# Set minimal log verbosity setVerbosity(MinimalLog) results_filename = 'CuH_results.hdf5' # Set up lattice vector_a = [14.45984, 0.0, 0.0]*Angstrom vector_b = [0.0, 14.45984, 0.0]*Angstrom vector_c = [0.0, 0.0, 14.45984]*Angstrom lattice = UnitCell(vector_a, vector_b, vector_c) # Define elements elements = [Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Copper, Hydrogen] # Define coordinates fractional_coordinates = [[ 0. , 0. , 0. ], [ 0. , 0. , 0.25 ], [ 0. , 0. , 0.5 ], [ 0. , 0. , 0.75 ], [ 0. , 0.25 , 0. ], [ 0. , 0.25 , 0.25 ], [ 0. , 0.25 , 0.5 ], [ 0. , 0.25 , 0.75 ], [ 0. , 0.5 , 0. ], [ 0. , 0.5 , 0.25 ], [ 0. , 0.5 , 0.5 ], [ 0. , 0.5 , 0.75 ], [ 0. , 0.75 , 0. ], [ 0. , 0.75 , 0.25 ], [ 0. , 0.75 , 0.5 ], [ 0. , 0.75 , 0.75 ], [ 0.25 , 0. , 0. ], [ 0.25 , 0. , 0.25 ], [ 0.25 , 0. , 0.5 ], [ 0.25 , 0. , 0.75 ], [ 0.25 , 0.25 , 0. ], [ 0.25 , 0.25 , 0.25 ], [ 0.25 , 0.25 , 0.5 ], [ 0.25 , 0.25 , 0.75 ], [ 0.25 , 0.5 , 0. ], [ 0.25 , 0.5 , 0.25 ], [ 0.25 , 0.5 , 0.5 ], [ 0.25 , 0.5 , 0.75 ], [ 0.25 , 0.75 , 0. ], [ 0.25 , 0.75 , 0.25 ], [ 0.25 , 0.75 , 0.5 ], [ 0.25 , 0.75 , 0.75 ], [ 0.5 , 0. , 0. ], [ 0.5 , 0. , 0.25 ], [ 0.5 , 0. , 0.5 ], [ 0.5 , 0. , 0.75 ], [ 0.5 , 0.25 , 0. ], [ 0.5 , 0.25 , 0.25 ], [ 0.5 , 0.25 , 0.5 ], [ 0.5 , 0.25 , 0.75 ], [ 0.5 , 0.5 , 0. ], [ 0.5 , 0.5 , 0.25 ], [ 0.5 , 0.5 , 0.5 ], [ 0.5 , 0.5 , 0.75 ], [ 0.5 , 0.75 , 0. ], [ 0.5 , 0.75 , 0.25 ], [ 0.5 , 0.75 , 0.5 ], [ 0.5 , 0.75 , 0.75 ], [ 0.75 , 0. , 0. ], [ 0.75 , 0. , 0.25 ], [ 0.75 , 0. , 0.5 ], [ 0.75 , 0. , 0.75 ], [ 0.75 , 0.25 , 0. ], [ 0.75 , 0.25 , 0.25 ], [ 0.75 , 0.25 , 0.5 ], [ 0.75 , 0.25 , 0.75 ], [ 0.75 , 0.5 , 0. ], [ 0.75 , 0.5 , 0.25 ], [ 0.75 , 0.5 , 0.5 ], [ 0.75 , 0.5 , 0.75 ], [ 0.75 , 0.75 , 0. ], [ 0.75 , 0.75 , 0.25 ], [ 0.75 , 0.75 , 0.5 ], [ 0.75 , 0.75 , 0.75 ], [ 0.125, 0.125, 0. ], [ 0.125, 0.125, 0.25 ], [ 0.125, 0.125, 0.5 ], [ 0.125, 0.125, 0.75 ], [ 0.125, 0.375, 0. ], [ 0.125, 0.375, 0.25 ], [ 0.125, 0.375, 0.5 ], [ 0.125, 0.375, 0.75 ], [ 0.125, 0.625, 0. ], [ 0.125, 0.625, 0.25 ], [ 0.125, 0.625, 0.5 ], [ 0.125, 0.625, 0.75 ], [ 0.125, 0.875, 0. ], [ 0.125, 0.875, 0.25 ], [ 0.125, 0.875, 0.5 ], [ 0.125, 0.875, 0.75 ], [ 0.375, 0.125, 0. ], [ 0.375, 0.125, 0.25 ], [ 0.375, 0.125, 0.5 ], [ 0.375, 0.125, 0.75 ], [ 0.375, 0.375, 0. ], [ 0.375, 0.375, 0.25 ], [ 0.375, 0.375, 0.5 ], [ 0.375, 0.375, 0.75 ], [ 0.375, 0.625, 0. ], [ 0.375, 0.625, 0.25 ], [ 0.375, 0.625, 0.5 ], [ 0.375, 0.625, 0.75 ], [ 0.375, 0.875, 0. ], [ 0.375, 0.875, 0.25 ], [ 0.375, 0.875, 0.5 ], [ 0.375, 0.875, 0.75 ], [ 0.625, 0.125, 0. ], [ 0.625, 0.125, 0.25 ], [ 0.625, 0.125, 0.5 ], [ 0.625, 0.125, 0.75 ], [ 0.625, 0.375, 0. ], [ 0.625, 0.375, 0.25 ], [ 0.625, 0.375, 0.5 ], [ 0.625, 0.375, 0.75 ], [ 0.625, 0.625, 0. ], [ 0.625, 0.625, 0.25 ], [ 0.625, 0.625, 0.5 ], [ 0.625, 0.625, 0.75 ], [ 0.625, 0.875, 0. ], [ 0.625, 0.875, 0.25 ], [ 0.625, 