!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : Tersoff_LAMMPS_Tersoff_1994_SiC__MO_794973922560_000 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 = 185.43056205507654 Forces: 1 -3.18923205e+01 -1.81913940e+01 -1.51720389e+01 2 -8.88887243e+01 1.25180756e+02 -3.42427378e+01 3 -6.13152145e+00 -1.97611302e+01 -1.43354810e+01 4 -2.31686049e+01 2.21751518e+01 1.48657602e+01 5 1.07247563e+02 -1.50966489e+02 -4.05029037e+00 6 2.31445681e+01 5.42720841e-01 -1.76715789e+01 7 1.33484290e+01 -7.65083823e+01 -5.52252500e+01 8 -7.53349663e+01 -6.04018056e+01 1.19586953e+01 9 -1.86108842e+01 -6.10749600e+00 -2.08078927e+01 10 -2.31687355e+01 3.81835462e+01 -5.19506558e+01 11 -4.69043867e+01 -4.55546125e+01 3.48386392e+00 12 -3.04205430e+01 1.59323170e+01 -2.12885053e+00 13 -9.03607751e+00 -2.60430385e+00 -1.11026976e+02 14 1.50140616e+01 1.28863867e+01 -5.98171466e+00 15 1.46629841e+02 4.88913081e+01 -1.82438406e+00 16 3.34592472e+01 8.57055816e+01 3.77226219e+01 17 -3.90324154e+01 -2.39746362e+01 -3.09722012e+01 18 1.16006546e+01 1.34081308e+01 -6.72855203e+00 19 3.26421124e+01 -2.98023243e+01 3.55208307e+01 20 -9.93614685e+00 3.11151972e+01 3.17597252e+01 21 -2.83666178e+01 -2.69965616e+01 3.94624692e+01 22 5.90310748e+01 1.40197615e+01 3.07603768e+01 23 9.36889610e+00 -8.83034422e-02 1.11887533e+01 24 3.66583131e+00 -1.94410349e+01 1.25042884e+01 25 -1.93831053e+01 -1.08791265e+01 -1.04317578e+01 26 -4.62467566e+01 5.44389635e+01 -1.55374202e+01 27 2.11172568e+01 -6.48643137e+01 4.98205245e+01 28 -9.23727500e+01 6.69764611e+01 -8.62673878e-01 29 -1.28696824e+01 -9.37571938e+00 3.67804691e+01 30 2.61931732e+01 1.72613681e+01 -5.08022463e+00 31 5.35407623e+01 -1.00475870e+01 3.69948571e+01 32 4.57607681e+01 2.88475700e+01 5.12074446e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = C (Configuration in file "config-T-C.xyz") ----------------------------------------------------------------------------------------------------- Energy = 185.43056205507654 Forces: 1 -3.18923205e+01 -1.81913940e+01 -1.51720389e+01 2 -8.88887243e+01 1.25180756e+02 -3.42427378e+01 3 -6.13152145e+00 -1.97611302e+01 -1.43354810e+01 4 -2.31686049e+01 2.21751518e+01 1.48657602e+01 5 1.07247563e+02 -1.50966489e+02 -4.05029037e+00 6 2.31445681e+01 5.42720841e-01 -1.76715789e+01 7 1.33484290e+01 -7.65083823e+01 -5.52252500e+01 8 -7.53349663e+01 -6.04018056e+01 1.19586953e+01 9 -1.86108842e+01 -6.10749600e+00 -2.08078927e+01 10 -2.31687355e+01 3.81835462e+01 -5.19506558e+01 11 -4.69043867e+01 -4.55546125e+01 3.48386392e+00 12 -3.04205430e+01 1.59323170e+01 -2.12885053e+00 13 -9.03607751e+00 -2.60430385e+00 -1.11026976e+02 14 1.50140616e+01 1.28863867e+01 -5.98171466e+00 15 1.46629841e+02 4.88913081e+01 -1.82438406e+00 16 3.34592472e+01 8.57055816e+01 3.77226219e+01 17 -3.90324154e+01 -2.39746362e+01 -3.09722012e+01 18 1.16006546e+01 1.34081308e+01 -6.72855203e+00 19 3.26421124e+01 -2.98023243e+01 3.55208307e+01 20 -9.93614685e+00 3.11151972e+01 3.17597252e+01 21 -2.83666178e+01 -2.69965616e+01 3.94624692e+01 22 5.90310748e+01 1.40197615e+01 