!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : EMT_Asap_Standard_JacobsenStoltzeNorskov_1996_Pt__MO_637493005914_001 Supported species : Pt random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Pt (Configuration in file "config-F-Pt.xyz") ----------------------------------------------------------------------------------------------------- Energy = 422.4216752934138 Forces: 1 -1.59929826e+01 -4.08151842e+01 -4.11259980e+01 2 -3.37511640e+01 3.92927095e+01 -2.55126679e+01 3 2.38212921e+01 -2.06000730e+01 -8.92127663e+00 4 -2.07963136e+01 3.17448446e+01 2.66803763e+01 5 2.65623926e+01 -6.53858581e+01 -9.48386658e+00 6 2.58731406e+01 1.42903318e+01 -2.58536604e+01 7 1.87256341e+01 -1.38014737e+02 -1.36502569e+02 8 -6.59584038e+01 -4.99324742e+01 -2.39809787e+00 9 -5.08372047e+01 -3.16804623e+01 -7.86369963e+01 10 -2.19060857e+01 8.50419690e+01 -8.88261843e+01 11 -2.34008046e+01 -6.59089584e+01 6.23360276e+01 12 -3.85830059e+01 5.12098117e+01 2.33481715e+01 13 -3.40663299e+01 -5.23186045e+01 -1.83156018e+02 14 3.20742030e+01 4.18302545e+01 -2.89936080e+01 15 1.53581074e+02 -4.33546916e+01 3.56928487e+01 16 2.00479889e+01 1.18208686e+02 6.50600029e+01 17 -7.85170682e+01 -5.43476922e+01 -2.86078671e+01 18 6.43977882e+01 8.32429412e+01 -7.92904932e+01 19 2.80432400e+01 -9.24160578e+01 5.72996518e+01 20 -6.50233205e+01 3.11053735e+01 7.50673839e+01 21 -5.68352503e+01 -3.94196237e+01 3.04492609e+01 22 8.65231347e+01 1.12697764e+02 1.10465944e+02 23 1.94734446e+01 -8.01526998e+00 2.59699051e+01 24 2.20651491e+01 2.10264902e+01 2.80140250e+01 25 -4.69770015e+01 -2.98843789e+01 -1.60678322e+01 26 -2.48907201e+01 7.97297843e+01 -4.41094157e+01 27 7.91926051e+01 -1.54428913e+02 5.75303614e+01 28 -1.35025485e+02 1.23236535e+02 2.85746696e+01 29 -3.63319365e+01 -4.64286235e+01 2.50798486e+01 30 4.06767551e+01 6.90718820e+01 3.73017675e+01 31 6.90656254e+01 -3.10437931e+01 4.41207676e+01 32 3.87696090e+01 6.22660174e+01 6.44955391e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Pt (Configuration in file "config-T-Pt.xyz") ----------------------------------------------------------------------------------------------------- Energy = 422.4216752934138 Forces: 1 -1.59929826e+01 -4.08151842e+01 -4.11259980e+01 2 -3.37511640e+01 3.92927095e+01 -2.55126679e+01 3 2.38212921e+01 -2.06000730e+01 -8.92127663e+00 4 -2.07963136e+01 3.17448446e+01 2.66803763e+01 5 2.65623926e+01 -6.53858581e+01 -9.48386658e+00 6 2.58731406e+01 1.42903318e+01 -2.58536604e+01 7 1.87256341e+01 -1.38014737e+02 -1.36502569e+02 8 -6.59584038e+01 -4.99324742e+01 -2.39809787e+00 9 -5.08372047e+01 -3.16804623e+01 -7.86369963e+01 10 -2.19060857e+01 8.50419690e+01 -8.88261843e+01 11 -2.34008046e+01 -6.59089584e+01 6.23360276e+01 12 -3.85830059e+01 5.12098117e+01 2.33481715e+01 13 -3.40663299e+01 -5.23186045e+01 -1.83156018e+02 14 3.20742030e+01 4.18302545e+01 -2.89936080e+01 15 1.53581074e+02 -4.33546916e+01 3.56928487e+01 16 2.00479889e+01 1.18208686e+02 6.50600029e+01 17 -7.85170682e+01 -5.43476922e+01 -2.86078671e+01 18 6.43977882e+01 8.32429412e+01 -7.92904932e+01 19 2.80432400e+01 -9.24160578e+01 5.72996518e+01 20 -6.50233205e+01 3.11053735e+01 7.50673839e+01 21 -5.68352503e+01 -3.94196237e+01 3.04492609e+01 22 8.65231347e+01 1.12697764e+02 1.10465944e+02 23 1.94734446e+01 -8.01526998e+00 2.59699051e+01 24 2.20651491e+01 2.10264902e+01 2.80140250e+01 25 -4.69770015e+01 -2.98843789e+01 -1.60678322e+01 26 -2.48907201e+01 7.97297843e+01 -4.41094157e+01 27 7.91926051e+01 -1.54428913e+02 5.75303614e+01 28 -1.35025485e+02 1.23236535e+02 2.85746696e+01 29 -3.63319365e+01 -4.64286235e+01 2.50798486e+01 30 4.06767551e+01 6.90718820e+01 3.73017675e+01 31 6.90656254e+01 -3.10437931e+01 4.41207676e+01 32 3.87696090e+01 6.22660174e+01 6.44955391e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==23872== Memcheck, a memory error detector ==23872== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==23872== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==23872== Command: python runner2.py EMT_Asap_Standard_JacobsenStoltzeNorskov_1996_Pt__MO_637493005914_001 ==23872== ==24657== Warning: invalid file descriptor 1048564 in syscall close() ==24657== Warning: invalid file descriptor 1048565 in syscall close() ==24657== Warning: invalid file descriptor 1048566 in syscall close() ==24657== Warning: invalid file descriptor 1048567 in syscall close() ==24657== Use --log-fd= to select an alternative log fd. ==24657== Warning: invalid file descriptor 1048568 in syscall close() ==24657== Warning: invalid file descriptor 1048569 in syscall close() ==24664== Warning: invalid file descriptor 1048564 in syscall close() ==24664== Warning: invalid file descriptor 1048565 in syscall close() ==24664== Warning: invalid file descriptor 1048566 in syscall close() ==24664== Warning: invalid file descriptor 1048567 in syscall close() ==24664== Use --log-fd= to select an alternative log fd. ==24664== Warning: invalid file descriptor 1048568 in syscall close() ==24664== Warning: invalid file descriptor 1048569 in syscall close() ==24736== Warning: invalid file descriptor 1048564 in syscall close() ==24736== Warning: invalid file descriptor 1048565 in syscall close() ==24736== Warning: invalid file descriptor 1048566 in syscall close() ==24736== Warning: invalid file descriptor 1048567 in syscall close() ==24736== Use --log-fd= to select an alternative log fd. ==24736== Warning: invalid file descriptor 1048568 in syscall close() ==24736== Warning: invalid file descriptor 1048569 in syscall close() ==24741== Warning: invalid file descriptor 1048564 in syscall close() ==24741== Warning: invalid file descriptor 1048565 in syscall close() ==24741== Warning: invalid file descriptor 1048566 in syscall close() ==24741== Warning: invalid file descriptor 1048567 in syscall close() ==24741== Use --log-fd= to select an alternative log fd. ==24741== Warning: invalid file descriptor 1048568 in syscall close() ==24741== Warning: invalid file descriptor 1048569 in syscall close() ==24749== Warning: invalid file descriptor 1048564 in syscall close() ==24749== Warning: invalid file descriptor 1048565 in syscall close() ==24749== Warning: invalid file descriptor 1048566 in syscall close() ==24749== Warning: invalid file descriptor 1048567 in syscall close() ==24749== Use --log-fd= to select an alternative log fd. ==24749== Warning: invalid file descriptor 1048568 in syscall close() ==24749== Warning: invalid file descriptor 1048569 in syscall close() ==24755== Warning: invalid file descriptor 1048564 in syscall close() ==24755== Warning: invalid file descriptor 1048565 in syscall close() ==24755== Warning: invalid file descriptor 1048566 in syscall close() ==24755== Warning: invalid file descriptor 1048567 in syscall close() ==24755== Use --log-fd= to select an alternative log fd. ==24755== Warning: invalid file descriptor 1048568 in syscall close() ==24755== Warning: invalid file descriptor 1048569 in syscall close() ==23872== ==23872== HEAP SUMMARY: ==23872== in use at exit: 1,718,292 bytes in 1,321 blocks ==23872== total heap usage: 30,944 allocs, 29,623 frees, 39,187,688 bytes allocated ==23872== ==23872== LEAK SUMMARY: ==23872== definitely lost: 0 bytes in 0 blocks ==23872== indirectly lost: 0 bytes in 0 blocks ==23872== possibly lost: 178,943 bytes in 97 blocks ==23872== still reachable: 1,539,349 bytes in 1,224 blocks ==23872== suppressed: 0 bytes in 0 blocks ==23872== Rerun with --leak-check=full to see details of leaked memory ==23872== ==23872== For counts of detected and suppressed errors, rerun with: -v ==23872== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16344 from 613) ================================================================================ 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.