!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_KinaciHaskinsSevik_2012_BNC__MO_105008013807_000 Supported species : B C N random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = B (Configuration in file "config-F-B.xyz") ----------------------------------------------------------------------------------------------------- Energy = 130.28050864540654 Forces: 1 -2.78922403e+01 -7.06542809e+00 -1.10756487e+01 2 2.40166547e+01 9.83935139e+00 -2.60687652e+01 3 -2.97952703e+00 -1.21969957e+01 -1.81923801e+00 4 -1.90921689e+01 -1.63869009e+00 -9.80228718e+00 5 7.77064827e+00 -1.89977256e+01 -2.78653507e+01 6 1.60252467e+01 -2.77249880e+01 -2.57107683e+01 7 -6.95942599e+00 1.64429269e+01 1.33762948e+01 8 1.89062949e+01 2.60498052e+00 -1.87477312e+01 9 8.13404628e+00 -8.13741688e+00 -1.78339496e+01 10 -1.47275939e+01 -9.19435274e+00 -3.17063204e+01 11 -2.55714253e+01 3.87290781e+01 -1.02107307e+01 12 -3.72717105e+01 2.93746098e+01 1.33597908e+01 13 -7.48306272e-01 -6.69436358e+00 -2.19866008e+01 14 -6.95937252e+01 -6.64182837e+00 1.33731593e+01 15 1.01074675e+02 2.69086686e+00 7.47636824e+00 16 1.30030573e+01 3.48850725e+01 5.68352019e+00 17 -1.00061022e+01 -8.14367349e+00 -1.97404839e+00 18 8.12456362e+00 -1.65740851e+01 1.11684091e+01 19 -5.69865247e+00 -2.61545821e+01 2.40837700e+01 20 4.19478753e+00 -8.84234951e-01 5.60428798e+00 21 1.38035533e-01 -7.50424336e+01 2.89332585e+01 22 2.36403000e+01 -1.23399839e+01 2.18685709e+00 23 1.44929167e+01 3.51049572e-01 1.59906758e+01 24 -1.25730080e+01 -1.07905974e+01 9.73053538e+00 25 -3.20935419e+01 3.60834291e+01 -2.13841776e-01 26 -1.38726967e+01 1.49907982e+01 -2.60847285e+01 27 -2.38823913e+00 1.60647170e+01 1.60541143e+01 28 -1.93145973e+01 9.52619137e+00 1.20500551e+01 29 2.25314896e-01 2.42789153e+01 8.06928016e+00 30 2.21238017e+01 7.72566597e+00 5.87764758e+00 31 2.82744210e+01 7.75575929e-01 1.39235409e+00 32 1.06381968e+01 3.85815124e+00 3.66896310e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = B (Configuration in file "config-T-B.xyz") ----------------------------------------------------------------------------------------------------- Energy = 130.28050864540654 Forces: 1 -2.78922403e+01 -7.06542809e+00 -1.10756487e+01 2 2.40166547e+01 9.83935139e+00 -2.60687652e+01 3 -2.97952703e+00 -1.21969957e+01 -1.81923801e+00 4 -1.90921689e+01 -1.63869009e+00 -9.80228718e+00 5 7.77064827e+00 -1.89977256e+01 -2.78653507e+01 6 1.60252467e+01 -2.77249880e+01 -2.57107683e+01 7 -6.95942599e+00 1.64429269e+01 1.33762948e+01 8 1.89062949e+01 2.60498052e+00 -1.87477312e+01 9 8.13404628e+00 -8.13741688e+00 -1.78339496e+01 10 -1.47275939e+01 -9.19435274e+00 -3.17063204e+01 11 -2.55714253e+01 3.87290781e+01 -1.02107307e+01 12 -3.72717105e+01 2.93746098e+01 1.33597908e+01 13 -7.48306272e-01 -6.69436358e+00 -2.19866008e+01 14 -6.95937252e+01 -6.64182837e+00 1.33731593e+01 15 1.01074675e+02 2.69086686e+00 7.47636824e+00 16 1.30030573e+01 3.48850725e+01 5.68352019e+00 17 -1.00061022e+01 -8.14367349e+00 -1.97404839e+00 18 8.12456362e+00 -1.65740851e+01 1.11684091e+01 19 -5.69865247e+00 -2.61545821e+01 2.40837700e+01 20 4.19478753e+00 -8.84234951e-01 5.60428798e+00 21 1.38035533e-01 -7.50424336e+01 2.89332585e+01 22 2.36403000e+01 -1.23399839e+01 2.18685709e+00 