!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 ----------------------------------------------------------------------------------------------------- Results for KIM Model : Tersoff_LAMMPS_Tersoff_PRB39_1989_GeSi__MO_350526375143_001 Supported species : Ge Si random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Ge (Configuration in file "config-F-Ge.xyz") ----------------------------------------------------------------------------------------------------- Energy = 336.071326508 Forces: 1 -1.53275356e+01 -3.27264998e+01 -3.85864339e+01 2 -1.61050808e+01 5.95823233e+00 -3.55863032e+01 3 6.68786397e+00 -3.94780405e+01 -1.43397412e+01 4 -2.23343961e+01 3.87733000e+01 1.81413808e+01 5 8.67050763e+00 -3.50086753e+01 -2.15439302e+01 6 2.16669562e+01 5.72316830e+00 -3.16624445e+01 7 2.74104006e+01 -5.65376850e+01 -5.06121826e+01 8 -2.69768761e+01 -3.21110281e+01 5.81721196e+00 9 -3.33541387e+01 -7.12761483e+00 -4.27734575e+01 10 -2.53150969e+01 5.71142817e+01 -4.37319314e+01 11 -3.81763393e+01 -3.42507379e+01 3.98819541e+01 12 -2.38529871e+01 3.32842872e+01 -1.49513763e+01 13 2.99423126e+01 -2.00142166e+01 -9.18125501e+01 14 1.96556967e+01 1.65771745e+01 -1.52318356e+01 15 7.31352928e+01 -4.95717255e+00 -5.19876971e+00 16 1.09259033e+01 7.07756012e+01 3.22115883e+01 17 -3.26093811e+01 -1.86141797e+01 7.57657179e+00 18 4.88872202e+00 2.59848687e+01 2.09196896e+01 19 6.80611076e+00 -2.41421311e+01 1.65356882e+01 20 -1.54712228e+01 1.17404871e+01 1.30781329e+01 21 -2.11376689e+01 -2.87423693e+01 2.20338132e+01 22 4.25085272e+01 4.13565457e+01 4.47472431e+01 23 1.51351543e+01 -9.82485743e+00 2.94085352e+01 24 2.84033129e+00 3.41686617e+00 1.72723383e+01 25 -2.66143841e+01 -2.93897522e+01 1.51987451e+01 26 -2.30473222e+01 5.73202533e+01 -4.39676707e+01 27 6.43422435e+00 -6.92137725e+01 4.05048644e+01 28 -5.45350768e+01 4.46845161e+01 2.39754151e+01 29 -1.49007532e+01 -2.56924730e+01 1.55709317e+01 30 3.23562868e+01 3.38136749e+01 1.38969837e+01 31 5.01160757e+01 -1.34128261e+01 2.55004935e+01 32 3.05778935e+01 3.47207748e+01 4.77270460e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ge (Configuration in file "config-T-Ge.xyz") ----------------------------------------------------------------------------------------------------- Energy = 717.482575362 Forces: 1 4.87941534e+01 -4.68569336e+01 -6.20746831e+00 2 -5.28992920e+01 1.23510426e+01 2.55873430e+01 3 1.16682226e+01 5.59394671e+00 -7.37942661e+00 4 3.77815952e+01 6.20213527e+01 8.34586937e+00 5 9.79334165e+00 -1.07457455e+01 -1.06448571e+01 6 -3.91010902e+01 6.29757995e+01 7.95186983e+00 7 -2.04067411e+01 -4.85854510e+01 -5.41139217e+01 8 -3.00899641e+01 -3.11105412e+01 8.21530005e+00 9 -5.55711376e+01 -4.69844206e+01 3.14862711e+01 10 -4.14683781e+01 3.59591408e+01 -1.38968557e+01 11 -3.69321547e+01 -4.52925894e+01 4.23172920e+01 12 1.93250880e+01 2.19446617e+00 -2.87395910e+01 13 3.40232815e+01 -2.81377831e+01 -6.91100106e+01 14 -6.04259438e-01 4.23267383e-01 -1.72615490e+01 15 5.59685620e+01 -7.23661771e+00 -6.56669855e+00 16 1.62666876e+01 4.64449587e+01 4.78415779e+01 17 2.43942301e+01 -2.81805834e+01 1.62603450e+01 18 6.92271857e+00 3.56403806e+01 1.79135167e+01 19 7.58612911e+00 2.09428321e+01 1.47905433e+01 20 3.61822489e+01 6.55062458e+01 -1.97846498e+01 21 -2.35593914e+01 1.48364758e+00 2.45828005e+01 22 -1.11426716e+01 8.07846256e+01 6.16614804e+01 23 -3.92481252e+01 -7.01643696e+01 -2.24484104e+01 24 3.81605295e+01 1.35566290e+01 -4.96016368e+01 25 -4.83519830e+00 -4.07734229e+01 9.60065494e+00 26 -1.63779504e+01 7.60981937e+00 -5.99564758e+01 27 4.05197106e+01 -7.78525270e+01 -1.42974344e+01 28 -6.28738550e+01 3.93293501e+01 -1.08458929e+01 29 -1.58964197e+01 -3.34084838e+01 1.48258415e+01 30 -1.50684302e+01 5.63699452e+00 3.76874382e+01 31 2.75084042e+01 -1.25593363e+01 1.68076428e+01 32 5.11801560e+01 2.94343060e+01 4.97909213e+00 MONOATOMIC STRUCTURE (pbc=False)-- Species = Si (Configuration in file "config-F-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 213.541866536 Forces: 1 -1.45014499e+01 -1.26561506e+01 -1.75997006e+01 2 -1.87390145e+01 -2.75160845e+01 -6.41361072e+01 3 1.61246375e+00 -2.12799028e+01 -5.40728619e+00 4 -4.57412120e+01 -4.46583404e+00 7.28275428e+00 5 5.52492834e+00 -3.21081841e+01 -2.47365855e+01 6 1.32178114e+01 4.93029312e+00 -9.84006627e+00 7 1.32844948e+01 -1.26397702e+01 -1.47116390e-01 8 3.89745678e+01 -2.34712674e+01 3.24703312e+01 9 -2.03990287e+01 6.37711383e+00 -1.68060008e+01 10 -3.98857792e+01 6.74410269e+01 -1.43805650e+01 11 -2.75558630e+01 2.90564780e+01 2.61423582e+00 12 -2.82422797e+01 4.77041892e+01 -5.47140163e+01 13 4.34435079e+01 -3.03398554e+01 -5.03162078e+01 14 2.10021302e+01 5.74708129e+00 -1.35923270e+01 15 2.83409731e+01 1.64912994e+01 -1.75410237e+01 16 3.80744541e+00 2.36274167e+01 1.87982312e+01 17 -4.51413161e+01 -1.38473156e+01 -1.51606786e+01 18 2.50446782e+01 -3.11681358e+01 7.70556359e+00 19 2.75960134e+01 -2.03641251e+01 2.68620028e+01 20 -2.75161611e+01 1.10969833e+01 3.41666259e+01 21 1.49377748e+01 -9.13001453e+00 1.14026200e+01 22 2.27291459e+01 -1.54293302e+01 -3.33147390e+00 23 3.50011183e+00 -5.10985087e+00 3.84968662e+00 24 2.32062931e+00 -3.17250549e+01 2.03622911e+01 25 -3.34585674e+01 -5.04220746e+01 2.34157854e+01 26 3.94907118e+01 5.81795727e+01 5.34648086e+00 27 -2.68228247e+01 1.46412642e+01 2.27046064e+01 28 -2.64094741e+01 1.24979014e+01 3.64371528e+01 29 2.01737914e+01 9.15646299e+00 4.00499392e+01 30 2.06088569e+01 1.08381294e+01 -1.89811995e+01 31 2.53824695e+01 9.55309520e-01 1.41420166e+01 32 -1.65795354e+01 2.29324287e+01 1.90800312e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Si (Configuration in file "config-T-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 564.060270283 Forces: 1 1.32787347e+01 -1.49937184e+01 -1.71845024e+01 2 -1.54048475e+01 -3.84160192e+01 -3.68493729e+01 3 3.44912717e+00 2.58926699e+01 -1.59732332e+01 4 -3.43309696e+01 -3.76804689e+00 2.06678052e+01 5 -3.89157125e+00 -1.78640152e+01 -1.38286859e+01 6 1.58489157e+00 1.52401605e+01 2.39068996e+01 