# -*- coding: utf-8 -*- # ------------------------------------------------------------- # Bulk Configuration # ------------------------------------------------------------- # Set up lattice vector_a = [19.4208291666, 0.0, 0.0]*Angstrom vector_b = [0.0, 19.4208291666, 0.0]*Angstrom vector_c = [0.0, 0.0, 21.7708]*Angstrom lattice = UnitCell(vector_a, vector_b, vector_c) # Define elements elements = [Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Platinum] # Define coordinates fractional_coordinates = [[ 0.071476891153, 0.071677939606, 0.095448841337], [ 0.21422958197 , 0.071767563389, 0.09551863341 ], [ 0.356980476979, 0.071733071169, 0.095431689739], [ 0.49992007245 , 0.07158378379 , 0.095165619418], [ 0.642837906088, 0.071473631863, 0.095045925408], [ 0.785797818457, 0.071436255218, 0.095035426227], [ 0.928737109658, 0.071569869326, 0.095311713306], [ 0.071619837528, 0.214433355378, 0.095720726718], [ 0.214331542408, 0.214585088388, 0.095987062411], [ 0.356945462178, 0.214633000271, 0.095938513878], [ 0.499789427236, 0.214569435451, 0.095589891744], [ 0.642684963764, 0.21445303171 , 0.09534440104 ], [ 0.785777183724, 0.214327566169, 0.095176886243], [ 0.928838266852, 0.214338566184, 0.095471359624], [ 0.071690444146, 0.357031542891, 0.095785874864], [ 0.214433123176, 0.357095222226, 0.096135332309], [ 0.356995448253, 0.35719049206 , 0.096135332309], [ 0.499738127283, 0.357254171394, 0.095785874864], [ 0.642583703389, 0.357228707917, 0.09549467485 ], [ 0.785714285714, 0.357142857143, 0.095240634258], [ 0.928844868039, 0.357057006369, 0.09549467485 ], [ 0.071639144193, 0.499716278835, 0.095589891744], [ 0.214483109251, 0.499652714015, 0.095938513878], [ 0.357097029021, 0.499700625898, 0.095987062411], [ 0.499808733901, 0.499852358908, 0.095720726718], [ 0.642590304576, 0.499947148102, 0.095471359624], [ 0.785651387705, 0.499958148117, 0.095176886243], [ 0.928743607665, 0.499832682576, 0.09534440104 ], [ 0.071508498979, 0.642701930495, 0.095165619418], [ 0.21444809445 , 0.642552643117, 0.095431689739], [ 0.357198989459, 0.642518150896, 0.09551863341 ], [ 0.499951680276, 0.642607774679, 0.095448841337], [ 0.642691461771, 0.642715844959, 0.095311713306], [ 0.785630752972, 0.642849459068, 0.095035426227], [ 0.928590665341, 0.642812082423, 0.095045925408], [ 0.071397585934, 0.785731914328, 0.094996964001], [ 0.214315482243, 0.785646265432, 0.095068100242], [ 0.357177382924, 0.785585242293, 0.095104608232], [ 0.500020669229, 0.785586020025, 0.095097447318], [ 0.642839294304, 0.785650480886, 0.095049611824], [ 0.785704376904, 0.785732960379, 0.094963613701], [ 0.928547876908, 0.785743876766, 0.094979809646], [ 0.0714079022 , 0.928699694261, 0.095097447318], [ 0.214251188505, 0.928700471993, 0.095104608232], [ 0.357113089185, 0.928639448854, 0.095068100242], [ 0.500030985495, 0.928553799958, 0.094996964001], [ 0.64288069452 , 0.92854183752 , 0.094979809646], [ 0.785724194524, 0.928552753907, 0.094963613701], [ 0.928589277125, 0.9286352334 , 0.095049611824], [-0.000012717108, -0.00001672564 , 0.181124437582], [ 0.142819437905, 0.000001517452, 0.181147232103], [ 0.285676903279, -0.000003682009, 0.181086027432], [ 0.428649866641, -0.00008531149 , 0.180924489997], [ 0.571483143524, -0.000050169787, 0.180917263641], [ 0.714293287926, -0.000062427867, 0.180921621119], [ 0.857074175205, -0.000100267729, 0.180949570318], [ 0.000143234997, 0.142995680047, 0.181633638761], [ 0.142777168782, 0.142985397039, 0.181738550078], [ 0.285542212126, 0.14304567233 , 0.181798444111], [ 0.428554874364, 0.142899877123, 0.181331019619], [ 0.571433954371, 0.142835473885, 0.181087280059], [ 0.714343400662, 0.142760548608, 0.180921837814], [ 0.857174963038, 0.142838300413, 0.181105088033], [ 