!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : Sim_LAMMPS_ModifiedTersoff_KumagaiIzumiHara_2007_Si__SM_773333226968_000 Supported species : Si random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Si (Configuration in file "config-F-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 120.68774869352576 Forces: 1 -1.28018960e+01 -1.31564448e+01 -1.93779045e+01 2 -1.31189907e+01 2.09294645e+01 -1.99795272e+01 3 1.00575968e-01 -2.12353277e+01 1.12355842e+01 4 -1.49666818e+01 1.11651439e+01 5.59780859e+00 5 1.60611905e+01 -2.87008690e+01 -1.36707925e+01 6 1.25341422e+01 3.22067937e+00 -1.66812240e+01 7 1.18722861e+01 -4.91571474e+01 -3.98627257e+01 8 -2.46242077e+01 -2.83914280e+01 3.46594328e+00 9 -7.01876788e+00 -2.31237545e+01 -2.79395467e+01 10 -6.59907819e+00 2.32725934e+01 -3.01202854e+01 11 -2.56180641e-02 -1.79063964e+01 -2.71599730e+01 12 -2.15440745e+01 2.70460691e+01 1.69400745e+01 13 -1.68471905e+01 -1.02690663e+01 -7.52795437e+01 14 1.34267288e+01 1.44173531e+01 -8.88419314e+00 15 7.29587916e+01 3.62970916e+00 1.96807928e+01 16 1.14400351e+01 5.53504969e+01 1.83619188e+01 17 -1.63642532e+01 -9.85846364e+00 -2.56077484e+00 18 4.92270572e+00 3.80251141e-01 9.60933863e+00 19 4.95227532e+00 -1.36049468e+01 1.15436365e+01 20 -7.61576609e+00 8.82912472e+00 8.01443412e+00 21 -2.11536386e+01 -2.34774710e+01 7.75721823e+00 22 3.49646911e+01 3.85413067e+01 3.64180545e+01 23 1.45638976e+01 -7.00145123e+00 1.18180206e+01 24 -6.46460705e+00 1.17476900e+01 1.32062687e+01 25 -4.51173229e+01 -2.53037822e+00 1.80173311e+01 26 -9.85888791e+00 4.16296737e+01 -1.03921835e+01 27 1.93017019e+01 -5.54296421e+01 2.48173644e+01 28 -4.63629783e+01 3.81726228e+01 9.36997240e+00 29 -1.81618668e+00 -2.38345190e+01 1.72293179e+01 30 1.58925532e+01 2.02840056e+01 -1.74509671e+00 31 2.42188931e+01 -1.40644905e+01 2.24696699e+01 32 1.50896783e+01 2.31256124e+01 2.81010218e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Si (Configuration in file "config-T-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 120.68774869352576 Forces: 1 -1.28018960e+01 -1.31564448e+01 -1.93779045e+01 2 -1.31189907e+01 2.09294645e+01 -1.99795272e+01 3 1.00575968e-01 -2.12353277e+01 1.12355842e+01 4 -1.49666818e+01 1.11651439e+01 5.59780859e+00 5 1.60611905e+01 -2.87008690e+01 -1.36707925e+01 6 1.25341422e+01 3.22067937e+00 -1.66812240e+01 7 1.18722861e+01 -4.91571474e+01 -3.98627257e+01 8 -2.46242077e+01 -2.83914280e+01 3.46594328e+00 9 -7.01876788e+00 -2.31237545e+01 -2.79395467e+01 10 -6.59907819e+00 2.32725934e+01 -3.01202854e+01 11 -2.56180641e-02 -1.79063964e+01 -2.71599730e+01 12 -2.15440745e+01 2.70460691e+01 1.69400745e+01 13 -1.68471905e+01 -1.02690663e+01 -7.52795437e+01 14 1.34267288e+01 1.44173531e+01 -8.88419314e+00 15 7.29587916e+01 3.62970916e+00 1.96807928e+01 16 1.14400351e+01 5.53504969e+01 1.83619188e+01 17 -1.63642532e+01 -9.85846364e+00 -2.56077484e+00 18 4.92270572e+00 3.80251141e-01 9.60933863e+00 19 4.95227532e+00 -1.36049468e+01 1.15436365e+01 20 -7.61576609e+00 8.82912472e+00 8.01443412e+00 21 -2.11536386e+01 -2.34774710e+01 7.75721823e+00 22 3.49646911e+01 3.85413067e+01 3.64180545e+01 23 1.45638976e+01 -7.00145123e+00 1.18180206e+01 24 -6.46460705e+00 1.17476900e+01 1.32062687e+01 25 -4.51173229e+01 -2.53037822e+00 1.80173311e+01 26 -9.85888791e+00 4.16296737e+01 -1.03921835e+01 27 1.93017019e+01 -5.54296421e+01 2.48173644e+01 28 -4.63629783e+01 3.81726228e+01 9.36997240e+00 29 -1.81618668e+00 -2.38345190e+01 1.72293179e+01 30 1.58925532e+01 2.02840056e+01 -1.74509671e+00 31 2.42188931e+01 -1.40644905e+01 2.24696699e+01 32 1.50896783e+01 2.31256124e+01 2.81010218e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==5869== Memcheck, a memory error detector ==5869== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==5869== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==5869== Command: