Extracting Optimised Structures from ABINIT Output Files Using Abipy

Overview

When performing structure optimisation calculations in ABINIT, the programme generates a HIST.nc file containing the complete trajectory of the optimisation process. The Abipy library provides convenient Python tools to extract and manipulate this data, enabling researchers to access final structures, analyse optimisation convergence, and export geometries in various standard formats.

Implementation

The following Python script demonstrates how to extract optimised structures from ABINIT output files and save them to a designated directory:

#!/usr/bin/env python
"""
Extract optimised structures from ABINIT output files
Process NetCDF output files using the Abipy library
"""

from abipy.dynamics.hist import HistFile
import os


def extract_structure_from_hist(hist_file, output_dir="../1_structures/optimized_structures"):
    """
    Extract optimised structure from HIST.nc file
    
    Parameters:
    -----------
    hist_file : str
        Path to the HIST.nc file
    output_dir : str
        Directory for saving structure files
    """
    
    # Create output directory
    os.makedirs(output_dir, exist_ok=True)
    
    # Open HIST file
    print(f"Reading file: {hist_file}")
    hist = HistFile(hist_file)
    
    # Retrieve the final optimised structure
    final_structure = hist.final_structure
    
    # Obtain calculation information
    base_name = os.path.basename(os.path.dirname(os.path.dirname(hist_file)))
    
    print(f"\nStructure information:")
    print(f"Lattice parameters: {final_structure.lattice}")
    print(f"Number of atoms: {final_structure.num_sites}")
    print(f"Chemical formula: {final_structure.composition}")
    
    # Save in multiple formats
    output_files = {
        "cif": os.path.join(output_dir, f"{base_name}_optimized.cif"),
        "poscar": os.path.join(output_dir, f"{base_name}_optimized.vasp"),
    }
    
    for fmt, filepath in output_files.items():
        final_structure.to(fmt=fmt, filename=filepath)
        print(f"Saved {fmt.upper()} format: {filepath}")
    
    # Display optimisation trajectory information
    all_structures = hist.structures
    print(f"\nOptimisation information:")
    print(f"Total optimisation steps: {len(all_structures)}")
    
    # Read energy information
    try:
        energies = hist.reader.read_value("etotal")
        print(f"Initial energy: {energies[0]:.6f} Ha")
        print(f"Final energy: {energies[-1]:.6f} Ha")
        print(f"Energy change: {energies[-1] - energies[0]:.6f} Ha")
    except Exception as e:
        print(f"Unable to read energy information: {e}")
    
    # Close file
    hist.close()
    
    return final_structure


if __name__ == "__main__":
    # Example usage
    # Extract structure from al_fcc calculation
    hist_file = "../2_calculations/al_fcc/outdata/out_HIST.nc"
    
    if os.path.exists(hist_file):
        structure = extract_structure_from_hist(hist_file)
        print("\n✓ Structure extraction complete!")
    else:
        print(f"Error: File not found {hist_file}")
        print("Please ensure the ABINIT calculation has completed and generated the HIST.nc file")

Key Features

Structure Extraction

The script utilises the HistFile class from Abipy to interface with ABINIT's NetCDF output. The final_structure attribute provides direct access to the optimised geometry after the relaxation process has converged.

Multiple Output Formats

The extracted structure is saved in two widely-used formats:

• CIF (Crystallographic Information File): A standard format for crystallographic data exchange
• VASP POSCAR: Compatible with VASP and other common DFT codes

This flexibility facilitates seamless integration with various computational chemistry and materials science workflows.

Optimisation Trajectory Analysis

Beyond retrieving the final structure, the script also extracts:

• Total number of optimisation steps
• Energy evolution throughout the relaxation process
• Initial and final total energies
• Overall energy change during optimisation

This information is valuable for assessing convergence quality and understanding the optimisation behaviour.

Usage

To use this script with your ABINIT calculations:

1. Ensure your ABINIT calculation has completed and generated a HIST.nc file
2. Update the hist_file path to point to your actual output file
3. Optionally modify the output_dir to specify where structures should be saved
4. Run the script to extract and save the optimised structure

Error Handling

The script includes basic error handling to:

• Check for file existence before processing
• Handle cases where energy information cannot be read
• Create output directories if they don't exist

This makes the workflow more robust when processing multiple calculations or automating structure extraction tasks.