CHANGELOG.md

Changelog

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v.0.15.0

full changelog

Added

• Added support for Python 3.11 [#227]
• Added FleurInputSchema.xsd and FleurOutputSchema.xsd for the MaX6.2 release of fleur (file version 0.37) [#240]
• KKR parser: Added keywords for Kkrimp BdG [#235]

Bugfixes

• Fixed order of added comments in readd_inpgen_comments. Previously they would end up in reverse order
• Fixed extraction of global magnetic moments from out.xml [#230]/[#231]

v.0.14.0

full changelog

Added

• Command masci-tools convert-inpgen to transform common structure formats, e.g. cif into inpgen files. Uses ase or pymatgen with the corresponding fleur plugins ase-fleur and pymatgen-io-fleur (install additional dependencies cmdline-extras)[#215]
• Functions get_inpgen_comments and readd_inpgen_comments to keep the comments of the inp.xml file containing the inpgen commandline and file content through functions using clear_xml

Improvements

• write/read_fleur_inpgen now supports the magnetic moment definitions in the inpgen input file introduced in MaX-6.1 (also the scf namelist) [#213]
• get_structuredata also reads out the magnetic moments [#213]
• FleurXMLModifier.modify_xmlfile now keeps the inpgen comments by default (controlled by option keep_inpgen_comments)

Bugfixes

• Serveral fixes for Fleur DOS plots [#212]:
  • Fixed wrong summation of atom weights for files containing 10 or more atomtypes
  • Fixed crashes using a custom weight not conforming to the naming scheme of weights in the banddos.hdf
  • Fixed specification of parameters by DOS label not working if the spin suffix is omitted

v.0.13.0

full changelog

Improvements

• set_kpointmesh now also writes out the nx/ny/nz attributes fro the dimensions of the kpoint mesh
• get_structure_data, get_parameter_data and get_kpoints_data are renamed to get_structuredata, get_parameterdata and get_kpointsdata to match the names of the corresponding functions in aiida-fleur. Old names are available with deprecations [#208]
• FleurXMLModifier now supports changes to input files with not yet available Fleur schemas, if the changes are compatible with the last available file schema [#209]

Bugfixes

• Bugfix in XML setters set_inpchanges and set_attrib_value, setting the xcFunctional key was previously not case-insensitive in constrast with all other keys
• Fixed crash in get_parameter_data. This function would previously crash if a kpoint mesh without nx/ny/nz attributes was used and the first point in the list was the gamma point

v.0.12.0

full changelog

Added

• Added XPath evaluation functions with runtime tpye checking of the results of the expressions [#181]
• Command masci-tools fleur-schema pull <branch> to update/add Fleur Schema files from the iffgit more easily [#184]
• New XML setters [#183]:
  • Setting XC functional explicitly + LibXC support (set_xcfunctional),
  • Creating a kpoint path using ase (set_kpointpath)
  • Creating a kpoint mesh with symmetry reduction using spglib. Should be equivalent to the gamma@grid=nx,ny,nz kpoint generator in inpgen (set_kpointmesh)
• Added FleurInputSchema.xsd and FleurOutputSchema.xsd for the MaX6.1 release of fleur (file version 0.36) [#196]

Bugfixes

• Add clearer error message if None is passed to the convert_to_xml functions. This would happen for example using the set_inpchanges function with {'minDistance': None} [#182]
• Fixed masci-tools fleur-schema add with --from-git flag. Previously it would still check for the existence of the Schema file locally [#184]
• get_fleur_modes: gw mode renamed to spex and now stores the actual integer value of the attribute [#185]
• Bugfix in clear_xml, when multiple XML comments are present outside the root element [#193]
• Bugfix in reverse_xinclude. This would previously break when reexcluding trees already containing a relaxation tag and would end up with two xi:include tags for the relax.xml [#194]
• Bugfix for FleurXMLModifier. The task_list property would incorrectly enter a kwargs key if the modifying function in question has an explicit **kwargs argument
• Bugfix in matplotlib plots with placement of multiple colorbars (e.g. weighted spin-polarized bandstructure) [#198]

v.0.11.3

full changelog

Improvements

• Changes to KKR plotting routine dispersionplot for compatibility with AiiDA v2.0
• Connecting vectors for intersite GreensFunction are now saved in Angstroem. For better interoperability with ase, pymatgen, AiiDA

