Supported File Formats¶

CHARMM crd file format (`charmm`)¶

CHARMM coordinate files contain information about the location of each atom in Cartesian space. The format of the ASCII (CARD) CHARMM coordinate files is: Title line(s), number of atoms in file and the coordinate lines (one for each atom in the file).

The coordinate lines contain specific information about each atom. These have the following structure: Atom number (sequential), residue number (specified relative to first residue in the PSF), residue name, atom type, x-coordinate, y-coordinate, z-coordinate, segment identifier, residue identifier and a weighting array value.

Filename patterns: *.crd

`iodata.formats.charmm.load_one()`¶

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

VASP 5 CHGCAR file format (`chgcar`)¶

This format is used by VASP 5.X and VESTA.

Note that even though the CHGCAR and LOCPOT files look very similar, they require different conversions to atomic units.

Filename patterns: CHGCAR*, AECCAR*

`iodata.formats.chgcar.load_one()`¶

Always loads atcoords, atnums, cellvecs, cube, title

CP2K ATOM output file format (`cp2klog`)¶

Filename patterns: *.cp2k.out

`iodata.formats.cp2klog.load_one()`¶

Always loads atcoords, atcorenums, atnums, energy, mo, obasis

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`)¶

Cube files are generated by various QC codes these days, including Gaussian, CP2K, GPAW, Q-Chem, …

Note that the second column in the geometry specification of the cube file is interpreted as the effective core charges.

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`)¶

The extended XYZ file format is defined in the ASE documentation.

Usually, the different frames in a trajectory describe different geometries of the same molecule, with atoms in the same order. The load_many function below can also handle an XYZ with different molecules, e.g. a molecular database.

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`)¶

Filename patterns: *.fchk, *.fch

`iodata.formats.fchk.load_one()`¶

Always loads atcharges, atcoords, atnums, atcorenums, energy, lot, mo, obasis, obasis_name, run_type, title
May load 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

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`)¶

Notes¶

This function works only for restricted wave-functions.
One- and two-electron integrals are stored in chemists’ notation in an FCIDUMP file, while IOData internally uses Physicist’s notation.
Keep in mind that the FCIDUMP format changed in MOLPRO 2012, so files generated with older versions are not supported.

Filename patterns: *FCIDUMP*

`iodata.formats.fcidump.load_one()`¶

Always loads core_energy, one_ints, nelec, spinpol, two_ints

`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.

GAMESS punch file format (`gamess`)¶

Filename patterns: *.dat

`iodata.formats.gamess.load_one()`¶

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

Gaussian Log file format (`gaussianlog`)¶

To write out the integrals in a Gaussian log file, which can be loaded with this module, you need to use the following Gaussian command line:

scf(conventional) iop(3/33=5) extralinks=l316 iop(3/27=999)

Filename patterns: *.log

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

Always loads
May load one_ints, two_ints

GROMACS gro file format (`gromacs`)¶

Files with the gro file extension contain a molecular structure in Gromos87 format. GROMACS gro files can be used as trajectory by simply concatenating files.

http://manual.gromacs.org/current/reference-manual/file-formats.html#gro

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

VASP 5 LOCPOT file format (`locpot`)¶

This format is used by VASP 5.X and VESTA.

Note that even though the CHGCAR and LOCPOT files look very similar, they require different conversions to atomic units.

Filename patterns: LOCPOT*

`iodata.formats.locpot.load_one()`¶

Always loads atcoords, atnums, cellvecs, cube, title

MOL2 file format (`mol2`)¶

There are different formats of mol2 files. Here the compatibility with AMBER software was the main objective to write out files with atomic charges used by antechamber.

Filename patterns: *.mol2

`iodata.formats.mol2.load_one()`¶

Always loads atcoords, atnums, atcharges, atffparams
May load title

`iodata.formats.mol2.dump_one()`¶

Requires atcoords, atnums
May dump atcharges, atffparams, title

`iodata.formats.mol2.load_many()`¶

Always loads atcoords, atnums, atcharges, atffparams
May load title

`iodata.formats.mol2.dump_many()`¶

Requires atcoords, atnums, atcharges
May dump title

Molden file format (`molden`)¶

Many QC codes can write out Molden files, e.g. Molpro, Orca, PSI4, Molden, Turbomole. Keep in mind that several of these write incorrect versions of the file format, but these errors are corrected when loading them with IOData.

