!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : ThreeBodyCluster_BH_BiswasHamann_1987_Si__MO_019616213550_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 = 459.0574656570972 Forces: 1 -1.96929128e+01 -1.95391902e+01 -2.85529313e+01 2 -1.83286988e+01 -8.52580881e+00 -6.20652568e+01 3 -6.70688639e+00 -6.09131681e+01 -1.45294469e+01 4 -4.87680406e+01 1.26170879e+01 -6.05526471e+00 5 5.66906486e+00 -4.50578665e+01 -3.71790423e+01 6 2.83617703e+01 -4.67157339e+00 -3.37215429e+01 7 4.45480999e+01 -5.60151493e+01 -2.24721054e+01 8 6.84053109e-01 -5.13884989e+01 -2.02191270e+01 9 -3.99689969e+01 -1.42327937e+01 -5.01815603e+01 10 -1.02709517e+01 6.63568207e+01 -6.27765330e+01 11 -6.48441637e+01 -1.22976548e+01 -8.53861352e+00 12 -5.25171624e+01 3.71349368e+01 1.01257102e+01 13 2.86801242e+01 -8.77867046e+00 -1.06447707e+02 14 3.61114339e+01 3.00996330e+01 -2.71017336e+01 15 1.05460031e+02 5.86068450e+00 -1.18132561e+01 16 1.76814488e+01 1.02043990e+02 3.76713694e+00 17 -4.67770443e+01 -3.12559220e+01 2.72479153e+00 18 -2.59831219e+01 -5.84538620e-01 2.45932742e+01 19 9.03020930e-01 -3.81243655e+01 4.29169486e+01 20 -2.64476991e+01 9.54880048e+00 3.27362814e+01 21 6.24939947e+00 -6.55881301e+01 2.03619477e+01 22 7.47493447e+01 -9.89554615e-01 2.00731323e+01 23 2.15871552e+01 -1.54867713e+01 2.52232168e+01 24 1.02137581e+00 -7.49156931e+00 5.70592356e+01 25 -6.61092863e+01 -4.46604728e+00 3.49362699e+00 26 -1.08304654e+01 7.59542572e+01 8.40866371e+00 27 -1.23780180e+01 -2.08359226e+01 5.84403878e+01 28 -3.73968688e+01 2.86214791e+01 2.51109384e+01 29 1.20212688e+01 9.12681526e+00 5.60964141e+01 30 4.03406362e+01 4.11929538e+01 1.04239202e+01 31 4.57901985e+01 6.93002053e+00 4.39749132e+01 32 1.71618917e+01 4.07557165e+01 4.61235811e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Si (Configuration in file "config-T-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 459.0574656570972 Forces: 1 -1.96929128e+01 -1.95391902e+01 -2.85529313e+01 2 -1.83286988e+01 -8.52580881e+00 -6.20652568e+01 3 -6.70688639e+00 -6.09131681e+01 -1.45294469e+01 4 -4.87680406e+01 1.26170879e+01 -6.05526471e+00 5 5.66906486e+00 -4.50578665e+01 -3.71790423e+01 6 2.83617703e+01 -4.67157339e+00 -3.37215429e+01 7 4.45480999e+01 -5.60151493e+01 -2.24721054e+01 8 6.84053109e-01 -5.13884989e+01 -2.02191270e+01 9 -3.99689969e+01 -1.42327937e+01 -5.01815603e+01 10 -1.02709517e+01 6.63568207e+01 -6.27765330e+01 11 -6.48441637e+01 -1.22976548e+01 -8.53861352e+00 12 -5.25171624e+01 3.71349368e+01 1.01257102e+01 13 2.86801242e+01 -8.77867046e+00 -1.06447707e+02 14 3.61114339e+01 3.00996330e+01 -2.71017336e+01 15 1.05460031e+02 5.86068450e+00 -1.18132561e+01 16 1.76814488e+01 1.02043990e+02 3.76713694e+00 17 -4.67770443e+01 -3.12559220e+01 2.72479153e+00 18 -2.59831219e+01 -5.84538620e-01 2.45932742e+01 19 9.03020930e-01 -3.81243655e+01 4.29169486e+01 20 -2.64476991e+01 9.54880048e+00 3.27362814e+01 21 6.24939947e+00 -6.55881301e+01 2.03619477e+01 22 7.47493447e+01 -9.89554615e-01 2.00731323e+01 23 2.15871552e+01 -1.54867713e+01 2.52232168e+01 24 1.02137581e+00 -7.49156931e+00 5.70592356e+01 25 -6.61092863e+01 -4.46604728e+00 3.49362699e+00 26 -1.08304654e+01 7.59542572e+01 8.40866371e+00 27 -1.23780180e+01 -2.08359226e+01 5.84403878e+01 28 -3.73968688e+01 2.86214791e+01 2.51109384e+01 29 1.20212688e+01 9.12681526e+00 5.60964141e+01 30 4.03406362e+01 4.11929538e+01 1.04239202e+01 31 4.57901985e+01 6.93002053e+00 4.39749132e+01 32 1.71618917e+01 4.07557165e+01 4.61235811e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==19893== Memcheck, a memory error detector ==19893== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==19893== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==19893== Command: python runner2.py ThreeBodyCluster_BH_BiswasHamann_1987_Si__MO_019616213550_000 ==19893== ==21737== Warning: invalid file descriptor 1048564 in syscall close() ==21737== Warning: invalid file descriptor 1048565 in syscall close() ==21737== Warning: invalid file descriptor 1048566 in syscall close() ==21737== Warning: invalid file descriptor 1048567 in syscall close() ==21737== Use --log-fd= to select an alternative log fd. ==21737== Warning: invalid file descriptor 1048568 in syscall close() ==21737== Warning: invalid file descriptor 1048569 in syscall close() ==21752== Warning: invalid file descriptor 1048564 in syscall close() ==21752== Warning: invalid file descriptor 1048565 in syscall close() ==21752== Warning: invalid file descriptor 1048566 in syscall close() ==21752== Warning: invalid file descriptor 1048567 in syscall close() ==21752== Use --log-fd= to select an alternative log fd. ==21752== Warning: invalid file descriptor 1048568 in syscall close() ==21752== Warning: invalid file descriptor 1048569 in syscall close() ==21899== Warning: invalid file descriptor 1048564 in syscall close() ==21899== Warning: invalid file descriptor 1048565 in syscall close() ==21899== Warning: invalid file descriptor 1048566 in syscall close() ==21899== Warning: invalid file descriptor 1048567 in syscall close() ==21899== Use --log-fd= to select an alternative log fd. ==21899== Warning: invalid file descriptor 1048568 in syscall close() ==21899== Warning: invalid file descriptor 1048569 in syscall close() ==21905== Warning: invalid file descriptor 1048564 in syscall close() ==21905== Warning: invalid file descriptor 1048565 in syscall close() ==21905== Warning: invalid file descriptor 1048566 in syscall close() ==21905== Warning: invalid file descriptor 1048567 in syscall close() ==21905== Use --log-fd= to select an alternative log fd. ==21905== Warning: invalid file descriptor 1048568 in syscall close() ==21905== Warning: invalid file descriptor 1048569 in syscall close() ==21921== Warning: invalid file descriptor 1048564 in syscall close() ==21921== Warning: invalid file descriptor 1048565 in syscall close() ==21921== Warning: invalid file descriptor 1048566 in syscall close() ==21921== Warning: invalid file descriptor 1048567 in syscall close() ==21921== Use --log-fd= to select an alternative log fd. ==21921== Warning: invalid file descriptor 1048568 in syscall close() ==21921== Warning: invalid file descriptor 1048569 in syscall close() ==21931== Warning: invalid file descriptor 1048564 in syscall close() ==21931== Warning: invalid file descriptor 1048565 in syscall close() ==21931== Warning: invalid file descriptor 1048566 in syscall close() ==21931== Warning: invalid file descriptor 1048567 in syscall close() ==21931== Use --log-fd= to select an alternative log fd. ==21931== Warning: invalid file descriptor 1048568 in syscall close() ==21931== Warning: invalid file descriptor 1048569 in syscall close() ==19893== ==19893== HEAP SUMMARY: ==19893== in use at exit: 1,718,292 bytes in 1,321 blocks ==19893== total heap usage: 31,015 allocs, 29,694 frees, 38,078,641 bytes allocated ==19893== ==19893== LEAK SUMMARY: ==19893== definitely lost: 0 bytes in 0 blocks ==19893== indirectly lost: 0 bytes in 0 blocks ==19893== possibly lost: 178,943 bytes in 97 blocks ==19893== still reachable: 1,539,349 bytes in 1,224 blocks ==19893== suppressed: 0 bytes in 0 blocks ==19893== Rerun with --leak-check=full to see details of leaked memory ==19893== ==19893== For counts of detected and suppressed errors, rerun with: -v ==19893== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16362 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.