Add support for reading displacement and force matrices from .npy files

Hrushikesh Sahasrabuddherequested to merge
hpsahasrabuddhe/pheasy:support-disp-force-matrix-input into develop

This commit adds support for directly reading displacement and force data from .npy matrix files, in addition to the existing file-based workflows, and relaxes the ASE dependency constraint. This functionality is specifically used to support the atomate2–pheasy workflow used to generate the 2nd-order harmonic phonon database, where displacement and force data are already available in matrix form.

Key changes:

  • Introduced optional input arguments:

    • DISP_MATRIX_FILE
    • FORCE_MATRIX_FILE

  • Added new CLI flags in basic_io.py:

    • --disp_matrix_file
    • --force_matrix_file

  • Implemented:

    • read_displacements_from_matrix()
    • load_interatomic_forces_from_matrix()

  • Updated workflow logic in constructors.py:

    • If DISP_MATRIX_FILE is provided, displacement configurations are read directly from the NumPy matrix instead of reconstructed from structure files.
    • If FORCE_MATRIX_FILE is provided, forces are loaded directly from the NumPy matrix instead of parsed from DFT outputs.

  • Preserved backward compatibility:

    • Existing DISP_FILE and default workflows remain unchanged.
    • New functionality is only triggered when matrix files are explicitly provided.

Dependency update:

  • Relaxed ASE version constraint from ==3.22.1 to >=3.22.1 to improve its compatibilty with atomate2 software.

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