!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_ReaxFF_KeithFantauzziJacob_2010_AuO__SM_974345878378_001 Supported species : Au O random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Au (Configuration in file "config-F-Au.xyz") ----------------------------------------------------------------------------------------------------- Energy = 368.5868170863069 Forces: 1 -1.35303430e+01 -2.25688251e+01 -2.43171035e+01 2 -8.94022547e+00 1.34645387e+01 -2.37873439e+01 3 1.47356609e+01 -4.00185016e+01 -1.54147902e+01 4 -3.13038252e+01 1.44356857e+01 4.87119955e-01 5 -3.39994447e+00 -3.72997334e+01 -1.31683324e+01 6 2.42146475e+01 1.30795344e+01 -2.61577908e+01 7 2.33251688e+01 -6.05086485e+01 -3.89347708e+01 8 -2.94081275e+01 -2.29443968e+01 -3.37741150e+00 9 -2.44575788e+01 -1.64888991e+01 -4.11359053e+01 10 -8.38717739e+00 4.49176260e+01 -4.55092541e+01 11 -1.00015963e+01 -2.89824980e+01 6.40428838e+00 12 -2.97051090e+01 3.82323195e+01 5.74394073e+00 13 -9.62597453e+00 -2.94196031e+01 -8.79674715e+01 14 2.30350129e+01 2.75732463e+01 -2.06782233e+01 15 7.96335719e+01 -1.83857185e+01 9.99246591e+00 16 7.22629042e+00 7.05729007e+01 2.50549379e+01 17 -4.45554005e+01 -2.88205785e+01 -5.94573237e+00 18 2.52388313e+01 2.94903102e+01 2.07149810e+01 19 1.62093359e+01 -2.45827526e+01 2.28503920e+01 20 -1.71564230e+01 1.96192595e+01 2.27072489e+01 21 -2.88907814e+01 -3.33303503e+01 9.07856821e+00 22 5.03149962e+01 4.40713503e+01 3.53390351e+01 23 3.01403405e+01 -1.79392448e+01 2.16481684e+01 24 -2.05038705e+01 1.90626105e+01 1.97068777e+01 25 -3.42698761e+01 -1.22138074e+01 1.73824738e+01 26 -1.20874838e+01 4.97868849e+01 -1.92533509e+01 27 2.00272131e+01 -6.73441569e+01 3.11853882e+01 28 -5.62611358e+01 4.61885306e+01 1.58877960e+01 29 -1.68745719e+01 -2.73318744e+01 2.21603846e+01 30 2.71321907e+01 3.75743214e+01 1.08153576e+01 31 3.82929250e+01 -1.57214588e+01 2.92459247e+01 32 1.98332594e+01 3.58319293e+01 3.92421316e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Au (Configuration in file "config-T-Au.xyz") ----------------------------------------------------------------------------------------------------- Energy = 368.5868170865506 Forces: 1 -1.35303430e+01 -2.25688251e+01 -2.43171035e+01 2 -8.94022547e+00 1.34645387e+01 -2.37873439e+01 3 1.47356609e+01 -4.00185016e+01 -1.54147902e+01 4 -3.13038252e+01 1.44356857e+01 4.87119955e-01 5 -3.39994447e+00 -3.72997334e+01 -1.31683324e+01 6 2.42146475e+01 1.30795344e+01 -2.61577908e+01 7 2.33251688e+01 -6.05086485e+01 -3.89347708e+01 8 -2.94081275e+01 -2.29443968e+01 -3.37741150e+00 9 -2.44575788e+01 -1.64888991e+01 -4.11359053e+01 10 -8.38717739e+00 4.49176260e+01 -4.55092541e+01 11 -1.00015963e+01 -2.89824980e+01 6.40428838e+00 12 -2.97051090e+01 3.82323195e+01 5.74394073e+00 13 -9.62597453e+00 -2.94196031e+01 -8.79674715e+01 14 2.30350129e+01 2.75732463e+01 -2.06782233e+01 