def check_state(self, atoms, tol=1e-15):
"""Check for system changes since last calculation."""
def compare_dict(d1, d2):
"""Helper function to compare dictionaries"""
# Use symmetric difference to find keys which aren't shared
# for python 2.7 compatiblity
if set(d1.keys()) ^ set(d2.keys()):
return False
# Check for differences in values
for key, value in d1.items():
if np.any(value != d2[key]):
return False
return True
# First we check for default changes
system_changes = FileIOCalculator.check_state(self, atoms, tol=tol)
# We now check if we have made any changes to the input parameters
# XXX: Should we add these parameters to all_changes?
for param_string, old_dict in self.param_state.items():
param_dict = getattr(self, param_string) # Get current param dict
if not compare_dict(param_dict, old_dict):
system_changes.append(param_string)
return system_changes
def check_state(self, atoms):
system_changes = FileIOCalculator.check_state(self, atoms)
# Ignore unit cell for molecules:
if not atoms.pbc.any() and 'cell' in system_changes:
system_changes.remove('cell')
if self.pcpot and self.pcpot.mmpositions is not None:
system_changes.append('positions')
return system_changes
def check_state(self, atoms):
system_changes = FileIOCalculator.check_state(self, atoms)
# Ignore unit cell for molecules:
if not atoms.pbc.any() and 'cell' in system_changes:
system_changes.remove('cell')
if self.pcpot and self.pcpot.mmpositions is not None:
system_changes.append('positions')
return system_changes
def check_state(self, atoms):
system_changes = FileIOCalculator.check_state(self, atoms)
# Ignore unit cell and boundary conditions:
if 'cell' in system_changes:
system_changes.remove('cell')
if 'pbc' in system_changes:
system_changes.remove('pbc')
return system_changes
def check_state(self, atoms):
system_changes = FileIOCalculator.check_state(self, atoms)
# Ignore unit cell and boundary conditions:
if 'cell' in system_changes:
system_changes.remove('cell')
if 'pbc' in system_changes:
system_changes.remove('pbc')
return system_changes
def check_state(self, atoms):
system_changes = FileIOCalculator.check_state(self, atoms)
# Ignore unit cell and boundary conditions:
if "cell" in system_changes:
system_changes.remove("cell")
if "pbc" in system_changes:
system_changes.remove("pbc")
return system_changes
def check_state(self, atoms):
system_changes = FileIOCalculator.check_state(self, atoms)
ignore = ['cell', 'pbc']
for change in system_changes:
if change in ignore:
system_changes.remove(change)
return system_changes
def check_state(self, atoms):
system_changes = FileIOCalculator.check_state(self, atoms)
ignore = ['cell', 'pbc']
for change in system_changes:
if change in ignore:
system_changes.remove(change)
return system_changes
def check_state(self, atoms=None):
"""Check if any changes exist that require new calculations."""
if atoms is None:
atoms = self.get_atoms()
log.debug('atoms IMM: {}'.format(atoms.get_initial_magnetic_moments()))
system_changes = FileIOCalculator.check_state(self, atoms)
# Ignore boundary conditions:
if 'pbc' in system_changes:
system_changes.remove('pbc')
s = 'FileIOCalculator reports these changes: {}'
log.debug(s.format(system_changes))
# if dir is empty, there is nothing to read here.
if self.get_state() == Vasp.EMPTY:
return system_changes
# Check if the parameters have changed
file_params = {}
file_params.update(self.read_incar())
if 'rwigs' in file_params:
# This gets read as a list.
with open(self.potcar) as f:
lines = f.readlines()
# symbols are in the # FIXME: first line of each potcar
symbols = [lines[0].split()[1]]
for i, line in enumerate(lines):
if 'End of Dataset' in line and i != len(lines) - 1:
symbols += [lines[i + 1].split()[1]]
file_params['rwigs'] = dict(
list(zip(symbols, file_params['rwigs'])))
file_params.update(self.read_potcar())
file_params.update(self.read_kpoints())
xc_keys = sorted(Vasp.xc_defaults,
key=lambda k: len(Vasp.xc_defaults[k]),
reverse=True)
for ex in xc_keys:
pd = {k: file_params.get(k, None) for k in Vasp.xc_defaults[ex]}
if pd == Vasp.xc_defaults[ex]:
file_params['xc'] = ex.lower()
break
# reconstruct ldau_luj if necessary
if 'ldauu' in file_params:
ldaul = file_params['ldaul']
ldauj = file_params['ldauj']
ldauu = file_params['ldauu']
with open(self.potcar) as f:
lines = f.readlines()
# symbols are in the first line of each potcar
symbols = [lines[0].split()[1]]
for i, line in enumerate(lines):
if 'End of Dataset' in line and i != len(lines) - 1:
symbols += [lines[i + 1].split()[1]]
ldau_luj = {}
for sym, l, j, u in zip(symbols, ldaul, ldauj, ldauu):
ldau_luj[sym] = {'L': l, 'U': u, 'J': j}
file_params['ldau_luj'] = ldau_luj
if not {
k: v
for k, v in list(self.parameters.items()) if v is not None
} == file_params:
new_keys = set(self.parameters.keys()) - set(file_params.keys())
missing_keys = (set(file_params.keys()) -
set(self.parameters.keys()))
log.debug('New keys: {}'.format(new_keys))
log.debug('Missing keys: {}'.format(missing_keys))
log.debug('params_on_file do not match.')
