Enter a model name: === Verification check vc-memory-leak start (2022-11-30 10:16:30) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_BonnyGrigorevTerentyev_2014EAM1_WHHe__MO_292520929154_000 Supported species : H He W random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = H (Configuration in file "config-F-H.xyz") ----------------------------------------------------------------------------------------------------- Energy = 9.42543676586091 Forces: 1 -2.67014183e-01 -6.05785125e-01 -5.11858760e-01 2 -1.78096536e-01 2.84360118e-01 -5.21216940e-01 3 1.71692153e-01 -4.74511294e-01 -6.15899705e-02 4 -4.46218390e-01 3.53937083e-01 3.29632292e-01 5 7.62408102e-02 -7.38282260e-01 -3.16311393e-01 6 4.36681206e-01 9.30212691e-02 -4.94982718e-01 7 4.02543311e-01 -9.31740349e-01 -5.65990012e-01 8 -4.05243363e-01 -3.62259196e-01 1.23024751e-01 9 -3.50611230e-01 -5.25784393e-01 -7.87544844e-01 10 4.47865936e-01 7.29762199e-01 -6.91566448e-01 11 -1.12559778e-01 -5.44345697e-01 -3.28547423e-01 12 -8.38150407e-01 6.46886526e-01 4.73904939e-01 13 -3.00386291e-01 -1.60963924e-01 -1.36725735e+00 14 3.89201057e-01 4.70952723e-01 -3.12273767e-01 15 1.25146275e+00 -4.06576611e-02 3.00858334e-01 16 1.86135970e-01 1.13962423e+00 7.45198344e-02 17 -7.37895431e-01 -4.25707464e-01 -1.96324901e-01 18 1.89503957e-01 3.11630046e-01 -2.24410440e-01 19 1.68329841e-01 -7.38455037e-01 4.88954134e-01 20 -4.71530464e-01 3.02851152e-01 4.98734290e-01 21 -3.57073128e-01 -5.28708675e-01 1.93851823e-01 22 7.71168686e-01 6.34141883e-01 5.16524321e-01 23 2.57939883e-01 -1.36713171e-01 4.25515496e-01 24 2.60233977e-01 1.20836939e-01 4.59463128e-01 25 -9.42243498e-01 -1.20220950e-01 1.92578116e-01 26 -1.80803858e-01 9.81799639e-01 -1.53626171e-01 27 2.03165039e-01 -8.16788651e-01 6.11924868e-01 28 -8.94083094e-01 7.32477364e-01 3.39996284e-01 29 -3.37858074e-02 -4.80291044e-01 2.93093257e-01 30 4.88751964e-01 6.97439899e-01 -1.62977342e-01 31 5.66475465e-01 -4.70147648e-01 6.52429458e-01 32 2.48303453e-01 6.01641468e-01 7.21473149e-01 MONOATOMIC STRUCTURE (pbc=True)-- Species = H (Configuration in file "config-T-H.xyz") ----------------------------------------------------------------------------------------------------- Energy = 9.42543676586091 Forces: 1 -2.67014183e-01 -6.05785125e-01 -5.11858760e-01 2 -1.78096536e-01 2.84360118e-01 -5.21216940e-01 3 1.71692153e-01 -4.74511294e-01 -6.15899705e-02 4 -4.46218390e-01 3.53937083e-01 3.29632292e-01 5 7.62408102e-02 -7.38282260e-01 -3.16311393e-01 6 4.36681206e-01 9.30212691e-02 -4.94982718e-01 7 4.02543311e-01 -9.31740349e-01 -5.65990012e-01 8 -4.05243363e-01 -3.62259196e-01 1.23024751e-01 9 -3.50611230e-01 -5.25784393e-01 -7.87544844e-01 10 4.47865936e-01 7.29762199e-01 -6.91566448e-01 11 -1.12559778e-01 -5.44345697e-01 -3.28547423e-01 12 -8.38150407e-01 6.46886526e-01 4.73904939e-01 13 -3.00386291e-01 -1.60963924e-01 -1.36725735e+00 14 3.89201057e-01 4.70952723e-01 -3.12273767e-01 15 1.25146275e+00 -4.06576611e-02 3.00858334e-01 16 1.86135970e-01 1.13962423e+00 7.45198344e-02 17 -7.37895431e-01 -4.25707464e-01 -1.96324901e-01 18 1.89503957e-01 3.11630046e-01 -2.24410440e-01 19 1.68329841e-01 -7.38455037e-01 4.88954134e-01 20 -4.71530464e-01 3.02851152e-01 4.98734290e-01 21 -3.57073128e-01 -5.28708675e-01 