!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : Sim_LAMMPS_MEAM_ParkFellingerLenosky_2012_Ta__SM_907764821792_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 = 174.73543909831082 Forces: 1 -1.98575781e+01 -2.24890195e+00 -5.79864510e+00 2 2.10524309e+01 -2.12670715e+01 -4.37001653e+01 3 -1.02438794e+01 -3.76720120e+01 9.23598480e+00 4 -4.41520647e+01 -1.21857228e+01 -1.38285813e+01 5 -1.39943283e+01 -4.91000386e+00 -1.72477080e+01 6 3.05771279e+01 -8.31809061e+00 -2.96666785e+01 7 5.86634694e+00 7.21837889e+00 1.82117408e+01 8 1.49748400e+01 3.59820381e+01 2.30672131e+01 9 -1.00995579e+01 1.69002178e+01 -1.25296248e+01 10 2.45906902e+01 1.45762166e+00 1.12142852e+01 11 -2.76376579e+01 2.53553386e+01 -7.64048278e+00 12 -2.62625058e+01 1.91450020e+01 -4.97266266e+00 13 9.31382312e+00 9.39588123e+00 8.85741429e-01 14 1.50293278e+01 1.24740444e+01 -8.36454922e+00 15 -1.69188044e+01 4.96524536e-01 -2.23662371e+01 16 -2.07812907e+01 9.40866726e+00 -2.01295035e+01 17 -2.12182751e+01 -2.20006420e+01 -5.71213582e+00 18 3.43293896e+01 -1.54879313e+01 8.97071494e+00 19 -9.10511251e+00 -1.91459746e+01 3.18292648e+01 20 -1.53158548e+01 4.32623036e-01 1.39611972e+01 21 1.44753964e+01 -3.32257791e+01 -7.04275501e+00 22 3.05239042e+01 -2.01907071e+01 -8.80671086e+00 23 7.90517703e+00 -6.13722495e+00 9.42084985e+00 24 -4.45764181e+00 -3.14978776e+00 3.11067033e+01 25 -8.54911206e+00 6.02264118e+00 -6.44211363e+00 26 1.83552884e+01 8.22033046e+00 -1.19153981e+01 27 -1.26066362e+01 1.43646384e+01 4.18991882e+01 28 -5.10026135e+00 5.65510692e+00 6.64070746e+00 29 4.24938435e+01 5.20758355e+00 2.12965656e-01 30 2.20686469e+01 1.08848322e+01 3.43262113e+00 31 -1.21116631e+01 8.69331028e+00 -1.32135982e+00 32 -1.31440090e+01 8.62506893e+00 1.73961335e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ta (Configuration in file "config-T-Ta.xyz") ----------------------------------------------------------------------------------------------------- Energy = 174.73543909831082 Forces: 1 -1.98575781e+01 -2.24890195e+00 -5.79864510e+00 2 2.10524309e+01 -2.12670715e+01 -4.37001653e+01 3 -1.02438794e+01 -3.76720120e+01 9.23598480e+00 4 -4.41520647e+01 -1.21857228e+01 -1.38285813e+01 5 -1.39943283e+01 -4.91000386e+00 -1.72477080e+01 6 3.05771279e+01 -8.31809061e+00 -2.96666785e+01 7 5.86634694e+00 7.21837889e+00 1.82117408e+01 8 1.49748400e+01 3.59820381e+01 2.30672131e+01 9 -1.00995579e+01 1.69002178e+01 -1.25296248e+01 10 2.45906902e+01 1.45762166e+00 1.12142852e+01 11 -2.76376579e+01 2.53553386e+01 -7.64048278e+00 12 -2.62625058e+01 1.91450020e+01 -4.97266266e+00 13 9.31382312e+00 9.39588123e+00 8.85741429e-01 14 1.50293278e+01 1.24740444e+01 -8.36454922e+00 15 -1.69188044e+01 4.96524536e-01 -2.23662371e+01 16 -2.07812907e+01 9.40866726e+00 -2.01295035e+01 17 -2.12182751e+01 -2.20006420e+01 -5.71213582e+00 18 3.43293896e+01 -1.54879313e+01 8.97071494e+00 19 -9.10511251e+00 -1.91459746e+01 3.18292648e+01 20 -1.53158548e+01 4.32623036e-01 1.39611972e+01 21 1.44753964e+01 -3.32257791e+01 -7.04275501e+00 22 3.05239042e+01 -2.01907071e+01 -8.80671086e+00 23 7.90517703e+00 -6.13722495e+00 9.42084985e+00 24 -4.45764181e+00 -3.14978776e+00 3.11067033e+01 25 -8.54911206e+00 6.02264118e+00 -6.44211363e+00 26 1.83552884e+01 8.22033046e+00 -1.19153981e+01 27 -1.26066362e+01 1.43646384e+01 4.18991882e+01 28 -5.10026135e+00 5.65510692e+00 6.64070746e+00 29 4.24938435e+01 5.20758355e+00 2.12965656e-01 30 2.20686469e+01 1.08848322e+01 3.43262113e+00 31 -1.21116631e+01 8.69331028e+00 -1.32135982e+00 32 -1.31440090e+01 8.62506893e+00 1.73961335e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==74951== Memcheck, a memory error detector ==74951== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==74951== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==74951== Command: python runner2.py Sim_LAMMPS_MEAM_ParkFellingerLenosky_2012_Ta__SM_907764821792_000 ==74951== ==76858== Warning: invalid file descriptor 1048564 in syscall close() ==76858== Warning: invalid file descriptor 1048565 in syscall close() ==76858== Warning: invalid file descriptor 1048566 in syscall close() ==76858== Warning: invalid file descriptor 1048567 in syscall close() ==76858== Use --log-fd= to select an alternative log fd. ==76858== Warning: invalid