.. _file_formats: Supported File Formats ###################### .. _format_charmm: CHARMM crd file format. (``charmm``) ==================================== See :py:mod:`iodata.formats.charmm` for details. Filename patterns: ``*.crd`` :py:func:`iodata.formats.charmm.load_one` ----------------------------------------- - Always loads ``atcoords``, ``atffparams``, ``atmasses``, ``extra`` - May load ``title`` .. _format_chgcar: VASP 5 CHGCAR file format. (``chgcar``) ======================================= See :py:mod:`iodata.formats.chgcar` for details. Filename patterns: ``CHGCAR*``, ``AECCAR*`` :py:func:`iodata.formats.chgcar.load_one` ----------------------------------------- - Always loads ``atcoords``, ``atnums``, ``cellvecs``, ``cube``, ``title`` .. _format_cp2klog: CP2K ATOM output file format. (``cp2klog``) =========================================== See :py:mod:`iodata.formats.cp2klog` for details. Filename patterns: ``*.cp2k.out`` :py:func:`iodata.formats.cp2klog.load_one` ------------------------------------------ - Always loads ``atcoords``, ``atcorenums``, ``atnums``, ``energy``, ``mo``, ``obasis`` Notes ----- This function assumes that the following subsections are present in the CP2K ATOM input file, in the section ``ATOM%PRINT``: .. code-block:: text &PRINT &POTENTIAL &END POTENTIAL &BASIS_SET &END BASIS_SET &ORBITALS &END ORBITALS &END PRINT .. _format_cube: Gaussian Cube file format. (``cube``) ===================================== See :py:mod:`iodata.formats.cube` for details. Filename patterns: ``*.cube``, ``*.cub`` :py:func:`iodata.formats.cube.load_one` --------------------------------------- - Always loads ``atcoords``, ``atcorenums``, ``atnums``, ``cellvecs``, ``cube`` :py:func:`iodata.formats.cube.dump_one` --------------------------------------- - Requires ``atcoords``, ``atnums``, ``cube`` - May dump ``title``, ``atcorenums`` .. _format_extxyz: Extended XYZ file format. (``extxyz``) ====================================== See :py:mod:`iodata.formats.extxyz` for details. Filename patterns: ``*.extxyz`` :py:func:`iodata.formats.extxyz.load_one` ----------------------------------------- - Always loads ``title`` - May load ``atcoords``, ``atgradient``, ``atmasses``, ``atnums``, ``cellvecs``, ``charge``, ``energy``, ``extra`` :py:func:`iodata.formats.extxyz.load_many` ------------------------------------------ - Always loads ``title`` - May load ``atcoords``, ``atgradient``, ``atmasses``, ``atnums``, ``cellvecs``, ``charge``, ``energy``, ``extra`` .. _format_fchk: Gaussian FCHK file format. (``fchk``) ===================================== See :py:mod:`iodata.formats.fchk` for details. Filename patterns: ``*.fchk``, ``*.fch`` :py:func:`iodata.formats.fchk.load_one` --------------------------------------- - Always loads ``atcharges``, ``atcoords``, ``atnums``, ``atcorenums``, ``lot``, ``mo``, ``obasis``, ``obasis_name``, ``run_type``, ``title`` - May load ``energy``, ``atfrozen``, ``atgradient``, ``athessian``, ``atmasses``, ``one_rdms``, ``extra``, ``moments`` :py:func:`iodata.formats.fchk.dump_one` --------------------------------------- - Requires ``atnums``, ``atcorenums`` - May dump ``atcharges``, ``atcoords``, ``atfrozen``, ``atgradient``, ``athessian``, ``atmasses``, ``charge``, ``energy``, ``lot``, ``mo``, ``one_rdms``, ``obasis_name``, ``extra``, ``moments`` :py:func:`iodata.formats.fchk.load_many` ---------------------------------------- - Always loads ``atcoords``, ``atgradient``, ``atnums``, ``atcorenums``, ``energy``, ``extra``, ``title`` Notes ----- Trajectories from a Gaussian optimization, relaxed scan or IRC calculation are written in groups of frames, called "points" in the Gaussian world, e.g. to discrimininate between different values of the constraint in a relaxed