Aim2dat

=============

**Enhancements:**

* A parser for xml output files of Quantum ESPRESSO is added (`PR 102 <https://github.com/aim2dat/aim2dat/pull/102>`_).
* Added interface to MOFXDB (https://mof.tech.northwestern.edu/) to the ``strct.StructureImporter`` class (`PR #94 <https://github.com/aim2dat/aim2dat/pull/94>`_).
* The ``strct.Structure`` class checks now for duplicate positions upon initialization (`PR 107 <https://github.com/aim2dat/aim2dat/pull/107>`_).
* ``strct.ext_analysis.determine_molecular_fragments`` offers additional parameters, allowing to exclude sites and restricting the size of the fragments (`PR 111 <https://github.com/aim2dat/aim2dat/pull/111>`_).
* Slight speed-up in distance based methods to calculate the coordination environment by sorting the pair-wise distances first.
* Added ``utils.element_properties.get_val_electrons`` function to return the number of valence electrons of the element (`PR 113 <https://github.com/aim2dat/aim2dat/pull/113>`_).
* Support CP2K versions 2025.1 (`PR 114 <https://github.com/aim2dat/aim2dat/pull/114>`_).
* Implemented BSSE parsing to ``io.cp2k.read_stdout`` function (`PR 115 <https://github.com/aim2dat/aim2dat/pull/115>`_ and `PR #116 <https://github.com/aim2dat/aim2dat/pull/116>`_).
* Added more units and fundamental constants to ``utils.units`` (`PR 122 <https://github.com/aim2dat/aim2dat/pull/122>`_).
* The ``strct.Structure.calculate_angle`` and ``strct.Structure.calculate_dihedral_angle`` now supports lists and ``None`` as input (`PR 126 <https://github.com/aim2dat/aim2dat/pull/126>`_).
* Several new functions have been added to the ``strct.ext_manipulation`` module, including ``add_structure_position``, ``translate_structure`` or ``rotate_structure``, each of the functions in this module now implement a common ``dist_threshold`` parameter to control the inter-atomic distances of the altered structures (`PR 105 <https://github.com/aim2dat/aim2dat/pull/105>`_, `PR #123 <https://github.com/aim2dat/aim2dat/pull/123>`_, `PR #129 <https://github.com/aim2dat/aim2dat/pull/129>`_).
* The ``strct.Structure`` class has now the property ``numbers`` to get the atomic number related to the element (`PR 130 <https://github.com/aim2dat/aim2dat/pull/130>`_).

**Fixes:**

* The ``internal`` backend of ``strct.Structure`` was not properly identifying the correct function to parse the file in all cases. Additionally, the ``io.cif.read_file`` function now uses the ``io.utils.custom_open`` function, allowing to pass on a string instead of the file path (`PR 99 <https://github.com/aim2dat/aim2dat/pull/99>`_).
* ``io.cp2k.read_restart_structure`` function now supports parsing files with "" delimiters for string values (`PR 100 <https://github.com/aim2dat/aim2dat/pull/100>`_).
* Improve the interface of ``strct.Structure`` to the ase ``Atoms`` class by transferring ``attributes`` to ``info`` and ``site_attributes`` to ``arrays`` (`PR 103 <https://github.com/aim2dat/aim2dat/pull/103>`_).
* Expose ``strct.Structure.attributes``, ``strct.Structure.site_attributes`` and ``strct.Structure.extras`` to ``strct.StructureCollection.append``, ``strct.Structure.from_ase_atoms`` and ``strct.Structure.from_pymatgen_structure`` functions (`PR 103 <https://github.com/aim2dat/aim2dat/pull/103>`_).
* Some str values were sometimes wrongly transformed into float numbers in the output parsers and cif parser checks more rigorously whether two atoms are occupying the same site (`PR 104 <https://github.com/aim2dat/aim2dat/pull/104>`_).
* Fix positions returned from ``strct.Structure.calculate_distance`` function (`PR 106 <https://github.com/aim2dat/aim2dat/pull/106>`_).
* ``io.cif.read_file`` was not properly parsing string values in loops with delimiters ("" or '') and without spaces (`PR 118 <https://github.com/aim2dat/aim2dat/pull/118>`_).
* Setting ``strct.Structure.site_attributes`` was not resetting the dictionary but instead adding the new key/value pairs (`PR 125 <https://github.com/aim2dat/aim2dat/pull/125>`_).
* The ``strct.StructureOperations.compare_sites_via_coordination``, ``strct.StructureOperations.find_eq_sites_via_coordination``, ``strct.ext_analysis.decorator.external_analysis_method`` decorator now properly handles unset keyword arguments (`PR 128 <https://github.com/aim2dat/aim2dat/pull/128>`_).

