def get_frequencies(self, current_directory, gasphase=False):
''' Returns a list of vibrational frequcencies
Vibrational frequency calculations are placed in a subdirectory
named 'vib'
Calculations from VASP or PHONONPY can be extracted
If no vibrational frequencies is found an empty list is returned
frequencies : list
'''
frequencies = []
# Check if directory 'vib' exists and get frequencies
if 'vib' in os.listdir(current_directory):
print(" 'vib' directory found")
if os.path.isfile(
os.path.join(current_directory, 'vib', self.outcarfile)):
viboutcar = OUTCAR(
os.path.join(current_directory, 'vib', self.outcarfile))
frequencies = viboutcar.read_vibrational_frequencies(
gasphase=gasphase)
elif os.path.isfile(
os.path.join(current_directory, 'vib', self.phononpyfile)):
from vasp_outcar import PHONONPY
viboutfile = PHONONPY(
os.path.join(current_directory, 'vib', self.phononpyfile))
frequencies = viboutfile.read_vibrational_frequencies_phononpy(
)
return frequencies
def get_frequencies(self, current_directory, gasphase = False):
''' Returns a list of vibrational frequcencies
Vibrational frequency calculations are placed in a subdirectory
named 'vib'
Calculations from VASP or PHONONPY can be extracted
If no vibrational frequencies is found an empty list is returned
frequencies : list
'''
frequencies = []
# Check if directory 'vib' exists and get frequencies
if 'vib' in os.listdir(current_directory):
print(" 'vib' directory found")
if os.path.isfile(os.path.join(
current_directory, 'vib', self.outcarfile)):
viboutcar = OUTCAR(os.path.join(
current_directory, 'vib', self.outcarfile))
frequencies = viboutcar.read_vibrational_frequencies(
gasphase=gasphase)
elif os.path.isfile(os.path.join(
current_directory, 'vib', self.phononpyfile)):
from vasp_outcar import PHONONPY
viboutfile = PHONONPY(
os.path.join(current_directory, 'vib', self.phononpyfile))
frequencies = viboutfile.read_vibrational_frequencies_phononpy()
return frequencies
def get_variables(self,
current_directory,
gasphase=False,
surface=False,
solid=False,
adsorbate=False,
ts=False,
species=None,
config=None,
system=None):
'''Get the variables surface_name, composition, species_name, state,
site_name, total_energy, frequencies, cell, positions, info
from the VASP calculations
'''
system_name = self.rootdir.split('/')[-1]
print('\nChecking --- ' + str(current_directory))
# Check if outcarfile and contcarfile ie in the current_directory
if (os.path.isfile(os.path.join(current_directory, self.outcarfile))
and os.path.isfile(
os.path.join(current_directory, self.contcarfile))):
outcar = OUTCAR(os.path.join(current_directory, self.outcarfile))
contcar = CONTCAR(os.path.join(current_directory,
self.contcarfile))
# Checks if the OUTCAR file has completed -- will be
# substituted with outcar.check_convergence
finished = outcar.outcar_check()
if finished is False:
if surface:
print(" ERROR --- OUTCAR is not complete --- Exiting")
sys.exit()
else:
print(" Warning --- OUTCAR file is not complete "
"--- This element is skipped")
variables = []
return variables
# if no contcar or outcar is in current_directory move to next
else:
print(" Warning --- No OUTCAR and/or CONTCAR file found "
"--- This element is skipped")
variables = []
return variables
# Check if calculation has converged
convergence = outcar.check_convergence()
if convergence:
print(' OUTCAR file - converged')
#else:
#print('WARNING --- Check convergency')
# get chemical composition
composition = contcar.read_composition(ordered=True)
# get the total energy of the system
total_energy = outcar.read_energy()
# get the atomic super cell
cell = contcar.read_cell()
# get the atomic position of all elements
positions = contcar.read_atoms_and_positions()
# info is set as the given directory
info = current_directory
if gasphase:
# check if atom/molecule is in defined molecules!!!! Add this
# Set surface, site, species names and bulk_structure for
# gasphase species
surface_name = 'gasphase'
species_name = contcar.read_composition(ordered=True, name=True)
site_name = 'None'
state = 'gasphase'
if surface:
# Set surface, site, species names and bulk_structure for
# gasphase species
surface_name = system_name
site_name = 'None'
species_name = contcar.read_composition(ordered=True)
state = 'surface'
if solid:
# Set surface, site, species names and bulk_structure for
# gasphase species
surface_name = system_name
site_name = 'None'
species_name = contcar.read_composition(ordered=True)
state = 'solid'
if adsorbate:
surface_name = system_name
site_name = config
surface_atoms = self.get_system_atoms(system=system)
species_name = contcar.read_composition(adsorbed=True,
surface=surface_atoms,
name=True)
state = species
if ts:
surface_name = system_name
site_name = config
surface_atoms = self.get_system_atoms(system=system)
species_name = contcar.read_composition(adsorbed=True,
surface=surface_atoms,
name=True)
state = species
image = []
for i in range(0, 40):
if i < 10:
image.append(str(0) + str(i))
else:
image.append(str(i))
if 'dim' in current_directory.split('/'):
print(' Dimer method - used')
elif current_directory.split('/')[-1] in image:
print(' (CI)-NEB method - used - image ' +
str(current_directory.split('/')[-1]) +
' set as transition state '
'--- Check that this is the correct transition state')
else:
print(' Method for finding transition state not given')
frequencies = self.get_frequencies(current_directory,
gasphase=gasphase)
# Check the number of imaginary frequencies
j = 0
for f in frequencies:
if isinstance(f, complex):
j = j + 1
if j > 0 and ts is False:
print(" WARNING --- " + str(j) + " imaginary frequencies found")
elif j > 1 and ts is True:
print(" WARNING --- " + str(j) +
" imaginary frequencies found - is this a true "
"transition state?")
