ezga-lib 0.0.44

A modular multi-objective genetic algorithm framework for atomistic structure exploration

EZGA — Evolutionary Structure Explorer (ezga-lib)

A modular multi-objective genetic algorithm (GA) framework for atomistic structure exploration, with first-class YAML configuration, plugin-style extensibility, and a Hierarchical Supercell Escalation (HiSE) workflow for coarse-to-fine supercell searches.

PyPI name: ezga-lib CLI entry point: ezga (via ezga.cli.run:app) License: GPL-3.0-only

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Features

• Clean YAML → Runtime: Pydantic-v2 validated configs; dotted imports & factory specs are materialized into live Python callables.

• Multi-objective selection: Boltzmann (default) plus alternative methods; repulsion & diversity control.

• Rich variation operators: Tunable mutation, crossover, and user-defined operators.

• ASE integration: Simple shorthand to wrap ASE calculators.

• HiSE manager: Orchestrates multi-stage, coarse-to-fine supercell exploration. Lifts previous results via:

  • tile (Partition-based generate_supercell),
  • best_compatible (find largest divisor supercell among previous stages),
  • ase (fallback tiling using ASE).

• Agentic mailbox: Stage-scoped shared directory for multi-agent workflows.

• Pretty CLI summaries: Rich panels with compact configuration overviews.

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Installation

From source (recommended during development)

git clone <your-repo-url>
cd ezga
pip install -U pip
pip install -e .

This installs the ezga command line app.

From PyPI (when available)

pip install ezga-lib

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Quick Start

Create a minimal ezga.yaml:

max_generations: 100
output_path: demo/run

population:
  dataset_path: config.xyz
  filter_duplicates: true

evaluator:
  features_funcs:
    factory: ezga.selection.features:feature_composition_vector
    args: [["C","H"]]         # features are composition counts
  objectives_funcs:
    - ezga.selection.objective:objective_energy

multiobjective:
  size: 256
  selection_method: boltzmann
  sampling_temperature: 0.9
  objective_temperature: 0.6
  random_seed: 73

variation:
  initial_mutation_rate: 3.0
  crossover_probability: 0.1

simulator:
  mode: sampling
  calculator:
    type: ase
    class: ase.calculators.lj:LennardJones
    kwargs: { epsilon: 0.0103, sigma: 3.4 }  # ASE params

Run:

ezga validate -c ezga.yaml --strict
ezga once -c ezga.yaml

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CLI

ezga once -c <config.yaml>
ezga validate -c <config.yaml> [--strict]

• once: Runs a single GA or delegates to HiSE if the YAML has an hise block.
• validate: Validates and prints a rich summary; --strict also builds the engine to catch wiring errors.

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Configuration

GAConfig (high level)

• population: dataset paths, constraints, duplicate filtering, …
• evaluator: features_funcs, objectives_funcs (dotted, factory, or list)
• multiobjective: selection params (size, method, temperatures, metric, …)
• variation: mutation & crossover knobs
• simulator: mode & calculator (ASE shorthand supported)
• convergence, hashmap, agentic: execution support
• hise (optional): HiSE manager block (see below)

All sections are validated by Pydantic-v2; unknown fields are forbidden.

Dotted imports & factories

Anywhere you need a callable/object, you can write:

• Dotted string: "package.module:attr" or "package.module.attr"

• Factory spec:

  key:
    factory: "pkg.mod:build_something"
    args: [1, 2]
    kwargs: { flag: true }
  

• ASE shorthand (calculator only):

  simulator:
    mode: sampling
    calculator:
      type: ase
      class: ase.calculators.lj:LennardJones
      kwargs: { epsilon: 0.0103, sigma: 3.4 }
  

The loader resolves these into live Python objects before the run.

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Constraints (Design of Experiments)

You can provide constraint generators as factories. Example using a custom generator:

population:
  constraints:
    - factory: ezga.DoE.DoE:ConstraintGenerator.sum_in_range
      args: [["C", "H"], 100, 100]

Tip Use ezga.DoE.DoE:ConstraintGenerator.sum_in_range (colon form). Avoid ezga.DoE.DoE.ConstraintGenerator:sum_in_range (that treats ConstraintGenerator as a module path).

If your constraint generator expects feature names, you can register a name→index mapping in your code (e.g., after features are known):

from ezga.DoE.DoE import ConstraintGenerator
ConstraintGenerator.set_name_mapping({"C": 0, "H": 1})

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HiSE — Hierarchical Supercell Escalation

HiSE runs a sequence of stages over growing supercells and replaces the base input at each stage with a lifted dataset derived from previous results.

