!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : Sim_LAMMPS_MEAM_HennigLenoskyTrinkle_2008_Ti__SM_318953488749_000 Supported species : Ti random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Ti (Configuration in file "config-F-Ti.xyz") ----------------------------------------------------------------------------------------------------- Energy = 52.89814246638538 Forces: 1 -1.10707247e+01 -9.63204780e+00 -7.86510021e+00 2 1.03031665e+01 1.90999715e+01 -5.07667444e+00 3 5.70108832e+00 -1.06460104e+01 4.50465843e+00 4 -6.13196389e+00 1.29028339e+01 1.09072646e+01 5 4.90277122e+00 -7.87134294e+00 -5.84186726e-01 6 4.72363847e+00 -1.17653044e+00 -6.02909783e+00 7 2.88824562e+00 -1.56308390e+01 -1.26389242e+01 8 -2.63513919e+01 -1.67660986e+01 1.15389016e+00 9 -4.36501491e+00 -4.41047841e+00 -7.90214349e+00 10 -6.44876638e+00 9.06069579e+00 -1.73768804e+01 11 7.95015389e+00 -1.91984120e+01 8.99351913e+00 12 -7.79627798e+00 5.48046439e+00 4.60490342e+00 13 -1.82377190e+01 -1.27579995e+01 -3.29748435e+01 14 1.17954622e+01 6.24497093e+00 -6.27475881e+00 15 3.96072633e+01 -8.05210398e+00 1.66741174e+00 16 -5.46253172e+00 2.75664971e+01 1.52332330e+01 17 -1.91250122e+01 -1.48631459e+01 -1.37648071e+01 18 1.43077586e+01 1.97768254e+01 -1.87261969e+01 19 1.83288868e+01 -8.82593193e+00 4.15094709e+00 20 -1.47870990e+01 1.84563448e+01 2.10657236e+01 21 -2.23964806e+00 -1.23961383e+01 -2.90865783e+00 22 5.20059452e+00 1.38409653e+01 4.44612300e+00 23 8.72371578e+00 -2.45946535e+00 8.37230433e+00 24 -8.35451556e+00 2.03400026e+00 5.96912542e+00 25 -7.47251702e+00 -9.93035705e+00 -2.40146732e-01 26 -3.50410161e+00 1.48836846e+01 -1.16697634e+01 27 -3.50587318e+00 -2.34578284e+01 9.31961939e+00 28 -1.40007109e+01 1.16417688e+01 1.98762117e+00 29 -1.06219316e+01 -7.95830623e+00 1.88830814e+01 30 1.21600097e+01 1.92815461e+01 1.36995663e+00 31 1.43529918e+01 -7.56194240e+00 1.04372833e+01 32 8.53005292e+00 1.33244097e+01 1.09655156e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ti (Configuration in file "config-T-Ti.xyz") ----------------------------------------------------------------------------------------------------- Energy = 52.89814246638538 Forces: 1 -1.10707247e+01 -9.63204780e+00 -7.86510021e+00 2 1.03031665e+01 1.90999715e+01 -5.07667444e+00 3 5.70108832e+00 -1.06460104e+01 4.50465843e+00 4 -6.13196389e+00 1.29028339e+01 1.09072646e+01 5 4.90277122e+00 -7.87134294e+00 -5.84186726e-01 6 4.72363847e+00 -1.17653044e+00 -6.02909783e+00 7 2.88824562e+00 -1.56308390e+01 -1.26389242e+01 8 -2.63513919e+01 -1.67660986e+01 1.15389016e+00 9 -4.36501491e+00 -4.41047841e+00 -7.90214349e+00 10 -6.44876638e+00 9.06069579e+00 -1.73768804e+01 11 7.95015389e+00 -1.91984120e+01 8.99351913e+00 12 -7.79627798e+00 5.48046439e+00 4.60490342e+00 13 -1.82377190e+01 -1.27579995e+01 -3.29748435e+01 14 1.17954622e+01 6.24497093e+00 -6.27475881e+00 15 3.96072633e+01 -8.05210398e+00 1.66741174e+00 16 -5.46253172e+00 2.75664971e+01 1.52332330e+01 17 -1.91250122e+01 -1.48631459e+01 -1.37648071e+01 18 1.43077586e+01 1.97768254e+01 -1.87261969e+01 19 1.83288868e+01 -8.82593193e+00 4.15094709e+00 20 -1.47870990e+01 1.84563448e+01 2.10657236e+01 21 -2.23964806e+00 -1.23961383e+01 -2.90865783e+00 22 5.20059452e+00 1.38409653e+01 4.44612300e+00 23 8.72371578e+00 -2.45946535e+00 8.37230433e+00 24 -8.35451556e+00 2.03400026e+00 5.96912542e+00 25 -7.47251702e+00 -9.93035705e+00 -2.40146732e-01 26 -3.50410161e+00 1.48836846e+01 -1.16697634e+01 27 -3.50587318e+00 -2.34578284e+01 9.31961939e+00 28 -1.40007109e+01 1.16417688e+01 1.98762117e+00 29 -1.06219316e+01 -7.95830623e+00 1.88830814e+01 30 1.21600097e+01 1.92815461e+01 1.36995663e+00 31 1.43529918e+01 -7.56194240e+00 1.04372833e+01 32 8.53005292e+00 1.33244097e+01 1.09655156e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==39560== Memcheck, a memory error detector ==39560== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==39560== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==39560== Command: python runner2.py Sim_LAMMPS_MEAM_HennigLenoskyTrinkle_2008_Ti__SM_318953488749_000 ==39560== ==40852== Warning: invalid file descriptor 1048564 in syscall close() ==40852== Warning: invalid file descriptor 1048565 in syscall close() ==40852== Warning: invalid file descriptor 1048566 in syscall close() ==40852== Warning: invalid file descriptor 1048567 in syscall