def parse_set_of_forces(displacements,
forces_filenames,
supercell,
disp_keyword='first_atoms',
is_distribute=True,
symprec=1e-5):
natom = supercell.get_number_of_atoms()
lattice = supercell.get_cell()
force_sets = []
for wien2k_filename, disp in zip(forces_filenames,
displacements[disp_keyword]):
# Parse wien2k case.scf file
wien2k_forces = get_forces_wien2k(wien2k_filename, lattice)
if is_distribute:
forces = _distribute_forces(supercell,
[disp['number'], disp['displacement']],
wien2k_forces, wien2k_filename,
symprec)
if not forces:
return []
else:
if not (natom == len(wien2k_forces)):
print("%s contains only forces of %d atoms" %
(wien2k_filename, len(wien2k_forces)))
return []
else:
forces = wien2k_forces
drift_force = get_drift_forces(forces, filename=wien2k_filename)
force_sets.append(np.array(forces) - drift_force)
return force_sets
def create_FORCE_SETS(forces_filenames,
displacements,
supercell,
filename='FORCE_SETS',
is_distribute=True,
symprec=1e-5):
natom = supercell.get_number_of_atoms()
lattice = supercell.get_cell()
for wien2k_filename, disp in zip(forces_filenames,
displacements['first_atoms']):
# Parse wien2k case.scf file
wien2k_forces = get_forces_wien2k(wien2k_filename, lattice)
if is_distribute:
force_set = distribute_forces(
supercell, [disp['number'], disp['displacement']],
wien2k_forces, wien2k_filename, symprec)
if not force_set:
return False
else:
if not (natom == len(wien2k_forces)):
print "%s contains only forces of %d atoms" % (
wien2k_filename, len(wien2k_forces))
return False
else:
force_set = wien2k_forces
drift_force = get_drift_forces(force_set, filename=wien2k_filename)
disp['forces'] = np.array(force_set) - drift_force
write_FORCE_SETS(displacements, filename=filename)
return True
def create_FORCE_SETS(forces_filenames,
displacements,
supercell,
filename='FORCE_SETS',
is_distribute=True,
symprec=1e-5):
natom = supercell.get_number_of_atoms()
lattice = supercell.get_cell()
for wien2k_filename, disp in zip(forces_filenames,
displacements['first_atoms']):
# Parse wien2k case.scf file
wien2k_forces = get_forces_wien2k(wien2k_filename, lattice)
if is_distribute:
force_set = distribute_forces(
supercell,
[disp['number'], disp['displacement']],
wien2k_forces,
wien2k_filename,
symprec)
if not force_set:
return False
else:
if not (natom == len(wien2k_forces)):
print "%s contains only forces of %d atoms" % (
wien2k_filename, len(wien2k_forces))
return False
else:
force_set = wien2k_forces
drift_force = get_drift_forces(force_set, filename=wien2k_filename)
disp['forces'] = np.array(force_set) - drift_force
write_FORCE_SETS(displacements, filename=filename)
return True
def parse_set_of_forces(displacements,
forces_filenames,
supercell,
disp_keyword='first_atoms',
is_distribute=True,
symprec=1e-5):
natom = supercell.get_number_of_atoms()
lattice = supercell.get_cell()
force_sets = []
for wien2k_filename, disp in zip(forces_filenames,
displacements[disp_keyword]):
# Parse wien2k case.scf file
wien2k_forces = get_forces_wien2k(wien2k_filename, lattice)
if is_distribute:
forces = _distribute_forces(
supercell,
[disp['number'], disp['displacement']],
wien2k_forces,
wien2k_filename,
symprec)
if not forces:
return []
else:
if not (natom == len(wien2k_forces)):
print("%s contains only forces of %d atoms" %
(wien2k_filename, len(wien2k_forces)))
return []
else:
forces = wien2k_forces
drift_force = get_drift_forces(forces, filename=wien2k_filename)
force_sets.append(np.array(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 = "cartesian forces (eV/Angstrom)"
force_sets = []
for filename in forces_filenames:
f = open(filename)
abinit_forces = collect_forces(f, num_atoms, hook, [1, 2, 3])
if not abinit_forces:
return []
drift_force = get_drift_forces(abinit_forces)
force_sets.append(np.array(abinit_forces) - drift_force)
return force_sets
def parse_set_of_forces(num_atoms, forces_filenames):
hook = 'cartesian forces (eV/Angstrom)'
force_sets = []
for filename in forces_filenames:
f = open(filename)
abinit_forces = collect_forces(f, num_atoms, hook, [1, 2, 3])
if not abinit_forces:
return []
drift_force = get_drift_forces(abinit_forces)
force_sets.append(np.array(abinit_forces) - drift_force)
return force_sets
def parse_set_of_forces(num_atoms, forces_filenames):
hook = "Forces :"
force_sets = []
for filename in forces_filenames:
f = open(filename)
elk_forces = collect_forces(f, num_atoms, hook, [3, 4, 5], word="total force")
if not elk_forces:
return []
drift_force = get_drift_forces(elk_forces)
force_sets.append(np.array(elk_forces) - drift_force)
return force_sets
def parse_set_of_forces(displacements, forces_filenames, num_atom):
hook = 'cartesian forces (eV/Angstrom)'
for abinit_filename, disp in zip(forces_filenames,
displacements['first_atoms']):
f = open(abinit_filename)
abinit_forces = collect_forces(f, num_atom, hook, [1, 2, 3])
if not abinit_forces:
return False
drift_force = get_drift_forces(abinit_forces)
disp['forces'] = np.array(abinit_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(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 = ''
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(displacements,
forces_filenames,
num_atom):
hook = 'cartesian forces (eV/Angstrom)'
for abinit_filename, disp in zip(forces_filenames,
displacements['first_atoms']):
f = open(abinit_filename)
abinit_forces = collect_forces(f, num_atom, hook, [1, 2, 3])
if not abinit_forces:
return False
drift_force = get_drift_forces(abinit_forces)
disp['forces'] = np.array(abinit_forces) - drift_force
return True
def parse_set_of_forces(displacements, forces_filenames, num_atom):
hook = 'Forces :'
for elk_filename, disp in zip(forces_filenames,
displacements['first_atoms']):
f = open(elk_filename)
elk_forces = collect_forces(f,
num_atom,
hook, [3, 4, 5],
word='total force')
if not elk_forces:
return False
drift_force = get_drift_forces(elk_forces)
disp['forces'] = np.array(elk_forces) - drift_force
return True
def parse_set_of_forces(num_atoms, forces_filenames):
hook = 'Forces :'
force_sets = []
for filename in forces_filenames:
f = open(filename)
elk_forces = collect_forces(f,
num_atoms,
hook, [3, 4, 5],
word='total force')
if not elk_forces:
return []
drift_force = get_drift_forces(elk_forces)
force_sets.append(np.array(elk_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(displacements,
forces_filenames,
num_atom):
hook = 'Forces :'
for elk_filename, disp in zip(forces_filenames,
displacements['first_atoms']):
f = open(elk_filename)
elk_forces = collect_forces(f,
num_atom,
hook,
[3, 4, 5],
word='total force')
if not elk_forces:
return False
drift_force = get_drift_forces(elk_forces)
disp['forces'] = np.array(elk_forces) - drift_force
return True