def sym_ana(fname):
# tol=float(sys.argv[2])
atoms = read_vasp(fname)
dataset0 = sp.get_symmetry_dataset(atoms, symprec=1e-5)
tempsg = dataset0
print '1e-5 precision', tempsg['international']
print '1e-5 precision', tempsg['origin_shift']
for i in range(800):
tol = 0.001 * i + 0.001
dataset = sp.get_symmetry_dataset(atoms, symprec=tol)
# sym=sp.get_spacegroup(atoms,symprec=tol)
# print sym
if tempsg['international'] != dataset['international']:
print 'group\t supergroup'
print tempsg['hall'], ';', dataset['hall']
print tempsg['international'], '\t', dataset['international']
print tempsg['number'], '\t', dataset['number']
print 'origin', tempsg['origin_shift'], '\t', dataset[
'origin_shift']
print 'wyckoff', tempsg['wyckoffs']
print 'new_wyckoff', dataset['wyckoffs']
print 'equivalent atoms old', tempsg['equivalent_atoms']
print 'equivalent atoms new', dataset['equivalent_atoms']
print 'tolerance', tol
print '--------------------------------------------------------------------------------------\n'
tempsg = dataset
if i == 800 - 1 and dataset0['international'] == dataset[
'international']:
print 'cannot find superSG, but initial sym is', dataset0[
'international'], dataset0['number']
def get_periodic_symmetry_group(atoms, error_tolerance=0.01, debug=False):
from pyspglib import spglib
print atoms
dataset = spglib.get_symmetry_dataset(atoms, symprec=error_tolerance)
print dataset['equivalent_atoms']
print dataset['international']
print dataset['hall']
print dataset['wyckoffs']
print dataset['transformation_matrix']
print "Number of symmetry operations %i" % len(dataset['rotations'])
return dataset['international']
def get_kspace_operations(ao,
methods=['atoms_info', 'spglib'],
symprec_spglib=1e-5):
# returns k-space operations for the atoms object ao
kops = None
for method in methods:
if method == 'atoms_info':
# get operations from ao.info
if ('spacegroup' in ao.info) and (ao.info['spacegroup'] != None):
if ('unit_cell' in ao.info):
if (ao.info['unit_cell'] == 'conventional'):
primitive_cell = False
else:
primitive_cell = True
else:
primitive_cell = True
print 'get_kspace_operations(): Warning, assuming primitive cell'
rot = ao.info['spacegroup'].rotations
p2c_dir = ao.info['spacegroup'].scaled_primitive_cell
p2c_rec = ao.info['spacegroup'].reciprocal_cell
kops = []
for iop in range(len(rot)):
if primitive_cell:
mat = dot(p2c_rec.T, dot(rot[iop], p2c_dir))
else:
mat = rot[iop]
newop = True
for i in range(len(kops)):
if cmp_mat(kops[i], mat):
newop = False
break
if newop:
kops.append(mat)
return kops
else:
print 'get_kspace_operations(): atoms object has no space group information'
if method == 'spglib':
if has_spglib:
rot = spglib.get_symmetry_dataset(
ao, symprec=symprec_spglib)['rotations']
kops = []
for iop in range(len(rot)):
mat = rot[iop]
newop = True
for i in range(len(kops)):
if cmp_mat(kops[i], mat):
newop = False
break
if newop:
kops.append(mat)
return kops
else:
print 'get_kspace_operations(): spglib not found'
def get_kspace_operations(ao, methods=['atoms_info','spglib'], symprec_spglib=1e-5):
# returns k-space operations for the atoms object ao
kops=None
for method in methods:
if method=='atoms_info':
# get operations from ao.info
if ('spacegroup' in ao.info) and (ao.info['spacegroup'] is not None):
if ('unit_cell' in ao.info):
if (ao.info['unit_cell']=='conventional'):
primitive_cell=False
else:
primitive_cell=True
else:
primitive_cell=True
print 'get_kspace_operations(): Warning, assuming primitive cell'
rot=ao.info['spacegroup'].rotations
p2c_dir=ao.info['spacegroup'].scaled_primitive_cell
p2c_rec=ao.info['spacegroup'].reciprocal_cell
kops=[]
for iop in range(len(rot)):
if primitive_cell:
mat=dot(p2c_rec.T, dot(rot[iop],p2c_dir))
else:
mat=rot[iop]
newop=True
for i in range(len(kops)):
if cmp_mat(kops[i],mat):
newop=False
break
if newop:
kops.append(mat)
return kops
else:
print 'get_kspace_operations(): atoms object has no space group information'
if method=='spglib':
if has_spglib:
rot=spglib.get_symmetry_dataset(ao, symprec=symprec_spglib)['rotations']
kops=[]
for iop in range(len(rot)):
mat=rot[iop]
newop=True
for i in range(len(kops)):
if cmp_mat(kops[i],mat):
newop=False
break
if newop:
kops.append(mat)
return kops
else:
print 'get_kspace_operations(): spglib not found'
for i in range(symmetry['rotations'].shape[0]):
print " --------------- %4d ---------------" % (i + 1)
rot = symmetry['rotations'][i]
trans = symmetry['translations'][i]
print " rotation:"
for x in rot:
print " [%2d %2d %2d]" % (x[0], x[1], x[2])
print " translation:"
print " (%8.5f %8.5f %8.5f)" % (trans[0], trans[1], trans[2])
print ""
print "[get_pointgroup]"
print " Pointgroup of Rutile is", spglib.get_pointgroup(
symmetry['rotations'])[0]
print ""
dataset = spglib.get_symmetry_dataset(rutile)
print "[get_symmetry_dataset] ['international']"
print " Spacegroup of Rutile is ", dataset['international']
print ""
print "[get_symmetry_dataset] ['wyckoffs']"
alphabet = "abcdefghijklmnopqrstuvwxyz"
print " Wyckoff letters of Rutile are: ", dataset['wyckoffs']
print ""
print "[get_symmetry_dataset] ['equivalent_atoms']"
print " Mapping to equivalent atoms of Rutile are: "
for i, x in enumerate(dataset['equivalent_atoms']):
print " %d -> %d" % (i + 1, x + 1)
print ""
print "[get_symmetry_dataset] ['rotations'], ['translations']"
print " Symmetry operations of Rutile unitcell are:"
for i, (rot,
symmetry = spglib.get_symmetry( rutile )
for i in range(symmetry['rotations'].shape[0]):
print " --------------- %4d ---------------" % (i+1)
rot = symmetry['rotations'][i]
trans = symmetry['translations'][i]
