- (:pr:`118`) Model string representations should be more user friendly and descriptive without overload the output.
- (:pr:`119`) The
molparse.to_stringkeyword-argreturn_datanow returns molecule keywords for GAMESS and NWChem. Themodels.Molecule.to_stringcan usereturn_datanow, too. - (:pr:`120`) Auto documentation tech is now built into the
ProtoModeland does not need an external function.
- (:pr:`114`) The Numpy einsum calls reference the top level functions and not core C functions. This fixes an issue which can result in NumPy version dependencies.
- (:pr:`85`, :pr:`87`) Msgpack is a new serialization option for Models. Serialization defaults to msgpack when
available (
conda install msgpack-python [-c conda-forge]), falling back to JSON otherwise. This results in substantial speedups for both serialization and deserialization actions and should be a transparent replacement for users within Elemental itself.
- (:pr:`78`) Molecular alignments can now be aligned on the derivatives of vector components.
- (:pr:`81`) Testing is now operated both on the minimal supported and the latest released versions of dependencies.
- (:pr:`82`) Molecule fragment grouping is now disabled by default to match expected behavior.
- (:pr:`84`) Testing without internet connection should now pass since PubChem testing is skipped with no connection.
- (:pr:`85`) Molecule switches from lists to numpy arrays for internal storage of per-atom fields.
- (:pr:`86`) Molecule performance and memory enhancements through reduced validation times and LRU caching of common validations.
- (:pr:`88`, :pr:`109`) The
MoleculeModel now has its attributes documented and in an on-the-fly manner derived from the Pydantic Schema of those attributes. - (:pr:`99`, :pr:`100`, :pr:`101`, :pr:`102`, :pr:`103`, :pr:`104`, :pr:`105`, :pr:`106`, :pr:`107`) Various documentation, type hints, and small changes.
- (:pr:`87`) Molecule objects built from Schema are run through validators for consistency.
- (:pr:`76`) Adds a built-in
Molecule.to_filefunction for easy serialization into.numpy,.json,.xyz,.psimol, and.psi4file formats.
- (:pr:`74`) Atom and fragment ordering are preserved when invoking
get_fragment.
- (:pr:`68`)
molparse.to_stringlearned parameterreturn_datathat contains aspects of themodels.Moleculenot expressible in the string. Implemented for dtypes xyz, cfour, psi4. - (:pr:`68`)
Datumgained an attributenumericthat reflects whether arithmetic ondatais valid.Datums that aren't numeric can now be created by initializing withnumeric=False.
- (:pr:`66`) Fix tests when networkx not installed.
- (:pr:`67`) Fix "unsupported format string passed to numpy.ndarray.__format__" on Mac for
testing.compare_values.
- (:pr:`51`) Changes
models.Moleculeconnectivity to default to None rather than an empty list. WARNING this change alters the hashes produced from theMolecule.get_hashfunctionality. - (:pr:`52`, :pr:`53`)
models.Moleculelearnednuclear_repulsion_energy,nelectrons, andto_stringfunctions. - (:pr:`54`)
models.ResultPropertiessupports CCSD and CCSD(T) properties. - (:pr:`56`) Algorithms Kabsch
molutil.kabsch_align, Hungarianutil.linear_sum_assignment, and Unoutil.unoadded. Utilities to generate random 3D rotationsutil.random_rotation_matrixand reindex a NumPy array into smaller blocksutil.blockwise_expandadded. - (:pr:`56`) Molecular alignment taking into account displacement, rotation, atom exchange, and mirror symmetry for
superimposable and differing geometries was added in
molutil.B787(basis NumPy function) andmodels.Molecule.align(far more convenient). Suitable for QM-sized molecules. Requires addition packagenetworkx. - (:pr:`58`)
utilslearnedwhich_importandwhichthat provide a path or boolean result for locating modules or commands, respectively. These were migrated from QCEngine along withsafe_versionandparse_versionto colocate the import utilities. - (:pr:`61`) Add molecular visualization to the
models.Moleculeobject through the optional 3dMol.js framework. - (:pr:`65`)
testing.compare_molrecslearned parameterrelative_geoms='align'that lets Molecules pass if geometries within a translation and rotation of each other. - (:pr:`65`)
testing.compare_recursivelearned parameterforgivethat is a list of paths that may differ without failing the comparison.
