!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_MendelevAckland_2007_Zr__MO_537826574817_000 Supported species : Zr random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Zr (Configuration in file "config-F-Zr.xyz") ----------------------------------------------------------------------------------------------------- Energy = 593.5664566232813 Forces: 1 -3.58473891e+01 -3.98030330e+01 -4.69479102e+01 2 -1.97717982e+01 2.38112923e+01 -6.05019582e+01 3 -6.26608585e+00 -5.57182159e+01 3.05685862e+01 4 -5.15663426e+01 1.39343138e+01 1.03987412e+01 5 3.59506388e+01 -6.40789813e+01 -3.93282814e+01 6 2.89523899e+01 6.55711695e+00 -4.03258075e+01 7 3.85531501e+01 -9.30627691e+01 -5.53867691e+01 8 -3.54494241e+01 -5.46742413e+01 -1.45603487e+01 9 -4.43489144e+01 -5.06385219e+00 -5.65586471e+01 10 -2.77256224e+01 8.05658719e+01 -6.96605845e+01 11 -3.61218556e+01 -3.25114342e+01 2.47380701e+00 12 -5.20161981e+01 6.83463792e+01 -1.92032142e+01 13 1.65951591e+01 -2.80728507e+01 -1.30497785e+02 14 3.50894920e+01 3.86095803e+01 -3.13290832e+01 15 1.24988127e+02 -4.79775668e+00 -2.02645175e+01 16 2.29973605e+01 1.16372755e+02 2.86044788e+01 17 -6.48154716e+01 -4.70793605e+01 -2.49782246e+01 18 2.82993050e+01 1.46617692e+01 4.07854398e+00 19 2.43903748e+01 -5.65609041e+01 4.53343292e+01 20 -3.86389313e+01 2.97763316e+01 4.95113560e+01 21 -3.77869522e+01 -6.37631823e+01 1.48029101e+01 22 8.70258550e+01 4.54134860e+01 5.28745617e+01 23 4.19185048e+01 -2.48413128e+01 3.67676667e+01 24 -1.43813010e+01 2.33038385e+01 4.20429551e+01 25 -7.03261047e+01 -2.79437614e+01 3.62985902e+01 26 -1.14397701e+01 8.14027780e+01 -8.41919707e+00 27 2.07059341e+01 -8.09470261e+01 5.77677860e+01 28 -7.74837632e+01 6.39246281e+01 3.16638750e+01 29 -2.58366910e+01 -1.97877123e+01 3.30689845e+01 30 5.39683719e+01 6.52570312e+01 2.58943798e+00 31 6.56799752e+01 -2.73450041e+01 7.61843379e+01 32 2.47079771e+01 5.41142262e+01 6.29313808e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Zr (Configuration in file "config-T-Zr.xyz") ----------------------------------------------------------------------------------------------------- Energy = 593.5664566232813 Forces: 1 -3.58473891e+01 -3.98030330e+01 -4.69479102e+01 2 -1.97717982e+01 2.38112923e+01 -6.05019582e+01 3 -6.26608585e+00 -5.57182159e+01 3.05685862e+01 4 -5.15663426e+01 1.39343138e+01 1.03987412e+01 5 3.59506388e+01 -6.40789813e+01 -3.93282814e+01 6 2.89523899e+01 6.55711695e+00 -4.03258075e+01 7 3.85531501e+01 -9.30627691e+01 -5.53867691e+01 8 -3.54494241e+01 -5.46742413e+01 -1.45603487e+01 9 -4.43489144e+01 -5.06385219e+00 -5.65586471e+01 10 -2.77256224e+01 8.05658719e+01 -6.96605845e+01 11 -3.61218556e+01 -3.25114342e+01 2.47380701e+00 12 -5.20161981e+01 6.83463792e+01 -1.92032142e+01 13 1.65951591e+01 -2.80728507e+01 -1.30497785e+02 14 3.50894920e+01 3.86095803e+01 -3.13290832e+01 15 1.24988127e+02 -4.79775668e+00 -2.02645175e+01 16 2.29973605e+01 1.16372755e+02 2.86044788e+01 17 -6.48154716e+01 -4.70793605e+01 -2.49782246e+01 18 2.82993050e+01 1.46617692e+01 4.07854398e+00 19 2.43903748e+01 -5.65609041e+01 4.53343292e+01 20 -3.86389313e+01 2.97763316e+01 4.95113560e+01 21 -3.77869522e+01 -6.37631823e+01 1.48029101e+01 22 8.70258550e+01 4.54134860e+01 5.28745617e+01 23 4.19185048e+01 -2.48413128e+01 3.67676667e+01 24 -1.43813010e+01 2.33038385e+01 4.20429551e+01 25 -7.03261047e+01 -2.79437614e+01 3.62985902e+01 26 -1.14397701e+01 8.14027780e+01 -8.41919707e+00 27 2.07059341e+01 -8.09470261e+01 5.77677860e+01 28 -7.74837632e+01 6.39246281e+01 3.16638750e+01 29 -2.58366910e+01 -1.97877123e+01 3.30689845e+01 30 5.39683719e+01 6.52570312e+01 2.58943798e+00 31 6.56799752e+01 -2.73450041e+01 7.61843379e+01 32 2.47079771e+01 5.41142262e+01 6.29313808e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==42634== Memcheck, a memory error detector ==42634== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==42634== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==42634== Command: python runner2.py EAM_Dynamo_MendelevAckland_2007_Zr__MO_537826574817_000 ==42634== ==43707== Warning: invalid file descriptor 1048564 in syscall close() ==43707== Warning: invalid file descriptor 1048565 in syscall close() ==43707== Warning: invalid file descriptor 1048566 in syscall close() ==43707== Warning: invalid file descriptor 1048567 in syscall close() ==43707== Use --log-fd= to select an alternative log fd. ==43707== Warning: invalid file descriptor 1048568 in syscall close() ==43707== Warning: invalid file descriptor 1048569 in syscall close() ==43708== Warning: invalid file descriptor 1048564 in syscall close() ==43708== Warning: invalid file descriptor 1048565 in syscall close() ==43708== Warning: invalid file descriptor 1048566 in syscall close() ==43708== Warning: invalid file descriptor 1048567 in syscall close() ==43708== Use --log-fd= to select an alternative log fd. ==43708== Warning: invalid file descriptor 1048568 in syscall close() ==43708== Warning: invalid file descriptor 1048569 in syscall close() ==43796== Warning: invalid file descriptor 1048564 in syscall close() ==43796== Warning: invalid file descriptor 1048565 in syscall close() ==43796== Warning: invalid file descriptor 1048566 in syscall close() ==43796== Warning: invalid file descriptor 1048567 in syscall close() ==43796== Use --log-fd= to select an alternative log fd. ==43796== Warning: invalid file descriptor 1048568 in syscall close() ==43796== Warning: invalid file descriptor 1048569 in syscall close() ==43802== Warning: invalid file descriptor 1048564 in syscall close() ==43802== Warning: invalid file descriptor 1048565 in syscall close() ==43802== Warning: invalid file descriptor 1048566 in syscall close() ==43802== Warning: invalid file descriptor 1048567 in syscall close() ==43802== Use --log-fd= to select an alternative log fd. ==43802== Warning: invalid file descriptor 1048568 in syscall close() ==43802== Warning: invalid file descriptor 1048569 in syscall close() ==43809== Warning: invalid file descriptor 1048564 in syscall close() ==43809== Warning: invalid file descriptor 1048565 in syscall close() ==43809== Warning: invalid file descriptor 1048566 in syscall close() ==43809== Warning: invalid file descriptor 1048567 in syscall close() ==43809== Use --log-fd= to select an alternative log fd. ==43809== Warning: invalid file descriptor 1048568 in syscall close() ==43809== Warning: invalid file descriptor 1048569 in syscall close() ==43816== Warning: invalid file descriptor 1048564 in syscall close() ==43816== Warning: invalid file descriptor 1048565 in syscall close() ==43816== Warning: invalid file descriptor 1048566 in syscall close() ==43816== Warning: invalid file descriptor 1048567 in syscall close() ==43816== Use --log-fd= to select an alternative log fd. ==43816== Warning: invalid file descriptor 1048568 in syscall close() ==43816== Warning: invalid file descriptor 1048569 in syscall close() ==42634== ==42634== HEAP SUMMARY: ==42634== in use at exit: 1,718,292 bytes in 1,321 blocks ==42634== total heap usage: 31,120 allocs, 29,799 frees, 47,288,427 bytes allocated ==42634== ==42634== LEAK SUMMARY: ==42634== definitely lost: 0 bytes in 0 blocks ==42634== indirectly lost: 0 bytes in 0 blocks ==42634== possibly lost: 178,943 bytes in 97 blocks ==42634== still reachable: 1,539,349 bytes in 1,224 blocks ==42634== suppressed: 0 bytes in 0 blocks ==42634== Rerun with --leak-check=full to see details of leaked memory ==42634== ==42634== For counts of detected and suppressed errors, rerun with: -v ==42634== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16337 from 612) ================================================================================ 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.