!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_PlummerTucker_2019_TiSiC__MO_751442731010_000 Supported species : C Si Ti random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = C (Configuration in file "config-F-C.xyz") ----------------------------------------------------------------------------------------------------- Energy = -61.80481669978791 Forces: 1 -1.17235091e+00 6.92580883e+00 3.38890996e+00 2 2.91227842e+00 -3.00096768e+00 -5.25541887e-02 3 1.29276252e+01 -3.66621678e+00 7.49123094e-01 4 -1.85852349e+00 -3.69847348e-01 -1.39964679e+00 5 -9.09154580e+00 3.19023575e+00 5.86995896e+00 6 -2.95402735e-02 -2.10699451e-01 3.40650630e-01 7 -3.86800650e+00 2.99706753e+00 -1.21006372e-03 8 7.80521150e-01 -7.94128170e-01 1.11065469e-01 9 3.12818644e+00 9.03068430e+00 8.62140868e+00 10 -2.02941764e+00 -3.05062804e+00 -2.05181671e+00 11 -6.12639567e+00 -2.29994533e+00 1.84036978e+00 12 1.92201156e+00 -1.16434444e+01 3.50019025e-01 13 -2.86537053e+00 1.24021454e+00 -7.71714851e-02 14 -1.73597610e+00 -5.46195072e+00 4.10403368e+00 15 4.57262964e+00 5.52713185e+00 -2.03236025e+00 16 -5.17834641e+00 5.41287545e+00 4.15619634e+00 17 4.45986137e+00 3.57381655e+00 7.84792666e+00 18 -4.95373522e+00 -3.64780021e+00 -7.45161327e+00 19 -7.05412465e+00 4.67442204e+00 -3.67215516e+00 20 3.08990083e+00 -6.67321976e+00 -5.21364458e+00 21 -4.59478125e+00 -4.65976671e+00 -7.18298042e-01 22 5.29401235e+00 -9.22403546e-01 1.26359963e+01 23 -2.21323434e+00 7.42949148e+00 -1.14075111e+01 24 3.58647127e+00 -1.89888610e+00 -4.15342910e-02 25 8.91020742e+00 1.09005701e+00 -2.54639488e+01 26 1.33623835e+01 -3.10446832e+00 -7.99202683e+00 27 3.52075100e+00 -9.37197913e+00 1.06472554e+01 28 -7.66907451e+00 1.23702289e+01 1.24876463e+01 29 -6.01730541e+00 -5.98532091e+00 4.97160526e+00 30 5.75815078e+00 1.27960828e+00 -3.87965624e-01 31 -8.52666539e+00 9.15891409e+00 -1.33681651e+00 32 7.59403139e-01 -7.13888396e+00 -8.82189189e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = C (Configuration in file "config-T-C.xyz") ----------------------------------------------------------------------------------------------------- Energy = -61.80481669978791 Forces: 1 -1.17235091e+00 6.92580883e+00 3.38890996e+00 2 2.91227842e+00 -3.00096768e+00 -5.25541887e-02 3 1.29276252e+01 -3.66621678e+00 7.49123094e-01 4 -1.85852349e+00 -3.69847348e-01 -1.39964679e+00 5 -9.09154580e+00 3.19023575e+00 5.86995896e+00 6 -2.95402735e-02 -2.10699451e-01 3.40650630e-01 7 -3.86800650e+00 2.99706753e+00 -1.21006372e-03 8 7.80521150e-01 -7.94128170e-01 1.11065469e-01 9 3.12818644e+00 9.03068430e+00 8.62140868e+00 10 -2.02941764e+00 -3.05062804e+00 -2.05181671e+00 11 -6.12639567e+00 -2.29994533e+00 1.84036978e+00 12 1.92201156e+00 -1.16434444e+01 3.50019025e-01 13 -2.86537053e+00 1.24021454e+00 -7.71714851e-02 14 -1.73597610e+00 -5.46195072e+00 4.10403368e+00 15 4.57262964e+00 5.52713185e+00 -2.03236025e+00 16 -5.17834641e+00 5.41287545e+00 4.15619634e+00 17 4.45986137e+00 3.57381655e+00 7.84792666e+00 18 -4.95373522e+00 -3.64780021e+00 -7.45161327e+00 19 -7.05412465e+00 4.67442204e+00 -3.67215516e+00 20 3.08990083e+00 -6.67321976e+00 -5.21364458e+00 21 -4.59478125e+00 -4.65976671e+00 -7.18298042e-01 22 5.29401235e+00 -9.22403546e-01 1.26359963e+01 23 -2.21323434e+00 7.42949148e+00 -1.14075111e+01 24 3.58647127e+00 -1.89888610e+00 -4.15342910e-02 25 8.91020742e+00 1.09005701e+00 -2.54639488e+01 26 1.33623835e+01 -3.10446832e+00 -7.99202683e+00 27 3.52075100e+00 -9.37197913e+00 1.06472554e+01 28 -7.66907451e+00 1.23702289e+01 1.24876463e+01 29 -6.01730541e+00 -5.98532091e+00 4.97160526e+00 30 5.75815078e+00 1.27960828e+00 -3.87965624e-01 31 -8.52666539e+00 9.15891409e+00 -1.33681651e+00 32 7.59403139e-01 -7.13888396e+00 -8.82189189e+00 MONOATOMIC STRUCTURE (pbc=False)-- Species = Si (Configuration in file "config-F-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 161.58732760590908 Forces: 1 -6.91403432e+00 -7.48905883e+00 -6.61006259e+00 2 -2.43080293e+01 2.77532282e+01 -7.30348127e+00 3 2.14215511e+00 -1.44539254e+01 -2.72019219e+01 4 -1.68094859e+01 -1.08280237e+01 8.30282404e+00 5 2.13988280e+01 -3.44680570e+01 -9.42850315e+00 6 2.03946154e+01 -1.05310817e+01 -1.64160621e+01 7 2.86101756e+01 -3.66826101e+01 -8.93578255e-01 8 -1.63127914e+01 1.80240666e+01 -8.35470913e+00 9 -1.87578855e+01 -6.70471951e+00 -1.77181226e+01 10 1.07313408e+01 1.77846154e+01 -2.13762804e+01 11 -3.81152457e+01 -1.99097692e+01 -3.41959856e+01 12 -1.35441856e+01 1.20896394e+01 9.16944935e+00 13 -4.15042655e+01 -7.78910027e+00 -5.87897861e+01 14 1.42598262e+01 1.79927662e+01 -2.11731120e+01 15 6.21251176e+01 -3.00232198e+00 3.21052330e+01 16 1.20159879e+01 5.23088572e+01 -2.85477380e+01 17 -2.60394203e+01 -4.77620534e+00 1.28944642e+01 18 -1.60220686e+01 -2.84795348e+01 7.94857414e+00 19 -3.88618148e+01 -4.70837581e+01 2.90968388e+01 20 -1.11617262e+01 -1.32263649e+01 1.26323842e+01 21 1.61642719e+01 -3.11444496e+01 -6.87727987e+00 22 2.96078706e+01 -1.30706778e+01 -1.55622103e+01 23 7.25342913e+00 -4.93831572e+00 4.12528115e+00 24 2.70465404e+01 3.26912401e+01 2.49686939e+01 25 -2.17362691e+01 -1.52715735e+00 -7.56324408e+00 26 -4.71861355e+01 5.51295691e+01 5.31624630e+00 27 1.08836802e+01 2.32780198e-01 2.42462510e+01 28 -1.96124880e+01 2.86046927e+01 1.30892579e+01 29 3.43718704e+01 -3.18818375e+01 1.31273050e+01 30 3.23254726e+01 1.99130037e+01 8.42828768e+00 31 1.24072586e+01 2.41354636e+01 4.03847087e+01 32 1.51474052e+01 2.13270466e+01 4.21762778e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Si (Configuration in file "config-T-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 161.58732760590908 Forces: 1 -6.91403432e+00 -7.48905883e+00 -6.61006259e+00 2 -2.43080293e+01 2.77532282e+01 -7.30348127e+00 3 2.14215511e+00 -1.44539254e+01 -2.72019219e+01 4 -1.68094859e+01 -1.08280237e+01 8.30282404e+00 5 2.13988280e+01 -3.44680570e+01 -9.42850315e+00 6 2.03946154e+01 -1.05310817e+01 -1.64160621e+01 7 2.86101756e+01 -3.66826101e+01 -8.93578255e-01 8 -1.63127914e+01 1.80240666e+01 -8.35470913e+00 9 -1.87578855e+01 -6.70471951e+00 -1.77181226e+01 10 1.07313408e+01 1.77846154e+01 -2.13762804e+01 11 -3.81152457e+01 -1.99097692e+01 -3.41959856e+01 12 -1.35441856e+01 1.20896394e+01 9.16944935e+00 13 -4.15042655e+01 -7.78910027e+00 -5.87897861e+01 14 1.42598262e+01 1.79927662e+01 -2.11731120e+01 15 6.21251176e+01 -3.00232198e+00 