!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : Sim_LAMMPS_Polymorphic_Zhou_2004_CuTa__SM_453737875254_000 Supported species : Cu Ta random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Cu (Configuration in file "config-F-Cu.xyz") ----------------------------------------------------------------------------------------------------- Energy = 6.795283121170529 Forces: 1 -2.77330394e+00 -6.21824589e+00 -6.63341976e+00 2 -8.09520413e+00 1.22987949e+01 -8.20332468e+00 3 7.40197013e-01 -8.46300136e+00 -1.43506401e+00 4 -4.02898827e+00 3.86143047e+00 3.90657639e+00 5 1.01418535e+01 -1.63245214e+01 -1.67039629e+00 6 3.00535097e+00 1.63557050e+00 -5.18982433e+00 7 3.75790045e+00 -2.17890636e+01 -2.02372174e+01 8 -7.75460153e+00 -8.89357307e+00 9.60551109e-01 9 -9.87088809e+00 -5.65714236e+00 -1.45102000e+01 10 -3.41366946e+00 1.63257746e+01 -1.58516918e+01 11 -2.29291193e+00 -1.27365795e+01 1.03561959e+01 12 -7.83208355e+00 1.34801506e+01 7.00827141e-02 13 -3.82456971e+00 -7.33117584e+00 -3.35003558e+01 14 5.31236745e+00 7.01771108e+00 -4.36122263e+00 15 2.85006770e+01 -3.91578621e+00 9.22238767e+00 16 3.69498981e+00 2.18083391e+01 1.16410007e+01 17 -8.64426726e+00 -3.50628499e+00 -3.54054239e+00 18 -2.88512811e+00 7.77074073e+00 3.17849316e+00 19 4.60959181e+00 -6.80891948e+00 5.21517241e+00 20 -2.96317178e+00 6.22600302e+00 3.98476778e+00 21 -8.10443436e+00 -8.21292469e+00 6.24425639e+00 22 1.33238409e+01 1.85747073e+01 1.61215007e+01 23 2.33364491e+00 -6.97980503e-01 4.35287537e+00 24 1.90659380e+00 8.46140963e-01 3.76993616e+00 25 -5.40145996e+00 -7.96653890e+00 9.86218846e+00 26 -5.40108426e+00 1.34104105e+01 -7.63864435e+00 27 8.49877250e+00 -2.52578101e+01 6.93391939e+00 28 -2.05003361e+01 1.70200347e+01 2.63161766e+00 29 -6.07155105e+00 -9.75577822e+00 3.18090609e+00 30 6.07015537e+00 1.02426154e+01 3.28094436e-01 31 1.14141228e+01 -7.81244329e+00 9.44139039e+00 32 6.54759525e+00 1.08293455e+01 1.13699905e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Cu (Configuration in file "config-T-Cu.xyz") ----------------------------------------------------------------------------------------------------- Energy = 6.795283121170529 Forces: 1 -2.77330394e+00 -6.21824589e+00 -6.63341976e+00 2 -8.09520413e+00 1.22987949e+01 -8.20332468e+00 3 7.40197013e-01 -8.46300136e+00 -1.43506401e+00 4 -4.02898827e+00 3.86143047e+00 3.90657639e+00 5 1.01418535e+01 -1.63245214e+01 -1.67039629e+00 6 3.00535097e+00 1.63557050e+00 -5.18982433e+00 7 3.75790045e+00 -2.17890636e+01 -2.02372174e+01 8 -7.75460153e+00 -8.89357307e+00 9.60551109e-01 9 -9.87088809e+00 -5.65714236e+00 -1.45102000e+01 10 -3.41366946e+00 1.63257746e+01 -1.58516918e+01 11 -2.29291193e+00 -1.27365795e+01 1.03561959e+01 12 -7.83208355e+00 1.34801506e+01 7.00827141e-02 13 -3.82456971e+00 -7.33117584e+00 -3.35003558e+01 14 5.31236745e+00 7.01771108e+00 -4.36122263e+00 15 2.85006770e+01 -3.91578621e+00 9.22238767e+00 16 3.69498981e+00 2.18083391e+01 1.16410007e+01 17 -8.64426726e+00 -3.50628499e+00 -3.54054239e+00 18 -2.88512811e+00 7.77074073e+00 3.17849316e+00 19 4.60959181e+00 -6.80891948e+00 5.21517241e+00 20 -2.96317178e+00 6.22600302e+00 3.98476778e+00 21 -8.10443436e+00 -8.21292469e+00 6.24425639e+00 22 1.33238409e+01 1.85747073e+01 