!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_2005SiII_SiC__MO_408791041969_002 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 = -61.804847065255274 Forces: 1 -1.17235019e+00 6.92581147e+00 3.38891270e+00 2 2.91228091e+00 -3.00097113e+00 -5.25534207e-02 3 1.29276260e+01 -3.66621376e+00 7.49123866e-01 4 -1.85852063e+00 -3.69849179e-01 -1.39964587e+00 5 -9.09155103e+00 3.19023903e+00 5.86996101e+00 6 -2.95402817e-02 -2.10699509e-01 3.40650725e-01 7 -3.86800911e+00 2.99707340e+00 -1.20484412e-03 8 7.80525672e-01 -7.94125108e-01 1.11066720e-01 9 3.12818937e+00 9.03068858e+00 8.62141392e+00 10 -2.02941566e+00 -3.05063384e+00 -2.05181256e+00 11 -6.12639578e+00 -2.29994264e+00 1.84036759e+00 12 1.92201276e+00 -1.16434494e+01 3.50019016e-01 13 -2.86537109e+00 1.24021745e+00 -7.71637118e-02 14 -1.73597840e+00 -5.46195498e+00 4.10403634e+00 15 4.57262302e+00 5.52713545e+00 -2.03236148e+00 16 -5.17835057e+00 5.41286991e+00 4.15619607e+00 17 4.45986750e+00 3.57382002e+00 7.84793007e+00 18 -4.95373951e+00 -3.64780521e+00 -7.45161646e+00 19 -7.05412973e+00 4.67442588e+00 -3.67215873e+00 20 3.08990329e+00 -6.67322395e+00 -5.21364842e+00 21 -4.59477766e+00 -4.65976510e+00 -7.18300388e-01 22 5.29400754e+00 -9.22409072e-01 1.26359968e+01 23 -2.21323567e+00 7.42949372e+00 -1.14075159e+01 24 3.58647237e+00 -1.89888667e+00 -4.15343114e-02 25 8.91021365e+00 1.09006080e+00 -2.54639526e+01 26 1.33623880e+01 -3.10447359e+00 -7.99202752e+00 27 3.52074333e+00 -9.37197021e+00 1.06472522e+01 28 -7.66906743e+00 1.23702203e+01 1.24876477e+01 29 -6.01730440e+00 -5.98531924e+00 4.97160224e+00 30 5.75815007e+00 1.27960510e+00 -3.87965572e-01 31 -8.52666984e+00 9.15891861e+00 -1.33681925e+00 32 7.59403460e-01 -7.13888709e+00 -8.82189586e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = C (Configuration in file "config-T-C.xyz") ----------------------------------------------------------------------------------------------------- Energy = -61.804847065255274 Forces: 1 -1.17235019e+00 6.92581147e+00 3.38891270e+00 2 2.91228091e+00 -3.00097113e+00 -5.25534207e-02 3 1.29276260e+01 -3.66621376e+00 7.49123866e-01 4 -1.85852063e+00 -3.69849179e-01 -1.39964587e+00 5 -9.09155103e+00 3.19023903e+00 5.86996101e+00 6 -2.95402817e-02 -2.10699509e-01 3.40650725e-01 7 -3.86800911e+00 2.99707340e+00 -1.20484412e-03 8 7.80525672e-01 -7.94125108e-01 1.11066720e-01 9 3.12818937e+00 9.03068858e+00 8.62141392e+00 10 -2.02941566e+00 -3.05063384e+00 -2.05181256e+00 11 -6.12639578e+00 -2.29994264e+00 1.84036759e+00 12 1.92201276e+00 -1.16434494e+01 3.50019016e-01 13 -2.86537109e+00 1.24021745e+00 -7.71637118e-02 14 -1.73597840e+00 -5.46195498e+00 4.10403634e+00 15 4.57262302e+00 5.52713545e+00 -2.03236148e+00 16 -5.17835057e+00 5.41286991e+00 4.15619607e+00 17 4.45986750e+00 3.57382002e+00 7.84793007e+00 18 -4.95373951e+00 -3.64780521e+00 -7.45161646e+00 19 -7.05412973e+00 4.67442588e+00 -3.67215873e+00 20 3.08990329e+00 -6.67322395e+00 -5.21364842e+00 21 -4.59477766e+00 -4.65976510e+00 -7.18300388e-01 22 5.29400754e+00 -9.22409072e-01 1.26359968e+01 23 -2.21323567e+00 7.42949372e+00 -1.14075159e+01 24 3.58647237e+00 -1.89888667e+00 -4.15343114e-02 25 8.91021365e+00 1.09006080e+00 -2.54639526e+01 26 1.33623880e+01 -3.10447359e+00 -7.99202752e+00 27 3.52074333e+00 -9.37197021e+00 1.06472522e+01 28 -7.66906743e+00 1.23702203e+01 1.24876477e+01 29 -6.01730440e+00 -5.98531924e+00 4.97160224e+00 30 5.75815007e+00 1.27960510e+00 -3.87965572e-01 31 -8.52666984e+00 9.15891861e+00 -1.33681925e+00 32 7.59403460e-01 -7.13888709e+00 -8.82189586e+00 MONOATOMIC STRUCTURE (pbc=False)-- Species = Si (Configuration in file "config-F-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 115.24656203973359 Forces: 1 -1.53792582e+01 -3.58361438e+00 -6.58641413e+00 2 -2.93478887e+01 2.33604846e+01 -8.84498246e+00 3 -6.45181471e+00 -1.23753664e+01 3.42404852e+00 4 -1.55875710e+01 -1.80616723e+01 -2.84930367e+01 5 2.90263944e+01 -3.40797501e+01 -1.40699594e+01 6 2.45386188e+01 -9.53599145e+00 -1.91840057e+01 7 2.72995122e+01 -3.06873451e+01 -1.03408198e+01 8 -2.14098795e+01 1.65165302e+01 -1.32241252e+01 9 -1.20377803e+01 -1.11380798e+01 -9.86970224e+00 10 1.31561470e+01 1.64120879e+01 -1.65527073e+01 11 -3.44607930e+01 3.16739469e+00 -3.38862356e+01 12 -1.71283998e+01 1.55447490e+01 8.22845832e+00 13 -4.44164101e+01 -8.92072723e+00 -4.60337227e+01 14 1.14207940e+01 1.58586374e+01 -1.84903865e+01 15 6.60623392e+01 -8.13179405e+00 3.39209060e+01 16 -8.04388596e+00 4.51957148e+01 -2.54945586e+01 17 -1.08659108e+01 -1.51738370e+01 3.38233196e+00 18 -2.22397127e+00 -3.30723704e+01 1.16429706e+01 19 -3.80903865e+01 -4.09371351e+01 2.13558630e+01 20 -1.59681001e+01 -2.50180025e+01 2.46825116e+01 21 9.53203727e+00 -2.15078257e+01 -8.99844904e+00 22 2.26087822e+01 4.36115721e+00 1.11493889e+01 23 1.02299721e+01 -9.00491481e+00 9.01236478e+00 24 2.76087246e+01 3.22584085e+01 2.23367927e+01 25 -2.09563236e+01 2.49771265e+01 2.21455810e+00 26 -4.17575943e+01 4.40718570e+01 -1.31148887e+01 27 1.03826352e+01 1.97842502e+01 2.47357226e+01 28 -9.99524759e+00 1.16186131e+01 4.99550678e+00 29 2.52441181e+01 -3.12417135e+01 1.48004461e+01 30 2.25588324e+01 1.50753961e+01 6.36412244e+00 31 1.65333063e+01 8.36419921e+00 1.72789374e+01 32 2.79190018e+01 1.59035333e+01 5.36590642e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Si (Configuration in file "config-T-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 115.24656203973359 Forces: 1 -1.53792582e+01 -3.58361438e+00 -6.58641413e+00 2 -2.93478887e+01 2.33604846e+01 -8.84498246e+00 3 -6.45181471e+00 -1.23753664e+01 3.42404852e+00 4 -1.55875710e+01 -1.80616723e+01 -2.84930367e+01 5 2.90263944e+01 -3.40797501e+01 -1.40699594e+01 6 2.45386188e+01 -9.53599145e+00 -1.91840057e+01 7 2.72995122e+01 -3.06873451e+01 -1.03408198e+01 8 -2.14098795e+01 1.65165302e+01 -1.32241252e+01 9 -1.20377803e+01 -1.11380798e+01 -9.86970224e+00 10 1.31561470e+01 1.64120879e+01 -1.65527073e+01 11 -3.44607930e+01 3.16739469e+00 -3.38862356e+01 12 -1.71283998e+01 1.55447490e+01 8.22845832e+00 13 -4.44164101e+01 -8.92072723e+00 -4.60337227e+01 14 1.14207940e+01 1.58586374e+01 -1.84903865e+01 15 6.60623392e+01 -8.13179405e+00 3.39209060e+01 16 -8.04388596e+00 4.51957148e+01 -2.54945586e+01 17 -1.08659108e+01 -1.51738370e+01 