!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_ParkFellingerLenosky_2012_Mo__SM_769176993156_000 Supported species : Mo random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Mo (Configuration in file "config-F-Mo.xyz") ----------------------------------------------------------------------------------------------------- Energy = 98.23716757390869 Forces: 1 -6.51538664e+00 -8.05659808e+00 -9.84327538e+00 2 -1.95135277e+00 -3.91475534e+00 -2.33961031e+01 3 5.81825105e+00 -1.85054762e+01 -3.37312036e+00 4 -2.06203203e+01 -7.06834890e-01 5.10767056e+00 5 -4.69566715e+00 -1.98570835e+01 -1.45602594e+01 6 1.73768810e+01 3.27313101e+00 -2.04872265e+01 7 1.42173576e+01 -1.44039216e+01 4.44027056e+00 8 -3.08642959e+00 -5.37847427e+00 4.56842846e+00 9 -1.23927821e+01 -2.41391803e-01 -2.00115870e+01 10 1.33406000e+00 2.49591510e+01 -1.36067758e+01 11 -6.90818063e+00 -9.71734098e+00 2.94033690e+00 12 -1.91190823e+01 1.70171390e+01 3.45543795e+00 13 1.14229465e+01 -5.97688111e+00 -2.37153379e+01 14 1.48487087e+01 1.77493015e+01 -1.49536134e+01 15 1.95389031e+01 -5.15486291e+00 -1.72772819e+00 16 -7.20514993e+00 2.56967623e+01 -2.95178239e+00 17 -2.50118972e+01 -1.36615286e+01 -5.80980311e+00 18 5.77080772e+00 9.14645773e+00 -2.09173098e+00 19 7.62390430e+00 -2.00328820e+01 1.75772491e+01 20 -1.43757846e+01 1.22735114e+01 1.55144100e+01 21 -1.01142418e+01 -2.13518224e+01 2.87084322e+00 22 2.49690923e+01 7.12654939e+00 2.38046236e+00 23 8.84542373e+00 -6.09130017e+00 1.28346662e+01 24 1.10674192e+00 8.09015226e-01 1.50306040e+01 25 -1.78509002e+01 -5.36272472e+00 2.61024190e+00 26 4.97708172e+00 2.48847384e+01 -3.50705827e+00 27 -3.62521484e+00 -1.16187120e+01 1.88988243e+01 28 -1.52462979e+01 7.96017855e+00 9.35907194e+00 29 -1.63465645e+00 -1.26178556e+01 1.13700919e+01 30 1.49017158e+01 1.71984280e+01 1.24792008e+00 31 1.35060390e+01 -3.82339129e+00 1.21695485e+01 32 4.09542996e+00 1.83794739e+01 1.76593241e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Mo (Configuration in file "config-T-Mo.xyz") ----------------------------------------------------------------------------------------------------- Energy = 98.23716757390869 Forces: 1 -6.51538664e+00 -8.05659808e+00 -9.84327538e+00 2 -1.95135277e+00 -3.91475534e+00 -2.33961031e+01 3 5.81825105e+00 -1.85054762e+01 -3.37312036e+00 4 -2.06203203e+01 -7.06834890e-01 5.10767056e+00 5 -4.69566715e+00 -1.98570835e+01 -1.45602594e+01 6 1.73768810e+01 3.27313101e+00 -2.04872265e+01 7 1.42173576e+01 -1.44039216e+01 4.44027056e+00 8 -3.08642959e+00 -5.37847427e+00 4.56842846e+00 9 -1.23927821e+01 -2.41391803e-01 -2.00115870e+01 10 1.33406000e+00 2.49591510e+01 -1.36067758e+01 11 -6.90818063e+00 -9.71734098e+00 2.94033690e+00 12 -1.91190823e+01 1.70171390e+01 3.45543795e+00 13 1.14229465e+01 -5.97688111e+00 -2.37153379e+01 14 1.48487087e+01 1.77493015e+01 -1.49536134e+01 15 1.95389031e+01 -5.15486291e+00 -1.72772819e+00 16 -7.20514993e+00 2.56967623e+01 -2.95178239e+00 17 -2.50118972e+01 -1.36615286e+01 -5.80980311e+00 18 5.77080772e+00 9.14645773e+00 -2.09173098e+00 19 7.62390430e+00 -2.00328820e+01 1.75772491e+01 20 -1.43757846e+01 1.22735114e+01 1.55144100e+01 21 -1.01142418e+01 -2.13518224e+01 2.87084322e+00 22 2.49690923e+01 7.12654939e+00 2.38046236e+00 23 8.84542373e+00 -6.09130017e+00 1.28346662e+01 24 1.10674192e+00 8.09015226e-01 1.50306040e+01 25 -1.78509002e+01 -5.36272472e+00 2.61024190e+00 26 4.97708172e+00 2.48847384e+01 -3.50705827e+00 27 -3.62521484e+00 -1.16187120e+01 1.88988243e+01 28 -1.52462979e+01 7.96017855e+00 9.35907194e+00 29 -1.63465645e+00 -1.26178556e+01 1.13700919e+01 30 1.49017158e+01 1.71984280e+01 1.24792008e+00 31 1.35060390e+01 -3.82339129e+00 1.21695485e+01 32 4.09542996e+00 1.83794739e+01 1.76593241e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==68557== Memcheck, a memory error detector ==68557== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==68557== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==68557== Command: python runner2.py Sim_LAMMPS_MEAM_ParkFellingerLenosky_2012_Mo__SM_769176993156_000 ==68557== ==69867== Warning: invalid file descriptor 1048564 in syscall close() ==69867== Warning: invalid file descriptor 1048565 in syscall close() ==69867== Warning: invalid file descriptor 1048566 in syscall close() ==69867== Warning: invalid file descriptor 1048567 in syscall close() ==69867== Use --log-fd= to select an alternative log fd. ==69867== Warning: invalid file descriptor 1048568 in syscall close() ==69867== Warning: invalid file descriptor 1048569 in syscall close() ==69868== Warning: invalid file descriptor 1048564 in syscall close() ==69868== Warning: invalid file descriptor 1048565 in syscall close() ==69868== Warning: invalid file descriptor 1048566 in syscall close() ==69868== Warning: invalid file descriptor 1048567 in syscall close() ==69868== Use --log-fd= to select an alternative log fd. ==69868== Warning: invalid file descriptor 1048568 in syscall close() ==69868== Warning: invalid file descriptor 1048569 in syscall close() ==69869== Warning: invalid file descriptor 1048564 in syscall close() ==69869== Warning: invalid file descriptor 1048565 in syscall close() ==69869== Warning: invalid file descriptor 1048566 in syscall close() ==69869== Warning: invalid file descriptor 1048567 in syscall close() ==69869== Use --log-fd= to select an alternative log fd. ==69869== Warning: invalid file descriptor 1048568 in syscall close() ==69869== Warning: invalid file descriptor 1048569 in syscall close() ==69871== Warning: invalid file descriptor 1048564 in syscall close() ==69871== Warning: invalid file descriptor 1048565 in syscall close() ==69871== Warning: invalid file descriptor 1048566 in syscall close() ==69871== Warning: invalid file descriptor 1048567 in syscall close() ==69871== Use --log-fd= to select an alternative log fd. ==69871== Warning: invalid file descriptor 1048568 in syscall close() ==69871== Warning: invalid file descriptor 1048569 in syscall close() ==69874== Warning: invalid file descriptor 1048564 in syscall close() ==69874== Warning: invalid file descriptor 1048565 in syscall close() ==69874== Warning: invalid file descriptor 1048566 in syscall close() ==69874== Warning: invalid file descriptor 1048567 in syscall close() ==69874== Use --log-fd= to select an alternative log fd. ==69874== Warning: invalid file descriptor 1048568 in syscall close() ==69874== Warning: invalid file descriptor 1048569 in syscall close() ==69876== Warning: invalid file descriptor 1048564 in syscall close() ==69876== Warning: invalid file descriptor 1048565 in syscall close() ==69876== Warning: invalid file descriptor 1048566 in syscall close() ==69876== Warning: invalid file descriptor 1048567 in syscall close() ==69876== Use --log-fd= to select an alternative log fd. ==69876== Warning: invalid file descriptor 1048568 in syscall close() ==69876== Warning: invalid file descriptor 1048569 in syscall close() ==69878== Warning: invalid file descriptor 1048564 in syscall close() ==69878== Warning: invalid file descriptor 1048565 in syscall close() ==69878== Warning: invalid file descriptor 1048566 in syscall close() ==69878== Warning: invalid file descriptor 1048567 in syscall close() ==69878== Use --log-fd= to select an alternative log fd. ==69878== Warning: invalid file descriptor 1048568 in syscall close() ==69878== Warning: invalid file descriptor 1048569 in syscall close() ==69880== Warning: invalid file descriptor 1048564 in syscall close() ==69880== Warning: invalid file descriptor 1048565 in syscall close() ==69880== Warning: invalid file descriptor 1048566 in syscall close() ==69880== Warning: invalid file descriptor 1048567 in syscall close() ==69880== Use --log-fd= to select an alternative log fd. ==69880== Warning: invalid file descriptor 1048568 in syscall close() ==69880== Warning: invalid file descriptor 1048569 in syscall close() ==68557== ==68557== HEAP SUMMARY: ==68557== in use at exit: 1,780,731 bytes in 1,488 blocks ==68557== total heap usage: 28,449 allocs, 26,961 frees, 42,733,124 bytes allocated ==68557== ==68557== LEAK SUMMARY: ==68557== definitely lost: 0 bytes in 0 blocks ==68557== indirectly lost: 0 bytes in 0 blocks ==68557== possibly lost: 178,423 bytes in 96 blocks ==68557== still reachable: 1,602,308 bytes in 1,392 blocks ==68557== suppressed: 0 bytes in 0 blocks ==68557== Rerun with --leak-check=full to see details of leaked memory ==68557== ==68557== For counts of detected and suppressed errors, rerun with: -v ==68557== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16448 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.