!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! VERIFICATION CHECK: vc-memory-leak !!!!! !!!!! !!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Description: Check that the model has no memory leaks. This is tested using the Valgrind memory debugging tool (http://valgrind.org) by performing a series of energy and force calculations on a randomly distorted face-centered cubic (FCC) cube base structure for both non-periodic and periodic boundary conditions. Separate configurations are tested for each species supported by the model, as well as one containing a random distribution of all species. Configurations used for testing are provided as auxiliary files. Author: Ellad Tadmor ----------------------------------------------------------------------------------------------------- Results for KIM Model : EAM_Dynamo_Hale_Wong_pairMorse_PdAgH__MO_108983864770_004 Supported species : Ag H Pd random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Ag (Configuration in file "config-F-Ag.xyz") ----------------------------------------------------------------------------------------------------- Energy = 195.308400718 Forces: 1 -7.72171665e+00 -1.67216718e+01 -1.43946995e+01 2 -5.59006790e+00 7.23722586e+00 -1.60200034e+01 3 5.51173978e+00 -1.56913944e+01 -2.85696750e+00 4 -1.46712079e+01 8.10858468e+00 6.85937388e+00 5 2.02288685e+00 -2.15819628e+01 -9.49820348e+00 6 1.28914400e+01 2.57427323e+00 -1.51896081e+01 7 1.30103421e+01 -2.58536865e+01 -1.40884584e+01 8 -1.09953982e+01 -1.07617966e+01 4.58638316e+00 9 -1.06603190e+01 -1.47908076e+01 -2.38454809e+01 10 1.27898972e+01 2.21251206e+01 -1.80382437e+01 11 1.80840034e+00 -1.33477345e+01 -9.36555105e+00 12 -2.42026693e+01 2.14184919e+01 1.05598932e+01 13 -8.98308266e+00 -5.48383211e+00 -4.02712957e+01 14 1.22771827e+01 1.50460149e+01 -1.26466477e+01 15 3.70568161e+01 -8.06709140e+00 5.13746442e+00 16 -1.40647282e+00 3.62932520e+01 2.98611921e+00 17 -2.37455766e+01 -1.47715538e+01 -5.48474505e+00 18 8.79219546e+00 1.03652322e+01 -1.85667499e+00 19 8.67567244e+00 -1.76878352e+01 1.51892424e+01 20 -1.29392227e+01 9.76918896e+00 1.52265054e+01 21 -1.19564596e+01 -1.50770657e+01 6.92382890e+00 22 2.23365047e+01 1.72218112e+01 1.24692826e+01 23 7.45909283e+00 -4.29807035e+00 1.26062594e+01 24 1.43075198e+00 -4.49419377e+00 1.14673001e+01 25 -2.96067798e+01 -1.92421667e+00 1.38808582e+01 26 -6.23807101e+00 2.92320650e+01 -5.88377741e+00 27 4.45571425e-01 -2.21159948e+01 1.65314175e+01 28 -2.35898502e+01 1.76347690e+01 7.67520604e+00 29 4.20975284e-01 -1.44321496e+01 8.08814006e+00 30 1.56264072e+01 1.76432933e+01 3.25282495e+00 31 2.08593672e+01 -7.09321998e+00 1.53966355e+01 32 8.89165066e+00 1.95249545e+01 2.06036219e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ag (Configuration in file "config-T-Ag.xyz") ----------------------------------------------------------------------------------------------------- Energy = 392.05428216 Forces: 1 1.59711477e+01 -1.33316242e+01 3.14147822e+00 2 -1.47343706e+01 3.32505402e+00 1.25507227e+01 3 4.62521449e+00 5.70080564e+00 9.75301609e-01 4 1.20142009e+01 1.41959507e+01 9.82715271e+00 5 3.96798370e+00 -7.37396675e+00 -3.28510340e+00 6 -2.07979007e+01 2.08431021e+01 1.41127539e+00 7 -3.09881016e+00 -1.61695161e+01 -1.20222530e+01 8 -1.24042269e+01 -1.05007766e+01 5.70599955e+00 9 -1.18716757e+01 -2.66586975e+01 5.54820382e+00 10 1.29115694e+01 1.05592036e+01 -1.55078467e+00 11 2.02811491e+00 -1.36707024e+01 -9.07968420e+00 12 -1.14963301e+00 6.44758397e+00 1.94216459e+01 13 -7.02148010e+00 -6.61873012e+00 -2.34418166e+01 14 -1.26402324e+01 5.64436920e+00 -1.39918643e+01 15 2.11136689e+01 -7.89642184e+00 6.09215577e+00 16 -1.94633629e-01 2.00948210e+01 4.17802498e+00 17 4.57345091e+00 -1.62673720e+01 -6.67288742e+00 18 1.19137265e+01 1.06528498e+01 -2.03029105e+00 19 8.79424566e+00 3.09300080e+00 6.24269567e+00 20 1.26254773e+01 2.54667523e+01 -4.89681559e+00 21 -1.22481675e+01 1.89049037e+00 8.02636271e+00 22 -2.70562159e+00 2.75625855e+01 1.12254009e+01 23 -2.03749737e+01 -2.08061727e+01 -9.52981184e+00 24 1.19706020e+01 2.59227576e+00 -1.80031855e+01 25 -1.55007255e+01 -5.27388532e+00 1.35562510e+01 26 -3.83923302e+00 7.83676763e+00 -7.93045506e+00 27 9.80903041e+00 -2.48490047e+01 -1.03811047e+01 28 -2.21655558e+01 1.25648856e+01 -1.16335784e+01 29 4.62493369e-01 -1.46060113e+01 8.03035410e+00 30 2.99849393e+00 2.61073294e+00 5.48381599e+00 31 1.27026728e+01 -8.68262849e+00 6.46930506e+00 32 1.22651473e+01 1.16242789e+01 6.56348970e+00 MONOATOMIC STRUCTURE (pbc=False)-- Species = H (Configuration in file "config-F-H.xyz") ----------------------------------------------------------------------------------------------------- Energy = -7.69702332176 Forces: 1 -1.42352312e+00 -1.99467311e+00 -1.91097933e+00 2 3.37662144e+00 -2.33512497e+00 -2.04199016e+00 3 3.74981801e+00 -6.62570611e+00 -2.84994653e+00 4 -4.81083565e+00 2.96172237e+00 -2.83576783e+00 5 -7.38128653e+00 -2.09470053e+00 -6.05120579e+00 6 3.58486947e+00 7.01498372e-01 -1.56167536e+00 7 7.04275573e+00 -1.74648301e+00 6.68783238e+00 8 3.96119684e+00 5.39712236e+00 -1.08665668e+01 9 -5.49886706e+00 1.51761419e+00 -2.39377490e+00 10 3.65103196e+00 1.03452059e+00 -3.53698536e+00 11 5.34325247e+00 3.01673674e+00 -8.16934554e-01 12 -2.55921692e+00 1.13912777e+00 2.94511909e+00 13 -2.95639395e+00 7.65692945e-01 -1.46874226e+00 14 3.91301747e+00 1.60594503e+00 -4.02760463e+00 15 6.80818563e+00 -3.46397646e+00 -1.01045965e+00 16 -6.72111268e+00 5.00028747e+00 2.66942636e+00 17 -3.18033090e+00 -2.77761550e+00 4.25680958e+00 18 -5.32233627e+00 