Merge pull request #210 from JuDFTteam/release-0.13.0

🚀 Release `0.13.0`

Author: janssenhenning

.github/workflows/ci.yml

@@ -112,8 +112,9 @@ jobs:
           - python-version: '3.7'
             experimental: false
             pytest-cmdline: '-o addopts="--cov=masci_tools --cov=tests --cov-report xml"'
-#           - python-version: '3.11-dev'
-#             experimental: true
+          #- python-version: '3.11.0-rc.2'
+          #  experimental: true
+          #  pytest-cmdline: ""
       fail-fast: false
 
     name: tests-python-${{ matrix.python-version }}
@@ -140,7 +141,7 @@ jobs:
       if: ${{ matrix.experimental }}
       run: |
         sudo apt-get update
-        sudo apt-get install -y libxml2-dev libxslt-dev libhdf5-serial-dev
+        sudo apt-get install -y libxml2-dev libxslt-dev libhdf5-serial-dev libopenblas-dev
         pip install --upgrade pip setuptools wheel
         pip install --upgrade cython
         pip list

CHANGELOG.md

@@ -1,10 +1,21 @@
 # Changelog
 
 ## latest
-[full changelog](https://github.com/JuDFTteam/masci-tools/compare/v0.12.0...develop)
+[full changelog](https://github.com/JuDFTteam/masci-tools/compare/v0.13.0...develop)
 
 Nothing here yet
 
+## v.0.13.0
+[full changelog](https://github.com/JuDFTteam/masci-tools/compare/v0.12.0...v0.13.0)
+
+### 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]](https://github.com/JuDFTteam/masci-tools/pull/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]](https://github.com/JuDFTteam/masci-tools/pull/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](https://github.com/JuDFTteam/masci-tools/compare/v0.11.3...v0.12.0)
 

