!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_ErhartAlbe_2005_SiC__MO_903987585848_003 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 = -61.804847720676065 Forces: 1 -1.17235019e+00 6.92581153e+00 3.38891274e+00 2 2.91228095e+00 -3.00097117e+00 -5.25534161e-02 3 1.29276261e+01 -3.66621376e+00 7.49123873e-01 4 -1.85852062e+00 -3.69849190e-01 -1.39964587e+00 5 -9.09155113e+00 3.19023907e+00 5.86996107e+00 6 -2.95402820e-02 -2.10699511e-01 3.40650728e-01 7 -3.86800915e+00 2.99707347e+00 -1.20480298e-03 8 7.80525713e-01 -7.94125090e-01 1.11066729e-01 9 3.12818941e+00 9.03068867e+00 8.62141402e+00 10 -2.02941566e+00 -3.05063390e+00 -2.05181254e+00 11 -6.12639582e+00 -2.29994263e+00 1.84036758e+00 12 1.92201278e+00 -1.16434495e+01 3.50019021e-01 13 -2.86537111e+00 1.24021748e+00 -7.71636482e-02 14 -1.73597843e+00 -5.46195505e+00 4.10403639e+00 15 4.57262299e+00 5.52713551e+00 -2.03236150e+00 16 -5.17835064e+00 5.41286990e+00 4.15619609e+00 17 4.45986758e+00 3.57382007e+00 7.84793015e+00 18 -4.95373958e+00 -3.64780527e+00 -7.45161653e+00 19 -7.05412982e+00 4.67442594e+00 -3.67215879e+00 20 3.08990333e+00 -6.67322402e+00 -5.21364849e+00 21 -4.59477767e+00 -4.65976512e+00 -7.18300409e-01 22 5.29400754e+00 -9.22409124e-01 1.26359969e+01 23 -2.21323570e+00 7.42949379e+00 -1.14075160e+01 24 3.58647240e+00 -1.89888669e+00 -4.15343119e-02 25 8.91021376e+00 1.09006085e+00 -2.54639528e+01 26 1.33623881e+01 -3.10447366e+00 -7.99202757e+00 27 3.52074327e+00 -9.37197017e+00 1.06472522e+01 28 -7.66906740e+00 1.23702203e+01 1.24876478e+01 29 -6.01730443e+00 -5.98531927e+00 4.97160224e+00 30 5.75815011e+00 1.27960508e+00 -3.87965570e-01 31 -8.52666992e+00 9.15891871e+00 -1.33681928e+00 32 7.59403469e-01 -7.13888716e+00 -8.82189594e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = C (Configuration in file "config-T-C.xyz") ----------------------------------------------------------------------------------------------------- Energy = -61.804847720676065 Forces: 1 -1.17235019e+00 6.92581153e+00 3.38891274e+00 2 2.91228095e+00 -3.00097117e+00 -5.25534161e-02 3 1.29276261e+01 -3.66621376e+00 7.49123873e-01 4 -1.85852062e+00 -3.69849190e-01 -1.39964587e+00 5 -9.09155113e+00 3.19023907e+00 5.86996107e+00 6 -2.95402820e-02 -2.10699511e-01 3.40650728e-01 7 -3.86800915e+00 2.99707347e+00 -1.20480298e-03 8 7.80525713e-01 -7.94125090e-01 1.11066729e-01 9 3.12818941e+00 9.03068867e+00 8.62141402e+00 10 -2.02941566e+00 -3.05063390e+00 -2.05181254e+00 11 -6.12639582e+00 -2.29994263e+00 1.84036758e+00 12 1.92201278e+00 -1.16434495e+01 3.50019021e-01 13 -2.86537111e+00 1.24021748e+00 -7.71636482e-02 14 -1.73597843e+00 -5.46195505e+00 4.10403639e+00 15 4.57262299e+00 5.52713551e+00 -2.03236150e+00 16 -5.17835064e+00 5.41286990e+00 4.15619609e+00 17 4.45986758e+00 3.57382007e+00 7.84793015e+00 18 -4.95373958e+00 -3.64780527e+00 -7.45161653e+00 19 -7.05412982e+00 4.67442594e+00 -3.67215879e+00 20 3.08990333e+00 -6.67322402e+00 -5.21364849e+00 21 -4.59477767e+00 -4.65976512e+00 -7.18300409e-01 22 5.29400754e+00 -9.22409124e-01 1.26359969e+01 23 -2.21323570e+00 7.42949379e+00 -1.14075160e+01 24 3.58647240e+00 -1.89888669e+00 -4.15343119e-02 25 8.91021376e+00 1.09006085e+00 -2.54639528e+01 26 1.33623881e+01 -3.10447366e+00 -7.99202757e+00 27 3.52074327e+00 -9.37197017e+00 1.06472522e+01 28 -7.66906740e+00 1.23702203e+01 1.24876478e+01 29 -6.01730443e+00 -5.98531927e+00 4.97160224e+00 30 5.75815011e+00 1.27960508e+00 -3.87965570e-01 31 -8.52666992e+00 9.15891871e+00 -1.33681928e+00 32 7.59403469e-01 -7.13888716e+00 -8.82189594e+00 MONOATOMIC STRUCTURE (pbc=False)-- Species = Si (Configuration in file "config-F-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 94.25915452273168 Forces: 1 -9.96024008e+00 -6.31902702e+00 -6.50160093e+00 2 -2.57060476e+01 2.35443154e+01 -6.46722999e+00 3 1.07869089e+01 -1.09009897e+01 -3.83607979e+01 4 -1.00684214e+01 -8.02759547e+00 -2.71741552e+00 5 2.17094065e+01 -3.94471945e+01 -1.21998172e+01 6 2.17502758e+01 -8.69403621e+00 -2.25872591e+01 7 2.11649987e+01 -3.11360768e+01 -2.77867362e+00 8 -2.89816993e+01 1.33875594e+01 3.80138952e+00 9 -1.06043266e+01 -5.41137850e+00 -9.73850090e+00 10 1.10800779e+01 1.25176029e+01 -1.41830961e+01 11 -2.26676903e+01 -1.14848269e+01 -3.91920717e+01 12 -1.08837066e+01 1.25844931e+01 6.44309920e+00 13 -4.61752707e+01 -4.99715332e+00 -4.87301878e+01 14 1.29914226e+01 1.75124985e+01 -2.08800052e+01 15 7.00266938e+01 -1.86034789e+01 3.57927780e+01 16 -1.70542561e+01 5.41219889e+01 -9.10538618e+00 17 -2.77454832e+01 -3.19489949e+00 2.67295218e+01 18 -6.91918721e+00 -2.02688061e+01 7.37685163e+00 19 -3.88771070e+01 -3.79617138e+01 2.51001088e+01 20 -9.59336594e+00 -1.26549854e+01 8.16942036e+00 21 2.08075358e+01 -1.65701884e+01 -7.28247936e+00 22 2.35550686e+01 8.06403854e-01 1.49559655e+01 23 8.30584618e+00 -6.43035887e+00 2.95076886e+00 24 2.54419682e+01 3.68366299e+01 1.99354290e+01 25 -1.58232551e+01 -4.69569815e+00 -1.01183717e+01 26 -2.90081030e+01 5.05717767e+01 8.31942640e+00 27 6.52779607e+00 5.46683306e+00 2.19451549e+01 28 -3.88619331e+00 1.87164961e+01 9.45997037e+00 29 2.20161754e+01 -2.94397981e+01 1.87735333e+01 30 2.69928109e+01 1.13537890e+01 -4.35159374e+00 31 1.40177899e+01 4.15059529e+00 1.45239613e+01 32 -3.22042157e+00 1.46672237e+01 3.09171082e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Si (Configuration in file "config-T-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 94.25915452273168 Forces: 1 -9.96024008e+00 -6.31902702e+00 -6.50160093e+00 2 -2.57060476e+01 2.35443154e+01 -6.46722999e+00 3 1.07869089e+01 -1.09009897e+01 -3.83607979e+01 4 -1.00684214e+01 -8.02759547e+00 -2.71741552e+00 5 2.17094065e+01 -3.94471945e+01 -1.21998172e+01 6 2.17502758e+01 -8.69403621e+00 -2.25872591e+01 7 2.11649987e+01 -3.11360768e+01 -2.77867362e+00 8 -2.89816993e+01 1.33875594e+01 3.80138952e+00 9 -1.06043266e+01 -5.41137850e+00 -9.73850090e+00 10 1.10800779e+01 1.25176029e+01 -1.41830961e+01 11 -2.26676903e+01 -1.14848269e+01 -3.91920717e+01 12 -1.08837066e+01 1.25844931e+01 6.44309920e+00 13 -4.61752707e+01 -4.99715332e+00 -4.87301878e+01 14 1.29914226e+01 1.75124985e+01 -2.08800052e+01 15 7.00266938e+01 -1.86034789e+01 3.57927780e+01 16 -1.70542561e+01 5.41219889e+01 -9.10538618e+00 17 -2.77454832e+01 -3.19489949e+00 