close() ==40852== Use --log-fd= to select an alternative log fd. ==40852== Warning: invalid file descriptor 1048568 in syscall close() ==40852== Warning: invalid file descriptor 1048569 in syscall close() ==40853== Warning: invalid file descriptor 1048564 in syscall close() ==40853== Warning: invalid file descriptor 1048565 in syscall close() ==40853== Warning: invalid file descriptor 1048566 in syscall close() ==40853== Warning: invalid file descriptor 1048567 in syscall close() ==40853== Use --log-fd= to select an alternative log fd. ==40853== Warning: invalid file descriptor 1048568 in syscall close() ==40853== Warning: invalid file descriptor 1048569 in syscall close() ==40854== Warning: invalid file descriptor 1048564 in syscall close() ==40854== Warning: invalid file descriptor 1048565 in syscall close() ==40854== Warning: invalid file descriptor 1048566 in syscall close() ==40854== Warning: invalid file descriptor 1048567 in syscall close() ==40854== Use --log-fd= to select an alternative log fd. ==40854== Warning: invalid file descriptor 1048568 in syscall close() ==40854== Warning: invalid file descriptor 1048569 in syscall close() ==40855== Warning: invalid file descriptor 1048564 in syscall close() ==40855== Warning: invalid file descriptor 1048565 in syscall close() ==40855== Warning: invalid file descriptor 1048566 in syscall close() ==40855== Warning: invalid file descriptor 1048567 in syscall close() ==40855== Use --log-fd= to select an alternative log fd. ==40855== Warning: invalid file descriptor 1048568 in syscall close() ==40855== Warning: invalid file descriptor 1048569 in syscall close() ==40856== Warning: invalid file descriptor 1048564 in syscall close() ==40856== Warning: invalid file descriptor 1048565 in syscall close() ==40856== Warning: invalid file descriptor 1048566 in syscall close() ==40856== Warning: invalid file descriptor 1048567 in syscall close() ==40856== Use --log-fd= to select an alternative log fd. ==40856== Warning: invalid file descriptor 1048568 in syscall close() ==40856== Warning: invalid file descriptor 1048569 in syscall close() ==40857== Warning: invalid file descriptor 1048564 in syscall close() ==40857== Warning: invalid file descriptor 1048565 in syscall close() ==40857== Warning: invalid file descriptor 1048566 in syscall close() ==40857== Warning: invalid file descriptor 1048567 in syscall close() ==40857== Use --log-fd= to select an alternative log fd. ==40857== Warning: invalid file descriptor 1048568 in syscall close() ==40857== Warning: invalid file descriptor 1048569 in syscall close() ==40858== Warning: invalid file descriptor 1048564 in syscall close() ==40858== Warning: invalid file descriptor 1048565 in syscall close() ==40858== Warning: invalid file descriptor 1048566 in syscall close() ==40858== Warning: invalid file descriptor 1048567 in syscall close() ==40858== Use --log-fd= to select an alternative log fd. ==40858== Warning: invalid file descriptor 1048568 in syscall close() ==40858== Warning: invalid file descriptor 1048569 in syscall close() ==40860== Warning: invalid file descriptor 1048564 in syscall close() ==40860== Warning: invalid file descriptor 1048565 in syscall close() ==40860== Warning: invalid file descriptor 1048566 in syscall close() ==40860== Warning: invalid file descriptor 1048567 in syscall close() ==40860== Use --log-fd= to select an alternative log fd. ==40860== Warning: invalid file descriptor 1048568 in syscall close() ==40860== Warning: invalid file descriptor 1048569 in syscall close() ==39560== ==39560== HEAP SUMMARY: ==39560== in use at exit: 1,780,731 bytes in 1,488 blocks ==39560== total heap usage: 28,441 allocs, 26,953 frees, 42,736,896 bytes allocated ==39560== ==39560== LEAK SUMMARY: ==39560== definitely lost: 0 bytes in 0 blocks ==39560== indirectly lost: 0 bytes in 0 blocks ==39560== possibly lost: 178,423 bytes in 96 blocks ==39560== still reachable: 1,602,308 bytes in 1,392 blocks ==39560== suppressed: 0 bytes in 0 blocks ==39560== Rerun with --leak-check=full to see details of leaked memory ==39560== ==39560== For counts of detected and suppressed errors, rerun with: -v ==39560== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16445 from 620) ================================================================================ 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.