# -*- coding: utf-8 -*- # ------------------------------------------------------------- # Bulk Configuration # ------------------------------------------------------------- # Set up lattice vector_a = [16.646425, 0.0, 0.0]*Angstrom vector_b = [-8.32321249999, 14.4162269322, 0.0]*Angstrom vector_c = [0.0, 0.0, 21.326457581]*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] # Define coordinates fractional_coordinates = [[ 0.055555555556, 0.111111111111, 0.10621977455 ], [ 0.222222222222, 0.111111111111, 0.10621977455 ], [ 0.388888888889, 0.111111111111, 0.10621977455 ], [ 0.555555555556, 0.111111111111, 0.10621977455 ], [ 0.722222222222, 0.111111111111, 0.10621977455 ], [ 0.888888888889, 0.111111111111, 0.10621977455 ], [ 0.055555555556, 0.277777777778, 0.10621977455 ], [ 0.222222222222, 0.277777777778, 0.10621977455 ], [ 0.388888888889, 0.277777777778, 0.10621977455 ], [ 0.555555555556, 0.277777777778, 0.10621977455 ], [ 0.722222222222, 0.277777777778, 0.10621977455 ], [ 0.888888888889, 0.277777777778, 0.10621977455 ], [ 0.055555555556, 0.444444444444, 0.10621977455 ], [ 0.222222222222, 0.444444444444, 0.10621977455 ], [ 0.388888888889, 0.444444444444, 0.10621977455 ], [ 0.555555555556, 0.444444444444, 0.10621977455 ], [ 0.722222222222, 0.444444444444, 0.10621977455 ], [ 0.888888888889, 0.444444444444, 0.10621977455 ], [ 0.055555555556, 0.611111111111, 0.10621977455 ], [ 0.222222222222, 0.611111111111, 0.10621977455 ], [ 0.388888888889, 0.611111111111, 0.10621977455 ], [ 0.555555555556, 0.611111111111, 0.10621977455 ], [ 0.722222222222, 0.611111111111, 0.10621977455 ], [ 0.888888888889, 0.611111111111, 0.10621977455 ], [ 0.055555555556, 0.777777777778, 0.10621977455 ], [ 0.222222222222, 0.777777777778, 0.10621977455 ], [ 0.388888888889, 0.777777777778, 0.10621977455 ], [ 0.555555555556, 0.777777777778, 0.10621977455 ], [ 0.722222222222, 0.777777777778, 0.10621977455 ], [ 0.888888888889, 0.777777777778, 0.10621977455 ], [ 0.055555555556, 0.944444444444, 0.10621977455 ], [ 0.222222222222, 0.944444444444, 0.10621977455 ], [ 0.388888888889, 0.944444444444, 0.10621977455 ], [ 0.555555555556, 0.944444444444, 0.10621977455 ], [ 0.722222222222, 0.944444444444, 0.10621977455 ], [ 0.888888888889, 0.944444444444, 0.10621977455 ], [ 0.000226807104, 0.000057875462, 0.212957342554], [ 0.1665498202 , -0.000072225052, 0.213294798732], [ 0.333173398868, 0.000159934466, 0.212690477142], [ 0.499697158812, -0.000492389747, 0.213281802769], [ 0.666917204855, 0.000202526408, 0.2124198855 ], [ 0.833873824125, 0.000198213493, 0.212123369397], [ 0.000125219109, 0.167032161884, 0.213034121588], [ 0.166689106049, 0.166644227284, 0.213422578363], [ 0.333405558386, 0.166783513134, 0.213294798732], [ 0.499766434426, 0.166486427943, 0.212979063596], [ 0.666521716357, 0.166403494494, 0.212795707393], [ 0.833742551658, 0.167112984582, 0.212521599186], [-0.000154326507, 0.33348765984 , 0.213320067478], [ 0.166301171449, 0.333208114225, 0.213034121588], [ 0.333275457871, 0.333106526229, 0.212957342554], [ 0.500169773591, 0.333073983426, 0.213071445019], [ 0.666737670072, 0.333200197506, 0.212854170252], [ 0.8334762873 , 0.333624688356, 0.212943876091], [-0.000291355022, 