print " rotation:"
for x in rot:
print " [%2d %2d %2d]" % (x[0], x[1], x[2])
print " translation:"
print " (%8.5f %8.5f %8.5f)" % (trans[0], trans[1], trans[2])
print ""
print "[get_pointgroup]"
print " Pointgroup of Rutile is", spglib.get_pointgroup(symmetry['rotations'])[0]
print ""
dataset = spglib.get_symmetry_dataset( rutile )
print "[get_symmetry_dataset] ['international']"
print " Spacegroup of Rutile is ", dataset['international']
print ""
print "[get_symmetry_dataset] ['wyckoffs']"
alphabet = "abcdefghijklmnopqrstuvwxyz"
print " Wyckoff letters of Rutile are: ", dataset['wyckoffs']
print ""
print "[get_symmetry_dataset] ['equivalent_atoms']"
print " Mapping to equivalent atoms of Rutile are: "
for i, x in enumerate( dataset['equivalent_atoms'] ):
print " %d -> %d" % ( i+1, x+1 )
print ""
print "[get_symmetry_dataset] ['rotations'], ['translations']"
print " Symmetry operations of Rutile unitcell are:"
for i, (rot,trans) in enumerate( zip( dataset['rotations'], dataset['translations'] ) ):
parser.set_defaults(mesh=None, qpoints=None)
parser.add_option("-m", "--mesh", dest="mesh", type="string", help="Mesh numbers")
parser.add_option("-q", "--qpoints", dest="qpoints", type="string", help="Stabilizers")
(options, args) = parser.parse_args()
if options.mesh == None:
mesh = [4, 4, 4]
else:
mesh = [int(x) for x in options.mesh.split()]
if options.qpoints == None:
qpoints = np.array([[0, 0, 0]], dtype=float)
else:
qpoints = np.array([float(x) for x in options.qpoints.split()]).reshape(-1, 3)
cell = read_vasp(args[0])
mapping_g, grid_point = spglib.get_ir_reciprocal_mesh(mesh, cell)
print mapping_g
dataset = spglib.get_symmetry_dataset(cell)
mapping, grid_point = spglib.get_stabilized_reciprocal_mesh(mesh, dataset["rotations"], qpoints=qpoints)
print mapping
print "%d / %d" % (np.sum((mapping_g == mapping) * 1), len(mapping))
# for i, m in enumerate(mapping):
# print i, grid_point[m]
def get_periodic_symmetry_operations(atoms, error_tolerance=0.01, debug=False):
from ase.utils import irotate
from ase.visualize import view
from pyspglib import spglib
#symmetry = spglib.get_symmetry(atoms, symprec=1e-5)
symmetry = spglib.get_symmetry(atoms, symprec=1e-2)
dataset = spglib.get_symmetry_dataset(atoms, symprec=1e-2)
result = []
if debug:
cell, scaled_positions, numbers = spglib.find_primitive(atoms,
symprec=1e-5)
a = Atoms(symbols='O4',
cell=cell,
scaled_positions=scaled_positions,
pbc=True)
#symmetry = spglib.get_symmetry(a, symprec=1e-2)
#dataset = spglib.get_symmetry_dataset(a, symprec=1e-2)
print dataset['equivalent_atoms']
print dataset['international']
print dataset['hall']
print dataset['wyckoffs']
print dataset['transformation_matrix']
print "Number of symmetry operations %i" % len(dataset['rotations'])
for i in range(dataset['rotations'].shape[0]):
new_atoms = atoms.copy()
test = atoms.copy()
rot = dataset['rotations'][i]
trans = dataset['translations'][i]
if debug:
x, y, z = irotate(rot)
#print x, y, z
print "------------------- %i -----------------------" % i
print "Rotation"
print rot
print "Translation"
print trans
new_pos = new_atoms.get_scaled_positions()
for l, pos in enumerate(new_atoms.get_scaled_positions()):
#print new_pos[l]
new_pos[l] = (numpy.dot(rot, pos))
new_pos[l] += trans
#print new_pos[l]
new_atoms.set_scaled_positions(new_pos)
equals = get_equals_periodic(atoms,
new_atoms,
error_tolerance=error_tolerance,
debug=debug)
if equals != None:
so = SymmetryOperation(str(i),
equals,
None,
vector=None,
magnitude=1,
rotation_matrix=rot,
translation_vector=trans)
#if debug:
# print so
result.append(so)
else:
print "Equivalent not found"
#view(test)
#view(new_atoms)
#raw_input()
return result
def main(argv=None):
print '========================================================='
print '|| CASTEP 2 BoltzTraP Interface ||'
print '|| version 1.0 ||'
print '|| 14 April 2016 ||'
print '||-----------------------------------------------------||'
if argv is None:
argv = sys.argv
if len(argv) < 2:
# Avoid ugly errors
print '|| Usage: castep2boltz <seedname> <optional arguments> ||'
print '|| optional arguments: "so" (for SOC runs) ... ||'
print '|| and "down" (for spin down calculations) ||'
print '||-----------------------------------------------------||'
print '|| UNSUCCESSFUL! READ Usage above ||'
print '...'
sys.exit()
# Define <seedname>
prefix = argv[1]
# Help menu, it shows the message and stops the process
help = ['h', '-h', '--h', 'help', '-help', '--help']
for i in help:
if i in argv:
print '|| Usage: castep2boltz <seedname> <optional arguments> ||'
print '|| optional arguments: "so" (for SOC runs) ... ||'
print '|| and "down" (for spin down calculations) ||'
print '========================================================='
sys.exit()
# Check if an argument for SOC is given
# so_on is defined here because it is used multiple times
if 'so' in argv or '-so' in argv:
so_on = 'so'
else:
so_on = None
# Set a proper suffix for the .energy file
if so_on == 'so':
energy_file = prefix + '.energyso'
else:
energy_file = prefix + '.energy'
# Names of output files
def_file = 'BoltzTraP.def'
intrans_file = prefix + '.intrans'
struct_file = prefix + '.struct'
#========================================================================================#
# Begin initial extraction of data from
# <seedname>.castep and <seedname>.bands
#========================================================================================#
# Open the .castep file and read it
castep_file = prefix + '.castep'
castep_file = open(castep_file, 'r')
castep_data = castep_file.readlines()
castep_file.close()
