!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_Ta__MO_568033730744_000 Supported species : Ta random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Ta (Configuration in file "config-F-Ta.xyz") ----------------------------------------------------------------------------------------------------- Energy = 12.26220426988192 Forces: 1 -6.40192208e+00 -1.26357786e+01 -1.31346057e+01 2 -1.37968090e+01 2.24809619e+01 -1.64865148e+01 3 -2.50254918e+00 -2.04876785e+01 -2.38609995e+00 4 -1.13216937e+01 5.17029487e+00 6.13410333e+00 5 2.02454359e+01 -2.93269780e+01 -7.05428997e+00 6 6.69819745e+00 1.29007662e+00 -1.24296330e+01 7 1.38243271e+01 -4.59545071e+01 -4.01213489e+01 8 -2.98179864e+01 -2.99750249e+01 -1.16162133e+01 9 -1.32751917e+01 -2.03922176e+01 -3.23645061e+01 10 -3.70176293e+00 2.83398001e+01 -3.19981463e+01 11 -5.76336388e+00 -2.00821280e+01 1.74408727e+00 12 -2.17011047e+01 2.96714524e+01 1.42568151e+01 13 -5.99129951e+00 -1.46538138e+01 -5.94018594e+01 14 1.11532308e+01 1.07462345e+01 -5.64078295e+00 15 6.75284404e+01 1.73519674e+01 5.45655230e+00 16 1.57496852e+01 4.58527866e+01 1.87565070e+01 17 -1.76799308e+01 -8.55678054e+00 -6.10563093e+00 18 -1.38460943e+01 1.06839107e+01 1.30807973e+01 19 7.77400098e+00 -1.50916270e+01 1.25754094e+01 20 -7.70044289e+00 1.10624232e+01 8.78388620e+00 21 -1.43540128e+01 -2.13653876e+01 1.41028869e+01 22 3.36219205e+01 2.92310631e+01 3.57159311e+01 23 5.61368965e+00 -2.84146405e+00 1.04622575e+01 24 4.02961217e+00 7.35637866e-01 1.11681558e+01 25 -2.32800421e+01 -6.57007490e+00 1.75668890e+01 26 -1.18145710e+01 3.16524791e+01 -1.23766299e+01 27 1.16600274e+01 -4.54118474e+01 1.79176633e+01 28 -3.75619456e+01 3.10588559e+01 6.49325973e+00 29 -7.80113508e+00 -9.37788022e+00 1.54237771e+01 30 1.31919261e+01 1.79054982e+01 -3.70449853e+00 31 2.40924951e+01 -1.43759153e+01 2.05209626e+01 32 1.31288688e+01 2.38656608e+01 2.46608187e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ta (Configuration in file "config-T-Ta.xyz") ----------------------------------------------------------------------------------------------------- Energy = 12.26220426988192 Forces: 1 -6.40192208e+00 -1.26357786e+01 -1.31346057e+01 2 -1.37968090e+01 2.24809619e+01 -1.64865148e+01 3 -2.50254918e+00 -2.04876785e+01 -2.38609995e+00 4 -1.13216937e+01 5.17029487e+00 6.13410333e+00 5 2.02454359e+01 -2.93269780e+01 -7.05428997e+00 6 6.69819745e+00 1.29007662e+00 -1.24296330e+01 7 1.38243271e+01 -4.59545071e+01 -4.01213489e+01 8 -2.98179864e+01 -2.99750249e+01 -1.16162133e+01 9 -1.32751917e+01 -2.03922176e+01 -3.23645061e+01 10 -3.70176293e+00 2.83398001e+01 -3.19981463e+01 11 -5.76336388e+00 -2.00821280e+01 1.74408727e+00 12 -2.17011047e+01 2.96714524e+01 1.42568151e+01 13 -5.99129951e+00 -1.46538138e+01 -5.94018594e+01 14 1.11532308e+01 1.07462345e+01 -5.64078295e+00 15 6.75284404e+01 1.73519674e+01 5.45655230e+00 16 1.57496852e+01 4.58527866e+01 1.87565070e+01 17 -1.76799308e+01 -8.55678054e+00 -6.10563093e+00 18 -1.38460943e+01 1.06839107e+01 1.30807973e+01 19 7.77400098e+00 -1.50916270e+01 1.25754094e+01 20 -7.70044289e+00 1.10624232e+01 8.78388620e+00 21 -1.43540128e+01 -2.13653876e+01 1.41028869e+01 22 3.36219205e+01 2.92310631e+01 3.57159311e+01 23 5.61368965e+00 -2.84146405e+00 1.04622575e+01 24 4.02961217e+00 7.35637866e-01 1.11681558e+01 25 -2.32800421e+01 -6.57007490e+00 1.75668890e+01 26 -1.18145710e+01 3.16524791e+01 -1.23766299e+01 27 1.16600274e+01 -4.54118474e+01 1.79176633e+01 28 -3.75619456e+01 3.10588559e+01 6.49325973e+00 29 -7.80113508e+00 -9.37788022e+00 1.54237771e+01 30 1.31919261e+01 1.79054982e+01 -3.70449853e+00 31 2.40924951e+01 -1.43759153e+01 2.05209626e+01 32 1.31288688e+01 2.38656608e+01 2.46608187e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==94299== Memcheck, a memory error detector ==94299== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==94299== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==94299== Command: python runner2.py EAM_Dynamo_ZhouWadleyJohnson_2001NISTretabulation_Ta__MO_568033730744_000 ==94299== ==96256== Warning: invalid file descriptor 1048564 in syscall close() ==96256== Warning: invalid file descriptor 1048565 in syscall close() ==96256== Warning: invalid file descriptor 1048566 in syscall close() ==96256== Warning: invalid file descriptor 1048567 in syscall close() ==96256== Use --log-fd= to select an alternative log fd. ==96256== Warning: invalid file descriptor 1048568 in syscall close() ==96256== Warning: invalid file descriptor 1048569 in syscall close() ==96264== Warning: invalid file descriptor 1048564 in syscall close() ==96264== Warning: invalid file descriptor 1048565 in syscall close() ==96264== Warning: invalid file descriptor 1048566 in syscall close() ==96264== Warning: invalid file descriptor 1048567 in syscall close() ==96264== Use --log-fd= to select an alternative log fd. ==96264== Warning: invalid file descriptor 1048568 in syscall close() ==96264== Warning: invalid file descriptor 1048569 in syscall close() ==96369== Warning: invalid file descriptor 1048564 in syscall close() ==96369== Warning: invalid file descriptor 1048565 in syscall close() ==96369== Warning: invalid file descriptor 1048566 in syscall close() ==96369== Warning: invalid file descriptor 1048567 in syscall close() ==96369== Use --log-fd= to select an alternative log fd. ==96369== Warning: invalid file descriptor 1048568 in syscall close() ==96369== Warning: invalid file descriptor 1048569 in syscall close() ==96374== Warning: invalid file descriptor 1048564 in syscall close() ==96374== Warning: invalid file descriptor 1048565 in syscall close() ==96374== Warning: invalid file descriptor 1048566 in syscall close() ==96374== Warning: invalid file descriptor 1048567 in syscall close() ==96374== Use --log-fd= to select an alternative log fd. ==96374== Warning: invalid file descriptor 1048568 in syscall close() ==96374== Warning: invalid file descriptor 1048569 in syscall close() ==96375== Warning: invalid file descriptor 1048564 in syscall close() ==96375== Warning: invalid file descriptor 1048565 in syscall close() ==96375== Warning: invalid file descriptor 1048566 in syscall close() ==96375== Warning: invalid file descriptor 1048567 in syscall close() ==96375== Use --log-fd= to select an alternative log fd. ==96375== Warning: invalid file descriptor 1048568 in syscall close() ==96375== Warning: invalid file descriptor 1048569 in syscall close() ==96383== Warning: invalid file descriptor 1048564 in syscall close() ==96383== Warning: invalid file descriptor 1048565 in syscall close() ==96383== Warning: invalid file descriptor 1048566 in syscall close() ==96383== Warning: invalid file descriptor 1048567 in syscall close() ==96383== Use --log-fd= to select an alternative log fd. ==96383== Warning: invalid file descriptor 1048568 in syscall close() ==96383== Warning: invalid file descriptor 1048569 in syscall close() ==94299== ==94299== HEAP SUMMARY: ==94299== in use at exit: 1,718,308 bytes in 1,321 blocks ==94299== total heap usage: 32,186 allocs, 30,865 frees, 42,654,757 bytes allocated ==94299== ==94299== LEAK SUMMARY: ==94299== definitely lost: 0 bytes in 0 blocks ==94299== indirectly lost: 0 bytes in 0 blocks ==94299== possibly lost: 178,943 bytes in 97 blocks ==94299== still reachable: 1,539,365 bytes in 1,224 blocks ==94299== suppressed: 0 bytes in 0 blocks ==94299== Rerun with --leak-check=full to see details of leaked memory ==94299== ==94299== For counts of detected and suppressed errors, rerun with: -v ==94299== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 13374 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.