!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_MunetohMotookaMoriguchi_2007_SiO__MO_501246546792_000 Supported species : O Si 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 = 3260.788818869596 Forces: 1 -9.38903892e+01 -1.94219559e+02 -2.97061836e+02 2 -1.77542579e+02 2.78481603e+02 -2.15858447e+02 3 1.73691962e+02 -2.22439386e+02 -1.37019395e+02 4 -1.81416894e+02 2.16906030e+02 9.89690850e+01 5 1.15362525e+02 -4.48312492e+02 1.14477691e+01 6 1.18088948e+02 -2.61433624e+01 -1.31986214e+02 7 -2.13192108e+02 -6.52512961e+02 -8.20960382e+02 8 -5.32580380e+01 -4.58918907e+02 -2.45054520e+01 9 -1.30325276e+02 -1.73012810e+02 -4.52477053e+02 10 -3.88028665e+00 5.13809284e+02 -6.20496534e+02 11 -2.55500339e+02 -5.57249892e+02 4.13768480e+00 12 -3.68149754e+02 2.64254517e+02 8.31334397e+01 13 -2.02175649e+02 2.25141761e+01 -9.09970732e+02 14 2.25075621e+02 2.42325680e+02 -2.10990838e+02 15 7.00946573e+02 -1.21654591e+01 3.64318049e+02 16 9.24668938e+01 4.54407788e+02 4.63286201e+02 17 -4.04882255e+02 -1.06497521e+02 3.84422584e+01 18 1.13722688e+02 2.84327468e+02 -1.97446204e+02 19 1.39814810e+02 -4.05735241e+02 2.17130108e+02 20 -2.12742644e+02 1.13096044e+02 2.58590050e+02 21 -1.74421866e+02 -1.72698194e+02 5.35042693e+01 22 6.05075617e+02 5.88600553e+02 7.67713880e+02 23 1.06505085e+02 -4.67718924e+01 1.46174381e+02 24 8.05798207e+01 -6.42199465e+00 2.14868382e+02 25 -3.59076815e+02 -4.12956794e+00 -5.25015910e+01 26 6.98672304e+01 4.24744388e+02 -1.88542213e+02 27 3.94366759e+02 -6.73985766e+02 2.62948033e+02 28 -9.21291541e+02 5.90874193e+02 2.25466648e+02 29 -9.08362431e+01 -1.18811267e+02 1.34032686e+02 30 2.75662136e+02 2.69278203e+02 2.18272678e+02 31 2.70557069e+02 -9.69748271e+01 2.61236718e+02 32 3.60798941e+02 1.13381175e+02 4.36144568e+02 MONOATOMIC STRUCTURE (pbc=True)-- Species = O (Configuration in file "config-T-O.xyz") ----------------------------------------------------------------------------------------------------- Energy = 3260.788818869596 Forces: 1 -9.38903892e+01 -1.94219559e+02 -2.97061836e+02 2 -1.77542579e+02 2.78481603e+02 -2.15858447e+02 3 1.73691962e+02 -2.22439386e+02 -1.37019395e+02 4 -1.81416894e+02 2.16906030e+02 9.89690850e+01 5 1.15362525e+02 -4.48312492e+02 1.14477691e+01 6 1.18088948e+02 -2.61433624e+01 -1.31986214e+02 7 -2.13192108e+02 -6.52512961e+02 -8.20960382e+02 8 -5.32580380e+01 -4.58918907e+02 -2.45054520e+01 9 -1.30325276e+02 -1.73012810e+02 -4.52477053e+02 10 -3.88028665e+00 5.13809284e+02 -6.20496534e+02 11 -2.55500339e+02 -5.57249892e+02 4.13768480e+00 12 -3.68149754e+02 2.64254517e+02 8.31334397e+01 13 -2.02175649e+02 2.25141761e+01 -9.09970732e+02 14 2.25075621e+02 2.42325680e+02 -2.10990838e+02 15 7.00946573e+02 -1.21654591e+01 3.64318049e+02 16 9.24668938e+01 4.54407788e+02 4.63286201e+02 17 -4.04882255e+02 -1.06497521e+02 3.84422584e+01 18 1.13722688e+02 2.84327468e+02 -1.97446204e+02 19 1.39814810e+02 -4.05735241e+02 2.17130108e+02 20 -2.12742644e+02 1.13096044e+02 2.58590050e+02 21 -1.74421866e+02 -1.72698194e+02 5.35042693e+01 22 6.05075617e+02 