import numpy from NL.Study.SurfaceProcessSimulation import SurfaceProcessSimulation # Set up lattice vector_a = [19.664, 0.0, 0.0]*Angstrom vector_b = [0.0, 17.029523540017202, 0.0]*Angstrom vector_c = [0.0, 0.0, 64.05420000000001]*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, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, 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, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, 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, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, 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, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, 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, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, 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, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, 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, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, 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, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, 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 = [[ 0.2250875 , 0.183275 , 0.020101990391], [ 0.4750875 , 0.183275 , 0.020101990391], [ 0.7250875 , 0.183275 , 0.020101990391], [ 0.9750875 , 0.183275 , 0.020101990391], [ 0.1000875 , 0.433275 , 0.020101990391], [ 0.3500875 , 0.433275 , 0.020101990391], [ 0.6000875 , 0.433275 , 0.020101990391], [ 0.8500875 , 0.433275 , 0.020101990391], [ 0.2250875 , 0.683275 , 0.020101990391], [ 0.4750875 , 0.683275 , 0.020101990391], [ 0.7250875 , 0.683275 , 0.020101990391], [ 0.9750875 , 0.683275 , 0.020101990391], [ 0.1000875 , 0.933275 , 0.020101990391], [ 0.3500875 , 0.933275 , 0.020101990391], [ 0.6000875 , 0.933275 , 0.020101990391], [ 0.8500875 , 0.933275 , 0.020101990391], [ 0.1000875 , 0.140025 , 0.028130065336], [ 0.3500875 , 0.140025 , 0.028130065336], [ 0.6000875 , 0.140025 , 0.028130065336], [ 0.8500875 , 0.140025 , 0.028130065336], [ 0.2250875 , 0.390025 , 0.028130065336], [ 0.4750875 , 0.390025 , 0.028130065336], [ 0.7250875 , 0.390025 , 0.028130065336], [ 0.9750875 , 0.390025 , 0.028130065336], [ 0.1000875 , 0.640025 , 0.028130065336], [ 0.3500875 , 0.640025 , 0.028130065336], [ 0.6000875 , 0.640025 , 0.028130065336], [ 0.8500875 , 0.640025 , 0.028130065336], [ 0.2250875 , 0.890025 , 0.028130065336], [ 0.4750875 , 0.890025 , 0.028130065336], [ 0.7250875 , 0.890025 , 0.028130065336], [ 0.9750875 , 0.890025 , 0.028130065336], [ 0.0263375 , 0.154075 , 0.038180665297], [ 0.2763375 , 0.154075 , 0.038180665297], [ 0.5263375 , 0.154075 , 0.038180665297], [ 0.7763375 , 0.154075 , 0.038180665297], [ 0.1513375 , 0.404075 , 0.038180665297], [ 0.4013375 , 0.404075 , 0.038180665297], [ 0.6513375 , 0.404075 , 0.038180665297], [ 0.9013375 , 0.404075 , 0.038180665297], [ 0.0263375 , 0.654075 , 0.038180665297], [ 0.2763375 , 0.654075 , 0.038180665297], [ 0.5263375 , 0.654075 , 0.038180665297], [ 0.7763375 , 0.654075 , 0.038180665297], [ 0.1513375 , 0.904075 , 0.038180665297], [ 0.4013375 , 0.904075 , 0.038180665297], [ 0.6513375 , 0.904075 , 0.038180665297], [ 0.9013375 , 0.904075 , 0.038180665297], [-0.001081432544, 0.07932984034 , 0.048749945551], [ 0.253449274633, 0.076998617204, 0.049434687108], [ 0.499581693561, 0.081917366123, 0.050019496886], [ 0.758333622335, 0.080756697574, 0.052004115907], [ 0.128928108734, 0.329942190906, 0.049246963457], [ 0.372658244644, 0.330482352902, 0.049026044191], [ 0.63050016974 , 