3_epc/ml_epc.py

#!/usr/bin/env python
"""
Compute AO brackets (U/V matrices + eigenvalues) for EPC from HPRO and DeepH-E3.

Pipeline:
  1. HPRO reconstruction for each EPC structure (scf_0 + group_1..12)
  2. DeepH-E3 inference on each structure
  3. AO bracket computation: U[n,m](k) = c_n^{d,dag} · S^{d,0}(k) · c_m^0(k)
  4. Save ao_brackets_hpro.npz and ao_brackets_e3.npz in displacements/scf_0/

Run after diamond.jl (create + run steps), before diamond_ml.jl.

Usage:
  python ml_epc.py [--hpro] [--e3] [--brackets]  (default: all steps)
  python ml_epc.py --hpro      # only HPRO reconstruction
  python ml_epc.py --e3        # only DeepH-E3 inference
  python ml_epc.py --brackets  # only AO bracket computation
"""
import argparse
import glob
import json
import os
import subprocess
import sys

import h5py
import numpy as np
from ase.io import read as ase_read
from scipy import linalg as la

SCRIPT_DIR   = os.path.dirname(os.path.abspath(__file__))
DISP_DIR     = os.path.join(SCRIPT_DIR, 'displacements')
DIAMOND_DIR  = os.path.dirname(SCRIPT_DIR)
AOBASIS_DIR  = os.path.join(DIAMOND_DIR, 'aobasis')
PSEUDOS_DIR  = os.path.join(DIAMOND_DIR, 'pseudos')
PARAMS_PATH  = os.path.join(DIAMOND_DIR, '1_data_prepare', 'params.json')
RESULTS_DIR  = os.path.join(DIAMOND_DIR, '2_training', 'hamiltonian', 'results')

NATOMS   = 2
NBANDS   = 8
K_MESH   = (6, 6, 6)

# FCC lattice vectors (Angstrom), rows = a1, a2, a3
_b = 3.567 / 2.0
LAT_MAT = np.array([[0, _b, _b], [_b, 0, _b], [_b, _b, 0]])
LAT_INV = np.linalg.inv(LAT_MAT)


# ============================================================
# Helpers: H(R) construction and diagonalization
# ============================================================

def generate_kgrid(n1, n2, n3):
    kpts = []
    for i in range(n1):
        for j in range(n2):
            for k in range(n3):
                kpts.append([i / n1, j / n2, k / n3])
    return np.array(kpts)


KGRID = generate_kgrid(*K_MESH)
NK = len(KGRID)


def read_h5_dict(fn):
    """Read DeePH/HPRO HDF5 file → dict {(R0,R1,R2,ia,ja): ndarray}."""
    d = {}
    with h5py.File(fn, 'r') as f:
        for key in f.keys():
            nk = tuple(map(int, key[1:-1].split(',')))
            d[nk] = np.array(f[key])
    return d


def get_orbital_info(aodir):
    """Return (site_norbits, norbits, csum) from orbital_types.dat."""
    with open(os.path.join(aodir, 'orbital_types.dat')) as f:
        site_norbits = np.array(
            [sum(2 * l + 1 for l in map(int, line.split())) for line in f]
        )
    norbits = int(sum(site_norbits))
    csum = np.cumsum(site_norbits)
    return site_norbits, norbits, csum


def build_HR(h5d, s5d, site_norbits, norbits, csum):
    """Assemble full H(R) and S(R) matrices from HDF5 dicts."""
    H_R, S_R = {}, {}
    for key in h5d:
        R, ai, aj = key[:3], key[3] - 1, key[4] - 1
        if R not in H_R:
            H_R[R] = np.zeros((norbits, norbits), dtype=np.complex128)
            S_R[R] = np.zeros((norbits, norbits), dtype=np.complex128)
        i0 = csum[ai] - site_norbits[ai]
        j0 = csum[aj] - site_norbits[aj]
        ni, nj = site_norbits[ai], site_norbits[aj]
        H_R[R][i0:i0 + ni, j0:j0 + nj] = h5d[key]
        if key in s5d:
            S_R[R][i0:i0 + ni, j0:j0 + nj] = s5d[key]
    return H_R, S_R