5.88600553e+02 7.67713880e+02 23 1.06505085e+02 -4.67718924e+01 1.46174381e+02 24 8.05798207e+01 -6.42199465e+00 2.14868382e+02 25 -3.59076815e+02 -4.12956794e+00 -5.25015910e+01 26 6.98672304e+01 4.24744388e+02 -1.88542213e+02 27 3.94366759e+02 -6.73985766e+02 2.62948033e+02 28 -9.21291541e+02 5.90874193e+02 2.25466648e+02 29 -9.08362431e+01 -1.18811267e+02 1.34032686e+02 30 2.75662136e+02 2.69278203e+02 2.18272678e+02 31 2.70557069e+02 -9.69748271e+01 2.61236718e+02 32 3.60798941e+02 1.13381175e+02 4.36144568e+02 MONOATOMIC STRUCTURE (pbc=False)-- Species = Si (Configuration in file "config-F-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 255.90090354987882 Forces: 1 -2.76113821e+01 -4.19664915e+01 -5.51943402e+01 2 1.74623491e+01 5.66156920e-01 -5.21772785e+01 3 1.53170943e+01 -3.80276289e+01 1.69721569e+01 4 -4.26976168e+01 3.32472241e+01 2.09647123e+01 5 6.59447186e+00 -1.60970866e+01 -2.13153156e+01 6 2.21486442e+01 2.55339442e+01 -4.50995631e+01 7 2.98831677e+01 -4.80118316e+01 1.98490442e+01 8 -1.12809060e+01 1.69336267e+01 1.87824792e+01 9 -1.22564420e+01 6.12367674e+00 -1.89935551e+01 10 -6.23331737e+01 4.85893728e+01 -3.71084734e+01 11 3.51405713e+01 -1.23306823e+00 -3.81696750e+01 12 -1.60950097e+01 2.19504310e+01 -3.39353839e+00 13 1.94470104e+01 -9.25961843e+01 -6.46426971e+01 14 3.17421870e+01 1.80587118e+01 -2.36696700e+01 15 2.89997324e+01 -1.48254879e+01 -2.32565094e+01 16 1.54768227e+01 7.62546852e+01 7.31167278e+01 17 -1.91187643e+01 -2.03302275e+01 3.26796876e+01 18 9.84182313e+00 -1.05967887e+01 3.33456707e+01 19 -1.27892178e+01 -7.89019522e+00 1.03359849e+01 20 -1.97500548e+01 -1.85440443e+01 9.54071506e+00 21 -9.42220111e+00 -2.08947677e+01 -2.21777918e+01 22 2.93639285e+01 -1.32476295e+01 -6.12670038e+00 23 2.22629907e+01 -1.43459007e+01 2.23181559e+01 24 -1.43239153e+01 7.81002072e+00 2.88458774e+01 25 -9.06406997e+01 -3.29612521e+01 2.73326902e+01 26 4.15391489e+01 6.19250728e+01 -1.33717789e+01 27 2.01435693e+01 -1.30346348e+01 3.25712954e+01 28 -3.43617299e+01 3.10825719e+01 2.85960664e+01 29 -1.65640290e+01 -8.34887004e+00 -9.75803750e+00 30 1.49518931e+01 3.49131091e+01 1.49636420e+01 31 2.33437519e+01 7.75143713e+00 2.83208344e+01 32 5.58598561e+00 2.22120483e+01 1.59191840e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Si (Configuration in file "config-T-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 255.90090354987882 Forces: 1 -2.76113821e+01 -4.19664915e+01 -5.51943402e+01 2 1.74623491e+01 5.66156920e-01 -5.21772785e+01 3 1.53170943e+01 -3.80276289e+01 1.69721569e+01 4 -4.26976168e+01 3.32472241e+01 2.09647123e+01 5 6.59447186e+00 -1.60970866e+01 -2.13153156e+01 6 2.21486442e+01 2.55339442e+01 -4.50995631e+01 7 2.98831677e+01 -4.80118316e+01 1.98490442e+01 8 -1.12809060e+01 1.69336267e+01 1.87824792e+01 9 -1.22564420e+01 6.12367674e+00 -1.89935551e+01 10 -6.23331737e+01 4.85893728e+01 -3.71084734e+01 11 3.51405713e+01 -1.23306823e+00 -3.81696750e+01 12 -1.60950097e+01 2.19504310e+01 -3.39353839e+00 13 1.94470104e+01 -9.25961843e+01 -6.46426971e+01 14 