Enter a model name: === Verification check vc-memory-leak start (2022-11-30 10:16:18) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_NordAlbeErhart_2003_GaN__MO_612061685362_004 Supported species : Ga N random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Ga (Configuration in file "config-F-Ga.xyz") ----------------------------------------------------------------------------------------------------- Energy = 48.35004349261608 Forces: 1 -4.98407714e+00 -4.97139870e+00 -6.93763334e+00 2 -5.28934598e+00 5.91336784e+00 -8.33580957e+00 3 -1.45222337e+00 -7.60567699e+00 4.15758062e+00 4 -7.08697905e+00 1.02767570e-01 2.63299742e+00 5 8.53780285e+00 -8.24658809e+00 -5.04825165e+00 6 5.53517115e+00 6.10290609e-02 -7.25493172e+00 7 4.55516291e+00 -1.87708470e+01 -1.24547112e+01 8 -8.33369529e+00 -1.07874435e+01 -1.39572480e+01 9 -1.14305022e+01 -3.41958969e+00 -1.38605355e+01 10 -5.26255487e+00 1.25395468e+01 -1.31949570e+01 11 -1.07317591e+01 -9.44446265e+00 5.65825660e+00 12 -1.19789319e+01 1.10926648e+01 2.40450087e+00 13 8.74886713e+00 -6.93747513e+00 -2.13098069e+01 14 6.95504679e+00 5.12186688e+00 -4.07180968e+00 15 2.35781474e+01 3.18036841e+00 -5.61070251e+00 16 7.71748882e+00 2.02015897e+01 6.42771806e+00 17 -9.36646955e+00 -6.93849618e+00 -3.98240993e+00 18 4.29241163e+00 4.52297246e+00 -4.22453272e+00 19 3.16901008e+00 -9.86586421e+00 8.49060505e+00 20 -5.50790230e+00 4.77656535e+00 6.76585612e+00 21 -5.60880482e+00 -9.32632066e+00 5.74164879e+00 22 1.55920964e+01 7.65640041e+00 8.76405484e+00 23 2.30928486e+00 -8.15074413e-01 8.00084040e+00 24 9.36857640e-01 -3.40476132e+00 1.25381109e+01 25 -1.49350247e+01 -1.44912963e+00 2.96728118e+00 26 -7.94742745e+00 1.35018779e+01 -2.40931288e+00 27 -7.76296476e+00 -1.16843041e+01 1.03647956e+01 28 -7.56216958e+00 5.53245870e+00 3.65846654e+00 29 2.07271887e+00 -1.49936181e+00 8.61634916e+00 30 1.00128635e+01 8.26110996e+00 2.62403526e-01 31 1.28376355e+01 -2.88246116e+00 1.59194256e+01 32 8.39026663e+00 1.55846694e+01 9.28176134e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ga (Configuration in file "config-T-Ga.xyz") ----------------------------------------------------------------------------------------------------- Energy = 48.35004349261608 Forces: 1 -4.98407714e+00 -4.97139870e+00 -6.93763334e+00 2 -5.28934598e+00 5.91336784e+00 -8.33580957e+00 3 -1.45222337e+00 -7.60567699e+00 4.15758062e+00 4 -7.08697905e+00 1.02767570e-01 2.63299742e+00 5 8.53780285e+00 -8.24658809e+00 -5.04825165e+00 6 5.53517115e+00 6.10290609e-02 -7.25493172e+00 7 4.55516291e+00 -1.87708470e+01 -1.24547112e+01 8 -8.33369529e+00 -1.07874435e+01 -1.39572480e+01 9 -1.14305022e+01 -3.41958969e+00 -1.38605355e+01 10 -5.26255487e+00 1.25395468e+01 -1.31949570e+01 11 -1.07317591e+01 -9.44446265e+00 5.65825660e+00 12 -1.19789319e+01 1.10926648e+01 2.40450087e+00 13 8.74886713e+00 -6.93747513e+00 -2.13098069e+01 14 6.95504679e+00 5.12186688e+00 -4.07180968e+00 15 2.35781474e+01 3.18036841e+00 -5.61070251e+00 16 7.71748882e+00 2.02015897e+01 6.42771806e+00 17 -9.36646955e+00 -6.93849618e+00 -3.98240993e+00 18 4.29241163e+00 4.52297246e+00 -4.22453272e+00 19 3.16901008e+00 -9.86586421e+00 8.49060505e+00 20 -5.50790230e+00 