!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_PunMishin_2009_NiAl__MO_751354403791_005 Supported species : Al Ni random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Al (Configuration in file "config-F-Al.xyz") ----------------------------------------------------------------------------------------------------- Energy = 15.74881648428885 Forces: 1 -3.32162158e+00 -2.71299971e+00 -3.36275367e+00 2 1.54871177e+00 -1.27660892e+00 -6.91169707e+00 3 2.36517643e+00 -6.00636379e+00 5.90552478e-01 4 -6.54962057e+00 2.23909845e+00 -1.91217239e-01 5 -1.06656288e+00 -4.38847395e+00 -3.37430506e+00 6 3.91511222e+00 1.32338286e+00 -3.92406625e+00 7 3.38281461e+00 -3.63218136e+00 -2.44533319e-01 8 -1.00222346e+00 -2.00451238e+00 1.11383455e+00 9 -4.44345872e+00 -3.71814364e-01 -5.60228672e+00 10 5.99657294e-01 6.29311274e+00 -4.91647983e+00 11 -2.64053171e+00 -2.60777671e+00 -4.18958185e-01 12 -5.78210713e+00 4.78440184e+00 1.07239303e+00 13 2.13438526e+00 -1.63800170e+00 -7.32135650e+00 14 4.45056666e+00 3.92477505e+00 -4.84225718e+00 15 6.95307966e+00 -1.92040864e+00 -6.87302186e-01 16 -2.10717441e+00 8.77559528e+00 -6.59958163e-01 17 -5.81740358e+00 -4.53392533e+00 1.98384203e-01 18 1.68181039e+00 5.03822886e-01 -5.29388452e-01 19 2.36383451e+00 -5.91260590e+00 3.58786898e+00 20 -4.53291479e+00 2.10375111e+00 5.28771958e+00 21 -2.22324012e+00 -4.54991933e+00 8.40257014e-01 22 5.67890486e+00 1.04095695e+00 5.70113066e-01 23 2.61351822e+00 -1.90940790e+00 4.18526159e+00 24 9.64955590e-01 -8.50095605e-01 4.75954611e+00 25 -6.20728140e+00 -1.12678777e+00 -7.12280631e-01 26 5.08469181e-01 7.22826008e+00 -1.14053196e+00 27 -1.09940780e+00 -1.37664061e+00 6.09638415e+00 28 -4.54191000e+00 3.00072398e+00 3.47790970e+00 29 3.69219636e-01 -3.17290458e+00 1.97507413e+00 30 5.34550408e+00 5.09108764e+00 1.76371831e+00 31 4.76341003e+00 -9.09565313e-01 4.24297627e+00 32 1.69632772e+00 4.59202499e+00 5.07737926e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Al (Configuration in file "config-T-Al.xyz") ----------------------------------------------------------------------------------------------------- Energy = 15.74881648428885 Forces: 1 -3.32162158e+00 -2.71299971e+00 -3.36275367e+00 2 1.54871177e+00 -1.27660892e+00 -6.91169707e+00 3 2.36517643e+00 -6.00636379e+00 5.90552478e-01 4 -6.54962057e+00 2.23909845e+00 -1.91217239e-01 5 -1.06656288e+00 -4.38847395e+00 -3.37430506e+00 6 3.91511222e+00 1.32338286e+00 -3.92406625e+00 7 3.38281461e+00 -3.63218136e+00 -2.44533319e-01 8 -1.00222346e+00 -2.00451238e+00 1.11383455e+00 9 -4.44345872e+00 -3.71814364e-01 -5.60228672e+00 10 5.99657294e-01 6.29311274e+00 -4.91647983e+00 11 -2.64053171e+00 -2.60777671e+00 -4.18958185e-01 12 -5.78210713e+00 4.78440184e+00 1.07239303e+00 13 2.13438526e+00 -1.63800170e+00 -7.32135650e+00 14 4.45056666e+00 3.92477505e+00 -4.84225718e+00 15 6.95307966e+00 -1.92040864e+00 -6.87302186e-01 16 -2.10717441e+00 8.77559528e+00 -6.59958163e-01 17 -5.81740358e+00 -4.53392533e+00 1.98384203e-01 18 1.68181039e+00 5.03822886e-01 -5.29388452e-01 19 2.36383451e+00 -5.91260590e+00 3.58786898e+00 20 -4.53291479e+00 2.10375111e+00 5.28771958e+00 21 -2.22324012e+00 -4.54991933e+00 8.40257014e-01 22 5.67890486e+00 1.04095695e+00 5.70113066e-01 23 2.61351822e+00 -1.90940790e+00 4.18526159e+00 24 9.64955590e-01 -8.50095605e-01 4.75954611e+00 25 -6.20728140e+00 -1.12678777e+00 -7.12280631e-01 26 5.08469181e-01 7.22826008e+00 -1.14053196e+00 27 -1.09940780e+00 -1.37664061e+00 6.09638415e+00 28 -4.54191000e+00 3.00072398e+00 3.47790970e+00 29 3.69219636e-01 -3.17290458e+00 1.97507413e+00 30 5.34550408e+00 5.09108764e+00 1.76371831e+00 31 4.76341003e+00 -9.09565313e-01 4.24297627e+00 32 1.69632772e+00 4.59202499e+00 5.07737926e+00 MONOATOMIC STRUCTURE (pbc=False)-- Species = Ni (Configuration in file "config-F-Ni.xyz") ----------------------------------------------------------------------------------------------------- Energy = -60.1994404349066 Forces: 1 -4.55689524e+00 -4.73911382e+00 -5.34661339e+00 2 3.30506869e+00 4.74719160e+00 -7.03792159e+00 3 3.31595876e+00 -7.93472804e+00 3.22578844e+00 4 -6.92709389e+00 4.50226203e+00 1.03005610e+00 5 -1.53184109e+00 -3.63654562e+00 -3.67033592e+00 6 3.24638982e+00 3.03657158e+00 -5.40072294e+00 7 5.05293909e+00 -3.93319612e+00 2.74038258e+00 8 4.01325085e-01 3.49766326e+00 3.02011222e+00 9 -2.11257630e+00 -1.50916749e+00 -3.11352536e+00 10 -3.64164318e+00 5.78822550e+00 -4.01567986e+00 11 3.33602760e+00 -1.95874112e+00 -7.19199358e-01 12 -4.89151539e+00 4.97743048e+00 -8.39784188e-01 13 3.80353495e-01 -6.07065443e+00 -4.31231345e+00 14 4.27676707e+00 2.27319567e+00 -3.81166823e+00 15 4.68312219e+00 -4.19226123e-01 -2.09778467e+00 16 -8.00324048e-01 4.74319542e+00 5.24234749e+00 17 -3.16358335e+00 -3.37191974e+00 3.25008777e+00 18 2.58591518e+00 -6.81443840e-02 2.74225034e+00 19 -1.25854242e+00 -8.48182136e-01 8.01618650e-01 20 -3.06398548e+00 -2.51465080e+00 2.64076870e+00 21 -2.53445345e+00 -3.95493316e+00 -2.43330276e+00 22 5.01432678e+00 -2.64647645e+00 -1.52618017e+00 23 2.74979139e+00 -2.51082678e+00 3.17031639e+00 24 -3.73851890e+00 1.19212554e+00 5.16205951e+00 25 -5.86986471e+00 -2.25427919e+00 2.40087949e+00 26 3.61580510e+00 5.44784886e+00 -3.27358845e+00 27 3.93892593e+00 -2.64063396e+00 5.09694433e+00 28 -3.96233286e+00 3.60439269e+00 2.43155156e+00 29 -4.48656249e+00 -1.99337316e+00 -3.11419982e+00 30 3.42092996e+00 4.56745723e+00 -6.84271524e-01 31 4.16415457e+00 3.47169209e-01 5.05801734e+00 32 -9.48067918e-01 4.28006346e+00 3.38391081e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ni (Configuration in file "config-T-Ni.xyz") ----------------------------------------------------------------------------------------------------- Energy = -60.1994404349066 Forces: 1 -4.55689524e+00 -4.73911382e+00 -5.34661339e+00 2 3.30506869e+00 4.74719160e+00 -7.03792159e+00 3 3.31595876e+00 -7.93472804e+00 3.22578844e+00 4 -6.92709389e+00 4.50226203e+00 1.03005610e+00 5 -1.53184109e+00 -3.63654562e+00 -3.67033592e+00 6 3.24638982e+00 3.03657158e+00 -5.40072294e+00 7 5.05293909e+00 -3.93319612e+00 2.74038258e+00 8 4.01325085e-01 3.49766326e+00 3.02011222e+00 9 -2.11257630e+00 -1.50916749e+00 -3.11352536e+00 10 -3.64164318e+00 5.78822550e+00 -4.01567986e+00 11 3.33602760e+00 -1.95874112e+00 -7.19199358e-01 12 -4.89151539e+00 4.97743048e+00 -8.39784188e-01 13 3.80353495e-01 -6.07065443e+00 -4.31231345e+00 14 4.27676707e+00 2.27319567e+00 -3.81166823e+00 15 4.68312219e+00 -4.19226123e-01 -2.09778467e+00 16 -8.00324048e-01 4.74319542e+00 5.24234749e+00 17 -3.16358335e+00 -3.37191974e+00 3.25008777e+00 18 2.58591518e+00 -6.81443840e-02 2.74225034e+00 19 -1.25854242e+00 -8.48182136e-01 8.01618650e-01 20 -3.06398548e+00 -2.51465080e+00 2.64076870e+00 21 -2.53445345e+00 -3.95493316e+00 -2.43330276e+00 22 5.01432678e+00 -2.64647645e+00 -1.52618017e+00 23 2.74979139e+00 -2.51082678e+00 3.17031639e+00 24 -3.73851890e+00 1.19212554e+00 5.16205951e+00 25 -5.86986471e+00 -2.25427919e+00 2.40087949e+00 26 3.61580510e+00 5.44784886e+00 -3.27358845e+00 27 3.93892593e+00 -2.64063396e+00 5.09694433e+00 28 -3.96233286e+00 3.60439269e+00 2.43155156e+00 29 -4.48656249e+00 -1.99337316e+00 -3.11419982e+00 30 3.42092996e+00 4.56745723e+00 -6.84271524e-01 31 4.16415457e+00 3.47169209e-01 5.05801734e+00 32 -9.48067918e-01 4.28006346e+00 3.38391081e+00 MIXED STRUCTURE (pbc=False)-- Species = Al Ni (Configuration in file "config-F-AlNi.xyz") ----------------------------------------------------------------------------------------------------- Energy = 17.074631404228196 Forces: 1 -1.27351425e+02 -1.28555828e+02 2.06647607e+01 2 1.27351696e+02 1.26867850e+02 -3.40758360e+01 3 8.57965490e-01 -7.01841405e+00 4.36470797e+00 4 -7.53258081e+00 2.75445603e-01 4.92339596e+00 5 9.22112021e-01 -5.04213064e+00 -6.38011374e+00 6 5.27941207e+00 5.40303741e-01 -5.01540345e+00 7 3.81935750e+00 -3.40350401e+00 1.92923067e+00 8 -1.87120888e+00 -2.55550482e+00 3.13840479e+00 9 -2.80433983e+00 5.50173008e+00 -1.77670527e+00 10 -3.10723457e+00 3.52840315e+00 -6.93173728e+00 11 -1.66542411e+00 -3.54751810e+00 -1.64915980e+00 12 -7.11734546e+00 6.79464861e+00 -3.43083308e+00 13 -4.26781798e-01 -8.63903682e-01 -1.00890171e+01 14 1.81917436e+00 2.81049464e+00 -2.44836867e+00 15 9.06151504e+00 1.14576329e+00 2.99286628e+00 16 2.70230623e+00 9.16566033e+00 4.74510931e+00 17 -6.48814080e+00 -9.39399642e+00 -3.53566913e-01 18 1.07401953e+02 6.67334303e+00 -9.08289604e+01 19 2.62979338e+00 -5.62390387e+00 8.26516247e+00 20 -1.09200805e+02 -3.56527088e+00 9.12706495e+01 21 7.53467639e-01 -6.10213664e+00 2.74297293e-01 22 3.98254588e+01 -6.99510485e+00 -3.55389741e+01 23 2.06983653e+00 -3.14233638e+00 2.52510578e+00 24 -3.61439914e+01 5.04216466e+00 3.65969735e+01 25 -9.57804101e+00 -6.01319261e-01 -2.75622585e+00 26 2.03329599e+00 1.08399961e+01 -1.21644316e+01 27 -1.27696634e-01 -8.83544794e+00 2.07746748e+01 28 -3.36791954e+00 3.95434558e+00 2.30303666e+00 29 -3.33753661e-01 5.40683834e-01 -2.91015910e-01 30 3.63647496e+00 4.51863465e+00 -3.74911160e+00 31 4.75962841e+00 1.02402042e+00 6.80292461e+00 32 2.19324083e+00 6.02283240e+00 5.90816036e+00 MIXED STRUCTURE (pbc=True)-- Species = Al Ni (Configuration in file "config-T-AlNi.xyz") ----------------------------------------------------------------------------------------------------- Energy = 23.939710443316052 Forces: 1 -1.25273438e+02 -1.27855787e+02 2.21958235e+01 2 1.25363065e+02 1.28776761e+02 -2.59206856e+01 3 -4.67856539e-01 -2.31949920e+00 4.60784709e+00 