!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_AcklandTichyVitek_1987v2_Ag__MO_055919219575_000 Supported species : Ag random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Ag (Configuration in file "config-F-Ag.xyz") ----------------------------------------------------------------------------------------------------- Energy = 170.1769806003144 Forces: 1 -7.86921663e+00 -1.38880688e+01 -1.24850032e+01 2 -4.32757778e+00 5.92388327e+00 -1.48490319e+01 3 5.18639953e+00 -1.47462564e+01 -2.31439996e+00 4 -1.37889213e+01 5.41496809e+00 5.15309742e+00 5 9.06661211e-01 -1.95303578e+01 -9.62084627e+00 6 1.25529405e+01 2.43690806e+00 -1.46188643e+01 7 1.27353989e+01 -2.15711325e+01 -9.34135543e+00 8 -9.73896431e+00 -9.13038635e+00 4.45470982e+00 9 -9.58902735e+00 -1.13645776e+01 -2.12453184e+01 10 9.17551529e+00 2.01820060e+01 -1.67100959e+01 11 -1.44154087e+00 -1.24713738e+01 -6.16650944e+00 12 -2.10268508e+01 1.91066103e+01 7.58679387e+00 13 -5.73901629e+00 -4.57807254e+00 -3.42063265e+01 14 1.16936357e+01 1.36392682e+01 -1.10919008e+01 15 3.21140066e+01 -6.41588664e+00 2.96324650e+00 16 -3.25513816e-01 3.24469347e+01 1.84107866e+00 17 -2.16527126e+01 -1.34893291e+01 -4.80664258e+00 18 8.40067699e+00 8.97364526e+00 -1.82912762e+00 19 7.81890226e+00 -1.66520416e+01 1.41287651e+01 20 -1.24537042e+01 8.43657767e+00 1.43324665e+01 21 -1.05171242e+01 -1.40658577e+01 5.57278298e+00 22 1.98527653e+01 1.36704572e+01 8.98265526e+00 23 7.04214466e+00 -4.23921697e+00 1.19822612e+01 24 8.80143706e-01 -3.50430872e+00 1.06263785e+01 25 -2.50292211e+01 -2.31036493e+00 1.00396439e+01 26 -4.74354132e+00 2.71488181e+01 -4.09749470e+00 27 6.75607498e-01 -1.77997970e+01 1.52642412e+01 28 -1.99878381e+01 1.58213178e+01 7.56700771e+00 29 -1.92466862e-01 -1.37404315e+01 8.07095022e+00 30 1.49061465e+01 1.69446947e+01 8.15510949e-01 31 1.84502997e+01 -7.26619443e+00 1.46254604e+01 32 6.03199329e+00 1.66175651e+01 1.93758667e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ag (Configuration in file "config-T-Ag.xyz") ----------------------------------------------------------------------------------------------------- Energy = 170.1769806003144 Forces: 1 -7.86921663e+00 -1.38880688e+01 -1.24850032e+01 2 -4.32757778e+00 5.92388327e+00 -1.48490319e+01 3 5.18639953e+00 -1.47462564e+01 -2.31439996e+00 4 -1.37889213e+01 5.41496809e+00 5.15309742e+00 5 9.06661211e-01 -1.95303578e+01 -9.62084627e+00 6 1.25529405e+01 2.43690806e+00 -1.46188643e+01 7 1.27353989e+01 -2.15711325e+01 -9.34135543e+00 8 -9.73896431e+00 -9.13038635e+00 4.45470982e+00 9 -9.58902735e+00 -1.13645776e+01 -2.12453184e+01 10 9.17551529e+00 2.01820060e+01 -1.67100959e+01 11 -1.44154087e+00 -1.24713738e+01 -6.16650944e+00 12 -2.10268508e+01 1.91066103e+01 7.58679387e+00 13 -5.73901629e+00 -4.57807254e+00 -3.42063265e+01 14 1.16936357e+01 1.36392682e+01 -1.10919008e+01 15 3.21140066e+01 -6.41588664e+00 2.96324650e+00 16 -3.25513816e-01 3.24469347e+01 1.84107866e+00 17 -2.16527126e+01 -1.34893291e+01 -4.80664258e+00 18 8.40067699e+00 8.97364526e+00 -1.82912762e+00 19 7.81890226e+00 -1.66520416e+01 1.41287651e+01 20 -1.24537042e+01 8.43657767e+00 1.43324665e+01 21 -1.05171242e+01 -1.40658577e+01 5.57278298e+00 22 1.98527653e+01 1.36704572e+01 8.98265526e+00 23 7.04214466e+00 -4.23921697e+00 1.19822612e+01 24 8.80143706e-01 -3.50430872e+00 1.06263785e+01 25 -2.50292211e+01 -2.31036493e+00 1.00396439e+01 26 -4.74354132e+00 2.71488181e+01 -4.09749470e+00 27 6.75607498e-01 -1.77997970e+01 1.52642412e+01 28 -1.99878381e+01 1.58213178e+01 7.56700771e+00 29 -1.92466862e-01 -1.37404315e+01 8.07095022e+00 30 1.49061465e+01 1.69446947e+01 8.15510949e-01 31 1.84502997e+01 -7.26619443e+00 1.46254604e+01 32 6.03199329e+00 1.66175651e+01 1.93758667e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==7351== Memcheck, a