4.77656535e+00 6.76585612e+00 21 -5.60880482e+00 -9.32632066e+00 5.74164879e+00 22 1.55920964e+01 7.65640041e+00 8.76405484e+00 23 2.30928486e+00 -8.15074413e-01 8.00084040e+00 24 9.36857640e-01 -3.40476132e+00 1.25381109e+01 25 -1.49350247e+01 -1.44912963e+00 2.96728118e+00 26 -7.94742745e+00 1.35018779e+01 -2.40931288e+00 27 -7.76296476e+00 -1.16843041e+01 1.03647956e+01 28 -7.56216958e+00 5.53245870e+00 3.65846654e+00 29 2.07271887e+00 -1.49936181e+00 8.61634916e+00 30 1.00128635e+01 8.26110996e+00 2.62403526e-01 31 1.28376355e+01 -2.88246116e+00 1.59194256e+01 32 8.39026663e+00 1.55846694e+01 9.28176134e+00 MONOATOMIC STRUCTURE (pbc=False)-- Species = N (Configuration in file "config-F-N.xyz") ----------------------------------------------------------------------------------------------------- Energy = -45.59496553715769 Forces: 1 1.12259271e+00 2.00437723e+00 1.40110393e+00 2 -7.78442693e-01 2.09164205e-01 -3.62385440e+00 3 -1.55262446e-01 -2.25164712e-01 -1.80864998e+00 4 -3.36706765e+00 -3.10338130e+00 -5.33535753e-01 5 1.92416724e+00 3.01598214e+00 8.52350315e-01 6 -5.83462707e+00 -2.46758800e+00 -6.97440006e-01 7 -3.06845551e+00 2.33580634e+00 1.71059363e+00 8 2.49103767e+00 -2.95518138e+00 8.15361063e-01 9 -2.96201537e-03 -5.71088882e-02 -7.75622880e-01 10 -2.66757747e-01 1.50814923e+00 4.15215980e-01 11 3.95257040e+00 -3.65732625e+00 -3.59605893e-01 12 -2.91381993e+00 3.34390823e+00 1.26525424e+00 13 5.83415015e+00 -1.86301267e+00 -1.54028833e+00 14 -2.70407715e+00 -2.95076997e+00 2.22544047e+00 15 3.52126076e-01 1.75227759e+00 2.96962839e-01 16 -2.23041052e-02 1.03058002e+00 -8.81481136e-02 17 1.86310184e+00 -1.99396835e+00 -1.40994395e+00 18 -1.99357404e+00 -1.63270377e+00 -1.69270526e+00 19 -1.26388798e+00 -5.01440025e+00 1.38294082e+00 20 -3.65358309e+00 4.36833998e+00 1.95366440e+00 21 4.90359872e+00 -5.22824270e+00 -3.59428313e+00 22 1.77770247e+00 4.21475871e+00 -2.70608017e+00 23 -1.98489811e+00 -6.35344999e-01 2.50587878e-01 24 4.88990400e+00 2.95743799e-01 6.05250823e+00 25 -2.40127715e+00 2.48466667e+00 2.24435449e+00 26 5.02041635e-01 1.59148953e+00 -2.21244488e+00 27 -3.24164021e+00 2.49920045e+00 1.64525483e+00 28 4.42865841e-01 -2.18476239e+00 -1.08345860e+00 29 5.56677995e+00 6.38107286e+00 1.54535119e+00 30 -3.87622446e+00 -3.37869822e+00 -4.27100443e-01 31 3.16975995e-01 -4.98657009e-01 -1.11699671e+00 32 1.58924667e+00 8.10793893e-01 -3.86785806e-01 MONOATOMIC STRUCTURE (pbc=True)-- Species = N (Configuration in file "config-T-N.xyz") ----------------------------------------------------------------------------------------------------- Energy = -45.59496553715769 Forces: 1 1.12259271e+00 2.00437723e+00 1.40110393e+00 2 -7.78442693e-01 2.09164205e-01 -3.62385440e+00 3 -1.55262446e-01 -2.25164712e-01 -1.80864998e+00 4 -3.36706765e+00 -3.10338130e+00 -5.33535753e-01 5 1.92416724e+00 3.01598214e+00 8.52350315e-01 6 -5.83462707e+00 -2.46758800e+00 -6.97440006e-01 7 -3.06845551e+00 2.33580634e+00 1.71059363e+00 8 2.49103767e+00 -2.95518138e+00 8.15361063e-01 9 -2.96201537e-03 -5.71088882e-02 -7.75622880e-01 10 -2.66757747e-01 1.50814923e+00 4.15215980e-01 11 3.95257040e+00 -3.65732625e+00 -3.59605893e-01 12 -2.91381993e+00 3.34390823e+00 