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_ErhartJuslinGoy_2006_ZnO__MO_616776018688_004 Supported species : O Zn 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 = -2.1820214295660567 Forces: 1 3.09097604e-01 -1.91816213e+00 -2.41918646e+00 2 -1.59778626e+00 -8.81623174e-01 -2.07089831e+00 3 1.50103028e+00 -4.65024448e+00 -6.21601378e+00 4 -2.31833612e+00 2.59233868e+00 2.10322812e+00 5 2.37805920e+00 -1.35890335e+00 -8.83421481e-01 6 4.23259068e-01 -1.72867333e+00 -1.03312163e+00 7 4.72835175e-01 -4.41033311e+00 -6.03861905e+00 8 -1.97477665e+00 -1.55044681e+00 8.36986880e-01 9 -7.51169209e-01 4.52696174e-01 -3.68515033e-01 10 -2.08413858e+00 3.42884030e-01 -1.77914219e+00 11 -1.21972208e-01 -1.07030287e+00 -2.26817263e+00 12 -2.83012826e-01 3.81888481e-01 -1.85322049e+00 13 -3.93273568e+00 -2.17114063e+00 -6.04206693e+00 14 1.60770387e+00 2.70268376e+00 -2.07812618e+00 15 5.31378410e+00 -7.33725590e-01 2.61374108e+00 16 2.48654496e+00 3.84060102e+00 2.11334167e-01 17 -5.22553063e+00 -2.90632950e+00 1.92369368e+00 18 3.12277323e+00 5.39589654e+00 3.70733061e+00 19 1.09935863e+00 -2.05065493e+00 1.83667326e+00 20 -1.98481047e+00 7.58280911e-01 4.48753718e-01 21 -1.64127306e-01 -1.06308225e+00 1.38342942e+00 22 3.70059440e+00 1.87517532e+00 4.55326113e+00 23 1.29841254e-01 -5.95265751e-02 -2.03117238e-01 24 6.74590152e-02 -2.22848112e-01 2.64078899e-01 25 -4.01804219e+00 4.32400021e-01 2.16217950e+00 26 -1.43548056e+00 3.49344148e+00 3.11474526e+00 27 1.67252298e+00 -2.82725806e+00 1.40664300e+00 28 -3.71274929e+00 3.16055323e+00 -2.50213675e-01 29 1.69221600e+00 1.29619662e+00 3.18758623e+00 30 6.51991838e-01 1.79060849e+00 2.78966312e+00 31 5.32493036e-01 2.22150843e-01 4.19953225e-01 32 2.44310334e+00 8.65459297e-01 5.40553762e-01 MONOATOMIC STRUCTURE (pbc=True)-- Species = O (Configuration in file "config-T-O.xyz") ----------------------------------------------------------------------------------------------------- Energy = -2.1820214295660567 Forces: 1 3.09097604e-01 -1.91816213e+00 -2.41918646e+00 2 -1.59778626e+00 -8.81623174e-01 -2.07089831e+00 3 1.50103028e+00 -4.65024448e+00 -6.21601378e+00 4 -2.31833612e+00 2.59233868e+00 2.10322812e+00 5 2.37805920e+00 -1.35890335e+00 -8.83421481e-01 6 4.23259068e-01 -1.72867333e+00 -1.03312163e+00 7 4.72835175e-01 -4.41033311e+00 -6.03861905e+00 8 -1.97477665e+00 -1.55044681e+00 8.36986880e-01 9 -7.51169209e-01 4.52696174e-01 -3.68515033e-01 10 -2.08413858e+00 3.42884030e-01 -1.77914219e+00 11 -1.21972208e-01 -1.07030287e+00 -2.26817263e+00 12 -2.83012826e-01 3.81888481e-01 -1.85322049e+00 13 -3.93273568e+00 -2.17114063e+00 -6.04206693e+00 14 1.60770387e+00 2.70268376e+00 -2.07812618e+00 15 5.31378410e+00 -7.33725590e-01 2.61374108e+00 16 2.48654496e+00 3.84060102e+00 2.11334167e-01 17 -5.22553063e+00 -2.90632950e+00 1.92369368e+00 18 3.12277323e+00 5.39589654e+00 3.70733061e+00 19 1.09935863e+00 -2.05065493e+00 1.83667326e+00 20 -1.98481047e+00 7.58280911e-01 4.48753718e-01 21 -1.64127306e-01 -1.06308225e+00 1.38342942e+00 22 3.70059440e+00 1.87517532e+00 4.55326113e+00 23 1.29841254e-01 -5.95265751e-02 -2.03117238e-01 