def write(self, name=None, **kwargs):
self.setting.update(kwargs)
univ.cornerCube(self)
inp, molecule = \
super(GaussianBasisInput, self).write(name, **self.setting)
# mode setup
if self.setting['mode'] == 'single_point':
operation = 'energy'
elif self.setting['mode'] == 'geopt':
operation = 'optimize'
# Theory setupt
dft = {
'pbe': 'xpbe96 cpbe96',
'pbe0': 'pbe0',
'blyp': 'becke88 lyp',
'b3lyp': 'b3lyp',
'bp91': 'becke88 perdew91',
'bp86': 'becke88 perdew86',
'pw91': 'xperdew91 perdew91',
}
scf = {
'rhf', 'rohf', 'uhf',
}
tce = {
'mp2', 'mp3', 'mp4',
'ccsd', 'ccsdt', 'lccsd',
'cisd', 'cisdt',
}
if self.setting['theory'] in dft:
module = 'dft'
xc = dft[self.setting['theory']]
elif self.setting['theory'] in scf:
module = 'scf'
elif self.setting['theory'] in tce:
module = 'tce'
else:
qtk.exit("theory %s is not implemented" % self.setting['theory'])
mul_dict = {1: 'singlet', 2: 'doublet', 3: 'triplet'}
# print file
inp.write('title %s\n' % name)
inp.write('start %s\n' % name)
inp.write('echo\n')
if self.setting['fix_molecule']\
and self.setting['fix_molecule']:
fix_mol = 'nocenter'
else:
fix_mol = ''
inp.write('\ngeometry units angstrom %s\n' % fix_mol)
if fix_mol:
inp.write('symmetry group c1\n')
if 'nuclear_charges' in self.setting:
new_Z = self.setting['nuclear_charges']
else:
new_Z = []
z_itr = 0
for i in range(molecule.N):
n_charge = ''
e_str = molecule.type_list[i]
if new_Z and z_itr < len(new_Z):
if new_Z[z_itr][0] == i:
Zn = molecule.Z[i]
n_charge = 'charge %.3f' % float(new_Z[z_itr][1] + Zn)
e_str = molecule.type_list[i] + '.' + new_Z[z_itr][2]
molecule.string[i] = e_str
z_itr = z_itr + 1
inp.write(' %-8s % 8.4f % 8.4f % 8.4f %s\n' % \
(e_str,
molecule.R[i, 0],
molecule.R[i, 1],
molecule.R[i, 2],
n_charge
))
inp.write('end\n\n')
inp.write('basis cartesian\n')
if self.setting['basis_set'] != 'gen':
eStr = []
for e in range(len(molecule.Z)):
if molecule.string[e]:
eString = molecule.string[e]
else:
eString = molecule.type_list[e]
if eString not in set(eStr):
eStr.append(eString)
inp.write(' %-8s library %2s %s\n' % (\
eString,
molecule.type_list[e],
self.setting['basis_set'].upper()),
)
inp.write('end\n\n')
if module == 'dft':
inp.write('dft\n')
inp.write(' xc %s\n' % xc)
if molecule.multiplicity > 1:
inp.write(' odft\n')
inp.write(' mult %d\n' % molecule.multiplicity)
if self.setting['wf_convergence'] != 1e-06:
inp.write(' convergence energy %e\n' % \
self.setting['wf_convergence'])
if 'scf_step' in self.setting:
inp.write(' maxiter %d\n' % self.setting['scf_step'])
if 'vdw' in self.setting:
if self.setting['vdw'] == 'd3':
inp.write(' disp vdw 3\n')
elif self.setting['vdw'] == 'd2':
inp.write(' disp vdw 2\n')
inp.write('end\n\n')
elif module == 'scf':
inp.write('scf\n')
if molecule.multiplicity <= 3:
inp.write(' %s\n' % mul_dict[molecule.multiplicity])
inp.write(' %s\n' % self.setting['theory'])
else:
qtk.exit('multiplicity > 3 is not yet implemented')
inp.write('end\n\n')
if module == 'tce':
_mult = False
if molecule.multiplicity > 1:
_mult = True
inp.write('scf\n')
inp.write(' %s\n' % mul_dict[molecule.multiplicity])
inp.write(' rohf\n')
inp.write('end\n\n')
inp.write('tce\n')
if _mult: inp.write(' scf\n')
inp.write(' %s\n' % self.setting['theory'])
inp.write('end\n\n')
if molecule.charge != 0:
inp.write('charge % 5.2f\n' % molecule.charge)
inp.write('\ntask %s %s\n' % (module, operation))
if self.setting['save_density']:
