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CHANGELOG-1.3.0.md

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APEX 1.3.0 Changelog

Highlights

APEX 1.3.0 introduces new structure-generation workflows, new property workflows, improved automatic supercell construction, stronger failure-handling behavior, and a substantially reworked GUI submission/retrieval workflow.

Major additions include:

  • Composition-aware automatic lattice constant estimation
  • Automatic supercell generation from composition tolerance
  • Sublattice-aware RSS generation for B2, L1_2, and L1_0 systems
  • RSS workflow support and example documentation
  • GammaSurface workflow support and example documentation
  • Grüneisen parameters and thermal expansion workflow support and example documentation
  • Finite-temperature lattice workflow improvements
  • Finite-temperature elasticity workflow support and example documentation
  • Annealing workflow support for LAMMPS
  • Shape-controlled automatic supercell generation
  • req_calc-based relaxation/property selection for joint workflows
  • GUI-side batched submission for large configuration sets
  • Multi-workflow progress tracking and retrieval in apex gui
  • Bohrium account defaults managed by apex account
  • Improved failed-step output retrieval, diagnostics, retry behavior, and early-break handling

Core Features

Automatic Structure Construction

  • Added automatic lattice constant estimation based on composition-weighted atomic radii.
  • Added automatic supercell generation from composition tolerance.
  • Added optional maximum atom budget for automatic supercell construction.
  • Added shape-control modes for automatic supercell generation:
    • near_cubic
    • xy_equal_z_free, mainly for gamma-surface and slab-like workflows.
  • Added support for sublattice-aware random solid solution generation for:
    • B2
    • L1_2
    • L1_0

RSS Workflow

  • Added RSS workflow support.
  • Added RSS example documentation.
  • Added support for prototype-aware and sublattice-aware RSS systems.
  • Added parent-lattice helpers, automatic parent-lattice resolution, and Warren-Cowley SRO-driven sampling utilities.

GammaSurface Workflow

  • Added GammaSurface workflow support.
  • Added GammaSurface example documentation.
  • Added shape-control support for slab-like gamma-surface supercells.
  • Added apex preview support for generating GIF previews of GammaSurface motion.

Grüneisen Parameters and Thermal Expansion Workflow

  • Added gruneisen workflow support based on phonon calculations at multiple symmetric volume strains.
  • Added both sign_only and full output modes; full can fit Birch-Murnaghan EOS data to estimate thermal expansion.
  • Extended LAMMPS/phonoLAMMPS and VASP paths for Grüneisen post-processing, and added dedicated tests and examples.

Finite-Temperature Lattice Workflow

  • Add finite-temperature lattice calculations with updated thermo output, temperature-aware reporting, pressure handling, and c/a post-processing.

Finite-Temperature Elasticity Workflow

  • Added finite-temperature elasticity workflow support.
  • Added finite-temperature elasticity example documentation.
  • Added finite-temperature elastic tensor fitting, stress post-processing, and derived elastic modulus output.

Annealing Workflow

  • Added LAMMPS annealing workflow support.
  • Improved generated annealing input scripts for heating, cooling, RDF output, and holding stages.

Workflow Selection and Submission

  • Added req_calc-based workflow selection for relaxation and property calculations.
  • Added support for skipping relaxation in joint workflows with "relaxation": {"req_calc": false} when property setup can use the structure-directory POSCAR directly.
  • Added explicit disabling of individual properties with "req_calc": false.
  • Added clearer submit-time path validation and workflow labeling support.
  • Added skip-completed behavior for already successful relaxation and property tasks when rerun is not requested.

Failure Handling and Retrieval

  • Added automatic break behavior when the relaxation step fails in joint workflows.
  • Added detailed failed-step diagnostics with last-step failure reasons, workflow IDs, and workflow UIDs.
  • Added failed-output retrieval support using debug artifacts and main logs from the latest failed steps.
  • Added archive-workflow retrieval support in apex retrieve, including UID-based fallback lookup when workflow-name lookup is insufficient.
  • Added retry-aware artifact download behavior for transient failures while avoiding retries for permanent missing-artifact cases.
  • Added per-task LAMMPS status records and debug artifacts, including:
    • apex_task_status.json
    • .debug.log
    • .debug.stdout
    • .debug.stderr

Reporting

  • Added richer report support for new and updated workflows, including finite-temperature lattice, finite-temperature elasticity, GammaSurface, and annealing outputs.
  • Added static-report support for finite-temperature lattice tables/plots and annealing artifact summaries.
  • Added report CLI controls for browser launch, host, and port.
  • Improved Dash report startup behavior and reduced duplicate report-page launches.

User Experience

  • Added apex gui, a web-based interface for common APEX operations.
  • Added GUI-side batched submission for large configuration sets.
  • Added aggregated multi-workflow progress tracking and retrieval in apex gui.
  • Added GUI support for structure upload, POSCAR-driven interaction auto-detection, VASP/ABACUS interaction-table editing, and profile-specific default templates.
  • Added GUI-side account management and report/retrieve orchestration.
  • Added apex account for saving Bohrium identity and cloud defaults for easier repeated submission.
  • Added automatic Bohrium default injection while preserving user-provided config overrides.
  • Added apex preview for visualizing GammaSurface movement before submission.
  • Added automatic interaction-type detection from POSCAR content.
  • Improved failed-step messages by printing the reason from the latest failed step.
  • Added default configuration templates for LAMMPS, VASP, ABACUS, and GUI submit groups.

Compatibility and Documentation

  • Updated README coverage for RSS, GUI usage, Bohrium account defaults, Gamma line/surface, req_calc, and finite-temperature elasticity.
  • Added runnable examples for RSS, GammaSurface, and finite-temperature elasticity.
  • Added GUI developer documentation.
  • Added monty to the package dependencies and constrained supported Python versions to <3.13.
  • Added support for Phonopy v4 in terms of phonon calculation.