For Developers

• Relaxed CI requirements for docs build. Nitpicky mode is no longer required to pass but is treated as a hint to look into the warnings

v.0.11.2

full changelog

Improvements

• Several changes in KKR IO functions to make them compatible with aiida-core>=2.0 [#175]
• Add function to calculate fourier transform of e.g. J_ij constants calculated from Green's functions (masci_tools.tools.greensf_calculations.heisenberg_reciprocal)

Bugfixes

• Fixed nondeterministic order in bokeh regression tests if multiple dictionaries with the same values but differing keys in the same list (e.g. Providing the same data for different columns)
• Fixed wrong names for columns entered in decompose_jij_tensor, i.e. J_ji -> J_ij

Deprecations

• Deprecated the unused modules util/kkr_rms_tracker.py and util/modify_potential.py

v.0.11.1

full changelog

Bugfixes

• Bugfix in reverse_xinclude. Version 0.11.0 broke this function for versions, where the relaxation tag was not allowed.

v.0.11.0

full changelog

This release adds some improvements to the XML and HDF5 handling mainly for better AiiDA-Fleur support. Also major updates to documentation configurations and Green's function calculations.

Added

• Added FleurElementMaker class. This can be used to create XML elements compatible with a given version from scratch. Has case-insensitivity and converts values to strings for XML [#159] Example

   from masci_tools.util.xml.builder import FleurElementMaker
   E = FleurElementMaker.fromVersion('0.35')
   new_kpointset = E.kpointlist(
       *(
           E.kpoint(kpoint, weight=weight, label=special_labels[indx]) if indx in special_labels else
           E.kpoint(kpoint, weight=weight) for indx, (kpoint, weight) in enumerate(zip(kpoints, weights))
       ),
       name=name,
       count=nkpts,
       type=kpoint_type)

• Function serialize_xml_arguments to masci_tools.util.xml.common_functions to remove XML elements/trees from positional/keyword arguments and replace them with string representations of the XML. Can be used in AiiDA-Fleur
• Module masci_tools.util.ipython and ipython extension (%load_ext masci_tools). Adds syntax highlighted XML tree output and creating HTML syntax highlighted diffs of XML trees [#158]
• Added calculation of Jij Tensor from intersite Green's functions [#170]

Improvements

• Added name entry to SchemaDict.tag_info which contains the tag name in the original case [#159]
• convert_to_xml is made more strict. Conversion int to str uses the {:d} format specifier and string conversion is no longer always attempted [#159]
• Improvements to Colorbar creation in matplotlib plotting methods. Limits are now set consistently with limits={'color': (low, high)} in the plot and colorbar. Spinpolarized bandplots now show two colorbars for the two colormaps if requested
• get_parameter_data now also extracts the gamma switch for kpoint generation for more consistent roundtrips. This is only set if the first kpoint in the mesh is the gamma point and there are multiple
• load_inpxml and load_outxml now consistently accept the XML file given as a string of the content. The content no longer has to be manually encoded as bytes
• The method FleurXMLModifier.modify_xmlfile now always returns two things. The modified XML tree and a dictionary with all additional file contents, e.g. n_mmp_mat.
• Support for aligning spin/real-space frames of Green's functions. Several further imporvements/bugfixes for Green's function modules [#170]