24 6.74590152e-02 -2.22848112e-01 2.64078899e-01 25 -4.01804219e+00 4.32400021e-01 2.16217950e+00 26 -1.43548056e+00 3.49344148e+00 3.11474526e+00 27 1.67252298e+00 -2.82725806e+00 1.40664300e+00 28 -3.71274929e+00 3.16055323e+00 -2.50213675e-01 29 1.69221600e+00 1.29619662e+00 3.18758623e+00 30 6.51991838e-01 1.79060849e+00 2.78966312e+00 31 5.32493036e-01 2.22150843e-01 4.19953225e-01 32 2.44310334e+00 8.65459297e-01 5.40553762e-01 MONOATOMIC STRUCTURE (pbc=False)-- Species = Zn (Configuration in file "config-F-Zn.xyz") ----------------------------------------------------------------------------------------------------- Energy = 126.94385519276116 Forces: 1 -1.82453146e+01 -1.48964214e+01 -1.29121152e+01 2 1.74959348e+01 2.23884581e+01 -1.50898129e+01 3 8.14471380e+00 -3.21558706e+01 -1.63477256e+01 4 -2.11478471e+01 1.50104577e+01 -9.26744227e+00 5 -5.01399805e+00 -8.24911441e+00 -7.99307582e+00 6 1.60576846e+01 3.36395843e+00 -1.15096589e+01 7 1.71470443e+01 -2.41209219e+01 -9.68612930e-01 8 -1.11486126e+01 1.31828944e+01 -2.37675034e+00 9 -4.94778484e+00 2.53168815e+00 -7.47568094e+00 10 -5.88884319e+00 3.08731189e+00 -2.04010726e+00 11 1.60180956e+01 -1.00454103e+01 -1.41024440e+01 12 -1.98819658e+01 2.49781737e+01 -2.68925127e+01 13 -4.30058537e+00 2.37366239e+00 -4.70102362e+00 14 6.73179837e+00 4.60140149e+00 -4.41537047e+00 15 1.33056680e+01 -6.89044458e+00 -6.68637265e+00 16 -8.08019810e+00 9.83158291e+00 -8.46444376e-01 17 -2.28088478e+01 -3.23800676e+01 1.58521996e+01 18 8.91377978e+00 3.01438640e+01 5.37204105e+00 19 -1.23970012e+01 -1.53875814e+01 2.60782659e+01 20 -1.55248575e+01 -1.53036907e+00 1.72028265e+01 21 1.85277271e+01 -2.01432217e+01 -6.13567719e+00 22 9.96401836e+00 1.10667253e+01 6.95953746e-01 23 4.68211602e-01 -8.81183318e+00 1.07165555e+01 24 7.73517116e+00 -2.30769306e+00 1.76377670e+01 25 -3.55185219e+01 -3.51946886e+01 -5.52196251e+00 26 3.16862811e+01 2.93135777e+01 -8.51446353e+00 27 2.22440649e+01 -1.66335782e+01 2.31613646e+01 28 -2.64348713e+01 3.33999715e+01 3.69272216e+01 29 -2.05747285e+00 7.26719291e+00 -1.24891041e+01 30 1.73587798e+01 1.18063052e+01 -5.53435313e+00 31 1.07984550e+01 -5.30836715e+00 1.65244283e+01 32 -9.20070618e+00 9.70835747e+00 1.16520868e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Zn (Configuration in file "config-T-Zn.xyz") ----------------------------------------------------------------------------------------------------- Energy = 126.94385519276116 Forces: 1 -1.82453146e+01 -1.48964214e+01 -1.29121152e+01 2 1.74959348e+01 2.23884581e+01 -1.50898129e+01 3 8.14471380e+00 -3.21558706e+01 -1.63477256e+01 4 -2.11478471e+01 1.50104577e+01 -9.26744227e+00 5 -5.01399805e+00 -8.24911441e+00 -7.99307582e+00 6 1.60576846e+01 3.36395843e+00 -1.15096589e+01 7 1.71470443e+01 -2.41209219e+01 -9.68612930e-01 8 -1.11486126e+01 1.31828944e+01 -2.37675034e+00 9 -4.94778484e+00 2.53168815e+00 -7.47568094e+00 10 -5.88884319e+00 3.08731189e+00 -2.04010726e+00 11 1.60180956e+01 -1.00454103e+01 -1.41024440e+01 12 -1.98819658e+01 2.49781737e+01 -2.68925127e+01 13 -4.30058537e+00 2.37366239e+00 -4.70102362e+00 14 6.73179837e+00 