def __getitem__(self, frames):
"""
Gets a subset of the trajectory if a slice is given, if an int is given, return a structure
Args:
frames (int, slice): int or slice of trajectory to return
Return:
(Trajectory, Structure) Subset of trajectory
"""
if isinstance(frames, int) and frames < self.frac_coords.shape[0]:
lattice = self.lattice if self.constant_lattice else self.lattice[frames]
site_properties = self.site_properties[frames] if self.site_properties else None
return Structure(Lattice(lattice), self.species, self.frac_coords[frames], site_properties=site_properties,
to_unit_cell=True)
if isinstance(frames, slice):
frames = np.arange(frames.start, frames.stop, frames.step)
elif not (isinstance(frames, list) or isinstance(frames, np.ndarray)):
try:
frames = np.asarray(frames)
except:
raise Exception('Given accessor is not of type int, slice, tuple, list, or array')
if (isinstance(frames, list) or isinstance(frames, np.ndarray)) and \
(np.asarray([frames]) < self.frac_coords.shape[0]).all():
if self.constant_lattice:
lattice = self.lattice
else:
lattice = self.lattice[frames, :]
return Trajectory(lattice, self.species, self.frac_coords[frames, :], self.time_step,
self.site_properties)
else:
warnings.warn('Some or all selected frames exceed trajectory length')
return
def delete_bt_layer(self, bt, tol=0.25, axis=2):
"""
Delete bottom or top layer of the structure.
Args:
bt (str): Specify whether it's a top or bottom layer delete. "b"
means bottom layer and "t" means top layer.
tol (float), Angstrom: Tolerance factor to determine whether two
atoms are at the same plane.
Default to 0.25
axis (int): The direction of top and bottom layers. 0: x, 1: y, 2: z
"""
if bt == "t":
l1, l2 = (-1, -2)
else:
l1, l2 = (0, 1)
l = self.lattice.abc[axis]
layers = self.sort_sites_in_layers(tol=tol, axis=axis)
l_dist = abs(layers[l1][0].coords[axis] - layers[l2][0].coords[axis])
l_vector = [1, 1]
l_vector.insert(axis, (l - l_dist) / l)
new_lat = Lattice(self.lattice.matrix * np.array(l_vector)[:, None])
layers.pop(l1)
sites = reduce(lambda x, y: np.concatenate((x, y), axis=0), layers)
new_sites = []
l_dist = 0 if bt == "t" else l_dist
l_vector = [0, 0]
l_vector.insert(axis, l_dist)
for i in sites:
new_sites.append(PeriodicSite(i.specie, i.coords - l_vector,
new_lat, coords_are_cartesian=True))
self._sites = new_sites
self._lattice = new_lat
def build_supercell_full_disorder(pstructure, scaling_matrix):
"""
get a supercell with all disordered sites inside, should be used to generate a certain config based on instruction
:param pstructure:
:param scaling_matrix:
:return:
"""
scale_matrix = np.array(scaling_matrix, np.int16)
if scale_matrix.shape != (3, 3):
scale_matrix = np.array(scale_matrix * np.eye(3), np.int16)
new_lattice = Lattice(np.dot(scale_matrix, pstructure._lattice.matrix))
f_lat = lattice_points_in_supercell(scale_matrix)
c_lat = new_lattice.get_cartesian_coords(f_lat)
new_sites = []
for site in pstructure.sites:
icell = 0
for v in c_lat:
site_properties = deepcopy(site.properties)
site_properties['icell'] = icell
s = PeriodicSite(site.species,
site.coords + v,
new_lattice,
properties=site_properties,
coords_are_cartesian=True,
to_unit_cell=False)
new_sites.append(s)
icell += 1
new_charge = pstructure._charge * np.linalg.det(
scale_matrix) if pstructure._charge else None
return Structure.from_sites(new_sites, charge=new_charge), len(c_lat)
def setUp(self):
self.si = Element("Si")
coords = list()
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
self.lattice = Lattice([[3.8401979337, 0.00, 0.00],
[1.9200989668, 3.3257101909, 0.00],
[0.00, -2.2171384943, 3.1355090603]])
self.struct = Structure(self.lattice, [self.si, self.si], coords)
def setUp(self):
l = Lattice([[3.52,0.0,2.033], [1.174,3.32,2.033], \
[0.0,0.0,4.066]])
s_bulk = Structure(l, ['Ga', 'As'], \
[[0.0000, 0.0000, 0.0000], \
[0.2500, 0.2500, 0.2500]])
defect_site = PeriodicSite('As', [0.25, 0.25, 0.25], l)
defect = Vacancy(s_bulk, defect_site, charge=1.)
defect_entry = DefectEntry(defect, 0.)
entries = [defect_entry]
vbm = 0.2
band_gap = 1.
