- (:pr:`340`, :issue:`330`) Add molecular charge and multiplicity to Molecule repr formula, so neutral singlet unchanged but radical cation has '2^formula+'.
- (:pr:`342`) Update some docs settings and requirements for newer tools.
- (:pr:`338`) Adapts for numpy v2 (only works with pint >= v0.24). v1 still compatible.
- (:pr:`335`, :issue:`334`) Numpy >=1.26 only works with pint >=0.21. @TyBalduf
- (:pr:`329`) Continues :pr:`328` adding
util.whichworkaround for only python v3.12.0 and psi4 (can be expanded) to correctly select among cmd, cmd.bat, cmd.exe.
- (:pr:`326`, :pr:`327`) New protocol option
occupations_and_eigenvaluesadded toWavefunctionPropertiesto store lightweight fields.
- (:pr:`322`) Allow
util.whichto raise a clearer error when handling pyenv shims. Improve docs.
- (:pr:`325`, :issue:`324`) Ensure
util.measure_coordinatesisn't returning NaN angles just - because floating-point errors are outside arccos's
[-1, 1]bounds.
- (:pr:`325`, :issue:`324`) Ensure
- (:pr:`315`) Stop resetting numpy print formatting.
- (:pr:`328`) Add workaround for only python v3.12.0 and psi4 (can be expanded) to handle
util.whichon Windows when a cmd (non-executable) and a cmd.<executable_extension> live side-by-side. Otherwise see[WinError 193] %1 is not a valid Win32 application.
- (:pr:`320`) Reset
blackformatting to 2022. - (:pr:`327`) Enable Python v3.12 in poetry.
- (:pr:`328`) Start Windows testing and cron testing.
- (:pr:`308`) Fix CI Pipelines. Dropped Python3.6. Bring CI pipelines into harmony with local dev experience. Lint and format entire code base. Accelerate CI pipelines. Update setup.py to correctly define extras packages. Breaking change due to dropped support for Python3.6. No code functionality was altered.
- Dropped support for dead Python 3.6. Minimum supported Python is now 3.7.
- Updated CONTRIBUTING.md to contain detailed instructions for developers on how to contribute.
- Fixed broken code that failed to prepend the "v" to version numbers.
- Updated CI to run without conda and using only packages defined in setup.py. CI is now much faster and runs the same way for local developers and GitHub Actions.
- Added test.sh and format.sh to devtools/scripts for easy execution of formatting and testing.
- Formatted all code with black. Sorted imports with isort.
- Added pre-commit to repo so code formatting, linting, and testing will all run as part of regular git workflow.
- (:pr:`310`) Modernize DevOps Tooling
- Added /scripts directory to root of project that contains scripts for testing, formatting code, and building docs.
- Updated build system from setuptools to modern pyproject.toml specification using poetry for the build backend.
- Removed complicated versioning code in favor of single source of truth in pyproject.toml. Using standard library importlib for looking up package version in __init__.py file.
- Added build_docs.sh script to /scrips and removed Makefile from /docs. Flattened /docs file structure.
- Removed travis-ci code from devtools
- Removed LGTM code (they no longer exist as a project).
- Bring all package directories under black, isort, and autoflake control.
- (:pr:`305`) Initialize Molecule.extras as empty dictionary.
- (:pr:`311`) Update docs location from RTD to GH pages. Resolve escape char warnings. Update changelog.
- (:pr:`311`) Clear up NumPy "Conversion of an array with ndim > 0 to a scalar is deprecated" in util.measure_coordinates called by Molecule.measure.
- (:pr:`314`) Import pydantic.v1 from pydantic v2 so that QCElemental can work with any >=1.8.2 pydantic until QCElemental is updated for v2.
- (:pr:`297`) Rearrange imports for compatibility with Pint v0.20. No new restrictions on pint version.