total_wf = int(sum(self.molecule.Z) / 2)
valence_wf = self.molecule.getValenceElectrons() / 2
wf_list = reversed([total_wf - i for i in range(valence_wf)])
cubeout = 'qmout'
if name: cubeout = name
inp.write('\ndplot\n')
inp.write(' output %s_density.cube\n' % cubeout)
inp.write(' vectors %s.movecs\n' % name)
inp.write(' LimitXYZ\n')
for i in range(3):
for j in range(2):
inp.write(' % 8.4f' % self.molecule.grid[i][j])
inp.write(' %d\n' % self.molecule.grid[i][2])
inp.write(' gaussian\n')
inp.write(' spin total\n')
inp.write(' orbitals; %d\n' % valence_wf)
for i in wf_list:
inp.write(' %d' % i)
inp.write('\nend\n')
inp.write('task dplot\n\n')
if self.setting['save_wf']:
for occ in self.setting['save_wf']:
if not self.molecule.grid:
self.setGrid()
cubeout = 'qmout'
if name: cubeout = name
inp.write('\ndplot\n')
inp.write(' output %s_wf%02d.cube\n' % (cubeout, occ))
inp.write(' vectors %s.movecs\n' % cubeout)
inp.write(' LimitXYZ\n')
for i in range(3):
for j in range(2):
inp.write(' % 8.4f' % self.molecule.grid[i][j])
inp.write(' %d\n' % self.molecule.grid[i][2])
inp.write(' gaussian\n')
inp.write(' spin total\n')
inp.write(' orbitals view\n')
inp.write(' 1; %d\n' % occ)
inp.write('end\n')
inp.write('task dplot\n\n')
inp.close()
return inp
def write(self, name=None, **kwargs):
self.setting.update(kwargs)
if 'geopt' in self.setting and self.setting['geopt']:
self.setting['mode'] = 'geopt'
univ.cornerCube(self)
inp, molecule = \
super(GaussianBasisInput, self).write(name, **self.setting)
# mode setup
if self.setting['mode'] == 'single_point':
operation = 'energy'
elif self.setting['mode'] == 'geopt':
operation = 'optimize'
# Theory setupt
dft = {
'pbe': 'xpbe96 cpbe96',
'pbe0': 'pbe0',
'blyp': 'becke88 lyp',
'b3lyp': 'b3lyp',
'bp91': 'becke88 perdew91',
'bp86': 'becke88 perdew86',
'pw91': 'xperdew91 perdew91',
}
scf = {
'rhf',
'rohf',
'uhf',
}
tce = {
'mp2',
'mp3',
'mp4',
'ccsd',
'ccsdt',
'lccsd',
'cisd',
'cisdt',
}
if self.setting['theory'] in dft:
module = 'dft'
xc = dft[self.setting['theory']]
elif self.setting['theory'] in scf:
module = 'scf'
elif self.setting['theory'] in tce:
module = 'tce'
else:
qtk.exit("theory %s is not implemented" % self.setting['theory'])
mul_dict = {1: 'singlet', 2: 'doublet', 3: 'triplet'}
# print file
inp.write('title %s\n' % name)
inp.write('start %s\n' % name)
inp.write('echo\n')
if self.setting['fix_molecule']\
and self.setting['fix_molecule']:
fix_mol = 'nocenter'
else:
fix_mol = ''
inp.write('\ngeometry units angstrom %s\n' % fix_mol)
if fix_mol:
inp.write('symmetry group c1\n')
if 'nuclear_charges' in self.setting:
new_Z = self.setting['nuclear_charges']
else:
new_Z = []
z_itr = 0
for i in range(molecule.N):
n_charge = ''
e_str = molecule.type_list[i]
if new_Z and z_itr < len(new_Z):
if new_Z[z_itr][0] == i:
Zn = molecule.Z[i]
n_charge = 'charge %.3f' % float(new_Z[z_itr][1] + Zn)
e_str = molecule.type_list[i] + '.' + new_Z[z_itr][2]
molecule.string[i] = e_str
z_itr = z_itr + 1
inp.write(' %-8s % 8.4f % 8.4f % 8.4f %s\n' % \
(e_str,
molecule.R[i, 0],
molecule.R[i, 1],
molecule.R[i, 2],
n_charge
))
inp.write('end\n\n')
inp.write('basis cartesian\n')
if self.setting['basis_set'] != 'gen':
eStr = []
for e in range(len(molecule.Z)):
if molecule.string[e]:
eString = molecule.string[e]
else:
eString = molecule.type_list[e]
if eString not in set(eStr):
eStr.append(eString)
inp.write(' %-8s library %2s %s\n' % (\