def build_Hk_Sk(H_R, S_R, kf, norbits):
    """Fourier-transform H(R), S(R) to k-space with Hermitianization."""
    Hk = np.zeros((norbits, norbits), dtype=np.complex128)
    Sk = np.zeros((norbits, norbits), dtype=np.complex128)
    for R in H_R:
        ph = np.exp(2j * np.pi * np.dot(kf, R))
        Hk += H_R[R] * ph
        if R in S_R:
            Sk += S_R[R] * ph
    return 0.5 * (Hk + Hk.conj().T), 0.5 * (Sk + Sk.conj().T)


def compute_eigenvectors(H_R, S_R, kpts, norbits, nbands=NBANDS):
    """Solve generalized eigenproblem at each k-point, return (eigs, evecs) lists."""
    all_eigs, all_evecs = [], []
    for kf in kpts:
        Hk, Sk = build_Hk_Sk(H_R, S_R, kf, norbits)
        eigs, evecs = la.eigh(Hk, Sk)
        idx = np.argsort(np.real(eigs))
        all_eigs.append(np.real(eigs[idx[:nbands]]))
        all_evecs.append(evecs[:, idx[:nbands]])
    return all_eigs, all_evecs


def build_cross_overlap_R(S0_raw, Sd_raw, displaced_atom_1based, site_norbits, norbits, csum):
    """Build S^{d,0}(R): use displaced-atom rows from Sd, others from S0."""
    S_cross = {}
    all_keys = set(S0_raw.keys()) | set(Sd_raw.keys())
    for key in all_keys:
        R = key[:3]
        ai, aj = key[3] - 1, key[4] - 1
        if R not in S_cross:
            S_cross[R] = np.zeros((norbits, norbits), dtype=np.complex128)
        i0 = csum[ai] - site_norbits[ai]
        j0 = csum[aj] - site_norbits[aj]
        ni, nj = site_norbits[ai], site_norbits[aj]
        if key[3] == displaced_atom_1based:
            if key in Sd_raw:
                S_cross[R][i0:i0 + ni, j0:j0 + nj] = Sd_raw[key]
        else:
            if key in S0_raw:
                S_cross[R][i0:i0 + ni, j0:j0 + nj] = S0_raw[key]
    return S_cross


_ORBPAIR_CACHE = None


def _get_orbpairs():
    """Initialize (and cache) HPRO OrbPair objects for Carbon DZP basis."""
    global _ORBPAIR_CACHE
    if _ORBPAIR_CACHE is None:
        from HPRO.orbutils import parse_siesta_ion, OrbPair, LinearRGD, grid_R2G
        from HPRO.constants import AOFT_QGRID_DEN
        ion_file = os.path.join(AOBASIS_DIR, 'C.ion')
        norb_rad, phirgrids = parse_siesta_ion(ion_file)
        Ecut = 50  # Hartree
        grid_nq = int(np.sqrt(Ecut) * AOFT_QGRID_DEN)
        gridQ = LinearRGD(0, np.sqrt(2 * Ecut), grid_nq)
        phiQlist = [grid_R2G(gridQ, g) for g in phirgrids]
        orbpairs = []
        for jorb in range(norb_rad):
            for iorb in range(norb_rad):
                r1, r2 = phirgrids[iorb].rcut, phirgrids[jorb].rcut
                orbpairs.append(OrbPair(phiQlist[iorb], phiQlist[jorb], r1 + r2, index=1))
        orbslices = [0]
        for g in phirgrids:
            orbslices.append(orbslices[-1] + 2 * g.l + 1)
        # Permutation: HPRO wiki → h5 (OpenMX) convention for Carbon ss*p^2d (13 orbs)
        perm_full = np.array(
            [0, 1]
            + [2 + i for i in [2, 0, 1]]       # p1: py,pz,px → px,py,pz
            + [5 + i for i in [2, 0, 1]]       # p2
            + [8 + i for i in [2, 4, 0, 3, 1]] # d: wiki → openmx
        )
        _ORBPAIR_CACHE = (orbpairs, orbslices, perm_full, norb_rad)
    return _ORBPAIR_CACHE


