!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : Morse_SigmoidalSmoothed_Jelinek_1972_Ar__MO_071460865933_002 Supported species : Ar random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Ar (Configuration in file "config-F-Ar.xyz") ----------------------------------------------------------------------------------------------------- Energy = 4.111448859247961 Forces: 1 -1.22689526e-01 -2.91390627e-01 -1.62725443e-01 2 -6.85262923e-03 7.86685669e-04 -2.68779345e-01 3 -2.48784789e-02 -2.76002275e-01 -7.06726487e-02 4 -2.60571784e-01 9.94462828e-02 8.07385715e-03 5 4.24693398e-02 -2.67386657e-01 -1.47393944e-01 6 1.49472629e-01 -3.67142136e-02 -1.44324435e-01 7 1.27975260e-01 -2.00259797e-01 -1.31602691e-01 8 -1.32464627e-01 -1.87661401e-01 9.83087278e-02 9 -1.10924728e-01 1.64129882e-02 -3.48021201e-01 10 -1.19692217e-01 4.05540928e-01 -3.98324715e-01 11 -7.57825520e-02 -2.02907973e-01 -9.37804364e-02 12 -2.88519565e-01 2.62212056e-01 -5.49748710e-02 13 2.11196196e-01 -4.05598197e-02 -4.69009056e-01 14 1.89182411e-01 1.55098187e-01 -1.44196623e-01 15 3.69701818e-01 -1.08380754e-01 -2.29528420e-01 16 3.69060233e-02 4.37698319e-01 2.02239815e-01 17 -3.41000947e-01 -2.23749322e-01 -5.63473974e-02 18 -5.88020280e-02 1.01152798e-01 -1.99555528e-04 19 1.57942662e-01 -2.47204996e-01 1.95410925e-01 20 -1.59499381e-01 1.34215749e-01 2.78227484e-01 21 2.89621392e-02 -2.75932503e-01 1.77839776e-01 22 3.57990679e-01 -7.35323581e-02 4.42050742e-02 23 1.32775931e-01 -5.30272529e-02 1.56396074e-01 24 1.80880558e-02 -6.68469983e-02 2.11028373e-01 25 -3.80052954e-01 3.09927387e-02 2.29860955e-01 26 -8.94733055e-02 3.26004438e-01 -1.76738776e-02 27 7.66865401e-02 -2.56148292e-01 1.91108742e-01 28 -4.95670247e-01 3.15030267e-01 1.15411740e-01 29 4.94679810e-02 1.40321624e-02 1.01963621e-01 30 3.22578847e-01 3.05802459e-01 -1.88696721e-02 31 2.94147036e-01 4.06009954e-02 3.95995198e-01 32 1.01331421e-01 1.62678183e-01 3.50353968e-01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ar (Configuration in file "config-T-Ar.xyz") ----------------------------------------------------------------------------------------------------- Energy = 4.111448859247961 Forces: 1 -1.22689526e-01 -2.91390627e-01 -1.62725443e-01 2 -6.85262923e-03 7.86685669e-04 -2.68779345e-01 3 -2.48784789e-02 -2.76002275e-01 -7.06726487e-02 4 -2.60571784e-01 9.94462828e-02 8.07385715e-03 5 4.24693398e-02 -2.67386657e-01 -1.47393944e-01 6 1.49472629e-01 -3.67142136e-02 -1.44324435e-01 7 1.27975260e-01 -2.00259797e-01 -1.31602691e-01 8 -1.32464627e-01 -1.87661401e-01 9.83087278e-02 9 -1.10924728e-01 1.64129882e-02 -3.48021201e-01 10 -1.19692217e-01 4.05540928e-01 -3.98324715e-01 11 -7.57825520e-02 -2.02907973e-01 -9.37804364e-02 12 -2.88519565e-01 2.62212056e-01 -5.49748710e-02 13 2.11196196e-01 -4.05598197e-02 -4.69009056e-01 14 1.89182411e-01 1.55098187e-01 -1.44196623e-01 15 3.69701818e-01 -1.08380754e-01 -2.29528420e-01 16 3.69060233e-02 4.37698319e-01 2.02239815e-01 17 -3.41000947e-01 -2.23749322e-01 -5.63473974e-02 18 -5.88020280e-02 1.01152798e-01 -1.99555528e-04 19 1.57942662e-01 -2.47204996e-01 1.95410925e-01 20 -1.59499381e-01 1.34215749e-01 2.78227484e-01 21 2.89621392e-02 -2.75932503e-01 1.77839776e-01 22 3.57990679e-01 -7.35323581e-02 4.42050742e-02 23 1.32775931e-01 -5.30272529e-02 1.56396074e-01 24 1.80880558e-02 -6.68469983e-02 2.11028373e-01 25 -3.80052954e-01 3.09927387e-02 2.29860955e-01 26 -8.94733055e-02 3.26004438e-01 -1.76738776e-02 27 7.66865401e-02 -2.56148292e-01 1.91108742e-01 28 -4.95670247e-01 3.15030267e-01 1.15411740e-01 29 4.94679810e-02 1.40321624e-02 1.01963621e-01 30 3.22578847e-01 3.05802459e-01 -1.88696721e-02 31 2.94147036e-01 4.06009954e-02 3.95995198e-01 32 1.01331421e-01 1.62678183e-01 3.50353968e-01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==73685== Memcheck, a memory error detector ==73685== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==73685== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==73685== Command: python runner2.py Morse_SigmoidalSmoothed_Jelinek_1972_Ar__MO_071460865933_002 ==73685== ==73825== Warning: invalid file descriptor 1048564 in syscall close() ==73825== Warning: invalid file descriptor 1048565 in syscall close() ==73825== Warning: invalid file descriptor 1048566 in syscall close() ==73825== Warning: invalid file descriptor 1048567 in syscall close() ==73825== Use --log-fd= to select an alternative log fd. ==73825== Warning: invalid file descriptor 1048568 in syscall close() ==73825== Warning: invalid file descriptor 1048569 in syscall close() ==73827== Warning: invalid file descriptor 1048564 in syscall close() ==73827== Warning: invalid file descriptor 1048565 in syscall close() ==73827== Warning: invalid file descriptor 1048566 in syscall close() ==73827== Warning: invalid file descriptor 1048567 in syscall close() ==73827== Use --log-fd= to select an alternative log fd. ==73827== Warning: invalid file descriptor 1048568 in syscall close() ==73827== Warning: invalid file descriptor 1048569 in syscall close() ==73841== Warning: invalid file descriptor 1048564 in syscall close() ==73841== Warning: invalid file descriptor 1048565 in syscall close() ==73841== Warning: invalid file descriptor 1048566 in syscall close() ==73841== Warning: invalid file descriptor 1048567 in syscall close() ==73841== Use --log-fd= to select an alternative log fd. ==73841== Warning: invalid file descriptor 1048568 in syscall close() ==73841== Warning: invalid file descriptor 1048569 in syscall close() ==73843== Warning: invalid file descriptor 1048564 in syscall close() ==73843== Warning: invalid file descriptor 1048565 in syscall close() ==73843== Warning: invalid file descriptor 1048566 in syscall close() ==73843== Warning: invalid file descriptor 1048567 in syscall close() ==73843== Use --log-fd= to select an alternative log fd. ==73843== Warning: invalid file descriptor 1048568 in syscall close() ==73843== Warning: invalid file descriptor 1048569 in syscall close() ==73845== Warning: invalid file descriptor 1048564 in syscall close() ==73845== Warning: invalid file descriptor 1048565 in syscall close() ==73845== Warning: invalid file descriptor 1048566 in syscall close() ==73845== Warning: invalid file descriptor 1048567 in syscall close() ==73845== Use --log-fd= to select an alternative log fd. ==73845== Warning: invalid file descriptor 1048568 in syscall close() ==73845== Warning: invalid file descriptor 1048569 in syscall close() ==73849== Warning: invalid file descriptor 1048564 in syscall close() ==73849== Warning: invalid file descriptor 1048565 in syscall close() ==73849== Warning: invalid file descriptor 1048566 in syscall close() ==73849== Warning: invalid file descriptor 1048567 in syscall close() ==73849== Use --log-fd= to select an alternative log fd. ==73849== Warning: invalid file descriptor 1048568 in syscall close() ==73849== Warning: invalid file descriptor 1048569 in syscall close() ==73685== ==73685== HEAP SUMMARY: ==73685== in use at exit: 1,718,308 bytes in 1,321 blocks ==73685== total heap usage: 31,669 allocs, 30,348 frees, 38,331,065 bytes allocated ==73685== ==73685== LEAK SUMMARY: ==73685== definitely lost: 0 bytes in 0 blocks ==73685== indirectly lost: 0 bytes in 0 blocks ==73685== possibly lost: 178,943 bytes in 97 blocks ==73685== still reachable: 1,539,365 bytes in 1,224 blocks ==73685== suppressed: 0 bytes in 0 blocks ==73685== Rerun with --leak-check=full to see details of leaked memory ==73685== ==73685== For counts of detected and suppressed errors, rerun with: -v ==73685== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16367 from 603) ================================================================================ 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.