3.21052330e+01 16 1.20159879e+01 5.23088572e+01 -2.85477380e+01 17 -2.60394203e+01 -4.77620534e+00 1.28944642e+01 18 -1.60220686e+01 -2.84795348e+01 7.94857414e+00 19 -3.88618148e+01 -4.70837581e+01 2.90968388e+01 20 -1.11617262e+01 -1.32263649e+01 1.26323842e+01 21 1.61642719e+01 -3.11444496e+01 -6.87727987e+00 22 2.96078706e+01 -1.30706778e+01 -1.55622103e+01 23 7.25342913e+00 -4.93831572e+00 4.12528115e+00 24 2.70465404e+01 3.26912401e+01 2.49686939e+01 25 -2.17362691e+01 -1.52715735e+00 -7.56324408e+00 26 -4.71861355e+01 5.51295691e+01 5.31624630e+00 27 1.08836802e+01 2.32780198e-01 2.42462510e+01 28 -1.96124880e+01 2.86046927e+01 1.30892579e+01 29 3.43718704e+01 -3.18818375e+01 1.31273050e+01 30 3.23254726e+01 1.99130037e+01 8.42828768e+00 31 1.24072586e+01 2.41354636e+01 4.03847087e+01 32 1.51474052e+01 2.13270466e+01 4.21762778e+01 MONOATOMIC STRUCTURE (pbc=False)-- Species = Ti (Configuration in file "config-F-Ti.xyz") ----------------------------------------------------------------------------------------------------- Energy = 71.91029235552645 Forces: 1 -2.05612565e+00 -1.35841166e+00 -1.83257959e+00 2 -1.28117791e+01 7.95349888e+00 -1.48632407e+01 3 -7.25641107e+00 -1.63294673e+01 -5.49004924e+00 4 -1.46819193e+01 -4.53192776e+00 -1.34505601e+01 5 9.81020301e+00 -2.04136601e+01 -1.19902856e+01 6 6.39954768e+00 3.41966766e+00 -1.07860418e+01 7 8.66954934e+00 -1.21493210e+01 2.91843029e+00 8 7.74862252e-01 -6.11426149e+00 -7.29109582e+00 9 -1.34827064e+01 -1.46925439e+00 -1.37517922e+01 10 -4.97116111e+00 9.02566027e+00 -1.77602387e+01 11 6.95703691e+00 -3.73092290e+00 -9.52000766e+00 12 -1.88662972e+01 1.72954876e+01 -4.09111159e+00 13 -8.58699616e+00 -9.20586672e+00 -2.34397110e+01 14 1.50947481e+01 1.75719928e+01 -8.29939619e+00 15 2.53680951e+01 -8.56042145e+00 -4.53191178e-01 16 1.17029397e+01 1.93047046e+01 -1.54115602e+00 17 -1.10741529e+01 -1.48390038e+01 4.27567695e+00 18 5.50556881e+00 -1.76662182e+01 -1.08718243e+01 19 6.35202261e+00 -2.09722828e+01 8.98465350e+00 20 -2.26073293e+01 2.26309481e+00 1.35388123e+01 21 7.61097924e+00 -1.58558702e+01 7.85579203e+00 22 2.73120207e+01 -1.97168733e+01 -6.45497749e+00 23 3.42088700e+00 -4.06276999e+00 3.54137145e+00 24 -2.30786326e+00 -1.55677369e+01 2.29669212e+01 25 -3.09664313e+01 1.29854016e+01 5.28974913e+00 26 -8.51560277e+00 2.05442844e+01 1.12409100e+01 27 -2.31564040e+00 1.89527385e+01 3.08952195e+01 28 -4.17240543e+00 4.07558658e+00 4.04985431e+00 29 -8.98505221e+00 1.23416132e+01 -5.90903990e+00 30 1.11983413e+01 1.57530737e+01 6.92737775e+00 31 2.18461170e+01 1.53364176e+01 2.83161718e+01 32 5.63495488e+00 1.57210477e+01 1.69953590e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ti (Configuration in file "config-T-Ti.xyz") ----------------------------------------------------------------------------------------------------- Energy = 71.91029235552645 Forces: 1 -2.05612565e+00 -1.35841166e+00 -1.83257959e+00 2 -1.28117791e+01 7.95349888e+00 -1.48632407e+01 3 -7.25641107e+00 -1.63294673e+01 -5.49004924e+00 4 -1.46819193e+01 -4.53192776e+00 -1.34505601e+01 5 9.81020301e+00 -2.04136601e+01 -1.19902856e+01 6 6.39954768e+00 3.41966766e+00 -1.07860418e+01 7 