# -*- coding: utf-8 -*- setVerbosity(MinimalLog) # ------------------------------------------------------------- # Bulk Configuration # ------------------------------------------------------------- # Set up lattice vector_a = [9.497426971725758, 0.0, 0.0]*Angstrom vector_b = [0.0, 9.497426971725758, 0.0]*Angstrom vector_c = [0.0, 0.0, 9.497426971725758]*Angstrom lattice = UnitCell(vector_a, vector_b, vector_c) # Define elements elements = [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, Hafnium, Hafnium, Hafnium, Hafnium, Hafnium, Hafnium, Hafnium, Hafnium, Hafnium, Hafnium, Hafnium, Hafnium, Hafnium, Hafnium, Hafnium, Hafnium, Hafnium, Hafnium, Hafnium, Hafnium] # Define coordinates fractional_coordinates = [[ 0.046849303132, 0.578048584239, 0.330834628862], [ 0.747486215681, 0.435180554111, 0.527295513093], [ 0.728887761335, 0.886922306732, 0.768860338684], [ 0.414425990171, 0.535354936092, 0.752008448713], [ 0.255345178522, 0.753701553286, 0.282131565008], [ 0.90036373387 , 0.145453898294, 0.91761587373 ], [ 0.374066511603, 0.307760711155, 0.497068077455], [ 1.001750691515, 0.826775399807, 0.767971573708], [ 0.499595292484, 0.810872894696, 0.200633139672], [ 0.73569352768 , 0.733148719396, 0.412714298573], [-0.040562971588, 0.573188171614, 0.660129132106], [ 0.520051379459, 0.103549730374, 0.306573957993], [ 0.754832828099, 0.760331884743, 0.032073457935], [ 0.226495603727, 1.066519311917, 0.230294586588], [ 0.073666311249, 0.222949067025, 0.422025179187], [ 0.229250922081, 1.016061409098, 0.510825242303], [ 0.351070436645, 0.22556170251 , 0.045638330736], [ 0.529866779197, 0.598981184289, 0.029685084869], [ 0.218593337763, 0.390693512083, 0.279656897794], [ 0.700494745201, 0.610231274156, 0.713194313872], [ 0.032452381159, 0.257328382205, 0.138954792242], [ 1.090090362588, 0.939570412957, 0.039249823067], [ 0.493734371776, 0.918447728982, 0.534857432958], [ 0.625707030726, 0.193798424052, 0.589531032883], [ 0.891181246874, 0.95284347295 , 0.46802753193 ], [ 0.589992811466, 0.328089179471, 0.108967920543], [ 0.9644318872 , 0.280931870331, 0.652147203356], [ 0.905813913574, 0.428478389797, 0.964274043418], [ 0.400084250597, 0.821303330657, 0.874952965449], [ 0.834679015026, 0.029420113918, 0.151709005136], [ 0.832984558616, 0.472748135559, 0.223176653472], [ 0.154519315133, 0.448726019407, 0.560259895709], [ 0.255496737936, 0.708732865978, 0.597386689053], [ 0.61936512292 , 0.353847688099, 0.809562728881], [ 0.821478501522, 0.211801165209, 0.335990745615], [ 0.219490629981, 0.353621117151, 0.826266199085], [ 0.488730235527, 0.512568404251, 0.350920527406], [ 0.301190752318, 0.502371188879, 0.081521311454], [ 0.233348375244, 0.080840790956, 0.782272506811], [ 0.129249284668, 0.642179113642, 0.966219325888], [ 0.262552811495, 0.566017036421, 0.407245798597], [ 0.414951250419, 0.295557205543, 0.255790072536], [ 0.330528046577, 0.720410601205, 0.070959634619], [ 0.156232927199, 0.14176776161 , 0.987993911627], [ 0.6885651968 , 0.056969405266, 0.446353090389], [ 0.830958665112, 0.410041054826, 0.761145385667], [ 0.321292346767, 0.904194231944, 0.676264889112], [ 0.848524561724, 0.767786200934, 0.615072765218], [ 0.063642600349, 0.485719269682, 0.125091384053], [ 0.170185141422, 