pyiron-workflow-vasp 0.1.0__tar.gz

pyiron_workflow_vasp-0.1.0/PKG-INFO

@@ -0,0 +1,231 @@
+Metadata-Version: 2.4
+Name: pyiron_workflow_vasp
+Version: 0.1.0
+Summary: A VASP workflow integration package for pyiron
+Author-email: pyiron Team <pyiron@mpie.de>
+License: BSD-3-Clause
+Project-URL: Homepage, https://github.com/pyiron/pyiron_workflow_vasp
+Project-URL: Documentation, https://github.com/pyiron/pyiron_workflow_vasp
+Project-URL: Repository, https://github.com/pyiron/pyiron_workflow_vasp.git
+Project-URL: Bug Tracker, https://github.com/pyiron/pyiron_workflow_vasp/issues
+Keywords: pyiron,vasp,workflow,dft,materials-science
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Physics
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Requires-Python: <3.13,>=3.10
+Description-Content-Type: text/markdown
+Requires-Dist: numpy<2.0.0,>=1.26.4
+Requires-Dist: pandas<4.0.0,>=3.0.0
+Requires-Dist: matplotlib<4.0.0,>=3.10.9
+Requires-Dist: ase<4.0.0,>=3.27.0
+Requires-Dist: scipy<2.0.0,>=1.17.0
+Requires-Dist: pyiron-workflow==0.15.6
+Requires-Dist: pyiron-workflow-atomistics==0.0.6
+Requires-Dist: pyiron_vasp==0.2.19
+Requires-Dist: pymatgen<2027.0.0,>=2026.5.4
+Requires-Dist: pyiron_snippets<2.0.0,>=1.2.1
+Requires-Dist: scikit-learn<2.0.0,>=1.8.0
+Requires-Dist: tqdm<5.0.0,>=4.67.3
+Provides-Extra: test
+Requires-Dist: pytest>=6.0; extra == "test"
+Requires-Dist: pytest-cov>=2.0; extra == "test"
+Requires-Dist: nbformat; extra == "test"
+Requires-Dist: nbclient; extra == "test"
+Provides-Extra: dev
+Requires-Dist: pytest>=6.0; extra == "dev"
+Requires-Dist: pytest-cov>=2.0; extra == "dev"
+Requires-Dist: black>=22.0; extra == "dev"
+Requires-Dist: isort>=5.0; extra == "dev"
+Requires-Dist: flake8>=4.0; extra == "dev"
+Requires-Dist: ruff>=0.5; extra == "dev"
+Provides-Extra: notebook
+Requires-Dist: jupyter>=1.0.0; extra == "notebook"
+Requires-Dist: notebook>=6.0.0; extra == "notebook"
+
+# pyiron_workflow_vasp
+
+A VASP workflow integration package for pyiron, providing tools and utilities for running and managing VASP calculations within the pyiron workflow framework.
+
+## Installation
+
+The package can be installed using pip:
+
+```bash
+# Basic installation
+pip install pyiron_workflow_vasp
+
+# Installation with development tools
+pip install "pyiron_workflow_vasp[dev]"
+
+# Installation with notebook support
+pip install "pyiron_workflow_vasp[notebook]"
+
+# Installation with all optional dependencies
+pip install "pyiron_workflow_vasp[dev,notebook]"
+```
+
+## Dependencies
+
+The package requires the following core dependencies:
+- Python >= 3.8
+- numpy >= 1.20.0
+- pandas >= 1.3.0
+- pymatgen >= 2023.0.0
+- pyiron_workflow >= 0.1.0
+- ase >= 3.22.0
+
+## Project Information
+
+- **License**: BSD-3-Clause
+- **Development Status**: Alpha
+- **Documentation**: [GitHub Repository](https://github.com/pyiron/pyiron_workflow_vasp)
+- **Bug Tracker**: [GitHub Issues](https://github.com/pyiron/pyiron_workflow_vasp/issues)
+
+## Usage
+
+The package provides a set of tools for running VASP calculations within pyiron workflows. A minimal end-to-end example:
+
+```python
+from ase.build import bulk
+from pymatgen.io.vasp.inputs import Incar
+from pyiron_workflow_vasp.vasp import VaspInput, vasp_job
+
+structure = bulk("Fe", cubic=True, a=2.83)
+incar = Incar.from_dict({
+    "ENCUT": 400,
+    "ISMEAR": 1,
+    "SIGMA": 0.1,
+    "ISPIN": 2,
+    "MAGMOM": "2*3.0",
+})
+
+# VaspInput bundles structure + INCAR (+ optional KPOINTS / explicit POTCARs).
