🚀 aiida-thermo_pw: immigrate aiida-thermo_pw to aiida-mechanical

.copier-answers.yml

@@ -1,7 +1,7 @@
 # Changes here will be overwritten by Copier; NEVER EDIT MANUALLY
 _commit: v0.11.1
 _src_path: https://github.com/mbercx/python-copier
-description: AiiDA plugin for thermo_pw software
+description: AiiDA plugin for mechanical properties
 doc_deploy: github
 docs: myst
-package_name: aiida-thermo_pw
+package_name: aiida-mechanical

.github/workflows/.ci.yml → .github/workflows/ci.yml

@@ -33,4 +33,4 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
       - run: pip install click==8.1.8 hatch
-      - run: hatch test
+      - run: hatch test --py ${{ matrix.python-version }}

.gitignore

@@ -173,7 +173,7 @@ cython_debug/
 #  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
-#.idea/
+.idea/
 
 # Abstra
 # Abstra is an AI-powered process automation framework.
@@ -186,7 +186,7 @@ cython_debug/
 #  that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
 #  and can be added to the global gitignore or merged into this file. However, if you prefer, 
 #  you could uncomment the following to ignore the entire vscode folder
-# .vscode/
+.vscode/
 
 # Ruff stuff:
 .ruff_cache/
@@ -209,6 +209,4 @@ __marimo__/
 # MyST documentation build
 docs/_build
 
-# Jupytext sync is a tool for writing notebooks in `.ipynb` format, and syncing them to a `.md` file
-# https://marketplace.visualstudio.com/items?itemName=caenrigen.jupytext-sync
-.jupytext-sync-ipynb
+dev/

