!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_ZopeMishin_2003_Al__MO_664470114311_005 Supported species : Al random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Al (Configuration in file "config-F-Al.xyz") ----------------------------------------------------------------------------------------------------- Energy = -27.761862732486225 Forces: 1 -1.95102485e+00 -2.10367614e+00 -2.58474938e+00 2 -9.11778305e-01 1.82615395e+00 -4.42878341e+00 3 1.04169289e+00 -3.85492454e+00 2.39685025e-01 4 -3.60410345e+00 1.62802809e+00 1.10020801e+00 5 1.72868324e+00 -4.65210113e+00 -1.70390202e+00 6 2.13735717e+00 1.19157729e+00 -2.86000879e+00 7 2.26438538e+00 -5.69590762e+00 -3.64019376e+00 8 -2.58157300e+00 -1.48317705e+00 -1.22254109e-01 9 -4.21016704e+00 -1.94649383e+00 -5.46388605e+00 10 -2.26193676e-01 6.80741526e+00 -5.76808686e+00 11 -3.06451581e+00 -5.34253948e+00 3.00956686e+00 12 -4.85335735e+00 3.99260640e+00 1.42215516e+00 13 4.35882543e+00 -2.36008288e+00 -7.88017455e+00 14 1.50620768e+00 1.36040053e+00 -1.61009906e+00 15 6.52350258e+00 -8.02393101e-01 -3.02882114e+00 16 1.97884683e+00 7.83158229e+00 3.54283466e+00 17 -4.87295734e+00 -2.79864212e+00 -1.16118702e+00 18 1.44411713e+00 3.10726771e+00 -1.65853585e+00 19 1.22118947e+00 -4.86536234e+00 3.53999910e+00 20 -3.06528731e+00 2.45759273e+00 3.08063355e+00 21 -2.16638609e+00 -4.59034522e+00 8.74777070e-01 22 6.04507757e+00 3.21536892e+00 2.88000471e+00 23 1.83071099e+00 -8.43758939e-01 2.77002775e+00 24 8.60009764e-01 1.72533832e+00 3.48156089e+00 25 -4.57703996e+00 -3.11642259e+00 -1.15142756e+00 26 1.43727943e+00 6.22311398e+00 -2.22180191e+00 27 1.75383447e+00 -5.59125170e+00 4.96582014e+00 28 -5.80198412e+00 4.12926352e+00 2.99282678e+00 29 -2.95782763e+00 -2.40906237e+00 2.65386174e+00 30 3.44719762e+00 5.43477872e+00 4.22421506e-01 31 3.79912700e+00 -2.53667889e+00 4.45851642e+00 32 1.46615128e+00 4.06233222e+00 3.84901211e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Al (Configuration in file "config-T-Al.xyz") ----------------------------------------------------------------------------------------------------- Energy = -27.761862732486225 Forces: 1 -1.95102485e+00 -2.10367614e+00 -2.58474938e+00 2 -9.11778305e-01 1.82615395e+00 -4.42878341e+00 3 1.04169289e+00 -3.85492454e+00 2.39685025e-01 4 -3.60410345e+00 1.62802809e+00 1.10020801e+00 5 1.72868324e+00 -4.65210113e+00 -1.70390202e+00 6 2.13735717e+00 1.19157729e+00 -2.86000879e+00 7 2.26438538e+00 -5.69590762e+00 -3.64019376e+00 8 -2.58157300e+00 -1.48317705e+00 -1.22254109e-01 9 -4.21016704e+00 -1.94649383e+00 -5.46388605e+00 10 -2.26193676e-01 6.80741526e+00 -5.76808686e+00 11 -3.06451581e+00 -5.34253948e+00 3.00956686e+00 12 -4.85335735e+00 3.99260640e+00 1.42215516e+00 13 4.35882543e+00 -2.36008288e+00 -7.88017455e+00 14 1.50620768e+00 1.36040053e+00 -1.61009906e+00 15 6.52350258e+00 -8.02393101e-01 -3.02882114e+00 16 1.97884683e+00 7.83158229e+00 3.54283466e+00 17 -4.87295734e+00 -2.79864212e+00 -1.16118702e+00 18 1.44411713e+00 3.10726771e+00 -1.65853585e+00 19 1.22118947e+00 -4.86536234e+00 3.53999910e+00 20 -3.06528731e+00 2.45759273e+00 3.08063355e+00 21 -2.16638609e+00 -4.59034522e+00 8.74777070e-01 22 6.04507757e+00 3.21536892e+00 2.88000471e+00 23 1.83071099e+00 -8.43758939e-01 2.77002775e+00 24 8.60009764e-01 1.72533832e+00 3.48156089e+00 25 -4.57703996e+00 -3.11642259e+00 -1.15142756e+00 26 1.43727943e+00 6.22311398e+00 -2.22180191e+00 27 1.75383447e+00 -5.59125170e+00 4.96582014e+00 28 -5.80198412e+00 4.12926352e+00 2.99282678e+00 29 -2.95782763e+00 -2.40906237e+00 2.65386174e+00 30 3.44719762e+00 5.43477872e+00 4.22421506e-01 31 3.79912700e+00 -2.53667889e+00 4.45851642e+00 32 1.46615128e+00 4.06233222e+00 3.84901211e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==773== Memcheck, a memory error detector ==773== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==773== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==773== Command: python runner2.py EAM_Dynamo_ZopeMishin_2003_Al__MO_664470114311_005 ==773== ==2715== Warning: invalid file descriptor 1048564 in syscall close() ==2715== Warning: invalid file descriptor 1048565 in syscall close() ==2715== Warning: invalid file descriptor 1048566 in syscall close() ==2715== Warning: invalid file descriptor 1048567 in syscall close() ==2715== Use --log-fd= to select an alternative log fd. ==2715== Warning: invalid file descriptor 1048568 in syscall close() ==2715== Warning: invalid file descriptor 1048569 in syscall close() ==2718== Warning: invalid file descriptor 1048564 in syscall close() ==2718== Warning: invalid file descriptor 1048565 in syscall close() ==2718== Warning: invalid file descriptor 1048566 in syscall close() ==2718== Warning: invalid file descriptor 1048567 in syscall close() ==2718== Use --log-fd= to select an alternative log fd. ==2718== Warning: invalid file descriptor 1048568 in syscall close() ==2718== Warning: invalid file descriptor 1048569 in syscall close() ==2866== Warning: invalid file descriptor 1048564 in syscall close() ==2866== Warning: invalid file descriptor 1048565 in syscall close() ==2866== Warning: invalid file descriptor 1048566 in syscall close() ==2866== Warning: invalid file descriptor 1048567 in syscall close() ==2866== Use --log-fd= to select an alternative log fd. ==2866== Warning: invalid file descriptor 1048568 in syscall close() ==2866== Warning: invalid file descriptor 1048569 in syscall close() ==2873== Warning: invalid file descriptor 1048564 in syscall close() ==2873== Warning: invalid file descriptor 1048565 in syscall close() ==2873== Warning: invalid file descriptor 1048566 in syscall close() ==2873== Warning: invalid file descriptor 1048567 in syscall close() ==2873== Use --log-fd= to select an alternative log fd. ==2873== Warning: invalid file descriptor 1048568 in syscall close() ==2873== Warning: invalid file descriptor 1048569 in syscall close() ==2879== Warning: invalid file descriptor 1048564 in syscall close() ==2879== Warning: invalid file descriptor 1048565 in syscall close() ==2879== Warning: invalid file descriptor 1048566 in syscall close() ==2879== Warning: invalid file descriptor 1048567 in syscall close() ==2879== Use --log-fd= to select an alternative log fd. ==2879== Warning: invalid file descriptor 1048568 in syscall close() ==2879== Warning: invalid file descriptor 1048569 in syscall close() ==2886== Warning: invalid file descriptor 1048564 in syscall close() ==2886== Warning: invalid file descriptor 1048565 in syscall close() ==2886== Warning: invalid file descriptor 1048566 in syscall close() ==2886== Warning: invalid file descriptor 1048567 in syscall close() ==2886== Use --log-fd= to select an alternative log fd. ==2886== Warning: invalid file descriptor 1048568 in syscall close() ==2886== Warning: invalid file descriptor 1048569 in syscall close() ==773== ==773== HEAP SUMMARY: ==773== in use at exit: 1,718,292 bytes in 1,321 blocks ==773== total heap usage: 31,120 allocs, 29,799 frees, 47,287,891 bytes allocated ==773== ==773== LEAK SUMMARY: ==773== definitely lost: 0 bytes in 0 blocks ==773== indirectly lost: 0 bytes in 0 blocks ==773== possibly lost: 178,943 bytes in 97 blocks ==773== still reachable: 1,539,349 bytes in 1,224 blocks ==773== suppressed: 0 bytes in 0 blocks ==773== Rerun with --leak-check=full to see details of leaked memory ==773== ==773== For counts of detected and suppressed errors, rerun with: -v ==773== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 11239 from 589) ================================================================================ 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.