+# Without an explicit potcar_paths kwarg, POTCAR generation uses the
+# pseudopotential library configured in ~/.pyiron_vasp_config.
+vasp_input = VaspInput(structure=structure, incar=incar)
+
+job = vasp_job(workdir="./bulk_fe_run", vasp_input=vasp_input)
+job.run()
+
+print("converged:", job.outputs.convergence_status.value)
+print("E_pot:    ", job.outputs.to_value_dict()["vasp_output"]["generic"]["energy_pot"])
+```
+
+For more examples — including an equation-of-state scan and a queued cluster
+run — see:
+
+- [`examples/run_bulk_fe.py`](examples/run_bulk_fe.py) — a runnable script with no hardcoded cluster paths.
+- [`example_notebooks/QuickStart.ipynb`](example_notebooks/QuickStart.ipynb) — the original walkthrough (uses MPIE cluster paths).
+- [`.pyiron_vasp_config.example`](.pyiron_vasp_config.example) — annotated template for the config file.
+
+## VASP Configuration
+
+The `.pyiron_vasp_config` file is essential for configuring the paths to the VASP pseudopotential files (POTCAR files) used in pyiron_workflow's VASP nodes. The file specifies the locations of different VASP potential sets and the default potential set to be used.
+
+For detailed configuration instructions, see [generate_vasp_pyiron_config.md](generate_vasp_pyiron_config.md), which includes:
+- Basic configuration setup
+- Configuring custom pseudopotential sets
+- Adding new pseudopotential variants to CSV files
+
+## 1. Determine the Locations of Your VASP POTCAR Files
+
+Before creating the `.pyiron_vasp_config` file, ensure that you know the locations of the different POTCAR sets on your system. The common VASP potential directories are `potpaw_64`, `potpaw_54`, and `potpaw_52`, but your setup may vary. The directory structure should look something like this:
+
+```
+/home/pyiron_resources_cmmc/vasp/potpaw_64/LDA
+/home/pyiron_resources_cmmc/vasp/potpaw_64/GGA
+/home/pyiron_resources_cmmc/vasp/potpaw_54/LDA
+/home/pyiron_resources_cmmc/vasp/potpaw_54/GGA
+/home/pyiron_resources_cmmc/vasp/potpaw_52/LDA
+/home/pyiron_resources_cmmc/vasp/potpaw_52/GGA
+```
+
+- **LDA** and **GGA** refer to the functional types for the VASP potentials.
+
+## 2. Create the .pyiron_vasp_config File
+
+1. Open a terminal and navigate to your home directory:
+
+    ```bash
+    cd ~
+    ```
+
+2. Use a text editor (such as `nano` or `vim`) to create and open the `.pyiron_vasp_config` file. For example:
+
+    ```bash
+    nano .pyiron_vasp_config
+    ```
+
+3. Add the following lines to the file. Make sure to modify the paths according to your setup.
+
+    ```ini
+    # Set the default POTCAR set
+    # Make sure that the default_POTCAR_set matches one of the suffixes in the vasp_POTCAR_path_*
+    default_POTCAR_set = potpaw64
+    
+    # Path to the root directory containing the VASP pseudopotential files
+    pyiron_vasp_resources = /home/pyiron_resources_cmmc/vasp
+    
+    # Path for different POTPAW versions (adjust these paths according to your setup)
+    vasp_POTCAR_path_potpaw64 = {pyiron_vasp_resources}/potpaw_64
+    vasp_POTCAR_path_potpaw54 = {pyiron_vasp_resources}/potpaw_54
+    vasp_POTCAR_path_potpaw52 = {pyiron_vasp_resources}/potpaw_52
+    # Note that pyiron vasp nodes can detect variants of vasp_POTCAR_path_{randomsuffix}
+    # So if you want to do something with custom pseudopotentials, you can... 