3.07603768e+01 23 9.36889610e+00 -8.83034422e-02 1.11887533e+01 24 3.66583131e+00 -1.94410349e+01 1.25042884e+01 25 -1.93831053e+01 -1.08791265e+01 -1.04317578e+01 26 -4.62467566e+01 5.44389635e+01 -1.55374202e+01 27 2.11172568e+01 -6.48643137e+01 4.98205245e+01 28 -9.23727500e+01 6.69764611e+01 -8.62673878e-01 29 -1.28696824e+01 -9.37571938e+00 3.67804691e+01 30 2.61931732e+01 1.72613681e+01 -5.08022463e+00 31 5.35407623e+01 -1.00475870e+01 3.69948571e+01 32 4.57607681e+01 2.88475700e+01 5.12074446e+01 MONOATOMIC STRUCTURE (pbc=False)-- Species = Si (Configuration in file "config-F-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 226.60149818015708 Forces: 1 -1.44223216e+01 -1.23576539e+01 -6.15219358e+00 2 -1.04416738e+01 -1.82991738e-01 -2.87537799e+01 3 -8.43031929e+00 -4.73513543e+01 1.55933658e+01 4 -4.58010630e+01 -2.11578530e-01 -1.37240926e+01 5 -1.97176843e+00 -3.35795599e+01 -3.52447928e+01 6 3.70745183e+01 3.60388722e+01 -5.45185900e+01 7 2.30242141e+01 -7.38895749e+01 1.65817531e+01 8 -2.39280167e+00 1.13273178e+01 1.14282110e+01 9 -7.70982485e+00 5.02699521e+00 -3.43140749e+00 10 -4.53055475e+00 9.54250116e+00 -8.91642638e+00 11 -2.31603185e+01 2.70130424e+01 -2.45758319e+01 12 -1.41670387e+01 7.49167451e+00 -9.11329593e+00 13 1.01334386e+01 2.99227911e+01 -3.31196342e+01 14 4.98394409e+00 6.49355115e+00 -1.46166747e+01 15 5.90807345e+01 7.60950076e+00 -3.35459107e+01 16 1.55277625e+01 2.31842810e+01 -3.95364251e+01 17 -3.50068920e+01 -3.72113965e+01 -9.01945848e+00 18 5.35222798e+00 -7.04031166e+00 -3.67099410e+00 19 -5.99522127e+00 -1.73858621e+01 5.66814795e+01 20 -1.16842578e+01 4.66536920e+00 1.54054252e+01 21 -1.01863801e+01 -3.64529248e+01 -4.60436387e+01 22 3.77648794e+01 1.27968951e+01 1.71626747e+01 23 4.76792736e+01 -2.04972762e+01 4.88304217e+01 24 -1.78898658e+01 -1.08404870e+01 2.22815909e+01 25 -3.55055590e+01 1.31837189e+01 4.86039250e+00 26 -1.47734090e+01 2.10741705e+01 2.14342032e+01 27 -1.66407426e+01 1.93925377e+01 3.19185670e+01 28 -1.04809102e+01 1.18733360e+01 1.89222023e+01 29 -2.57339708e+01 -1.66771564e+01 4.23605418e+01 30 3.43859209e+01 3.72697896e+01 2.48781490e+01 31 3.94200041e+01 1.83256378e+01 4.04822536e+00 32 2.49797520e+00 1.14461462e+01 1.15959435e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Si (Configuration in file "config-T-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 226.60149818015708 Forces: 1 -1.44223216e+01 -1.23576539e+01 -6.15219358e+00 2 -1.04416738e+01 -1.82991738e-01 -2.87537799e+01 3 -8.43031929e+00 -4.73513543e+01 1.55933658e+01 4 -4.58010630e+01 -2.11578530e-01 -1.37240926e+01 5 -1.97176843e+00 -3.35795599e+01 -3.52447928e+01 6 3.70745183e+01 3.60388722e+01 -5.45185900e+01 7 2.30242141e+01 -7.38895749e+01 1.65817531e+01 8 -2.39280167e+00 1.13273178e+01 1.14282110e+01 9 -7.70982485e+00 5.02699521e+00 -3.43140749e+00 10 -4.53055475e+00 9.54250116e+00 -8.91642638e+00 11 -2.31603185e+01 2.70130424e+01 -2.45758319e+01 12 -1.41670387e+01 7.49167451e+00 -9.11329593e+00 13 1.01334386e+01 2.99227911e+01 -3.31196342e+01 14 