Index

A

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

add_symbols() (mcal.utils.cif_reader.FileIO method) atom_weight() (in module mcal.mcal) atomic_pair_transfer_analysis() (mcal.calculations.tcal.Tcal method) ATOMIC_WEIGHTS (mcal.utils.cif_reader.CifReader attribute)

C

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

check_reorganization_energy_completion() (in module mcal.mcal) check_transfer_integral_completion() (in module mcal.mcal) CifReader (class in mcal.utils.cif_reader) close() (mcal.utils.gaus_log_reader.FileReader method) convert_cart_to_frac() (mcal.utils.cif_reader.CifReader method) convert_frac_to_cart() (mcal.utils.cif_reader.CifReader method) convert_xyz_to_gjf() (mcal.calculations.tcal.Tcal method) COVALENT_RADII (mcal.utils.cif_reader.CifReader attribute) create_chk_file() (mcal.utils.gjf_maker.GjfMaker method) create_cube_file() (mcal.calculations.tcal.Tcal method) create_monomer_file() (mcal.calculations.tcal.Tcal method) create_reorg_gjf() (in module mcal.mcal) create_rwf_file() (mcal.utils.gjf_maker.GjfMaker method) create_ti_gjf() (in module mcal.mcal) custom_atomic_pair_transfer_analysis() (mcal.calculations.tcal.Tcal method)

D

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

diffusion_coefficient_tensor_MC() (in module mcal.calculations.hopping_mobility_model) diffusion_coefficient_tensor_ODE() (in module mcal.calculations.hopping_mobility_model)

E

ELEMENT_PROP (mcal.utils.cif_reader.CifReader attribute) (mcal.utils.gjf_maker.GjfMaker attribute) ElementPropertiesIsNotDefinedError ELEMENTS_NUM (mcal.utils.gjf_maker.GjfMaker attribute) EV (mcal.calculations.tcal.Tcal attribute) expand_mols() (mcal.utils.cif_reader.CifReader method)

export_gjf() (mcal.utils.gjf_maker.GjfMaker method) export_mol_file() (mcal.utils.cif_reader.FileIO method) export_unit_cell_file() (mcal.utils.cif_reader.CifReader method) export_xyz_file() (mcal.utils.cif_reader.FileIO method) extract_coordinates() (mcal.calculations.tcal.Tcal static method) extract_energy() (mcal.calculations.rcal.Rcal method) extract_num() (mcal.calculations.tcal.Tcal static method)

F

FileIO (class in mcal.utils.cif_reader)

FileReader (class in mcal.utils.gaus_log_reader)

G

GausTermError

GjfMaker (class in mcal.utils.gjf_maker)

M

main() (in module mcal.calculations.rcal) (in module mcal.calculations.tcal) (in module mcal.mcal) marcus_rate() (in module mcal.calculations.hopping_mobility_model) mcal module mcal.calculations module mcal.calculations.hopping_mobility_model module mcal.calculations.rcal module mcal.calculations.tcal 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.calculations.hopping_mobility_model) module mcal mcal.calculations mcal.calculations.hopping_mobility_model mcal.calculations.rcal mcal.calculations.tcal mcal.mcal mcal.utils mcal.utils.cif_reader mcal.utils.gaus_log_reader mcal.utils.gjf_maker

O

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

output_csv() (mcal.calculations.tcal.Tcal static method) output_detail() (mcal.utils.gjf_maker.GjfMaker method)

P

PairAnalysis (class in mcal.calculations.tcal) parent_dir (mcal.utils.cif_reader.CifReader attribute) (mcal.utils.gjf_maker.GjfMaker attribute) print_apta() (mcal.calculations.tcal.Tcal method) print_element_pairs() (mcal.calculations.tcal.PairAnalysis method) print_largest_pairs() (mcal.calculations.tcal.PairAnalysis method) print_matrix() (mcal.calculations.tcal.Tcal static method) 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.calculations.tcal.Tcal static method) print_tranfer_integral_diff_levels() (mcal.calculations.tcal.Tcal method) print_transfer_integral() (in module mcal.mcal) print_transfer_integrals() (mcal.calculations.tcal.Tcal method)

R

Rcal (class in mcal.calculations.rcal) read_dimer() (mcal.calculations.tcal.Tcal method) read_matrix() (mcal.calculations.tcal.Tcal static method) read_monomer1() (mcal.calculations.tcal.Tcal method) read_monomer2() (mcal.calculations.tcal.Tcal method)

read_pickle() (in module mcal.mcal) read_symmetric_matrix() (mcal.calculations.tcal.Tcal static method) remove_duplicates() (mcal.utils.cif_reader.CifReader method) reset_variable() (mcal.utils.gjf_maker.GjfMaker method) reversed_readline() (mcal.utils.gaus_log_reader.FileReader method) run_gaussian() (mcal.calculations.tcal.Tcal method)

S

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

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

T

Tcal (class in mcal.calculations.tcal)

Z

ZValueIsNotMatchError