iodata package

Subpackages

• iodata.formats package
  • Submodules
    • iodata.formats.charmm module
      • load_one()
    • iodata.formats.chgcar module
      • load_one()
    • iodata.formats.cp2klog module
      • load_one()
    • iodata.formats.cube module
      • dump_one()
      • load_one()
    • iodata.formats.extxyz module
      • load_many()
      • load_one()
    • iodata.formats.fchk module
      • dump_one()
      • load_many()
      • load_one()
      • prepare_dump()
    • iodata.formats.fcidump module
      • dump_one()
      • load_one()
    • iodata.formats.gamess module
      • load_one()
    • iodata.formats.gaussianinput module
      • load_one()
    • iodata.formats.gaussianlog module
      • load_one()
    • iodata.formats.gromacs module
      • load_many()
      • load_one()
    • iodata.formats.json_qcschema module
      • General Usage
      • Schema Definitions
      • dump_one()
      • load_one()
      • prepare_dump()
    • iodata.formats.locpot module
      • load_one()
    • iodata.formats.mol2 module
      • dump_many()
      • dump_one()
      • load_many()
      • load_one()
    • iodata.formats.molden module
      • dump_one()
      • load_one()
      • prepare_dump()
    • iodata.formats.molekel module
      • dump_one()
      • load_one()
      • prepare_dump()
    • iodata.formats.mwfn module
      • load_one()
    • iodata.formats.orcalog module
      • load_one()
    • iodata.formats.pdb module
      • dump_many()
      • dump_one()
      • load_many()
      • load_one()
    • iodata.formats.poscar module
      • dump_one()
      • load_one()
    • iodata.formats.qchemlog module
      • load_one()
      • load_qchemlog_low()
    • iodata.formats.sdf module
      • dump_many()
      • dump_one()
      • load_many()
      • load_one()
    • iodata.formats.wfn module
      • build_obasis()
      • dump_one()
      • get_mocoeff_scales()
      • load_one()
      • load_wfn_low()
      • prepare_dump()
    • iodata.formats.wfx module
      • dump_one()
      • load_data_wfx()
      • load_one()
      • parse_wfx()
      • prepare_dump()
    • iodata.formats.xyz module
      • dump_many()
      • dump_one()
      • load_many()
      • load_one()
  • Module contents
• iodata.inputs package
  • Submodules
    • iodata.inputs.common module
      • write_input_base()
    • iodata.inputs.gaussian module
      • default_atom_line()
      • write_input()
    • iodata.inputs.orca module
      • default_atom_line()
      • write_input()
  • Module contents
• iodata.test package
  • Subpackages
    • iodata.test.data package
      • Module contents
  • Submodules
    • iodata.test.common module
      • check_orthonormal()
      • compare_mols()
      • compute_1rdm()
      • compute_mulliken_charges()
      • create_generalized_contraction()
      • create_generalized_orbitals()
      • load_one_warning()
      • truncated_file()
    • iodata.test.test_api module
      • test_dump_many_generator()
      • test_dump_many_missing_attribute_first()
      • test_dump_many_missing_attribute_second()
      • test_dump_one_missing_attribute_no_file()
      • test_empty_dump_many_no_file()
      • test_json_no_pattern()
      • test_nodump()
      • test_noinput()
      • test_nonexisting_format()
    • iodata.test.test_attrutils module
      • FooBar
      • NoName0
      • NoName1
      • NoName2
      • NoName3
      • Spam
      • test_convert_array_to_assign()
      • test_convert_array_to_init()
      • test_validate_shape_assign()
      • test_validate_shape_exceptions()
      • test_validate_shape_init()
    • iodata.test.test_basis module
      • test_angmom_its()
      • test_angmom_sti()
