!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_Tersoff_1994_SiC__MO_794973922560_000 Supported species : C Si 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 = 3889.1394737074834 Forces: 1 -1.35008662e+02 -2.36758516e+02 -3.15522643e+02 2 -8.31740104e+01 6.69421312e+01 -3.45182137e+02 3 4.11193618e+01 -3.87701192e+02 -9.64728588e+01 4 -3.16567616e+02 1.54455367e+02 1.40027258e+01 5 -1.27428424e+01 -4.10168418e+02 -9.45716285e+01 6 1.60485675e+02 -6.83996254e+01 -1.69146610e+02 7 -1.18955534e+02 -2.53382725e+02 -8.32040875e+01 8 3.03453919e+02 -6.17492751e+02 -5.44102015e+01 9 -1.73086414e+02 -7.56549024e+01 -4.68609435e+02 10 -3.59539897e+01 4.45374151e+02 -5.34489399e+02 11 -1.55197737e+02 -4.46823198e+02 -6.76046375e+01 12 -3.94959263e+02 3.52399421e+02 -7.24123153e+01 13 -2.72009868e+02 -1.12957120e+01 -1.10432944e+03 14 1.96883301e+02 2.30302180e+02 -2.08300764e+02 15 7.09039493e+02 5.60760948e+02 1.79391816e+02 16 1.72569911e+02 5.23402276e+02 2.50550633e+02 17 -4.99734321e+02 -3.29639221e+02 -4.97732139e+01 18 1.24146328e+02 2.06943719e+02 5.35364595e+00 19 2.61062460e+02 -3.27454680e+02 2.36510055e+02 20 -1.77576585e+02 2.09195767e+02 3.63229316e+02 21 -8.96983217e+00 -3.77208145e+02 3.38111419e+02 22 4.44609488e+02 -4.97208528e+01 6.33409978e+01 23 1.64596571e+02 -5.92607410e+01 2.07280518e+02 24 -1.36644651e+01 -4.36583978e+01 2.01017961e+02 25 -5.22869714e+02 -2.10174580e+01 6.40818478e+01 26 1.67910118e+02 5.36954787e+02 -3.03576034e+01 27 3.54084117e+02 -5.66799117e+02 3.26740486e+02 28 -9.01889636e+02 5.26124669e+02 3.18032084e+02 29 -2.47123686e+02 -1.46128114e+02 1.40517157e+02 30 4.02282904e+02 4.32860841e+02 7.49464805e+01 31 3.94300528e+02 -5.81136283e+01 5.83163989e+02 32 1.72939999e+02 2.40961138e+02 3.28115839e+02 MONOATOMIC STRUCTURE (pbc=True)-- Species = C (Configuration in file "config-T-C.xyz") ----------------------------------------------------------------------------------------------------- Energy = 3889.1394737074834 Forces: 1 -1.35008662e+02 -2.36758516e+02 -3.15522643e+02 2 -8.31740104e+01 6.69421312e+01 -3.45182137e+02 3 4.11193618e+01 -3.87701192e+02 -9.64728588e+01 4 -3.16567616e+02 1.54455367e+02 1.40027258e+01 5 -1.27428424e+01 -4.10168418e+02 -9.45716285e+01 6 1.60485675e+02 -6.83996254e+01 -1.69146610e+02 7 -1.18955534e+02 -2.53382725e+02 -8.32040875e+01 8 3.03453919e+02 -6.17492751e+02 -5.44102015e+01 9 -1.73086414e+02 -7.56549024e+01 -4.68609435e+02 10 -3.59539897e+01 4.45374151e+02 -5.34489399e+02 11 -1.55197737e+02 -4.46823198e+02 -6.76046375e+01 12 -3.94959263e+02 3.52399421e+02 -7.24123153e+01 13 -2.72009868e+02 -1.12957120e+01 -1.10432944e+03 14 1.96883301e+02 2.30302180e+02 -2.08300764e+02 15 7.09039493e+02 5.60760948e+02 1.79391816e+02 16 1.72569911e+02 5.23402276e+02 2.50550633e+02 17 -4.99734321e+02 -3.29639221e+02 -4.97732139e+01 18 1.24146328e+02 2.06943719e+02 5.35364595e+00 19 2.61062460e+02 -3.27454680e+02 2.36510055e+02 20 -1.77576585e+02 2.09195767e+02 3.63229316e+02 21 -8.96983217e+00 -3.77208145e+02 3.38111419e+02 22 4.44609488e+02 -4.97208528e+01 