15 7.96335719e+01 -1.83857185e+01 9.99246591e+00 16 7.22629042e+00 7.05729007e+01 2.50549379e+01 17 -4.45554005e+01 -2.88205785e+01 -5.94573237e+00 18 2.52388313e+01 2.94903102e+01 2.07149810e+01 19 1.62093359e+01 -2.45827526e+01 2.28503920e+01 20 -1.71564230e+01 1.96192595e+01 2.27072489e+01 21 -2.88907814e+01 -3.33303503e+01 9.07856821e+00 22 5.03149962e+01 4.40713503e+01 3.53390351e+01 23 3.01403405e+01 -1.79392448e+01 2.16481684e+01 24 -2.05038705e+01 1.90626105e+01 1.97068777e+01 25 -3.42698761e+01 -1.22138074e+01 1.73824738e+01 26 -1.20874838e+01 4.97868849e+01 -1.92533509e+01 27 2.00272131e+01 -6.73441569e+01 3.11853882e+01 28 -5.62611358e+01 4.61885306e+01 1.58877960e+01 29 -1.68745719e+01 -2.73318744e+01 2.21603846e+01 30 2.71321907e+01 3.75743214e+01 1.08153576e+01 31 3.82929250e+01 -1.57214588e+01 2.92459247e+01 32 1.98332594e+01 3.58319293e+01 3.92421316e+01 MONOATOMIC STRUCTURE (pbc=False)-- Species = O (Configuration in file "config-F-O.xyz") ----------------------------------------------------------------------------------------------------- Energy = 32.44665732771034 Forces: 1 -1.12954315e+00 -8.51592229e-01 -1.00629066e+00 2 -2.82589901e+00 2.16095856e+00 -1.86325415e+00 3 5.21523645e+00 -4.96300433e+00 5.43338765e+00 4 -3.85482437e+00 -9.99906361e-01 -1.00498591e+00 5 5.44684234e-01 -1.04365827e+00 -5.47064550e-01 6 1.32394477e+00 -1.93837044e+00 -2.55983746e-01 7 6.54453534e-01 2.54599735e+00 -7.54056873e-01 8 1.98745088e+00 -6.73543711e-01 -1.73561211e+00 9 1.85032650e+00 -6.09058503e-01 -6.37425456e-01 10 -2.46547769e+00 1.28336313e+00 -1.29367896e+00 11 2.56267282e-01 2.35457299e+00 -1.15726658e+00 12 -5.24522142e-01 3.98077581e-01 -1.99534168e+00 13 2.67065367e-01 -3.02763042e+00 -4.80797971e+00 14 -9.47549670e-03 1.13052575e-01 9.55015486e-01 15 5.44463224e+00 4.14525270e+00 -2.34024137e-02 16 -1.32167403e+00 1.63093068e+00 -1.81496026e-01 17 1.45979622e+00 4.46543106e-02 8.42788755e-01 18 -1.34444179e+00 -1.30523909e+00 -6.11812690e+00 19 -8.45903842e-02 -1.04405010e+00 -1.46682309e+00 20 -1.92250238e+00 7.42347928e-01 4.26139172e-03 21 -7.93808083e+00 -2.10248639e+00 -2.01042622e+00 22 2.58623642e+00 -3.79492797e+00 3.81272499e-02 23 1.44173322e+00 3.85923999e-01 -3.31090224e-01 24 1.67641346e+00 -5.19135121e+00 4.76504461e+00 25 -5.08365643e+00 -2.40116136e+00 1.66339076e+00 26 -2.19084891e+00 3.64574895e+00 9.13100991e-01 27 4.40284886e-01 7.59967461e+00 6.98744024e+00 28 -6.09386428e-01 8.19724492e-01 6.72331738e-02 29 -3.57891954e+00 -4.29743413e+00 2.23373883e+00 30 5.61640202e+00 1.58216110e+00 -5.85403785e-01 31 2.75861820e+00 3.36604433e+00 8.62272281e-01 32 1.36029690e+00 1.42492922e+00 3.00990763e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = O (Configuration in file "config-T-O.xyz") ----------------------------------------------------------------------------------------------------- Energy = 32.44665732864196 Forces: 1 -1.12954315e+00 -8.51592229e-01 -1.00629066e+00 2 -2.82589901e+00 2.16095856e+00 -1.86325415e+00 3 5.21523645e+00 -4.96300433e+00 5.43338765e+00 4 -3.85482437e+00 -9.99906361e-01 -1.00498591e+00 5 5.44684234e-01 -1.04365827e+00 -5.47064550e-01 6 1.32394477e+00 -1.93837044e+00 -2.55983746e-01 7 6.54453534e-01 2.54599735e+00 -7.54056873e-01 8 1.98745088e+00 -6.73543711e-01 -1.73561211e+00 9 1.85032650e+00 -6.09058504e-01 -6.37425456e-01 10 -2.46547769e+00 1.28336313e+00 -1.29367896e+00 11 2.56267282e-01 2.35457299e+00 -1.15726658e+00 12 -5.24522142e-01 3.98077581e-01 -1.99534168e+00 13 2.67065367e-01 -3.02763042e+00 -4.80797971e+00 14 -9.47549667e-03 1.13052575e-01 9.55015486e-01 15 5.44463224e+00 4.14525270e+00 -2.34024137e-02 16 -1.32167403e+00 1.63093068e+00 -1.81496026e-01 17 1.45979622e+00 4.46543106e-02 8.42788755e-01 18 -1.34444179e+00 -1.30523909e+00 -6.11812690e+00 19 -8.45903842e-02 -1.04405010e+00 -1.46682309e+00 20 -1.92250238e+00 7.42347928e-01 4.26139171e-03 21 -7.93808083e+00 -2.10248639e+00 -2.01042622e+00 22 2.58623642e+00 -3.79492797e+00 3.81272499e-02 23 1.44173322e+00 3.85923999e-01 -3.31090224e-01 24 1.67641346e+00 -5.19135121e+00 4.76504461e+00 25 -5.08365643e+00 -2.40116136e+00 1.66339076e+00 26 -2.19084891e+00 3.64574895e+00 9.13100991e-01 27 4.40284886e-01 7.59967461e+00 6.98744024e+00 28 -6.09386428e-01 8.19724492e-01 6.72331738e-02 29 -3.57891954e+00 -4.29743413e+00 2.23373883e+00 30 5.61640202e+00 1.58216110e+00 -5.85403785e-01 31 2.75861820e+00 3.36604433e+00 8.62272281e-01 32 1.36029690e+00 1.42492922e+00 3.00990763e+00 MIXED STRUCTURE (pbc=False)-- Species = Au O (Configuration in file "config-F-AuO.xyz") ----------------------------------------------------------------------------------------------------- Energy = 110.49810860243205 Forces: 1 -5.00992012e+00 -4.26041272e+00 -7.97271701e+00 2 1.79721323e+00 1.30282440e+00 -8.57043369e+00 3 2.76900391e+00 -6.78342599e+00 3.90249668e+00 4 -7.30590895e+00 3.90910309e+00 -9.83279812e+00 5 -4.11357912e-01 -3.16508788e+00 -4.62329473e+00 6 3.95966689e+00 -4.05501221e+00 -2.94282088e+00 7 3.83208164e+00 -9.75130045e-01 -9.36820449e-01 8 -8.77091628e+00 -3.19726882e+01 -9.28773995e+00 9 -2.30308815e+00 2.89297790e+00 -2.73605466e+00 10 -3.57826750e+01 1.20555366e+01 -2.28968457e+01 11 3.05743563e+00 -8.11142369e-01 -4.59297659e+00 12 -5.09167472e+00 7.21034830e+00 -2.42306054e+00 13 1.09058464e+01 -1.68767624e+01 -3.59779819e+01 14 1.32201686e+00 1.45112600e-01 -4.42983363e-01 15 2.65484162e+01 2.71390921e+00 -8.52824130e+00 16 1.25045655e+01 4.63452012e+01 6.06336075e-01 17 -2.52045514e+00 -1.33888638e+01 9.03935734e+00 18 3.05719413e+00 -9.04855307e-01 -2.95264158e+00 19 2.51830122e+00 -5.50239254e+00 4.35901492e+00 20 -5.76996122e+00 1.45746285e+00 9.21145051e+00 21 7.33621948e-01 -6.29428136e+00 -1.49898378e-01 22 1.51446351e+01 -4.60140152e+00 -7.65784046e+00 23 3.60789901e+00 -1.38436194e+01 1.30873662e+01 24 -3.16351395e+00 6.47961507e-01 8.58108564e+00 25 -3.32894949e+01 -5.13521954e+00 -1.58020247e+01 26 -9.65036575e+00 6.10720425e+01 -3.21060402e+00 27 1.02142560e+01 -3.65613415e+01 4.74138912e+01 28 -1.45280194e+01 1.39204484e+01 1.39669213e+01 29 1.28254805e+01 -2.40150085e+01 1.39316221e+01 30 9.74938294e+00 2.92323623e+01 -5.55548630e+00 31 8.00867968e+00 -7.58836906e+00 2.84083569e+01 32 1.04165470e+00 3.82972342e+00 4.58536548e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==20424== Memcheck, a memory error detector ==20424== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==20424== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==20424== Command: python runner2.py Sim_LAMMPS_ReaxFF_KeithFantauzziJacob_2010_AuO__SM_974345878378_001 ==20424== ==20424== Conditional jump or move depends on uninitialised value(s) ==20424== at 0x4FCBE77: __wcsnlen_avx2 (strlen-avx2.S:261) ==20424== by 0x4EF9EC1: wcsrtombs (wcsrtombs.c:104) ==20424== by 0x4E7FB20: wcstombs (wcstombs.c:34) ==20424== by 0x547A3F: ??? (in /usr/bin/python3.6) ==20424== by 0x63345D: _Py_stat (in /usr/bin/python3.6) ==20424== by 0x5BA640: ??? (in /usr/bin/python3.6) ==20424== by 0x551B80: ??? (in /usr/bin/python3.6) ==20424== by 0x5AA6EB: _PyObject_FastCallKeywords (in /usr/bin/python3.6) ==20424== by 0x50ABB2: ??? (in /usr/bin/python3.6) ==20424== by 0x50C5B8: _PyEval_EvalFrameDefault (in /usr/bin/python3.6) ==20424== by 0x509D47: ??? (in /usr/bin/python3.6) ==20424== by 0x50AA7C: ??? (in /usr/bin/python3.6) ==20424== ==20424== Conditional jump or move depends on uninitialised value(s) ==20424== at 0x4E63408: internal_utf8_loop (loop.c:298) ==20424== by 0x4E63408: __gconv_transform_internal_utf8 (skeleton.c:609) ==20424== by 0x4EF9EF4: wcsrtombs (wcsrtombs.c:110) ==20424== by 0x4E7FB20: wcstombs (wcstombs.c:34) ==20424== by 0x547A3F: ??? (in /usr/bin/python3.6) ==20424== by 0x63345D: _Py_stat (in /usr/bin/python3.6) ==20424== by 0x5BA640: ??? (in /usr/bin/python3.6) ==20424== by 0x551B80: ??? (in /usr/bin/python3.6) ==20424== by 0x5AA6EB: _PyObject_FastCallKeywords (in /usr/bin/python3.6) ==20424== by 0x50ABB2: ??? (in /usr/bin/python3.6) ==20424== by 0x50C5B8: _PyEval_EvalFrameDefault (in /usr/bin/python3.6) ==20424== by 0x509D47: ??? (in /usr/bin/python3.6) ==20424== by 0x50AA7C: ??? (in /usr/bin/python3.6) ==20424== ==20424== Conditional jump or move depends on uninitialised value(s) ==20424== at 0x4E63411: internal_utf8_loop (loop.c:303) ==20424== by 0x4E63411: __gconv_transform_internal_utf8 (skeleton.c:609) ==20424== by 0x4EF9EF4: wcsrtombs (wcsrtombs.c:110) ==20424== by 0x4E7FB20: wcstombs (wcstombs.c:34) ==20424== by 0x547A3F: ??? (in /usr/bin/python3.6) ==20424== by 0x63345D: _Py_stat (in /usr/bin/python3.6) ==20424== by 