iodata.formats.fchk module

Gaussian FCHK file format.

dump_one(f, data)[source]

Dump a single frame into a Gaussian Formatted Checkpoint file.

Parameters:

  • f (TextIO) – A writeable file object.

  • data (IOData) – An IOData instance which must have the following attributes initialized: atnums, atcorenums. If the following attributes are present, they are also dumped into the file: atcharges, atcoords, atfrozen, atgradient, athessian, atmasses, charge, energy, lot, mo, one_rdms, obasis_name, extra, moments.

Notes

load_many(lit)[source]

Load multiple frames from a XYZ file.

Parameters:

lit (LineIterator) – The line iterator to read the data from.

Yields:

result (dict) – A dictionary with IOData attributes. The following attribtues are guaranteed to be loaded: atcoords, atgradient, atnums, atcorenums, energy, extra, title.

Return type:

Iterator[dict]

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.

load_one(lit)[source]

Load a single frame from a Gaussian Formatted Checkpoint file.

Parameters:

lit (LineIterator) – The line iterator to read the data from.

Return type:

dict

Returns:

result (dict) – A dictionary with IOData attributes. The following attributes are guaranteed to be loaded: atcharges, atcoords, atnums, atcorenums, lot, mo, obasis, obasis_name, run_type, title. The following may be loaded if present in the file: energy, atfrozen, atgradient, athessian, atmasses, one_rdms, extra, moments.

prepare_dump(data, allow_changes, filename)[source]

Check the compatibility of the IOData object with the FCHK format.

Parameters:

  • data (IOData) – The IOData instance to be checked.

  • allow_changes (bool) – Whether conversion of the IOData object to a compatible form is allowed or not. (not relevant for FCHK, present for API consistency)

  • filename (str) – The file to be written to, only used for error messages.

Return type:

IOData

Returns:

data – The given IOData object.

Raises:

PrepareDumpError – If the given IOData instance is not compatible with the WFN format.