concat_for_train.py

from ase.io import read, write
from ase.atoms import Atoms
from ase.stress import voigt_6_to_full_3x3_stress
from pathlib import Path
import numpy as np
from tqdm import tqdm

from csp.utils.find_molecs import split_and_wrap_molecs

def get_wrapped_pos(atoms):
    """Needed for computing intra virials."""
    atoms_copy = atoms.copy()
    mol_id = split_and_wrap_molecs(atoms_copy, cutoff_multiplier=1.2, cutoff_shift=0.0)
    assert "molID" in atoms_copy.arrays.keys()
    return atoms_copy.positions


output_filename = Path(__file__).parent / "residualized_32k_1Jan2025.extxyz"
output_verbose_filename = Path(__file__).parent / "residualized_32k_1Jan2025_verbose.extxyz"

index = ":" 
dft_total = read("/home/ubuntu/efs/ajc/csp/csp-prod/csp_42ktrain_processed/B86bPBEXDM_total_45k_30Dec2025.extxyz", index=index)
dft_intra = read("/home/ubuntu/efs/ajc/csp/csp-prod/csp_42ktrain_processed/B86bPBEXDM_intra_32k_30Dec2025.extxyz", index=index)

fukui_2L = read("/home/ubuntu/efs/ajc/csp/csp-prod/csp_42ktrain_processed/fukui_2L_42k_1Jan2026.extxyz", index=index)
xdm = read("/home/ubuntu/efs/ajc/csp/csp_raw_dft/model_outputs_42k/xdm_atoms.extxyz", index=index)


ids_total = [atom.info["identifier"] for atom in dft_total]
ids_intra = [atom.info["identifier"] for atom in dft_intra]
ids_fukui = [atom.info["identifier"] for atom in fukui_2L]
ids_xdm = [atom.info["identifier"] for atom in xdm]

# Take intersection of all ids. 
ids_all = set(ids_total) & set(ids_intra) & set(ids_fukui) & set(ids_xdm)
print(len(ids_all))
for id in tqdm(ids_all):
    dft_total_a = dft_total[ids_total.index(id)]
    dft_intra_a = dft_intra[ids_intra.index(id)]
    fukui_2L_a = fukui_2L[ids_fukui.index(id)]
    xdm_a = xdm[ids_xdm.index(id)]

    new_atoms = Atoms(
        symbols=dft_total_a.get_chemical_symbols(),
        positions=dft_total_a.get_positions(),
        cell=dft_total_a.get_cell(),
        pbc=dft_total_a.get_pbc(),
    )

    new_atoms.info["identifier"] = id
    dft_energy_interm = dft_total_a.get_potential_energy() - dft_intra_a.get_potential_energy()
    dft_forces_interm = dft_total_a.get_forces() - dft_intra_a.get_forces()

    # Get stress (using virials for intra).
    volume = dft_total_a.get_volume()
    if "molID" in dft_intra_a.arrays.keys():
        del dft_intra_a.arrays["molID"] 
    wrapped_pos = get_wrapped_pos(dft_intra_a)
    intra_fhi_aims_virials = np.einsum("ni,nj->ij", wrapped_pos, dft_intra_a.get_forces())
    intra_fhi_aims_stress = -intra_fhi_aims_virials / volume
    dft_stress_interm = (
        dft_total_a.get_stress(voigt=False) - intra_fhi_aims_stress
    ).flatten()

    fukui_energy_interm = fukui_2L_a.info['full_system_energy'] - fukui_2L_a.info['intra_energy']
    fukui_forces_interm = fukui_2L_a.arrays['full_system_forces'] - fukui_2L_a.arrays['intra_forces']
    fukui_stress_intra = -(np.einsum("ni,nj->ij", wrapped_pos, fukui_2L_a.arrays['intra_forces']) / volume).flatten()
    fukui_stress_total = voigt_6_to_full_3x3_stress(fukui_2L_a.info['full_system_stress']).flatten()
    fukui_stress_interm = fukui_stress_total - fukui_stress_intra
    xdm_energy_interm = xdm_a.info["xdm_energy"]
    xdm_forces_interm = xdm_a.arrays['xdm_forces']
    xdm_stress_interm = xdm_a.info['xdm_stress'].flatten()

    # Put it together. 
    energy_interm = dft_energy_interm - fukui_energy_interm - xdm_energy_interm
    forces_interm = dft_forces_interm - fukui_forces_interm - xdm_forces_interm
    stress_interm = dft_stress_interm - fukui_stress_interm - xdm_stress_interm

    new_atoms.info["energy_interm"] = energy_interm
    new_atoms.arrays["forces_interm"] = forces_interm
    new_atoms.info["stress_interm"] = stress_interm

    write(images=new_atoms, format="extxyz", filename=output_filename, append=True)

    new_atoms.info["dft_energy_interm"] = dft_energy_interm
    new_atoms.info["dft_energy_total"] = dft_total_a.get_potential_energy()
    new_atoms.info["dft_intra_energy"] = dft_intra_a.get_potential_energy()
    new_atoms.arrays["dft_forces_total"] = dft_total_a.get_forces()
    new_atoms.arrays["dft_forces_intra"] = dft_intra_a.get_forces()
    new_atoms.arrays["dft_forces_interm"] = dft_forces_interm
    new_atoms.info["dft_stress_interm"] = dft_stress_interm
    new_atoms.info["dft_stress_total"] = dft_total_a.get_stress(voigt=False).flatten()
    new_atoms.info["dft_stress_intra"] = intra_fhi_aims_stress.flatten()
    new_atoms.info["fukui_energy_interm"] = fukui_energy_interm
    new_atoms.arrays["fukui_forces_interm"] = fukui_forces_interm
    new_atoms.info["fukui_stress_interm"] = fukui_stress_interm
    new_atoms.info["fukui_stress_total"] = fukui_stress_total
    new_atoms.info["fukui_stress_intra"] = fukui_stress_intra
    new_atoms.arrays["fukui_forces_total"] = fukui_2L_a.arrays['full_system_forces']
    new_atoms.arrays["fukui_forces_intra"] = fukui_2L_a.arrays['intra_forces']
    new_atoms.info["fukui_intra_energy"] = fukui_2L_a.info['intra_energy']
    new_atoms.info["fukui_energy_total"] = fukui_2L_a.info['full_system_energy']
    new_atoms.info["xdm_energy_interm"] = xdm_energy_interm
    new_atoms.arrays["xdm_forces_interm"] = xdm_forces_interm
    new_atoms.info["xdm_stress_interm"] = xdm_stress_interm
    new_atoms.info["xdm_energy_total"] = xdm_a.info['xdm_total_energy']
    new_atoms.info["xdm_intra_energy"] = xdm_a.info['xdm_intra_energy']
    write(images=new_atoms, format="extxyz", filename=output_verbose_filename, append=True)