def create_FORCE_SETS(interface_mode,
force_filenames,
symprec=1e-5,
is_wien2k_p1=False,
force_sets_zero_mode=False,
disp_filename='disp.yaml',
force_sets_filename='FORCE_SETS',
log_level=0):
if (interface_mode is None or interface_mode == 'vasp'
or interface_mode == 'pwmat' or interface_mode == 'abinit'
or interface_mode == 'elk' or interface_mode == 'pwscf'
or interface_mode == 'siesta' or interface_mode == 'crystal'):
disp_dataset = parse_disp_yaml(filename=disp_filename)
num_atoms = disp_dataset['natom']
num_displacements = len(disp_dataset['first_atoms'])
if force_sets_zero_mode:
num_displacements += 1
force_sets = get_force_sets(interface_mode,
num_atoms,
num_displacements,
force_filenames,
disp_filename,
verbose=(log_level > 0))
elif interface_mode == 'wien2k':
disp_dataset, supercell = parse_disp_yaml(filename=disp_filename,
return_cell=True)
from phonopy.interface.wien2k import parse_set_of_forces
num_displacements = len(disp_dataset['first_atoms'])
if force_sets_zero_mode:
num_displacements += 1
if _check_number_of_files(num_displacements, force_filenames,
disp_filename):
force_sets = []
else:
disps = [[d['number'], d['displacement']]
for d in disp_dataset['first_atoms']]
force_sets = parse_set_of_forces(disps,
force_filenames,
supercell,
is_distribute=(not is_wien2k_p1),
symprec=symprec,
verbose=(log_level > 0))
else:
force_sets = []
if force_sets:
if force_sets_zero_mode:
force_sets = _subtract_residual_forces(force_sets)
for forces, disp in zip(force_sets, disp_dataset['first_atoms']):
disp['forces'] = forces
write_FORCE_SETS(disp_dataset, filename=force_sets_filename)
if log_level > 0:
if force_sets:
print("%s has been created." % force_sets_filename)
else:
print("%s could not be created." % force_sets_filename)
return 0
def create_FORCE_SETS(interface_mode,
force_filenames,
symprec,
is_wien2k_p1=False,
force_sets_zero_mode=False,
log_level=0):
if (interface_mode is None or
interface_mode == 'vasp' or
interface_mode == 'abinit' or
interface_mode == 'elk' or
interface_mode == 'pwscf' or
interface_mode == 'siesta'):
displacements = parse_disp_yaml(filename='disp.yaml')
num_atoms = displacements['natom']
if _check_number_of_files(displacements,
force_filenames,
force_sets_zero_mode):
return 1
force_sets = _get_force_sets(interface_mode, num_atoms, force_filenames)
elif interface_mode == 'wien2k':
displacements, supercell = parse_disp_yaml(filename='disp.yaml',
return_cell=True)
from phonopy.interface.wien2k import parse_set_of_forces
if _check_number_of_files(displacements,
force_filenames,
force_sets_zero_mode):
return 1
force_sets = parse_set_of_forces(
displacements,
force_filenames,
supercell,
disp_keyword='first_atoms',
is_distribute=(not is_wien2k_p1),
symprec=symprec)
else:
force_sets = []
if force_sets:
if force_sets_zero_mode:
force_sets = _subtract_residual_forces(force_sets)
for forces, disp in zip(force_sets, displacements['first_atoms']):
disp['forces'] = forces
write_FORCE_SETS(displacements, filename='FORCE_SETS')
if log_level > 0:
if force_sets:
print("FORCE_SETS has been created.")
else:
print("FORCE_SETS could not be created.")
return 0
def create_FORCE_SETS(interface_mode,
force_filenames,
symprec,
is_wien2k_p1=False,
log_level=0):
if (interface_mode is None or
interface_mode == 'vasp' or
interface_mode == 'abinit' or
interface_mode == 'elk' or
interface_mode == 'pwscf' or
interface_mode == 'siesta'):
displacements = parse_disp_yaml(filename='disp.yaml')
num_atoms = displacements['natom']
if len(displacements['first_atoms']) != len(force_filenames):
print('')
print("Number of files to be read don't match "
"to number of displacements in disp.yaml.")
return 1
force_sets = get_force_sets(interface_mode, num_atoms, force_filenames)
elif interface_mode == 'wien2k':
displacements, supercell = parse_disp_yaml(filename='disp.yaml',
return_cell=True)
if len(displacements['first_atoms']) != len(force_filenames):
print('')
print("Number of files to be read don't match "
"to number of displacements in disp.yaml.")
return 1
from phonopy.interface.wien2k import parse_set_of_forces
force_sets = parse_set_of_forces(
displacements,
force_filenames,
supercell,
disp_keyword='first_atoms',
is_distribute=(not is_wien2k_p1),
symprec=symprec)
else:
force_sets = []
if force_sets:
for forces, disp in zip(force_sets, displacements['first_atoms']):
disp['forces'] = forces
write_FORCE_SETS(displacements, filename='FORCE_SETS')
if log_level > 0:
if force_sets:
print("FORCE_SETS has been created.")