1.82376792e+00 7.63806007e+00 19 4.61942307e-01 -7.61820631e-01 -1.46946985e-01 20 -9.89538953e-01 -2.55521178e-01 1.45415791e+00 21 2.59135121e+00 -9.33193330e+00 7.43701264e+00 22 3.01409387e+00 3.11388009e-01 -2.43503887e+00 23 1.42716572e+00 -4.17152897e+00 1.97117065e+00 24 -2.92922038e+00 1.52265233e+00 1.48520331e+00 25 -4.49354363e+00 3.31775022e+00 2.39265790e+00 26 -9.42070697e-01 1.27570189e+00 -2.46284262e+00 27 2.39687367e+00 -1.98323797e+00 2.18462322e+00 28 -2.12659371e+00 1.54694763e+00 7.09177448e-02 29 -2.60845942e+00 2.97782456e+00 2.75042960e+00 30 7.27058118e-01 3.43734228e-01 -2.26761220e-01 31 2.61264108e+00 -9.43169299e-01 1.16287692e+00 32 -7.18545139e-01 2.22545642e+00 1.53792548e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = H (Configuration in file "config-T-H.xyz") ----------------------------------------------------------------------------------------------------- Energy = -21.7779232387 Forces: 1 -4.13565524e-01 -2.92823076e+00 -1.43594751e+00 2 2.75884961e+00 -1.27585247e+00 1.14923293e+00 3 5.49993618e+00 -2.60038390e+00 -3.55765769e+00 4 -4.75959106e+00 2.75707964e+00 -3.30434210e+00 5 -8.76249350e+00 -1.47457375e+00 -4.93447408e+00 6 4.17576046e+00 2.76480128e+00 4.33238638e+00 7 6.35103309e+00 8.00889358e-01 6.58731741e+00 8 4.24896392e+00 5.08786719e+00 -1.11048796e+01 9 -4.73264643e+00 2.24937676e+00 -1.09028847e+00 10 3.50856268e+00 2.24703832e+00 -1.77436621e+00 11 5.12334227e+00 3.31192849e+00 -1.06414301e+00 12 -3.73316207e+00 -3.07023949e+00 2.30042794e+00 13 -4.11986899e+00 3.06061477e+00 3.45937124e+00 14 4.51867328e+00 3.39739567e+00 -6.82697862e-01 15 6.19879136e+00 -3.12141636e+00 -1.34991627e+00 16 -7.49862662e+00 3.13256818e+00 3.17199718e+00 17 1.46773700e+00 -2.06024345e+00 3.62604346e+00 18 -5.46377063e+00 1.63881359e+00 7.92142669e+00 19 1.07037814e+00 -2.22354157e+00 -1.99446141e+00 20 1.15633922e+00 -2.45937169e-01 4.37553502e-01 21 4.07751339e+00 -7.32792676e+00 7.35405514e+00 22 -2.04568123e+00 1.81220930e+00 -2.89189187e+00 23 1.40600766e+00 -6.26742485e+00 -9.88275444e-01 24 -4.56608900e+00 -6.12637889e-01 -5.46854143e+00 25 -3.26217257e+00 4.32179216e+00 2.74158787e+00 26 -1.85474453e+00 -2.30399108e+00 -8.59448332e-01 27 2.37930555e+00 -2.38463839e+00 1.09203111e-01 28 3.93584617e+00 3.13025230e+00 2.24116863e+00 29 -2.33287648e+00 3.17388170e+00 3.01089642e+00 30 -3.90160291e+00 -2.05092155e+00 -2.94618973e+00 31 8.84795837e-01 -5.07691766e+00 -3.82606899e+00 32 -1.31494425e+00 2.13836840e+00 8.30922146e-01 MONOATOMIC STRUCTURE (pbc=False)-- Species = Pd (Configuration in file "config-F-Pd.xyz") ----------------------------------------------------------------------------------------------------- Energy = 65.1458528159 Forces: 1 -3.84062618e+00 -3.96990781e+00 -4.58409859e+00 2 -1.61427736e+00 -4.61183766e+00 -1.53116429e+01 3 1.77245763e+00 -1.49135186e+01 -3.63824933e+00 4 -1.91471980e+01 -3.21510464e+00 4.96710825e-01 5 1.76798490e+00 -8.41491362e+00 -8.22992632e+00 6 1.25230723e+01 -3.62630809e+00 -9.93343617e+00 7 7.46103881e+00 -1.15016138e+01 -3.32862367e+00 8 -1.63725471e+00 -4.44010055e+00 -4.52692883e+00 9 -1.22285557e+01 2.18723521e+00 -1.43812112e+01 10 1.45688597e+00 1.16639477e+01 -1.07469358e+01 11 3.54837214e+00 4.51203509e+00 3.01475791e+00 12 -1.20451566e+01 1.04472779e+01 -1.00547465e+00 13 1.09155905e+00 5.97407494e+00 -1.79863567e+01 14 3.14717617e+00 2.14456764e+00 -2.61647250e+00 15 1.81275529e+01 7.64520371e+00 -3.38190527e+00 16 9.70888543e-01 1.23981156e+01 1.90035791e+00 17 -1.09364467e+01 -9.50563092e+00 4.03655324e+00 18 -6.72691907e+00 -2.43544525e+00 -1.16283283e+01 19 -4.24700984e+00 -1.81108677e+01 1.25369013e+01 20 -1.61031500e+01 -6.31599382e+00 1.30128612e+01 21 3.89046900e+00 -2.06222760e+01 6.12295650e-01 22 1.95422209e+01 -6.47605581e+00 -7.57741036e-01 23 3.51652990e+00 -6.16113420e+00 5.94459761e+00 24 8.23097221e+00 -8.60982331e+00 2.49181440e+01 25 -2.06997960e+01 2.09877840e+00 -3.03074287e+00 26 2.37486411e+00 1.53794885e+01 -4.21340984e+00 27 -3.83578098e+00 8.51611916e+00 2.28215933e+01 28 -6.19888688e+00 7.06210616e+00 6.82716869e+00 29 3.94077734e+00 8.34397941e+00 -4.75577755e+00 30 1.09411398e+01 1.59258825e+01 -8.11272713e-01 31 1.25377581e+01 3.90874004e+00 1.59260825e+01 32 2.41933832e+00 1.47229798e+01 1.28205101e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Pd (Configuration in file "config-T-Pd.xyz") ----------------------------------------------------------------------------------------------------- Energy = 300.12067126 Forces: 1 -1.22138799e+00 2.36604826e+00 9.90627696e-01 2 3.88247826e-01 -1.83515930e+00 2.72404034e+00 3 8.72170437e+00 1.35318187e+00 -2.97922059e+00 4 3.70847086e-01 -6.96917018e+00 1.98517755e+00 5 7.13028861e+00 -1.24258458e+01 8.02626256e+00 6 -1.14186584e+00 -7.07818483e+00 -9.45526059e+00 7 1.27840175e+00 6.22682534e-01 -7.61266329e-01 8 -7.42931742e+00 -2.84423516e+00 -2.09151906e+00 9 -4.64452124e+00 5.18869546e+00 -1.00790449e+01 10 8.90148351e+00 2.37999678e+00 -6.57175780e+00 11 9.95801602e+00 3.44666872e+00 7.35259911e+00 12 -6.94526267e+00 -4.43087137e+00 4.76234824e-01 13 -5.91041784e-01 9.21103273e+00 -8.14139711e+00 14 -8.73494646e+00 -4.38610114e+00 -7.35469234e+00 15 6.13931889e-01 1.21820096e+01 3.95538864e-01 16 -6.22070439e+00 2.12052859e+00 3.23438223e+00 17 -1.10333855e+00 -1.23671435e+00 3.53711486e+00 18 -3.50253627e+00 4.33147425e-02 -1.59124570e+01 19 -7.83296917e+00 -1.28648630e+01 2.80125112e-01 20 -5.94454509e+00 -3.43117689e+00 7.08654501e+00 21 3.98133622e+00 -1.24159458e+01 -3.11038739e+00 22 3.86596315e-01 -5.85013736e+00 -9.07884871e-01 23 -7.72407132e+00 -4.36981328e+00 2.74498245e+00 24 9.30844208e+00 -2.76297629e+00 8.77614787e+00 25 -5.14137169e+00 3.42310365e+00 -6.37707589e+00 26 8.47201988e+00 -2.26098671e-01 -3.63036587e+00 27 -5.84600174e-01 9.71984426e+00 1.41994156e+01 28 2.95089045e+00 3.17751265e+00 3.79598924e+00 29 8.72444288e-01 7.42383583e+00 -7.47219841e+00 30 -2.03403942e+00 1.12631558e+01 -3.74904286e+00 31 3.46506903e-01 4.34387224e+00 1.24791858e+01 32 7.11536226e+00 4.86180970e+00 1.05092019e+01 MIXED STRUCTURE (pbc=False)-- Species = Ag H Pd (Configuration in file "config-F-AgHPd.xyz") ----------------------------------------------------------------------------------------------------- Energy = 0.836727212537 Forces: 1 -2.07837178e-01 1.85544983e-01 1.25293213e-01 2 -6.67001946e+00 3.56221175e+00 -8.79838466e+00 3 -5.40867066e+00 -6.77024935e+00 7.81526244e+00 4 -5.57573116e+00 -3.77922398e+00 -1.50591680e-01 5 1.19395788e+01 -7.14333426e+00 -3.00505385e+00 6 6.68572472e+00 -1.05124714e+01 -1.41385223e+01 7 2.08593277e-01 -1.56788060e+00 -3.93102525e-01 8 -2.39572993e+00 7.94988144e-01 -2.69447030e+00 9 -4.05833427e+00 6.58833061e-01 -4.43740267e+00 10 -2.56903679e+00 1.22910611e+01 -8.58843224e+00 11 -3.32773721e+00 -4.64813751e+00 8.31524634e-01 12 -7.41617969e+00 5.56813381e+00 -3.21963138e+00 13 7.17256344e+00 -2.49472706e+00 -5.76506789e-01 14 6.33008155e-01 1.62127366e+00 -4.95236265e-01 15 1.21732176e+00 7.79658075e+00 1.33726672e+01 16 4.71443215e+00 2.42306130e+00 -1.42905273e+00 17 -9.16449822e-01 -5.14420502e-01 -1.64294765e+00 18 3.02942851e+00 -7.88394864e+00 -5.79730440e-01 19 -1.95127839e+00 -4.28341749e-01 4.99825567e+00 20 -3.74745349e-01 4.97436540e-01 8.16968880e-01 21 3.28422471e+00 7.58745585e-02 -2.84319134e+00 22 2.41592809e+00 1.64704958e+00 3.31491318e+00 23 1.24413192e+01 -9.13410740e+00 -3.06559122e+00 24 -1.17898923e+01 4.53074712e+00 2.12393853e+00 25 -1.40681336e+01 -1.40582459e+01 -9.67581998e+00 26 9.03767640e+00 1.22670838e+01 -2.24630550e+00 27 -1.16909960e+00 -2.48491548e+00 1.36327004e+01 28 -7.37066480e+00 1.39680460e+01 2.16028896e+01 29 -7.29705904e+00 -8.02041783e+00 -7.35520772e+00 30 1.57747324e+01 2.23466777e+01 -1.35080773e+01 31 3.93707976e+00 -1.13532451e+01 1.86344643e+01 32 7.49877032e-02 5.59062978e-01 1.57438051e+00 MIXED STRUCTURE (pbc=True)-- Species = Ag H Pd (Configuration in file "config-T-AgHPd.xyz") ----------------------------------------------------------------------------------------------------- Energy = 120.154693802 Forces: 1 2.19669047e+00 9.70130590e-01 4.15121306e-01 2 -1.95245061e+01 -5.08987548e+00 9.79660923e+00 3 1.78990969e+00 1.45451666e+01 4.34463697e+00 4 1.17066326e+01 -1.05430114e+01 1.15808512e+01 5 4.71038805e+00 -8.50722391e+00 7.44562215e+00 6 -1.53684237e+01 -3.30935482e+01 -7.66519308e+00 7 4.02437631e-01 -8.93831945e-01 2.01918775e+00 8 -3.43397079e+00 9.11240140e-02 -7.65924213e-01 9 2.03973156e+01 1.54516626e+01 -4.23196036e+00 10 -2.31914179e+00 8.93513330e+00 -7.66079834e+00 11 -1.91411485e+00 -4.68243647e+00 2.40608059e+00 12 -9.97194408e+00 5.55919298e+00 2.45874284e-01 13 9.14954502e+00 1.64136387e-01 1.11749482e+01 14 -3.51101213e+00 2.75782306e+00 1.25782752e+01 15 -1.34823664e+01 9.29029177e+00 1.73056575e+01 16 6.92650926e+00 -2.17365720e+00 -8.84445612e-01 17 8.18411152e-01 1.31311157e+00 -4.12828898e+00 18 3.75057327e+00 -8.00001693e+00 -1.46821053e-01 19 -2.87660885e+00 1.01723223e+00 5.60103386e+00 20 2.60492731e+00 -1.51335762e-01 -3.19917434e+00 21 4.01079959e+00 2.56448895e+00 -2.63247639e+00 22 2.20694380e+00 -3.73984913e-01 1.93866709e+00 23 1.13741663e+01 2.64651161e+00 -1.46559545e+01 24 -3.41604742e+00 5.02574194e+00 -1.79949077e+01 25 1.38957621e+01 -2.47628753e+01 -1.21977059e+01 26 6.80777840e+00 3.56984797e+00 6.46973093e+00 27 -5.81976181e+00 1.43638930e+00 -9.93990275e+00 28 1.25869223e+01 1.53092148e+01 1.25739165e+01 29 -1.05526597e+01 -8.68067302e+00 -9.95096190e+00 30 -1.30479894e+01 3.17781082e+01 -2.06685213e+01 31 -8.85801250e+00 -1.73862475e+01 1.04307990e+01 32 -1.23915303e+00 1.91341018e+00 3.96024623e-01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==2745== Memcheck, a memory error detector ==2745== Copyright (C) 2002-2015, and GNU GPL'd, by Julian Seward et al. ==2745== Using Valgrind-3.11.0 and LibVEX; rerun with -h for copyright info ==2745== Command: python runner2.py EAM_Dynamo_Hale_Wong_pairMorse_PdAgH__MO_108983864770_004 ==2745== ==2745== ==2745== HEAP SUMMARY: ==2745== in use at exit: 4,110,439 bytes in 5,852 blocks ==2745== total heap usage: 65,921 allocs, 60,069 frees, 77,840,150 bytes allocated ==2745== ==2745== LEAK SUMMARY: ==2745== definitely lost: 0 bytes in 0 blocks ==2745== indirectly lost: 0 bytes in 0 blocks ==2745== possibly lost: 172,751 bytes in 105 blocks ==2745== still reachable: 3,937,688 bytes in 5,747 blocks ==2745== suppressed: 0 bytes in 0 blocks ==2745== Rerun with --leak-check=full to see details of leaked memory ==2745== ==2745== For counts of detected and suppressed errors, rerun with: -v ==2745== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 2433 from 125) ================================================================================ To pass this verification check the number of bytes that are "definitely lost" or "indirectly lost" must be zero. NOTE that Valgrind will typically report non-zero "possibly lost" bytes due to Python's internal memory allocation and garbage collection that it does not monitor. Full Valgrind output written to auxiliary file "valgrind.out" Grade: P Comment: No memory leak detected.