Index

_

__init__() (BaseFileError method) (BaseFileWarning method) (Cube method) (DumpError method) (DumpWarning method) (FileFormatError method) (GaussianOverlap method) (IOData method) (LineIterator method) (LoadError method) (LoadWarning method) (MolecularBasis method) (MolecularOrbitals method) (PrepareDumpError method) (PrepareDumpWarning method) (Shell method) (WriteInputError method)

A

add_note() (BaseFileError method) (BaseFileWarning method) (DumpError method) (DumpWarning method) (FileFormatError method) (LoadError method) (LoadWarning method) (PrepareDumpError method) (PrepareDumpWarning 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) (PrepareDumpWarning 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_load_dump_consistency() (in module iodata.test.test_xyz) check_water() (in module iodata.test.test_gaussianinput) (in module iodata.test.test_gromacs) (in module iodata.test.test_xyz) coeffs (MolecularOrbitals attribute) (Shell attribute) coeffsa (MolecularOrbitals property)

coeffsb (MolecularOrbitals property) compute_overlap() (in module iodata.overlap) compute_overlap_gaussian_1d() (GaussianOverlap method) conventions (MolecularBasis attribute) convert_array_to() (in module iodata.attrutils) convert_conventions() (in module iodata.convert) convert_to_segmented() (in module iodata.convert) convert_to_unrestricted() (in module iodata.convert) core_energy (IOData attribute) 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_qcschema) (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

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

G

g_rot (IOData attribute) GaussianOverlap (class in iodata.overlap)

get_mocoeff_scales() (in module iodata.formats.wfn) gob_cart_normalization() (in module iodata.overlap)

I

icenter (Shell attribute) iodata module IOData (class in iodata.iodata) iodata.api module iodata.attrutils module iodata.basis module iodata.convert 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_qcschema 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.prepare module iodata.test module iodata.test.data module iodata.test.test_charmm module iodata.test.test_chgcar module iodata.test.test_cube module iodata.test.test_extxyz 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_locpot module iodata.test.test_mwfn module iodata.test.test_orcalog module iodata.test.test_poscar module iodata.test.test_qchemlog module iodata.test.test_xyz module iodata.utils module irreps (MolecularOrbitals attribute) irrepsa (MolecularOrbitals property) irrepsb (MolecularOrbitals property) iter_cart_alphabet() (in module iodata.convert)

K

kind (MolecularOrbitals attribute)

kinds (Shell attribute)

L

LineIterator (class in iodata.utils) load_data_wfx() (in module iodata.formats.wfx) 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_qcschema) (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_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.convert 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_qcschema 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.prepare iodata.test iodata.test.data iodata.test.test_charmm iodata.test.test_chgcar iodata.test.test_cube iodata.test.test_extxyz iodata.test.test_fcidump iodata.test.test_gamess iodata.test.test_gaussianinput iodata.test.test_gaussianlog iodata.test.test_gromacs iodata.test.test_locpot iodata.test.test_mwfn iodata.test.test_orcalog iodata.test.test_poscar iodata.test.test_qchemlog 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) nexp (Shell property) norb (MolecularOrbitals property) norba (MolecularOrbitals attribute) norbb (MolecularOrbitals attribute)

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)

P

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

prepare_segmented() (in module iodata.prepare) prepare_unrestricted_aminusb() (in module iodata.prepare) PrepareDumpError PrepareDumpWarning 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) spinpol (IOData property) (MolecularOrbitals property) strtobool() (in module iodata.utils)

T

test_dump_load_fcidimp_consistency_ao() (in module iodata.test.test_fcidump) 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_load_aelta() (in module iodata.test.test_cube) 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_dump_ch4_6points() (in module iodata.test.test_cube) test_load_dump_consistency() (in module iodata.test.test_poscar) (in module iodata.test.test_xyz) 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_xyz) test_load_dump_nh3_7points() (in module iodata.test.test_cube) 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_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_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_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_one_gamess_punch() (in module iodata.test.test_gamess) test_load_one_h2o_dimer_eda2() (in module iodata.test.test_qchemlog) 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_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_water() (in module iodata.test.test_gromacs) 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_number() (in module iodata.test.test_orcalog) (in module iodata.test.test_xyz) test_nelec_charge() (in module iodata.test.test_mwfn) title (IOData attribute) 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) (PrepareDumpWarning 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