- (:pr:`285`) Standardized default on
AtomicResult.native_filesto{}fromNone. May break strict logic. - (:pr:`289`, :pr:`290`) Transition from some early documentation tools (class
AutodocBaseSettingsandqcarchive_sphinx_theme) to externally maintained ones (project https://github.com/mansenfranzen/autodoc_pydantic andsphinx_rtd_theme). Expand API docs.
- (:pr:`286`) Sphinx autodocumentation with typing of
qcelemental.testing.compare_recursiveno longer warns about circular import.
- (:pr:`275`)
AtomicResultgains anative_filesfield of a dictionary of file names (or generic'input') and text (not binary) contents that the CMS program may have generated but which haven't necessarily been harvested into QCSchema. Contents controlled by a new native_files protocol analogous to stdout protocol.
- (:pr:`281`)
TorsionDriveInputnow accepts a list ofMoleculeobjects as theinitial_moleculeto seed the torsiondrive with multiple conformations.
- (:pr:`276`)
AtomicResultProperties.dict()no longer forces arrays to JSON flat lists but now allows NumPy arrays. That is,AtomicResultPropertiesnow behaves like every other QCElemental model. Expected to be disruptive to QCFractal. - (:pr:`280`) Examples of QCSchema from test cases are now saved at branch https://github.com/MolSSI/QCElemental/tree/qcschema-examples . These have passed validation as models by Pydantic and as JSON by schema generated from Pydantic models.
- (:pr:`277`) Documentation is now served from https://molssi.github.io/QCElemental/ and built by https://github.com/MolSSI/QCElemental/blob/master/.github/workflows/CI.yml . https://qcelemental.readthedocs.io/en/latest/ will soon be retired.
- (:pr:`274`) The molecule
from_stringparser when no dtype specified learned to return the most specialized error message among the dtypes, not the full input string. - (:pr:`276`)
Molecule.to_string(..., dtype="nwchem")learned to handle ghosts (real=False) correctly. It also now prints the user label, which is used downstream for custom basis sets and shows up in a NWChem output file. QCEngine will be edited to process the label, but other uses may need modification. - (:pr:`276`)
Molecule.alignlearned a new keywordgeneric_ghosts=Trueso that it can act on molecules that have centers with content Gh, not Gh(He).
- (:pr:`276`)
Molecule.to_string(..., dtype="gamess")learned to handle ghosts (real=False) correctly forcoord=unique. Note that QCEngine usescoord=prinaxis, so actual ghosts are still NOT interpretable by downstream GAMESS.
- (:pr:`268`) Add provisional models that store the inputs to and outputs of a torsion drive procedure. @SimonBoothroyd
- (:pr:`272`) Add SCF and return gradient and Hessian fields to
AtomicResultProperties.
- (:pr:`271`)
Moleculelearned to create instances with geometry rounded to other than 8 decimal places throughMolecule(..., geometry_noise=<13>)to optionally overrideqcel.models.molecule.GEOMETRY_NOISE = 8. This should be used sparingly, as it will make more molecules unique in the QCA database. But it is sometimes necessary for accurate finite difference steps and to preserve intrinsic symmetry upon geometry rotation. Previous route was to reset the qcel module variable for the duration of instance creation. - (:pr:`271`)
Molecule.alignandMolecule.scramblelearned to return a fuller copy of self than previously. Now has aligned atom_labels, real, and mass_numbers as well as incidentals like Identifiers. Fragmentation still not addressed. - (:pr:`271`)
Molecule.to_string(dtype="gamess")learned to write symmetry information to the prinaxis output if passed in through field fix_symmetry. This is provisional, as we'd like the field to be uniform across qcprogs.
- (:pr:`271`) Testing function
compare_values()on arrays corrected the RMS maximum o-e value displayed and added a relative value.
- (:pr:`267`) Serialization learned msgpack mode that, in contrast to msgpack-ext, doesn't embed NumPy objects.
- (:pr:`266`) Testing function
compare_values()learned to print RMS and MAX statistics for arrays.