else:
print("FORCE_SETS could not be created.")
return 0
def create_FORCE_SETS(interface_mode,
force_filenames,
options,
log_level=0):
if (interface_mode == 'vasp' or
interface_mode == 'abinit' or
interface_mode == 'elk' or
interface_mode == 'pwscf' or
interface_mode == 'siesta'):
displacements = parse_disp_yaml(filename='disp.yaml')
num_atoms = displacements['natom']
if len(displacements['first_atoms']) != len(force_filenames):
print('')
print("Number of files to be read don't match "
"to number of displacements in disp.yaml.")
return 1
force_sets = get_force_sets(interface_mode, num_atoms, force_filenames)
elif interface_mode == 'wien2k':
displacements, supercell = parse_disp_yaml(filename='disp.yaml',
return_cell=True)
if len(displacements['first_atoms']) != len(force_filenames):
print('')
print("Number of files to be read don't match "
"to number of displacements in disp.yaml.")
return 1
from phonopy.interface.wien2k import parse_set_of_forces
force_sets = parse_set_of_forces(
displacements,
force_filenames,
supercell,
disp_keyword='first_atoms',
is_distribute=(not options.is_wien2k_p1),
symprec=options.symprec)
else:
force_sets = []
if force_sets:
for forces, disp in zip(force_sets, displacements['first_atoms']):
disp['forces'] = forces
write_FORCE_SETS(displacements, filename='FORCE_SETS')
if log_level > 0:
if force_sets:
print("FORCE_SETS has been created.")
else:
print("FORCE_SETS could not be created.")
return 0
def read_phonopy(sposcar='SPOSCAR',
sc_mat=np.eye(3),
force_constants=None,
disp_yaml=None,
force_sets=None):
if force_constants is None and (disp_yaml is None or force_sets is None):
raise ValueError(
"Either FORCE_CONSTANTS or (disp.yaml&FORCE_SETS) file should be provided."
)
atoms = read(sposcar)
#vesta_view(atoms)
primitive_matrix = inv(sc_mat)
bulk = PhonopyAtoms(symbols=atoms.get_chemical_symbols(),
scaled_positions=atoms.get_scaled_positions(),
cell=atoms.get_cell())
phonon = Phonopy(
bulk,
supercell_matrix=np.eye(3),
primitive_matrix=primitive_matrix,
#factor=factor,
#symprec=symprec
)
if disp_yaml is not None:
disp = parse_disp_yaml(filename=disp_yaml)
phonon.set_displacement_dataset(disp)
if force_sets is not None:
fc = parse_FORCE_SETS(filename=force_sets)
phonon.set_forces(fc)
fc = parse_FORCE_CONSTANTS(force_constants)
phonon.set_force_constants(fc)
return phonon
def test_parse_wien2k_struct(self):
cell, npts, r0s, rmts = parse_wien2k_struct("BaGa2.struct")
lattice = cell.get_cell().T
displacements, supercell = parse_disp_yaml("disp_BaGa2.yaml",
return_cell=True)
symmetry = Symmetry(cell)
print(PhonopyAtoms(atoms=cell))
sym_op = symmetry.get_symmetry_operations()
print(symmetry.get_international_table())
for i, (r, t) in enumerate(
zip(sym_op['rotations'], sym_op['translations'])):
print("--- %d ---" % (i + 1))
print(r)
print(t)
def parse_set_of_forces(num_atoms, forces_filenames, verbose=False):
hook = 'CONVERGED'
force_sets = []
for fplo_filename in forces_filenames:
fplo_forces = iter_collect_forces(fplo_filename,
num_atoms,
hook, [6, 7, 8],
word='TOTAL NEUTRAL FORCES')
# rotate forces from the FPLO xyz coordinate system
# into the coordinate system of phonopy
# read the phonopy lattice vectors
conf, cell = parse_disp_yaml(return_cell=True)
ppy_lat = cell.get_cell()
# read the fplo output file
f = open(fplo_filename, 'r')
outf = f.readlines()
f.close
# search lattice vectors
fp_lat = np.zeros((3, 3))
for j in np.arange(len(outf)):
if outf[j].find("lattice vectors") == 0:
for i in np.arange(3):
fp_lat[i, :] = list(
map(float,
outf[j + i + 1].split(":")[1].split())) # [bohr]
if np.allclose(fp_lat, np.zeros((3, 3))):
sys.exit("(EE) The lattice vectors were not found in: " +
fplo_filename)
T = np.dot(np.linalg.inv(ppy_lat), fp_lat)
if not np.allclose(np.dot(T.T, T), np.eye(3)):
sys.exit("(EE) The basis transformation is wrong!")