LICENSE

@@ -1,21 +1,91 @@
-MIT License
-
-Copyright (c) 2025 Marnik Bercx
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+Non-Commercial, End-User Software License Agreement for AiiDA-Supercon
+
+Copyright (c), 2021-2025, University of Bremen, Germany (U Bremen Excellence Chair),
+École Polytechnique Fédérale de Lausanne (Theory and Simulation of Materials (THEOS)
+and National Centre for Computational Design and Discovery of Novel Materials
+(NCCR MARVEL)), Switzerland and Paul Scherrer Institut (Laboratory for Materials
+ Simulations (LMS)), Switzerland. All rights reserved.
+
+INTRODUCTION
+
+- This license agreement sets forth the terms and conditions under which the
+  Authors and their Institutions (hereafter "LICENSORS") of the program
+"AiiDA-Supercon" (hereafter "PROGRAM"), will grant you (hereafter
+"LICENSEE") a fully-paid, non-exclusive, and non-transferable license for
+academic, non-commercial purposes only (hereafter "LICENSE") to use the PROGRAM
+computer software and associated documentation furnished hereunder.
+
+- LICENSEE acknowledges that the PROGRAM is a research tool still in the
+  development stage, that is being supplied "as is", without any related
+services, improvements or warranties from LICENSORS and that this license is
+entered into in order to enable others to utilize the PROGRAM in their academic
+activities.
+
+TERMS AND CONDITIONS OF THE LICENSE
+
+1. LICENSORS grant to LICENSEE a fully-paid up, non-exclusive, and
+non-transferable license to use the PROGRAM for academic, non-commercial
+purposes, upon the terms and conditions hereinafter set out and until
+termination of this license as set forth below.
+
+2. LICENSEE acknowledges that the PROGRAM is a research tool still in the
+development stage. The PROGRAM is provided "as is", without any related
+services or improvements from LICENSORS and that the LICENSE is entered into in
+order to enable others to utilize the PROGRAM in their academic activities.
+
+3. LICENSORS MAKES NO REPRESENTATIONS OR WARRANTIES, EXPRESS OR IMPLIED,
+INCLUDING WITHOUT LIMITATION ANY REPRESENTATIONS OR WARRANTIES OF
+MERCHANTABILITY OR FITNESS FOR PARTICULAR PURPOSE OR THAT THE USE OF THE
+PROGRAM WILL NOT INFRINGE ANY PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER RIGHTS.
+LICENSORS shall not be liable for any direct, indirect or consequential damages
+with respect to any claim by LICENSEE or any third party arising from this
+Agreement or use of the PROGRAM.
+
+4. LICENSEE agrees that it will use the PROGRAM, and any modifications,
+improvements, or derivatives to PROGRAM that LICENSEE may create (collectively,
+"IMPROVEMENTS") solely for academic, non-commercial purposes and shall not
+distribute or transfer the PROGRAM or any IMPROVEMENTS to any person without
+prior written permission from LICENSORS. The terms "academic, non-commercial",
+as used in this Agreement, mean academic or other scholarly research which (a)
+is not undertaken for profit, or (b) is not intended to produce works,
+services, or data for commercial use, or (c) is neither conducted, nor funded,
+by a person or an entity engaged in the commercial use, application or
+exploitation of works similar to the PROGRAM.
+
+5. LICENSEE agrees that he/she shall make the following acknowledgement in
+publications resulting from the use of the PROGRAM: "Sebastiaan. P. Huber, Spyros Zoupanos,
+Martin Uhrin, Leopold Talirz, Leonid Kahle, Rico Häuselmann, Dominik Gresch,
+Tiziano Müller, Aliaksandr V. Yakutovich, Casper W. Andersen, Francisco F.
+Ramirez, Carl S. Adorf, Fernando Gargiulo, Snehal Kumbhar, Elsa Passaro,
+Conrad Johnston, Andrius Merkys, Andrea Cepellotti, Nicolas Mounet, Nicola
+Marzari, Boris Kozinsky, and Giovanni Pizzi, AiiDA 1.0, a scalable computational
+infrastructure for automated reproducible workflows and data provenance,
+Scientific Data 7, 300 (2020), DOI: 10.1038/s41597-020-00638-4"
+(http://www.aiida.net), plus any additional reference explicitly mentioned in
+the custom workflow used. Except for the above-mentioned acknowledgment,
+LICENSEE shall not use the PROGRAM title or the names or logos of LICENSORS,
+nor any adaptation thereof, nor the names of any of its employees or
+laboratories, in any advertising, promotional or sales material without prior
+written consent obtained from LICENSORS in each case.
+
+6. Ownership of all rights, including copyright in the PROGRAM and in any
+material associated therewith, shall at all times remain with LICENSORS, and
+LICENSEE agrees to preserve the same. LICENSEE agrees not to use any portion of
+the PROGRAM or of any IMPROVEMENTS in any machine-readable form outside the
+PROGRAM, nor to make any copies except for its internal use, without prior
+written consent of LICENSORS. LICENSEE agrees to place the following copyright
+notice on any such copies: © All rights reserved. Paul Scherrer Institut, Switzerland,
+Laboratory for Materials Simulations (LMS), 2025; Authors: Marnik Bercx and Nicola
+Marzari.
+
+7. The LICENSE shall not be construed to confer any rights upon LICENSEE by
+implication or otherwise except as specifically set forth herein.
+
+8. This Agreement shall be governed by the material laws of Switzerland and any
+dispute arising out of this Agreement or use of the PROGRAM shall be brought
+before the courts of Lausanne, Switzerland.
+
+9. This Agreement and the LICENSE shall remain effective until expiration of
+the copyrights of the PROGRAM except that upon any breach of this Agreement by
+LICENSEE, LICENSORS shall have the right to terminate the LICENSE immediately
+upon notice to LICENSEE.

LICENSE.txt

@@ -0,0 +1,24 @@
+The MIT License (MIT)
+
+Copyright (c), 2015-2020, ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE
+(Theory and Simulation of Materials (THEOS) and National Centre for
+Computational Design and Discovery of Novel Materials (NCCR MARVEL)).
+All rights reserved.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

README.md

@@ -1,5 +1,3 @@
-[![Templated from python-copier](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/mbercx/python-copier/refs/heads/main/docs/img/badge.json)](https://github.com/mbercx/python-copier)
+# `aiida-mechanical`
 
-# `aiida-thermo_pw`
-
-AiiDA plugin for thermo_pw software
+AiiDA plugin package with workflows for mechanical properties

docs/developer.md

@@ -11,7 +11,7 @@ First clone the repository from GitHub
 
 and install the package locally in **editable** mode (`-e`):
 
-    cd aiida-thermo_pw
+    cd aiida-mechanical
     pip install -e .
 
