Source code for wavefunction_analysis.utils.chiral_geom

from wavefunction_analysis import sys, np
from wavefunction_analysis.utils import print_matrix
from wavefunction_analysis.utils.sec_mole import read_symbols_coords, write_symbols_coords



def swap_atoms_coords(coords, atoms_idx):
    """
    change two atoms a, b positions from the center atom c
    """
    a, c, b = atoms_idx

    va, vb = coords[a]-coords[c], coords[b]-coords[c]
    da, db = np.linalg.norm(va), np.linalg.norm(vb)

    # change a and b coords and scale by the distances
    coords[a], coords[b] = (da/db)* coords[b], (db/da)* coords[a]
    return coords





def spin_square_biortho(mf):
    mo_coeff = mf.mo_coeff
    mo_occ = mf.mo_occ
    ovlp = mf.get_ovlp()

    moa, mob = mo_coeff[0][:, mo_occ[0]>0], mo_coeff[1][:, mo_occ[1]>0]

    s = np.einsum('mi,mn,nj->ij', moa, ovlp, mob)
    u, s, vt = np.linalg.svd(s)
    print_matrix('s:', s)
    moa, mob = np.einsum('mi,ik->mk', moa, u), np.einsum('mi,ki->mk', mob, vt)

    return mf.spin_square([moa, mob], ovlp)





def run_gtensor(symbols, coords, charge=1, spin=1, functional='hf', basis='3-21g'):
    from pyscf import gto, scf
    from pyscf.prop import gtensor
    from wavefunction_analysis.utils.pyscf_parser import build_atom

    atom = build_atom(symbols, coords)
    mol = gto.M(
            atom = atom,
            basis = basis,
            charge = charge,
            spin = spin,
            )

    mf = scf.UKS(mol)
    mf.xc = functional
    mf.kernel()

    gobj = gtensor.UKS(mf)
    gobj.para_soc2e = None
    gobj.dia_soc2e = None
    gobj.so_eff_charge = False
    gmat = gobj.kernel()
    print('gmat:\n', gmat)

    return mf, gobj



if __name__ == '__main__':
    charge = 1
    spin = 1
    functional = 'hf'

    xyzfile = sys.argv[1]
    symbols, coords = read_symbols_coords(xyzfile)
    write_symbols_coords('stdout', symbols, coords)
    mf, gobj = run_gtensor(symbols, coords, charge, spin, functional)

    s2, s2p1 = spin_square_biortho(mf)
    print('s2, s2p1:', s2, s2p1)
    print('')

    atoms_idx = [2, 0, 3]
    coords = swap_atoms_coords(coords, atoms_idx)
    write_symbols_coords('stdout', symbols, coords)
    mf, gobj = run_gtensor(symbols, coords, charge, spin, functional)