+    # Each of these dirs must have a "GGA" and "LDA" subdirectory structure
+    # i.e. 
+    # The structure should look like
+    # .../vasp/potpaw_64/LDA
+    # .../vasp/potpaw_64/GGA
+    # .../vasp/potpaw_54/LDA etc.
+    ```
+
+4. After you have added the configuration details, save the file:
+   - If you're using `nano`, press `Ctrl + O`, then `Enter` to save. Press `Ctrl + X` to exit.
+   - If you're using `vim`, press `Esc`, type `:wq`, and press `Enter` to save and exit.
+
+## 3. Verify File Permissions
+
+Ensure that your `.pyiron_vasp_config` file and the POTCAR directories are readable by your user. Run the following command to check the file permissions of the `.pyiron_vasp_config`:
+
+```bash
+ls -l ~/.pyiron_vasp_config
+```
+
+If necessary, you can modify the permissions to ensure read access:
+
+```bash
+chmod 644 ~/.pyiron_vasp_config
+```
+
+Also, verify that you have read/copy access to the files inside the VASP resource directories (`potpaw_64`, `potpaw_54`, etc.):
+
+```bash
+ls -l /home/pyiron_resources_cmmc/vasp/potpaw_64
+```
+
+## 4. Testing Your Configuration
+
+To verify that pyiron is correctly reading the `.pyiron_vasp_config` file, you can either check within your pyiron scripts or write a simple Python script to test the configuration:
+
+```python
+import os
+from pathlib import Path
+
+# Read the config file
+config_file = Path.home().joinpath(".pyiron_vasp_config")
+with open(config_file, "r") as f:
+    print(f.read())
+```
+
+This should print out the contents of your `.pyiron_vasp_config`, and you can check if the paths are correctly generated.
+
+### Additional Notes:
+- **Ensure Correct Paths**: Double-check that the paths to your POTCAR directories are correct. Incorrect paths will lead to pyiron not being able to find the necessary POTCAR files for your VASP calculations.
+
+By following these instructions, you'll have a correctly configured `.pyiron_vasp_config` file that points to the appropriate VASP pseudopotential directories.

pyiron_workflow_vasp-0.1.0/README.md

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+# pyiron_workflow_vasp
+
+A VASP workflow integration package for pyiron, providing tools and utilities for running and managing VASP calculations within the pyiron workflow framework.
+
+## Installation
+
+The package can be installed using pip:
+
+```bash
+# Basic installation
+pip install pyiron_workflow_vasp
+
+# Installation with development tools
+pip install "pyiron_workflow_vasp[dev]"
+
+# Installation with notebook support
+pip install "pyiron_workflow_vasp[notebook]"
+
+# Installation with all optional dependencies
+pip install "pyiron_workflow_vasp[dev,notebook]"
+```
+
+## Dependencies
+
+The package requires the following core dependencies:
+- Python >= 3.8
+- numpy >= 1.20.0
+- pandas >= 1.3.0
+- pymatgen >= 2023.0.0
+- pyiron_workflow >= 0.1.0
+- ase >= 3.22.0
+
+## Project Information
+
+- **License**: BSD-3-Clause
+- **Development Status**: Alpha
+- **Documentation**: [GitHub Repository](https://github.com/pyiron/pyiron_workflow_vasp)
+- **Bug Tracker**: [GitHub Issues](https://github.com/pyiron/pyiron_workflow_vasp/issues)
+
+## Usage
+
+The package provides a set of tools for running VASP calculations within pyiron workflows. A minimal end-to-end example:
+
+```python
+from ase.build import bulk
+from pymatgen.io.vasp.inputs import Incar
+from pyiron_workflow_vasp.vasp import VaspInput, vasp_job
+
+structure = bulk("Fe", cubic=True, a=2.83)
+incar = Incar.from_dict({
+    "ENCUT": 400,
+    "ISMEAR": 1,
+    "SIGMA": 0.1,
+    "ISPIN": 2,
+    "MAGMOM": "2*3.0",
+})
+
+# VaspInput bundles structure + INCAR (+ optional KPOINTS / explicit POTCARs).
