# Set up lattice vector_a = [16.2918, 0.0, 0.0]*Angstrom vector_b = [0.0, 16.2918, 0.0]*Angstrom vector_c = [0.0, 0.0, 120.0]*Angstrom lattice = UnitCell(vector_a, vector_b, vector_c) # Define elements elements = [Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Germanium, Germanium, Germanium, Germanium, Germanium, Germanium, Germanium, Germanium, Germanium, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Germanium, Germanium, Germanium, Germanium, Germanium, Germanium, Germanium, Germanium, Germanium, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Germanium, Germanium, Germanium, Germanium, Germanium, Germanium, Germanium, Germanium, Germanium, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Germanium, Germanium, Germanium, Germanium, Germanium, Germanium, Germanium, Germanium, Germanium, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Germanium, Germanium, Germanium, Germanium, Germanium, Germanium, Germanium, Germanium, Germanium, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Germanium, Germanium, Germanium, Germanium, Germanium, Germanium, Germanium, Germanium, Germanium, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Germanium, Germanium, Germanium, Germanium, Germanium, Germanium, Germanium, Germanium, Germanium, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Germanium, Germanium, Germanium, Germanium, Germanium, Germanium, Germanium, Germanium, Germanium, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon] # Define coordinates fractional_coordinates = [[ 0.054235628727, 0.013748064291, 0.210673025109], [ 0.038044906868, 0.37381152921 , 0.210457088502], [ 0.071542169214, 0.665391115471, 0.211344276698], [ 0.375731178859, 0.034933508088, 0.209141376095], [ 0.375459473603, 0.375015689193, 0.209962585283], [ 0.376324096784, 0.710033575219, 0.208733503147], [ 0.711945787572, 0.043648212506, 0.210348546943], [ 0.695027888284, 0.389825301836, 0.212468355638], [ 0.708338334975, 0.707511256162, 0.210039027784], [ 0.041958124945, 0.042471172657, 0.254919383021], [ 0.049435614058, 0.37142367878 , 0.255808606566], [ 0.046821887515, 0.705555738042, 0.254928867141], [ 0.368559864135, 0.035947230647, 0.25519703213 ], [ 0.369576018651, 0.376135464648, 0.254861340258], [ 0.372214731594, 0.707434754362, 0.254435007345], [ 0.712354166078, 0.044502781486, 0.254871126447], [ 0.710563582615, 0.37317778341 , 0.255461259985], [ 0.701872974175, 0.704710073554, 0.254321570482], [ 0.041071418754, 0.042139597028, 0.300742996878], [ 0.043764331627, 0.371547189877, 0.300339064317], [ 0.041167725817, 0.705394848423, 0.299783766519], [ 0.383194876333, 0.040978829672, 0.299708342913], [ 0.381790213233, 0.372580909976, 0.301470466748], [ 0.38721916316 , 0.70678511912 , 0.300166016121], [ 0.710335523252, 0.032472737099, 0.300787710514], [ 0.70640230758 , 0.375310882972, 0.300549715285], [ 0.713660493539, 0.714082369065, 0.300134719947], [ 0.043299692492, 0.043649373092, 0.346417149036], [ 0.041296823473, 0.373815015786, 0.346210553679], [ 0.042079250109, 0.706977436056, 0.346315047025], [ 0.375285807595, 0.039639396024, 0.346331679874], [ 0.372705197042, 0.372508079823, 0.345967086152], [ 0.375865408344, 0.702150367261, 0.34578879971 ], [ 0.706719004541, 0.038211555108, 0.345381060315], [ 0.717385925094, 0.372955435795, 0.345739809885], [ 0.711150380911, 0.70646712823 , 0.346565360493], [ 0.046860483499, 0.040566583247, 0.390729317584], [ 0.041307560353, 0.379042682727, 0.391141253456], [ 0.039175496912, 0.711615685415, 0.3913310645 ], [ 0.371560221067, 