Index

_

__init__() (BaseFileError method) (BaseFileWarning method) (Cube method) (DumpError method) (DumpWarning method) (FileFormatError method) (FooBar method) (GaussianOverlap method) (IOData method) (LineIterator method) (LoadError method) (LoadWarning method) (MolecularBasis method) (MolecularOrbitals method) (NoName0 method) (NoName1 method) (NoName2 method) (NoName3 method) (PrepareDumpError method) (Shell method) (Spam method) (WriteInputError method)

A

add_note() (BaseFileError method) (BaseFileWarning method) (DumpError method) (DumpWarning method) (FileFormatError method) (LoadError method) (LoadWarning method) (PrepareDumpError method) (WriteInputError method) angmom_its() (in module iodata.basis) angmom_sti() (in module iodata.basis) angmoms (Shell attribute) args (BaseFileError attribute) (BaseFileWarning attribute) (DumpError attribute) (DumpWarning attribute) (FileFormatError attribute) (LoadError attribute) (LoadWarning attribute) (PrepareDumpError attribute) (WriteInputError attribute)

atcharges (IOData attribute) atcoords (IOData attribute) atcorenums (IOData property) atffparams (IOData attribute) atfrozen (IOData attribute) atgradient (IOData attribute) athessian (IOData attribute) atmasses (IOData attribute) atnums (IOData attribute) axes (Cube attribute)

B

back() (LineIterator method) BaseFileError BaseFileWarning

basisdef (IOData attribute) bonds (IOData attribute) build_obasis() (in module iodata.formats.wfn)

C

cellvecs (IOData attribute) charge (IOData property) check_dm() (in module iodata.utils) check_example() (in module iodata.test.test_mol2) (in module iodata.test.test_sdf) check_load_azirine() (in module iodata.test.test_fchk) check_load_dump_consistency() (in module iodata.test.test_fchk) (in module iodata.test.test_mol2) (in module iodata.test.test_molekel) (in module iodata.test.test_sdf) (in module iodata.test.test_wfn) (in module iodata.test.test_wfx) (in module iodata.test.test_xyz) check_load_input_and_compare() (in module iodata.test.test_inputs) check_load_nitrogen() (in module iodata.test.test_fchk) check_normalization_dm_azirine() (in module iodata.test.test_fchk) check_orthonormal() (in module iodata.test.common) check_trj_basics() (in module iodata.test.test_fchk) check_water() (in module iodata.test.test_gaussianinput) (in module iodata.test.test_gromacs) (in module iodata.test.test_pdb) (in module iodata.test.test_xyz)

check_wfn() (in module iodata.test.test_wfn) coeffs (MolecularOrbitals attribute) (Shell attribute) coeffsa (MolecularOrbitals property) coeffsb (MolecularOrbitals property) compare_mols() (in module iodata.test.common) compare_mols_diff_formats() (in module iodata.test.test_molekel) compare_mulliken_charges() (in module iodata.test.test_wfx) compute_1rdm() (in module iodata.test.common) compute_mulliken_charges() (in module iodata.test.common) compute_overlap() (in module iodata.overlap) compute_overlap_gaussian_1d() (GaussianOverlap method) conventions (MolecularBasis attribute) convert_array_to() (in module iodata.attrutils) convert_convention_shell() (in module iodata.basis) convert_conventions() (in module iodata.basis) core_energy (IOData attribute) create_generalized() (in module iodata.test.common) Cube (class in iodata.utils) cube (IOData attribute)

D

data (Cube attribute) default_atom_line() (in module iodata.inputs.gaussian) (in module iodata.inputs.orca) derive_naturals() (in module iodata.utils) document_dump_many() (in module iodata.docstrings) document_dump_one() (in module iodata.docstrings) document_load_many() (in module iodata.docstrings) document_load_one() (in module iodata.docstrings) document_write_input() (in module iodata.docstrings) dump_many() (in module iodata.api) (in module iodata.formats.mol2) (in module iodata.formats.pdb) (in module iodata.formats.sdf) (in module iodata.formats.xyz) dump_one() (in module iodata.api) (in module iodata.formats.cube) (in module iodata.formats.fchk) (in module iodata.formats.fcidump) (in module iodata.formats.json) (in module iodata.formats.mol2) (in module iodata.formats.molden) (in module iodata.formats.molekel) (in module iodata.formats.pdb) (in module iodata.formats.poscar) (in module iodata.formats.sdf) (in module iodata.formats.wfn) (in module iodata.formats.wfx) (in module iodata.formats.xyz)