for i in np.arange(len(fplo_forces)):
fplo_forces[i] = np.dot(T, np.array(fplo_forces[i]))
# Calculate the drift_force (sum over all forces has to be zero) and
# normalize the forces.
drift_force = get_drift_forces(fplo_forces, fplo_filename, verbose)
force_sets.append(np.array(fplo_forces) - drift_force)
return force_sets
def create_FORCE_SETS(interface_mode,
force_filenames,
symmetry_tolerance=None,
is_wien2k_p1=False,
force_sets_zero_mode=False,
disp_filename='disp.yaml',
force_sets_filename='FORCE_SETS',
log_level=0):
if log_level > 0:
if interface_mode:
print("Calculator interface: %s" % interface_mode)
print("Displacements were read from \"%s\"." % disp_filename)
if disp_filename == 'disp.yaml':
print('')
print("NOTE:")
print(" From phonopy v2.0, displacements are written into "
"\"phonopy_disp.yaml\".")
print(" \"disp.yaml\" is still supported for reading, but is "
"deprecated.")
print('')
if force_sets_zero_mode:
print("Forces in %s are subtracted from forces in all "
"other files." % force_filenames[0])
if interface_mode in (None, 'vasp', 'abinit', 'elk', 'qe', 'siesta',
'cp2k', 'crystal', 'dftbp', 'turbomole'):
disp_dataset = parse_disp_yaml(filename=disp_filename)
num_atoms = disp_dataset['natom']
num_displacements = len(disp_dataset['first_atoms'])
if force_sets_zero_mode:
num_displacements += 1
force_sets = get_force_sets(interface_mode,
num_atoms,
num_displacements,
force_filenames,
disp_filename=disp_filename,
check_number_of_files=True,
verbose=(log_level > 0))
elif interface_mode == 'wien2k':
disp_dataset, supercell = parse_disp_yaml(filename=disp_filename,
return_cell=True)
from phonopy.interface.wien2k import parse_set_of_forces
num_displacements = len(disp_dataset['first_atoms'])
if force_sets_zero_mode:
num_displacements += 1
if _check_number_of_files(num_displacements,
force_filenames,
disp_filename):
force_sets = []
else:
disps = [[d['number'], d['displacement']]
for d in disp_dataset['first_atoms']]
force_sets = parse_set_of_forces(
disps,
force_filenames,
supercell,
is_distribute=(not is_wien2k_p1),
symmetry_tolerance=symmetry_tolerance,
verbose=(log_level > 0))
else:
force_sets = []
if force_sets:
if force_sets_zero_mode:
force_sets = _subtract_residual_forces(force_sets)
for forces, disp in zip(force_sets, disp_dataset['first_atoms']):
disp['forces'] = forces
write_FORCE_SETS(disp_dataset, filename=force_sets_filename)
if log_level > 0:
if force_sets:
print("%s has been created." % force_sets_filename)
else:
print("%s could not be created." % force_sets_filename)
return 0
def create_FORCE_SETS(interface_mode,
force_filenames,
symprec=1e-5,
is_wien2k_p1=False,
force_sets_zero_mode=False,
disp_filename='disp.yaml',
force_sets_filename='FORCE_SETS',
log_level=0):
if (interface_mode is None or
interface_mode == 'vasp' or
interface_mode == 'abinit' or
interface_mode == 'elk' or
interface_mode == 'lmto' or
interface_mode == 'qe' or
interface_mode == 'siesta' or
interface_mode == 'cp2k' or
interface_mode == 'crystal'):
disp_dataset = parse_disp_yaml(filename=disp_filename)
num_atoms = disp_dataset['natom']
num_displacements = len(disp_dataset['first_atoms'])
if force_sets_zero_mode:
num_displacements += 1
force_sets = get_force_sets(interface_mode,
num_atoms,
num_displacements,
force_filenames,
disp_filename,
verbose=(log_level > 0))
elif interface_mode == 'wien2k':
disp_dataset, supercell = parse_disp_yaml(filename=disp_filename,
return_cell=True)
from phonopy.interface.wien2k import parse_set_of_forces
num_displacements = len(disp_dataset['first_atoms'])
if force_sets_zero_mode:
num_displacements += 1
if _check_number_of_files(num_displacements,
force_filenames,
disp_filename):
force_sets = []
else:
disps = [[d['number'], d['displacement']]
for d in disp_dataset['first_atoms']]
force_sets = parse_set_of_forces(
disps,
force_filenames,
supercell,
is_distribute=(not is_wien2k_p1),
symprec=symprec,
verbose=(log_level > 0))
else:
force_sets = []
if force_sets:
if force_sets_zero_mode:
force_sets = _subtract_residual_forces(force_sets)
for forces, disp in zip(force_sets, disp_dataset['first_atoms']):
disp['forces'] = forces
write_FORCE_SETS(disp_dataset, filename=force_sets_filename)
if log_level > 0:
if force_sets:
print("%s has been created." % force_sets_filename)
else:
print("%s could not be created." % force_sets_filename)
return 0
def create_FORCE_SETS(interface_mode,
force_filenames,
symmetry_tolerance=None,
wien2k_P1_mode=False,
force_sets_zero_mode=False,
disp_filename='disp.yaml',
force_sets_filename='FORCE_SETS',
log_level=0):
"""Create FORCE_SETS from phonopy_disp.yaml and calculator output files.