0.330722234483, 0.051239863446], [ 0.882714354991, 0.330799438985, 0.051446213901], [-0.000552860472, 0.578361478484, 0.050294971707], [ 0.245985309735, 0.585503632465, 0.049866546491], [ 0.500595749574, 0.579681583656, 0.050824052955], [ 0.752232091546, 0.574535730492, 0.04889014947 ], [ 0.125955417602, 0.82463912082 , 0.047844044515], [ 0.37254553922 , 0.831386188047, 0.049763619333], [ 0.62350211644 , 0.834838215251, 0.051198045995], [ 0.874893320824, 0.827653841228, 0.048191565961], [ 0.037882682228, 0.220283723303, 0.05502675622 ], [ 0.286688344001, 0.219461115652, 0.054662823251], [ 0.53125812394 , 0.222830231881, 0.054461836075], [ 0.789075017217, 0.226811297848, 0.051789834594], [ 0.16055883538 , 0.474792371047, 0.053494604074], [ 0.413141598408, 0.467558697034, 0.055292780135], [ 0.659352939484, 0.474006185964, 0.053533903812], [ 0.909298662507, 0.47572843573 , 0.05329871715 ], [ 0.035921479747, 0.716406244656, 0.055902817293], [ 0.279936891814, 0.726068985151, 0.052693539379], [ 0.53946138596 , 0.721875685582, 0.053207099214], [ 0.785008230764, 0.716009796745, 0.05727258636 ], [ 0.166900222994, 0.967770625826, 0.055679544793], [ 0.408716423579, 0.974974183835, 0.053700824777], [ 0.65858111944 , 0.984289559119, 0.051260030645], [ 0.911402319441, 0.973692113472, 0.053745295902], [ 0.211554278183, 0.03174814934 , 0.067072253166], [ 0.454047428512, 0.035576735304, 0.065918570496], [ 0.709925468465, 0.032816295683, 0.065667333402], [ 0.961674859881, 0.028933009311, 0.065011327869], [ 0.082450409728, 0.283062959313, 0.065157301849], [ 0.333493283683, 0.282210323228, 0.065326214637], [ 0.579387130545, 0.282740111759, 0.066287130393], [ 0.840653590318, 0.273192461772, 0.065537128238], [ 0.211892595043, 0.531024617472, 0.066068603294], [ 0.4583859056 , 0.530900456776, 0.067183309573], [ 0.711065030696, 0.532342198177, 0.066074506967], [ 0.955226488434, 0.533671221045, 0.065866903595], [ 0.082783362896, 0.780727505764, 0.064824181858], [ 0.331134525482, 0.781863868185, 0.064743221455], [ 0.58112096029 , 0.78345558128 , 0.066523390048], [ 0.834812676858, 0.7823107998 , 0.066004520067], [ 0.169710778005, 0.093326664171, 0.079238391572], [ 0.418371003757, 0.08915361472 , 0.082095501986], [ 0.664736101524, 0.088901351678, 0.079689918883], [ 0.919719848687, 0.089119779509, 0.07939724887 ], [ 0.036600965772, 0.334224750023, 0.079541133152], [ 0.28769163552 , 0.335627452099, 0.078204814405], [ 0.539103359401, 0.341573959707, 0.079737980168], [ 0.79835495142 , 0.337281868689, 0.078780950842], [ 0.162270576682, 0.58048138931 , 0.080390049125], [ 0.411300413432, 0.579208753772, 0.082570152011], [ 0.668199538612, 0.588070670841, 0.08036262387 ], [ 0.917618101849, 0.584662283291, 0.082494439858], [ 0.050676934771, 0.84179840553 , 0.080948961725], [ 0.294607519092, 0.842980699766, 0.080271614194], [ 0.533398403081, 0.833058555652, 0.080382964113], [ 0.791931570936, 0.836467862031, 0.080925541479], [ 0.009348151425, -0.018707269729, 0.080031772033], [ 0.262326062527, -0.013006164948, 0.082986090365], [ 0.500091857597, -0.022973158047, 0.078832292755], [ 0.742713808465, -0.026564955754, 0.081085160159], [ 0.127983018507, 0.234352696208, 0.081162046339], [ 0.383921619636, 0.230687443461, 0.079967772421], [ 0.627614481683, 0.232874804782, 0.081312813762], [ 0.883044568236, 0.228509106496, 0.081393324991], [ 0.004338655377, 0.477683165965, 0.079663723855], [ 0.255770473895, 0.481128049192, 0.082733601437], [ 0.51057233225 , 0.48338113362 , 0.080806022903], [ 