!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_ADP_MishinMehlPapaconstantopoulos_2005_Ni__SM_477692857359_000 Supported species : Ni random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Ni (Configuration in file "config-F-Ni.xyz") ----------------------------------------------------------------------------------------------------- Energy = -55.52405382494054 Forces: 1 -1.46451743e+00 -2.53023279e+00 -2.82294795e+00 2 -1.54547017e+00 1.71126970e+00 -3.74797877e+00 3 1.57347061e+00 -4.26303233e+00 3.54099690e-02 4 -3.47434538e+00 1.13841994e+00 5.91490761e-01 5 2.32759823e+00 -4.54328202e+00 -1.81194128e+00 6 9.27202849e-01 1.72483373e+00 -2.03545542e+00 7 3.16642896e+00 -6.06919049e+00 -3.65034611e+00 8 -3.09505790e+00 -3.23080977e+00 -1.31465496e+00 9 -4.20400382e+00 -2.89843065e+00 -6.05965239e+00 10 -1.94030374e-01 8.32431100e+00 -6.53000142e+00 11 -2.10937025e+00 -5.74836070e+00 3.06556698e+00 12 -4.59225751e+00 5.62532588e+00 1.37636027e+00 13 4.76829021e+00 -2.75158100e+00 -8.84191882e+00 14 9.67212166e-01 1.48670868e+00 -8.95108851e-01 15 7.57498420e+00 -1.35606514e+00 -3.40514614e+00 16 2.64491723e+00 8.61811364e+00 2.19946935e+00 17 -5.94111702e+00 -3.19612192e+00 -1.76944354e+00 18 1.47685640e+00 4.15737697e+00 4.75308655e-01 19 2.22988467e+00 -4.60933260e+00 3.56101995e+00 20 -2.01044220e+00 3.90630379e+00 2.63917947e+00 21 -3.79569444e+00 -4.60399593e+00 1.08418015e+00 22 6.03841896e+00 3.76747076e+00 3.55881287e+00 23 1.92391863e+00 -8.27487443e-01 2.56648756e+00 24 -2.35714111e-01 1.02363338e+00 2.20298107e+00 25 -3.68779031e+00 -1.99325700e+00 3.43920760e+00 26 -1.32600643e+00 6.54366415e+00 -2.51229348e+00 27 3.76002204e-02 -6.88848798e+00 3.96694757e+00 28 -4.68943948e+00 3.26593897e+00 1.78450897e+00 29 -3.37942103e+00 -3.96813888e+00 3.10986876e+00 30 2.96334442e+00 6.27215552e+00 3.57405532e-01 31 4.98885293e+00 -2.87979978e+00 4.16597513e+00 32 2.13569716e+00 4.79208028e+00 5.21670850e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ni (Configuration in file "config-T-Ni.xyz") ----------------------------------------------------------------------------------------------------- Energy = -55.52405382494054 Forces: 1 -1.46451743e+00 -2.53023279e+00 -2.82294795e+00 2 -1.54547017e+00 1.71126970e+00 -3.74797877e+00 3 1.57347061e+00 -4.26303233e+00 3.54099690e-02 4 -3.47434538e+00 1.13841994e+00 5.91490761e-01 5 2.32759823e+00 -4.54328202e+00 -1.81194128e+00 6 9.27202849e-01 1.72483373e+00 -2.03545542e+00 7 3.16642896e+00 -6.06919049e+00 -3.65034611e+00 8 -3.09505790e+00 -3.23080977e+00 -1.31465496e+00 9 -4.20400382e+00 -2.89843065e+00 -6.05965239e+00 10 -1.94030374e-01 8.32431100e+00 -6.53000142e+00 11 -2.10937025e+00 -5.74836070e+00 3.06556698e+00 12 -4.59225751e+00 5.62532588e+00 1.37636027e+00 13 4.76829021e+00 -2.75158100e+00 -8.84191882e+00 14 9.67212166e-01 1.48670868e+00 -8.95108851e-01 15 7.57498420e+00 -1.35606514e+00 -3.40514614e+00 16 2.64491723e+00 8.61811364e+00 2.19946935e+00 17 -5.94111702e+00 -3.19612192e+00 -1.76944354e+00 18 1.47685640e+00 4.15737697e+00 4.75308655e-01 19 2.22988467e+00 -4.60933260e+00 3.56101995e+00 20 -2.01044220e+00 3.90630379e+00 2.63917947e+00 21 -3.79569444e+00 -4.60399593e+00 1.08418015e+00 22 6.03841896e+00 3.76747076e+00 3.55881287e+00 23 1.92391863e+00 -8.27487443e-01 2.56648756e+00 24 -2.35714111e-01 1.02363338e+00 2.20298107e+00 25 -3.68779031e+00 -1.99325700e+00 3.43920760e+00 26 -1.32600643e+00 6.54366415e+00 -2.51229348e+00 27 3.76002204e-02 -6.88848798e+00 3.96694757e+00 28 -4.68943948e+00 3.26593897e+00 1.78450897e+00 29 -3.37942103e+00 -3.96813888e+00 3.10986876e+00 30 2.96334442e+00 6.27215552e+00 3.57405532e-01 31 4.98885293e+00 -2.87979978e+00 4.16597513e+00 32 2.13569716e+00 4.79208028e+00 5.21670850e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==52709== Memcheck, a memory error detector ==52709== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==52709== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==52709== Command: python runner2.py Sim_LAMMPS_ADP_MishinMehlPapaconstantopoulos_2005_Ni__SM_477692857359_000 ==52709== ==54534== Warning: invalid file descriptor 1048564 in syscall close() ==54534== Warning: invalid file descriptor 1048565 in syscall close() ==54534== Warning: invalid file descriptor 1048566 in syscall close() ==54534== Warning: invalid file descriptor 1048567 in syscall