!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_Tersoff_PRB39_1989_CSi__MO_171585019474_001 Supported species : C Si random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = C (Configuration in file "config-F-C.xyz") ----------------------------------------------------------------------------------------------------- Energy = 3570.26251664 Forces: 1 -1.25206729e+02 -2.12517132e+02 -2.90959734e+02 2 -8.61262690e+01 7.91379388e+01 -3.05647352e+02 3 3.89700180e+01 -3.48769336e+02 -8.95578518e+01 4 -2.77523125e+02 1.57398309e+02 1.71647035e+01 5 -1.12675160e+01 -3.79505368e+02 -8.76232798e+01 6 1.49689151e+02 -6.54642281e+01 -1.56031061e+02 7 -1.08131735e+02 -2.23899833e+02 -8.18816265e+01 8 2.72823955e+02 -5.21325755e+02 -1.88012735e+01 9 -1.59042695e+02 -7.15983108e+01 -4.03268360e+02 10 -3.38360686e+01 4.04047219e+02 -5.12201261e+02 11 -2.41232219e+02 -4.17759322e+02 -1.01023011e+02 12 -3.58215444e+02 2.87073212e+02 -3.35732291e+00 13 -2.32094690e+02 -5.84038769e+00 -9.96420633e+02 14 1.95439009e+02 2.08437471e+02 -1.67363755e+02 15 7.15126989e+02 5.47731822e+02 3.32260340e+02 16 2.79804436e+02 4.70525221e+02 -2.10273505e+01 17 -4.71855632e+02 -2.93315756e+02 -6.16149899e+01 18 1.23549959e+02 1.68526915e+02 6.15550242e+00 19 2.63746804e+02 -2.91358105e+02 2.35285328e+02 20 -1.38740743e+02 2.07935628e+02 3.39178310e+02 21 -5.10163026e+01 -3.41229758e+02 2.59474460e+02 22 4.06663246e+02 -7.24711145e+00 6.82228023e+01 23 1.95678813e+02 -8.22367013e+01 1.81620338e+02 24 -5.71179850e+01 -4.47275193e+01 2.22625068e+02 25 -4.66752267e+02 -7.96525089e+01 6.53667990e+00 26 -1.24261671e+02 5.14273856e+02 2.72548575e+02 27 3.41797191e+02 -4.27860458e+02 2.38061479e+02 28 -7.33692537e+02 5.37654899e+02 2.46827283e+02 29 -7.01042206e+01 -1.71289219e+02 2.29003339e+02 30 3.47479329e+02 3.53660071e+02 -4.16248232e+01 31 3.04655069e+02 -1.78690416e+02 3.73693211e+02 32 1.10793880e+02 2.27884666e+02 3.09746267e+02 MONOATOMIC STRUCTURE (pbc=True)-- Species = C (Configuration in file "config-T-C.xyz") ----------------------------------------------------------------------------------------------------- Energy = 3570.26251664 Forces: 1 -1.25206729e+02 -2.12517132e+02 -2.90959734e+02 2 -8.61262690e+01 7.91379388e+01 -3.05647352e+02 3 3.89700180e+01 -3.48769336e+02 -8.95578518e+01 4 -2.77523125e+02 1.57398309e+02 1.71647035e+01 5 -1.12675160e+01 -3.79505368e+02 -8.76232798e+01 6 1.49689151e+02 -6.54642281e+01 -1.56031061e+02 7 -1.08131735e+02 -2.23899833e+02 -8.18816265e+01 8 2.72823955e+02 -5.21325755e+02 -1.88012735e+01 9 -1.59042695e+02 -7.15983108e+01 -4.03268360e+02 10 -3.38360686e+01 4.04047219e+02 -5.12201261e+02 11 -2.41232219e+02 -4.17759322e+02 -1.01023011e+02 12 -3.58215444e+02 2.87073212e+02 -3.35732291e+00 13 -2.32094690e+02 -5.84038769e+00 -9.96420633e+02 14 1.95439009e+02 2.08437471e+02 -1.67363755e+02 15 7.15126989e+02 5.47731822e+02 3.32260340e+02 16 2.79804436e+02 4.70525221e+02 -2.10273505e+01 17 -4.71855632e+02 -2.93315756e+02 -6.16149899e+01 18 1.23549959e+02 1.68526915e+02 6.15550242e+00 19 2.63746804e+02 -2.91358105e+02 2.35285328e+02 20 -1.38740743e+02 2.07935628e+02 3.39178310e+02 21 -5.10163026e+01 -3.41229758e+02 2.59474460e+02 22 4.06663246e+02 -7.24711145e+00 6.82228023e+01 23 1.95678813e+02 -8.22367013e+01 1.81620338e+02 24 -5.71179850e+01 -4.47275193e+01 2.22625068e+02 25 -4.66752267e+02 -7.96525089e+01 6.53667990e+00 26 -1.24261671e+02 5.14273856e+02 2.72548575e+02 27 3.41797191e+02 -4.27860458e+02 2.38061479e+02 28 -7.33692537e+02 5.37654899e+02 2.46827283e+02 29 -7.01042206e+01 -1.71289219e+02 2.29003339e+02 30 3.47479329e+02 3.53660071e+02 -4.16248232e+01 31 3.04655069e+02 -1.78690416e+02 3.73693211e+02 32 1.10793880e+02 2.27884666e+02 3.09746267e+02 MONOATOMIC STRUCTURE (pbc=False)-- Species = Si (Configuration in file "config-F-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 205.161263861 Forces: 1 -3.39656730e+01 -1.50127382e+01 -3.26705555e+01 2 -2.30879515e+01 7.23333677e+00 -5.79257151e+01 3 7.57622288e+00 -3.77880231e+01 3.49042680e+01 4 -2.78940534e+01 -2.41101393e+01 -2.00737183e+01 5 1.97939903e+01 -3.03611032e+01 -2.06958244e+01 6 3.33108008e+01 -1.37102130e+01 -1.96402669e+01 7 1.98761644e+01 -4.38902574e+01 -2.87811286e+01 8 1.12493965e+01 7.08542908e+00 1.06675860e+01 9 -7.37606836e+00 2.88134410e+00 -1.93918772e+01 10 -7.06560911e+00 1.54600937e+01 -1.76321142e+01 11 5.31680095e-01 3.67703970e+01 -9.59637705e+00 12 -1.03383887e+01 3.29544709e+01 -2.36456353e+00 13 -5.44500455e-01 1.28824829e+01 -2.66723279e+01 14 5.48352845e+00 1.29787454e+01 -8.64569520e+00 15 1.89085543e+01 9.46496980e+00 1.41332338e+01 16 2.08394064e+01 2.13037487e+01 -1.82362167e+01 17 -9.44676058e+00 -1.17117050e+01 7.43343302e+00 18 -8.00125427e+00 -1.42135382e+01 2.84742190e+01 19 -8.28782515e+00 -1.18114135e+01 9.68456459e+00 20 -1.71623117e+01 2.84141142e+00 1.31354320e+01 21 -1.94697395e+01 -3.39581499e+01 8.76988260e+00 22 2.96964608e+01 3.02697748e+01 1.51727457e+01 23 1.42473243e+01 -9.14597065e+00 2.39450874e+01 24 1.01595649e+01 -3.24873395e+01 4.65981767e+01 25 -2.82188238e+01 8.40570006e+00 3.43537639e+01 26 -4.50829765e+01 2.56895644e+01 -1.62403898e+01 27 -5.44616313e+01 -2.14167695e+01 5.06084365e+01 28 -9.62569412e+00 4.42040517e+00 3.91260688e+00 29 1.43298191e+01 -1.53689490e+01 -5.67421655e+01 30 5.57752183e+01 3.48482580e+01 -3.21203115e+01 31 4.01084035e+01 -1.18085704e+01 2.79259794e+01 32 8.14272620e+00 6.13047477e+01 5.77098318e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Si (Configuration in file "config-T-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 528.017287643 Forces: 1 -3.72100870e+01 -4.89644335e+00 -2.53295532e+01 2 -2.50292246e+01 4.12363406e+01 -1.66225775e+01 3 9.72532486e+00 -9.17843003e+00 3.80923662e+01 4 5.01027887e+01 -3.87765204e+01 -3.78381565e+00 5 2.27262695e+01 1.68013511e+01 -6.77000661e+00 6 -1.91951597e+01 -1.92174336e+01 -3.72127634e+01 7 -1.31783885e+00 -2.94632058e+01 -3.92895053e+01 8 6.01855588e+00 8.58731569e+00 1.24024621e+01 9 3.76156928e+01 -7.97200424e+00 1.28393838e+00 10 -1.66958549e+01 1.04208761e+00 3.90894111e+01 11 4.68272153e+00 3.36793933e+01 -6.45245257e+00 12 1.40025548e+00 1.70808708e+01 1.15869542e+00 13 -9.65689697e+00 8.85758014e+00 3.16312456e+01 14 1.19826663e+01 -8.52854329e+00 6.55072196e+00 15 -5.53524316e+01 2.33652295e+01 -4.87462954e-01 16 2.51287488e+01 -4.85698859e+00 -1.25268156e+01 17 4.89858932e+01 -2.25952203e+01 1.97502919e+01 18 -2.97741928e+00 -1.37657805e+01 2.65348851e+01 19 -1.50086294e+01 -3.83206831e+00 -4.24940385e+01 20 4.53416475e+00 1.28247951e+01 7.95171090e+00 21 -3.06757238e+01 -5.79274494e+00 7.24763467e+00 22 -2.85722522e+01 4.17310654e+01 1.84944125e+01 23 -1.15334819e+00 -1.02812767e+01 2.32238809e+01 24 1.04322343e+01 -3.93518107e+01 1.76154120e+01 25 2.37543808e+01 2.71021458e+01 7.11301482e+01 26 -4.83104394e+01 1.51869410e+01 -2.54617995e+01 27 -6.58148536e+01 -6.52554976e+01 -3.69462052e+00 28 8.20330188e+00 3.81319993e+00 -1.74053252e+01 29 1.18614248e+01 -1.66668778e+01 -7.16368846e+01 30 4.22860321e+01 8.21578367e+00 -4.37432299e+01 31 2.22870266e+01 -1.19458432e+01 -1.11468403e+01 32 1.52426772e+01 5.28525897e+01 4.19004745e+01 MIXED STRUCTURE (pbc=False)-- Species = C Si (Configuration in file "config-F-CSi.xyz") ----------------------------------------------------------------------------------------------------- Energy = -32.7326803745 Forces: 1 -2.87871439e+00 -1.75286371e+01 -1.10223929e+01 2 2.80457792e+00 2.44185304e+00 -1.30461636e+01 3 -8.80261235e+00 -1.07867256e+01 -2.08662827e+01 4 -1.45737792e+01 1.48013185e+01 8.14145309e+00 5 -2.28656491e+00 5.27131170e-01 -1.70728838e+00 6 -4.21607609e+00 2.38846994e-01 1.07210464e+00 7 5.64714969e+00 1.69653836e+00 -1.82714293e-01 8 1.34780617e+01 -1.86608915e+00 7.82258907e-01 9 2.53194912e+00 1.70274297e-01 -1.96039438e+00 10 -7.53413157e+00 3.97996375e+00 -9.32730004e+00 11 -2.58875504e+01 -4.03356711e+00 1.50473144e+01 12 -2.97094401e+00 2.63706720e+00 7.40269947e+00 13 1.01500781e+01 -1.29030713e+01 -3.48664965e+01 14 1.38719379e+01 3.61210081e+00 -8.88025855e+00 15 4.45711484e+00 -6.59923068e+00 4.44531741e+00 16 1.89484536e+00 2.44345819e+01 2.04800284e+01 17 -1.02268334e+01 -7.54583366e+00 -3.73108048e+00 18 -4.44921213e+00 1.15494667e+01 3.09389388e+00 19 -2.73359346e+00 -4.68664859e+00 8.19255410e+00 20 -5.74438254e+00 1.07261078e+01 2.88246123e+00 21 1.88794697e+01 -1.34117635e+01 8.94401739e+00 22 4.64878278e+00 1.72599849e+00 -3.88761774e+00 23 8.86124045e+00 -7.65351242e+00 4.69694649e+00 24 4.84717719e+00 6.37784714e+00 1.03923978e+01 25 -2.77271314e+01 -1.60723279e+01 -3.60448993e+00 26 1.15495193e+01 1.11002741e+01 -4.75593718e+00 27 7.64305384e+00 4.50487399e+00 1.63983505e+01 28 -1.92717640e+00 1.21757544e+00 4.76082271e-01 29 1.04593518e+01 2.94626198e+00 4.95196146e+00 30 -2.28822586e+00 -1.14957050e+01 5.06622601e+00 31 