1.26525424e+00 13 5.83415015e+00 -1.86301267e+00 -1.54028833e+00 14 -2.70407715e+00 -2.95076997e+00 2.22544047e+00 15 3.52126076e-01 1.75227759e+00 2.96962839e-01 16 -2.23041052e-02 1.03058002e+00 -8.81481136e-02 17 1.86310184e+00 -1.99396835e+00 -1.40994395e+00 18 -1.99357404e+00 -1.63270377e+00 -1.69270526e+00 19 -1.26388798e+00 -5.01440025e+00 1.38294082e+00 20 -3.65358309e+00 4.36833998e+00 1.95366440e+00 21 4.90359872e+00 -5.22824270e+00 -3.59428313e+00 22 1.77770247e+00 4.21475871e+00 -2.70608017e+00 23 -1.98489811e+00 -6.35344999e-01 2.50587878e-01 24 4.88990400e+00 2.95743799e-01 6.05250823e+00 25 -2.40127715e+00 2.48466667e+00 2.24435449e+00 26 5.02041635e-01 1.59148953e+00 -2.21244488e+00 27 -3.24164021e+00 2.49920045e+00 1.64525483e+00 28 4.42865841e-01 -2.18476239e+00 -1.08345860e+00 29 5.56677995e+00 6.38107286e+00 1.54535119e+00 30 -3.87622446e+00 -3.37869822e+00 -4.27100443e-01 31 3.16975995e-01 -4.98657009e-01 -1.11699671e+00 32 1.58924667e+00 8.10793893e-01 -3.86785806e-01 MIXED STRUCTURE (pbc=False)-- Species = Ga N (Configuration in file "config-F-GaN.xyz") ----------------------------------------------------------------------------------------------------- Energy = 246.18211344988256 Forces: 1 -1.87556359e+01 -1.85647039e+01 -2.13829967e+01 2 -2.23637487e+01 2.44459953e+01 -5.48397440e+01 3 -3.84398801e+00 -5.42733146e+01 3.79006571e+01 4 -7.30173033e+01 3.63483482e+01 -3.12271685e+01 5 2.58725573e+01 -2.32122201e+01 -3.17897896e+01 6 1.60164101e+01 -1.02661066e+00 -6.17066829e+00 7 7.18858767e-01 -2.86696380e+00 -5.18707444e+00 8 9.27223283e+01 7.93525293e+00 -2.40735772e+01 9 -1.95548352e+01 -1.29858332e+01 -1.73759816e+01 10 2.27600071e+00 1.66526918e+01 -1.29221096e+01 11 -7.98099744e+00 -2.11414160e+01 -3.65756904e+01 12 -2.92946885e+01 3.65537070e+01 1.30677980e+01 13 1.81820555e+01 1.46118834e+01 -2.08611759e+01 14 1.75934431e+01 4.42389585e+01 -6.92248328e+01 15 2.74541852e+01 -4.42040931e+01 3.08684178e+01 16 -1.28249725e+01 1.91424401e+01 1.46674908e+01 17 -1.86196035e+01 -5.52607081e+01 7.06266008e-01 18 -2.52106877e+01 -2.24631780e+01 3.21881896e+01 19 -2.82459334e+00 -3.50000614e+01 4.18227430e+01 20 -2.17097663e+01 2.16265636e+01 4.42028668e+01 21 -5.37772263e+00 -6.13282672e+01 -5.88250431e+01 22 2.62162083e+01 9.02964007e+00 -8.08651216e+00 23 1.13471094e+01 -1.05106992e+01 1.44700467e+01 24 2.72316344e+01 4.38644803e+01 6.97812844e+01 25 -3.69330479e+01 2.93056449e+00 -5.96188675e+00 26 -1.12192724e+00 4.40029374e+01 2.34842211e+01 27 1.77271480e+01 -4.00133229e+01 3.17430815e+01 28 -3.36834299e+01 4.07676008e+01 5.58524889e+00 29 2.25474513e+01 7.82087371e+00 2.15575761e+01 30 9.78218898e+00 1.61356337e+01 1.25223672e+01 31 4.23879775e+00 -1.79053322e+00 9.58263392e+00 32 1.31905707e+01 1.85343542e+01 3.53362050e-01 MIXED STRUCTURE (pbc=True)-- Species = Ga N (Configuration in file "config-T-GaN.xyz") ----------------------------------------------------------------------------------------------------- Energy = 481.2199318421281 Forces: 1 -2.80822041e+01 6.91832200e+00 -4.11286165e+01 2 -1.80597247e+01 3.65694936e+01 -4.08390152e+01 3 -6.29339806e-02 -1.79052923e+01 5.20818736e+01 4 -6.18216466e+01 5.21069250e+01 -2.51255320e+01 5 2.42701829e+01 -8.11038497e+00 -1.52432768e+01 6 3.73656133e+00 1.78950220e+01 -2.53128044e+00 7 -1.77195933e+01 -1.33947943e+01 5.33537319e-01 8 8.99904047e+01 1.16824303e+01 -2.23766987e+01 9 -8.52207708e+00 -3.16042075e+01 4.54371783e+01 10 1.07436795e+01 -3.08476304e+01 -2.36480394e+01 11 -1.28153968e+01 -1.36795885e+01 -3.60978502e+01 12 -1.11623425e+01 2.66718395e+01 1.41363283e+01 13 2.48662060e+01 1.45333260e+01 -5.93568622e+00 14 5.63058073e+01 1.60882982e+01 -3.74126754e+01 15 6.76062964e+00 -4.14917693e+01 2.72601582e+00 16 -2.30664802e+01 -5.78802581e+00 3.52211691e+01 17 2.64851376e+00 -5.39343715e+01 1.79888392e+01 18 -2.51429682e+01 -2.03953254e+01 3.31140437e+01 19 -6.37193118e+00 -2.54476150e+01 2.98176885e+01 20 -1.41512618e+01 2.23662759e+01 2.49833141e+01 21 -5.30095012e+00 -5.14508857e+01 -7.16187155e+01 22 1.12153897e+01 2.49440640e+01 -7.57037820e+00 23 -3.68070052e+00 -1.74070220e+01 1.51400052e+01 24 2.96918345e+01 5.10471136e+01 6.22640827e+01 25 -2.03698259e+01 -9.87755959e-01 -1.86833814e+01 26 -8.85220014e-02 2.11788247e+01 2.23886677e+01 27 3.03190457e+01 -5.25595110e+01 1.88060887e+01 28 -3.03675118e+01 8.52269661e+01 -3.32002460e+01 29 1.94898010e+01 -1.71961707e+00 2.15891373e+01 30 -1.45983438e+00 4.33131465e+00 1.52670142e+01 31 -2.19196483e+01 -1.05056501e+01 9.39934837e+00 32 1.27497472e-01 5.66923128e+00 -3.94829402e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==1819522== Memcheck, a memory error detector ==1819522== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==1819522== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info ==1819522== Command: python runner2.py Tersoff_LAMMPS_NordAlbeErhart_2003_GaN__MO_612061685362_004 ==1819522== ==1820807== Warning: invalid file descriptor 1024 in syscall close() ==1820807== Warning: invalid file descriptor 1025 in syscall close() ==1820807== Warning: invalid file descriptor 1026 in syscall close() ==1820807== Warning: invalid file descriptor 1027 in syscall close() ==1820807== Use --log-fd= to select an alternative log fd. ==1820807== Warning: invalid file descriptor 1028 in syscall close() ==1820807== Warning: invalid file descriptor 1029 in syscall close() ==1819522== ==1819522== HEAP SUMMARY: ==1819522== in use at exit: 2,259,511 bytes in 1,705 blocks ==1819522== total heap usage: 88,718 allocs, 87,013 frees, 66,837,721 bytes allocated ==1819522== ==1819522== LEAK SUMMARY: ==1819522== definitely lost: 0 bytes in 0 blocks ==1819522== indirectly lost: 0 bytes in 0 blocks ==1819522== possibly lost: 180,827 bytes in 103 blocks ==1819522== still reachable: 2,078,652 bytes in 1,601 blocks ==1819522== of which reachable via heuristic: ==1819522== stdstring : 38 bytes in 1 blocks ==1819522== suppressed: 32 bytes in 1 blocks ==1819522== Rerun with --leak-check=full to see details of leaked memory ==1819522== ==1819522== For lists of detected and suppressed errors, rerun with: -s ==1819522== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 8034 from 565) ================================================================================ 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. === Verification check vc-memory-leak end (2022-11-30 10:16:49) ===