0.000195097537, 0.28568783172 , 0.181742707791], [ 0.142872288062, 0.285726413306, 0.182116056576], [ 0.285680596071, 0.285896897262, 0.182453658608], [ 0.428528165244, 0.285916495106, 0.181987019307], [ 0.571253972425, 0.285895624673, 0.18164222053 ], [ 0.714261055087, 0.285733041115, 0.181119051752], [ 0.857190685903, 0.285692649147, 0.181164583893], [ 0.000174599004, 0.428390089613, 0.18164222053 ], [ 0.142900406184, 0.428369219179, 0.181987019307], [ 0.285747975357, 0.428388817024, 0.182453658608], [ 0.428556283366, 0.42855930098 , 0.182116056576], [ 0.571233473891, 0.428597882566, 0.181742707791], [ 0.714237885526, 0.428593065139, 0.181164583893], [ 0.857167516341, 0.428552673171, 0.181119051752], [-0.000005382942, 0.5714502404 , 0.181087280059], [ 0.142873697064, 0.571385837163, 0.181331019619], [ 0.285886359302, 0.571240041955, 0.181798444111], [ 0.428651402647, 0.571300317246, 0.181738550078], [ 0.571285336432, 0.571290034239, 0.181633638761], [ 0.714253608391, 0.571447413873, 0.181105088033], [ 0.857085170767, 0.571525165677, 0.180921837814], [-0.000054572095, 0.714335884073, 0.180917263641], [ 0.142778704788, 0.714371025776, 0.180924489997], [ 0.285751668149, 0.714289396294, 0.181086027432], [ 0.428609133524, 0.714284196834, 0.181147232103], [ 0.571441288537, 0.714302439925, 0.181124437582], [ 0.714354396223, 0.714385982015, 0.180949570318], [ 0.857135283503, 0.714348142153, 0.180921621119], [-0.000048867931, 0.857141634459, 0.180949858897], [ 0.142819009425, 0.857161056544, 0.180926261853], [ 0.285714285714, 0.857142857143, 0.180908567489], [ 0.428609562004, 0.857124657742, 0.180926261853], [ 0.57147743936 , 0.857144079827, 0.180949858897], [ 0.71430797318 , 0.857154417719, 0.180956088687], [ 0.857120598248, 0.857131296567, 0.180956088687], [ 0.071433652552, 0.071229121209, 0.270479482749], [ 0.214131311274, 0.071155568545, 0.270470164741], [ 0.357440394596, 0.070970722986, 0.270104166083], [ 0.500175762874, 0.071214746057, 0.270210099866], [ 0.642938087144, 0.071221799256, 0.270165054873], [ 0.785615032917, 0.071282269905, 0.270208307842], [ 0.928220184302, 0.071044369006, 0.270093906973], [ 0.07165748343 , 0.214578116471, 0.271567235372], [ 0.213564907097, 0.214330279453, 0.271447345349], [ 0.357290365187, 0.214225448398, 0.270780793152], [ 0.500060803547, 0.214101539502, 0.270473157899], [ 0.643164672788, 0.21394056988 , 0.270046227352], [ 0.785723423343, 0.214170838699, 0.270217112819], [ 0.928453316576, 0.214297306875, 0.270463308773], [ 0.071698187409, 0.356716310973, 0.27158044433 ], [ 0.213796409502, 0.35683333889 , 0.271875772856], [ 0.357632161927, 0.357452375396, 0.271875772856], [ 0.499730384019, 0.357569403313, 0.27158044433 ], [ 0.642948307719, 0.357241791472, 0.2704459205 ], [ 0.785714285714, 0.357142857143, 0.270237497122], [ 0.928480263709, 0.357043922814, 0.2704459205 ], [ 0.071367767882, 0.500184174784, 0.270473157899], [ 0.214138206242, 0.500060265888, 0.270780793152], [ 0.357863664331, 0.499955434833, 0.271447345349], [ 0.499771087998, 0.499707597815, 0.271567235372], [ 0.642975254853, 0.499988407411, 0.270463308773], [ 0.785705148085, 0.500114875586, 0.270217112819], [ 0.928263898641, 0.500345144405, 0.270046227352], [ 0.071252808555, 0.643070968229, 0.270210099866], [ 0.213988176833, 0.643314991299, 0.270104166083], [ 0.357297260155, 0.64313014574 , 0.270470164741], [ 0.499994918877, 0.643056593077, 0.270479482749], [ 0.643208387127, 0.643241345279, 0.270093906973], [ 0.785813538512, 0.643003444381, 0.270208307842], [ 0.928490484285, 0.643063915029, 0.270165054873], [ 0.071339969561, 0.78576824882 , 0.270141438736], [ 0.214225852162, 0.785856036447, 0.270126800266], [ 0.357178845883, 0.785837391922, 0.270167558266], [ 0.500076398396, 