Bugfixes

• Bugfix for outxml_parser returning a nested list for Hubbard 1 distances, where a flat list was expected. Removed force_list argument from the parsing task definition
• Fixes in plot_fleur_bands, when providing custom weights without spin suffixes, i.e. _up/_down
• Fix in HDF5Reader. IO like objects without an attached filename would lead to an early error. This is the case for example for some readers in the file repository implementation used in AiiDA v2.0
• Fix in HDF5Reader. The file handles for compressed files in the AiiDA v2 repository have to be copied into a temporary file first before they can be used

For Developers

• Docs: Updated sphinx and sphinx-autodoc-typehints versions and build docs on python 3.10 [#156]
• Docs: Converted to MyST markdown and where appropriate introduced myst-nb for executing code cells in the documentation, e.g. generate plotting examples [#157]
• Bokeh regression tests now strip out the bokeh version from the test files
• Added pre-commit hook, which generates the docstrings for the FleurXMLModifier registration methods from their XML setter function counterparts [#166]

v0.10.1

full changelog

Bugfixes

• Remove accidentally left in debug print in outxml_parser

v.0.10.0

full changelog

This release provides several new features in the XML modification/evaluation for Fleur XML files and bugfixes. Multiple problems when working with DFT+U density matrix files are also fixed.

Added

• New XML setter align_nmmpmat_to_sqa to rotate the density matrix file according to SQAs specified either for noco or second variation SOC [#140]

• Added task_list property to FleurXMLModifier to construct a list which can be used to replicate the same FleurXMLModifier with the fromList() classmethod [#149]

• Added FleurXMLContext, which acts as a holder of th XML elements, schema dictionary, constants and logger to reduce the amount of information/clutter in functions evaluating things from the XML file [#152]

  Note: The class ParseTasks used in the outxml_parser was simplified and placed into the outxml_parser module and the decorator register_parsing_function was removed. This was done without deprecation since they were exclusively used in the outxml_parser and were the main cause of cyclic import problems previously

• Added several predefined conversions to/from input version 0.35 to inpxml_converter [#153]

Improvements

• Added inverse argument to nmmpmat XML setters. These will correctly produce the inverse rotation operation for the given angles. Also allow setting orbital='all' in rotate_nmmpmat to rotate all blocks by the given angles [#140]
• The XML setters create_tag, replace_tag and their low-level equivalents now also accept XML strings, i.e. <example attribute="1"/>, as arguments for the elements to create/replace [#145]

Bugfixes

• Fix for XML setters operating on the DFT+U density matrix file. Previously these functions would not map the density matrix blocks correctly if multiple atomgroups shared the same species containing ldaU tags [#140]
• Added missing prefactor (-1)^(m-mp) to get_wigner_matrix()
• Added basic tests of masci_tools.tools.greensfunction module and fixed several bugs found due to this [#150]
• Fixed bug in XML setters operating on the DFT+U density matrix file not correctly extracting the number of spin blocks when only setting l_mperp
• Fixed bug, when using the FleurXMLModifier directly (not in aiida-fleur), included XML files were not handled
• Fixed bug in outxml_parser, when the XML file had to be repaired and more than one iteration was present the wrong iteration was chosen as the last stable iteration [#152]

Deprecated

• The module masci_tools.io.io_fleurxml is renamed to masci_tools.io.fleur_xml [#152]
• The module masci_tools.util.parse_task_decorator is removed. All decorators are now availaibe under masci_tools.io.parsers.fleur [#152]

For Developers

• Added py.typed marker to masci-tools, since a large part of the outside facing code (especially the XML APIs are typed). With this marker other packages can use the typehints in this package

v.0.9.1

full changelog

Added

• Standalone function masci_tools.tools.fleur_inpxml_converter.convert_inpxml to allow conversions of inp.xml files within a python runtime without needing to go via the commandline

Bugfixes

• Fixed bug in bokeh testing fixtures using the wrong folder for fallback versions
• Fixed bug not correctly converting complex numbers from the Fleur xml files if they have whitespace at beginning/end

v.0.9.0

full changelog

Added

• New bokeh plot routine for matrix plot of rectangle patches with added texts [#124]
• Added TS contribution to free energy to output of outxml_parser