- (:pr:`265`) Fix search path construction. @sheepforce
- (:pr:`266`) Bump minimum pydantic to 1.8.2 to avoid security hole -- https://github.com/samuelcolvin/pydantic/security/advisories/GHSA-5jqp-qgf6-3pvh .
- (:pr:`257`)
PhysicalConstantsContextlearned to write a Fortran header. @awvwgk
- (:pr:`261`) Documentation became type-aware and grew more links.
- (:pr:`253`) Fixed incompatibility with Pydantic >=1.8.
- (:pr:`237`) Exports models to JSON Schema with
make schema. - (:pr:`237`) Build bank of JSON examples from Pydantic models defined in tests. Test that bank against exported schema with
pytest --validate qcelemental/. - (:pr:`237`) Many model descriptions edited, dimensions added to array properties,
AtomicInput.model.basisnow takesBasisSetobject not just string, several properties added to match QCSchema, several limitations on number and uniqueness imposed.
- (:pr:`237`) Improve mypy conformance including dynamic provenance. Necessitates Pydantic >=1.5.
- (:pr:`237`)
a0without underscore added as computable pint unit. - (:pr:`246`, :pr:`250`) Removes types deprecated in NumPy v1.20.0.
- (:pr:`244`) Fixes where in code validation throws if
center_datamissing fromBasisSetmodel. - (:pr:`249`) Fixes web tests that weren't marked.
- (:pr:`238`)
molparse.to_stringMRChem dtype developed.
- (:pr:`231`)
compare,compare_values, andcompare_recursivelearned new keywordequal_phasethat whenTrueallows eithercomputedor-computedto pass the comparison. Forcompare_recursive, the leniency can be restricted to specific leaves of the iterable by passing a list of allowed leaves.
- (:pr:`229`)
Molecule.aligntold the full truth in its documentation that themol_alignargument can take a float.
- (:pr:`228`) Fix testing bug for installed module, which was missing a dummy directory.
- (:pr:`182`) Added experimental protocol for controlling autocorrection attemps. (That is, when a calculation throws a known error that QCEngine thinks it can tweak the input and rerun.) Currently in trial for NWChem.
- (:pr:`186`, :pr:`223`)
molparse.to_stringOrca and MADNESS dtypes developed. - (:pr:`226`) Allow
which_importto distinguish between ordinary and namespace packages. - (:pr:`227`) Add non-default
strictargument toperiodictable.to_Z,to_symbol, andto_elementthat fails when isotope information is given. - (:pr:`227`) Allow nonphysical masses to pass validation in
molparse.from_schema(..., nonphysical=True). Also allowed in formingqcel.models.Molecule(..., nonphysical=True).
- (:pr:`227`) Fixed deception described in issue 225 where
qcel.models.Molecule(..., symbols=["O18"])accepted "O18" but did not influence the isotope, as user might have expected. That now raisesNotAnElementError, and an example of correctly setting isotope/masses has been added. This error now caught atqcel.molparse.from_arraysso general.
- (:pr:`211`) Improve testing reliability by excusing PubChem when internet flaky.
- (:pr:`216`) "CODATA2018" constants now tested.
- (:pr:`207`) Multipoles exist in
AtomicResultPropertiesas ndarray with order-dimensional shape. Propertyscf_quadrupole_momentdefined.
- (:pr:`216`) Fixes a bug where "CODATA2018" constants could not be used with
conversion_factor. - (:pr:`217`) Can now run
.schema()on pydantic classes containingArrayfields (allowing ndarray in place of List).
- (:pr:`209`) Added the option to Hill-order molecular formulas.
- (:pr:`208`) Fixes a Molecule hashing issue due to order of operations changes in
Molecule.from_data. The order of operations changed inMolecule.from_dataand occasionally resulted in different hashes for Molecules undergoing orient operations. This issue was introduced in 0.13.0 and is unlikely to have any serious negative effects as this did not affect hash integrity.
