def ChargeMomentOfInertia(picklestruct):
SPA = psa.SpacegroupAnalyzer(picklestruct)
picklestruct = SPA.get_conventional_standard_structure()
Rcm = CenterofMass(picklestruct)
#fractional coords
I = 0
for site in picklestruct.sites:
elemCharge = site.specie.max_oxidation_state
coords = site._fcoords
dist = coords - Rcm
I += elemCharge * np.dot(dist, dist)
return I
def MassMomentOfInertia(picklestruct):
SPA = psa.SpacegroupAnalyzer(picklestruct)
picklestruct = SPA.get_conventional_standard_structure()
Rcm = CenterofMass(picklestruct)
#fractional coords
I = 0
for site in picklestruct.sites:
Mass = site.specie.data['Atomic mass']
coords = site._fcoords
dist = coords - Rcm
I += Mass * np.dot(dist, dist)
return I
def CenterofMass(picklestruct):
'''
centerofmass in terms of fractional coordinates
:param picklestruct:
:return:
'''
symmetryfinder = psa.SpacegroupAnalyzer(picklestruct)
numerator = np.array([0.0, 0.0, 0.0])
denominator = list()
for sites in picklestruct.sites:
mass = sites.specie.data['Atomic mass']
cellPosition = sites.frac_coords
#normalized
numerator += cellPosition * mass
denominator.append(mass)
return numerator / (np.mean(denominator))
def structure_symmetry():
if is_pbc():
struct = readstructure(crystal=True, molecule=False)
ast = analyzer.SpacegroupAnalyzer(struct)
print("{} : {}".format('Structure Type', 'periodicity'))
print("{} : {}".format('Lattice Type', ast.get_lattice_type()))
print("{} : {}".format('Space Group ID', ast.get_space_group_number()))
print("{} : {}".format('International Symbol',
ast.get_space_group_symbol()))
print("{} : {}".format('Hall Symbol', ast.get_hall()))
return
else:
struct = readstructure(crystal=False, molecule=True)
ast = analyzer.PointGroupAnalyzer(struct)
print("{} : {}".format('Structure Type', 'non-periodicity'))
print("{} : {}".format('International Symbol', ast.get_pointgroup()))
return
def ChargeMomentOfInertia(picklestruct):
'''
moment of inertia seems sort of extraneous
:param picklestruct:
:return:
'''
def CenterofMass(picklestruct): #function needs to be imbedded
'''
centerofmass in terms of fractional coordinates
:param picklestruct:
:return:
'''
numerator = np.array([0.0, 0.0, 0.0])
denominator = list()
for sites in picklestruct.sites:
mass = sites.specie.data['Atomic mass']
cellPosition = sites.frac_coords
# normalized
numerator += cellPosition * mass
denominator.append(mass)
return numerator / (np.mean(denominator))
SPA = psa.SpacegroupAnalyzer(picklestruct)
picklestruct = SPA.get_conventional_standard_structure()
Rcm = CenterofMass(picklestruct)
#fractional coords
I = 0
for site in picklestruct.sites:
elemCharge = site.specie.max_oxidation_state
coords = site._fcoords
dist = coords - Rcm
I += elemCharge * np.dot(dist, dist)
data = {
'charge moment of inertia': I
}
return data
def getSpacegroup(kind,inittraj): if kind == 'bulk': pmg = pmgase.AseAtomsAdaptor().get_structure(pickle.loads(inittraj)) return psa.SpacegroupAnalyzer(pmg).get_space_group_number() else: return None
def getCellSymmetryOps(picklestruct):
symmetry = psa.SpacegroupAnalyzer(picklestruct)
numSGOps = len(symmetry.get_symmetry_operations())
data = {'symmetry ops': numSGOps}
return data
def getCellSymmetryOps(picklestruct):
symmetry = psa.SpacegroupAnalyzer(picklestruct);
numSGOps = len(symmetry.get_symmetry_operations());
return numSGOps;
def getCrystalSystem(picklestruct):
symmetry = psa.SpacegroupAnalyzer(picklestruct);
numeric = cs.CrystalSysClassFeat(symmetry.get_crystal_system());
return numeric;
def Hall_Number(picklestruct): #return hall_number, which is just another way of listing a spacegroup number
symmetryDat = psa.SpacegroupAnalyzer(picklestruct);
return symmetryDat.get_symmetry_dataset()['hall_number'];
def rewrite_cif(path: str,
outdir: str,
remove_disorder: bool = True,
remove_duplicates: bool = True,
p1: bool = False,
clean_symmetry: float = None) -> str:
"""
Reads cif file and keeps only the relevant parts defined in RELEVANT_KEYS.