Improvements

• Several arguments in XML setter functions were renamed for more consistent signatures. The main changes are

  • attributedict/change_dict -> changes
  • attributename/attribv -> name/value
  • add_number -> number_to_add

  The old signatures are still supported with deprecations if called via the FleurXMLModifier [#118]

• Remove constraint on bokeh version (previously <=1.4.0) [#122]

• Add only_spin option and calculate complete non-spinpolarized DOS for spinpol=False in plot_fleur_dos [#125]

• Refactored CFCalculation, i.e. naming of attributes handling of cutoffs. Added classmethod to construct instance directly from numpy arrays [#127]

• Refactored plotting methods for CFCalculation to allow the same parameter freedom as for the other matplolib routines [#127]

• Improvement to labels and legends in DOS/bandstructure plots. Matplotlib plots now put the legend centered below the plot and added latex labels to axis and ticks in bokeh (version 2.4.0 needed) [#133]

• io_nmmpmat: Allow negative indices in read_nmmpmat_block and raise error for invalid index

Bugfixes

• Fix for signatures of set_text/set_first_text. These contained names of attribute setting functions [#118]
• Fix for validating arguments in FleurXMLModifier not accepting an argument named name when passed by keyword. [#118]
• Fixed problems in masci_tools.testing.bokeh when adding files for new bokeh versions [#122]
• Several fixes for plot_fleur_dos. Using the area_plot or specifying color explicitly could mess up the color order [#132]
• Fixed bug in validate_nmmpmat and consequently FleurXMLModifier not correctly validating denisty matrix files with certain off-diagonal elements being negative [#135]
• Fix for HDF5Reader for compatibility for file handles in aiida-core 2.0. The file handles coming from the file repository have no directly attached extension so the check if the file is a hdf file cannot be performed

For developers

• Fixed upload of pytest-mpl results artifacts to include the whole directory with images and not just the HTML file [#117]
• Updated typing to newer version of lxml-stubs (0.4.0) [#123]

v.0.8.0

full changelog

Added

• Added FleurInputSchema.xsd and FleurOutputSchema.xsd for the MaX6 release of fleur (file version 0.35) [#112]
• New XML getter function: get_special_kpoints extracts the labelled kpoints from a kpoint list (for now only implemented for Max5 or later)
• Added extraction of Hubbard 1 input and distances in the outxml_parser for fleur (distances only available starting from version 0.35) [#108]
• Added extraction of global vector of magnetic moments in non-collinear calculations in outxml_parser under the key magnetic_vec_moments starting from version 0.35

Improvements

• Fleur schema parsing functions now recognize a new alias from the fleur schemas FortranComplex which is a number of the form (float,float). Converters for complex values are added. (Note: Complex numbers should not yet be used in the outxml_parser, since AiiDA (<2.0) does not support complex numbers yet) [#106]
• Added IncompatibleSchemaVersions error when a combination of output and input version for OutputSchemaDict is given, for which it is known that no XML schema can be compiled
• xml_getters functions can now be used in the task definitions of the outxml_parser to keep information consistent. This example definition will insert the structure data, i.e. a tuple of atoms, bravais matrix and periodic boundary conditions into the output dictionary. {'parse_type':'xmlGetter', 'name': 'get_structure_data'} [#107]
• The _conversions key in the outxml_parser now accepts namedtuples Conversion to enable passing additional arguments to these functions. [#109]
• Adjusted get_cell to understand the bravaisMatrixFilm input introduced with the MaX6 release of fleur [#110]
• Improved detection, whether a given xpath contains a tag including stripping predicates. Added function contains_tag in masci_tools.util.xml.common_functions [#113]
• Refactored bokeh plot routine periodic_table_plot to make use of the plot parameters utilities [#114]
• get_parameter_data now extracts LOs with higher energy derivatives or HELO type, as they are supported by the newest versions of the inpgen. The old behaviour of dropping all non SCLO and eDeriv="0" LOs is available via the option allow_special_los=False