DumpError DumpWarning

E

egg0 (Spam attribute) egg1 (Spam attribute) egg2 (Spam attribute) egg3 (Spam attribute) energies (MolecularOrbitals attribute)

energiesa (MolecularOrbitals property) energiesb (MolecularOrbitals property) energy (IOData attribute) exponents (Shell attribute) extcharges (IOData attribute) extra (IOData attribute)

F

factorial2() (in module iodata.overlap)

FileFormatError FooBar (class in iodata.test.test_attrutils)

G

g_rot (IOData attribute) GaussianOverlap (class in iodata.overlap) get_default_conventions() (in module iodata.basis)

get_mocoeff_scales() (in module iodata.formats.wfn) get_segmented() (MolecularBasis method) gob_cart_normalization() (in module iodata.overlap)

H

helper_load_data_wfx() (in module iodata.test.test_wfx)

helper_load_wfn_low() (in module iodata.test.test_wfn)

I

icenter (Shell attribute) iodata module IOData (class in iodata.iodata) iodata.api module iodata.attrutils module iodata.basis module iodata.docstrings module iodata.formats module iodata.formats.charmm module iodata.formats.chgcar module iodata.formats.cp2klog module iodata.formats.cube module iodata.formats.extxyz module iodata.formats.fchk module iodata.formats.fcidump module iodata.formats.gamess module iodata.formats.gaussianinput module iodata.formats.gaussianlog module iodata.formats.gromacs module iodata.formats.json module iodata.formats.locpot module iodata.formats.mol2 module iodata.formats.molden module iodata.formats.molekel module iodata.formats.mwfn module iodata.formats.orcalog module iodata.formats.pdb module iodata.formats.poscar module iodata.formats.qchemlog module iodata.formats.sdf module iodata.formats.wfn module iodata.formats.wfx module iodata.formats.xyz module iodata.inputs module iodata.inputs.common module iodata.inputs.gaussian module iodata.inputs.orca module iodata.iodata module iodata.orbitals module iodata.overlap module iodata.overlap_cartpure module iodata.periodic module

iodata.test module iodata.test.common module iodata.test.data module iodata.test.test_api module iodata.test.test_attrutils module iodata.test.test_basis module iodata.test.test_charmm module iodata.test.test_chgcar module iodata.test.test_cli module iodata.test.test_cp2klog module iodata.test.test_cube module iodata.test.test_extxyz module iodata.test.test_fchk module iodata.test.test_fcidump module iodata.test.test_gamess module iodata.test.test_gaussianinput module iodata.test.test_gaussianlog module iodata.test.test_gromacs module iodata.test.test_inputs module iodata.test.test_iodata module iodata.test.test_json module iodata.test.test_locpot module iodata.test.test_mol2 module iodata.test.test_molden module iodata.test.test_molekel module iodata.test.test_mwfn module iodata.test.test_orbitals module iodata.test.test_orcalog module iodata.test.test_overlap module iodata.test.test_pdb module iodata.test.test_poscar module iodata.test.test_qchemlog module iodata.test.test_sdf module iodata.test.test_utils module iodata.test.test_wfn module iodata.test.test_wfx module iodata.test.test_xyz module iodata.utils module irreps (MolecularOrbitals attribute) irrepsa (MolecularOrbitals property) irrepsb (MolecularOrbitals property) iter_cart_alphabet() (in module iodata.basis)

K

kind (MolecularOrbitals attribute)

kinds (Shell attribute)

L

leg (Spam attribute) LineIterator (class in iodata.utils) load_data_wfx() (in module iodata.formats.wfx) load_fchk_helper() (in module iodata.test.test_fchk) load_fchk_trj_helper() (in module iodata.test.test_fchk) load_helper() (in module iodata.test.test_mwfn) load_log_helper() (in module iodata.test.test_gaussianlog) load_many() (in module iodata.api) (in module iodata.formats.extxyz) (in module iodata.formats.fchk) (in module iodata.formats.gromacs) (in module iodata.formats.mol2) (in module iodata.formats.pdb) (in module iodata.formats.sdf) (in module iodata.formats.xyz) load_one() (in module iodata.api) (in module iodata.formats.charmm) (in module iodata.formats.chgcar) (in module iodata.formats.cp2klog) (in module iodata.formats.cube) (in module iodata.formats.extxyz) (in module iodata.formats.fchk) (in module iodata.formats.fcidump) (in module iodata.formats.gamess) (in module iodata.formats.gaussianinput) (in module iodata.formats.gaussianlog) (in module iodata.formats.gromacs) (in module iodata.formats.json) (in module iodata.formats.locpot) (in module iodata.formats.mol2) (in module iodata.formats.molden) (in module iodata.formats.molekel) (in module iodata.formats.mwfn) (in module iodata.formats.orcalog) (in module iodata.formats.pdb) (in module iodata.formats.poscar) (in module iodata.formats.qchemlog) (in module iodata.formats.sdf) (in module iodata.formats.wfn) (in module iodata.formats.wfx) (in module iodata.formats.xyz)