      • test_angmom_sti_uppercase()
      • test_nbasis1()
      • test_shell_exceptions()
      • test_shell_info_propertes()
      • test_shell_validators()
    • iodata.test.test_charmm module
      • test_load_crambin()
    • iodata.test.test_chgcar module
      • test_load_chgcar_oxygen()
      • test_load_chgcar_water()
    • iodata.test.test_cli module
      • test_convert_many_autofmt()
      • test_convert_many_manfmt()
      • test_convert_one_autofmt()
      • test_convert_one_autofmt_changes()
      • test_convert_one_manfmt()
      • test_convert_one_manfmt_changes()
      • test_convert_one_nonexisting_infmt()
      • test_convert_one_nonexisting_outfmt()
    • iodata.test.test_convert module
      • obasis()
      • test_conventions()
      • test_convert_convention_obasis()
      • test_convert_convention_obasis_duplicate()
      • test_convert_convention_obasis_empty()
      • test_convert_convention_obasis_invalid()
      • test_convert_convention_shell()
      • test_convert_exceptions()
      • test_convert_to_segmented()
      • test_convert_to_segmented_empty()
      • test_convert_to_segmented_sp()
      • test_convert_to_unrestricted_aminusb()
      • test_convert_to_unrestricted_full()
      • test_convert_to_unrestricted_generalized()
      • test_convert_to_unrestricted_minimal()
      • test_convert_to_unrestricted_occ_float()
      • test_convert_to_unrestricted_occ_integer()
      • test_convert_to_unrestricted_pass_through()
      • test_iter_cart_alphabet()
    • iodata.test.test_cp2klog module
      • test_atom_o_rks()
      • test_atom_si_uks()
      • test_carbon_gs_ae_contracted()
      • test_carbon_gs_ae_uncontracted()
      • test_carbon_gs_pp_contracted()
      • test_carbon_gs_pp_uncontracted()
      • test_carbon_sc_ae_contracted()
      • test_carbon_sc_ae_uncontracted()
      • test_carbon_sc_pp_contracted()
      • test_carbon_sc_pp_uncontracted()
      • test_errors()
    • iodata.test.test_cube module
      • test_load_aelta()
      • test_load_dump_ch4_6points()
      • test_load_dump_h2o_5points()
      • test_load_dump_load_aelta()
      • test_load_dump_nh3_7points()
    • iodata.test.test_extxyz module
      • test_load_fcc_extended()
      • test_load_many_extended()
      • test_load_mgo()
    • iodata.test.test_fchk module
      • check_load_azirine()
      • check_load_dump_consistency()
      • check_load_nitrogen()
      • check_normalization_dm_azirine()
      • check_trj_basics()
      • load_fchk_helper()
      • load_fchk_trj_helper()
      • test_atfrozen()
      • test_atgradient()
      • test_athessian()
      • test_atmasses()
      • test_dump_fchk_from_molden()
      • test_dump_fchk_from_molekel()
      • test_dump_fchk_from_wfn()
      • test_dump_fchk_from_wfn_fci_lif()
      • test_dump_fchk_from_wfn_fci_lih_cation()
      • test_dump_fchk_from_wfx()
      • test_dump_fchk_from_wfx_lih_cisd_cation()
      • test_fchk_generalized_contraction()
      • test_generalized_orbitals()
      • test_load_azirine_cc()
      • test_load_azirine_ci()
      • test_load_azirine_mp2()
      • test_load_azirine_mp3()
      • test_load_dump_consistence_fchk()
      • test_load_fchk_ch3_rohf_g03()
      • test_load_fchk_ghost_atoms()
      • test_load_fchk_h_sto3g_num()
      • test_load_fchk_hf_sto3g_num()
      • test_load_fchk_hf_water_atcharges()
      • test_load_fchk_lih_321g_hf()
      • test_load_fchk_nonexistent()
      • test_load_fchk_o2_cc_pvtz_cart_num()
      • test_load_fchk_o2_cc_pvtz_pure_num()
      • test_load_fchk_water_sto3g_hf()
      • test_load_fchk_water_sto3g_hf_qchem()
      • test_load_monosilicic_acid_hf_lan()