def _compute_overlap_block(Rvec_cart_bohr, orbpairs, orbslices, norb_rad):
    """Compute nao×nao overlap at given inter-atomic vector (Bohr) via OrbPair."""
    nao = orbslices[-1]
    S = np.zeros((nao, nao))
    Rv = np.array(Rvec_cart_bohr).reshape(1, 3)
    idx = 0
    for jorb in range(norb_rad):
        for iorb in range(norb_rad):
            s1 = slice(orbslices[iorb], orbslices[iorb + 1])
            s2 = slice(orbslices[jorb], orbslices[jorb + 1])
            S[s1, s2] = orbpairs[idx].calc(Rv)[0]
            idx += 1
    return S


def _get_delta_cart_ang(scf0_dir, struct_dir_d, atom_1based):
    """Cartesian displacement (Ang) of atom_1based between two QE scf.in files."""
    s0 = ase_read(os.path.join(scf0_dir, 'scf.in'), format='espresso-in')
    sd = ase_read(os.path.join(struct_dir_d, 'scf.in'), format='espresso-in')
    return sd.get_positions()[atom_1based - 1] - s0.get_positions()[atom_1based - 1]


def build_cross_overlap_R_exact(S0_raw, Sd_raw, displaced_atom_1based,
                                 site_norbits, norbits, csum, delta_cart_ang):
    """
    Exact cross-overlap S^{d,0}(R): same as build_cross_overlap_R but replaces
    the (kappa,kappa) blocks with OrbPair evaluated at R_cart - delta_cart.

    For the self-overlap block of the displaced atom:
        S^{d,0}_{kk}(R) = <phi(r - tau_k - delta) | phi(r - tau_k - R*lat)>
                        = OrbPair(R_cart - delta)
    instead of OrbPair(R_cart) used in the approximate version.
    """
    from HPRO.constants import bohr2ang
    orbpairs, orbslices, perm_full, norb_rad = _get_orbpairs()
    nao_per_atom = orbslices[-1]
    P = np.eye(nao_per_atom)[perm_full]

    kappa = displaced_atom_1based
    ai_kappa = kappa - 1
    i0 = csum[ai_kappa] - site_norbits[ai_kappa]
    ni = site_norbits[ai_kappa]
    delta_bohr = np.array(delta_cart_ang) / bohr2ang

    S_cross = build_cross_overlap_R(S0_raw, Sd_raw, kappa, site_norbits, norbits, csum)

    for R in list(S_cross.keys()):
        key_kk = R + (kappa, kappa)
        if key_kk not in S0_raw and key_kk not in Sd_raw:
            continue
        R_cart_bohr = np.array(R) @ LAT_MAT / bohr2ang
        R_cross_bohr = R_cart_bohr - delta_bohr
        S_wiki = _compute_overlap_block(R_cross_bohr, orbpairs, orbslices, norb_rad)
        S_cross[R][i0:i0 + ni, i0:i0 + ni] = P @ S_wiki @ P.T

    return S_cross


def build_Sk_cross(S_cross_R, kf, norbits):
    """Fourier-transform cross-overlap (no Hermitianization)."""
    Sk = np.zeros((norbits, norbits), dtype=np.complex128)
    for R in S_cross_R:
        ph = np.exp(2j * np.pi * np.dot(kf, R))
        Sk += S_cross_R[R] * ph
    return Sk


def compute_brackets(c_disp, c_undisp, S_cross_k, nbands=NBANDS):
    """U[n,m] = c_n^{d,dag} · S^{d,0}(k) · c_m^0."""
    return c_disp[:, :nbands].conj().T @ S_cross_k @ c_undisp[:, :nbands]


# ============================================================
# Step 1: HPRO reconstruction
# ============================================================

def run_hpro_for_structure(struct_dir, label):
    """Run HPRO PW2AOkernel reconstruction for one EPC structure."""
    recon_dir = os.path.join(struct_dir, 'reconstruction')
    aodir     = os.path.join(recon_dir, 'aohamiltonian')
    out_h5    = os.path.join(aodir, 'hamiltonians.h5')

    if os.path.exists(out_h5):
        print(f'  [{label}] HPRO already done')
        return True