load_one_warning() (in module iodata.test.common) load_qchemlog_low() (in module iodata.formats.qchemlog) load_wfn_low() (in module iodata.formats.wfn) LoadError LoadWarning lot (IOData attribute)

M

mo (IOData attribute) module iodata iodata.api iodata.attrutils iodata.basis iodata.docstrings iodata.formats iodata.formats.charmm iodata.formats.chgcar iodata.formats.cp2klog iodata.formats.cube iodata.formats.extxyz iodata.formats.fchk iodata.formats.fcidump iodata.formats.gamess iodata.formats.gaussianinput iodata.formats.gaussianlog iodata.formats.gromacs iodata.formats.json iodata.formats.locpot iodata.formats.mol2 iodata.formats.molden iodata.formats.molekel iodata.formats.mwfn iodata.formats.orcalog iodata.formats.pdb iodata.formats.poscar iodata.formats.qchemlog iodata.formats.sdf iodata.formats.wfn iodata.formats.wfx iodata.formats.xyz iodata.inputs iodata.inputs.common iodata.inputs.gaussian iodata.inputs.orca iodata.iodata iodata.orbitals iodata.overlap iodata.overlap_cartpure iodata.periodic iodata.test iodata.test.common iodata.test.data iodata.test.test_api iodata.test.test_attrutils iodata.test.test_basis iodata.test.test_charmm iodata.test.test_chgcar iodata.test.test_cli iodata.test.test_cp2klog iodata.test.test_cube iodata.test.test_extxyz iodata.test.test_fchk iodata.test.test_fcidump iodata.test.test_gamess iodata.test.test_gaussianinput iodata.test.test_gaussianlog iodata.test.test_gromacs iodata.test.test_inputs iodata.test.test_iodata iodata.test.test_json iodata.test.test_locpot iodata.test.test_mol2 iodata.test.test_molden iodata.test.test_molekel iodata.test.test_mwfn iodata.test.test_orbitals iodata.test.test_orcalog iodata.test.test_overlap iodata.test.test_pdb iodata.test.test_poscar iodata.test.test_qchemlog iodata.test.test_sdf iodata.test.test_utils iodata.test.test_wfn iodata.test.test_wfx iodata.test.test_xyz iodata.utils

MolecularBasis (class in iodata.basis) MolecularOrbitals (class in iodata.orbitals) moments (IOData attribute)

N

natom (IOData property) nbasis (MolecularBasis property) (MolecularOrbitals property) (Shell property) ncon (Shell property) nelec (IOData property) (MolecularOrbitals property)

NoName0 (class in iodata.test.test_attrutils) NoName1 (class in iodata.test.test_attrutils) NoName2 (class in iodata.test.test_attrutils) NoName3 (class in iodata.test.test_attrutils) norb (MolecularOrbitals property) norba (MolecularOrbitals attribute) norbb (MolecularOrbitals attribute) nprim (Shell property)

O

obasis (IOData attribute) obasis_name (IOData attribute) occs (MolecularOrbitals attribute) occs_aminusb (MolecularOrbitals attribute) occsa (MolecularOrbitals property)

occsb (MolecularOrbitals property) one_ints (IOData attribute) one_rdms (IOData attribute) origin (Cube attribute) other (NoName3 attribute)

P

parse_wfx() (in module iodata.formats.wfx) prepare_dump() (in module iodata.formats.fchk) (in module iodata.formats.json) (in module iodata.formats.molden) (in module iodata.formats.molekel) (in module iodata.formats.wfn) (in module iodata.formats.wfx)

PrepareDumpError primitive_normalization (MolecularBasis attribute)

R

run_type (IOData attribute)

S

set_four_index_element() (in module iodata.utils) shape (Cube property) Shell (class in iodata.basis) shells (MolecularBasis attribute)