      • test_load_nbasis_indep()
      • test_load_nitrogen_cc()
      • test_load_nitrogen_ci()
      • test_load_nitrogen_mp2()
      • test_load_nitrogen_mp3()
      • test_load_water_hfs_321g()
      • test_nelec_charge()
      • test_normalization_dm_azirine_cc()
      • test_normalization_dm_azirine_ci()
      • test_normalization_dm_azirine_mp2()
      • test_normalization_dm_azirine_mp3()
      • test_peroxide_irc()
      • test_peroxide_opt()
      • test_peroxide_relaxed_scan()
      • test_peroxide_tsopt()
      • test_spinpol()
    • iodata.test.test_fcidump module
      • test_dump_load_fcidimp_consistency_ao()
      • test_load_fcidump_molpro_h2()
      • test_load_fcidump_psi4_h2()
    • iodata.test.test_gamess module
      • test_load_one_gamess_punch()
    • iodata.test.test_gaussianinput module
      • check_water()
      • test_load_error()
      • test_load_multi_link()
      • test_load_multi_route()
      • test_load_multi_title()
      • test_load_water_com()
      • test_load_water_gjf()
    • iodata.test.test_gaussianlog module
      • load_log_helper()
      • test_load_operators_water_ccpvdz_pure_hf_g03()
      • test_load_operators_water_sto3g_hf_g03()
    • iodata.test.test_gromacs module
      • check_water()
      • test_load_many()
      • test_load_water()
    • iodata.test.test_inputs module
      • check_load_input_and_compare()
      • test_input_gaussian_atom_line()
      • test_input_gaussian_from_fchk()
      • test_input_gaussian_from_iodata()
      • test_input_gaussian_from_xyz()
      • test_input_orca_from_iodata()
      • test_input_orca_from_molden()
      • test_input_orca_from_xyz()
    • iodata.test.test_iodata module
      • test_charge_nelec1()
      • test_charge_nelec10()
      • test_charge_nelec11()
      • test_charge_nelec12()
      • test_charge_nelec13()
      • test_charge_nelec14()
      • test_charge_nelec15()
      • test_charge_nelec2()
      • test_charge_nelec3()
      • test_charge_nelec4()
      • test_charge_nelec5()
      • test_charge_nelec6()
      • test_charge_nelec7()
      • test_charge_nelec8()
      • test_charge_nelec9()
      • test_derived1()
      • test_derived2()
      • test_dm_ch3_rohf_g03()
      • test_dm_lih_sto3g_hf()
      • test_dm_water_sto3g_hf()
      • test_natom()
      • test_spinpol1()
      • test_spinpol2()
      • test_typecheck()
      • test_typecheck_raises()
      • test_undefined()
      • test_unknown_format()
    • iodata.test.test_json_qcschema module
      • test_bad_qcschema_files()
      • test_ghost()
      • test_inout_molssi_qcschema_molecule()
      • test_inout_qcschema_input()
      • test_inout_qcschema_molecule()
      • test_inout_qcschema_output()
      • test_molssi_qcschema_molecule()
      • test_passthrough_qcschema_input()
      • test_passthrough_qcschema_molecule()
      • test_qcschema_input()
      • test_qcschema_molecule()
      • test_qcschema_output()
    • iodata.test.test_locpot module
      • test_load_locpot_oxygen()
    • iodata.test.test_mol2 module
      • check_example()
      • check_load_dump_consistency()
      • test_bondtypes_benzene()
      • test_load_dump_consistency()
      • test_load_dump_many_consistency()
      • test_load_dump_wrong_bond_num()
      • test_load_many()
      • test_load_water_bonds_warning()
      • test_mol2_formaterror()
      • test_mol2_load_one()
      • test_mol2_symbol()
    • iodata.test.test_molden module
      • test_generalized_orbitals()
      • test_load_be_cisd_321g_psi4()
      • test_load_dump_consistency()
      • test_load_molden_cfour()
      • test_load_molden_f()
      • test_load_molden_h2o_6_31g_d_cart_psi4()
      • test_load_molden_h2o_orca()