geometry. In most cases, e.g. IRC or conventional optimization, there is only one "point". Within one "point", one can have multiple geometries and their properties. This information is stored in the ``extra`` attribute: - ``ipoint`` is the counter for a point - ``npoint`` is the total number of points. - ``istep`` is the counter within one "point" - ``nstep`` is the total number of geometries within in a "point". - ``reaction_coordinate`` is only present in case of an IRC calculation. .. _format_fcidump: Molpro 2012 FCIDUMP file format. (``fcidump``) ============================================== See :py:mod:`iodata.formats.fcidump` for details. Filename patterns: ``*FCIDUMP*``, ``*.fcidump`` :py:func:`iodata.formats.fcidump.load_one` ------------------------------------------ - Always loads ``core_energy``, ``one_ints``, ``nelec``, ``spinpol``, ``two_ints`` Notes ----- IOData stores four-index objects in physicists' notation internally and assumes they are stored in an FCIDUMP file in chemists' notation. :py:func:`iodata.formats.fcidump.dump_one` ------------------------------------------ - Requires ``one_ints``, ``two_ints`` - May dump ``core_energy``, ``nelec``, ``spinpol`` The dictionary ``one_ints`` must contain a field ``core_mo``. Similarly, ``two_ints`` must contain ``two_mo``. IOData stores four-index objects in physicists' notation internally and dumps them to an FCIDUMP file in chemists' notation. .. _format_gamess: GAMESS punch file format. (``gamess``) ====================================== See :py:mod:`iodata.formats.gamess` for details. Filename patterns: ``*.dat`` :py:func:`iodata.formats.gamess.load_one` ----------------------------------------- - Always loads ``title``, ``energy``, ``grot``, ``atgradient``, ``athessian``, ``atmasses``, ``atnums``, ``atcoords`` .. _format_gaussianinput: Gaussian input format. (``gaussianinput``) ========================================== See :py:mod:`iodata.formats.gaussianinput` for details. Filename patterns: ``*.com``, ``*.gjf`` :py:func:`iodata.formats.gaussianinput.load_one` ------------------------------------------------ - Always loads ``atcoords``, ``atnums``, ``title`` .. _format_gaussianlog: Gaussian Log file format. (``gaussianlog``) =========================================== See :py:mod:`iodata.formats.gaussianlog` for details. Filename patterns: ``*.log`` :py:func:`iodata.formats.gaussianlog.load_one` ---------------------------------------------- - Always loads - May load ``one_ints``, ``two_ints`` Notes ----- Note that Gaussian writes four-center integrals in chemists' notation. They will be reordered into physicists' notation when loading them with IOData. .. _format_gromacs: GROMACS gro file format. (``gromacs``) ====================================== See :py:mod:`iodata.formats.gromacs` for details. Filename patterns: ``*.gro`` :py:func:`iodata.formats.gromacs.load_one` ------------------------------------------ - Always loads ``atcoords``, ``atffparams``, ``cellvecs``, ``extra``, ``title`` :py:func:`iodata.formats.gromacs.load_many` ------------------------------------------- - Always loads ``atcoords``, ``atffparams``, ``cellvecs``, ``extra``, ``title`` .. _format_json_qcschema: QCSchema JSON file format. (``json_qcschema``) ============================================== See :py:mod:`iodata.formats.json_qcschema` for details. Filename patterns: :py:func:`iodata.formats.json_qcschema.load_one` ------------------------------------------------ - Always loads ``atnums``, ``atcorenums``, ``atcoords``, ``charge``, ``nelec``, ``spinpol`` - May load ``atmasses``, ``bonds``, ``energy``, ``g_rot``, ``lot``, ``obasis``, ``obasis_name``, ``title``, ``extra`` :py:func:`iodata.formats.json_qcschema.dump_one` ------------------------------------------------ - Requires ``atnums``, ``atcoords``, ``charge``, ``spinpol`` - May dump ``title``, ``atcorenums``, ``atmasses``, ``bonds``, ``g_rot``, ``extra`` .. _format_locpot: VASP 5 LOCPOT file format. (``locpot``) ======================================= See :py:mod:`iodata.formats.locpot` for details. Filename patterns: ``LOCPOT*`` :py:func:`iodata.formats.locpot.load_one` ----------------------------------------- - Always loads ``atcoords``, ``atnums``, ``cellvecs``, ``cube``, ``title`` .. _format_mol2: MOL2 file format. (``mol2``) ============================ See :py:mod:`iodata.formats.mol2` for details. Filename patterns: ``*.mol2`` :py:func:`iodata.formats.mol2.load_one` --------------------------------------- - Always loads ``atcoords``, ``atnums``, ``atcharges``, ``atffparams`` - May load ``title`` :py:func:`iodata.formats.mol2.dump_one` --------------------------------------- - Requires ``atcoords``, ``atnums`` - May dump ``atcharges``, ``atffparams``, ``title`` :py:func:`iodata.formats.mol2.load_many` ---------------------------------------- - Always loads ``atcoords``, ``atnums``, ``atcharges``, ``atffparams`` - May load ``title`` :py:func:`iodata.formats.mol2.dump_many` ---------------------------------------- - Requires ``atcoords``, ``atnums``, ``atcharges`` - May dump ``title`` .. _format_molden: Molden file format. (``molden``) ================================ See :py:mod:`iodata.formats.molden` for details. Filename patterns: ``*.molden.input``, ``*.molden`` :py:func:`iodata.formats.molden.load_one` ----------------------------------------- - Always loads ``atcoords``, ``atnums``, ``atcorenums``, ``mo``, ``obasis`` - May load ``title`` - Keyword arguments ``norm_threshold`` :py:func:`iodata.formats.molden.dump_one` ----------------------------------------- - Requires ``atcoords``, ``atnums``, ``mo``, ``obasis`` - May dump ``atcorenums``, ``title`` .. _format_molekel: Molekel file format. (``molekel``) ================================== See :py:mod:`iodata.formats.molekel` for details. Filename patterns: ``*.mkl`` :py:func:`iodata.formats.molekel.load_one` ------------------------------------------ - Always loads ``atcoords``, ``atnums``, ``mo``, ``obasis`` - May load ``atcharges`` - Keyword arguments ``norm_threshold`` :py:func:`iodata.formats.molekel.dump_one` ------------------------------------------ - Requires ``atcoords``, ``atnums``, ``mo``, ``obasis`` - May dump ``atcharges`` .. _format_mwfn: Multiwfn MWFN file format. (``mwfn``) ===================================== See :py:mod:`iodata.formats.mwfn` for details. Filename patterns: ``*.mwfn`` :py:func:`iodata.formats.mwfn.load_one` --------------------------------------- - Always loads ``atcoords``, ``atnums``, ``atcorenums``, ``energy``, ``mo``, ``obasis``, ``extra``, ``title`` .. _format_orcalog: Orca output file format. (``orcalog``) ====================================== See :py:mod:`iodata.formats.orcalog` for details. Filename patterns: ``*.out`` :py:func:`iodata.formats.orcalog.load_one` ------------------------------------------ - Always loads ``atcoords``, ``atnums``, ``energy``, ``moments``, ``extra`` .. _format_pdb: PDB file format. (``pdb``) ========================== See :py:mod:`iodata.formats.pdb` for details. Filename patterns: ``*.pdb`` :py:func:`iodata.formats.pdb.load_one` -------------------------------------- - Always loads ``atcoords``, ``atnums``, ``atffparams``, ``extra`` - May load ``title``, ``bonds`` :py:func:`iodata.formats.pdb.dump_one` -------------------------------------- - Requires ``atcoords``, ``atnums``, ``extra`` - May dump ``atffparams``, ``title``, ``bonds`` :py:func:`iodata.formats.pdb.load_many` --------------------------------------- - Always loads ``atcoords``, ``atnums``, ``atffparams``, ``extra`` - May