!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 and Daniel S. Karls ----------------------------------------------------------------------------------------------------- Results for KIM Model : EAM_Dynamo_TehranchiCurtin_2010_NiH__MO_535504325462_003 Supported species : H Ni random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = H (Configuration in file "config-F-H.xyz") ----------------------------------------------------------------------------------------------------- Energy = -28.286567769735566 Forces: 1 1.00675795e+00 1.76489279e+00 1.88266935e+00 2 6.88769462e-01 -1.52280136e+00 1.15127759e+00 3 -9.72376868e-01 1.67904632e+00 4.97540141e-01 4 1.41330322e+00 -9.64249229e-01 -9.41380366e-01 5 -5.79668687e-01 2.45608866e+00 6.51082381e-01 6 -1.15057212e+00 -7.27985625e-01 1.23301260e+00 7 -1.33678074e+00 2.45665654e+00 1.71339395e+00 8 1.53051597e+00 5.45789601e-01 3.84199251e-01 9 1.35855562e+00 1.04706319e+00 2.80849601e+00 10 5.20995948e-02 -2.07126619e+00 2.02616570e+00 11 -1.86249765e+00 1.25639141e+00 -2.77961659e-01 12 1.83512527e+00 -2.49373462e+00 -6.37143991e-01 13 7.68533835e-01 1.50240458e+00 2.57628416e+00 14 -1.29004210e+00 -1.61398545e+00 1.11716604e+00 15 -2.37994273e+00 1.42828851e+00 -1.02727590e-01 16 -1.40634850e-01 -2.05573103e+00 -8.82985148e-01 17 2.73736277e+00 1.53683120e+00 8.34665977e-01 18 -5.85548057e-01 -2.03207473e+00 5.62841284e-01 19 -1.05185201e+00 2.61870309e+00 -1.65636604e+00 20 1.34073437e+00 -1.67997503e+00 -1.69436752e+00 21 1.63157107e+00 1.76264828e+00 -5.11298327e-01 22 -2.20384759e+00 -2.26057659e+00 -1.13048649e+00 23 -1.03897100e+00 5.57319420e-01 -1.62159201e+00 24 -5.30746934e-01 -6.45143195e-01 -1.31613933e+00 25 2.02927776e+00 9.45256267e-01 -9.97781702e-01 26 4.92178016e-01 -2.32765155e+00 1.19908022e+00 27 -8.08336785e-01 2.88469937e+00 -1.46973482e+00 28 2.50675347e+00 -2.23342155e+00 -9.93812670e-01 29 1.02394767e+00 1.16302237e+00 -2.76656684e-01 30 -1.42796495e+00 -2.13006765e+00 -7.05052120e-01 31 -2.29646506e+00 1.09000280e+00 -1.47584476e+00 32 -7.59237901e-01 -1.93644058e+00 -1.94654343e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = H (Configuration in file "config-T-H.xyz") ----------------------------------------------------------------------------------------------------- Energy = -28.286567769735566 Forces: 1 1.00675795e+00 1.76489279e+00 1.88266935e+00 2 6.88769462e-01 -1.52280136e+00 1.15127759e+00 3 -9.72376868e-01 1.67904632e+00 4.97540141e-01 4 1.41330322e+00 -9.64249229e-01 -9.41380366e-01 5 -5.79668687e-01 2.45608866e+00 6.51082381e-01 6 -1.15057212e+00 -7.27985625e-01 1.23301260e+00 7 -1.33678074e+00 2.45665654e+00 1.71339395e+00 8 1.53051597e+00 5.45789601e-01 3.84199251e-01 9 1.35855562e+00 1.04706319e+00 2.80849601e+00 10 5.20995948e-02 -2.07126619e+00 2.02616570e+00 11 -1.86249765e+00 1.25639141e+00 -2.77961659e-01 12 1.83512527e+00 -2.49373462e+00 -6.37143991e-01 13 7.68533835e-01 1.50240458e+00 2.57628416e+00 14 -1.29004210e+00 -1.61398545e+00 1.11716604e+00 15 -2.37994273e+00 1.42828851e+00 -1.02727590e-01 16 -1.40634850e-01 -2.05573103e+00 -8.82985148e-01 17 2.73736277e+00 1.53683120e+00 8.34665977e-01 18 -5.85548057e-01 -2.03207473e+00 5.62841284e-01 19 -1.05185201e+00 2.61870309e+00 -1.65636604e+00 20 1.34073437e+00 -1.67997503e+00 -1.69436752e+00 21 1.63157107e+00 1.76264828e+00 -5.11298327e-01 22 -2.20384759e+00 -2.26057659e+00 -1.13048649e+00 23 -1.03897100e+00 5.57319420e-01 -1.62159201e+00 24 -5.30746934e-01 -6.45143195e-01 -1.31613933e+00 25 2.02927776e+00 9.45256267e-01 -9.97781702e-01 26 4.92178016e-01 -2.32765155e+00 1.19908022e+00 27 -8.08336785e-01 2.88469937e+00 -1.46973482e+00 28 2.50675347e+00 -2.23342155e+00 -9.93812670e-01 29 1.02394767e+00 1.16302237e+00 -2.76656684e-01 30 -1.42796495e+00 -2.13006765e+00 -7.05052120e-01 31 -2.29646506e+00 1.09000280e+00 -1.47584476e+00 32 -7.59237901e-01 -1.93644058e+00 -1.94654343e+00 MONOATOMIC STRUCTURE (pbc=False)-- Species = Ni (Configuration in file "config-F-Ni.xyz") ----------------------------------------------------------------------------------------------------- Energy = -36.11069175823841 Forces: 1 -3.07338251e+00 -2.66907108e+00 -4.01671233e+00 2 2.60965303e+00 9.44282157e-01 -9.01436292e+00 3 5.45445391e+00 -1.44114004e+01 -6.02039784e+00 4 -1.27914913e+01 8.71333005e+00 4.08648266e+00 5 2.95735832e+00 -7.35598600e+00 -6.16123184e+00 6 7.47832076e+00 -4.24696322e+00 -5.45305691e+00 7 8.54260631e+00 -1.08870006e+01 -4.25212077e+00 8 -4.81276337e+00 3.20114851e+00 -5.93300378e+00 9 -1.20450251e+01 -1.01491740e+00 -9.70321538e+00 10 2.15768535e-01 7.24416180e+00 -9.79576551e+00 11 9.22426449e+00 -4.90532352e+00 1.17165002e+01 12 -6.18633429e+00 1.23190004e+01 -3.11150243e+00 13 -4.15339089e+00 4.72693961e+00 -7.43403360e+00 14 3.03209857e+00 4.86095778e-01 -2.64842036e+00 15 1.06278782e+01 8.17993506e+00 -9.83477340e-01 16 1.05589188e+00 4.05839609e+00 6.53710573e+00 17 -7.61510845e+00 -6.90583575e+00 4.94229097e+00 18 -6.58856078e+00 1.28101882e+01 3.73073918e+00 19 4.07806150e+00 -8.49540684e+00 4.28073983e+00 20 -6.76671481e+00 7.22390303e+00 1.70015665e+00 21 2.55412179e+00 -1.38041579e+01 6.69933957e+00 22 9.78216470e+00 -9.28622928e-01 7.11636686e+00 23 1.17917670e+00 -1.09620613e+00 7.21029802e-01 24 2.89405737e+00 3.20366743e+00 6.78432671e+00 25 -3.30125846e+00 -8.47052376e+00 7.24364277e+00 26 -4.26537557e+00 8.59415072e+00 -1.15041688e+01 27 -5.51499168e+00 -1.14918793e+01 6.39444679e+00 28 -3.96240771e+00 2.48574876e+00 2.16033985e+00 29 -7.56959134e+00 5.70442021e+00 2.41767490e+00 30 1.89402639e+00 3.63216279e+00 -3.56938957e+00 31 6.10240850e+00 -4.08059797e+00 5.87211166e+00 32 8.96408530e+00 7.23636207e+00 7.19756519e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ni (Configuration in file "config-T-Ni.xyz") ----------------------------------------------------------------------------------------------------- Energy = -36.11069175823841 Forces: 1 -3.07338251e+00 -2.66907108e+00 -4.01671233e+00 2 2.60965303e+00 9.44282157e-01 -9.01436292e+00 3 5.45445391e+00 -1.44114004e+01 -6.02039784e+00 4 -1.27914913e+01 8.71333005e+00 4.08648266e+00 5 2.95735832e+00 -7.35598600e+00 -6.16123184e+00 6 7.47832076e+00 -4.24696322e+00 -5.45305691e+00 7 8.54260631e+00 -1.08870006e+01 -4.25212077e+00 8 -4.81276337e+00 3.20114851e+00 -5.93300378e+00 9 -1.20450251e+01 -1.01491740e+00 -9.70321538e+00 10 2.15768535e-01 7.24416180e+00 -9.79576551e+00 