1.61215007e+01 23 2.33364491e+00 -6.97980503e-01 4.35287537e+00 24 1.90659380e+00 8.46140963e-01 3.76993616e+00 25 -5.40145996e+00 -7.96653890e+00 9.86218846e+00 26 -5.40108426e+00 1.34104105e+01 -7.63864435e+00 27 8.49877250e+00 -2.52578101e+01 6.93391939e+00 28 -2.05003361e+01 1.70200347e+01 2.63161766e+00 29 -6.07155105e+00 -9.75577822e+00 3.18090609e+00 30 6.07015537e+00 1.02426154e+01 3.28094436e-01 31 1.14141228e+01 -7.81244329e+00 9.44139039e+00 32 6.54759525e+00 1.08293455e+01 1.13699905e+01 MONOATOMIC STRUCTURE (pbc=False)-- Species = Ta (Configuration in file "config-F-Ta.xyz") ----------------------------------------------------------------------------------------------------- Energy = 189.9767398463904 Forces: 1 -1.27089811e+01 -1.71216401e+01 -2.02439217e+01 2 -2.88348293e+01 -2.05806198e+01 -6.77742624e+01 3 2.58386760e+01 -7.10748747e+01 -3.08399916e+01 4 -6.07431023e+01 4.80965350e+01 -4.34615882e+01 5 -4.39797163e+00 -2.73598587e+01 -2.88935629e+01 6 2.69383691e+01 -1.15502567e+01 -3.15337938e+01 7 2.13598175e+01 -1.62001530e+01 -2.99718401e+00 8 4.54429154e+01 -3.34337051e+01 1.84921877e+01 9 -1.09812593e+01 -1.63121867e+00 -1.05171633e+01 10 -5.32750191e+00 1.48723021e+01 -1.81119481e+01 11 -7.96046513e+01 2.98420011e+01 2.57984183e+01 12 -1.94577798e+01 2.30535501e+01 -1.27099140e+01 13 3.39684612e+01 2.54854448e+01 -8.99694937e+01 14 7.63811186e+00 9.71452397e+00 -1.10733687e+01 15 4.40738737e+01 1.82700881e+01 2.39116362e+01 16 2.75558758e+01 4.15766356e+01 -3.08886180e+01 17 -6.67132747e+01 -8.70565875e+01 4.73249130e+01 18 3.72773249e+01 4.89593416e+01 1.37559849e+01 19 1.32082206e+01 -4.03482978e+01 4.88573884e+01 20 -4.21876784e+01 1.67671661e+01 3.07676046e+01 21 -2.65330704e+01 -4.19859608e+01 -2.52763313e+01 22 4.16049695e+01 2.27054364e+01 -2.39017707e+01 23 5.26734619e+01 -4.32398989e+01 4.80739347e+01 24 -3.29378488e+01 3.27650860e+01 3.61349153e+01 25 -2.18699257e+01 -3.68772261e+00 8.48239139e+00 26 -2.52937566e+01 2.98349863e+01 4.15284176e+01 27 1.96808754e+01 -1.41003686e+01 1.56196832e+01 28 -2.03026054e+01 2.46936569e+01 7.64131976e+00 29 2.75179841e+01 1.58536609e+01 5.62805930e+01 30 2.85916127e+01 1.49055891e+01 -7.10930812e+00 31 2.56120384e+01 -5.54460441e+00 9.92886584e+00 32 -2.10883514e+01 1.75197634e+01 2.27039667e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ta (Configuration in file "config-T-Ta.xyz") ----------------------------------------------------------------------------------------------------- Energy = 189.9767398463904 Forces: 1 -1.27089811e+01 -1.71216401e+01 -2.02439217e+01 2 -2.88348293e+01 -2.05806198e+01 -6.77742624e+01 3 2.58386760e+01 -7.10748747e+01 -3.08399916e+01 4 -6.07431023e+01 4.80965350e+01 -4.34615882e+01 5 -4.39797163e+00 -2.73598587e+01 -2.88935629e+01 6 2.69383691e+01 -1.15502567e+01 -3.15337938e+01 7 2.13598175e+01 -1.62001530e+01 -2.99718401e+00 8 4.54429154e+01 -3.34337051e+01 1.84921877e+01 9 -1.09812593e+01 -1.63121867e+00 -1.05171633e+01 10 -5.32750191e+00 1.48723021e+01 -1.81119481e+01 11 -7.96046513e+01 2.98420011e+01 2.57984183e+01 12 -1.94577798e+01 2.30535501e+01 -1.27099140e+01 13 3.39684612e+01 2.54854448e+01 -8.99694937e+01 14 7.63811186e+00 9.71452397e+00 -1.10733687e+01 15 4.40738737e+01 1.82700881e+01 