!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 ----------------------------------------------------------------------------------------------------- Results for KIM Model : Tersoff_LAMMPS_Nord_Albe_Erhart_Nordlund_GaN__MO_612061685362_000 Supported species : Ga N random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Ga (Configuration in file "config-F-Ga.xyz") ----------------------------------------------------------------------------------------------------- Energy = 55.4193682096 Forces: 1 -7.91401421e+00 -7.65208419e+00 -1.22205429e+01 2 -3.60418190e+00 3.67378909e+00 -1.36714785e+01 3 5.30265836e+00 -2.15498660e+01 -2.67697842e-01 4 -1.34583072e+01 1.08893488e+01 6.03626179e+00 5 2.22203549e+00 -1.33110704e+01 -6.43678241e+00 6 7.68391143e+00 4.05809673e+00 -9.57723035e+00 7 4.35888298e+00 -1.00612268e+01 1.02915399e+00 8 -1.03811267e+00 -2.30896600e+01 -1.03469482e+01 9 -1.06002505e+01 -6.24255588e+00 -1.47001564e+01 10 -1.11212205e+00 1.10577406e+01 -8.52284966e+00 11 -1.21283347e+01 1.90505541e+00 3.03419728e+00 12 -9.25739565e+00 9.91074154e+00 3.32104447e+00 13 7.55299084e+00 1.75325303e+00 -2.49077628e+01 14 3.65525467e+00 4.97442321e+00 -4.80476300e+00 15 3.19348092e+01 1.83256604e+00 -7.32301721e+00 16 6.60424353e+00 1.47195051e+01 -5.34998634e+00 17 -1.11040013e+01 -7.67091607e+00 -2.12683440e+00 18 2.79195666e+00 5.80641845e+00 -5.29544574e-02 19 4.67473004e+00 -1.32750427e+01 1.08021424e+01 20 -9.41246889e+00 4.79660991e+00 7.97166606e+00 21 -4.17327060e-01 -6.06447271e+00 1.68092089e+00 22 1.10103689e+01 1.01720712e+00 6.67726450e+00 23 1.25778611e+00 -7.18168825e-01 2.52596784e+00 24 4.48166128e+00 -1.49593104e+00 8.50632546e+00 25 -1.38809504e+01 3.95999403e-02 1.83807652e+00 26 -1.55779746e+01 2.07812524e+01 1.13519314e+01 27 2.00482453e+00 -7.21938828e+00 6.48556002e+00 28 -7.39857331e+00 1.00019891e+01 3.70500991e+00 29 2.50107529e+00 -2.33321535e+00 2.33928726e+01 30 6.59390593e+00 9.25201159e+00 -1.23029960e+00 31 1.09912353e+01 -6.47381136e+00 1.42764745e+01 32 1.28168390e+00 1.06878016e+01 8.90443443e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ga (Configuration in file "config-T-Ga.xyz") ----------------------------------------------------------------------------------------------------- Energy = 222.141667153 Forces: 1 7.39611289e-01 -1.41100711e+00 -4.67951144e+00 2 -8.29809844e+00 1.32192262e+01 -2.80612415e-01 3 1.48400367e+01 -1.19744909e+01 8.26767371e-01 4 4.51414344e+00 2.38980594e+01 7.93617177e+00 5 4.24907602e+00 -1.56742360e+01 -3.31437985e+00 6 -4.30815890e+00 1.59638655e+01 -1.34489483e+01 7 -1.19085521e+01 -2.96638624e+00 1.48130472e+01 8 -7.71930940e+00 -2.20534612e+01 -8.78015640e+00 9 -1.23702490e+01 -2.34971130e+01 -9.10135159e+00 10 7.11958142e+00 -1.33235374e+00 -4.61615873e+00 11 -1.23570934e+01 1.77695433e+00 7.29995891e+00 12 4.02291270e+00 -5.70723142e+00 1.24276501e+01 13 1.28216382e+01 1.83540097e+00 -1.54522732e+01 14 -2.14034131e+01 2.18564425e-01 -2.16022688e+01 15 2.62807254e+01 -3.26820670e+00 -7.48101511e+00 16 4.14007571e+00 9.37459667e+00 1.51471352e+00 17 4.77331650e+00 -7.67239310e+00 -8.17241044e+00 18 4.16664220e+00 1.27913453e+01 1.13286690e-02 19 1.01469524e+01 -8.83057257e+00 8.81324971e+00 20 -5.78627020e+00 1.87335516e+01 1.31405041e+00 21 -5.61904669e+00 1.23422029e+01 5.64320416e+00 22 1.21809120e+00 1.56117409e+01 1.05482106e+01 23 -7.21494543e+00 1.88040237e+00 -1.07288806e+01 24 6.40332500e+00 -2.51620885e+00 -5.78964976e+00 25 -6.50330282e+00 -3.62501005e+00 1.07745132e+00 26 -1.52703019e+01 6.95444512e+00 1.29082253e+01 27 3.91954258e+00 -1.07866714e+01 -7.75784090e+00 28 -7.52362878e+00 1.03404612e+00 -3.26415703e+00 29 3.10100725e+00 -1.04747062e+01 2.36049640e+01 30 1.16379334e-01 -2.72112915e+00 6.20320142e+00 31 1.02441915e+01 -1.62029635e+01 1.43407945e+01 32 3.46512136e+00 1.50797393e+01 -4.81337427e+00 MONOATOMIC STRUCTURE (pbc=False)-- Species = N (Configuration in file "config-F-N.xyz") ----------------------------------------------------------------------------------------------------- Energy = -42.1349880785 Forces: 1 -2.48285005e-01 3.62111057e+00 2.07101887e+00 2 1.59802691e+00 -1.82323818e+00 -2.64789734e+00 3 2.85979162e+00 -5.54566513e+00 -2.72923925e+00 4 -2.23947800e+00 -6.50368863e+00 -2.46171326e+00 5 -1.92527231e+00 8.10385566e-01 -1.97775328e+00 6 1.34447541e+00 8.25164794e-01 -1.65558392e+00 7 2.22005131e+00 -1.27053742e+00 1.80625297e+00 8 -4.99473208e-01 -1.87506314e+00 7.49094533e-01 9 -9.72764629e+00 2.28462138e-02 -1.07052762e+01 10 -1.19448043e+00 -8.94082401e-01 8.67268599e-01 11 6.47519726e+00 5.57831648e+00 5.45061881e+00 12 9.19847049e-01 5.52996474e-01 1.47321881e+00 13 3.23576302e+00 6.51451104e-01 -2.90130229e+00 14 -1.73148288e+00 -5.82330587e-01 4.94716085e-01 15 6.90967056e-01 -8.45651859e-03 2.25278912e+00 16 2.54129382e+00 3.26717042e+00 -5.29735372e+00 17 -3.01981782e+00 -1.52075631e+00 -3.28295246e-01 18 -5.27976467e-01 6.19126251e+00 6.09319639e+00 19 -1.44081869e+00 -7.94228795e-01 9.83623683e-01 20 1.41340242e+00 1.85438988e+00 -9.06849379e-01 21 1.19069184e+00 -2.20265024e-01 1.17403021e+00 22 1.80866802e+00 1.31529240e+00 8.20925189e-01 23 -4.50315337e-01 1.16101097e+00 -1.63942817e+00 24 -8.81752128e-01 -7.23462505e-01 8.93409854e-01 25 -1.10285731e+00 -2.40850166e-01 2.92265087e+00 26 -5.54133851e-01 -9.78070091e-02 3.94213794e+00 27 -1.31881966e+00 -1.65043484e+00 1.72678815e-01 28 1.02246325e+00 -4.55424126e-01 -4.09564970e-01 29 -2.55347606e+00 -2.06558347e+00 2.82381061e+00 30 -1.42961710e-01 -1.86598191e+00 2.22763251e+00 31 7.63878370e-01 2.93249611e+00 -2.49381338e+00 32 1.47452981e+00 -6.46037337e-01 -1.06500346e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = N (Configuration in file "config-T-N.xyz") ----------------------------------------------------------------------------------------------------- Energy = -33.7687702525 Forces: 1 1.58837059e-01 -8.21024813e-01 1.01751224e-01 2 -3.47272131e-02 -9.19483395e-01 -3.08119970e+00 3 3.59241149e+00 -4.10451431e+00 -5.77404359e+00 4 2.64418274e-01 -3.06142745e+00 4.32256423e-02 5 -4.15469745e+00 -1.99937810e+00 -1.96830142e+00 6 -8.50132931e-01 2.52110617e+00 -3.49445361e+00 7 3.28510025e+00 -3.49128094e-01 3.29022468e+00 8 2.94798755e-01 -7.87253915e-01 1.40667588e+00 9 -9.55920002e+00 2.17801948e-01 -9.03569450e+00 10 -2.80648357e+00 2.62356032e+00 3.90061798e+00 11 8.67908068e+00 4.40149551e+00 7.21910698e+00 12 2.16888695e-01 -1.07923305e+00 -3.13386757e+00 13 3.22322327e+00 -8.93190126e-01 -1.33865809e+00 14 6.92324258e-01 1.55618841e+00 -1.01329818e+00 15 -6.50619975e-01 -5.63298937e-01 2.11729613e+00 16 1.15975825e+00 3.14425073e+00 -4.67035509e+00 17 -2.93494284e+00 2.16459839e+00 3.69900472e+00 18 1.31855380e+00 7.50212288e+00 6.07563411e+00 19 -1.48275613e+00 -1.50380454e+00 2.29900645e-02 20 1.20424003e+00 -6.50756164e-02 -8.99886956e-01 21 1.14901447e+00 2.51039061e-01 -1.00832361e-01 22 -1.00725354e+00 1.40331021e+00 1.83700185e+00 23 -2.95000717e-01 2.47838609e+00 -1.23735342e+00 24 -3.28472859e-01 1.64381370e+00 1.74335324e-02 