Enter a model name: === Verification check vc-memory-leak start (2022-11-30 10:16:29) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : EAM_Dynamo_HaleWongZimmerman_2008PairHybrid_PdAgH__MO_104806802344_005 Supported species : Ag H Pd random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Ag (Configuration in file "config-F-Ag.xyz") ----------------------------------------------------------------------------------------------------- Energy = 195.3084007180693 Forces: 1 -7.72171666e+00 -1.67216718e+01 -1.43946995e+01 2 -5.59006791e+00 7.23722586e+00 -1.60200034e+01 3 5.51173979e+00 -1.56913944e+01 -2.85696750e+00 4 -1.46712079e+01 8.10858468e+00 6.85937388e+00 5 2.02288685e+00 -2.15819628e+01 -9.49820348e+00 6 1.28914401e+01 2.57427321e+00 -1.51896081e+01 7 1.30103421e+01 -2.58536865e+01 -1.40884584e+01 8 -1.09953982e+01 -1.07617966e+01 4.58638316e+00 9 -1.06603190e+01 -1.47908076e+01 -2.38454809e+01 10 1.27898972e+01 2.21251206e+01 -1.80382437e+01 11 1.80840034e+00 -1.33477345e+01 -9.36555105e+00 12 -2.42026693e+01 2.14184919e+01 1.05598932e+01 13 -8.98308267e+00 -5.48383210e+00 -4.02712957e+01 14 1.22771827e+01 1.50460149e+01 -1.26466477e+01 15 3.70568161e+01 -8.06709139e+00 5.13746443e+00 16 -1.40647282e+00 3.62932520e+01 2.98611921e+00 17 -2.37455766e+01 -1.47715538e+01 -5.48474505e+00 18 8.79219546e+00 1.03652322e+01 -1.85667499e+00 19 8.67567244e+00 -1.76878352e+01 1.51892424e+01 20 -1.29392227e+01 9.76918896e+00 1.52265054e+01 21 -1.19564596e+01 -1.50770657e+01 6.92382890e+00 22 2.23365047e+01 1.72218112e+01 1.24692826e+01 23 7.45909283e+00 -4.29807034e+00 1.26062594e+01 24 1.43075198e+00 -4.49419377e+00 1.14673001e+01 25 -2.96067798e+01 -1.92421667e+00 1.38808582e+01 26 -6.23807101e+00 2.92320650e+01 -5.88377741e+00 27 4.45571428e-01 -2.21159948e+01 1.65314175e+01 28 -2.35898501e+01 1.76347690e+01 7.67520603e+00 29 4.20975284e-01 -1.44321496e+01 8.08814006e+00 30 1.56264072e+01 1.76432933e+01 3.25282495e+00 31 2.08593672e+01 -7.09321998e+00 1.53966355e+01 32 8.89165066e+00 1.95249545e+01 2.06036219e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ag (Configuration in file "config-T-Ag.xyz") ----------------------------------------------------------------------------------------------------- Energy = 195.3084007180693 Forces: 1 -7.72171666e+00 -1.67216718e+01 -1.43946995e+01 2 -5.59006791e+00 7.23722586e+00 -1.60200034e+01 3 5.51173979e+00 -1.56913944e+01 -2.85696750e+00 4 -1.46712079e+01 8.10858468e+00 6.85937388e+00 5 2.02288685e+00 -2.15819628e+01 -9.49820348e+00 6 1.28914401e+01 2.57427321e+00 -1.51896081e+01 7 1.30103421e+01 -2.58536865e+01 -1.40884584e+01 8 -1.09953982e+01 -1.07617966e+01 4.58638316e+00 9 -1.06603190e+01 -1.47908076e+01 -2.38454809e+01 10 1.27898972e+01 2.21251206e+01 -1.80382437e+01 11 1.80840034e+00 -1.33477345e+01 -9.36555105e+00 12 -2.42026693e+01 2.14184919e+01 1.05598932e+01 13 -8.98308267e+00 -5.48383210e+00 -4.02712957e+01 14 1.22771827e+01 1.50460149e+01 -1.26466477e+01 15 3.70568161e+01 -8.06709139e+00 5.13746443e+00 16 -1.40647282e+00 3.62932520e+01 2.98611921e+00 17 -2.37455766e+01 -1.47715538e+01 -5.48474505e+00 18 8.79219546e+00 1.03652322e+01 -1.85667499e+00 19 8.67567244e+00 -1.76878352e+01 1.51892424e+01 20 -1.29392227e+01 9.76918896e+00 1.52265054e+01 21 -1.19564596e+01 -1.50770657e+01 6.92382890e+00 22 2.23365047e+01 1.72218112e+01 1.24692826e+01 23 7.45909283e+00 -4.29807034e+00 1.26062594e+01 24 1.43075198e+00 -4.49419377e+00 1.14673001e+01 25 -2.96067798e+01 -1.92421667e+00 1.38808582e+01 26 -6.23807101e+00 2.92320650e+01 -5.88377741e+00 27 4.45571428e-01 -2.21159948e+01 1.65314175e+01 28 -2.35898501e+01 1.76347690e+01 7.67520603e+00 29 4.20975284e-01 -1.44321496e+01 8.08814006e+00 30 1.56264072e+01 1.76432933e+01 3.25282495e+00 31 2.08593672e+01 -7.09321998e+00 1.53966355e+01 32 8.89165066e+00 1.95249545e+01 2.06036219e+01 MONOATOMIC STRUCTURE (pbc=False)-- Species = H (Configuration in file "config-F-H.xyz") ----------------------------------------------------------------------------------------------------- Energy = -7.697023321756065 Forces: 1 -1.42352312e+00 -1.99467311e+00 -1.91097933e+00 2 3.37662144e+00 -2.33512497e+00 -2.04199016e+00 3 3.74981801e+00 -6.62570611e+00 -2.84994653e+00 4 -4.81083565e+00 2.96172237e+00 -2.83576783e+00 5 -7.38128653e+00 -2.09470053e+00 -6.05120579e+00 6 3.58486947e+00 7.01498372e-01 -1.56167536e+00 7 7.04275573e+00 -1.74648301e+00 6.68783238e+00 8 3.96119684e+00 5.39712236e+00 -1.08665668e+01 9 -5.49886706e+00 1.51761419e+00 -2.39377490e+00 10 3.65103196e+00 1.03452059e+00 -3.53698536e+00 11 5.34325247e+00 3.01673674e+00 -8.16934554e-01 12 -2.55921692e+00 1.13912777e+00 2.94511909e+00 13 -2.95639395e+00 7.65692945e-01 -1.46874226e+00 14 3.91301747e+00 1.60594503e+00 -4.02760463e+00 15 6.80818563e+00 -3.46397646e+00 -1.01045965e+00 16 -6.72111268e+00 5.00028747e+00 2.66942636e+00 17 -3.18033090e+00 -2.77761550e+00 4.25680958e+00 18 -5.32233627e+00 1.82376792e+00 7.63806007e+00 19 4.61942307e-01 -7.61820631e-01 -1.46946985e-01 20 -9.89538953e-01 -2.55521178e-01 1.45415791e+00 21 2.59135121e+00 -9.33193330e+00 7.43701264e+00 22 3.01409387e+00 3.11388009e-01 -2.43503887e+00 23 1.42716572e+00 -4.17152897e+00 1.97117065e+00 24 -2.92922038e+00 1.52265233e+00 1.48520331e+00 25 -4.49354363e+00 3.31775022e+00 2.39265790e+00 26 -9.42070697e-01 1.27570189e+00 -2.46284262e+00 27 2.39687367e+00 -1.98323797e+00 2.18462322e+00 28 -2.12659371e+00 1.54694763e+00 7.09177448e-02 29 -2.60845942e+00 2.97782456e+00 2.75042960e+00 30 7.27058118e-01 3.43734228e-01 -2.26761220e-01 31 2.61264108e+00 -9.43169299e-01 1.16287692e+00 32 -7.18545139e-01 2.22545642e+00 1.53792548e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = H (Configuration in file "config-T-H.xyz") ----------------------------------------------------------------------------------------------------- Energy = -7.697023321756065 Forces: 1 -1.42352312e+00 -1.99467311e+00 -1.91097933e+00 2 3.37662144e+00 -2.33512497e+00 -2.04199016e+00 3 3.74981801e+00 -6.62570611e+00 -2.84994653e+00 4 -4.81083565e+00 2.96172237e+00 -2.83576783e+00 5 -7.38128653e+00 -2.09470053e+00 -6.05120579e+00 6 3.58486947e+00 7.01498372e-01 -1.56167536e+00 7 7.04275573e+00 -1.74648301e+00 6.68783238e+00 8 3.96119684e+00 5.39712236e+00 -1.08665668e+01 9 -5.49886706e+00 1.51761419e+00 -2.39377490e+00 10 3.65103196e+00 1.03452059e+00 -3.53698536e+00 11 5.34325247e+00 3.01673674e+00 -8.16934554e-01 12 -2.55921692e+00 1.13912777e+00 2.94511909e+00 13 -2.95639395e+00 7.65692945e-01 -1.46874226e+00 14 3.91301747e+00 1.60594503e+00 -4.02760463e+00 15 