4.98394409e+00 6.49355115e+00 -1.46166747e+01 15 5.90807345e+01 7.60950076e+00 -3.35459107e+01 16 1.55277625e+01 2.31842810e+01 -3.95364251e+01 17 -3.50068920e+01 -3.72113965e+01 -9.01945848e+00 18 5.35222798e+00 -7.04031166e+00 -3.67099410e+00 19 -5.99522127e+00 -1.73858621e+01 5.66814795e+01 20 -1.16842578e+01 4.66536920e+00 1.54054252e+01 21 -1.01863801e+01 -3.64529248e+01 -4.60436387e+01 22 3.77648794e+01 1.27968951e+01 1.71626747e+01 23 4.76792736e+01 -2.04972762e+01 4.88304217e+01 24 -1.78898658e+01 -1.08404870e+01 2.22815909e+01 25 -3.55055590e+01 1.31837189e+01 4.86039250e+00 26 -1.47734090e+01 2.10741705e+01 2.14342032e+01 27 -1.66407426e+01 1.93925377e+01 3.19185670e+01 28 -1.04809102e+01 1.18733360e+01 1.89222023e+01 29 -2.57339708e+01 -1.66771564e+01 4.23605418e+01 30 3.43859209e+01 3.72697896e+01 2.48781490e+01 31 3.94200041e+01 1.83256378e+01 4.04822536e+00 32 2.49797520e+00 1.14461462e+01 1.15959435e+01 MIXED STRUCTURE (pbc=False)-- Species = C Si (Configuration in file "config-F-CSi.xyz") ----------------------------------------------------------------------------------------------------- Energy = 19.92505422077393 Forces: 1 -1.51510033e+01 -3.32106534e+01 -4.67605014e+01 2 -5.85436811e+00 -4.11927177e+00 -9.26648671e+00 3 1.70317737e+01 -1.57427883e+01 1.41886583e+01 4 -2.12164892e+01 4.29160164e+01 3.18635546e+01 5 1.18213139e+01 -7.92831125e+00 -1.18084217e+01 6 1.93556552e+00 2.26386838e+00 -6.75288621e+00 7 7.69960391e+00 -7.30099790e+00 -6.34865108e+00 8 -2.05029420e-01 2.44795793e+00 4.57829539e+00 9 -1.44663772e+01 -1.14936889e+00 -7.03087989e+00 10 -1.47587717e+01 3.72716728e+01 -3.99022653e+01 11 -3.16255757e+01 -2.79631393e+01 3.90903034e+01 12 -1.63021323e+01 6.59282105e+00 5.69156642e+00 13 5.03541230e+01 -1.25033561e+01 -4.03229632e+01 14 -5.04596637e+00 -2.66558035e+00 2.64010012e+00 15 5.57310657e+00 1.39936218e+00 6.90426521e+00 16 3.04078395e+01 2.16584367e+01 1.67309091e+01 17 -2.02392634e+01 -1.58300766e+01 -1.06654767e+01 18 5.64851593e+00 1.71328861e+00 -1.33702327e+01 19 8.95267772e-02 -1.82904423e+01 2.97316790e+01 20 -2.48501469e+01 -8.31238183e+00 1.64823545e+01 21 5.20162039e-01 -1.14144736e+01 -4.32962515e+00 22 7.06317199e+00 6.97688082e+00 5.82999397e+00 23 7.75824909e+00 1.43130796e+00 5.54742385e+00 24 1.16328684e+01 5.05063864e+00 1.09270141e+01 25 -2.19987499e+01 -5.45867726e-01 -1.78758301e+01 26 5.91966131e+00 3.08169067e+01 -1.23964618e+01 27 5.63998321e+00 -5.08394686e-01 3.69379472e+01 28 1.33256390e-01 2.77321667e-01 4.95892831e-01 29 8.61283921e+00 -7.87318765e-01 -6.08822267e+00 30 2.49787422e+00 1.28289713e+00 -2.19035857e+00 31 2.51692318e+00 -2.28544300e+00 1.52674897e+00 32 8.85751566e+00 8.45848878e+00 5.94255624e+00 MIXED STRUCTURE (pbc=True)-- Species = C Si (Configuration in file "config-T-CSi.xyz") ----------------------------------------------------------------------------------------------------- Energy = 74.71615721757016 Forces: 1 9.89483042e+00 -1.32298302e+01 -6.87392863e+01 2 -7.56461631e-01 -6.20349224e+00 -1.83900325e+00 3 3.48712453e+01 