Reading disp.yaml instead of phonopy_disp.yaml is deprecated.
"""
if log_level > 0:
if interface_mode:
print("Calculator interface: %s" % interface_mode)
print("Displacements were read from \"%s\"." % disp_filename)
if disp_filename == 'disp.yaml':
print('')
print("NOTE:")
print(" From phonopy v2.0, displacements are written into "
"\"phonopy_disp.yaml\".")
print(" \"disp.yaml\" is still supported for reading except for "
"Wien2k interface, ")
print(" but is deprecated.")
print('')
if force_sets_zero_mode:
print("Forces in %s are subtracted from forces in all "
"other files." % force_filenames[0])
if disp_filename == 'disp.yaml':
if interface_mode == 'wien2k':
disp_dataset, supercell = parse_disp_yaml(filename=disp_filename,
return_cell=True)
else:
disp_dataset = parse_disp_yaml(filename=disp_filename)
else:
phpy = PhonopyYaml()
phpy.read(disp_filename)
supercell = phpy.supercell
disp_dataset = phpy.dataset
if 'natom' in disp_dataset: # type-1 dataset
num_atoms = disp_dataset['natom']
num_displacements = len(disp_dataset['first_atoms'])
dataset_type = 1
elif 'displacements' in disp_dataset: # type-2 dataset
num_atoms = disp_dataset['displacements'].shape[1]
num_displacements = disp_dataset['displacements'].shape[0]
dataset_type = 2
else:
raise RuntimeError("Number of atoms could not be retrieved from %s" %
disp_filename)
if force_sets_zero_mode:
num_displacements += 1
if not check_number_of_force_files(num_displacements, force_filenames,
disp_filename):
force_sets = []
elif interface_mode == 'wien2k':
force_sets = get_force_sets_wien2k(
num_displacements,
force_filenames,
disp_filename,
supercell,
disp_dataset,
wien2k_P1_mode=wien2k_P1_mode,
symmetry_tolerance=symmetry_tolerance,
verbose=(log_level > 0))
else:
force_sets = get_force_sets(interface_mode,
num_atoms,
num_displacements,
force_filenames,
disp_filename=disp_filename,
verbose=(log_level > 0))
if force_sets:
if force_sets_zero_mode:
force_sets = _subtract_residual_forces(force_sets)
if dataset_type == 1:
for forces, disp in zip(force_sets, disp_dataset['first_atoms']):
disp['forces'] = forces
elif dataset_type == 2:
disp_dataset['forces'] = np.array(force_sets,
dtype='double',
order='C')
else:
raise RuntimeError("FORCE_SETS could not be created.")
write_FORCE_SETS(disp_dataset, filename=force_sets_filename)
if log_level > 0:
if force_sets:
print("%s has been created." % force_sets_filename)
else:
print("%s could not be created." % force_sets_filename)
return 0
def on_all_ok(self):
"""
This method is called once the `Work` is completed i.e. when all the tasks
have reached status S_OK. Here we get the forces from the output files, and
we call phonopy to compute the inter-atomic force constants.
"""
phonon = self.phonon
# Write POSCAR with initial unit cell.
structure = structure_from_atoms(phonon.get_primitive())
structure.to(filename=self.outdir.path_in("POSCAR"))
# Write yaml file with displacements.
supercell = phonon.get_supercell()
displacements = phonon.get_displacements()
#directions = phonon.get_displacement_directions()
file_IO.write_disp_yaml(
displacements,
supercell, # directions=directions,
filename=self.outdir.path_in('disp.yaml'))
# Extract forces from the main Abinit output files.
forces_filenames = [
task.output_file.path for task in self.phonopy_tasks
]
num_atoms = supercell.get_number_of_atoms()
force_sets = parse_set_of_forces(num_atoms, forces_filenames)
# Write FORCE_SETS file.
displacements = file_IO.parse_disp_yaml(
filename=self.outdir.path_in('disp.yaml'))
num_atoms = displacements['natom']
for forces, disp in zip(force_sets, displacements['first_atoms']):
disp['forces'] = forces
file_IO.write_FORCE_SETS(displacements,
filename=self.outdir.path_in('FORCE_SETS'))
