!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_ZhouJohnsonWadley_2004_Pb__MO_116920074573_005 Supported species : Pb random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Pb (Configuration in file "config-F-Pb.xyz") ----------------------------------------------------------------------------------------------------- Energy = 680.0181029755818 Forces: 1 -1.98882170e+01 -4.50176391e+01 -3.78438609e+01 2 -1.45786248e+01 4.40917043e+00 -4.75855156e+01 3 6.59233408e+00 -5.06655960e+01 -1.60594743e+01 4 -3.72429412e+01 2.55235474e+01 2.29409430e+01 5 8.81097376e+00 -5.28594903e+01 -2.60031284e+01 6 3.13108681e+01 4.14125650e+00 -3.73199103e+01 7 3.30870261e+01 -7.34815232e+01 -4.60542396e+01 8 -2.16363671e+01 -3.43153792e+01 4.87318037e+00 9 -4.62000169e+01 1.36190401e+00 -5.37686290e+01 10 -2.41726465e+01 7.75588904e+01 -6.06164995e+01 11 -4.69007639e+01 -3.49338981e+01 3.57558731e+01 12 -3.55741120e+01 3.77088218e+01 -6.22797068e+00 13 3.73557658e+01 -1.87856119e+01 -1.09325771e+02 14 2.55372845e+01 2.56659269e+01 -2.34971603e+01 15 8.64003487e+01 3.47507463e+00 5.66087394e+00 16 2.35346886e+01 9.07315393e+01 2.92186060e+01 17 -4.72777822e+01 -2.32090049e+01 -7.68215409e-03 18 -2.90956807e+00 2.01880826e+01 1.46537341e+01 19 6.64551837e+00 -3.78284491e+01 2.87461262e+01 20 -2.54988627e+01 1.22097370e+01 2.56202393e+01 21 -2.22517919e+01 -4.44900342e+01 1.91232742e+01 22 5.94370678e+01 4.41801386e+01 4.15833461e+01 23 2.30912513e+01 -1.39079675e+01 3.02453810e+01 24 1.95320021e+00 6.13653019e+00 3.16900671e+01 25 -5.10315572e+01 -3.28594800e+01 -1.53913359e+01 26 -1.92363955e+01 8.26112379e+01 -1.62442025e+01 27 2.06671912e+01 -6.43930546e+01 6.13605958e+01 28 -6.72040435e+01 6.25411238e+01 3.35384282e+01 29 1.58792130e+01 -4.01592269e+01 1.94452139e+01 30 3.24838943e+01 3.91959692e+01 7.82484917e+00 31 4.14830261e+01 -1.72343754e+01 3.05807911e+01 32 2.73340387e+01 4.65017799e+01 5.30838575e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Pb (Configuration in file "config-T-Pb.xyz") ----------------------------------------------------------------------------------------------------- Energy = 680.0181029755818 Forces: 1 -1.98882170e+01 -4.50176391e+01 -3.78438609e+01 2 -1.45786248e+01 4.40917043e+00 -4.75855156e+01 3 6.59233408e+00 -5.06655960e+01 -1.60594743e+01 4 -3.72429412e+01 2.55235474e+01 2.29409430e+01 5 8.81097376e+00 -5.28594903e+01 -2.60031284e+01 6 3.13108681e+01 4.14125650e+00 -3.73199103e+01 7 3.30870261e+01 -7.34815232e+01 -4.60542396e+01 8 -2.16363671e+01 -3.43153792e+01 4.87318037e+00 9 -4.62000169e+01 1.36190401e+00 -5.37686290e+01 10 -2.41726465e+01 7.75588904e+01 -6.06164995e+01 11 -4.69007639e+01 -3.49338981e+01 3.57558731e+01 12 -3.55741120e+01 3.77088218e+01 -6.22797068e+00 13 3.73557658e+01 -1.87856119e+01 -1.09325771e+02 14 2.55372845e+01 2.56659269e+01 -2.34971603e+01 15 8.64003487e+01 3.47507463e+00 5.66087394e+00 16 2.35346886e+01 9.07315393e+01 2.92186060e+01 17 -4.72777822e+01 -2.32090049e+01 -7.68215409e-03 18 -2.90956807e+00 2.01880826e+01 1.46537341e+01 19 6.64551837e+00 -3.78284491e+01 2.87461262e+01 20 -2.54988627e+01 1.22097370e+01 2.56202393e+01 21 -2.22517919e+01 -4.44900342e+01 1.91232742e+01 22 5.94370678e+01 4.41801386e+01 4.15833461e+01 23 2.30912513e+01 -1.39079675e+01 3.02453810e+01 24 1.95320021e+00 6.13653019e+00 3.16900671e+01 25 -5.10315572e+01 -3.28594800e+01 -1.53913359e+01 26 -1.92363955e+01 8.26112379e+01 -1.62442025e+01 27 2.06671912e+01 -6.43930546e+01 6.13605958e+01 28 -6.72040435e+01 6.25411238e+01 3.35384282e+01 29 1.58792130e+01 -4.01592269e+01 1.94452139e+01 30 3.24838943e+01 3.91959692e+01 7.82484917e+00 31 4.14830261e+01 -1.72343754e+01 3.05807911e+01 32 2.73340387e+01 4.65017799e+01 5.30838575e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==83226== Memcheck, a memory error