1.95256789e+01 2.95733556e+01 4 1.78716673e+00 7.12961454e+01 3.62737752e+01 5 1.39521317e+01 5.34828549e+00 -1.71853090e+01 6 -8.42459364e+00 1.03996883e+01 -9.70219588e+00 7 -4.87795222e+01 -1.81164564e+01 1.43187787e+01 8 -3.83011622e-01 4.57139819e-01 3.92503721e+00 9 -1.63231277e+01 -4.19719965e-01 -5.94439005e+00 10 -1.14963682e+01 1.21345293e+01 -4.84230310e+01 11 -3.15526686e+01 -4.07889839e+01 4.07341183e+01 12 -2.12236045e+01 -3.41782204e+01 1.62083216e+01 13 4.53125802e+01 -1.37756598e+01 -3.40830185e+01 14 -1.11054052e+01 -9.25823262e+00 -1.94306853e+00 15 6.41883976e+00 2.13090295e+00 8.90324139e+00 16 3.37494366e+01 1.11461922e+01 2.14823895e+01 17 -9.86877066e+00 -1.39614188e+01 -1.09334850e+01 18 3.65134881e+00 2.17717592e-01 -1.37111233e+01 19 5.93264903e-01 -2.30085144e+00 3.22326522e+01 20 -1.58886153e+01 1.60763790e+00 7.89678995e+00 21 1.99614435e+00 -3.95878577e+00 -6.05926307e+00 22 3.33643719e+00 9.98701108e+00 4.81612748e+00 23 -9.10882524e+00 -8.32587993e+00 4.05849173e+00 24 1.15246766e+01 5.13688520e+00 9.51583997e+00 25 -2.06625744e+01 1.11877163e+00 -1.84036654e+01 26 3.50381293e+00 1.14658975e+01 -2.15078892e+01 27 7.98282042e+00 1.16882179e+00 3.05753473e+01 28 -2.89633457e+00 -3.03975574e+00 2.15758089e+00 29 8.16746846e+00 -1.07699832e-01 -5.97280886e+00 30 5.54665209e+00 6.05703443e-01 -4.90660943e+00 31 5.09811220e+00 1.73632078e+00 -3.41595342e+00 32 1.10829150e+01 2.18165769e+00 1.00982531e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==95645== Memcheck, a memory error detector ==95645== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==95645== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info ==95645== Command: python runner2.py Tersoff_LAMMPS_Tersoff_1994_SiC__MO_794973922560_000 ==95645== ==96805== Warning: invalid file descriptor 255988 in syscall close() ==96805== Warning: invalid file descriptor 255989 in syscall close() ==96805== Warning: invalid file descriptor 255990 in syscall close() ==96805== Warning: invalid file descriptor 255991 in syscall close() ==96805== Use --log-fd= to select an alternative log fd. ==96805== Warning: invalid file descriptor 255992 in syscall close() ==96805== Warning: invalid file descriptor 255993 in syscall close() ==95645== ==95645== HEAP SUMMARY: ==95645== in use at exit: 2,259,527 bytes in 1,705 blocks ==95645== total heap usage: 89,330 allocs, 87,625 frees, 58,442,144 bytes allocated ==95645== ==95645== LEAK SUMMARY: ==95645== definitely lost: 0 bytes in 0 blocks ==95645== indirectly lost: 0 bytes in 0 blocks ==95645== possibly lost: 180,827 bytes in 103 blocks ==95645== still reachable: 2,078,668 bytes in 1,601 blocks ==95645== of which reachable via heuristic: ==95645== stdstring : 38 bytes in 1 blocks ==95645== suppressed: 32 bytes in 1 blocks ==95645== Rerun with --leak-check=full to see details of leaked memory ==95645== ==95645== For lists of detected and suppressed errors, rerun with: -s ==95645== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 8144 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.