def write_FORCES(lattice,
forces_filenames,
displacements,
filename='FORCE_SETS',
amplitude=0.01,
mode='vasp',
is_zero_point=False,
is_fropho_disp=False):
if mode == "vasp":
try:
from lxml import etree
except ImportError:
print "You need to install python-lxml."
sys.exit(1)
if is_zero_point:
force_files = forces_filenames[1:]
if mode == "wien2k":
zero_forces = wien2k.get_forces_wien2k(forces_filenames[0],
lattice)
else: # "vasp" case
zero_forces = \
vasp.get_forces_vasprun_xml(etree.iterparse(
vasp.VasprunWrapper(forces_filenames[0]),
tag='varray'))
else:
force_files = forces_filenames
zero_forces = None
displacements = sort_displacements(displacements)
forces = []
# Show progress
print >> sys.stderr, "counter (file index):",
for i in range(len(displacements)):
if mode == "wien2k": # wien2k
forces.append(wien2k.get_forces_wien2k(force_files[i], lattice))
else: # vasp
forces.append(
vasp.get_forces_vasprun_xml(
etree.iterparse(vasp.VasprunWrapper(force_files[i]),
tag='varray')))
write_FORCES_from_forces(lattice,
forces,
displacements,
amplitude,
filename,
zero_forces,
is_fropho_disp,
verbose=True)
# Show progress
print >> sys.stderr, "\n"
def write_FORCES( lattice,
forces_filenames,
displacements,
filename='FORCE_SETS',
amplitude=0.01,
mode='vasp',
is_zero_point=False,
is_fropho_disp=False ):
if mode == "vasp":
try:
from lxml import etree
except ImportError:
print "You need to install python-lxml."
sys.exit(1)
if is_zero_point:
force_files = forces_filenames[1:]
if mode == "wien2k":
zero_forces = wien2k.get_forces_wien2k(forces_filenames[0], lattice)
else: # "vasp" case
zero_forces = \
vasp.get_forces_vasprun_xml(etree.iterparse(
vasp.VasprunWrapper( forces_filenames[0] ),
tag='varray' ) )
else:
force_files = forces_filenames
zero_forces = None
displacements = sort_displacements( displacements )
forces = []
# Show progress
print >> sys.stderr, "counter (file index):",
for i in range( len( displacements ) ):
if mode == "wien2k": # wien2k
forces.append( wien2k.get_forces_wien2k( force_files[i], lattice ) )
else: # vasp
forces.append(
vasp.get_forces_vasprun_xml( etree.iterparse(
vasp.VasprunWrapper( force_files[i] ),
tag='varray') ) )
write_FORCES_from_forces( lattice,
forces,
displacements,
amplitude,
filename,
zero_forces,
is_fropho_disp,
verbose=True )
# Show progress
print >> sys.stderr, "\n"
def write_FORCE_SETS_wien2k(forces_filenames,
displacements,
supercell,
filename='FORCE_SETS',
is_zero_point=False,
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 = wien2k.get_forces_wien2k(wien2k_filename, lattice)
if is_distribute:
force_set = wien2k.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 = np.sum(force_set, axis=0) / len(force_set)
print "Drift force of %s" % wien2k_filename
print "%12.8f %12.8f %12.8f" % tuple(drift_force)
print "This drift force was subtracted from forces."
print
disp['forces'] = np.array(force_set) - drift_force
write_FORCE_SETS(displacements, filename=filename)
return True
def write_FORCE_SETS_wien2k(forces_filenames,
displacements,
supercell,
filename='FORCE_SETS',
is_zero_point=False,
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 = wien2k.get_forces_wien2k(wien2k_filename, lattice)
if is_distribute:
force_set = wien2k.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 = np.sum(force_set, axis=0) / len(force_set)
print "Drift force of %s" % wien2k_filename
print "%12.8f %12.8f %12.8f" % tuple(drift_force)
print "This drift force was subtracted from forces."
print
disp['forces'] = np.array(force_set) - drift_force
write_FORCE_SETS(displacements, filename=filename)
return True
