Supported File Formats¶

CHARMM crd file format. (`charmm`)¶

See iodata.formats.charmm for details.

Filename patterns: *.crd

`iodata.formats.charmm.load_one()`¶

Always loads atcoords, atffparams, atmasses, extra
May load title

VASP 5 CHGCAR file format. (`chgcar`)¶

See iodata.formats.chgcar for details.

Filename patterns: CHGCAR*, AECCAR*

`iodata.formats.chgcar.load_one()`¶

Always loads atcoords, atnums, cellvecs, cube, title

CP2K ATOM output file format. (`cp2klog`)¶

See iodata.formats.cp2klog for details.

Filename patterns: *.cp2k.out

`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:

&PRINT
  &POTENTIAL
  &END POTENTIAL
  &BASIS_SET
  &END BASIS_SET
  &ORBITALS
  &END ORBITALS
&END PRINT

Gaussian Cube file format. (`cube`)¶

See iodata.formats.cube for details.

Filename patterns: *.cube, *.cub

`iodata.formats.cube.load_one()`¶

Always loads atcoords, atcorenums, atnums, cellvecs, cube

`iodata.formats.cube.dump_one()`¶

Requires atcoords, atnums, cube
May dump title, atcorenums

Extended XYZ file format. (`extxyz`)¶

See iodata.formats.extxyz for details.

Filename patterns: *.extxyz

`iodata.formats.extxyz.load_one()`¶

Always loads title
May load atcoords, atgradient, atmasses, atnums, cellvecs, charge, energy, extra

`iodata.formats.extxyz.load_many()`¶

Always loads title
May load atcoords, atgradient, atmasses, atnums, cellvecs, charge, energy, extra

Gaussian FCHK file format. (`fchk`)¶

See iodata.formats.fchk for details.

Filename patterns: *.fchk, *.fch

`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

`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

`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.

Molpro 2012 FCIDUMP file format. (`fcidump`)¶

See iodata.formats.fcidump for details.

Filename patterns: *FCIDUMP*, *.fcidump

`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.

`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.

GAMESS punch file format. (`gamess`)¶

See iodata.formats.gamess for details.

Filename patterns: *.dat

`iodata.formats.gamess.load_one()`¶

Always loads title, energy, grot, atgradient, athessian, atmasses, atnums, atcoords

Gaussian input format. (`gaussianinput`)¶

See iodata.formats.gaussianinput for details.

Filename patterns: *.com, *.gjf

`iodata.formats.gaussianinput.load_one()`¶

Always loads atcoords, atnums, title

Gaussian Log file format. (`gaussianlog`)¶

See iodata.formats.gaussianlog for details.

Filename patterns: *.log

`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.

GROMACS gro file format. (`gromacs`)¶

See iodata.formats.gromacs for details.

Filename patterns: *.gro

`iodata.formats.gromacs.load_one()`¶

Always loads atcoords, atffparams, cellvecs, extra, title

`iodata.formats.gromacs.load_many()`¶

Always loads atcoords, atffparams, cellvecs, extra, title

QCSchema JSON file format. (`json_qcschema`)¶

See iodata.formats.json_qcschema for details.

Filename patterns:

`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