dpd = DefectPhaseDiagram(entries, vbm, band_gap)
self.dp = DefectPlotter(dpd)
def __getitem__(self, frames):
"""
Gets a subset of the trajectory if a slice is given, if an int is given, return a structure
Args:
frames (int, slice): int or slice of trajectory to return
Return:
(Trajectory, Structure) Subset of trajectory
"""
# If trajectory is in displacement mode, return the displacements at that frame
if self.coords_are_displacement:
if isinstance(frames, int):
if frames >= np.shape(self.frac_coords)[0]:
raise ValueError(
"Selected frame exceeds trajectory length")
# For integer input, return the displacements at that timestep
return self.frac_coords[frames]
if isinstance(frames, slice):
# For slice input, return a list of the displacements
start, stop, step = frames.indices(len(self))
return [self.frac_coords[i] for i in range(start, stop, step)]
if isinstance(frames, (list, np.ndarray)):
# For list input, return a list of the displacements
pruned_frames = [
i for i in frames if i < len(self)
] # Get rid of frames that exceed trajectory length
if len(pruned_frames) < len(frames):
warnings.warn(
"Some or all selected frames exceed trajectory length")
return [self.frac_coords[i] for i in pruned_frames]
raise Exception(
"Given accessor is not of type int, slice, list, or array")
# If trajectory is in positions mode, return a structure for the given frame or trajectory for the given frames
if isinstance(frames, int):
if frames >= np.shape(self.frac_coords)[0]:
raise ValueError("Selected frame exceeds trajectory length")
# For integer input, return the structure at that timestep
lattice = self.lattice if self.constant_lattice else self.lattice[
frames]
site_properties = (self.site_properties[frames]
if self.site_properties else None)
site_properties = (self.site_properties[frames]
if self.site_properties else None)
return Structure(
Lattice(lattice),
self.species,
self.frac_coords[frames],
site_properties=site_properties,
to_unit_cell=True,
)
if isinstance(frames, slice):
# For slice input, return a trajectory of the sliced time
start, stop, step = frames.indices(len(self))
pruned_frames = range(start, stop, step)
lattice = (self.lattice if self.constant_lattice else
[self.lattice[i] for i in pruned_frames])
frac_coords = [self.frac_coords[i] for i in pruned_frames]
if self.site_properties is not None:
site_properties = [
self.site_properties[i] for i in pruned_frames
]
else:
site_properties = None
if self.frame_properties is not None:
frame_properties = {}
for key, item in self.frame_properties.items():
frame_properties[key] = [item[i] for i in pruned_frames]
else:
frame_properties = None
return Trajectory(
lattice,
self.species,
frac_coords,
time_step=self.time_step,
site_properties=site_properties,
frame_properties=frame_properties,
constant_lattice=self.constant_lattice,
coords_are_displacement=False,
base_positions=self.base_positions,
)
if isinstance(frames, (list, np.ndarray)):
# For list input, return a trajectory of the specified times
pruned_frames = [
i for i in frames if i < len(self)
] # Get rid of frames that exceed trajectory length
if len(pruned_frames) < len(frames):
warnings.warn(
"Some or all selected frames exceed trajectory length")
lattice = (self.lattice if self.constant_lattice else
[self.lattice[i] for i in pruned_frames])
frac_coords = [self.frac_coords[i] for i in pruned_frames]
if self.site_properties is not None:
site_properties = [
self.site_properties[i] for i in pruned_frames
]
else:
site_properties = None
if self.frame_properties is not None:
frame_properties = {}
for key, item in self.frame_properties.items():
frame_properties[key] = [item[i] for i in pruned_frames]
else:
frame_properties = None
return Trajectory(
lattice,
self.species,
frac_coords,
time_step=self.time_step,
site_properties=site_properties,
frame_properties=frame_properties,
constant_lattice=self.constant_lattice,
coords_are_displacement=False,
base_positions=self.base_positions,
)
raise Exception(
"Given accessor is not of type int, slice, tuple, list, or array")
crystal = Structure.from_file(
filename=each_original_vasp) # vasp file read -> structure 정보 접근
for i in range(
num_noised_files): # original vasp file로부터 noised vasp 파일을 횟수만큼 생성
# -------------------------- lattice 구조에 noise 부여하기 -----------------------------------------
lattice_shell = np.zeros(
shape=crystal.lattice.matrix.shape) # 새로운 lattice matrix shell 생성
noised_lattice = gaussian_noise_level * np.random.normal(
0, 1, 9).reshape((3, 3)) # 기존 lattice matrix에 넣을 noise 생성
new_lattice_matrix = crystal.lattice.matrix + noised_lattice # 기존 lattice matrix에 noise 추가
noised_lattice = Lattice(new_lattice_matrix) # noise 추가된 새로운 lattice
noised_crystal = Structure(
noised_lattice, crystal.species,
crystal.frac_coords) # unitcell에 noise 추가된 결정구조
# -----------------------------------------------------------------------------------------------
# --------------------------- 결정구조 안의 각 원자에 대해 좌표 noise 부여 -------------------------
for j in range(
len(noised_crystal)): # For each atom in the crystal structure
noised_coord = list(gaussian_noise_level * np.random.normal(
0, 1, 3).reshape(-1)) # internal coordinate noise
noised_crystal[j] = noised_crystal[j].specie.name, noised_crystal[
j].frac_coords + noised_coord # 각 원자 좌표에 noise 추가
# -----------------------------------------------------------------------------------------------
# vasp file saved