# -*- coding: utf-8 -*- # ------------------------------------------------------------- # Bulk Configuration # ------------------------------------------------------------- # Set up lattice vector_a = [10.559292205578911, 0.0, 0.0]*Angstrom vector_b = [0.0, 10.559292205578911, 0.0]*Angstrom vector_c = [0.0, 0.0, 10.559292205578911]*Angstrom lattice = UnitCell(vector_a, vector_b, vector_c) # Define elements elements = [Hafnium, Hafnium, Hafnium, Hafnium, Hafnium, Hafnium, Hafnium, Hafnium, Hafnium, Hafnium, Hafnium, Hafnium, Hafnium, Hafnium, Hafnium, Hafnium, Hafnium, Hafnium, Hafnium, Hafnium, Hafnium, Hafnium, Hafnium, Hafnium, Hafnium, Hafnium, Hafnium, Hafnium, Hafnium, Hafnium, Hafnium, Hafnium, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen] # Define coordinates fractional_coordinates = [[ 0.24941383618 , 0.588908558001, 0.721482382728], [ 0.902855608094, 0.719311096057, 0.503324733774], [ 0.667773850045, 0.680021940826, 0.315112130795], [ 0.366051408441, 0.397870673559, 0.419761956664], [ 0.402185685125, 0.937865521348, 0.738330840107], [ 0.721933221283, 0.651477971505, 0.011405373011], [ 0.802870790841, 0.390726574845, 0.139927625652], [ 0.320785363317, 0.164137591684, 0.033560443696], [ 0.375926436776, 0.719763134578, 0.333932254362], [ 0.00348302074 , 0.086709693209, 0.911120104968], [ 0.20771836228 , 0.83015833482 , 0.991715244064], [ 0.362695814842, 0.096344858485, 0.431126156569], [ 0.476717433039, 0.876712805957, 0.068670223918], [ 0.351358665305, 0.519692883241, 0.094315300364], [ 0.525217288218, 0.437052464567, 0.879633151035], [ 0.705196705606, 0.855428643414, 0.791629278211], [ 0.878184581399, 0.927916545828, 0.217583615261], [ 0.23207171114 , 0.217455358051, 0.735154359269], [ 0.671706736126, 0.117231777413, 0.963643600579], [ 0.817282805511, 0.36340170513 , 0.804152093636], [ 0.594174398458, 0.620649184791, 0.636499414818], [ 0.903516534077, 0.096908590632, 0.561614408785], [ 0.185317578193, 0.882930422275, 0.509346537725], [ 0.762405231515, 0.38849340748 , 0.492784744308], [ 0.544162451925, 0.25195397921 , 0.653169201868], [ 0.608950103883, 0.93025028558 , 0.50702464697 ], [ 0.066129448571, 0.200104512632, 0.304150389092], [ 0.608394526732, 0.176018727799, 0.23702966881 ], [ 0.066496464619, 0.442434451326, 0.536037242962], [ 0.05433759723 , 0.641201369156, 0.25423989688 ], [ 0.98891732283 , 0.795803846329, 0.772234112962], [ 0.057808815739, 0.561230452414, 0.983634394272], [ 0.279068727518, 0.537498897632, 0.525608287916], [ 0.44008248514 , 0.564742799056, 0.737874139022], [ 0.170521217557, 0.055030482874, 0.401934159979], [ 0.686165221727, 0.534594390296, 0.201618176546], [ 0.440718428366, 0.241177468471, 0.319172982909], [ 0.523289806344, 0.680287129434, 0.457252989328], [ 0.657745322496, 0.443610277121, 0.702753349166], [ 0.73874647351 , 0.043944835248, 0.144572597241], [ 0.733330682334, 0.462139189608, 0.954685122268], [ 0.404919684943, 0.320456174065, 0.770299948873], [ 0.588738214224, 0.004274694557, 0.829722659715], [ 0.893013107766, 0.431415314967, 0.634955021664], [ 0.113237652051, 0.932540729764, 0.858198025755], [ 0.740479066476, 0.583727295913, 0.479122990855], [ 0.344110892442, 0.249432914223, 0.550136813505], [ 0.517935583258, 0.580214580029, 0.015414590368], [ 0.758162359153, 0.981278439109, 0.618883784773], [ 0.966623275059, 0.795937585934, 0.336476453353], [ 0.382304240773, 0.833884248634, 0.901043024078], [ 0.909482297748, 0.054799823918, 0.367091498701], [ 0.843201367225, 0.190372412267, 0.900254184443], [ 0.159699260491, 0.200203661295, 0.922240974345], [ 0.053968934598, 0.645430123217, 0.622085493361], [ 0.925826052659, 0.540892818164, 0.134289561292], [ 0.165416319115, 0.398670669672, 0.691544111348], [ 0.665733443228, 