!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_AsadiZaeemNouranian_2015_Ni__SM_078420412697_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 = -23.812393739274622 Forces: 1 -5.67124900e+00 -5.53867787e+00 -1.02946001e+01 2 -1.13936202e+01 1.85518699e+01 -6.65103679e+00 3 1.12207631e+01 -8.83730880e+00 -1.07023794e+00 4 -5.55988405e+00 7.37514264e+00 2.42970118e+00 5 1.27928809e+01 -2.04969803e+01 2.64650175e+00 6 1.69362154e+00 1.31915998e+00 -2.62583994e+00 7 1.18412872e+00 -2.76901454e+01 -3.07734446e+01 8 -1.21741826e+01 -8.19519141e+00 -3.24305522e+00 9 -5.94995077e+00 -4.97651693e+00 -9.08712387e+00 10 -7.90755783e+00 1.66309418e+01 -1.60151082e+01 11 -1.93421385e+01 -1.42726708e+01 1.43316802e+01 12 -4.39286141e+00 8.07738276e+00 3.17860001e+00 13 1.38711074e+00 -1.06449482e+01 -4.27932588e+01 14 4.15414109e+00 6.80663436e+00 -3.94907690e+00 15 3.05786796e+01 -3.16975022e+00 1.73898840e+01 16 9.66583631e+00 2.38571814e+01 1.51018626e+01 17 -1.30277851e+01 -6.06527947e+00 -4.96974991e-01 18 6.04686745e+00 9.11659754e+00 -2.76721483e+00 19 3.74296481e+00 -8.47085798e+00 7.27585449e+00 20 -3.94522058e+00 6.41009044e+00 5.64789364e+00 21 -1.14117370e+01 -1.14546742e+01 6.15356365e+00 22 2.08941925e+01 2.60882061e+01 2.31638867e+01 23 3.42335905e+00 -2.23089862e+00 3.74712291e+00 24 -1.59473506e-02 4.94503150e+00 4.76331857e+00 25 -3.93220920e+00 -5.84525883e+00 -1.24693974e+00 26 -4.01754735e+00 9.70623909e+00 -8.33784991e+00 27 2.04902291e+01 -3.41984011e+01 5.98516554e+00 28 -3.11071834e+01 2.81144209e+01 6.94085249e+00 29 -6.25662850e+00 -5.73660911e+00 4.26379854e+00 30 5.68895854e+00 1.18047037e+01 -7.10153592e+00 31 7.42683833e+00 -1.18720043e+01 1.16911265e+01 32 5.71513104e+00 1.08925714e+01 1.17424849e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ni (Configuration in file "config-T-Ni.xyz") ----------------------------------------------------------------------------------------------------- Energy = -23.812393739274622 Forces: 1 -5.67124900e+00 -5.53867787e+00 -1.02946001e+01 2 -1.13936202e+01 1.85518699e+01 -6.65103679e+00 3 1.12207631e+01 -8.83730880e+00 -1.07023794e+00 4 -5.55988405e+00 7.37514264e+00 2.42970118e+00 5 1.27928809e+01 -2.04969803e+01 2.64650175e+00 6 1.69362154e+00 1.31915998e+00 -2.62583994e+00 7 1.18412872e+00 -2.76901454e+01 -3.07734446e+01 8 -1.21741826e+01 -8.19519141e+00 -3.24305522e+00 9 -5.94995077e+00 -4.97651693e+00 -9.08712387e+00 10 -7.90755783e+00 1.66309418e+01 -1.60151082e+01 11 -1.93421385e+01 -1.42726708e+01 1.43316802e+01 12 -4.39286141e+00 8.07738276e+00 3.17860001e+00 13 1.38711074e+00 -1.06449482e+01 -4.27932588e+01 14 4.15414109e+00 6.80663436e+00 -3.94907690e+00 15 3.05786796e+01 -3.16975022e+00 1.73898840e+01 16 9.66583631e+00 2.38571814e+01 1.51018626e+01 17 -1.30277851e+01 -6.06527947e+00 -4.96974991e-01 18 6.04686745e+00 9.11659754e+00 -2.76721483e+00 19 3.74296481e+00 -8.47085798e+00 7.27585449e+00 20 -3.94522058e+00 6.41009044e+00 5.64789364e+00 21 -1.14117370e+01 -1.14546742e+01 6.15356365e+00 22 2.08941925e+01 2.60882061e+01 2.31638867e+01 23 3.42335905e+00 -2.23089862e+00 3.74712291e+00 24 -1.59473506e-02 