close() ==54534== Use --log-fd= to select an alternative log fd. ==54534== Warning: invalid file descriptor 1048568 in syscall close() ==54534== Warning: invalid file descriptor 1048569 in syscall close() ==54545== Warning: invalid file descriptor 1048564 in syscall close() ==54545== Warning: invalid file descriptor 1048565 in syscall close() ==54545== Warning: invalid file descriptor 1048566 in syscall close() ==54545== Warning: invalid file descriptor 1048567 in syscall close() ==54545== Use --log-fd= to select an alternative log fd. ==54545== Warning: invalid file descriptor 1048568 in syscall close() ==54545== Warning: invalid file descriptor 1048569 in syscall close() ==54555== Warning: invalid file descriptor 1048564 in syscall close() ==54555== Warning: invalid file descriptor 1048565 in syscall close() ==54555== Warning: invalid file descriptor 1048566 in syscall close() ==54555== Warning: invalid file descriptor 1048567 in syscall close() ==54555== Use --log-fd= to select an alternative log fd. ==54555== Warning: invalid file descriptor 1048568 in syscall close() ==54555== Warning: invalid file descriptor 1048569 in syscall close() ==54557== Warning: invalid file descriptor 1048564 in syscall close() ==54557== Warning: invalid file descriptor 1048565 in syscall close() ==54557== Warning: invalid file descriptor 1048566 in syscall close() ==54557== Warning: invalid file descriptor 1048567 in syscall close() ==54557== Use --log-fd= to select an alternative log fd. ==54557== Warning: invalid file descriptor 1048568 in syscall close() ==54557== Warning: invalid file descriptor 1048569 in syscall close() ==54560== Warning: invalid file descriptor 1048564 in syscall close() ==54560== Warning: invalid file descriptor 1048565 in syscall close() ==54560== Warning: invalid file descriptor 1048566 in syscall close() ==54560== Warning: invalid file descriptor 1048567 in syscall close() ==54560== Use --log-fd= to select an alternative log fd. ==54560== Warning: invalid file descriptor 1048568 in syscall close() ==54560== Warning: invalid file descriptor 1048569 in syscall close() ==54565== Warning: invalid file descriptor 1048564 in syscall close() ==54565== Warning: invalid file descriptor 1048565 in syscall close() ==54565== Warning: invalid file descriptor 1048566 in syscall close() ==54565== Warning: invalid file descriptor 1048567 in syscall close() ==54565== Use --log-fd= to select an alternative log fd. ==54565== Warning: invalid file descriptor 1048568 in syscall close() ==54565== Warning: invalid file descriptor 1048569 in syscall close() ==54568== Warning: invalid file descriptor 1048564 in syscall close() ==54568== Warning: invalid file descriptor 1048565 in syscall close() ==54568== Warning: invalid file descriptor 1048566 in syscall close() ==54568== Warning: invalid file descriptor 1048567 in syscall close() ==54568== Use --log-fd= to select an alternative log fd. ==54568== Warning: invalid file descriptor 1048568 in syscall close() ==54568== Warning: invalid file descriptor 1048569 in syscall close() ==54570== Warning: invalid file descriptor 1048564 in syscall close() ==54570== Warning: invalid file descriptor 1048565 in syscall close() ==54570== Warning: invalid file descriptor 1048566 in syscall close() ==54570== Warning: invalid file descriptor 1048567 in syscall close() ==54570== Use --log-fd= to select an alternative log fd. ==54570== Warning: invalid file descriptor 1048568 in syscall close() ==54570== Warning: invalid file descriptor 1048569 in syscall close() ==52709== ==52709== HEAP SUMMARY: ==52709== in use at exit: 1,779,759 bytes in 1,487 blocks ==52709== total heap usage: 28,430 allocs, 26,943 frees, 57,232,808 bytes allocated ==52709== ==52709== LEAK SUMMARY: ==52709== definitely lost: 0 bytes in 0 blocks ==52709== indirectly lost: 0 bytes in 0 blocks ==52709== possibly lost: 178,423 bytes in 96 blocks ==52709== still reachable: 1,601,336 bytes in 1,391 blocks ==52709== suppressed: 0 bytes in 0 blocks ==52709== Rerun with --leak-check=full to see details of leaked memory ==52709== ==52709== For counts of detected and suppressed errors, rerun with: -v ==52709== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 13432 from 603) ================================================================================ 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.