def get_nelec(self, geom, multiplicity):
atoms = manage_xyz.get_atoms(geom)
elements = [ELEMENT_TABLE.from_symbol(atom) for atom in atoms]
atomic_num = [ele.atomic_num for ele in elements]
self.n_electrons = sum(atomic_num) - self.charge
if self.n_electrons < 0:
raise ValueError("Molecule has fewer than 0 electrons!!!")
self.check_multiplicity(multiplicity)
return
def __init__(self, options, **kwargs):
self.Data = options
# => Read in the coordinates <= #
# important first try to read in geom
t0 = time()
if self.Data['geom'] is not None:
print(" getting cartesian coordinates from geom")
atoms = manage_xyz.get_atoms(self.Data['geom'])
xyz = manage_xyz.xyz_to_np(self.Data['geom'])
elif self.Data['fnm'] is not None:
print(" reading cartesian coordinates from file")
if self.Data['ftype'] is None:
self.Data['ftype'] = os.path.splitext(self.Data['fnm'])[1][1:]
if not os.path.exists(self.Data['fnm']):
#logger.error('Tried to create Molecule object from a file that does not exist: %s\n' % self.Data['fnm'])
raise IOError
geom = manage_xyz.read_xyz(self.Data['fnm'], scale=1.)
xyz = manage_xyz.xyz_to_np(geom)
atoms = manage_xyz.get_atoms(geom)
else:
raise RuntimeError
t1 = time()
print(" Time to get coords= %.3f" % (t1 - t0))
#resid=[]
#for a in ob.OBMolAtomIter(mol.OBMol):
# res = a.GetResidue()
# resid.append(res.GetName())
#self.resid = resid
# Perform all the sanity checks and cache some useful attributes
# TODO make PES property
self.PES = type(self.Data['PES']).create_pes_from(
PES=self.Data['PES'],
options={'node_id': self.Data['node_id']},
copy_wavefunction=self.Data['copy_wavefunction'])
if not hasattr(atoms, "__getitem__"):
raise TypeError("atoms must be a sequence of atomic symbols")
for a in atoms:
if not isinstance(a, str):
raise TypeError("atom symbols must be strings")
if type(xyz) is not np.ndarray:
raise TypeError("xyz must be a numpy ndarray")
if xyz.shape != (len(atoms), 3):
raise ValueError("xyz must have shape natoms x 3")
self.Data['xyz'] = xyz.copy()
# create a dictionary from atoms
# atoms contain info you need to know about the atoms
self.atoms = [ELEMENT_TABLE.from_symbol(atom) for atom in atoms]
tx = time()
print(" Time to create PES,elements %.3f" % (tx - t1))
t1 = tx
if not isinstance(self.Data['comment'], str):
raise TypeError("comment for a Molecule must be a string")
# Create the coordinate system
if self.Data['coord_obj'] is not None:
print(" getting coord_object from options")
self.coord_obj = self.Data['coord_obj']
else:
print(
" Disabling this feature, Molecule cannot create coordinate system"
)
raise NotImplementedError
#elif self.Data['coordinate_type'] == "Cartesian":
# self.coord_obj = CartesianCoordinates.from_options(xyz=self.xyz,atoms=self.atoms)
#elif self.Data['coordinate_type'] == "DLC":
# print(" building coordinate object")
# self.coord_obj = DelocalizedInternalCoordinates.from_options(xyz=self.xyz,atoms=self.atoms,connect=True,extra_kwargs =self.Data['top_settings'])
#elif self.Data['coordinate_type'] == "HDLC":
# self.coord_obj = DelocalizedInternalCoordinates.from_options(xyz=self.xyz,atoms=self.atoms,addcart=True,extra_kwargs =self.Data['top_settings'])
#elif self.Data['coordinate_type'] == "TRIC":
# self.coord_obj = DelocalizedInternalCoordinates.from_options(xyz=self.xyz,atoms=self.atoms,addtr=True,extra_kwargs =self.Data['top_settings'])
self.Data['coord_obj'] = self.coord_obj
t2 = time()
print(" Time to build coordinate system= %.3f" % (t2 - t1))
#TODO
self.gradrms = 0.
self.isTSnode = False
self.bdist = 0.