0.785849263811, 0.270217674024], [ 0.642955238054, 0.785870795689, 0.270228525631], [ 0.785736446002, 0.78577320504 , 0.270228424297], [ 0.928497702356, 0.78574598852 , 0.27017690571 ], [ 0.071352173032, 0.928436450475, 0.270217674024], [ 0.214249725546, 0.928448322364, 0.270167558266], [ 0.357202719266, 0.928429677839, 0.270126800266], [ 0.500088601867, 0.928517465466, 0.270141438736], [ 0.642930869072, 0.928539725765, 0.27017690571 ], [ 0.785692125427, 0.928512509246, 0.270228424297], [ 0.928473333375, 0.928414918597, 0.270228525631], [-0.000158672329, -0.000551335153, 0.359559690166], [ 0.142772290027, -0.000455881976, 0.359510089248], [ 0.285744010348, -0.000643115537, 0.3595307305 ], [ 0.428728350758, -0.000313000084, 0.359439782983], [ 0.571572000162, -0.000228704153, 0.35950216726 ], [ 0.714302883669, -0.000140424356, 0.359535601826], [ 0.857001619348, -0.000195472029, 0.359530780415], [-0.001214894278, 0.141610906204, 0.358793392157], [ 0.142687648435, 0.142514226501, 0.360382514462], [ 0.286696541246, 0.141247902158, 0.358880604612], [ 0.429046113335, 0.142331603508, 0.359562815992], [ 0.571679234074, 0.142294886679, 0.359540233021], [ 0.714262266065, 0.142621029528, 0.359486534668], [ 0.856685630829, 0.142650928964, 0.359548957615], [-0.000235846804, 0.285646440373, 0.360459004359], [ 0.142308340235, 0.285559047346, 0.36520633436 ], [ 0.28460866694 , 0.284621840088, 0.359853315812], [ 0.428938390463, 0.285455644606, 0.360307424668], [ 0.572604358026, 0.28461375266 , 0.358803850796], [ 0.714590983911, 0.285607768683, 0.359490363682], [ 0.856932346129, 0.285634918839, 0.359492280028], [-0.001175786597, 0.429671961626, 0.358803850796], [ 0.142490180965, 0.42883006968 , 0.360307424668], [ 0.286819904488, 0.429663874198, 0.359853315812], [ 0.429120231193, 0.42872666694 , 0.36520633436 ], [ 0.571664418232, 0.428639273913, 0.360459004359], [ 0.714496225299, 0.428650795447, 0.359492280028], [ 0.856837587517, 0.428677945603, 0.359490363682], [-0.000250662646, 0.571990827606, 0.359540233021], [ 0.142382458094, 0.571954110778, 0.359562815992], [ 0.284732030182, 0.573037812127, 0.358880604612], [ 0.428740922994, 0.571771487785, 0.360382514462], [ 0.572643465706, 0.572674808082, 0.358793392157], [ 0.7147429406 , 0.571634785322, 0.359548957615], [ 0.857166305363, 0.571664684758, 0.359486534668], [-0.000143428733, 0.714514418439, 0.35950216726 ], [ 0.14270022067 , 0.71459871437 , 0.359439782983], [ 0.285684561081, 0.714928829823, 0.3595307305 ], [ 0.428656281402, 0.714741596262, 0.359510089248], [ 0.571587243757, 0.714837049439, 0.359559690166], [ 0.71442695208 , 0.714481186315, 0.359530780415], [ 0.857125687759, 0.714426138641, 0.359535601826], [-0.000118163791, 0.856996705446, 0.359506935376], [ 0.142772290193, 0.857053384075, 0.359444287355], [ 0.285714285714, 0.857142857143, 0.35945833579 ], [ 0.428656281235, 0.857232330211, 0.359444287355], [ 0.571546735219, 0.85728900884 , 0.359506935376], [ 0.714343127611, 0.857180250463, 0.359549064322], [ 0.857085443817, 0.857105463823, 0.359549064322], [ 0.071407580151, 0.070021064407, 0.446256838403], [ 0.214073296263, 0.070013834592, 0.446271784778], [ 0.357449175134, 0.070499508547, 0.445711601263], [ 0.500243867747, 0.070782578525, 0.445699248215], [ 0.64297938693 , 0.071147122611, 0.445680148407], [ 0.785571106133, 0.071223358891, 0.445653546069], [ 0.928201620286, 0.071001904567, 0.445654739735], [ 0.066199138865, 0.209008203896, 0.446353891489], [ 0.218708266694, 0.209050682643, 0.446472180934], [ 0.358333775661, 0.212962703464, 0.446889811833], [ 0.500402431209, 0.213045403121, 0.446310980677], [ 0.643172572366, 0.213913180699, 0.445680672236], [ 0.785361352689, 0.214120271601, 0.445678021377], [ 0.927277080644, 0.214257448043, 