# Set minimal log verbosity setVerbosity(MinimalLog) # %% Copper_Hydrogen # 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 = [[-0.000042654769, 0.000127477445, 0.000030028663], [-0.000100822353, -0.000022713401, 0.249845444146], [ 0.000041461119, -0.000200371119, 0.499903441763], [ 0.000085358314, -0.000053490558, 0.750106370007], [ 0.00007551707 , 0.249974681348, -0.000201890057], [ 0.000046271849, 0.250078466383, 0.249855230811], [-0.00000538891 , 0.249921347952, 0.499990137564], [ 0.000010958309, 0.249842691294, 0.750061967354], [-0.000160363637, 0.499977788665, -0.000238872702], [-0.000099866265, 0.499984234451, 0.249767441298], [-0.000104080849, 0.500133569129, 0.500055524446], [-0.000086911482, 0.500089590687, 0.750168820788], [-0.00027402157 , 0.750202643301, -0.00001642029 ], [-0.000236175208, 0.750006291727, 0.249826649834], [-0.000051644555, 0.750106624175, 0.499970111488], [-0.00004632484 , 0.750249391779, 0.75014291577 ], [ 0.250174444383, -0.000204603343, -0.000134421419], [ 0.24997761557 , -0.000162108064, 0.24984918576 ], [ 0.249876997539, -0.000221742981, 0.499812852317], [ 0.250083502543, -0.000237681858, 0.750026124673], [ 0.250074257968, 0.249904454795, -0.000154127162], [ 0.24945993756 , 0.249516430987, 0.249351524267], [ 0.249357212463, 0.249488056611, 0.500561960122], [ 0.249949306853, 0.249854535179, 0.749955376147], [ 0.250011061468, 0.500167630433, -0.000132173504], [ 0.249459251441, 0.500767219075, 0.249314490804], [ 0.249321612858, 0.500735703786, 0.500608158376], [ 0.249823513889, 0.500160587445, 0.75011875861 ], [ 0.250052883944, 0.750216473852, -0.000093287862], [ 0.249978387138, 0.749954812416, 0.249746327894], [ 0.249958499351, 0.749945054351, 0.499982986722], [ 0.249987559793, 0.750119383169, 0.750251521004], [ 0.50012036781 , -0.0001919754 , -0.000198304617], [ 0.500103559892, -0.000112205463, 0.249934654823], [ 0.500019091037, -0.000187698847, 0.499946491654], [ 0.499999883823, -0.000200167058, 0.749928635444], [ 0.499957169414, 0.249972874669, -0.000172678118], [ 0.500492516958, 0.249361335225, 0.249408491041], [ 0.500541864053, 0.249372371016, 0.500563604932], [ 0.500053052962, 0.249905670801, 0.74991637881 ], [ 0.500077219599, 0.500029516273, -0.000138764656], [ 0.500712463127, 0.500685170668, 0.249442681586], [ 0.500697970901, 0.500635992837, 0.500719483319], [ 0.500126311735, 0.500020555412, 0.750036439257], [ 0.500389060442, 0.750090533634, -0.000159708147], [ 0.500321974607, 0.750033023708, 0.249923126748], [ 0.500110055503, 0.750010225102, 0.500095982016], [ 0.50016124489 , 0.749991432552, 0.750121994148], [ 0.749990281996, 0.000200376515, -0.000051430352], [ 0.750197107722, 0.000043220047, 0.249984111557], [ 0.750227227591, -0.000137005314, 0.499990369735], [ 0.75006318056 , 0.000037343757, 0.750034408955], [ 0.750034676156, 0.250021375508, -0.000175555767], [ 0.75003750715 , 0.24999648025 , 0.249952456507], [ 0.750185247268, 0.249846632879, 0.50000131289 ], [ 0.750173575821, 0.249820299241, 0.750020477526], [ 0.750151433128, 0.499853126214, -0.000285552784], [ 0.750017565522, 0.499918880147, 0.249940868301], [ 0.750148962886, 0.500049203852, 0.500118855562], [ 0.750243527134, 0.499941888193, 0.750060972834], [ 0.75015660727 , 0.750097827262, -0.000102337351], [ 0.750246086687, 0.750122872092, 0.250014777788], [ 0.750223684542, 0.75022855851 , 0.500084481219], [ 0.750175588701, 0.750189066363, 0.750030191807], [ 