!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_AsadiZaeemNouranian_2015_Fe__SM_042630680993_000 Supported species : Fe random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Fe (Configuration in file "config-F-Fe.xyz") ----------------------------------------------------------------------------------------------------- Energy = -26.938003538837204 Forces: 1 -3.68597978e+00 -4.34419323e+00 -6.00393514e+00 2 -5.16461590e+00 7.04653625e+00 -4.97458808e+00 3 2.17870509e+00 -3.72053830e+00 4.53270706e+00 4 -3.09467606e+00 3.28012791e+00 3.20864152e+00 5 5.74967235e+00 -9.51756498e+00 -3.11108914e+00 6 4.68582527e+00 -2.67230293e+00 -6.73285277e+00 7 6.05122779e+00 -1.70314731e+01 -1.85084308e+01 8 -2.00336161e+01 -1.38286401e+01 1.86909423e+00 9 -5.31267778e+00 -3.10929591e+00 -7.91250019e+00 10 -3.91510437e+00 1.02239746e+01 -1.10176023e+01 11 -4.88943719e+00 -7.48940329e+00 4.10928218e+00 12 -4.69362644e+00 6.18383107e+00 9.81811602e-01 13 -5.13323728e+00 -1.24696646e+00 -2.47178934e+01 14 3.69768023e+00 3.97682225e+00 -1.62856261e+00 15 3.05839948e+01 9.94730405e+00 7.39410420e+00 16 5.05430266e+00 1.63422201e+01 7.89764636e+00 17 -6.41678543e+00 -4.33397685e+00 -3.79425550e+00 18 2.99433254e+00 5.65569099e+00 -6.14064415e+00 19 3.76828512e+00 -7.94588105e+00 6.45118417e+00 20 -4.28826337e+00 3.90840644e+00 5.04529798e+00 21 -1.06727203e+01 -6.55945961e+00 7.31318057e+00 22 1.26244500e+01 9.69155331e+00 1.13604829e+01 23 3.57605873e+00 -4.84227704e-01 5.89598361e+00 24 3.22013174e-01 -2.42567898e+00 3.77440187e+00 25 -7.00289041e+00 -4.37295894e+00 9.17088982e-01 26 -3.57439315e+00 1.11968320e+01 -4.65964438e+00 27 1.29204283e+01 -2.23483247e+01 7.47191514e+00 28 -2.15220262e+01 1.90810256e+01 3.47540525e+00 29 -3.41699864e+00 -4.88937290e+00 3.79575499e+00 30 3.99577343e+00 6.10187791e+00 -1.09945943e+00 31 9.58184465e+00 -4.01486806e+00 6.46536501e+00 32 5.03245426e+00 7.69892459e+00 8.34211023e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Fe (Configuration in file "config-T-Fe.xyz") ----------------------------------------------------------------------------------------------------- Energy = -26.938003538837204 Forces: 1 -3.68597978e+00 -4.34419323e+00 -6.00393514e+00 2 -5.16461590e+00 7.04653625e+00 -4.97458808e+00 3 2.17870509e+00 -3.72053830e+00 4.53270706e+00 4 -3.09467606e+00 3.28012791e+00 3.20864152e+00 5 5.74967235e+00 -9.51756498e+00 -3.11108914e+00 6 4.68582527e+00 -2.67230293e+00 -6.73285277e+00 7 6.05122779e+00 -1.70314731e+01 -1.85084308e+01 8 -2.00336161e+01 -1.38286401e+01 1.86909423e+00 9 -5.31267778e+00 -3.10929591e+00 -7.91250019e+00 10 -3.91510437e+00 1.02239746e+01 -1.10176023e+01 11 -4.88943719e+00 -7.48940329e+00 4.10928218e+00 12 -4.69362644e+00 6.18383107e+00 9.81811602e-01 13 -5.13323728e+00 -1.24696646e+00 -2.47178934e+01 14 3.69768023e+00 3.97682225e+00 -1.62856261e+00 15 3.05839948e+01 9.94730405e+00 7.39410420e+00 16 5.05430266e+00 1.63422201e+01 7.89764636e+00 17 -6.41678543e+00 -4.33397685e+00 -3.79425550e+00 18 2.99433254e+00 5.65569099e+00 -6.14064415e+00 19 3.76828512e+00 -7.94588105e+00 6.45118417e+00 20 -4.28826337e+00 3.90840644e+00 5.04529798e+00 21 -1.06727203e+01 -6.55945961e+00 7.31318057e+00 22 1.26244500e+01 9.69155331e+00 1.13604829e+01 23 3.57605873e+00 -4.84227704e-01 5.89598361e+00 24 3.22013174e-01 -2.42567898e+00 3.77440187e+00 25 -7.00289041e+00 -4.37295894e+00 9.17088982e-01 26 -3.57439315e+00 1.11968320e+01 -4.65964438e+00 27 1.29204283e+01 -2.23483247e+01 7.47191514e+00 28 -2.15220262e+01 1.90810256e+01 3.47540525e+00 29 -3.41699864e+00 -4.88937290e+00 3.79575499e+00 30 3.99577343e+00 6.10187791e+00 -1.09945943e+00 31 9.58184465e+00 -4.01486806e+00 6.46536501e+00 32 5.03245426e+00 7.69892459e+00 8.34211023e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==26576== Memcheck, a memory error detector ==26576== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==26576== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==26576== Command: python runner2.py Sim_LAMMPS_MEAM_AsadiZaeemNouranian_2015_Fe__SM_042630680993_000 ==26576== ==29777== Warning: invalid file descriptor 1048564 in syscall close() ==29777== Warning: invalid file descriptor 1048565 in syscall close() ==29777== Warning: invalid file descriptor 1048566 in syscall close() ==29777== Warning: invalid file descriptor 1048567 in syscall