tesliper.writing.gjf_writer

Export of Gaussian input files (.gjf) for setting up new calculation step.

Classes

GjfWriter(destination[, mode, link0, route, ...])

Generates Gaussian input files for each conformer given.
class tesliper.writing.gjf_writer.GjfWriter(destination: Union[str, pathlib.Path], mode: str = 'x', link0: Optional[Dict[str, Union[str, bool]]] = None, route: str = '', comment: str = 'No information provided.', post_spec: str = '')[source]

Generates Gaussian input files for each conformer given.

Parameters

  • destination (str or pathlib.Path) – Directory, to which generated files should be written.

  • mode (str, optional) – Specifies how writing to file should be handled. Should be one of characters: “a” (append to existing file); “x” (only write if file doesn’t exist yet); or “w” (overwrite file if it already exists). Defaults to “x”.

  • link0 (Dict[str, Union[str, bool]], optional) – Link0 commands that should be included in generated files, as a dictionary of {“command”: “value”}. Refer to link0 for more information. If omitted, no link0 commands are added.

  • route (str) – Calculation directives for Gaussan, refer to the Gaussian documentation for information on how to construct the calculations route.

  • comment (str, optional) – Additional text, describing the calculations, by default “No information provided.”

  • post_spec (str, optional) – Additional specification written after the molecule specification, written to generated files as provided by the user (you need to take care of line breaks). If omitted, no additional specification is added.

geometry(geometry: tesliper.glassware.arrays.Geometry, charge: Optional[Union[tesliper.glassware.arrays.IntegerArray, Sequence[int], int]] = None, multiplicity: Optional[Union[tesliper.glassware.arrays.IntegerArray, Sequence[int], int]] = None, name_template: Union[str, string.Template] = '${conf}.${ext}')[source]

Write given conformers’ geometries to multiple Gaussian input files.

Parameters

  • geometry (Geometry) – Geometry object containing data for each confomer that should be exported as Gaussian input file.

  • charge (Union[IntegerArray, Sequence[int], int, None], optional) – Molecule’s charge for each conformer. May be a sequence of values or one value that will be repeated for each conformer. By default 0 for each.

  • multiplicity (Union[IntegerArray, Sequence[int], int, None], optional) – Molecule’s multiplicity for each conformer. May be a sequence of values or one value that will be repeated for each conformer. By default 1 for each.

  • name_template (Union[str, Template], optional) – Template that will be used to generate filenames, by default “${conf}.${ext}”. Refer to make_name() documentation for details on supported placeholders.

_get_handle(template: Union[str, string.Template], template_params: dict, open_params: Optional[dict] = None) → Iterator[IO]

Helper method for creating files. Given additional kwargs will be passed to Path.open() method. Implemented as context manager for use with with statement.

Parameters

  • template (str or string.Template) – Template that will be used to generate filenames.

  • template_params (dict) – Dictionary of {identifier: value} for .make_name method.

  • open_params (dict, optional) – Arguments for Path.open() used to open file.

Yields

  • IO – file handle, will be closed automatically after with statement exits

  • meta public:

_iter_handles(filenames: Iterable[str], template: Union[str, string.Template], template_params: dict, open_params: Optional[dict] = None) → Iterator[IO]

Helper method for iteration over generated files. Given additional kwargs will be passed to Path.open() method.

Parameters

  • filenames (list of str) – list of source filenames, used as value for ${conf} placeholder in name_template

  • template_params (dict) – Dictionary of {identifier: value} for .make_name method.

  • open_params (dict, optional) – arguments for Path.open() used to open file.

Yields

  • TextIO – file handle, will be closed automatically on next iteration

  • meta public:

property destination: pathlib.Path

Directory, to which generated files should be written.

Raises

FileNotFoundError – If given destination doesn’t exist or is not a directory.

Type

pathlib.Path

static distribute_data(data: List) → Tuple[Dict[str, List], Dict[str, Any]]

Sorts given data by genre category for use by specialized writing methods.

Returns

  • distr (dict) – Dictionary with DataArray-like objects, sorted by their type. Each {key: value} pair is {name of the type in lowercase format: list of DataArray objects of this type}.

  • extras (dict) – Spacial-case genres: extra information used by some writer methods when exporting data. Available {key: value} pairs (if given in data) are:

    corrections: dict of {“energy genre”: FloatArray},
    frequencies: Bands,
    wavelengths: Bands,
    excitation: Bands,
    stoichiometry: InfoArray,
    charge: IntegerArray,
    multiplicity: IntegerArray

energies(energies: tesliper.glassware.arrays.Energies, corrections: Optional[tesliper.glassware.arrays.FloatArray] = None, name_template: Union[str, string.Template] = '')

Interface for writing energies values, and optionally their corrections. Evoked when handling Energies objects.