0.27030104043 , 0.085098136345], [ 0.282483316799, 0.786253470408, 0.653037521779], [ 0.173209147742, 0.35429440692 , 0.393576993577], [ 0.962210703148, 0.27100432793 , 0.47105163203 ], [ 0.65491740313 , 0.666378789789, 0.819675632631], [ 0.974112975927, 0.421409643317, 0.894372042151], [ 0.259824979584, 0.030232543926, 0.626385150949], [ 0.820749958436, 0.746258146649, 0.671512093507], [ 0.896015209182, 0.685048874803, 0.913407674178], [ 0.000802912835, 0.006003393166, 0.090941440308], [ 0.298147168479, 0.968372352246, 0.089306954055], [ 0.729665916716, 0.307145499105, 0.322405853303], [ 0.076474450163, 0.740809301522, 0.092488519106], [ 0.37222270705 , 0.899283890626, 0.426985393272], [ 0.784014922167, 0.759411172403, 0.174067084567], [ 0.168403482866, 0.51991729442 , 0.155216845056], [ 0.554826279748, 0.82363245738 , 0.657957284668], [ 0.3287726963 , 0.725156788691, 0.128929595389], [ 0.738256801819, 0.225122614513, 0.595458330136], [ 0.646163421945, 0.836535442404, 0.986390847321], [ 0.134918140314, 0.69592600534 , 0.852968772801], [ 0.498251781913, 0.067868400654, 0.594930954447], [ 0.025292079595, 0.148412684824, 0.706236792884], [ 0.624139981164, 0.259315995186, 0.833783994032], [ 0.569547861564, 0.04540227083 , 0.365772506996], [ 0.411388952542, 0.343261752668, 0.032043272541], [ 0.220572417983, 0.19714194811 , 0.190840977687], [ 0.947974714731, 0.276665306637, 0.177529342417], [ 0.869013638066, 0.939693437027, 0.851562567373], [ 0.352304382485, 0.091298512383, 0.848633137133], [ 0.507068863785, 0.078739681492, 0.081120908203], [ 0.191515178593, 0.734685592687, 0.371755703642], [ 0.40055984606 , 0.530829320339, 0.282988602457], [ 0.549769330001, 0.388670168995, 0.502944191824], [ 0.008816974987, 0.889659572675, 0.58704419235 ], [ 0.972656965386, 0.552146944663, 0.404502024642], [ 0.531051809837, 0.794173156049, 0.236180870299], [ 0.740293266149, 0.822730667041, 0.421446693542], [ 0.256830517134, 0.523327690969, 0.92422328655 ]] # Set up configuration bulk_configuration = BulkConfiguration( bravais_lattice=lattice, elements=elements, fractional_coordinates=fractional_coordinates ) nlsave('active-learning.hdf5', bulk_configuration) #------------------------------------------------------------- # Reference Calculator # ------------------------------------------------------------- k_point_sampling = KpointDensity( density_a=4.0*Angstrom, ) numerical_accuracy_parameters = NumericalAccuracyParameters( density_mesh_cutoff=125.0*Hartree, k_point_sampling=k_point_sampling, ) calculator = LCAOCalculator( numerical_accuracy_parameters=numerical_accuracy_parameters, ) # compile initial training data #--------------------------------------------- #initial data be crystalTrainingRandomDisplacements object #--------------------------------------------- training_set=nlread('initial_training_sets.hdf5') if(len(training_set)>1): training_set=[item for i in training_set for item in i] #--------------------------------------------- #uncomment only if data is a Trajectory or MDTrajectory object #Reference configurations loaded from a trajectory object from file, #trajectory may contain energy, force and stress data as well #extract 100 snapshots (uniformly distributed) from the trajectory and recompute using the calculator set above #for multiple trajetories create training_set_1, training_set_2, etc #https://docs.quantumatk.com/manual/Types/TrainingSet/TrainingSet.html #--------------------------------------------- #trajectory=nlread('initial_training_sets.hdf5',Trajectory)[-1] #trajectory=nlread('initial_training_sets.hdf5',MDTrajectory)[-1] #training_set = TrainingSet(trajectory, # #sample_size=100, # calculator=calculator, # recalculate_training_data=True) # compute