Spam (class in iodata.test.test_attrutils) spam (FooBar attribute) spinpol (IOData property) (MolecularOrbitals property) strtobool() (in module iodata.utils)

T

test_amu() (in module iodata.test.test_utils) test_angmom_its() (in module iodata.test.test_basis) test_angmom_sti() (in module iodata.test.test_basis) test_angmom_sti_uppercase() (in module iodata.test.test_basis) test_atfrozen() (in module iodata.test.test_fchk) test_atgradient() (in module iodata.test.test_fchk) test_athessian() (in module iodata.test.test_fchk) test_atmasses() (in module iodata.test.test_fchk) test_atom_o_rks() (in module iodata.test.test_cp2klog) test_atom_si_uks() (in module iodata.test.test_cp2klog) test_bad_qcschema_files() (in module iodata.test.test_json) test_bondtypes_benzene() (in module iodata.test.test_mol2) test_carbon_gs_ae_contracted() (in module iodata.test.test_cp2klog) test_carbon_gs_ae_uncontracted() (in module iodata.test.test_cp2klog) test_carbon_gs_pp_contracted() (in module iodata.test.test_cp2klog) test_carbon_gs_pp_uncontracted() (in module iodata.test.test_cp2klog) test_carbon_sc_ae_contracted() (in module iodata.test.test_cp2klog) test_carbon_sc_ae_uncontracted() (in module iodata.test.test_cp2klog) test_carbon_sc_pp_contracted() (in module iodata.test.test_cp2klog) test_carbon_sc_pp_uncontracted() (in module iodata.test.test_cp2klog) test_charge_nelec1() (in module iodata.test.test_iodata) test_charge_nelec10() (in module iodata.test.test_iodata) test_charge_nelec11() (in module iodata.test.test_iodata) test_charge_nelec12() (in module iodata.test.test_iodata) test_charge_nelec13() (in module iodata.test.test_iodata) test_charge_nelec14() (in module iodata.test.test_iodata) test_charge_nelec15() (in module iodata.test.test_iodata) test_charge_nelec2() (in module iodata.test.test_iodata) test_charge_nelec3() (in module iodata.test.test_iodata) test_charge_nelec4() (in module iodata.test.test_iodata) test_charge_nelec5() (in module iodata.test.test_iodata) test_charge_nelec6() (in module iodata.test.test_iodata) test_charge_nelec7() (in module iodata.test.test_iodata) test_charge_nelec8() (in module iodata.test.test_iodata) test_charge_nelec9() (in module iodata.test.test_iodata) test_conventions() (in module iodata.test.test_basis) test_convert_array_to_assign() (in module iodata.test.test_attrutils) test_convert_array_to_init() (in module iodata.test.test_attrutils) test_convert_convention_obasis() (in module iodata.test.test_basis) test_convert_convention_shell() (in module iodata.test.test_basis) test_convert_exceptions() (in module iodata.test.test_basis) test_convert_many_autofmt() (in module iodata.test.test_cli) test_convert_many_manfmt() (in module iodata.test.test_cli) test_convert_one_autofmt() (in module iodata.test.test_cli) test_convert_one_manfmt() (in module iodata.test.test_cli) test_derived1() (in module iodata.test.test_iodata) test_derived2() (in module iodata.test.test_iodata) test_dm_ch3_rohf_g03() (in module iodata.test.test_iodata) test_dm_lih_sto3g_hf() (in module iodata.test.test_iodata) test_dm_water_sto3g_hf() (in module iodata.test.test_iodata) test_dump_fchk_from_molden() (in module iodata.test.test_fchk) test_dump_fchk_from_molekel() (in module iodata.test.test_fchk) test_dump_fchk_from_wfn() (in module iodata.test.test_fchk) test_dump_fchk_from_wfn_fci_lif() (in module iodata.test.test_fchk) test_dump_fchk_from_wfn_fci_lih_cation() (in module iodata.test.test_fchk) test_dump_fchk_from_wfx() (in module iodata.test.test_fchk) test_dump_fchk_from_wfx_lih_cisd_cation() (in module iodata.test.test_fchk) test_dump_load_fcidimp_consistency_ao() (in module iodata.test.test_fcidump) test_dump_many_generator() (in module iodata.test.test_api) test_dump_many_missing_attribute_first() (in module iodata.test.test_api) test_dump_many_missing_attribute_second() (in module iodata.test.test_api) test_dump_one() (in module iodata.test.test_wfx) test_dump_one_from_molden_neon() (in module iodata.test.test_wfx) test_dump_one_match() (in module iodata.test.test_wfx) test_dump_one_missing_attribute_no_file() (in module iodata.test.test_api) test_dump_one_pure_functions() (in module iodata.test.test_wfn) (in module iodata.test.test_wfx) test_dump_xyz_fcc() (in module iodata.test.test_xyz) test_dump_xyz_water_element() (in module iodata.test.test_xyz) test_dump_xyz_water_number() (in module iodata.test.test_xyz) test_empty_dump_many_no_file() (in module iodata.test.test_api) test_errors() (in module iodata.test.test_cp2klog) test_factorial2_float_arguments() (in module iodata.test.test_overlap) test_factorial2_float_array_argument() (in module iodata.test.test_overlap) test_factorial2_integer_arguments() (in module