+# Without an explicit potcar_paths kwarg, POTCAR generation uses the
+# pseudopotential library configured in ~/.pyiron_vasp_config.
+vasp_input = VaspInput(structure=structure, incar=incar)
+
+job = vasp_job(workdir="./bulk_fe_run", vasp_input=vasp_input)
+job.run()
+
+print("converged:", job.outputs.convergence_status.value)
+print("E_pot:    ", job.outputs.to_value_dict()["vasp_output"]["generic"]["energy_pot"])
+```
+
+For more examples — including an equation-of-state scan and a queued cluster
+run — see:
+
+- [`examples/run_bulk_fe.py`](examples/run_bulk_fe.py) — a runnable script with no hardcoded cluster paths.
+- [`example_notebooks/QuickStart.ipynb`](example_notebooks/QuickStart.ipynb) — the original walkthrough (uses MPIE cluster paths).
+- [`.pyiron_vasp_config.example`](.pyiron_vasp_config.example) — annotated template for the config file.
+
+## VASP Configuration
+
+The `.pyiron_vasp_config` file is essential for configuring the paths to the VASP pseudopotential files (POTCAR files) used in pyiron_workflow's VASP nodes. The file specifies the locations of different VASP potential sets and the default potential set to be used.
+
+For detailed configuration instructions, see [generate_vasp_pyiron_config.md](generate_vasp_pyiron_config.md), which includes:
+- Basic configuration setup
+- Configuring custom pseudopotential sets
+- Adding new pseudopotential variants to CSV files
+
+## 1. Determine the Locations of Your VASP POTCAR Files
+
+Before creating the `.pyiron_vasp_config` file, ensure that you know the locations of the different POTCAR sets on your system. The common VASP potential directories are `potpaw_64`, `potpaw_54`, and `potpaw_52`, but your setup may vary. The directory structure should look something like this:
+
+```
+/home/pyiron_resources_cmmc/vasp/potpaw_64/LDA
+/home/pyiron_resources_cmmc/vasp/potpaw_64/GGA
+/home/pyiron_resources_cmmc/vasp/potpaw_54/LDA
+/home/pyiron_resources_cmmc/vasp/potpaw_54/GGA
+/home/pyiron_resources_cmmc/vasp/potpaw_52/LDA
+/home/pyiron_resources_cmmc/vasp/potpaw_52/GGA
+```
+
+- **LDA** and **GGA** refer to the functional types for the VASP potentials.
+
+## 2. Create the .pyiron_vasp_config File
+
+1. Open a terminal and navigate to your home directory:
+
+    ```bash
+    cd ~
+    ```
+
+2. Use a text editor (such as `nano` or `vim`) to create and open the `.pyiron_vasp_config` file. For example:
+
+    ```bash
+    nano .pyiron_vasp_config
+    ```
+
+3. Add the following lines to the file. Make sure to modify the paths according to your setup.
+
+    ```ini
+    # Set the default POTCAR set
+    # Make sure that the default_POTCAR_set matches one of the suffixes in the vasp_POTCAR_path_*
+    default_POTCAR_set = potpaw64
+    
+    # Path to the root directory containing the VASP pseudopotential files
+    pyiron_vasp_resources = /home/pyiron_resources_cmmc/vasp
+    
+    # Path for different POTPAW versions (adjust these paths according to your setup)
+    vasp_POTCAR_path_potpaw64 = {pyiron_vasp_resources}/potpaw_64
+    vasp_POTCAR_path_potpaw54 = {pyiron_vasp_resources}/potpaw_54
+    vasp_POTCAR_path_potpaw52 = {pyiron_vasp_resources}/potpaw_52
+    # Note that pyiron vasp nodes can detect variants of vasp_POTCAR_path_{randomsuffix}
+    # So if you want to do something with custom pseudopotentials, you can... 