0.758205625435, 0.475055384758, 0.080481020429], [ 0.139951809107, 0.729562626809, 0.076825460887], [ 0.382138120554, 0.730807762769, 0.07859488851 ], [ 0.627516518553, 0.73121224655 , 0.081845751751], [ 0.889544895326, 0.730701930912, 0.079452467846], [ 0.15117244109 , 0.163783472403, 0.094765021158], [ 0.404387348041, 0.1601880897 , 0.09639744549 ], [ 0.652089938108, 0.159347328306, 0.095086205089], [ 0.902842551143, 0.156910369114, 0.095613795395], [ 0.021209829382, 0.407368583177, 0.093373671517], [ 0.270908302272, 0.400138988402, 0.094263416148], [ 0.527866976314, 0.411578850563, 0.095594952805], [ 0.778078140223, 0.405190087192, 0.094452515632], [ 0.146919936452, 0.657280372053, 0.093242648755], [ 0.397025651999, 0.660609372292, 0.094224222391], [ 0.648614358159, 0.653436963948, 0.095156105519], [ 0.899562601408, 0.660953145718, 0.095320063095], [ 0.025524920596, 0.911430318587, 0.094918338071], [ 0.27697257175 , 0.90845208608 , 0.095985385885], [ 0.524954909131, 0.908429519561, 0.09499274618 ], [ 0.76704471266 , 0.901439371092, 0.096099924575], [ 0.212527133222, 0.178057036452, 0.109325426525], [ 0.469155741741, 0.180997014962, 0.109460618601], [ 0.716084641114, 0.181602155699, 0.107259886852], [ 0.964411186414, 0.17484554196 , 0.110247176463], [ 0.082000917373, 0.41923039301 , 0.109001617303], [ 0.332927172861, 0.410029063847, 0.109778027445], [ 0.584409425934, 0.409124054371, 0.112802303241], [ 0.831179933059, 0.425801273891, 0.111730586367], [ 0.210304120774, 0.681972557477, 0.106068352631], [ 0.464438299276, 0.678722646931, 0.10810174614 ], [ 0.708611903 , 0.670947424475, 0.110120545502], [ 0.957873406149, 0.684618335015, 0.111109518805], [ 0.08635180636 , 0.933495564221, 0.111138422182], [ 0.333348189027, 0.923658353384, 0.112068789183], [ 0.591269769783, 0.928860717582, 0.108223914466], [ 0.83048530316 , 0.925830508686, 0.110522871147], [ 0.086911364327, 0.143542010481, 0.108401169987], [ 0.341328746046, 0.145997678006, 0.109744619757], [ 0.595925777998, 0.139183986418, 0.110528800733], [ 0.83844319708 , 0.142140927486, 0.109762882523], [ 0.205253994251, 0.37641487398 , 0.106571713546], [ 0.459283419684, 0.387145248066, 0.10689221113 ], [ 0.71041348079 , 0.378006261947, 0.105655097873], [ 0.959800090199, 0.390438307665, 0.107971127671], [ 0.082526853445, 0.664265557953, 0.105815145845], [ 0.332893640025, 0.650523756556, 0.107803080743], [ 0.584364491534, 0.634845857469, 0.108353210776], [ 0.831813894891, 0.643711644843, 0.106894064256], [ 0.209314584028, 0.889796356549, 0.109065732055], [ 0.460124316359, 0.894972517411, 0.108823463213], [ 0.711125947394, 0.876496043599, 0.112048337667], [ 0.960407289447, 0.88572817651 , 0.107272361275], [ 0.026488405474, 0.157458766042, 0.124320607136], [ 0.276476874302, 0.162371626453, 0.123421880903], [ 0.527385752336, 0.150563569275, 0.124184486603], [ 0.774832382621, 0.164950172219, 0.122712069034], [ 0.150372946489, 0.40302827693 , 0.122787384732], [ 0.396019807042, 0.392543849936, 0.123108584784], [ 0.655782535405, 0.394757093223, 0.122913460489], [ 0.899102850889, 0.406324629901, 0.12338156642 ], [ 0.024507844858, 0.664925746631, 0.123220039264], [ 0.269886906605, 0.668615284348, 0.122227895214], [ 0.521693735241, 0.653105001376, 0.12295026722 ], [ 0.774224880992, 0.657888620586, 0.12312193237 ], [ 0.148111102219, 0.908319901523, 0.124554760142], [ 0.398194443622, 0.902547681482, 0.124724700157], [ 0.64490924193 , 0.90949245559 , 0.124945469195], [ 0.898543798842, 0.909831122129, 