2.51352024e+00 9.75906466e+00 -5.23816510e+00 32 9.09816096e-03 1.35965770e-01 6.10514207e-01 MIXED STRUCTURE (pbc=True)-- Species = C Si (Configuration in file "config-T-CSi.xyz") ----------------------------------------------------------------------------------------------------- Energy = 62.9107512993 Forces: 1 -2.72370393e+01 2.65895350e+01 1.28918203e+01 2 2.79166263e+00 3.94865694e+00 -4.86970743e+00 3 -1.56529472e+01 -7.62682359e-01 -1.62557284e+01 4 -6.57050605e+00 2.59830796e+01 8.09680906e+00 5 -4.30514266e+00 1.09427697e+01 2.95381606e+01 6 2.60169357e+00 4.31634137e+00 1.50466451e+00 7 -2.45309939e+01 1.51907796e+01 -4.85767882e+00 8 1.10241282e+01 -3.39359466e+00 1.33030594e+00 9 -1.02571321e+01 -5.35550178e+00 7.72310000e+00 10 2.52032814e+01 -4.61748548e+01 1.88194317e+01 11 -2.50197243e+01 -5.22399687e+00 1.99062129e+01 12 -1.50629319e-01 -5.76591415e+00 1.46984434e+01 13 2.34717957e+01 -3.56854306e+00 -9.98491866e-02 14 4.99907246e+00 -2.52159735e+01 -1.26497270e+01 15 9.48548116e+00 -8.79845827e+00 6.52921466e+00 16 7.49733372e-01 1.01770160e+01 2.05692305e+01 17 2.04037895e+01 -3.18309738e+00 3.00801619e+00 18 -7.98620199e+00 8.73987229e+00 9.54642109e-01 19 -1.01309038e+01 2.09200664e+01 -4.68769317e+01 20 -1.81935183e+00 1.48271617e+01 2.67686722e+00 21 1.67329306e+01 -8.60230981e+00 1.09863624e+01 22 4.47170911e-01 3.77419876e+00 -5.93095989e+00 23 2.61995688e+01 9.84905434e-01 -1.35186469e+01 24 6.45065936e+00 7.10386643e+00 -1.14874071e+01 25 -2.69089461e+01 -2.26291421e+01 -1.35761333e+01 26 1.28779119e+01 1.31135452e+01 -5.55009277e+00 27 -8.50280629e+00 -1.12194857e+01 -2.04998649e+01 28 -3.10954667e+00 -1.33011593e+00 8.78701703e-01 29 1.08729788e+01 3.08047238e+00 6.77952034e+00 30 -8.23439221e+00 -1.66913140e+01 -2.39132641e+00 31 -1.08251166e+00 1.91733741e+00 -1.62553478e+00 32 7.18691709e+00 -3.69461983e+00 -6.70191510e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==28277== Memcheck, a memory error detector ==28277== Copyright (C) 2002-2015, and GNU GPL'd, by Julian Seward et al. ==28277== Using Valgrind-3.11.0 and LibVEX; rerun with -h for copyright info ==28277== Command: python runner2.py Tersoff_LAMMPS_Tersoff_PRB39_1989_CSi__MO_171585019474_001 ==28277== ==28277== ==28277== HEAP SUMMARY: ==28277== in use at exit: 4,113,290 bytes in 5,863 blocks ==28277== total heap usage: 99,651 allocs, 93,788 frees, 65,240,384 bytes allocated ==28277== ==28277== LEAK SUMMARY: ==28277== definitely lost: 0 bytes in 0 blocks ==28277== indirectly lost: 0 bytes in 0 blocks ==28277== possibly lost: 172,751 bytes in 105 blocks ==28277== still reachable: 3,940,539 bytes in 5,758 blocks ==28277== suppressed: 0 bytes in 0 blocks ==28277== Rerun with --leak-check=full to see details of leaked memory ==28277== ==28277== For counts of detected and suppressed errors, rerun with: -v ==28277== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 2420 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.