self.newHess = 5
if self.Data['Hessian'] is None and self.Data['Form_Hessian']:
if self.Data['Primitive_Hessian'] is None and type(
self.coord_obj) is not CartesianCoordinates:
self.form_Primitive_Hessian()
t3 = time()
print(" Time to build Prim Hessian %.3f" % (t3 - t2))
if self.Data['Primitive_Hessian'] is not None:
print(" forming Hessian in basis")
self.form_Hessian_in_basis()
else:
self.form_Hessian()
#logger.info("Molecule %s constructed.", repr(self))
#logger.debug("Molecule %s constructed.", repr(self))
print(" molecule constructed")
def __init__(
self,
options,
):
""" Constructor """
self.options = options
# properties
self.Energy = namedtuple('Energy', 'value unit')
self.Gradient = namedtuple('Gradient', 'value unit')
self.Coupling = namedtuple('Coupling', 'value unit')
self._Energies = {}
self._Gradients = {}
self._Couplings = {}
# count number of states
singlets = self.search_tuple(self.states, 1)
doublets = self.search_tuple(self.states, 2)
triplets = self.search_tuple(self.states, 3)
quartets = self.search_tuple(self.states, 4)
quintets = self.search_tuple(self.states, 5)
#TODO do this for all states, since it catches if states are put in lazy e.g [(1,1)]
if singlets:
len_singlets = max(singlets, key=lambda x: x[1])[1] + 1
else:
len_singlets = 0
len_doublets = len(doublets)
len_triplets = len(triplets)
len_quartets = len(quartets)
len_quintets = len(quintets)
# DO this before fixing states if put in lazy
if self.options['gradient_states'] == None and self.calc_grad:
print(" Assuming gradient states are ", self.states)
self.options['gradient_states'] = self.options['states']
if len(
self.states
) < len_singlets + len_doublets + len_triplets + len_quartets + len_quintets:
print('fixing states to be proper length')
tmp = []
# TODO put in rest of fixed states
for i in range(len_singlets):
tmp.append((1, i))
for i in range(len_triplets):
tmp.append((3, i))
self.states = tmp
print(' New states ', self.states)
self.geom = self.options['geom']
if self.geom is not None:
print(" initializing LOT from geom")
elif self.options['fnm'] is not None:
print(" initializing LOT from file")
if not os.path.exists(self.options['fnm']):
logger.error(
'Tried to create LOT object from a file that does not exist: %s\n'
% self.options['fnm'])
raise IOError
self.geom = manage_xyz.read_xyz(self.options['fnm'], scale=1.)
else:
raise RuntimeError("Need to initialize LOT object")
# Cache some useful atributes - other useful attributes are properties
self.currentCoords = manage_xyz.xyz_to_np(self.geom)
self.atoms = manage_xyz.get_atoms(self.geom)
self.ID = self.options['ID']
self.nproc = self.options['nproc']
self.charge = self.options['charge']
self.node_id = self.options['node_id']
self.lot_inp_file = self.options['lot_inp_file']
# Bools for running
self.hasRanForCurrentCoords = False
self.has_nelectrons = False
# Read file options if they exist and not already set
if self.file_options is None:
self.file_options = File_Options(self.lot_inp_file)
#package specific implementation
#TODO MOVE to specific package !!!
# tc cloud
self.options['job_data']['orbfile'] = self.options['job_data'].get(
'orbfile', '')
# pytc? TODO
self.options['job_data']['lot'] = self.options['job_data'].get(
'lot', None)
print(" making folder scratch/{:03}/{}".format(self.ID, self.node_id))
os.system('mkdir -p scratch/{:03}/{}'.format(self.ID, self.node_id))
# self.nodes[-1].energy = self.nodes[0].energy
# self.nodes[-1].gradrms = 0.
if __name__ == '__main__':
from level_of_theories.dummy_lot import Dummy
from potential_energy_surfaces.pes import PES
from coordinate_systems.delocalized_coordinates import DelocalizedInternalCoordinates, PrimitiveInternalCoordinates, Topology
from optimizers import eigenvector_follow
geoms = manage_xyz.read_molden_geoms(
'../growing_string_methods/opt_converged_000.xyz')
lot = Dummy.from_options(geom=geoms[0])
pes = PES.from_options(lot=lot, ad_idx=0, multiplicity=1)
atom_symbols = manage_xyz.get_atoms(geoms[0])
ELEMENT_TABLE = elements.ElementData()
atoms = [ELEMENT_TABLE.from_symbol(atom) for atom in atom_symbols]
xyz1 = manage_xyz.xyz_to_np(geoms[0])
xyz2 = manage_xyz.xyz_to_np(geoms[-1])
top1 = Topology.build_topology(
xyz1,
atoms,
)
# find union bonds
xyz2 = manage_xyz.xyz_to_np(geoms[-1])
top2 = Topology.build_topology(
xyz2,