iodata.test.test_overlap) test_factorial2_integer_array_argument() (in module iodata.test.test_overlap) test_generalized() (in module iodata.test.test_fchk) (in module iodata.test.test_molden) (in module iodata.test.test_molekel) (in module iodata.test.test_wfn) (in module iodata.test.test_wfx) test_generalized_coeffs() (in module iodata.test.test_orbitals) test_generalized_empty() (in module iodata.test.test_orbitals) test_generalized_energies() (in module iodata.test.test_orbitals) test_generalized_irreps() (in module iodata.test.test_orbitals) test_generalized_occs() (in module iodata.test.test_orbitals) test_generalized_occs_aminusb() (in module iodata.test.test_orbitals) test_get_segmented() (in module iodata.test.test_basis) test_ghost() (in module iodata.test.test_json) test_indomethacin_dimer() (in module iodata.test.test_pdb) test_inout_molssi_qcschema_molecule() (in module iodata.test.test_json) test_inout_qcschema_input() (in module iodata.test.test_json) test_inout_qcschema_molecule() (in module iodata.test.test_json) test_inout_qcschema_output() (in module iodata.test.test_json) test_input_gaussian_atom_line() (in module iodata.test.test_inputs) test_input_gaussian_from_fchk() (in module iodata.test.test_inputs) test_input_gaussian_from_iodata() (in module iodata.test.test_inputs) test_input_gaussian_from_xyz() (in module iodata.test.test_inputs) test_input_orca_from_iodata() (in module iodata.test.test_inputs) test_input_orca_from_molden() (in module iodata.test.test_inputs) test_input_orca_from_xyz() (in module iodata.test.test_inputs) test_iter_cart_alphabet() (in module iodata.test.test_basis) test_load_2bcw() (in module iodata.test.test_pdb) test_load_aelta() (in module iodata.test.test_cube) test_load_azirine_cc() (in module iodata.test.test_fchk) test_load_azirine_ci() (in module iodata.test.test_fchk) test_load_azirine_mp2() (in module iodata.test.test_fchk) test_load_azirine_mp3() (in module iodata.test.test_fchk) test_load_be_cisd_321g_psi4() (in module iodata.test.test_molden) test_load_ch5plus_bonds() (in module iodata.test.test_pdb) test_load_chgcar_oxygen() (in module iodata.test.test_chgcar) test_load_chgcar_water() (in module iodata.test.test_chgcar) test_load_crambin() (in module iodata.test.test_charmm) test_load_data_wfx_h2() (in module iodata.test.test_wfx) test_load_data_wfx_h2o_error() (in module iodata.test.test_wfx) test_load_data_wfx_water() (in module iodata.test.test_wfx) test_load_dump_ch4_6points() (in module iodata.test.test_cube) test_load_dump_consistence_fchk() (in module iodata.test.test_fchk) test_load_dump_consistency() (in module iodata.test.test_mol2) (in module iodata.test.test_molden) (in module iodata.test.test_molekel) (in module iodata.test.test_pdb) (in module iodata.test.test_poscar) (in module iodata.test.test_sdf) (in module iodata.test.test_wfn) (in module iodata.test.test_xyz) test_load_dump_consistency_from_fchk_h2o() (in module iodata.test.test_wfn) test_load_dump_consistency_from_molden_nh3() (in module iodata.test.test_wfn) test_load_dump_consistency_h2() (in module iodata.test.test_wfx) test_load_dump_consistency_lih_cation_cisd() (in module iodata.test.test_wfx) test_load_dump_consistency_lih_cation_rohf() (in module iodata.test.test_wfx) test_load_dump_consistency_lih_cation_uhf() (in module iodata.test.test_wfx) test_load_dump_consistency_water() (in module iodata.test.test_wfx) test_load_dump_h2o_5points() (in module iodata.test.test_cube) test_load_dump_load_aelta() (in module iodata.test.test_cube) test_load_dump_many_consistency() (in module iodata.test.test_mol2) (in module iodata.test.test_pdb) (in module iodata.test.test_sdf) (in module iodata.test.test_xyz) test_load_dump_nh3_7points() (in module iodata.test.test_cube) test_load_dump_wrong_bond_num() (in module iodata.test.test_mol2) test_load_dump_xyz_consistency() (in module iodata.test.test_pdb) test_load_error() (in module iodata.test.test_gaussianinput) test_load_fcc_columns() (in module iodata.test.test_xyz) test_load_fcc_extended() (in module iodata.test.test_extxyz) test_load_fchk_ch3_rohf_g03() (in module iodata.test.test_fchk) test_load_fchk_ghost_atoms() (in module iodata.test.test_fchk) test_load_fchk_h_sto3g_num() (in module iodata.test.test_fchk) test_load_fchk_hf_sto3g_num() (in module iodata.test.test_fchk) (in module iodata.test.test_overlap) test_load_fchk_hf_water_atcharges() (in module iodata.test.test_fchk) test_load_fchk_lih_321g_hf() (in module iodata.test.test_fchk) test_load_fchk_nonexistent() (in module iodata.test.test_fchk) test_load_fchk_o2_cc_pvtz_cart_num() (in module iodata.test.test_fchk) (in module iodata.test.test_overlap) test_load_fchk_o2_cc_pvtz_pure_num() (in module iodata.test.test_fchk) (in module iodata.test.test_overlap)