detector ==83226== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==83226== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==83226== Command: python runner2.py EAM_Dynamo_ZhouJohnsonWadley_2004_Pb__MO_116920074573_005 ==83226== ==85251== Warning: invalid file descriptor 1048564 in syscall close() ==85251== Warning: invalid file descriptor 1048565 in syscall close() ==85251== Warning: invalid file descriptor 1048566 in syscall close() ==85251== Warning: invalid file descriptor 1048567 in syscall close() ==85251== Use --log-fd= to select an alternative log fd. ==85251== Warning: invalid file descriptor 1048568 in syscall close() ==85251== Warning: invalid file descriptor 1048569 in syscall close() ==85258== Warning: invalid file descriptor 1048564 in syscall close() ==85258== Warning: invalid file descriptor 1048565 in syscall close() ==85258== Warning: invalid file descriptor 1048566 in syscall close() ==85258== Warning: invalid file descriptor 1048567 in syscall close() ==85258== Use --log-fd= to select an alternative log fd. ==85258== Warning: invalid file descriptor 1048568 in syscall close() ==85258== Warning: invalid file descriptor 1048569 in syscall close() ==85348== Warning: invalid file descriptor 1048564 in syscall close() ==85348== Warning: invalid file descriptor 1048565 in syscall close() ==85348== Warning: invalid file descriptor 1048566 in syscall close() ==85348== Warning: invalid file descriptor 1048567 in syscall close() ==85348== Use --log-fd= to select an alternative log fd. ==85348== Warning: invalid file descriptor 1048568 in syscall close() ==85348== Warning: invalid file descriptor 1048569 in syscall close() ==85355== Warning: invalid file descriptor 1048564 in syscall close() ==85355== Warning: invalid file descriptor 1048565 in syscall close() ==85355== Warning: invalid file descriptor 1048566 in syscall close() ==85355== Warning: invalid file descriptor 1048567 in syscall close() ==85355== Use --log-fd= to select an alternative log fd. ==85355== Warning: invalid file descriptor 1048568 in syscall close() ==85355== Warning: invalid file descriptor 1048569 in syscall close() ==85363== Warning: invalid file descriptor 1048564 in syscall close() ==85363== Warning: invalid file descriptor 1048565 in syscall close() ==85363== Warning: invalid file descriptor 1048566 in syscall close() ==85363== Warning: invalid file descriptor 1048567 in syscall close() ==85363== Use --log-fd= to select an alternative log fd. ==85363== Warning: invalid file descriptor 1048568 in syscall close() ==85363== Warning: invalid file descriptor 1048569 in syscall close() ==85368== Warning: invalid file descriptor 1048564 in syscall close() ==85368== Warning: invalid file descriptor 1048565 in syscall close() ==85368== Warning: invalid file descriptor 1048566 in syscall close() ==85368== Warning: invalid file descriptor 1048567 in syscall close() ==85368== Use --log-fd= to select an alternative log fd. ==85368== Warning: invalid file descriptor 1048568 in syscall close() ==85368== Warning: invalid file descriptor 1048569 in syscall close() ==83226== ==83226== HEAP SUMMARY: ==83226== in use at exit: 1,718,292 bytes in 1,321 blocks ==83226== total heap usage: 31,120 allocs, 29,799 frees, 40,376,686 bytes allocated ==83226== ==83226== LEAK SUMMARY: ==83226== definitely lost: 0 bytes in 0 blocks ==83226== indirectly lost: 0 bytes in 0 blocks ==83226== possibly lost: 178,943 bytes in 97 blocks ==83226== still reachable: 1,539,349 bytes in 1,224 blocks ==83226== suppressed: 0 bytes in 0 blocks ==83226== Rerun with --leak-check=full to see details of leaked memory ==83226== ==83226== For counts of detected and suppressed errors, rerun with: -v ==83226== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16333 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.