eString,
molecule.type_list[e],
self.setting['basis_set'].upper()),
)
inp.write('end\n\n')
if module == 'dft':
inp.write('dft\n')
inp.write(' xc %s\n' % xc)
if molecule.multiplicity > 1:
inp.write(' odft\n')
inp.write(' mult %d\n' % molecule.multiplicity)
if self.setting['wf_convergence'] != 1e-06:
inp.write(' convergence energy %e\n' % \
self.setting['wf_convergence'])
if 'scf_step' in self.setting:
inp.write(' maxiter %d\n' % self.setting['scf_step'])
if 'vdw' in self.setting:
if self.setting['vdw'] == 'd3':
inp.write(' disp vdw 3\n')
elif self.setting['vdw'] == 'd2':
inp.write(' disp vdw 2\n')
inp.write('end\n\n')
elif module == 'scf':
inp.write('scf\n')
if molecule.multiplicity <= 3:
inp.write(' %s\n' % mul_dict[molecule.multiplicity])
inp.write(' %s\n' % self.setting['theory'])
else:
qtk.exit('multiplicity > 3 is not yet implemented')
inp.write('end\n\n')
if module == 'tce':
_mult = False
if molecule.multiplicity > 1:
_mult = True
inp.write('scf\n')
inp.write(' %s\n' % mul_dict[molecule.multiplicity])
inp.write(' rohf\n')
inp.write('end\n\n')
inp.write('tce\n')
if _mult: inp.write(' scf\n')
inp.write(' %s\n' % self.setting['theory'])
inp.write('end\n\n')
if molecule.charge != 0:
inp.write('charge % 5.2f\n' % molecule.charge)
inp.write('\ntask %s %s\n' % (module, operation))
if self.setting['save_density']:
total_wf = int(sum(self.molecule.Z) / 2)
valence_wf = self.molecule.getValenceElectrons() / 2
wf_list = reversed([total_wf - i for i in range(valence_wf)])
cubeout = 'qmout'
if name: cubeout = name
inp.write('\ndplot\n')
inp.write(' output %s_density.cube\n' % cubeout)
inp.write(' vectors %s.movecs\n' % name)
inp.write(' LimitXYZ\n')
for i in range(3):
for j in range(2):
inp.write(' % 8.4f' % self.molecule.grid[i][j])
inp.write(' %d\n' % self.molecule.grid[i][2])
inp.write(' gaussian\n')
inp.write(' spin total\n')
inp.write(' orbitals; %d\n' % valence_wf)
for i in wf_list:
inp.write(' %d' % i)
inp.write('\nend\n')
inp.write('task dplot\n\n')
if self.setting['save_wf']:
for occ in self.setting['save_wf']:
if not self.molecule.grid:
self.setGrid()
cubeout = 'qmout'
if name: cubeout = name
inp.write('\ndplot\n')
inp.write(' output %s_wf%02d.cube\n' % (cubeout, occ))
inp.write(' vectors %s.movecs\n' % cubeout)
inp.write(' LimitXYZ\n')
for i in range(3):
for j in range(2):
inp.write(' % 8.4f' % self.molecule.grid[i][j])
inp.write(' %d\n' % self.molecule.grid[i][2])
inp.write(' gaussian\n')
inp.write(' spin total\n')
inp.write(' orbitals view\n')
inp.write(' 1; %d\n' % occ)
inp.write('end\n')
inp.write('task dplot\n\n')
inp.close()
return inp
def write(self, name=None, **kwargs):
self.setting.update(kwargs)
univ.cornerCube(self)
inp, molecule = \
super(GaussianBasisInput, self).write(name, **self.setting)
theory_dict = {
'pbe': 'pbepbe',
'pbe0': 'pbe1pbe',
}
if self.setting['theory'] in theory_dict:
theory = theory_dict[self.setting['theory']]
else:
theory = self.setting['theory']
if 'cc' in theory:
try:
ind = self.setting['gaussian_setting'].index('force')
del self.setting['gaussian_setting'][ind]
except:
pass
if 'openshell' in self.setting:
if self.setting['openshell'] == 'restricted':
theory = 'ro' + theory
elif self.setting['openshell'] == 'unrestricted':
theory = 'u' + theory
if 'geopt' in self.setting and self.setting['geopt']:
self.setting['gaussian_setting'].append('opt')
if 'force' in self.setting['gaussian_setting']:
ind = self.setting['gaussian_setting'].index('force')
del self.setting['gaussian_setting'][ind]
if 'print_polarizability' in self.setting\
and self.setting['print_polarizability']:
self.setting['gaussian_setting'].append('polar')
if 'force' in self.setting['gaussian_setting']:
ind = self.setting['gaussian_setting'].index('force')
del self.setting['gaussian_setting'][ind]
basis = self.setting['basis_set']
if type(basis) is str:
if 'def2' in basis.lower():
basis = basis.replace('-', '')
if 'charge_multiplicity' not in self.setting:
charge, multiplicity = \
self.molecule.charge, self.molecule.multiplicity
else:
charge, multiplicity = \
self.setting['charge_multiplicity']
if (charge + sum(self.molecule.Z) + 1) % 2 != multiplicity % 2:
qtk.exit("charge: %3.1f and multiplicity %d is " \
% (float(charge), multiplicity) +
"not competible with number of electron %d\n"
% sum(self.molecule.Z))
gaussian_setting = self.setting['gaussian_setting']
chk_flag = False
save_list = [
'save_density',
'ks_states',
'save_wf',
'save_restart',
]
for s in save_list:
if s in self.setting and self.setting[s]:
chk_flag = True
if 'threads' in self.setting:
inp.write('%%nproc=%d\n' % self.setting['threads'])
else:
inp.write('%nproc=\n')
if chk_flag:
if name:
inp.write('%%chk=%s.chk\n' % name)
else:
inp.write('%chk=tmp.chk\n')
density_dict = {'ccsd', 'mp2', 'mp3', 'ccd', 'cid', 'cisd'}
if 'save_density' in self.setting\
and self.setting['save_density']:
if theory.lower() in density_dict\
and 'Density=Current' not in self.setting['gaussian_setting']:
self.setting['gaussian_setting'].append('Density=Current')
if 'nuclear_charges' in self.setting:
gaussian_setting.append('Charge')
if 'vdw' in self.setting:
if self.setting['vdw'] == 'd3':
gaussian_setting.append('EmpiricalDispersion=GD3')
elif self.setting['vdw'] == 'd2':
gaussian_setting.append('EmpiricalDispersion=GD2')
if 'print_energy' in self.setting and self.setting['print_energy']:
gaussian_setting.append('ExtraLinks=L608')
if 'mode' in self.setting and self.setting['mode'] == 'geopt':
gaussian_setting.append('Opt')
if type(basis) is str:
inp.write("# %s/%s" % (theory, basis))
else:
inp.write("# %s/gen" % theory)
for s in list(set(gaussian_setting)):
inp.write(" %s" % s)
inp.write("\n\n%s\n\n" % self.molecule.name)
inp.write("%d %d\n" % (charge, multiplicity))
for i in range(molecule.N):
inp.write('%-2s % 8.4f % 8.4f % 8.4f\n' % \
(molecule.type_list[i],
molecule.R[i, 0],
molecule.R[i, 1],
molecule.R[i, 2]))
if 'nuclear_charges' in self.setting:
new_Z = self.setting['nuclear_charges']
else:
new_Z = []
if new_Z:
inp.write('\n')
for chg_list in new_Z:
for i in range(molecule.N):
if chg_list[0] == i:
Ri = molecule.R[i]
charge = chg_list[1]
inp.write('% 8.4f % 8.4f % 8.4f % .3f\n' %\
(Ri[0], Ri[1], Ri[2], charge))
if type(basis) is dict:
inp.write('\n')
l_dict = {0: 'S', 1: 'P', 2: 'D', 3: 'F', 4: 'G'}
for atom in set(molecule.type_list):
if atom not in basis:
qtk.exit("basis function for atom %s is missing" % atom)
inp.write("%-2s 0\n" % atom)
for b in basis[atom]:
inp.write("%s %2d 1.00\n" % (l_dict[b[0]], len(b) - 1))
for ec in b[1:]:
inp.write(" %16.8f %16.8f\n" % (ec[0], ec[1]))
inp.write('****\n')
inp.write('\n\n')
inp.close()
return inp
def write(self, name=None, **kwargs):
self.setting.update(kwargs)
univ.cornerCube(self)
inp, molecule = \
super(GaussianBasisInput, self).write(name, **self.setting)
