!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_Tersoff_1988T3_Si__MO_186459956893_002 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 = 239.76178394351032 Forces: 1 -1.22056310e+01 -2.79414078e+01 -4.18754720e+01 2 -2.03170579e+01 1.71063520e+01 -2.68580080e+01 3 1.35313683e+01 -3.70395034e+01 -1.38962378e+01 4 -1.84713375e+01 3.88189878e+01 1.40662002e+01 5 9.66813543e+00 -3.11816493e+01 -1.19326578e+01 6 2.20277770e+01 2.87754287e+00 -2.37555430e+01 7 1.44876126e+01 -6.28494172e+01 -4.13193949e+01 8 -2.63034552e+01 -3.20407974e+01 1.79462454e+00 9 -1.25873879e+01 -2.79277499e+01 -3.13072732e+01 10 -9.80017670e+00 2.64622273e+01 -3.31551105e+01 11 5.52816717e+00 -2.79408316e+01 -4.99611573e+01 12 -3.28019982e+01 3.39527660e+01 1.24673393e+01 13 -1.56079059e+01 -1.22733193e+01 -8.28720948e+01 14 2.18902625e+01 1.80037675e+01 -1.10854475e+01 15 8.74009746e+01 1.20397904e+01 1.57801870e+01 16 1.72026733e+01 6.28261569e+01 1.69207814e+01 17 -2.78015181e+01 -1.53839899e+01 1.37187928e+01 18 5.89908310e+00 1.67631623e+01 2.72642873e+01 19 9.26034084e+00 -1.75041273e+01 1.49633753e+01 20 -1.25173916e+01 9.92632085e+00 1.54005231e+01 21 -2.02134025e+01 -2.26204283e+01 1.79423190e+01 22 4.04263616e+01 4.32591625e+01 3.55472272e+01 23 7.94446549e+00 -4.66316947e+00 1.75342315e+01 24 -8.50193329e-01 -5.81093567e+00 1.86685374e+01 25 -7.39677257e+01 1.43187647e+00 3.50765320e+01 26 -1.78399917e+01 5.10895190e+01 -8.46143915e+00 27 5.46989294e+00 -5.99962902e+01 3.07550748e+01 28 -5.24134361e+01 4.01014336e+01 8.61919269e+00 29 2.24378341e+01 -2.82578609e+01 2.17860995e+01 30 2.17398400e+01 2.35363189e+01 -1.52432273e+00 31 2.83115820e+01 -1.38515302e+01 2.74385023e+01 32 2.04722386e+01 2.90876237e+01 3.22603313e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Si (Configuration in file "config-T-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 239.76178394351032 Forces: 1 -1.22056310e+01 -2.79414078e+01 -4.18754720e+01 2 -2.03170579e+01 1.71063520e+01 -2.68580080e+01 3 1.35313683e+01 -3.70395034e+01 -1.38962378e+01 4 -1.84713375e+01 3.88189878e+01 1.40662002e+01 5 9.66813543e+00 -3.11816493e+01 -1.19326578e+01 6 2.20277770e+01 2.87754287e+00 -2.37555430e+01 7 1.44876126e+01 -6.28494172e+01 -4.13193949e+01 8 -2.63034552e+01 -3.20407974e+01 1.79462454e+00 9 -1.25873879e+01 -2.79277499e+01 -3.13072732e+01 10 -9.80017670e+00 2.64622273e+01 -3.31551105e+01 11 5.52816717e+00 -2.79408316e+01 -4.99611573e+01 12 -3.28019982e+01 3.39527660e+01 1.24673393e+01 13 -1.56079059e+01 -1.22733193e+01 -8.28720948e+01 14 2.18902625e+01 1.80037675e+01 -1.10854475e+01 15 8.74009746e+01 1.20397904e+01 1.57801870e+01 16 1.72026733e+01 6.28261569e+01 1.69207814e+01 17 -2.78015181e+01 -1.53839899e+01 1.37187928e+01 18 5.89908310e+00 1.67631623e+01 2.72642873e+01 19 9.26034084e+00 -1.75041273e+01 1.49633753e+01 20 -1.25173916e+01 9.92632085e+00 1.54005231e+01 21 -2.02134025e+01 -2.26204283e+01 1.79423190e+01 22 4.04263616e+01 4.32591625e+01 3.55472272e+01 23 7.94446549e+00 -4.66316947e+00 1.75342315e+01 24 -8.50193329e-01 -5.81093567e+00 1.86685374e+01 25 -7.39677257e+01 1.43187647e+00 3.50765320e+01 26 -1.78399917e+01 5.10895190e+01 -8.46143915e+00 27 5.46989294e+00 -5.99962902e+01 3.07550748e+01 28 -5.24134361e+01 4.01014336e+01 8.61919269e+00 29 2.24378341e+01 -2.82578609e+01 2.17860995e+01 30 2.17398400e+01 2.35363189e+01 -1.52432273e+00 31 2.83115820e+01 -1.38515302e+01 2.74385023e+01 32 2.04722386e+01 2.90876237e+01 3.22603313e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==8242== Memcheck, a memory error detector ==8242== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==8242== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==8242== Command: python runner2.py Tersoff_LAMMPS_Tersoff_1988T3_Si__MO_186459956893_002 ==8242== ==8242== Conditional jump or move depends on uninitialised value(s) ==8242== at 0x4FCBE77: __wcsnlen_avx2 (strlen-avx2.S:261) ==8242== by 0x4EF9EC1: wcsrtombs (wcsrtombs.c:104) ==8242== by 0x4E7FB20: wcstombs (wcstombs.c:34) ==8242== by 0x547A3F: ??? (in /usr/bin/python3.6) ==8242== by 0x63345D: _Py_stat (in /usr/bin/python3.6) ==8242== by 0x5BA640: ??? (in /usr/bin/python3.6) ==8242== by 0x551B80: ??? (in /usr/bin/python3.6) ==8242== by 0x5AA6EB: _PyObject_FastCallKeywords (in /usr/bin/python3.6) ==8242== by 0x50ABB2: ??? (in /usr/bin/python3.6) ==8242== by 0x50C5B8: _PyEval_EvalFrameDefault (in /usr/bin/python3.6) ==8242== by 0x509D47: ??? (in /usr/bin/python3.6) ==8242== by 0x50AA7C: ??? (in /usr/bin/python3.6) ==8242== ==8242== Conditional jump or move depends on uninitialised value(s) ==8242== at 0x4E63408: internal_utf8_loop (loop.c:298) ==8242== by 0x4E63408: __gconv_transform_internal_utf8 (skeleton.c:609) ==8242== by 0x4EF9EF4: wcsrtombs (wcsrtombs.c:110) ==8242== by 0x4E7FB20: wcstombs (wcstombs.c:34) ==8242== by 0x547A3F: ??? (in /usr/bin/python3.6) ==8242== by 0x63345D: _Py_stat (in /usr/bin/python3.6) ==8242== by 0x5BA640: ??? (in /usr/bin/python3.6) ==8242== by 0x551B80: ??? (in /usr/bin/python3.6) ==8242== by 0x5AA6EB: _PyObject_FastCallKeywords (in /usr/bin/python3.6) ==8242== by 0x50ABB2: ??? (in /usr/bin/python3.6) ==8242== by 0x50C5B8: _PyEval_EvalFrameDefault (in /usr/bin/python3.6) ==8242== by 0x509D47: ??? (in /usr/bin/python3.6) ==8242== by 0x50AA7C: ??? (in /usr/bin/python3.6) ==8242== ==8242== Conditional jump or move depends on uninitialised value(s) ==8242== at 0x4E63411: internal_utf8_loop (loop.c:303) ==8242== by 0x4E63411: __gconv_transform_internal_utf8 (skeleton.c:609) ==8242== by 0x4EF9EF4: wcsrtombs (wcsrtombs.c:110) ==8242== by 0x4E7FB20: wcstombs (wcstombs.c:34) ==8242== by 0x547A3F: ??? (in /usr/bin/python3.6) ==8242== by 0x63345D: _Py_stat (in /usr/bin/python3.6) ==8242== by 0x5BA640: ??? (in /usr/bin/python3.6) ==8242== by 0x551B80: ??? (in /usr/bin/python3.6) ==8242== by 0x5AA6EB: _PyObject_FastCallKeywords (in /usr/bin/python3.6) ==8242== by 0x50ABB2: ??? (in /usr/bin/python3.6) ==8242== by 0x50C5B8: _PyEval_EvalFrameDefault (in /usr/bin/python3.6) ==8242== by 0x509D47: ??? (in /usr/bin/python3.6) ==8242== by 0x50AA7C: ??? (in /usr/bin/python3.6) ==8242== ==8242== Conditional jump or move depends on uninitialised value(s) ==8242== at 0x4E63458: internal_utf8_loop (loop.c:298) ==8242== by 0x4E63458: __gconv_transform_internal_utf8 (skeleton.c:609) ==8242== by 0x4EF9EF4: wcsrtombs (wcsrtombs.c:110) ==8242== by 0x4E7FB20: wcstombs (wcstombs.c:34) ==8242== by 0x547A3F: ??? (in /usr/bin/python3.6) ==8242== by 0x63345D: _Py_stat (in /usr/bin/python3.6) ==8242== by 0x5BA640: ??? (in /usr/bin/python3.6) ==8242== by 0x551B80: ??? (in /usr/bin/python3.6) ==8242== by 0x5AA6EB: _PyObject_FastCallKeywords (in /usr/bin/python3.6) ==8242== by 0x50ABB2: ??? (in /usr/bin/python3.6) ==8242== by 0x50C5B8: _PyEval_EvalFrameDefault (in /usr/bin/python3.6) ==8242== by 0x509D47: ??? (in /usr/bin/python3.6) ==8242== by 0x50AA7C: ??? (in /usr/bin/python3.6) ==8242== ==8242== Conditional jump or move depends on uninitialised value(s) ==8242== at 0x4FCBCEC: __wcsnlen_avx2 (strlen-avx2.S:103) ==8242== by 0x4EF9EC1: wcsrtombs (wcsrtombs.c:104) ==8242== by 0x4E7FB20: wcstombs (wcstombs.c:34) ==8242== by 0x547A3F: ??? (in /usr/bin/python3.6) ==8242== by 0x547D20: PyUnicode_FSConverter (in /usr/bin/python3.6) ==8242== by 0x4C51E6: ??? (in /usr/bin/python3.6) ==8242== by 0x4F8388: ??? (in /usr/bin/python3.6) ==8242== by 0x4FBD83: ??? (in /usr/bin/python3.6) ==8242== by 0x4FC914: _PyArg_ParseStack_SizeT (in /usr/bin/python3.6) ==8242== by 0x4C6C88: ??? (in /usr/bin/python3.6) ==8242== by 0x50A9D9: ??? (in /usr/bin/python3.6) ==8242== by 0x50C5B8: _PyEval_EvalFrameDefault (in /usr/bin/python3.6) ==8242== ==8242== ==8242== HEAP SUMMARY: ==8242== in use at exit: 2,764,995 bytes in 1,647 blocks ==8242== total heap usage: 36,318 allocs, 34,671 frees, 61,242,051 bytes allocated ==8242== ==8242== LEAK SUMMARY: ==8242== definitely lost: 0 bytes in 0 blocks ==8242== indirectly lost: 0 bytes in 0 blocks ==8242== possibly lost: 146,155 bytes in 87 blocks ==8242== still reachable: 2,618,840 bytes in 1,560 blocks ==8242== suppressed: 0 bytes in 0 blocks ==8242== Rerun with --leak-check=full to see details of leaked memory ==8242== ==8242== For counts of detected and suppressed errors, rerun with: -v ==8242== Use --track-origins=yes to see where uninitialised values come from ==8242== ERROR SUMMARY: 6672 errors from 5 contexts (suppressed: 12396 from 655) ================================================================================ 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.