Parameters

  • energies – Conformers’ energies. Mandatory in custom implementation.

  • corrections – Correction of energies values. Mandatory in custom implementation. May be None when method evoked by handler.

  • name_template – Template that defines naming scheme for files generated by this method. May be omitted in custom implementation.

Raises

NotImplementedError – Whenever called, this is an interface that should not be used directly.

generic(data: List[Union[tesliper.glassware.arrays.DataArray, tesliper.glassware.arrays.IntegerArray, tesliper.glassware.arrays.FloatArray, tesliper.glassware.arrays.BooleanArray, tesliper.glassware.arrays.InfoArray]], name_template: Union[str, string.Template] = '')

Interface for writing generic data: any that provides one value for each conformer. Evoked when handling DataArray, IntegerArray, FloatArray, BooleanArray, or InfoArray.

Parameters

data – List of objects that provide one value for each conformer.

Raises

NotImplementedError – Whenever called, this is an interface that should not be used directly.

make_name(template: Union[str, string.Template], conf: str = '', num: Union[str, int] = '', genre: str = '', cat: str = '', det: str = '', ext: str = '') → str

Create filename using given template and given or global values for known identifiers. The identifier should be used in the template as "${identifier}" where “identifier” is the name of identifier. Available names and their meaning are:

${ext} - appropriate file extension
${conf} - name of the conformer
${num} - number of the file according to internal counter
${genre} - genre of exported data
${cat} - category of produced output
${det} - category-specific detail

The ${ext} identifier is filled with the value of Writers extension attribute if not explicitly given as parameter to this method’s call. Values for other identifiers should be provided by the caller.

Parameters

  • template (str or string.Template) – Template that will be used to generate filenames. It should contain only known identifiers, listed above.

  • conf (str) – value for ${conf} identifier, defaults to empty string.

  • num (str or int) – value for ${str} identifier, defaults to empty string.

  • genre (str) – value for ${genre} identifier, defaults to empty string.

  • cat (str) – value for ${cat} identifier, defaults to empty string.

  • det (str) – value for ${det} identifier, defaults to empty string.

  • ext (str) – value for ${ext} identifier, defaults to empty string.

Raises

ValueError – If given template or string contains any unexpected identifiers.

Examples

Must be first subclassed and instantiated:

>>> class MyWriter(WriterBase):
>>>     extension = "foo"
>>> wrt = MyWriter("/path/to/some/directory/")

>>> wrt.make_name(template="somefile.${ext}")
"somefile.foo"
>>> wrt.make_name(template="${conf}.${ext}")
".foo"  # conf is empty string by default
>>> wrt.make_name(template="${conf}.${ext}", conf="conformer")
"conformer.foo"
>>> wrt.make_name(template="Unknown_identifier_${bla}.${ext}")
Traceback (most recent call last):
ValueError: Unexpected identifiers given: bla.
property mode

Specifies how writing to file should be handled. Should be one of characters: “a”, “x”, or “w”. “a” - append to existing file; “x” - only write if file doesn’t exist yet; “w” - overwrite file if it already exists.

Raises

ValueError – If given anything other than “a”, “x”, or “w”.

overview(energies: Sequence[tesliper.glassware.arrays.Energies], frequencies: Optional[tesliper.glassware.arrays.Bands] = None, stoichiometry: Optional[tesliper.glassware.arrays.InfoArray] = None, name_template: Union[str, string.Template] = '')

Intercafe for generating an overview of known conformers: values of energies, number of imaginary frequencies, and stoichiometry for each conformer. Evoked when handling Energies objects.

Parameters

  • energies – List of objects representing different energies genres for each conformer. Mandatory in custom implementation.

  • frequencies – Bands of “freq” genre, with list of frequencies for each conformer. Mandatory in custom implementation. May be None when method evoked by handler.

  • stoichiometry – Stoichiometry of each conformer. Mandatory in custom implementation. May be None when method evoked by handler.

  • name_template – Template that defines naming scheme for files generated by this method. May be omitted in custom implementation.

Raises

NotImplementedError – Whenever called, this is an interface that should not be used directly.

single_spectrum(spectrum: tesliper.glassware.spectra.SingleSpectrum, name_template: Union[str, string.Template] = '')

Interface for writing a single spectrum to disk: calculated for one conformer or averaged. Evoked when handling SingleSpectrum objects.