0x5BA640: ??? (in /usr/bin/python3.6) ==20424== by 0x551B80: ??? (in /usr/bin/python3.6) ==20424== by 0x5AA6EB: _PyObject_FastCallKeywords (in /usr/bin/python3.6) ==20424== by 0x50ABB2: ??? (in /usr/bin/python3.6) ==20424== by 0x50C5B8: _PyEval_EvalFrameDefault (in /usr/bin/python3.6) ==20424== by 0x509D47: ??? (in /usr/bin/python3.6) ==20424== by 0x50AA7C: ??? (in /usr/bin/python3.6) ==20424== ==20424== Conditional jump or move depends on uninitialised value(s) ==20424== at 0x4E63458: internal_utf8_loop (loop.c:298) ==20424== by 0x4E63458: __gconv_transform_internal_utf8 (skeleton.c:609) ==20424== by 0x4EF9EF4: wcsrtombs (wcsrtombs.c:110) ==20424== by 0x4E7FB20: wcstombs (wcstombs.c:34) ==20424== by 0x547A3F: ??? (in /usr/bin/python3.6) ==20424== by 0x63345D: _Py_stat (in /usr/bin/python3.6) ==20424== by 0x5BA640: ??? (in /usr/bin/python3.6) ==20424== by 0x551B80: ??? (in /usr/bin/python3.6) ==20424== by 0x5AA6EB: _PyObject_FastCallKeywords (in /usr/bin/python3.6) ==20424== by 0x50ABB2: ??? (in /usr/bin/python3.6) ==20424== by 0x50C5B8: _PyEval_EvalFrameDefault (in /usr/bin/python3.6) ==20424== by 0x509D47: ??? (in /usr/bin/python3.6) ==20424== by 0x50AA7C: ??? (in /usr/bin/python3.6) ==20424== ==20424== Conditional jump or move depends on uninitialised value(s) ==20424== at 0x4FCBCEC: __wcsnlen_avx2 (strlen-avx2.S:103) ==20424== by 0x4EF9EC1: wcsrtombs (wcsrtombs.c:104) ==20424== by 0x4E7FB20: wcstombs (wcstombs.c:34) ==20424== by 0x547A3F: ??? (in /usr/bin/python3.6) ==20424== by 0x547D20: PyUnicode_FSConverter (in /usr/bin/python3.6) ==20424== by 0x4C51E6: ??? (in /usr/bin/python3.6) ==20424== by 0x4F8388: ??? (in /usr/bin/python3.6) ==20424== by 0x4FBD83: ??? (in /usr/bin/python3.6) ==20424== by 0x4FC914: _PyArg_ParseStack_SizeT (in /usr/bin/python3.6) ==20424== by 0x4C6C88: ??? (in /usr/bin/python3.6) ==20424== by 0x50A9D9: ??? (in /usr/bin/python3.6) ==20424== by 0x50C5B8: _PyEval_EvalFrameDefault (in /usr/bin/python3.6) ==20424== ==20424== ==20424== HEAP SUMMARY: ==20424== in use at exit: 3,061,613 bytes in 1,949 blocks ==20424== total heap usage: 60,149 allocs, 58,200 frees, 140,980,370 bytes allocated ==20424== ==20424== LEAK SUMMARY: ==20424== definitely lost: 0 bytes in 0 blocks ==20424== indirectly lost: 0 bytes in 0 blocks ==20424== possibly lost: 151,315 bytes in 96 blocks ==20424== still reachable: 2,910,298 bytes in 1,853 blocks ==20424== suppressed: 0 bytes in 0 blocks ==20424== Rerun with --leak-check=full to see details of leaked memory ==20424== ==20424== For counts of detected and suppressed errors, rerun with: -v ==20424== Use --track-origins=yes to see where uninitialised values come from ==20424== ERROR SUMMARY: 6672 errors from 5 contexts (suppressed: 11111 from 657) ================================================================================ 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.