load ``title`` :py:func:`iodata.formats.pdb.dump_many` --------------------------------------- - Requires ``atcoords``, ``atnums``, ``extra`` - May dump ``atffparams``, ``title`` .. _format_poscar: VASP 5 POSCAR file format. (``poscar``) ======================================= See :py:mod:`iodata.formats.poscar` for details. Filename patterns: ``POSCAR*`` :py:func:`iodata.formats.poscar.load_one` ----------------------------------------- - Always loads ``atcoords``, ``atnums``, ``cellvecs``, ``title`` :py:func:`iodata.formats.poscar.dump_one` ----------------------------------------- - Requires ``atcoords``, ``atnums``, ``cellvecs`` - May dump ``title`` .. _format_qchemlog: Q-Chem Log file format. (``qchemlog``) ====================================== See :py:mod:`iodata.formats.qchemlog` for details. Filename patterns: ``*.qchemlog`` :py:func:`iodata.formats.qchemlog.load_one` ------------------------------------------- - Always loads ``atcoords``, ``atmasses``, ``atnums``, ``energy``, ``g_rot``, ``mo``, ``lot``, ``obasis_name``, ``run_type``, ``extra`` - May load ``athessian`` .. _format_sdf: SDF file format. (``sdf``) ========================== See :py:mod:`iodata.formats.sdf` for details. Filename patterns: ``*.sdf`` :py:func:`iodata.formats.sdf.load_one` -------------------------------------- - Always loads ``atcoords``, ``atnums``, ``bonds``, ``title`` :py:func:`iodata.formats.sdf.dump_one` -------------------------------------- - Requires ``atcoords``, ``atnums`` - May dump ``title``, ``bonds`` :py:func:`iodata.formats.sdf.load_many` --------------------------------------- - Always loads ``atcoords``, ``atnums``, ``bonds``, ``title`` :py:func:`iodata.formats.sdf.dump_many` --------------------------------------- - Requires ``atcoords``, ``atnums`` - May dump ``title``, ``bonds`` .. _format_wfn: Gaussian/GAMESS-US WFN file format. (``wfn``) ============================================= See :py:mod:`iodata.formats.wfn` for details. Filename patterns: ``*.wfn`` :py:func:`iodata.formats.wfn.load_one` -------------------------------------- - Always loads ``atcoords``, ``atnums``, ``energy``, ``mo``, ``obasis``, ``title``, ``extra`` :py:func:`iodata.formats.wfn.dump_one` -------------------------------------- - Requires ``atcoords``, ``atnums``, ``mo``, ``obasis`` - May dump ``energy``, ``title``, ``extra`` .. _format_wfx: AIM/AIMAll WFX file format. (``wfx``) ===================================== See :py:mod:`iodata.formats.wfx` for details. Filename patterns: ``*.wfx`` :py:func:`iodata.formats.wfx.load_one` -------------------------------------- - Always loads ``atcoords``, ``atgradient``, ``atnums``, ``energy``, ``extra``, ``mo``, ``obasis``, ``title`` :py:func:`iodata.formats.wfx.dump_one` -------------------------------------- - Requires ``atcoords``, ``atnums``, ``atcorenums``, ``mo``, ``obasis``, ``charge`` - May dump ``title``, ``energy``, ``spinpol``, ``lot``, ``atgradient``, ``extra`` .. _format_xyz: XYZ file format. (``xyz``) ========================== See :py:mod:`iodata.formats.xyz` for details. Filename patterns: ``*.xyz`` :py:func:`iodata.formats.xyz.load_one` -------------------------------------- - Always loads ``atcoords``, ``atnums``, ``title`` - Keyword arguments ``atom_columns`` :py:func:`iodata.formats.xyz.dump_one` -------------------------------------- - Requires ``atcoords``, ``atnums`` - May dump ``title`` - Keyword arguments ``atom_columns`` :py:func:`iodata.formats.xyz.load_many` --------------------------------------- - Always loads ``atcoords``, ``atnums``, ``title`` - Keyword arguments ``atom_columns`` :py:func:`iodata.formats.xyz.dump_many` --------------------------------------- - Requires ``atcoords``, ``atnums`` - May dump ``title`` - Keyword arguments ``atom_columns``