0.122936833946], [ 0.007061380939, 0.081618714549, 0.135914092259], [ 0.259810184312, 0.085329646623, 0.136807408606], [ 0.508797157058, 0.07684968057 , 0.137730065764], [ 0.750436367249, 0.095715778309, 0.137027800525], [ 0.13548891647 , 0.336824111829, 0.139672779592], [ 0.390713011346, 0.324179159264, 0.141158378966], [ 0.641904458943, 0.321911925322, 0.138467884925], [ 0.886575570458, 0.338518704475, 0.139529242104], [ 0.006281351794, 0.584753126487, 0.137014037583], [ 0.260866109469, 0.593364112836, 0.137064284838], [ 0.501667180277, 0.580039157362, 0.13803224524 ], [ 0.763696993965, 0.578995995195, 0.135757626525], [ 0.132683820452, 0.829868648651, 0.138207131001], [ 0.382453736602, 0.833708190688, 0.140425454129], [ 0.621020112937, 0.840221932256, 0.139112250511], [ 0.885640566091, 0.830379668826, 0.135657204417], [ 0.042258293093, 0.234468426672, 0.138430207611], [ 0.291014232532, 0.233190399155, 0.13911358911 ], [ 0.548177519606, 0.21951204869 , 0.140380593199], [ 0.785785395582, 0.240647212607, 0.136675585768], [ 0.173364665458, 0.481361971418, 0.132572726733], [ 0.41432087058 , 0.470274893294, 0.134442804542], [ 0.680318277136, 0.464506540185, 0.136536907048], [ 0.914065080625, 0.477288273061, 0.137821269714], [ 0.036650199492, 0.735886324303, 0.138307389582], [ 0.288405550126, 0.737702593155, 0.137881719987], [ 0.538683252249, 0.724563206588, 0.136664479279], [ 0.793439398779, 0.723726491203, 0.138529460764], [ 0.170331943455, 0.973685180025, 0.139831465206], [ 0.418235629622, 0.970770166817, 0.13983062409 ], [ 0.671567500533, 0.980978735773, 0.13805356563 ], [ 0.918970211273, 0.974068303564, 0.139392687022], [ 0.216766627616, 0.034346772385, 0.151564808907], [ 0.460370144472, 0.029800108973, 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2.013755430024e-03, -4.055340407077e-03, -7.785247528921e-04], [-3.478906750023e-04, -6.639545715863e-03, 1.423030940704e-03], [-4.698252055867e-03, 1.575608388739e-03, -1.679496893345e-03], [ 5.534517604412e-03, -2.190310003145e-05, -2.818222994825e-03], [ 1.660290277674e-03, -4.232161814904e-03, -4.146379549844e-03], [-3.934380360840e-03, 4.799533897198e-03, 1.674833010320e-03], [ 6.715650584814e-03, -1.540101424630e-03, 1.050865677594e-03], [ 3.314309862337e-03, 2.901025084989e-03, 3.336020809715e-03], [ 1.279769426675e-03, 4.997794554811e-03, 1.515045075346e-03], [-1.608064519346e-03, -1.525680651384e-04, 1.613012028971e-03], [-3.472626187833e-03, 6.917966175431e-03, 2.408746903720e-03], [-2.214146979253e-03, -1.834649538132e-03, -1.832364060437e-03], [ 1.503111269666e-04, 3.775144750982e-03, 2.113295163750e-03], [-5.374191645583e-03, 9.576218347596e-05, -6.334014555646e-04], [-1.753743294611e-03, 9.566316192831e-04, -7.466428172172e-04], [ 2.574396691894e-03, 1.495358551622e-04, 3.246709065081e-05], [ 8.307546658373e-05, -8.865713411026e-04, 4.776464305797e-03], [-5.985117120075e-03, 1.596927457439e-03, 9.988108827713e-03], [ 2.986050330293e-03, 6.158525617845e-03, -2.501655485048e-04], [ 3.047460893370e-03, -6.506871317968e-03, -4.118089857161e-03], [ 1.356155558568e-03, -6.313721370842e-04, 4.445959414068e-03], [-1.080564446145e-02, -2.322292838177e-03, -1.393679748081e-03], [ 3.898061798558e-03, -5.546391945007e-04, 9.577560559220e-03], [-1.686917812792e-04, -2.139262848223e-04, -8.483350275367e-04], [-1.273206058579e-03, -4.389228280922e-03, -4.596606121096e-04], [ 2.332300301004e-03, 2.454779907937e-03, 3.021197446183e-03], [ 1.965293626504e-03, 1.848154786451e-03, 2.009097632073e-03], [ 