cliff.helpers package

Submodules

cliff.helpers.cell module

class cliff.helpers.cell.Cell(cellh)

Bases: object

Cell geometry

classmethod lattice_parameters(a, b, c, alpha=90.0, beta=90.0, gamma=90.0)

Units: distance in Angstroem, angles in degrees.

pbc_distance(coords1, coords2)

cliff.helpers.constants module

cliff.helpers.options module

class cliff.helpers.options.Options(config_file='config.ini', name=None)

Bases: object

Class to parse and store options

load_atomic_density_options()

load_disp_options()

load_elst_options()

load_exch_options()

load_hirsh_options()

load_indu_options()

load_multipole_options()

set_atomicdensity_cutoff(val)

set_atomicdensity_krr_kernel(val)

set_atomicdensity_krr_lambda(val)

set_atomicdensity_krr_sigma(val)

set_atomicdensity_ref_adens(val)

set_atomicdensity_refpath(val)

set_atomicdensity_save_path(val)

set_atomicdensity_save_to_disk(val)

set_atomicdensity_training(val)

set_damping_exponents(val)

set_disp_beta(val)

set_disp_coeffs(val)

set_disp_method(val)

set_disp_radius(val)

set_elst_type(val)

set_exchange_int_params(val)

set_hirsh_save_path(val)

set_hirsh_save_to_disk(val)

set_hirshfeld_cutoff(val)

set_hirshfeld_file_read(val)

set_hirshfeld_filepath(val)

set_hirshfeld_krr_kernel(val)

set_hirshfeld_krr_lambda(val)

set_hirshfeld_krr_sigma(val)

set_hirshfeld_max_neighbors(val)

set_hirshfeld_ref_hirsh(val)

set_hirshfeld_training(val)

set_indu_smearing_coeff(val)

set_induction_conv(val)

set_induction_omega(val)

set_induction_sr_params(val)

set_logger_level(val)

set_mtp_to_disk(val)

set_multipole_correct_charge(val)

set_multipole_kernel(val)

set_multipole_krr_lambda(val)

set_multipole_krr_sigma(val)

set_multipole_ml_method(val)

set_multipole_rcut(val)

set_multipole_ref_mtp(val)

set_multipole_ref_path(val)

set_multipole_save_path(val)

set_multipole_training(val)

set_name(name)

set_pol_exponent(val)

set_pol_scs_cutoff(val)

cliff.helpers.system module

class cliff.helpers.system.System(options, xyz=None, log=False)

Bases: object

Common system class for molecular system

build_slatm(mbtypes, cutoff, xyz=None)

compute_basis()

Basis for multipole expansion

expand_multipoles()

Expand coefficients along basis set to compute multipoles

identify_atom_types(logger=None)

Identifies the atom type and bonds of every atom in the molecule

initialize_multipoles()

Initialize multipoles to 0

load_qcel_mol(mol, name)

load_xyz(logger)

save_mtp()

set_mtp_save_path(path)

set_properties(props)

cliff.helpers.utils module

cliff.helpers.utils.build_coulomb_matrix(coords, atom_types, central_atom_id, max_neighbors, direction=None)

Build Coulomb matrix ordered by distance to central_atom_id

cliff.helpers.utils.build_r(c1, c2, cell)

cliff.helpers.utils.cart_to_sphere(cart)

Convert cartesian to spherical multipoles

cliff.helpers.utils.extract_atomic_numbers(cartesian, atom_types)

Extract atomic number from name of atom type

cliff.helpers.utils.file_finder(fname, ref=None, jobdir=None)

Compiles xyz files for multiple computations

dirs points to directories, one for each computation

cliff.helpers.utils.neighboring_vectors(coords, atom_types, central_atom_id)

Returns neighboring pairwise vectors starting from central atom up to 3. If it’s less than 3, complete by orthogonal vectors.

cliff.helpers.utils.read_file(infile)

Read file and return content

cliff.helpers.utils.reorder_atoms(coords, atom_types, central_atom_id, max_neighbors)

Reorder list of atoms from the central atom and by its distance

cliff.helpers.utils.set_logger_level(level)

cliff.helpers.utils.slater_mbis(cell, coord_i, N_i, v_i, U_i, coord_j, N_j, v_j, U_j)

Returns overlap of two atoms scaled by global parameters

@params:

cliff.helpers.utils.slater_mbis_funcform(rij, N_i, v_i, N_j, v_j)

cliff.helpers.utils.slater_ovp_mat(r, v1, v2)

cliff.helpers.utils.spher_to_cart(quad, stone_convention=True)

convert spherical to cartesian multipoles

Module contents