6.33409978e+01 23 1.64596571e+02 -5.92607410e+01 2.07280518e+02 24 -1.36644651e+01 -4.36583978e+01 2.01017961e+02 25 -5.22869714e+02 -2.10174580e+01 6.40818478e+01 26 1.67910118e+02 5.36954787e+02 -3.03576034e+01 27 3.54084117e+02 -5.66799117e+02 3.26740486e+02 28 -9.01889636e+02 5.26124669e+02 3.18032084e+02 29 -2.47123686e+02 -1.46128114e+02 1.40517157e+02 30 4.02282904e+02 4.32860841e+02 7.49464805e+01 31 3.94300528e+02 -5.81136283e+01 5.83163989e+02 32 1.72939999e+02 2.40961138e+02 3.28115839e+02 MONOATOMIC STRUCTURE (pbc=False)-- Species = Si (Configuration in file "config-F-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 205.16126386103954 Forces: 1 -3.39656730e+01 -1.50127382e+01 -3.26705555e+01 2 -2.30879515e+01 7.23333677e+00 -5.79257151e+01 3 7.57622288e+00 -3.77880231e+01 3.49042680e+01 4 -2.78940534e+01 -2.41101393e+01 -2.00737183e+01 5 1.97939903e+01 -3.03611032e+01 -2.06958244e+01 6 3.33108008e+01 -1.37102130e+01 -1.96402669e+01 7 1.98761644e+01 -4.38902574e+01 -2.87811286e+01 8 1.12493965e+01 7.08542908e+00 1.06675860e+01 9 -7.37606836e+00 2.88134410e+00 -1.93918772e+01 10 -7.06560911e+00 1.54600937e+01 -1.76321142e+01 11 5.31680095e-01 3.67703970e+01 -9.59637705e+00 12 -1.03383887e+01 3.29544709e+01 -2.36456353e+00 13 -5.44500455e-01 1.28824829e+01 -2.66723279e+01 14 5.48352845e+00 1.29787454e+01 -8.64569520e+00 15 1.89085543e+01 9.46496980e+00 1.41332338e+01 16 2.08394064e+01 2.13037487e+01 -1.82362167e+01 17 -9.44676058e+00 -1.17117050e+01 7.43343302e+00 18 -8.00125427e+00 -1.42135382e+01 2.84742190e+01 19 -8.28782515e+00 -1.18114135e+01 9.68456459e+00 20 -1.71623117e+01 2.84141142e+00 1.31354320e+01 21 -1.94697395e+01 -3.39581499e+01 8.76988260e+00 22 2.96964608e+01 3.02697748e+01 1.51727457e+01 23 1.42473243e+01 -9.14597065e+00 2.39450874e+01 24 1.01595649e+01 -3.24873395e+01 4.65981767e+01 25 -2.82188238e+01 8.40570006e+00 3.43537639e+01 26 -4.50829765e+01 2.56895644e+01 -1.62403898e+01 27 -5.44616313e+01 -2.14167695e+01 5.06084365e+01 28 -9.62569412e+00 4.42040517e+00 3.91260688e+00 29 1.43298191e+01 -1.53689490e+01 -5.67421655e+01 30 5.57752183e+01 3.48482580e+01 -3.21203115e+01 31 4.01084035e+01 -1.18085704e+01 2.79259794e+01 32 8.14272620e+00 6.13047477e+01 5.77098318e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Si (Configuration in file "config-T-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 205.16126386103954 Forces: 1 -3.39656730e+01 -1.50127382e+01 -3.26705555e+01 2 -2.30879515e+01 7.23333677e+00 -5.79257151e+01 3 7.57622288e+00 -3.77880231e+01 3.49042680e+01 4 -2.78940534e+01 -2.41101393e+01 -2.00737183e+01 5 1.97939903e+01 -3.03611032e+01 -2.06958244e+01 6 3.33108008e+01 -1.37102130e+01 -1.96402669e+01 7 1.98761644e+01 -4.38902574e+01 -2.87811286e+01 8 1.12493965e+01 7.08542908e+00 1.06675860e+01 9 -7.37606836e+00 2.88134410e+00 -1.93918772e+01 10 -7.06560911e+00 1.54600937e+01 -1.76321142e+01 11 5.31680095e-01 3.67703970e+01 -9.59637705e+00 12 -1.03383887e+01 3.29544709e+01 -2.36456353e+00 13 -5.44500455e-01 1.28824829e+01 -2.66723279e+01 14 5.48352845e+00 