!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_DuLenoskyHennig_2011_Si__SM_662785656123_000 Supported species : Si random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Si (Configuration in file "config-F-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 148.80938429613087 Forces: 1 -7.54997140e+00 -6.08084848e+00 -7.97156077e+00 2 -4.03399025e+00 -8.86133751e+00 -3.49529110e+01 3 -1.52121695e+01 -4.23836131e+01 -6.05148664e+00 4 -2.99950682e+01 -4.91618053e+00 -5.17520319e+00 5 4.76042474e+00 -1.56401107e+01 -1.70097827e+01 6 1.10737580e+01 -6.44510101e+00 -1.66644925e+01 7 2.01794263e+01 -2.36453983e+01 -7.12004186e+00 8 1.34648918e+01 -2.11153052e+01 -1.28879166e+01 9 -1.54505920e+01 2.02989621e+00 -1.95498675e+01 10 -7.53885402e+00 1.97599510e+01 -2.10021043e+01 11 -2.97081925e+01 6.18333203e+00 -1.37430598e+01 12 -1.76416699e+01 1.47713883e+01 -4.86590783e+00 13 1.38784287e+01 7.65676119e+00 -4.49019312e+01 14 1.04793609e+01 9.11129478e+00 -8.13288004e+00 15 4.65874183e+01 1.13577131e+01 -1.18442188e+01 16 8.46464575e+00 4.93762119e+01 -1.25457192e+01 17 -1.39141538e+01 -1.16171473e+01 3.85856800e+00 18 -1.52596562e+01 -1.60200696e+01 1.42232122e+01 19 -3.92335592e+00 -1.24427066e+01 1.43453762e+01 20 -1.19653162e+01 -4.55725197e+00 1.03083545e+01 21 7.69901579e+00 -3.10998567e+01 1.18348263e+01 22 3.54609230e+01 -1.15039456e+01 4.31799126e+00 23 5.99800403e+00 -2.25921726e+00 9.18931048e+00 24 1.32844344e+00 -9.54228304e+00 3.56596935e+01 25 -4.26218821e+01 4.03813300e+00 7.42413412e+00 26 -1.16245609e+01 4.04576192e+01 1.27742854e+01 27 -1.35671363e+01 7.39451465e+00 3.33858391e+01 28 -1.06744195e+01 5.71351720e+00 8.78461079e+00 29 2.02663314e+01 1.42339241e+01 2.54908545e+01 30 2.23843082e+01 1.84548077e+01 7.52974912e+00 31 2.01617816e+01 -1.64544830e-01 2.27128754e+01 32 8.49382661e+00 1.77558536e+01 2.25794033e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Si (Configuration in file "config-T-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 148.80938429613087 Forces: 1 -7.54997140e+00 -6.08084848e+00 -7.97156077e+00 2 -4.03399025e+00 -8.86133751e+00 -3.49529110e+01 3 -1.52121695e+01 -4.23836131e+01 -6.05148664e+00 4 -2.99950682e+01 -4.91618053e+00 -5.17520319e+00 5 4.76042474e+00 -1.56401107e+01 -1.70097827e+01 6 1.10737580e+01 -6.44510101e+00 -1.66644925e+01 7 2.01794263e+01 -2.36453983e+01 -7.12004186e+00 8 1.34648918e+01 -2.11153052e+01 -1.28879166e+01 9 -1.54505920e+01 2.02989621e+00 -1.95498675e+01 10 -7.53885402e+00 1.97599510e+01 -2.10021043e+01 11 -2.97081925e+01 6.18333203e+00 -1.37430598e+01 12 -1.76416699e+01 1.47713883e+01 -4.86590783e+00 13 1.38784287e+01 7.65676119e+00 -4.49019312e+01 14 1.04793609e+01 9.11129478e+00 -8.13288004e+00 15 4.65874183e+01 1.13577131e+01 -1.18442188e+01 16 8.46464575e+00 4.93762119e+01 -1.25457192e+01 17 -1.39141538e+01 -1.16171473e+01 3.85856800e+00 18 -1.52596562e+01 -1.60200696e+01 1.42232122e+01 19 -3.92335592e+00 -1.24427066e+01 1.43453762e+01 20 -1.19653162e+01 -4.55725197e+00 1.03083545e+01 21 7.69901579e+00 -3.10998567e+01 1.18348263e+01 22 3.54609230e+01 -1.15039456e+01 4.31799126e+00 23 5.99800403e+00 -2.25921726e+00 9.18931048e+00 24 1.32844344e+00 -9.54228304e+00 3.56596935e+01 25 -4.26218821e+01 4.03813300e+00 7.42413412e+00 26 -1.16245609e+01 4.04576192e+01 1.27742854e+01 27 -1.35671363e+01 7.39451465e+00 3.33858391e+01 28 -1.06744195e+01 5.71351720e+00 8.78461079e+00 29 2.02663314e+01 1.42339241e+01 2.54908545e+01 30 2.23843082e+01 1.84548077e+01 7.52974912e+00 31 2.01617816e+01 -1.64544830e-01 2.27128754e+01 32 8.49382661e+00 1.77558536e+01 2.25794033e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==64075== Memcheck, a memory error detector ==64075== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==64075== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==64075== Command: python runner2.py Sim_LAMMPS_MEAM_DuLenoskyHennig_2011_Si__SM_662785656123_000 ==64075== ==64771== Warning: invalid file descriptor 1048564 in syscall close() ==64771== Warning: invalid file descriptor 1048565 in syscall close() ==64771== Warning: invalid file descriptor 1048566 in syscall close() ==64771== Warning: invalid file descriptor 1048567 in syscall close() ==64771== Use --log-fd= to select an alternative log fd. ==64771== Warning: invalid file descriptor 1048568 in syscall close() ==64771== Warning: invalid file descriptor 1048569 in syscall close() ==64772== Warning: invalid file descriptor 1048564 in syscall close() ==64772== Warning: invalid file descriptor 1048565 in syscall close() ==64772== Warning: invalid file descriptor 1048566 in syscall close() ==64772== Warning: invalid file descriptor 1048567 in syscall close() ==64772== Use --log-fd= to select an alternative log fd. ==64772== Warning: invalid file descriptor 1048568 in syscall close() ==64772== Warning: invalid file descriptor 1048569 in syscall close() ==64773== Warning: invalid file descriptor 1048564 in syscall close() ==64773== Warning: invalid file descriptor 1048565 in syscall close() ==64773== Warning: invalid file descriptor 1048566 in syscall close() ==64773== Warning: invalid file descriptor 1048567 in syscall close() ==64773== Use --log-fd= to select an alternative log fd. ==64773== Warning: invalid file descriptor 1048568 in syscall close() ==64773== Warning: invalid file descriptor 1048569 in syscall close() ==64774== Warning: invalid file descriptor 1048564 in syscall close() ==64774== Warning: invalid file descriptor 1048565 in syscall close() ==64774== Warning: invalid file descriptor 1048566 in syscall close() ==64774== Warning: invalid file descriptor 1048567 in syscall close() ==64774== Use --log-fd= to select an alternative log fd. ==64774== Warning: invalid file descriptor 1048568 in syscall close() ==64774== Warning: invalid file descriptor 1048569 in syscall close() ==64775== Warning: invalid file descriptor 1048564 in syscall close() ==64775== Warning: invalid file descriptor 1048565 in syscall close() ==64775== Warning: invalid file descriptor 1048566 in syscall close() ==64775== Warning: invalid file descriptor 1048567 in syscall close() ==64775== Use --log-fd= to select an alternative log fd. ==64775== Warning: invalid file descriptor 1048568 in syscall close() ==64775== Warning: invalid file descriptor 1048569 in syscall close() ==64776== Warning: invalid file descriptor 1048564 in syscall close() ==64776== Warning: invalid file descriptor 1048565 in syscall close() ==64776== Warning: invalid file descriptor 1048566 in syscall close() ==64776== Warning: invalid file descriptor 1048567 in syscall close() ==64776== Use --log-fd= to select an alternative log fd. ==64776== Warning: invalid file descriptor 1048568 in syscall close() ==64776== Warning: invalid file descriptor 1048569 in syscall close() ==64777== Warning: invalid file descriptor 1048564 in syscall close() ==64777== Warning: invalid file descriptor 1048565 in syscall close() ==64777== Warning: invalid file descriptor 1048566 in syscall close() ==64777== Warning: invalid file descriptor 1048567 in syscall close() ==64777== Use --log-fd= to select an alternative log fd. ==64777== Warning: invalid file descriptor 1048568 in syscall close() ==64777== Warning: invalid file descriptor 1048569 in syscall close() ==64778== Warning: invalid file descriptor 1048564 in syscall close() ==64778== Warning: invalid file descriptor 1048565 in syscall close() ==64778== Warning: invalid file descriptor 1048566 in syscall close() ==64778== Warning: invalid file descriptor 1048567 in syscall close() ==64778== Use --log-fd= to select an alternative log fd. ==64778== Warning: invalid file descriptor 1048568 in syscall close() ==64778== Warning: invalid file descriptor 1048569 in syscall close() ==64075== ==64075== HEAP SUMMARY: ==64075== in use at exit: 1,780,671 bytes in 1,488 blocks ==64075== total heap usage: 28,445 allocs, 26,957 frees, 42,733,582 bytes allocated ==64075== ==64075== LEAK SUMMARY: ==64075== definitely lost: 0 bytes in 0 blocks ==64075== indirectly lost: 0 bytes in 0 blocks ==64075== possibly lost: 178,423 bytes in 96 blocks ==64075== still reachable: 1,602,248 bytes in 1,392 blocks ==64075== suppressed: 0 bytes in 0 blocks ==64075== Rerun with --leak-check=full to see details of leaked memory ==64075== ==64075== For counts of detected and suppressed errors, rerun with: -v ==64075== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16446 from 605) ================================================================================ 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.