Enter a model name: === Verification check vc-memory-leak start (2019-08-08 23:26:04) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : EAM_MagneticCubic_MendelevHanSrolovitz_2003_Fe__MO_856295952425_002 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 = -12.952720171829725 Forces: 1 -5.87390507e+00 -4.84725585e+00 -8.96036533e+00 2 -9.51453644e+00 1.81155169e+01 -5.95879056e+00 3 9.44585509e+00 -8.06745996e+00 -1.11574291e+00 4 -6.44851549e+00 4.99687440e+00 2.42348449e+00 5 1.12301562e+01 -1.88081719e+01 1.99660501e+00 6 2.20036414e+00 1.52072896e+00 -2.88523803e+00 7 1.54555860e+00 -2.80440210e+01 -3.27455228e+01 8 -1.10151713e+01 -8.67682859e+00 -9.12131017e+00 9 -2.83012543e+00 -4.89971308e+00 -8.22294628e+00 10 -6.36218002e+00 8.28876764e+00 -1.44713700e+01 11 -1.92942790e+00 -7.84689209e+00 -5.03420064e-03 12 -5.78101278e+00 1.08945057e+01 1.76584798e+00 13 -1.40928840e+01 -1.23163327e+01 -3.86032105e+01 14 6.99241990e+00 1.16790911e+01 -8.64130727e+00 15 3.02632571e+01 -1.30592957e+01 1.62195601e+01 16 1.62651102e+00 2.22182786e+01 1.75475705e+01 17 -1.61418710e+01 -2.23070778e+00 -5.73034865e+00 18 1.58347484e+00 4.25906315e+00 2.13663464e+00 19 1.37563803e+01 -1.00153907e+01 1.04492599e+01 20 -5.48635884e+00 9.23896265e+00 3.89280793e+00 21 -1.12800633e+01 -9.97077310e+00 8.01845674e+00 22 2.00727711e+01 2.29259044e+01 2.27547286e+01 23 9.70757114e+00 -5.27105869e+00 5.26362629e+00 24 -8.39078336e+00 6.29691079e+00 3.76629100e+00 25 -8.58804680e+00 -6.52143864e+00 6.14567984e+00 26 1.43759992e+00 1.20868384e+01 -7.17963245e+00 27 2.19335344e+01 -3.65076645e+01 7.82346708e+00 28 -3.21540754e+01 2.72412502e+01 3.55139704e+00 29 -7.45086421e+00 2.08132725e+00 9.99799526e+00 30 5.71752038e+00 9.73752321e+00 5.72126280e+00 31 1.03391007e+01 -4.54757039e+00 6.76153368e+00 32 5.48774659e+00 1.00490313e+01 7.40461028e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Fe (Configuration in file "config-T-Fe.xyz") ----------------------------------------------------------------------------------------------------- Energy = -12.952720171829725 Forces: 1 -5.87390507e+00 -4.84725585e+00 -8.96036533e+00 2 -9.51453644e+00 1.81155169e+01 -5.95879056e+00 3 9.44585509e+00 -8.06745996e+00 -1.11574291e+00 4 -6.44851549e+00 4.99687440e+00 2.42348449e+00 5 1.12301562e+01 -1.88081719e+01 1.99660501e+00 6 2.20036414e+00 1.52072896e+00 -2.88523803e+00 7 1.54555860e+00 -2.80440210e+01 -3.27455228e+01 8 -1.10151713e+01 -8.67682859e+00 -9.12131017e+00 9 -2.83012543e+00 -4.89971308e+00 -8.22294628e+00 10 -6.36218002e+00 8.28876764e+00 -1.44713700e+01 11 -1.92942790e+00 -7.84689209e+00 -5.03420064e-03 12 -5.78101278e+00 1.08945057e+01 1.76584798e+00 13 -1.40928840e+01 -1.23163327e+01 -3.86032105e+01 14 6.99241990e+00 1.16790911e+01 -8.64130727e+00 15 3.02632571e+01 -1.30592957e+01 1.62195601e+01 16 1.62651102e+00 2.22182786e+01 1.75475705e+01 17 -1.61418710e+01 -2.23070778e+00 -5.73034865e+00 18 1.58347484e+00 4.25906315e+00 2.13663464e+00 19 1.37563803e+01 -1.00153907e+01 1.04492599e+01 20 -5.48635884e+00 9.23896265e+00 3.89280793e+00 21 -1.12800633e+01 -9.97077310e+00 8.01845674e+00 22 2.00727711e+01 2.29259044e+01 2.27547286e+01 23 9.70757114e+00 -5.27105869e+00 5.26362629e+00 24 -8.39078336e+00 6.29691079e+00 3.76629100e+00 25 -8.58804680e+00 -6.52143864e+00 6.14567984e+00 26 1.43759992e+00 1.20868384e+01 -7.17963245e+00 27 2.19335344e+01 -3.65076645e+01 7.82346708e+00 28 -3.21540754e+01 2.72412502e+01 3.55139704e+00 29 -7.45086421e+00 2.08132725e+00 9.99799526e+00 30 5.71752038e+00 9.73752321e+00 5.72126280e+00 31 1.03391007e+01 -4.54757039e+00 6.76153368e+00 32 5.48774659e+00 1.00490313e+01 7.40461028e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==11762== Memcheck, a memory error detector ==11762== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==11762== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==11762== Command: python runner2.py EAM_MagneticCubic_MendelevHanSrolovitz_2003_Fe__MO_856295952425_002 ==11762== ==12938== Warning: invalid file descriptor 