# Write README and configuration files.
examples_url = "http://atztogo.github.io/phonopy/examples.html"
doctags_url = "http://atztogo.github.io/phonopy/setting-tags.html#setting-tags"
kptbounds = np.array([k.frac_coords for k in structure.hsym_kpoints])
path_coords = " ".join(str(rc) for rc in kptbounds.flat)
path_labels = " ".join(k.name for k in structure.hsym_kpoints)
ngqpt = structure.calc_ngkpt(nksmall=30)
with open(self.outdir.path_in("band.conf"), "wt") as fh:
fh.write("#" + doctags_url + "\n")
fh.write("DIM = %d %d %d\n" % tuple(self.scdims))
fh.write("BAND = %s\n" % path_coords)
fh.write("BAND_LABELS = %s\n" % path_labels)
fh.write("BAND_POINTS = 101\n")
fh.write("#BAND_CONNECTION = .TRUE.\n")
with open(self.outdir.path_in("dos.conf"), "wt") as fh:
fh.write("#" + doctags_url + "\n")
fh.write("DIM = %d %d %d\n" % tuple(self.scdims))
fh.write("MP = %d %d %d\n" % tuple(ngqpt))
fh.write("#GAMMA_CENTER = .TRUE.\n")
with open(self.outdir.path_in("band-dos.conf"), "wt") as fh:
fh.write("#" + doctags_url + "\n")
fh.write("DIM = %d %d %d\n" % tuple(self.scdims))
fh.write("BAND = %s\n" % path_coords)
fh.write("BAND_LABELS = %s\n" % path_labels)
fh.write("BAND_POINTS = 101\n")
fh.write("#BAND_CONNECTION = .TRUE.\n")
fh.write("MP = %d %d %d\n" % tuple(ngqpt))
fh.write("#GAMMA_CENTER = .TRUE.\n")
with open(self.outdir.path_in("README.md"), "wt") as fh:
fh.write("To plot bands, use:\n\tphonopy -p band.conf\n\n")
fh.write("To plot phonon dos, use:\n\tphonopy -p dos.conf\n\n")
fh.write(
"To plot bands and dos, use:\n\tphonopy -p band-dos.conf\n\n")
fh.write("See also:\n")
fh.write("\t" + examples_url + "\n")
fh.write("\t" + doctags_url + "\n")
if self.cpdata2dst:
self.outdir.copy_r(self.cpdata2dst)
return super(PhonopyWork, self).on_all_ok()
def create_FORCE_SETS(interface_mode, force_filenames, options, log_level):
if interface_mode == 'vasp':
displacements = parse_disp_yaml(filename='disp.yaml')
if (interface_mode == 'wien2k' or interface_mode == 'abinit'
or interface_mode == 'pwscf'):
displacements, supercell = parse_disp_yaml(filename='disp.yaml',
return_cell=True)
num_disp_files = len(force_filenames)
if options.force_sets_zero_mode:
num_disp_files -= 1
if len(displacements['first_atoms']) != num_disp_files:
print
print(
"Number of files to be read don't match "
"to number of displacements in disp.yaml.")
return 1
if interface_mode == 'vasp':
from phonopy.interface.vasp import parse_set_of_forces
is_parsed = parse_set_of_forces(
displacements,
force_filenames,
is_zero_point=options.force_sets_zero_mode)
if interface_mode == 'abinit':
from phonopy.interface.abinit import parse_set_of_forces
print "**********************************************************"
print "**** Abinit FORCE_SETS support is experimental. ****"
print "**** Your feedback would be appreciated. ****"
print "**********************************************************"
is_parsed = parse_set_of_forces(displacements, force_filenames,
supercell.get_number_of_atoms())
if interface_mode == 'pwscf':
from phonopy.interface.pwscf import parse_set_of_forces
print "**********************************************************"
print "**** Pwscf FORCE_SETS support is experimental. ****"
print "**** Your feedback would be appreciated. ****"
print "**********************************************************"
is_parsed = parse_set_of_forces(displacements, force_filenames,
supercell.get_number_of_atoms())
if interface_mode == 'wien2k':
from phonopy.interface.wien2k import parse_set_of_forces
print "**********************************************************"
print "**** Wien2k FORCE_SETS support is experimental. ****"
print "**** Your feedback would be appreciated. ****"
print "**********************************************************"
is_parsed = parse_set_of_forces(
displacements,
force_filenames,
supercell,
is_distribute=(not options.is_wien2k_p1),
symprec=options.symprec)
if is_parsed:
write_FORCE_SETS(displacements, filename='FORCE_SETS')
if log_level > 0:
if is_parsed:
print "FORCE_SETS has been created."
else:
print "FORCE_SETS could not be created."
return 0
def create_FORCE_SETS(interface_mode,
force_filenames,
options,
log_level):
if interface_mode == 'vasp':
displacements = parse_disp_yaml(filename='disp.yaml')
if (interface_mode == 'wien2k' or
interface_mode == 'abinit' or
interface_mode == 'pwscf'):
displacements, supercell = parse_disp_yaml(filename='disp.yaml',
return_cell=True)
num_disp_files = len(force_filenames)
if options.force_sets_zero_mode:
num_disp_files -= 1
if len(displacements['first_atoms']) != num_disp_files:
print
print ("Number of files to be read don't match "
"to number of displacements in disp.yaml.")
