def get_system_atoms(self, system=None):
"""
Returns a list of the atom kinds and number of atoms of the surface or solid system
atom_kind : list
atom_number : list
"""
if system == 'surface':
system_directory = self.sysdir_check()[0]
if system == 'solid':
system_directory = self.sysdir_check()[1]
contcar = CONTCAR(os.path.join(system_directory, self.contcarfile))
atom_kind = contcar.read_atomkinds()
atom_number = contcar.read_atomnumbers()
return atom_kind, atom_number
def get_system_atoms(self, system=None):
"""
Returns a list of the atom kinds and number of atoms of the surface '
'or solid system
atom_kind : list
atom_number : list
"""
if system == 'surface':
system_directory = self.sysdir_check()[0]
if system == 'solid':
system_directory = self.sysdir_check()[1]
contcar = CONTCAR(os.path.join(system_directory, self.contcarfile))
atom_kind = contcar.read_atomkinds()
atom_number = contcar.read_atomnumbers()
return atom_kind, atom_number
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_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