close() ==29777== Use --log-fd= to select an alternative log fd. ==29777== Warning: invalid file descriptor 1048568 in syscall close() ==29777== Warning: invalid file descriptor 1048569 in syscall close() ==29784== Warning: invalid file descriptor 1048564 in syscall close() ==29784== Warning: invalid file descriptor 1048565 in syscall close() ==29784== Warning: invalid file descriptor 1048566 in syscall close() ==29784== Warning: invalid file descriptor 1048567 in syscall close() ==29784== Use --log-fd= to select an alternative log fd. ==29784== Warning: invalid file descriptor 1048568 in syscall close() ==29784== Warning: invalid file descriptor 1048569 in syscall close() ==29797== Warning: invalid file descriptor 1048564 in syscall close() ==29797== Warning: invalid file descriptor 1048565 in syscall close() ==29797== Warning: invalid file descriptor 1048566 in syscall close() ==29797== Warning: invalid file descriptor 1048567 in syscall close() ==29797== Use --log-fd= to select an alternative log fd. ==29797== Warning: invalid file descriptor 1048568 in syscall close() ==29797== Warning: invalid file descriptor 1048569 in syscall close() ==29809== Warning: invalid file descriptor 1048564 in syscall close() ==29809== Warning: invalid file descriptor 1048565 in syscall close() ==29809== Warning: invalid file descriptor 1048566 in syscall close() ==29809== Warning: invalid file descriptor 1048567 in syscall close() ==29809== Use --log-fd= to select an alternative log fd. ==29809== Warning: invalid file descriptor 1048568 in syscall close() ==29809== Warning: invalid file descriptor 1048569 in syscall close() ==29825== Warning: invalid file descriptor 1048564 in syscall close() ==29825== Warning: invalid file descriptor 1048565 in syscall close() ==29825== Warning: invalid file descriptor 1048566 in syscall close() ==29825== Warning: invalid file descriptor 1048567 in syscall close() ==29825== Use --log-fd= to select an alternative log fd. ==29825== Warning: invalid file descriptor 1048568 in syscall close() ==29825== Warning: invalid file descriptor 1048569 in syscall close() ==29834== Warning: invalid file descriptor 1048564 in syscall close() ==29834== Warning: invalid file descriptor 1048565 in syscall close() ==29834== Warning: invalid file descriptor 1048566 in syscall close() ==29834== Warning: invalid file descriptor 1048567 in syscall close() ==29834== Use --log-fd= to select an alternative log fd. ==29834== Warning: invalid file descriptor 1048568 in syscall close() ==29834== Warning: invalid file descriptor 1048569 in syscall close() ==29841== Warning: invalid file descriptor 1048564 in syscall close() ==29841== Warning: invalid file descriptor 1048565 in syscall close() ==29841== Warning: invalid file descriptor 1048566 in syscall close() ==29841== Warning: invalid file descriptor 1048567 in syscall close() ==29841== Use --log-fd= to select an alternative log fd. ==29841== Warning: invalid file descriptor 1048568 in syscall close() ==29841== Warning: invalid file descriptor 1048569 in syscall close() ==29850== Warning: invalid file descriptor 1048564 in syscall close() ==29850== Warning: invalid file descriptor 1048565 in syscall close() ==29850== Warning: invalid file descriptor 1048566 in syscall close() ==29850== Warning: invalid file descriptor 1048567 in syscall close() ==29850== Use --log-fd= to select an alternative log fd. ==29850== Warning: invalid file descriptor 1048568 in syscall close() ==29850== Warning: invalid file descriptor 1048569 in syscall close() ==26576== ==26576== HEAP SUMMARY: ==26576== in use at exit: 1,780,719 bytes in 1,488 blocks ==26576== total heap usage: 28,624 allocs, 27,136 frees, 48,637,497 bytes allocated ==26576== ==26576== LEAK SUMMARY: ==26576== definitely lost: 0 bytes in 0 blocks ==26576== indirectly lost: 0 bytes in 0 blocks ==26576== possibly lost: 178,423 bytes in 96 blocks ==26576== still reachable: 1,602,296 bytes in 1,392 blocks ==26576== suppressed: 0 bytes in 0 blocks ==26576== Rerun with --leak-check=full to see details of leaked memory ==26576== ==26576== For counts of detected and suppressed errors, rerun with: -v ==26576== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16441 from 621) ================================================================================ 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.