[i] * ratio
self.R = qtk.fractional2xyz(self.R_scale, self.celldm)
else:
self.R = self.R * ratio
def read_cif(self, name, **kwargs):
xyz = open(name, 'r')
content = xyz.readlines()
xyz.close()
l_list = filter(lambda x: '_cell_length_' in x, content)
a_list = filter(lambda x: '_cell_angle_' in x, content)
l = [float(filter(None, l_str.split(' '))[1]) for l_str in l_list]
a = [float(filter(None, a_str.split(' '))[1]) for a_str in a_list]
a = np.cos(np.array(a) * (np.pi / 180.))
fx, fy, fz = map(len, [
filter(lambda x: '_atom_site_fract_x' in x, content),
filter(lambda x: '_atom_site_fract_y' in x, content),
filter(lambda x: '_atom_site_fract_z' in x, content),
])
if (fx, fy, fz) != (1, 1, 1):
qtk.exit("Failed! Only fractional coordingates are implemented")
r_flag = filter(lambda x: '_atom_site_occupancy' in x, content)
r_ind = content.index(r_flag[0]) + 1
atoms = np.array(
[filter(None, r_str.split(' ')) for r_str in content[r_ind:]]
)
self.periodic = True
self.celldm = np.concatenate([l, a])
self.R_scale = atoms[:, 3:6].astype(float)
self.R = qtk.fractional2xyz(self.R_scale, self.celldm)
self.type_list = atoms[:, 0].tolist()
self.Z = np.array(map(qtk.n2Z, atoms[:, 0]))
self.N = len(self.Z)
self.string = ['' for _ in range(self.N)]
self.name = name
def expand(self, ratio):
if self.celldm:
for i in range(3):
self.celldm[i] = self.celldm[i] * ratio
self.R = qtk.fractional2xyz(self.R_scale, self.celldm)
else:
self.R = self.R * ratio
def read_xyz(self, name, **kwargs):
xyz = open(name, 'r')
content = xyz.readlines()
xyz.close()
content = [line.replace('\t', ' ') for line in content]
prop_list = ['charge', 'celldm', 'scale', 'symmetry']
for prop in prop_list:
try:
prop_str = filter(lambda x: prop in x, content)[0]
prop_str = re.sub('.*:', '', prop_str)
prop_data = prop_str.split(' ')
prop_data = filter(None, prop_data)
if len(prop_data) == 1:
try:
setattr(self, prop, float(prop_data[0]))
except Exception as exc:
if prop == 'symmetry':
setattr(self, prop, prop_data[0].strip())
elif len(prop_data) > 1:
setattr(self, prop, [float(_) for _ in prop_data])
except ValueError as exc:
setattr(self, prop, False)
qtk.warning("setting attribute %s with error: %s" % \
(prop, exc))
except:
setattr(self, prop, False)
if not self.charge:
self.charge = 0
if self.celldm or self.scale:
self.periodic = True
if self.celldm:
assert len(self.celldm) == 6
self.N = int(content[0])
coord_list = content[2 : self.N + 2]
coord = [filter(None,[a for a in entry.split(' ')])
for entry in coord_list]
type_list = list(np.array(coord)[:,0])
self.type_list = [str(elem) for elem in type_list]
self.Z = [qtk.n2Z(elem) for elem in self.type_list]
self.Z = np.array(self.Z)
self.R = np.array(coord)[:,1:4].astype(float)
self.box = False
if self.celldm:
self.periodic = True
angle = self.celldm[3:]
angle_sum = sum([abs(entry) for entry in angle])
if angle_sum == 0:
self.box = self.celldm[:3]
self.R_scale = copy.deepcopy(self.R)
self.R = qtk.fractional2xyz(self.R_scale, self.celldm)
def read_xyz(self, name, **kwargs):
xyz = open(name, 'r')
content = xyz.readlines()
xyz.close()
content = [line.replace('\t', ' ') for line in content]
prop_list = ['charge', 'celldm', 'scale', 'symmetry', 'isolated']
for prop in prop_list:
try:
prop_str = filter(lambda x: prop in x, content)[0]
prop_str = re.sub('.*:', '', prop_str)
prop_data = prop_str.split(' ')
prop_data = filter(None, prop_data)
if len(prop_data) == 1:
try:
setattr(self, prop, float(prop_data[0]))
except Exception as exc:
if prop == 'symmetry' or prop == 'isolated':
setattr(self, prop, prop_data[0].strip())
elif len(prop_data) > 1:
setattr(self, prop, [float(_) for _ in prop_data])
except ValueError as exc:
setattr(self, prop, False)
qtk.warning("setting attribute %s with error: %s" % \
(prop, exc))
except:
setattr(self, prop, False)
# convert celldm acoording to proper symmetry is still not working
# universally due to abinit and vasp k-point sampling
# require explicity reciprocal coordinate
#if hasattr(self, 'symmetry') and self.symmetry in ['bcc', 'fcc']:
# new_dm = copy.deepcopy(self.celldm)
# if np.linalg.norm(np.array(new_dm[3:])) < 1E-5:
# lattice_cube = np.array(new_dm[:3]) * np.eye(3)
# if self.symmetry == 'fcc':
# vec1 = (lattice_cube[1] + lattice_cube[2])/2
# vec2 = (lattice_cube[0] + lattice_cube[2])/2
# vec3 = (lattice_cube[0] + lattice_cube[1])/2
# elif self.symmetry == 'bcc':
# vec1 = (-lattice_cube[0] + lattice_cube[1] + lattice_cube[2])/2
# vec2 = ( lattice_cube[0] - lattice_cube[1] + lattice_cube[2])/2
# vec3 = ( lattice_cube[0] + lattice_cube[1] - lattice_cube[2])/2
# nv1 = vec1 / np.linalg.norm(vec1)
# nv2 = vec2 / np.linalg.norm(vec2)
# nv3 = vec3 / np.linalg.norm(vec3)
# new_dm = [
# np.linalg.norm(vec1),
# np.linalg.norm(vec2),
# np.linalg.norm(vec3),
# np.dot(nv2, nv3),
# np.dot(nv1, nv3),
# np.dot(nv1, nv2),
# ]
# qtk.warning(
# "symmetry is %s but celldm is set to cubic, reset from %s to %s"\
# % (self.symmetry, str(self.celldm), str(new_dm))
# )
# self.celldm = new_dm
if not self.charge:
self.charge = 0
if self.celldm or self.scale:
self.periodic = True
if self.celldm:
assert len(self.celldm) == 6
self.N = int(content[0])
prop_list = content[1]
try:
self.prop_list = np.array(prop_list.split(' ')).astype(float)
except:
self.prop_list = prop_list
coord_list = content[2 : self.N + 2]
coord = [filter(None,[a for a in entry.replace("\n", '').split(' ')])
for entry in coord_list]
type_list = list(np.array(coord)[:,0])
self.type_list = [str(elem) for elem in type_list]
self.Z = [qtk.n2Z(elem) for elem in self.type_list]
self.Z = np.array(self.Z)
self.R = np.array(coord)[:,1:4].astype(float)
self.box = False
if self.celldm:
self.periodic = True
angle = self.celldm[3:]
angle_sum = sum([abs(entry) for entry in angle])
if angle_sum == 0:
self.box = self.celldm[:3]
if not self.isolated:
self.R_scale = copy.deepcopy(self.R)
self.R = qtk.fractional2xyz(self.R_scale, self.celldm)