Sometimes, it is good to loose information ...
Args:
path (str): Path to input file
outdir (str): Path to output directory
remove_disorder (bool): If True (default), then disorder groups other than 1 and . are removed.
p1 (bool): If True, then we will set the symmetry to P1.
clean_symmetry (float): uses spglib to symmetrize the structure with the specified tolerance, set to None
if you do not want to use it
Returns:
outpath (str)
"""
# ToDo: I want to have it pretty strict with pre-defined keys but maybe a regex can take care of captitiliaztion
RELEVANT_KEYS = [
'_cell_volume',
'_cell_angle_gamma',
'_cell_angle_beta',
'_cell_angle_alpha',
'_cell_length_a',
'_cell_length_b',
'_cell_length_c',
'_atom_site_label',
'_atom_site_fract_x',
'_atom_site_fract_y',
'_atom_site_fract_z',
'_atom_site_charge',
'_atom_site_type_symbol',
]
RELEVANT_KEYS_NON_P1 = [
'_symmetry_cell_setting',
'_space_group_crystal_system',
'_space_group_name_hall',
'_space_group_crystal_system',
'_space_group_it_number',
'_symmetry_space_group_name_h-m',
'_symmetry_int_tables_number',
'_space_group_name_h-m_alt',
'_symmetry_tnt_tables_number',
'_symmetry_space_group_name_hall',
'_symmetry_equiv_pos_as_xyz',
'_space_group_symop_operation_xyz',
]
LOOP_KEYS = [
'_atom_site_label', '_atom_site_fract_x', '_atom_site_fract_y',
'_atom_site_fract_z', '_atom_site_charge', '_atom_site_occupancy'
]
NUMERIC_LOOP_KEYS = [
'_atom_site_fract_x', '_atom_site_fract_y', '_atom_site_fract_z',
'_atom_site_charge', '_atom_site_occupancy'
]
CELL_PROPERTIES = [
'_cell_volume',
'_cell_angle_gamma',
'_cell_angle_beta',
'_cell_angle_alpha',
'_cell_length_a',
'_cell_length_b',
'_cell_length_c',
]
try:
cf = CifFile.ReadCif(path)
image = cf[cf.keys()[0]]
if ('_atom_site_fract_x' not in image.keys()) or (
'_atom_site_fract_y' not in image.keys()) or (
'_atom_site_fract_z' not in image.keys()):
raise ValueError
except ValueError:
logger.error(
'the file %s seems to be invalid because we were unable to find '
'the atomic positions will return input path but '
'this file will likely cause errors and needs to be checked',
path)
return path
except FileNotFoundError:
logger.error('the file %s was not found', path)
return path
except Exception:
logger.error(
'the file %s seems to be invalid will return input path but '
'this file will likely cause errors and needs to be checked',
path)
return path
else:
# First, make sure we have proper atom type labels.
if ('_atom_site_type_symbol' not in image.keys()) and (
'_atom_site_symbol' not in image.keys()):
# then loop over the label and strip all the floats
type_symbols = []
for label in image['_atom_site_label']:
type_symbols.append(re.sub('[^a-zA-Z]+', '', label))
image.AddItem('_atom_site_type_symbol', type_symbols)
image.AddLoopName('_atom_site_label', '_atom_site_type_symbol')
if remove_disorder and '_atom_site_disorder_group' in image.keys():
indices_to_drop = []
logger.info('Removing disorder groups in %s', path)
for i, dg in enumerate(image['_atom_site_disorder_group']):
if dg not in ('.', '1'):
indices_to_drop.append(i)
if indices_to_drop:
image['_atom_site_type_symbol'] = [
i
for j, i in enumerate(image['_atom_site_type_symbol'])
if j not in indices_to_drop
]
for key in LOOP_KEYS:
if key in image.keys():
loop_fixed = [
i for j, i in enumerate(image[key])
if j not in indices_to_drop
]
image.RemoveItem(key)
image.AddItem(key, loop_fixed)
image.AddLoopName('_atom_site_type_symbol', key)
if not p1:
RELEVANT_KEYS += RELEVANT_KEYS_NON_P1
for key in image.keys():
