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Implement write_FORCES_FC4

This commit is contained in:
Atsushi Togo 2015-01-23 13:18:27 +09:00
parent f353c57524
commit ebde17ae01
2 changed files with 96 additions and 29 deletions
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44
anharmonic/file_IO.py
View File

@ -161,6 +161,15 @@ def write_disp_fc2_yaml(dataset, supercell, filename='disp_fc2.yaml'):
return num_first
def write_FORCES_FC4_vasp(vaspruns,
disp_dataset,
filename='FORCES_FC4'):
natom = disp_dataset['natom']
forces = get_forces_from_vasprun_xmls(vaspruns, natom)
w = open(filename, 'w')
write_FORCES_FC4(disp_dataset, forces, fp=w)
w.close()
def write_FORCES_FC3_vasp(vaspruns,
disp_dataset,
filename='FORCES_FC3'):
@ -236,6 +245,41 @@ def write_FORCES_FC3(disp_dataset, forces_fc3, fp=None, filename="FORCES_FC3"):
for j in range(natom):
w.write("%15.10f %15.10f %15.10f\n" % (0, 0, 0))
count += 1
def write_FORCES_FC4(disp_dataset, forces_fc4, fp=None, filename="FORCES_FC4"):
if fp is None:
w = open(filename, 'w')
else:
w = fp
natom = disp_dataset['natom']
num_disp1 = len(disp_dataset['first_atoms'])
num_disp2 = 0
for disp1 in disp_dataset['first_atoms']:
num_disp2 += len(disp1['second_atoms'])
count = num_disp1 + num_disp2
write_FORCES_FC3(disp_dataset, forces_fc3=forces_fc4, fp=w)
for i, disp1 in enumerate(disp_dataset['first_atoms']):
atom1 = disp1['number']
for disp2 in disp1['second_atoms']:
atom2 = disp2['number']
for disp3 in disp2['third_atoms']:
atom3 = disp3['number']
w.write("# File: %-5d\n" % (count + 1))
w.write("# %-5d " % (atom1 + 1))
w.write("%20.16f %20.16f %20.16f\n" %
tuple(disp1['displacement']))
w.write("# %-5d " % (atom2 + 1))
w.write("%20.16f %20.16f %20.16f\n" %
tuple(disp2['displacement']))
w.write("# %-5d " % (atom3 + 1))
w.write("%20.16f %20.16f %20.16f\n" %
tuple(disp3['displacement']))
for forces in forces_fc4[count]:
w.write("%15.10f %15.10f %15.10f\n" % tuple(forces))
count += 1
def write_FORCES_THIRD(vaspruns,
disp_dataset,

81
scripts/phono4py
View File

@ -46,7 +46,7 @@ from phonopy.units import VaspToTHz
from phonopy.harmonic.force_constants import show_drift_force_constants
from anharmonic.phonon3.fc3 import show_drift_fc3
from anharmonic.file_IO import parse_disp_fc4_yaml,\
write_FORCES_FOURTH, parse_FORCES_FC4, \
write_FORCES_FC4_vasp, parse_FORCES_FC4, \
read_fc4_from_hdf5, read_fc3_from_hdf5, read_fc2_from_hdf5, \
write_fc4_to_hdf5, write_fc3_to_hdf5, write_fc2_to_hdf5, \
write_freq_shifts_to_hdf5, write_disp_fc4_yaml
@ -72,16 +72,33 @@ def print_end():
\___|_| |_|\__,_|
"""
def print_error():
print """ ___ _ __ _ __ ___ _ __
/ _ \ '__| '__/ _ \| '__|
| __/ | | | | (_) | |
\___|_| |_| \___/|_|
"""
def print_error(message):
print message
def file_exists(filename, log_level):
if os.path.exists(filename):
return True
else:
error_text = "%s not found." % filename
print_error_message(error_text)
if log_level > 0:
print_error()
sys.exit(1)
# Parse options
parser = OptionParser()
parser.set_defaults(band_indices=None,
cell_poscar=None,
displacement_distance=None,
factor=None,
forces_fourth_mode=False,
forces_fc4_mode=False,
grid_points=None,
input_filename=None,
input_output_filename=None,
@ -114,9 +131,9 @@ parser.add_option("-c", "--cell", dest="cell_poscar",
action="store", type="string",
help="Read unit cell", metavar="FILE")
parser.add_option("--cf4", "--create_f4",
dest="forces_fourth_mode",
dest="forces_fc4_mode",
action="store_true",
help="Create FORCES_FOURTH")
help="Create FORCES_FC4")
parser.add_option("-d", "--disp", dest="is_displacement",
action="store_true",
help="As first stage, get least displacements")
@ -211,17 +228,33 @@ if options.input_output_filename is not None:
input_filename = options.input_output_filename
output_filename = options.input_output_filename
# Create FC2_FOURTH_SETS
if options.forces_fourth_mode:
displacements = parse_disp_fc4_yaml()
write_FORCES_FOURTH(args, displacements)
print_end()
exit(0)
# Title
if log_level:
print_phono4py()
#####################
# Create FORCES_FC4 #
#####################
if options.forces_fc4_mode:
if input_filename is None:
filename = 'disp_fc4.yaml'
else:
filename = 'disp_fc4.' + input_filename + '.yaml'
file_exists(filename, log_level)
if log_level:
print "Displacement dataset is read from %s." % filename
disp_dataset = parse_disp_fc4_yaml()
write_FORCES_FC4_vasp(args, disp_dataset)
if log_level:
print "FORCES_FC4 has been created."
print_end()
exit(0)
##################
# Parse settings #
##################
if len(args) > 0:
phono3py_conf = Phono3pyConfParser(filename=args[0],
options=options,
@ -233,26 +266,16 @@ else:
option_list=option_list)
settings = phono3py_conf.get_settings()
# Read POSCAR
###################################
# Read crystal structure (POSCAR) #
###################################
if options.cell_poscar is None:
if os.path.exists('POSCAR'):
unitcell_filename = 'POSCAR'
else:
print_error("POSCAR could not be found.")
if log_level:
print_end()
sys.exit(1)
file_exists('POSCAR', log_level)
unitcell_filename = 'POSCAR'
else:
if os.path.exists(options.cell_poscar):
unitcell_filename = options.cell_poscar
else:
print_error("%s not found" % options.cell_poscar)
if log_level:
print_end()
sys.exit(1)
unitcell = read_vasp(unitcell_filename,
settings.get_chemical_symbols())
file_exists(options.cell_poscar, log_level)
unitcell_filename = options.cell_poscar
unitcell = read_vasp(unitcell_filename, settings.get_chemical_symbols())
#################################################
# Create supercells with displacements and exit #