3.17421870e+01 1.80587118e+01 -2.36696700e+01 15 2.89997324e+01 -1.48254879e+01 -2.32565094e+01 16 1.54768227e+01 7.62546852e+01 7.31167278e+01 17 -1.91187643e+01 -2.03302275e+01 3.26796876e+01 18 9.84182313e+00 -1.05967887e+01 3.33456707e+01 19 -1.27892178e+01 -7.89019522e+00 1.03359849e+01 20 -1.97500548e+01 -1.85440443e+01 9.54071506e+00 21 -9.42220111e+00 -2.08947677e+01 -2.21777918e+01 22 2.93639285e+01 -1.32476295e+01 -6.12670038e+00 23 2.22629907e+01 -1.43459007e+01 2.23181559e+01 24 -1.43239153e+01 7.81002072e+00 2.88458774e+01 25 -9.06406997e+01 -3.29612521e+01 2.73326902e+01 26 4.15391489e+01 6.19250728e+01 -1.33717789e+01 27 2.01435693e+01 -1.30346348e+01 3.25712954e+01 28 -3.43617299e+01 3.10825719e+01 2.85960664e+01 29 -1.65640290e+01 -8.34887004e+00 -9.75803750e+00 30 1.49518931e+01 3.49131091e+01 1.49636420e+01 31 2.33437519e+01 7.75143713e+00 2.83208344e+01 32 5.58598561e+00 2.22120483e+01 1.59191840e+01 MIXED STRUCTURE (pbc=False)-- Species = O Si (Configuration in file "config-F-OSi.xyz") ----------------------------------------------------------------------------------------------------- Energy = 13.81120493397865 Forces: 1 -1.40490746e+00 -5.71037141e+00 -8.07804907e+00 2 -5.14243669e+00 -3.29886439e+00 -1.35867257e+01 3 9.11091343e+00 -1.44034356e+01 -8.99967753e+00 4 -1.58709973e+01 1.33637480e+01 7.51192564e+00 5 4.81172095e+00 4.01094522e-01 -1.92483227e+00 6 9.18674512e+00 -1.16048246e+01 -9.95535550e+00 7 6.47872633e+00 -3.47826723e+00 -2.45071979e+00 8 1.03047709e+01 -1.19911969e+01 -3.87608511e+01 9 4.21342421e+00 3.54097287e+00 -2.97785619e-01 10 1.44615190e+00 -4.53255600e+00 1.99214061e+00 11 -6.51267127e+00 6.05030996e+00 2.14879964e+00 12 4.47290117e-01 -7.33884417e-02 2.94413314e+00 13 -3.90056502e+00 6.61707595e+00 -1.12301068e+01 14 2.52864046e+01 4.04683132e+00 -3.16672806e+01 15 3.22925481e+01 -1.58660302e+01 -1.18241474e+01 16 -3.87316528e+01 1.21625035e+01 1.41121550e+01 17 -1.06600365e+01 -7.27078923e+00 9.49615047e-01 18 -2.53197933e+01 -5.06921363e+00 1.81306336e+01 19 4.86326557e+00 -1.47767532e+01 8.88025038e+00 20 -1.17672960e+01 -1.67041934e+01 3.10249455e+01 21 3.76705734e+00 -1.24419577e+01 -1.76940463e+00 22 2.35490678e+00 8.51518107e+00 -5.28242963e+00 23 1.03120358e+01 -8.46530936e+00 6.08914668e+00 24 -6.66188483e+00 4.88792076e+00 1.07338671e+01 25 -1.08397810e+01 1.14200217e+01 -3.34106164e+01 26 -2.05362016e+00 3.56007680e+00 -2.02191254e+00 27 8.76234770e+00 4.78692402e+00 4.01949731e+00 28 -7.11443725e-01 1.96619405e+01 1.10146468e+01 29 -6.14113368e+00 1.48181958e+01 3.14386912e+01 30 7.88224327e+00 3.14998341e+01 4.88596374e+00 31 4.54403389e+00 -1.37213428e+01 2.07890547e+01 32 -3.46366227e-01 4.07586314e+00 4.59442839e+00 MIXED STRUCTURE (pbc=True)-- Species = O Si (Configuration in file "config-T-OSi.xyz") ----------------------------------------------------------------------------------------------------- Energy = 30.01673284184878 Forces: 1 1.17061941e+00 -1.40070063e+01 8.93531449e+00 2 -4.39566999e-01 -7.31855539e+00 -1.18789247e+01 3 8.99630426e+00 -1.42856560e+01 -7.81066747e+00 4 -1.41360967e+01 1.37313487e+01 7.77608382e+00 5 3.14399587e+00 1.97152190e+00 -3.17246033e+00 6 5.02452541e+00 -4.80779125e+00 -9.12381977e+00 7 1.86534072e+00 -2.15731651e+00 4.49341400e-01 8 1.55707430e+01 -1.65917451e+01 -3.86471345e+01 9 -2.01210006e+00 -6.41479828e-01 3.24964868e+00 10 7.49005727e+00 2.94221488e+00 7.70232874e-01 11 -6.52251623e+00 6.47757969e+00 -3.18922090e-02 12 -5.00125129e+00 3.62837434e+00 1.65667743e+00 13 -4.59150638e+00 6.41953048e+00 -1.01183347e+01 14 2.66051867e+01 3.53705327e+00 -2.71897144e+01 15 2.72000503e+01 -1.61765890e+01 -2.22222116e+01 16 -4.05706404e+01 1.01556453e+01 2.00101837e+01 17 -1.11653597e+01 -6.50150357e+00 3.12829192e-01 18 -2.52718944e+01 -4.84192350e+00 1.83542801e+01 19 8.49787064e+00 8.77491727e+00 2.93695499e+00 20 -1.71360359e+00 -1.73423879e+01 2.96933481e+01 21 4.03027384e+00 -1.22595464e+01 -3.91694023e+00 22 -1.52407788e+00 3.37472352e+00 -8.14177447e+00 23 5.12581864e-01 -4.95917312e+00 6.52633602e+00 24 -6.26430080e+00 9.47331552e+00 9.76687374e+00 25 1.43079488e+01 3.22301790e+00 -4.21449750e+01 26 -2.58494816e-02 -1.05636289e+00 -3.75383471e+00 27 9.97708793e+00 4.97776033e+00 2.80825662e+00 28 1.14382476e+01 1.77631844e+01 1.31082552e+01 29 -6.47617996e+00 1.49266372e+01 3.14530488e+01 30 3.93261501e+00 3.44920143e+01 -7.53507349e+00 31 -3.10213480e+01 -1.23211081e+01 3.26929429e+01 32 6.97284317e+00 -1.06006940e+01 5.18714946e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==5086== Memcheck, a memory error detector ==5086== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==5086== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info ==5086== Command: python runner2.py Tersoff_LAMMPS_MunetohMotookaMoriguchi_2007_SiO__MO_501246546792_000 ==5086== ==5642== Warning: invalid file descriptor 255988 in syscall close() ==5642== Warning: invalid file descriptor 255989 in syscall close() ==5642== Warning: invalid file descriptor 255990 in syscall close() ==5642== Warning: invalid file descriptor 255991 in syscall close() ==5642== Use --log-fd= to select an alternative log fd. ==5642== Warning: invalid file descriptor 255992 in syscall close() ==5642== Warning: invalid file descriptor 255993 in syscall close() ==5086== ==5086== HEAP SUMMARY: ==5086== in use at exit: 2,207,767 bytes in 1,649 blocks ==5086== total heap usage: 91,307 allocs, 89,658 frees, 71,844,296 bytes allocated ==5086== ==5086== LEAK SUMMARY: ==5086== definitely lost: 0 bytes in 0 blocks ==5086== indirectly lost: 0 bytes in 0 blocks ==5086== possibly lost: 198,622 bytes in 101 blocks ==5086== still reachable: 2,009,113 bytes in 1,547 blocks ==5086== suppressed: 32 bytes in 1 blocks ==5086== Rerun with --leak-check=full to see details of leaked memory ==5086== ==5086== For lists of detected and suppressed errors, rerun with: -s ==5086== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 9402 from 558) ================================================================================ 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.