+    # Each of these dirs must have a "GGA" and "LDA" subdirectory structure
+    # i.e. 
+    # The structure should look like
+    # .../vasp/potpaw_64/LDA
+    # .../vasp/potpaw_64/GGA
+    # .../vasp/potpaw_54/LDA etc.
+    ```
+
+4. After you have added the configuration details, save the file:
+   - If you're using `nano`, press `Ctrl + O`, then `Enter` to save. Press `Ctrl + X` to exit.
+   - If you're using `vim`, press `Esc`, type `:wq`, and press `Enter` to save and exit.
+
+## 3. Verify File Permissions
+
+Ensure that your `.pyiron_vasp_config` file and the POTCAR directories are readable by your user. Run the following command to check the file permissions of the `.pyiron_vasp_config`:
+
+```bash
+ls -l ~/.pyiron_vasp_config
+```
+
+If necessary, you can modify the permissions to ensure read access:
+
+```bash
+chmod 644 ~/.pyiron_vasp_config
+```
+
+Also, verify that you have read/copy access to the files inside the VASP resource directories (`potpaw_64`, `potpaw_54`, etc.):
+
+```bash
+ls -l /home/pyiron_resources_cmmc/vasp/potpaw_64
+```
+
+## 4. Testing Your Configuration
+
+To verify that pyiron is correctly reading the `.pyiron_vasp_config` file, you can either check within your pyiron scripts or write a simple Python script to test the configuration:
+
+```python
+import os
+from pathlib import Path
+
+# Read the config file
+config_file = Path.home().joinpath(".pyiron_vasp_config")
+with open(config_file, "r") as f:
+    print(f.read())
+```
+
+This should print out the contents of your `.pyiron_vasp_config`, and you can check if the paths are correctly generated.
+
+### Additional Notes:
+- **Ensure Correct Paths**: Double-check that the paths to your POTCAR directories are correct. Incorrect paths will lead to pyiron not being able to find the necessary POTCAR files for your VASP calculations.
+
+By following these instructions, you'll have a correctly configured `.pyiron_vasp_config` file that points to the appropriate VASP pseudopotential directories.

pyiron_workflow_vasp-0.1.0/pyiron_workflow_vasp/__init__.py

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+"""pyiron_workflow_vasp - VASP integration for the pyiron workflow system.
+
+Public API:
+    VaspEngine - satisfies pyiron_workflow_atomistics.engine.Engine
+                  for Static + Minimize modes; wraps the helpers in
+                  vasp.py and vasp_parser/output.py.
+
+Plus the existing standalone helper functions in vasp and generic
+(re-exported via wildcard for backwards compatibility with the 0.0.x
+script-style API).
+"""
+
+from ._version import get_versions
+from .engine import VaspEngine
+from .generic import *  # noqa: F401,F403  -- legacy helpers
+from .vasp import *  # noqa: F401,F403      -- legacy helpers
+
+__version__ = get_versions()["version"]
+__all__ = ["VaspEngine"]

pyiron_workflow_vasp-0.1.0/pyiron_workflow_vasp/_run.py

@@ -0,0 +1,202 @@
+"""Internal: assemble VASP inputs, run the binary, parse -> EngineOutput.
+
+Not part of the public API - callers should go through
+``VaspEngine.get_calculate_fn`` which returns this function as its
+callable. The kwargs surface mirrors the keys VaspEngine bakes into
+the return tuple.