0.044395429057, 0.390230306665], [ 0.369211272131, 0.373530114005, 0.391016722381], [ 0.369812204115, 0.708097648183, 0.391399963548], [ 0.706288126307, 0.042388894305, 0.391769516553], [ 0.709001687051, 0.374554412122, 0.391292599844], [ 0.709035410016, 0.713520486681, 0.391383114633], [ 0.043914393449, 0.042809711059, 0.436567287749], [ 0.043287668666, 0.378794660242, 0.436741280547], [ 0.044604985623, 0.713286950169, 0.436173751016], [ 0.369175033288, 0.04327349983 , 0.435567340468], [ 0.378843169613, 0.375404448198, 0.437343902159], [ 0.378332414054, 0.713126397972, 0.436005192636], [ 0.709701177352, 0.047843271844, 0.435826739008], [ 0.710089185281, 0.373753072927, 0.436038516209], [ 0.703944592279, 0.706469453326, 0.436458812839], [ 0.042128162745, 0.039821296276, 0.482021713105], [ 0.042125447561, 0.376976866303, 0.481021182589], [ 0.035884453075, 0.704836483969, 0.481620529162], [ 0.374467353762, 0.044367428157, 0.48133962078 ], [ 0.373769392438, 0.374318349978, 0.48137961309 ], [ 0.37437946463 , 0.716468112272, 0.481911595467], [ 0.704244716138, 0.044626944063, 0.481356924715], [ 0.710661128454, 0.379423081078, 0.481963216078], [ 0.713621255265, 0.706796508347, 0.481399664117], [ 0.043296659558, 0.034664761398, 0.529621787157], [ 0.040272967946, 0.371183614599, 0.530164124721], [ 0.041232761191, 0.713459946079, 0.529027874122], [ 0.371892401429, 0.046592199909, 0.528758265829], [ 0.368624836062, 0.370549179625, 0.530002381638], [ 0.37559414565 , 0.705981281954, 0.529463390815], [ 0.703853985933, 0.050575350354, 0.529109438632], [ 0.706781704852, 0.379587398123, 0.53044954176 ], [ 0.715127646628, 0.709605933061, 0.528795398745], [ 0.037475145765, 0.044909937846, 0.575488355555], [ 0.043993857379, 0.377419077416, 0.575378300092], [ 0.0414941562 , 0.698998334266, 0.574388316481], [ 0.378071050626, 0.042590591411, 0.575407359786], [ 0.376261750114, 0.376331735199, 0.575190102435], [ 0.374669276164, 0.706586005412, 0.575914439345], [ 0.713077061605, 0.040571241649, 0.574509830032], [ 0.705441548266, 0.371285767542, 0.574399684145], [ 0.713744807536, 0.709334321599, 0.574887249201], [ 0.036524394457, 0.038138823265, 0.620838189979], [ 0.037573045746, 0.367157017075, 0.620823212135], [ 0.040964431045, 0.708270705704, 0.620112486681], [ 0.372151316845, 0.041266322716, 0.620675118796], [ 0.37097009149 , 0.374985167561, 0.620110481381], [ 0.370907148758, 0.705762838814, 0.62042612118 ], [ 0.70223959991 , 0.048551888476, 0.620719902414], [ 0.701770818349, 0.369141825627, 0.619746985102], [ 0.718789053831, 0.700560596124, 0.620021147528], [ 0.037012841986, 0.040487955063, 0.665444085978], [ 0.039021236558, 0.375548334888, 0.665352342313], [ 0.039085466655, 0.710001077566, 0.666149526273], [ 0.376309004194, 0.042088969455, 0.665479626336], [ 0.371724703006, 0.383428908725, 0.664748367463], [ 0.371068131451, 0.717647490034, 0.666252552281], [ 0.709053500876, 0.048498712133, 0.666199643671], [ 0.702536066431, 0.378541185255, 0.664891860715], [ 0.707573593616, 0.704776032621, 0.665467927868], [ 0.042727333341, 0.044356228644, 0.711683166524], [ 0.045939295497, 0.375164397859, 0.711036795822], [ 0.045651026689, 0.713124783233, 0.711148078429], [ 0.370375474665, 0.042488820419, 0.712345527245], [ 0.377557388837, 0.378830038358, 0.710793950981], [ 0.373894339431, 0.70817494773 , 0.711425947006], [ 0.708013096993, 0.039918361379, 0.710831098625], [ 0.711982848596, 0.373132587859, 0.710685956369], [ 0.713882961698, 0.704169796612, 0.711355945313], [ 0.040710787217, 