0.125085373663, 0.124857327319, -0.000193415089], [ 0.124675780579, 0.124668672138, 0.249643049736], [ 0.124615189147, 0.124530064323, 0.500124770753], [ 0.125033600451, 0.124751845611, 0.750098429304], [ 0.125060976754, 0.37501397608 , -0.000172674576], [ 0.124798088873, 0.375143218095, 0.249512962967], [ 0.124657277951, 0.375131551495, 0.500400418761], [ 0.12487314015 , 0.375009375862, 0.75007568971 ], [ 0.124776173882, 0.625255108782, -0.000184083445], [ 0.124488676993, 0.625398313188, 0.2495057632 ], [ 0.124538376589, 0.625454168777, 0.500263977972], [ 0.124805942636, 0.625293199987, 0.750346853893], [ 0.124952440695, 0.875112632677, 0.00003500071 ], [ 0.124905481603, 0.874883055573, 0.24981356675 ], [ 0.125022650625, 0.874865793604, 0.499870732001], [ 0.125024585292, 0.875004178314, 0.75015909854 ], [ 0.37507849204 , 0.124823425584, -0.000148825768], [ 0.374971689057, 0.12466470478 , 0.24954994222 ], [ 0.374924918051, 0.124638803918, 0.500225628108], [ 0.375035622234, 0.124824930483, 0.749819467095], [ 0.374978127541, 0.375033101835, -0.000725312005], [ 0.375051870013, 0.375120198749, 0.24727572538 ], [ 0.374958873236, 0.375143141834, 0.502772683482], [ 0.374931038767, 0.375024466838, 0.750508065643], [ 0.375174056933, 0.6251648 , -0.000106428722], [ 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0.249612962104, 0.625316428884], [ 0.624968737008, 0.249956233613, 0.87491009863 ], [ 0.62544907111 , 0.500201048169, 0.12452686674 ], [ 0.625366496227, 0.500359648626, 0.375112969558], [ 0.625580714477, 0.500224326882, 0.625475493155], [ 0.625141494426, 0.49990821129 , 0.874907453779], [ 0.625433710625, 0.75016414503 , 0.124894084128], [ 0.625237773073, 0.750121134093, 0.37507026177 ], [ 0.625216868881, 0.750205070296, 0.625152517444], [ 0.625260641352, 0.750042789141, 0.874954774691], [ 0.874977598946, 0.000202256186, 0.124938665634], [ 0.875121560299, -0.000009159385, 0.374912074268], [ 0.875148950392, -0.000059574216, 0.625014059522], [ 0.875000256465, 0.000178420832, 0.875086131425], [ 0.8750372445 , 0.250085305845, 0.124911608946], [ 0.875096211073, 0.249891071757, 0.374944946806], [ 0.875122621235, 0.249807778701, 0.624967887402], [ 0.875094093309, 0.249923171693, 0.874916154192], [ 0.874928583496, 0.499856418317, 0.124793470759], [ 0.874976240703, 0.500115157396, 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0.000009030798, 0.874929490948, 0.374846422223], [ 0.000074354604, 0.875025572924, 0.625029414759], [-0.000067471987, 0.875209495736, 0.875149908397], [ 0.249820964862, 0.124518875666, 0.124540038097], [ 0.249589067142, 0.124720338311, 0.374882056571], [ 0.249731728066, 0.124461946792, 0.625225562552], [ 0.250172656899, 0.124840378925, 0.874900809763], [ 0.249740917169, 0.375152502822, 0.124656841637], [ 0.247250876157, 0.375196662498, 0.375000696538], [ 0.24950600014 , 0.375099096616, 0.625295154771], [ 0.249853190055, 0.374996981343, 0.87489174657 ], [ 0.249767813035, 0.625517184692, 0.124429493958], [ 0.2496151118 , 0.625291474464, 0.374888251896], [ 0.249659421923, 0.625469123756, 0.625536633106], [ 0.249964117452, 0.625196485458, 0.875117118167], [ 0.25004297244 , 0.874942370672, 0.12491825152 ], [ 0.249852881024, 0.87478162066 , 0.374780795755], [ 0.249987174564, 0.874888290499, 0.624975352804], [ 0.250142466668, 0.874973610102, 0.875045616325], [ 0.50022763044 , 0.124541989795, 0.124525807847], [ 0.500333224421, 0.124644529569, 0.374957883151], [ 