python runner2.py Sim_LAMMPS_ModifiedTersoff_KumagaiIzumiHara_2007_Si__SM_773333226968_000 ==5869== ==5869== Conditional jump or move depends on uninitialised value(s) ==5869== at 0x4FCBE77: __wcsnlen_avx2 (strlen-avx2.S:261) ==5869== by 0x4EF9EC1: wcsrtombs (wcsrtombs.c:104) ==5869== by 0x4E7FB20: wcstombs (wcstombs.c:34) ==5869== by 0x547A3F: ??? (in /usr/bin/python3.6) ==5869== by 0x63345D: _Py_stat (in /usr/bin/python3.6) ==5869== by 0x5BA640: ??? (in /usr/bin/python3.6) ==5869== by 0x551B80: ??? (in /usr/bin/python3.6) ==5869== by 0x5AA6EB: _PyObject_FastCallKeywords (in /usr/bin/python3.6) ==5869== by 0x50ABB2: ??? (in /usr/bin/python3.6) ==5869== by 0x50C5B8: _PyEval_EvalFrameDefault (in /usr/bin/python3.6) ==5869== by 0x509D47: ??? (in /usr/bin/python3.6) ==5869== by 0x50AA7C: ??? (in /usr/bin/python3.6) ==5869== ==5869== Conditional jump or move depends on uninitialised value(s) ==5869== at 0x4E63408: internal_utf8_loop (loop.c:298) ==5869== by 0x4E63408: __gconv_transform_internal_utf8 (skeleton.c:609) ==5869== by 0x4EF9EF4: wcsrtombs (wcsrtombs.c:110) ==5869== by 0x4E7FB20: wcstombs (wcstombs.c:34) ==5869== by 0x547A3F: ??? (in /usr/bin/python3.6) ==5869== by 0x63345D: _Py_stat (in /usr/bin/python3.6) ==5869== by 0x5BA640: ??? (in /usr/bin/python3.6) ==5869== by 0x551B80: ??? (in /usr/bin/python3.6) ==5869== by 0x5AA6EB: _PyObject_FastCallKeywords (in /usr/bin/python3.6) ==5869== by 0x50ABB2: ??? (in /usr/bin/python3.6) ==5869== by 0x50C5B8: _PyEval_EvalFrameDefault (in /usr/bin/python3.6) ==5869== by 0x509D47: ??? (in /usr/bin/python3.6) ==5869== by 0x50AA7C: ??? (in /usr/bin/python3.6) ==5869== ==5869== Conditional jump or move depends on uninitialised value(s) ==5869== at 0x4E63411: internal_utf8_loop (loop.c:303) ==5869== by 0x4E63411: __gconv_transform_internal_utf8 (skeleton.c:609) ==5869== by 0x4EF9EF4: wcsrtombs (wcsrtombs.c:110) ==5869== by 0x4E7FB20: wcstombs (wcstombs.c:34) ==5869== by 0x547A3F: ??? (in /usr/bin/python3.6) ==5869== by 0x63345D: _Py_stat (in /usr/bin/python3.6) ==5869== by 0x5BA640: ??? (in /usr/bin/python3.6) ==5869== by 0x551B80: ??? (in /usr/bin/python3.6) ==5869== by 0x5AA6EB: _PyObject_FastCallKeywords (in /usr/bin/python3.6) ==5869== by 0x50ABB2: ??? (in /usr/bin/python3.6) ==5869== by 0x50C5B8: _PyEval_EvalFrameDefault (in /usr/bin/python3.6) ==5869== by 0x509D47: ??? (in /usr/bin/python3.6) ==5869== by 0x50AA7C: ??? (in /usr/bin/python3.6) ==5869== ==5869== Conditional jump or move depends on uninitialised value(s) ==5869== at 0x4E63458: internal_utf8_loop (loop.c:298) ==5869== by 0x4E63458: __gconv_transform_internal_utf8 (skeleton.c:609) ==5869== by 0x4EF9EF4: wcsrtombs (wcsrtombs.c:110) ==5869== by 0x4E7FB20: wcstombs (wcstombs.c:34) ==5869== by 0x547A3F: ??? (in /usr/bin/python3.6) ==5869== by 0x63345D: _Py_stat (in /usr/bin/python3.6) ==5869== by 0x5BA640: ??? (in /usr/bin/python3.6) ==5869== by 0x551B80: ??? (in /usr/bin/python3.6) ==5869== by 0x5AA6EB: _PyObject_FastCallKeywords (in /usr/bin/python3.6) ==5869== by 0x50ABB2: ??? (in /usr/bin/python3.6) ==5869== by 0x50C5B8: _PyEval_EvalFrameDefault (in /usr/bin/python3.6) ==5869== by 0x509D47: ??? (in /usr/bin/python3.6) ==5869== by 0x50AA7C: ??? (in /usr/bin/python3.6) ==5869== ==5869== Conditional jump or move depends on uninitialised value(s) ==5869== at 0x4FCBCEC: __wcsnlen_avx2 (strlen-avx2.S:103) ==5869== by 0x4EF9EC1: wcsrtombs (wcsrtombs.c:104) ==5869== by 0x4E7FB20: wcstombs (wcstombs.c:34) ==5869== by 0x547A3F: ??? (in /usr/bin/python3.6) ==5869== by 0x547D20: PyUnicode_FSConverter (in /usr/bin/python3.6) ==5869== by 0x4C51E6: ??? (in /usr/bin/python3.6) ==5869== by 0x4F8388: ??? (in /usr/bin/python3.6) ==5869== by 0x4FBD83: ??? (in /usr/bin/python3.6) ==5869== by 0x4FC914: _PyArg_ParseStack_SizeT (in /usr/bin/python3.6) ==5869== by 0x4C6C88: ??? (in /usr/bin/python3.6) ==5869== by 0x50A9D9: ??? (in /usr/bin/python3.6) ==5869== by 0x50C5B8: _PyEval_EvalFrameDefault (in /usr/bin/python3.6) ==5869== --5869-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --5869-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --5869-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --5869-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --5869-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --5869-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --5869-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --5869-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --5869-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --5869-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --5869-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --5869-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --5869-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --5869-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --5869-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --5869-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --5869-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --5869-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --5869-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --5869-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --5869-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --5869-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --5869-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --5869-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --5869-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --5869-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --5869-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --5869-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --5869-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --5869-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --5869-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --5869-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --5869-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --5869-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --5869-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --5869-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --5869-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --5869-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --5869-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --5869-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --5869-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --5869-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --5869-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --5869-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --5869-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --5869-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --5869-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --5869-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 ==5869== ==5869== HEAP SUMMARY: ==5869== in use at exit: 3,061,549 bytes in 1,950 blocks ==5869== total heap usage: 46,065 allocs, 44,115 frees, 73,074,077 bytes allocated ==5869== ==5869== LEAK SUMMARY: ==5869== definitely lost: 0 bytes in 0 blocks ==5869== indirectly lost: 0 bytes in 0 blocks ==5869== possibly lost: 151,315 bytes in 96 blocks ==5869== still reachable: 2,910,234 bytes in 1,854 blocks ==5869== suppressed: 0 bytes in 0 blocks ==5869== Rerun with --leak-check=full to see details of leaked memory ==5869== ==5869== For counts of detected and suppressed errors, rerun with: -v ==5869== Use --track-origins=yes to see where uninitialised values come from ==5869== ERROR SUMMARY: 6672 errors from 5 contexts (suppressed: 11064 from 675) ================================================================================ 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.