23 1.44929167e+01 3.51049572e-01 1.59906758e+01 24 -1.25730080e+01 -1.07905974e+01 9.73053538e+00 25 -3.20935419e+01 3.60834291e+01 -2.13841776e-01 26 -1.38726967e+01 1.49907982e+01 -2.60847285e+01 27 -2.38823913e+00 1.60647170e+01 1.60541143e+01 28 -1.93145973e+01 9.52619137e+00 1.20500551e+01 29 2.25314896e-01 2.42789153e+01 8.06928016e+00 30 2.21238017e+01 7.72566597e+00 5.87764758e+00 31 2.82744210e+01 7.75575929e-01 1.39235409e+00 32 1.06381968e+01 3.85815124e+00 3.66896310e+01 MONOATOMIC STRUCTURE (pbc=False)-- Species = C (Configuration in file "config-F-C.xyz") ----------------------------------------------------------------------------------------------------- Energy = 4417.542384287916 Forces: 1 -1.65703939e+02 -7.98752615e+01 -2.10895168e+02 2 1.10055970e+02 -2.61288180e+02 -4.03521597e+02 3 5.87838563e+01 -2.75152192e+02 -1.02769499e+02 4 -4.02516723e+02 -1.29927547e+02 -2.82272381e+02 5 -3.05355040e+01 -9.49809221e+01 -1.19331883e+02 6 2.93097915e+02 -3.09843770e+02 -2.50151250e+02 7 2.69964743e+02 -3.10471964e+02 -1.44743087e+02 8 -3.03941257e+02 -1.20771746e+02 -7.24446783e+02 9 -2.74398679e+02 -7.14886615e+00 -4.51716612e+02 10 -7.32125035e+01 3.06517990e+02 -2.39742603e+02 11 -2.79610985e+02 1.11271207e+02 -6.11872863e+02 12 -2.67214606e+02 2.84223367e+02 1.02273337e+02 13 -9.72861392e+01 1.53308080e+02 -1.89984863e+02 14 1.26274223e+02 9.91518478e+01 -4.50607920e+01 15 4.66507263e+02 3.85208871e+02 -1.05079691e+02 16 -7.18693012e+01 5.34207388e+02 -1.52215626e+02 17 -7.81172327e+02 -4.43799382e+02 -2.28324963e+02 18 2.06596044e+02 -4.83181348e+02 5.25794186e+01 19 4.08969346e+02 -4.46234323e+02 7.71264537e+02 20 -4.42857962e+02 -8.36054050e+01 3.35017633e+02 21 -2.47949799e+02 -5.82261659e+02 7.67116913e+01 22 7.16304326e+02 -1.21585246e+02 3.48576571e+02 23 2.89233308e+02 -3.06363951e+02 3.44007012e+02 24 1.42347560e+02 1.15341924e+01 3.85300026e+02 25 -9.32569942e+02 4.52790711e+02 -8.60585333e+01 26 -8.54057640e+01 5.10034613e+02 2.28046030e+02 27 8.27441090e+01 2.39671904e+02 7.96018736e+02 28 -2.37022264e+02 2.51871951e+02 2.01984665e+02 29 7.14007721e+02 2.07763631e+02 3.54236032e+02 30 4.41441029e+02 2.29862169e+02 7.18802443e+01 31 2.92948777e+02 8.42134102e+01 9.83885649e+01 32 7.39915027e+01 1.94860433e+02 1.81903695e+02 MONOATOMIC STRUCTURE (pbc=True)-- Species = C (Configuration in file "config-T-C.xyz") ----------------------------------------------------------------------------------------------------- Energy = 4417.542384287916 Forces: 1 -1.65703939e+02 -7.98752615e+01 -2.10895168e+02 2 1.10055970e+02 -2.61288180e+02 -4.03521597e+02 3 5.87838563e+01 -2.75152192e+02 -1.02769499e+02 4 -4.02516723e+02 -1.29927547e+02 -2.82272381e+02 5 -3.05355040e+01 -9.49809221e+01 -1.19331883e+02 6 2.93097915e+02 -3.09843770e+02 -2.50151250e+02 7 2.69964743e+02 -3.10471964e+02 -1.44743087e+02 8 -3.03941257e+02 -1.20771746e+02 -7.24446783e+02 9 -2.74398679e+02 -7.14886615e+00 -4.51716612e+02 10 -7.32125035e+01 3.06517990e+02 -2.39742603e+02 11 -2.79610985e+02 1.11271207e+02 -6.11872863e+02 12 -2.67214606e+02 2.84223367e+02 1.02273337e+02 13 -9.72861392e+01 1.53308080e+02 -1.89984863e+02 14 1.26274223e+02 9.91518478e+01 -4.50607920e+01 15 4.66507263e+02 3.85208871e+02 -1.05079691e+02 