!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : Tersoff_LAMMPS_Erhart_Juslin_Goy_Nordlund_Mueller_Albe_ZnO__MO_616776018688_000 Supported species : O Zn random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = O (Configuration in file "config-F-O.xyz") ----------------------------------------------------------------------------------------------------- Energy = 0.000926607341691 Forces: 1 -8.21955760e-01 -2.61205032e+00 -3.69884876e+00 2 -2.98365726e+00 4.51376673e-01 -3.16328340e+00 3 1.83602085e+00 -3.91517164e+00 1.60594122e+00 4 -2.83690868e+00 3.14280803e+00 2.21314290e+00 5 9.46756486e-01 -1.12287974e+00 -4.93400293e-01 6 1.12091990e-01 -1.37715584e+00 -9.03456666e-01 7 3.45727598e+00 -1.46832202e+00 -4.03078980e+00 8 -2.59272787e+00 -1.37205193e+01 5.03258728e+00 9 -1.85351862e+00 5.94111134e-01 -2.76430092e+00 10 7.02199406e-01 1.49282678e+00 -2.59413285e-02 11 -3.01881585e-01 -7.90655200e-01 -7.23488018e-01 12 -1.81102723e+00 9.79520263e-01 -1.38864874e+00 13 -6.44575528e+00 4.86580126e+00 -1.76353248e+01 14 -1.56831168e-01 1.39492409e-01 -7.93068992e-02 15 1.44946625e+01 9.20684374e+00 5.38532351e+00 16 4.14816974e-01 4.02895173e+00 -2.43970432e+00 17 -8.54897407e-01 -9.66817019e-01 3.86923775e-01 18 7.32405582e-01 -7.32617008e-01 7.19801613e-01 19 1.89831769e+00 -9.40322238e-01 5.16241451e-01 20 -2.06939205e+00 1.27133396e+00 4.08958577e-01 21 -5.83959533e+00 -2.15585533e+00 3.38681572e+00 22 3.27478627e+00 -7.15057170e-01 8.31579723e-01 23 2.26151136e+00 2.00796281e-01 1.95486293e+00 24 -7.29519627e-01 -1.41264629e+00 7.96846515e-01 25 -9.56386774e-02 1.07130276e+00 3.05441593e+00 26 -3.03218395e-01 1.28851012e+00 2.68343333e+00 27 7.35813483e+00 -6.55715223e+00 2.32436740e-01 28 -8.47787009e+00 6.31326453e+00 6.09547494e-01 29 -2.33937658e+00 4.63811777e-01 3.24275087e+00 30 1.19207134e+00 1.53806321e+00 -2.26708049e-02 31 2.38266100e+00 9.83172059e-01 3.75672499e+00 32 -5.49940633e-01 4.55234615e-01 5.50830160e-01 MONOATOMIC STRUCTURE (pbc=True)-- Species = O (Configuration in file "config-T-O.xyz") ----------------------------------------------------------------------------------------------------- Energy = 26.5679384716 Forces: 1 -1.62441712e-01 -6.03062909e+00 -4.76258573e+00 2 -1.56623655e+00 3.86801914e+00 -1.39746264e+00 3 2.59960719e+00 -3.82004722e+00 2.94180827e+00 4 -4.35924692e-01 5.98082834e+00 4.01712653e+00 5 1.29532433e+00 -2.23099800e-01 -4.18434336e-01 6 -3.36011296e+00 1.73372134e+00 -1.31559127e+00 7 2.87589156e+00 -1.37063043e+00 -5.30802482e+00 8 -3.58537292e+00 -1.39261826e+01 5.69204296e+00 9 -4.60383548e+00 -4.28470993e+00 3.31900794e+00 10 2.58802962e+00 2.32579481e+00 1.20618768e+00 11 3.06778891e-01 -1.30063549e+00 -5.42446601e-02 12 7.64972540e-01 3.74032084e-01 -1.57501309e-01 13 -8.15728485e+00 3.80884101e+00 -1.58767209e+01 14 -4.56168660e-01 1.23000627e+00 -9.13715170e-01 15 1.31299572e+01 8.36146448e+00 5.99150953e+00 16 4.58635968e-02 1.77854757e+00 -1.72931792e+00 17 7.96666914e+00 -8.17996859e+00 6.87943450e-01 18 7.07902860e-01 -1.35845668e-01 4.38100398e-01 19 3.14213047e+00 -2.16250074e+00 -1.23508142e+00 20 -2.76066077e+00 5.76086439e+00 -1.17402291e+00 21 -9.02024785e+00 -4.44365630e-01 2.86771779e+00 22 -4.87720713e+00 8.89544991e+00 1.35793960e+00 23 2.60266472e+00 -1.31319416e+00 4.54073809e+00 24 -9.78678574e-01 -3.00472317e-01 -5.38616305e-01 25 1.39197386e+00 -7.74953329e-01 2.87028150e+00 26 -1.38348454e+00 5.51943592e-01 2.31541523e+00 27 1.25747102e+01 -1.18187868e+01 -5.03745503e+00 