memory error detector ==7351== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==7351== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==7351== Command: python runner2.py EAM_Dynamo_AcklandTichyVitek_1987v2_Ag__MO_055919219575_000 ==7351== ==8559== Warning: invalid file descriptor 1048564 in syscall close() ==8559== Warning: invalid file descriptor 1048565 in syscall close() ==8559== Warning: invalid file descriptor 1048566 in syscall close() ==8559== Warning: invalid file descriptor 1048567 in syscall close() ==8559== Use --log-fd= to select an alternative log fd. ==8559== Warning: invalid file descriptor 1048568 in syscall close() ==8559== Warning: invalid file descriptor 1048569 in syscall close() ==8560== Warning: invalid file descriptor 1048564 in syscall close() ==8560== Warning: invalid file descriptor 1048565 in syscall close() ==8560== Warning: invalid file descriptor 1048566 in syscall close() ==8560== Warning: invalid file descriptor 1048567 in syscall close() ==8560== Use --log-fd= to select an alternative log fd. ==8560== Warning: invalid file descriptor 1048568 in syscall close() ==8560== Warning: invalid file descriptor 1048569 in syscall close() ==8581== Warning: invalid file descriptor 1048564 in syscall close() ==8581== Warning: invalid file descriptor 1048565 in syscall close() ==8581== Warning: invalid file descriptor 1048566 in syscall close() ==8581== Warning: invalid file descriptor 1048567 in syscall close() ==8581== Use --log-fd= to select an alternative log fd. ==8581== Warning: invalid file descriptor 1048568 in syscall close() ==8581== Warning: invalid file descriptor 1048569 in syscall close() ==8586== Warning: invalid file descriptor 1048564 in syscall close() ==8586== Warning: invalid file descriptor 1048565 in syscall close() ==8586== Warning: invalid file descriptor 1048566 in syscall close() ==8586== Warning: invalid file descriptor 1048567 in syscall close() ==8586== Use --log-fd= to select an alternative log fd. ==8586== Warning: invalid file descriptor 1048568 in syscall close() ==8586== Warning: invalid file descriptor 1048569 in syscall close() ==8590== Warning: invalid file descriptor 1048564 in syscall close() ==8590== Warning: invalid file descriptor 1048565 in syscall close() ==8590== Warning: invalid file descriptor 1048566 in syscall close() ==8590== Warning: invalid file descriptor 1048567 in syscall close() ==8590== Use --log-fd= to select an alternative log fd. ==8590== Warning: invalid file descriptor 1048568 in syscall close() ==8590== Warning: invalid file descriptor 1048569 in syscall close() ==8599== Warning: invalid file descriptor 1048564 in syscall close() ==8599== Warning: invalid file descriptor 1048565 in syscall close() ==8599== Warning: invalid file descriptor 1048566 in syscall close() ==8599== Warning: invalid file descriptor 1048567 in syscall close() ==8599== Use --log-fd= to select an alternative log fd. ==8599== Warning: invalid file descriptor 1048568 in syscall close() ==8599== Warning: invalid file descriptor 1048569 in syscall close() ==7351== ==7351== HEAP SUMMARY: ==7351== in use at exit: 1,718,308 bytes in 1,321 blocks ==7351== total heap usage: 31,217 allocs, 29,896 frees, 47,302,089 bytes allocated ==7351== ==7351== LEAK SUMMARY: ==7351== definitely lost: 0 bytes in 0 blocks ==7351== indirectly lost: 0 bytes in 0 blocks ==7351== possibly lost: 178,943 bytes in 97 blocks ==7351== still reachable: 1,539,365 bytes in 1,224 blocks ==7351== suppressed: 0 bytes in 0 blocks ==7351== Rerun with --leak-check=full to see details of leaked memory ==7351== ==7351== For counts of detected and suppressed errors, rerun with: -v ==7351== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16331 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.