0.499857046033, 0.212943876091], [ 0.166220348751, 0.499590781676, 0.212521599186], [ 0.33313511984 , 0.499459509208, 0.212123369397], [ 0.500185914573, 0.499723106796, 0.212348843097], [ 0.666843950707, 0.499742296271, 0.212937651166], [ 0.833263923839, 0.500069409495, 0.212832110441], [ 0.000133135828, 0.666595663261, 0.212854170251], [ 0.16692983884 , 0.666811616976, 0.212795707393], [ 0.333130806925, 0.666416128478, 0.2124198855 ], [ 0.499694891549, 0.666689265423, 0.212082523144], [ 0.666786880922, 0.666546452411, 0.21221766124 ], [ 0.833591037062, 0.666489382626, 0.212937651166], [ 0.000259349907, 0.833163559742, 0.213071445019], [ 0.16684690539 , 0.833566898907, 0.212979063596], [ 0.33382572308 , 0.833636174521, 0.213281802769], [ 0.499841161374, 0.833492171959, 0.213111429333], [ 0.666644067911, 0.833638441784, 0.212082523144], [ 0.833610226537, 0.83314741876 , 0.212348843097], [ 0.110818500675, 0.055096949888, 0.318817357301], [ 0.277720756341, 0.055612576992, 0.318292731222], [ 0.443712511578, 0.054888162345, 0.31774049646 ], [ 0.610790480742, 0.054403394682, 0.317652081492], [ 0.779118628009, 0.05596059045 , 0.316254564139], [ 0.944862251124, 0.056202175621, 0.317492084274], [ 0.111073410793, 0.22225992254 , 0.31854419333 ], [ 0.278236383445, 0.222514832658, 0.318817357301], [ 0.444729802774, 0.222395446075, 0.318950979773], [ 0.610814774861, 0.221921061669, 0.317507995065], [ 0.778033654963, 0.22249834792 , 0.317198379173], [ 0.944242881119, 0.222521708834, 0.31861958654 ], [ 0.110811624499, 0.389090452214, 0.31861958654 ], [ 0.277131157712, 0.388471082209, 0.317492084274], [ 0.444822819156, 0.388841821777, 0.317606793093], [ 0.611427210921, 0.38851320443 , 0.318337039449], [ 0.777930594203, 0.389460177488, 0.31786517137 ], [ 0.944326603694, 0.38900672964 , 0.318987903693], [ 0.110834985414, 0.55529967837 , 0.317198379173], [ 0.277372742883, 0.554214705324, 0.316254564139], [ 0.444593094099, 0.555443912753, 0.315874469959], [ 0.611412279252, 0.555682396824, 0.317023344467], [ 0.777743558639, 0.555589774694, 0.318374635382], [ 0.943873155846, 0.555402739131, 0.31786517137 ], [ 0.111412271665, 0.722518558473, 0.317507995065], [ 0.278929938652, 0.722542852592, 0.317652081492], [ 0.443636383948, 0.721831317076, 0.317279545541], [ 0.610974604266, 0.722358729068, 0.315586932234], [ 0.777650936509, 0.721921054081, 0.317023344467], [ 0.944820128903, 0.721906122412, 0.318337039449], [ 0.110937887258, 0.888603530559, 0.318950979774], [ 0.278445170988, 0.889620821755, 0.31774049646 ], [ 0.445046405994, 0.88828692734 , 0.320381590022], [ 0.611502016258, 0.889696949385, 0.317279545541], [ 0.77788942058 , 0.888740239234, 0.315874469959], [ 0.944491511557, 0.888510514177, 0.317606793093], [ 0.055146104225, 0.110692907698, 0.425256329559], [ 0.222308941692, 0.111024391641, 0.42517270049 ], [ 0.3892713168 , 0.111152196357, 0.425114568602], [ 0.554953000491, 0.109708581171, 0.421935330867], [ 0.723174784513, 0.109917656766, 0.420779399355], [ 0.888926496451, 0.111024007556, 0.425262258365], [ 0.055215727794, 0.27811760554 , 0.425144603061], [ 0.222640425636, 0.278187229108, 0.425256329559], [ 0.390638166676, 0.280200458307, 0.426397471882], [ 0.556485313525, 