Index

A

add_adjacency_mat() (mcal.utils.cif_reader.FileIO method) add_coordinates() (mcal.utils.cif_reader.FileIO method) add_link() (mcal.GjfMaker method) (mcal.utils.gjf_maker.GjfMaker method) add_root() (mcal.GjfMaker method) (mcal.utils.gjf_maker.GjfMaker method)

add_symbols() (mcal.utils.cif_reader.FileIO method) atom_weight() (in module mcal) (in module mcal.mcal) ATOMIC_WEIGHTS (mcal.CifReader attribute) (mcal.utils.cif_reader.CifReader attribute)

C

cal_cen_of_weight() (in module mcal) (in module mcal.mcal) cal_distance_between_cen_of_weight() (in module mcal) (in module mcal.mcal) cal_eigenvalue_decomposition() (in module mcal.mcal) cal_min_distance() (in module mcal) (in module mcal.mcal) cal_moment_of_inertia() (in module mcal) (in module mcal.mcal) cal_pinv() (in module mcal) (in module mcal.calculations.hopping_mobility_model) calc_cen_of_weight() (mcal.CifReader method) (mcal.utils.cif_reader.CifReader method) calc_reorganization() (mcal.calculations.rcal.Rcal method) (mcal.calculations.rcal_pyscf.RcalPySCF method) (mcal.Rcal method) (mcal.RcalPySCF method) check_error_term() (mcal.calculations.rcal.Rcal static method) (mcal.Rcal static method) check_extension_log() (mcal.calculations.rcal.Rcal method) (mcal.Rcal method) check_normal_termination() (in module mcal) (in module mcal.utils.gaus_log_reader)

check_reorganization_energy_completion() (in module mcal.mcal) check_reorganization_energy_completion_pyscf() (in module mcal.mcal) check_transfer_integral_completion() (in module mcal.mcal) check_transfer_integral_completion_pyscf() (in module mcal.mcal) CifReader (class in mcal) (class in mcal.utils.cif_reader) close() (mcal.FileReader method) (mcal.utils.gaus_log_reader.FileReader method) convert_cart_to_frac() (mcal.CifReader method) (mcal.utils.cif_reader.CifReader method) convert_frac_to_cart() (mcal.CifReader method) (mcal.utils.cif_reader.CifReader method) COVALENT_RADII (mcal.CifReader attribute) (mcal.utils.cif_reader.CifReader attribute) create_chk_file() (mcal.GjfMaker method) (mcal.utils.gjf_maker.GjfMaker method) create_reorg_gjf() (in module mcal.mcal) create_reorg_xyz() (in module mcal.mcal) create_rwf_file() (mcal.GjfMaker method) (mcal.utils.gjf_maker.GjfMaker method) create_ti_gjf() (in module mcal.mcal) create_ti_xyz() (in module mcal.mcal)

D

demo() (in module mcal.calculations.hopping_mobility_model)

diffusion_coefficient_tensor() (in module mcal) (in module mcal.calculations.hopping_mobility_model)

E

ELEMENT_PROP (mcal.CifReader attribute) (mcal.GjfMaker attribute) (mcal.utils.cif_reader.CifReader attribute) (mcal.utils.gjf_maker.GjfMaker attribute) ElementPropertiesIsNotDefinedError ELEMENTS_NUM (mcal.GjfMaker attribute) (mcal.utils.gjf_maker.GjfMaker attribute) expand_mols() (mcal.CifReader method) (mcal.utils.cif_reader.CifReader method)

export_gjf() (mcal.GjfMaker method) (mcal.utils.gjf_maker.GjfMaker method) export_mol_file() (mcal.utils.cif_reader.FileIO method) export_unit_cell_file() (mcal.CifReader method) (mcal.utils.cif_reader.CifReader method) export_xyz_file() (mcal.utils.cif_reader.FileIO method) extract_energy() (mcal.calculations.rcal.Rcal method) (mcal.Rcal method)

F

FileIO (class in mcal.utils.cif_reader)

FileReader (class in mcal) (class in mcal.utils.gaus_log_reader)

G

GausTermError

GjfMaker (class in mcal) (class in mcal.utils.gjf_maker)

H

HARTREE_TO_EV (mcal.calculations.rcal_pyscf.RcalPySCF attribute) (mcal.RcalPySCF attribute)

M

main() (in module mcal.calculations.rcal) (in module mcal.mcal) marcus_rate() (in module mcal) (in module mcal.calculations.hopping_mobility_model) mcal module mcal.calculations module mcal.calculations.hopping_mobility_model module mcal.calculations.rcal module mcal.calculations.rcal_pyscf module mcal.mcal module mcal.utils module

mcal.utils.cif_reader module mcal.utils.gaus_log_reader module mcal.utils.gjf_maker module mobility_tensor() (in module mcal) (in module mcal.calculations.hopping_mobility_model) module mcal mcal.calculations mcal.calculations.hopping_mobility_model mcal.calculations.rcal mcal.calculations.rcal_pyscf mcal.mcal mcal.utils mcal.utils.cif_reader mcal.utils.gaus_log_reader mcal.utils.gjf_maker

O

opt() (mcal.GjfMaker method) (mcal.utils.gjf_maker.GjfMaker method)

OSCTypeError, [1] output_detail() (mcal.GjfMaker method) (mcal.utils.gjf_maker.GjfMaker method)

P

parent_dir (mcal.CifReader attribute) (mcal.GjfMaker attribute) (mcal.utils.cif_reader.CifReader attribute) (mcal.utils.gjf_maker.GjfMaker attribute) plot_mobility_2d() (in module mcal.mcal) print_mobility() (in module mcal.mcal)

print_reorg_energy() (in module mcal.mcal) print_tensor() (in module mcal.calculations.hopping_mobility_model) (in module mcal.mcal) print_timestamp() (mcal.calculations.rcal.Rcal static method) (mcal.Rcal static method) print_transfer_integral() (in module mcal.mcal)

R

Rcal (class in mcal) (class in mcal.calculations.rcal) RcalPySCF (class in mcal) (class in mcal.calculations.rcal_pyscf) read_pickle() (in module mcal.mcal)

remove_duplicates() (mcal.CifReader method) (mcal.utils.cif_reader.CifReader method) reset_variable() (mcal.GjfMaker method) (mcal.utils.gjf_maker.GjfMaker method) reversed_readline() (mcal.FileReader method) (mcal.utils.gaus_log_reader.FileReader method)

S

set_charge_spin() (mcal.GjfMaker method) (mcal.utils.gjf_maker.GjfMaker method) set_coordinates() (mcal.GjfMaker method) (mcal.utils.gjf_maker.GjfMaker method) set_function() (mcal.GjfMaker method) (mcal.utils.gjf_maker.GjfMaker method)

set_resource() (mcal.GjfMaker method) (mcal.utils.gjf_maker.GjfMaker method) set_symbols() (mcal.GjfMaker method) (mcal.utils.gjf_maker.GjfMaker method) set_title() (mcal.GjfMaker method) (mcal.utils.gjf_maker.GjfMaker method) SymmetryIsNotDefinedError

Z

ZValueIsNotMatchError