import itertools # %% List_of_SMIs_Config # %% Configuration # Define elements elements = [Hydrogen, Carbon, Hydrogen, Hydrogen, Carbon, Oxygen, Oxygen, Hydrogen] # Define coordinates cartesian_coordinates = [[ 0.748765, -0.127722, -1.46492 ], [-0.209816, -0.194167, -0.933683], [-0.836558, 0.642786, -1.268776], [-0.701067, -1.128721, -1.232691], [-0.001295, -0.142614, 0.547721], [-0.296097, -0.967368, 1.393966], [ 0.600553, 0.98165 , 1.006038], [ 0.695512, 0.936156, 1.952344]]*Angstrom # Set up configuration configuration_0 = MoleculeConfiguration( elements=elements, cartesian_coordinates=cartesian_coordinates ) # Add bonds bonds = [[0, 1], [1, 2], [1, 3], [1, 4], [4, 5], [4, 6], [6, 7]] configuration_0.setBonds(bonds) configuration_name_0 = "Acetic acid" configuration_table = Table() configuration_table.addInstanceColumn(key='configurations', types=MoleculeConfiguration) configuration_table.append(configuration_0) configuration_names_table = Table() configuration_names_table.addStringColumn(key='configuration_names') configuration_names_table.append(configuration_name_0) # %% List_of_cluster_model # %% Configuration # Define elements elements = [Aluminium, Nitrogen, Hydrogen, Nitrogen, Hydrogen, Nitrogen, Hydrogen, Hydrogen, Hydrogen, Hydrogen] # Define coordinates cartesian_coordinates = [[ 9.865768213117, 12.383377293118, 11.748123418484], [ 10.669928205505, 13.645245174255, 10.058539260268], [ 11.634771653761, 13.378964418898, 9.709224345954], [ 10.604212310744, 10.469469434034, 10.809099556215], [ 11.654520764871, 10.322933671824, 10.861739632734], [ 10.622061370086, 13.790527070005, 13.296477200545], [ 11.433508645293, 14.437456397798, 13.164253165495], [ 10.069368922141, 14.458709581093, 9.746148012834], [ 9.916597400124, 9.891134033957, 10.25249843707 ], [ 9.923287172717, 13.530771082121, 14.034338129733]]*Angstrom # Set up configuration configuration_0 = MoleculeConfiguration( elements=elements, cartesian_coordinates=cartesian_coordinates ) # Add tags configuration_0.addTags('H_N', [7, 8, 9]) # Add bonds bonds = [[0, 1], [0, 3], [0, 5], [1, 2], [1, 7], [3, 4], [3, 8], [5, 6], [5, 9]] configuration_0.setBonds(bonds) configuration_name_0 = "AlNH2" configuration_table_1 = Table() configuration_table_1.addInstanceColumn(key='configurations', types=MoleculeConfiguration) configuration_table_1.append(configuration_0) configuration_names_table_1 = Table() configuration_names_table_1.addStringColumn(key='configuration_names') configuration_names_table_1.append(configuration_name_0) # %% ForceFieldCalculator potentialSet = TorchX_MACE_MP_0_L0_2023(dtype='float32', enforceLTX=False) calculator = TremoloXCalculator(parameters=potentialSet) # %% generate_complex def generate_complex(smis, surface_models, name_surface_models, name_smis): # Extract matching columns from tables config_smis = smis.column('configurations') surf_config = surface_models.column('configurations') name_surf = name_surface_models.column('configuration_names') name_smi = name_smis.column('configuration_names') # Defined variables. central_atoms = '[Al, Si]' # Script. from generateAcidDerivativeComplex import generateAcidDerivativeComplex table_of_complex_config = generateAcidDerivativeComplex( config_smis, surf_config, name_surf, name_smi, central_atoms ) return table_of_complex_config table_of_complex_config = generate_complex( configuration_table, configuration_table_1, configuration_names_table_1, configuration_names_table, ) nlsave('AdsorptionEnergies_AcidDerivatives.hdf5', table_of_complex_config) # %% Array Table Iteration # Array Table Iteration(preparation) for row_index in range(table_of_complex_config.numberOfRows()): surf_cluster, name_surf, smi_mol, name_smi, complex_config, products = ( table_of_complex_config[ row_index, [ 'surf_cluster', 'name_surf', 'config_mol', 'name_smi', 'complex_config', 'product_1', ], ] ) # %% Create table for calculations def create_table_for_calculations(surf_cluster, smi_mol, complex_config, products): # This custom script supports atkpython syntax # and can perform almost any procedure. configuration_table = Table() configuration_table.addInstanceColumn( key='configuration', types=BulkConfiguration ) configuration_table.append(surf_cluster) configuration_table.append(smi_mol) configuration_table.append(complex_config) configuration_table.append(products) energy = Table() energy.addInstanceColumn(key='energy', types=TotalEnergy) return configuration_table, energy configuration_table_2, energy = create_table_for_calculations( surf_cluster, smi_mol, complex_config, products ) nlsave( 'AdsorptionEnergies_AcidDerivatives.hdf5', configuration_table_2, object_id='configuration_table_2_Create_table_for_calculations', ) nlsave( 'AdsorptionEnergies_AcidDerivatives.hdf5', energy, object_id='energy_Create_table_for_calculations', ) # %% Table Iteration # Table Iteration(preparation) for row_index_1 in range(configuration_table_2.numberOfRows()): configuration = configuration_table_2[row_index_1, ['configuration']] # %% Set Calculator configuration.setCalculator(calculator) configuration.update() nlsave( 'AdsorptionEnergies_AcidDerivatives.hdf5', configuration, object_id=f'configuration_Set_Calculator_row_index_1_{row_index_1}_row_index_{row_index}', ) # %% OptimizeGeometry restart_strategy = RestartFromTrajectory( trajectory_filename='AdsorptionEnergies_AcidDerivatives.hdf5', object_id=f'optimized_configuration_optimize_trajectory_row_index_1_{row_index_1}_row_index_{row_index}', ) optimized_configuration = OptimizeGeometry( configuration=configuration, max_forces=0.05 * eV / Angstrom, constraints=[BravaisLatticeConstraint()], trajectory_filename='AdsorptionEnergies_AcidDerivatives.hdf5', trajectory_object_id=f'optimized_configuration_optimize_trajectory_row_index_1_{row_index_1}_row_index_{row_index}', optimizer_method=FIRE(), restart_strategy=restart_strategy, ) nlsave( 'AdsorptionEnergies_AcidDerivatives.hdf5', optimized_configuration, object_id=f'optimized_configuration_optgeom_row_index_1_{row_index_1}_row_index_{row_index}', ) # %% TotalEnergy total_energy = TotalEnergy(configuration=optimized_configuration) nlsave( 'AdsorptionEnergies_AcidDerivatives.hdf5', total_energy, object_id=f'total_energy_TotalEnergy_row_index_1_{row_index_1}_row_index_{row_index}', ) # %% Save energies to Table def save_energies_to_table(energy, energy_total): # This custom script supports atkpython syntax # and can perform almost any procedure. energy.append(energy_total) return energy energy = save_energies_to_table(energy, total_energy) nlsave( 'AdsorptionEnergies_AcidDerivatives.hdf5', energy, object_id='energy_Save_energies_to_Table', ) # %% AdsorptionEnergy def adsorption_energy(energies): # Extract matching columns from tables energy = energies.column('energy') # Calculate bond dissociation energy # original_mol = surf_cluster.hillFormula() # ligand = smi_mol.hillFormula() Energy_all = energies.column(0) Binding_energy = ( Energy_all[3].evaluate() + Energy_all[2].evaluate() - Energy_all[1].evaluate() - Energy_all[0].evaluate() ) return Binding_energy binding__energy = adsorption_energy(energy) nlsave( 'AdsorptionEnergies_AcidDerivatives.hdf5', binding__energy, object_id=f'binding__energy_AdsorptionEnergy_row_index_{row_index}_1', ) # %% CollectResults if 'collect_results' not in locals(): collect_results = Table( 'AdsorptionEnergies_AcidDerivatives.hdf5', object_id='table' ) collect_results.addInstanceColumn(key='model', types=BulkConfiguration) collect_results.addStringColumn(key='name_surf') collect_results.addInstanceColumn(key='adsorbate', types=BulkConfiguration) collect_results.addStringColumn(key='name_smi') collect_results.addQuantityColumn(key='adsorption_energy', unit=eV) collect_results.setMetatext('CollectResults') collect_results.append(surf_cluster, name_surf, smi_mol, name_smi, binding__energy) # %% SaveResults def save_results(table): # Extract matching columns from tables model = table.column('model') name_surf = table.column('name_surf') adsorbate = table.column('adsorbate') name_smi = table.column('name_smi') adsorption_energy = table.column('adsorption_energy') nlsave('E_ADS.hdf5', table) return save_results(collect_results)