def test_scan(self):
gau = GaussianOutput(os.path.join(test_dir, "so2_scan.log"))
d = gau.read_scan()
self.assertAlmostEqual(-548.02102, d["energies"][-1])
self.assertEqual(len(d["coords"]), 1)
self.assertEqual(len(d["energies"]), len(gau.energies))
self.assertEqual(len(d["energies"]), 21)
def test_multiple_parameters(self):
"""
This test makes sure that input files with multi-parameter keywords
and route cards with multiple lines can be parsed accurately.
"""
filepath = os.path.join(test_dir, "l-cysteine.out")
route = {
"test": None,
"integral": {
"grid": "UltraFine"
},
"opt": {
"Z-Matrix": None,
"maxcycles": "80",
"tight": None
},
}
gout = GaussianOutput(filepath)
self.assertEqual(gout.dieze_tag, "#n")
self.assertEqual(gout.functional, "B3LYP")
self.assertEqual(gout.basis_set, "6-31+G**")
self.assertEqual(gout.route_parameters, route)
self.assertEqual(gout.title, "L-cysteine neutral")
self.assertEqual(gout.charge, 0)
self.assertEqual(gout.spin_multiplicity, 1)
def FindTorsionEnergies(rotdihed_dir, out_dir):
"""
Iterates through rotdihed_dir and finds energies for each torsion angle
for the molecule. It then creates a energy cvs file for the molecule.
"""
mols = [m for m in os.listdir(rotdihed_dir) if os.path.isdir(os.path.join(rotdihed_dir,m))]
for m in mols:
mol_name = m.split('.')[0]
mpath = os.path.join(rotdihed_dir,m)
log_file = [x for x in os.listdir(mpath) if x.endswith('.log')][0]
log_path = os.path.join(mpath,log_file)
mol = GaussianOutput(log_path)
if mol.properly_terminated:
normal = 0
with open(log_path) as fn:
log = fn.readlines()
for line in log:
if re.search(' Optimized Parameters',line):
normal = 1
break
else:
continue
if normal == 0:
print("Error. {} job had a normal termination but did not have optimized parameters.".format(mol_name))
else:
normal = 0
print("Error. {} job did not have a normal termination.".format(mol_name))
if normal == 1:
energy = mol.final_energy
with open('{}/energies.cvs'.format(out_dir),'a') as fout:
fout.write(mol_name + ',' + str(energy) + '\n')
print("Dihedral rotations energies collected for {}!".format(mol_name))
def assimilate(self, path):
"""
Assimilate data in a directory path into a ComputedEntry object.
Args:
path: directory path
Returns:
ComputedEntry
"""
try:
gaurun = GaussianOutput(path)
except Exception as ex:
logger.debug("error in {}: {}".format(path, ex))
return None
param = {}
for p in self._parameters:
param[p] = getattr(gaurun, p)
data = {}
for d in self._data:
data[d] = getattr(gaurun, d)
if self._inc_structure:
entry = ComputedStructureEntry(gaurun.final_structure,
gaurun.final_energy,
parameters=param,
data=data)
else:
entry = ComputedEntry(
gaurun.final_structure.composition,
gaurun.final_energy,
parameters=param,
data=data,
)
return entry
def mol_object(log_fn):
"""
Get pymatgen object in preparation for further processing
Returns:
A pymatgen object
"""
try:
return GaussianOutput(log_fn)
except FileNotFoundError:
print("File does not exist: {}".format(log_fn))
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 test_pop(self):
gau = GaussianOutput(os.path.join(test_dir, "H2O_gau.out"))
self.assertEqual(gau.num_basis_func, 13)
self.assertEqual(gau.electrons, (5, 5))
self.assertEqual(gau.is_spin, True)
self.assertListEqual(gau.eigenvalues[Spin.down], [-20.55343, -1.35264,
-0.72655, -0.54824,
-0.49831, 0.20705,
0.30297, 1.10569,
1.16144, 1.16717,
1.20460, 1.38903,
1.67608])
mo = gau.molecular_orbital
self.assertEqual(len(mo), 2) # la 6
self.assertEqual(len(mo[Spin.down]), 13)
self.assertEqual(len(mo[Spin.down][0]), 3)
self.assertEqual(mo[Spin.down][5][0]["1S"], -0.08771)