**Deprecations:**

* The ``strct.Structure.import_methods``, ``strct.Structure.export_methods``, ``strct.Structure.analysis_methods``, ``strct.Structure.manipulation_methods``, ``strct.StructureOperations.analysis_methods`` and ``strct.StructureOperaions.manipulation_methods`` functions are now deprecated since Python dropped the support for class properties. The methods are replaced by the ``list_*_methods`` class methods, making this Package compatible with Python 3.13 (`PR 132 <https://github.com/aim2dat/aim2dat/pull/132>`_).

**Breaking Changes:**

* ``strct.ext_analysis.determine_molecular_fragments`` now considers the same site multiple times if it is connected, returns a list of ``strct.Structure`` objects and does not shift the position of the first atom to zero (`PR 111 <https://github.com/aim2dat/aim2dat/pull/111>`_).
* ``strct.ext_analysis.create_graph`` now only outputs the graphviz graph if the ``get_graphviz_graph`` parameter is set to ``True`` and networkx is added to the core dependencies (`PR 112 <https://github.com/aim2dat/aim2dat/pull/112>`_).
* All units and constants now rely on an internal implementation which is based on CODATA 2022 instead of 2014 (`PR 122 <https://github.com/aim2dat/aim2dat/pull/122>`_).
* The ``strct.Structure.calculate_distance``, ``strct.Structure.calculate_angle`` and ``strct.Structure.calculate_dihedral_angle`` now return all possible combinations from the given indices instead of pairwise tuples (`PR 126 <https://github.com/aim2dat/aim2dat/pull/126>`_).
* The ``strct.ext_analysis.determine_molecular_fragments``, ``strct.ext_analysis.create_graph`` and ``strct.ext_manipulation.add_structure_coord`` functions now implement ``**cn_kwargs`` as container for the arguments forwarded to the ``strct.Structure.calculate_coordination`` function (`PR 128 <https://github.com/aim2dat/aim2dat/pull/128>`_).
* The default value for the ``method`` parameter of the ``strct.Structure.calculate_coordination`` is now set to ``atomic_radius`` as this method seems more reliable and equally fast as ``minimum_distance`` (`PR 128 <https://github.com/aim2dat/aim2dat/pull/128>`_).
* The ``aim2dat.strct.ext_manipulation.add_structure_random`` function now uses the numpy random number generator and now offers more keyword arguments to control the used random numbers (`PR 134 <https://github.com/aim2dat/aim2dat/pull/134>`_).

