!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_TersoffZBL_ByggmastarGranberg_2020_Fe__SM_958863895234_000 Supported species : Fe random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Fe (Configuration in file "config-F-Fe.xyz") ----------------------------------------------------------------------------------------------------- Energy = -27.007072907842286 Forces: 1 -3.25317566e+00 -5.50944575e+00 -5.92892713e+00 2 -7.48224837e+00 1.30028821e+01 -6.66995515e+00 3 4.68485630e+00 -4.99003334e+00 1.98636476e-01 4 -5.12603082e+00 4.17656656e+00 4.21136090e+00 5 8.54100249e+00 -1.52608127e+01 -6.16453809e-01 6 4.40152151e+00 1.31411931e+00 -5.78352770e+00 7 3.10062006e+00 -2.30682759e+01 -2.31440732e+01 8 -1.17849554e+01 -1.03748517e+01 5.71066025e+00 9 -4.90025791e+00 -5.86795859e+00 -9.68459353e+00 10 -3.83374014e+00 1.04614141e+01 -1.28906883e+01 11 -4.79925167e+00 -8.26116826e+00 3.28098169e+00 12 -5.49069552e+00 7.42563017e+00 4.47229776e+00 13 -8.65346990e+00 -7.09967898e+00 -3.35982359e+01 14 4.70116348e+00 6.62886691e+00 -4.21026087e+00 15 2.83749879e+01 -8.55914041e+00 6.37476767e+00 16 3.66914616e+00 2.33707083e+01 9.96561583e+00 17 -1.07327819e+01 -4.99376241e+00 -3.96442414e+00 18 5.70010018e+00 9.71584800e+00 -6.73417128e+00 19 5.88704092e+00 -1.05035107e+01 8.53339618e+00 20 -5.23984165e+00 6.00902203e+00 6.35498335e+00 21 -1.26306979e+01 -5.33301401e+00 1.69581344e+00 22 1.31048355e+01 2.01157084e+01 1.80927722e+01 23 5.09653596e+00 -7.73879490e-01 7.81931758e+00 24 -1.61129871e-01 -2.19920728e+00 3.37324634e+00 25 -9.83566982e+00 -7.46893362e+00 -3.74759437e+00 26 -3.38692793e+00 1.49378314e+01 -7.38414246e+00 27 1.19559465e+01 -2.51941752e+01 1.25493915e+01 28 -2.20993406e+01 2.09552845e+01 4.24458551e+00 29 -4.95706882e+00 -1.07232270e+01 4.78736894e+00 30 6.00441700e+00 1.13107910e+01 6.37712020e+00 31 1.28726564e+01 -3.57338299e+00 6.03102646e+00 32 6.27245353e+00 1.03297854e+01 1.02837056e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Fe (Configuration in file "config-T-Fe.xyz") ----------------------------------------------------------------------------------------------------- Energy = -27.007072907842286 Forces: 1 -3.25317566e+00 -5.50944575e+00 -5.92892713e+00 2 -7.48224837e+00 1.30028821e+01 -6.66995515e+00 3 4.68485630e+00 -4.99003334e+00 1.98636476e-01 4 -5.12603082e+00 4.17656656e+00 4.21136090e+00 5 8.54100249e+00 -1.52608127e+01 -6.16453809e-01 6 4.40152151e+00 1.31411931e+00 -5.78352770e+00 7 3.10062006e+00 -2.30682759e+01 -2.31440732e+01 8 -1.17849554e+01 -1.03748517e+01 5.71066025e+00 9 -4.90025791e+00 -5.86795859e+00 -9.68459353e+00 10 -3.83374014e+00 1.04614141e+01 -1.28906883e+01 11 -4.79925167e+00 -8.26116826e+00 3.28098169e+00 12 -5.49069552e+00 7.42563017e+00 4.47229776e+00 13 -8.65346990e+00 -7.09967898e+00 -3.35982359e+01 14 4.70116348e+00 6.62886691e+00 -4.21026087e+00 15 2.83749879e+01 -8.55914041e+00 6.37476767e+00 16 3.66914616e+00 2.33707083e+01 9.96561583e+00 17 -1.07327819e+01 -4.99376241e+00 -3.96442414e+00 18 5.70010018e+00 9.71584800e+00 -6.73417128e+00 19 5.88704092e+00 -1.05035107e+01 8.53339618e+00 20 -5.23984165e+00 6.00902203e+00 6.35498335e+00 21 -1.26306979e+01 -5.33301401e+00 1.69581344e+00 22 1.31048355e+01 2.01157084e+01 1.80927722e+01 23 5.09653596e+00 -7.73879490e-01 7.81931758e+00 24 -1.61129871e-01 -2.19920728e+00 3.37324634e+00 25 -9.83566982e+00 -7.46893362e+00 -3.74759437e+00 26 -3.38692793e+00 1.49378314e+01 -7.38414246e+00 27 1.19559465e+01 -2.51941752e+01 1.25493915e+01 28 -2.20993406e+01 2.09552845e+01 4.24458551e+00 29 -4.95706882e+00 -1.07232270e+01 4.78736894e+00 30 6.00441700e+00 1.13107910e+01 6.37712020e+00 31 1.28726564e+01 -3.57338299e+00 6.03102646e+00 32 6.27245353e+00 1.03297854e+01 1.02837056e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==1172== Memcheck, a memory error detector ==1172== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==1172== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==1172== Command: python runner2.py Sim_LAMMPS_TersoffZBL_ByggmastarGranberg_2020_Fe__SM_958863895234_000 ==1172== ==1172== Conditional jump or move depends on uninitialised value(s) ==1172== at 0x4FCBE77: __wcsnlen_avx2 (strlen-avx2.S:261) ==1172== by 0x4EF9EC1: wcsrtombs (wcsrtombs.c:104) ==1172== by 0x4E7FB20: wcstombs (wcstombs.c:34) ==1172== by 0x547A3F: ??? (in /usr/bin/python3.6) ==1172== by 0x63345D: _Py_stat (in /usr/bin/python3.6) ==1172== by 0x5BA640: ??? (in /usr/bin/python3.6) ==1172== by 0x551B80: ??? (in /usr/bin/python3.6) ==1172== by 0x5AA6EB: _PyObject_FastCallKeywords (in /usr/bin/python3.6) ==1172== by 0x50ABB2: ??? (in /usr/bin/python3.6) ==1172== by 0x50C5B8: _PyEval_EvalFrameDefault (in /usr/bin/python3.6) ==1172== by 0x509D47: ??? (in /usr/bin/python3.6) ==1172== by 0x50AA7C: ??? (in /usr/bin/python3.6) ==1172== ==1172== Conditional jump or move depends on uninitialised value(s) ==1172== at 0x4E63408: internal_utf8_loop (loop.c:298) ==1172== by 0x4E63408: __gconv_transform_internal_utf8 (skeleton.c:609) ==1172== by 0x4EF9EF4: wcsrtombs (wcsrtombs.c:110) ==1172== by 0x4E7FB20: wcstombs (wcstombs.c:34) ==1172== by 0x547A3F: ??? (in /usr/bin/python3.6) ==1172== by 0x63345D: _Py_stat (in /usr/bin/python3.6) ==1172== by 0x5BA640: ??? (in /usr/bin/python3.6) ==1172== by 0x551B80: ??? (in /usr/bin/python3.6) ==1172== by 0x5AA6EB: _PyObject_FastCallKeywords (in /usr/bin/python3.6) ==1172== by 0x50ABB2: ??? (in /usr/bin/python3.6) ==1172== by 0x50C5B8: _PyEval_EvalFrameDefault (in /usr/bin/python3.6) ==1172== by 0x509D47: ??? (in /usr/bin/python3.6) ==1172== by 0x50AA7C: ??? (in /usr/bin/python3.6) ==1172== ==1172== Conditional jump or move depends on uninitialised value(s) ==1172== at 0x4E63411: internal_utf8_loop (loop.c:303) ==1172== by 0x4E63411: __gconv_transform_internal_utf8 (skeleton.c:609) ==1172== by 0x4EF9EF4: wcsrtombs (wcsrtombs.c:110) ==1172== by 0x4E7FB20: wcstombs (wcstombs.c:34) ==1172== by 0x547A3F: ??? (in /usr/bin/python3.6) ==1172== by 0x63345D: _Py_stat (in /usr/bin/python3.6) ==1172== by 0x5BA640: ??? (in /usr/bin/python3.6) ==1172== by 0x551B80: ??? (in /usr/bin/python3.6) ==1172== by 0x5AA6EB: _PyObject_FastCallKeywords (in /usr/bin/python3.6) ==1172== by 0x50ABB2: ??? (in /usr/bin/python3.6) ==1172== by 0x50C5B8: _PyEval_EvalFrameDefault (in /usr/bin/python3.6) ==1172== by 0x509D47: ??? (in /usr/bin/python3.6) ==1172== by 0x50AA7C: ??? (in /usr/bin/python3.6) ==1172== ==1172== Conditional jump or move depends on uninitialised value(s) ==1172== at 0x4E63458: internal_utf8_loop (loop.c:298) ==1172== by 0x4E63458: __gconv_transform_internal_utf8 (skeleton.c:609) ==1172== by 0x4EF9EF4: wcsrtombs (wcsrtombs.c:110) ==1172== by 0x4E7FB20: wcstombs (wcstombs.c:34) ==1172== by 0x547A3F: ??? (in /usr/bin/python3.6) ==1172== by 0x63345D: _Py_stat (in /usr/bin/python3.6) ==1172== by 0x5BA640: ??? (in /usr/bin/python3.6) ==1172== by 0x551B80: ??? (in /usr/bin/python3.6) ==1172== by 0x5AA6EB: _PyObject_FastCallKeywords (in /usr/bin/python3.6) ==1172== by 0x50ABB2: ??? (in /usr/bin/python3.6) ==1172== by 0x50C5B8: _PyEval_EvalFrameDefault (in /usr/bin/python3.6) ==1172== by 0x509D47: ??? (in /usr/bin/python3.6) ==1172== by 0x50AA7C: ??? (in /usr/bin/python3.6) ==1172== ==1172== Conditional jump or move depends on uninitialised value(s) ==1172== at 0x4FCBCEC: __wcsnlen_avx2 (strlen-avx2.S:103) ==1172== by 0x4EF9EC1: wcsrtombs (wcsrtombs.c:104) ==1172== by 0x4E7FB20: wcstombs (wcstombs.c:34) ==1172== by 0x547A3F: ??? (in /usr/bin/python3.6) ==1172== by 0x547D20: PyUnicode_FSConverter (in /usr/bin/python3.6) ==1172== by 0x4C51E6: ??? (in /usr/bin/python3.6) ==1172== by 0x4F8388: ??? (in /usr/bin/python3.6) ==1172== by 0x4FBD83: ??? (in /usr/bin/python3.6) ==1172== by 0x4FC914: _PyArg_ParseStack_SizeT (in /usr/bin/python3.6) ==1172== by 0x4C6C88: ??? (in /usr/bin/python3.6) ==1172== by 0x50A9D9: ??? (in /usr/bin/python3.6) ==1172== by 0x50C5B8: _PyEval_EvalFrameDefault (in /usr/bin/python3.6) ==1172== --1172-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --1172-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --1172-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --1172-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --1172-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --1172-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --1172-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --1172-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --1172-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --1172-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --1172-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --1172-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --1172-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --1172-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --1172-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --1172-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --1172-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --1172-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --1172-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --1172-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --1172-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --1172-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --1172-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --1172-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --1172-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --1172-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --1172-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --1172-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --1172-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --1172-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --1172-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --1172-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --1172-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --1172-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --1172-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --1172-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --1172-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --1172-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --1172-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --1172-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --1172-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --1172-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --1172-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --1172-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --1172-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --1172-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --1172-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 --1172-- Warning: DWARF2 CFI reader: unhandled DW_OP_ opcode 0x13 ==1172== ==1172== HEAP SUMMARY: ==1172== in use at exit: 3,063,785 bytes in 1,953 blocks ==1172== total heap usage: 46,500 allocs, 44,547 frees, 73,718,377 bytes allocated ==1172== ==1172== LEAK SUMMARY: ==1172== definitely lost: 0 bytes in 0 blocks ==1172== indirectly lost: 0 bytes in 0 blocks ==1172== possibly lost: 151,931 bytes in 97 blocks ==1172== still reachable: 2,911,854 bytes in 1,856 blocks ==1172== suppressed: 0 bytes in 0 blocks ==1172== Rerun with --leak-check=full to see details of leaked memory ==1172== ==1172== For counts of detected and suppressed errors, rerun with: -v ==1172== Use --track-origins=yes to see where uninitialised values come from ==1172== ERROR SUMMARY: 6672 errors from 5 contexts (suppressed: 11338 from 708) ================================================================================ 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.