Point defects in metals#194
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…_coeff for metal-metal, Ne-Ne, H-M and H-Ne interaction in WaterPotential node (values taken from IonPotential node). Added node for FixAtoms, where Atom species, z-coordiate or atom indexes can be defined.
…ng HEA structures
* Edit gitignore, add pipeline and env for testing, add sample test * Fix CI workflow paths and smoke-test checks * Update CI pipeline to run tests and checks on all files * Configure Ruff, Black, and Mypy without pyproject * Format black * Fix CI paths for branch checks and tests * Match executorlib CI behavior * Restore assyst import cleanup * Format black * Use DEPENDABOT_WORKFLOW_TOKEN instead of GITHUB_TOKEN * Temporarily remove ruff * Add back ruff check * Update pipeline.yml * Update pipeline.yml Temporarily disable ruff, mypy and project install * Set python version to 3.12 and update smoke test to use unittest * Format black --------- Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: pyiron-runner <pyiron@mpie.de>
Edit default password type hint
…mestep is not being recorded as the value from the dataclass, presently the CreateLammpsInput node seems to use the default timestep.
JNmpi
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Jun 30, 2026
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While the individual node functions have good doc strings, the module would also benefit from a detailed description. Similarly, one or a few example workflows would be really helpful.
Refactor RunLammpsCalculation to support threading and optional executor. Added input port for the executor and modified input port 'cores' to 'threads_per_core' in accordance with the keys in executorlib.
… static calculations. Merge multiple parsers into one
…files - Add coverage configuration in .coveragerc - Update pipeline.yml to include coverage reporting - Create integration and unit test directories with initial test files for LAMMPS functionality
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #194 +/- ##
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+ Coverage 3.48% 15.04% +11.56%
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Files 80 85 +5
Lines 6537 8519 +1982
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+ Hits 228 1282 +1054
- Misses 6309 7237 +928 ☔ View full report in Codecov by Harness. 🚀 New features to boost your workflow:
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…ect_type API
Collapses the 12 near-duplicate Create{Vacancy,Substitution,Interstitial}{FromIds,FromSeed,BatchFromIds,BatchFromSeed}
functions into 4 (CreateDefectFromIds, CreateDefectFromSeed, CreateDefectBatchFromIds,
CreateDefectBatchFromSeed) dispatched on a defect_type literal, since each family shared
the same parent-resolution/event-bookkeeping logic and only differed in the site-selection
and mutation step. Verified behaviorally identical to the original functions via diff
against the pre-merge implementation.
Also extracts shared helpers for the pairwise PBC distance calculations and the
Voronoi/Delaunay interstitial site-finding pipeline, dedupes the stoichiometry/
operations-short logic that was implemented twice (module-level vs. StructureContainer
staticmethod), and adds node wrappers for four previously-unexposed functions
(GetStoichiometry, ValidateStructure, ElementUids, FindStructureIndex).
Adds an example workflow (Workflows/point_defects_metals.py) demonstrating the merged
API: one independent defect of each type, plus chaining a second defect onto an
existing one via parent_defect_index=-1.
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Wires the container_new defect-creation example (point_defects_metals.py) into the GRACE-based energy/formation-energy pipeline from point_def_energies.py: one vacancy, substitution, and interstitial defect plus a chained defect, each run through a static energy calculation and fed into the chemical-potential / formation-energy machinery in atomistic/thermodynamics/defect_phases.py. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
…tion test tests/unit/structure/test_container_new.py: 37 fast, dependency-free tests covering AddPristine, CreateDefectFromIds/FromSeed/Batch* for all three defect types, chaining via parent_defect_index, error handling, the newly-added node wrappers (GetStoichiometry, ValidateStructure, ElementUids, FindStructureIndex), the pairwise-PBC-distance getters (checked against ase.Atoms.get_distance), the Voronoi/Delaunay site finders, and a couple of filter functions. tests/integration/structure/test_point_defects_metals_lammps.py: builds a small defect workflow (pristine + vacancy + interstitial, as in Workflows/point_defects_metals.py) and computes real static energies via LAMMPS (CreateLammpsStaticInput, as in Workflows/lammps_static_basic.py) rather than the slower GRACE ML-potential path, then checks the resulting vacancy/interstitial formation energies are physically sane. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
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