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_2014EAM2_WHHe__MO_626183701337_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 = 4.326006134147404 Forces: 1 -1.48067328e-01 -1.65755881e-01 -1.50735872e-01 2 7.63157426e-02 2.51038061e-02 -1.90691664e-01 3 1.17656515e-01 -2.73570924e-01 -9.12899519e-02 4 -2.98751975e-01 1.18251085e-01 -4.13533596e-02 5 1.28856875e-02 -1.85088019e-01 -1.40445036e-01 6 1.38407828e-01 4.65370400e-03 -1.96882141e-01 7 1.06022534e-01 -3.94420657e-01 -2.37440841e-01 8 -6.45495597e-02 -1.01235328e-01 -4.31837220e-02 9 -1.97152662e-01 -6.00455508e-02 -2.73553340e-01 10 3.40013613e-03 3.14715149e-01 -2.85523659e-01 11 -8.44642276e-02 -1.47582032e-01 -1.00676882e-02 12 -2.77181803e-01 2.24839296e-01 5.39824459e-02 13 5.75354572e-03 -1.29888643e-01 -4.01201748e-01 14 1.69649227e-01 1.93354491e-01 -1.40139875e-01 15 3.60464778e-01 -5.96676941e-02 -1.80619187e-02 16 4.56930832e-02 3.93648186e-01 6.97549437e-02 17 -3.24287062e-01 -2.18732276e-01 3.40909908e-02 18 7.06438664e-02 9.56158206e-02 8.68771519e-02 19 -1.47588825e-02 -2.61239907e-01 2.20751259e-01 20 -1.60084504e-01 8.14400223e-02 1.70972101e-01 21 -5.71147427e-02 -2.99545031e-01 -3.59003224e-04 22 3.89163362e-01 2.55377212e-01 1.98217549e-01 23 2.06321111e-01 -1.00191766e-01 1.92286686e-01 24 -4.35927020e-02 1.59550484e-01 2.04237438e-01 25 -2.88137485e-01 -7.63587761e-02 -1.64819121e-02 26 -6.05674879e-03 3.72972487e-01 -7.22791685e-02 27 2.65520257e-01 -4.21680339e-01 2.70929332e-01 28 -4.70860400e-01 3.99801944e-01 2.05738252e-01 29 -1.38473321e-02 -1.16357821e-01 1.42409202e-01 30 2.02399100e-01 2.55167194e-01 -4.18510159e-03 31 2.03778359e-01 -1.05972754e-01 2.05731603e-01 32 7.48322815e-02 2.22842518e-01 2.57897046e-01 MONOATOMIC STRUCTURE (pbc=True)-- Species = H (Configuration in file "config-T-H.xyz") ----------------------------------------------------------------------------------------------------- Energy = 4.326006134147404 Forces: 1 -1.48067328e-01 -1.65755881e-01 -1.50735872e-01 2 7.63157426e-02 2.51038061e-02 -1.90691664e-01 3 1.17656515e-01 -2.73570924e-01 -9.12899519e-02 4 -2.98751975e-01 1.18251085e-01 -4.13533596e-02 5 1.28856875e-02 -1.85088019e-01 -1.40445036e-01 6 1.38407828e-01 4.65370400e-03 -1.96882141e-01 7 1.06022534e-01 -3.94420657e-01 -2.37440841e-01 8 -6.45495597e-02 -1.01235328e-01 -4.31837220e-02 9 -1.97152662e-01 -6.00455508e-02 -2.73553340e-01 10 3.40013613e-03 3.14715149e-01 -2.85523659e-01 11 -8.44642276e-02 -1.47582032e-01 -1.00676882e-02 12 -2.77181803e-01 2.24839296e-01 5.39824459e-02 13 5.75354572e-03 -1.29888643e-01 -4.01201748e-01 14 1.69649227e-01 1.93354491e-01 -1.40139875e-01 15 3.60464778e-01 -5.96676941e-02 -1.80619187e-02 16 4.56930832e-02 3.93648186e-01 6.97549437e-02 17 -3.24287062e-01 -2.18732276e-01 3.40909908e-02 18 7.06438664e-02 9.56158206e-02 8.68771519e-02 19 -1.47588825e-02 -2.61239907e-01 2.20751259e-01 20 -1.60084504e-01 8.14400223e-02 1.70972101e-01 21 -5.71147427e-02 -2.99545031e-01 -3.59003224e-04 22 3.89163362e-01 2.55377212e-01 1.98217549e-01 23 2.06321111e-01 -1.00191766e-01 1.92286686e-01 24 -4.35927020e-02 1.59550484e-01 2.04237438e-01 25 -2.88137485e-01 -7.63587761e-02 -1.64819121e-02 26 -6.05674879e-03 3.72972487e-01 -7.22791685e-02 27 2.65520257e-01 -4.21680339e-01 2.70929332e-01 28 -4.70860400e-01 3.99801944e-01 2.05738252e-01 29 -1.38473321e-02 -1.16357821e-01 1.42409202e-01 30 2.02399100e-01 2.55167194e-01 -4.18510159e-03 31 2.03778359e-01 -1.05972754e-01 2.05731603e-01 32 7.48322815e-02 2.22842518e-01 2.57897046e-01 MONOATOMIC STRUCTURE (pbc=False)-- Species = He (Configuration in file "config-F-He.xyz") ----------------------------------------------------------------------------------------------------- Energy = -0.0664677253547798 Forces: 1 -7.19077384e-03 2.09756968e-01 2.28181401e-01 2 2.09999284e-02 -1.59900384e-01 -9.49451403e-03 3 4.82107305e-01 2.49579991e-01 -1.32845697e-01 4 3.39344063e-02 -5.14252562e-01 1.74972948e-01 5 2.09794674e-02 3.62644521e-01 1.29568992e+00 6 -1.49935183e-01 -5.20687103e-01 5.57664159e-01 7 -8.75073187e-01 1.12427164e+00 -1.18356921e+00 8 6.34153671e-01 -7.90495362e-01 -1.69095765e-01 9 -1.52011470e-01 9.70975451e-02 -1.75229954e-02 10 -1.60401257e-02 6.33937722e-02 -9.10691422e-02 11 -7.93611055e-01 6.80061587e-01 1.40914920e-01 12 7.91677248e-01 -5.71411822e-01 -2.92530544e-02 13 2.27264725e-02 -4.15426350e-02 -9.57171780e-02 14 2.75540764e-02 3.94548490e-02 -5.46176134e-02 15 -4.57473896e-02 -2.46650257e-02 5.05962260e-02 16 5.95468232e-02 1.65641514e-01 1.43546569e-02 17 5.65689735e-01 6.46848437e-01 -5.35115341e-01 18 -1.00403524e+00 -2.87493798e-01 -4.63633680e-01 19 6.49033812e-01 1.37016785e-01 -5.78888387e-01 20 4.57515325e-01 7.57923305e-01 -1.05270412e-01 21 -3.49336753e-01 2.73078648e-01 1.65939292e+00 22 7.32667475e-02 -1.88403460e-01 -6.07056287e-02 23 -3.53732451e-02 -2.05120092e-01 -1.68165227e-01 24 -2.30305141e-01 -3.77418334e-01 -6.41703950e-01 25 3.04323101e-01 -7.52586777e-01 1.09037685e-01 26 -8.33798643e-01 -4.68307785e-02 8.69137168e-01 27 -5.96334794e-01 -6.22016247e-03 -3.28466698e-01 28 8.57532071e-01 -3.57988159e-01 -5.51126507e-01 29 6.81989692e-02 -5.99168117e-02 -4.33207307e-02 30 8.11783244e-02 1.15222779e-01 -2.22240921e-02 31 -2.28413607e-01 2.15141276e-01 1.61671999e-01 32 1.66789130e-01 -2.32200349e-01 2.01918216e-02 MONOATOMIC STRUCTURE (pbc=True)-- Species = He (Configuration in file "config-T-He.xyz") ----------------------------------------------------------------------------------------------------- Energy = -0.0664677253547798 Forces: 1 -7.19077384e-03 2.09756968e-01 2.28181401e-01 2 2.09999284e-02 -1.59900384e-01 -9.49451403e-03 3 4.82107305e-01 2.49579991e-01 -1.32845697e-01 4 3.39344063e-02 -5.14252562e-01 1.74972948e-01 5 2.09794674e-02 3.62644521e-01 1.29568992e+00 6 -1.49935183e-01 -5.20687103e-01 5.57664159e-01 7 -8.75073187e-01 1.12427164e+00 -1.18356921e+00 8 6.34153671e-01 -7.90495362e-01 -1.69095765e-01 9 -1.52011470e-01 9.70975451e-02 -1.75229954e-02 10 -1.60401257e-02 6.33937722e-02 -9.10691422e-02 11 -7.93611055e-01 6.80061587e-01 1.40914920e-01 12 7.91677248e-01 -5.71411822e-01 -2.92530544e-02 13 2.27264725e-02 -4.15426350e-02 -9.57171780e-02 14 2.75540764e-02 3.94548490e-02 -5.46176134e-02 15 -4.57473896e-02 -2.46650257e-02 5.05962260e-02 16 5.95468232e-02 1.65641514e-01 1.43546569e-02 17 5.65689735e-01 6.46848437e-01 -5.35115341e-01 18 -1.00403524e+00 -2.87493798e-01 -4.63633680e-01 