self.assertEqual(mo[Spin.down][5][0]["2PZ"], -0.21625)
self.assertListEqual(gau.eigenvectors[Spin.up][:, 5].tolist(), [-0.08771,
0.10840,
0.00000,
0.00000,
-0.21625,
1.21165,
0.00000,
0.00000,
-0.44481,
-0.06348,
-1.00532,
-0.06348,
-1.00532])
self.assertListEqual(gau.atom_basis_labels[0], ["1S", "2S", "2PX", "2PY",
"2PZ", "3S", "3PX", "3PY",
"3PZ"])
self.assertListEqual(gau.atom_basis_labels[2], ["1S", "2S"])
gau = GaussianOutput(os.path.join(test_dir, "H2O_gau_vib.out"))
self.assertEqual(gau.bond_orders[(0, 1)], 0.7582)
self.assertEqual(gau.bond_orders[(1, 2)], 0.0002)
def MakeJSON(mol_dir,omega_file,json_file):
"""
For a molecule rotation directory, mol_dir, this finds the energy, xyz, and
degree of rotation and places those into json_file.
"""
mol_name = str(mol_dir.split('/')[-1])
energy = 0
mol_xyz = 0
try:
# if 0 == 0:
log_fn = [x for x in os.listdir(mol_dir) if x.endswith('opt_0.log')][0]
log_path = os.path.join(mol_dir,log_fn)
mol = GaussianOutput(log_path)
if mol.properly_terminated:
num_electrons = mol.electrons[0]
eigens = list(mol.eigenvalues.values())[0]
h**o = eigens[num_electrons - 1] * 27.2114
lumo = eigens[num_electrons] * 27.2114
homo_lumo_gap = lumo - h**o
pymat_mol = Molecule.from_file(log_path)
smi_mol = pmgmol_to_rdmol(pymat_mol)[1]
with open(omega_file,'r') as fn:
omega_data = fn.readlines()[-2].split()[1]
omega = "0{}".format(omega_data.split('.')[1])
normal = 1
else:
normal = 0
print("Error. wtuning for did not properly terminate for {}".format(mol_name))
except Exception as e:
normal = 0
print("Error. Data NOT collected for {}. Energy calculations for dihedral rotations may not have finished!".format(mol_name))
print(e)
if normal == 1:
json_data = {
"molecule_name" : mol_name,
"smiles" : smi_mol,
"tuned_omega" : omega,
"h**o" : h**o,
"lumo" : lumo,
"homo_lumo_gap" : homo_lumo_gap
}
with open(json_file,'w+') as fn:
json.dump(json_data, fn)
print("Data collected for {}".format(mol_name))
else:
pass
try:
json_file.close()
omega_file.close()
except:
pass
def test_geo_opt(self):
"""
Test an optimization where no "input orientation" is outputted
"""
gau = GaussianOutput(
os.path.join(test_dir, "acene-n_gaussian09_opt.out"))
self.assertAlmostEqual(-1812.58399675, gau.energies[-1])
self.assertEqual(len(gau.structures), 6)
# Test the first 3 atom coordinates
coords = [[-13.642932, 0.715060, 0.000444],
[-13.642932, -0.715060, 0.000444],
[-12.444202, 1.416837, 0.000325]]
self.assertAlmostEqual(gau.opt_structures[-1].cart_coords[:3].tolist(),
coords)
def get_run_folders(molecule_dir, out_dir, nflag=''):
mol_name = molecule_dir.split('/')[-1].split('.')[0]
opt_log = os.path.join(molecule_dir, 'opt.log')
opt_gjf = os.path.join(molecule_dir, 'opt.gjf')
freq_gjf = os.path.join(molecule_dir, 'freq.gjf')
tddft_gjf = os.path.join(molecule_dir, 'tddft.gjf')
tddft_log = os.path.join(molecule_dir, 'tddft.log')
if os.path.isfile(tddft_gjf):
mol_tddft = GaussianOutput(tddft_log)
if mol_tddft.properly_terminated:
print("{} TD-DFT terminated normally".format(mol_name))
else:
txt_file = os.path.join(out_dir, 'folders_to_run_tddft.txt')
with open(txt_file, 'a+') as fn:
fn.write(molecule_dir + '\n')
return None
normal = None
if os.path.isfile(opt_log):
with open(opt_log) as fn:
log_fn = fn.readlines()
for line in log_fn:
if re.search(' Optimized Parameters', line):
last_line = log_fn[-1]
if re.search('Normal termination', last_line):
if os.path.isfile(freq_gjf):
txt_file = os.path.join(out_dir,
'folders_to_run_freq.txt')
with open(txt_file, 'a+') as fn:
fn.write(molecule_dir + '\n')
else:
print(
"{} is finished optimizing, but there is not freq.gjf file."