0.044194845557, 0.756873427587], [ 0.046098237801, 0.367442116876, 0.757030869578], [ 0.045202380225, 0.712074139463, 0.756447506955], [ 0.374074553985, 0.049629545422, 0.756797180826], [ 0.382017439766, 0.374990406614, 0.756923502896], [ 0.379437140374, 0.712135074515, 0.755774660877], [ 0.707980076825, 0.048882314335, 0.755679290612], [ 0.707006126403, 0.377624068533, 0.755984174516], [ 0.707294790543, 0.706406722006, 0.755687051104], [ 0.129651559868, 0.113579782383, 0.219969015603], [ 0.112705240165, 0.463211089712, 0.221849823887], [ 0.119415412546, 0.780343805759, 0.221098033016], [ 0.451931830474, 0.122370504383, 0.220904776728], [ 0.453928345246, 0.459928560447, 0.220665259741], [ 0.452527565276, 0.79447282694 , 0.219921926233], [ 0.798052706834, 0.121539545165, 0.220598497026], [ 0.789939979522, 0.455593637835, 0.222396284053], [ 0.788280075684, 0.783159088219, 0.221815840985], [ 0.126601051932, 0.118268780313, 0.267499527037], [ 0.124528695695, 0.457433208919, 0.267337072012], [ 0.132057276172, 0.787042744793, 0.266533366673], [ 0.45178211808 , 0.115999889578, 0.267257679497], [ 0.463406149371, 0.454792498468, 0.265855749628], [ 0.45824057887 , 0.790596472464, 0.266014497038], [ 0.793762662523, 0.126095138564, 0.267054289624], [ 0.786264105575, 0.457111716167, 0.266507859854], [ 0.785804663914, 0.785666065342, 0.266281494885], [ 0.123552090347, 0.133258016398, 0.312997756432], [ 0.128496757875, 0.457028903234, 0.311546309362], [ 0.123391908481, 0.786950381225, 0.311761457869], [ 0.455316051609, 0.121517282631, 0.312338297191], [ 0.460164839482, 0.460920188471, 0.312429878799], [ 0.458725015759, 0.789616555194, 0.313501342006], [ 0.789169663737, 0.123050108948, 0.311539484147], [ 0.787828177611, 0.455372375912, 0.311452344708], [ 0.789759087704, 0.797362938846, 0.313290118051], [ 0.122300458554, 0.12410476634 , 0.357409759423], [ 0.123113023423, 0.45920092015 , 0.357755852435], [ 0.130333636808, 0.788192834046, 0.357205135447], [ 0.458357499204, 0.130929627329, 0.357483279351], [ 0.46488306353 , 0.456628179471, 0.356621117258], [ 0.459561208204, 0.786201768842, 0.35747595714 ], [ 0.789731754569, 0.12061024532 , 0.356760853704], [ 0.798743719271, 0.457098563034, 0.356133879913], [ 0.792362873343, 0.789263414398, 0.357562144761], [ 0.127960068825, 0.128967412237, 0.401420662631], [ 0.125884643184, 0.457794532793, 0.402775966744], [ 0.124451559489, 0.794688079044, 0.402602006291], [ 0.444900265422, 0.121409982606, 0.402978829884], [ 0.450484749458, 0.458967565614, 0.401631774613], [ 0.454555251495, 0.79556268717 , 0.402379750542], [ 0.789325080538, 0.121216634796, 0.402370563426], [ 0.7910578186 , 0.455374128212, 0.4022511822 ], [ 0.791823950647, 0.794766766682, 0.402342429435], [ 0.125086369444, 0.129582687562, 0.447540117287], [ 0.128866121926, 0.461877653471, 0.447160440702], [ 0.128376482253, 0.795098270945, 0.447341537876], [ 0.449075143812, 0.122713265616, 0.447589903325], [ 0.461706133838, 0.457055482377, 0.448061200253], [ 0.461101192215, 0.795714039542, 0.447413470012], [ 0.793671434203, 0.129535259157, 0.44648957228 ], [ 0.790808525124, 0.456309873584, 0.447068379105], [ 0.784971713551, 0.785597433266, 0.448695882227], [ 0.122538719111, 0.129008535869, 0.49402075206 ], [ 0.126221829101, 0.458062716089, 0.49339490268 ], [ 0.121188783809, 0.786370130887, 0.493370388446], [ 0.453606260849, 0.126697602383, 0.493885779508], [ 0.453840191249, 0.457673929426, 0.493655586773], [ 0.457571253212, 0.799061239622, 0.493663307069], [ 0.788713973022, 0.127482505528, 