      • test_load_molden_he2_ghost_psi4_1()
      • test_load_molden_high_am_orca()
      • test_load_molden_high_am_psi4()
      • test_load_molden_li2_orca()
      • test_load_molden_li2_orca_huge_threshold()
      • test_load_molden_low_nh3_molden_cart()
      • test_load_molden_neon_turbomole()
      • test_load_molden_nh3_aug_cc_pvqz_cart_psi4()
      • test_load_molden_nh3_molden_cart()
      • test_load_molden_nh3_molden_pure()
      • test_load_molden_nh3_molpro2012()
      • test_load_molden_nh3_orca()
      • test_load_molden_nh3_psi4()
      • test_load_molden_nh3_psi4_1()
      • test_load_molden_nh3_turbomole()
      • test_mixed_pure_cartesian()
    • iodata.test.test_molekel module
      • check_load_dump_consistency()
      • compare_mols_diff_formats()
      • test_generalized_orbitals()
      • test_load_dump_consistency()
      • test_load_mkl_ethanol()
      • test_load_mkl_h2()
      • test_load_mkl_h2_huge_threshold()
      • test_load_mkl_li2()
      • test_load_wrong_spin_mult()
    • iodata.test.test_mwfn module
      • load_helper()
      • test_load_mwfn_ch3_hf_g03()
      • test_load_mwfn_ch3_rohf_g03()
      • test_load_mwfn_he_spdfgh_g03()
      • test_nelec_charge()
    • iodata.test.test_orbitals module
      • test_generalized_coeffs()
      • test_generalized_empty()
      • test_generalized_energies()
      • test_generalized_irreps()
      • test_generalized_occs()
      • test_generalized_occs_aminusb()
      • test_restricted_coeffs()
      • test_restricted_empty()
      • test_restricted_energies()
      • test_restricted_irreps()
      • test_restricted_occs()
      • test_restricted_occs_aminusb()
      • test_unrestricted_coeffs()
      • test_unrestricted_empty()
      • test_unrestricted_energies()
      • test_unrestricted_irreps()
      • test_unrestricted_occs()
      • test_unrestricted_occs_aminusb()
      • test_wrong_kind()
    • iodata.test.test_orcalog module
      • test_load_water_number()
    • iodata.test.test_overlap module
      • test_factorial2_float_arguments()
      • test_factorial2_float_array_argument()
      • test_factorial2_integer_arguments()
      • test_factorial2_integer_array_argument()
      • test_load_fchk_hf_sto3g_num()
      • test_load_fchk_o2_cc_pvtz_cart_num()
      • test_load_fchk_o2_cc_pvtz_pure_num()
      • test_normalization_basics_generalized()
      • test_normalization_basics_segmented()
      • test_overlap_l1()
      • test_overlap_two_basis_different()
      • test_overlap_two_basis_exceptions()
      • test_overlap_two_basis_same()
    • iodata.test.test_pdb module
      • check_water()
      • test_indomethacin_dimer()
      • test_load_2bcw()
      • test_load_ch5plus_bonds()
      • test_load_dump_consistency()
      • test_load_dump_many_consistency()
      • test_load_dump_xyz_consistency()
      • test_load_many()
      • test_load_peptide_2luv()
      • test_load_water()
      • test_load_water_no_end()
    • iodata.test.test_poscar module
      • test_load_dump_consistency()
      • test_load_poscar_cubicbn_cartesian()
      • test_load_poscar_cubicbn_direct()
      • test_load_poscar_water()
    • iodata.test.test_prepare module
      • test_dump_occs_aminusb()
      • test_segmented_generalized()
      • test_segmented_no_basis()
      • test_segmented_not_generalized()
      • test_segmented_sp()
      • test_unrestricted_aminusb_generaized()
      • test_unrestricted_aminusb_no_mo()
      • test_unrestricted_aminusb_pass_error()
      • test_unrestricted_aminusb_pass_through1()
      • test_unrestricted_aminusb_pass_through2()
      • test_unrestricted_aminusb_pass_warning()
    • iodata.test.test_qchemlog module
