!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_2007v3_Zr__MO_004835508849_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 = 593.5664566558469 Forces: 1 -3.58473807e+01 -3.98030341e+01 -4.69479105e+01 2 -1.97718448e+01 2.38112976e+01 -6.05019583e+01 3 -6.26610568e+00 -5.57182289e+01 3.05685769e+01 4 -5.15663484e+01 1.39343113e+01 1.03987248e+01 5 3.59506348e+01 -6.40789744e+01 -3.93282863e+01 6 2.89523942e+01 6.55712239e+00 -4.03258000e+01 7 3.85531745e+01 -9.30627985e+01 -5.53867716e+01 8 -3.54494046e+01 -5.46742435e+01 -1.45603411e+01 9 -4.43489117e+01 -5.06386525e+00 -5.65586484e+01 10 -2.77256079e+01 8.05658632e+01 -6.96605745e+01 11 -3.61218442e+01 -3.25114246e+01 2.47380345e+00 12 -5.20161910e+01 6.83463700e+01 -1.92032009e+01 13 1.65951504e+01 -2.80728556e+01 -1.30497780e+02 14 3.50894976e+01 3.86095841e+01 -3.13290883e+01 15 1.24988117e+02 -4.79772662e+00 -2.02645325e+01 16 2.29973578e+01 1.16372758e+02 2.86044814e+01 17 -6.48154871e+01 -4.70793637e+01 -2.49782296e+01 18 2.82992778e+01 1.46617850e+01 4.07853005e+00 19 2.43903672e+01 -5.65609040e+01 4.53343319e+01 20 -3.86389217e+01 2.97763434e+01 4.95113570e+01 21 -3.77869148e+01 -6.37632032e+01 1.48029207e+01 22 8.70258612e+01 4.54134843e+01 5.28745485e+01 23 4.19185108e+01 -2.48413183e+01 3.67676753e+01 24 -1.43813066e+01 2.33038512e+01 4.20429585e+01 25 -7.03260865e+01 -2.79437540e+01 3.62985951e+01 26 -1.14397552e+01 8.14027634e+01 -8.41919423e+00 27 2.07059278e+01 -8.09470127e+01 5.77678011e+01 28 -7.74837669e+01 6.39246212e+01 3.16638623e+01 29 -2.58366984e+01 -1.97877030e+01 3.30689911e+01 30 5.39683583e+01 6.52570294e+01 2.58944169e+00 31 6.56799684e+01 -2.73449935e+01 7.61843379e+01 32 2.47079777e+01 5.41142197e+01 6.29313785e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Zr (Configuration in file "config-T-Zr.xyz") ----------------------------------------------------------------------------------------------------- Energy = 593.5664566558469 Forces: 1 -3.58473807e+01 -3.98030341e+01 -4.69479105e+01 2 -1.97718448e+01 2.38112976e+01 -6.05019583e+01 3 -6.26610568e+00 -5.57182289e+01 3.05685769e+01 4 -5.15663484e+01 1.39343113e+01 1.03987248e+01 5 3.59506348e+01 -6.40789744e+01 -3.93282863e+01 6 2.89523942e+01 6.55712239e+00 -4.03258000e+01 7 3.85531745e+01 -9.30627985e+01 -5.53867716e+01 8 -3.54494046e+01 -5.46742435e+01 -1.45603411e+01 9 -4.43489117e+01 -5.06386525e+00 -5.65586484e+01 10 -2.77256079e+01 8.05658632e+01 -6.96605745e+01 11 -3.61218442e+01 -3.25114246e+01 2.47380345e+00 12 -5.20161910e+01 6.83463700e+01 -1.92032009e+01 13 1.65951504e+01 -2.80728556e+01 -1.30497780e+02 14 3.50894976e+01 3.86095841e+01 -3.13290883e+01 15 1.24988117e+02 -4.79772662e+00 -2.02645325e+01 16 2.29973578e+01 1.16372758e+02 2.86044814e+01 17 -6.48154871e+01 -4.70793637e+01 -2.49782296e+01 18 2.82992778e+01 1.46617850e+01 4.07853005e+00 19 2.43903672e+01 -5.65609040e+01 4.53343319e+01 20 -3.86389217e+01 2.97763434e+01 4.95113570e+01 21 -3.77869148e+01 -6.37632032e+01 1.48029207e+01 22 8.70258612e+01 4.54134843e+01 5.28745485e+01 23 4.19185108e+01 -2.48413183e+01 3.67676753e+01 24 -1.43813066e+01 2.33038512e+01 4.20429585e+01 25 -7.03260865e+01 -2.79437540e+01 3.62985951e+01 26 -1.14397552e+01 8.14027634e+01 -8.41919423e+00 27 2.07059278e+01 -8.09470127e+01 5.77678011e+01 28 -7.74837669e+01 6.39246212e+01 3.16638623e+01 29 -2.58366984e+01 -1.97877030e+01 3.30689911e+01 30 5.39683583e+01 6.52570294e+01 2.58944169e+00 31 6.56799684e+01 -2.73449935e+01 7.61843379e+01 32 2.47079777e+01 5.41142197e+01 6.29313785e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==43235== Memcheck, a memory error detector ==43235== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==43235== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==43235== Command: