def set_atoms(self, atoms):
if self.atoms == atoms:
return
# performs an update of the atoms
Calculator.set_atoms(self, atoms)
write_turbomole('coord', atoms)
# energy and forces must be re-calculated
self.update_energy = True
self.update_forces = True
def set_atoms(self, atoms):
if self.atoms == atoms:
return
# performs an update of the atoms
Calculator.set_atoms(self, atoms)
write_turbomole("coord", atoms)
# energy and forces must be re-calculated
self.update_energy = True
self.update_forces = True
def __init__(self, label='ase', ioplist=list(), basisfile=None,
directory=None, **kwargs):
Calculator.__init__(self)
# Form a set of dictionaries for each input variable type
self.link0_int_params = dict()
self.link0_str_params = dict()
self.route_str_params = dict()
self.route_int_params = dict()
self.route_float_params = dict()
self.route_bool_params = dict()
self.route_self_params = dict()
for key in link0_int_keys:
self.link0_int_params[key] = None
for key in link0_str_keys:
self.link0_str_params[key] = None
for key in route_str_keys:
self.route_str_params[key] = None
for key in route_int_keys:
self.route_int_params[key] = None
for key in route_float_keys:
self.route_float_params[key] = None
for key in route_bool_keys:
self.route_bool_params[key] = None
for key in route_self_keys:
self.route_self_params[key] = None
self.set(**kwargs)
self.atoms = None
self.positions = None
self.old_positions = None
self.old_link0_str_params = None
self.old_link0_int_params = None
self.old_route_str_params = None
self.old_route_int_params = None
self.old_route_float_params = None
self.old_route_bool_params = None
self.old_route_self_params = None
self.old_basisfile = None
self.old_label = None
self.old_ioplist = None
self.basisfile = basisfile
self.label = label
self.ioplist = list(ioplist)[:]
self.directory = directory
self.multiplicity = 1
self.converged = False
def set_atoms(self, atoms):
if self.atoms == atoms:
if (self.updated and os.path.isfile('coord')):
self.updated = False
a = read('coord').get_positions()
if np.allclose(a, atoms.get_positions(), rtol=0, atol=1e-13):
return
else:
return
# performs an update of the atoms
write('coord', atoms)
Calculator.set_atoms(self, atoms)
# energy and forces must be re-calculated
self.update_energy = True
self.update_forces = True
def set_atoms(self, atoms):
if self.atoms == atoms:
if (self.updated and os.path.isfile('coord')):
self.updated = False
a = read('coord').get_positions()
if np.allclose(a, atoms.get_positions(), rtol=0, atol=1e-13):
return
else:
return
# performs an update of the atoms
write('coord', atoms)
Calculator.set_atoms(self, atoms)
# energy and forces must be re-calculated
self.update_energy = True
self.update_forces = True
def set_atoms(self, atoms):
if self.atoms == atoms:
return
# performs an update of the atoms
Calculator.set_atoms(self, atoms)
#
# We may reside in a clean directory,
# Write 'control' and auxiliary files:
#
self.store2files(TURBOMOLE_INPUT_FILES)
write_turbomole('coord', atoms)
# energy and forces must be re-calculated
self.update_energy = True
self.update_forces = True
def set_atoms(self, atoms):
# Delete old coord control, ... files, if exist
for f in [
'coord', 'basis', 'energy', 'gradients', 'alpha', 'beta',
'mos', 'forceapprox', 'statistics', 'dscf_problem', 'control'
]:
if os.path.exists(f):
os.remove(f)
# if self.atoms == atoms:
# if (self.updated and os.path.isfile('coord')):
# self.updated = False
# a = read('coord').get_positions()
# if np.allclose(a, atoms.get_positions(), rtol=0, atol=1e-13):
# return
# else:
# return
# performs an update of the atoms
write('coord', atoms)
if not self.key_parameters["basis"] == 'cefine':
string = '\n\na coord\n*\nno\nb all ' + self.key_parameters[
'basis'] + '\n*\neht\n\n' + str(
self.key_parameters['charge']
) + '\n\nscf\niter\n' + str(
self.key_parameters['maxit']
) + '\n\ncc\nmemory\n1000\n*\ndft\non\nfunc\n' + self.key_parameters[
'method'] + '\n*\nri\non\nm\n3000\n*\n*'
self.define_str = string
with open('def.inp', 'w') as f:
f.write(self.define_str)
command = 'define < def.inp > define.out'
else:
self.define_str = self.key_parameters['method'] + '-chrg ' + str(
self.key_parameters['charge'])
command = self.define_str + ' > cefine.out'
# run define
proc = Popen([command], shell=True, stderr=PIPE)
error = proc.communicate()[1]
if 'abnormally' in error:
raise OSError(error)
Calculator.set_atoms(self, atoms)
# energy and forces must be re-calculated
self.update_energy = True
self.update_forces = True