Parameters

  • spectrum – Single calculated spectrum. Mandatory in custom implementation.

  • name_template – Template that defines naming scheme for files generated by this method. May be omitted in custom implementation.

Raises

NotImplementedError – Whenever called, this is an interface that should not be used directly.

spectra(spectra: tesliper.glassware.spectra.Spectra, name_template: Union[str, string.Template] = '')

Interface for writing a set of spectra of one type calculated for many conformers. Evoked when handling Spectra objects.

Parameters

  • spectra – Spectra of one type calculated for multiple conformers. Mandatory in custom implementation.

  • name_template – Template that defines naming scheme for files generated by this method. May be omitted in custom implementation.

Raises

NotImplementedError – Whenever called, this is an interface that should not be used directly.

spectral_activities(band: tesliper.glassware.arrays.Bands, data: List[tesliper.glassware.arrays.SpectralActivities], name_template: Union[str, string.Template] = '')

Interface for writing multiple objects with spectral activities (data that may be converted to signal intensity). Evoked when handling one of the: VibrationalActivities, ElectronicActivities, ScatteringActivities objects.

Parameters

  • band – Band at which transitions occur for each conformer. Mandatory in custom implementation.

  • data – List of objects representing different spectral activities genres. Mandatory in custom implementation.

  • name_template – Template that defines naming scheme for files generated by this method. May be omitted in custom implementation.

Raises

NotImplementedError – Whenever called, this is an interface that should not be used directly.

spectral_data(band: tesliper.glassware.arrays.Bands, data: List[tesliper.glassware.arrays.SpectralData], name_template: Union[str, string.Template] = '')

Interface for writing multiple objects with spectral data that is not a spectral activity (cannot be converted to signal intensity). Evoked when handling one of the: VibrationalData, ElectronicData, ScatteringData objects.

Parameters

  • band – Band at which transitions occur for each conformer. Mandatory in custom implementation.

  • data – List of objects representing different spectral data genres (but not spectral activities). Mandatory in custom implementation.

  • name_template – Template that defines naming scheme for files generated by this method. May be omitted in custom implementation.

Raises

NotImplementedError – Whenever called, this is an interface that should not be used directly.

transitions(transitions: tesliper.glassware.arrays.Transitions, wavelengths: tesliper.glassware.arrays.Bands, only_highest: bool = True, name_template: Union[str, string.Template] = '')

Interface for writing single object with electronic transitions data. Evoked when handling Transitions objects.

Parameters

  • transitions – List of objects representing different spectral data genres (but not spectral_activities). Mandatory in custom implementation.

  • wavelengths – Wavelengths at which transitions occur for each conformer. Mandatory in custom implementation.

  • only_highest – Boolean flag indicating if all transitions should be written to disk or only these transition that contributes the most for each wavelength/ May be omitted in custom implementation.

  • name_template – Template that defines naming scheme for files generated by this method. May be omitted in custom implementation.

Raises

NotImplementedError – Whenever called, this is an interface that should not be used directly.

write(data: List) → None

Writes DataArray-like objects to disk, decides how to write them based on the type of each object. If some types of given objects are not supported by this writer, data of this type is ignored and a warning is emitted.

Parameters

data (List) – DataArray-like objects that should be written to disk.

property link0: Dict[str, Union[str, bool]]

Link0 commands, in a form of {"command": "value"}, that will be placed in the beginning of each Gaussian input file created. If anny command is an unknown keword, an exception will be raised. Accepted command keywords are as follows:

Mem

str specifying required memory

Chk

str with file path

OldChk

str with file path

SChk

str with file path

RWF

str with file path

OldMatrix

str with file path

OldRawMatrix

str with file path

Int

str with spec

D2E

str with spec

KJob

str with link number and, optionally, space-separated number

Save

boolean

ErrorSave

boolean

NoSave

boolean, same as ErrorSave

Subst

str with link number and space-separated file path

Commands that provide a file path as a value may be parametrized for each conformer. You can put a placeholder inside a given string path, that will be parametrized when writing to file. See make_name() to see available placeholders. You may use any of values listed there, however ${conf} and ${num} will probably be the most useful.

property route: str

Also known as # lines, specifies desired calculation type, model chemistry, and other options for Gaussian. If pound sign is missing, it is added in the beginning. For supported keywords and syntax refer to the Gaussian’s documentation.