ATST-Tools 2.2.1

2.2.1：Agent-facing 增量（结构化 NDJSON 进度、plot 可视化、结果 schema 可选扩展）+ 完整路径 launcher version 探测修复 + Sella 未收敛可见性 + efermi 解析容错。按仓库版本语义（patch 承担小功能/优化）承载。

ATST-Tools 2.2.0

ATST-Tools 2.2.0 Release Notes

Version: 2.2.0
Date: 2026-07-24
Branch: main
Tag: v2.2.0

Summary

ATST-Tools 2.2.0 publishes the stable Python API with final CLI and
image-parallel compatibility safeguards. The release is additive: existing YAML
workflow and command-line entry points are retained.

Highlights

• Adds a stable, schema-backed Python API for workflow execution and embedded
  CCQN use, with a clean-installed wheel release gate.
• Adds the installed python -m atst_tools.api.runner process boundary with
  root-only atst-api-result-v1 JSON handoff, stable 0/2/1 exit codes, and
  no scheduler or MPI-launcher ownership.
• Preserves legacy CLI behavior: CLI-owned workflows do not gain API artifact
  manifests, missing or directory YAML paths retain their filesystem
  exceptions, and the installed atst console command exits successfully
  without printing a Python WorkflowResult representation.
• Adds synchronized pre-run construction for parallel NEB and both ATST and
  native ASE AutoNEB backends so local calculator, engine, optimizer, and
  trajectory-writer failures exit all ranks before optimizer collectives; the
  native ASE NEB receives the caller-supplied communicator.
• Classifies a missing cyipopt module as an optional dependency error while
  retaining solver/runtime failures as workflow execution errors.

Validation

• Focused API, CLI, MPI, and package metadata tests in the atst-dev
  environment.
• python scripts/verify_wheel_api.py --mpi-smoke runs a bounded two-rank API runner dry-run, plus in-process optimizer- and engine-construction failure-synchronization regressions, from a clean wheel installation.
• git diff --check for source and documentation changes.

Compatibility

• Package version: 2.2.0.
• Python support remains >=3.10.
• Existing YAML schemas and normal single-rank CLI execution retain their
  established behavior.

v2.1.4

ATST-Tools 2.1.4 Release Notes

Version: 2.1.4
Date: 2026-07-07
Branch: main

Summary

ATST-Tools 2.1.4 publishes the governed main branch after the experimental
DMF integration, abacuslite snapshot fixes, the ATST banner command, and CI
hardening work. This release keeps the package metadata aligned with the code
now available on origin/main.

Highlights

• Experimental DMF workflow:

  • Adds calculation.type: dmf and D2S rough_method: dmf support for Direct
    MaxFlux candidate generation.
  • Vendors PyDMF under src/atst_tools/external/pydmf for source-tree
    reproducibility.
  • Adds DMF examples, validation utilities, and SAI-oriented production
    validation materials.

• ABACUS / abacuslite backend fixes:

  • Preserves abacuslite numbered backups.
  • Validates property keyword conflicts.
  • Removes unsupported dipole property handling.
  • Syncs vendored abacuslite keyword handling and magmom reorder behavior with
    upstream expectations.
  • Adds an abacuslite snapshot drift checker.

• CLI and user experience:

  • Adds atst banner and shared banner rendering.
  • Documents the banner command in CLI references and operational skill docs.

• CI and governance:

  • Runs the full unit suite on pull requests.
  • Adds abacuslite ASE interface checks for vendored backend changes.
  • Adds snapshot drift tests to guard the vendored abacuslite copy.

Validation

• conda run -n atst-dev python -c "import atst_tools; print(atst_tools.__version__)"
• conda run -n atst-dev pytest tests -q
• git diff --check -- pyproject.toml

Compatibility

• Package version: 2.1.4.
• Python support remains >=3.10.
• YAML schema migration is not required for existing non-DMF workflows.
• DMF remains experimental. It requires cyipopt/IPOPT at runtime and produces
  TS candidates or rough paths, not independently validated transition states.

v2.1.3

What's Changed

• fix: preserve ABACUS STRU mobility in NEB inputs by @QuantumMisaka in #32
  Full Changelog: v2.1.2...v2.1.3

v2.1.2

Simples patches

v2.1.1

ATST-Tools 2.1.1 Release Notes

Version: 2.1.1
Date: 2026-06-10
Branch: main

Summary

ATST-Tools 2.1.1 is a maintenance release focused on unit test improvements,
legacy code cleanup, and small robustness enhancements to the Dimer module.
It keeps full backward compatibility with 2.1.0 inputs.