if key not in RELEVANT_KEYS:
image.RemoveItem(key)
image['_atom_site_label'] = image['_atom_site_type_symbol']
if p1:
image.AddItem('_symmetry_space_group_name_H-M', 'P 1')
image.ChangeItemOrder('_symmetry_space_group_name_h-m', -1)
image.AddItem('_space_group_name_Hall', 'P 1')
image.ChangeItemOrder('_space_group_name_Hall', -1)
# remove uncertainty brackets
for key in NUMERIC_LOOP_KEYS:
if key in image.keys():
image[key] = [
float(re.sub(r'\([^)]*\)', '', s)) for s in image[key]
]
for prop in CELL_PROPERTIES:
if prop in image.keys():
image[prop] = float(re.sub(r'\([^)]*\)', '', image[prop]))
# make filename that is safe
name = slugify(Path(path).stem)
outpath = os.path.join(outdir, '.'.join([name, 'cif']))
with open(outpath, 'w') as f:
f.write(cf.WriteOut() + '\n')
if clean_symmetry:
crystal = Structure.from_file(outpath)
spa = analyzer.SpacegroupAnalyzer(crystal, 0.1)
crystal = spa.get_refined_structure()
crystal.to(filename=outpath)
if remove_duplicates:
atoms = read(outpath)
get_duplicate_atoms(atoms, 0.5, delete=True)
write(outpath, atoms)
return outpath
def elastic_analysis():
filename = 'OUTCAR'
step_count = 1
check_file(filename)
proc_str = "Reading Data From " + filename + " File ..."
procs(proc_str, step_count, sp='-->>')
outcar = Outcar(filename)
outcar.read_elastic_tensor()
cij_tensor = np.array(outcar.data['elastic_tensor'])
filename = 'vasprun.xml'
step_count += 1
check_file(filename)
proc_str = "Reading Data From " + filename + " File ..."
procs(proc_str, step_count, sp='-->>')
vsr = Vasprun(filename)
struct0 = vsr.structures[0]
natom = struct0.num_sites
weight = struct0.composition.weight
volume = struct0.lattice.volume
## converting the units
volume *= 1.0e-30 ## from Angstrom to meters
weight *= weight * 1.0e-3 ## from gram to kg
density = weight / (volume * Avogadro)
asa = analyzer.SpacegroupAnalyzer(struct0)
# lat_type=asa.get_crystal_system()
crys_type = asa.get_lattice_type()
## Redefining the Cij matrix into the correct Voigt notation since VASP's OUTCAR has a different order
## In VASP: Columns and rows are listed as: 1, 2, 3, 6, 4, 5
## In this format OUTCAR's C44 values would be actually C66, C55 would be C44, and C66 would be C55.
## OUTCAR follows the below order:
## [C11 C12 C13 C16 C14 C15]
## [C21 C22 C23 C26 C24 C25]
## [C31 C32 C33 C36 C34 C35]
## [C61 C62 C63 C66 C64 C65]
## [C41 C42 C43 C46 C44 C45]
## [C51 C52 C53 C56 C54 C55]
cnew = np.zeros((6, 6))
snew = np.zeros((6, 6))
cnew = np.copy(cij_tensor)
for j in range(0, 6):
cnew[3][j] = cij_tensor[4][j]
cnew[4][j] = cij_tensor[5][j]
cnew[5][j] = cij_tensor[3][j]
ctemp = np.zeros((6, 6))
ctemp = np.copy(cnew)
for i in range(0, 6):
cnew[i][3] = cnew[i][4]
cnew[i][4] = cnew[i][5]
cnew[i][5] = ctemp[i][3]
# Change the units of Cij from kBar to GPa
cnew = cnew / 10.0
proc_str = "\n Modified elastic tensor in correct order (in GPa units)"
print(proc_str)
fmt = "%7.3f " * 6
for i in range(6):
print(fmt % tuple(cnew[i, :]))
def check_symmetric(a, tol=1e-8):
return np.allclose(a, a.T, atol=tol)
print(
'\n Checking if the elastic tensor is symmetric: i.e. Cij = Cji: %5s'
% check_symmetric(cnew))
print("\n Eigen Values of the elastic tensor:")
evals = LA.eigvals(cnew)
print(fmt % tuple(evals))
if np.all(evals) > 0.0:
print("\n All eigen values are positive indicating elastic stability.")
else:
print(
"\n ATTENTION: One or more eigen values are negative indicating elastic instability."
)
calc_elastic_prop(cnew, snew, crys_type, density, weight, natom)