!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_Dynamo_ZhouWadleyJohnson_2001NISTretabulation_W__MO_914556822329_000 Supported species : W random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = W (Configuration in file "config-F-W.xyz") ----------------------------------------------------------------------------------------------------- Energy = 329.3571002305523 Forces: 1 -1.54331235e+01 -3.19212671e+01 -3.32207456e+01 2 -3.38624344e+01 5.54086668e+01 -3.94581490e+01 3 5.40787307e+00 -2.14075663e+01 9.99473668e+00 4 -1.98429693e+01 2.33616652e+01 2.01555340e+01 5 4.93268259e+01 -7.29325985e+01 -1.22373159e+01 6 1.56368923e+01 5.63019097e+00 -2.57774348e+01 7 2.21389296e+01 -1.05730072e+02 -9.88124939e+01 8 -5.63936297e+01 -4.04734460e+01 2.21040974e+00 9 -4.39839949e+01 -2.52558950e+01 -6.60987892e+01 10 -1.72957468e+01 7.34693740e+01 -7.39471026e+01 11 -2.51620141e+01 -5.87985210e+01 5.01941067e+01 12 -3.55790851e+01 4.44007135e+01 1.94123064e+01 13 -2.03647213e+01 -4.42068981e+01 -1.53319536e+02 14 2.93869059e+01 3.63415524e+01 -2.68628520e+01 15 1.31061057e+02 -3.55116292e+01 2.39454191e+01 16 1.23419260e+01 1.07301404e+02 5.05552228e+01 17 -6.58113148e+01 -4.58767777e+01 -2.31691681e+01 18 5.15422153e+01 6.67112632e+01 -6.32619541e+01 19 2.35824860e+01 -7.67150669e+01 4.82319241e+01 20 -5.44371052e+01 2.62544808e+01 6.10372914e+01 21 -4.67065235e+01 -3.55794955e+01 2.36096491e+01 22 7.18283770e+01 8.24429363e+01 8.00405169e+01 23 1.67227814e+01 -7.44505775e+00 2.39810474e+01 24 1.91015341e+01 1.79067970e+01 2.52726444e+01 25 -4.24426045e+01 -2.51485285e+01 -1.46803044e+01 26 -1.93288642e+01 7.04595791e+01 -3.64000907e+01 27 5.11864038e+01 -1.14622863e+02 5.28235878e+01 28 -9.98990942e+01 8.95157218e+01 2.53180469e+01 29 -2.99191187e+01 -4.29331347e+01 2.65230995e+01 30 3.81276610e+01 5.87906789e+01 3.07488847e+01 31 5.64655811e+01 -2.64350210e+01 3.75940123e+01 32 3.26048942e+01 5.29988150e+01 5.55974964e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = W (Configuration in file "config-T-W.xyz") ----------------------------------------------------------------------------------------------------- Energy = 329.3571002305523 Forces: 1 -1.54331235e+01 -3.19212671e+01 -3.32207456e+01 2 -3.38624344e+01 5.54086668e+01 -3.94581490e+01 3 5.40787307e+00 -2.14075663e+01 9.99473668e+00 4 -1.98429693e+01 2.33616652e+01 2.01555340e+01 5 4.93268259e+01 -7.29325985e+01 -1.22373159e+01 6 1.56368923e+01 5.63019097e+00 -2.57774348e+01 7 2.21389296e+01 -1.05730072e+02 -9.88124939e+01 8 -5.63936297e+01 -4.04734460e+01 2.21040974e+00 9 -4.39839949e+01 -2.52558950e+01 -6.60987892e+01 10 -1.72957468e+01 7.34693740e+01 -7.39471026e+01 11 -2.51620141e+01 -5.87985210e+01 5.01941067e+01 12 -3.55790851e+01 4.44007135e+01 1.94123064e+01 13 -2.03647213e+01 -4.42068981e+01 -1.53319536e+02 14 2.93869059e+01 3.63415524e+01 -2.68628520e+01 15 1.31061057e+02 -3.55116292e+01 2.39454191e+01 16 1.23419260e+01 1.07301404e+02 5.05552228e+01 17 -6.58113148e+01 -4.58767777e+01 -2.31691681e+01 18 5.15422153e+01 6.67112632e+01 -6.32619541e+01 19 2.35824860e+01 -7.67150669e+01 4.82319241e+01 20 -5.44371052e+01 2.62544808e+01 6.10372914e+01 21 -4.67065235e+01 -3.55794955e+01 2.36096491e+01 22 7.18283770e+01 8.24429363e+01 8.00405169e+01 23 1.67227814e+01 -7.44505775e+00 2.39810474e+01 24 1.91015341e+01 1.79067970e+01 2.52726444e+01 25 -4.24426045e+01 -2.51485285e+01 -1.46803044e+01 26 -1.93288642e+01 7.04595791e+01 -3.64000907e+01 27 5.11864038e+01 -1.14622863e+02 5.28235878e+01 28 -9.98990942e+01 8.95157218e+01 2.53180469e+01 29 -2.99191187e+01 -4.29331347e+01 2.65230995e+01 30 3.81276610e+01 5.87906789e+01 3.07488847e+01 31 5.64655811e+01 -2.64350210e+01 3.75940123e+01 32 3.26048942e+01 5.29988150e+01 5.55974964e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==95503== Memcheck, a memory error detector ==95503== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==95503== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==95503== Command: python runner2.py EAM_Dynamo_ZhouWadleyJohnson_2001NISTretabulation_W__MO_914556822329_000 ==95503== ==97211== Warning: invalid file descriptor 1048564 in syscall close() ==97211== Warning: invalid file descriptor 1048565 in syscall close() ==97211== Warning: invalid file descriptor 1048566 in syscall close() ==97211== Warning: invalid file descriptor 1048567 in syscall close() ==97211== Use --log-fd= to select an alternative log fd. ==97211== Warning: invalid file descriptor 1048568 in syscall close() ==97211== Warning: invalid file descriptor 1048569 in syscall close() ==97212== Warning: invalid file descriptor 1048564 in syscall close() ==97212== Warning: invalid file descriptor 1048565 in syscall close() ==97212== Warning: invalid file descriptor 1048566 in syscall close() ==97212== Warning: invalid file descriptor 1048567 in syscall close() ==97212== Use --log-fd= to select an alternative log fd. ==97212== Warning: invalid file descriptor 1048568 in syscall close() ==97212== Warning: invalid file descriptor 1048569 in syscall close() ==97287== Warning: invalid file descriptor 1048564 in syscall close() ==97287== Warning: invalid file descriptor 1048565 in syscall close() ==97287== Warning: invalid file descriptor 1048566 in syscall close() ==97287== Warning: invalid file descriptor 1048567 in syscall close() ==97287== Use --log-fd= to select an alternative log fd. ==97287== Warning: invalid file descriptor 1048568 in syscall close() ==97287== Warning: invalid file descriptor 1048569 in syscall close() ==97292== Warning: invalid file descriptor 1048564 in syscall close() ==97292== Warning: invalid file descriptor 1048565 in syscall close() ==97292== Warning: invalid file descriptor 1048566 in syscall close() ==97292== Warning: invalid file descriptor 1048567 in syscall close() ==97292== Use --log-fd= to select an alternative log fd. ==97292== Warning: invalid file descriptor 1048568 in syscall close() ==97292== Warning: invalid file descriptor 1048569 in syscall close() ==97299== Warning: invalid file descriptor 1048564 in syscall close() ==97299== Warning: invalid file descriptor 1048565 in syscall close() ==97299== Warning: invalid file descriptor 1048566 in syscall close() ==97299== Warning: invalid file descriptor 1048567 in syscall close() ==97299== Use --log-fd= to select an alternative log fd. ==97299== Warning: invalid file descriptor 1048568 in syscall close() ==97299== Warning: invalid file descriptor 1048569 in syscall close() ==97301== Warning: invalid file descriptor 1048564 in syscall close() ==97301== Warning: invalid file descriptor 1048565 in syscall close() ==97301== Warning: invalid file descriptor 1048566 in syscall close() ==97301== Warning: invalid file descriptor 1048567 in syscall close() ==97301== Use --log-fd= to select an alternative log fd. ==97301== Warning: invalid file descriptor 1048568 in syscall close() ==97301== Warning: invalid file descriptor 1048569 in syscall close() ==95503== ==95503== HEAP SUMMARY: ==95503== in use at exit: 1,718,292 bytes in 1,321 blocks ==95503== total heap usage: 31,120 allocs, 29,799 frees, 40,378,460 bytes allocated ==95503== ==95503== LEAK SUMMARY: ==95503== definitely lost: 0 bytes in 0 blocks ==95503== indirectly lost: 0 bytes in 0 blocks ==95503== possibly lost: 178,943 bytes in 97 blocks ==95503== still reachable: 1,539,349 bytes in 1,224 blocks ==95503== suppressed: 0 bytes in 0 blocks ==95503== Rerun with --leak-check=full to see details of leaked memory ==95503== ==95503== For counts of detected and suppressed errors, rerun with: -v ==95503== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 13370 from 596) ================================================================================ 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.