.format(mol_name))
return None
if re.search('Error termination', line):
normal = 0
txt_file = os.path.join(out_dir,
'folders_to_run{}.txt'.format(nflag))
with open(txt_file, 'a+') as fn:
fn.write(molecule_dir + '\n')
print("Error in termination for {}".format(mol_name))
return None
else:
print("{} does not have an opt.log file.")
if os.path.isfile(opt_gjf):
print("{} may still be running".format(mol_name))
else:
print("Error. {} does not contain a gjf file.".format(mol_name))
def make_json(mol_dir, dihed_atoms_file, json_file):
"""
For a molecule rotation directory, mol_dir, this finds the energy, xyz, and
degree of rotation and places those into json_file.
"""
mol_name = str(mol_dir.split('/')[-1])
try:
log_fn = [x for x in os.listdir(dpath) if x.endswith('deg.log')][0]
log_path = os.path.join(dpath, log_fn)
except IndexError:
print("Error. No log file for {} at {} degrees.".format(
mol_name, degree))
return None
if check_normal_optimization(log_path):
mol = GaussianOutput(log_path)
num_electrons = mol.electrons[0]
eigens = list(mol.eigenvalues.values())[0]
h**o = eigens[num_electrons - 1] * 27.2114
lumo = eigens[num_electrons] * 27.2114
homo_lumo_gap = lumo - h**o
energy = mol.final_energy * 27.2114
imol = IMolecule.from_file(log_path)
with open(dihed_atoms_file, 'r') as lines:
data = lines.readlines()
dihedral1 = data[0].split(',')[0]
d1atom1_num = int(dihedral1.split()[0])
d1atom2_num = int(dihedral1.split()[1])
d1atom3_num = int(dihedral1.split()[2])
d1atom4_num = int(dihedral1.split()[3])
di_angle = imol.get_dihedral(d1atom1_num, d1atom2_num, d1atom3_num,
d1atom4_num)
json_data = {
"molecule_name": mol_name,
"dihedral_angle": di_angle,
"energy": energy,
"h**o": h**o,
"lumo": lumo,
"homo_lumo_gap": homo_lumo_gap
}
write_json(json_data, json_file)
print("Data collected for {}".format(mol_name))
else:
normal = 0
print("Error. GeomOpt calculation did not properly terminate for {}".
format(mol_name))
def make_json(mol_dir, mol_name, json_file):
"""
For a molecule directory, mol_dir, this finds the energy, xyz, charge, h**o,
lumo, homo_lumo_gap, and runtime and places those into json_file.
