def parse_set_of_forces(num_atoms,
forces_filenames,
verbose=True):
hook = 'Forces acting on atoms'
is_parsed = True
force_sets = []
for i, filename in enumerate(forces_filenames):
if verbose:
sys.stdout.write("%d. " % (i + 1))
pwscf_forces = iter_collect_forces(filename,
num_atoms,
hook,
[6, 7, 8],
word='force')
if check_forces(pwscf_forces, num_atoms, filename, verbose=verbose):
drift_force = get_drift_forces(pwscf_forces,
filename=filename,
verbose=verbose)
force_sets.append(np.array(pwscf_forces) - drift_force)
else:
is_parsed = False
if is_parsed:
return force_sets
else:
return []
def parse_set_of_forces(num_atoms, forces_filenames, verbose=True):
hook = 'ATOM X Y Z'
force_sets = []
for i, filename in enumerate(forces_filenames):
if verbose:
sys.stdout.write("%d. " % (i + 1))
crystal_forces = iter_collect_forces(filename, num_atoms, hook,
[2, 3, 4])
if check_forces(crystal_forces, num_atoms, filename, verbose=verbose):
is_parsed = True
drift_force = get_drift_forces(crystal_forces,
filename=filename,
verbose=verbose)
# Convert forces Hartree / Bohr -> eV / Angstrom
# This avoids confusion with the units. CRYSTAL uses Angstroms for
# coordinates, but Hartree / Bohr for forces. This would lead in mixed
# units hartree / (Angstrom * Bohr) for force constants, requiring
# additional tweaks for unit conversions in other parts of the code
force_sets.append(
np.multiply(
np.array(crystal_forces) - drift_force, Hartree / Bohr))
else:
is_parsed = False
if is_parsed:
return force_sets
else:
return []
def parse_set_of_forces(num_atoms,
forces_filenames,
verbose=True):
hook = 'ATOM X Y Z'
force_sets = []
for i, filename in enumerate(forces_filenames):
if verbose:
sys.stdout.write("%d. " % (i + 1))
crystal_forces = iter_collect_forces(filename,
num_atoms,
hook,
[2, 3, 4])
if check_forces(crystal_forces, num_atoms, filename, verbose=verbose):
is_parsed = True
drift_force = get_drift_forces(crystal_forces,
filename=filename,
verbose=verbose)
# Convert forces Hartree / Bohr -> eV / Angstrom
# This avoids confusion with the units. CRYSTAL uses Angstroms for
# coordinates, but Hartree / Bohr for forces. This would lead in mixed
# units hartree / (Angstrom * Bohr) for force constants, requiring
# additional tweaks for unit conversions in other parts of the code
force_sets.append(np.multiply(np.array(crystal_forces) - drift_force, Hartree / Bohr))
else:
is_parsed = False
if is_parsed:
return force_sets
else:
return []
def parse_set_of_forces(num_atoms,
forces_filenames,
verbose=True):
hook = 'Forces acting on atoms'
is_parsed = True
force_sets = []
for i, filename in enumerate(forces_filenames):
if verbose:
sys.stdout.write("%d. " % (i + 1))
pwscf_forces = iter_collect_forces(filename,
num_atoms,
hook,
[6, 7, 8],
word='force')
if check_forces(pwscf_forces, num_atoms, filename, verbose=verbose):
drift_force = get_drift_forces(pwscf_forces,
filename=filename,
verbose=verbose)
force_sets.append(np.array(pwscf_forces) - drift_force)
else:
is_parsed = False
if is_parsed:
return force_sets
else:
return []
def parse_set_of_forces(displacements, forces_filenames, num_atom):
hook = ''
for siesta_filename, disp in zip(forces_filenames,
displacements['first_atoms']):
siesta_forces = iter_collect_forces(siesta_filename,
num_atom,
hook, [1, 2, 3],
word='')
drift_force = get_drift_forces(siesta_forces)
disp['forces'] = np.array(siesta_forces) - drift_force
return True
def parse_set_of_forces(num_atoms, forces_filenames):
hook = '' # Just for skipping the first line
force_sets = []
for filename in forces_filenames:
siesta_forces = iter_collect_forces(filename,
num_atoms,
hook, [1, 2, 3],
word='')
if not siesta_forces:
return []
drift_force = get_drift_forces(siesta_forces)