16 -7.18693012e+01 5.34207388e+02 -1.52215626e+02 17 -7.81172327e+02 -4.43799382e+02 -2.28324963e+02 18 2.06596044e+02 -4.83181348e+02 5.25794186e+01 19 4.08969346e+02 -4.46234323e+02 7.71264537e+02 20 -4.42857962e+02 -8.36054050e+01 3.35017633e+02 21 -2.47949799e+02 -5.82261659e+02 7.67116913e+01 22 7.16304326e+02 -1.21585246e+02 3.48576571e+02 23 2.89233308e+02 -3.06363951e+02 3.44007012e+02 24 1.42347560e+02 1.15341924e+01 3.85300026e+02 25 -9.32569942e+02 4.52790711e+02 -8.60585333e+01 26 -8.54057640e+01 5.10034613e+02 2.28046030e+02 27 8.27441090e+01 2.39671904e+02 7.96018736e+02 28 -2.37022264e+02 2.51871951e+02 2.01984665e+02 29 7.14007721e+02 2.07763631e+02 3.54236032e+02 30 4.41441029e+02 2.29862169e+02 7.18802443e+01 31 2.92948777e+02 8.42134102e+01 9.83885649e+01 32 7.39915027e+01 1.94860433e+02 1.81903695e+02 MONOATOMIC STRUCTURE (pbc=False)-- Species = N (Configuration in file "config-F-N.xyz") ----------------------------------------------------------------------------------------------------- Energy = 69.9833042817161 Forces: 1 -1.12463623e+01 -1.07358970e+01 -8.84552914e+00 2 2.14225677e+00 -2.21480158e+00 -2.02074903e+01 3 -6.98752478e+00 -8.42093815e+00 -1.95263190e+00 4 -2.42722913e+01 -9.22513190e+00 -8.56581481e+00 5 5.17951694e+00 -1.60807811e+01 -1.54323170e+01 6 5.95678536e+00 -7.96672776e+00 -7.07359376e+00 7 1.14313139e+01 -6.44444165e+00 -1.62612756e+00 8 3.26009709e-01 -1.60903165e+01 -7.49046295e+00 9 -6.04692653e+00 4.72670488e+00 -5.54361242e+00 10 -1.45733866e+01 1.50231451e+01 -2.43745464e+01 11 5.69334851e+00 1.46248017e+01 -1.19768655e+01 12 -9.23164425e+00 1.08949296e+01 -1.23966710e+01 13 3.21303616e+00 -3.00074157e+00 -1.69318660e+01 14 7.46565123e+00 1.05614870e+01 -7.29908581e+00 15 1.87214211e+01 1.37256425e+01 -6.11487770e+00 16 1.99592199e+01 5.97475075e+00 6.07288430e+00 17 -6.63761220e+00 -1.64142494e+01 -5.63313392e+00 18 -3.08120139e+00 -1.26635078e+01 1.24355654e+01 19 1.16225501e+00 -6.95992634e+00 1.43443436e+01 20 -1.52594357e+01 -2.39499587e+00 1.04190477e+01 21 4.98713271e+00 -1.56255377e+01 8.90207159e+00 22 1.49160115e+01 -2.85503704e-01 1.12273464e+01 23 9.09755125e-01 -2.27596092e-01 2.75333989e-01 24 1.11929196e+01 -6.28639419e+00 1.31395029e+01 25 -3.14059478e+01 1.28550190e+00 1.10263059e+01 26 1.01123584e-01 2.14634824e+01 7.60172952e+00 27 1.03588632e+00 7.73243273e+00 2.18269690e+01 28 -9.51522460e+00 1.21498566e+01 8.65617853e+00 29 6.17428340e+00 1.19633394e+01 1.51722413e+01 30 4.53531437e-01 3.41227790e+00 2.32457540e+00 31 1.57888115e+01 1.34107901e+00 1.04204143e+01 32 1.44728770e+00 6.15805685e+00 7.62011631e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = N (Configuration in file "config-T-N.xyz") ----------------------------------------------------------------------------------------------------- Energy = 69.9833042817161 Forces: 1 -1.12463623e+01 -1.07358970e+01 -8.84552914e+00 2 2.14225677e+00 -2.21480158e+00 -2.02074903e+01 3 -6.98752478e+00 -8.42093815e+00 -1.95263190e+00 4 -2.42722913e+01 -9.22513190e+00 -8.56581481e+00 5 5.17951694e+00 -1.60807811e+01 -1.54323170e+01 6 5.95678536e+00 -7.96672776e+00 -7.07359376e+00 7 1.14313139e+01 -6.44444165e+00 -1.62612756e+00 8 3.26009709e-01 -1.60903165e+01 -7.49046295e+00 9 -6.04692653e+00 4.72670488e+00 -5.54361242e+00 10 -1.45733866e+01 1.50231451e+01 -2.43745464e+01 11 5.69334851e+00 1.46248017e+01 -1.19768655e+01 12 -9.23164425e+00 1.08949296e+01 -1.23966710e+01 13 3.21303616e+00 -3.00074157e+00 -1.69318660e+01 14 7.46565123e+00 1.05614870e+01 -7.29908581e+00 15 1.87214211e+01 1.37256425e+01 -6.11487770e+00 16 1.99592199e+01 5.97475075e+00 6.07288430e+00 17 -6.63761220e+00 -1.64142494e+01 -5.63313392e+00 18 -3.08120139e+00 -1.26635078e+01 1.24355654e+01 19 1.16225501e+00 -6.95992634e+00 1.43443436e+01 20 -1.52594357e+01 -2.39499587e+00 1.04190477e+01 21 4.98713271e+00 -1.56255377e+01 8.90207159e+00 22 1.49160115e+01 -2.85503704e-01 1.12273464e+01 23 9.09755125e-01 -2.27596092e-01 2.75333989e-01 24 1.11929196e+01 -6.28639419e+00 1.31395029e+01 25 -3.14059478e+01 1.28550190e+00 1.10263059e+01 26 1.01123584e-01 2.14634824e+01 7.60172952e+00 27 1.03588632e+00 7.73243273e+00 2.18269690e+01 28 -9.51522460e+00 1.21498566e+01 8.65617853e+00 29 6.17428340e+00 1.19633394e+01 1.51722413e+01 30 4.53531437e-01 3.41227790e+00 2.32457540e+00 31 1.57888115e+01 1.34107901e+00 1.04204143e+01 32 1.44728770e+00 6.15805685e+00 7.62011631e+00 MIXED STRUCTURE (pbc=False)-- Species = B C N (Configuration in file "config-F-BCN.xyz") ----------------------------------------------------------------------------------------------------- Energy = 4242.007539837175 Forces: 1 -1.20659680e+03 -7.92224557e+02 -1.71516015e+03 2 3.60724225e+02 1.19093763e+02 -3.92244383e+02 3 1.15615225e+03 -9.83009067e+02 5.60315131e+02 4 -8.40853289e+02 1.09058107e+03 1.05408116e+03 5 -3.85607712e+02 -4.77810223e+02 -4.05187578e+02 6 6.85140872e+02 -3.92477274e+01 -8.00652239e+02 7 3.15421837e+02 -2.38135250e+02 1.57124989e+02 8 3.95811743e+02 -3.43537246e+02 3.98213714e+02 9 -3.28645009e+02 2.05613087e+02 -2.80830346e+01 10 7.97500469e+01 1.96391889e+02 -2.27297941e+02 11 -1.12189433e+01 -1.71510740e+02 -2.98716323e+02 12 -2.10865955e+02 1.87734739e+02 -4.45514684e+01 13 -4.64347718e+02 3.91599910e+02 -3.51102017e+02 14 1.31663915e+02 2.70333611e+02 -1.42495607e+02 15 3.69454180e+02 2.42653458e+02 4.77032167e+02 16 1.52790231e+01 1.66207592e+02 -1.02074226e+02 17 -4.05786531e+02 -4.82685556e+01 -2.97246821e+02 18 -4.21421118e+02 5.33511976e+02 -3.36883681e+01 19 -1.10586278e+02 -7.52484810e+02 8.60392324e+02 20 -4.36523789e+02 -3.17827977e+02 1.90803176e+02 21 8.01288045e+02 -4.38644759e+02 -2.48735569e+02 22 2.49393219e+02 -1.43451962e+01 3.43000704e+01 23 4.55528157e+02 -4.83107791e+02 7.29479467e+01 24 -3.30594672e+02 3.51699770e+02 1.55819557e+02 25 -3.97838683e+02 2.34140499e+02 1.72047309e+02 26 -1.90168792e+02 3.76497710e+02 -2.99183177e+01 27 2.40455971e+02 4.19450109e+02 3.64290812e+02 28 -6.18157947e+01 1.54095397e+02 2.27017163e+02 29 -3.15859951e+02 -3.73892607e+02 -8.09829400e+01 30 2.80252434e+02 4.67357850e+02 -3.25410344e+00 31 4.79672006e+02 -2.29703278e+02 1.83835347e+02 32 1.02743103e+02 2.96787357e+02 2.93170214e+02 MIXED STRUCTURE (pbc=True)-- Species = B C N (Configuration in file "config-T-BCN.xyz") ----------------------------------------------------------------------------------------------------- Energy = 6337.219753121708 Forces: 1 -1.05034977e+03 -6.62797952e+02 -1.61127234e+03 2 4.55651249e+02 