    # VSC is in outdir from ElectronPhonon.jl (outdir = "./tmp/")
    vscdir = os.path.join(struct_dir, 'tmp')
    if not os.path.exists(os.path.join(vscdir, 'VSC')):
        print(f'  [{label}] WARNING: VSC not found at {vscdir}/VSC — run diamond.jl first')
        return False

    params = json.load(open(PARAMS_PATH))
    ecutwfn = params['hpro']['ecutwfn']

    os.makedirs(recon_dir, exist_ok=True)
    orig_dir = os.getcwd()
    os.chdir(recon_dir)
    try:
        from HPRO import PW2AOkernel
        print(f'  [{label}] Running HPRO reconstruction...')
        kernel = PW2AOkernel(
            lcao_interface='siesta',
            lcaodata_root=AOBASIS_DIR,
            hrdata_interface='qe-bgw',
            vscdir=vscdir,
            upfdir=PSEUDOS_DIR,
            ecutwfn=ecutwfn,
        )
        kernel.run_pw2ao_rs('./aohamiltonian')
        print(f'  [{label}] HPRO done → {aodir}')
    finally:
        os.chdir(orig_dir)
    return True


def run_all_hpro():
    struct_labels = [('scf_0', os.path.join(DISP_DIR, 'scf_0'))]
    for i in range(1, NATOMS * 6 + 1):
        struct_labels.append((f'group_{i}', os.path.join(DISP_DIR, f'group_{i}')))

    print('=' * 60)
    print('Step 1: HPRO reconstruction')
    print('=' * 60)
    for label, struct_dir in struct_labels:
        if not os.path.isdir(struct_dir):
            print(f'  [{label}] not found — run diamond.jl (create + run) first')
            continue
        run_hpro_for_structure(struct_dir, label)


# ============================================================
# Step 2: DeepH-E3 inference
# ============================================================

def find_latest_model():
    dirs = sorted(glob.glob(os.path.join(RESULTS_DIR, '*')))
    dirs = [d for d in dirs if os.path.isdir(d)
            and os.path.exists(os.path.join(d, 'best_model.pkl'))]
    return dirs[-1] if dirs else None


def run_e3_inference(struct_dir, label, model_dir, params):
    """Run DeepH-E3 inference for one structure, output hamiltonians_pred_e3.h5."""
    aodir    = os.path.join(struct_dir, 'reconstruction', 'aohamiltonian')
    pred_h5  = os.path.join(aodir, 'hamiltonians_pred_e3.h5')

    if os.path.exists(pred_h5):
        print(f'  [{label}] DeepH-E3 prediction already exists')
        return True
    if not os.path.exists(os.path.join(aodir, 'hamiltonians.h5')):
        print(f'  [{label}] SKIP — no hamiltonians.h5 (run HPRO first)')
        return False

    infer_dir   = os.path.join(struct_dir, 'infer_e3')
    dataset_dir = os.path.join(infer_dir, 'dataset')
    graph_dir   = os.path.join(infer_dir, 'graph')
    output_dir  = os.path.join(infer_dir, 'output')
    ini_path    = os.path.join(infer_dir, 'eval.ini')

    # Build dataset directory with symlinks to aodir
    dest = os.path.join(dataset_dir, '00')
    os.makedirs(dest, exist_ok=True)
    for fname in os.listdir(aodir):
        link = os.path.join(dest, fname)
        if not os.path.exists(link):
            os.symlink(os.path.join(aodir, fname), link)
    os.makedirs(graph_dir, exist_ok=True)
    os.makedirs(output_dir, exist_ok=True)

    # Write eval.ini
    t = params.get('hamiltonian', {})
    conda_env = t.get('conda_env', 'deeph')
    deeph_e3_dir = t.get('deeph_e3_dir', '/home/apolyukhin/Development/DeepH-E3')
    device = t.get('device', 'cuda')

    ini = f"""; DeepH-E3 eval config — generated by ml_epc.py

[basic]
device = {device}
dtype = float
trained_model_dir = {model_dir}
output_dir = {output_dir}
target = hamiltonian
inference = False
test_only = False

[data]
graph_dir =
DFT_data_dir =
processed_data_dir = {dataset_dir}
save_graph_dir = {graph_dir}
target_data = hamiltonian
dataset_name = diamond_qe_e3_epc_{label}
get_overlap = False
"""
    with open(ini_path, 'w') as f:
        f.write(ini)

