def get_plams_settings(self):
"""Returns a plams setting object."""
sett = plams.Settings()
sett.input.basis.type = self.basis_name.upper()
if self.basis_name.upper() in self.additional_basis_type:
sett.input.basis.path = self.additional_basis_path
sett.input.basis.core = 'None'
sett.input.symmetry = 'nosym'
if self.scf.lower() == 'hf':
sett.input.XC.HartreeFock = ''
elif self.scf.lower() == 'dft':
sett.input.XC.LDA = 'VWN'
# correct unit
if self.units == 'angs':
sett.input.units.length = 'Angstrom'
elif self.units == 'bohr':
sett.input.units.length = 'Bohr'
# total energy
sett.input.totalenergy = True
return sett
def __init__(self, mol_file, job_name, settings=None, geo_opt=False):
self.job_name = job_name
self.mol = plams.Molecule(mol_file)
#sort atoms to prevent errors in ADF
self.mol.atoms.sort(key=lambda x: x.symbol)
self.settings = plams.Settings()
self._set_std_settings(geo_opt)
if settings is not None:
self.settings.update(settings)
def test_saving_plams_settings(historian: mincepy.Historian):
from scm import plams
settings = plams.Settings()
settings.sub.a = 'a'
settings.sub.b = 'b'
settings.top = 'top'
settings_id = historian.save(settings)
del settings
loaded = historian.load(settings_id)
assert isinstance(loaded.sub, plams.Settings)
assert loaded.sub.a == 'a'
assert loaded.sub.b == 'b'
assert loaded.top == 'top'
def adf_grads():
"""
Settings for running gradients calculation
"""
adf = plams.Settings()
adf.input.SYMMETRY = 'NOSYM'
adf.input.BASIS.type = 'DZP'
adf.input.BASIS.core = 'Large'
adf.input.XC.GGA = 'BP86'
adf.input.RESPONSE.Dipole = ""
adf.input.RESPONSE.AllComponents = ""
# adf.input.XC.DISPERSION = 'GRIMME3 BJDAMP'
#adf.input.RESTART.File = '/Users/janani/Desktop/Raman_trials/ADF_new_version_trials/H2/H2_bp86_sp/H2_bp86_sp.t21'
#adf.input.RESTART.nogeo = ''
adf.input.Gradient = ""
return adf
def run(self):
"""Run the calculation
Raises:
ValueError: [description]
Returns:
np.ndarray -- molecular orbital matrix
"""
wd = ''.join(self.atoms) + '_' + self.basis_name
t21_name = wd + '.t21'
plams_wd = './plams_workdir'
t21_path = os.path.join(plams_wd, os.path.join(wd, t21_name))
if os.path.isfile(t21_name):
print('Reusing previous calculation from ', t21_name)
kf = plams.KFFile(t21_name)
e = kf.read('Total Energy', 'Total energy')
else:
# init PLAMS
plams.init()
plams.config.log.stdout = -1
plams.config.erase_workdir = True
# create the molecule
mol = plams.Molecule()
for at, xyz in zip(self.atoms, self.atom_coords):
mol.add_atom(plams.Atom(symbol=at, coords=tuple(xyz)))
# settings in PLAMS
sett = plams.Settings()
sett.input.basis.type = self.basis_name.upper()
sett.input.basis.core = 'None'
sett.input.symmetry = 'nosym'
sett.input.XC.HartreeFock = ''
# correct unit
if self.units == 'angs':
sett.input.units.length = 'Angstrom'
elif self.units == 'bohr':
sett.input.units.length = 'Bohr'
# total energy
sett.input.totalenergy = True
# run the ADF job
job = plams.ADFJob(molecule=mol, settings=sett, name=wd)
job.run()
# read the energy from the t21 file
e = job.results.readkf('Total Energy', 'Total energy')
# make a copy of the t21 file
shutil.copyfile(t21_path, t21_name)
shutil.rmtree(plams_wd)
# print energy
print('== SCF Energy : ', e)
self.out_file = t21_name
functionals = ['PBE']
print(
f'Starting singlepoint DFT and DFTB vibration calculations for {len(mol_names)} molecules from the {dataset_name} dataset:'
)
print('Molecules:')
[print('\t' + str(i + 1), n) for i, n in enumerate(mol_names)]
for f in functionals:
print(
f'Starting geo-opt DFT vibration calculations for {len(mol_names)} molecules from the {dataset_name} dataset with functional {f}'
)
for n, p in zip(mol_names, mol_paths):
settings = plams.Settings()
if f == 'PBE':
settings.input.XC.GGA = 'PBE'
kf_DFT = jobs.DFTJob(p, job_name=f'{n}_DFT',
geo_opt=True).run(init=False)
shutil.copy2(kf_DFT, f'{kf_dir}/{n}_DFT.t21')
if f == 'DFTB3':
settings.input.DFTB.Model = 'DFTB3'
settings.input.DFTB.ResourcesDir = 'DFTB.org/3ob-3-1'
kf_DFTB = jobs.DFTBJob(p, job_name=f'{n}_{f}_DFTB',
geo_opt=True).run(init=False)
shutil.copy2(kf_DFTB, f'{kf_dir}/{n}_{f}_DFTB.rkf')