- (:pr:`52`, :pr:`53`)
molparse.to_stringNWChem and GAMESS dtypes developed. - (:pr:`57`)
molparse.to_stringlearneddtype='terachem'for writing the separate XYZ file required by TeraChem. Angstroms or Bohr allowed, though the latter requires extra in input file. - (:pr:`60`)
util.whichadded the Python interpreter path to the default search$PATH. - (:pr:`62`) Added
*to parameter list of many functions requiring subsequent to be keyword only. Code relying heavily on positional arguments may get broken. - (:pr:`63`)
util.whichlearned parameterenvto use an alternate search$PATH. - (:pr:`63`)
util.whichandutil.which_importlearned parametersraise_errorandraise_msgwhich raisesModuleNotFoundError(for both functions) when not located. It error will have a generic error message which can be extended byraise_msg. It is strongly encouraged to add specific remedies (like how to install) through this parameter. This is the third exit pattern possible from the "which" functions, of which path/None is the default, True/error happens whenraise_error=True, and True/False happens otherwise whenreturn_bool=True. - (:pr:`65`) Testing functions
compare,compare_values,compare_recursivelearned parameterreturn_handlerthat lets other printing, logging, and pass/fail behavior to be interjected.
- (:pr:`63`)
util.whichusesos.pathseprather than Linux-focused:. - (:pr:`65`) Fixed some minor printing and tolerance errors in molecule alignment.
- (:pr:`65`)
testing.compare_recursivestopped doingatol=10**-atolforatol>=1, bringing it in line with other compare functions.
- (:pr:`49`) Precompute some mass number and mass lookups and store on
qcel.periodic_table. Also move staticre.compileexpressions out of fns on to module. Mol validation .127s --> .005s.
- (:pr:`47`)
models.DriverEnumnow has aderivative_intfunction to return 1 forgradient, etc., for easy math.propertiesreturns 0. - (:pr:`47`) Optional
fix_symmetryfield in qcschema_molecule was missing frommodels.Moleculeso Pydantic got mad at Psi4. Now calmed.
- (:pr:`48`) If Molecule object has passed through molparse validation because it was created with a molparse
constructor (e.g.,
from_string), save some time by not passing it through again atmodel.Moleculecreation time.
- (:pr:`48`) Fixed a
Molecule.get_fragmentbug where ghosted fragments still asserted charge/multiplicity to the validator, which was rightly confused.
- (:pr:`37`) Documentation now pulls from the custom QC Archive Sphinx Theme, but can fall back to the standard RTD theme. This allows all docs across QCA to appear consistent with each other.
- (:pr:`41`) Conda-build recipe removed to avoid possible confusion for everyone who isn't a Conda-Forge
recipe maintainer. Tests now rely on the
conda envsetups. - (:pr:`44`) Molecule objects are now always validated against a more rigorous model and fragment multiplicities are
fixed at the correct times, even when no multiplicities are provided. Molecule defaults to
dtype=2.
- (:pr:`39`) Fixed
setup.pyto callpytestinstead ofunittestwhen running tests on install - (:pr:`41`) Pinned a minimum Pytest version to make sure errors are not because of too old of a pytest version
- (:pr:`33`)
molparse.to_schemarecognizesdtype=2in keeping with GH:MolSSI/QCSchema#60 with internalschema_name=qcschema_moleculeandschema_version=2fields.molparse.from_schemarecognizes external fields (existing functionality), internal fields (dtype=2), and mixed. - (:pr:`33`) Pydantic molecule model now contains schema_name and schema_version=2 information.
- (:pr:`35`) Models now have an
extrafield for extra attributes, no additional base keys are allowed.
- (:pr:`34`) Converts
qcel.Datumto Pydantic model. Changes: (a) comment, doi, glossary fields must be accessed by keyword, (b)to_dict()becomesdict()and instead of only label, units, data fields in dict, now comment, doi, glossary present _if_ non-default, (c) complex values no longer list-ified byto_dict(). - (:pr:`36`) Changelog and Models documentation.