test_load_fchk_water_sto3g_hf() (in module iodata.test.test_fchk) test_load_fchk_water_sto3g_hf_qchem() (in module iodata.test.test_fchk) test_load_fcidump_molpro_h2() (in module iodata.test.test_fcidump) test_load_fcidump_psi4_h2() (in module iodata.test.test_fcidump) test_load_locpot_oxygen() (in module iodata.test.test_locpot) test_load_many() (in module iodata.test.test_gromacs) (in module iodata.test.test_mol2) (in module iodata.test.test_pdb) (in module iodata.test.test_sdf) (in module iodata.test.test_xyz) test_load_many_dataset_emptylines() (in module iodata.test.test_xyz) test_load_many_extended() (in module iodata.test.test_extxyz) test_load_mgo() (in module iodata.test.test_extxyz) test_load_mkl_ethanol() (in module iodata.test.test_molekel) test_load_mkl_h2() (in module iodata.test.test_molekel) test_load_mkl_h2_huge_threshold() (in module iodata.test.test_molekel) test_load_mkl_li2() (in module iodata.test.test_molekel) test_load_molden_cfour() (in module iodata.test.test_molden) test_load_molden_f() (in module iodata.test.test_molden) test_load_molden_h2o_6_31g_d_cart_psi4() (in module iodata.test.test_molden) test_load_molden_h2o_orca() (in module iodata.test.test_molden) test_load_molden_he2_ghost_psi4_1() (in module iodata.test.test_molden) test_load_molden_high_am_orca() (in module iodata.test.test_molden) test_load_molden_high_am_psi4() (in module iodata.test.test_molden) test_load_molden_li2_orca() (in module iodata.test.test_molden) test_load_molden_li2_orca_huge_threshold() (in module iodata.test.test_molden) test_load_molden_low_nh3_molden_cart() (in module iodata.test.test_molden) test_load_molden_neon_turbomole() (in module iodata.test.test_molden) test_load_molden_nh3_aug_cc_pvqz_cart_psi4() (in module iodata.test.test_molden) test_load_molden_nh3_molden_cart() (in module iodata.test.test_molden) test_load_molden_nh3_molden_pure() (in module iodata.test.test_molden) test_load_molden_nh3_molpro2012() (in module iodata.test.test_molden) test_load_molden_nh3_orca() (in module iodata.test.test_molden) test_load_molden_nh3_psi4() (in module iodata.test.test_molden) test_load_molden_nh3_psi4_1() (in module iodata.test.test_molden) test_load_molden_nh3_turbomole() (in module iodata.test.test_molden) test_load_monosilicic_acid_hf_lan() (in module iodata.test.test_fchk) test_load_multi_link() (in module iodata.test.test_gaussianinput) test_load_multi_route() (in module iodata.test.test_gaussianinput) test_load_multi_title() (in module iodata.test.test_gaussianinput) test_load_mwfn_ch3_hf_g03() (in module iodata.test.test_mwfn) test_load_mwfn_ch3_rohf_g03() (in module iodata.test.test_mwfn) test_load_mwfn_he_spdfgh_g03() (in module iodata.test.test_mwfn) test_load_nbasis_indep() (in module iodata.test.test_fchk) test_load_nitrogen_cc() (in module iodata.test.test_fchk) test_load_nitrogen_ci() (in module iodata.test.test_fchk) test_load_nitrogen_mp2() (in module iodata.test.test_fchk) test_load_nitrogen_mp3() (in module iodata.test.test_fchk) test_load_one_cah110_hf_sto3g_g09() (in module iodata.test.test_wfn) test_load_one_gamess_punch() (in module iodata.test.test_gamess) test_load_one_h2() (in module iodata.test.test_wfx) test_load_one_h2o() (in module iodata.test.test_wfx) test_load_one_h2o_dimer_eda2() (in module iodata.test.test_qchemlog) test_load_one_lih_cation_cisd() (in module iodata.test.test_wfn) (in module