Filename patterns: *.molden.input, *.molden

`iodata.formats.molden.load_one()`¶

Always loads atcoords, atnums, atcorenums, mo, obasis
May load title

`iodata.formats.molden.dump_one()`¶

Requires atcoords, atnums, mo, obasis
May dump atcorenums, title

Molekel file format (`molekel`)¶

This format is used by two programs: Molekel and Orca.

Filename patterns: *.mkl

`iodata.formats.molekel.load_one()`¶

Always loads atcoords, atnums, mo, obasis
May load atcharges

`iodata.formats.molekel.dump_one()`¶

Requires atcoords, atnums, mo, obasis
May dump atcharges

Orca output file format (`orcalog`)¶

Filename patterns: *.out

`iodata.formats.orcalog.load_one()`¶

Always loads atcoords, atnums, energy, moments, extra

PDB file format (`pdb`)¶

There are different formats of pdb files. The convention used here is the last updated one and is described in this link: http://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html

Filename patterns: *.pdb

`iodata.formats.pdb.load_one()`¶

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

`iodata.formats.pdb.dump_one()`¶

Requires atcoords, atnums, extra
May dump atffparams, title

`iodata.formats.pdb.load_many()`¶

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

`iodata.formats.pdb.dump_many()`¶

Requires atcoords, atnums, extra
May dump atffparams, title

VASP 5 POSCAR file format (`poscar`)¶

This format is used by VASP 5.X and VESTA.

Filename patterns: POSCAR*

`iodata.formats.poscar.load_one()`¶

Always loads atcoords, atnums, cellvecs, title

`iodata.formats.poscar.dump_one()`¶

Requires atcoords, atnums, cellvecs
May dump title

Q-Chem Log file format (`qchemlog`)¶

This module will load Q-Chem log file into IODATA.

Filename patterns: *.qchemlog

`iodata.formats.qchemlog.load_one()`¶

Always loads atcoords, atmasses, atnums, energy, g_rot, mo, lot, obasis_name, run_type, extra
May load athessian

SDF file format (`sdf`)¶

Usually, the different frames in a trajectory describe different geometries of the same molecule, with atoms in the same order. The load_many and dump_many functions below can also handle an SDF file with different molecules, e.g. a molecular database.

Filename patterns: *.sdf

`iodata.formats.sdf.load_one()`¶

Always loads atcoords, atnums, title

`iodata.formats.sdf.dump_one()`¶

Requires atcoords, atnums
May dump title

`iodata.formats.sdf.load_many()`¶

Always loads atcoords, atnums, title

`iodata.formats.sdf.dump_many()`¶

Requires atcoords, atnums
May dump title

Gaussian/GAMESS-US WFN file format (`wfn`)¶

Only use this format if the program that generated it does not offer any alternatives that HORTON can load. The WFN format has the disadvantage that it cannot represent contractions and therefore expands all orbitals into a decontracted basis. This makes the post-processing less efficient compared to formats that do support contractions of Gaussian functions.

Filename patterns: *.wfn

`iodata.formats.wfn.load_one()`¶

Always loads atcoords, atnums, energy, mo, obasis, title, extra

`iodata.formats.wfn.dump_one()`¶

Requires atcoords, atnums, energy, mo, obasis, title, extra

AIM/AIMAll WFX file format (`wfx`)¶

See http://aim.tkgristmill.com/wfxformat.html

Filename patterns: *.wfx

`iodata.formats.wfx.load_one()`¶

Always loads atcoords, atgradient, atnums, energy, extra, mo, obasis, title

`iodata.formats.wfx.dump_one()`¶

Requires atcoords, atnums, atcorenums, mo, obasis, charge
May dump title, energy, spinpol, lot, atgradient, extra

XYZ file format (`xyz`)¶

Usually, the different frames in a trajectory describe different geometries of the same molecule, with atoms in the same order. The load_many and dump_many functions below can also handle an XYZ with different molecules, e.g. a molecular database.