# Check if there are any symmetry operations.
for index, line in enumerate(castep_data):
if 'Number of symmetry operations' in line:
n_symm_ops = int(float(line.split()[5]))
symmetry = True
elif 'There are no symmetry operations specified' in line:
symmetry = False
# Open the .bands file and read it
bands_file = prefix + '.bands'
bands_file = open(bands_file, 'r')
bands_data = bands_file.readlines()
bands_file.close()
# Here we will store some of the data
kpoints_frac_coordinates = []
eigenenergies = [] # spin 1 (up)
eigenenergies_spin2 = [] # spin 2 (down)
unit_cell = [] # Crystal lattice
# Extract number of kpoints, spin components,
# electrons, eigenvalues from the <seedname>.bands file
# Extract values for Fermi energy, kpoints frac coordinates.
for line in bands_data:
if 'Number of k-points' in line:
n_kpoints = float(line.split()[3])
elif 'Number of spin components' in line:
spin_components = float(line.split()[4])
elif 'Number of electrons' in line:
if spin_components == 1:
n_electrons = float(line.split()[3])
n_electrons_down = None
elif spin_components == 2:
n_electrons = float(line.split()[3])
n_electrons_down = float(line.split()[4])
# Can you have different number of eigenvalues for
# spin up and down channels? If yes, this part
# should be rewritten. n_eigenvalues is used when
# the .energy file is cooked and might give
# wrong results if n_eigenvalues != n_eigenvalues_down
elif 'Number of eigenvalues' in line:
n_eigenvalues = float(line.split()[3])
# This is present when there is 1 spin component
elif 'Fermi energy' in line:
# castep output is in Hartree, this converts
# Fermi energy into Rydberg; Ry=2*Hartree
efermi = float(line.split()[5]) * 2
# Set Fermi energy for spin down electrons to None
# This might be used later for a quick check
efermi_down = None
# This is present when there are 2 spin components
elif 'Fermi energies' in line:
efermi_up = float(line.split()[5]) * 2
efermi_down = float(line.split()[6]) * 2
efermi = efermi_up
elif 'K-point' in line:
kpoints_frac_coordinates.append([
float(line.split()[2]),
float(line.split()[3]),
float(line.split()[4])
])
# Get eigenenergies and unit cell from .bands file
for index, line in enumerate(bands_data):
if 'Spin component 1' in line:
eigenenergy_starting_line = index + 1
for i in range(int(n_eigenvalues)):
eigenenergies.append('{:3.10f}'.format(
float(bands_data[eigenenergy_starting_line].split()[0]) *
2))
eigenenergy_starting_line += 1
elif 'Spin component 2' in line:
eigenenergy_starting_line2 = index + 1
for i in range(int(n_eigenvalues)):
eigenenergies_spin2.append('{:3.10f}'.format(
float(bands_data[eigenenergy_starting_line2].split()[0]) *
2))
eigenenergy_starting_line2 += 1
elif 'Unit cell vectors' in line:
start = index + 1
for j in range(3):
unit_cell.append([
'{:3.10f}'.format(float(bands_data[start].split()[0])),
'{:3.10f}'.format(float(bands_data[start].split()[1])),
'{:3.10f}'.format(float(bands_data[start].split()[2]))
])
start += 1
#========================================================================================#
#========================================================================================#
#========================================================================================#
# SPGLIB SECTION #
#----------------------------------------------------------------------------------------#
# spglib will generate symmetry operations even if CASTEP doesn't use symmetry_generate #
#----------------------------------------------------------------------------------------#
# If symmetry_generate IS used in CASTEP, spglib SYMMETRY OPERATIONS #
# will be added to the .struct file. #
# #
# If symmetry_generate is NOT used, then the IDENTITY MATRIX #
# will be added to the .struct file. #
#----------------------------------------------------------------------------------------#
# At the end of the section there is an if clause which checks if the number of CASTEP #
# symmetry operations is the same as the number of the ones generated by spglib. #
# If they are different, a warning will pop up. #
#========================================================================================#
positions = []
a_symbols = []
unit_cell_from_castep = []
# Find the total number of ions
for line in castep_data:
if 'Total number of ions' in line:
num_ions = int(line.split()[7])
# Get unit cell from <seedname>.castep.
for index, line in enumerate(castep_data):
# Crystal lattice in (A) units. <seedname>.bands file also contains
# this information. However, it uses Bohr units and this creates
# some problems when symmetry operations are generated with spglib.
if 'Real Lattice(A)' in line:
start = index + 1
for j in range(3):
unit_cell_from_castep.append([
float(castep_data[start].split()[0]),
float(castep_data[start].split()[1]),
float(castep_data[start].split()[2])
])
start += 1
break # avoid double counting
# Get atomic positions and symbols from .castep
# Use the total number of ions and append the position of every atom to positions = []
for index, line in enumerate(castep_data):
if 'Cell Contents' in line:
for i in range(0, num_ions):
positions.append([
float(castep_data[index + 10 + i].split()[3]),
float(castep_data[index + 10 + i].split()[4]),
float(castep_data[index + 10 + i].split()[5])
])
a_symbols.append(str(castep_data[index + 10 + i].split()[1]))
break # avoid double counting
# if multiple castep runs are present in one .castep file
# For debugging
# print 'positions',positions, 'atoms_symbols',a_symbols,'total num of ions', num_ions
# print 'Unit cell', unit_cell
# print 'unit_cell_from_castep' ,unit_cell_from_castep
# Create an argument needed by spglib to generate symmetries
all_atoms = Atoms(symbols=a_symbols,
cell=unit_cell_from_castep,
scaled_positions=positions,
pbc=True)
# Taken from the VASP interface, it checks if two symm ops are identical.
# If they are, then don't add them to the list of operations.
def cmp_mat(mat1, mat2):
absdiff = abs(mat1 - mat2)
value = sum(sum(absdiff))
if value > 1.0e-10:
return False
else:
return True
############################################################################################
# Debugging part
# dataset = spglib.get_symmetry_dataset( all_atoms )
# for i, (rot,trans) in enumerate( zip( dataset['rotations'], dataset['translations'] ) ):
# print " --------------- %4d ---------------" % (i+1)
# print " rotation:"
# for x in rot:
# print " [%2d %2d %2d]" % (x[0], x[1], x[2])
# print " translation:"
# print " (%8.5f %8.5f %8.5f)" % (trans[0], trans[1], trans[2])
#############################################################################################
# Time for spglib
# Check if spglib is present.
if has_spglib and symmetry:
# Use spglib and get rotational operations
print '|| spglib found. ||'
rotations = spglib.get_symmetry_dataset(all_atoms,
symprec=1e-5)['rotations']
symm_ops_spglib = []
# Append every value from rotations to symm_ops_spglib ...
for i in range(len(rotations)):
new_rot = rotations[i]