"""
# Gather info from log file in mol_dir
try:
log_fn = [x for x in os.listdir(mol_dir) if x.endswith('.log')][0]
log_path = os.path.join(mol_dir, log_fn)
mol = GaussianOutput(log_path)
if mol.properly_terminated:
structure = mol.final_structure
xyz = structure.to(fmt="xyz")
charge = mol.charge
energy = mol.final_energy * 27.2114
num_electrons = mol.electrons[0]
eigens = list(mol.eigenvalues.values())[0]
h**o = eigens[num_electrons - 1] * 27.2114
lumo = eigens[num_electrons] * 27.2114
homo_lumo_gap = lumo - h**o
runtime = runtime_from_log(log_path)
normal = 1
else:
normal = 0
print("Error. Calculation did not properly terminate for {}".format(mol_name))
except:
normal = 0
print("Error. Data NOT collected for {}. Energy calculations may not have finished!".format(mol_name))
# write json file if data was correctly gathered
if normal == 1:
json_data = {
"molecule_name": mol_name,
"charge": charge,
"structure": xyz,
"energy": energy,
"h**o": h**o,
"lumo": lumo,
"homo_lumo_gap": homo_lumo_gap,
"runtime": runtime
}
write_json(json_data, json_file)
print("Data collected for {}".format(mol_name))
def read_mol(filename):
"""
Reads a molecule based on file extension. For example, anything ending in
a "xyz" is assumed to be a XYZ file. Supported formats include xyz,
gaussian input (gjf|g03|g09|com|inp), Gaussian output (.out|and
pymatgen's JSON serialized molecules. Using openbabel,
many more extensions are supported but requires openbabel to be installed.
Args:
filename (str): A filename to read from.
Returns:
A Molecule object.
"""
fname = os.path.basename(filename)
if fnmatch(fname.lower(), "*.xyz*"):
return XYZ.from_file(filename).molecule
elif any([
fnmatch(fname.lower(), "*.{}*".format(r))
for r in ["gjf", "g03", "g09", "com", "inp"]
]):
return GaussianInput.from_file(filename).molecule
elif any([
fnmatch(fname.lower(), "*.{}*".format(r))
for r in ["out", "lis", "log"]
]):
return GaussianOutput(filename).final_structure
elif fnmatch(fname, "*.json*") or fnmatch(fname, "*.mson*"):
with zopen(filename) as f:
s = json.load(f, cls=MontyDecoder)
if type(s) != Molecule:
raise IOError("File does not contain a valid serialized "
"molecule")
return s
else:
m = re.search("\.(pdb|mol|mdl|sdf|sd|ml2|sy2|mol2|cml|mrv)",
filename.lower())
if m:
return BabelMolAdaptor.from_file(filename, m.group(1)).pymatgen_mol
raise ValueError("Unrecognized file extension!")
def setUp(self):
self.gauout = GaussianOutput(os.path.join(test_dir, "methane.log"))
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')
def make_json(mol_dir, json_file, omega_file=None):
"""
For a molecule directory, mol_dir, this finds the molecule_name, smiles, and tuned omega
for the polymer. It then finds the optimized structures, energies, homos, lumos, and
runtimes for each degree of rotation and places those into a json_file.
"""
mol_name = mol_dir.split('/')[-1]
xyz_dict, energy_dict, homo_dict, lumo_dict, runtime_dict = {}, {}, {}, {}, {}
mol_smiles, omega = None, None
if os.path.isfile(omega_file):
with open(omega_file, 'r') as fn:
try:
omega_data = fn.readlines()[-1].split()[1]
omega = "0{}".format(omega_data.split('.')[1])
except IndexError:
print('Error. wtuning for {} may not have finished'.format(
mol_name))
return None
deg_folders = [
deg for deg in os.listdir(mol_dir)
if os.path.isdir(os.path.join(mol_dir, deg))
]
for deg in deg_folders:
dpath = os.path.join(mol_dir, deg)
if os.path.isdir(dpath):
degree = str((deg.split('_')[-1])[:-3])
try:
log_fn = [
x for x in os.listdir(dpath) if x.endswith('deg.log')
][0]
log_path = os.path.join(dpath, log_fn)
except IndexError:
print("Error. No log file for {} at {} degrees.".format(
mol_name, degree))
continue
if check_normal_optimization(log_path):
runtime = runtime_from_log(log_path)
mol = IMolecule.from_file(log_path)
mol_xyz = mol.to(fmt="xyz")
out_mol = GaussianOutput(log_path)
num_electrons = out_mol.electrons[0]
eigens = list(out_mol.eigenvalues.values())[0]
h**o = eigens[num_electrons - 1] * 27.2114
lumo = eigens[num_electrons] * 27.2114
energy = out_mol.final_energy * 27.2114
if mol_smiles is None:
mol_smiles = pmgmol_to_rdmol(mol)[1]
else:
print(
"Error. Optimization did not properly terminate for {} at {} degrees."