1.29787454e+01 -8.64569520e+00 15 1.89085543e+01 9.46496980e+00 1.41332338e+01 16 2.08394064e+01 2.13037487e+01 -1.82362167e+01 17 -9.44676058e+00 -1.17117050e+01 7.43343302e+00 18 -8.00125427e+00 -1.42135382e+01 2.84742190e+01 19 -8.28782515e+00 -1.18114135e+01 9.68456459e+00 20 -1.71623117e+01 2.84141142e+00 1.31354320e+01 21 -1.94697395e+01 -3.39581499e+01 8.76988260e+00 22 2.96964608e+01 3.02697748e+01 1.51727457e+01 23 1.42473243e+01 -9.14597065e+00 2.39450874e+01 24 1.01595649e+01 -3.24873395e+01 4.65981767e+01 25 -2.82188238e+01 8.40570006e+00 3.43537639e+01 26 -4.50829765e+01 2.56895644e+01 -1.62403898e+01 27 -5.44616313e+01 -2.14167695e+01 5.06084365e+01 28 -9.62569412e+00 4.42040517e+00 3.91260688e+00 29 1.43298191e+01 -1.53689490e+01 -5.67421655e+01 30 5.57752183e+01 3.48482580e+01 -3.21203115e+01 31 4.01084035e+01 -1.18085704e+01 2.79259794e+01 32 8.14272620e+00 6.13047477e+01 5.77098318e+01 MIXED STRUCTURE (pbc=False)-- Species = C Si (Configuration in file "config-F-CSi.xyz") ----------------------------------------------------------------------------------------------------- Energy = 16.32878613618865 Forces: 1 -2.04380555e+01 -2.12051669e+01 -2.41150153e+01 2 -8.18485193e+00 8.60123176e+00 -1.26583774e+01 3 -1.51613196e+01 -2.80186743e+01 5.18325233e+00 4 -4.98230895e+00 1.88347355e+01 1.02659162e+01 5 1.48619607e+01 -3.20466676e+01 -3.05300753e+01 6 2.32218756e+01 -5.20563128e-01 -1.42815449e+01 7 1.18204544e+01 -8.40822306e+00 1.13726151e+01 8 1.63536038e+01 1.10182556e+01 1.71857511e+01 9 1.10641711e-01 3.27197476e-01 -6.53404240e-01 10 -2.42235985e-01 -4.00536006e-02 -3.81182335e+00 11 -1.17150020e+01 5.97760678e+00 -3.88995646e+00 12 3.31424107e+00 -5.22508277e-01 9.48621349e+00 13 -4.78724501e+00 2.70916423e+01 -2.80287472e+01 14 1.47530672e+01 -8.06159235e-01 -4.27356839e+00 15 6.62203506e+00 3.31953786e+00 3.23992318e-01 16 -9.74623588e+00 6.10308236e+00 5.25202893e+00 17 -4.05459052e+01 -1.85540491e+01 1.04598908e+01 18 1.17712701e+01 1.13208048e+01 3.08866022e+00 19 -3.82579873e+00 -2.41878328e+00 1.33076219e+01 20 -2.80165327e+01 -3.38264374e+01 3.33326374e+01 21 1.29623560e+01 -1.04596709e+01 -5.45516691e+00 22 2.14746120e+01 1.59374792e+01 -1.96366291e+01 23 1.59836845e+01 -2.65055556e+01 1.62178826e+01 24 -2.74576641e+01 1.53020528e+01 1.05314133e+01 25 -1.54167105e+01 7.85961102e+00 -3.98688731e+01 26 -1.87495887e+01 1.03962383e+01 -2.05454725e-02 27 3.71133003e+01 1.90362586e+01 1.44994825e+01 28 -5.78271909e+00 1.73809929e+01 9.96577459e+00 29 1.16363027e+01 2.90875024e+00 5.25984334e+00 30 1.03383760e+01 2.07406506e+01 -1.09786830e+01 31 3.50635595e+00 -1.30659310e+01 2.11090990e+01 32 -7.91962924e-01 -5.75768459e+00 1.36033514e+00 MIXED STRUCTURE (pbc=True)-- Species = C Si (Configuration in file "config-T-CSi.xyz") ----------------------------------------------------------------------------------------------------- Energy = 58.78332133488683 Forces: 1 -2.05833401e+01 -1.38531464e+01 -3.93683647e+01 2 -6.14220435e+00 3.59649982e+00 -5.21207606e+00 3 -1.24199528e+01 -1.83223547e+01 1.22727607e+01 