    # Write launcher
    launcher = os.path.join(infer_dir, '_eval_launcher.py')
    with open(launcher, 'w') as f:
        f.write(f"""import sys, torch
torch.serialization.add_safe_globals([slice])
try:
    from torch_geometric.data.data import DataEdgeAttr, DataTensorAttr
    from torch_geometric.data.storage import GlobalStorage
    torch.serialization.add_safe_globals([DataEdgeAttr, DataTensorAttr, GlobalStorage])
except ImportError:
    pass
sys.path.insert(0, '{deeph_e3_dir}')
from deephe3 import DeepHE3Kernel
kernel = DeepHE3Kernel()
kernel.eval('{ini_path}')
""")

    conda_base = params['paths']['conda_base']
    activate   = (f'source {conda_base}/etc/profile.d/conda.sh'
                  f' && conda activate {conda_env}')
    print(f'  [{label}] Running DeepH-E3 inference...')
    subprocess.run(['bash', '-c', f'{activate} && python {launcher}'], check=True)

    # Copy prediction to aodir
    pred_out = os.path.join(output_dir, '00', 'hamiltonians_pred.h5')
    if os.path.exists(pred_out):
        import shutil
        shutil.copy(pred_out, pred_h5)
        print(f'  [{label}] Inference done → {pred_h5}')
        return True
    else:
        print(f'  [{label}] WARNING: {pred_out} not found after inference')
        return False


def run_all_e3():
    params = json.load(open(PARAMS_PATH))
    model_dir = find_latest_model()
    if model_dir is None:
        print('ERROR: No trained model found in 2_training/hamiltonian/results/')
        sys.exit(1)
    print(f'Using model: {os.path.basename(model_dir)}')

    struct_labels = [('scf_0', os.path.join(DISP_DIR, 'scf_0'))]
    for i in range(1, NATOMS * 6 + 1):
        struct_labels.append((f'group_{i}', os.path.join(DISP_DIR, f'group_{i}')))

    print('=' * 60)
    print('Step 2: DeepH-E3 inference')
    print('=' * 60)
    for label, struct_dir in struct_labels:
        if not os.path.isdir(struct_dir):
            continue
        run_e3_inference(struct_dir, label, model_dir, params)


# ============================================================
# Step 3: AO bracket computation
# ============================================================

def load_structure(struct_dir, ham_file):
    """Load H_raw, S_raw, orbital info for one structure."""
    aodir = os.path.join(struct_dir, 'reconstruction', 'aohamiltonian')
    H_raw = read_h5_dict(os.path.join(aodir, ham_file))
    S_raw = read_h5_dict(os.path.join(aodir, 'overlaps.h5'))
    site_norbits, norbits, csum = get_orbital_info(aodir)
    return H_raw, S_raw, site_norbits, norbits, csum


def compute_ao_brackets(source):
    """
    Compute U/V brackets and eigenvalues for all 6 displacement directions.

    source: 'hpro' or 'e3'
    Saves to displacements/scf_0/ao_brackets_{source}.npz
    """
    ham_file = 'hamiltonians.h5' if source == 'hpro' else 'hamiltonians_pred_e3.h5'
    label    = source.upper()
    out_file = os.path.join(DISP_DIR, 'scf_0', f'ao_brackets_{source}.npz')

    if os.path.exists(out_file):
        print(f'  [{label}] ao_brackets_{source}.npz already exists')
        return

    print(f'\n{"=" * 60}')
    print(f'Computing AO brackets ({label})')
    print(f'{"=" * 60}')

    # Load undisplaced structure
    scf0_dir = os.path.join(DISP_DIR, 'scf_0')
    H0_raw, S0_raw, site_norbits, norbits, csum = load_structure(scf0_dir, ham_file)
    H0_R, S0_R = build_HR(H0_raw, S0_raw, site_norbits, norbits, csum)

    print(f'  Undisplaced: norbits={norbits}')
    print(f'  Computing eigenvectors at {NK} k-points...')
    eigs_0, evecs_0 = compute_eigenvectors(H0_R, S0_R, KGRID, norbits)

    n_disp_dirs = NATOMS * 3  # 6
    U_arr  = np.zeros((n_disp_dirs, NK, NK, NBANDS, NBANDS), dtype=np.complex128)
    V_arr  = np.zeros((n_disp_dirs, NK, NK, NBANDS, NBANDS), dtype=np.complex128)
    ek_arr = np.array(eigs_0)                                # (NK, NBANDS)
    ep_arr = np.zeros((n_disp_dirs, NK, NBANDS))
    epm_arr = np.zeros((n_disp_dirs, NK, NBANDS))

    for d in range(n_disp_dirs):
        gp = 2 * d + 1   # positive displacement group index
        gm = 2 * d + 2   # negative displacement group index
        atom = d // 3 + 1  # displaced atom (1-based)
        print(f'\n  d={d} (atom {atom}, groups {gp}/{gm})...')