.format(mol_name, degree))
continue
xyz_dict[degree] = mol_xyz
energy_dict[degree] = energy
homo_dict[degree] = h**o
lumo_dict[degree] = lumo
runtime_dict[degree] = runtime
json_data = {
# Polymer data
"molecule_name": mol_name,
"smiles": mol_smiles,
"tuned_omega": omega,
# Rotation dictionaries
"structures": xyz_dict,
"energies": energy_dict,
"homos": homo_dict,
"lumos": lumo_dict,
"runtimes": runtime_dict
}
write_json(json_data, json_file)
print("Data collected for {}".format(mol_name))
def test_td(self):
gau = GaussianOutput(os.path.join(test_dir, "so2_td.log"))
transitions = gau.read_excitation_energies()
self.assertEqual(len(transitions), 4)
self.assertAlmostEqual(transitions[0], (3.9281, 315.64, 0.0054))
def extract_abs(fn):
return GaussianOutput(fn).read_excitation_energies()
def extract_energy(fn):
return GaussianOutput(fn).final_energy
def extract_data_from_tar_file(tar_file):
with tarfile.open(tar_file, 'r:gz') as tar:
tar.extractall()
folder = tar_file.replace('.tar.gz', '')
with cd(folder):
tdout = GaussianOutput('td.log')
td_exit = tdout.read_excitation_energies()
td_triplet = [e for e in td_exit if 'triplet' in e[3].lower()][0][0]
td_singlet = [e for e in td_exit if 'singlet' in e[3].lower()][0][0]
tdaout = GaussianOutput('tda.log')
tda_exit = tdaout.read_excitation_energies()
tda_triplet = [e for e in tda_exit if 'triplet' in e[3].lower()][0][0]
tda_singlet = [e for e in tda_exit if 'singlet' in e[3].lower()][0][0]
nicssout = GaussianOutput('nics_singlet.log')
# occasionally some jobs fail here
if not nicssout.properly_terminated:
return False
nicss_mag = nicssout.read_magnetic_shielding()
nicss_six_ring_above = (abs(nicss_mag[-8]['isotropic']) +
abs(nicss_mag[-6]['isotropic']))/2
nicss_six_ring_below = (abs(nicss_mag[-7]['isotropic']) +
abs(nicss_mag[-5]['isotropic']))/2
nicss_five_ring_above = (abs(nicss_mag[-4]['isotropic']) +
abs(nicss_mag[-2]['isotropic']))/2
nicss_five_ring_below = (abs(nicss_mag[-3]['isotropic']) +
abs(nicss_mag[-1]['isotropic']))/2
nicstout = GaussianOutput('nics_triplet.log')
if not nicstout.properly_terminated:
return False
nicst_mag = nicstout.read_magnetic_shielding()
nicst_six_ring_above = (abs(nicst_mag[-8]['isotropic']) +
abs(nicst_mag[-6]['isotropic']))/2
nicst_six_ring_below = (abs(nicst_mag[-7]['isotropic']) +
abs(nicst_mag[-5]['isotropic']))/2
nicst_five_ring_above = (abs(nicst_mag[-4]['isotropic']) +
abs(nicst_mag[-2]['isotropic']))/2
nicst_five_ring_below = (abs(nicst_mag[-3]['isotropic']) +
abs(nicst_mag[-1]['isotropic']))/2
data = {'td_singlet': td_singlet, 'td_triplet': td_triplet,
'tda_singlet': tda_singlet, 'tda_triplet': tda_triplet,
'nicss_six_ring_above': nicss_six_ring_above,
'nicss_six_ring_below': nicss_six_ring_below,
'nicss_five_ring_above': nicss_five_ring_above,
'nicss_five_ring_below': nicss_five_ring_below,
'nicst_six_ring_above': nicst_six_ring_above,