8.371435860471e-03, -4.049034105928e-04, -6.741681996375e-04], [ 8.373883120258e-04, -2.597851878901e-03, -2.553267101266e-04], [ 1.507587472254e-03, -1.719062660535e-04, 7.228414823480e-04], [ 1.983957218801e-05, 2.585231986128e-03, -2.526560332628e-03], [ 2.890581920835e-04, 1.649549635247e-03, -2.190344134739e-03], [-2.963985611663e-03, -2.098449841099e-03, -1.567659869451e-03], [-2.445750112361e-04, -2.209223480617e-03, -3.196023026517e-03], [ 2.023084691935e-03, 6.923697754924e-04, 5.350298425711e-03], [-3.819300097480e-03, -2.192520847499e-03, -4.490093346506e-03], [-2.212479824103e-03, 3.289479678331e-03, -6.835115995950e-04], [-2.350240028695e-03, 2.562432900150e-03, 3.269240405874e-03], [-4.649607925953e-03, -8.523796007858e-04, 4.796059970845e-04], [ 9.366273766554e-04, -1.269862898486e-03, 2.277314561130e-04], [ 5.120877257175e-03, -2.918016143297e-03, 1.501495736751e-03], [-3.336201234612e-03, 7.538198317114e-04, 2.679037715012e-03], [ 5.902615220397e-03, -1.677480088496e-03, -2.925402673594e-03], [-3.995347680728e-03, 2.232117894996e-03, -1.091626268239e-03], [ 3.927174497783e-04, 2.632794205383e-03, -1.739625612960e-04], [ 2.820498383739e-03, 4.064466174744e-03, 8.919430959010e-03], [ 5.257097663184e-03, 1.496018992360e-03, -9.503779382573e-04], [ 2.634008140117e-03, 8.468941757566e-07, -7.059439795355e-04], [ 2.218336591038e-03, 7.068955749533e-03, -1.156352495389e-03], [ 3.898480094125e-03, -3.267617388812e-03, 1.045486978541e-02], [ 2.423708155608e-03, 4.953067152062e-03, 5.896246858920e-03], [-2.197445496156e-03, 1.622434450915e-03, -1.622574687094e-03], [-6.484587088970e-03, 3.807059485273e-03, 4.949595921259e-03], [ 3.312991223888e-03, 6.464114873985e-04, -2.791493470332e-04], [-7.464957987367e-03, 6.604457727812e-03, 1.412203508388e-03], [-2.237150928084e-03, -3.206240579181e-03, 2.981961006576e-03], [ 5.760149705364e-03, -3.367485391638e-03, -3.912905461917e-04], [ 3.330323775514e-03, 4.948271421876e-03, -1.244606634785e-03], [-1.347235346782e-03, 5.685045756547e-03, 6.162385329558e-03], [-2.607427605464e-03, -2.071759270767e-03, -2.334961403826e-03], [ 5.057107890908e-03, -1.048160674778e-03, -9.706777862046e-04], [ 5.081812936115e-04, 8.596341758596e-04, 2.796383144014e-03], [-2.951364640280e-03, -2.020303160054e-03, 5.628350403901e-04], [-8.717023715906e-03, 8.082234544177e-03, 5.029112995136e-03], [-1.372710307234e-03, 5.506215367645e-03, 2.253235376107e-03], [-1.770062775283e-03, 1.817780017283e-03, -1.413718635124e-03], [-3.644257890819e-03, -2.128081503915e-03, -6.959201616888e-03], [ 1.604474639952e-03, 2.148226771993e-03, -2.793257292794e-03], [ 1.324980134269e-03, 9.147312885132e-03, -2.067608256050e-03], [-6.287940595013e-03, 3.025388903425e-03, -1.747892095324e-03], [ 5.148083473658e-03, -8.176712702318e-04, 4.841593689626e-03], [ 1.754558110254e-04, -3.559280730318e-03, 4.417672729552e-03], [ 5.098610202379e-03, 2.408763952621e-03, -3.371305906290e-03], [ 4.896081970419e-03, -2.378169461781e-03, -8.082040009314e-04], [-9.370117776386e-04, 1.590290096792e-03, 2.786261947412e-03], [ 3.313875593611e-03, 2.029710523973e-03, -4.412505857923e-04], [-1.393021620876e-03, 1.393673917966e-03, 3.320060099481e-04], [ 2.502771345192e-03, 3.107516453530e-04, 5.254033038953e-05], [ 1.380358139373e-03, -1.105188215554e-03, -1.512224166058e-03], [ 3.692581391254e-03, -1.444361928263e-03, 1.313779274386e-03], [-2.538136883651e-03, 2.233368346252e-03, -9.417679620250e-04], [ 2.625385068864e-03, -1.217468558742e-03, 