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JaGeojanosh
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Tutorials for QHA and Grüneisen workflows (#1122)
* add info on jobflow remote and lobster workflow * remove file and fix linting * add another phonon example * add tutorial for phonons including mock_vasp * add tutorial test * test tutorial test * test tutorial test * test tutorial test * test tutorial test * split up workflow again * split up workflow again * split up workflow again * split up workflow again * add automerge * add automerge * add mock lobster and a lobster tutorial * fix bug in tutorial and fix calc summary * add plot * fix linting * fix linting * more type hints * fix linting * fix linting * fix linting * fix linting * fix more linting * fix final linting * Update pyproject.toml * adapt tutorial * fix linting and add a tmp dir to tutorial execution * remove file * print ref and actual values in testing.lobster.verify_inputs ValueError * add a qha tutorial * add unit in document * add tutorials to doc * fix linting * fix syntax * add tutorials to doc attempt2 * fix line length * fix line length * final fix linting * test fixing the linter again * update tests * fix linting * fix linting * fix more linting * fix more linting * fix more linting * fix tutorial * update gruneisen workflow * update gruneisen workflow * update gruneisen workflow * update test * fix linting * fix linting * fix linting * fix linting * hopefully fix linting errors * exclude grunisen file from ruff * ADD COMMENTS --------- Co-authored-by: Janosh Riebesell <[email protected]>
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‎.github/workflows/docs.yml‎

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python -m pip install --upgrade pip
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pip install .[strict,docs]
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- name: Copy tutorials
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run: |
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cp -r tutorials docs/
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jupyter nbconvert --to markdown docs/tutorials/*.ipynb
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jupyter nbconvert --to markdown docs/tutorials/*/*.ipynb
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- name: Build
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run: sphinx-build docs docs_build
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‎.gitignore‎

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docs/_build/*/*
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docs/_build/*/*/*
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docs_build/*
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docs/tutorials/*
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docs/tutorials/*/*
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# C extensions
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*.so

‎.pre-commit-config.yaml‎

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hooks:
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- id: ruff
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args: [--fix]
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exclude: tutorials/grueneisen_workflow.ipynb
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- id: ruff-format
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v5.0.0

‎docs/index.md‎

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‎src/atomate2/common/flows/eos.py‎

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@@ -95,6 +95,12 @@ def make(self, structure: Structure, prev_dir: str | Path = None) -> Flow:
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)
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relax_flow.name = "EOS equilibrium relaxation"
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try:
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if len(relax_flow.jobs) > 1:
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for job in relax_flow.jobs:
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job.append_name(" EOS equilibrium relaxation")
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except AttributeError:
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pass
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flow_output["initial_relax"] = {
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"E0": relax_flow.output.output.energy,
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"V0": relax_flow.output.structure.volume,
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prev_dir=prev_dir,
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)
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relax_job.name += f" deformation {frame_idx}"
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try:
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if len(relax_job.jobs) > 1:
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for job in relax_job.jobs:
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job.append_name(f" deformation {frame_idx}")
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except AttributeError:
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pass
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jobs["relax"].append(relax_job)
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if self.static_maker:

‎src/atomate2/common/schemas/qha.py‎

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)
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helmholtz_volume: Optional[list[list[float]]] = Field(
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None,
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description="Free energies at temperatures and volumes."
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"shape (temperatures, volumes)",
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description="Free energies (eV) at temperatures and volumes (Angstrom^3)."
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"shape (temperatures, volumes)", # TODO: add units here
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)
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volume_temperature: Optional[list[float]] = Field(
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None,

‎tests/aims/test_flows/test_eos.py‎

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# mapping from job name to directory containing test files
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ref_paths = {
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"Relaxation calculation 1": "double-relax-si/relax-1",
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"Relaxation calculation 2": "double-relax-si/relax-2",
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"Relaxation calculation 1 EOS equilibrium relaxation": "double-relax-si/relax-1",
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"Relaxation calculation 2 EOS equilibrium relaxation": "double-relax-si/relax-2",
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"Relaxation calculation (fixed cell) deformation 0": "eos-si/0",
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"Relaxation calculation (fixed cell) deformation 1": "eos-si/1",
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"Relaxation calculation (fixed cell) deformation 2": "eos-si/2",

‎tests/test_data/vasp/Si_gruneisen_tutorial/dft_phonon_static_1_1_ground_24/inputs/INCAR.gz‎

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‎tests/test_data/vasp/Si_gruneisen_tutorial/dft_phonon_static_1_1_ground_24/inputs/POSCAR.gz‎

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‎tests/test_data/vasp/Si_gruneisen_tutorial/dft_phonon_static_1_1_ground_24/inputs/POTCAR.spec.gz‎

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