2.39116362e+01 16 2.75558758e+01 4.15766356e+01 -3.08886180e+01 17 -6.67132747e+01 -8.70565875e+01 4.73249130e+01 18 3.72773249e+01 4.89593416e+01 1.37559849e+01 19 1.32082206e+01 -4.03482978e+01 4.88573884e+01 20 -4.21876784e+01 1.67671661e+01 3.07676046e+01 21 -2.65330704e+01 -4.19859608e+01 -2.52763313e+01 22 4.16049695e+01 2.27054364e+01 -2.39017707e+01 23 5.26734619e+01 -4.32398989e+01 4.80739347e+01 24 -3.29378488e+01 3.27650860e+01 3.61349153e+01 25 -2.18699257e+01 -3.68772261e+00 8.48239139e+00 26 -2.52937566e+01 2.98349863e+01 4.15284176e+01 27 1.96808754e+01 -1.41003686e+01 1.56196832e+01 28 -2.03026054e+01 2.46936569e+01 7.64131976e+00 29 2.75179841e+01 1.58536609e+01 5.62805930e+01 30 2.85916127e+01 1.49055891e+01 -7.10930812e+00 31 2.56120384e+01 -5.54460441e+00 9.92886584e+00 32 -2.10883514e+01 1.75197634e+01 2.27039667e+01 MIXED STRUCTURE (pbc=False)-- Species = Cu Ta (Configuration in file "config-F-CuTa.xyz") ----------------------------------------------------------------------------------------------------- Energy = 164.8210632234266 Forces: 1 -1.16007138e+01 -6.97479288e+00 -1.21318313e+01 2 -2.13838694e+01 3.83994883e+01 -3.88445908e+01 3 -3.06022509e+01 -3.17860767e+01 4.22369727e+01 4 -1.67078164e+01 1.50213901e+01 -1.75134722e+01 5 2.09228445e+01 -4.85360393e+01 -5.50968292e+01 6 2.02521020e+01 8.02370919e+00 -2.08720542e+01 7 3.88047843e+01 -2.68698949e+01 1.64716448e+01 8 6.39142507e+00 1.06315162e+01 2.09094323e+01 9 -1.87048859e+01 -1.53671896e+01 -1.32880020e+01 10 1.31738726e+01 2.54044152e+01 -3.12559161e+01 11 5.86300504e+00 -2.54557736e+01 -2.09387086e+01 12 -3.68244700e+01 2.87696978e+01 -1.52829920e+01 13 -1.46563050e+00 1.52818171e+01 -2.14946343e+01 14 6.31804335e+00 6.64338010e+00 -3.64195799e+00 15 1.68322456e+01 -2.68500122e+00 -6.69081391e+00 16 7.37241634e+00 2.77677563e+01 -1.53558724e+01 17 -1.36665005e+01 -2.24700387e+01 1.82207096e+01 18 -8.11926207e+00 1.10306049e+01 -3.18324910e+01 19 -2.97503081e+01 -3.54487723e+01 5.40715259e+01 20 -4.30809681e+01 -2.85430291e+01 3.14051663e+01 21 1.19208876e+01 -6.47166113e+01 -4.75673628e+01 22 2.59502069e+01 1.72187631e+01 -8.06357232e+00 23 5.77717604e+01 -3.92457717e+01 3.18587765e+01 24 -1.87920478e+01 4.94842092e+01 2.98046574e+01 25 -6.93653183e+01 -2.28580449e+01 -2.63684924e+01 26 3.23423103e+01 6.75784819e+01 2.38904739e+01 27 5.43980135e+01 2.93990585e+01 5.51659149e+01 28 -2.35685254e+01 1.70395738e+01 2.09303827e+01 29 7.99311532e+00 -1.78555820e+01 2.26588499e+01 30 3.31931035e+01 1.29130772e+01 -1.61621460e+01 31 7.71621008e+00 4.37231833e+00 4.14925715e+00 32 -2.35837792e+01 3.83336101e+00 3.06279751e+01 MIXED STRUCTURE (pbc=True)-- Species = Cu Ta (Configuration in file "config-T-CuTa.xyz") ----------------------------------------------------------------------------------------------------- Energy = 221.85843967319553 Forces: 1 -5.53339241e+00 -2.38053393e+01 2.22673268e+00 2 -1.59856598e+01 3.94995768e+01 -2.59560040e+01 3 -2.91682352e+01 -2.44249674e+01 4.28441976e+01 4 -1.16087180e+01 1.74879029e+01 -1.73152141e+01 5 3.03667295e+01 -3.21725817e+01 -3.87455597e+01 6 1.13801818e+01 9.65717001e+00 -6.78356512e+00 7 2.91144587e+01 -1.44761170e+01 1.57460936e+01 8 7.40789466e+00 1.12874005e+01 