def parse_set_of_forces(num_atoms, forces_filenames, verbose=True):
"""Parse forces from output files."""
hook = "Forces :"
is_parsed = True
force_sets = []
for i, filename in enumerate(forces_filenames):
if verbose:
sys.stdout.write("%d. " % (i + 1))
f = open(filename)
elk_forces = collect_forces(f,
num_atoms,
hook, [3, 4, 5],
word="total force")
if check_forces(elk_forces, num_atoms, filename, verbose=verbose):
drift_force = get_drift_forces(elk_forces,
filename=filename,
verbose=verbose)
force_sets.append(np.array(elk_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 = 'Forces :'
is_parsed = True
force_sets = []
for i, filename in enumerate(forces_filenames):
if verbose:
sys.stdout.write("%d. " % (i + 1))
f = open(filename)
elk_forces = collect_forces(f,
num_atoms,
hook,
[3, 4, 5],
word='total force')
if check_forces(elk_forces, num_atoms, filename, verbose=verbose):
drift_force = get_drift_forces(elk_forces,
filename=filename,
verbose=verbose)
force_sets.append(np.array(elk_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 = '1 #'
is_parsed = True
force_sets = []
for i, filename in enumerate(forces_filenames):
if verbose:
sys.stdout.write("%d. " % (i + 1))
f = open(filename)
fleur_forces = collect_forces(f,
num_atoms,
hook, [0, 1, 2],
word='force')
if check_forces(fleur_forces, num_atoms, filename, verbose=verbose):
drift_force = get_drift_forces(fleur_forces,
filename=filename,
verbose=verbose)
force_sets.append(np.array(fleur_forces) - drift_force)
else:
is_parsed = False
if is_parsed:
return force_sets
else:
return []
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(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 = "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 = '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 = '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(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, verbose=True):
hook = '# Atom Kind Element'
force_sets = []
for i, filename in enumerate(forces_filenames):
if verbose:
sys.stdout.write("%d. " % (i + 1))
with open(filename) as fhandle:
cp2k_forces = collect_forces(fhandle, num_atoms, hook, [3, 4, 5])
if check_forces(cp2k_forces, num_atoms, filename, verbose=verbose):
drift_force = get_drift_forces(cp2k_forces,
filename=filename,
verbose=verbose)
force_sets.append(np.array(cp2k_forces) - drift_force)
else:
return [] # if one file is invalid, the whole thing is broken
return force_sets
def parse_set_of_forces(num_atoms, forces_filenames, verbose=True):
hook = 'cartesian forces (eV/Angstrom)'
is_parsed = True
force_sets = []
for i, filename in enumerate(forces_filenames):
if verbose:
sys.stdout.write("%d. " % (i + 1))
f = open(filename)
abinit_forces = collect_forces(f, num_atoms, hook, [1, 2, 3])
if check_forces(abinit_forces, num_atoms, filename, verbose=verbose):
drift_force = get_drift_forces(abinit_forces,
filename=filename,
verbose=verbose)
force_sets.append(np.array(abinit_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 = 'cartesian forces (eV/Angstrom)'
is_parsed = True
force_sets = []
for i, filename in enumerate(forces_filenames):
if verbose:
sys.stdout.write("%d. " % (i + 1))
f = open(filename)
abinit_forces = collect_forces(f, num_atoms, hook, [1, 2, 3])
if check_forces(abinit_forces, num_atoms, filename, verbose=verbose):
drift_force = get_drift_forces(abinit_forces,
filename=filename,
verbose=verbose)
force_sets.append(np.array(abinit_forces) - drift_force)
else:
is_parsed = False
if is_parsed:
return force_sets
else:
return []