4 5.86799321e+00 5.45384470e+00 5.76831521e+00 5 7.45239168e-01 -4.67894279e+00 -1.21720517e-01 6 1.98479032e+00 1.22726882e+00 -4.77003673e+00 7 -8.58546513e+00 -7.75857632e+00 6.13546274e+00 8 -1.10106927e+00 -3.21340317e+00 3.07511262e+00 9 -2.75119007e+00 5.00890930e+00 1.03635637e+00 10 -3.20093053e+00 3.22913521e+00 -4.76132275e+00 11 -1.97509233e+00 -3.13602816e+00 -2.50256950e+00 12 -6.53437308e+00 5.59599696e+00 -3.83507600e+00 13 7.44034919e-01 3.63519298e-01 -8.63085457e+00 14 4.55184035e-01 -1.97288144e+00 -4.12205121e+00 15 5.15383758e+00 2.42775227e+00 2.19264013e+00 16 3.58395750e+00 4.73090306e+00 3.34914046e+00 17 -5.70471200e+00 -6.66333233e+00 -2.24341554e+00 18 1.07647178e+02 6.53560229e+00 -9.10242262e+01 19 2.79033692e+00 -7.14453723e+00 -1.85258752e+00 20 -1.08334267e+02 -3.62287846e+00 8.77755502e+01 21 2.67456709e+00 -1.22996873e+00 7.42505677e-01 22 3.78725828e+01 -7.69511402e+00 -3.62522912e+01 23 3.53767682e+00 -3.02031727e+00 -5.88173147e-01 24 -3.57965908e+01 4.93167814e+00 3.53740907e+01 25 -4.62399839e+00 -1.30755995e+00 -2.13562315e+00 26 9.64188521e-01 9.48087040e+00 -1.18339394e+01 27 6.96186259e-01 -8.51693456e+00 1.54102060e+01 28 6.40672053e-01 4.72777091e+00 5.36094742e+00 29 3.28665953e-02 9.39703357e-01 1.04212287e-01 30 -1.40876420e+00 4.86880711e+00 -5.46887387e+00 31 1.81666814e+00 1.91249562e-01 7.71149135e+00 32 3.18672250e+00 1.64598774e+00 5.22374526e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==1397729== Memcheck, a memory error detector ==1397729== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==1397729== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info ==1397729== Command: python runner2.py EAM_Dynamo_PunMishin_2009_NiAl__MO_751354403791_005 ==1397729== ==1399075== Warning: invalid file descriptor 1024 in syscall close() ==1399075== Warning: invalid file descriptor 1025 in syscall close() ==1399075== Warning: invalid file descriptor 1026 in syscall close() ==1399075== Warning: invalid file descriptor 1027 in syscall close() ==1399075== Use --log-fd= to select an alternative log fd. ==1399075== Warning: invalid file descriptor 1028 in syscall close() ==1399075== Warning: invalid file descriptor 1029 in syscall close() ==1397729== ==1397729== HEAP SUMMARY: ==1397729== in use at exit: 2,257,751 bytes in 1,704 blocks ==1397729== total heap usage: 82,936 allocs, 81,232 frees, 173,068,334 bytes allocated ==1397729== ==1397729== LEAK SUMMARY: ==1397729== definitely lost: 0 bytes in 0 blocks ==1397729== indirectly lost: 0 bytes in 0 blocks ==1397729== possibly lost: 180,827 bytes in 103 blocks ==1397729== still reachable: 2,076,892 bytes in 1,600 blocks ==1397729== of which reachable via heuristic: ==1397729== stdstring : 38 bytes in 1 blocks ==1397729== suppressed: 32 bytes in 1 blocks ==1397729== Rerun with --leak-check=full to see details of leaked memory ==1397729== ==1397729== For lists of detected and suppressed errors, rerun with: -s ==1397729== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 7867 from 545) ================================================================================ 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.