UniPath/remote/DiffCSP-official/diffcsp/script_utils.py

import chemparse
import numpy as np
import torch
from torch.utils.data import Dataset
from torch_geometric.data import Data

chemical_symbols = [
    # 0
    'X',
    # 1
    'H', 'He',
    # 2
    'Li', 'Be', 'B', 'C', 'N', 'O', 'F', 'Ne',
    # 3
    'Na', 'Mg', 'Al', 'Si', 'P', 'S', 'Cl', 'Ar',
    # 4
    'K', 'Ca', 'Sc', 'Ti', 'V', 'Cr', 'Mn', 'Fe', 'Co', 'Ni', 'Cu', 'Zn',
    'Ga', 'Ge', 'As', 'Se', 'Br', 'Kr',
    # 5
    'Rb', 'Sr', 'Y', 'Zr', 'Nb', 'Mo', 'Tc', 'Ru', 'Rh', 'Pd', 'Ag', 'Cd',
    'In', 'Sn', 'Sb', 'Te', 'I', 'Xe',
    # 6
    'Cs', 'Ba', 'La', 'Ce', 'Pr', 'Nd', 'Pm', 'Sm', 'Eu', 'Gd', 'Tb', 'Dy',
    'Ho', 'Er', 'Tm', 'Yb', 'Lu',
    'Hf', 'Ta', 'W', 'Re', 'Os', 'Ir', 'Pt', 'Au', 'Hg', 'Tl', 'Pb', 'Bi',
    'Po', 'At', 'Rn',
    # 7
    'Fr', 'Ra', 'Ac', 'Th', 'Pa', 'U', 'Np', 'Pu', 'Am', 'Cm', 'Bk',
    'Cf', 'Es', 'Fm', 'Md', 'No', 'Lr',
    'Rf', 'Db', 'Sg', 'Bh', 'Hs', 'Mt', 'Ds', 'Rg', 'Cn', 'Nh', 'Fl', 'Mc',
    'Lv', 'Ts', 'Og']


class SampleDataset(Dataset):

    def __init__(self, formula, num_evals):
        super().__init__()
        self.formula = formula
        self.num_evals = num_evals
        self.get_structure()

    def get_structure(self):
        self.composition = chemparse.parse_formula(self.formula)
        chem_list = []
        for elem in self.composition:
            num_int = int(self.composition[elem])
            chem_list.extend([chemical_symbols.index(elem)] * num_int)
        self.chem_list = chem_list

    def __len__(self) -> int:
        return self.num_evals

    def __getitem__(self, index):
        return Data(
            atom_types=torch.LongTensor(self.chem_list),
            num_atoms=len(self.chem_list),
            num_nodes=len(self.chem_list),
        )


train_dist = {
    'perov_5': [0, 0, 0, 0, 0, 1],
    'carbon_24': [0.0,
                0.0,
                0.0,
                0.0,
                0.0,
                0.0,
                0.3250697750779839,
                0.0,
                0.27795107535708424,
                0.0,
                0.15383352487276308,
                0.0,
                0.11246100804465604,
                0.0,
                0.04958134953209654,
                0.0,
                0.038745690362830404,
                0.0,
                0.019044491873255624,
                0.0,
                0.010178952552946971,
                0.0,
                0.007059596125430964,
                0.0,
                0.006074536200952225],
    'perov': [0, 0, 0, 0, 0, 1],
    'carbon': [0.0,
                0.0,
                0.0,
                0.0,
                0.0,
                0.0,
                0.3250697750779839,
                0.0,
                0.27795107535708424,
                0.0,
                0.15383352487276308,
                0.0,
                0.11246100804465604,
                0.0,
                0.04958134953209654,
                0.0,
                0.038745690362830404,
                0.0,
                0.019044491873255624,
                0.0,
                0.010178952552946971,
                0.0,
                0.007059596125430964,
                0.0,
                0.006074536200952225],
    'mp_20' : [0.0,
            0.0021742334905660377,
            0.021079009433962265,
            0.019826061320754717,
            0.15271226415094338,
            0.047132959905660375,
            0.08464770047169812,
            0.021079009433962265,
            0.07808814858490566,
            0.03434551886792453,
            0.0972877358490566,
            0.013303360849056603,
            0.09669811320754718,
            0.02155807783018868,
            0.06522700471698113,
            0.014372051886792452,
            0.06703272405660378,
            0.00972877358490566,
            0.053176591981132074,
            0.010576356132075472,
            0.08995430424528301]
}


class GenDataset(Dataset):

    def __init__(self, dataset, total_num):
        super().__init__()
        self.total_num = total_num
        self.distribution = train_dist[dataset]
        self.num_atoms = np.random.choice(len(self.distribution), total_num, p = self.distribution)
        self.is_carbon = dataset == 'carbon_24'

    def __len__(self) -> int:
        return self.total_num

    def __getitem__(self, index):

        num_atom = self.num_atoms[index]
        data = Data(
            num_atoms=torch.LongTensor([num_atom]),
            num_nodes=num_atom,
        )
        if self.is_carbon:
            data.atom_types = torch.LongTensor([6] * num_atom)
        return data