0.493226679935], [ 0.790387899228, 0.455625122462, 0.493911224141], [ 0.79258119377 , 0.788396552007, 0.493374204515], [ 0.119114550503, 0.12824866279 , 0.541109896658], [ 0.128007710976, 0.460626793939, 0.540750360774], [ 0.125203802078, 0.794889014831, 0.540070757307], [ 0.462881214586, 0.129310202349, 0.540852546954], [ 0.461596403116, 0.461693728588, 0.540505672306], [ 0.45757916617 , 0.788808194182, 0.54127189995 ], [ 0.791607439506, 0.125868046016, 0.541044541821], [ 0.79686932489 , 0.46465355608 , 0.540961489871], [ 0.792290459333, 0.796438140542, 0.540595056334], [ 0.126563583072, 0.129796721713, 0.585659657227], [ 0.130251116007, 0.46449859892 , 0.586445005851], [ 0.122499380599, 0.787186467954, 0.586563492968], [ 0.461500655934, 0.127399175057, 0.586351856278], [ 0.458024670855, 0.4625883908 , 0.585522169503], [ 0.454140557644, 0.788065980577, 0.586920328786], [ 0.79080439554 , 0.128859883047, 0.586216073546], [ 0.789011869979, 0.46321755584 , 0.586087314525], [ 0.791933453219, 0.788680731414, 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0.286437582054, 0.425115025183], [ 0.791756952141, 0.624023178383, 0.42552450278 ], [ 0.794831067382, 0.960829327779, 0.425315226992], [ 0.12360005508 , 0.29365235534 , 0.468879061142], [ 0.12021766429 , 0.627382709213, 0.46952287895 ], [ 0.12980452056 , 0.957277530112, 0.470727140687], [ 0.454785689741, 0.29066952381 , 0.470223799094], [ 0.456399123821, 0.628115613808, 0.469942379405], [ 0.462267959667, 0.966557907611, 0.469627917078], [ 0.794065737463, 0.293699613216, 0.470617728495], [ 0.789263291564, 0.624933513551, 0.46966422365 ], [ 0.793583227935, 0.956127502695, 0.469712173276], [ 0.120902763337, 0.295802417265, 0.517763358028], [ 0.12257486424 , 0.630154448237, 0.518023642142], [ 0.122643309956, 0.958886115035, 0.516706858819], [ 0.454687531098, 0.299730210052, 0.517940776216], [ 0.461133657239, 0.632672775709, 0.517362740872], [ 0.462144085146, 0.958679490735, 0.518978285531], [ 0.790476087965, 0.296963428803, 0.518361685769], [ 0.800167899918, 0.628191638587, 0.51767206234 ], [ 0.78875836772 , 0.961775148284, 0.517660921531], [ 0.122753551948, 0.297504805356, 0.563935545023], [ 0.127464479646, 0.626686611599, 0.562191840262], [ 0.11649903932 , 0.958314131461, 0.56391465724 ], [ 0.457687669606, 0.296866118504, 0.563341688255], [ 0.458935626232, 0.630492520361, 0.56386661738 ], [ 0.459255882918, 0.954586970315, 0.563772671748], [ 0.796277847701, 0.289662382931, 0.562376173851], [ 0.793853983856, 0.627648599931, 0.562695689598], [ 0.79289833494 , 0.953794222494, 0.563574179745], [ 0.125779649001, 0.294687102603, 0.609035151267], [ 0.119623406244, 0.624546251108, 0.608922810461], [ 0.122527565315, 0.95686011529 , 0.609839838982], [ 0.457717944179, 0.292324042458, 0.607874079031], [ 0.452529464096, 0.625384208196, 0.608932604418], [ 0.460409773728, 0.956568122836, 0.609335795941], [ 0.79594823313 , 0.292804576147, 0.608053417459], [ 0.802028794628, 0.621409442945, 0.608352054242], [ 0.790212751125, 0.965271239378, 0.609475058843], [ 0.124635609052, 0.28805337285 , 0.654141148436], [ 0.122142682899, 0.630368903477, 0.653638853385], [ 0.119619494452, 0.959122406749, 0.654593710053], [ 0.452273324569, 0.288931944736, 0.654014730007], [ 0.454259723804, 0.629477824993, 0.654269600201], [ 0.462454438173, 0.96112078968 , 0.653553184759], [ 0.781954977935, 0.287798197732, 0.653848933549], [ 0.791571705864, 0.621322814008, 0.654150039146], [ 0.792023788102, 0.96241286092 , 0.655018592882], [ 0.121335121148, 0.296174944759, 