3.38233196e+00 18 -2.22397127e+00 -3.30723704e+01 1.16429706e+01 19 -3.80903865e+01 -4.09371351e+01 2.13558630e+01 20 -1.59681001e+01 -2.50180025e+01 2.46825116e+01 21 9.53203727e+00 -2.15078257e+01 -8.99844904e+00 22 2.26087822e+01 4.36115721e+00 1.11493889e+01 23 1.02299721e+01 -9.00491481e+00 9.01236478e+00 24 2.76087246e+01 3.22584085e+01 2.23367927e+01 25 -2.09563236e+01 2.49771265e+01 2.21455810e+00 26 -4.17575943e+01 4.40718570e+01 -1.31148887e+01 27 1.03826352e+01 1.97842502e+01 2.47357226e+01 28 -9.99524759e+00 1.16186131e+01 4.99550678e+00 29 2.52441181e+01 -3.12417135e+01 1.48004461e+01 30 2.25588324e+01 1.50753961e+01 6.36412244e+00 31 1.65333063e+01 8.36419921e+00 1.72789374e+01 32 2.79190018e+01 1.59035333e+01 5.36590642e+01 MIXED STRUCTURE (pbc=False)-- Species = C Si (Configuration in file "config-F-CSi.xyz") ----------------------------------------------------------------------------------------------------- Energy = 79.76211146411052 Forces: 1 -5.01264364e+01 -1.59027033e+01 -6.68839987e+01 2 6.68786677e+00 4.64221002e+01 -3.56800031e+01 3 1.36220398e+01 -5.39268920e+01 4.61379157e+01 4 -1.84274617e+01 1.35067052e+01 1.30829816e+01 5 2.14131599e+01 -3.29153769e+01 -2.34811857e+01 6 1.41436911e+01 2.48999711e+01 -1.20620238e+01 7 3.45417654e+00 -1.53073419e+01 1.20231977e+01 8 3.00590692e+01 5.48391867e+00 -2.41216669e+01 9 -1.80925911e+00 -3.31412943e-01 -4.94828878e+00 10 -4.72911605e+00 7.76867945e-01 3.40435470e+00 11 3.37057916e+00 1.02500941e+01 -4.79236190e+01 12 -2.20623648e-03 5.88176131e+00 -5.86695118e+00 13 -2.67360031e+00 -3.87509170e+00 -8.95818901e+00 14 1.03233693e+01 4.78801893e+00 -1.34554463e+01 15 1.13136265e+01 2.84263780e-02 4.83403632e+00 16 -6.58968599e+00 1.56031024e+01 8.00700828e+00 17 -2.11074019e+01 -5.02795707e+00 2.21474481e+01 18 -3.49038330e+01 1.53428612e+01 2.98073601e+01 19 -1.91606962e+01 -1.16593769e+01 2.45938973e+01 20 -5.39284224e+00 -2.05096737e+00 6.01311617e+00 21 5.36450683e+01 -4.60809434e+01 -9.28942682e+00 22 2.19954383e+00 1.08882457e+01 -1.04993239e+01 23 6.00584985e+00 -9.43735232e+00 1.13660258e+01 24 1.62500060e+00 1.02745200e+01 1.38397393e+01 25 -4.40320229e+01 -1.10149413e+01 1.10680090e+01 26 1.90078415e+01 4.44851897e+01 1.25079717e+01 27 1.40798965e+01 -8.79867331e+00 2.11114846e+01 28 -1.33182409e+01 1.44033069e+01 1.11009388e+01 29 1.05846444e+01 -6.05498807e+00 6.75286382e+00 30 3.27579398e-01 -4.78036559e+00 3.14412286e+00 31 2.24023995e+00 2.97281661e+00 2.64716492e-01 32 -1.83043977e+00 1.15647759e+00 1.96293484e+00 MIXED STRUCTURE (pbc=True)-- Species = C Si (Configuration in file "config-T-CSi.xyz") ----------------------------------------------------------------------------------------------------- Energy = 139.73431305274573 Forces: 1 -5.21041474e+01 -1.64028889e+01 -5.87705761e+01 2 5.92122301e+00 4.41227739e+01 -2.08998701e+01 3 9.94695344e+00 -2.84717057e+01 6.56286719e+01 4 -1.09981715e+01 1.83489512e+01 1.55467216e+01 5 2.40043391e+01 -1.20180208e+01 -2.42028783e+01 6 7.36951425e+00 3.47271512e+01 -9.24828102e+00 7 8.46824912e-01 -1.71458802e+01 1.74628406e+01 8 3.08908430e+01 6.34004897e+00 -2.40837992e+01 9 -3.70501673e+00 -1.42231644e+00 -2.76967259e+00 10 3.93004098e-01 -2.36210852e+01 -4.51973714e+00 11 7.15199747e+00 9.91722526e+00 -4.59198193e+01 12 -6.99811770e+00 3.99542212e+00 7.12888340e+00 13 5.11177604e+00 -6.06325523e+00 -8.87805169e-01 14 1.71638265e+01 -1.00164365e+01 -1.51756110e+01 15 -9.21580543e+00 1.49666330e+00 -7.51968768e+00 16 -6.80988831e+00 4.54448762e+00 1.24542264e+01 17 -2.22219950e+01 -1.32824268e+00 1.24830497e+01 18 -3.58451815e+01 1.56678707e+01 3.14349593e+01 19 -1.81014713e+01 1.58564199e+00 1.04685533e+01 20 -6.22639181e+00 -5.08562560e+00 -2.89840712e-01 21 5.71183402e+01 -3.86982096e+01 -1.20414940e+01 22 -3.73817158e-01 1.15654290e+01 -9.85733236e+00 23 4.04528367e+00 -2.82865795e+00 4.20840974e+00 24 4.14069076e+00 1.22600801e+01 4.77188092e+00 25 -2.54674755e+01 -2.00195575e+01 2.09119930e+01 26 1.99303851e+01 2.34633024e+01 8.91850606e+00 27 1.45412625e+01 -6.31926024e+00 1.34371674e+00 28 -9.29339876e+00 1.38213182e+01 1.38387411e+01 29 9.92335071e+00 -5.86847650e+00 7.32831351e+00 30 -6.23507944e+00 1.26305767e+00 -1.65102203e+00 31 -6.95931176e+00 -3.36082331e+00 1.23067161e+00 32 2.05565441e+00 -4.44898123e+00 2.67728771e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==7822== Memcheck, a memory error detector ==7822== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==7822== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==7822== Command: python runner2.py Tersoff_LAMMPS_ErhartAlbe_2005SiII_SiC__MO_408791041969_002 ==7822== ==7822== Conditional jump or move depends on uninitialised value(s) ==7822== at 0x4FCBE77: __wcsnlen_avx2 (strlen-avx2.S:261) ==7822== by 0x4EF9EC1: wcsrtombs (wcsrtombs.c:104) ==7822== by 0x4E7FB20: wcstombs (wcstombs.c:34) ==7822== by 0x547A3F: ??? (in /usr/bin/python3.6) ==7822== by 0x63345D: _Py_stat (in /usr/bin/python3.6) ==7822== by 0x5BA640: ??? (in /usr/bin/python3.6) ==7822== by 0x551B80: ??? (in /usr/bin/python3.6) ==7822== by 0x5AA6EB: _PyObject_FastCallKeywords (in /usr/bin/python3.6) ==7822== by 0x50ABB2: ??? (in /usr/bin/python3.6) ==7822== by 0x50C5B8: _PyEval_EvalFrameDefault (in /usr/bin/python3.6) ==7822== by 0x509D47: ??? (in /usr/bin/python3.6) ==7822== by 0x50AA7C: ??? (in /usr/bin/python3.6) ==7822== ==7822== Conditional jump or move depends on uninitialised value(s) ==7822== at 0x4E63408: internal_utf8_loop (loop.c:298) ==7822== by 0x4E63408: __gconv_transform_internal_utf8 (skeleton.c:609) ==7822== by 0x4EF9EF4: wcsrtombs (wcsrtombs.c:110) ==7822== by 0x4E7FB20: wcstombs (wcstombs.c:34) ==7822== by 0x547A3F: ??? (in /usr/bin/python3.6) ==7822== by 0x63345D: _Py_stat (in /usr/bin/python3.6) ==7822== by 0x5BA640: ??? (in /usr/bin/python3.6) ==7822== by 0x551B80: ??? (in /usr/bin/python3.6) ==7822== by 0x5AA6EB: _PyObject_FastCallKeywords (in /usr/bin/python3.6) ==7822== by 0x50ABB2: ??? (in /usr/bin/python3.6) ==7822== by 0x50C5B8: _PyEval_EvalFrameDefault (in /usr/bin/python3.6) ==7822== by 0x509D47: ??? (in /usr/bin/python3.6) ==7822== by 0x50AA7C: ??? (in /usr/bin/python3.6) ==7822== ==7822== Conditional jump or move depends on uninitialised value(s) ==7822== at 0x4E63411: internal_utf8_loop (loop.c:303) ==7822== by 0x4E63411: __gconv_transform_internal_utf8 (skeleton.c:609) ==7822== by 0x4EF9EF4: wcsrtombs (wcsrtombs.c:110) ==7822== by 0x4E7FB20: wcstombs (wcstombs.c:34) ==7822== by 0x547A3F: ??? (in /usr/bin/python3.6) ==7822== by 0x63345D: _Py_stat (in /usr/bin/python3.6) ==7822== by 0x5BA640: ??? (in /usr/bin/python3.6) ==7822== by 0x551B80: ??? (in /usr/bin/python3.6) ==7822== by 0x5AA6EB: _PyObject_FastCallKeywords (in /usr/bin/python3.6) ==7822== by 0x50ABB2: ??? (in /usr/bin/python3.6) ==7822== by 0x50C5B8: _PyEval_EvalFrameDefault (in /usr/bin/python3.6) ==7822== by 0x509D47: ??? (in /usr/bin/python3.6) ==7822== by 0x50AA7C: ??? (in /usr/bin/python3.6) ==7822== ==7822== Conditional jump or move depends on uninitialised value(s) ==7822== at 0x4E63458: internal_utf8_loop (loop.c:298) ==7822== by 0x4E63458: __gconv_transform_internal_utf8 (skeleton.c:609) ==7822== by 0x4EF9EF4: wcsrtombs (wcsrtombs.c:110) ==7822== by 0x4E7FB20: wcstombs (wcstombs.c:34) ==7822== by 0x547A3F: ??? (in /usr/bin/python3.6) ==7822== by 0x63345D: _Py_stat (in /usr/bin/python3.6) ==7822== by 0x5BA640: ??? (in /usr/bin/python3.6) ==7822== by 0x551B80: ??? (in /usr/bin/python3.6) ==7822== by 0x5AA6EB: _PyObject_FastCallKeywords (in /usr/bin/python3.6) ==7822== by 0x50ABB2: ??? (in /usr/bin/python3.6) ==7822== by 0x50C5B8: _PyEval_EvalFrameDefault (in /usr/bin/python3.6) ==7822== by 0x509D47: ??? (in /usr/bin/python3.6) ==7822== by 0x50AA7C: ??? (in /usr/bin/python3.6) ==7822== ==7822== Conditional jump or move depends on uninitialised value(s) ==7822== at 0x4FCBCEC: __wcsnlen_avx2 (strlen-avx2.S:103) ==7822== by 0x4EF9EC1: wcsrtombs (wcsrtombs.c:104) ==7822== by 0x4E7FB20: wcstombs (wcstombs.c:34) ==7822== by 0x547A3F: ??? (in /usr/bin/python3.6) ==7822== by 0x547D20: PyUnicode_FSConverter (in /usr/bin/python3.6) ==7822== by 0x4C51E6: ??? (in /usr/bin/python3.6) ==7822== by 0x4F8388: ??? (in /usr/bin/python3.6) ==7822== by 0x4FBD83: ??? (in /usr/bin/python3.6) ==7822== by 0x4FC914: _PyArg_ParseStack_SizeT (in /usr/bin/python3.6) ==7822== by 0x4C6C88: ??? (in /usr/bin/python3.6) ==7822== by 0x50A9D9: ??? (in /usr/bin/python3.6) ==7822== by 0x50C5B8: _PyEval_EvalFrameDefault (in /usr/bin/python3.6) ==7822== ==7822== ==7822== HEAP SUMMARY: ==7822== in use at exit: 2,766,803 bytes in 1,649 blocks ==7822== total heap usage: 54,869 allocs, 53,220 frees, 67,442,444 bytes allocated ==7822== ==7822== LEAK SUMMARY: ==7822== definitely lost: 0 bytes in 0 blocks ==7822== indirectly lost: 0 bytes in 0 blocks ==7822== possibly lost: 146,155 bytes in 87 blocks ==7822== still reachable: 2,620,648 bytes in 1,562 blocks ==7822== suppressed: 0 bytes in 0 blocks ==7822== Rerun with --leak-check=full to see details of leaked memory ==7822== ==7822== For counts of detected and suppressed errors, rerun with: -v ==7822== Use --track-origins=yes to see where uninitialised values come from ==7822== ERROR SUMMARY: 6672 errors from 5 contexts (suppressed: 12420 from 654) ================================================================================ 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.