return 1
if interface_mode == 'vasp':
from phonopy.interface.vasp import parse_set_of_forces
is_parsed = parse_set_of_forces(
displacements,
force_filenames,
is_zero_point=options.force_sets_zero_mode)
if interface_mode == 'abinit':
from phonopy.interface.abinit import parse_set_of_forces
print "**********************************************************"
print "**** Abinit FORCE_SETS support is experimental. ****"
print "**** Your feedback would be appreciated. ****"
print "**********************************************************"
is_parsed = parse_set_of_forces(
displacements,
force_filenames,
supercell.get_number_of_atoms())
if interface_mode == 'pwscf':
from phonopy.interface.pwscf import parse_set_of_forces
print "**********************************************************"
print "**** Pwscf FORCE_SETS support is experimental. ****"
print "**** Your feedback would be appreciated. ****"
print "**********************************************************"
is_parsed = parse_set_of_forces(
displacements,
force_filenames,
supercell.get_number_of_atoms())
if interface_mode == 'wien2k':
from phonopy.interface.wien2k import parse_set_of_forces
print "**********************************************************"
print "**** Wien2k FORCE_SETS support is experimental. ****"
print "**** Your feedback would be appreciated. ****"
print "**********************************************************"
is_parsed = parse_set_of_forces(
displacements,
force_filenames,
supercell,
is_distribute=(not options.is_wien2k_p1),
symprec=options.symprec)
if is_parsed:
write_FORCE_SETS(displacements,
filename='FORCE_SETS')
if log_level > 0:
if is_parsed:
print "FORCE_SETS has been created."
else:
print "FORCE_SETS could not be created."
return 0
def create_FORCE_SETS(
interface_mode,
force_filenames,
symmetry_tolerance=None,
wien2k_P1_mode=False,
force_sets_zero_mode=False,
disp_filename="disp.yaml",
force_sets_filename="FORCE_SETS",
write_forcesets_yaml=False,
log_level=0,
):
"""Create FORCE_SETS from phonopy_disp.yaml and calculator output files.
Reading disp.yaml instead of phonopy_disp.yaml is deprecated.
"""
if log_level > 0:
if interface_mode:
print("Calculator interface: %s" % interface_mode)
print('Displacements were read from "%s".' % disp_filename)
if disp_filename == "disp.yaml":
print("")
print("NOTE:")
print(" From phonopy v2.0, displacements are written into "
'"phonopy_disp.yaml".')
print(' "disp.yaml" is still supported for reading except for '
"Wien2k interface, ")
print(" but is deprecated.")
print("")
if force_sets_zero_mode:
print("Forces in %s are subtracted from forces in all "
"other files." % force_filenames[0])
if disp_filename == "disp.yaml":
if interface_mode == "wien2k":
disp_dataset, supercell = parse_disp_yaml(filename=disp_filename,
return_cell=True)
else:
disp_dataset = parse_disp_yaml(filename=disp_filename)
else:
phpy_yaml = PhonopyYaml()
phpy_yaml.read(disp_filename)
supercell = phpy_yaml.supercell
disp_dataset = phpy_yaml.dataset
if "natom" in disp_dataset: # type-1 dataset
num_atoms = disp_dataset["natom"]
num_displacements = len(disp_dataset["first_atoms"])
dataset_type = 1
elif "displacements" in disp_dataset: # type-2 dataset
num_atoms = disp_dataset["displacements"].shape[1]
num_displacements = disp_dataset["displacements"].shape[0]
dataset_type = 2
else:
raise RuntimeError("Number of atoms could not be retrieved from %s" %
disp_filename)
if force_sets_zero_mode:
num_displacements += 1
if not check_number_of_force_files(num_displacements, force_filenames,
disp_filename):
force_sets = []
elif interface_mode == "wien2k":
force_sets = get_force_sets_wien2k(
force_filenames,
supercell,
disp_dataset,
wien2k_P1_mode=wien2k_P1_mode,
symmetry_tolerance=symmetry_tolerance,
verbose=(log_level > 0),
)
else:
force_sets = get_force_sets(
interface_mode,
num_atoms,
force_filenames,
verbose=(log_level > 0),
)
if force_sets:
if force_sets_zero_mode:
force_sets = _subtract_residual_forces(force_sets)
if dataset_type == 1:
for forces, disp in zip(force_sets, disp_dataset["first_atoms"]):
disp["forces"] = forces
elif dataset_type == 2:
disp_dataset["forces"] = np.array(force_sets,
dtype="double",
order="C")
else:
raise RuntimeError("FORCE_SETS could not be created.")
write_FORCE_SETS(disp_dataset, filename=force_sets_filename)
if log_level > 0:
print('"%s" has been created.' % force_sets_filename)
if disp_filename != "disp.yaml" and write_forcesets_yaml:
phpy_yaml.dataset = disp_dataset
with open("phonopy_force_sets.yaml", "w") as w:
w.write(str(phpy_yaml))
if log_level > 0:
print('"%s" has been created.' % "phonopy_force_sets.yaml")
else:
if log_level > 0:
print("%s could not be created." % force_sets_filename)
def on_all_ok(self):
"""
This method is called once the `Work` is completed i.e. when all the tasks
have reached status S_OK. Here we get the forces from the output files, and
we call phonopy to compute the inter-atomic force constants.
