!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : SW_StillingerWeber_1985_Si__MO_405512056662_005 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 = 533.506832247138 Forces: 1 -2.04948361e+01 -2.91919025e+01 -2.63264859e+01 2 -8.04133993e+00 -1.10097731e+01 -6.20205520e+01 3 -1.02395709e+01 -5.74654688e+01 -1.30722707e+01 4 -5.65695595e+01 -1.67768387e+00 -5.08854178e-01 5 5.73599437e+00 -4.26791872e+01 -3.21509847e+01 6 3.50466281e+01 -9.22661000e+00 -3.97247932e+01 7 3.56174263e+01 -6.01646637e+01 -2.81673467e+01 8 9.49408978e-01 -3.56186623e+01 -1.43180135e+00 9 -3.01165774e+01 1.31478277e+01 -4.74969609e+01 10 -1.95557866e+01 4.62453898e+01 -5.11010026e+01 11 -4.22403251e+01 -1.29738051e+00 -1.69251770e+01 12 -4.46145393e+01 4.13379074e+01 -1.34666386e+01 13 2.95210692e+00 9.45003316e+00 -1.00464339e+02 14 2.60723372e+01 2.19809179e+01 -2.30919788e+01 15 1.02397663e+02 8.51819347e+00 -1.40679549e-01 16 1.88893344e+01 8.99930748e+01 -1.58216316e+01 17 -3.68392763e+01 -2.23809160e+01 7.23859078e+00 18 -1.73856849e+01 -7.80403367e+00 2.20899331e+01 19 -3.13197593e-01 -2.54795875e+01 3.44178671e+01 20 -2.12040804e+01 3.15660088e+00 2.22488615e+01 21 5.12561630e+00 -5.28695875e+01 2.14728228e+01 22 6.34180309e+01 6.43499441e+00 2.65051682e+01 23 1.95062230e+01 -1.28056964e+01 2.46644553e+01 24 2.46484419e+00 -1.00123147e+01 5.20409356e+01 25 -6.95962574e+01 -1.15728583e+01 2.43898131e+01 26 -1.91574142e+01 7.41261175e+01 1.13435844e+01 27 -1.14685895e+01 -3.01316941e+01 5.67111251e+01 28 -4.78840740e+01 3.19460970e+01 2.45615574e+01 29 2.15453041e+01 2.87437742e+00 3.90088546e+01 30 4.82924106e+01 3.73484051e+01 5.50852849e+00 31 5.11616906e+01 -5.04947057e+00 4.55365100e+01 32 1.65460900e+01 3.98775543e+01 5.41728889e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Si (Configuration in file "config-T-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 533.506832247138 Forces: 1 -2.04948361e+01 -2.91919025e+01 -2.63264859e+01 2 -8.04133993e+00 -1.10097731e+01 -6.20205520e+01 3 -1.02395709e+01 -5.74654688e+01 -1.30722707e+01 4 -5.65695595e+01 -1.67768387e+00 -5.08854178e-01 5 5.73599437e+00 -4.26791872e+01 -3.21509847e+01 6 3.50466281e+01 -9.22661000e+00 -3.97247932e+01 7 3.56174263e+01 -6.01646637e+01 -2.81673467e+01 8 9.49408978e-01 -3.56186623e+01 -1.43180135e+00 9 -3.01165774e+01 1.31478277e+01 -4.74969609e+01 10 -1.95557866e+01 4.62453898e+01 -5.11010026e+01 11 -4.22403251e+01 -1.29738051e+00 -1.69251770e+01 12 -4.46145393e+01 4.13379074e+01 -1.34666386e+01 13 2.95210692e+00 9.45003316e+00 -1.00464339e+02 14 2.60723372e+01 2.19809179e+01 -2.30919788e+01 15 1.02397663e+02 8.51819347e+00 -1.40679549e-01 16 1.88893344e+01 8.99930748e+01 -1.58216316e+01 17 -3.68392763e+01 -2.23809160e+01 7.23859078e+00 18 -1.73856849e+01 -7.80403367e+00 2.20899331e+01 19 -3.13197593e-01 -2.54795875e+01 3.44178671e+01 20 -2.12040804e+01 3.15660088e+00 2.22488615e+01 21 5.12561630e+00 -5.28695875e+01 2.14728228e+01 22 6.34180309e+01 6.43499441e+00 2.65051682e+01 23 1.95062230e+01 -1.28056964e+01 2.46644553e+01 24 2.46484419e+00 -1.00123147e+01 5.20409356e+01 25 -6.95962574e+01 -1.15728583e+01 2.43898131e+01 26 -1.91574142e+01 7.41261175e+01 1.13435844e+01 27 -1.14685895e+01 -3.01316941e+01 5.67111251e+01 28 -4.78840740e+01 3.19460970e+01 2.45615574e+01 29 2.15453041e+01 2.87437742e+00 3.90088546e+01 30 4.82924106e+01 3.73484051e+01 5.50852849e+00 31 5.11616906e+01 -5.04947057e+00 4.55365100e+01 32 1.65460900e+01 3.98775543e+01 5.41728889e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==78592== Memcheck, a memory error detector ==78592== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==78592== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==78592== Command: python