28 -1.11863218e+01 1.02805895e+01 -4.30901577e+00 29 -3.20977051e+00 -2.64922771e-01 2.70657635e+00 30 1.17543306e+00 1.99716451e+00 -1.26058756e-01 31 3.17694788e+00 -1.17872387e+00 3.66029498e+00 32 -6.01108216e-01 5.82401553e-01 -2.58841310e-01 MONOATOMIC STRUCTURE (pbc=False)-- Species = Zn (Configuration in file "config-F-Zn.xyz") ----------------------------------------------------------------------------------------------------- Energy = 135.168602647 Forces: 1 -3.12147534e+00 -3.19536058e+00 -3.29985688e+00 2 -3.26586622e+01 1.95209444e+01 -2.91797109e+01 3 -3.76967969e+01 -2.71936961e+01 3.51307581e+01 4 -2.32751067e+01 2.01752993e-01 -1.73280666e+01 5 5.25523428e+01 -2.25608353e+01 -4.46069511e+01 6 8.03194727e+00 -3.06302221e+00 -4.93571241e+00 7 9.26396929e+00 -9.78630667e+00 -1.03597391e+01 8 1.29978937e+01 3.68243250e+00 1.86712858e+01 9 -1.47124414e+01 -1.11071532e+01 -7.28213097e+00 10 1.20252410e+01 1.31620828e+01 -4.17877367e+00 11 6.42170936e+00 2.17185312e+01 -1.46682563e+01 12 -6.82141517e+00 1.05734963e+01 -3.76381063e+00 13 -7.31476533e+00 5.65051747e+00 -1.17758583e+01 14 7.30564389e+00 6.98640165e+00 -9.73583430e-01 15 1.63682947e+01 9.15280124e+00 -1.36129462e+01 16 6.08276212e+00 1.16479401e+01 -1.32684953e+01 17 -9.89434608e+00 -1.80744798e+01 4.26844280e+00 18 1.28533920e+01 -1.03730771e+01 1.69724348e+01 19 3.50773662e+00 -6.71693737e+00 4.88732664e+00 20 -1.05510550e+01 6.89017634e-01 7.52818874e+00 21 -8.00654985e+00 -1.39593041e+01 -6.38437202e+00 22 3.19136363e+01 1.14672258e+01 -1.43367676e+01 23 5.85138594e+01 -8.52426179e+01 2.73419943e+01 24 -7.31680342e+01 7.02749536e+01 2.68733331e+01 25 -1.42841649e+01 -1.54399471e+01 -4.19762891e+00 26 -3.93458783e+00 1.43539259e+01 7.72919214e+00 27 1.78280133e+00 3.50571565e+00 1.53401722e+01 28 -5.76103399e+00 1.38506945e+01 1.87051196e+01 29 2.07246903e+00 -7.19108974e-01 9.92992502e+00 30 4.92136588e+00 8.51454290e+00 1.54467998e+00 31 1.35088936e+01 -9.46248656e+00 3.98431186e+00 32 -8.92352332e+00 1.19413562e+01 5.24549510e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Zn (Configuration in file "config-T-Zn.xyz") ----------------------------------------------------------------------------------------------------- Energy = 252.848258246 Forces: 1 -2.59666590e+00 1.49186102e+01 -1.20920520e+01 2 -3.04328330e+01 1.69759346e+01 -1.88271401e+01 3 -3.60814510e+01 -6.61971362e+00 4.16462368e+01 4 9.02501299e+00 1.40876861e+01 -1.87890244e+01 5 5.51562119e+01 -1.99218420e+01 -4.21940347e+01 6 -3.27896489e+00 -8.80231735e+00 7.08338437e+00 7 -2.81624781e+01 -1.67829625e+01 -1.70902214e+01 8 1.24914363e+01 3.97990269e+00 1.93130854e+01 9 2.29024922e+00 -1.71073288e+01 1.01123053e+01 10 1.79361537e+01 -8.75171407e+00 -3.48327159e+00 11 8.80188983e+00 2.13122759e+01 -1.41643701e+01 12 9.90258077e+00 -1.18105871e+01 -1.54609273e+01 13 -1.40589108e+01 -5.17866406e-01 2.13419338e+00 14 -7.00062126e+00 2.22981511e+01 2.40715367e+01 15 5.81239769e+00 9.59202331e+00 -1.43127906e+01 16 1.06923577e+01 -3.48737988e+00 -1.45078601e+01 17 1.55009760e+01 -2.51136531e+00 1.94304739e+01 18 1.38819269e+01 -8.92159374e+00 1.62791893e+01 19 6.26647208e+00 1.14884696e+01 1.99494586e+00 20 3.59373975e+00 2.34902568e-01 4.89329494e+00 21 -6.48297153e+00 1.47730004e+00 -5.95790765e+00 22 1.43801446e+01 2.12343405e+01 -1.49693155e+01 23 5.58379372e+01 -8.27759085e+01 2.85488083e+01 24 -7.57823049e+01 7.37045735e+01 2.23292157e+01 25 1.97821599e+00 -2.39705435e+01 -3.69818612e+00 26 -4.93132045e+00 -2.64477740e+00 1.52548127e+00 27 2.81275303e+00 7.11518391e+00 3.08302984e+00 28 8.44895414e+00 2.04245513e+01 7.10871302e+00 29 1.62542897e+00 -1.32847222e+00 9.35603866e+00 30 -2.95887779e+01 -1.47925184e+00 7.17351532e+00 31 -1.63981945e+00 -3.02894442e+01 -2.63944162e+01 32 -1.63977194e+01 8.87916307e+00 -4.14193053e+00 MIXED STRUCTURE (pbc=False)-- Species = O Zn (Configuration in file "config-F-OZn.xyz") ----------------------------------------------------------------------------------------------------- Energy = 478.789885612 Forces: 1 -1.81318656e+01 -1.15443241e+01 -3.33096983e+01 2 1.03447953e+01 1.46141200e+01 -2.46373980e+01 3 1.02681111e+01 -4.75241256e+01 1.21094459e+00 4 -3.62934082e+01 3.27739305e+01 8.56601430e+00 5 -3.94844708e+01 -2.11685053e+01 -4.63765665e+01 6 -4.54814395e-01 1.62597740e+01 -3.88133264e+01 7 7.24082004e+01 -4.38805537e+01 3.04580449e+01 8 1.11131063e+01 1.08284110e+02 -1.71474023e+02 9 -3.03645671e+01 -4.76250916e+01 -3.81265156e+01 10 -1.88580147e+01 9.01889556e+01 -3.88776287e+01 11 -3.42855031e+01 -5.10898090e+01 -2.93551652e+01 12 -1.94603504e+01 4.86743939e+01 2.12368201e+01 13 2.75071981e+01 -6.33499497e+01 -3.86431760e+01 14 7.19665374e+00 1.33996371e+01 -7.79826079e+00 15 5.88824502e+01 -1.33898765e+01 -6.22657339e+01 16 2.02376658e+01 4.59715820e+01 2.92522925e+01 17 -1.15144808e+01 -3.06717451e+01 8.83732191e+00 18 -9.85954244e+01 4.27462814e+01 -1.39276174e+01 19 1.13579008e+01 -1.84735477e+01 1.46784214e+01 20 -2.22689105e+01 4.67497663e+00 1.59237814e+01 21 3.01639976e+01 -2.00125623e+02 1.62362753e+02 22 7.07442596e+01 -3.06635260e+01 2.54602353e+01 23 2.55651802e+01 -1.93700804e+01 2.44291700e+01 24 -2.23034612e+01 -1.84301935e+01 4.40595792e+01 25 -2.62323728e+01 -2.10803138e+01 -1.13811677e+01 26 6.57107093e+00 5.02028994e+01 3.37090448e+01 27 1.53941470e+01 1.16017627e+01 3.07118421e+01 28 -4.17042528e+00 1.07140388e+01 1.49765929e+01 29 -3.39923808e+01 1.12195279e+02 4.63848376e+01 30 -1.78911252e+00 2.65999118e+01 1.89741788e+00 31 4.75606511e+01 -2.06469292e+00 3.82075051e+01 32 -7.11582541e+00 1.15503056e+01 2.62365832e+00 MIXED STRUCTURE (pbc=True)-- Species = O Zn (Configuration in file "config-T-OZn.xyz") ----------------------------------------------------------------------------------------------------- Energy = 1162.72436184 Forces: 1 3.34459443e+01 9.33952597e+01 -2.21720384e+01 2 -2.13399729e+01 3.07529843e+01 4.81130433e+01 3 2.73464966e+01 7.37776660e+01 3.00107685e+00 4 8.31198441e+01 1.23665737e+02 1.46274437e+00 5 -8.86207591e+01 6.76497738e+01 -4.58511560e+01 6 3.31980303e+01 4.99711013e+01 9.20172641e+00 7 -3.74603696e+01 -1.54365826e+02 1.10286183e+02 8 1.78888249e+00 1.29232020e+02 -1.85637419e+02 9 -1.25803536e+01 -2.47152928e+02 4.76337290e+01 10 -1.67841494e+01 8.91027807e+00 -4.91416460e+01 11 -1.97568882e+01 -6.41655221e+01 -2.79864505e+01 12 -2.67132676e+01 3.95896979e+01 5.00803258e+01 13 7.44592539e+01 -8.75176751e+01 1.27530735e+02 14 -5.87018863e+01 5.25337767e+01 -2.85109440e+00 15 2.65594951e+01 -4.28768148e+01 -5.76653993e+01 16 1.86166333e+01 -1.81551770e+01 8.58442322e+01 17 -9.60216837e+00 -7.23453345e+01 3.10753447e+00 18 -9.76827126e+01 5.60979358e+01 -2.10885119e+01 19 2.39802273e+01 -3.87526162e+01 -4.60871107e+01 20 -2.85393773e+00 3.89874981e+01 1.06711528e+01 21 3.84511348e+01 -2.06358650e+02 1.83146332e+02 22 5.35700322e+01 3.40505184e-01 2.27470410e+01 23 -1.35814061e+00 -8.38955511e+01 -3.18223058e+01 24 -5.09741480e+01 -1.52015557e+01 -4.90433970e+01 25 1.66686299e+01 -4.68839663e+01 -2.42399728e+01 26 1.40988720e+01 3.99124806e+01 3.68272842e+01 27 -1.79640956e+01 1.51337837e+01 -1.12619034e+02 28 4.01544179e+01 1.02806519e+02 -8.00569246e+01 29 -3.87824645e+01 1.18625404e+02 3.26568360e+01 30 -7.11381808e+00 4.71200585e+01 -3.27496133e+00 31 2.93897379e+01 -2.62640272e+01 2.44880068e+01 32 -6.55849984e+00 1.54331643e+01 -3.72605610e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==24350== Memcheck, a memory error detector ==24350== Copyright (C) 2002-2015, and GNU GPL'd, by Julian Seward et al. ==24350== Using Valgrind-3.11.0 and LibVEX; rerun with -h for copyright info ==24350== Command: python runner2.py Tersoff_LAMMPS_Erhart_Juslin_Goy_Nordlund_Mueller_Albe_ZnO__MO_616776018688_000 ==24350== ==24350== Warning: set address range perms: large range [0x20fe9000, 0x314e9000) (defined) ==24350== Warning: set address range perms: large range [0x2122d000, 0x314e9000) (defined) ==24350== Warning: set address range perms: large range [0x20fe9000, 0x314e9000) (noaccess) ==24350== Warning: set address range perms: large range [0x23029000, 0x33529000) (defined) ==24350== Warning: set address range perms: large range [0x2326d000, 0x33529000) (defined) ==24350== Warning: set address range perms: large range [0x23029000, 0x33529000) (noaccess) ==24350== Warning: set address range perms: large range [0x23029000, 0x33529000) (defined) ==24350== Warning: set address range perms: large range [0x2326d000, 0x33529000) (defined) ==24350== Warning: set address range perms: large range [0x23029000, 0x33529000) (noaccess) ==24350== Warning: set address range perms: large range [0x23029000, 0x33529000) (defined) ==24350== Warning: set address range perms: large range [0x2326d000, 0x33529000) (defined) ==24350== Warning: set address range perms: large range [0x23029000, 0x33529000) (noaccess) ==24350== Warning: set address range perms: large range [0x23429000, 0x33929000) (defined) ==24350== Warning: set address range perms: large range [0x2366d000, 0x33929000) (defined) ==24350== Warning: set address range perms: large range [0x23429000, 0x33929000) (noaccess) ==24350== Warning: set address range perms: large range [0x23429000, 0x33929000) (defined) ==24350== Warning: set address range perms: large range [0x2366d000, 0x33929000) (defined) ==24350== Warning: set address range perms: large range [0x23429000, 0x33929000) (noaccess) ==24350== Warning: set address range perms: large range [0x23429000, 0x33929000) (defined) ==24350== Warning: set address range perms: large range [0x2366d000, 0x33929000) (defined) ==24350== Warning: set address range perms: large range [0x23429000, 0x33929000) (noaccess) ==24350== ==24350== HEAP SUMMARY: ==24350== in use at exit: 4,040,223 bytes in 5,778 blocks ==24350== total heap usage: 150,714 allocs, 144,936 frees, 59,329,102 bytes allocated ==24350== ==24350== LEAK SUMMARY: ==24350== definitely lost: 0 bytes in 0 blocks ==24350== indirectly lost: 0 bytes in 0 blocks ==24350== possibly lost: 162,822 bytes in 96 blocks ==24350== still reachable: 3,877,401 bytes in 5,682 blocks ==24350== suppressed: 0 bytes in 0 blocks ==24350== Rerun with --leak-check=full to see details of leaked memory ==24350== ==24350== For counts of detected and suppressed errors, rerun with: -v ==24350== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 2414 from 156) ================================================================================ 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.