4 -5.04781476e-01 2.74639423e+01 1.08781680e+01 5 2.45318978e+01 -2.06301660e+01 -3.49504604e+01 6 1.76733095e+01 3.39840117e+00 -1.08841448e+01 7 -1.20178668e+01 -7.33617746e+00 1.89650300e+01 8 1.67581147e+01 1.17038400e+01 1.75480328e+01 9 -8.43309367e-01 -2.04287062e+00 5.68525244e+00 10 1.01995970e+01 -1.89374895e+01 -1.01560082e+00 11 -1.17136438e+01 6.87704372e+00 -4.49162384e+00 12 4.29465835e-01 -9.60300000e+00 1.30384307e+01 13 2.68331626e+00 2.51651704e+01 -9.90543600e+00 14 1.98959040e+01 -1.05768977e+00 -6.54425838e+00 15 7.04949217e+00 -5.64564090e-03 1.13169632e+00 16 -1.33647335e+01 -2.44259694e+00 1.14429715e+01 17 -3.09665102e+01 -1.51026897e+01 1.68553389e+01 18 1.09144846e+01 1.22754601e+01 4.82892860e+00 19 -1.63877598e+00 -3.61430154e+00 1.29962630e+01 20 -2.25825092e+01 -3.59362710e+01 2.97975622e+01 21 1.38767492e+01 -8.35002038e+00 -4.29223489e+00 22 1.45291282e+01 1.58697874e+01 -2.73436101e+01 23 9.13960549e+00 -2.53340857e+01 1.97803455e+01 24 -2.48099962e+01 1.29102169e+01 1.02915753e+01 25 -1.47043165e+00 3.40788991e+00 -4.94271239e+01 26 -1.36018633e+01 7.84883208e+00 1.72898003e+00 27 2.30535947e+01 1.45224325e+01 -4.96938593e+00 28 1.19060804e+01 2.30341546e+01 1.38638412e+01 29 1.10635483e+01 2.19737355e+00 4.79046330e+00 30 -7.05345406e+00 2.38957478e+01 -2.11875796e+01 31 -1.32380069e+01 -1.58121983e+01 1.72881502e+01 32 -7.52908553e-01 4.21391157e+00 -3.59189129e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==216436== Memcheck, a memory error detector ==216436== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==216436== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info ==216436== Command: python runner2.py Tersoff_LAMMPS_Tersoff_1994_SiC__MO_794973922560_000 ==216436== ==217087== Warning: invalid file descriptor 255988 in syscall close() ==217087== Warning: invalid file descriptor 255989 in syscall close() ==217087== Warning: invalid file descriptor 255990 in syscall close() ==217087== Warning: invalid file descriptor 255991 in syscall close() ==217087== Use --log-fd= to select an alternative log fd. ==217087== Warning: invalid file descriptor 255992 in syscall close() ==217087== Warning: invalid file descriptor 255993 in syscall close() ==216436== ==216436== HEAP SUMMARY: ==216436== in use at exit: 2,205,015 bytes in 1,646 blocks ==216436== total heap usage: 91,195 allocs, 89,549 frees, 71,851,464 bytes allocated ==216436== ==216436== LEAK SUMMARY: ==216436== definitely lost: 0 bytes in 0 blocks ==216436== indirectly lost: 0 bytes in 0 blocks ==216436== possibly lost: 198,622 bytes in 101 blocks ==216436== still reachable: 2,006,361 bytes in 1,544 blocks ==216436== suppressed: 32 bytes in 1 blocks ==216436== Rerun with --leak-check=full to see details of leaked memory ==216436== ==216436== For lists of detected and suppressed errors, rerun with: -s ==216436== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 9288 from 551) ================================================================================ 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.