Highlights

• Unit test maintenance:
    - Added tests/helpers.py with shared test fixtures (DummyCalc, FakeWorld, FakeReducingWorld)
    - Added root artifact leak guard in conftest.py to prevent md_final.traj and md_post_summary.json from polluting the repository root
    - Enhanced test coverage for reactive_modes.py, post.py, dimer.py, and autoneb.py
    - Added test_reactive_modes.py for reactive modes analysis path
    - Added governance tests to verify legacy NEB scripts are not exposed

• Legacy code cleanup:
    - Deleted unregistered neb_make.py and neb_post.py scripts (functionality is available via unified atst CLI)

• Dimer module improvements:
    - Stricter validation for displacement vectors (requires one vector per atom)
    - Better calculator directory precedence (calc_config directory overrides backend_config directory)
    - Explicit error for unsupported init_eigenmode_method values

• Documentation:
    - Added UNIT_TEST_MAINTENANCE_2026-06-10.md report
    - Updated DOCUMENTATION_STATUS_REPORT.md

Validation

• All unit tests pass in the atst-dev environment
• Documentation governance checks pass
• No root artifacts left by test runs
• Version commands report 2.1.1 from the source tree

Compatibility

• Package version: 2.1.1.
• Fully backward compatible with 2.0.x and 2.1.0 inputs. No YAML semantics changed.
• All existing workflows (NEB, AutoNEB, Dimer, Sella, CCQN, D2S, Relax, Vibration, IRC, MD) remain unchanged.

2.1.0

ATST-Tools 2.1.0 Release Notes

Version: 2.1.0
Date: 2026-06-07
Branch: develop

Summary

ATST-Tools 2.1.0 is a feature release focused on expanding ASE-native
workflows with molecular dynamics support and a dedicated MD
post-processing path. It keeps the project on the governed YAML/CLI/document
structure while extending the runtime surface in a way that remains backward
compatible with existing 2.0.x inputs.

Highlights

• Added calculation.type: md with two execution paths:
  ASE-driven MD using ABACUS or DeePMD-kit calculators, and ABACUS-native MD
  using abacuslite-managed input preparation and run monitoring.
• Added atst md summary and atst md post for trajectory summary and
  conversion/post-processing.
• Wired MD workflow completion to trigger the summary post-processing step
  automatically after successful runs.
• Added the Li-Si MD example set based on the existing 01_neb_Li-Si initial
  structure, covering ASE+DP, ASE+ABACUS, and ABACUS-native configurations.
• Updated the feature matrix, CLI reference, configuration reference, examples
  overview, and documentation governance records to reflect the new MD support.

Validation

• Unit tests pass in the atst-dev environment for the MD workflow and
  MD post-processing coverage.
• Documentation governance checks pass for the active user, developer, and
  project-manager entry points.
• Version commands report 2.1.0 from the source tree after the version bump.

Compatibility

• Package version: 2.1.0.
• Existing 2.0.x YAML inputs remain valid. The new MD workflow is additive and
  does not change the semantics of existing NEB, AutoNEB, Dimer, Sella, CCQN,
  D2S, Relax, Vibration, or IRC inputs.
• GA remains unsupported. The ASE 3.28.0 GA implementation is still outside
  the project's supported workflow set.

v2.0.1

ATST-Tools 2.0.1 Release Notes

Version: 2.0.1
Date: 2026-06-03
Branch: develop

Summary

ATST-Tools 2.0.1 is a focused 2.0.x maintenance and feature-completion release.
It updates the package version to reflect the post-2.0.0 workflow, validation,
and documentation-governance additions. The obsolete YAML config_version
marker was removed; the active schema is governed by the installed package
version.

Highlights

• Completed the P0/P1 transition-state workflow iteration: CCQN automatic
  reactive-mode enumeration, product alignment, mode manifests, diagnostics,
  artifact manifests, TS validation, NEB two-stage warm-up, endpoint relaxation,
  and descent IRC examples.
• Added and validated CCQN support as a standalone workflow and D2S refinement
  option, including perturbed H2-Au ABACUS validation against the Sella example.
• Added DPA-3.1 DP example validation evidence and curated DP reference results
  for the supported DP-backed examples.
• Added image-level MPI NEB/AutoNEB support and Cy-Pt SAI E2E validation
  examples with curated outputs.
• Added documentation governance checks, report ledger maintenance, and
  archival cleanup for superseded plans and outdated reports.