iodata.test.test_wfx) test_load_one_lih_cation_rohf() (in module iodata.test.test_wfn) (in module iodata.test.test_wfx) test_load_one_lih_cation_uhf() (in module iodata.test.test_wfn) (in module iodata.test.test_wfx) test_load_one_qchemlog_freq() (in module iodata.test.test_qchemlog) test_load_operators_water_ccpvdz_pure_hf_g03() (in module iodata.test.test_gaussianlog) test_load_operators_water_sto3g_hf_g03() (in module iodata.test.test_gaussianlog) test_load_peptide_2luv() (in module iodata.test.test_pdb) test_load_poscar_cubicbn_cartesian() (in module iodata.test.test_poscar) test_load_poscar_cubicbn_direct() (in module iodata.test.test_poscar) test_load_poscar_water() (in module iodata.test.test_poscar) test_load_qchemlog_low_h2o() (in module iodata.test.test_qchemlog) test_load_qchemlog_low_qchemlog_h2o_dimer_eda2() (in module iodata.test.test_qchemlog) test_load_truncated_h2o() (in module iodata.test.test_wfx) test_load_water() (in module iodata.test.test_gromacs) (in module iodata.test.test_pdb) test_load_water_bonds_warning() (in module iodata.test.test_mol2) test_load_water_com() (in module iodata.test.test_gaussianinput) test_load_water_element() (in module iodata.test.test_xyz) test_load_water_gjf() (in module iodata.test.test_gaussianinput) test_load_water_hfs_321g() (in module iodata.test.test_fchk) test_load_water_no_end() (in module iodata.test.test_pdb) test_load_water_number() (in module iodata.test.test_orcalog) (in module iodata.test.test_xyz) test_load_wfn_h2_ccpvqz_virtual() (in module iodata.test.test_wfn) test_load_wfn_h2o_sto3g() (in module iodata.test.test_wfn) test_load_wfn_h2o_sto3g_decontracted() (in module iodata.test.test_wfn) test_load_wfn_li_sp() (in module iodata.test.test_wfn) test_load_wfn_li_sp_virtual() (in module iodata.test.test_wfn) test_load_wfn_lif_fci() (in module iodata.test.test_wfn) test_load_wfn_lih_cation_fci() (in module iodata.test.test_wfn) test_load_wfn_low_h2o() (in module iodata.test.test_wfn) test_load_wfn_low_he_s() (in module iodata.test.test_wfn) test_load_wfn_o2() (in module iodata.test.test_wfn) test_load_wfn_o2_virtual() (in module iodata.test.test_wfn) test_mol2_formaterror() (in module iodata.test.test_mol2) test_mol2_load_one() (in module iodata.test.test_mol2) test_mol2_symbol() (in module iodata.test.test_mol2) test_molssi_qcschema_molecule() (in module iodata.test.test_json) test_natom() (in module iodata.test.test_iodata) test_nbasis1() (in module iodata.test.test_basis) test_nelec_charge() (in module iodata.test.test_fchk) (in module iodata.test.test_mwfn) test_normalization_basics_generalized() (in module iodata.test.test_overlap) test_normalization_basics_segmented() (in module iodata.test.test_overlap) test_normalization_dm_azirine_cc() (in module iodata.test.test_fchk) test_normalization_dm_azirine_ci() (in module iodata.test.test_fchk) test_normalization_dm_azirine_mp2() (in module iodata.test.test_fchk) test_normalization_dm_azirine_mp3() (in module iodata.test.test_fchk) test_overlap_l1() (in module iodata.test.test_overlap) test_overlap_two_basis_different() (in module iodata.test.test_overlap) test_overlap_two_basis_exceptions() (in module iodata.test.test_overlap) test_overlap_two_basis_same() (in module iodata.test.test_overlap) test_parse_wfx_missing_tag_h2o() (in module iodata.test.test_wfx) test_passthrough_qcschema_input() (in module