        # Positive displacement
        gp_dir = os.path.join(DISP_DIR, f'group_{gp}')
        Hp_raw, Sp_raw, _, _, _ = load_structure(gp_dir, ham_file)
        Hp_R, Sp_R = build_HR(Hp_raw, Sp_raw, site_norbits, norbits, csum)
        eigs_p, evecs_p = compute_eigenvectors(Hp_R, Sp_R, KGRID, norbits)
        ep_arr[d] = np.array(eigs_p)

        delta_p = _get_delta_cart_ang(scf0_dir, gp_dir, atom)
        S_cross_p = build_cross_overlap_R_exact(S0_raw, Sp_raw, atom,
                                                 site_norbits, norbits, csum, delta_p)
        for ik in range(NK):
            Sk_cross = build_Sk_cross(S_cross_p, KGRID[ik], norbits)
            U_arr[d, ik, ik] = compute_brackets(evecs_p[ik], evecs_0[ik], Sk_cross)

        # Negative displacement
        gm_dir = os.path.join(DISP_DIR, f'group_{gm}')
        Hm_raw, Sm_raw, _, _, _ = load_structure(gm_dir, ham_file)
        Hm_R, Sm_R = build_HR(Hm_raw, Sm_raw, site_norbits, norbits, csum)
        eigs_m, evecs_m = compute_eigenvectors(Hm_R, Sm_R, KGRID, norbits)
        epm_arr[d] = np.array(eigs_m)

        delta_m = _get_delta_cart_ang(scf0_dir, gm_dir, atom)
        S_cross_m = build_cross_overlap_R_exact(S0_raw, Sm_raw, atom,
                                                 site_norbits, norbits, csum, delta_m)
        for ik in range(NK):
            Sk_cross = build_Sk_cross(S_cross_m, KGRID[ik], norbits)
            V_arr[d, ik, ik] = compute_brackets(evecs_m[ik], evecs_0[ik], Sk_cross)

        print(f'  d={d} done')

    np.savez(out_file,
             U_list=U_arr, V_list=V_arr,
             ek_list=ek_arr, ep_list=ep_arr, epm_list=epm_arr)
    print(f'\n  Saved: {out_file}')
    print(f'  U_list shape: {U_arr.shape}  (n_dirs, nk, nk, nbands, nbands)')


def run_all_brackets():
    print('=' * 60)
    print('Step 3: AO bracket computation')
    print('=' * 60)
    for source in ('hpro', 'e3'):
        aodir_0 = os.path.join(DISP_DIR, 'scf_0', 'reconstruction', 'aohamiltonian')
        ham_file = 'hamiltonians.h5' if source == 'hpro' else 'hamiltonians_pred_e3.h5'
        if not os.path.exists(os.path.join(aodir_0, ham_file)):
            print(f'  [{source.upper()}] {ham_file} not found in scf_0 — skipping')
            continue
        compute_ao_brackets(source)


# ============================================================
# Main
# ============================================================

def main():
    parser = argparse.ArgumentParser(description='ml_epc.py: EPC AO bracket pipeline')
    parser.add_argument('--hpro',     action='store_true', help='Run only HPRO reconstruction')
    parser.add_argument('--e3',       action='store_true', help='Run only DeepH-E3 inference')
    parser.add_argument('--brackets', action='store_true', help='Run only AO bracket computation')
    args = parser.parse_args()

    run_all = not (args.hpro or args.e3 or args.brackets)

    if run_all or args.hpro:
        run_all_hpro()

    if run_all or args.e3:
        run_all_e3()

    if run_all or args.brackets:
        run_all_brackets()

    print('\nml_epc.py done.')
    print('Run diamond_ml.jl to compute EPC with AO brackets and compare with DFT.')


if __name__ == '__main__':
    main()