alomancy 0.1.1

Active Learning framework for atomistic simulations with flexible workflows and HPC submission.

ALomancy 🔮

Modular Active Learning Workflows for Modern Computational Chemistry

Installation • Quick Start • Documentation • Examples • Contributing

---

🎯 Overview

ALomnacy is a Python framework for running active learning (AL) workflows for training machine-learned inter-atomic potentials (MLIPs). This package focusses on customization and reproducibility to build robust training datasets and train MLIPs.

Key Features

• 🚀 Automated AL Workflows: End-to-end active learning with minimal manual intervention
• 🔧 HPC Integration: Built-in support for remote job submission on HPC clusters
• ⚡ Parallelization: Ensures that jobs run concurrently where possible increasing speed to results
• 🔄 Extensible Design: Abstract base classes for easy customization and extension
• 📊 Analysis Tools: Built-in utilities for monitoring and analyzing AL progress

Workflow Overview

flowchart TD
    A((Initial Dataset)) --> B[Train MLIP Committee]
    B --> C[Structure Generation]
    C --> D((Uncertainty-based Selection))
    D --> E[High-Accuracy Evaluation]
    E --> F((Update Training Dataset))
    F --> B

    style A fill:#e66027
    style B fill:#e87322
    style C fill:#eb861e
    style D fill:#efa119
    style E fill:#708e4c
    style F fill:#328566

🚀 Installation

From PyPI (Recommended)

pip install alomancy

From Source

git clone https://github.com/yourusername/ALomnacy.git
cd ALomnacy
pip install -e ".[dev]"

Dependencies

• Python 3.9+
• ASE - Atomic Simulation Environment
• WFL - Workflow for atomistic simulations
• Expyre - Remote job execution

⚡ Quick Start

1. Basic Active Learning Workflow

from alomancy.core import StandardActiveLearningWorkflow
from pathlib import Path

# Initialize workflow
workflow = StandardActiveLearningWorkflow(
    initial_train_file_path="train_set.xyz",
    initial_test_file_path="test_set.xyz",
    config_file_path="config.yaml",
    number_of_al_loops=5,
    verbose=1
)

# Run the active learning workflow
workflow.run()

2. Configuration File

Create a config.yaml file to specify your computational setup:

mlip_committee:
  name: "mace_training"
  size_of_committee: 4
  epochs: 1000
  max_time: "24:00:00"
  hpc:
    hpc_name: "gpu_cluster"
    partitions: ["gpu"]
    pre_cmds: ["module load cuda", "source activate mace"]

structure_generation:
  name: "md_generation"
  number_of_concurrent_jobs: 8
  desired_number_of_structures: 100
  max_time: "12:00:00"
  hpc:
    hpc_name: "gpu_cluster"
    partitions: ["gpu"]
    pre_cmds: ["module load cuda", "source activate mace"]

high_accuracy_evaluation:
  name: "dft_evaluation"
  max_time: "48:00:00"
  hpc:
    hpc_name: "cpu_cluster"
    partitions: ["cpu"]
    pre_cmds: ["module load quantum-espresso"]
    node_info:
      ranks_per_system: 32
      ranks_per_node: 32
      threads_per_rank: 1
      max_mem_per_node: "128GB"
    pwx_path: "/path/to/pw.x"
    pp_path: "/path/to/pseudopotentials"
    pseudo_dict:
      H: "H.pbe-rrkjus_psl.1.0.0.UPF"
      O: "O.pbe-n-kjpaw_psl.1.0.0.UPF"

3. Custom Workflow Implementation

Extend the base class for specialized workflows:

from alomancy.core import BaseActiveLearningWorkflow
from ase import Atoms
import pandas as pd

class CustomActiveLearningWorkflow(BaseActiveLearningWorkflow):

    def train_mlip(self, base_name: str, mlip_committee_job_dict: dict, **kwargs):
        """Custom MLIP training implementation"""
        # Your custom training logic here
        return "path/to/trained/model.pt"

    def evaluate_mlip(self, mlip_committee_job_dict: dict, **kwargs) -> pd.DataFrame:
        """Custom model evaluation"""
        # Your evaluation logic here
        return pd.DataFrame({"rmse": [0.1], "mae": [0.05]})

    def generate_structures(self, base_name: str, job_dict: dict,
                          train_data: list[Atoms], **kwargs) -> list[Atoms]:
        """Custom structure generation"""
        # Your structure generation logic here
        return generated_structures

    def high_accuracy_evaluation(self, base_name: str,
                               high_accuracy_eval_job_dict: dict,
                               structures: list[Atoms], **kwargs) -> list[Atoms]:
        """Custom high-accuracy evaluation"""
        # Your high-accuracy calculation logic here
        return evaluated_structures

📚 Examples

Check out the examples/ directory for complete workflow examples:

• Basic Usage: Simple active learning workflow setup
• Custom HPC Configuration: Advanced cluster configuration
• Analysis Scripts: Post-processing and visualization tools

🏗️ Project Structure

alomancy/
├── analysis/           # Analysis and visualization tools
├── configs/           # Configuration management
├── core/              # Core active learning framework
├── high_accuracy_evaluation/  # DFT calculation modules
├── mlip/              # Machine learning potential training
├── structure_generation/      # MD and structure generation
└── utils/             # Utility functions and helpers

🔧 Key Components

Core Framework

• BaseActiveLearningWorkflow: Abstract base class for AL workflows
• StandardActiveLearningWorkflow: Ready-to-use implementation

MLIP Training

• MACE Integration: Committee training with uncertainty quantification
• Remote Submission: HPC job management for GPU-accelerated training

Structure Generation

• Molecular Dynamics: ASE-based MD simulations with MACE potentials
• Uncertainty Sampling: Intelligent structure selection based on model disagreement

High-Accuracy Evaluation

• Quantum Espresso: Automated DFT calculations for reference data
• Job Management: Parallel submission and monitoring of DFT jobs

🤝 Contributing

We welcome contributions! Please see our Contributing Guide for details.

Development Setup

# Clone the repository
git clone https://github.com/yourusername/ALomnacy.git
cd ALomnacy

# Install in development mode
pip install -e ".[dev]"

# Run tests
pytest

# Run linting
ruff check .
ruff format .

Running Tests

# Run all tests
pytest

# Run specific test categories
pytest tests/core_tests/
pytest tests/mlip_train_tests/
pytest tests/high_acc_tests/

# Run with coverage
pytest --cov=alomancy

📝 Citation

If you use ALomnacy in your research, please cite:

@software{alomancy2025,
  title={ALomnacy: Modular Active Learning Workflows for Modern Computational Chemistry},
  author={Julian Holland},
  year={2025},
  url={https://github.com/yourusername/ALomnacy},
  version={0.1.0}
}

📄 License

This project is licensed under the MIT License - see the LICENSE file for details.

🙏 Acknowledgments

• The Fritz Haber Institute

📞 Support

• 📖 Documentation: https://alomancy.readthedocs.io
• 🐛 Bug Reports: GitHub Issues
• 💬 Discussions: GitHub Discussions
• 📧 Email: [e-mail]

---