0.570617214913, 0.754224329446], [ 0.803233430653, 0.256977991098, 0.104950251227], [ 0.546998081622, 0.402095501559, 0.59679733679 ], [ 0.369865336928, 0.942237013356, 0.341297492104], [ 0.942213547077, 0.403206696145, 0.439938812898], [ 0.664057568462, 0.647503486697, 0.229862535733], [ 0.005501956376, 0.059369530507, 0.29825977379 ], [ 0.183507487754, 0.227621365202, 0.613164544886], [ 0.44074326472 , 0.399616721589, 0.937065786032], [ 0.889764293264, 0.923155092107, 0.940716933301], [ 0.607199787647, 0.728431830883, 0.865394444287]] # Define velocities velocities = [[-1.696580250855e-02, 1.457001145269e-02, -7.184740254696e-03], [-3.131746995789e-03, 2.534983832653e-03, -9.882157986733e-03], [-5.769552749414e-03, 3.218205180341e-04, -2.219335824301e-02], [ 1.772054196800e-02, -1.383634874481e-02, 1.492380996053e-02], [-1.430712860988e-02, 7.077377533187e-03, -1.062838510734e-03], [ 1.683880846738e-02, 1.746790228741e-03, -8.635135529429e-04], [ 3.959646995992e-03, -6.706804791711e-04, -5.407956995707e-03], [-2.876649389428e-03, 1.075286773103e-03, 2.322664933880e-03], [-2.309507994169e-02, 8.411263540726e-03, -1.306859044801e-03], [ 6.630135840514e-03, 2.668440553874e-03, 1.862788244342e-02], [ 1.801351557124e-02, -7.515552779359e-03, 1.321834467776e-02], [ 2.571510517324e-02, 1.480949057662e-02, 3.886138043709e-03], [-1.451403976765e-02, 7.239859289853e-03, 5.101782050010e-05], [-1.816164286881e-02, 1.054766587589e-02, -1.368827808805e-02], [ 9.005527153282e-03, -1.212415532897e-02, -3.856324775962e-03], [-4.583058774760e-03, -7.886765988656e-03, 1.093365961048e-02], [-5.067098610516e-03, -7.962934985918e-03, -8.228774755095e-03], [-8.242725697357e-04, 2.068752643069e-03, 8.625565416900e-03], [ 1.374460986230e-02, -3.338244770370e-03, -1.413370987872e-02], [-6.883156257166e-03, -1.150058508020e-03, 5.485092723725e-03], [-6.487397786190e-03, -4.992052112256e-04, -2.559824514658e-04], [-3.267323757774e-02, -1.210340638781e-02, -1.740204202893e-02], [-2.301048959165e-02, -1.045577924621e-02, -1.102679467791e-02], [-2.460939149525e-02, 1.949342881719e-02, 1.819374410425e-03], [-8.252971336415e-03, 2.070679718519e-02, 9.518449565472e-03], [-1.552752839880e-02, -5.381355595456e-03, -1.284932778699e-02], [-2.454903512569e-02, 4.077285339012e-03, -8.961924431063e-03], [-6.719967593734e-03, 8.086739311696e-03, 1.704612879614e-02], [-1.257561716793e-02, -9.229093553670e-03, -1.120434238416e-04], [ 1.619720495135e-02, -3.277484356317e-02, 6.009512237017e-03], [ 1.645790232317e-03, 1.561816208047e-02, -1.268717629904e-02], [ 8.899058812628e-03, -1.223364599234e-02, -5.564443911452e-03], [-1.792658603537e-03, 5.420856989598e-03, -1.420688689700e-02], [ 1.544414164208e-02, -7.151286005892e-03, 3.998779171079e-03], [ 2.069452364627e-02, 3.272449032905e-03, -8.818055755476e-03], [ 2.556430963006e-03, -8.017668663144e-03, 1.225991855537e-02], [-1.895039250712e-02, 5.308140294287e-03, -8.160184370211e-03], [ 3.571475093748e-03, 1.409839644879e-02, 9.210704607059e-03], [ 1.884899793066e-02, 1.602263032151e-02, -2.382924948166e-03], [-3.571468829186e-03, -7.645291930146e-03, 4.511244990108e-03], [ 1.850769292865e-03, -6.019001358779e-03, 2.062524343668e-03], [ 2.509099644103e-03, 