theory_dict = {
'pbe': 'pbepbe',
'pbe0': 'pbe1pbe',
}
if self.setting['theory'] in theory_dict:
theory = theory_dict[self.setting['theory']]
else:
theory = self.setting['theory']
if 'cc' in theory:
try:
ind = self.setting['gaussian_setting'].index('force')
del self.setting['gaussian_setting'][ind]
except:
pass
if 'openshell' in self.setting :
if self.setting['openshell'] == 'restricted':
theory = 'ro' + theory
elif self.setting['openshell'] == 'unrestricted':
theory = 'u' + theory
if 'geopt' in self.setting and self.setting['geopt']:
self.setting['gaussian_setting'].append('opt')
if 'force' in self.setting['gaussian_setting']:
ind = self.setting['gaussian_setting'].index('force')
del self.setting['gaussian_setting'][ind]
if 'print_polarizability' in self.setting\
and self.setting['print_polarizability']:
self.setting['gaussian_setting'].append('polar')
if 'force' in self.setting['gaussian_setting']:
ind = self.setting['gaussian_setting'].index('force')
del self.setting['gaussian_setting'][ind]
basis = self.setting['basis_set']
if 'def2' in basis.lower():
basis = basis.replace('-', '')
if 'charge_multiplicity' not in self.setting:
charge, multiplicity = \
self.molecule.charge, self.molecule.multiplicity
else:
charge, multiplicity = \
self.setting['charge_multiplicity']
if (charge + sum(self.molecule.Z) + 1) % 2 != multiplicity % 2:
qtk.exit("charge: %3.1f and multiplicity %d is " \
% (float(charge), multiplicity) +
"not competible with number of electron %d\n"
% sum(self.molecule.Z))
gaussian_setting = self.setting['gaussian_setting']
chk_flag = False
save_list = [
'save_density',
'ks_states',
'save_wf',
'save_restart',
]
for s in save_list:
if s in self.setting and self.setting[s]:
chk_flag = True
if 'threads' in self.setting:
inp.write('%%nproc=%d\n' % self.setting['threads'])
else:
inp.write('%nproc=\n')
if chk_flag:
if name:
inp.write('%%chk=%s.chk\n' % name)
else:
inp.write('%chk=tmp.chk\n')
density_dict = {'ccsd', 'mp2', 'mp3', 'ccd', 'cid', 'cisd'}
if 'save_density' in self.setting\
and self.setting['save_density']:
if theory.lower() in density_dict\
and 'Density=Current' not in self.setting['gaussian_setting']:
self.setting['gaussian_setting'].append('Density=Current')
if 'nuclear_charges' in self.setting:
gaussian_setting.append('Charge')
if 'vdw' in self.setting:
if self.setting['vdw'] == 'd3':
gaussian_setting.append('EmpiricalDispersion=GD3')
elif self.setting['vdw'] == 'd2':
gaussian_setting.append('EmpiricalDispersion=GD2')
if 'print_energy' in self.setting and self.setting['print_energy']:
gaussian_setting.append('ExtraLinks=L608')
if 'mode' in self.setting and self.setting['mode'] == 'geopt':
gaussian_setting.append('Opt')
inp.write("# %s/%s" % (theory, basis))
for s in list(set(gaussian_setting)):
inp.write(" %s" % s)
inp.write("\n\n%s\n\n" % self.molecule.name)
inp.write("%d %d\n" % (charge, multiplicity))
for i in range(molecule.N):
inp.write('%-2s % 8.4f % 8.4f % 8.4f\n' % \
(molecule.type_list[i],
molecule.R[i, 0],
molecule.R[i, 1],
molecule.R[i, 2]))
if 'nuclear_charges' in self.setting:
new_Z = self.setting['nuclear_charges']
else:
new_Z = []
if new_Z:
inp.write('\n')
for chg_list in new_Z:
for i in range(molecule.N):
if chg_list[0] == i:
Ri = molecule.R[i]
charge = chg_list[1]
inp.write('% 8.4f % 8.4f % 8.4f % .3f\n' %\
(Ri[0], Ri[1], Ri[2], charge))
inp.write('\n\n')
inp.close()
return inp