 :::{note}

docs/index.md

@@ -1,5 +1,5 @@
 # Introduction
 
-This is the documentation of the `aiida-thermo_pw` Python package.
+This is the documentation of the `aiida-mechanical` Python package.
 
-AiiDA plugin for thermo_pw software
+AiiDA plugin for mechanical properties

docs/myst.yml

@@ -1,8 +1,8 @@
 # See docs at: https://mystmd.org/guide/frontmatter
 version: 1
 project:
-  title: aiida-thermo_pw
-  description: AiiDA plugin for thermo_pw software
+  title: aiida-mechanical
+  description: AiiDA plugin for mechanical properties
   # keywords: []
   # authors: []
   # github: https://github.com/

examples/example_01.py

@@ -0,0 +1,58 @@
+#!/usr/bin/env python
+"""Run a ``Thermo_pwBaseWorkChain`` for a scf calculation.
+
+Usage: ./example_01.py
+"""
+
+import click
+
+from aiida import cmdline, orm
+
+from aiida_mechanical.workflows.base import Thermo_pwBaseWorkChain
+
+from aiida_mechanical.cli.params import RUN
+from aiida_mechanical.utils.structure import read_structure
+from aiida_mechanical.utils.workflows.builder.serializer import print_builder
+from aiida_mechanical.utils.workflows.builder.setter import set_parallelization
+from aiida_mechanical.utils.workflows.builder.submit import (
+    submit_and_add_group,
+)
+
+
+def submit(
+    code: orm.Code,
+    structure: orm.StructureData,
+    group: orm.Group = None,
+    run: bool = False,
+):
+    """Submit a ``Thermo_pwBaseWorkChain`` to calculate the thermodynamic properties."""
+    builder = Thermo_pwBaseWorkChain.get_builder_from_protocol(
+        code, structure=structure
+    )
+
+    # You can change parallelization here
+    parallelization = {
+        "num_mpiprocs_per_machine": 8,
+        "npool": 4,
+    }
+    set_parallelization(builder, parallelization, process_class=Thermo_pwBaseWorkChain)
+
+    print_builder(builder)
+
+    if run:
+        submit_and_add_group(builder, group)
+
+
+@click.command()
+@cmdline.utils.decorators.with_dbenv()
+@cmdline.params.options.CODE(help="The pw.x code identified by its ID, UUID or label.")
+@cmdline.params.options.GROUP(help="The group to add the submitted workchain.")
+@click.argument("filename", type=click.Path(exists=True))
+@RUN()
+def cli(filename, code, group, run):
+    """Run a ``Thermo_pwBaseWorkChain`` to calculate the scf.
+
+    FILENAME: a crystal structure file, e.g., ``structures/Si.xsf``.
+    """
+    struct = read_structure(filename, store=True)
+    submit(code, struct, group, run)

examples/structures/Pb.xsf

@@ -0,0 +1,8 @@
+CRYSTAL
+PRIMVEC 1
+      0.0000000000       2.4595782679       2.4595782679
+      2.4595782679       0.0000000000       2.4595782679
+      2.4595782679       2.4595782679       0.0000000000
+PRIMCOORD 1
+1 1
+82       0.0000000000       0.0000000000       0.0000000000

examples/structures/Si.xsf

@@ -0,0 +1,9 @@
+CRYSTAL
+PRIMVEC 1
+      0.0000000000       2.7164586260       2.7164586260
+      2.7164586260       0.0000000000       2.7164586260
+      2.7164586260       2.7164586260       0.0000000000
+PRIMCOORD 1
+2 1
+14       1.3582293131       4.0746879391       1.3582293131
+14      -0.0000000000      -0.0000000000       2.7164586260