docs/source/devel_guide/fleur_parser.md

@@ -6,6 +6,12 @@
 .. currentmodule:: masci_tools.io.parsers.fleur_schema
 ```
 
+:::{note}
+A more detailed walkthrough of the important design decisions concerning the implementation
+Fleur XML parsers and IO capabilities can be found in this
+[document](https://python-fleur-xml-design.readthedocs.io/en/latest/)
+:::
+
 Each input and output file for Fleur has a correspong XML-Schema, where the structure
 of these files are defined.
 

docs/source/user_guide/fleur_parser.md

@@ -104,11 +104,11 @@ in the {py:mod}`~masci_tools.util.xml.xml_getters` module. The following are ava
 - {py:func}`get_nkpts()`: Get the (for older versions approximate if not `kPointList` is
   used) number of kpoints to be used in the calculation
 - {py:func}`get_cell()`: Get the Bravais matrix of the system
-- {py:func}`get_parameter_data()`: Get the information about the calculation parameters
+- {py:func}`get_parameterdata()`: Get the information about the calculation parameters
   needed to reproduce a calculation starting from the inpgen
-- {py:func}`get_structure_data()`: Get the structure from the xml file
+- {py:func}`get_structuredata()`: Get the structure from the xml file
   (atom positions + unit cell)
-- {py:func}`get_kpoints_data()`: Get the defined kpoint sets (single/multiple)
+- {py:func}`get_kpointsdata()`: Get the defined kpoint sets (single/multiple)
   from the xml file (kpoints + weights + unit cell)
 - {py:func}`get_relaxation_information()`: Get the relaxation history and current displacements
 - {py:func}`get_symmetry_information()`: Get the symmetry operations used in the calculation

masci_tools/__init__.py

@@ -21,7 +21,7 @@
 __copyright__ = ('Copyright (c), Forschungszentrum Jülich GmbH, IAS-1/PGI-1, Germany. '
                  'All rights reserved.')
 __license__ = 'MIT license, see LICENSE.txt file.'
-__version__ = '0.12.0'
+__version__ = '0.13.0'
 __authors__ = 'The JuDFT team. Also see AUTHORS.txt file.'
 
 logging.getLogger(__name__).addHandler(logging.NullHandler())

masci_tools/cmdline/commands/parse.py

@@ -103,11 +103,11 @@ def parse_structure_data(xml_file):
     """
     Parse the structure information in the given Fleur xml file
     """
-    from masci_tools.util.xml.xml_getters import get_structure_data
+    from masci_tools.util.xml.xml_getters import get_structuredata
 
     xmltree, schema_dict = _load_xml_file(xml_file)
 
-    atoms, cell, pbc = get_structure_data(xmltree, schema_dict)
+    atoms, cell, pbc = get_structuredata(xmltree, schema_dict)
 
     echo.echo_info('Atoms found:')
     echo.echo_formatted_list(atoms, ['symbol', 'kind', 'position'])
@@ -139,11 +139,11 @@ def parse_parameter_data(xml_file):
     """
     Parse the calculation parameters of the given xml file
     """
-    from masci_tools.util.xml.xml_getters import get_parameter_data
+    from masci_tools.util.xml.xml_getters import get_parameterdata
 
     xmltree, schema_dict = _load_xml_file(xml_file)
 
-    params = get_parameter_data(xmltree, schema_dict)
+    params = get_parameterdata(xmltree, schema_dict)
 
     echo.echo_info('LAPW parameters:')
     echo.echo_dictionary(params)
@@ -169,10 +169,10 @@ def parse_kpoints_data(xml_file):
     """
     Parse the used kpoints from the given xml-file
     """
-    from masci_tools.util.xml.xml_getters import get_kpoints_data
+    from masci_tools.util.xml.xml_getters import get_kpointsdata
 
     xmltree, schema_dict = _load_xml_file(xml_file)
-    kpoints, weights, cell, pbc = get_kpoints_data(xmltree, schema_dict, only_used=True)
+    kpoints, weights, cell, pbc = get_kpointsdata(xmltree, schema_dict, only_used=True)
 
     echo.echo_info('Bravais matrix:')
     echo.echo(str(cell))

masci_tools/io/fleurxmlmodifier.py

@@ -29,7 +29,8 @@
     from typing_extensions import Literal  #type: ignore
 
 from masci_tools.util.xml.collect_xml_setters import XPATH_SETTERS, SCHEMA_DICT_SETTERS, NMMPMAT_SETTERS
-from masci_tools.util.xml.common_functions import clear_xml
+from masci_tools.util.xml.xml_setters_names import set_attrib_value
+from masci_tools.util.xml.common_functions import clear_xml, eval_xpath_one
 from masci_tools.util.schema_dict_util import ensure_relaxation_xinclude
 from masci_tools.io.fleur_xml import load_inpxml
 from masci_tools.util.typing import XMLFileLike, FileLike
@@ -217,7 +218,8 @@ def apply_modifications(cls,
                             xmltree: etree._ElementTree,
                             nmmp_lines: list[str] | None,
                             modification_tasks: list[ModifierTask],
