!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_pairHybrid_PdAgH__MO_104806802344_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 -7.72171666e+00 -1.67216718e+01 -1.43946995e+01 2 -5.59006791e+00 7.23722586e+00 -1.60200034e+01 3 5.51173979e+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 1.28914401e+01 2.57427321e+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 -8.98308267e+00 -5.48383210e+00 -4.02712957e+01 14 1.22771827e+01 1.50460149e+01 -1.26466477e+01 15 3.70568161e+01 -8.06709139e+00 5.13746443e+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 -4.29807034e+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 4.45571428e-01 -2.21159948e+01 1.65314175e+01 28 -2.35898501e+01 1.76347690e+01 7.67520603e+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 = -17.4318484102 Forces: 1 -9.17255946e-02 2.04366322e-01 2.04512959e-01 2 -3.78832226e+00 3.52284628e+00 -6.69685909e+00 3 -3.29595434e+00 -5.99704981e+00 5.69542321e+00 4 -5.63558022e+00 -3.78208300e+00 -2.50576506e-01 5 7.04834614e+00 -5.05205496e+00 -2.42632882e+00 6 5.02213281e+00 -4.97157210e+00 -6.17091966e+00 7 5.15641147e-01 -1.69072966e+00 -1.52580935e-01 8 -2.04622283e+00 1.09408485e-01 -2.71640198e+00 9 -2.79210518e+00 1.49046902e-01 -4.40734760e+00 10 -2.98851634e-01 5.31002879e+00 -3.88785023e+00 11 -1.51348032e+00 9.97018626e-02 -6.95380814e-01 12 -5.07805063e+00 4.49288394e+00 8.10650679e-02 13 -1.89345543e+00 -2.05706539e+00 -3.33057329e+00 14 2.58505211e+00 4.14216228e+00 -1.12151818e+00 15 5.38557133e+00 1.63725015e+00 6.72792605e+00 16 1.26952376e+00 1.35908566e+00 -2.44057905e+00 17 -1.57638393e-01 1.14668205e-01 -7.85469331e-01 18 1.34492908e+00 -6.52056744e+00 -2.74302609e-01 19 -8.10468487e-01 4.43238896e-03 1.58195799e+00 20 -9.71579975e-01 -4.39813180e-01 3.57382666e-01 21 1.04730782e+00 -1.07609877e+00 -9.58187044e-02 22 2.70665743e+00 1.31279552e+00 3.28473708e+00 23 4.34955573e+00 -3.98200538e+00 -1.59795252e+00 24 -4.24586480e+00 -1.14862293e+00 2.34196496e+00 25 -1.28618899e+01 -1.39053248e+01 -1.36360938e+01 26 8.03571364e+00 1.09130492e+01 -5.38715516e+00 27 3.76255272e+00 -5.24806429e+00 1.12941882e+01 28 -8.60436116e+00 1.63768422e+01 2.05825200e+01 29 -4.39118853e+00 -2.32295912e+00 -4.20832116e+00 30 9.79411528e+00 1.11121481e+01 -4.56833035e+00 31 6.19195776e+00 -3.44380319e+00 1.06599056e+01 32 -5.82317029e-01 7.77097768e-01 2.03877599e+00 MIXED STRUCTURE (pbc=True)-- Species = Ag H Pd (Configuration in file "config-T-AgHPd.xyz") ----------------------------------------------------------------------------------------------------- Energy = 100.231422891 Forces: 1 6.67274729e-01 3.69337427e-01 3.86734458e-01 2 -8.81516126e+00 -5.93722804e+00 5.99608088e+00 3 1.85921608e+00 1.16183632e+01 3.65702954e+00 4 5.61006519e+00 -1.03294056e+01 7.08705868e+00 5 4.23673937e-01 -4.78366074e+00 7.36529104e+00 6 -1.59709993e+00 -1.32946116e+01 1.52382978e+00 7 -5.61266390e-01 -1.10689978e+00 5.47725347e-01 8 -3.03777624e+00 -6.21356008e-01 -7.39972246e-01 9 1.07922209e+01 4.41406446e+00 -1.83651708e+00 10 3.62029255e-01 1.43139894e+00 -4.44950373e+00 11 -2.45960090e-01 6.02449132e-01 3.99592788e-01 12 -5.05318758e+00 5.05923641e+00 2.79368404e+00 13 -6.80385071e+00 1.48669755e-01 7.09975380e+00 14 8.23142517e-01 1.24766100e+00 1.10326318e+01 15 -8.69793928e+00 2.78244984e+00 1.26501725e+01 16 2.66751328e+00 -3.12374265e+00 -2.97952819e+00 17 2.03651744e+00 -6.54839298e-03 9.74172475e-01 18 1.92271049e+00 -6.67399668e+00 8.08950899e-02 19 -1.89359926e-01 1.85298225e+00 1.70056027e+00 20 2.73839459e+00 -1.94266648e+00 -4.14150135e+00 21 1.18674686e+00 2.85031772e+00 1.69454648e+00 22 1.87291971e+00 -2.35674218e-01 1.83494674e+00 23 6.28994252e+00 7.15226067e+00 -1.30100959e+01 24 -2.67202491e+00 5.42078819e-01 -1.39121985e+01 25 1.29977014e+01 -2.46735140e+01 -1.55846731e+01 26 5.59188619e+00 2.80145145e+00 3.27441606e+00 27 1.57059111e+00 -1.29713290e+00 -6.81364188e+00 28 8.78505495e+00 1.79821268e+01 1.49695195e+01 29 -7.93567157e+00 -2.98694329e+00 -7.18196168e+00 30 -1.73814491e+01 2.15100136e+01 -1.30458748e+01 31 -2.07503349e+00 -7.88028968e+00 -3.49040336e-01 32 -3.13182072e+00 2.52880862e+00 -1.02413260e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==32061== Memcheck, a memory error detector ==32061== Copyright (C) 2002-2015, and GNU GPL'd, by Julian Seward et al. ==32061== Using Valgrind-3.11.0 and LibVEX; rerun with -h for copyright info ==32061== Command: python runner2.py EAM_Dynamo_Hale_Wong_pairHybrid_PdAgH__MO_104806802344_004 ==32061== ==32061== ==32061== HEAP SUMMARY: ==32061== in use at exit: 4,109,935 bytes in 5,851 blocks ==32061== total heap usage: 65,633 allocs, 59,782 frees, 77,802,143 bytes allocated ==32061== ==32061== LEAK SUMMARY: ==32061== definitely lost: 0 bytes in 0 blocks ==32061== indirectly lost: 0 bytes in 0 blocks ==32061== possibly lost: 172,751 bytes in 105 blocks ==32061== still reachable: 3,937,184 bytes in 5,746 blocks ==32061== suppressed: 0 bytes in 0 blocks ==32061== Rerun with --leak-check=full to see details of leaked memory ==32061== ==32061== For counts of detected and suppressed errors, rerun with: -v ==32061== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 2449 from 133) ================================================================================ 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.