!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : EAM_Dynamo_ZhouWadleyJohnson_2001_Pt__MO_102190350384_005 Supported species : Pt random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Pt (Configuration in file "config-F-Pt.xyz") ----------------------------------------------------------------------------------------------------- Energy = 91.8126263894708 Forces: 1 -1.08494195e+01 -1.29201988e+01 -1.65211470e+01 2 -8.02249431e+00 1.25660246e+01 -1.95645933e+01 3 -2.14035963e+00 -1.70684299e+01 1.08799511e+01 4 -1.46318045e+01 9.79095309e+00 5.12178388e+00 5 1.58161059e+01 -2.27258025e+01 -1.39248472e+01 6 8.64629535e+00 2.07878137e+00 -1.36220773e+01 7 1.44577212e+01 -3.66500941e+01 -2.36646598e+01 8 -1.58592883e+01 -2.53015758e+01 -8.51561702e+00 9 -9.58950184e+00 -1.20861574e+01 -2.22008819e+01 10 -7.18673670e+00 2.40706971e+01 -2.60968236e+01 11 -1.95903168e+01 -1.65602346e+01 -1.87320282e+01 12 -1.86587477e+01 1.94287428e+01 8.71390675e+00 13 2.40881676e+00 -1.34310499e+01 -5.07828200e+01 14 1.09054212e+01 1.07352010e+01 -9.64268041e+00 15 5.06664725e+01 -4.15445013e-01 -6.63349695e+00 16 9.84719858e+00 5.02915977e+01 5.10592137e+00 17 -1.90357013e+01 -1.10518705e+01 -3.41948008e+00 18 2.74501922e+00 3.98352333e+00 -5.70045587e+00 19 8.35426128e+00 -2.48725042e+01 1.74204635e+01 20 -1.62623377e+01 9.92670799e+00 1.26284676e+01 21 -1.30413297e+01 -2.04268132e+01 1.28597825e+01 22 3.19797644e+01 1.63019270e+01 2.41600899e+01 23 5.61687847e+00 -3.27002499e+00 9.90031238e+00 24 3.82079007e+00 -1.05737878e+01 1.75630451e+01 25 -3.66779265e+01 -4.17820169e+00 6.61357807e+00 26 -1.22537247e+01 4.40645842e+01 -1.94395026e+00 27 -4.88953073e+00 -2.41736339e+01 2.73338091e+01 28 -2.51673293e+01 1.96585288e+01 1.04750665e+01 29 1.02306984e+01 -1.00733054e+01 2.36337456e+01 30 1.77971649e+01 2.11304055e+01 9.06567102e+00 31 2.49107047e+01 -3.69136053e+00 1.47321086e+01 32 1.56532360e+01 2.54428157e+01 2.47578559e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Pt (Configuration in file "config-T-Pt.xyz") ----------------------------------------------------------------------------------------------------- Energy = 91.8126263894708 Forces: 1 -1.08494195e+01 -1.29201988e+01 -1.65211470e+01 2 -8.02249431e+00 1.25660246e+01 -1.95645933e+01 3 -2.14035963e+00 -1.70684299e+01 1.08799511e+01 4 -1.46318045e+01 9.79095309e+00 5.12178388e+00 5 1.58161059e+01 -2.27258025e+01 -1.39248472e+01 6 8.64629535e+00 2.07878137e+00 -1.36220773e+01 7 1.44577212e+01 -3.66500941e+01 -2.36646598e+01 8 -1.58592883e+01 -2.53015758e+01 -8.51561702e+00 9 -9.58950184e+00 -1.20861574e+01 -2.22008819e+01 10 -7.18673670e+00 2.40706971e+01 -2.60968236e+01 11 -1.95903168e+01 -1.65602346e+01 -1.87320282e+01 12 -1.86587477e+01 1.94287428e+01 8.71390675e+00 13 2.40881676e+00 -1.34310499e+01 -5.07828200e+01 14 1.09054212e+01 1.07352010e+01 -9.64268041e+00 15 5.06664725e+01 -4.15445013e-01 -6.63349695e+00 16 9.84719858e+00 5.02915977e+01 5.10592137e+00 17 -1.90357013e+01 -1.10518705e+01 -3.41948008e+00 18 2.74501922e+00 3.98352333e+00 -5.70045587e+00 19 8.35426128e+00 -2.48725042e+01 1.74204635e+01 20 -1.62623377e+01 9.92670799e+00 1.26284676e+01 21 -1.30413297e+01 -2.04268132e+01 1.28597825e+01 22 3.19797644e+01 1.63019270e+01 2.41600899e+01 23 5.61687847e+00 -3.27002499e+00 9.90031238e+00 24 3.82079007e+00 -1.05737878e+01 1.75630451e+01 25 -3.66779265e+01 -4.17820169e+00 6.61357807e+00 26 -1.22537247e+01 4.40645842e+01 -1.94395026e+00 27 -4.88953073e+00 -2.41736339e+01 2.73338091e+01 28 -2.51673293e+01 1.96585288e+01 1.04750665e+01 29 1.02306984e+01 -1.00733054e+01 2.36337456e+01 30 1.77971649e+01 2.11304055e+01 9.06567102e+00 31 2.49107047e+01 -3.69136053e+00 1.47321086e+01 32 1.56532360e+01 2.54428157e+01 2.47578559e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==98494== Memcheck, a memory error detector ==98494== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==98494== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==98494== Command: python runner2.py EAM_Dynamo_ZhouWadleyJohnson_2001_Pt__MO_102190350384_005 ==98494== ==99932== Warning: invalid file descriptor 1048564 in syscall close() ==99932== Warning: invalid file descriptor 1048565 in syscall close() ==99932== Warning: invalid file descriptor 1048566 in syscall close() ==99932== Warning: invalid file descriptor 1048567 in syscall close() ==99932== Use --log-fd= to select an alternative log fd. ==99932== Warning: invalid file descriptor 1048568 in syscall close() ==99932== Warning: invalid file descriptor 1048569 in syscall close() ==99942== Warning: invalid file descriptor 1048564 in syscall close() ==99942== Warning: invalid file descriptor 1048565 in syscall close() ==99942== Warning: invalid file descriptor 1048566 in syscall close() ==99942== Warning: invalid file descriptor 1048567 in syscall close() ==99942== Use --log-fd= to select an alternative log fd. ==99942== Warning: invalid file descriptor 1048568 in syscall close() ==99942== Warning: invalid file descriptor 1048569 in syscall close() ==362== Warning: invalid file descriptor 1048564 in syscall close() ==362== Warning: invalid file descriptor 1048565 in syscall close() ==362== Warning: invalid file descriptor 1048566 in syscall close() ==362== Warning: invalid file descriptor 1048567 in syscall close() ==362== Use --log-fd= to select an alternative log fd. ==362== Warning: invalid file descriptor 1048568 in syscall close() ==362== Warning: invalid file descriptor 1048569 in syscall close() ==368== Warning: invalid file descriptor 1048564 in syscall close() ==368== Warning: invalid file descriptor 1048565 in syscall close() ==368== Warning: invalid file descriptor 1048566 in syscall close() ==368== Warning: invalid file descriptor 1048567 in syscall close() ==368== Use --log-fd= to select an alternative log fd. ==368== Warning: invalid file descriptor 1048568 in syscall close() ==368== Warning: invalid file descriptor 1048569 in syscall close() ==375== Warning: invalid file descriptor 1048564 in syscall close() ==375== Warning: invalid file descriptor 1048565 in syscall close() ==375== Warning: invalid file descriptor 1048566 in syscall close() ==375== Warning: invalid file descriptor 1048567 in syscall close() ==375== Use --log-fd= to select an alternative log fd. ==375== Warning: invalid file descriptor 1048568 in syscall close() ==375== Warning: invalid file descriptor 1048569 in syscall close() ==381== Warning: invalid file descriptor 1048564 in syscall close() ==381== Warning: invalid file descriptor 1048565 in syscall close() ==381== Warning: invalid file descriptor 1048566 in syscall close() ==381== Warning: invalid file descriptor 1048567 in syscall close() ==381== Use --log-fd= to select an alternative log fd. ==381== Warning: invalid file descriptor 1048568 in syscall close() ==381== Warning: invalid file descriptor 1048569 in syscall close() ==98494== ==98494== HEAP SUMMARY: ==98494== in use at exit: 1,718,292 bytes in 1,321 blocks ==98494== total heap usage: 31,120 allocs, 29,799 frees, 40,376,686 bytes allocated ==98494== ==98494== LEAK SUMMARY: ==98494== definitely lost: 0 bytes in 0 blocks ==98494== indirectly lost: 0 bytes in 0 blocks ==98494== possibly lost: 178,943 bytes in 97 blocks ==98494== still reachable: 1,539,349 bytes in 1,224 blocks ==98494== suppressed: 0 bytes in 0 blocks ==98494== Rerun with --leak-check=full to see details of leaked memory ==98494== ==98494== For counts of detected and suppressed errors, rerun with: -v ==98494== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16338 from 599) ================================================================================ 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.