4.60140149e+00 -4.41537047e+00 15 1.33056680e+01 -6.89044458e+00 -6.68637265e+00 16 -8.08019810e+00 9.83158291e+00 -8.46444376e-01 17 -2.28088478e+01 -3.23800676e+01 1.58521996e+01 18 8.91377978e+00 3.01438640e+01 5.37204105e+00 19 -1.23970012e+01 -1.53875814e+01 2.60782659e+01 20 -1.55248575e+01 -1.53036907e+00 1.72028265e+01 21 1.85277271e+01 -2.01432217e+01 -6.13567719e+00 22 9.96401836e+00 1.10667253e+01 6.95953746e-01 23 4.68211602e-01 -8.81183318e+00 1.07165555e+01 24 7.73517116e+00 -2.30769306e+00 1.76377670e+01 25 -3.55185219e+01 -3.51946886e+01 -5.52196251e+00 26 3.16862811e+01 2.93135777e+01 -8.51446353e+00 27 2.22440649e+01 -1.66335782e+01 2.31613646e+01 28 -2.64348713e+01 3.33999715e+01 3.69272216e+01 29 -2.05747285e+00 7.26719291e+00 -1.24891041e+01 30 1.73587798e+01 1.18063052e+01 -5.53435313e+00 31 1.07984550e+01 -5.30836715e+00 1.65244283e+01 32 -9.20070618e+00 9.70835747e+00 1.16520868e+01 MIXED STRUCTURE (pbc=False)-- Species = O Zn (Configuration in file "config-F-OZn.xyz") ----------------------------------------------------------------------------------------------------- Energy = 841.1729497967672 Forces: 1 -7.90230758e+00 -4.49403551e+01 -4.20124236e+01 2 5.74192275e+01 -2.50451476e+01 -6.37165240e+01 3 7.15456745e+01 -1.76427214e+02 -4.44347938e+01 4 -1.65784484e+02 1.07191023e+02 3.97119984e+01 5 6.93890463e+01 -2.43955592e+01 -5.85386472e+01 6 1.27232960e+01 -6.95135552e+00 -2.86104156e+01 7 9.24708814e+01 -3.01971782e+01 -8.33977820e+01 8 3.85836109e+01 -3.19888402e+01 -1.40621440e+02 9 -7.54328250e+01 2.10247568e+01 -2.33342510e+01 10 5.01666107e+01 1.03994061e+02 -1.33068457e+02 11 -7.40314692e+01 -6.24682260e+01 7.10682063e+01 12 -7.71034863e+01 1.78649904e+01 3.72359242e+00 13 3.57012027e+01 -2.51500067e+01 -7.73597124e+01 14 1.40000393e+01 2.00189937e+01 -9.29290401e+00 15 5.87528214e+01 -2.47429328e+00 -3.89060160e+01 16 7.21926875e+01 7.83543000e+01 1.81758042e+01 17 -8.75652687e+01 -5.81504066e+01 3.46766825e+01 18 1.80722544e+01 3.34609677e+01 -4.18006178e+01 19 -5.06914649e+01 -6.16479163e+01 1.20833978e+02 20 -3.23188400e+01 -8.80181736e+00 7.88818357e+01 21 -5.65116693e+01 -1.11127801e+02 7.25882625e+01 22 5.96491942e+01 1.51993060e+01 9.02628328e+00 23 1.90996824e+01 -2.57280406e+01 3.44684814e+01 24 5.90908971e+01 -2.40827545e+01 7.52207737e+01 25 -8.53189839e+01 -1.51448427e+01 -5.40537704e+01 26 1.54344246e+01 7.99484693e+01 5.74698163e+01 27 -1.45027543e+01 5.36796703e+01 7.34459946e+01 28 -2.15152890e+01 2.07681444e+01 3.44734498e+01 29 -5.79261201e+01 1.13098198e+02 6.75668104e+01 30 1.96658522e+01 2.70774928e+01 -8.49234659e+00 31 1.52249410e+01 -2.93317154e+00 2.99640352e+01 32 2.74226186e+01 4.59745520e+01 2.63440970e+01 MIXED STRUCTURE (pbc=True)-- Species = O Zn (Configuration in file "config-T-OZn.xyz") ----------------------------------------------------------------------------------------------------- Energy = 1423.8977737126286 Forces: 1 -1.25014865e+01 -2.26560730e+01 -5.37020235e+01 2 9.28416270e+01 -1.46121617e+01 -1.72959736e+01 3 5.68008151e+01 -1.17733620e+02 -5.16917780e+01 4 -1.64717548e+02 1.27648138e+02 9.56454293e+01 