0.500242621911, 0.124509187033, 0.625235018101], [ 0.499964395485, 0.124930447532, 0.874858454429], [ 0.500307136278, 0.375022244482, 0.124685314878], [ 0.502744904335, 0.375033514596, 0.375094472168], [ 0.50040826206 , 0.374990856298, 0.625269379441], [ 0.50009537795 , 0.375000655466, 0.874858062814], [ 0.500568940446, 0.625457943335, 0.124507263853], [ 0.500568201096, 0.625311879796, 0.375067134569], [ 0.500390152213, 0.625376627812, 0.625488635504], [ 0.500219311109, 0.624948994978, 0.875011139041], [ 0.50029958393 , 0.874957212325, 0.124951459842], [ 0.500214486706, 0.874932241077, 0.374965165694], [ 0.500013230378, 0.87488359426 , 0.624971772795], [ 0.500165079493, 0.874906662244, 0.874904835553], [ 0.750107879119, 0.125093797284, 0.124870092714], [ 0.750151944344, 0.124930258998, 0.374982482428], [ 0.750227788903, 0.124792272444, 0.625018629881], [ 0.749995244741, 0.12504139679 , 0.874987993805], [ 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[-7.315352192558e-04, 1.996804088105e-03, -1.667607047825e-03], [ 1.606167371954e-03, 1.758449586708e-03, -1.778138857265e-04], [-6.656397954815e-04, -1.024873904487e-03, -2.513738866808e-03], [-6.624787915054e-04, -2.388507143059e-03, 5.149294615369e-04], [ 2.140976096363e-03, 4.349121716109e-03, -2.085793304844e-03], [ 1.901610302424e-03, 6.715303409252e-04, 8.861654465241e-04], [ 3.852276853903e-04, 2.818092257182e-03, -1.063139563166e-03], [-7.601907146980e-04, 3.251237573814e-03, 7.036263883776e-04], [ 3.308868546712e-03, -2.258528029364e-04, -7.413395805387e-04], [-3.873339127036e-03, 3.111350994120e-03, -1.422880646251e-03], [ 3.040524553579e-03, -2.176210629155e-03, 1.117669897631e-03], [ 7.210076828975e-04, -1.904742115292e-03, 4.504676309215e-03], [-2.303395024244e-03, 1.532037281504e-04, -6.209527789865e-04], [ 4.739086351163e-04, -1.551856397385e-03, 9.897752179653e-04], [ 6.050187537634e-04, -3.072088690429e-05, 5.062548977146e-04], [ 2.886530110098e-05, -3.473735837266e-04, 1.052761022700e-03], [ 4.803668353155e-04, 2.924762289878e-04, -1.639625968384e-03], [ 1.271356829907e-03, -1.554367135972e-03, 2.047325894764e-03], [-3.809632343099e-03, 8.142455201573e-04, 5.823795789468e-04], [-2.394279920300e-03, 1.713257632269e-03, -7.892240594910e-04], [ 1.215838708654e-04, 1.316351998905e-03, 1.068350319832e-03], [-1.826039768157e-03, -1.797752588405e-03, -1.402188830522e-03], [-2.325655220681e-04, 2.552016496015e-04, -2.782026997167e-04], [-2.220964478869e-03, -9.773860554954e-04, 5.859981614715e-04], [-1.106671138892e-03, -1.139894141334e-03, 1.959085708982e-03], [-4.172114590436e-03, -1.688278470763e-03, 1.069117510949e-03], [ 3.453266155780e-03, -8.441706320726e-04, 2.731421785649e-04], [-1.852701591373e-03, -3.924960982565e-03, 1.559348499834e-03], [-9.742732104358e-04, 1.610966356508e-03, 2.894351885685e-03], [-3.311905038339e-04, -1.191193633134e-03, 3.906422298625e-03], [ 2.171916947942e-03, 1.267241740933e-03, 3.413919067365e-04], [-7.405682553962e-04, -1.253486413952e-03, 2.145694313297e-03], [ 9.760896019401e-04, 1.172742653085e-03, -1.429132732143e-03], [-2.651308990427e-04, -2.696653428523e-04, 1.523449812303e-03], [ 1.306048845744e-04, 1.343294219944e-03, -4.466587624917e-03], [-1.721569620225e-03, -1.023122778774e-03, -1.754696966488e-03], [-8.792325191099e-04, 2.024421159131e-03, -4.301634285397e-04], [ 2.032445083924e-03, -6.621700617028e-04, 3.174300086863e-04], [-3.245207973149e-03, -6.207560553160e-04, 