newop = True
# ... but first use the VASP function to see
# if the symmetry operation is unique ...
# [I don't think this is needed but it doesn't hurt to have it]
for k in range(len(symm_ops_spglib)):
if cmp_mat(symm_ops_spglib[k], new_rot):
# If the operation is not unique don't add it
newop = False
break
# ... eventually when a new operation is found
# append it symm_ops_spglib
if newop:
symm_ops_spglib.append(new_rot)
if len(symm_ops_spglib) < 10:
print '||', len(
symm_ops_spglib
), 'symmetry operations generated by spglib. ||'
elif len(symm_ops_spglib) >= 10:
print '||', len(
symm_ops_spglib
), 'symmetry operations generated by spglib. ||'
# Check if the number of symmetry operations generated by spglib
# is the same as the number of symmetry operations in CASTEP
if len(symm_ops_spglib) != n_symm_ops:
print '|| ||'
print '|| WARNING: ||'
if n_symm_ops < 10:
print '||', n_symm_ops, 'symmetry operations found in %s.castep. ||' % prefix
elif n_symm_ops >= 10:
print '||', n_symm_ops, 'symmetry operations found in %s.castep. ||' % prefix
print '||', len(
symm_ops_spglib
), 'symmetry operations generated by spglib. ||'
print '|| CASTEP tolerance might be too loose. ||'
print '|| Proceed with CAUTION. ||'
# If spglib is not found pop a warning
else:
if symmetry:
print '|| ||'
print '|| WARNING: ||'
print '|| Symmetry operations ARE present... ||'
print '|| ...but spglib was NOT found. ||'
print '|| Proceed with CAUTION. ||'
print '|| TRY installing spglib: sudo pip install pyspglib ||'
if not symmetry:
print '|| ||'
print '|| MESSAGE: ||'
print '|| Symmetry operations NOT used in CASTEP calculation. ||'
print '|| Continue NORMALLY. ||'
#========================================================================================#
#========================================================================================#
#========================================================================================#
#
# Create the <seedname>.energy file
#
#========================================================================================#
#---------------------------------- Spin 1/ Spin up PART --------------------------------#
# First line is a comment, in this case it is the name of the structure
f_energy = prefix + '\n'
# Number of k-points
f_energy += str(int(n_kpoints)) + '\n'
# K-point coordinates and number of eigenvalues
for ik in range(int(n_kpoints)):
for j in range(3):
f_energy += str(kpoints_frac_coordinates[ik][j]) + ' '
f_energy += str(int(n_eigenvalues)) + '\n'
start_pos_for_next_k_point = ik * int(n_eigenvalues)
# Eigenvalues for a given k-point
# if you want to exclude bands change range to
# range(int(n_excluded:n_eigenvalues)) and
# add this as offset to start_pos ------> this would only exclude the bottom bands
for ib in range(int(n_eigenvalues)):
f_energy += str(eigenenergies[start_pos_for_next_k_point]) + '\n'
start_pos_for_next_k_point += 1
#------------------------------- Spin 2/ Spin down PART ---------------------------------#
# Similar to Spin 1 PART
if spin_components == 2:
f_energy_down = prefix + ' down ' + '\n'
f_energy_down += str(int(n_kpoints)) + '\n'
for ik in range(int(n_kpoints)):
for j in range(3):
f_energy_down += str(kpoints_frac_coordinates[ik][j]) + ' '
f_energy_down += str(int(n_eigenvalues)) + '\n'
start_pos_for_next_k_point = ik * int(n_eigenvalues)
# if you want to exclude bands change range to
# range(int(n_excluded:n_eigenvalues)) and
# add this as offset to start_pos ------> this would only exclude the bottom bands
for ib in range(int(n_eigenvalues)):
f_energy_down += str(
eigenenergies_spin2[start_pos_for_next_k_point]) + '\n'
start_pos_for_next_k_point += 1
else:
pass
f = open(energy_file, 'w')
# Choose whether spin up or spin down energies
# will be written to the .energy file
if 'down' in argv or '-down' in argv:
# Check if there are spin down eigenvalues...
if spin_components == 2:
f.write(f_energy_down)
f.close()
print '|| ||'
print '|| Spin down energy file cooked and ready to go. ||'
# ...if not, use normal values.
else:
print '|| ||'
print '|| Spin polarisation not present, no spin down values. ||'
print '|| Default settings used instead. ||'
f.write(f_energy)
f.close()
else:
f.write(f_energy)
f.close()
# IMPORTANT: If a kpoint is repeated BoltzTraP will give an error,
# CASTEP BS calculations might have such point defined in the path
# and it needs to be removed.
#========================================================================================#
#========================================================================================#
#========================================================================================#
#
# Create the BoltzTraP.def file
#
#========================================================================================#
f_def = '5, \'' + prefix + '.intrans\', \'old\', \'formatted\',0\n'
f_def += '6,\'' + prefix + '.outputtrans\', \'unknown\', \'formatted\',0\n'
f_def += '20,\'' + prefix + '.struct\', \'old\', \'formatted\',0\n'
if so_on == 'so':
f_def += '10,\'' + prefix + '.energyso\', \'old\', \'formatted\',0\n'
else:
f_def += '10,\'' + prefix + '.energy\', \'old\', \'formatted\',0\n'
f_def += '48,\'' + prefix + '.engre\', \'unknown\', \'unformatted\',0\n'
f_def += '49,\'' + prefix + '.transdos\', \'unknown\', \'formatted\',0\n'
f_def += '50,\'' + prefix + '.sigxx\', \'unknown\', \'formatted\',0\n'
f_def += '51,\'' + prefix + '.sigxxx\', \'unknown\', \'formatted\',0\n'
f_def += '21,\'' + prefix + '.trace\', \'unknown\', \'formatted\',0\n'
f_def += '22,\'' + prefix + '.condtens\', \'unknown\', \'formatted\',0\n'
f_def += '24,\'' + prefix + '.halltens\', \'unknown\', \'formatted\',0\n'
f_def += '30,\'' + prefix + '_BZ.dx\', \'unknown\', \'formatted\',0\n'
f_def += '31,\'' + prefix + '_fermi.dx\', \'unknown\', \'formatted\',0\n'
f_def += '32,\'' + prefix + '_sigxx.dx\', \'unknown\', \'formatted\',0\n'
f_def += '33,\'' + prefix + '_sigyy.dx\', \'unknown\', \'formatted\',0\n'
f_def += '34,\'' + prefix + '_sigzz.dx\', \'unknown\', \'formatted\',0\n'
f_def += '35,\'' + prefix + '_band.dat\', \'unknown\', \'formatted\',0\n'
f_def += '36,\'' + prefix + '_band.gpl\', \'unknown\', \'formatted\',0\n'
f_def += '37,\'' + prefix + '_deriv.dat\', \'unknown\', \'formatted\',0\n'
f_def += '38,\'' + prefix + '_mass.dat\', \'unknown\', \'formatted\',0\n'
f = open(def_file, 'w')
f.write(f_def)
f.close()
#========================================================================================#
#========================================================================================#
#========================================================================================#
#
# Create the <seedname>.intrans file
#
#========================================================================================#
deltae = 0.0005
ecut = 0.4
lpfac = 5
efcut = 0.15
tmax = 800.0
deltat = 50.0
ecut2 = -1.0
# efermi is only for spin up at the moment, add an if statement if spin down is present
f_intrans = 'GENE # Format of DOS\n'
f_intrans += '0 0 0 0.0 # iskip (not presently used) idebug setgap shiftgap\n'
if 'down' in argv or '-down' in argv:
if spin_components == 2:
f_intrans += str(efermi_down) + ' ' + str(deltae) + ' ' + str(
ecut
) + ' ' + str(
n_electrons_down
) + ' # Fermilevel (Ry), energygrid, energy span around Fermilevel, number of electrons\n'
else:
# This could be regarded as an error or a typo.
# This part is also present in the .energy file section and should pop a warning if triggered.
f_intrans += str(efermi) + ' ' + str(deltae) + ' ' + str(
ecut
) + ' ' + str(
n_electrons
) + ' # Fermilevel (Ry), energygrid, energy span around Fermilevel, number of electrons\n'
else:
f_intrans += str(efermi) + ' ' + str(deltae) + ' ' + str(
ecut
) + ' ' + str(
n_electrons
) + ' # Fermilevel (Ry), energygrid, energy span around Fermilevel, number of electrons\n'
f_intrans += 'CALC # CALC (calculate expansion coeff), NOCALC read from file\n'
f_intrans += str(
lpfac
) + ' # lpfac, number of latt-points per k-point\n'
f_intrans += 'BOLTZ # run mode (only BOLTZ is supported)\n'
f_intrans += str(
efcut
) + ' # (efcut) energy range of chemical potential\n'
f_intrans += str(tmax) + ' ' + str(
deltat) + ' # Tmax, temperature grid\n'
f_intrans += str(
ecut2
) + ' # energyrange of bands given individual DOS output sig_xxx and dos_xxx (xxx is band number)\n'
f_intrans += 'HISTO #Scheme to obtain DOS. HISTO/TETRA: histogram/thetrahedron sampling\n'
f = open(intrans_file, 'w')
f.write(f_intrans)
f.close()
#========================================================================================#
#========================================================================================#
#========================================================================================#
#
# Create the <seedname>.struct file
#
#========================================================================================#
# First line is a comment, name of the structure in this case.
f_struct = prefix + '\n'
# Crystal lattice from <seedname>.bands file
for i in range(3):
for j in range(3):
f_struct += str(unit_cell[i][j]) + ' '
f_struct += '\n'
# Check if symmetry operations and spglib are present
if symmetry is True and has_spglib:
f_struct += str(len(symm_ops_spglib)) + '\n'
for i in range(int(len(symm_ops_spglib))):
for j in range(3):
for k in range(3):
f_struct += str(symm_ops_spglib[i][j][k]) + ' '
f_struct += '\n'
# If there are no symmetry operations, append an identity matrix
# to the .struct file. BoltzTraP doesn't run otherwise.
elif symmetry is False or not has_spglib:
f_struct += '1' + '\n'
f_struct += '1 0 0 0 1 0 0 0 1'
f = open(struct_file, 'w')
f.write(f_struct)
f.close()
#========================================================================================#
#========================================================================================#
if so_on == 'so':
print '|| ||'
print '|| SOC .energyso file cooked and ready to go. ||'
print '|| ||'
print '|| Done. ||'
print '========================================================='
def main(argv = None):
print '========================================================='
print '|| CASTEP 2 BoltzTraP Interface ||'
print '|| version 1.2 ||'
print '|| 30 Jan 2018 ||'
print '||-----------------------------------------------------||'
if not ase_atoms:
print '|| ase library not found. ||'
print '|| TRY installing ase: sudo pip install --upgrade ase ||'
print '|| UNSUCCESSFUL! ||'
print '...'
sys.exit()
if argv is None:
argv = sys.argv
if len(argv) < 2:
# Avoid ugly errors
print '|| Usage: castep2boltz.py <seedname> <opt. arguments> ||'
print '|| optional arguments: "so" (for SOC runs) ... ||'
print '|| and "up/dn" (for spin polarised calc.) ||'
print '||-----------------------------------------------------||'
print '|| Needed input:<seedname>.bands and <seedname>.castep ||'
print '|| UNSUCCESSFUL! READ Usage above ||'
print '...'
sys.exit()
# Define <seedname>
prefix = argv[1]
# Help menu, it shows the message and stops the process
help = ['h', '-h','--h', 'help', '-help', '--help']
for i in help:
if i in argv:
print '|| Usage: castep2boltz.py <seedname> <opt. arguments> ||'
print '|| optional arguments: "so" (for SOC runs) ... ||'
print '|| and "up/dn" (for spin polarised calc.) ||'
print '|| Needed input:<seedname>.bands and <seedname>.castep ||'
print '========================================================='
sys.exit()
# Check if an argument for SOC is given
# so_on is defined here because it is used multiple times
if 'so' in argv or '-so' in argv:
so_on = True
else :
so_on = False
# Check if an argument for spin down calculations is given
if 'down' in argv or '-down' in argv or 'dn' in argv or '-dn' in argv:
spin_dn = True
else :
spin_dn = False
# Check if an argument for spin down calculations is given
if 'up' in argv or '-up' in argv:
spin_up = True
else :
spin_up = False
# Set a proper suffix for the .energy file
if so_on:
energy_file = prefix + '.energyso'
elif spin_up:
energy_file = prefix + '.energyup'
elif spin_dn:
energy_file = prefix + '.energydn'
else:
energy_file = prefix + '.energy'
# Names of output files
def_file = 'BoltzTraP.def'
intrans_file = prefix + '.intrans'
struct_file = prefix + '.struct'
#========================================================================================#
# Begin initial extraction of data from
# <seedname>.castep and <seedname>.bands
#========================================================================================#
# Open the .castep file and read it
castep_file = prefix + '.castep'
castep_file = open(castep_file, 'r')
castep_data = castep_file.readlines()
castep_file.close()