2.67295218e+01 18 -6.91918721e+00 -2.02688061e+01 7.37685163e+00 19 -3.88771070e+01 -3.79617138e+01 2.51001088e+01 20 -9.59336594e+00 -1.26549854e+01 8.16942036e+00 21 2.08075358e+01 -1.65701884e+01 -7.28247936e+00 22 2.35550686e+01 8.06403854e-01 1.49559655e+01 23 8.30584618e+00 -6.43035887e+00 2.95076886e+00 24 2.54419682e+01 3.68366299e+01 1.99354290e+01 25 -1.58232551e+01 -4.69569815e+00 -1.01183717e+01 26 -2.90081030e+01 5.05717767e+01 8.31942640e+00 27 6.52779607e+00 5.46683306e+00 2.19451549e+01 28 -3.88619331e+00 1.87164961e+01 9.45997037e+00 29 2.20161754e+01 -2.94397981e+01 1.87735333e+01 30 2.69928109e+01 1.13537890e+01 -4.35159374e+00 31 1.40177899e+01 4.15059529e+00 1.45239613e+01 32 -3.22042157e+00 1.46672237e+01 3.09171082e+01 MIXED STRUCTURE (pbc=False)-- Species = C Si (Configuration in file "config-F-CSi.xyz") ----------------------------------------------------------------------------------------------------- Energy = 66.02832579951162 Forces: 1 -4.69911707e+01 -1.42008929e+01 -4.99167020e+01 2 6.38644440e+00 4.29948505e+01 -3.22495226e+01 3 1.23767353e+01 -4.83496518e+01 4.90379167e+01 4 -1.75986526e+01 1.25743872e+01 1.51830624e+01 5 2.03593128e+01 -2.97670531e+01 -2.40669443e+01 6 1.17244099e+01 2.50733003e+01 -1.21219056e+01 7 3.04803512e+00 -1.51832625e+01 1.27171713e+01 8 2.81795146e+01 8.90463614e+00 -2.82702978e+01 9 -2.13720120e+00 -1.71631732e-01 -4.61639434e+00 10 -4.67610383e+00 9.38072572e-01 3.30223700e+00 11 -7.44243982e+00 4.94334786e+00 -3.33324516e+01 12 -2.84722715e+00 9.48054428e+00 -1.28784842e+01 13 -1.96547602e+00 -4.41481139e+00 -8.75795444e+00 14 1.06571474e+01 4.17809367e+00 -1.29206714e+01 15 1.25596274e+01 -1.76489582e+00 6.64415599e+00 16 -5.01406263e+00 9.29099911e+00 1.15401001e+01 17 -1.88469541e+01 -6.58482775e+00 7.14269249e-01 18 -3.48963748e+01 1.47298889e+01 2.59334218e+01 19 -1.32875666e+01 -1.04321831e+01 2.26477367e+01 20 -6.84769135e+00 -8.00553410e+00 1.16102224e+01 21 4.18393840e+01 -4.58307776e+01 -4.65667642e+00 22 2.25688354e+01 1.53887813e+01 -1.69031162e+01 23 1.57245450e+01 -1.58570525e+01 1.01003452e+01 24 -1.72515627e+01 1.11088235e+01 2.18748084e+01 25 -3.43157890e+01 -1.66210095e+01 -3.16014912e+00 26 1.82461828e+01 4.16223017e+01 1.42007382e+01 27 1.83444941e+01 6.39014481e-01 1.70779276e+01 28 -1.36067560e+01 1.63433492e+01 1.75614510e+01 29 6.77230922e+00 2.16506718e+00 5.75591378e+00 30 3.00823582e-01 -2.72516460e+00 3.06009884e-01 31 -6.22805219e-01 1.20610479e+00 -1.43965707e+00 32 -7.39967314e-01 -1.67281438e+00 -9.16560594e-01 MIXED STRUCTURE (pbc=True)-- Species = C Si (Configuration in file "config-T-CSi.xyz") ----------------------------------------------------------------------------------------------------- Energy = 100.92996292670877 Forces: 1 -4.82444904e+01 -1.65359905e+01 -5.00948755e+01 2 8.00875409e+00 3.77169211e+01 -2.06736867e+01 3 8.86193431e+00 -2.27086162e+01 6.38212831e+01 4 -1.12720757e+01 1.87253801e+01 1.86348153e+01 5 2.16320550e+01 -9.99098862e+00 -2.50132473e+01 6 4.39735937e+00 3.36256424e+01 -1.31473152e+01 7 6.65256617e-01 -1.71803573e+01 1.83393142e+01 8 2.92545875e+01 9.60843695e+00 -2.76985866e+01 9 -4.03473975e+00 -7.74975959e-01 -2.39239433e+00 10 4.56965188e-01 -2.45896261e+01 -8.40488363e+00 11 -3.11379827e+00 4.71783671e+00 -3.34661319e+01 12 -9.37038903e+00 5.54393624e+00 -5.34155159e+00 13 4.26818800e+00 -7.67607702e+00 2.64276683e+00 14 1.82718956e+01 -7.25540961e+00 -1.52659035e+01 15 2.95499192e+00 -2.01314526e+00 -7.92990060e-01 16 -5.36088536e+00 -1.21467712e+00 1.56484599e+01 17 -1.95468824e+01 -1.94475629e+00 3.35070450e+00 18 -3.62562440e+01 1.53887114e+01 2.80993724e+01 19 -8.11925049e+00 -2.60821464e+00 1.52202327e+01 20 -8.14648317e+00 -1.17834176e+01 4.46035322e+00 21 4.31633943e+01 -4.21450074e+01 -6.68389795e+00 22 1.93214685e+01 1.19072149e+01 -1.91964259e+01 23 1.52240420e+01 -9.33533192e+00 4.73169906e+00 24 -1.65565121e+01 1.37927073e+01 2.01468856e+01 25 -2.37700544e+01 -2.50615263e+01 3.87895798e-01 26 1.76062299e+01 2.97146934e+01 1.04863936e+01 27 1.66446141e+01 4.08341353e+00 -7.18651400e-01 28 -1.65052189e+01 1.36779035e+01 2.01487135e+01 29 6.64507978e+00 1.78346316e+00 5.61217404e+00 30 -5.48544269e+00 6.01276098e+00 -6.98413361e+00 31 -2.55498772e+00 -2.87727928e+00 7.24724655e+00 32 9.60638054e-01 -6.03624651e-01 -3.10363525e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==7901== Memcheck, a memory error detector ==7901== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==7901== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==7901== Command: python runner2.py Tersoff_LAMMPS_ErhartAlbe_2005_SiC__MO_903987585848_003 ==7901== ==7901== Conditional jump or move depends on uninitialised value(s) ==7901== at 0x4FCBE77: __wcsnlen_avx2 (strlen-avx2.S:261) ==7901== by 0x4EF9EC1: wcsrtombs (wcsrtombs.c:104) ==7901== by 0x4E7FB20: wcstombs (wcstombs.c:34) ==7901== by 0x547A3F: ??? (in /usr/bin/python3.6) ==7901== by 0x63345D: _Py_stat (in /usr/bin/python3.6) ==7901== by 0x5BA640: ??? (in /usr/bin/python3.6) ==7901== by 0x551B80: ??? (in /usr/bin/python3.6) ==7901== by 0x5AA6EB: _PyObject_FastCallKeywords (in /usr/bin/python3.6) ==7901== by 0x50ABB2: ??? (in /usr/bin/python3.6) ==7901== by 0x50C5B8: _PyEval_EvalFrameDefault (in /usr/bin/python3.6) ==7901== by 0x509D47: ??? (in /usr/bin/python3.6) ==7901== by 0x50AA7C: ??? (in /usr/bin/python3.6) ==7901== ==7901== Conditional jump or move depends on uninitialised value(s) ==7901== at 0x4E63408: internal_utf8_loop (loop.c:298) ==7901== by 0x4E63408: __gconv_transform_internal_utf8 (skeleton.c:609) ==7901== by 0x4EF9EF4: wcsrtombs (wcsrtombs.c:110) ==7901== by 0x4E7FB20: wcstombs (wcstombs.c:34) ==7901== by 0x547A3F: ??? (in /usr/bin/python3.6) ==7901== by 0x63345D: _Py_stat (in /usr/bin/python3.6) ==7901== by 0x5BA640: ??? (in /usr/bin/python3.6) ==7901== by 0x551B80: ??? (in /usr/bin/python3.6) ==7901== by 0x5AA6EB: _PyObject_FastCallKeywords (in /usr/bin/python3.6) ==7901== by 0x50ABB2: ??? (in /usr/bin/python3.6) ==7901== by 0x50C5B8: _PyEval_EvalFrameDefault (in /usr/bin/python3.6) ==7901== by 0x509D47: ??? (in /usr/bin/python3.6) ==7901== by 0x50AA7C: ??? (in /usr/bin/python3.6) ==7901== ==7901== Conditional jump or move depends on uninitialised value(s) ==7901== at 0x4E63411: internal_utf8_loop (loop.c:303) ==7901== by 0x4E63411: __gconv_transform_internal_utf8 (skeleton.c:609) ==7901== by 0x4EF9EF4: wcsrtombs (wcsrtombs.c:110) ==7901== by 0x4E7FB20: wcstombs (wcstombs.c:34) ==7901== by 0x547A3F: ??? (in /usr/bin/python3.6) ==7901== by 0x63345D: _Py_stat (in /usr/bin/python3.6) ==7901== by 0x5BA640: ??? (in /usr/bin/python3.6) ==7901== by 0x551B80: ??? (in /usr/bin/python3.6) ==7901== by 0x5AA6EB: _PyObject_FastCallKeywords (in /usr/bin/python3.6) ==7901== by 0x50ABB2: ??? (in /usr/bin/python3.6) ==7901== by 0x50C5B8: _PyEval_EvalFrameDefault (in /usr/bin/python3.6) ==7901== by 0x509D47: ??? (in /usr/bin/python3.6) ==7901== by 0x50AA7C: ??? (in /usr/bin/python3.6) ==7901== ==7901== Conditional jump or move depends on uninitialised value(s) ==7901== at 0x4E63458: internal_utf8_loop (loop.c:298) ==7901== by 0x4E63458: __gconv_transform_internal_utf8 (skeleton.c:609) ==7901== by 0x4EF9EF4: wcsrtombs (wcsrtombs.c:110) ==7901== by 0x4E7FB20: wcstombs (wcstombs.c:34) ==7901== by 0x547A3F: ??? (in /usr/bin/python3.6) ==7901== by 0x63345D: _Py_stat (in /usr/bin/python3.6) ==7901== by 0x5BA640: ??? (in /usr/bin/python3.6) ==7901== by 0x551B80: ??? (in /usr/bin/python3.6) ==7901== by 0x5AA6EB: _PyObject_FastCallKeywords (in /usr/bin/python3.6) ==7901== by 0x50ABB2: ??? (in /usr/bin/python3.6) ==7901== by 0x50C5B8: _PyEval_EvalFrameDefault (in /usr/bin/python3.6) ==7901== by 0x509D47: ??? (in /usr/bin/python3.6) ==7901== by 0x50AA7C: ??? (in /usr/bin/python3.6) ==7901== ==7901== Conditional jump or move depends on uninitialised value(s) ==7901== at 0x4FCBCEC: __wcsnlen_avx2 (strlen-avx2.S:103) ==7901== by 0x4EF9EC1: wcsrtombs (wcsrtombs.c:104) ==7901== by 0x4E7FB20: wcstombs (wcstombs.c:34) ==7901== by 0x547A3F: ??? (in /usr/bin/python3.6) ==7901== by 0x547D20: PyUnicode_FSConverter (in /usr/bin/python3.6) ==7901== by 0x4C51E6: ??? (in /usr/bin/python3.6) ==7901== by 0x4F8388: ??? (in /usr/bin/python3.6) ==7901== by 0x4FBD83: ??? (in /usr/bin/python3.6) ==7901== by 0x4FC914: _PyArg_ParseStack_SizeT (in /usr/bin/python3.6) ==7901== by 0x4C6C88: ??? (in /usr/bin/python3.6) ==7901== by 0x50A9D9: ??? (in /usr/bin/python3.6) ==7901== by 0x50C5B8: _PyEval_EvalFrameDefault (in /usr/bin/python3.6) ==7901== ==7901== ==7901== HEAP SUMMARY: ==7901== in use at exit: 2,766,803 bytes in 1,649 blocks ==7901== total heap usage: 55,096 allocs, 53,447 frees, 67,442,817 bytes allocated ==7901== ==7901== LEAK SUMMARY: ==7901== definitely lost: 0 bytes in 0 blocks ==7901== indirectly lost: 0 bytes in 0 blocks ==7901== possibly lost: 146,155 bytes in 87 blocks ==7901== still reachable: 2,620,648 bytes in 1,562 blocks ==7901== suppressed: 0 bytes in 0 blocks ==7901== Rerun with --leak-check=full to see details of leaked memory ==7901== ==7901== For counts of detected and suppressed errors, rerun with: -v ==7901== Use --track-origins=yes to see where uninitialised values come from ==7901== ERROR SUMMARY: 6672 errors from 5 contexts (suppressed: 12448 from 653) ================================================================================ 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.