def write_gau_input(species, coords, iframe, jobname="run_gau", **kwargs):
""" write a gaussian input file """
path = kwargs["path"]
functional = kwargs["functional"]
basis_set = kwargs["basis_set"]
nprocs = kwargs["nprocs"]
# get first letter of atom name => element
species = [specie[0] for specie in species]
# convert nm to angstrom
coords = np.array(coords) * 10
# build Molecule and Gaussian object
mol = mg.Molecule(species, coords, validate_proximity=True)
ginp = GaussianInput(
mol,
charge=0,
title="Written by gro2qm - snapshot %d" % iframe,
functional=functional, basis_set=basis_set,
route_parameters={"pop": "(MK, MBS)"},
link0_parameters={"%nprocs": nprocs},
dieze_tag="#"
)
basename = "gau_%05d" % iframe
ginp.write_file(os.path.join(path, basename + ".com"), cart_coords=True)
mol.to(fmt="xyz", filename=os.path.join(path, basename + ".xyz"))
return "sbatch -J snap_%05d %s %s.com" % (iframe, jobname, basename)
def better_guess(cls,
gaussian_cmd,
input_file,
output_file,
stderr_file='stderr.txt',
backup=True,
cart_coords=True):
orig_input = GaussianInput.from_file(input_file)
yield (GaussianJob(gaussian_cmd=gaussian_cmd,
input_file=input_file,
output_file=output_file,
stderr_file=stderr_file,
suffix='.guess1',
backup=backup))
if GaussianErrorHandler.activate_better_guess:
# TODO: check why it comes here only if the lower job is not
# failing and not in the else condition
# continue only if other corrections are invalid or failed
lower_output = GaussianOutput(output_file)
if len(lower_output.errors) == 0:
# if the calculation at the lower level of theory succeeded
if not filter(os.listdir('.'), '*.[Cc][Hh][Kk]'):
raise FileNotFoundError(
'Missing checkpoint file. Required '
'to read initial guesses')
gin = GaussianInput(
mol=None,
charge=orig_input.charge,
spin_multiplicity=orig_input.spin_multiplicity,
title=orig_input.title,
functional=orig_input.functional,
basis_set=orig_input.basis_set,
route_parameters=lower_output.route_parameters,
input_parameters=orig_input.input_parameters,
link0_parameters=orig_input.link0_parameters,
dieze_tag=orig_input.dieze_tag,
gen_basis=orig_input.gen_basis)
gin.route_parameters['Guess'] = 'Read'
gin.route_parameters['Geom'] = 'Checkpoint'
gin.write_file(input_file, cart_coords=cart_coords)
yield (GaussianJob(gaussian_cmd=gaussian_cmd,
input_file=input_file,
output_file=output_file,
stderr_file=stderr_file,
suffix='.guess2',
backup=backup))
else:
logger.info('Failed to generate a better initial guess')
else:
logger.info('Calculation completed normally without having to '
'generate a better initial guess')
def gauss_in_gen(name, mol, type, func, basis, charge, spin, route_params,
link0_params):
mol_in = GaussianInput(
mol,
charge=charge,
spin_multiplicity=spin,
functional=func,
basis_set=basis,
route_parameters=route_params,
link0_parameters=link0_params,
)
fn = '{}_{}.gjf'.format(name, type)
mol_in.write_file(filename=fn, cart_coords=True)
return fn
def MakesGauInputs(mol_file, dihed_atoms_file, w, num_conform=19):
"""
Creates Gaussian input files in its own folder for mol_file structues that
freezes the central angle at iterations of 180/num_conform degrees. This
function requires Gaussian output file of molecule in question and file
with dihedral atoms to be in the current working directory.