11 9.22426449e+00 -4.90532352e+00 1.17165002e+01 12 -6.18633429e+00 1.23190004e+01 -3.11150243e+00 13 -4.15339089e+00 4.72693961e+00 -7.43403360e+00 14 3.03209857e+00 4.86095778e-01 -2.64842036e+00 15 1.06278782e+01 8.17993506e+00 -9.83477340e-01 16 1.05589188e+00 4.05839609e+00 6.53710573e+00 17 -7.61510845e+00 -6.90583575e+00 4.94229097e+00 18 -6.58856078e+00 1.28101882e+01 3.73073918e+00 19 4.07806150e+00 -8.49540684e+00 4.28073983e+00 20 -6.76671481e+00 7.22390303e+00 1.70015665e+00 21 2.55412179e+00 -1.38041579e+01 6.69933957e+00 22 9.78216470e+00 -9.28622928e-01 7.11636686e+00 23 1.17917670e+00 -1.09620613e+00 7.21029802e-01 24 2.89405737e+00 3.20366743e+00 6.78432671e+00 25 -3.30125846e+00 -8.47052376e+00 7.24364277e+00 26 -4.26537557e+00 8.59415072e+00 -1.15041688e+01 27 -5.51499168e+00 -1.14918793e+01 6.39444679e+00 28 -3.96240771e+00 2.48574876e+00 2.16033985e+00 29 -7.56959134e+00 5.70442021e+00 2.41767490e+00 30 1.89402639e+00 3.63216279e+00 -3.56938957e+00 31 6.10240850e+00 -4.08059797e+00 5.87211166e+00 32 8.96408530e+00 7.23636207e+00 7.19756519e+00 MIXED STRUCTURE (pbc=False)-- Species = H Ni (Configuration in file "config-F-HNi.xyz") ----------------------------------------------------------------------------------------------------- Energy = -52.94055021202526 Forces: 1 -1.29967643e+01 -8.26414485e+00 -7.20456619e+00 2 1.23922913e+01 1.19614137e+01 -9.45826946e+00 3 8.71970410e+00 -9.57846137e+00 1.15014029e+01 4 -4.07669905e+00 7.19311544e-01 1.14930943e+01 5 2.07155442e-02 -4.59239848e-01 -3.00417648e-01 6 5.60835893e-01 1.96615212e-02 -2.69548993e-01 7 -3.83376923e-01 -2.20287509e+00 -1.81564525e+00 8 -4.50201976e-01 2.45309459e-01 4.46947335e-01 9 -2.63544446e+00 3.01448915e+00 -9.10692629e+00 10 -2.23545175e+00 1.94967694e+00 -3.50874664e+00 11 -7.12461735e-01 -3.91087904e-01 6.21724119e-01 12 6.97322537e-01 3.42355767e+00 4.24779451e+00 13 1.24689897e+00 -1.88034608e+00 -2.75315884e-01 14 -2.43439006e-01 2.00261450e-01 3.64766472e-02 15 1.86075484e-01 3.83578215e-01 2.03219066e-01 16 -4.73606252e-01 -1.29412978e+00 1.06301092e+00 17 1.66957100e-01 -2.59661156e+00 -1.92880113e+00 18 -1.52421415e-01 -3.39634600e-02 1.25337247e-01 19 -1.22069298e-01 4.22507395e-02 2.62973853e-01 20 1.03360727e+00 2.53114881e+00 1.51632380e+00 21 1.86726453e-01 -9.62680665e-02 5.58305848e-02 22 -2.15511141e-02 3.15928921e+00 -6.71197683e-01 23 1.24388149e-01 -2.15977405e-01 2.09187270e-01 24 -5.35956576e+00 -3.94313586e+00 3.88715818e-01 25 -4.05772449e-01 1.82082163e-01 3.35302622e-02 26 -6.14833893e-02 2.79957855e-01 2.58190803e-02 27 -4.65732750e-02 -1.73119200e-01 3.47996335e-01 28 1.41885407e-01 -1.57428954e-01 -2.13337207e-01 29 5.84276219e-01 6.26396549e-02 -1.74202610e-02 30 3.91122950e+00 1.62198195e+00 -1.46611707e+00 31 6.20496425e+00 -2.33128498e-01 3.16500000e+00 32 -5.80099604e+00 1.72330788e+00 4.91925703e-01 MIXED STRUCTURE (pbc=True)-- Species = H Ni (Configuration in file "config-T-HNi.xyz") ----------------------------------------------------------------------------------------------------- Energy = -58.63463741116635 Forces: 1 -1.16747697e+01 -1.41782015e+01 -3.36479181e+00 2 1.59727991e+01 1.13982933e+01 -5.63710777e+00 3 7.71311458e+00 -6.57918616e+00 1.27516965e+01 4 4.65489201e-02 2.03153740e+00 1.00271619e+01 5 -2.46996502e-01 -7.24058046e-01 -2.42538223e-01 6 7.27420294e-01 4.05613250e-01 -4.32967462e-01 7 -2.48973709e+00 -5.05595662e+00 -2.18606841e+00 8 -1.00528831e+00 7.24610717e-01 4.45309884e-01 9 -3.44096859e+00 4.36769936e+00 -8.01792114e+00 10 -3.93015647e+00 1.81846789e+00 -3.07021702e+00 11 -7.95694387e-01 -9.78549043e-01 1.17743035e+00 12 -9.60452995e-01 3.85421080e+00 5.02799896e+00 13 1.72121796e+00 -2.42529919e+00 -4.15417254e-01 14 -2.15209844e-01 -6.70391527e-02 -1.44539831e-01 15 2.69605407e-01 4.44216729e-01 1.98574074e-01 16 8.31072028e-01 -1.42884091e+00 1.23249409e+00 17 2.55457343e-01 -5.23132292e+00 -2.12637385e+00 18 3.32538588e-01 3.04958791e-01 -1.77494326e-01 19 1.86280103e-02 1.00652080e-01 4.16506461e-01 20 -3.35339261e+00 7.59975305e+00 -8.95193151e+00 21 3.09607669e-01 -1.00145725e-01 -7.15515568e-02 22 -2.08152463e+00 3.66829685e+00 6.67512026e-01 23 3.46359786e-01 -2.32319081e-02 -1.70416676e-01 24 -5.86280203e+00 -6.10794556e+00 2.01284292e+00 25 -2.56885585e-01 -1.08637569e-01 -1.91748261e-01 26 -1.62173699e-01 2.28737816e-01 -1.81059898e-01 27 -9.62654203e-02 -2.41766757e-01 3.32889065e-01 28 -5.01560645e-01 1.82458576e-01 -6.87647163e-02 29 3.31062791e-01 -4.91824598e-02 -2.77557170e-01 30 5.68039002e+00 3.30642926e+00 -1.33383452e+00 31 7.87726284e+00 -4.92936131e-02 4.93738061e+00 32 -5.35920684e+00 2.91272125e+00 -2.16549536e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==1304769== Memcheck, a memory error detector ==1304769== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==1304769== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info ==1304769== Command: python runner2.py EAM_Dynamo_TehranchiCurtin_2010_NiH__MO_535504325462_003 ==1304769== ==1306145== Warning: invalid file descriptor 1024 in syscall close() ==1306145== Warning: invalid file descriptor 1025 in syscall close() ==1306145== Warning: invalid file descriptor 1026 in syscall close() ==1306145== Warning: invalid file descriptor 1027 in syscall close() ==1306145== Use --log-fd= to select an alternative log fd. ==1306145== Warning: invalid file descriptor 1028 in syscall close() ==1306145== Warning: invalid file descriptor 1029 in syscall close() ==1304769== ==1304769== HEAP SUMMARY: ==1304769== in use at exit: 2,257,767 bytes in 1,704 blocks ==1304769== total heap usage: 82,926 allocs, 81,222 frees, 78,626,623 bytes allocated ==1304769== ==1304769== LEAK SUMMARY: ==1304769== definitely lost: 0 bytes in 0 blocks ==1304769== indirectly lost: 0 bytes in 0 blocks ==1304769== possibly lost: 180,827 bytes in 103 blocks ==1304769== still reachable: 2,076,908 bytes in 1,600 blocks ==1304769== of which reachable via heuristic: ==1304769== stdstring : 38 bytes in 1 blocks ==1304769== suppressed: 32 bytes in 1 blocks ==1304769== Rerun with --leak-check=full to see details of leaked memory ==1304769== ==1304769== For lists of detected and suppressed errors, rerun with: -s ==1304769== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 7965 from 556) ================================================================================ 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.