+"""
+
+from __future__ import annotations
+
+import os
+from pathlib import Path
+from typing import Any
+
+from ase import Atoms
+from pyiron_workflow_atomistics.engine import (
+    CalcInputMinimize,
+    CalcInputStatic,
+    EngineOutput,
+)
+
+
+def run_vasp(
+    structure: Atoms,
+    working_directory: str,
+    engine_input: CalcInputStatic | CalcInputMinimize,
+    potcar_config_file: Path | None,
+    functional: str,
+    encut: float,
+    kpoints_density: float,
+    command: str,
+    mode: str,
+) -> EngineOutput:
+    """Run a VASP single-point or relaxation and return an EngineOutput.
+
+    Workflow:
+        1. mkdir working_directory
+        2. write POSCAR (via ASE)
+        3. write INCAR (built from engine_input + mode + encut)
+        4. write KPOINTS (built from kpoints_density)
+        5. write POTCAR (via potcar_config_file)
+        6. shell out to `command`
+        7. parse via pyiron_vasp.vasp.output.parse_vasp_output
+        8. map parsed dict -> EngineOutput
+    """
+    from pyiron_vasp.vasp.output import parse_vasp_output
+
+    from pyiron_workflow_vasp.generic import shell
+    from pyiron_workflow_vasp.vasp import (
+        VaspInput,
+        get_default_POTCAR_paths,
+        read_potcar_config,
+        write_INCAR,
+        write_KPOINTS,
+        write_POSCAR,
+        write_POTCAR,
+    )
+
+    os.makedirs(working_directory, exist_ok=True)
+
+    # 1. POSCAR (via the existing helper - ASE-Atoms-aware)
+    write_POSCAR(workdir=working_directory, structure=structure)
+
+    # 2. INCAR - build dict from engine_input + mode, hand to pymatgen Incar
+    incar = _build_incar(engine_input=engine_input, mode=mode, encut=encut)
+    write_INCAR(workdir=working_directory, incar=incar)
+
+    # 3. KPOINTS - automatic density via pymatgen Kpoints
+    kpoints = _build_kpoints(structure=structure, kpoints_density=kpoints_density)
+    write_KPOINTS(workdir=working_directory, kpoints=kpoints)
+
+    # 4. POTCAR - resolve via potcar_config_file
+    if potcar_config_file is not None:
+        config = read_potcar_config(potcar_config_file)
+        pseudopot_lib_path = config["default_POTCAR_library_path"]
+    else:
+        pseudopot_lib_path = None
+
+    potcar_paths = get_default_POTCAR_paths(
+        structure=structure,
+        pseudopot_lib_path=pseudopot_lib_path,
+        pseudopot_functional=functional,
+    )
+    vasp_input = VaspInput(
+        structure=structure,
+        potcar_paths=potcar_paths,
+        pseudopot_lib_path=pseudopot_lib_path,
+        pseudopot_functional=functional,
+    )
+    write_POTCAR(workdir=working_directory, vasp_input=vasp_input)
+
+    # 5. Run the binary - shell is a pyiron_workflow Node; use the raw callable
+    shell.node_function(command=command, workdir=working_directory)
+
+    # 6. Parse the output
+    parsed = parse_vasp_output(working_directory=working_directory)
+
+    # 7. Map -> EngineOutput
+    return _to_engine_output(parsed=parsed)
+
+
+def _build_incar(
+    engine_input: CalcInputStatic | CalcInputMinimize,
+    mode: str,
+    encut: float,
+):
+    """Build a pymatgen Incar from the engine_input + mode + encut."""