# Check if there are any symmetry operations.
for index, line in enumerate(castep_data):
if 'Number of symmetry operations' in line:
n_symm_ops = int(float(line.split()[5]))
if n_symm_ops != 1:
symmetry = True
else:
symmetry = False
elif 'There are no symmetry operations specified' in line:
symmetry = False
# Open the .bands file and read it
bands_file = prefix + '.bands'
bands_file = open(bands_file, 'r')
bands_data = bands_file.readlines()
bands_file.close()
# Here we will store some of the data
kpoints_frac_coordinates = []
eigenenergies = [] # spin 1 (up)
eigenenergies_spin2 = [] # spin 2 (down)
unit_cell = [] # Crystal lattice
# Extract number of kpoints, spin components,
# electrons, eigenvalues from the <seedname>.bands file
# Extract values for Fermi energy, kpoints frac coordinates.
for line in bands_data:
if 'Number of k-points' in line:
n_kpoints = float(line.split()[3])
elif 'Number of spin components' in line:
spin_components = float(line.split()[4])
elif 'Number of electrons' in line:
if spin_components == 1:
n_electrons = float(line.split()[3])
n_electrons_down = None
elif spin_components == 2:
n_electrons_up = float(line.split()[3])
n_electrons_down = float(line.split()[4])
n_electrons = n_electrons_up + n_electrons_down
# Can you have different number of eigenvalues for
# spin up and down channels? If yes, this part
# should be rewritten. n_eigenvalues is used when
# the .energy file is cooked and might give
# wrong results if n_eigenvalues != n_eigenvalues_down
elif 'Number of eigenvalues' in line:
n_eigenvalues = float(line.split()[3])
# This is present when there is 1 spin component
elif 'Fermi energy' in line:
# castep output is in Hartree, this converts
# Fermi energy into Rydberg; Ry=2*Hartree
efermi = float(line.split()[5])*2
# Set Fermi energy for spin down electrons to None
# This might be used later for a quick check
efermi_down = None
# This is present when there are 2 spin components
elif 'Fermi energies' in line:
efermi_up = float(line.split()[5])*2
efermi_down = float(line.split()[6])*2
efermi=efermi_up
elif 'K-point' in line:
kpoints_frac_coordinates.append([float(line.split()[2]),
float(line.split()[3]),
float(line.split()[4])])
# Get eigenenergies and unit cell from .bands file
for index, line in enumerate(bands_data):
if 'Spin component 1' in line:
eigenenergy_starting_line = index + 1
for i in range(int(n_eigenvalues)):
eigenenergies.append('{0:3.10f}'.format(
float(bands_data[eigenenergy_starting_line].split()[0])*2))
eigenenergy_starting_line += 1
elif 'Spin component 2' in line:
eigenenergy_starting_line2 = index + 1
for i in range(int(n_eigenvalues)):
eigenenergies_spin2.append('{0:3.10f}'.format(
float(bands_data[eigenenergy_starting_line2].split()[0])*2))
eigenenergy_starting_line2 += 1
elif 'Unit cell vectors' in line:
start = index + 1
for j in range (3):
unit_cell.append(['{0:3.10f}'.format(float(bands_data[start].split()[0])),
'{0:3.10f}'.format(float(bands_data[start].split()[1])),
'{0:3.10f}'.format(float(bands_data[start].split()[2]))])
start += 1
#========================================================================================#
#========================================================================================#
#========================================================================================#
# SPGLIB SECTION #
#----------------------------------------------------------------------------------------#
# spglib will generate symmetry operations even if CASTEP doesn't use symmetry_generate #
#----------------------------------------------------------------------------------------#
# If symmetry_generate IS used in CASTEP, spglib SYMMETRY OPERATIONS #
# will be added to the .struct file. #
# #
# If symmetry_generate is NOT used, then the IDENTITY MATRIX #
# will be added to the .struct file. #
#----------------------------------------------------------------------------------------#
# At the end of the section there is an if clause which checks if the number of CASTEP #
# symmetry operations is the same as the number of the ones generated by spglib. #
# If they are different, a warning will pop up. #
#========================================================================================#
positions = []
a_symbols = []
unit_cell_from_castep = []
# Find the total number of ions
for line in castep_data:
if 'Total number of ions' in line:
num_ions = int(line.split()[7])
elif 'Cell is a supercell' in line:
sup_cell = True
num_sup_cells = int(line.split()[5])
sup_cell_msg = line
#print num_sup_cells
# Get unit cell from <seedname>.castep.
for index, line in enumerate(castep_data):
# Crystal lattice in (A) units. <seedname>.bands file also contains
# this information. However, it uses Bohr units and this creates
# some problems when symmetry operations are generated with spglib.
if 'Real Lattice(A)' in line:
start = index + 1
for j in range (3):
unit_cell_from_castep.append(
[float(castep_data[start].split()[0]),
float(castep_data[start].split()[1]),
float(castep_data[start].split()[2])])
start += 1
break # avoid double counting
# Get atomic positions and symbols from .castep
# Use the total number of ions and append the position of every atom to positions = []
for index, line in enumerate(castep_data):
if 'Cell Contents' in line:
for i in range(0, num_ions):
positions.append([float(castep_data[index+10+i].split()[3]),
float(castep_data[index+10+i].split()[4]),
float(castep_data[index+10+i].split()[5])])
a_symbols.append(str(castep_data[index+10+i].split()[1]))
break # avoid double counting
# if multiple castep runs are present in one .castep file
# Create an argument needed by spglib to generate symmetries
all_atoms = Atoms(symbols = a_symbols,
cell=unit_cell_from_castep,
scaled_positions=positions,
pbc=True)
# Translational symm ops are not considered by boltztrap
# Add only unique rotational symm ops
def compare_elements(element1, element2):
absdiff = abs(element1 - element2)
value = sum(sum(absdiff))
if value > 1.0e-10:
return False
else:
return True
# Check if spglib is present.
if has_spglib and symmetry:
# Use spglib and get rotational operations
print '|| spglib found. ||'
# used for debugging
#cell_symm = spglib.get_symmetry(all_atoms, symprec=symmetry_tol)
#translations = spglib.get_symmetry_dataset(all_atoms, symprec=symmetry_tol)['translations']
rotations = spglib.get_symmetry_dataset(all_atoms, symprec=symmetry_tol)['rotations']
symm_ops_spglib = []
for i in range(len(rotations)):
new_rot = rotations[i]
newop=True
for i in range(len(symm_ops_spglib)):
if compare_elements(symm_ops_spglib[i],new_rot):
newop=False
break
if newop:
symm_ops_spglib.append(new_rot)
def max_length(msg):
max_length1 = abs(57-len(msg))
return max_length1
# print number of symmetry operations generated by spglib.
mess = '|| %s ' %len(symm_ops_spglib) + 'symmetry operations generated by spglib. '
print '%s' %mess + '{0:>{width}}'.format("||", width=max_length(mess))
# Check if the number of symmetry operations generated by spglib
# is the same as the number of symmetry operations in CASTEP
if len(symm_ops_spglib) != n_symm_ops:
print '|| ||'
print '|| WARNING: ||'
err_mess = '|| %s ' %n_symm_ops + 'symmetry operations found in %s.castep. ' % prefix
print '%s' %err_mess + '{0:>{width}}'.format("||", width=max_length(err_mess))
err_mess = '|| %s ' %len(symm_ops_spglib) + 'symmetry operations generated by spglib. '
print '%s' %err_mess + '{0:>{width}}'.format("||", width=max_length(err_mess))
if sup_cell:
if len(symm_ops_spglib)*num_sup_cells == n_symm_ops:
sup_cell_msg = '|| Cell is a supercell containing %s ' %num_sup_cells + 'primitive cells '
print '|| ||'
print '%s' %sup_cell_msg + '{0:>{width}}'.format("||", width=max_length(sup_cell_msg))
print '|| and translational sym. ops. are not needed. ||'
print '|| Everything should be fine. ||'
else:
sup_cell_msg = '|| Cell is a supercell containing %s ' %num_sup_cells + 'primitive cells. '
print '|| ||'
print '%s' %sup_cell_msg + '{0:>{width}}'.format("||", width=max_length(sup_cell_msg))
print '|| However, the number of sym. ops. is unexpected. ||'
print '|| Check symmetry operations tolerance in CASTEP. ||'
print '|| Proceed with CAUTION. ||'
else:
print '|| Check symmetry operations tolerance in CASTEP. ||'
print '|| Proceed with CAUTION. ||'
# If spglib is not found pop a warning
else:
if symmetry:
print '|| ||'
print '|| WARNING: ||'
print '|| Symmetry operations ARE present... ||'
print '|| ...but spglib was NOT found. ||'
print '|| Proceed with CAUTION. ||'
print '|| TRY installing spglib: sudo pip install pyspglib ||'
if not symmetry:
print '|| ||'
print '|| MESSAGE: ||'
print '|| Symmetry operations NOT used in CASTEP calculation. ||'
print '|| Continue NORMALLY. ||'
#========================================================================================#
#========================================================================================#
#========================================================================================#
#
# Create the <seedname>.energy file
#
#========================================================================================#
#---------------------------------- Spin 1/ Spin up PART --------------------------------#
# First line is a comment, in this case it is the name of the structure
f_energy = prefix + '\n'
# Number of k-points
f_energy += str(int(n_kpoints)) + '\n'
# K-point coordinates and number of eigenvalues
for ik in range(int(n_kpoints)):
for j in range(3):
f_energy += str(kpoints_frac_coordinates[ik][j]) + ' '
f_energy += str(int(n_eigenvalues)) + '\n'
start_pos_for_next_k_point = ik*int(n_eigenvalues)
# Eigenvalues for a given k-point
# if you want to exclude bands change range to
# range(int(n_excluded:n_eigenvalues)) and
# add this as offset to start_pos ------> this would only exclude the bottom bands
for ib in range(int(n_eigenvalues)):
f_energy += str(eigenenergies[start_pos_for_next_k_point]) + '\n'
start_pos_for_next_k_point += 1
#------------------------------- Spin 2/ Spin down PART ---------------------------------#
# Similar to Spin 1 PART
if spin_components == 2:
f_energy_down = prefix + ' down ' + '\n'
f_energy_down += str(int(n_kpoints)) + '\n'
for ik in range(int(n_kpoints)):
for j in range(3):
f_energy_down += str(kpoints_frac_coordinates[ik][j]) + ' '
f_energy_down += str(int(n_eigenvalues)) + '\n'
start_pos_for_next_k_point = ik*int(n_eigenvalues)
# if you want to exclude bands change range to
# range(int(n_excluded:n_eigenvalues)) and
# add this as offset to start_pos ------> this would only exclude the bottom bands
for ib in range(int(n_eigenvalues)):
f_energy_down += str(eigenenergies_spin2[start_pos_for_next_k_point]) + '\n'
start_pos_for_next_k_point += 1
else:
pass
f = open(energy_file, 'w')
# Choose whether spin up or spin down energies
# will be written to the .energy file
if 'down' in argv or '-down' in argv or 'dn' in argv or '-dn' in argv:
# Check if there are spin down eigenvalues...
if spin_components == 2:
f.write(f_energy_down)
f.close()
print '|| ||'
print '|| Spin down energy file cooked and ready to go. ||'
# ...if not, use normal values.
else:
print '|| ||'
print '|| Spin polarisation not present, no spin down values. ||'
print '|| Default settings used instead. ||'
f.write(f_energy)
f.close()
else:
f.write(f_energy)
f.close()
