Atomic distances between atom in different C20 molecules,, QML/develop branch

test_c20.py

#!/usr/bin/env python3

import numpy as np

# The development version of QML
import qml

from qml.fchl import generate_representation
from qml.fchl import get_atomic_kernels
from qml.fchl import get_global_symmetric_kernels
from qml.data import Compound

np.set_printoptions(linewidth=99999999, suppress=True)

REP_ARGS = {
    "max_size": 20,
    "cut_distance": 1e6,
}

KERNEL_ARGS = {
    "kernel_args": {
        "sigma": [0.1],
    },
    "alchemy": "off",
    "cut_distance": 1e6,
}

if __name__ == "__main__":

    c1 = Compound(xyz="c20.xyz")
    c2 = Compound(xyz="c20-other.xyz") # [6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 6, 7, 6, 6, 6, 6]
    c3 = Compound(xyz="c20-opposite.xyz") # [6, 6, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 6]


    r1 = generate_representation(c1.coordinates, c1.nuclear_charges, **REP_ARGS)
    r2 = generate_representation(c2.coordinates, c2.nuclear_charges, **REP_ARGS)
    r3 = generate_representation(c3.coordinates, c3.nuclear_charges, **REP_ARGS)

    K12 = get_atomic_kernels(r2, r3, **KERNEL_ARGS)[0]
    print(K12)

    all_reps = np.array([r1, r2, r3])
    K12 = get_global_symmetric_kernels(all_reps, **KERNEL_ARGS)[0]
    print(K12)