log.debug('file-params: {}'.format(file_params))
log.debug('compared to: {}'.format({
k: v
for k, v in list(self.parameters.items()) if v is not None
}))
system_changes += ['params_on_file']
log.debug('System changes: {}'.format(system_changes))
return system_changes
def check_state(self, atoms):
system_changes = FileIOCalculator.check_state(self, atoms)
# Ignore boundary conditions (ELK always uses them):
if 'pbc' in system_changes:
system_changes.remove('pbc')
return system_changes
def check_state(self, atoms):
# from the standard ase.calculators
system_changes = FileIOCalculator.check_state(self, atoms)
return system_changes
def check_state(self, atoms):
system_changes = FileIOCalculator.check_state(self, atoms)
# Ignore unit cell for molecules:
if not atoms.pbc.any() and 'cell' in system_changes:
system_changes.remove('cell')
return system_changes
def check_state(self, atoms):
system_changes = FileIOCalculator.check_state(self, atoms)
return system_changes
def check_state(self, atoms):
system_changes = FileIOCalculator.check_state(self, atoms)
# Ignore unit cell for molecules:
if not atoms.pbc.any() and 'cell' in system_changes:
system_changes.remove('cell')
return system_changes
def check_state(self, atoms):
system_changes = FileIOCalculator.check_state(self, atoms)
# Ignore boundary conditions (ELK always uses them):
if 'pbc' in system_changes:
system_changes.remove('pbc')
return system_changes
def check_state(self, atoms):
system_changes = FileIOCalculator.check_state(self, atoms)
return system_changes
def check_state(self, atoms, tol=1e-15):
system_changes = FileIOCalculator.check_state(self, atoms)
# Ignore boundary conditions:
if 'pbc' in system_changes:
system_changes.remove('pbc')
return system_changes
def check_state(self, atoms=None):
"""Check if any changes exist that require new calculations."""
if atoms is None:
atoms = self.get_atoms()
log.debug('atoms IMM: {}'.format(atoms.get_initial_magnetic_moments()))
system_changes = FileIOCalculator.check_state(self, atoms)
# Ignore boundary conditions:
if 'pbc' in system_changes:
system_changes.remove('pbc')
s = 'FileIOCalculator reports these changes: {}'
log.debug(s.format(system_changes))
# if dir is empty, there is nothing to read here.
if self.get_state() == Vasp.EMPTY:
return system_changes
# Check if the parameters have changed
file_params = {}
file_params.update(self.read_incar())
file_params.update(self.read_potcar())
file_params.update(self.read_kpoints())
xc_keys = sorted(Vasp.xc_defaults,
key=lambda k: len(Vasp.xc_defaults[k]),
reverse=True)
for ex in xc_keys:
pd = {k: file_params.get(k, None)
for k in Vasp.xc_defaults[ex]}
if pd == Vasp.xc_defaults[ex]:
file_params['xc'] = ex.lower()
break
# reconstruct ldau_luj if necessary
if 'ldauu' in file_params:
ldaul = file_params['ldaul']
ldauj = file_params['ldauj']
ldauu = file_params['ldauu']
with open(self.potcar) as f:
lines = f.readlines()
# symbols are in the first line of each potcar
symbols = [lines[0].split()[1]]
for i, line in enumerate(lines):
if 'End of Dataset' in line and i != len(lines) - 1:
symbols += [lines[i + 1].split()[1]]
ldau_luj = {}
for sym, l, j, u in zip(symbols, ldaul, ldauj, ldauu):
ldau_luj[sym] = {'L': l, 'U': u, 'J': j}
file_params['ldau_luj'] = ldau_luj
if not {k: v for k, v in self.parameters.iteritems()
if v is not None} == file_params:
new_keys = set(self.parameters.keys()) - set(file_params.keys())
missing_keys = (set(file_params.keys()) -
set(self.parameters.keys()))
log.debug('New keys: {}'.format(new_keys))
log.debug('Missing keys: {}'.format(missing_keys))
log.debug('params_on_file do not match.')
log.debug('file-params: {}'.format(file_params))
log.debug('compared to: {}'.format({k: v for k, v in
self.parameters.iteritems()
if v is not None}))
system_changes += ['params_on_file']
log.debug('System changes: {}'.format(system_changes))
return system_changes