"""
molecule_name = mol_file.split('/')[-1][:-12]
mol_pymat = Molecule.from_file(mol_file)
molecule = pmgmol_to_rdmol(mol_pymat)[0]
with open(dihed_atoms_file, 'r') as fn:
data = fn.readlines()
dihedral1 = data[0].split(',')[0]
dihedral2 = data[0].split(',')[1]
d1atom1_num = int(dihedral1.split()[0])
d1atom2_num = int(dihedral1.split()[1])
d1atom3_num = int(dihedral1.split()[2])
d1atom4_num = int(dihedral1.split()[3])
phi = np.linspace(start=0, stop=180, num=num_conform)
for P in phi:
dir_name = "{}/{}_{:.0f}deg/".format(os.getcwd(), molecule_name, P)
os.mkdir(dir_name)
file_name = "{}/{}_{:.0f}deg".format(dir_name, molecule_name, P)
SetDihedralDeg(molecule.GetConformer(), d1atom1_num, d1atom2_num,
d1atom3_num, d1atom4_num, P)
with open(dir_name + "temp.xyz", 'w+') as fout:
fout.write(str(MolToXYZBlock(molecule)))
mol = Molecule.from_file(dir_name + 'temp.xyz')
os.remove(dir_name + 'temp.xyz')
gau = GaussianInput(mol=mol,
charge=0,
spin_multiplicity=1,
functional='uLC-wPBE',
basis_set='cc-pVDZ',
route_parameters={
"iop(3/107={}, 3/108={})".format(w, w): "",
"opt": "modredundant"
},
link0_parameters={
'%mem': '5GB',
'%chk':
'{}.chk'.format(file_name.split('/')[-1])
})
gjf_file = gau.write_file(dir_name + 'temp.gjf')
with open(dir_name + 'temp.gjf') as temp:
lines = temp.readlines()
os.remove(dir_name + 'temp.gjf')
with open(file_name + '.gjf', 'w') as gjf:
gjf.writelines([item for item in lines[:-2]])
gjf.write("D * {} {} * F\n\n".format(d1atom2_num + 1,
d1atom3_num + 1))
print(
"Torsion Gaussian input files for {} finsihed!".format(molecule_name))
def generate_gjf(in_fn,
out_dir,
functional='LC-wHPBE',
basis_set='TZVP',
charge=0,
calculation='opt',
omega=None,
oldchk=None):
"""
Convert an individually inputted xyz file to a gjf Gaussian input file
"""
mol = Molecule.from_file(in_fn)
mol.perturb(0.1)
mol_name = in_fn.split('/')[-1][:14]
link0_parameters = {'%mem': '5GB', '%chk': '{}.chk'.format(calculation)}
route_parameters = {
calculation: '',
'SCF': '(MaxCycle=250)',
'Int': '(Grid=Ultrafine)'
}
if calculation == 'tddft':
route_parameters = {'TD(NStates=5, 50-50)': ''}
if omega is not None:
route_parameters["iop(3/107={}, 3/108={})".format(omega, omega)] = ''
if oldchk:
link0_parameters['%oldchk'] = '{}.chk'.format(oldchk)
route_parameters['Geom'] = 'AllCheck'
gau = GaussianInput(mol=mol,
charge=charge,
functional=functional,
basis_set=basis_set,
route_parameters=route_parameters,
link0_parameters=link0_parameters)
gjf_file = gau.write_file('{}/{}.gjf'.format(out_dir, calculation))
return gjf_file
def MakesGauInputs(fn,w):
"""
Convert an individually imputted xyz file to a gjf Gaussian input file
"""
mol = Molecule.from_file(fn)
mol_name = fn.split('/')[-1][:-12]
gau = GaussianInput(mol=mol,charge=0,spin_multiplicity=1,functional='uLC-wPBE',basis_set='cc-pVDZ', route_parameters={"iop(3/107={}, 3/108={})".format(w,w):"","opt":"modredundant"}, link0_parameters={'%mem':'5GB','%chk':'{}.chk'.format(mol_name)})
gjf_file = gau.write_file('{}.gjf'.format(fn.split('.')[0]))
return gjf_file
def XYZtoGJF(xyz_fn, out_dir, functional, basis_set, charge=0):
"""
Convert an individually imputted xyz file to a gjf Gaussian input file
"""
mol = Molecule.from_file(xyz_fn)
mol_name = xyz_fn.split('/')[-1].split('.')[0]
gau = GaussianInput(mol=mol,
charge=charge,
functional=functional,
basis_set=basis_set,
route_parameters={"opt": ""},
link0_parameters={
'%mem': '5GB',
'%chk': '{}.chk'.format(mol_name)
})
gjf_file = gau.write_file('{}/{}.gjf'.format(out_dir, mol_name))
return gjf_file
def XYZtoGJF(fn):
"""
Convert an individually imputted xyz file to a gjf Gaussian input file
"""
mol = Molecule.from_file(fn)
gau = GaussianInput(mol=mol,
charge=0,
spin_multiplicity=1,
functional='PM6',