+    from pymatgen.io.vasp.inputs import Incar
+
+    params: dict[str, Any] = {
+        "ENCUT": encut,
+        "PREC": "Accurate",
+        "EDIFF": 1e-5,
+        "ISMEAR": 0,
+        "SIGMA": 0.05,
+        "LREAL": "Auto",
+    }
+
+    if mode == "static":
+        params["NSW"] = 0
+        params["IBRION"] = -1
+    elif mode == "minimize":
+        assert isinstance(engine_input, CalcInputMinimize)
+        params["NSW"] = engine_input.max_iterations
+        params["IBRION"] = 2  # conjugate gradient
+        params["EDIFFG"] = -abs(engine_input.force_convergence_tolerance)
+        params["ISIF"] = 3 if engine_input.relax_cell else 2
+        if engine_input.energy_convergence_tolerance is not None:
+            params["EDIFF"] = engine_input.energy_convergence_tolerance
+    else:
+        raise ValueError(f"Unknown mode {mode!r}")
+
+    return Incar.from_dict(params)
+
+
+def _build_kpoints(structure: Atoms, kpoints_density: float):
+    """Build a pymatgen Kpoints using automatic density (A^-1)."""
+    from pymatgen.io.ase import AseAtomsAdaptor
+    from pymatgen.io.vasp.inputs import Kpoints
+
+    pmg_structure = AseAtomsAdaptor.get_structure(structure)
+    return Kpoints.automatic_density(
+        structure=pmg_structure,
+        kppa=int(1000 / max(kpoints_density, 0.01)),  # rough density mapping
+    )
+
+
+def _to_engine_output(parsed: dict) -> EngineOutput:
+    """Map the pyiron_vasp parse_vasp_output return dict to EngineOutput.
+
+    The parse_vasp_output result is structured as
+        {"generic": {"energy_tot": [...], "positions": [...], "cells": [...],
+                     "forces": [...], "stresses": [...], ...},
+         "converged": bool, ...}
+    Specific keys depend on pyiron_vasp version - adapt here.
+    """
+    from ase import Atoms as ASEAtoms
+
+    generic = parsed.get("generic", parsed)
+
+    # Trajectory
+    energies = list(generic.get("energy_pot", generic.get("energy_tot", [])))
+    forces_traj = list(generic.get("forces", []))
+    stresses_traj = list(generic.get("stresses", generic.get("pressures", [])))
+
+    # Reconstruct trajectory structures if cell/positions are present
+    structures_traj: list = []
+    cells = generic.get("cells")
+    positions = generic.get("positions")
+    indices = generic.get("indices")
+    if cells is not None and positions is not None and indices is not None:
+        species = parsed.get("species") or parsed.get("species_list")
+        for c, p, idx in zip(cells, positions, indices):
+            if species is None:
+                # Best effort: fall back to atom symbols from initial structure
+                continue
+            symbols = [species[i] for i in idx]
+            structures_traj.append(
+                ASEAtoms(symbols=symbols, positions=p, cell=c, pbc=True)
+            )
+
+    final_structure = (
+        structures_traj[-1] if structures_traj else parsed.get("final_structure")
+    )
+    final_energy = energies[-1] if energies else parsed.get("final_total_energy")
+    converged = bool(parsed.get("converged", False))
+
+    return EngineOutput(
+        final_structure=final_structure,
+        final_energy=final_energy,
+        converged=converged,
+        final_forces=forces_traj[-1] if forces_traj else None,
+        final_stress=stresses_traj[-1] if stresses_traj else None,
+        final_volume=(
+            final_structure.get_volume() if final_structure is not None else None
+        ),
+        energies=energies or None,
+        forces=forces_traj or None,
+        stresses=stresses_traj or None,
+        structures=structures_traj or None,
+        n_ionic_steps=len(energies) if energies else None,
+    )

pyiron_workflow_vasp-0.1.0/pyiron_workflow_vasp/_version.py

@@ -0,0 +1,21 @@
+
+# This file was generated by 'versioneer.py' (0.29) from
+# revision-control system data, or from the parent directory name of an
+# unpacked source archive. Distribution tarballs contain a pre-generated copy
+# of this file.
+
+import json
+
+version_json = '''
+{
+ "date": "2026-05-13T01:47:14+0200",
+ "dirty": true,
+ "error": null,
+ "full-revisionid": "b5ee3cfb986b43d9a19f5fe54e30dc867c5a2ae8",
+ "version": "0.1.0"
+}
+'''  # END VERSION_JSON
+
+
+def get_versions():
+    return json.loads(version_json)