1.07287115e+02 -2.30658409e+02 3 1.25622731e+03 -9.85656456e+02 6.96667371e+02 4 -6.22470531e+02 1.11490646e+03 1.15522674e+03 5 -5.24142248e+02 -2.47862597e+02 -3.62722292e+02 6 5.04939537e+02 2.07083853e+02 -3.12740159e+02 7 1.45715972e+02 -2.06200686e+02 3.31786868e+02 8 2.57932470e+02 -3.09362579e+02 6.55825394e+02 9 -1.28321976e+02 2.48229921e+02 1.14170515e+02 10 2.62138753e+02 1.60353555e+02 -2.49177247e-01 11 1.18820675e+02 -1.56232398e+02 -2.35690365e+02 12 -4.52931294e+01 4.35177586e+01 3.36513489e+01 13 -5.90696187e+02 4.88010054e+02 -1.39841488e+02 14 -6.33206416e+01 2.00399984e+02 -1.62732475e+01 15 1.48274919e+02 2.77188983e+02 5.58913477e+02 16 4.76406732e+01 -1.86881209e+02 3.30861074e+01 17 -3.53662563e+02 1.78306337e+01 -3.53624688e+02 18 -3.85322750e+02 6.52891585e+02 -1.20030517e+02 19 -1.00324987e+02 -6.76787979e+02 6.90003592e+02 20 -2.51796713e+02 -3.84841031e+02 -1.69195143e+01 21 8.00121304e+02 -2.53501843e+02 -2.60211139e+02 22 6.98652173e+01 -3.62616871e+00 4.24105707e+01 23 4.64632655e+02 -6.23354056e+02 -3.00262447e+02 24 -3.94808935e+02 2.66288175e+02 -5.67917488e+02 25 -4.79735774e+01 2.47433482e+02 -4.33650662e+01 26 -1.64460877e+02 8.64041134e+01 -7.38139158e+01 27 3.40763187e+02 4.36513638e+02 2.01451347e+02 28 1.72202334e+02 2.20155425e+02 1.73345620e+02 29 -3.45179014e+02 -4.64104474e+02 -1.56632347e+02 30 1.82772071e+02 4.30855175e+02 -7.69630706e+01 31 -2.44035380e+02 -2.86712289e+02 3.05872016e+01 32 8.44609540e+01 2.42571807e+02 1.62061523e+02 ================================================================================ VALGRIND OUTPUT ================================================================================ ==16027== Memcheck, a memory error detector ==16027== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==16027== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info ==16027== Command: python runner2.py Tersoff_LAMMPS_KinaciHaskinsSevik_2012_BNC__MO_105008013807_000 ==16027== ==17376== Warning: invalid file descriptor 4096 in syscall close() ==17376== Warning: invalid file descriptor 4097 in syscall close() ==17376== Warning: invalid file descriptor 4098 in syscall close() ==17376== Warning: invalid file descriptor 4099 in syscall close() ==17376== Use --log-fd= to select an alternative log fd. ==17376== Warning: invalid file descriptor 4100 in syscall close() ==17376== Warning: invalid file descriptor 4101 in syscall close() ==16027== ==16027== HEAP SUMMARY: ==16027== in use at exit: 2,203,223 bytes in 1,644 blocks ==16027== total heap usage: 117,500 allocs, 115,856 frees, 70,045,362 bytes allocated ==16027== ==16027== LEAK SUMMARY: ==16027== definitely lost: 0 bytes in 0 blocks ==16027== indirectly lost: 0 bytes in 0 blocks ==16027== possibly lost: 198,622 bytes in 101 blocks ==16027== still reachable: 2,004,569 bytes in 1,542 blocks ==16027== suppressed: 32 bytes in 1 blocks ==16027== Rerun with --leak-check=full to see details of leaked memory ==16027== ==16027== For lists of detected and suppressed errors, rerun with: -s ==16027== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 9399 from 586) ================================================================================ 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.