iodata.test.test_json) test_passthrough_qcschema_molecule() (in module iodata.test.test_json) test_peroxide_irc() (in module iodata.test.test_fchk) test_peroxide_opt() (in module iodata.test.test_fchk) test_peroxide_relaxed_scan() (in module iodata.test.test_fchk) test_peroxide_tsopt() (in module iodata.test.test_fchk) test_qcschema_input() (in module iodata.test.test_json) test_qcschema_molecule() (in module iodata.test.test_json) test_qcschema_output() (in module iodata.test.test_json) test_restricted_coeffs() (in module iodata.test.test_orbitals) test_restricted_empty() (in module iodata.test.test_orbitals) test_restricted_energies() (in module iodata.test.test_orbitals) test_restricted_irreps() (in module iodata.test.test_orbitals) test_restricted_occs() (in module iodata.test.test_orbitals) test_restricted_occs_aminusb() (in module iodata.test.test_orbitals) test_script_many_autofmt() (in module iodata.test.test_cli) test_script_many_manfmt() (in module iodata.test.test_cli) test_script_one_autofmt() (in module iodata.test.test_cli) test_script_one_manfmt() (in module iodata.test.test_cli) test_sdf_formaterror() (in module iodata.test.test_sdf) test_sdf_load_one_example() (in module iodata.test.test_sdf) test_sdf_load_one_formamide() (in module iodata.test.test_sdf) test_shell_exceptions() (in module iodata.test.test_basis) test_shell_info_propertes() (in module iodata.test.test_basis) test_shell_validators() (in module iodata.test.test_basis) test_spinpol() (in module iodata.test.test_fchk) test_spinpol1() (in module iodata.test.test_iodata) test_spinpol2() (in module iodata.test.test_iodata) test_strtobool() (in module iodata.test.test_utils) test_typecheck() (in module iodata.test.test_iodata) test_typecheck_raises() (in module iodata.test.test_iodata) test_undefined() (in module iodata.test.test_iodata) test_unknown_format() (in module iodata.test.test_iodata) test_unrestricted_coeffs() (in module iodata.test.test_orbitals) test_unrestricted_empty() (in module iodata.test.test_orbitals) test_unrestricted_energies() (in module iodata.test.test_orbitals) test_unrestricted_irreps() (in module iodata.test.test_orbitals) test_unrestricted_occs() (in module iodata.test.test_orbitals) test_unrestricted_occs_aminusb() (in module iodata.test.test_orbitals) test_v2000_check() (in module iodata.test.test_sdf) test_validate_shape_assign() (in module iodata.test.test_attrutils) test_validate_shape_exceptions() (in module iodata.test.test_attrutils) test_validate_shape_init() (in module iodata.test.test_attrutils) test_wrong_kind() (in module iodata.test.test_orbitals) title (IOData attribute) truncated_file() (in module iodata.test.common) two_ints (IOData attribute) two_rdms (IOData attribute)

V

validate_norbab() (in module iodata.orbitals) validate_occs_aminusb() (in module iodata.orbitals)

validate_shape() (in module iodata.attrutils) volume() (in module iodata.utils)

W

with_traceback() (BaseFileError method) (BaseFileWarning method) (DumpError method) (DumpWarning method) (FileFormatError method) (LoadError method) (LoadWarning method) (PrepareDumpError method) (WriteInputError method)

write_input() (in module iodata.api) (in module iodata.inputs.gaussian) (in module iodata.inputs.orca) write_input_base() (in module iodata.inputs.common) WriteInputError

X

xxx (NoName0 attribute) (NoName1 attribute) (NoName2 attribute) (NoName3 attribute)