# make list containing information about surface species, species,
# state, site, energy,
# frequencies, cell, positions and info
variables = [
surface_name, composition, species_name, state, site_name,
total_energy, frequencies, cell, positions, info
]
print(' ' + str(variables[0:6]))
return variables
def get_tslist(self, system=None):
"""
Returns the calculated data regarding the transition states.
Transition states data calculated using (CI-)NEB or dimer method can
extracted
Some updated are needed.
"""
print("\n************ TRANSITION STATES ****************")
# get the surface atom species and numbers
#surface_atoms = self.get_surface_atoms()
transition_state_dir, transition_states = self.tsdir_check(
system=system)
transition_state_list = []
for transition_state in transition_states:
# Get list of transition state configurations for ts
config_dir = os.path.join(transition_state_dir, transition_state)
configs = os.listdir(config_dir)
for config in configs:
ts_directory = os.path.join(config_dir, config)
if os.path.isdir(ts_directory):
names = []
for i in os.listdir(ts_directory):
if os.path.isdir(ts_directory + '/' + i):
names.append(i)
# Check if dimer method is used
# If dim is present, results from dimer method will be used
if 'dim' in names:
if os.path.isfile(
os.path.join(ts_directory, 'dim',
self.outcarfile)):
ts_dir = os.path.join(ts_directory, 'dim')
else:
print(
' WARNING --- No OUTCAR/CONTCAR file found')
break
# Check if CI-NEB method is used
elif len(names) > 1:
# make a list with image number and energies
# the image with the highest energy is treated as the
# transition stat
# this can be changede
image_list = []
energy_list = []
for image in names:
if (image.startswith('0') or image.startswith('1')
or image.startswith('2')):
# Make script for OUTCAR is .gz file
if os.path.isfile(
os.path.join(ts_directory, image,
self.outcarfile)):
outcar = OUTCAR(
os.path.join(ts_directory, image,
self.outcarfile))
else:
print(' WARNING --- No OUTCAR/CONTCAR '
'file found')
break
tot_energy = outcar.read_energy()
energy_list.append(tot_energy)
image_list.append(image)
# Find transition state energy and image number
index = energy_list.index(max(energy_list))
# Transition state image
ts_dir = os.path.join(ts_directory, image_list[index])
# The transisition state calculation is directly under
# the config_dir
elif os.path.isfile(
os.path.join(ts_directory, self.outcarfile)):
ts_dir = ts_directory
# No transition state is found
else:
print(' Warning --- no transition state files '
'found for ' + str(ts_directory))
break
# get the variable for the adsorbed species
variables = self.get_variables(ts_dir,
ts=True,
species=transition_state,
config=config,
system=system)
variables_text = '\t'.join([str(w) for w in variables])
transition_state_list.append(variables_text)
return transition_state_list
def get_variables(self, current_directory, gasphase=False, surface=False,
solid=False, adsorbate=False, ts=False, species=None,
config=None, system=None):
'''Get the variables surface_name, composition, species_name, state,
site_name, total_energy, frequencies, cell, positions, info
from the VASP calculations
'''
system_name = self.rootdir.split('/')[-1]
print('\nChecking --- ' + str(current_directory))
# Check if outcarfile and contcarfile ie in the current_directory
if (os.path.isfile(os.path.join(
current_directory, self.outcarfile)) and
os.path.isfile(os.path.join(
current_directory, self.contcarfile))):
outcar = OUTCAR(os.path.join(current_directory, self.outcarfile))
contcar = CONTCAR(os.path.join(current_directory, self.contcarfile))
# Checks if the OUTCAR file has completed -- will be
# substituted with outcar.check_convergence
finished = outcar.outcar_check()
if finished is False:
if surface:
print(" ERROR --- OUTCAR is not complete --- Exiting")
sys.exit()
else:
print(" Warning --- OUTCAR file is not complete "
"--- This element is skipped")
variables = []
return variables
# if no contcar or outcar is in current_directory move to next
else:
print(" Warning --- No OUTCAR and/or CONTCAR file found "
"--- This element is skipped")
variables = []
return variables
# Check if calculation has converged
convergence = outcar.check_convergence()
if convergence:
print(' OUTCAR file - converged')
#else:
#print('WARNING --- Check convergency')
# get chemical composition
composition = contcar.read_composition(ordered=True)
# get the total energy of the system
total_energy = outcar.read_energy()
# get the atomic super cell
cell = contcar.read_cell()
# get the atomic position of all elements
positions = contcar.read_atoms_and_positions()
# info is set as the given directory
info = current_directory
if gasphase:
# check if atom/molecule is in defined molecules!!!! Add this
# Set surface, site, species names and bulk_structure for
# gasphase species
surface_name = 'gasphase'
species_name = contcar.read_composition(ordered=True, name=True)
site_name = 'None'
state = 'gasphase'
if surface:
# Set surface, site, species names and bulk_structure for
# gasphase species
surface_name = system_name
site_name = 'None'
species_name = contcar.read_composition(ordered=True)
state = 'surface'
if solid:
# Set surface, site, species names and bulk_structure for
# gasphase species
surface_name = system_name
site_name = 'None'
species_name = contcar.read_composition(ordered=True)
state = 'solid'
if adsorbate:
surface_name = system_name
site_name = config
surface_atoms = self.get_system_atoms(system=system)
species_name = contcar.read_composition(
adsorbed=True, surface=surface_atoms, name=True)
state = species
if ts:
surface_name = system_name
site_name = config
surface_atoms = self.get_system_atoms(system=system)
species_name = contcar.read_composition(
adsorbed=True, surface=surface_atoms, name=True)
state = species
image = []
for i in range(0,40):
if i < 10:
image.append(str(0)+str(i))
else:
image.append(str(i))
if 'dim' in current_directory.split('/'):
print(' Dimer method - used')
elif current_directory.split('/')[-1] in image:
print(' (CI)-NEB method - used - image ' +
str(current_directory.split('/')[-1]) +
' set as transition state '
'--- Check that this is the correct transition state')
else:
print(' Method for finding transition state not given')
frequencies = self.get_frequencies(
current_directory, gasphase = gasphase)
# Check the number of imaginary frequencies
j = 0
for f in frequencies:
if isinstance(f, complex):
j = j + 1
if j > 0 and ts is False:
print(" WARNING --- " + str(j) + " imaginary frequencies found")
elif j > 1 and ts is True:
print(" WARNING --- " + str(j) +
" imaginary frequencies found - is this a true "
"transition state?")
# make list containing information about surface species, species,
# state, site, energy,
# frequencies, cell, positions and info
variables = [surface_name, composition, species_name, state, site_name,
total_energy, frequencies,
cell, positions, info]
print(' ' + str(variables[0:6]))
return variables
def get_tslist(self, system=None):
"""
Returns the calculated data regarding the transition states.
Transition states data calculated using (CI-)NEB or dimer method can
extracted
Some updated are needed.
"""
print("\n************ TRANSITION STATES ****************")
# get the surface atom species and numbers
#surface_atoms = self.get_surface_atoms()
transition_state_dir, transition_states = self.tsdir_check(
system=system)
transition_state_list = []
for transition_state in transition_states:
# Get list of transition state configurations for ts
config_dir = os.path.join(transition_state_dir, transition_state)
configs = os.listdir(config_dir)
for config in configs:
ts_directory = os.path.join(config_dir, config)
if os.path.isdir(ts_directory):
names = []
for i in os.listdir(ts_directory):
if os.path.isdir(ts_directory + '/' + i):
names.append(i)
# Check if dimer method is used
# If dim is present, results from dimer method will be used
if 'dim' in names:
if os.path.isfile(os.path.join(
ts_directory, 'dim', self.outcarfile)):
ts_dir = os.path.join(ts_directory, 'dim')
else:
print(
' WARNING --- No OUTCAR/CONTCAR file found')
break
# Check if CI-NEB method is used
elif len(names) > 1:
# make a list with image number and energies
# the image with the highest energy is treated as the
# transition stat
# this can be changede
image_list = []
energy_list = []
for image in names:
if (image.startswith('0') or
image.startswith('1') or
image.startswith('2')):
# Make script for OUTCAR is .gz file
if os.path.isfile(os.path.join(
ts_directory, image, self.outcarfile)):
outcar = OUTCAR(os.path.join(
ts_directory, image, self.outcarfile))
else:
print(' WARNING --- No OUTCAR/CONTCAR '
'file found')
break
tot_energy = outcar.read_energy()
energy_list.append(tot_energy)
image_list.append(image)
# Find transition state energy and image number
index = energy_list.index(max(energy_list))
# Transition state image
ts_dir = os.path.join(ts_directory, image_list[index])
# The transisition state calculation is directly under
# the config_dir
elif os.path.isfile(
os.path.join(ts_directory, self.outcarfile)):
ts_dir = ts_directory
# No transition state is found
else:
print(' Warning --- no transition state files '
'found for ' + str(ts_directory))
break
# get the variable for the adsorbed species
variables = self.get_variables(
ts_dir, ts=True, species=transition_state, config=config,
system=system)
variables_text = '\t'.join([str(w) for w in variables])
transition_state_list.append(variables_text)
return transition_state_list