0.277508029239, 0.426303095696], [ 0.72234117094 , 0.278090625746, 0.422290154414], [ 0.887463188045, 0.277296613959, 0.426238608102], [ 0.056036719375, 0.445870145288, 0.426238608102], [ 0.222309325777, 0.444406836883, 0.425262258365], [ 0.388566536535, 0.445350730844, 0.421329001259], [ 0.557039749406, 0.446177403736, 0.423169739262], [ 0.722095230003, 0.44488613944 , 0.425631787714], [ 0.888639334418, 0.444693998915, 0.425398544438], [ 0.055242707588, 0.610992162394, 0.422290154414], [ 0.223415676567, 0.610158548821, 0.420779399355], [ 0.387973861147, 0.609176302405, 0.421028550692], [ 0.555318835583, 0.612407269925, 0.420417257754], [ 0.721652794621, 0.611680538712, 0.42380995177 ], [ 0.888447193893, 0.61123810333 , 0.425631787714], [ 0.055825304094, 0.776848019808, 0.426303095696], [ 0.223624752162, 0.778380332842, 0.421935330867], [ 0.389370894537, 0.775378409674, 0.428888439055], [ 0.555764857106, 0.777568476228, 0.419941943731], [ 0.720926063409, 0.77801449775 , 0.420417257754], [ 0.887155929597, 0.776293583928, 0.423169739262], [ 0.053132875026, 0.942695166657, 0.426397471882], [ 0.222181136976, 0.944062016533, 0.425114568602], [ 0.389681571963, 0.943651761371, 0.425892342233], [ 0.557954923659, 0.943962438796, 0.428888439055], [ 0.724157030928, 0.945359472187, 0.421028550692], [ 0.887982602489, 0.944766796799, 0.421329001259], [ 0.663869215142, -0.159318974778, 0.527135142406], [ 0.667986298432, 0.16202082192 , 0.52747531414 ], [ 0.494256781527, 0.49745847521 , 0.527937523563], [ 0.492652308111, 0.669464118192, 0.527135142406], [ 0.171312511413, 0.665347034902, 0.52747531414 ], [ 0.665022776926, 0.668310556408, 0.528124315299], [-0.164125141877, 0.839076551806, 0.527937523563]] # 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]) bulk_configuration.addTags('Selection 1', [ 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]) # Morse-potential potentialSet = TremoloXPotentialSet(name='Pt-Morse') potentialSet.addParticleType(ParticleType.fromElement(Platinum)) potentialSet.addPotential(MorsePotential( 'Pt', 'Pt', r_0=2.897*Angstrom, k=1.6047*Angstrom**-1, E_0=0.7102*eV, r_i=6.5*Angstrom, r_cut=9.5*Angstrom) ) calculator = TremoloXCalculator(parameters=potentialSet) bulk_configuration.setCalculator(calculator) # ------------------------------------------------------------- # Adaptive Kinetic Monte Carlo # ------------------------------------------------------------- htst_parameters = HTSTParameters( assumed_prefactor=1e+13*1/Second, ) if os.path.isfile('akmc_markov_chain.hdf5'): markov_chain = nlread('akmc_markov_chain.hdf5')[-1] else: markov_chain = MarkovChain( configuration=bulk_configuration, configuration_energy=TotalEnergy(bulk_configuration).evaluate(), ) if os.path.isfile('akmc_kmc.hdf5'): kmc = nlread('akmc_kmc.hdf5')[-1] 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] akmc = AdaptiveKineticMonteCarlo( markov_chain=markov_chain, kmc_temperature=300.0*Kelvin, md_temperature=2000.0*Kelvin, calculator=bulk_configuration.calculator(), kmc=kmc, superbasin_threshold=20, htst_parameters=htst_parameters, constraints=constraints, confidence=0.99, filename_prefix='akmc', ) akmc.run(max_searches=200, max_kmc_steps=10000)