6.80818563e+00 -3.46397646e+00 -1.01045965e+00 16 -6.72111268e+00 5.00028747e+00 2.66942636e+00 17 -3.18033090e+00 -2.77761550e+00 4.25680958e+00 18 -5.32233627e+00 1.82376792e+00 7.63806007e+00 19 4.61942307e-01 -7.61820631e-01 -1.46946985e-01 20 -9.89538953e-01 -2.55521178e-01 1.45415791e+00 21 2.59135121e+00 -9.33193330e+00 7.43701264e+00 22 3.01409387e+00 3.11388009e-01 -2.43503887e+00 23 1.42716572e+00 -4.17152897e+00 1.97117065e+00 24 -2.92922038e+00 1.52265233e+00 1.48520331e+00 25 -4.49354363e+00 3.31775022e+00 2.39265790e+00 26 -9.42070697e-01 1.27570189e+00 -2.46284262e+00 27 2.39687367e+00 -1.98323797e+00 2.18462322e+00 28 -2.12659371e+00 1.54694763e+00 7.09177448e-02 29 -2.60845942e+00 2.97782456e+00 2.75042960e+00 30 7.27058118e-01 3.43734228e-01 -2.26761220e-01 31 2.61264108e+00 -9.43169299e-01 1.16287692e+00 32 -7.18545139e-01 2.22545642e+00 1.53792548e+00 MONOATOMIC STRUCTURE (pbc=False)-- Species = Pd (Configuration in file "config-F-Pd.xyz") ----------------------------------------------------------------------------------------------------- Energy = 65.14585281590932 Forces: 1 -3.84062618e+00 -3.96990781e+00 -4.58409859e+00 2 -1.61427736e+00 -4.61183766e+00 -1.53116429e+01 3 1.77245763e+00 -1.49135186e+01 -3.63824933e+00 4 -1.91471980e+01 -3.21510464e+00 4.96710825e-01 5 1.76798490e+00 -8.41491362e+00 -8.22992632e+00 6 1.25230723e+01 -3.62630809e+00 -9.93343617e+00 7 7.46103881e+00 -1.15016138e+01 -3.32862367e+00 8 -1.63725471e+00 -4.44010055e+00 -4.52692883e+00 9 -1.22285557e+01 2.18723521e+00 -1.43812112e+01 10 1.45688597e+00 1.16639477e+01 -1.07469358e+01 11 3.54837214e+00 4.51203509e+00 3.01475791e+00 12 -1.20451566e+01 1.04472779e+01 -1.00547465e+00 13 1.09155905e+00 5.97407494e+00 -1.79863567e+01 14 3.14717617e+00 2.14456764e+00 -2.61647250e+00 15 1.81275529e+01 7.64520371e+00 -3.38190527e+00 16 9.70888543e-01 1.23981156e+01 1.90035791e+00 17 -1.09364467e+01 -9.50563092e+00 4.03655324e+00 18 -6.72691907e+00 -2.43544525e+00 -1.16283283e+01 19 -4.24700984e+00 -1.81108677e+01 1.25369013e+01 20 -1.61031500e+01 -6.31599382e+00 1.30128612e+01 21 3.89046900e+00 -2.06222760e+01 6.12295650e-01 22 1.95422209e+01 -6.47605581e+00 -7.57741036e-01 23 3.51652990e+00 -6.16113420e+00 5.94459761e+00 24 8.23097221e+00 -8.60982331e+00 2.49181440e+01 25 -2.06997960e+01 2.09877840e+00 -3.03074287e+00 26 2.37486411e+00 1.53794885e+01 -4.21340984e+00 27 -3.83578098e+00 8.51611916e+00 2.28215933e+01 28 -6.19888688e+00 7.06210616e+00 6.82716869e+00 29 3.94077734e+00 8.34397941e+00 -4.75577755e+00 30 1.09411398e+01 1.59258825e+01 -8.11272713e-01 31 1.25377581e+01 3.90874004e+00 1.59260825e+01 32 2.41933832e+00 1.47229798e+01 1.28205101e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Pd (Configuration in file "config-T-Pd.xyz") ----------------------------------------------------------------------------------------------------- Energy = 65.14585281590932 Forces: 1 -3.84062618e+00 -3.96990781e+00 -4.58409859e+00 2 -1.61427736e+00 -4.61183766e+00 -1.53116429e+01 3 1.77245763e+00 -1.49135186e+01 -3.63824933e+00 4 -1.91471980e+01 -3.21510464e+00 4.96710825e-01 5 1.76798490e+00 -8.41491362e+00 -8.22992632e+00 6 1.25230723e+01 -3.62630809e+00 -9.93343617e+00 7 7.46103881e+00 -1.15016138e+01 -3.32862367e+00 8 -1.63725471e+00 -4.44010055e+00 -4.52692883e+00 9 -1.22285557e+01 2.18723521e+00 -1.43812112e+01 10 1.45688597e+00 1.16639477e+01 -1.07469358e+01 11 3.54837214e+00 4.51203509e+00 3.01475791e+00 12 -1.20451566e+01 1.04472779e+01 -1.00547465e+00 13 1.09155905e+00 5.97407494e+00 -1.79863567e+01 14 3.14717617e+00 2.14456764e+00 -2.61647250e+00 15 1.81275529e+01 7.64520371e+00 -3.38190527e+00 16 9.70888543e-01 1.23981156e+01 1.90035791e+00 17 -1.09364467e+01 -9.50563092e+00 4.03655324e+00 18 -6.72691907e+00 -2.43544525e+00 -1.16283283e+01 19 -4.24700984e+00 -1.81108677e+01 1.25369013e+01 20 -1.61031500e+01 -6.31599382e+00 1.30128612e+01 21 3.89046900e+00 -2.06222760e+01 6.12295650e-01 22 1.95422209e+01 -6.47605581e+00 -7.57741036e-01 23 3.51652990e+00 -6.16113420e+00 5.94459761e+00 24 8.23097221e+00 -8.60982331e+00 2.49181440e+01 25 -2.06997960e+01 2.09877840e+00 -3.03074287e+00 26 2.37486411e+00 1.53794885e+01 -4.21340984e+00 27 -3.83578098e+00 8.51611916e+00 2.28215933e+01 28 -6.19888688e+00 7.06210616e+00 6.82716869e+00 29 3.94077734e+00 8.34397941e+00 -4.75577755e+00 30 1.09411398e+01 1.59258825e+01 -8.11272713e-01 31 1.25377581e+01 3.90874004e+00 1.59260825e+01 32 2.41933832e+00 1.47229798e+01 1.28205101e+01 MIXED STRUCTURE (pbc=False)-- Species = Ag H Pd (Configuration in file "config-F-AgHPd.xyz") ----------------------------------------------------------------------------------------------------- Energy = -5.715488350950677 Forces: 1 -2.07472592e+01 -9.32810064e+00 -1.82493893e+01 2 5.24801356e+00 7.62572939e+00 -1.48527625e+01 3 1.45331033e+01 -1.49466793e+01 1.80859618e+01 4 -1.05535733e+01 9.12406975e+00 6.96516426e+00 5 -3.53247213e-03 -1.44938532e+00 -2.32451585e+00 6 3.96394420e+00 2.84416278e-01 -1.46480690e+00 7 3.62995505e+00 -2.21864654e+00 -3.60517819e+00 8 5.51890884e+00 2.56545193e+00 4.56525445e+00 9 -4.53822785e+00 -1.50348234e+00 -7.22558563e+00 10 -4.48210646e+00 3.59824706e-01 -1.01003448e+01 11 3.57857742e+00 1.51429546e+00 5.73973096e+00 12 -9.15784949e+00 3.28658943e+00 -6.99237080e+00 13 7.08543994e-01 -7.82829922e-01 -2.42738371e+00 14 4.28901640e+00 -9.39868340e-01 -2.92168050e+00 15 2.71895618e+00 1.91582435e+00 -2.22785379e+00 16 3.45691678e+00 5.28430938e+00 4.76710535e+00 17 -2.18410180e+00 -9.05848693e-01 8.38391790e-01 18 2.74523466e-01 -1.33145384e+00 -1.43177577e+00 19 1.32609548e+00 -9.88773246e+00 -4.95620334e-02 20 -5.69954005e+00 3.60699417e+00 1.83435810e+00 21 -5.16967622e+00 -2.43175645e+00 3.19252678e+00 22 4.24863354e+00 9.66681178e-01 3.28540432e+00 23 1.55306802e+00 -1.82042614e+00 3.66533024e-02 24 2.13672000e-01 -2.17606349e-01 3.38006383e+00 25 -5.44743207e+00 -1.09103812e+01 -9.37877655e-02 26 5.84740774e+00 9.27649116e+00 -3.30572492e+00 27 4.96190161e-01 1.73293757e+00 3.19577845e+00 28 -6.50887670e+00 5.53632279e+00 1.15129903e+01 29 -4.72899690e+00 -2.77399848e+00 -5.26001401e+00 30 5.35922126e+00 4.39605406e+00 -7.60953466e-01 31 8.25257883e+00 -2.27014971e-01 7.45510077e+00 32 4.00384625e+00 4.19921943e+00 8.43920544e+00 MIXED STRUCTURE (pbc=True)-- Species = Ag H Pd (Configuration in file "config-T-AgHPd.xyz") ----------------------------------------------------------------------------------------------------- Energy = 91.68427118097348 Forces: 1 -1.83505554e+01 -4.29837589e+00 -4.19070354e+00 2 7.19311495e+00 