0.699268296405], [ 0.123290629994, 0.626204586849, 0.699684730688], [ 0.123144495435, 0.955460743064, 0.699731868695], [ 0.455870663954, 0.291532075424, 0.699662096964], [ 0.461681519605, 0.628382861904, 0.699974637957], [ 0.460881602415, 0.962838003125, 0.700443591735], [ 0.796801104622, 0.294242751676, 0.699224530986], [ 0.783758156432, 0.618907086762, 0.69957545505 ], [ 0.797955277507, 0.957488152534, 0.699550458173], [ 0.132769681849, 0.28959936925 , 0.745362232705], [ 0.133819186182, 0.625247027921, 0.745626891543], [ 0.122973545814, 0.959556475072, 0.745529684185], [ 0.462198563221, 0.292322075062, 0.744727202898], [ 0.459407848064, 0.625966081131, 0.7446055014 ], [ 0.457994420013, 0.959749842319, 0.745512071201], [ 0.790995443782, 0.291469604993, 0.744220267627], [ 0.790108716154, 0.62566003526 , 0.744977612674], [ 0.794459798113, 0.951829372452, 0.744236396103], [ 0.125892576796, 0.297335542197, 0.790567923441], [ 0.130341819431, 0.617540591124, 0.790718128208], [ 0.118743054671, 0.953269876683, 0.789083284051], [ 0.468509885011, 0.28551391633 , 0.790607667519], [ 0.465118522254, 0.623474535601, 0.790561331524], [ 0.465941263299, 0.950621666267, 0.788399432489], [ 0.795295069272, 0.290863999305, 0.791435389531], [ 0.794297686382, 0.632925225544, 0.789844341884], [ 0.797985704291, 0.949600325845, 0.790124066237]] # Set up configuration bulk_configuration = BulkConfiguration( bravais_lattice=lattice, elements=elements, fractional_coordinates=fractional_coordinates, ) # Add tags bulk_configuration.addTags('heat_sink', [ 108, 109, 110, 111, 112, 113, 114, 115, 116, 225, 226, 227, 228, 229, 230, 231, 232, 233, 342, 343, 344, 345, 346, 347, 348, 349, 350, 459, 460, 461, 462, 463, 464, 465, 466, 467, 576, 577, 578, 579, 580, 581, 582, 583, 584, 693, 694, 695, 696, 697, 698, 699, 700, 701, 810, 811, 812, 813, 814, 815, 816, 817, 818, 927, 928, 929, 930, 931, 932, 933, 934, 935, ]) bulk_configuration.addTags('heat_source', [ 0, 1, 2, 3, 4, 5, 6, 7, 8, 117, 118, 119, 120, 121, 122, 123, 124, 125, 234, 235, 236, 237, 238, 239, 240, 241, 242, 351, 352, 353, 354, 355, 356, 357, 358, 359, 468, 469, 470, 471, 472, 473, 474, 475, 476, 585, 586, 587, 588, 589, 590, 591, 592, 593, 702, 703, 704, 705, 706, 707, 708, 709, 710, 819, 820, 821, 822, 823, 824, 825, 826, 827, ]) # ------------------------------------------------------------- # Calculator # ------------------------------------------------------------- potentialSet = Tersoff_SiGe_1989() calculator = TremoloXCalculator(parameters=potentialSet) bulk_configuration.setCalculator(calculator) # ------------------------------------------------------------- # Molecular Dynamics # ------------------------------------------------------------- initial_velocity = MaxwellBoltzmannDistribution( temperature=300.0*Kelvin, remove_center_of_mass_momentum=True ) method = NVEVelocityVerlet( time_step=1*femtoSecond, initial_velocity=initial_velocity, ) # Use a heating power of 50 nW. heating_power = 50.0e-9*Joule/Second momentum_exchange_hook = NonEquilibriumHeatExchange( configuration=bulk_configuration, heating_power=heating_power, heat_source='heat_source', heat_sink='heat_sink', update_profile_interval=10, profile_resolution=2.0*Ang ) md_trajectory = MolecularDynamics( bulk_configuration, constraints=[], trajectory_filename='Si_w_Ge_layer_NEMD.hdf5', steps=100000, log_interval=500, post_step_hook=momentum_exchange_hook, method=method ) # Print the information from the NEMD heat flow simulation. nlprint(momentum_exchange_hook)