1048564 in syscall close() ==12938== Warning: invalid file descriptor 1048565 in syscall close() ==12938== Warning: invalid file descriptor 1048566 in syscall close() ==12938== Warning: invalid file descriptor 1048567 in syscall close() ==12938== Use --log-fd= to select an alternative log fd. ==12938== Warning: invalid file descriptor 1048568 in syscall close() ==12938== Warning: invalid file descriptor 1048569 in syscall close() ==12939== Warning: invalid file descriptor 1048564 in syscall close() ==12939== Warning: invalid file descriptor 1048565 in syscall close() ==12939== Warning: invalid file descriptor 1048566 in syscall close() ==12939== Warning: invalid file descriptor 1048567 in syscall close() ==12939== Use --log-fd= to select an alternative log fd. ==12939== Warning: invalid file descriptor 1048568 in syscall close() ==12939== Warning: invalid file descriptor 1048569 in syscall close() Potential info: Fe Mendelev potential Atomic number: 26 ==12940== Warning: invalid file descriptor 1048564 in syscall close() ==12940== Warning: invalid file descriptor 1048565 in syscall close() ==12940== Warning: invalid file descriptor 1048566 in syscall close() ==12940== Warning: invalid file descriptor 1048567 in syscall close() ==12940== Use --log-fd= to select an alternative log fd. ==12940== Warning: invalid file descriptor 1048568 in syscall close() ==12940== Warning: invalid file descriptor 1048569 in syscall close() ==12941== Warning: invalid file descriptor 1048564 in syscall close() ==12941== Warning: invalid file descriptor 1048565 in syscall close() ==12941== Warning: invalid file descriptor 1048566 in syscall close() ==12941== Warning: invalid file descriptor 1048567 in syscall close() ==12941== Use --log-fd= to select an alternative log fd. ==12941== Warning: invalid file descriptor 1048568 in syscall close() ==12941== Warning: invalid file descriptor 1048569 in syscall close() ==12942== Warning: invalid file descriptor 1048564 in syscall close() ==12942== Warning: invalid file descriptor 1048565 in syscall close() ==12942== Warning: invalid file descriptor 1048566 in syscall close() ==12942== Warning: invalid file descriptor 1048567 in syscall close() ==12942== Use --log-fd= to select an alternative log fd. ==12942== Warning: invalid file descriptor 1048568 in syscall close() ==12942== Warning: invalid file descriptor 1048569 in syscall close() ==12943== Warning: invalid file descriptor 1048564 in syscall close() ==12943== Warning: invalid file descriptor 1048565 in syscall close() ==12943== Warning: invalid file descriptor 1048566 in syscall close() ==12943== Warning: invalid file descriptor 1048567 in syscall close() ==12943== Use --log-fd= to select an alternative log fd. ==12943== Warning: invalid file descriptor 1048568 in syscall close() ==12943== Warning: invalid file descriptor 1048569 in syscall close() Potential info: Fe Mendelev potential Atomic number: 26 Potential info: Fe Mendelev potential Atomic number: 26 ==11762== ==11762== HEAP SUMMARY: ==11762== in use at exit: 1,718,292 bytes in 1,321 blocks ==11762== total heap usage: 31,082 allocs, 29,761 frees, 38,170,437 bytes allocated ==11762== ==11762== LEAK SUMMARY: ==11762== definitely lost: 0 bytes in 0 blocks ==11762== indirectly lost: 0 bytes in 0 blocks ==11762== possibly lost: 178,943 bytes in 97 blocks ==11762== still reachable: 1,539,349 bytes in 1,224 blocks ==11762== suppressed: 0 bytes in 0 blocks ==11762== Rerun with --leak-check=full to see details of leaked memory ==11762== ==11762== For counts of detected and suppressed errors, rerun with: -v ==11762== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16378 from 616) ================================================================================ 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. === Verification check vc-memory-leak end (2019-08-08 23:26:26) === Potential info: Fe Mendelev potential Atomic number: 26 Potential info: Fe Mendelev potential Atomic number: 26 Potential info: Fe Mendelev potential Atomic number: 26