- (:pr:`183`, :pr:`187`) Added metadata about DFT functionals (
qcelemental.info.dftfunctionalinfo). - (:pr:`184`) Optional PubChem identifiers were added to molecules.
- (:pr:`187`, :pr:`192`, :pr:`195`) Added metadata about CPUs (
qcelemental.info.cpu_info).
- (:pr:`179`, :pr:`181`) QCElemental works with Python 3.8 at the expense of needing a new 0.10 pint (rather than generic install). Pint 0.10 has optional NumPy dependency of >=1.12.0, so QCElemental that requires both NumPy and pint needs this constraint.
- (:pr:`172`, :pr:`173`, :pr:`202`, :pr:`203`) Contribution improvements, including GitHub Actions checking,
make formatguidance, and updatedCONTRIBUTING.md. - (:pr:`189`, :pr:`196`) Constants and unit conversion based on 2018 CODATA are available (but 2014 remains the default).
- (:pr:`197`, :pr:`199`, :pr:`200`) Added more atomic units and aliases (e.g.
au_length = bohr). - (:pr:`190`, :pr:`191`, :pr:`201`) Slim molecules. Many fields in
Moleculeobjects may be optionally inferred.
- (:pr:`174`) Fix
compare_recursivefor whenexpectedis a list butcomputedis not. - (:pr:`177`) Spelling and type hint fixes.
- (:pr:`180`) Better test coverage.
- (:pr:`156`)
Moleculescan now be correctly compared with==. - (:pr:`157`)
molparse.to_stringQ-Chem dtype developed. Psi4 dtype now includes label and doesn't have extraneous info for single fragment systems. - (:pr:`162`) New protocol
stdoutadded toResultProtocolscontrolling whetherstdoutfield (which generally contains the primary logfile, whether a program writes it to file or stdout) is returned. - (:pr:`165`) The code base is now Black formatted.
- (:pr:`156`)
Molecule.compareis deprecated and will be removed in v0.13.0. - (:pr:`167`, :pr:`168`)
ResultInput,Result,Optimizationhave been removed in favor ofAtomicInput,AtomicResult, andOptimizationResultand will be removed in v0.13.0.
- (:pr:`170`)
ProtoModelsubclasses now correctly allow custom__repr__and__str__methods. - (:pr:`164`, :pr:`166`)
nglview-sdfmolecule string format now correctly uses correct sdf format widths fixing some issues with very large molecules.
- (:pr:`152`) Patches
Molecule.from_fileandMolecule.from_datato read XYZ+ format and correctly handle keyword arguments. - Patches
Molecule.to_fileto write XYZ+ format as the default for XYZ and XYZ+ files.
- (:pr:`152`) Patches
- (:pr:`147`) Updates Pydantic to the 1.0 release and fixes a number of breaking changes.
- (:pr:`148`) Switches from Py3dMoljs to NGLView for molecular visualization due to Jupyter Widget integration.
- (:pr:`149`) Adds statC and Debye to the units registry.
- (:pr:`150`) Patches
which_importto correctly handle submodules.
- (:pr:`137`, :pr:`138`) Coordinates can now be output in
Turbomoleformat in addition to all other formats. - (:pr:`139`) A wavefunction property have been added to the
ResultModel. Adds the ability for Engine and other programs to store and fetch wavefunction data. - (:pr:`140`)
Protocolshave been added toQCInputSpecificationwhich allows data to pre-pruned by different specifications. Main intention is to reduce wavefunction data which may be re-computed cheaply rather than storing all of it. This does change the input model, so requires a minor version bump.
- (:pr:`132`)
BasisSetandResult's documentations have been brought up to the standards of other models.
- (:pr:`123`) QCElemental now passes MyPy!
- (:pr:`127`, :pr:`131`) Adds van der Waals radii data available through
vdwradii.get(atom)function.
- (:pr:`125`) Add back a consistency check that had been optimized out.
- (: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 (line 23) 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).