Misc. functionalities

molbe.misc.libint2pyscf(xyzfile, hcore, basis, hcore_skiprows=1, use_df=False, unrestricted=False, spin=0, charge=0)

Build a pyscf Mole and RHF/UHF object using the given xyz file and core Hamiltonian (in libint standard format) c.f. In libint standard format, the basis sets appear in the order atom# n l m 0 1 0 0 1s 0 2 0 0 2s 0 2 1 -1 2py 0 2 1 0 2pz 0 2 1 1 2px … In pyscf, the basis sets appear in the order atom # n l m 0 1 0 0 1s 0 2 0 0 2s 0 2 1 1 2px 0 2 1 -1 2py 0 2 1 0 2pz … For higher angular momentum, both use [-l, -l+1, …, l-1, l] ordering.

Parameters:

• xyzfile (string) – Path to the xyz file

• hcore (string) – Path to the core Hamiltonian

• basis (string) – Name of the basis set

• hcore_skiprows (int, optional) – # of first rows to skip from the core Hamiltonian file, by default 1

• use_df (bool, optional) – If true, use density-fitting to evaluate the two-electron integrals

• unrestricted (bool, optional) – If true, use UHF bath

• spin (int, optional) – 2S, Difference between the number of alpha and beta electrons

• charge (int, optional) – Total charge of the system

Return type:

(pyscf.gto.Mole, pyscf.scf.RHF or pyscf.scf.UHF)

molbe.misc.be2fcidump(be_obj, fcidump_prefix, basis)

Construct FCIDUMP file for each fragment in a given BE object Assumes molecular, restricted BE calculation

Parameters:

• be_obj (molbe.mbe.BE) – BE object

• fcidump_prefix (string) – Prefix for path & filename to the output fcidump files Each file is named [fcidump_prefix]_f0, …

• basis (string) – ‘embedding’ to get the integrals in the embedding basis ‘fragment_mo’ to get the integrals in the fragment MO basis

molbe.misc.ube2fcidump(be_obj, fcidump_prefix, basis)

Construct FCIDUMP file for each fragment in a given BE object Assumes molecular, restricted BE calculation

Parameters:

• be_obj (molbe.mbe.BE) – BE object

• fcidump_prefix (string) – Prefix for path & filename to the output fcidump files Each file is named [fcidump_prefix]_f0, …

• basis (string) – ‘embedding’ to get the integrals in the embedding basis ‘fragment_mo’ to get the integrals in the fragment MO basis

molbe.misc.be2puffin(xyzfile, basis, hcore=None, libint_inp=False, pts_and_charges=None, jk=None, use_df=False, charge=0, spin=0, nproc=1, ompnum=1, be_type='be1', df_aux_basis=None, frozen_core=True, localization_method='lowdin', localization_basis=None, unrestricted=False, from_chk=False, checkfile=None, ecp=None)

Front-facing API bridge tailored for SCINE Puffin Returns the CCSD oneshot energies - QM/MM notes: Using QM/MM alongside big basis sets, especially with a frozen core, can cause localization and numerical stability problems. Use with caution. Additional work to this end on localization, frozen core, ECPs, and QM/MM in this capacity is ongoing. - If running unrestricted QM/MM calculations, with ECPs, in a large basis set, do not freeze the core. Using an ECP for heavy atoms improves the localization numerics, but this is not yet compatible with frozen core on the rest of the atoms.

Parameters:

• xyzfile (string) – Path to the xyz file

• basis (string) – Name of the basis set

• hcore (numpy.array) – Two-dimensional array of the core Hamiltonian

• libint_inp (bool) – True for hcore provided in Libint format. Else, hcore input is in PySCF format Default is False, i.e., hcore input is in PySCF format

• pts_and_charges (tuple of numpy.array) – QM/MM (points, charges). Use pyscf’s QM/MM instead of starting Hamiltonian

• jk (numpy.array) – Coulomb and Exchange matrices (pyscf will calculate this if not given)

• use_df (bool, optional) – If true, use density-fitting to evaluate the two-electron integrals

• charge (int, optional) – Total charge of the system

• spin (int, optional) – Total spin of the system, pyscf definition

• nproc (int, optional) –

• ompnum (int, optional) – Set number of processors and ompnum for the jobs

• frozen_core (bool, optional) – Whether frozen core approximation is used or not, by default True

• localization_method (string, optional) – For now, lowdin is best supported for all cases. IAOs to be expanded By default ‘lowdin’

• localization_basis (string, optional) – IAO minimal-like basis, only nead specification with IAO localization By default None

• unrestricted (bool, optional) – Unrestricted vs restricted HF and CCSD, by default False

• from_chk (bool, optional) – Run calculation from converged RHF/UHF checkpoint. By default False

• checkfile (string, optional) – if not None: - if from_chk: specify the checkfile to run the embedding calculation - if not from_chk: specify where to save the checkfile By default None

• ecp (string, optional) – specify the ECP for any atoms, accompanying the basis set syntax: {‘Atom_X’: ‘ECP_for_X’; ‘Atom_Y’: ‘ECP_for_Y’} By default None