-                            validate_changes: bool = True) -> tuple[etree._ElementTree, list[str] | None]:
+                            validate_changes: bool = True,
+                            adjust_version_for_dev_version: bool = True) -> tuple[etree._ElementTree, list[str] | None]:
         """
         Applies given modifications to the fleurinp lxml tree.
         It also checks if a new lxml tree is validated against schema.
@@ -228,6 +230,10 @@ def apply_modifications(cls,
         :param modification_tasks: a list of modification tuples
         :param validate_changes: bool optional (default True), if True after all tasks are performed
                                  both the xmltree and nmmp_lines are checked for consistency
+        :param adjust_version_for_dev_version: bool optional (default True), if True and the schema_dict
+                                               and file version differ, e.g. a development version is used
+                                               the version is temporarily modified to swallow the validation
+                                               error that would occur
 
         :returns: a modified lxml tree and a modified n_mmp_mat file
         """
@@ -236,6 +242,9 @@ def apply_modifications(cls,
         xmltree, schema_dict = load_inpxml(xmltree)
         xmltree, _ = clear_xml(xmltree)
 
+        file_version = eval_xpath_one(xmltree, '//@fleurInputVersion', str)
+        is_dev_version = schema_dict['inp_version'] != file_version
+
         for task in modification_tasks:
             if task.name in cls.xpath_functions:
                 action = cls.xpath_functions[task.name]
@@ -253,7 +262,12 @@ def apply_modifications(cls,
                 raise ValueError(f'Unknown task {task.name}')
 
         if validate_changes:
-            schema_dict.validate(xmltree, header='Changes were not valid')
+            if is_dev_version and adjust_version_for_dev_version:
+                set_attrib_value(xmltree, schema_dict, 'fleurinputversion', schema_dict['inp_version'])
+                schema_dict.validate(xmltree, header='Changes were not valid')
+                set_attrib_value(xmltree, schema_dict, 'fleurinputversion', file_version)
+            else:
+                schema_dict.validate(xmltree, header='Changes were not valid')
             try:
                 validate_nmmpmat(xmltree, nmmp_lines, schema_dict)
             except ValueError as exc:
@@ -349,7 +363,8 @@ def changes(self) -> list[ModifierTask]:
     def modify_xmlfile(self,
                        original_inpxmlfile: XMLFileLike,
                        original_nmmp_file: FileLike | list[str] | None = None,
-                       validate_changes: bool = True) -> tuple[etree._ElementTree, dict[str, str]]:
+                       validate_changes: bool = True,
+                       adjust_version_for_dev_version: bool = True) -> tuple[etree._ElementTree, dict[str, str]]:
         """
         Applies the registered modifications to a given inputfile
 
@@ -375,10 +390,12 @@ def modify_xmlfile(self,
         else:
             original_nmmp_lines = None
 
-        new_xmltree, new_nmmp_lines = self.apply_modifications(original_xmltree,
-                                                               original_nmmp_lines,
-                                                               self._tasks,
-                                                               validate_changes=validate_changes)
+        new_xmltree, new_nmmp_lines = self.apply_modifications(
+            original_xmltree,
+            original_nmmp_lines,
+            self._tasks,
+            validate_changes=validate_changes,
+            adjust_version_for_dev_version=adjust_version_for_dev_version)
 
         ensure_relaxation_xinclude(new_xmltree, schema_dict)
         etree.indent(new_xmltree)

masci_tools/io/kkr_params.py

@@ -18,7 +18,7 @@
 __copyright__ = ('Copyright (c), 2017, Forschungszentrum Jülich GmbH,'
                  'IAS-1/PGI-1, Germany. All rights reserved.')
 __license__ = 'MIT license, see LICENSE.txt file'
-__version__ = '1.8.7'
+__version__ = '1.8.8'
 __contributors__ = 'Philipp Rüßmann'
 
 # This defines the default parameters for KKR used in the aiida plugin:
@@ -448,6 +448,8 @@ def __init__(self, **kwargs):
                 None, '%f', False,
                 'Superconductivity: Scaling factor for lambda_BdG (e.g. used to deactivate BdG coupling in some layers by setting the value to 0)'
             ]),
+            ('<PHASE_BDG>',
