RodrigoAVargasHdz/huxel_molecule_desing

Hückel model + JAX

Inverse molecular design with automatic differentiation: Hückel + JAX

Using JAX we optimize the type of atoms given an adjacency matrix of a molecular graph and the target observable. All observables were computed with the Hückel model.

Otpimization of HOMO-LUMO gap , and polarizability ,

Our code only considers three different optimizers,

1. BFGS
2. Gradient descent
3. Adam

To extended to other optimization methods, check wrapper_opt_method in huxel/minimize.py.

Example (benzene)

Adjacency matrix for benzene (run_benzene.py)

    import jax.numpy as jnp

    from huxel import myMolecule
    from huxel import optimization as _opt

    atom_types = ["X", "X", "X", "X", "X", "X"]
    smile = "C6" # name label

    connectivity_matrix = jnp.array(
        [
            [0, 1, 0, 0, 0, 1],
            [1, 0, 1, 0, 0, 0],
            [0, 1, 0, 1, 0, 0],
            [0, 0, 1, 0, 1, 0],
            [0, 0, 0, 1, 0, 1],
            [1, 0, 0, 0, 1, 0],
        ],
        dtype=int,
    )

    xyz = jnp.array([[ 1.40000000e+00,  3.70074342e-17,  0.00000000e+00],
       [ 7.00000000e-01, -1.21243557e+00,  0.00000000e+00],
       [-7.00000000e-01, -1.21243557e+00,  0.00000000e+00],
       [-1.40000000e+00,  2.08457986e-16,  0.00000000e+00],
       [-7.00000000e-01,  1.21243557e+00,  0.00000000e+00],
       [ 7.00000000e-01,  1.21243557e+00,  0.00000000e+00]])

    molec = myMolecule(
        "benzene",
        smile,
        atom_types,
        connectivity_matrix,
        xyz
    )

    l = 0
    _opt(l, molec,'homo_lumo','BFGS')

Optimization of different molecules

We considered eight different molecules.

execute run_molecule_i.py where the options are,

1. --l, integer (to initialize jax.random.PRNGKey(l))
2. --s, integer for smile data set (range [1, ..., 8])
3. --obj, objective to optimize options [homo_lumo, polarizability]
4. --opt, optimization method [adam, GD, BFGS]
5. --extfield, external field magnitude (only for polarizability)

Requirements

jax, optax, jaxopt

Paper