runner2.py SW_StillingerWeber_1985_Si__MO_405512056662_005 ==78592== ==79813== Warning: invalid file descriptor 1048564 in syscall close() ==79813== Warning: invalid file descriptor 1048565 in syscall close() ==79813== Warning: invalid file descriptor 1048566 in syscall close() ==79813== Warning: invalid file descriptor 1048567 in syscall close() ==79813== Use --log-fd= to select an alternative log fd. ==79813== Warning: invalid file descriptor 1048568 in syscall close() ==79813== Warning: invalid file descriptor 1048569 in syscall close() ==79814== Warning: invalid file descriptor 1048564 in syscall close() ==79814== Warning: invalid file descriptor 1048565 in syscall close() ==79814== Warning: invalid file descriptor 1048566 in syscall close() ==79814== Warning: invalid file descriptor 1048567 in syscall close() ==79814== Use --log-fd= to select an alternative log fd. ==79814== Warning: invalid file descriptor 1048568 in syscall close() ==79814== Warning: invalid file descriptor 1048569 in syscall close() ==79815== Warning: invalid file descriptor 1048564 in syscall close() ==79815== Warning: invalid file descriptor 1048565 in syscall close() ==79815== Warning: invalid file descriptor 1048566 in syscall close() ==79815== Warning: invalid file descriptor 1048567 in syscall close() ==79815== Use --log-fd= to select an alternative log fd. ==79815== Warning: invalid file descriptor 1048568 in syscall close() ==79815== Warning: invalid file descriptor 1048569 in syscall close() ==79816== Warning: invalid file descriptor 1048564 in syscall close() ==79816== Warning: invalid file descriptor 1048565 in syscall close() ==79816== Warning: invalid file descriptor 1048566 in syscall close() ==79816== Warning: invalid file descriptor 1048567 in syscall close() ==79816== Use --log-fd= to select an alternative log fd. ==79816== Warning: invalid file descriptor 1048568 in syscall close() ==79816== Warning: invalid file descriptor 1048569 in syscall close() ==79817== Warning: invalid file descriptor 1048564 in syscall close() ==79817== Warning: invalid file descriptor 1048565 in syscall close() ==79817== Warning: invalid file descriptor 1048566 in syscall close() ==79817== Warning: invalid file descriptor 1048567 in syscall close() ==79817== Use --log-fd= to select an alternative log fd. ==79817== Warning: invalid file descriptor 1048568 in syscall close() ==79817== Warning: invalid file descriptor 1048569 in syscall close() ==79818== Warning: invalid file descriptor 1048564 in syscall close() ==79818== Warning: invalid file descriptor 1048565 in syscall close() ==79818== Warning: invalid file descriptor 1048566 in syscall close() ==79818== Warning: invalid file descriptor 1048567 in syscall close() ==79818== Use --log-fd= to select an alternative log fd. ==79818== Warning: invalid file descriptor 1048568 in syscall close() ==79818== Warning: invalid file descriptor 1048569 in syscall close() ==78592== ==78592== HEAP SUMMARY: ==78592== in use at exit: 1,718,308 bytes in 1,321 blocks ==78592== total heap usage: 31,346 allocs, 30,025 frees, 38,179,813 bytes allocated ==78592== ==78592== LEAK SUMMARY: ==78592== definitely lost: 0 bytes in 0 blocks ==78592== indirectly lost: 0 bytes in 0 blocks ==78592== possibly lost: 178,943 bytes in 97 blocks ==78592== still reachable: 1,539,365 bytes in 1,224 blocks ==78592== suppressed: 0 bytes in 0 blocks ==78592== Rerun with --leak-check=full to see details of leaked memory ==78592== ==78592== For counts of detected and suppressed errors, rerun with: -v ==78592== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 11250 from 588) ================================================================================ 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.