file descriptor 1048568 in syscall close() ==76858== Warning: invalid file descriptor 1048569 in syscall close() ==76861== Warning: invalid file descriptor 1048564 in syscall close() ==76861== Warning: invalid file descriptor 1048565 in syscall close() ==76861== Warning: invalid file descriptor 1048566 in syscall close() ==76861== Warning: invalid file descriptor 1048567 in syscall close() ==76861== Use --log-fd= to select an alternative log fd. ==76861== Warning: invalid file descriptor 1048568 in syscall close() ==76861== Warning: invalid file descriptor 1048569 in syscall close() ==76863== Warning: invalid file descriptor 1048564 in syscall close() ==76863== Warning: invalid file descriptor 1048565 in syscall close() ==76863== Warning: invalid file descriptor 1048566 in syscall close() ==76863== Warning: invalid file descriptor 1048567 in syscall close() ==76863== Use --log-fd= to select an alternative log fd. ==76863== Warning: invalid file descriptor 1048568 in syscall close() ==76863== Warning: invalid file descriptor 1048569 in syscall close() ==76865== Warning: invalid file descriptor 1048564 in syscall close() ==76865== Warning: invalid file descriptor 1048565 in syscall close() ==76865== Warning: invalid file descriptor 1048566 in syscall close() ==76865== Warning: invalid file descriptor 1048567 in syscall close() ==76865== Use --log-fd= to select an alternative log fd. ==76865== Warning: invalid file descriptor 1048568 in syscall close() ==76865== Warning: invalid file descriptor 1048569 in syscall close() ==76866== Warning: invalid file descriptor 1048564 in syscall close() ==76866== Warning: invalid file descriptor 1048565 in syscall close() ==76866== Warning: invalid file descriptor 1048566 in syscall close() ==76866== Warning: invalid file descriptor 1048567 in syscall close() ==76866== Use --log-fd= to select an alternative log fd. ==76866== Warning: invalid file descriptor 1048568 in syscall close() ==76866== Warning: invalid file descriptor 1048569 in syscall close() ==76867== Warning: invalid file descriptor 1048564 in syscall close() ==76867== Warning: invalid file descriptor 1048565 in syscall close() ==76867== Warning: invalid file descriptor 1048566 in syscall close() ==76867== Warning: invalid file descriptor 1048567 in syscall close() ==76867== Use --log-fd= to select an alternative log fd. ==76867== Warning: invalid file descriptor 1048568 in syscall close() ==76867== Warning: invalid file descriptor 1048569 in syscall close() ==76872== Warning: invalid file descriptor 1048564 in syscall close() ==76872== Warning: invalid file descriptor 1048565 in syscall close() ==76872== Warning: invalid file descriptor 1048566 in syscall close() ==76872== Warning: invalid file descriptor 1048567 in syscall close() ==76872== Use --log-fd= to select an alternative log fd. ==76872== Warning: invalid file descriptor 1048568 in syscall close() ==76872== Warning: invalid file descriptor 1048569 in syscall close() ==76874== Warning: invalid file descriptor 1048564 in syscall close() ==76874== Warning: invalid file descriptor 1048565 in syscall close() ==76874== Warning: invalid file descriptor 1048566 in syscall close() ==76874== Warning: invalid file descriptor 1048567 in syscall close() ==76874== Use --log-fd= to select an alternative log fd. ==76874== Warning: invalid file descriptor 1048568 in syscall close() ==76874== Warning: invalid file descriptor 1048569 in syscall close() ==74951== ==74951== HEAP SUMMARY: ==74951== in use at exit: 1,780,731 bytes in 1,488 blocks ==74951== total heap usage: 28,449 allocs, 26,961 frees, 42,734,880 bytes allocated ==74951== ==74951== LEAK SUMMARY: ==74951== definitely lost: 0 bytes in 0 blocks ==74951== indirectly lost: 0 bytes in 0 blocks ==74951== possibly lost: 178,423 bytes in 96 blocks ==74951== still reachable: 1,602,308 bytes in 1,392 blocks ==74951== suppressed: 0 bytes in 0 blocks ==74951== Rerun with --leak-check=full to see details of leaked memory ==74951== ==74951== For counts of detected and suppressed errors, rerun with: -v ==74951== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16445 from 620) ================================================================================ 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.