19 6.49033812e-01 1.37016785e-01 -5.78888387e-01 20 4.57515325e-01 7.57923305e-01 -1.05270412e-01 21 -3.49336753e-01 2.73078648e-01 1.65939292e+00 22 7.32667475e-02 -1.88403460e-01 -6.07056287e-02 23 -3.53732451e-02 -2.05120092e-01 -1.68165227e-01 24 -2.30305141e-01 -3.77418334e-01 -6.41703950e-01 25 3.04323101e-01 -7.52586777e-01 1.09037685e-01 26 -8.33798643e-01 -4.68307785e-02 8.69137168e-01 27 -5.96334794e-01 -6.22016247e-03 -3.28466698e-01 28 8.57532071e-01 -3.57988159e-01 -5.51126507e-01 29 6.81989692e-02 -5.99168117e-02 -4.33207307e-02 30 8.11783244e-02 1.15222779e-01 -2.22240921e-02 31 -2.28413607e-01 2.15141276e-01 1.61671999e-01 32 1.66789130e-01 -2.32200349e-01 2.01918216e-02 MONOATOMIC STRUCTURE (pbc=False)-- Species = W (Configuration in file "config-F-W.xyz") ----------------------------------------------------------------------------------------------------- Energy = 119.65673956896016 Forces: 1 -1.15031169e+01 -2.57418459e+01 -3.04633939e+01 2 -1.60905571e+01 -2.13178483e+01 -3.65668165e+01 3 1.11238335e+01 -3.42597084e+01 -1.80767973e+01 4 -3.33796511e+01 3.23854067e+01 6.75525221e+00 5 -1.86123089e+01 -2.70968255e+01 -3.54078702e+01 6 1.74619511e+01 2.00645737e+01 -1.82903345e+01 7 2.79583056e+01 -2.33314908e+01 2.45090514e+01 8 2.46736343e+01 2.06859823e+01 6.48162454e+00 9 -2.20959972e+01 -1.48705889e+01 -2.15712620e+01 10 5.26165820e+00 3.11136382e+01 -9.22158435e+00 11 -7.83645211e+00 2.16311725e+01 2.74026590e+01 12 -1.84885388e+01 1.87354898e+01 4.95249250e+00 13 2.99765318e+01 1.62392174e+00 -2.43939705e+01 14 7.44320127e+00 8.31658931e+00 -9.79004107e+00 15 1.87855823e+01 -1.87983816e+01 -1.35202610e+01 16 -1.28719007e+01 2.18861646e+01 -1.29499069e+01 17 -2.74233787e+01 -2.90129409e+01 1.91543529e+01 18 -1.23346939e+01 1.64905391e+01 1.38889163e+01 19 -7.67198943e+00 -1.09310267e+01 2.23334824e+01 20 -1.51036185e+01 -6.40889027e+00 1.84708654e+01 21 1.59953040e+01 -3.16716545e+01 -7.32656418e+00 22 3.02173773e+01 -5.75947565e+00 -2.62620036e+01 23 1.97885793e+01 -2.76591907e+01 2.34359246e+01 24 -1.12855265e+01 -1.81029467e+01 4.24148530e+01 25 -2.15386064e+01 -1.14298284e+01 -1.10043459e+01 26 1.69007616e+01 2.53643613e+01 -7.06153192e+00 27 -1.73094264e+01 -8.09974053e+00 3.03555844e+01 28 -2.24187084e+01 1.74410067e+01 2.09309287e+01 29 -5.41258987e+00 4.82987854e+00 -4.05544522e+01 30 2.66130180e+01 3.57322963e+01 -2.01423803e+00 31 3.84839109e+01 1.90302355e+00 3.24423016e+01 32 -9.30658824e+00 3.62883396e+01 3.09470849e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = W (Configuration in file "config-T-W.xyz") ----------------------------------------------------------------------------------------------------- Energy = 119.65673956896016 Forces: 1 -1.15031169e+01 -2.57418459e+01 -3.04633939e+01 2 -1.60905571e+01 -2.13178483e+01 -3.65668165e+01 3 1.11238335e+01 -3.42597084e+01 -1.80767973e+01 4 -3.33796511e+01 3.23854067e+01 6.75525221e+00 5 -1.86123089e+01 -2.70968255e+01 -3.54078702e+01 6 1.74619511e+01 2.00645737e+01 -1.82903345e+01 7 2.79583056e+01 -2.33314908e+01 2.45090514e+01 8 2.46736343e+01 2.06859823e+01 6.48162454e+00 9 -2.20959972e+01 -1.48705889e+01 -2.15712620e+01 10 5.26165820e+00 3.11136382e+01 -9.22158435e+00 11 -7.83645211e+00 2.16311725e+01 2.74026590e+01 12 -1.84885388e+01 1.87354898e+01 4.95249250e+00 13 2.99765318e+01 1.62392174e+00 -2.43939705e+01 14 7.44320127e+00 8.31658931e+00 -9.79004107e+00 15 1.87855823e+01 -1.87983816e+01 -1.35202610e+01 16 -1.28719007e+01 2.18861646e+01 -1.29499069e+01 17 -2.74233787e+01 -2.90129409e+01 1.91543529e+01 18 -1.23346939e+01 1.64905391e+01 1.38889163e+01 19 -7.67198943e+00 -1.09310267e+01 2.23334824e+01 20 -1.51036185e+01 -6.40889027e+00 1.84708654e+01 21 1.59953040e+01 -3.16716545e+01 -7.32656418e+00 22 3.02173773e+01 -5.75947565e+00 -2.62620036e+01 23 1.97885793e+01 -2.76591907e+01 2.34359246e+01 24 -1.12855265e+01 -1.81029467e+01 4.24148530e+01 25 -2.15386064e+01 -1.14298284e+01 -1.10043459e+01 26 1.69007616e+01 2.53643613e+01 -7.06153192e+00 27 -1.73094264e+01 -8.09974053e+00 3.03555844e+01 28 -2.24187084e+01 1.74410067e+01 2.09309287e+01 29 -5.41258987e+00 4.82987854e+00 -4.05544522e+01 30 2.66130180e+01 3.57322963e+01 -2.01423803e+00 31 3.84839109e+01 1.90302355e+00 3.24423016e+01 32 -9.30658824e+00 3.62883396e+01 3.09470849e+01 MIXED STRUCTURE (pbc=False)-- Species = H He W (Configuration in file "config-F-HHeW.xyz") ----------------------------------------------------------------------------------------------------- Energy = -177.67084144346566 Forces: 1 -2.49370676e+00 -1.59003279e+00 -5.53341033e+00 2 4.36713099e+00 7.19253039e+00 -7.75740091e+00 3 1.67873743e+01 -2.47822850e+01 -5.93566984e+00 4 -1.98742613e+01 2.95220832e+01 5.34617142e+00 5 1.18844410e+00 1.93957252e-01 -1.01713226e+00 6 9.86571570e-01 -1.35946100e+00 4.28538038e-01 7 -2.40017825e+00 2.27129357e+00 -1.07108408e+00 8 -4.78536539e-01 -1.38093515e+01 1.36568806e+01 9 -2.25329241e+00 -3.31272648e-01 -2.95561837e+00 10 4.62339120e+00 7.94292491e-01 -5.35082103e+00 11 -1.20612769e+01 -1.43194353e-01 1.43834758e+01 12 -8.87822906e+00 8.52924504e-01 -5.18965291e-01 13 8.85482526e+00 8.67527736e+00 -1.84217191e+01 14 7.24279768e-01 6.77483556e-01 -1.73619331e-01 15 3.27523359e+00 -6.85038629e-01 1.39296180e-01 16 -2.96094160e+00 3.43347421e+00 -5.93787318e+00 17 -2.84559125e+00 -5.35563759e+00 9.22782701e+00 18 1.08959498e+00 -2.57099874e+00 -7.59689713e+00 19 5.09383720e+00 -1.22397626e+00 -2.49749236e+00 20 -1.40251861e+01 -7.76165621e+00 -1.33808840e+00 21 1.10009645e+01 5.38745724e+00 1.49935042e+01 22 -3.43646898e+00 9.96326036e-01 -4.78687502e-01 23 -3.68751683e+00 4.40569925e+00 -3.28969528e+00 24 1.41212881e+01 -1.51364992e+01 -8.72820019e-01 25 -2.38577301e+00 2.76535748e-02 2.82151445e-01 26 -1.33134346e+01 1.95040145e+01 -6.32267893e+00 27 -1.28446323e+01 1.37525521e+01 2.54146822e+01 28 -2.30957889e+00 -4.08253938e-01 9.13706920e-01 29 1.44620990e+01 -2.20574501e+01 -2.61086349e+01 30 5.55280218e+00 1.85345716e+00 3.05721954e+00 31 1.08009427e+01 -8.99944684e+00 1.19095902e+01 32 3.31982533e+00 6.67407848e+00 3.42526467e+00 MIXED STRUCTURE (pbc=True)-- Species = H He W (Configuration in file "config-T-HHeW.xyz") ----------------------------------------------------------------------------------------------------- Energy = -198.24848243863775 Forces: 1 -1.89251888e+00 -1.72104423e+00 -5.85338347e+00 2 3.40722196e+00 6.17196213e+00 -8.61347084e+00 3 2.41188841e+01 -6.06153270e+00 -9.56204890e+00 4 -2.21653315e+01 2.68937125e+01 3.90496469e+00 5 1.12878143e+00 5.60742665e-01 -1.54455180e+00 6 -4.86539685e-01 -2.18450437e+00 1.61926845e+00 7 1.77996624e+00 7.95208970e-01 -1.18188795e+00 8 2.76749280e-01 -1.34728348e+01 1.19785022e+01 9 -2.51209794e+00 1.75128374e-01 -1.04424373e+00 10 4.33961705e+00 -1.29796440e-01 -6.21703225e+00 11 -1.20435648e+01 6.61598398e-01 1.30891638e+01 12 -1.73620303e+01 -1.32820410e+01 -1.55195265e+00 13 1.26132733e+01 1.19729213e+01 -1.11306331e+01 14 -4.32359313e-01 2.03368809e+00 -7.62805710e-01 15 1.78761940e+00 -1.18609269e+00 7.52172701e-01 16 -2.65490828e+00 1.96380596e+00 -6.48196269e+00 17 -3.93814426e+00 -5.51422312e+00 9.99690287e+00 18 7.79783214e-01 -2.85296170e+00 -7.22232815e+00 19 4.63138197e+00 -4.27773814e+00 -2.16913146e-01 20 -1.04285488e+01 -9.30766278e+00 -1.97560193e+00 21 1.27696443e+01 1.13942418e+01 1.07838297e+01 22 3.07518980e-01 4.84936445e-01 -7.00863690e-01 23 -2.23695758e+00 -1.46004501e+00 7.53921631e-01 24 1.44926628e+01 -1.60188095e+01 5.63917344e-01 25 -1.90494862e+00 5.01401117e-02 -8.44065167e-01 26 -1.76516575e+01 1.56144254e+01 -5.93213107e-01 27 -2.07118684e+01 1.33030733e+01 1.70913441e+01 28 -2.67306321e+00 6.95497662e-01 2.65005788e+00 29 1.40843827e+01 -1.86148576e+01 -2.39685188e+01 30 5.62852141e+00 8.36297466e-01 3.94339957e+00 31 1.35101435e+01 -3.32158483e+00 8.17599783e+00 32 3.43838733e+00 5.79834842e+00 4.16203436e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==4159802== Memcheck, a memory error detector ==4159802== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==4159802== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info ==4159802== Command: python runner2.py EAM_Dynamo_BonnyGrigorevTerentyev_2014EAM2_WHHe__MO_626183701337_000 ==4159802== ==4161143== Warning: invalid file descriptor 1024 in syscall close() ==4161143== Warning: invalid file descriptor 1025 in syscall close() ==4161143== Warning: invalid file descriptor 1026 in syscall close() ==4161143== Warning: invalid file descriptor 1027 in syscall close() ==4161143== Use --log-fd= to select an alternative log fd. ==4161143== Warning: invalid file descriptor 1028 in syscall close() ==4161143== Warning: invalid file descriptor 1029 in syscall close() ==4159802== ==4159802== HEAP SUMMARY: ==4159802== in use at exit: 2,257,767 bytes in 1,704 blocks ==4159802== total heap usage: 102,441 allocs, 100,737 frees, 215,693,414 bytes allocated ==4159802== ==4159802== LEAK SUMMARY: ==4159802== definitely lost: 0 bytes in 0 blocks ==4159802== indirectly lost: 0 bytes in 0 blocks ==4159802== possibly lost: 180,827 bytes in 103 blocks ==4159802== still reachable: 2,076,908 bytes in 1,600 blocks ==4159802== of which reachable via heuristic: ==4159802== stdstring : 38 bytes in 1 blocks ==4159802== suppressed: 32 bytes in 1 blocks ==4159802== Rerun with --leak-check=full to see details of leaked memory ==4159802== ==4159802== For lists of detected and suppressed errors, rerun with: -s ==4159802== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 8101 from 591) ================================================================================ 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) ===