0.446275442333], [ 0.066292666057, 0.36200883283 , 0.446522096182], [ 0.217538719928, 0.362471126593, 0.446978556975], [ 0.3538898515 , 0.351814587692, 0.446978556975], [ 0.505135905371, 0.352276881456, 0.446522096182], [ 0.644014463225, 0.357257732494, 0.446281125061], [ 0.785714285714, 0.357142857143, 0.445694018003], [ 0.927414108204, 0.357027981792, 0.446281125061], [ 0.07102614022 , 0.501240311165, 0.446310980677], [ 0.213094795767, 0.501323010822, 0.446889811833], [ 0.352720304735, 0.505235031643, 0.446472180934], [ 0.505229432563, 0.505277510389, 0.446353891489], [ 0.644151490785, 0.500028266242, 0.446275442333], [ 0.786067218739, 0.500165442684, 0.445678021377], [ 0.928255999062, 0.500372533586, 0.445680672236], [ 0.071184703682, 0.64350313576 , 0.445699248215], [ 0.213979396295, 0.643786205739, 0.445711601263], [ 0.357355275166, 0.644271879694, 0.446271784778], [ 0.500020991278, 0.644264649879, 0.446256838403], [ 0.643226951143, 0.643283809719, 0.445654739735], [ 0.785857465296, 0.643062355394, 0.445653546069], [ 0.928449184499, 0.643138591675, 0.445680148407], [ 0.071323360742, 0.785779791072, 0.445659876884], [ 0.214184925594, 0.785943464028, 0.445671622751], [ 0.357186864398, 0.786227490853, 0.445694024532], [ 0.500101164093, 0.786277157419, 0.445676874968], [ 0.642993179581, 0.785935275009, 0.445652099244], [ 0.785737431589, 0.785791195979, 0.445648594725], [ 0.928489259161, 0.785761889409, 0.44567115802 ], [ 0.071327407336, 0.928008556866, 0.445676874968], [ 0.21424170703 , 0.928058223433, 0.445694024532], [ 0.357243645835, 0.928342250257, 0.445671622751], [ 0.500105210687, 0.928505923213, 0.445659876884], [ 0.642939312268, 0.928523824877, 0.44567115802 ], [ 0.785691139839, 0.928494518307, 0.445648594725], [ 0.928435391848, 0.928350439277, 0.445652099244], [ 0.142023940953, 0.284983847074, 0.509401001692], [ 0.429404630476, 0.429301867212, 0.509401001692]] # Set up configuration bulk_configuration = BulkConfiguration( bravais_lattice=lattice, elements=elements, fractional_coordinates=fractional_coordinates ) # Add tags bulk_configuration.addTags('Selection 0', [ 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]) # ------------------------------------------------------------- # Calculator # ------------------------------------------------------------- potentialSet = EAM_Pt_2004() calculator = TremoloXCalculator(parameters=potentialSet) calculator.setVerletListsDelta(0.25*Angstrom) bulk_configuration.setCalculator(calculator) bulk_configuration.update() # ------------------------------------------------------------- # Adaptive Kinetic Monte Carlo # ------------------------------------------------------------- htst_parameters = HTSTParameters( assumed_prefactor=1e14/Second, ) # If the the markov chain already exists, read it from file, # otherwise create a new object. if os.path.isfile('akmc_markov_chain.nc'): markov_chain = nlread('akmc_markov_chain.nc')[0] else: markov_chain = MarkovChain( configuration=bulk_configuration, configuration_energy=TotalEnergy(bulk_configuration).evaluate(), ) # If the the kinetic Monte Carlo already exists, read it from file to resume it, # otherwise create a new kinetic Monte Carlo object. if os.path.isfile('akmc_kmc.nc'): kmc = nlread('akmc_kmc.nc')[0] else: kmc = None constraints = [ 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] saddle_search = MDSaddleSearch( temperature=1000.0*Kelvin, constraints=constraints, ) akmc = AdaptiveKineticMonteCarlo( markov_chain=markov_chain, kmc_temperature=300.0*Kelvin, calculator=bulk_configuration.calculator(), kmc=kmc, confidence=0.99, htst_parameters=htst_parameters, filename_prefix='akmc', saddle_search_method=saddle_search ) akmc.run(max_searches=50, max_kmc_steps=10000)