# This is example aims to reproduce results reported in Section 4.2 of the following paper:
#  * Mauro Bracconi, and Matteo Maestri. Training set design for machine learning techniques
#    applied to the approximation of computationally intensive first-principles kinetic models
#    Chemical Engineering Journal 2022 (400) 125469
#
# The original model is described in:
#  * K. Reuter, M. Scheffler, First-principles kinetic Monte Carlo simulations for
#    heterogeneous catalysis: application to the CO oxidation at RuO2(110)
#    Phys. Rev. B – Condens. Matter Mater. Phys. 73 (2006) 1–17

import scm.pyzacros as pz


class ReuterScheffler:

    def __init__(self, repeat_cell=[10, 20]):

        # ---------------------------------------------
        # Species:
        # ---------------------------------------------
        # Gas-species:
        O2_gas = pz.Species("O2")
        CO_gas = pz.Species("CO")
        CO2_gas = pz.Species("CO2", gas_energy=-3.072)

        # Surface species:
        s0 = pz.Species("*", 1)  # Empty adsorption site
        O_ads = pz.Species("O*", 1)
        CO_ads = pz.Species("CO*", 1)

        # ---------------------------------------------
        # Lattice setup:
        # ---------------------------------------------
        self.lattice = pz.Lattice(
            cell_vectors=[[6.43, 0.00], [0.00, 3.12]],
            repeat_cell=repeat_cell,
            site_types=["cus", "brg"],
            site_coordinates=[[0.25, 0.50], [0.75, 0.50]],
            neighboring_structure=[
                [(0, 1), pz.Lattice.SELF],
                [(0, 0), pz.Lattice.NORTH],
                [(0, 1), pz.Lattice.NORTH],
                [(1, 1), pz.Lattice.NORTH],
                [(1, 0), pz.Lattice.NORTH],
                [(1, 0), pz.Lattice.NORTHEAST],
                [(1, 0), pz.Lattice.EAST],
                [(1, 0), pz.Lattice.SOUTHEAST],
            ],
        )

        # ---------------------------------------------
        # Clusters & Cluster expansion
        # ---------------------------------------------
        O_point_brg = pz.Cluster(species=[O_ads], site_types=["brg"], multiplicity=1, energy=-2.3, label="O_point_brg")
        O_point_cus = pz.Cluster(species=[O_ads], site_types=["cus"], multiplicity=1, energy=-1.0, label="O_point_cus")

        CO_point_brg = pz.Cluster(
            species=[CO_ads], site_types=["brg"], multiplicity=1, energy=-1.6, label="CO_point_brg"
        )
        CO_point_cus = pz.Cluster(
            species=[CO_ads], site_types=["cus"], multiplicity=1, energy=-1.3, label="CO_point_cus"
        )

        O_brg_O_brg_1NN = pz.Cluster(
            species=[O_ads, O_ads],
            site_types=["brg", "brg"],
            neighboring=[(0, 1)],
            multiplicity=2,
            energy=0.0,
            label="O_brg_O_brg_1NN",
        )
        O_cus_O_cus_1NN = pz.Cluster(
            species=[O_ads, O_ads],
            site_types=["cus", "cus"],
            neighboring=[(0, 1)],
            multiplicity=2,
            energy=0.0,
            label="O_cus_O_cus_1NN",
        )
        O_cus_O_brg_1NN = pz.Cluster(
            species=[O_ads, O_ads],
            site_types=["cus", "brg"],
            neighboring=[(0, 1)],
            multiplicity=2,
            energy=0.0,
            label="O_cus_O_brg_1NN",
        )

        CO_brg_CO_brg_1NN = pz.Cluster(
            species=[CO_ads, CO_ads],
            site_types=["brg", "brg"],
            neighboring=[(0, 1)],
            multiplicity=2,
            energy=0.0,
            label="CO_brg_CO_brg_1NN",
        )
        CO_cus_CO_cus_1NN = pz.Cluster(
            species=[CO_ads, CO_ads],
            site_types=["cus", "cus"],
            neighboring=[(0, 1)],
            multiplicity=2,
            energy=0.0,
            label="CO_cus_CO_cus_1NN",
        )
        CO_cus_CO_brg_1NN = pz.Cluster(
            species=[CO_ads, CO_ads],
            site_types=["cus", "brg"],
            neighboring=[(0, 1)],
            multiplicity=2,
            energy=0.0,
            label="CO_cus_CO_brg_1NN",
        )