      • test_load_one_h2o_dimer_eda2()
      • test_load_one_qchemlog_freq()
      • test_load_qchemlog_low_h2o()
      • test_load_qchemlog_low_qchemlog_h2o_dimer_eda2()
    • iodata.test.test_sdf module
      • check_example()
      • check_load_dump_consistency()
      • test_load_dump_consistency()
      • test_load_dump_many_consistency()
      • test_load_many()
      • test_sdf_formaterror()
      • test_sdf_load_one_example()
      • test_sdf_load_one_formamide()
      • test_v2000_check()
    • iodata.test.test_utils module
      • test_amu()
      • test_strtobool()
    • iodata.test.test_wfn module
      • check_load_dump_consistency()
      • check_wfn()
      • helper_load_wfn_low()
      • test_dump_one_pure_functions()
      • test_generalized_orbitals()
      • test_load_dump_consistency()
      • test_load_dump_consistency_from_fchk_h2o()
      • test_load_dump_consistency_from_molden_nh3()
      • test_load_one_cah110_hf_sto3g_g09()
      • test_load_one_lih_cation_cisd()
      • test_load_one_lih_cation_rohf()
      • test_load_one_lih_cation_uhf()
      • test_load_wfn_h2_ccpvqz_virtual()
      • test_load_wfn_h2o_sto3g()
      • test_load_wfn_h2o_sto3g_decontracted()
      • test_load_wfn_li_sp()
      • test_load_wfn_li_sp_virtual()
      • test_load_wfn_lif_fci()
      • test_load_wfn_lih_cation_fci()
      • test_load_wfn_low_h2o()
      • test_load_wfn_low_he_s()
      • test_load_wfn_o2()
      • test_load_wfn_o2_virtual()
    • iodata.test.test_wfx module
      • check_load_dump_consistency()
      • compare_mulliken_charges()
      • helper_load_data_wfx()
      • test_dump_one()
      • test_dump_one_from_molden_neon()
      • test_dump_one_match()
      • test_dump_one_pure_functions()
      • test_generalized_orbitals()
      • test_load_data_wfx_h2()
      • test_load_data_wfx_h2o_error()
      • test_load_data_wfx_water()
      • test_load_dump_consistency_h2()
      • test_load_dump_consistency_lih_cation_cisd()
      • test_load_dump_consistency_lih_cation_rohf()
      • test_load_dump_consistency_lih_cation_uhf()
      • test_load_dump_consistency_water()
      • test_load_one_h2()
      • test_load_one_h2o()
      • test_load_one_lih_cation_cisd()
      • test_load_one_lih_cation_rohf()
      • test_load_one_lih_cation_uhf()
      • test_load_truncated_h2o()
      • test_parse_wfx_missing_tag_h2o()
    • iodata.test.test_xyz module
      • check_load_dump_consistency()
      • check_water()
      • test_dump_xyz_fcc()
      • test_dump_xyz_water_element()
      • test_dump_xyz_water_number()
      • test_load_dump_consistency()
      • test_load_dump_many_consistency()
      • test_load_fcc_columns()
      • test_load_many()
      • test_load_many_dataset_emptylines()
      • test_load_water_element()
      • test_load_water_number()
  • Module contents

Submodules

• iodata.api module
  • dump_many()
  • dump_one()
  • load_many()
  • load_one()
  • write_input()
• iodata.attrutils module
  • convert_array_to()
  • validate_shape()
• iodata.basis module
  • MolecularBasis
    • MolecularBasis.__init__()
    • MolecularBasis.conventions
    • MolecularBasis.nbasis
    • MolecularBasis.primitive_normalization
    • MolecularBasis.shells
  • Shell
    • Shell.__init__()
    • Shell.angmoms
    • Shell.coeffs
    • Shell.exponents
    • Shell.icenter
    • Shell.kinds
    • Shell.nbasis
    • Shell.ncon
    • Shell.nexp
  • angmom_its()
  • angmom_sti()
• iodata.convert module
  • convert_conventions()
  • convert_to_segmented()
  • convert_to_unrestricted()
  • iter_cart_alphabet()
• iodata.docstrings module
  • document_dump_many()
  • document_dump_one()