"""
phonon = self.phonon
# Write POSCAR with initial unit cell.
structure = structure_from_atoms(phonon.get_primitive())
structure.to(filename=self.outdir.path_in("POSCAR"))
# Write yaml file with displacements.
supercell = phonon.get_supercell()
displacements = phonon.get_displacements()
#directions = phonon.get_displacement_directions()
file_IO.write_disp_yaml(displacements, supercell, # directions=directions,
filename=self.outdir.path_in('disp.yaml'))
# Extract forces from the main Abinit output files.
forces_filenames = [task.output_file.path for task in self.phonopy_tasks]
num_atoms = supercell.get_number_of_atoms()
force_sets = parse_set_of_forces(num_atoms, forces_filenames)
# Write FORCE_SETS file.
displacements = file_IO.parse_disp_yaml(filename=self.outdir.path_in('disp.yaml'))
num_atoms = displacements['natom']
for forces, disp in zip(force_sets, displacements['first_atoms']):
disp['forces'] = forces
file_IO.write_FORCE_SETS(displacements, filename=self.outdir.path_in('FORCE_SETS'))
# Write README and configuration files.
examples_url = "http://atztogo.github.io/phonopy/examples.html"
doctags_url = "http://atztogo.github.io/phonopy/setting-tags.html#setting-tags"
kptbounds = np.array([k.frac_coords for k in structure.hsym_kpoints])
path_coords = " ".join(str(rc) for rc in kptbounds.flat)
path_labels = " ".join(k.name for k in structure.hsym_kpoints)
ngqpt = structure.calc_ngkpt(nksmall=30)
with open(self.outdir.path_in("band.conf"), "wt") as fh:
fh.write("#" + doctags_url + "\n")
fh.write("DIM = %d %d %d\n" % tuple(self.scdims))
fh.write("BAND = %s\n" % path_coords)
fh.write("BAND_LABELS = %s\n" % path_labels)
fh.write("BAND_POINTS = 101\n")
fh.write("#BAND_CONNECTION = .TRUE.\n")
with open(self.outdir.path_in("dos.conf"), "wt") as fh:
fh.write("#" + doctags_url + "\n")
fh.write("DIM = %d %d %d\n" % tuple(self.scdims))
fh.write("MP = %d %d %d\n" % tuple(ngqpt))
fh.write("#GAMMA_CENTER = .TRUE.\n")
with open(self.outdir.path_in("band-dos.conf"), "wt") as fh:
fh.write("#" + doctags_url + "\n")
fh.write("DIM = %d %d %d\n" % tuple(self.scdims))
fh.write("BAND = %s\n" % path_coords)
fh.write("BAND_LABELS = %s\n" % path_labels)
fh.write("BAND_POINTS = 101\n")
fh.write("#BAND_CONNECTION = .TRUE.\n")
fh.write("MP = %d %d %d\n" % tuple(ngqpt))
fh.write("#GAMMA_CENTER = .TRUE.\n")
with open(self.outdir.path_in("README.md"), "wt") as fh:
fh.write("To plot bands, use:\n\tphonopy -p band.conf\n\n")
fh.write("To plot phonon dos, use:\n\tphonopy -p dos.conf\n\n")
fh.write("To plot bands and dos, use:\n\tphonopy -p band-dos.conf\n\n")
fh.write("See also:\n")
fh.write("\t" + examples_url + "\n")
fh.write("\t" + doctags_url + "\n")
if self.cpdata2dst:
self.outdir.copy_r(self.cpdata2dst)
return super(PhonopyWork, self).on_all_ok()
def create_FORCE_SETS(interface_mode,
force_filenames,
symmetry_tolerance=None,
is_wien2k_p1=False,
force_sets_zero_mode=False,
disp_filename='disp.yaml',
force_sets_filename='FORCE_SETS',
log_level=0):
if log_level > 0:
if interface_mode:
print("Calculator interface: %s" % interface_mode)
print("Displacements were read from \"%s\"." % disp_filename)
if disp_filename == 'disp.yaml':
print('')
print("NOTE:")
print(" From phonopy v2.0, displacements are written into "
"\"phonopy_disp.yaml\".")
print(" \"disp.yaml\" is still supported for reading, but is "
"deprecated.")