        CO_brg_O_brg_1NN = pz.Cluster(
            species=[CO_ads, O_ads],
            site_types=["brg", "brg"],
            neighboring=[(0, 1)],
            multiplicity=2,
            energy=0.0,
            label="CO_brg_O_brg_1NN",
        )
        CO_cus_O_cus_1NN = pz.Cluster(
            species=[CO_ads, O_ads],
            site_types=["cus", "cus"],
            neighboring=[(0, 1)],
            multiplicity=2,
            energy=0.0,
            label="CO_cus_O_cus_1NN",
        )
        CO_cus_O_brg_1NN = pz.Cluster(
            species=[CO_ads, O_ads],
            site_types=["cus", "brg"],
            neighboring=[(0, 1)],
            multiplicity=2,
            energy=0.0,
            label="CO_cus_O_brg_1NN",
        )
        CO_brg_O_cus_1NN = pz.Cluster(
            species=[CO_ads, O_ads],
            site_types=["brg", "cus"],
            neighboring=[(0, 1)],
            multiplicity=2,
            energy=0.0,
            label="CO_brg_O_cus_1NN",
        )

        self.cluster_expansion = pz.ClusterExpansion(
            [
                O_point_brg,
                O_point_cus,
                CO_point_brg,
                CO_point_cus,
                O_brg_O_brg_1NN,
                O_cus_O_cus_1NN,
                O_cus_O_brg_1NN,
                CO_brg_CO_brg_1NN,
                CO_cus_CO_cus_1NN,
                CO_cus_CO_brg_1NN,
                CO_brg_O_brg_1NN,
                CO_cus_O_cus_1NN,
                CO_cus_O_brg_1NN,
                CO_brg_O_cus_1NN,
            ]
        )

        # ---------------------------------------------
        # Elementary Reactions & Mechanism
        # ---------------------------------------------

        CO_brg_adsorption = pz.ElementaryReaction(
            initial=[s0, CO_gas],
            final=[CO_ads],
            site_types=["brg"],
            reversible=True,
            pre_expon=2.04e08,
            pe_ratio=1.33e-10,
            activation_energy=0.0,
            prox_factor=0.0,
            label="CO_brg_adsorption",
        )

        CO_cus_adsorption = pz.ElementaryReaction(
            initial=[s0, CO_gas],
            final=[CO_ads],
            site_types=["cus"],
            reversible=True,
            pre_expon=2.04e08,
            pe_ratio=1.53e-10,
            activation_energy=0.0,
            prox_factor=0.0,
            label="CO_cus_adsorption",
        )

        O_brg_adsorption = pz.ElementaryReaction(
            initial=[s0, s0, O2_gas],
            final=[O_ads, O_ads],
            site_types=["brg", "brg"],
            neighboring=[(0, 1)],
            reversible=True,
            pre_expon=1.91e08,
            pe_ratio=5.33e-11,
            activation_energy=0.000,
            prox_factor=0.0,
            label="O_brg_adsorption",
        )

        O_cus_adsorption = pz.ElementaryReaction(
            initial=[s0, s0, O2_gas],
            final=[O_ads, O_ads],
            site_types=["cus", "cus"],
            neighboring=[(0, 1)],
            reversible=True,
            pre_expon=1.91e08,
            pe_ratio=5.33e-11,
            activation_energy=0.000,
            prox_factor=0.0,
            label="O_cus_adsorption",
        )

        O_cus_O_brg_adsorption = pz.ElementaryReaction(
            initial=[s0, s0, O2_gas],
            final=[O_ads, O_ads],
            site_types=["cus", "brg"],
            neighboring=[(0, 1)],
            reversible=True,
            pre_expon=1.91e08,
            pe_ratio=5.33e-11,
            activation_energy=0.000,
            prox_factor=0.0,
            label="O_cus_O_brg_adsorption",
        )

        CO_brg_O_cus_oxidation = pz.ElementaryReaction(
            initial=[CO_ads, O_ads],
            final=[s0, s0, CO2_gas],
            site_types=["brg", "cus"],
            neighboring=[(0, 1)],
            reversible=False,
            pre_expon=6.25e12,
            activation_energy=0.76,
            prox_factor=0.0,
            label="CO_brg_O_cus_oxidation",
        )

        CO_brg_O_brg_oxidation = pz.ElementaryReaction(
            initial=[CO_ads, O_ads],
            final=[s0, s0, CO2_gas],
            site_types=["brg", "brg"],
            neighboring=[(0, 1)],
            reversible=False,
            pre_expon=6.25e12,
            activation_energy=1.54,
            prox_factor=0.0,
            label="CO_brg_O_brg_oxidation",
        )

        CO_cus_O_cus_oxidation = pz.ElementaryReaction(
            initial=[CO_ads, O_ads],
            final=[s0, s0, CO2_gas],
            site_types=["cus", "cus"],
            neighboring=[(0, 1)],
            reversible=False,
            pre_expon=6.25e12,
            activation_energy=0.89,
            prox_factor=0.0,
            label="CO_cus_O_cus_oxidation",
        )

        CO_cus_O_brg_oxidation = pz.ElementaryReaction(
            initial=[CO_ads, O_ads],
            final=[s0, s0, CO2_gas],
            site_types=["cus", "brg"],
            neighboring=[(0, 1)],
            reversible=False,
            pre_expon=6.25e12,
            activation_energy=1.25,
            prox_factor=0.0,
            label="CO_cus_O_brg_oxidation",
        )

        self.mechanism = pz.Mechanism(
            [
                CO_brg_adsorption,
                CO_cus_adsorption,
                O_brg_adsorption,
                O_cus_adsorption,
                O_cus_O_brg_adsorption,
                CO_brg_O_cus_oxidation,
                CO_brg_O_brg_oxidation,
                CO_cus_O_cus_oxidation,
                CO_cus_O_brg_oxidation,
            ]
        )