=============

**Enhancements:**

* All larger parser functions moved from ``aiida_workflows`` to ``io`` such that they can used outside of the AiiDA framework (`PR 20 <https://github.com/aim2dat/aim2dat/pull/20>`_).
* ``io.qe.read_total_density_of_states`` parses now the Fermi energy as well (`PR 20 <https://github.com/aim2dat/aim2dat/pull/20>`_).
* ``plots.base_plot`` added new property `subplot_align_ylabels` to adjust y labels in subplots for backend `matplotlib` (`PR 23 <https://github.com/aim2dat/aim2dat/pull/23>`_).
* ``strct.Structure`` added new file formats `.cssr`, `.v1` and `.cuc` to `to_file` for postprocessing in Zeo++ (`PR 26 <https://github.com/aim2dat/aim2dat/pull/26>`_).
* ``strct.StructureOperaions`` now supports, in addition to a ``strct.StructureCollection`` object, a list of ``Structure`` objects upon initialization (`PR 29 <https://github.com/aim2dat/aim2dat/pull/29>`_).
* ``fct.smearing`` functions have a new parameter ``sampling_width`` to control the distance between x-values (`PR 32 <https://github.com/aim2dat/aim2dat/pull/32>`_).
* ``strct.Structure.to_dict`` returns a dictionary of a ``Structure`` object (`PR 34 <https://github.com/aim2dat/aim2dat/pull/34>`_).
* Structure manipulation methods maintain ``kinds`` information and ``strct.Structure.substitute_elements`` has now the addiational ``remove_kind`` parameter (`PR 34 <https://github.com/aim2dat/aim2dat/pull/34>`_).
* ``utils.element_properties.get_atomic_radius`` supports now the set of radii determined in :doi:`10.1039/C9RA07327B` (`PR 35 <https://github.com/aim2dat/aim2dat/pull/35>`_).
* ``strct.Structure.calculate_coordination`` supports the calculation of the coordination environment based on the sum of the corresponding atomic radii (`PR 35 <https://github.com/aim2dat/aim2dat/pull/35>`_).
* ``strct.ext_manipulation.add_structure_coord`` replaces the ``strct.ext_manipulation.add_functional_group`` function allowing ``Structure`` objects as input and adding methods to define the orientation and position of the guest structure in more detail (`PR 37 <https://github.com/aim2dat/aim2dat/pull/37>`_, `PR #65 <https://github.com/aim2dat/aim2dat/pull/65>`_, `PR #85 <https://github.com/aim2dat/aim2dat/pull/85>`_).
* ``strct.Structure`` has now site attributes which store site specific information (`PR 39 <https://github.com/aim2dat/aim2dat/pull/39>`_).
* ``utils.element_properties.get_atomic_radius`` supports now Van der Waals radii determined in :doi:`10.26434/chemrxiv-2024-m3rtp-v2` (`PR 44 <https://github.com/aim2dat/aim2dat/pull/44>`_).
* An internal cif-parser is added to parse additional information (`PR 47 <https://github.com/aim2dat/aim2dat/pull/47>`_).
* Support CP2K versions 2022.1-2024.1 (`PR 51 <https://github.com/aim2dat/aim2dat/pull/51>`_).
* The newly implemented ``strct.ext_manipulation.add_structure_random`` function adds a guest structure at a random position and orientation (`PR 53 <https://github.com/aim2dat/aim2dat/pull/53>`_).
* ``strct.Structure.from_file`` interfaces functions from the ``io`` sub-package via the internal ``'backend'`` and adds more parameters to control the ``'ase'`` backend (`PR 56 <https://github.com/aim2dat/aim2dat/pull/56>`_).
* The methods to find duplicate structures of ``strct.StructureOperations`` are sped up by comparing the chemical formulas prior to more expensive checks (`PR 61 <https://github.com/aim2dat/aim2dat/pull/61>`_).
* H2 is added to the pre-defined structures (`PR 65 <https://github.com/aim2dat/aim2dat/pull/65>`_).
* ``io.cp2k.read_atom_proj_density_of_states`` now also supports LDOS files (`PR 76 <https://github.com/aim2dat/aim2dat/pull/76>`_).
* ``strct.StructureOperations.compare_*`` functions can now be run in parallel (`PR 78 <https://github.com/aim2dat/aim2dat/pull/78>`_).
* Added ``custom_hatch`` to all ``plots`` classes to allow plotting hatched bars using the matplotlib backend (`PR 89 <https://github.com/aim2dat/aim2dat/pull/89>`_).