print('')
if force_sets_zero_mode:
print("Forces in %s are subtracted from forces in all "
"other files." % force_filenames[0])
if disp_filename == 'disp.yaml':
disp_dataset, supercell = parse_disp_yaml(filename=disp_filename,
return_cell=True)
else:
phpy = PhonopyYaml()
phpy.read(disp_filename)
supercell = phpy.supercell
disp_dataset = phpy.dataset
if 'natom' in disp_dataset: # type-1 dataset
num_atoms = disp_dataset['natom']
num_displacements = len(disp_dataset['first_atoms'])
dataset_type = 1
elif 'displacements' in disp_dataset: # type-2 dataset
num_atoms = disp_dataset['displacements'].shape[1]
num_displacements = disp_dataset['displacements'].shape[0]
dataset_type = 2
else:
raise RuntimeError("Number of atoms could not be retrieved from %s" %
disp_filename)
if force_sets_zero_mode:
num_displacements += 1
if interface_mode in (None, 'vasp', 'abinit', 'elk', 'qe', 'siesta',
'cp2k', 'crystal', 'dftbp', 'turbomole'):
force_sets = get_force_sets(interface_mode,
num_atoms,
num_displacements,
force_filenames,
disp_filename=disp_filename,
check_number_of_files=True,
verbose=(log_level > 0))
elif interface_mode == 'wien2k':
from phonopy.interface.wien2k import parse_set_of_forces
if not _check_number_of_files(num_displacements, force_filenames,
disp_filename):
force_sets = []
else:
disps, _ = get_displacements_and_forces(disp_dataset)
force_sets = parse_set_of_forces(
disps,
force_filenames,
supercell,
is_distribute=(not is_wien2k_p1),
symmetry_tolerance=symmetry_tolerance,
verbose=(log_level > 0))
else:
force_sets = []
if force_sets:
if force_sets_zero_mode:
force_sets = _subtract_residual_forces(force_sets)
if dataset_type == 1:
for forces, disp in zip(force_sets, disp_dataset['first_atoms']):
disp['forces'] = forces
elif dataset_type == 2:
disp_dataset['forces'] = np.array(force_sets,
dtype='double',
order='C')
else:
raise RuntimeError("FORCE_SETS could not be created.")
write_FORCE_SETS(disp_dataset, filename=force_sets_filename)
if log_level > 0:
if force_sets:
print("%s has been created." % force_sets_filename)
else:
print("%s could not be created." % force_sets_filename)
return 0
def create_FORCE_SETS(interface_mode, force_filenames, options, log_level):
if interface_mode == "vasp":
displacements = parse_disp_yaml(filename="disp.yaml")
if (
interface_mode == "wien2k"
or interface_mode == "abinit"
or interface_mode == "elk"
or interface_mode == "pwscf"
or interface_mode == "siesta"
):
displacements, supercell = parse_disp_yaml(filename="disp.yaml", return_cell=True)
num_disp_files = len(force_filenames)
if options.force_sets_zero_mode:
num_disp_files -= 1
if len(displacements["first_atoms"]) != num_disp_files:
print("")
print("Number of files to be read don't match " "to number of displacements in disp.yaml.")
return 1
if interface_mode == "vasp":
from phonopy.interface.vasp import parse_set_of_forces
is_parsed = parse_set_of_forces(displacements, force_filenames, is_zero_point=options.force_sets_zero_mode)
if interface_mode == "abinit":
from phonopy.interface.abinit import parse_set_of_forces
print("**********************************************************")
print("**** Abinit FORCE_SETS support is experimental. ****")
print("**** Your feedback would be appreciated. ****")
print("**********************************************************")
is_parsed = parse_set_of_forces(displacements, force_filenames, supercell.get_number_of_atoms())
if interface_mode == "pwscf":
from phonopy.interface.pwscf import parse_set_of_forces
print("**********************************************************")
print("**** Pwscf FORCE_SETS support is experimental. ****")
print("**** Your feedback would be appreciated. ****")
print("**********************************************************")
is_parsed = parse_set_of_forces(displacements, force_filenames, supercell.get_number_of_atoms())
if interface_mode == "wien2k":
from phonopy.interface.wien2k import parse_set_of_forces
print("**********************************************************")
print("**** Wien2k FORCE_SETS support is experimental. ****")
print("**** Your feedback would be appreciated. ****")
print("**********************************************************")
is_parsed = parse_set_of_forces(
displacements, force_filenames, supercell, is_distribute=(not options.is_wien2k_p1), symprec=options.symprec
)
if interface_mode == "elk":
from phonopy.interface.elk import parse_set_of_forces
print("**********************************************************")
print("**** Elk FORCE_SETS support is experimental. ****")
print("**** Your feedback would be appreciated. ****")
print("**********************************************************")
is_parsed = parse_set_of_forces(displacements, force_filenames, supercell.get_number_of_atoms())
if interface_mode == "siesta":
from phonopy.interface.siesta import parse_set_of_forces
print("**********************************************************")
print("**** Siesta FORCE_SETS support is experimental. ****")
print("**** Your feedback would be appreciated. ****")
print("**********************************************************")
is_parsed = parse_set_of_forces(displacements, force_filenames, supercell.get_number_of_atoms())
if is_parsed:
write_FORCE_SETS(displacements, filename="FORCE_SETS")
if log_level > 0:
if is_parsed:
print("FORCE_SETS has been created.")
else:
print("FORCE_SETS could not be created.")
return 0