Bugfixes

• Fix in load_inpxml and load_outxml (this also effects the inpxml/outxml_parser). Previously file handle like objects not directly subclassing io.IOBase would lead to an exception
• Added patch for OutputSchemaDict objects with FleurOutputSchema.xsd files before version 0.35. The attribute qPoints in the DMI output was actually called qpoints in these schemas, making it impossible to retrieve this attribute
• Fixed behaviour of relative XPath methods of SchemaDict which did not correctly handle root tags, whose names are contained in other tag names, for example bravaisMatrix and bravaisMatrixFilm from the new file version 0.35

Deprecated

• Passing strings in the _conversions key in task definitions for the outxml_parser. Use masci_tools.util.parse_utils.Conversion instead. [#109]

For developers

• Reorganized visualization tests, making the regeneration of baseline images with pytest-mpl easier [#101]
• Switched build system from setuptools to flit, since this way all the configuration can be specified in the pyproject.toml and a lot of duplication of information is avoided (e.g. version numbers) [#102]

v.0.7.2

full changelog

Bugfixes

• Fixed regression in set_atomgroup_label and set_species_label. These functions could be used in previous versions with atom labels, that do not exist. This is not possible in v.0.7.1. Since some parts of the aiida-fleur plugin relied on this the behaviour has to be kept.

v.0.7.1

full changelog

Added

• XPathBuilder class for specifying complex conditions on xpaths with a dictionary. Added filters argument to schema_dict_util and xml_setters functions for this dictionary [#96]

Bugfixes

• Fixed issue with MANIFEST.in, where non-python files from the tools subpackage were not included in the built packages
• Fixed bug not correctly processing the plot limits in plot_fleur_bands in excluding points outside the plot area for better performance
• Fix for HDF5 transformation add_partial_sums if not all formatted patterns are present in the dataset, e.g. if a bandstructure/DOS is calculated for only selected atoms

For developers

• More strict mypy configuration and moved a lot of the annotations to modern syntax with from __future__ import annotations
• Added pyupgrade hook to automatically do some easy refactoring, i.e. removing compatibility workarounds move to modern syntax. Set to apply changes compatible with 3.7 and later

v.0.7.0

full changelog

Commandline interface, refactoring of SchemaDict/XML functions and major improvements for package configuration/tooling for developers. Added support for python 3.10. Dropped testing for python 3.6.

Added

• Added click command line interface (available as masci-tools). Can add Fleur XML Schema files with validation (Also directly pulled from the Fleur git), use the XML parsing functions and interface to the fleur visualization routines [#49]
• Added Tabulator for use of creating pandas.Dataframes from attributes of python objects. Used in aiida-jutools to tabulate attributes of aiida nodes
• Added optional_tasks argument to outxml_parser. Adds tasks marked with '_optional': True to the performed tasks [#81]
• Added visualization routine for spectral functions (colormesh plot with path though Brillouin zone)
• Added tool for converting inp.xml files between different file versions (Available through the click CLI masci-tools inpxml) [#88]
• Added three new XML setters: clone_species (Create and modify a species starting from an existing one), switch_species/switch_species_label for switching the species attribute of atom groups with additional checks
• outxml_parser: Total Energy is now taken from the output freeEnergy in the out.xml