0.875, 0.5 ], [ 0.625, 0.875, 0.75 ], [ 0.875, 0.125, 0. ], [ 0.875, 0.125, 0.25 ], [ 0.875, 0.125, 0.5 ], [ 0.875, 0.125, 0.75 ], [ 0.875, 0.375, 0. ], [ 0.875, 0.375, 0.25 ], [ 0.875, 0.375, 0.5 ], [ 0.875, 0.375, 0.75 ], [ 0.875, 0.625, 0. ], [ 0.875, 0.625, 0.25 ], [ 0.875, 0.625, 0.5 ], [ 0.875, 0.625, 0.75 ], [ 0.875, 0.875, 0. ], [ 0.875, 0.875, 0.25 ], [ 0.875, 0.875, 0.5 ], [ 0.875, 0.875, 0.75 ], [ 0.125, 0. , 0.125], [ 0.125, 0. , 0.375], [ 0.125, 0. , 0.625], [ 0.125, 0. , 0.875], [ 0.125, 0.25 , 0.125], [ 0.125, 0.25 , 0.375], [ 0.125, 0.25 , 0.625], [ 0.125, 0.25 , 0.875], [ 0.125, 0.5 , 0.125], [ 0.125, 0.5 , 0.375], [ 0.125, 0.5 , 0.625], [ 0.125, 0.5 , 0.875], [ 0.125, 0.75 , 0.125], [ 0.125, 0.75 , 0.375], [ 0.125, 0.75 , 0.625], [ 0.125, 0.75 , 0.875], [ 0.375, 0. , 0.125], [ 0.375, 0. , 0.375], [ 0.375, 0. , 0.625], [ 0.375, 0. , 0.875], [ 0.375, 0.25 , 0.125], [ 0.375, 0.25 , 0.375], [ 0.375, 0.25 , 0.625], [ 0.375, 0.25 , 0.875], [ 0.375, 0.5 , 0.125], [ 0.375, 0.5 , 0.375], [ 0.375, 0.5 , 0.625], [ 0.375, 0.5 , 0.875], [ 0.375, 0.75 , 0.125], [ 0.375, 0.75 , 0.375], [ 0.375, 0.75 , 0.625], [ 0.375, 0.75 , 0.875], [ 0.625, 0. , 0.125], [ 0.625, 0. , 0.375], [ 0.625, 0. , 0.625], [ 0.625, 0. , 0.875], [ 0.625, 0.25 , 0.125], [ 0.625, 0.25 , 0.375], [ 0.625, 0.25 , 0.625], [ 0.625, 0.25 , 0.875], [ 0.625, 0.5 , 0.125], [ 0.625, 0.5 , 0.375], [ 0.625, 0.5 , 0.625], [ 0.625, 0.5 , 0.875], [ 0.625, 0.75 , 0.125], [ 0.625, 0.75 , 0.375], [ 0.625, 0.75 , 0.625], [ 0.625, 0.75 , 0.875], [ 0.875, 0. , 0.125], [ 0.875, 0. , 0.375], [ 0.875, 0. , 0.625], [ 0.875, 0. , 0.875], [ 0.875, 0.25 , 0.125], [ 0.875, 0.25 , 0.375], [ 0.875, 0.25 , 0.625], [ 0.875, 0.25 , 0.875], [ 0.875, 0.5 , 0.125], [ 0.875, 0.5 , 0.375], [ 0.875, 0.5 , 0.625], [ 0.875, 0.5 , 0.875], [ 0.875, 0.75 , 0.125], [ 0.875, 0.75 , 0.375], [ 0.875, 0.75 , 0.625], [ 0.875, 0.75 , 0.875], [ 0. , 0.125, 0.125], [ 0. , 0.125, 0.375], [ 0. , 0.125, 0.625], [ 0. , 0.125, 0.875], [ 0. , 0.375, 0.125], [ 0. , 0.375, 0.375], [ 0. , 0.375, 0.625], [ 0. , 0.375, 0.875], [ 0. , 0.625, 0.125], [ 0. , 0.625, 0.375], [ 0. , 0.625, 0.625], [ 0. , 0.625, 0.875], [ 0. , 0.875, 0.125], [ 0. , 0.875, 0.375], [ 0. , 0.875, 0.625], [ 0. , 0.875, 0.875], [ 0.25 , 0.125, 0.125], [ 0.25 , 0.125, 0.375], [ 0.25 , 0.125, 0.625], [ 0.25 , 0.125, 0.875], [ 0.25 , 0.375, 0.125], [ 0.25 , 0.375, 0.375], [ 0.25 , 0.375, 0.625], [ 0.25 , 0.375, 0.875], [ 0.25 , 0.625, 0.125], [ 0.25 , 0.625, 0.375], [ 0.25 , 0.625, 0.625], [ 0.25 , 0.625, 0.875], [ 0.25 , 0.875, 0.125], [ 0.25 , 0.875, 0.375], [ 0.25 , 0.875, 0.625], [ 0.25 , 0.875, 0.875], [ 0.5 , 0.125, 0.125], [ 0.5 , 0.125, 0.375], [ 0.5 , 0.125, 0.625], [ 0.5 , 0.125, 0.875], [ 0.5 , 0.375, 0.125], [ 0.5 , 0.375, 0.375], [ 0.5 , 0.375, 0.625], [ 0.5 , 0.375, 0.875], [ 0.5 , 0.625, 0.125], [ 0.5 , 0.625, 0.375], [ 0.5 , 0.625, 0.625], [ 0.5 , 0.625, 0.875], [ 0.5 , 0.875, 0.125], [ 0.5 , 0.875, 0.375], [ 0.5 , 0.875, 0.625], [ 0.5 , 0.875, 0.875], [ 0.75 , 0.125, 0.125], [ 0.75 , 0.125, 0.375], [ 0.75 , 0.125, 0.625], [ 0.75 , 0.125, 0.875], [ 0.75 , 0.375, 0.125], [ 0.75 , 0.375, 0.375], [ 0.75 , 0.375, 0.625], [ 0.75 , 0.375, 0.875], [ 0.75 , 0.625, 0.125], [ 0.75 , 0.625, 0.375], [ 0.75 , 0.625, 0.625], [ 0.75 , 0.625, 0.875], [ 0.75 , 0.875, 0.125], [ 0.75 , 0.875, 0.375], [ 0.75 , 0.875, 0.625], [ 0.75 , 0.875, 0.875], [ 0.375, 0.375, 0.375]] # Set up configuration copper = BulkConfiguration( bravais_lattice=lattice, elements=elements, fractional_coordinates=fractional_coordinates ) copper.addTags('hydrogen', [256]) copper.addTags('constrain', [100]) # %% ForceFieldCalculator potentialSet = TorchX_M3GNet_MP_DIRECT_PES_2021(dtype='float32') calculator = TremoloXCalculator(parameters=potentialSet) # %% Set Calculator copper.setCalculator(calculator) # Constrain one atom to fix the lattice in place. fix_atom_index = copper.indicesFromTags(['constrain']) constraints = [FixAtomConstraints(fix_atom_index), BravaisLatticeConstraint()] restart_strategy = RestartFromTrajectory( trajectory_filename='copper_1_results.hdf5', object_id='optimize_trajectory' ) # Optimize the initial geometry optimized_configuration = OptimizeGeometry( configuration=copper, max_forces=0.01 * eV / Angstrom, constraints=constraints, trajectory_filename='copper_1_results.hdf5', trajectory_object_id='optimize_trajectory', restart_strategy=restart_strategy, ) nlsave('copper_results.hdf5', optimized_configuration, object_id='optgeom') # %% TotalEnergy total_energy = TotalEnergy(configuration=optimized_configuration) nlsave('copper_1_results.hdf5', total_energy) # %% AdaptiveKineticMonteCarlo saddle_search_parameters = SaddleSearchParameters(max_neb_images=5) if os.path.isfile('akmc_markov_chain.nc'): markov_chain = nlread('akmc_markov_chain.nc')[-1] else: markov_chain = MarkovChain( configuration=optimized_configuration, configuration_energy=total_energy.evaluate(), ) if os.path.isfile('akmc_kmc.nc'): kmc = nlread('akmc_kmc.nc')[-1] else: kmc = None # Set up the direction generator for the saddle search. direction_generator = HypersphereDirection( order=Furthest, magnitude=(0.5*Angstrom, 1.0*Angstrom), ) # Set up the LanczosSaddleSearch object. We are interested in the hydrogen atom, so we set the # index_selector to the index of the hydrogen atom. hydrogen_index = copper.indicesFromTags(['hydrogen']) saddle_search = LanczosSaddleSearch( initial_direction_generator=direction_generator, constraints=optimized_configuration.indicesFromTags(['constrain']), index_selector=hydrogen_index, ) akmc = AdaptiveKineticMonteCarlo( markov_chain=markov_chain, kmc_temperature=300.0 * Kelvin, calculator=optimized_configuration.calculator(), kmc=kmc, saddle_search_method=saddle_search ) akmc.run(max_searches=10, max_kmc_steps=1000)