1.93851823e-01 22 7.71168686e-01 6.34141883e-01 5.16524321e-01 23 2.57939883e-01 -1.36713171e-01 4.25515496e-01 24 2.60233977e-01 1.20836939e-01 4.59463128e-01 25 -9.42243498e-01 -1.20220950e-01 1.92578116e-01 26 -1.80803858e-01 9.81799639e-01 -1.53626171e-01 27 2.03165039e-01 -8.16788651e-01 6.11924868e-01 28 -8.94083094e-01 7.32477364e-01 3.39996284e-01 29 -3.37858074e-02 -4.80291044e-01 2.93093257e-01 30 4.88751964e-01 6.97439899e-01 -1.62977342e-01 31 5.66475465e-01 -4.70147648e-01 6.52429458e-01 32 2.48303453e-01 6.01641468e-01 7.21473149e-01 MONOATOMIC STRUCTURE (pbc=False)-- Species = He (Configuration in file "config-F-He.xyz") ----------------------------------------------------------------------------------------------------- Energy = -18.2269530864704 Forces: 1 4.69654768e-01 1.79927491e-01 3.32510006e-01 2 1.02435137e+00 -1.83006948e-01 1.62088544e+00 3 2.23231590e-01 1.24140966e+00 -1.25266293e-01 4 8.77850903e-01 5.46392527e-01 1.84403635e-01 5 3.03409604e-01 1.35172761e+00 7.95077489e-01 6 -9.20405682e-01 -7.72705691e-02 1.24195823e+00 7 -9.89890071e-01 8.44141515e-01 -1.76957885e-03 8 -8.39486700e-02 3.08599872e-01 -6.28521780e-01 9 8.85617730e-01 4.68798310e-01 1.04313430e+00 10 -6.75265737e-01 -6.94356266e-01 8.85273204e-01 11 1.17937690e-01 -5.30282895e-01 1.91771098e-01 12 8.97307171e-01 -1.01243271e+00 -4.69383625e-01 13 -4.94788617e-01 -4.43811866e-01 8.44070184e-01 14 -5.50686700e-01 -9.25025506e-01 5.61123679e-01 15 -1.08226987e+00 -4.71856867e-01 -4.94930676e-01 16 8.46022674e-02 -1.00295954e+00 4.33904651e-01 17 6.85262396e-01 8.01542064e-01 2.22146301e-01 18 5.85419086e-01 9.88953055e-02 4.22036984e-01 19 5.03399186e-01 1.17877132e+00 -1.00971895e+00 20 8.75276253e-01 3.25595264e-01 -1.04720266e+00 21 -2.94855196e-01 1.49468317e+00 3.33020697e-01 22 -1.05676463e+00 -1.86036343e-01 3.00948987e-02 23 -8.21686941e-01 4.63204615e-01 -4.21587103e-01 24 -2.28096046e-01 -2.73985662e-01 -1.65215372e+00 25 1.07012674e+00 -4.95844032e-01 1.29915788e-01 26 1.13396790e+00 -1.08471550e+00 -6.91847240e-01 27 -4.68840511e-01 6.04520679e-02 -1.62074553e+00 28 2.07109417e-02 -7.87251647e-01 2.18287205e-01 29 -7.80999723e-01 -2.96803946e-01 -3.13819938e-01 30 -8.54399784e-01 -6.82864368e-01 4.57151863e-01 31 -6.00882722e-01 5.02585148e-01 -5.50298276e-01 32 1.45655296e-01 -7.18221272e-01 -9.19520282e-01 MONOATOMIC STRUCTURE (pbc=True)-- Species = He (Configuration in file "config-T-He.xyz") ----------------------------------------------------------------------------------------------------- Energy = -18.2269530864704 Forces: 1 4.69654768e-01 1.79927491e-01 3.32510006e-01 2 1.02435137e+00 -1.83006948e-01 1.62088544e+00 3 2.23231590e-01 1.24140966e+00 -1.25266293e-01 4 8.77850903e-01 5.46392527e-01 1.84403635e-01 5 3.03409604e-01 1.35172761e+00 7.95077489e-01 6 -9.20405682e-01 -7.72705691e-02 1.24195823e+00 7 -9.89890071e-01 8.44141515e-01 -1.76957885e-03 8 -8.39486700e-02 3.08599872e-01 -6.28521780e-01 9 8.85617730e-01 4.68798310e-01 1.04313430e+00 10 -6.75265737e-01 -6.94356266e-01 8.85273204e-01 11 1.17937690e-01 -5.30282895e-01 1.91771098e-01 12 8.97307171e-01 -1.01243271e+00 -4.69383625e-01 13 -4.94788617e-01 -4.43811866e-01 8.44070184e-01 14 -5.50686700e-01 -9.25025506e-01 5.61123679e-01 15 -1.08226987e+00 -4.71856867e-01 -4.94930676e-01 16 8.46022674e-02 -1.00295954e+00 4.33904651e-01 17 6.85262396e-01 8.01542064e-01 2.22146301e-01 18 5.85419086e-01 9.88953055e-02 4.22036984e-01 19 5.03399186e-01 1.17877132e+00 -1.00971895e+00 20 8.75276253e-01 3.25595264e-01 -1.04720266e+00 21 -2.94855196e-01 1.49468317e+00 3.33020697e-01 22 -1.05676463e+00 -1.86036343e-01 3.00948987e-02 23 -8.21686941e-01 4.63204615e-01 -4.21587103e-01 24 -2.28096046e-01 -2.73985662e-01 -1.65215372e+00 25 1.07012674e+00 -4.95844032e-01 1.29915788e-01 26 1.13396790e+00 -1.08471550e+00 -6.91847240e-01 27 -4.68840511e-01 6.04520679e-02 -1.62074553e+00 28 2.07109417e-02 -7.87251647e-01 2.18287205e-01 29 -7.80999723e-01 -2.96803946e-01 -3.13819938e-01 30 -8.54399784e-01 -6.82864368e-01 4.57151863e-01 31 -6.00882722e-01 5.02585148e-01 -5.50298276e-01 32 1.45655296e-01 -7.18221272e-01 -9.19520282e-01 MONOATOMIC STRUCTURE (pbc=False)-- Species = W (Configuration in file "config-F-W.xyz") ----------------------------------------------------------------------------------------------------- Energy = 136.5940577958009 Forces: 1 -1.03465326e+01 -1.91022111e+01 -2.45801000e+01 2 5.13033425e+00 -1.47611345e+01 -1.80548744e+01 3 1.13648743e+01 -2.45299844e+01 -1.04967863e+00 4 -2.36539643e+01 1.61556138e+01 1.11798569e+01 5 -1.57671920e+01 -2.30973084e+01 -2.63231526e+01 6 2.14910277e+01 2.88343101e+00 -2.57679510e+01 7 4.39558267e+01 -2.63985051e+01 2.55081843e+00 8 -2.02948254e+01 7.08478347e+00 -1.63391004e+01 9 -3.88403806e+01 -1.09276400e+01 -4.30535828e+01 10 4.55089617e+00 4.71910881e+01 -4.09373074e+01 11 1.61542189e+01 -2.43674062e+01 2.96514477e+01 12 -4.74595656e+01 3.96630712e+01 2.28069566e+01 13 8.47288993e+00 -6.25533182e+00 -2.89301682e+01 14 1.69696108e+01 8.96398913e+00 -6.72052846e+00 15 3.00313606e+01 2.58868449e+01 -1.49101150e+01 16 1.67709254e+01 2.21808702e+01 2.63578272e+01 17 -1.58654295e+01 -1.39483369e+01 1.63438129e+01 18 -3.31148951e+01 -2.66468576e+01 4.68054047e+00 19 -5.63515746e+00 -2.88365929e+01 5.04718225e+00 20 -1.76509028e+01 3.19845509e+00 1.12252234e+01 21 -1.24506747e+01 -3.36234116e+01 1.58139416e+01 22 3.37161271e+01 -1.06638259e+01 1.79822669e+01 23 1.71859274e+01 -1.35448476e+01 1.52181162e+01 24 9.58939678e+00 1.64377577e+01 2.12921056e+01 25 -3.90215577e+01 -1.82759659e+01 -1.74527073e+01 26 9.77496900e+00 3.67494437e+01 -3.20772509e+01 27 1.21337317e+01 -1.55468137e+01 4.18793409e+01 28 -2.31718455e+01 2.47433043e+01 2.56609831e+01 29 1.49545797e+01 3.45101206e+01 5.21851561e+00 30 1.88112417e+01 1.04724365e+01 -1.51997580e+01 31 1.01727532e+01 3.28602856e+00 1.70160002e+01 32 2.04223184e+00 1.11189354e+01 2.14713390e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = W (Configuration in file "config-T-W.xyz") ----------------------------------------------------------------------------------------------------- Energy = 136.5940577958009 Forces: 1 -1.03465326e+01 -1.91022111e+01 -2.45801000e+01 2 5.13033425e+00 -1.47611345e+01 -1.80548744e+01 3 1.13648743e+01 -2.45299844e+01 -1.04967863e+00 4 -2.36539643e+01 1.61556138e+01 1.11798569e+01 5 -1.57671920e+01 -2.30973084e+01 -2.63231526e+01 6 2.14910277e+01 2.88343101e+00 -2.57679510e+01 7 4.39558267e+01 -2.63985051e+01 2.55081843e+00 8 -2.02948254e+01 7.08478347e+00 -1.63391004e+01 