def __init__(self, molecule, options, basisset):
# verify that the minimal version is used if CPPE is provided
# from outside the Psi4 ecosystem
min_version = "0.3.1"
if parse_version(cppe.__version__) < parse_version(min_version):
raise ModuleNotFoundError("CPPE version {} is required at least. "
"Version {}"
" was found.".format(min_version,
cppe.__version__))
# setup the initial CppeState
self.molecule = molecule
self.options = options
self.pe_ecp = self.options.pop("pe_ecp", False)
self.basisset = basisset
self.mints = core.MintsHelper(self.basisset)
def callback(output):
core.print_out(f"{output}\n")
self.cppe_state = cppe.CppeState(self.options, psi4mol_to_cppemol(self.molecule), callback)
core.print_out("CPPE Options:\n")
core.print_out(f"PE(ECP) repulsive potentials = {self.pe_ecp}\n")
for k in cppe.valid_option_keys:
core.print_out(f"{k} = {self.cppe_state.options[k]}\n")
core.print_out("-------------------------\n\n")
self.cppe_state.calculate_static_energies_and_fields()
# obtain coordinates of polarizable sites
self._enable_induction = False
if self.cppe_state.get_polarizable_site_number():
self._enable_induction = True
coords = self.cppe_state.positions_polarizable
self.polarizable_coords = core.Matrix.from_array(coords)
self.V_es = None
if self.pe_ecp:
self._setup_pe_ecp()
def __init__(self, molecule, options, basisset):
# verify that the minimal version is used if CPPE is provided
# from outside the Psi4 ecosystem
min_version = "0.2.0"
if parse_version(cppe.__version__) < parse_version(min_version):
raise ModuleNotFoundError("CPPE version {} is required at least. "
"Version {}"
" was found.".format(min_version,
cppe.__version__))
# setup the initial CppeState
self.molecule = molecule
self.options = options
self.basisset = basisset
self.mints = core.MintsHelper(self.basisset)
def callback(output):
core.print_out("{}\n".format(output))
self.cppe_state = cppe.CppeState(self.options, psi4mol_to_cppemol(self.molecule), callback)
self.cppe_state.calculate_static_energies_and_fields()
# obtain coordinates of polarizable sites
self._enable_induction = False
if self.cppe_state.get_polarizable_site_number():
self._enable_induction = True
coords = np.array([site.position for site in self.cppe_state.potentials if site.is_polarizable])
self.polarizable_coords = core.Matrix.from_array(coords)
self.V_es = None
def _create_cppe_state(self, mol):
cppe_mol = cppe.Molecule()
for z, coord in zip(mol.atom_charges(), mol.atom_coords()):
cppe_mol.append(cppe.Atom(z, *coord))
def callback(output):
logger.info(self, output)
cppe_state = cppe.CppeState(self.options, cppe_mol, callback)
cppe_state.calculate_static_energies_and_fields()
return cppe_state
def __init__(self, molecule, options, basisset):
# setup the initial CppeState
self.molecule = molecule
self.options = options
self.basisset = basisset
self.mints = core.MintsHelper(self.basisset)
def callback(output):
core.print_out("{}\n".format(output))
self.cppe_state = cppe.CppeState(self.options, psi4mol_to_cppemol(self.molecule), callback)
self.cppe_state.calculate_static_energies_and_fields()
# obtain coordinates of polarizable sites
self._enable_induction = False
if self.cppe_state.get_polarizable_site_number():
self._enable_induction = True
coords = np.array([site.position for site in self.cppe_state.potentials if site.is_polarizable])
self.polarizable_coords = core.Matrix.from_array(coords)
self.V_es = None