25 -7.68186961e-02 -1.52122066e+00 2.40415146e+00 26 2.16433882e-01 -5.07617971e-01 3.88399375e+00 27 3.86194164e-01 -4.56198738e+00 -4.62777237e+00 28 -1.58188492e-01 -1.87371845e+00 2.73453977e+00 29 -2.72453131e+00 -3.29531902e+00 3.59906118e+00 30 -4.11702578e-01 -1.74922197e+00 9.22789750e-01 31 3.12051605e-01 2.52592387e-01 -9.53530246e-01 32 1.32219939e+00 -5.04367999e-01 -1.94625161e+00 MIXED STRUCTURE (pbc=False)-- Species = Ga N (Configuration in file "config-F-GaN.xyz") ----------------------------------------------------------------------------------------------------- Energy = 201.867939445 Forces: 1 -3.82292141e+00 -7.40821875e+00 -8.07816946e+00 2 7.62072255e+01 -6.87455885e+01 -2.60101484e+01 3 -2.25924692e+01 -2.38956555e+01 -3.31302642e+01 4 -4.19077081e+01 1.14021329e+01 -2.76996185e+01 5 1.08157400e+01 -1.50953213e+01 -1.66258636e+01 6 1.68490352e+01 -1.04168637e+01 -1.87305698e+01 7 2.79705222e+01 -2.25505229e+01 -2.92965299e+01 8 8.10838866e+00 2.07070589e+01 5.48258620e+00 9 -9.32492939e+01 6.48372983e+01 -1.24939416e+00 10 6.95398670e+00 1.46320488e+01 -1.05946447e+01 11 -1.02594105e+01 -1.39021248e+01 1.70503692e+01 12 -2.37528035e+01 3.60696829e+01 -1.11418870e+01 13 1.40233919e+00 -6.96782280e+00 -2.77032782e+01 14 9.72045825e+00 7.65778069e+00 -6.79497910e+00 15 2.28595218e+01 8.13842875e+00 1.65529762e+01 16 4.57226294e+00 4.32971809e+01 -2.64969558e+01 17 -2.98425644e+01 -4.54378448e+01 2.24055880e+01 18 1.56772403e+01 2.24890661e+01 1.05039067e+01 19 3.32862690e+00 -1.20995893e+01 1.08944030e+01 20 -5.64520964e+01 -4.87832592e+01 4.89571394e-01 21 1.87566811e+01 -1.94476821e+01 6.58450730e+01 22 1.54558710e+01 1.89589112e+01 -1.90243780e+01 23 7.22280359e-01 -2.87929644e+01 1.30851847e+01 24 1.19128069e+00 -1.38486404e+01 1.23772485e+01 25 -1.89076408e+01 -2.41978338e+00 -3.85629254e+00 26 -3.98624048e+01 4.45589816e+01 2.76068838e+01 27 3.63433363e+01 4.42803089e+01 4.53204756e+01 28 3.28385180e+00 1.04072773e+01 7.43018125e+00 29 3.60041655e+01 -3.88200318e+01 -7.41971008e+00 30 1.98661861e+01 1.36516925e+01 2.42266084e-01 31 1.07903071e+01 1.72948687e+00 8.51771674e+00 32 -6.22999456e+00 1.58145771e+01 1.00482528e+01 MIXED STRUCTURE (pbc=True)-- Species = Ga N (Configuration in file "config-T-GaN.xyz") ----------------------------------------------------------------------------------------------------- Energy = 515.598098621 Forces: 1 -3.11397979e+00 -2.03846181e+01 2.33176577e+01 2 8.48944700e+01 -1.01062295e+02 3.88326658e+01 3 -4.49992921e+01 3.03710092e+01 -1.59985969e+01 4 -1.47760373e+01 2.21546233e+01 -1.33670702e+01 5 4.44191896e+00 -1.50871408e+01 8.17708242e+00 6 2.15128538e+00 -1.27571796e+01 -1.19135803e+01 7 -2.24151516e+01 8.36493739e+00 -6.60307733e+00 8 5.16456287e+00 3.76716834e+01 1.06639446e+01 9 -8.96065234e+01 8.33065125e+01 3.24969650e+01 10 1.48371337e+01 1.14402645e+01 -5.32679755e+00 11 2.38007694e-01 -1.55303884e+01 1.60430008e+01 12 -2.58965489e+01 -7.99373800e+00 -1.34876075e+01 13 -1.21948667e-01 -1.72085669e+01 -1.42959737e+01 14 2.27217146e+00 -2.42330274e+01 -2.29779533e+01 15 6.76837266e+00 4.41302812e+00 1.89990144e+01 16 1.61511438e+01 9.98695224e-01 -3.40875589e+01 17 -3.21360915e+01 -4.69323291e+00 1.38568509e+01 18 1.63079748e+01 2.90482293e+01 9.69942214e+00 19 5.45916383e+01 6.35433124e+01 -6.07055516e+01 20 -6.35497020e+01 -7.12908317e+01 -3.83677882e+01 21 6.78571058e+00 1.79024286e+01 6.94470475e+01 22 8.78569701e+00 2.87569007e+01 -2.10008568e+01 23 3.40408537e+00 -3.37598612e+01 1.19214233e+01 24 