**Fixes:**

* ``utils.chem_formula.transform_str_to_dict`` supports now recurring elements and nested brackets (`PR 13 <https://github.com/aim2dat/aim2dat/pull/13>`_).
* ``strct.Structure.calculate_voronoi_tessellation`` now sorts the the neighbouring sites (`PR 31 <https://github.com/aim2dat/aim2dat/pull/31>`_).
* ``io.fhi_aims.read_atom_proj_density_of_states`` supports now higher azimuth quantum numbers up to i (`PR 33 <https://github.com/aim2dat/aim2dat/pull/33>`_).
* External structure manipulation methods now share the same interface as their internal counterparts (`PR 34 <https://github.com/aim2dat/aim2dat/pull/34>`_).
* A few smaller bug fixes in CP2K output parser (`PR 36 <https://github.com/aim2dat/aim2dat/pull/36>`_).
* Fix interface to spglib to support version 2.5 and above (`PR 54 <https://github.com/aim2dat/aim2dat/pull/54>`_).
* Small fixes to the Materials Project open-api interface (`PR 58 <https://github.com/aim2dat/aim2dat/pull/58>`_).
* The optimade interface was not working as soon as one supplier could not be reached (`PR 62 <https://github.com/aim2dat/aim2dat/pull/62>`_).
* ``strct.Structure.calculate_distance`` now correctly backfolds positions into the unit cell (`PR 63 <https://github.com/aim2dat/aim2dat/pull/63>`_).
* ``strct.ext_manipulation.add_structure_coord`` or ``strct.ext_manipulation.add_functional_group`` were not in all cases dealing correctly with planar coordination geometry (`PR 64 <https://github.com/aim2dat/aim2dat/pull/64>`_).
* Fixed error in ``strct.StructureOperations`` when index slices were used (`PR 71 <https://github.com/aim2dat/aim2dat/pull/71>`_).
* Fixed bug in ``plots.PartialChargesPlot`` occurring when a data labels was part of another data label (`PR 77 <https://github.com/aim2dat/aim2dat/pull/77>`_).

**Deprecations:**

* ``strct.ext_manipulation.add_functional_group`` is replaced by ``strct.ext_manipulation.add_structure_coord`` (`PR 37 <https://github.com/aim2dat/aim2dat/pull/37>`_).
* ``aim2dat.io.cp2k.read_optimized_structure`` is replaced by ``aim2dat.io.cp2k.read_restart_structure`` (`PR 56 <https://github.com/aim2dat/aim2dat/pull/56>`_).

**Breaking Changes:**

* Moved ``dict_*`` functions from ``aiida_workflows.utils`` to ``utils.dict_tools`` (`PR 36 <https://github.com/aim2dat/aim2dat/pull/36>`_).
* Space group and symmetry related keys now conform to the attributes returned by spglib (`PR 54 <https://github.com/aim2dat/aim2dat/pull/54>`_).
As such, the keys ``'sg_number'``, ``'int_symbol'``, ``'point_group_symbol'``, ``'schoenflies_symbol'`` are replaced by ``'number'``, ``'international'``, ``'pointgroup'``, ``'schoenflies'``, respectively.
* ``utils.chem_formula.reduce_formula`` tries now to find a formula only having natural numbers as quantities; this way utils.chem_formula.compare_formulas`` works for all use-cases (`PR 60 <https://github.com/aim2dat/aim2dat/pull/60>`_).
* Structure manipulation methods now in general maintain ``kinds``, ``attributes`` and ``site_attributes`` if not otherwise noted (`PR 63 <https://github.com/aim2dat/aim2dat/pull/63>`_).
* The interface of``strct.StructureOperations`` was changed in order to be more consistent with ``strct.Structure`` (`PR 72 <https://github.com/aim2dat/aim2dat/pull/72>`_).
* ``strct.Structure.kinds`` now always returns a tuple instead of ``None`` (`PR 73 <https://github.com/aim2dat/aim2dat/pull/73>`_).
* ``io.critic2.read_stdout`` now returns the value of 'version' as string (`PR 74 <https://github.com/aim2dat/aim2dat/pull/74>`_).
* ``strct.Structure.calculate_distance`` treats ``r_max`` as a cut-off value for the distance (`PR 83 <https://github.com/aim2dat/aim2dat/pull/83>`_, `PR #90 <https://github.com/aim2dat/aim2dat/pull/90>`_).

=============

* First published version.