  • document_load_many()
  • document_load_one()
  • document_write_input()
• iodata.iodata module
  • IOData
    • IOData.__init__()
    • IOData.atcharges
    • IOData.atcoords
    • IOData.atcorenums
    • IOData.atffparams
    • IOData.atfrozen
    • IOData.atgradient
    • IOData.athessian
    • IOData.atmasses
    • IOData.atnums
    • IOData.basisdef
    • IOData.bonds
    • IOData.cellvecs
    • IOData.charge
    • IOData.core_energy
    • IOData.cube
    • IOData.energy
    • IOData.extcharges
    • IOData.extra
    • IOData.g_rot
    • IOData.lot
    • IOData.mo
    • IOData.moments
    • IOData.natom
    • IOData.nelec
    • IOData.obasis
    • IOData.obasis_name
    • IOData.one_ints
    • IOData.one_rdms
    • IOData.run_type
    • IOData.spinpol
    • IOData.title
    • IOData.two_ints
    • IOData.two_rdms
• iodata.orbitals module
  • MolecularOrbitals
    • MolecularOrbitals.__init__()
    • MolecularOrbitals.coeffs
    • MolecularOrbitals.coeffsa
    • MolecularOrbitals.coeffsb
    • MolecularOrbitals.energies
    • MolecularOrbitals.energiesa
    • MolecularOrbitals.energiesb
    • MolecularOrbitals.irreps
    • MolecularOrbitals.irrepsa
    • MolecularOrbitals.irrepsb
    • MolecularOrbitals.kind
    • MolecularOrbitals.nbasis
    • MolecularOrbitals.nelec
    • MolecularOrbitals.norb
    • MolecularOrbitals.norba
    • MolecularOrbitals.norbb
    • MolecularOrbitals.occs
    • MolecularOrbitals.occs_aminusb
    • MolecularOrbitals.occsa
    • MolecularOrbitals.occsb
    • MolecularOrbitals.spinpol
  • validate_norbab()
  • validate_occs_aminusb()
• iodata.overlap module
  • GaussianOverlap
    • GaussianOverlap.__init__()
    • GaussianOverlap.compute_overlap_gaussian_1d()
  • compute_overlap()
  • factorial2()
  • gob_cart_normalization()
• iodata.overlap_cartpure module
• iodata.periodic module
• iodata.prepare module
  • prepare_segmented()
  • prepare_unrestricted_aminusb()
• iodata.utils module
  • BaseFileError
    • BaseFileError.__init__()
    • BaseFileError.add_note()
    • BaseFileError.args
    • BaseFileError.with_traceback()
  • BaseFileWarning
    • BaseFileWarning.__init__()
    • BaseFileWarning.add_note()
    • BaseFileWarning.args
    • BaseFileWarning.with_traceback()
  • Cube
    • Cube.__init__()
    • Cube.axes
    • Cube.data
    • Cube.origin
    • Cube.shape
  • DumpError
    • DumpError.__init__()
    • DumpError.add_note()
    • DumpError.args
    • DumpError.with_traceback()
  • DumpWarning
    • DumpWarning.__init__()
    • DumpWarning.add_note()
    • DumpWarning.args
    • DumpWarning.with_traceback()
  • FileFormatError
    • FileFormatError.__init__()
    • FileFormatError.add_note()
    • FileFormatError.args
    • FileFormatError.with_traceback()
  • LineIterator
    • LineIterator.__init__()
    • LineIterator.back()
  • LoadError
    • LoadError.__init__()
    • LoadError.add_note()
    • LoadError.args
    • LoadError.with_traceback()
  • LoadWarning
    • LoadWarning.__init__()
    • LoadWarning.add_note()
    • LoadWarning.args
    • LoadWarning.with_traceback()
  • PrepareDumpError
    • PrepareDumpError.__init__()
    • PrepareDumpError.add_note()
    • PrepareDumpError.args
    • PrepareDumpError.with_traceback()
  • PrepareDumpWarning
    • PrepareDumpWarning.__init__()
    • PrepareDumpWarning.add_note()
    • PrepareDumpWarning.args
    • PrepareDumpWarning.with_traceback()
  • WriteInputError
    • WriteInputError.__init__()
    • WriteInputError.add_note()
    • WriteInputError.args
    • WriteInputError.with_traceback()
  • check_dm()
  • derive_naturals()
  • set_four_index_element()
  • strtobool()
  • volume()

Module contents

Input and Output Module.