1.02018266e+01 -1.30937846e+01 -1.21466163e+01 25 -8.83134162e+00 1.29082373e+00 -1.95545112e+00 26 -3.87520491e+01 4.06891213e+01 2.17139795e+01 27 4.22137219e+01 7.85348643e+01 -1.66942705e+01 28 -7.58232422e+00 -5.52762371e+01 2.76068365e+01 29 3.72879368e+01 -5.22253207e+01 -9.16486501e+00 30 3.42224167e+01 -1.66251960e+01 -7.70154880e-01 31 -1.61628579e-01 -1.03837257e+00 -8.37303781e+00 32 1.22254414e+00 3.77335759e+00 4.46091762e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==24519== Memcheck, a memory error detector ==24519== Copyright (C) 2002-2015, and GNU GPL'd, by Julian Seward et al. ==24519== Using Valgrind-3.11.0 and LibVEX; rerun with -h for copyright info ==24519== Command: python runner2.py Tersoff_LAMMPS_Nord_Albe_Erhart_Nordlund_GaN__MO_612061685362_000 ==24519== ==24519== Warning: set address range perms: large range [0x20fe9000, 0x314e9000) (defined) ==24519== Warning: set address range perms: large range [0x2122d000, 0x314e9000) (defined) ==24519== Warning: set address range perms: large range [0x20fe9000, 0x314e9000) (noaccess) ==24519== Warning: set address range perms: large range [0x23029000, 0x33529000) (defined) ==24519== Warning: set address range perms: large range [0x2326d000, 0x33529000) (defined) ==24519== Warning: set address range perms: large range [0x23029000, 0x33529000) (noaccess) ==24519== Warning: set address range perms: large range [0x23029000, 0x33529000) (defined) ==24519== Warning: set address range perms: large range [0x2326d000, 0x33529000) (defined) ==24519== Warning: set address range perms: large range [0x23029000, 0x33529000) (noaccess) ==24519== Warning: set address range perms: large range [0x23029000, 0x33529000) (defined) ==24519== Warning: set address range perms: large range [0x2326d000, 0x33529000) (defined) ==24519== Warning: set address range perms: large range [0x23029000, 0x33529000) (noaccess) ==24519== Warning: set address range perms: large range [0x23429000, 0x33929000) (defined) ==24519== Warning: set address range perms: large range [0x2366d000, 0x33929000) (defined) ==24519== Warning: set address range perms: large range [0x23429000, 0x33929000) (noaccess) ==24519== Warning: set address range perms: large range [0x23429000, 0x33929000) (defined) ==24519== Warning: set address range perms: large range [0x2366d000, 0x33929000) (defined) ==24519== Warning: set address range perms: large range [0x23429000, 0x33929000) (noaccess) ==24519== Warning: set address range perms: large range [0x23429000, 0x33929000) (defined) ==24519== Warning: set address range perms: large range [0x2366d000, 0x33929000) (defined) ==24519== Warning: set address range perms: large range [0x23429000, 0x33929000) (noaccess) ==24519== ==24519== HEAP SUMMARY: ==24519== in use at exit: 4,043,539 bytes in 5,784 blocks ==24519== total heap usage: 150,786 allocs, 145,002 frees, 59,363,890 bytes allocated ==24519== ==24519== LEAK SUMMARY: ==24519== definitely lost: 0 bytes in 0 blocks ==24519== indirectly lost: 0 bytes in 0 blocks ==24519== possibly lost: 162,822 bytes in 96 blocks ==24519== still reachable: 3,880,717 bytes in 5,688 blocks ==24519== suppressed: 0 bytes in 0 blocks ==24519== Rerun with --leak-check=full to see details of leaked memory ==24519== ==24519== For counts of detected and suppressed errors, rerun with: -v ==24519== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 2415 from 158) ================================================================================ 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.