- (:pr:`32`) Updates compliance with Pydantic v0.20.
- (:pr:`31`) Lints the code base preparing for a release and minor test improvements.
- (:pr:`30`) Fixes
dihedralmeasurement code for incorrect phase in certain quadrants.
- (:pr:`27`) Adds a new
measurefeature to Molecule for distances, angles, and dihedrals. - (:pr:`25`) Adds a new
testingmodule which contains testing routines for arrays, dictionaries, and molecules.
- (:pr:`28`) Reduces loading time from ~1 second to 200 ms by delaying
pintimport and ensuring git tags are only computed once.
- (:pr:`24`) Update models to be compatible with QCFractal and MongoDB objects in the QCArchive Ecosystem.
Also enhances the
Moleculemodel'sjsonfunction to acceptas_dictkeyword, permitting a return as a dictionary of Pydantic-serialized python (primitive) objects, instead of a string.
- (:pr:`21`) Molparse's
from_schemamethod now correctly parses the newqcschema_Xstrings for schema names. - (:pr:`23`) Pydantic model serializations now correctly handle Numpy Array objects in nested
BaseModels. Model serialization testing added to catch these in the future.
- (:pr:`20`) Moves several Molecule parsing functions to the molparse module.
- now requires Python 3.6+
- now requires Pydantic
- (:pr:`14`, :pr:`16`, :pr:`17`) Added new Pydantic models for Molecules, Results, and Optimizations to make common objects used in the QCArchive project all exist in one central, always imported module.
- (:pr:`13`) Function
util.unnpthat recursively list-ifies ndarray in a dict now handles lists and flattens.
- (:pr:`12`) Adds "connectivity" validation and storage consistent with QCSchema.
- (:pr:`12`) Adds single dictionary provenance consistent with QCSchema rather than previous list o'dicts.
- (:pr:`10`) Adds covalent radii data available through
covalentradii.get(atom)function. - (:pr:`10`) Adds
to_units(unit)toDatumclass to access the data in non-native units. - (:pr:`10`) Adds
periodictable.to_period(atom)andto_group(atom)functions to address periodic table.
- (:pr:`7`, :pr:`9`) Adds "comment" and "provenance" fields to internal repr to better match QCSchema.
- (:pr:`7`) Adds provenance stamp to
from_string,from_arrays,from_schemafunctions.
- (:pr:`7`) Adds outer schema_name/schema_version to
to_schema(..., dtype=1)output so is inverse tofrom_schema.
- (:pr:`8`) Tests pass for installed module now that comparison tests are xfail.
This is the first alpha release of QCElemental containing the primary three components.
- (:pr:`6`) Updated molparse to write new Molecule QCSchema fields in keeping with GH:MolSSI/QCSchema#44
- Periodic Table data from NIST SRD144 (c. pre-2015?) collected into
qcelemental.periodictableinstance, with accessorsto_Z,to_element,to_E,to_mass,to_A(and redundant accessorsto_mass_number,to_atomic_number,to_symbol,to_name) infloatandDecimalformats. Also includes functionality to write a corresponding "C" header. - Physical Constants data from NIST SRD121 (CODATA 2014) collected into
qcelemental.constantsinstance, with access throughqcelemental.constants.Faraday_constant(exact capitalization;floatresult) orget(free capitalization;floatorDecimalresult). Also includes functionality to write a corresponding "C" header. molparsesubmodule wherefrom_string,from_array,from_schemaconstructors parse and rearrange (if necessary) and validate molecule topology inputs from the QC and EFP domains into a QCSchema-like data structure. Current deficiencies from QCSchema are non-contiguous fragments and "provenance" fields. Accessorsto_stringandto_schemaare highly customizable.- A pint context has been built around the NIST physical constants
data so that
qcelemental.constants.conversion_factor(from_unit, to_unit)uses the QCElemental values in its conversions. Resultingfloatis within uncertainty range of NIST constants but won't be exact for conversions involving multiple fundamental dimensions orwavelength -> energy != 1 / (energy -> wavelength).