def parse_FORCE_SETS( num_atom,
is_translational_invariance = False,
filename = "FORCE_SETS" ):
set_of_forces = []
file = open(filename, 'r')
natom_from_disp_yaml = int( get_line_ignore_blank( file ) )
if not num_atom==natom_from_disp_yaml:
return None
num_displacements = int( get_line_ignore_blank( file ) )
for i in range(num_displacements):
line = get_line_ignore_blank( file )
atom_number = int( line )
line = get_line_ignore_blank( file ).split()
displacement = np.array([ float(x) for x in line ])
forces_tmp = []
for j in range( num_atom ):
line = get_line_ignore_blank( file ).split()
forces_tmp.append(np.array( [ float(x) for x in line ] ) )
forces = Forces( atom_number-1, displacement, forces_tmp )
if is_translational_invariance:
forces.set_translational_invariance()
set_of_forces.append(forces)
return set_of_forces
def parse_FORCES(cell, is_translational_invariance=False, filename="FORCES"):
set_of_forces = []
f = open(filename, 'r')
num_displacements = int(f.readline().strip())
for i in range(num_displacements):
line = f.readline().strip().split()
atom_number = int(line[0])
displacement = np.array([float(line[x]) for x in (1, 2, 3)])
displacement = np.dot(displacement, cell.get_cell())
forces_tmp = []
for j in range(cell.get_number_of_atoms()):
forces_tmp.append(
np.array([float(x) for x in f.readline().strip().split()]))
forces = Forces(atom_number - 1, displacement, forces_tmp)
if is_translational_invariance:
forces.set_translational_invariance()
set_of_forces.append(forces)
return set_of_forces
def parse_FORCES( cell,
is_translational_invariance = False,
filename = "FORCES" ):
set_of_forces = []
file = open(filename, 'r')
num_displacements = int(file.readline().strip())
for i in range(num_displacements):
line = file.readline().strip().split()
atom_number = int( line[0] )
displacement = np.array([ float(line[x]) for x in (1,2,3)])
displacement = np.dot( displacement, cell.get_cell() )
forces_tmp = []
for j in range(cell.get_number_of_atoms()):
forces_tmp.append(np.array(
[ float(x) for x in file.readline().strip().split() ]))
forces = Forces( atom_number-1, displacement, forces_tmp )
if is_translational_invariance:
forces.set_translational_invariance()
set_of_forces.append(forces)
return set_of_forces
def get_set_of_forces(f, num_atom, is_translational_invariance):
set_of_forces = []
natom_from_disp_yaml = int(get_line_ignore_blank(f))
if not num_atom==natom_from_disp_yaml:
return None
num_displacements = int(get_line_ignore_blank(f))
for i in range(num_displacements):
line = get_line_ignore_blank(f)
atom_number = int(line)
line = get_line_ignore_blank(f).split()
displacement = np.array([float(x) for x in line])
forces_tmp = []
for j in range(num_atom):
line = get_line_ignore_blank(f).split()
forces_tmp.append(np.array([float(x) for x in line]))
forces = Forces(atom_number-1, displacement, forces_tmp)
if is_translational_invariance:
forces.set_translational_invariance()
set_of_forces.append(forces)
return set_of_forces
def get_set_of_forces(f, num_atom, is_translational_invariance):
set_of_forces = []
natom_from_disp_yaml = int(get_line_ignore_blank(f))
if not num_atom == natom_from_disp_yaml:
return None
num_displacements = int(get_line_ignore_blank(f))
for i in range(num_displacements):
line = get_line_ignore_blank(f)
atom_number = int(line)
line = get_line_ignore_blank(f).split()
displacement = np.array([float(x) for x in line])
forces_tmp = []
for j in range(num_atom):
line = get_line_ignore_blank(f).split()
forces_tmp.append(np.array([float(x) for x in line]))
forces = Forces(atom_number - 1, displacement, forces_tmp)
if is_translational_invariance:
forces.set_translational_invariance()
set_of_forces.append(forces)
return set_of_forces
def set_forces(self, sets_of_forces):
forces = []
for i, disp in enumerate(self._displacements):
forces.append(Forces(disp[0], disp[1:4], sets_of_forces[i]))
self._set_of_forces_objects = forces