1.18642409e+01 6.04326745e-01 3 1.40889863e+01 7.31030938e-01 1.89571086e+01 4 -2.94508675e+00 8.90846638e+00 1.56257700e+01 5 1.08823861e+00 -5.56402055e-01 -2.84356868e+00 6 -9.23574500e+00 5.51316925e+00 1.98765551e+00 7 -1.56609616e+00 -2.06151486e+00 -5.80176391e+00 8 5.09505731e+00 2.98538695e+00 6.46505684e+00 9 -7.40329330e+00 2.57477366e-01 -3.34308470e+00 10 2.90211966e-01 -1.47196743e+01 -4.19857017e+00 11 4.10726777e+00 1.70805949e+00 6.21791066e+00 12 -6.22097663e+00 -4.02192859e+00 -6.54145864e+00 13 -3.16862614e-01 -4.29583422e-01 -1.48411590e+00 14 -2.55117065e+00 -3.14353687e+00 -2.85886830e+00 15 1.41470887e+00 2.15123175e+00 -1.47876096e+00 16 6.74395031e+00 -1.21827190e+00 5.08273685e+00 17 4.03316738e+00 -6.55187041e-01 2.96997712e+00 18 8.58109409e-01 -8.12450153e-01 -2.36458392e+00 19 6.39547699e+00 2.03981447e+00 -8.53344318e+00 20 -1.22229072e+00 6.23839953e+00 -1.01104015e+01 21 -5.64411608e+00 -1.83148226e+00 3.22449375e+00 22 2.00259219e+00 2.04298618e+00 3.80593343e+00 23 -1.12491358e+01 -6.35859603e-01 -3.83206196e+00 24 5.86224963e+00 2.67731568e-02 -7.50889078e+00 25 5.43020793e+00 -1.39744305e+01 -2.59176634e+00 26 1.20847934e+01 2.18546076e+00 -5.89997139e+00 27 3.20161893e+00 2.53835114e+00 -1.67420781e+00 28 -6.06735702e+00 -3.24842422e+00 1.12090482e+01 29 -4.02132139e+00 -2.69509560e+00 -5.54829721e+00 30 -1.33054670e+01 5.46924537e+00 -3.58472312e+00 31 -1.38336602e+00 3.67665029e-01 3.21457339e+00 32 1.15930886e+01 -7.25541419e-01 5.02465102e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==1443533== Memcheck, a memory error detector ==1443533== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==1443533== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info ==1443533== Command: python runner2.py EAM_Dynamo_HaleWongZimmerman_2008PairHybrid_PdAgH__MO_104806802344_005 ==1443533== ==1445026== Warning: invalid file descriptor 1024 in syscall close() ==1445026== Warning: invalid file descriptor 1025 in syscall close() ==1445026== Warning: invalid file descriptor 1026 in syscall close() ==1445026== Warning: invalid file descriptor 1027 in syscall close() ==1445026== Use --log-fd= to select an alternative log fd. ==1445026== Warning: invalid file descriptor 1028 in syscall close() ==1445026== Warning: invalid file descriptor 1029 in syscall close() ==1443533== ==1443533== HEAP SUMMARY: ==1443533== in use at exit: 2,257,767 bytes in 1,704 blocks ==1443533== total heap usage: 102,152 allocs, 100,448 frees, 101,134,804 bytes allocated ==1443533== ==1443533== LEAK SUMMARY: ==1443533== definitely lost: 0 bytes in 0 blocks ==1443533== indirectly lost: 0 bytes in 0 blocks ==1443533== possibly lost: 180,827 bytes in 103 blocks ==1443533== still reachable: 2,076,908 bytes in 1,600 blocks ==1443533== of which reachable via heuristic: ==1443533== stdstring : 38 bytes in 1 blocks ==1443533== suppressed: 32 bytes in 1 blocks ==1443533== Rerun with --leak-check=full to see details of leaked memory ==1443533== ==1443533== For lists of detected and suppressed errors, rerun with: -s ==1443533== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 8228 from 585) ================================================================================ 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 10:17:03) ===