Chemistry files (qcip_tools.chemistry_files)

Read/write files commonly used in quantum chemistry.

Concepts

Human readable text files are widely used in the field of quantum chemistry, but there is large syntaxic differences from one to another (when there IS a syntax). This is especially true for input files, which follows rigorous syntax, while output files are more or less incoherent. This module implement access to different formats.

All classes derive from ChemistryFile. You need to override the read() method to read from a file.

Thanks to the dispatcher pattern, derivation from this class allow to define taylor-made accessors: use the @Class.define_property(property_name) decorator to give the ability to use this callback function with property(property_name[, optional kwargs ...]). Callbacks should have the form callback_func(obj, **kwargs), where obj is the current object. In the code, those callbacks have the form property__*(obj, **kwargs). One can check if a property is available with has_property() (which does not mean that the file actually contains this property, but that it can be carry out).

There is some mixins and derived classes to add functionnalities:

• WithMoleculeMixin adds self.molecule, which is accessible trough get_molecule(). It also provides a Class.from_molecule(molecule, *args, **kwargs) class method to ease creation of a file from scratch (if defined in subclass).

• WithIdentificationMixin adds Class.possible_file_extensions() and Class.attempt_identification() to allow file recognition by helpers.

  • possible_file_extensions() helps to avoid some possibilities if the extension is trusted. The helper expects a list of possible extentions (without the dot).

  • attempt_identification() actually make the recognition of the file: given f (the file open in read mode), the helper function expects True or False if it is a file corresponding to a given objects. This recognition is usually based on patterns or words (like the name of the program) that frequently appears.

• WithOutputMixin, which gives the ability to write() in a new file. Note that it is easier to override to_string() in this case.

• ChemistryLogFile (derived class) keeps the whole file in memory (in self.lines) and allow to divide the file in chunks to ease their manipulation. The chunk_exists() function check if a given chunk is present in the file. The mixins defines a apply_function() method to apply a given function (with apply_over_list(), see here) to the lines (to carry out information for example). Based on that, it also defines a search() function, which returns the line where the information was found.

Note

If one would like to construct the chemistry files from scratch (without using read() on an existing file) or get additional information from it, the different class members are given in the documentation. Also check if from_molecule() is defined.

API documentation

• Base (chemistry_files)
  • ChemistryFile
  • ChemistryLogFile
  • FormatError
  • PropertyNotDefined
  • PropertyNotPresent
  • WithIdentificationMixin
  • WithMoleculeMixin
  • WithOutputMixin
  • apply_over_list()
  • chemistry_file__property__file_type()
  • chemistry_file__property__molecule()
• Helpers (chemistry_files.helpers)
  • ProbablyNotAChemistryFile
  • create_open_chemistry_file_action()
  • identifiable_chemistry_file_objects()
  • open_chemistry_file()
• XYZ files (chemistry_files.xyz)
  • File
  • XYZFormatError
• PDB files (chemistry_files.pdb)
  • File
• Gaussian files (chemistry_files.gaussian)
  • BasisSet
  • BasisSetFormatError
  • ChargeTransferInformation
  • Cube
  • CubeFormatError
  • FCHK
  • FCHKChunkInformation
  • FCHKFormatError
  • Input
  • InputFormatError
  • LinkCalled
  • Output
  • OutputFormatError
  • beta_EOP_from_fchk()
  • beta_SHG_from_fchk()
  • gamma_from_gaussian()
  • gaussian__fchk__property__computed_energies()
  • gaussian__fchk__property__electrical_derivatives()
  • gaussian__fchk__property__excitations()
  • gaussian__fchk__property__geometrical_derivatives()
  • gaussian__output__get_computed_energies()
  • gaussian__output__property__electrical_derivatives()
  • gaussian__output__property__excitations()
  • make_cartesian_hessian_from_fchk()
• Dalton files (chemistry_files.dalton)
  • ALLOWED_LEVEL_0_MODULES
  • ArchiveOutput
  • Input
  • InputCard
  • InputFormatError
  • InputModule
  • InputModuleError
  • MoleculeInput
  • Output
  • OutputFormatError
  • OutputSection
  • WrongNumberOfData
  • check_module()
  • dalton__archive_output__property__computed_energies()
  • dalton__archive_output__property__electrical_derivatives()
  • dalton__archive_output__property__excitations()
  • dalton__archive_output__property__geometrical_derivatives()
  • dalton__output__computed_energies()
  • dalton__output__get_geometrical_derivatives()
• GAMESS files (chemistry_files.gamess)
  • Input
  • InputFormatError
  • InputModule
  • Output
  • OutputFormatError
  • OutputStep
  • gamess__log__property__computed_energies()
  • gamess__log__property__geometrical_derivatives()
• CRYSTAL17 files (chemistry_files.crystal)
  • Output
  • crystal__output__property__electrical_derivatives()
• Chemistry data files (chemistry_files.chemistry_datafile)
  • BadChemistryDataFile
  • ChemistryDataFile
  • chemistry_datafile__property__electrical_derivatives()
  • chemistry_datafile__property__geometrical_derivatives()
• Tensor in CSV format (chemistry_files.csv_tensor)
  • CSVTensor
  • csvtensor__property__electrical_derivatives()
  • csvtensor__property__excitations()
  • csvtensor__property__geometrical_derivatives()

More precisely,

Class	Description	Identifier	Input	Ouput
xyz.File	XYZ file (.xyz)	XYZ	Yes	Yes
gaussian.BasisSet	Gaussian basis set (.gbs ?)	GAUSSIAN_BS	Yes	Yes
gaussian.Cube	Gaussian Cube file (.cub)	GAUSSIAN_CUBE	Yes	Yes
gaussian.FCHK	Gaussian formated checkpoint file (.fchk)	GAUSSIAN_FCHK	Yes	No
gaussian.Input	Gaussian input file (.com, .gau or .inp)	GAUSSIAN_INP	Yes	Yes
gaussian.Output	Gaussian output (.log or .out)	GAUSSIAN_LOG	Yes	No
dalton.ArchiveOutput	Dalton archive (.tar.gz)	DALTON_ARCHIVE	Yes	No
dalton.Input	Dalton input file (.dal)	DALTON_DAL	Yes	Yes
dalton.MoleculeInput	Dalton molecule file (.mol)	DALTON_MOL	Yes	Yes
dalton.Output	Dalton output file (.out)	DALTON_LOG	Yes	No
gamess.Input	GAMESS input (.inp)	GAMESS_INP	Yes	Yes
gamess.Output	GAMESS output (.log or .out)	GAMESS_LOG	Yes	No
chemistry_datafile.ChemistryDataFile	QCIP chemistry data file (.h5)	QCIP_CDF	Yes	Yes