9.811918490498e-04, -4.329894855033e-03], [ 4.908760593883e-03, 2.873673465066e-03, -4.066930530408e-03], [-7.344679291964e-03, -8.490111461062e-03, -3.225747643865e-03], [-2.832678073286e-03, 2.298249110927e-04, 6.626791052081e-03], [ 1.394358142592e-03, 3.945568808851e-03, 1.971651011112e-03], [ 2.853681275203e-03, -8.748439946074e-04, -3.072415162012e-03], [ 3.187122769515e-03, -5.495272467071e-03, 4.056113041792e-03], [-1.529700971427e-03, 8.732656042273e-04, -2.496934183424e-03], [-1.146882669149e-04, 3.171546653427e-03, -1.850680819685e-03], [-3.632023976919e-03, 3.622308816317e-03, -4.251602415766e-03], [ 4.212637336031e-04, 4.740006218425e-03, -5.422969928190e-04], [-6.752743502465e-04, -7.535127585223e-04, -4.108305055283e-03], [-1.217419664633e-03, 9.842445642216e-03, 6.276308490177e-03], [-1.232235522555e-03, 5.827502916814e-03, 1.828381158681e-03], [-3.440044988692e-04, -5.197429198377e-03, 3.549952255471e-03], [ 6.099225631952e-03, -6.232499430705e-03, -1.265020037692e-04], [ 4.497075495982e-03, 3.485572654714e-03, 3.278846728088e-03], [-1.400031512446e-03, -1.818150678573e-03, 1.062487636660e-03], [ 1.154041792376e-03, -6.970979431843e-03, 1.641852492513e-03]]*Angstrom/fs # Set up configuration bulk_configuration = BulkConfiguration( bravais_lattice=lattice, elements=elements, fractional_coordinates=fractional_coordinates, velocities=velocities ) # ------------------------------------------------------------- # Calculator # ------------------------------------------------------------- potentialSet = TremoloXPotentialSet(name = 'HfO2_MTP_10.2021') potentialSet.addParticleType(ParticleType( symbol = 'O', mass = 15.9994*atomic_mass_unit, charge = None, sigma = 3.11814551349*Angstrom, sigma14 = 3.11814551349*Angstrom, epsilon = 0.06*kiloCaloriePerMol, epsilon14 = 0.06*kiloCaloriePerMol, atomicNumber = 8, tags = [], )) potentialSet.addParticleType(ParticleType( symbol = 'Hf', mass = 178.49*atomic_mass_unit, charge = None, sigma = 2.79831287368*Angstrom, sigma14 = 2.79831287368*Angstrom, epsilon = 0.072*kiloCaloriePerMol, epsilon14 = 0.072*kiloCaloriePerMol, atomicNumber = 72, tags = [], )) _potential = MTPPotential( file = './mtp_potential.mtp', suppress_intercept = False, ) potentialSet.addPotential(_potential) calculator = TremoloXCalculator(parameters=potentialSet) calculator.setVerletListsDelta(1.0*Angstrom) bulk_configuration.setCalculator(calculator) nlprint(bulk_configuration) bulk_configuration.update() nlsave('HfO2_MTP_3000K_md.hdf5', bulk_configuration) # ------------------------------------------------------------- # Molecular Dynamics # ------------------------------------------------------------- initial_velocity = MaxwellBoltzmannDistribution( temperature=3000.0*Kelvin, remove_center_of_mass_momentum=True, random_seed=None, enforce_temperature=True, ) method = Langevin( time_step=1*femtoSecond, reservoir_temperature=3000*Kelvin, friction=0.01*femtoSecond**-1, initial_velocity=initial_velocity, heating_rate=0*Kelvin/picoSecond, ) constraints = [FixCenterOfMass()] md_trajectory = MolecularDynamics( bulk_configuration, constraints=constraints, trajectory_filename='HfO2_MTP_3000K_md.hdf5', steps=100000, log_interval=500, method=method ) bulk_configuration = md_trajectory.lastImage()