dscribe

import numpy as np from ase.build import molecule from dscribe.descriptors import SOAP, CoulombMatrix # Define atomic structures samples = [molecule("H2O"), molecule("NO2"), molecule("CO2")] # Setup CoulombMatrix descriptor cm_desc = CoulombMatrix(n_atoms_max=3, permutation="sorted_l2") # Setup SOAP descriptor (using modern parameter names and compression) soap_desc = SOAP(species=["C", "H", "O", "N"], r_cut=5, n_max=8, l_max=6, compression="crossover") # Create descriptors for a single system water = samples[0] coulomb_matrix_h2o = cm_desc.create(water) soap_h2o = soap_desc.create(water, centers=[0]) print("Coulomb Matrix for H2O:\n", coulomb_matrix_h2o) print("SOAP for Oxygen in H2O:\n", soap_h2o) # Create descriptors for multiple systems (can be parallelized) coulomb_matrices_all = cm_desc.create(samples, n_jobs=2) oxygen_indices = [np.where(x.get_atomic_numbers() == 8)[0] for x in samples] oxygen_soap_all = soap_desc.create(samples, oxygen_indices, n_jobs=2) print("Coulomb Matrices for all samples shape:", coulomb_matrices_all.shape) print("SOAP for Oxygen in all samples shape:", oxygen_soap_all.shape) # Descriptors also allow calculating derivatives der, des = soap_desc.derivatives(samples[0], return_descriptor=True) print("SOAP derivatives shape:", der.shape) print("SOAP descriptor from derivatives shape:", des.shape)