+             [None, '%f', False, 'Superconductivity: Atom dependent phase factor for superconducting coupling.']),
             ('<MIXFAC_BDG>', [
                 None, '%f', False,
                 'Superconductivity: Mixing factor used in the mixing of the BdG Delta (defaults to 0.1)'
@@ -489,6 +491,7 @@ def __init__(self, **kwargs):
                 None, '%f', False,
                 'Renormalization factor for energy integration weights (can be used to shift the Fermi level around).'
             ]),
+            ('NQDOSMAXPOINTS', [None, '%i', False, 'Max number of q-points per batch.']),
             # array dimensions
             ('NSHELD', [None, '%i', False, 'Array dimension: number of shells (default: 300)']),
             ('IEMXD', [None, '%i', False, 'Array dimension: number of energy points (default: 101)']),
@@ -556,6 +559,8 @@ def __init__(self, **kwargs):
                 None, '%l', False,
                 "Run option: do not add some energy terms (coulomb, XC, eff. pot.) to total energy (former: 'NoMadel')"
             ]),
+            ('<NONCOBFIELD>', [None, '%l', False,
+                               'Run option: use non-collinear exteranl fields read from bfield.dat']),
             ('<PRINT_GIJ>',
              [None, '%l', False, "Run option: print cluster G_ij matrices to outfile (former: 'Gmatij')"]),
             ('<PRINT_GMAT>', [None, '%l', False, "Run option: print Gmat to outfile (former: 'Gmat')"]),
@@ -1256,16 +1261,23 @@ def _check_input_consistency(self, set_lists_only=False, verbose=False):
 
             #yapf: disable
             listargs = dict([
-                ['<RBASIS>', naez], ['<RBLEFT>', nlbasis], ['<RBRIGHT>', nrbasis], ['<SHAPE>', natyp],
-                ['<ZATOM>', natyp], ['<SOCSCL>', natyp], ['<SITE>', natyp], ['<CPA-CONC>', natyp],
-                ['<KAOEZL>', nlbasis], ['<KAOEZR>', nrbasis], ['XINIPOL', natyp], ['<RMTREF>', natyp],
-                ['<RMTREFL>', nlbasis], ['<RMTREFR>', nrbasis], ['<FPRADIUS>', natyp], ['BZDIVIDE', 3],
-                ['<RBLEFT>', nlbasis], ['ZPERIODL', 3], ['<RBRIGHT>', nrbasis], ['ZPERIODR', 3],
-                ['LDAU_PARA', 5], ['CPAINFO', 2], ['<DELTAE>', 2], ['FILES', 2], ['DECIFILES', 2],
-                ['<RMTCORE>', naez], ['<MTWAU>', naez], ['<RTMTWAU>',nrbasis ], ['<LFMTWAU>', nlbasis],
-                ['<MTWAL>', naez], ['<RTMTWAL>',nrbasis ], ['<LFMTWAL>', nlbasis],
-                ['<AT_SCALE_BDG>', natyp], ['<LM_SCALE_BDG>', (lmax + 1)**2],
+                ['BZDIVIDE', 3], ['ZPERIODL', 3], ['ZPERIODR', 3], ['LDAU_PARA', 5],
+                ['CPAINFO', 2], ['<DELTAE>', 2], ['FILES', 2], ['DECIFILES', 2],
             ])
+            if naez is not None:
+                for key in ['<RBASIS>',  '<RMTCORE>',  '<MTWAU>',  '<MTWAL>']:
+                    listargs[key] = naez
+            if natyp is not None:
+                for key in ['<SHAPE>', '<ZATOM>', '<SOCSCL>', '<SITE>', '<CPA-CONC>', 'XINIPOL', '<RMTREF>', '<FPRADIUS>', '<AT_SCALE_BDG>', '<PHASE_BDG>']:
+                    listargs[key] = natyp
+            if nlbasis is not None:
+                for key in ['<RBLEFT>', '<KAOEZL>', '<RMTREFL>', '<RBLEFT>', '<LFMTWAU>', '<LFMTWAL>']:
+                    listargs[key] = nlbasis
+            if nrbasis is not None:
+                for key in ['<RBRIGHT>', '<KAOEZR>', '<RMTREFR>', '<RBRIGHT>', '<RTMTWAU>', '<RTMTWAL>']:
+                    listargs[key] = nrbasis
+            if lmax is not None:
+                listargs['<LM_SCALE_BDG>'] = (lmax + 1)**2
             #yapf: enable
 
             # deal with special stuff for voronoi:
@@ -1799,7 +1811,9 @@ def read_keywords_from_inputcard(self, inputcard='inputcard', verbose=False):
         rbr = self.get_value('<RBRIGHT>')
         zper_l = self.get_value('ZPERIODL')
         zper_r = self.get_value('ZPERIODR')
-        alat2ang = self.get_value('ALATBASIS') * get_aBohr2Ang()
+        alat2ang = self.get_value('ALATBASIS')
+        if alat2ang is not None:
+            alat2ang *= get_aBohr2Ang()
         if rbl is not None:
             self.set_value('<RBLEFT>', array(rbl) * alat2ang)
         if rbr is not None:

masci_tools/io/parsers/fleur/default_parse_tasks.py

@@ -256,7 +256,7 @@
         '_conversions': [Conversion(name='convert_relax_info')],
         'parsed_relax_info': {
             'parse_type': 'xmlGetter',
-            'name': 'get_structure_data',
+            'name': 'get_structuredata',
             'kwargs': {
                 'convert_to_angstroem': False,
                 'include_relaxations': False