Improvements

• Refactored SchemaDict code. Moved routines get_tag_xpath and similar to methods on the SchemaDict. If the path cannot be determined custom exceptions NoPathFound and NoUniquePathFound are now raised [#84]
• Added utility to OutputSchemaDict to create absolute paths into iteration elements in out.xml. Added support for this option in schema_dict_util functions with iteration_path=True
• All basic XML modification functions now accept either a ElementTree or Element. and warn they find no nodes to operate on
• Improved capabilities of green's function tool, can now be used with radially resolved/k-resolved Green's functions
• Improved performance of Fleur XML Schema parsing by switching from the xpath method on the ElementTree to constructing a XPathEvaluator object [#89]
• All xml_getters functions can now also be used with out.xml files
• set_atomgroup/set_atomgroup_label now use switch_species if the species attribute is changed
• set_atomgroup now supports the all-<search string> syntax for species argument, equivalent to set_species
• Improved behaviour of spin-polarized DOS plots for duplicating all plot parameters for spin-down components (previously only color was repeated)

Bugfixes

• Fixed several issues in version handling of Schema dictionaries. It is now possible to add a new schema and have it work (with warnings) without needing to change any code (masci-tools fleur-schema add <path/to/schema>)
• Bugfix in evaluate_tag not handling the combination of options subtags=True and text=True correctly. Previously some results were overwritten.
• Fixed accidental change in write_inpgen_file in comparison to old aiida-fleur implementation. Now the species name is always appended to the position in the inpgen file if it is not equal to the atom symbol
• Fixed behaviour of get_parameter_data for inputs with local orbitals with higher energy derivatives. These cannot be created by the inpgen and so are dropped
• Fixes in xml_setters to allow consistent creation of multiple tags for setting text or attributes

Deprecated

• The fleur_schema subpackage was moved from masci_tools.io.parsers.fleur to masci_tools.io.parsers to avoid circular import issues [#87]

Removed

• get_structure_data now returns AtomSiteProperties for the atom information by default. The default value of site_namedtuple is now True

For developers

• Moved configuration of yapf, pylint and pytest into pyproject.toml
• Made test suite executable from the root-folder (Some file paths were not transferrable when changing the execution directory)
• Added test_file fixture, which constructs the absolute filepath to files in the tests/files folder to reduce the difficulty of moving test files around and reorganizing the pytest suite
• Updated pylint (2.11), pytest (6.0) in setup.py
• Added mypy pre-commit hook. Checked files are specified explicitly [#86].
• Added typing to majority of XML functions (with stubs package lxml-stubs) and large parts of the io and util subpackages
• Dropped testing for python 3.6 in CI

v.0.6.2

full changelog

Small bugfixes and refactoring for plotting routines

Added

• Common plot routines for equation of states eos_plot and plotting scf convergence convergence_plot
• Replaced old convergence plot routines with single routines for bokeh/matplotlib named plot_convergence

Improvements

• Moved eos and convergence plots to use PlotData class
• Fixed some edge cases of bokeh testing fixtures. Previously some plots would crash the code for normalizing the json

Bugfixes

• Fixed bugs in convergence routines for using them in aiida-fleur

v.0.6.1

Release fixing a small issue with publishing version 0.6.0 to zenodo

v.0.6.0

full changelog

This release contains major improvements to plotting methods and new tools. Also the fleur parsing functions were improved

Added

• PlotData class for handling data passed to plotting methods very flexibly [#54] (For more information see the relevant users guide or developers guide sections in the documentation)
• masci_tools.vis.common module for plotting methods with common interfaces for bokeh/matplotlib [#71]
• get_parameter_data also extracts kpt mesh specifications for the input generator
• Exposed and improved bokeh testing fixtures in masci_tools.testing.bokeh for use in higher level packages
• greensf_calculations module in tools with sample functions for calculating properties with green's functions from fleur
• Added two options line_plot and separate_bands to bandstructure plots. While line_plot is obvious (no weighted bandstructures possible), separate_bands allows to set parameters for single selected bands. These options can also be combined