# IMPORTANT: If a kpoint is repeated BoltzTraP will give an error,
# CASTEP BS calculations might have a such point defined in the path
# and it needs to be removed.
#========================================================================================#
#========================================================================================#
#========================================================================================#
#
# Create the BoltzTraP.def file
#
#========================================================================================#
f_def = '5, \'' + prefix + '.intrans\', \'old\', \'formatted\',0\n'
f_def += '6,\'' + prefix + '.outputtrans\', \'unknown\', \'formatted\',0\n'
f_def += '20,\'' + prefix + '.struct\', \'old\', \'formatted\',0\n'
if so_on:
f_def += '10,\'' + prefix + '.energyso\', \'old\', \'formatted\',0\n'
elif spin_up:
f_def += '10,\'' + prefix + '.energyup\', \'old\', \'formatted\',0\n'
elif spin_dn:
f_def += '10,\'' + prefix + '.energydn\', \'old\', \'formatted\',0\n'
else:
f_def += '10,\'' + prefix + '.energy\', \'old\', \'formatted\',0\n'
f_def += '48,\'' + prefix + '.engre\', \'unknown\', \'unformatted\',0\n'
f_def += '49,\'' + prefix + '.transdos\', \'unknown\', \'formatted\',0\n'
f_def += '50,\'' + prefix + '.sigxx\', \'unknown\', \'formatted\',0\n'
f_def += '51,\'' + prefix + '.sigxxx\', \'unknown\', \'formatted\',0\n'
f_def += '21,\'' + prefix + '.trace\', \'unknown\', \'formatted\',0\n'
f_def += '22,\'' + prefix + '.condtens\', \'unknown\', \'formatted\',0\n'
f_def += '24,\'' + prefix + '.halltens\', \'unknown\', \'formatted\',0\n'
f_def += '30,\'' + prefix + '_BZ.dx\', \'unknown\', \'formatted\',0\n'
f_def += '31,\'' + prefix + '_fermi.dx\', \'unknown\', \'formatted\',0\n'
f_def += '32,\'' + prefix + '_sigxx.dx\', \'unknown\', \'formatted\',0\n'
f_def += '33,\'' + prefix + '_sigyy.dx\', \'unknown\', \'formatted\',0\n'
f_def += '34,\'' + prefix + '_sigzz.dx\', \'unknown\', \'formatted\',0\n'
f_def += '35,\'' + prefix + '_band.dat\', \'unknown\', \'formatted\',0\n'
f_def += '36,\'' + prefix + '_band.gpl\', \'unknown\', \'formatted\',0\n'
f_def += '37,\'' + prefix + '_deriv.dat\', \'unknown\', \'formatted\',0\n'
f_def += '38,\'' + prefix + '_mass.dat\', \'unknown\', \'formatted\',0\n'
f = open(def_file, 'w')
f.write(f_def)
f.close()
#========================================================================================#
#========================================================================================#
#========================================================================================#
#
# Create the <seedname>.intrans file
#
#========================================================================================#
deltae = 0.0005
ecut = 0.4
lpfac = 5
efcut = 0.15
tmax = 800.0
deltat = 50.0
ecut2 = -1.0
# efermi is only for spin up at the moment, add an if statement if spin down is present
f_intrans = 'GENE # Format of DOS\n'
f_intrans += '0 0 0 0.0 # iskip (not presently used) idebug setgap shiftgap\n'
if 'down' in argv or '-down' in argv:
if spin_components == 2:
f_intrans += str(efermi_down) + ' ' + str(deltae) + ' ' + str(ecut) + ' ' + str(n_electrons) + ' # Fermilevel (Ry), energygrid, energy span around Fermilevel, number of electrons\n'
else:
# This could be regarded as an error or a typo.
# This part is also present in the .energy file section and should pop a warning if triggered.
f_intrans += str(efermi) + ' ' + str(deltae) + ' ' + str(ecut) + ' ' + str(n_electrons) + ' # Fermilevel (Ry), energygrid, energy span around Fermilevel, number of electrons\n'
else:
f_intrans += str(efermi) + ' ' + str(deltae) + ' ' + str(ecut) + ' ' + str(n_electrons) + ' # Fermilevel (Ry), energygrid, energy span around Fermilevel, number of electrons\n'
f_intrans += 'CALC # CALC (calculate expansion coeff), NOCALC read from file\n'
f_intrans += str(lpfac) + ' # lpfac, number of latt-points per k-point\n'
f_intrans += 'BOLTZ # run mode (only BOLTZ is supported)\n'
f_intrans += str(efcut) + ' # (efcut) energy range of chemical potential\n'
f_intrans += str(tmax) + ' ' + str(deltat) + ' # Tmax, temperature grid\n'
f_intrans += str(ecut2) + ' # energyrange of bands given individual DOS output sig_xxx and dos_xxx (xxx is band number)\n'
f_intrans += 'HISTO # Scheme to obtain DOS. HISTO/TETRA: histogram/thetrahedron sampling\n'
f_intrans += '#0 0 0 0 0 # tau-model. Not documented\n'
f_intrans += '#14 # number of fixed dopings\n'
f_intrans += '#1E20 5E20 1E21 2E21 3E21 5E21 1E22 5E22 -1E20 -5E20 -1E21 -2.5E21 -5E21 -1E22 # example of fixed doping levels in cm^3\n'
f = open(intrans_file, 'w')
f.write(f_intrans)
f.close()
#========================================================================================#
#========================================================================================#
#========================================================================================#
#
# Create the <seedname>.struct file
#
#========================================================================================#
# First line is a comment, name of the structure in this case.
f_struct = prefix + '\n'
# Crystal lattice from <seedname>.bands file
for i in range(3):
for j in range(3):
f_struct += str(unit_cell[i][j]) + ' '
f_struct +='\n'
# Check if symmetry operations and spglib are present
if symmetry is True and has_spglib:
f_struct += str(len(symm_ops_spglib)) + '\n'
for i in range(int(len(symm_ops_spglib))):
for j in range(3):
for k in range(3):
f_struct += str(symm_ops_spglib[i][j][k]) + ' '
f_struct += '\n'
# If there are no symmetry operations, append an identity matrix
# to the .struct file. BoltzTraP doesn't run otherwise.
elif symmetry is False or not has_spglib:
f_struct += '1' + '\n'
f_struct += '1 0 0 0 1 0 0 0 1'
f = open(struct_file, 'w')
f.write(f_struct)
f.close()
#========================================================================================#
#========================================================================================#
if so_on:
print '|| ||'
print '|| SOC .energyso file cooked and ready to go. ||'
print '|| ||'
print '|| Done. ||'
print '========================================================='
help="Mesh numbers")
parser.add_option("-f",
dest="filename",
type="string",
help="Filename of triplets at q")
parser.add_option("-g", dest="grid_point", type="int", help="A grid point")
(options, args) = parser.parse_args()
if options.mesh == None:
mesh = [4, 4, 4]
else:
mesh = [int(x) for x in options.mesh.split()]
cell = read_vasp(args[0])
dataset = spglib.get_symmetry_dataset(cell)
weights, third_q, grid_points = \
spglib.get_triplets_reciprocal_mesh_at_q(options.grid_point,
mesh,
dataset['rotations'])
if options.filename == None:
for i, (w, q) in enumerate(zip(weights, third_q)):
if w > 0:
print options.grid_point, i, q, w
else:
triplets_in, weights_in = parse_triplets(options.filename)
count = 0
for i, (w, q) in enumerate(zip(weights, third_q)):
if w > 0:
if triplets_in[count][0] == options.grid_point and \
