initial commit

Author: jan-janssen

.github/workflows/pyiron.yml

@@ -0,0 +1,28 @@
+name: pyiron
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - uses: conda-incubator/setup-miniconda@v3
+      with:
+        auto-update-conda: true
+        python-version: "3.12"
+        environment-file: environment.yml
+        auto-activate-base: false
+    - name: Tests
+      shell: bash -l {0}
+      run: |
+        pip install -e adis_tools
+        pip install -e python_workflow_definition
+        conda install -c conda-forge jupyter papermill
+        export ESPRESSO_PSEUDO=$(pwd)/espresso/pseudo
+        papermill universal_qe_to_pyiron_base.ipynb universal_qe_to_pyiron_base_out.ipynb -k "python3"

adis_tools/pyproject.toml

@@ -0,0 +1,20 @@
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "adis_tools"
+version = "0.0.1"
+description = "Common functions for the Ab initio Description of Iron and Steel (ADIS2023): Digitalization and Workflows workshop"
+authors = [
+  { name = "Jan Janssen", email = "janssen@mpie.de" },
+  { name = "Janine George", email = "janine.geogre@bam.de" },
+  { name = "Marnik Bercx", email = "marnik.bercx@psi.ch" },
+  { name = "Christina Ertural", email = "christina.ertural@bam.de" },
+  { name = "Joerg Schaarschmidt", email = "joerg.schaarschmidt@kit.edu" },
+  { name = "Sam Dareska" },
+  { name = "Leopold Talirz", email = "leopold.talirz@gmail.com" },
+  { name = "Julian Geiger", email = "julian.geiger@psi.ch" },
+]
+license = { text = "MIT" }
+dependencies = ["numpy", "xmlschema", "qe_tools", "ase"]

adis_tools/src/adis_tools/__init__.py

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+import numpy
+
+from xmlschema import XMLSchema
+from qe_tools import CONSTANTS
+
+from ase import Atoms
+from importlib.resources import files
+
+from . import schemas
+
+
+def parse_pw(xml_file):
+    """Parse a Quantum Espresso XML output file."""
+
+    xml_dict = XMLSchema(str(files(schemas) / 'qes_230310.xsd')).to_dict(xml_file)
+
+    parsed_results = {}
+
+    try:
+        cell = numpy.array(
+            [ v for v in xml_dict['output']['atomic_structure']['cell'].values()]
+        ) * CONSTANTS.bohr_to_ang
+        symbols = [el['@name'] for el in xml_dict['output']['atomic_structure']['atomic_positions']['atom']]
+        positions = numpy.array(
+            [el['$'] for el in xml_dict['output']['atomic_structure']['atomic_positions']['atom']]
+        ) * CONSTANTS.bohr_to_ang
+
+        parsed_results['ase_structure'] = Atoms(
+            cell=cell,
+            positions=positions,
+            symbols=symbols,
+            pbc=True,
+        )
+    except KeyError:
+        pass
+
+    try:
+        parsed_results['energy'] = xml_dict['output']['total_energy']['etot'] * CONSTANTS.ry_to_ev
+    except KeyError:
+        pass
+
+    try:
+        parsed_results['forces'] = (
+            numpy.array(xml_dict['output']['forces']['$']).reshape(xml_dict['output']['forces']['@dims'])
+            * 2 * CONSTANTS.ry_to_ev / CONSTANTS.bohr_to_ang
+        )
+    except KeyError:
+        pass
+
+    return parsed_results