8.66954934e+00 -1.21493210e+01 2.91843029e+00 8 7.74862252e-01 -6.11426149e+00 -7.29109582e+00 9 -1.34827064e+01 -1.46925439e+00 -1.37517922e+01 10 -4.97116111e+00 9.02566027e+00 -1.77602387e+01 11 6.95703691e+00 -3.73092290e+00 -9.52000766e+00 12 -1.88662972e+01 1.72954876e+01 -4.09111159e+00 13 -8.58699616e+00 -9.20586672e+00 -2.34397110e+01 14 1.50947481e+01 1.75719928e+01 -8.29939619e+00 15 2.53680951e+01 -8.56042145e+00 -4.53191178e-01 16 1.17029397e+01 1.93047046e+01 -1.54115602e+00 17 -1.10741529e+01 -1.48390038e+01 4.27567695e+00 18 5.50556881e+00 -1.76662182e+01 -1.08718243e+01 19 6.35202261e+00 -2.09722828e+01 8.98465350e+00 20 -2.26073293e+01 2.26309481e+00 1.35388123e+01 21 7.61097924e+00 -1.58558702e+01 7.85579203e+00 22 2.73120207e+01 -1.97168733e+01 -6.45497749e+00 23 3.42088700e+00 -4.06276999e+00 3.54137145e+00 24 -2.30786326e+00 -1.55677369e+01 2.29669212e+01 25 -3.09664313e+01 1.29854016e+01 5.28974913e+00 26 -8.51560277e+00 2.05442844e+01 1.12409100e+01 27 -2.31564040e+00 1.89527385e+01 3.08952195e+01 28 -4.17240543e+00 4.07558658e+00 4.04985431e+00 29 -8.98505221e+00 1.23416132e+01 -5.90903990e+00 30 1.11983413e+01 1.57530737e+01 6.92737775e+00 31 2.18461170e+01 1.53364176e+01 2.83161718e+01 32 5.63495488e+00 1.57210477e+01 1.69953590e+01 MIXED STRUCTURE (pbc=False)-- Species = C Si Ti (Configuration in file "config-F-CSiTi.xyz") ----------------------------------------------------------------------------------------------------- Energy = 40.577168485891995 Forces: 1 -2.30409729e+01 -2.68175915e+01 -1.76548800e+01 2 1.14989280e+01 4.99132932e+01 -6.39161528e+01 3 1.18192058e+01 -3.58618961e+01 3.12606058e+01 4 -2.53859592e+01 5.50498392e+00 1.90335054e+01 5 5.40601682e+00 -2.90519607e+01 -2.14403102e+01 6 3.55406260e+01 -6.61583700e+00 -3.09520559e+01 7 2.93251160e+01 -1.76116776e+01 -2.09491846e+01 8 -4.41012236e+01 -1.34277623e+00 3.46925606e+01 9 -3.00886366e+01 5.09632861e+00 -4.57756801e+01 10 -1.75037784e+01 1.05214576e+01 -4.53289221e+01 11 3.39781594e+01 -1.14044102e+01 2.75119715e+01 12 -4.93334828e+01 1.77052065e+01 -4.43629412e+01 13 1.11473610e+00 1.69240648e+01 -2.40264620e+01 14 4.82271936e-01 -4.23896412e+00 -1.58463628e+01 15 3.46608568e+01 2.49679621e+01 2.76480901e+01 16 1.64593462e+01 2.36201071e+01 3.11822666e+01 17 -1.62956364e+01 -1.46736928e+01 1.06493270e+01 18 -1.84019681e+01 -4.42044485e+01 -3.81104364e+01 19 8.13915386e+00 -1.65364827e+01 1.14858905e+01 20 -3.18879486e+01 -1.06036799e+01 2.16104111e+01 21 -3.18799659e+01 -1.88623086e+01 2.62011881e+01 22 2.29384514e+01 8.36485617e+00 5.51131400e+00 23 3.24757738e+00 -6.16011627e+00 1.05188667e+01 24 2.04973901e+01 -1.94878842e+01 1.12084308e+01 25 -4.09920012e+01 -2.01327485e+01 1.03476593e+01 26 6.94431464e+01 3.29758809e+01 8.38648951e+00 27 -6.63995316e+00 3.48219799e+01 3.37997511e+01 28 -2.17123359e+01 9.12354375e+00 3.80593974e+01 29 4.83127348e+01 1.71676779e-01 -2.39340357e+01 30 -6.04979957e-01 -6.23908128e-01 -1.79093345e-01 31 4.06080752e+00 9.79723139e+00 9.87462039e+00 32 9.44317894e-01 3.47218103e+01 2.34941713e+01 MIXED STRUCTURE (pbc=True)-- Species = C Si Ti (Configuration in file "config-T-CSiTi.xyz") ----------------------------------------------------------------------------------------------------- Energy = 238.95227912462664 Forces: 1 -1.99426724e+01 -2.28441813e+01 -2.70935191e+01 2 -3.64423538e+00 4.32733441e+01 -8.47568337e+00 3 1.82802762e+01 -3.27166729e+01 4.37799897e+01 4 -6.76508455e+00 1.07310254e+01 2.16589734e+01 5 1.22082679e+01 -2.37222996e+00 -3.73406843e+01 6 -4.34386959e-01 -2.30037990e+01 -3.20068562e+01 7 -1.01494189e+01 -1.33894815e+00 -3.23283792e+01 8 -4.62360818e+01 3.90126561e+00 3.99100578e+01 9 -5.16112888e+00 3.55764139e+01 -3.15772589e+01 10 -2.44483603e+01 9.30978714e+00 -3.26690405e+01 11 2.94829394e+01 -1.49058386e+01 3.34491725e+01 12 -3.22574740e+01 -3.44927091e+01 -7.41641243e+01 13 1.42721700e+01 3.87383613e+01 1.33788289e+01 14 -1.19239641e+00 -3.59642785e+00 -1.74286806e+01 15 2.58442429e+01 2.40626674e+01 2.55812232e+01 16 6.80818712e+00 -1.73848087e+01 4.74239605e+01 17 -1.04543411e+01 4.09133040e+01 4.44312866e+01 18 -1.50032274e+01 -4.55913075e+01 -4.13109013e+01 19 8.33238252e+00 -1.41517176e+01 -9.62462885e+00 20 1.65131709e+00 -2.41203434e+01 2.58307660e+01 21 -3.34944887e+01 -1.31158938e+01 3.28373695e+01 22 -6.07151441e+00 1.34736618e+01 -2.77231093e+00 23 -4.18402789e-01 -9.61533420e+00 2.75487591e+00 24 3.60636005e+01 -4.13626310e+01 -4.14442326e+01 25 -2.23380570e+01 -2.66539404e+01 -8.48914771e-01 26 9.33706612e+01 -1.42263227e+00 -3.75111822e+00 27 -7.00624372e+00 3.42909098e+01 -1.01815274e+01 28 6.62849893e+00 8.42720832e+00 8.75369824e+01 29 4.59948959e+01 1.14750369e+01 -1.75575897e+01 30 -4.86106984e+01 -3.75935469e+00 -1.68185961e+01 31 -2.40280695e+01 3.03801693e+01 1.85131296e+00 32 1.87188429e+01 2.78956154e+01 1.69692470e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==4444== Memcheck, a memory error detector ==4444== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==4444== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info ==4444== Command: python runner2.py Tersoff_LAMMPS_PlummerTucker_2019_TiSiC__MO_751442731010_000 ==4444== ==4500== Warning: invalid file descriptor 4096 in syscall close() ==4500== Warning: invalid file descriptor 4097 in syscall close() ==4500== Warning: invalid file descriptor 4098 in syscall close() ==4500== Warning: invalid file descriptor 4099 in syscall close() ==4500== Use --log-fd= to select an alternative log fd. ==4500== Warning: invalid file descriptor 4100 in syscall close() ==4500== Warning: invalid file descriptor 4101 in syscall close() ==4444== ==4444== HEAP SUMMARY: ==4444== in use at exit: 2,203,191 bytes in 1,644 blocks ==4444== total heap usage: 115,183 allocs, 113,539 frees, 69,775,863 bytes allocated ==4444== ==4444== LEAK SUMMARY: ==4444== definitely lost: 0 bytes in 0 blocks ==4444== indirectly lost: 0 bytes in 0 blocks ==4444== possibly lost: 198,622 bytes in 101 blocks ==4444== still reachable: 2,004,537 bytes in 1,542 blocks ==4444== suppressed: 32 bytes in 1 blocks ==4444== Rerun with --leak-check=full to see details of leaked memory ==4444== ==4444== For lists of detected and suppressed errors, rerun with: -s ==4444== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 9318 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.