Validation

• Unit tests pass in atst-dev with pytest tests -q.
• Documentation governance checks pass with
  python scripts/check_docs_governance.py.
• Active evidence reports cover DP/DPA3 examples, P0/P1 runtime smoke,
  CCQN ABACUS validation, and image-level MPI NEB/AutoNEB E2E validation.

Compatibility

• Package version: 2.0.1.
• YAML config_version has been removed. The installed package version defines
  the active YAML schema, and unknown top-level fields are rejected during schema
  validation.
• Existing 2.0.0 YAML inputs remain valid unless they relied on intentionally
  archived temporary plans or outdated validation notes.

v2.0.0

ATST-Tools 2.0.0 Release Notes

Version: 2.0.0
Date: 2026-05-25

Summary

ATST-Tools 2.0.0 completes the transition from the legacy script collection to
a pip-installable ASE workflow package. Production calculations use the unified
atst run CONFIG.yaml entry point, while atst neb, atst dimer,
atst relax, atst vibration, and atst traj provide lightweight
pre/post-processing utilities.

Major Capabilities

• ASE workflow package: NEB/DyNEB, AutoNEB, Dimer, Sella, D2S, Relax,
  Vibration, and Sella-backed IRC are available through the CLI/YAML interface.
• Calculator backends: ABACUS is integrated through abacuslite; DeePMD-kit
  is integrated through deepmd.calculator.DP.
• YAML governance: user-facing inputs are defined by Pydantic schema models,
  normalized before dispatch, and exported to user documentation.
• NEB endpoint governance: chains made from pure structures are repaired by
  endpoint single-point calculations before NEB/AutoNEB starts.
• D2S endpoint optimization: optional endpoint optimization is enabled by
  default and skipped when endpoint structures already carry valid results.
• DP multi-head support: DPA/DPA3 multi-head models pass calculator.dp.head
  directly to DeePMD-kit; the 2.0.0 validation path uses DPA-3.1-3M with the
  Omat24 head.

IRC Integration Position

The IRC workflow intentionally follows the main-branch application pattern:
read a TS structure, assign an ASE calculator, construct sella.IRC, run
forward and/or reverse directions, then write a normalized trajectory for
combined runs. ATST-Tools owns the orchestration, YAML configuration, calculator
construction, trajectory naming, restart handling, and diagnostics. The IRC
integration algorithm itself is delegated to the upstream Sella package.

Known flat-endpoint and inner-loop stops are reported as controlled
IRCBoundaryError diagnostics with the Sella exception type and trajectory
frame count. These diagnostics indicate that ATST-Tools reached the current
supported Sella-backed IRC boundary; they are not treated as calculator factory
or YAML orchestration failures.

Validation Status

• Local unit tests, example dry-runs, and compile checks pass in the atst-dev
  environment.
• ABACUS examples have existing SAI GPU validation evidence for the core
  workflows.
• DP examples were run on SAI GPU with
  temp_repos/dp_model/DPA-3.1-3M.pt and head: Omat24. NEB, AutoNEB,
  Dimer, Sella, D2S, Relax, and Vibration completed; the IRC example reaches a
  controlled Sella IRC boundary reported as IRCBoundaryError.
• The 2.0.0 release-ready process builds sdist/wheel artifacts and installs the
  wheel in a clean virtual environment for CLI smoke checks.
• Final release verification on 2026-05-25 confirmed the local test suite,
  example YAML dry-runs, compile checks, CLI version, and sdist/wheel build
  from the develop release branch.

Supported Workflows

Workflow	Status	Notes
NEB / DyNEB	Supported	Endpoint single-point governance enabled by default.
AutoNEB	Supported	Final-chain export is available through atst neb post.
Dimer	Supported	Can consume displacement vectors from NEB post-processing.
Sella	Supported	ASE/Sella saddle search through atst run.
D2S	Supported	Rough DyNEB followed by Dimer or Sella.
Relax	Supported	ASE optimizer based structure optimization.
Vibration	Supported	Harmonic and ideal-gas thermochemistry helpers.
IRC	Supported	Sella-backed application mode with controlled boundary diagnostics.
MD	Not included	Planned as a post-2.0.0 ASE workflow extension.

Installation

Development install:

pip install -e .

Wheel install after local build:

python -m build
pip install dist/atst_tools-2.0.0-py3-none-any.whl

ABACUS users need an executable ABACUS runtime plus pseudopotential/orbital
files referenced by YAML. DP users need DeePMD-kit installed and a model file
available outside git-tracked paths.

v1.5.0

• Dimer and Sella usage
• NEB2Dimer and NEB2Sella usage
• Examples update
• Pymatgen IDPP update
• Other minor fixing