Example

hise:
  supercells:
    - [1,1,1]
    - [2,1,1]
    - [2,2,1]

  input_from: final_dataset            # or: latest_generation
  stage_dir_pattern: "supercell_{a}_{b}_{c}"
  restart: false
  carry: all
  reseed_fraction: 1.0
  lift_method: tile                    # tile | best_compatible | ase

  overrides:
    multiobjective.size:               [10, 20, 30]
    max_generations:                   [ 2,  3,  5]
    variation.initial_mutation_rate:   [ 1,  2,  3]
    population.constraints:
      - factory: ezga.DoE.DoE:ConstraintGenerator.sum_in_range
        args: [['C', 'H'], 100, 100]
      - factory: ezga.DoE.DoE:ConstraintGenerator.sum_in_range
        args: [['C', 'H'], 200, 200]
      - factory: ezga.DoE.DoE:ConstraintGenerator.sum_in_range
        args: [['C', 'H'], 400, 400]

Lift methods

• tile: Partition-based lifting using container.AtomPositionManager.generate_supercell(repeat=(ra, rb, rc)) (requires sage_lib.partition.Partition).
• best_compatible: Scans all previous stages and picks the largest supercell (by volume) that divides the target coordinate-wise; lifts via Partition.
• ase: Simple tiling via ASE.Atoms.repeat. No Partition dependency (fallback).

Input source

• final_dataset: uses stage_root/config.xyz
• latest_generation: concatenates stage_root/generation/*/config.xyz

Stage directories

For each supercell (a,b,c) the HiSE manager creates:

<output_path>/
  supercell_{a}_{b}_{c}/
    input_lifted.xyz           # if lifting writes to disk
    config.xyz                 # final dataset (engine may write this)
    generation/...

Agentic shared dir

If agentic.shared_dir is set in the base config, each stage receives a stage-scoped mailbox:

<base_shared>/<relative_stage_dir>/

All agents of a given stage share this directory.

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Directory Layout (source tree)

src/ezga/
  cli/
    run.py                    # Typer app (ezga entry point)
    runners.py                # once / validate / hise dispatchers
  core/
    config.py                 # GAConfig + submodels (Pydantic v2)
    engine.py                 # GA main loop
    population.py             # population & DoE validation
  selection/
    features.py, objective.py # feature/ objective factories
  DoE/
    DoE.py                    # ConstraintGenerator and DoE
  hise/
    manager.py                # HiSE orchestrator
  io/
    config_loader.py          # YAML loader & materializer
  simulator/
    ase_calculator.py         # ASE adapter (shorthand support)

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Logging & Output

• Logs and artifacts are written under output_path (and per-stage subdirs in HiSE).
• The CLI prints a rich summary of the configuration before running.

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Developing

Tests

We use pytest. Example structure:

tests/
  test_loader.py
  test_hise_manager.py
  test_constraints.py
  conftest.py

Run:

pip install -e ".[test]"   # if you add an extra in pyproject
pytest -q

Example unit test for loader materialization:

# tests/test_loader.py
from ezga.io.config_loader import _materialize_factories

def test_factory_resolution():
    spec = {"factory": "math:prod", "args": [[2,3,4]]}
    fn = _materialize_factories(spec)
    assert callable(fn)
    assert fn([2,3,4]) == 24

Code style

• Type hints everywhere.
• Docstrings follow Google style.
• Avoid side effects in import time; factories should be cheap to resolve.

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Troubleshooting

• TypeError: 'dict' object is not callable You likely passed a factory dict (not materialized) directly into a runtime component. Ensure your keys live in the YAML under sections that the loader post-processes, or put them under hise.overrides if you need stage-specific values. The loader will materialize population.constraints, evaluator.*, mutation_funcs, crossover_funcs, and simulator.calculator.

• ModuleNotFoundError or wrong dotted form Use colon form: pkg.mod:attr (preferred). For our DoE example: ezga.DoE.DoE:ConstraintGenerator.sum_in_range.

• Pydantic model errors Ensure pydantic>=2.x is installed. Unknown fields are rejected (extra='forbid').

• Permission error exporting input_lifted.xyz Ensure the path is writable. The exporter writes a new file; if you manage files manually, don’t open the same file elsewhere.

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Roadmap

• Additional selection methods & visual diagnostics.
• More HiSE lift strategies (symmetry-aware mapping).
• Native viewers for generation trajectories.
• Optional async physics backends.

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Citation

If this software helps your research, please cite the repository (add DOI when available).

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License

GPL-3.0-only. See LICENSE.

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Acknowledgments

• ASE for atomistic infrastructure.
• pydantic, typer, ruamel.yaml, rich for the developer experience.
• sage_lib for partition and supercell lifting utilities.