Improvements

• Added option only_used to get_kpoints_data to get only the kPointList referenced in the kPointListSelection tag
• Made constants argument to schema_dict_util functions completely optional. Will raise an exception if a undefined constant is encountered
• Bandstructure plots now exclude points outside the plotting area to speed up these plots significantly for systems with a large number of bands
• Refactored attribute/text type definitions in SchemaDict objects. Now unified under one structure. Both attributes and texts can now be recognized to contain multiple values [#64]
• Added spin_arrows option to toggle spin arrows in plot_spinpol_dos for matplotlib. Previously this was only possible for bokeh
• Added options to create different types of bar plots to barchart: Available are 'stacked' (default), 'grouped', 'independent' (positions can be defined for each data set)
• Exceptions occurring in transforms for HDF5Reader are now bundled into HDF5TransformationError to allow easier error handling
• Added MT keys to kkrparams

Bugfixes

• Fix for write_inpgen_file, which was incorrectly inserting the 'X' (empty sphere) element into inpgen files
• Fix for read_inpgen_file, which could not handle inpgen files with comments on certain lines in the inpgen file
• Several fixes for plot_fleur_dos not using the standard DOS calculation but orbital decompositions and so on
• Adjusted default dpi for matplotlib to 100 to avoid problems with size when using plt.show() instead of saving

v.0.5.0

full changelog

This release contains fleur inpgen IO capabilities and many major improvements

Added

• IO routines for reading/writing inpgen input files
• get_structure_data now returns the relaxed structure if a relaxation section is present
• get_parameter_data can read in the electron configuration if requested
• get_symmetry_information xml getter to get all defined symmetry operations
• get_structure_data and get_parameter_data now norm the species names to get consistent ids for usage in the inpgen files [#70]

Improvements

• Added another possible value to environment variable MASCI_TOOLS_USE_OLD_CONSTANTS to get the values of constants in between commits c171563 and 66953f8 [#66]
• spex attribute is now used in addition to old gw attribute to determine whether a fleur input file is from a SPEX calculation
• evaluate_tag can now also get the text and recursively parse all subtags
• Changed default of multiply_by_eqiv_atoms in plot_fleur_dos to True
• barchart can now make horizontal bar charts
• get_cell now also takes the scale attribute into account
• Made conversion to angstroem optional (done by default) in the xml getters. Can be turned off with the options convert_to/from_angstroem
• Deprecated: Old atom position output in get_structure_data. Use option site_namedtuple=True to get new output (includes species information)

Bugfixes

• Fixes to make plot_convex_hull_2d work
• Fix in evaluate_text make constants argument optional
• Fix for get_structure_data; Added missing unit conversion for z-coordinate of film positions

v.0.4.10

full changelog

This release contains bugifxes for the visualization routines

Bugfixes

• Fixed issue for histogram plot, which prevented usage for e.g. stacked histograms with multiple datasets
• Fixed usage of dictionary arguments in plot_fleur_dos, that should not be used to specify parameters for multiple datasets (e.g. limits, lines)
• Updated documentation table of plot parameters to put all dictionaries into literal blocks. Otherwise single quotes appear differently on read the docs

v.0.4.9

full changelog

Improvements

• Added saving/loading of plot defaults in json files to Plotter class (No exposed functions yet in plot_methods or bokeh_plots)
• DOS plot parameters in plot_fleur_dos can now be specifified by label, e.g. color={'Total_up': 'blue'}

Bugfixes

• Various Bugfixes and improvements to ChemicalElements class, greensfunction tools and plotting methods
• Fixed wrong atom label generation in DOS plots (#55)

v.0.4.8

full changelog

Added

• Tool to analyze/work with greensfunctions calculated by Fleur masci_tools.tools.greensfunction

Improvements

• Several improvements of KKR parsers/parameters [#13]
• Introduced patching functions for the schema dictionaries to manually correct ambiguities [#48]
• Improvements of the HDF5Reader and recipes for Fleur DOS/bandstructure calculation
• For devs:
  • pylint warnings are no longer fatal for the CI jobs
  • tests folder moved outside package directory