5 6.21924191e+01 4.67523705e+01 -8.59720341e+01 6 2.38173985e+01 -1.94888992e+01 -7.22533488e+01 7 1.10605080e+02 7.53548103e+01 -9.75994341e+01 8 2.88328501e+01 -1.97135793e+01 -1.28600005e+02 9 -7.60573492e+01 2.11101878e+01 1.74254170e+00 10 1.17891198e+02 4.28705844e+01 -1.21341226e+02 11 -7.48620955e+01 -6.84948449e+01 7.71831996e+01 12 -9.25303722e+01 3.98394848e+00 -1.42498012e+01 13 3.00512619e+01 -4.29246852e+01 -6.44114710e+01 14 1.53843668e+01 1.97779652e+01 2.10785147e+01 15 1.69961292e+01 -1.33378535e+01 1.33021910e+01 16 9.91448719e+01 -5.61680051e+01 5.41516997e+01 17 -6.37346842e+01 -5.26203482e+00 2.49797695e+01 18 1.71643687e+01 7.28973760e+01 -6.65770509e+01 19 -4.23365133e+01 -5.62287772e+01 8.55217811e+01 20 -4.11670365e+01 -2.87459613e+01 9.62663430e+01 21 -9.91359467e+01 -8.84930163e+01 1.13046081e+02 22 4.15486032e+01 3.40496291e+01 -2.03035524e+01 23 -1.21786554e+01 -2.46837061e+01 5.93500543e+01 24 5.99644654e+01 -1.43152435e+01 5.35565331e+01 25 -7.38398742e+01 -4.36311964e+01 -7.49659901e+01 26 4.31671949e+01 1.02746112e+01 6.08083523e+01 27 -1.23295800e+01 5.20705432e+01 1.55278205e+00 28 3.89287967e-01 3.03201968e+01 3.15224478e+00 29 -5.91640017e+01 1.09327979e+02 6.66176137e+01 30 1.71769646e+01 -1.68884596e+01 2.11454626e+01 31 -3.80553806e+01 -1.31402783e+01 -7.43754291e+00 32 2.86416212e+01 2.00800551e+01 2.73006373e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==1819516== Memcheck, a memory error detector ==1819516== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==1819516== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info ==1819516== Command: python runner2.py Tersoff_LAMMPS_ErhartJuslinGoy_2006_ZnO__MO_616776018688_004 ==1819516== ==1820801== Warning: invalid file descriptor 1024 in syscall close() ==1820801== Warning: invalid file descriptor 1025 in syscall close() ==1820801== Warning: invalid file descriptor 1026 in syscall close() ==1820801== Warning: invalid file descriptor 1027 in syscall close() ==1820801== Use --log-fd= to select an alternative log fd. ==1820801== Warning: invalid file descriptor 1028 in syscall close() ==1820801== Warning: invalid file descriptor 1029 in syscall close() ==1819516== ==1819516== HEAP SUMMARY: ==1819516== in use at exit: 2,259,511 bytes in 1,705 blocks ==1819516== total heap usage: 88,763 allocs, 87,058 frees, 66,825,700 bytes allocated ==1819516== ==1819516== LEAK SUMMARY: ==1819516== definitely lost: 0 bytes in 0 blocks ==1819516== indirectly lost: 0 bytes in 0 blocks ==1819516== possibly lost: 180,827 bytes in 103 blocks ==1819516== still reachable: 2,078,652 bytes in 1,601 blocks ==1819516== of which reachable via heuristic: ==1819516== stdstring : 38 bytes in 1 blocks ==1819516== suppressed: 32 bytes in 1 blocks ==1819516== Rerun with --leak-check=full to see details of leaked memory ==1819516== ==1819516== For lists of detected and suppressed errors, rerun with: -s ==1819516== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 8126 from 572) ================================================================================ 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) ===