basis_set='',
route_parameters={'': ''},
link0_parameters={
'%mem': '5GB',
'%nproc': '1',
'%chk': '{}.chk'.format(fn.split('.')[0])
})
gjf_file = gau.write_file('{}.gjf'.format(fn.split('.')[0]))
return gjf_file
def calculate_properties(rin, directory):
with cd(directory):
# found that the relax often crashed or didn't finish, so will restart
# the calculation in these cases
try:
rout = GaussianOutput('relax.log')
if not rout.properly_terminated:
logging.info('restarting {}'.format(directory))
route = rout.route
route['integral'] = '(acc2e=12)'
rout.to_input('relax.com',
cart_coords=True,
route_parameters=route)
os.system('g09 < relax.com > relax.log')
except IOError:
# relaxation hasn't been run yet
logging.info('started processing {}'.format(directory))
rin.write_file('relax.com', cart_coords=True)
os.system('g09 < relax.com > relax.log')
except IndexError, AttributeError:
# the relax calculation used the wrong header, fix this and restart
rin = GaussianInput.from_file('relax.com')
rin.route_parameters['integral'] = '(acc2e=12)'
rin.write_file('relax.com', cart_coords=True)
os.system('g09 < relax.com > relax.log')
rout = GaussianOutput('relax.log')
if not rout.properly_terminated:
logging.error(
'{} relaxation did not terminate correctly'.format(directory))
return 0
# do the TD-DFT calculation
tdin = GaussianInput(rout.final_structure,
charge=0,
title=rin.title,
functional=functional,
spin_multiplicity=1,
basis_set=basis_set,
dieze_tag=dieze_tag,
link0_parameters=link0,
route_parameters=td_params)
td_done = False
if os.path.isfile('td.log'):
tdout = GaussianOutput('td.log')
if tdout.properly_terminated:
td_done = True
if not td_done:
tdin.write_file('td.com', cart_coords=True)
os.system('g09 < td.com > td.log')
tdout = GaussianOutput('td.log')
if not tdout.properly_terminated:
logging.error(
'{} TD-DFT did not terminate correctly'.format(directory))
return 0
# do the TD-DFT calculation w. Tamm-Dancoff approx
tdain = GaussianInput(rout.final_structure,
charge=0,
title=rin.title,
spin_multiplicity=1,
functional=functional,
basis_set=basis_set,
dieze_tag=dieze_tag,
link0_parameters=link0,
route_parameters=tda_params)
tda_done = False
if os.path.isfile('tda.log'):
tdaout = GaussianOutput('tda.log')
if tdaout.properly_terminated:
tda_done = True
if not tda_done:
tdain.write_file('tda.com', cart_coords=True)
os.system('g09 < tda.com > tda.log')
tdaout = GaussianOutput('tda.log')
if not tdaout.properly_terminated:
logging.error(
'{} TDA-DFT did not terminate correctly'.format(directory))
return 0
# add the dummy atoms for the NICS(1)_zz calculations
mol_nics = rout.final_structure
mol_nics = add_dummy_atoms(mol_nics, six_mem_a)
mol_nics = add_dummy_atoms(mol_nics, six_mem_b)
mol_nics = add_dummy_atoms(mol_nics, five_mem_a)
mol_nics = add_dummy_atoms(mol_nics, five_mem_b)
# run NICS on the ground state and triplet state
nicssin = GaussianInput(mol_nics,
charge=0,
title=rin.title,
spin_multiplicity=1,
functional=functional,
basis_set=basis_set,
dieze_tag=dieze_tag,
link0_parameters=link0,
route_parameters=nmr_params)
nicssin.write_file('nics_singlet.com', cart_coords=True)
# work around as pymatgen does not allow Bq as an element
os.system("sed -i 's/X-Bq0+/Bq/g' nics_singlet.com")
os.system('g09 < nics_singlet.com > nics_singlet.log')
# can't have NICS job completion check due to above mentioned pmg bug
nicstin = GaussianInput(mol_nics,
charge=0,
title=rin.title,
spin_multiplicity=3,
functional=functional,
basis_set=basis_set,
dieze_tag=dieze_tag,
link0_parameters=link0,
route_parameters=nmr_params)
nicstin.write_file('nics_triplet.com', cart_coords=True)
os.system("sed -i 's/X-Bq0+/Bq/g' nics_triplet.com")
os.system('g09 < nics_triplet.com > nics_triplet.log')
