def write_input(self, atoms, properties=None, systems_changes=None):
from ase.io import write
atoms.write(self.label + '.xyz', 'xyz')
self.mopac_calc = Mopac(label=self.label)
self.mopac_calc.parameters.update(self.mopacdict)
self.ddmc_calc = dDMC(label=self.label)
self.ddmc_calc.parameters.update(self.ddmcdict)
def __init__(self, label='dftbddmc', atoms=None, dftbdict={}, ddmcdict={}, **kwargs):
"""Construct a DFTB+ and a dDMC calculator.
"""
os.environ['ASE_DFTBDDMC_COMMAND'] = ''
self.label = label
self.dftbdict = dftbdict
self.ddmcdict = ddmcdict
ddmc_default_parameters = {}
ddmc_default_parameters['param_a'] = 1.85705835084132
ddmc_default_parameters['param_b'] = 1.01824853175310
ddmc_default_parameters['param_c'] = 23.0
ddmc_default_parameters['dftype'] = 3
ddmc_default_parameters['tagtype'] = 'dftbp'
for param in ddmc_default_parameters.keys():
if not param in self.ddmcdict.keys():
self.ddmcdict[param] = ddmc_default_parameters[param]
restart = None
ignore_bad_restart_file = None
FileIOCalculator.__init__(self, restart, ignore_bad_restart_file,
label, atoms, **kwargs)
self.dftb_calc = Dftb(label=self.label)
self.ddmc_calc = dDMC(label=self.label)
def __setASECalculator(self):
"""Initialize the calculator and set the parameters"""
method = self.definedParams['method']
if method == 'dftb_std-dDMC':
self.__setdDMCParams()
from ase.calculators.dftbddmc import DftbdDMC
self.calculator = DftbdDMC(atoms=self.mol,label='cazzo',dftbdict=self.__dftb_parameters, ddmcdict=self.__ddmc_parameters)
elif method == 'dftb_std' or method == 'dftb_mio11':
from ase.calculators.dftb import Dftb
self.calculator = Dftb(atoms=self.mol,label='cazzo')
elif method == 'dftb_std-D3':
from ase.calculators.dftbd3h4 import DftbD3H4
self.calculator = DftbD3H4(atoms=self.mol,label='cazzo',dftbdict=self.__dftb_parameters )
elif method == 'dftb_std-D3H4':
from ase.calculators.dftbd3h4 import DftbD3H4
self.calculator = DftbD3H4(atoms=self.mol,label='cazzo',dftbdict=self.__dftb_parameters )
elif method == 'dDMC':
self.__setdDMCParams()
from ase.calculators.ddmc import dDMC
self.calculator = dDMC(atoms=self.mol, label='cazzo')
else:
raise ImplementationError(method,'Calculator for this method is not implemented')
if self.definedParams['method'].find('dftb') > -1:
self.calculator.parameters.update(self.__dftb_parameters)
else:
self.calculator.parameters.update(self.__ddmc_parameters)
def write_input(self, atoms, properties=None, systems_changes=None):
from ase.io import write
atoms.write(self.label+'.xyz','xyz')
self.mopac_calc = Mopac(label=self.label)
self.mopac_calc.parameters.update(self.mopacdict)
self.ddmc_calc = dDMC(label=self.label)
self.ddmc_calc.parameters.update(self.ddmcdict)
def __init__(self,
label='dftbddmc',
atoms=None,
dftbdict={},
ddmcdict={},
**kwargs):
"""Construct a DFTB+ and a dDMC calculator.