python runner2.py EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_000 ==43235== ==44285== Warning: invalid file descriptor 1048564 in syscall close() ==44285== Warning: invalid file descriptor 1048565 in syscall close() ==44285== Warning: invalid file descriptor 1048566 in syscall close() ==44285== Warning: invalid file descriptor 1048567 in syscall close() ==44285== Use --log-fd= to select an alternative log fd. ==44285== Warning: invalid file descriptor 1048568 in syscall close() ==44285== Warning: invalid file descriptor 1048569 in syscall close() ==44286== Warning: invalid file descriptor 1048564 in syscall close() ==44286== Warning: invalid file descriptor 1048565 in syscall close() ==44286== Warning: invalid file descriptor 1048566 in syscall close() ==44286== Warning: invalid file descriptor 1048567 in syscall close() ==44286== Use --log-fd= to select an alternative log fd. ==44286== Warning: invalid file descriptor 1048568 in syscall close() ==44286== Warning: invalid file descriptor 1048569 in syscall close() ==44296== Warning: invalid file descriptor 1048564 in syscall close() ==44296== Warning: invalid file descriptor 1048565 in syscall close() ==44296== Warning: invalid file descriptor 1048566 in syscall close() ==44296== Warning: invalid file descriptor 1048567 in syscall close() ==44296== Use --log-fd= to select an alternative log fd. ==44296== Warning: invalid file descriptor 1048568 in syscall close() ==44296== Warning: invalid file descriptor 1048569 in syscall close() ==44297== Warning: invalid file descriptor 1048564 in syscall close() ==44297== Warning: invalid file descriptor 1048565 in syscall close() ==44297== Warning: invalid file descriptor 1048566 in syscall close() ==44297== Warning: invalid file descriptor 1048567 in syscall close() ==44297== Use --log-fd= to select an alternative log fd. ==44297== Warning: invalid file descriptor 1048568 in syscall close() ==44297== Warning: invalid file descriptor 1048569 in syscall close() ==44298== Warning: invalid file descriptor 1048564 in syscall close() ==44298== Warning: invalid file descriptor 1048565 in syscall close() ==44298== Warning: invalid file descriptor 1048566 in syscall close() ==44298== Warning: invalid file descriptor 1048567 in syscall close() ==44298== Use --log-fd= to select an alternative log fd. ==44298== Warning: invalid file descriptor 1048568 in syscall close() ==44298== Warning: invalid file descriptor 1048569 in syscall close() ==44299== Warning: invalid file descriptor 1048564 in syscall close() ==44299== Warning: invalid file descriptor 1048565 in syscall close() ==44299== Warning: invalid file descriptor 1048566 in syscall close() ==44299== Warning: invalid file descriptor 1048567 in syscall close() ==44299== Use --log-fd= to select an alternative log fd. ==44299== Warning: invalid file descriptor 1048568 in syscall close() ==44299== Warning: invalid file descriptor 1048569 in syscall close() ==43235== ==43235== HEAP SUMMARY: ==43235== in use at exit: 1,718,292 bytes in 1,321 blocks ==43235== total heap usage: 31,120 allocs, 29,799 frees, 47,288,657 bytes allocated ==43235== ==43235== LEAK SUMMARY: ==43235== definitely lost: 0 bytes in 0 blocks ==43235== indirectly lost: 0 bytes in 0 blocks ==43235== possibly lost: 178,943 bytes in 97 blocks ==43235== still reachable: 1,539,349 bytes in 1,224 blocks ==43235== suppressed: 0 bytes in 0 blocks ==43235== Rerun with --leak-check=full to see details of leaked memory ==43235== ==43235== For counts of detected and suppressed errors, rerun with: -v ==43235== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16327 from 599) ================================================================================ 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.