1.399305244164e-03], [-4.254815482218e-04, 1.499627301517e-03, -3.953892575589e-04], [ 3.896259356754e-04, -7.629168181559e-04, 3.674195218276e-03], [ 2.053649556164e-03, 2.681010770630e-04, 1.966370856263e-03], [-1.069476484482e-04, 2.202821318555e-03, -1.495441631680e-03], [-2.650280332284e-03, 1.474415394497e-03, 1.069904061650e-03], [ 2.390169395165e-03, 1.370773759126e-03, 3.556943031495e-03], [-1.833353390227e-03, 6.930049659477e-05, -2.627817275871e-03], [ 4.733318288094e-03, -1.391398140460e-03, -2.229483495450e-03], [-1.771962315584e-04, -3.359561247485e-03, 3.606220685601e-03], [-1.227965297622e-03, -3.274654690030e-04, -2.898979634025e-03], [ 5.083797589710e-04, 3.110772700087e-04, 1.390806260685e-03], [-1.318597048308e-02, 2.312252199835e-02, 3.882365806430e-03]]*Angstrom/fs # Set up configuration copper_hydrogen = BulkConfiguration( bravais_lattice=lattice, elements=elements, fractional_coordinates=fractional_coordinates, velocities=velocities ) # Add tags copper_hydrogen.addTags('Copper', [ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255]) copper_hydrogen.addTags('Frozen', [255]) copper_hydrogen.addTags('Hydrogen', [256]) copper_hydrogen_name = "Copper_Hydrogen" # %% Set MachineLearnedForceFieldCalculator # %% MachineLearnedForceFieldCalculator potentialSet = QuantumATK_MTP_CuH_2025_06() calculator = TremoloXCalculator(parameters=potentialSet) # %% Set Calculator copper_hydrogen.setCalculator(calculator) nlsave('CVHD_CuH_Diffusion_Example_results.hdf5', copper_hydrogen) # %% MolecularDynamics - Equilibration method = Langevin() constraints = [FixStrain(True, True, True), FixCenterOfMass()] md_trajectory = MolecularDynamics( configuration=copper_hydrogen, constraints=constraints, trajectory_filename='CVHD_CuH_Diffusion_Example_results.hdf5', steps=50000, log_interval=1000, method=method, trajectory_interval=10000, trajectory_object_id='md', ) last_image = md_trajectory.lastImage() nlsave('CVHD_CuH_Diffusion_Example_results.hdf5', last_image, object_id='md_1') # %% HookFunctions # Post-step hook functions hyperdynamics_position_distortion_1 = HyperdynamicsPositionDistortion( atom_tag='Hydrogen', maximum_radius=1.05 * Angstrom ) collective_variable_hyperdynamics = CollectiveVariableHyperdynamics( distortions=[hyperdynamics_position_distortion_1], gaussian_width=0.05, gaussian_height=0.25 * kiloJoulePerMole, gaussian_frequency=500, bias_damping_temperature=2000.0 * Kelvin, gaussian_limit=0.9, reaction_steps=2500, measurement_frequency=100, tracked_atoms_tag='Hydrogen', ) pre_step_hooks = [] post_step_hooks = [ collective_variable_hyperdynamics, ] measurement_hooks = [] hook_functions = HookFunctions( pre_step_hooks=pre_step_hooks, post_step_hooks=post_step_hooks, measurement_hooks=measurement_hooks, ) nlsave('CVHD_CuH_Diffusion_Example_results.hdf5', hook_functions) # %% MolecularDynamics - CVHD method = Langevin( initial_velocity=ConfigurationVelocities(remove_center_of_mass_momentum=False) ) constraints = [FixStrain(True, True, True), FixCenterOfMass()] md_trajectory_1 = MolecularDynamics( configuration=last_image, constraints=constraints, trajectory_filename='CVHD_CuH_Diffusion_Example_results.hdf5', steps=1000000, log_interval=1000, method=method, hook_functions=hook_functions, trajectory_object_id='md_2', ) last_image_1 = md_trajectory_1.lastImage() nlsave('CVHD_CuH_Diffusion_Example_results.hdf5', last_image_1, object_id='md_3')