!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_Wagner_2007_Ni__SM_168413969663_000 Supported species : Ni random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Ni (Configuration in file "config-F-Ni.xyz") ----------------------------------------------------------------------------------------------------- Energy = 3332.3300252755016 Forces: 1 1.24536312e+02 5.59117250e+01 -1.46753954e+02 2 -2.13884989e+02 6.92361027e+01 -1.22543108e+02 3 -2.42728128e+02 -3.18396576e+02 4.51373190e+02 4 -1.26055221e+02 1.17682408e+02 8.51248680e+01 5 9.20811258e+01 -8.22181453e+01 -1.23537899e+01 6 -2.79719364e+01 2.24473171e+01 2.45272024e+00 7 1.49392235e+02 -2.70520384e+02 -1.08345218e+02 8 -2.14288369e+02 -2.25026668e+02 2.07452066e+02 9 -1.21994187e+01 -1.03289536e+02 -8.10525176e+01 10 -5.91732471e+01 7.08373816e+01 -1.71460535e+01 11 5.50282149e+01 1.85134169e+01 4.01256211e+01 12 1.77018406e+01 1.98205330e+01 6.04202870e+01 13 -1.20747676e+04 -8.49175686e+03 -2.74749760e+02 14 1.21550058e+04 8.41421217e+03 1.89243277e+02 15 2.62043336e+02 3.57572891e+02 -2.21187529e+01 16 -1.70358853e+01 3.21929095e+01 2.70090237e+01 17 -3.80904376e+03 4.17871892e+03 1.88199267e+03 18 3.65684138e+02 3.87292111e+02 6.78473923e+01 19 7.48588167e+03 -3.03700454e+03 1.04224069e+03 20 -3.75466139e+03 -1.28117007e+03 -3.45315929e+03 21 -3.37323285e+02 -9.89527734e+02 -1.94335393e+03 22 -1.68898964e+02 1.69991867e+02 -4.69254189e+01 23 -7.08657443e+02 1.34779950e+03 9.37503394e+02 24 1.04654690e+03 -3.50551900e+02 1.03085581e+03 25 -2.64050152e+04 2.80183499e+04 7.38484591e+03 26 -4.44047009e+01 2.12134059e+01 3.17658102e+01 27 3.97651473e+04 -1.21099953e+04 3.92298518e+04 28 -1.33315214e+04 -1.59847942e+04 -4.64341569e+04 29 3.13657576e+01 -2.95421667e+01 6.61981953e+00 30 3.17672209e+01 2.78233338e+01 -1.04096323e+02 31 -5.94371295e+00 -1.08598343e+02 3.93251344e+01 32 -2.86071223e+01 5.27765004e+01 5.07054862e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ni (Configuration in file "config-T-Ni.xyz") ----------------------------------------------------------------------------------------------------- Energy = 3332.3300252755016 Forces: 1 1.24536312e+02 5.59117250e+01 -1.46753954e+02 2 -2.13884989e+02 6.92361027e+01 -1.22543108e+02 3 -2.42728128e+02 -3.18396576e+02 4.51373190e+02 4 -1.26055221e+02 1.17682408e+02 8.51248680e+01 5 9.20811258e+01 -8.22181453e+01 -1.23537899e+01 6 -2.79719364e+01 2.24473171e+01 2.45272024e+00 7 1.49392235e+02 -2.70520384e+02 -1.08345218e+02 8 -2.14288369e+02 -2.25026668e+02 2.07452066e+02 9 -1.21994187e+01 -1.03289536e+02 -8.10525176e+01 10 -5.91732471e+01 7.08373816e+01 -1.71460535e+01 11 5.50282149e+01 1.85134169e+01 4.01256211e+01 12 1.77018406e+01 1.98205330e+01 6.04202870e+01 13 -1.20747676e+04 -8.49175686e+03 -2.74749760e+02 14 1.21550058e+04 8.41421217e+03 1.89243277e+02 15 2.62043336e+02 3.57572891e+02 -2.21187529e+01 16 -1.70358853e+01 3.21929095e+01 2.70090237e+01 17 -3.80904376e+03 4.17871892e+03 1.88199267e+03 18 3.65684138e+02 3.87292111e+02 6.78473923e+01 19 7.48588167e+03 -3.03700454e+03 1.04224069e+03 20 -3.75466139e+03 -1.28117007e+03 -3.45315929e+03 21 -3.37323285e+02 -9.89527734e+02 -1.94335393e+03 22 -1.68898964e+02 1.69991867e+02 -4.69254189e+01 23 -7.08657443e+02 1.34779950e+03 9.37503394e+02 24 1.04654690e+03 -3.50551900e+02 1.03085581e+03 25 -2.64050152e+04 2.80183499e+04 7.38484591e+03 26 -4.44047009e+01 2.12134059e+01 3.17658102e+01 27 3.97651473e+04 -1.21099953e+04 3.92298518e+04 28 -1.33315214e+04 -1.59847942e+04 -4.64341569e+04 29 3.13657576e+01 -2.95421667e+01 6.61981953e+00 30 3.17672209e+01 2.78233338e+01 -1.04096323e+02 31 -5.94371295e+00 -1.08598343e+02 3.93251344e+01 32 -2.86071223e+01 5.27765004e+01 5.07054862e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==30658== Memcheck, a memory error detector ==30658== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==30658== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==30658== Command: python runner2.py Sim_LAMMPS_MEAM_Wagner_2007_Ni__SM_168413969663_000 ==30658== ==30864== Warning: invalid file descriptor 1048564 in syscall close() ==30864== Warning: invalid file descriptor 1048565 in syscall close() ==30864== Warning: invalid file descriptor 1048566 in syscall close() ==30864== Warning: invalid file descriptor 1048567 in syscall close() ==30864== Use --log-fd= to select an alternative log fd. ==30864== Warning: invalid file descriptor 1048568 in syscall close() ==30864== Warning: invalid file descriptor 1048569 in syscall close() ==30865== Warning: invalid file descriptor 1048564 in syscall close() ==30865== Warning: invalid file descriptor 1048565 in syscall close() ==30865== Warning: invalid file descriptor 1048566 in syscall close() ==30865== Warning: invalid file descriptor 1048567 in syscall close() ==30865== Use --log-fd= to select an alternative log fd. ==30865== Warning: invalid file descriptor 1048568 in syscall close() ==30865== Warning: invalid file descriptor 1048569 in syscall close() ==30866== Warning: invalid file descriptor 1048564 in syscall close() ==30866== Warning: invalid file descriptor 1048565 in syscall close() ==30866== Warning: invalid file descriptor 1048566 in syscall close() ==30866== Warning: invalid file descriptor 1048567 in syscall close() ==30866== Use --log-fd= to select an alternative log fd. ==30866== Warning: invalid file descriptor 1048568 in syscall close() ==30866== Warning: invalid file descriptor 1048569 in syscall close() ==30867== Warning: invalid file descriptor 1048564 in syscall close() ==30867== Warning: invalid file descriptor 1048565 in syscall close() ==30867== Warning: invalid file descriptor 1048566 in syscall close() ==30867== Warning: invalid file descriptor 1048567 in syscall close() ==30867== Use --log-fd= to select an alternative log fd. ==30867== Warning: invalid file descriptor 1048568 in syscall close() ==30867== Warning: invalid file descriptor 1048569 in syscall close() ==30868== Warning: invalid file descriptor 1048564 in syscall close() ==30868== Warning: invalid file descriptor 1048565 in syscall close() ==30868== Warning: invalid file descriptor 1048566 in syscall close() ==30868== Warning: invalid file descriptor 1048567 in syscall close() ==30868== Use --log-fd= to select an alternative log fd. ==30868== Warning: invalid file descriptor 1048568 in syscall close() ==30868== Warning: invalid file descriptor 1048569 in syscall close() ==30869== Warning: invalid file descriptor 1048564 in syscall close() ==30869== Warning: invalid file descriptor 1048565 in syscall close() ==30869== Warning: invalid file descriptor 1048566 in syscall close() ==30869== Warning: invalid file descriptor 1048567 in syscall close() ==30869== Use --log-fd= to select an alternative log fd. ==30869== Warning: invalid file descriptor 1048568 in syscall close() ==30869== Warning: invalid file descriptor 1048569 in syscall close() ==30870== Warning: invalid file descriptor 1048564 in syscall close() ==30870== Warning: invalid file descriptor 1048565 in syscall close() ==30870== Warning: invalid file descriptor 1048566 in syscall close() ==30870== Warning: invalid file descriptor 1048567 in syscall close() ==30870== Use --log-fd= to select an alternative log fd. ==30870== Warning: invalid file descriptor 1048568 in syscall close() ==30870== Warning: invalid file descriptor 1048569 in syscall close() ==30871== Warning: invalid file descriptor 1048564 in syscall close() ==30871== Warning: invalid file descriptor 1048565 in syscall close() ==30871== Warning: invalid file descriptor 1048566 in syscall close() ==30871== Warning: invalid file descriptor 1048567 in syscall close() ==30871== Use --log-fd= to select an alternative log fd. ==30871== Warning: invalid file descriptor 1048568 in syscall close() ==30871== Warning: invalid file descriptor 1048569 in syscall close() ==30658== ==30658== HEAP SUMMARY: ==30658== in use at exit: 1,780,563 bytes in 1,488 blocks ==30658== total heap usage: 28,788 allocs, 27,300 frees, 48,648,731 bytes allocated ==30658== ==30658== LEAK SUMMARY: ==30658== definitely lost: 0 bytes in 0 blocks ==30658== indirectly lost: 0 bytes in 0 blocks ==30658== possibly lost: 178,423 bytes in 96 blocks ==30658== still reachable: 1,602,140 bytes in 1,392 blocks ==30658== suppressed: 0 bytes in 0 blocks ==30658== Rerun with --leak-check=full to see details of leaked memory ==30658== ==30658== For counts of detected and suppressed errors, rerun with: -v ==30658== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 11327 from 594) ================================================================================ 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.