Bugfixes

• Bugfixes and improvements in the plotting functions for DOS/bandstructures
• Bugfixes in xml_setters and fleurxmlmodifier modules

v.0.4.7

full changelog

Added

• Introduced higher level XML modification functions for xml_delete_tag, xml_delete_att, xml_replace_tag

Improvements

• moving conversion factors for energy and bohr to angstroem conversion to NIST values in KKR parts of the code. This can also be disabled for backwards compatibility by setting the environment flag MASCI_TOOLS_USE_OLD_CONSTANTS
• Added missing energy unit alias for Fleur input files
• xml_delete_tag, xml_delete_att, xml_replace_tag now also support the occurrences argument
• FleurXMLModifier improvements. Modification registration methods will now test the given arguments against the modifying functions immediately to fail early for errors. fromList classmethod allows the instantiation with a known list of tasks to perform. These are passed through the same procedure as the normal registration of changes

v.0.4.6

full changelog

Bugfixes

• Fix for the clear_xml function, where comments could end up in the set of included tags. This lead to failures in aiida-fleur

v.0.4.5

full changelog

Added

• Introduced function to split a xmltree back up into the included subtrees and the main tree with xi:include tags
• clear_xml now returns a set of the tags, that were included

Bugfixes

• various bugfixes for xml modifying functions
• A special case for theta, phi and ef_shift attributes of forceTheorem tags, since they are not correctly typed in the Inputschema

v.0.4.4

full changelog

Added

• XML getter methods for number of kpoints and relaxation information
• XML setter methods for manipulating kpoints

Improvements

• top level create_tag now also accepts a etree.Element
• XML getters now also accept etree.Element
• Added etree.indent calls to keep modified inp.xml clean (raises lxml dependency constraint to 4.5)
• io_fleurxml functions now pass keyword arguments to XMLParser
• Re-add fleur_modes to output_dict

Bugfixes

• Bugfix for relative xpaths

v.0.4.3

full changelog

Added

• Added utility for creating schema dictionary version specific functions
• Added XML getter functions adapted from aiida-fleur fleurinpdata methods [#40]

Improvements

• Improved logging and failure handling of XML parser functions [#39]
• Improved handling of schema_dict_util functions with nodes away from the XML root of the file [#41]

v.0.4.2

full changelog

Added

• Added key descriptions to Plotter objects and get_mpl_help and get_bokeh_help functions in plotting modules for getting descriptions of parameters
• Two new recipes for HDF5Reader for bandstructures (for reading in no or specific weights besides eigenvalues)

Improvements

• MatplotlibPlotter and BokehPlotter now have a autogenerated table of descriptions and default values in the docstring (not as nicely formatted) and in the sphinx build (really nicely formatted)
• save_format in matplotlib plots can now be a list of formats
• Various visual improvements to band/DOS plots:
  • Bandstructure size scaling adjusted to not produce massive bands
  • Bandstrcuture spin up components are now potted on top by default
  • size/color scaling now done with respect to the maximum in the plotting region
  • DOS added spin arrows in spin-polarized case
  • DOS inverted x-axis in vertical plot (spin down now on the right side)
  • DOS added symmetric limits in DOS direction for spin-polarized plots
  • DOS default figsize flipped for vertical plots

v.0.4.1

full changelog

Bugfixes

• Fix for plot_lattice_constant to make it work in aiida-fleur

v.0.4.0

full changelog

Added

• Parsers for Fleur inp.xml/out.xml files. These are robust with respect to changing file versions [#3]
• General parser for .hdf files [#30]
• Functionality for modifying inp.xml files [#23]
• Fleur visualization routines plot_fleur_dos and plot_fleur_bands
• IO Module for creating/reading and manipulating n_mmp_mat files for LDA+U calculations in fleur [#31]
• Tool for calculating crystal field coefficients [#22]

Improvements

• Refactored parameter handling in plotting methods. Introduced Plotter class for consistent behaviour and easy extendability of plotting capabilities [#6]