Enter a model name: === Verification check vc-memory-leak start (2019-08-08 23:28:53) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : Morse_Shifted_GirifalcoWeizer_1959HighCutoff_Fe__MO_147603128437_003 Supported species : Fe random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Fe (Configuration in file "config-F-Fe.xyz") ----------------------------------------------------------------------------------------------------- Energy = 102.07149300594095 Forces: 1 -4.82319807e+00 -1.01518316e+01 -1.08572682e+01 2 -4.82694804e+00 8.31874758e+00 -8.44719407e+00 3 5.91309747e+00 -1.59708124e+01 -7.40108955e+00 4 -8.89809478e+00 7.68719229e+00 4.89920877e+00 5 -1.77537917e+00 -1.68022305e+01 -4.19919072e+00 6 1.00735693e+01 7.55955932e+00 -1.08380348e+01 7 9.45768280e+00 -3.12274698e+01 -2.26637898e+01 8 -1.50336914e+01 -1.12280400e+01 -3.18867848e+00 9 -1.03569012e+01 -9.42494048e+00 -1.84266403e+01 10 -4.75420772e+00 2.05751854e+01 -2.17511362e+01 11 -4.49001168e+00 -1.60210871e+01 4.73788720e+00 12 -1.22493143e+01 1.73564439e+01 3.40969407e+00 13 -7.76090028e+00 -1.65400839e+01 -4.48319005e+01 14 9.64596089e+00 1.21565684e+01 -8.47614181e+00 15 4.02363157e+01 -1.00961900e+01 7.75223836e+00 16 4.36414647e+00 3.40394938e+01 1.49111272e+01 17 -1.71465521e+01 -8.71997102e+00 -5.00407745e+00 18 5.56267706e+00 1.43952601e+01 8.80146774e+00 19 8.52342745e+00 -1.03532155e+01 9.60858423e+00 20 -6.00234521e+00 1.03397397e+01 8.16483147e+00 21 -1.51822924e+01 -1.37753388e+01 4.42647428e+00 22 2.29460575e+01 2.46760671e+01 2.30571282e+01 23 9.23350762e+00 -5.45180049e+00 7.03376121e+00 24 -5.52242395e+00 8.16477099e+00 6.96541014e+00 25 -1.40698647e+01 -9.36789249e+00 8.79919122e+00 26 -6.40926239e+00 2.25442147e+01 -1.11028842e+01 27 1.31691057e+01 -3.77780627e+01 1.29611964e+01 28 -2.92809985e+01 2.44076313e+01 5.94357908e+00 29 -9.35045826e+00 -1.36232595e+01 1.01663226e+01 30 1.09616683e+01 1.69904444e+01 5.17993020e+00 31 1.78666416e+01 -9.17578579e+00 1.27927031e+01 32 9.97898626e+00 1.64966929e+01 1.75772907e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Fe (Configuration in file "config-T-Fe.xyz") ----------------------------------------------------------------------------------------------------- Energy = 102.07149300594095 Forces: 1 -4.82319807e+00 -1.01518316e+01 -1.08572682e+01 2 -4.82694804e+00 8.31874758e+00 -8.44719407e+00 3 5.91309747e+00 -1.59708124e+01 -7.40108955e+00 4 -8.89809478e+00 7.68719229e+00 4.89920877e+00 5 -1.77537917e+00 -1.68022305e+01 -4.19919072e+00 6 1.00735693e+01 7.55955932e+00 -1.08380348e+01 7 9.45768280e+00 -3.12274698e+01 -2.26637898e+01 8 -1.50336914e+01 -1.12280400e+01 -3.18867848e+00 9 -1.03569012e+01 -9.42494048e+00 -1.84266403e+01 10 -4.75420772e+00 2.05751854e+01 -2.17511362e+01 11 -4.49001168e+00 -1.60210871e+01 4.73788720e+00 12 -1.22493143e+01 1.73564439e+01 3.40969407e+00 13 -7.76090028e+00 -1.65400839e+01 -4.48319005e+01 14 9.64596089e+00 1.21565684e+01 -8.47614181e+00 15 4.02363157e+01 -1.00961900e+01 7.75223836e+00 16 4.36414647e+00 3.40394938e+01 1.49111272e+01 17 -1.71465521e+01 -8.71997102e+00 -5.00407745e+00 18 5.56267706e+00 1.43952601e+01 8.80146774e+00 19 8.52342745e+00 -1.03532155e+01 9.60858423e+00 20 -6.00234521e+00 1.03397397e+01 8.16483147e+00 21 -1.51822924e+01 -1.37753388e+01 4.42647428e+00 22 2.29460575e+01 2.46760671e+01 2.30571282e+01 23 9.23350762e+00 -5.45180049e+00 7.03376121e+00 24 -5.52242395e+00 8.16477099e+00 6.96541014e+00 25 -1.40698647e+01 -9.36789249e+00 8.79919122e+00 26 -6.40926239e+00 2.25442147e+01 -1.11028842e+01 27 1.31691057e+01 -3.77780627e+01 1.29611964e+01 28 -2.92809985e+01 2.44076313e+01 5.94357908e+00 29 -9.35045826e+00 -1.36232595e+01 1.01663226e+01 30 1.09616683e+01 1.69904444e+01 5.17993020e+00 31 1.78666416e+01 -9.17578579e+00 1.27927031e+01 32 9.97898626e+00 1.64966929e+01 1.75772907e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==46312== Memcheck, a memory error detector ==46312== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==46312== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==46312== Command: python runner2.py Morse_Shifted_GirifalcoWeizer_1959HighCutoff_Fe__MO_147603128437_003 ==46312== ==47861== Warning: invalid file descriptor 1048564 in syscall close() ==47861== Warning: invalid file descriptor 1048565 in syscall close() ==47861== Warning: invalid file descriptor 1048566 in syscall close() ==47861== Warning: invalid file descriptor 1048567 in syscall close() ==47861== Use --log-fd= to select an alternative log fd. ==47861== Warning: invalid file descriptor 1048568 in syscall close() ==47861== Warning: invalid file descriptor 1048569 in syscall close() ==47873== Warning: invalid file descriptor 1048564 in syscall close() ==47873== Warning: invalid file descriptor 1048565 in syscall close() ==47873== Warning: invalid file descriptor 1048566 in syscall close() ==47873== Warning: invalid file descriptor 1048567 in syscall close() ==47873== Use --log-fd= to select an alternative log fd. ==47873== Warning: invalid file descriptor 1048568 in syscall close() ==47873== Warning: invalid file descriptor 1048569 in syscall close() ==48037== Warning: invalid file descriptor 1048564 in syscall close() ==48037== Warning: invalid file descriptor 1048565 in syscall close() ==48037== Warning: invalid file descriptor 1048566 in syscall close() ==48037== Warning: invalid file descriptor 1048567 in syscall close() ==48037== Use --log-fd= to select an alternative log fd. ==48037== Warning: invalid file descriptor 1048568 in syscall close() ==48037== Warning: invalid file descriptor 1048569 in syscall close() ==48042== Warning: invalid file descriptor 1048564 in syscall close() ==48042== Warning: invalid file descriptor 1048565 in syscall close() ==48042== Warning: invalid file descriptor 1048566 in syscall close() ==48042== Warning: invalid file descriptor 1048567 in syscall close() ==48042== Use --log-fd= to select an alternative log fd. ==48042== Warning: invalid file descriptor 1048568 in syscall close() ==48042== Warning: invalid file descriptor 1048569 in syscall close() ==48050== Warning: invalid file descriptor 1048564 in syscall close() ==48050== Warning: invalid file descriptor 1048565 in syscall close() ==48050== Warning: invalid file descriptor 1048566 in syscall close() ==48050== Warning: invalid file descriptor 1048567 in syscall close() ==48050== Use --log-fd= to select an alternative log fd. ==48050== Warning: invalid file descriptor 1048568 in syscall close() ==48050== Warning: invalid file descriptor 1048569 in syscall close() ==48063== Warning: invalid file descriptor 1048564 in syscall close() ==48063== Warning: invalid file descriptor 1048565 in syscall close() ==48063== Warning: invalid file descriptor 1048566 in syscall close() ==48063== Warning: invalid file descriptor 1048567 in syscall close() ==48063== Use --log-fd= to select an alternative log fd. ==48063== Warning: invalid file descriptor 1048568 in syscall close() ==48063== Warning: invalid file descriptor 1048569 in syscall close() ==46312== ==46312== HEAP SUMMARY: ==46312== in use at exit: 1,718,292 bytes in 1,321 blocks ==46312== total heap usage: 31,396 allocs, 30,075 frees, 38,295,359 bytes allocated ==46312== ==46312== LEAK SUMMARY: ==46312== definitely lost: 0 bytes in 0 blocks ==46312== indirectly lost: 0 bytes in 0 blocks ==46312== possibly lost: 178,943 bytes in 97 blocks ==46312== still reachable: 1,539,349 bytes in 1,224 blocks ==46312== suppressed: 0 bytes in 0 blocks ==46312== Rerun with --leak-check=full to see details of leaked memory ==46312== ==46312== For counts of detected and suppressed errors, rerun with: -v ==46312== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16351 from 613) ================================================================================ 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. === Verification check vc-memory-leak end (2019-08-08 23:29:14) ===