Add quantum espresso eample (#1)

* Add quantum espresso eample

* add hatchling

Author: jan-janssen

.github/workflows/pipeline.yml

@@ -21,6 +21,8 @@ jobs:
     - name: Test
       shell: bash -l {0}
       run: |
+        export ESPRESSO_PSEUDO=$(pwd)/espresso/pseudo
+        pip install --no-deps --no-build-isolation -e qe_xml_parser
         verdi presto --profile-name pwd
         echo -e 'from aiida import load_profile\nload_profile()\n\nfrom python_workflow_definition.aiida import load_workflow_json\n\n\nif __name__ == "__main__":\n    workgraph = load_workflow_json(file_name="workflow.json")\n    workgraph.run()' > test_with_aiida.py
         python test_with_aiida.py
@@ -40,6 +42,8 @@ jobs:
     - name: Test
       shell: bash -l {0}
       run: |
+        export ESPRESSO_PSEUDO=$(pwd)/espresso/pseudo
+        pip install --no-deps --no-build-isolation -e qe_xml_parser
         echo -e 'from jobflow.managers.local import run_locally\nfrom python_workflow_definition.jobflow import load_workflow_json\n\n\nif __name__ == "__main__":\n    flow = load_workflow_json(file_name="workflow.json")\n    print(run_locally(flow))' > test_with_jobflow.py
         python test_with_jobflow.py
 
@@ -58,5 +62,7 @@ jobs:
     - name: Test
       shell: bash -l {0}
       run: |
+        export ESPRESSO_PSEUDO=$(pwd)/espresso/pseudo
+        pip install --no-deps --no-build-isolation -e qe_xml_parser
         echo -e 'from python_workflow_definition.pyiron_base import load_workflow_json\n\n\nif __name__ == "__main__":\n    delayed_object_lst = load_workflow_json(file_name="workflow.json")\n    print(delayed_object_lst[-1].pull())' > test_with_pyiron.py
         python test_with_pyiron.py

README.md

@@ -1,30 +1,4 @@
-# Arithmetic Example Workflow
-[![Pipeline](https://github.com/pythonworkflow/example-workflow/actions/workflows/pipeline.yml/badge.svg)](https://github.com/pythonworkflow/example-workflow/actions/workflows/pipeline.yml)
-
-Template repository for publishing an interoperable workflow based on the Python Workflow Definition. 
-
-## Content 
-The minimal workflow consists of three files:
-
-| File              | Explanation                                             |
-|-------------------|---------------------------------------------------------|
-| `environment.yml` | Conda environment for software dependencies             |
-| `workflow.py`     | Python functions representing the nodes of the workflow |
-| `workflow.json`   | Workflow graph consisting of nodes and edges            |
-
-Additional optional files for the publication of the workflow: 
-
-| File                             | Explanation                              |
-|----------------------------------|------------------------------------------|
-| `README.md`                      | Readme file to introduce the workflow    |
-| `.github/workflows/pipeline.yml` | Github Actions to test the workflow      |
-
-## Publish your workflow
-You can publish your workflow in five simple steps:
-* Fork the repository and clone your fork locally.
-* Export your workflow to the Python Workflow Definition using the `python_workflow_definition` Python package, by calling the `write_workflow_json()` function.  
-* Replace the `environment.yml`, `workflow.py` and `workflow.json` in your local folder with the files for your workflow. In addition, you can add additional files if they are required and update the `README.md` to explain your workflow.
-* Commit the files locally using `git add -A` and `git commit -m "add my workflow"`
-* Push your workflow to Github `git push`
-
+# Quantum Espresso Bulk Modulus Workflow
+[![Pipeline](https://github.com/pythonworkflow/quantum-espresso-bulk-modulus-workflow/actions/workflows/pipeline.yml/badge.svg)](https://github.com/pythonworkflow/quantum-espresso-bulk-modulus-workflow/actions/workflows/pipeline.yml)
 
+Workflow to calculate the equilibrium bulk modulus with the [quantum ESPRESSO](https://www.quantum-espresso.org) density functional theory simulation code. This repository demonstrates the use of the [python-workflow-definition](https://github.com/pythonworkflow/python-workflow-definition) Python package and the [example-workflow](https://github.com/pythonworkflow/example-workflow) repository template.

environment.yml

@@ -2,5 +2,12 @@ channels:
 - conda-forge
 dependencies:
 - python =3.12
+- ase=3.24.0
+- hatchling =1.27.0
+- matplotlib=3.10.1
+- xmlschema=3.4.3
+- optimade=1.2.3
+- qe=7.2
+- qe-tools=2.0.0
 - pip:
   - python-workflow-definition==0.0.1

espresso/pseudo/Al.pbe-n-kjpaw_psl.1.0.0.UPF

@@ -0,0 +1,13 @@
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "qe_xml_parser"
+version = "0.0.1"
+description = "Quantum Espresso xml output parser"
+authors = [
+  { name = "Marnik Bercx", email = "marnik.bercx@psi.ch" },
+]
+license = { text = "MIT" }
+dependencies = ["numpy", "xmlschema", "qe_tools", "ase"]

qe_xml_parser/pyproject.toml

@@ -0,0 +1,70 @@
+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