reference data using the above loaded calculator #--------------------------------------------- #set up MTP training #for multiple training_sets, use [training_set_1, training_set_2] #--------------------------------------------- moment_tensor_potential_training = MomentTensorPotentialTraining( filename="reference-data.hdf5", object_id='reference calculation', training_sets=training_set, calculator=calculator, calculate_stress=True, random_seed=13345, number_of_processes_per_task=8, log_filename_prefix='mtp_' ) #--------------------------------------------- #fit MTP #--------------------------------------------- moment_tensor_potential_training.update() initial_training_data=[moment_tensor_potential_training] # Set MTP training parameters #--------------------------------------------- # Set up non-linear coefficients with optimization. #https://docs.quantumatk.com/manual/Types/NonLinearCoefficientsParameters/NonLinearCoefficientsParameters.html #--------------------------------------------- non_linear_coefficients_parameters = NonLinearCoefficientsParameters( perform_optimization=True, random_seed=500, max_steps=1, energy_only=True, ) #--------------------------------------------- #use default MTP fitting parameters #https://docs.quantumatk.com/manual/Types/MomentTensorPotentialFittingParameters/MomentTensorPotentialFittingParameters.html #--------------------------------------------- fitting_parameters = MomentTensorPotentialFittingParameters( basis_size=300, inner_cutoff_radii=1.0 * Angstrom, tapering_cutoff_radii=1.1 * Angstrom, outer_cutoff_radii= 5.0 * Angstrom, mtp_filename='mtp_potential.mtp', forces_cap= 100.0 * eV / Angstrom, non_linear_coefficients_parameters=non_linear_coefficients_parameters, ) # Set up active learning MD #--------------------------------------------- # Set up active learning #--------------------------------------------- active_learning = ActiveLearningSimulation( fitting_parameters=fitting_parameters, initial_training_data=initial_training_data, mtp_study_filename='HfO2-final-dataset', mtp_study_object_id='HfO2 amorphous', reference_calculator=calculator, candidate_threshold=1.0, retrain_threshold=3.0, check_interval=20, max_forces_check=10.0*eV/Ang, candidate_trajectory_filename='active_learning_candidates.hdf5', ) #--------------------------------------------- # Set up a high-temperature MD at 3000 K. # uncomment below the MD ensemble of interest #--------------------------------------------- initial_velocity = MaxwellBoltzmannDistribution( temperature=3000.0*Kelvin, remove_center_of_mass_momentum=True, random_seed=None, enforce_temperature=True, ) #------------------- #NPT #------------------- method = NPTMartynaTobiasKlein( time_step=1*femtoSecond, reservoir_temperature=3000*Kelvin, reservoir_pressure=1*bar, thermostat_timescale=100*femtoSecond, barostat_timescale=500*femtoSecond, initial_velocity=initial_velocity, heating_rate=0*Kelvin/picoSecond, compression_rate=0*bar/femtoSecond, chain_length=3, ) #------------------------ #Langevin #------------------------ #method = Langevin( # time_step=1*femtoSecond, # reservoir_temperature=6000*Kelvin, # friction=0.05*femtoSecond**-1, # initial_velocity=initial_velocity, #) constraints = [FixCenterOfMass()] #--------------------------------------------- # Run the MD simulation using bulk_configuration through the active learning object. #--------------------------------------------- # Scale the volume to facilitate melting. bulk_configuration.scaleVolume(1.1) md_trajectory = active_learning.runMolecularDynamics( bulk_configuration, constraints=constraints, trajectory_filename='active_learning_3000K.hdf5', steps=200000, log_interval=500, method=method, domain_decomposition_pattern=[1, 1, 1], )