4.577327101568e-03], [-4.235417050536e-03, 1.410261081126e-03, 4.107609045985e-03], [ 6.949917915106e-04, -3.405933712297e-05, 2.276782096120e-03], [ 2.001930906483e-03, -1.233718632093e-03, 3.872007400895e-03], [ 1.601852525180e-03, -3.436110049943e-05, 2.068347392092e-03], [-4.427821751121e-03, 2.411843987744e-03, -3.782236186540e-03], [ 3.340584986682e-03, 9.898368729600e-04, 6.204623920426e-03], [ 1.587672408078e-03, 6.957920642892e-03, -9.354232812135e-03], [ 7.237955693733e-03, 1.179919753981e-03, -9.822016143161e-04], [-1.993122779707e-03, 3.107450922535e-06, 8.124307725268e-03], [ 3.991736268074e-03, -4.345414824647e-03, -1.498250630144e-03], [ 6.575819251062e-03, 3.389861586735e-04, 3.868285149584e-03], [-6.345214222551e-03, -1.942789787427e-03, -6.158569712726e-04], [ 2.780965741863e-03, 4.382755700408e-04, -3.383092970607e-03], [-6.354236421016e-03, -3.665307977657e-03, -2.768518257552e-03], [-6.544331046262e-04, 2.821904722091e-03, -2.092903238650e-03], [-4.251083176842e-03, 2.965342202150e-03, 4.447268226203e-03], [ 2.410163805908e-03, -1.006705277584e-02, -2.760707678092e-03], [-4.030970815428e-04, 2.049774718934e-03, 6.943000749554e-03], [ 2.271503081444e-03, -4.226916331761e-03, 3.010924765599e-03], [-4.511279907728e-03, 9.249255035849e-04, -3.170339292369e-03], [ 1.624551297979e-05, 2.988862132722e-03, 5.639915802361e-03], [ 2.248634254563e-03, 1.034102419943e-03, 2.067880827352e-03], [-4.431754363538e-04, 5.510240423803e-03, -9.884425912009e-04], [-5.044180983433e-03, -7.422535416048e-03, -1.709910418370e-03], [-5.550776663734e-04, -2.001271892660e-03, -1.784789259500e-03], [-1.156287414864e-03, -1.255697069028e-03, 2.975106994690e-03], [-2.623138745318e-03, 1.573166209722e-03, 2.173380993750e-06], [ 3.906583550981e-03, -2.298334073595e-03, -1.243884980362e-03], [ 2.941683616905e-03, 5.101777413308e-03, 7.284738632465e-03], [ 4.672973496657e-03, 3.847104391556e-03, -1.433590216683e-03], [ 1.825900888174e-03, -2.099660996852e-03, -3.642137786930e-04], [ 2.075751935252e-03, -2.992921398726e-03, -1.630999808523e-03], [-3.575136269405e-03, -1.134108392946e-03, -1.534562967433e-03], [-1.940632146709e-03, 5.045316303855e-03, 8.031159713939e-03], [-6.853807997590e-03, 9.280819658520e-04, -9.615825171078e-03], [-6.433782348197e-03, 1.839211007063e-03, 7.618904105258e-03], [-9.206680485474e-03, -1.436133211357e-03, -1.415026223167e-03], [-6.479854056632e-04, 2.813657053856e-03, -3.844846190451e-03]]*Angstrom/fs # Set up configuration bulk_configuration = BulkConfiguration( bravais_lattice=lattice, elements=elements, fractional_coordinates=fractional_coordinates, velocities=velocities ) # Attach ReaxFF calculator. potentialSet = ReaxFF_CHONSSi_2012(strict_bondpairs = None) calculator = TremoloXCalculator(parameters=potentialSet) calculator.setVerletListsDelta(0.25*Angstrom) bulk_configuration.setCalculator(calculator) surface_process_simulation = SurfaceProcessSimulation( substrate=bulk_configuration, filename='sio2_n_etching.hdf5', object_id='sps_0', random_seed=7, temperature=300.0*Kelvin, fixed_thickness=4.0*Angstrom, thermostat_thickness=8*Angstrom, log_interval=10, ) # Run 5 deposition events, each 20 ps long. surface_process_simulation.addSequence( molecule=Nitrogen, number_of_events=5, md_time=20*ps, time_step=1.0*fs, mean_kinetic_energy=25*eV, mean_incident_angle=0*Degrees, std_kinetic_energy=0.3*eV, std_incident_angle=2*Degrees, post_md_hooks=[RemoveElementFromSubstrate(Nitrogen)], ) surface_process_simulation.update()