'nicst_six_ring_below': nicst_six_ring_below,
'nicst_five_ring_above': nicst_five_ring_above,
'nicst_five_ring_below': nicst_five_ring_below}
return data
name = names_dict.get(mol)
if not name:
continue
print(mol, name)
mol_name_path = os.path.join(name_path, name)
if not os.path.isdir(mol_name_path): os.mkdir(mol_name_path)
gas_opt_dir = os.path.join(mol_path, 'computation', 'gaussian')
if os.path.isdir(gas_opt_dir):
for zip_file in [
f for f in os.listdir(gas_opt_dir)
if f.endswith('.zip') and 'freq' not in f
]:
zip_path = os.path.join(gas_opt_dir, zip_file)
with ZipFile(zip_path, "r") as target_zip:
target_zip.extractall(mol_name_path)
log_file = os.path.join(mol_name_path, 'opt_groundState.log')
if os.path.isfile(log_file):
pmg_mol = GaussianOutput(log_file)
num_electrons = pmg_mol.electrons[0]
eigens = list(pmg_mol.eigenvalues.values())[0]
h**o = eigens[num_electrons - 1] * 27.2114
lumo = eigens[num_electrons] * 27.2114
energy = min(pmg_mol.energies) * 27.2114
master_dict["h**o"][name] = round(h**o, 3)
master_dict["lumo"][name] = round(lumo, 3)
master_dict["energy"][name] = round(energy, 3)
with open("individual_rings_data.json", 'w') as fn:
json.dump(master_dict, fn, indent=2)
def test_props(self):
gau = self.gauout
self.assertEqual(len(gau.energies), 3)
self.assertAlmostEqual(gau.energies[-1], -39.9768775602)
self.assertEqual(len(gau.structures), 4)
for mol in gau.structures:
self.assertEqual(mol.formula, "H4 C1")
self.assertIn("opt", gau.route_parameters)
self.assertEqual("Minimum", gau.stationary_type)
self.assertEqual("hf", gau.functional)
self.assertEqual("3-21G", gau.basis_set)
self.assertEqual(17, gau.num_basis_func)
d = gau.as_dict()
self.assertEqual(d["input"]["functional"], "hf")
self.assertAlmostEqual(d["output"]["final_energy"], -39.9768775602)
self.assertEqual(len(gau.cart_forces), 3)
self.assertEqual(gau.cart_forces[0][5], 0.009791094)
self.assertEqual(gau.cart_forces[0][-1], -0.003263698)
self.assertEqual(gau.cart_forces[2][-1], -0.000000032)
self.assertEqual(gau.eigenvalues[Spin.up][-1], 1.95586)
self.assertEqual(gau.num_basis_func, 17)
self.assertEqual(gau.is_spin, False)
ch2o_co2 = GaussianOutput(os.path.join(test_dir, "CH2O_CO2.log"))
self.assertEqual(len(ch2o_co2.frequencies), 2)
self.assertEqual(len(ch2o_co2.frequencies[0]), 6)
self.assertEqual(len(ch2o_co2.frequencies[1]), 4)
self.assertEqual(ch2o_co2.frequencies[0][0]["frequency"], 1203.1940)
self.assertEqual(ch2o_co2.frequencies[0][0]["symmetry"], 'A"')
self.assertEqual(ch2o_co2.frequencies[0][3]["IR_intensity"], 60.9575)
self.assertEqual(ch2o_co2.frequencies[0][3]["r_mass"], 3.7543)
self.assertEqual(ch2o_co2.frequencies[0][4]["f_constant"], 5.4175)
self.assertListEqual(
ch2o_co2.frequencies[0][1]["mode"],
[
0.15,
0.00,
0.00,
-0.26,
0.65,
0.00,
-0.26,
-0.65,
0.00,
-0.08,
0.00,
0.00,
],
)
self.assertListEqual(
ch2o_co2.frequencies[1][3]["mode"],
[0.00, 0.00, 0.88, 0.00, 0.00, -0.33, 0.00, 0.00, -0.33],