7 3.22502461e+01 3.17005359e+01 2.50885503e+01 8 3.81796376e+01 -2.15014285e+01 3.97209677e+01 9 -1.41789628e+01 5.83132063e+00 2.89616897e+01 10 -4.57512564e+01 7.03099659e+01 1.52586125e+01 11 -2.65001349e+01 1.92010316e+01 5.71302442e+00 12 -1.40300761e+01 2.39171953e+01 -6.81602332e+01 13 8.63230133e+01 -9.78024398e+00 2.97030928e+01 14 2.36172203e+01 -3.27090112e+00 4.14125756e+01 15 1.30342969e+01 1.39375101e+01 -1.94176098e+01 16 -3.13925591e+01 -3.29613440e+01 2.07482877e+01 17 -2.84449920e+01 5.39059001e+01 -3.00263786e+01 18 3.26048075e+01 -2.92330241e+01 6.18356503e+00 19 2.83586084e+01 2.69214923e+01 4.45222385e+01 20 -1.58112852e+01 7.70841760e+00 1.63997167e+00 21 8.78464666e+00 2.71464336e+01 6.05303302e+00 22 8.20165268e+00 -8.94123927e+00 -1.27282575e+01 23 -1.27983793e+00 4.78326680e+01 -3.16463639e+00 24 -4.15905498e-01 -2.85209592e+01 -2.16316498e+01 25 -2.21574485e+01 -6.47971138e+01 1.67967957e+01 26 5.69582018e+01 -8.83282122e+00 -1.75403632e+01 27 -5.84182181e+01 -1.47380756e+01 -7.26166121e+01 28 3.74367964e+01 -3.95243911e+00 5.41915364e+01 29 1.96205200e+01 1.00261886e+00 3.84959982e+01 30 -4.26542289e+01 -2.10531864e+01 -5.78983464e+01 31 -8.41813329e+00 -5.22025964e+01 -1.38639407e+01 32 -4.06019740e+01 4.27925227e+00 -1.81808219e+01 MIXED STRUCTURE (pbc=False)-- Species = Ge Si (Configuration in file "config-F-GeSi.xyz") ----------------------------------------------------------------------------------------------------- Energy = 209.054509934 Forces: 1 -1.53707547e+01 -3.24469830e+01 -3.60849134e+01 2 1.11399731e+01 1.08026246e+01 -2.57686484e+01 3 1.65682326e+01 -1.81942684e+01 4.53781768e+00 4 -3.38166217e+01 1.45914757e+01 7.96146642e+00 5 3.86038808e+00 -2.31940867e+01 -1.29618599e+01 6 1.29537538e+01 1.16151761e+01 -3.34187451e+01 7 1.67726906e+01 -3.31582364e+01 3.12827206e+00 8 -5.04937612e-02 -2.38813011e+01 4.97555852e-01 9 -1.45861443e+01 1.42890569e+01 -1.52606532e+01 10 -7.59763189e+00 1.47061873e+01 -8.38114042e+00 11 -3.81050231e+01 1.19325962e+01 -3.75867010e+00 12 -8.75234412e+00 1.32412229e+01 -9.29433308e+00 13 2.66294885e+01 -4.69194706e+00 -2.76458899e+01 14 9.57242007e+00 4.91808741e+00 -8.19293951e+00 15 3.82441763e+01 9.72152522e+00 -1.69136605e+01 16 -1.47328015e+01 3.91935791e+01 -2.48052493e+01 17 -2.50481549e+01 -2.00886419e+01 8.23170472e+00 18 -1.55467463e+01 -8.54686078e+00 -4.36773427e+01 19 -1.42417059e+01 -6.13247454e+01 3.01226399e+01 20 -3.72480277e+01 1.45734656e+01 1.64885871e+01 21 1.03150133e+01 -3.61938461e+01 -1.66415989e+01 22 1.51147692e+01 6.30777049e+00 1.91391514e+01 23 1.25405072e+01 -1.25168109e+01 1.13168316e+01 24 4.61362913e+01 2.08942064e+01 4.55236605e+01 25 -2.06786242e+01 9.71242546e-01 7.48288846e+00 26 -2.85291099e+01 2.35502329e+01 -1.93861833e+01 27 -1.18967161e+01 2.35312422e+01 5.27015172e+01 28 -1.69265747e+01 1.26115680e+01 1.26758933e+01 29 -1.44985943e+01 -3.82593632e+01 7.62441922e+00 30 7.43878837e+01 4.44380804e+01 1.08407796e+01 31 1.42955073e+01 -6.60063057e+00 3.01889959e+01 