force_sets.append(np.array(siesta_forces) - drift_force)
return force_sets
def parse_set_of_forces(displacements,
forces_filenames,
num_atom):
hook = 'Forces acting on atoms'
for pwscf_filename, disp in zip(forces_filenames,
displacements['first_atoms']):
pwscf_forces = iter_collect_forces(pwscf_filename,
num_atom,
hook,
[6, 7, 8],
word='force')
drift_force = get_drift_forces(pwscf_forces)
disp['forces'] = np.array(pwscf_forces) - drift_force
return True
def parse_set_of_forces(num_atoms, forces_filenames):
hook = 'Forces acting on atoms'
force_sets = []
for filename in forces_filenames:
pwscf_forces = iter_collect_forces(filename,
num_atoms,
hook, [6, 7, 8],
word='force')
if not pwscf_forces:
return []
drift_force = get_drift_forces(pwscf_forces)
force_sets.append(np.array(pwscf_forces) - drift_force)
return force_sets
def parse_set_of_forces(displacements,
forces_filenames,
num_atom):
hook = ''
for siesta_filename, disp in zip(forces_filenames,
displacements['first_atoms']):
siesta_forces = iter_collect_forces(siesta_filename,
num_atom,
hook,
[1, 2, 3],
word='')
drift_force = get_drift_forces(siesta_forces)
disp['forces'] = np.array(siesta_forces) - drift_force
return True
def parse_set_of_forces(num_atoms, forces_filenames):
hook = '' # Just for skipping the first line
force_sets = []
for filename in forces_filenames:
siesta_forces = iter_collect_forces(filename,
num_atoms,
hook,
[1, 2, 3],
word='')
if not siesta_forces:
return []
drift_force = get_drift_forces(siesta_forces)
force_sets.append(np.array(siesta_forces) - drift_force)
return force_sets
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 parse_set_of_forces(num_atoms, forces_filenames):
hook = 'Forces acting on atoms'
force_sets = []
for filename in forces_filenames:
pwscf_forces = iter_collect_forces(filename,
num_atoms,
hook,
[6, 7, 8],
word='force')
if not pwscf_forces:
return []
drift_force = get_drift_forces(pwscf_forces)
force_sets.append(np.array(pwscf_forces) - drift_force)
return force_sets
def parse_set_of_forces(num_atoms, forces_filenames, verbose=True):
force_sets = []
for i, filename in enumerate(forces_filenames):
if verbose:
sys.stdout.write("%d. " % (i + 1))
forces = iter_collect_forces(filename, num_atoms,
'# Atom Kind Element', [3, 4, 5])
if not check_forces(forces, num_atoms, filename, verbose=verbose):
return [] # if one file is invalid, the whole thing is broken
drift_force = get_drift_forces(forces,
filename=filename,
verbose=verbose)
force_sets.append(np.array(forces) - drift_force)
return force_sets
def parse_set_of_forces(num_atoms, forces_filenames, verbose=True):
hook = '' # Just for skipping the first line
is_parsed = True
force_sets = []
for i, filename in enumerate(forces_filenames):
if verbose:
sys.stdout.write("%d. " % (i + 1))
siesta_forces = iter_collect_forces(filename,
num_atoms,
hook, [1, 2, 3],
word='')
if check_forces(siesta_forces, num_atoms, filename, verbose=verbose):
drift_force = get_drift_forces(siesta_forces,
filename=filename,
verbose=verbose)
force_sets.append(np.array(siesta_forces) - drift_force)
else:
is_parsed = False
if is_parsed:
return force_sets
else:
return []
def parse_set_of_forces(num_atoms, forces_filenames, verbose=True):
hook = '' # Just for skipping the first line
is_parsed = True
force_sets = []
for i, filename in enumerate(forces_filenames):
if verbose:
sys.stdout.write("%d. " % (i + 1))
siesta_forces = iter_collect_forces(filename,
num_atoms,
hook,
[1, 2, 3],
word='')
if check_forces(siesta_forces, num_atoms, filename, verbose=verbose):
drift_force = get_drift_forces(siesta_forces,
filename=filename,
verbose=verbose)
force_sets.append(np.array(siesta_forces) - drift_force)
else:
is_parsed = False
if is_parsed:
return force_sets
else:
return []