1.98959383e+01 9 -1.13482128e+01 -5.67156228e+00 1.09028228e+01 10 5.32518608e+00 1.03013801e+01 -2.62580230e+01 11 5.89823729e+00 -2.48518184e+01 -2.15542884e+01 12 -2.45051525e+01 1.91878247e+01 -2.04471930e+01 13 -1.52832580e+00 1.41703697e+01 -1.84550521e+01 14 2.24471705e+00 4.18485828e+00 -1.63608066e+00 15 2.48389362e-01 -3.27914257e+00 -9.74503233e+00 16 5.20960563e+00 1.34951169e+01 -1.53974293e+01 17 -3.29077320e+00 -1.30510760e+01 1.86518031e+01 18 -9.13240563e+00 1.13511251e+01 -3.20644158e+01 19 -4.02073194e+01 -2.88223762e+01 3.74844285e+01 20 -2.11295483e+01 -3.41192708e+01 -2.53922397e+00 21 3.12657308e+00 -3.87122149e+01 -5.52218172e+01 22 2.15597540e+01 1.88600192e+01 -7.80437301e+00 23 5.73707976e+01 -1.56286924e+01 3.62488436e+01 24 -1.97609877e+01 5.07655846e+01 2.42202695e+01 25 -5.46947626e+01 -2.68780842e+01 -2.39072408e+01 26 3.15718960e+01 5.91873700e+01 2.15198473e+01 27 5.75909244e+01 2.87656658e+01 4.72166387e+01 28 -9.93813508e+00 1.67615475e+01 2.63659065e+01 29 8.72447343e+00 -1.72459643e+01 2.26244536e+01 30 2.29084464e+01 -1.06779961e+01 -2.69459819e+01 31 -1.63515726e+01 1.57896085e+01 -5.52994261e+00 32 -2.58650641e+01 -2.69353169e+01 3.03584614e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==73525== Memcheck, a memory error detector ==73525== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==73525== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==73525== Command: python runner2.py Sim_LAMMPS_Polymorphic_Zhou_2004_CuTa__SM_453737875254_000 ==73525== ==73525== Conditional jump or move depends on uninitialised value(s) ==73525== at 0x4FCBE77: __wcsnlen_avx2 (strlen-avx2.S:261) ==73525== by 0x4EF9EC1: wcsrtombs (wcsrtombs.c:104) ==73525== by 0x4E7FB20: wcstombs (wcstombs.c:34) ==73525== by 0x54744F: ??? (in /usr/bin/python3.6) ==73525== by 0x6332BD: _Py_stat (in /usr/bin/python3.6) ==73525== by 0x5BA510: ??? (in /usr/bin/python3.6) ==73525== by 0x551760: ??? (in /usr/bin/python3.6) ==73525== by 0x5AA69B: _PyObject_FastCallKeywords (in /usr/bin/python3.6) ==73525== by 0x50AB52: ??? (in /usr/bin/python3.6) ==73525== by 0x50C548: _PyEval_EvalFrameDefault (in /usr/bin/python3.6) ==73525== by 0x509CE7: ??? (in /usr/bin/python3.6) ==73525== by 0x50AA1C: ??? (in /usr/bin/python3.6) ==73525== ==73525== Conditional jump or move depends on uninitialised value(s) ==73525== at 0x4E63408: internal_utf8_loop (loop.c:298) ==73525== by 0x4E63408: __gconv_transform_internal_utf8 (skeleton.c:609) ==73525== by 0x4EF9EF4: wcsrtombs (wcsrtombs.c:110) ==73525== by 0x4E7FB20: wcstombs (wcstombs.c:34) ==73525== by 0x54744F: ??? (in /usr/bin/python3.6) ==73525== by 0x6332BD: _Py_stat (in /usr/bin/python3.6) ==73525== by 0x5BA510: ??? (in /usr/bin/python3.6) ==73525== by 0x551760: ??? (in /usr/bin/python3.6) ==73525== by 0x5AA69B: _PyObject_FastCallKeywords (in /usr/bin/python3.6) ==73525== by 0x50AB52: ??? (in /usr/bin/python3.6) ==73525== by 0x50C548: _PyEval_EvalFrameDefault (in /usr/bin/python3.6) ==73525== by 0x509CE7: ??? (in /usr/bin/python3.6) ==73525== by 0x50AA1C: ??? (in /usr/bin/python3.6) ==73525== ==73525== Conditional jump or move depends on uninitialised value(s) ==73525== at 0x4E63411: internal_utf8_loop (loop.c:303) ==73525== by 0x4E63411: __gconv_transform_internal_utf8 (skeleton.c:609) ==73525== by 0x4EF9EF4: wcsrtombs (wcsrtombs.c:110) ==73525== by 0x4E7FB20: wcstombs (wcstombs.c:34) ==73525== by 0x54744F: ??? (in /usr/bin/python3.6) ==73525== by 0x6332BD: _Py_stat (in /usr/bin/python3.6) ==73525== by 0x5BA510: ??? (in /usr/bin/python3.6) ==73525== by 0x551760: ??? (in /usr/bin/python3.6) ==73525== by 0x5AA69B: _PyObject_FastCallKeywords (in /usr/bin/python3.6) ==73525== by 0x50AB52: ??? (in /usr/bin/python3.6) ==73525== by 0x50C548: _PyEval_EvalFrameDefault (in /usr/bin/python3.6) ==73525== by 0x509CE7: ??? (in /usr/bin/python3.6) ==73525== by 0x50AA1C: ??? (in /usr/bin/python3.6) ==73525== ==73525== Conditional jump or move depends on uninitialised value(s) ==73525== at 0x4E63458: internal_utf8_loop (loop.c:298) ==73525== by 0x4E63458: __gconv_transform_internal_utf8 (skeleton.c:609) ==73525== by 0x4EF9EF4: wcsrtombs (wcsrtombs.c:110) ==73525== by 0x4E7FB20: wcstombs (wcstombs.c:34) ==73525== by 0x54744F: ??? (in /usr/bin/python3.6) ==73525== by 0x6332BD: _Py_stat (in /usr/bin/python3.6) ==73525== by 0x5BA510: ??? (in /usr/bin/python3.6) ==73525== by 0x551760: ??? (in /usr/bin/python3.6) ==73525== by 0x5AA69B: _PyObject_FastCallKeywords (in /usr/bin/python3.6) ==73525== by 0x50AB52: ??? (in /usr/bin/python3.6) ==73525== by 0x50C548: _PyEval_EvalFrameDefault (in /usr/bin/python3.6) ==73525== by 0x509CE7: ??? (in /usr/bin/python3.6) ==73525== by 0x50AA1C: ??? (in /usr/bin/python3.6) ==73525== ==73525== Conditional jump or move depends on uninitialised value(s) ==73525== at 0x4FCBCEC: __wcsnlen_avx2 (strlen-avx2.S:103) ==73525== by 0x4EF9EC1: wcsrtombs (wcsrtombs.c:104) ==73525== by 0x4E7FB20: wcstombs (wcstombs.c:34) ==73525== by 0x54744F: ??? (in /usr/bin/python3.6) ==73525== by 0x547730: PyUnicode_FSConverter (in /usr/bin/python3.6) ==73525== by 0x4CABB1: ??? (in /usr/bin/python3.6) ==73525== by 0x551760: ??? (in /usr/bin/python3.6) ==73525== by 0x5AA69B: _PyObject_FastCallKeywords (in /usr/bin/python3.6) ==73525== by 0x50AB52: ??? (in /usr/bin/python3.6) ==73525== by 0x50C548: _PyEval_EvalFrameDefault (in /usr/bin/python3.6) ==73525== by 0x509CE7: ??? (in /usr/bin/python3.6) ==73525== by 0x50AA1C: ??? (in /usr/bin/python3.6) ==73525== ==73525== ==73525== HEAP SUMMARY: ==73525== in use at exit: 11,857,447 bytes in 2,511 blocks ==73525== total heap usage: 53,362 allocs, 50,851 frees, 88,824,398 bytes allocated ==73525== ==73525== LEAK SUMMARY: ==73525== definitely lost: 8,280 bytes in 69 blocks ==73525== indirectly lost: 8,672,000 bytes in 542 blocks ==73525== possibly lost: 309,057 bytes in 104 blocks ==73525== still reachable: 2,868,110 bytes in 1,796 blocks ==73525== suppressed: 0 bytes in 0 blocks ==73525== Rerun with --leak-check=full to see details of leaked memory ==73525== ==73525== For counts of detected and suppressed errors, rerun with: -v ==73525== Use --track-origins=yes to see where uninitialised values come from ==73525== ERROR SUMMARY: 6672 errors from 5 contexts (suppressed: 15522 from 626) ================================================================================ 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" (Search for the word "lost" in the file to identify memory leaks.) Grade: F Comment: Memory leak detected.