9 -3.88403806e+01 -1.09276400e+01 -4.30535828e+01 10 4.55089617e+00 4.71910881e+01 -4.09373074e+01 11 1.61542189e+01 -2.43674062e+01 2.96514477e+01 12 -4.74595656e+01 3.96630712e+01 2.28069566e+01 13 8.47288993e+00 -6.25533182e+00 -2.89301682e+01 14 1.69696108e+01 8.96398913e+00 -6.72052846e+00 15 3.00313606e+01 2.58868449e+01 -1.49101150e+01 16 1.67709254e+01 2.21808702e+01 2.63578272e+01 17 -1.58654295e+01 -1.39483369e+01 1.63438129e+01 18 -3.31148951e+01 -2.66468576e+01 4.68054047e+00 19 -5.63515746e+00 -2.88365929e+01 5.04718225e+00 20 -1.76509028e+01 3.19845509e+00 1.12252234e+01 21 -1.24506747e+01 -3.36234116e+01 1.58139416e+01 22 3.37161271e+01 -1.06638259e+01 1.79822669e+01 23 1.71859274e+01 -1.35448476e+01 1.52181162e+01 24 9.58939678e+00 1.64377577e+01 2.12921056e+01 25 -3.90215577e+01 -1.82759659e+01 -1.74527073e+01 26 9.77496900e+00 3.67494437e+01 -3.20772509e+01 27 1.21337317e+01 -1.55468137e+01 4.18793409e+01 28 -2.31718455e+01 2.47433043e+01 2.56609831e+01 29 1.49545797e+01 3.45101206e+01 5.21851561e+00 30 1.88112417e+01 1.04724365e+01 -1.51997580e+01 31 1.01727532e+01 3.28602856e+00 1.70160002e+01 32 2.04223184e+00 1.11189354e+01 2.14713390e+01 MIXED STRUCTURE (pbc=False)-- Species = H He W (Configuration in file "config-F-HHeW.xyz") ----------------------------------------------------------------------------------------------------- Energy = 21.768458356579576 Forces: 1 -1.19837408e+00 -1.81456137e+00 -4.09204963e+00 2 8.68568586e+00 -9.13116290e+00 -2.33224136e+00 3 2.03607398e+01 -1.19370106e+01 -1.89180074e+01 4 -4.86506568e+00 5.18908181e+00 6.85245660e-01 5 -2.00003605e-01 -2.64409707e+00 -1.93878916e+00 6 4.15468938e+00 -2.90355885e+00 -1.84356249e+00 7 7.48589600e-01 -5.46912836e+00 -5.56223681e+00 8 -2.31668624e+00 4.63534041e-01 3.69874409e+00 9 -1.97434435e+01 -6.94666113e+00 -2.62908358e+00 10 1.45697719e+01 1.77334083e+01 -5.32462779e+00 11 1.74081596e+00 -1.13644372e+00 4.92421674e+00 12 -5.53768029e+00 7.13270967e-01 5.65365035e+00 13 -1.24662326e+01 -1.09855590e+01 -3.36480076e+00 14 1.34044038e+01 1.66894549e+01 -4.99818763e+00 15 1.69055165e+00 -2.87648117e+00 2.33955869e+00 16 -3.72846530e+00 5.39127442e-01 5.41150039e+00 17 -1.99245875e+01 -2.16476548e+00 1.54207862e+01 18 3.25263972e+00 8.91008055e+00 4.44283010e+00 19 5.13601664e-01 3.27454881e-01 6.57483342e-01 20 -1.36057743e-01 -9.74041050e-01 1.22215656e+00 21 2.30915758e-01 -1.27104742e+00 1.15308471e+00 22 6.46962147e-01 7.55538735e+00 3.21909161e-01 23 -2.68457814e-01 -1.34333254e+00 1.01691599e+00 24 -1.80669155e+00 -4.14080360e-01 2.20254207e+00 25 -4.39979986e+00 -3.64581884e+00 -9.76293384e-01 26 5.32287912e+00 2.23907199e+01 -2.83194724e+01 27 1.99677424e+01 -3.03686647e+01 1.65599852e+01 28 -2.73949715e+01 1.87567807e+01 1.45656743e+01 29 7.78902863e+00 -4.98322087e+00 -2.29805138e+00 30 6.92795028e-01 2.25663241e-01 2.31472107e-02 31 1.61461674e-01 1.37576649e+00 1.34995374e+00 32 5.32431738e-02 1.39904923e-01 9.48019322e-01 MIXED STRUCTURE (pbc=True)-- Species = H He W (Configuration in file "config-T-HHeW.xyz") ----------------------------------------------------------------------------------------------------- Energy = 39.13244446351276 Forces: 1 -1.05319998e+00 1.31140454e+00 -4.51156295e+00 2 8.57395420e+00 -9.40071417e+00 -2.31387447e+00 3 1.89686552e+01 -6.12567501e+00 -1.76268443e+01 4 -4.37768193e+00 5.18386130e+00 6.16079855e-01 5 -3.60632731e-01 -2.49278747e+00 -1.91905320e+00 6 4.05813424e+00 -2.98860061e+00 -1.83150593e+00 7 3.20370395e-01 -5.23575849e+00 -5.74809147e+00 8 -2.31397604e+00 4.58071768e-01 3.70470646e+00 9 -1.94819734e+01 -2.18649608e+01 1.31013267e+01 10 2.50853888e+01 2.03865219e+01 1.86685484e+01 11 1.73596583e+00 -1.19002114e+00 5.24197120e+00 12 -4.84224351e+00 -9.70761728e-01 6.54880074e+00 13 -9.16400052e+00 -1.06947018e+01 -1.48661222e+00 14 4.08633479e+00 2.19143916e+01 -1.43489176e+00 15 -9.92778798e-01 -2.03732787e+00 4.48240495e+00 16 -3.74389446e+00 4.58780081e-01 5.47365457e+00 17 -1.22800594e+01 -4.82410168e+00 1.35772505e+01 18 3.39129143e+00 8.95906712e+00 4.43151207e+00 19 7.95548574e-01 2.35169884e+00 9.70029088e-01 20 -1.82640945e-01 -2.25689510e+00 9.41686239e-01 21 7.51063150e-01 -8.37825891e-01 1.08136541e+00 22 -4.39965708e+00 1.21514753e+01 8.40059310e-02 23 -2.00300606e+00 -4.23756938e-01 1.61640149e+00 24 -1.91719842e+00 -4.11241629e-01 1.73138003e+00 25 -4.28200576e+00 -3.68284660e+00 -7.76361023e-01 26 6.37726600e+00 1.61678844e+01 -2.48559661e+01 27 2.26717146e+01 -3.36224382e+01 5.31271616e-01 28 -3.29057195e+01 2.47046951e+01 -1.74850278e+01 29 7.77997412e+00 -4.94631491e+00 -2.39037776e+00 30 4.08009138e-01 2.56619476e-01 1.23233861e-01 31 -7.31410138e-01 -6.70460422e-01 -1.17145330e+00 32 2.84081856e-02 3.72718904e-01 6.25993056e-01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==4159867== Memcheck, a memory error detector ==4159867== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==4159867== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info ==4159867== Command: python runner2.py EAM_Dynamo_BonnyGrigorevTerentyev_2014EAM1_WHHe__MO_292520929154_000 ==4159867== ==4161160== Warning: invalid file descriptor 1024 in syscall close() ==4161160== Warning: invalid file descriptor 1025 in syscall close() ==4161160== Warning: invalid file descriptor 1026 in syscall close() ==4161160== Warning: invalid file descriptor 1027 in syscall close() ==4161160== Use --log-fd= to select an alternative log fd. ==4161160== Warning: invalid file descriptor 1028 in syscall close() ==4161160== Warning: invalid file descriptor 1029 in syscall close() ==4159867== ==4159867== HEAP SUMMARY: ==4159867== in use at exit: 2,257,767 bytes in 1,704 blocks ==4159867== total heap usage: 102,152 allocs, 100,448 frees, 214,821,516 bytes allocated ==4159867== ==4159867== LEAK SUMMARY: ==4159867== definitely lost: 0 bytes in 0 blocks ==4159867== indirectly lost: 0 bytes in 0 blocks ==4159867== possibly lost: 180,827 bytes in 103 blocks ==4159867== still reachable: 2,076,908 bytes in 1,600 blocks ==4159867== of which reachable via heuristic: ==4159867== stdstring : 38 bytes in 1 blocks ==4159867== suppressed: 32 bytes in 1 blocks ==4159867== Rerun with --leak-check=full to see details of leaked memory ==4159867== ==4159867== For lists of detected and suppressed errors, rerun with: -s ==4159867== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 8092 from 589) ================================================================================ 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 10:17:12) ===