"""
os.environ['ASE_DFTBDDMC_COMMAND'] = ''
self.label = label
self.dftbdict = dftbdict
self.ddmcdict = ddmcdict
ddmc_default_parameters = {}
ddmc_default_parameters['param_a'] = 1.85705835084132
ddmc_default_parameters['param_b'] = 1.01824853175310
ddmc_default_parameters['param_c'] = 23.0
ddmc_default_parameters['dftype'] = 3
ddmc_default_parameters['tagtype'] = 'dftbp'
for param in ddmc_default_parameters.keys():
if not param in self.ddmcdict.keys():
self.ddmcdict[param] = ddmc_default_parameters[param]
restart = None
ignore_bad_restart_file = None
FileIOCalculator.__init__(self, restart, ignore_bad_restart_file,
label, atoms, **kwargs)
self.dftb_calc = Dftb(label=self.label)
self.ddmc_calc = dDMC(label=self.label)
def __setASECalculator(self):
"""Initialize the calculator and set the parameters"""
method = self.definedParams['method']
if method == 'dftb_std-dDMC':
self.__setdDMCParams()
from ase.calculators.dftbddmc import DftbdDMC
self.calculator = DftbdDMC(atoms=self.mol,
label='cazzo',
dftbdict=self.__dftb_parameters,
ddmcdict=self.__ddmc_parameters)
elif method == 'dftb_std' or method == 'dftb_mio11':
from ase.calculators.dftb import Dftb
self.calculator = Dftb(atoms=self.mol, label='cazzo')
elif method == 'dftb_std-D3':
from ase.calculators.dftbd3h4 import DftbD3H4
self.calculator = DftbD3H4(atoms=self.mol,
label='cazzo',
dftbdict=self.__dftb_parameters)
elif method == 'dftb_std-D3H4':
from ase.calculators.dftbd3h4 import DftbD3H4
self.calculator = DftbD3H4(atoms=self.mol,
label='cazzo',
dftbdict=self.__dftb_parameters)
elif method == 'dDMC':
self.__setdDMCParams()
from ase.calculators.ddmc import dDMC
self.calculator = dDMC(atoms=self.mol, label='cazzo')
else:
raise ImplementationError(
method, 'Calculator for this method is not implemented')
if self.definedParams['method'].find('dftb') > -1:
self.calculator.parameters.update(self.__dftb_parameters)
else:
self.calculator.parameters.update(self.__ddmc_parameters)
def write_input(self, atoms, properties=None, systems_changes=None):
self.gaus_calc = Gaussian(label=self.label)
self.gaus_calc.parameters.update(self.gausdict)
self.ddmc_calc = dDMC(label=self.label)
self.ddmc_calc.parameters.update(self.ddmcdict)
fd = open('%s.%d%s.pckl' % (name, a, 'xyz'[i]),
'w')
pickle.dump(force, fd)
fd.close()
if parallel is not None:
world.sum(F_ai)
return F_ai
#test = Atoms('2N',positions=[(0.,0.,0.),(0.,0.,4.10)])
#test = molecule('C2H2')
test = sys.argv[1]
#test = Atoms('2Ar', position=[(0.,0.,0.),(0.,0.,3.)])
test.set_calculator(dDMC(label='S668-24BenzeneBenzenepipi-090',atoms=test,dftype='3',tagtype='column'))
print test.get_potential_energy()
numer = numeric_forces(test, indices=None, axes=(0, 1, 2), d=0.001,
parallel=None, name=None)
anal = test.get_forces()
print 'Numerical Gradient: '
print numer
print
print 'Analitical Gradient: '
print anal
print
print 'Numerical/Analytical:'
print numer/anal
'w')
pickle.dump(force, fd)
fd.close()
if parallel is not None:
world.sum(F_ai)
return F_ai
#test = Atoms('2N',positions=[(0.,0.,0.),(0.,0.,4.10)])
#test = molecule('C2H2')
test = sys.argv[1]
#test = Atoms('2Ar', position=[(0.,0.,0.),(0.,0.,3.)])
test.set_calculator(
dDMC(label='S668-24BenzeneBenzenepipi-090',
atoms=test,
dftype='3',
tagtype='column'))
print test.get_potential_energy()
numer = numeric_forces(test,
indices=None,
axes=(0, 1, 2),
d=0.001,
parallel=None,
name=None)
anal = test.get_forces()
print 'Numerical Gradient: '
print numer
print
def write_input(self, atoms, properties=None, systems_changes=None):
self.gaus_calc = Gaussian(label=self.label)
self.gaus_calc.parameters.update(self.gausdict)
self.ddmc_calc = dDMC(label=self.label)
self.ddmc_calc.parameters.update(self.ddmcdict)