)
self.assertEqual(ch2o_co2.frequencies[1][3]["symmetry"], "SGU")
self.assertEqual(ch2o_co2.eigenvalues[Spin.up][3], -1.18394)
h2o = GaussianOutput(os.path.join(test_dir, "H2O_gau_vib.out"))
self.assertEqual(len(h2o.frequencies[0]), 3)
self.assertEqual(h2o.frequencies[0][0]["frequency"], 1662.8033)
self.assertEqual(h2o.frequencies[0][1]["symmetry"], "A'")
self.assertEqual(h2o.hessian[0, 0], 0.356872)
self.assertEqual(h2o.hessian.shape, (9, 9))
self.assertEqual(
h2o.hessian[8, :].tolist(),
[
-0.143692e-01,
0.780136e-01,
-0.362637e-01,
-0.176193e-01,
0.277304e-01,
-0.583237e-02,
0.319885e-01,
-0.105744e00,
0.420960e-01,
],
)
def test_td(self):
gau = GaussianOutput(os.path.join(test_dir, "so2_td.log"))
transitions = gau.read_excitation_energies()
self.assertEqual(len(transitions), 4)
self.assertAlmostEqual(transitions[0], (3.9281, 315.64, 0.0054))
def MakeJSON(mol_dir, json_file, master_json_file):
"""
For a molecule rotation directory, mol_dir, this finds the energy, xyz, and
degree of rotation and places those into json_file.
"""
mol_name = str(mol_dir.split('/')[-1])
try:
log_fn = [x for x in os.listdir(mol_dir) if x.endswith('.log')][0]
log_path = os.path.join(mol_dir, log_fn)
mol = GaussianOutput(log_path)
if mol.properly_terminated:
num_electrons = mol.electrons[0]
eigens = list(mol.eigenvalues.values())[0]
h**o = eigens[num_electrons - 1] * 27.2114
lumo = eigens[num_electrons] * 27.2114
homo_lumo_gap = lumo - h**o
energy = mol.final_energy * 27.2114
structure = mol.final_structure
mol_xyz = structure.to(fmt="xyz")
runtime = runtime_from_log(log_path)
functional = mol.functional
basis_set = mol.basis_set
normal = 1
else:
normal = 0
print(
"Error. Calculation did not properly terminate for {}".format(
mol_name))
print(mol_dir)
except:
normal = 0
print(
"Error. Data NOT collected for {}. Energy calculations may not have finished!"
.format(mol_name))
print(mol_dir)
try:
catpath = os.path.join(mol_dir, 'cation/')
log_fn = [x for x in os.listdir(catpath) if x.endswith('.log')][0]
log_path = os.path.join(catpath, log_fn)
cat = GaussianOutput(log_path)
if cat.properly_terminated:
cat_energy = cat.final_energy * 27.2114
cnormal = 1
else:
cnormal = 0
print(
"Error. Calculation did not properly terminate for {} cation with {} and {}"
.format(mol_name, functional, basis_set))
print(mol_dir)
except:
cnormal = 0
print(
"Error. Data NOT collected for {} cation. Energy calculations for cation may not have finished!"
.format(mol_name))
print(mol_dir)
if normal == 1 and cnormal == 1:
json_data = {
"molecule_name": mol_name,
"energy": energy,
"cation_energy": cat_energy,
"runtime": runtime,
"functional": functional,
"basis_set": basis_set,
"h**o": h**o,
"lumo": lumo,
"structure": mol_xyz,
"homo_lumo_gap": homo_lumo_gap
}
write_json(json_data, json_file)
print("Data collected for {} with {} and {}".format(
mol_name, functional, basis_set))