32 9.09497401e+00 2.72083817e+01 3.37296470e+01 MIXED STRUCTURE (pbc=True)-- Species = Ge Si (Configuration in file "config-T-GeSi.xyz") ----------------------------------------------------------------------------------------------------- Energy = 652.008110069 Forces: 1 -1.57725096e+01 -2.79233056e+00 -1.76267807e+01 2 2.20391901e+01 2.63694799e+01 1.53104482e+01 3 5.17188217e+01 2.55825237e+01 6.55917542e+00 4 6.95908486e+01 3.22465275e+01 2.78708413e+01 5 -7.83529466e+00 2.28224430e+01 1.13630246e+01 6 -6.09571139e+01 2.08094710e+01 -5.73873693e+01 7 -6.72191444e+01 -3.54781863e+01 -1.70877883e+01 8 -1.76128392e+01 -1.70565855e+01 2.23372786e+00 9 -1.79108495e+01 1.03630693e+01 1.85306975e+01 10 -1.29802676e+01 -3.54049586e+01 6.15680502e+01 11 -3.78795945e+01 1.11393674e+01 -2.92142363e+00 12 -1.16619080e+01 -6.29890476e+01 -5.25432174e+00 13 2.49937013e+01 -1.95778487e+01 -4.29695812e+00 14 1.72016635e+01 -4.38052144e+01 4.05588614e+01 15 -8.76226597e+01 3.64799210e-01 -9.75823370e+01 16 -1.76620687e+01 -9.69487532e+00 -3.42759554e+01 17 5.21147294e+01 -4.62160018e+01 6.84351669e+01 18 -1.31096707e+01 -6.86992958e+00 -5.54111480e+01 19 -1.69103985e+01 -4.74660015e+00 -1.36268358e+01 20 -1.29015242e+01 2.22716251e+01 7.47563774e+00 21 -4.67233314e+00 9.03002934e+00 -1.10332797e+01 22 -4.76736401e+01 3.38977775e+01 1.96718186e+01 23 1.37939301e+01 2.07084171e+01 -5.24791240e+01 24 5.31235672e+01 2.84874500e+01 2.87701711e+01 25 1.17184431e+02 4.11326524e+01 9.13107490e+01 26 -2.84855482e+01 4.71999021e+00 -2.41679592e+01 27 7.93400711e+00 2.20401393e+01 1.32890884e+01 28 -4.14948172e+01 -1.71868170e+01 -3.32056765e+01 29 -1.72771062e+01 -4.18122674e+01 9.96072237e-01 30 6.17019142e+01 4.11723535e+01 9.95555358e+00 31 -2.68494832e+00 -1.58912837e+01 1.28795784e+01 32 4.89274325e+01 -1.36361689e+01 -1.04217052e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==29298== Memcheck, a memory error detector ==29298== Copyright (C) 2002-2015, and GNU GPL'd, by Julian Seward et al. ==29298== Using Valgrind-3.11.0 and LibVEX; rerun with -h for copyright info ==29298== Command: python runner2.py Tersoff_LAMMPS_Tersoff_PRB39_1989_GeSi__MO_350526375143_001 ==29298== ==29298== ==29298== HEAP SUMMARY: ==29298== in use at exit: 4,107,467 bytes in 5,848 blocks ==29298== total heap usage: 99,845 allocs, 93,997 frees, 65,285,213 bytes allocated ==29298== ==29298== LEAK SUMMARY: ==29298== definitely lost: 0 bytes in 0 blocks ==29298== indirectly lost: 0 bytes in 0 blocks ==29298== possibly lost: 172,751 bytes in 105 blocks ==29298== still reachable: 3,934,716 bytes in 5,743 blocks ==29298== suppressed: 0 bytes in 0 blocks ==29298== Rerun with --leak-check=full to see details of leaked memory ==29298== ==29298== For counts of detected and suppressed errors, rerun with: -v ==29298== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 2422 from 128) ================================================================================ 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.