Exciting mapping parser (#2)

* Initial exciting parser

* Fix commit

* Add more quantities

* Rename schema package

* Add files

Author: ladinesa

.gitignore

@@ -0,0 +1,130 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+.pyenv
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/

pyproject.toml

@@ -19,7 +19,7 @@ dynamic = ["version"]
 readme = "README.md"
 requires-python = ">=3.9"
 authors = [
-    { name = "Esma B. Boydas, email = "esma.boydas@physik.hu-berlin.de" },
+    { name = "Esma B. Boydas", email = "esma.boydas@physik.hu-berlin.de" },
     { name = "Nathan Daelman", email = "ndaelman@physik.hu-berlin.de" },
     { name = "Alvin N. Ladines", email = "ladinesa@physik.hu-berlin.de" },
     { name = "Bernadette Mohr", email = "mohrbern@physik.hu-berlin.de" },
@@ -120,8 +120,8 @@ where = ["src"]
 [tool.setuptools_scm]
 
 [project.entry-points.'nomad.plugin']
-parser_entry_point = "nomad_simulation_parsers.parsers:parser_entry_point"
-schema_package_entry_point = "nomad_simulation_parsers.schema_packages:schema_package_entry_point"
+exciting_parser_entry_point = "nomad_simulation_parsers.parsers:exciting_parser_entry_point"
+exciting_schema_package_entry_point = "nomad_simulation_parsers.schema_packages:exciting_schema_package_entry_point"
 
 
 

src/nomad_simulation_parsers/parsers/__init__.py

@@ -1,18 +1,23 @@
 from nomad.config.models.plugins import ParserEntryPoint
-from pydantic import Field
 
 
-class NewParserEntryPoint(ParserEntryPoint):
-    parameter: int = Field(0, description='Custom configuration parameter')
-
+class EntryPoint(ParserEntryPoint):
     def load(self):
-        from nomad_simulation_parsers.parsers.parser import NewParser
+        from nomad.parsing.parser import MatchingParserInterface
 
-        return NewParser(**self.dict())
+        return MatchingParserInterface(
+            parser_class_name='nomad_simulation_parsers.parsers.exciting.parser.ExcitingParser',
+            **self.dict(),
+        )
 
 
-parser_entry_point = NewParserEntryPoint(
-    name='NewParser',
-    description='New parser entry point configuration.',
-    mainfile_name_re='.*\.newmainfilename',
+exciting_parser_entry_point = EntryPoint(
+    name='parsers/exciting',
+    aliases=['parsers/exciting'],
+    description='NOMAD parser for EXCITING.',
+    python_package='nomad_simulation_parsers',
+    mainfile_contents_re=r'EXCITING.*started[\s\S]+?All units are atomic ',
+    mainfile_name_re=r'^.*.OUT(\.[^/]*)?$',
+    code_name='exciting',
+    code_homepage='http://exciting-code.org/',
 )

src/nomad_simulation_parsers/parsers/exciting/eigval_reader.py

@@ -0,0 +1,33 @@
+import numpy as np
+from nomad.parsing.file_parser.text_parser import Quantity, TextParser
+
+
+def str_to_eigenvalues(val_in: str) -> dict[str, np.ndarray]:
+    val = val_in[: val_in.rfind('\n \n')].strip()
+    val = np.array([v.split() for v in val.split('\n')], dtype=float)
+    val = np.transpose(val)
+    occs = val[-1]
+    eigs = val[-2]
+
+    tol = 0.1
+    nspin = 1 if np.any(occs > 1 + tol) else 2
+    data = dict()
+    data['occupancies'] = np.reshape(occs, (nspin, len(occs) // nspin))
+    data['eigenvalues'] = np.reshape(eigs, (nspin, len(eigs) // nspin))
+    return data
+
+
+class EigvalReader(TextParser):
+    def init_quantities(self):
+        self._quantities = [
+            Quantity('k_points', r'\s*\d+\s*([\d\.Ee\- ]+):\s*k\-point', repeats=True),
+            Quantity(
+                'eigenvalues_occupancies',
+                r'\(state\, eigenvalue and occupancy below\)\s*'
+                r'([\d\.Ee\-\s]+?(?:\n *\n))',
+                str_operation=str_to_eigenvalues,
+                repeats=True,
+            ),
+            Quantity('n_k_points', r'(\d+) +\: +nkpt', dtype=int),
+            Quantity('n_states', r'(\d+) +\: +nstsv', dtype=int),
+        ]