The load_* and dump_* functions all accept the optional argument atom_columns. This argument fixes the meaning of the columns to be loaded from or dumped to an XYZ file. The following example defines, in addition to the conventional columns, also a column with atomic charges and three columns with atomic forces.

atom_columns = iodata.formats.xyz.DEFAULT_ATOM_COLUMNS + [
    # Atomic charges are stored in a dictionary atcharges and they key
    # refers to the name of the partitioning method.
    ("atcharges", "mulliken", (), float, float, "{:10.5f}".format),
    # Note that in IOData, the energy gradient is stored, which contains the
    # negative forces.
    ("atgradient", None, (3,), float,
     (lambda word: -float(word)),
     (lambda value: "{:15.10f}".format(-value)))
]

mol = load_one("test.xyz", atom_columns=atom_columns)
# The following attributes are present:
print(mol.atnums)
print(mol.atcoords)
print(mol.atcharges["mulliken"])
print(mol.atgradient)

When defining atom_columns, no columns can be skipped, such that all information loaded from a file can also be written back out when dumping it.

Filename patterns: *.xyz

`iodata.formats.xyz.load_one()`¶

Always loads atcoords, atnums, title
Keyword arguments atom_columns

`iodata.formats.xyz.dump_one()`¶

Requires atcoords, atnums
May dump title
Keyword arguments atom_columns

`iodata.formats.xyz.load_many()`¶

Always loads atcoords, atnums, title
Keyword arguments atom_columns

`iodata.formats.xyz.dump_many()`¶

Requires atcoords, atnums
May dump title
Keyword arguments atom_columns

Supported File Formats¶

CHARMM crd file format (charmm)¶

VASP 5 CHGCAR file format (chgcar)¶

CP2K ATOM output file format (cp2klog)¶

Gaussian Cube file format (cube)¶

Extended XYZ file format (extxyz)¶

Gaussian FCHK file format (fchk)¶

Molpro 2012 FCIDUMP file format (fcidump)¶

Notes¶

GAMESS punch file format (gamess)¶

Gaussian Log file format (gaussianlog)¶

GROMACS gro file format (gromacs)¶

VASP 5 LOCPOT file format (locpot)¶

MOL2 file format (mol2)¶

Molden file format (molden)¶

Molekel file format (molekel)¶

Orca output file format (orcalog)¶

PDB file format (pdb)¶

VASP 5 POSCAR file format (poscar)¶

Q-Chem Log file format (qchemlog)¶

SDF file format (sdf)¶

Gaussian/GAMESS-US WFN file format (wfn)¶

AIM/AIMAll WFX file format (wfx)¶

XYZ file format (xyz)¶

CHARMM crd file format (`charmm`)¶

VASP 5 CHGCAR file format (`chgcar`)¶

CP2K ATOM output file format (`cp2klog`)¶

Gaussian Cube file format (`cube`)¶

Extended XYZ file format (`extxyz`)¶

Gaussian FCHK file format (`fchk`)¶

Molpro 2012 FCIDUMP file format (`fcidump`)¶

GAMESS punch file format (`gamess`)¶

Gaussian Log file format (`gaussianlog`)¶

GROMACS gro file format (`gromacs`)¶

VASP 5 LOCPOT file format (`locpot`)¶

MOL2 file format (`mol2`)¶

Molden file format (`molden`)¶

Molekel file format (`molekel`)¶

Orca output file format (`orcalog`)¶

PDB file format (`pdb`)¶

VASP 5 POSCAR file format (`poscar`)¶

Q-Chem Log file format (`qchemlog`)¶

SDF file format (`sdf`)¶

Gaussian/GAMESS-US WFN file format (`wfn`)¶

AIM/AIMAll WFX file format (`wfx`)¶

XYZ file format (`xyz`)¶