4.94503150e+00 4.76331857e+00 25 -3.93220920e+00 -5.84525883e+00 -1.24693974e+00 26 -4.01754735e+00 9.70623909e+00 -8.33784991e+00 27 2.04902291e+01 -3.41984011e+01 5.98516554e+00 28 -3.11071834e+01 2.81144209e+01 6.94085249e+00 29 -6.25662850e+00 -5.73660911e+00 4.26379854e+00 30 5.68895854e+00 1.18047037e+01 -7.10153592e+00 31 7.42683833e+00 -1.18720043e+01 1.16911265e+01 32 5.71513104e+00 1.08925714e+01 1.17424849e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==27732== Memcheck, a memory error detector ==27732== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==27732== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==27732== Command: python runner2.py Sim_LAMMPS_MEAM_AsadiZaeemNouranian_2015_Ni__SM_078420412697_000 ==27732== ==30646== Warning: invalid file descriptor 1048564 in syscall close() ==30646== Warning: invalid file descriptor 1048565 in syscall close() ==30646== Warning: invalid file descriptor 1048566 in syscall close() ==30646== Warning: invalid file descriptor 1048567 in syscall close() ==30646== Use --log-fd= to select an alternative log fd. ==30646== Warning: invalid file descriptor 1048568 in syscall close() ==30646== Warning: invalid file descriptor 1048569 in syscall close() ==30659== Warning: invalid file descriptor 1048564 in syscall close() ==30659== Warning: invalid file descriptor 1048565 in syscall close() ==30659== Warning: invalid file descriptor 1048566 in syscall close() ==30659== Warning: invalid file descriptor 1048567 in syscall close() ==30659== Use --log-fd= to select an alternative log fd. ==30659== Warning: invalid file descriptor 1048568 in syscall close() ==30659== Warning: invalid file descriptor 1048569 in syscall close() ==30661== Warning: invalid file descriptor 1048564 in syscall close() ==30661== Warning: invalid file descriptor 1048565 in syscall close() ==30661== Warning: invalid file descriptor 1048566 in syscall close() ==30661== Warning: invalid file descriptor 1048567 in syscall close() ==30661== Use --log-fd= to select an alternative log fd. ==30661== Warning: invalid file descriptor 1048568 in syscall close() ==30661== Warning: invalid file descriptor 1048569 in syscall close() ==30663== Warning: invalid file descriptor 1048564 in syscall close() ==30663== Warning: invalid file descriptor 1048565 in syscall close() ==30663== Warning: invalid file descriptor 1048566 in syscall close() ==30663== Warning: invalid file descriptor 1048567 in syscall close() ==30663== Use --log-fd= to select an alternative log fd. ==30663== Warning: invalid file descriptor 1048568 in syscall close() ==30663== Warning: invalid file descriptor 1048569 in syscall close() ==30666== Warning: invalid file descriptor 1048564 in syscall close() ==30666== Warning: invalid file descriptor 1048565 in syscall close() ==30666== Warning: invalid file descriptor 1048566 in syscall close() ==30666== Warning: invalid file descriptor 1048567 in syscall close() ==30666== Use --log-fd= to select an alternative log fd. ==30666== Warning: invalid file descriptor 1048568 in syscall close() ==30666== Warning: invalid file descriptor 1048569 in syscall close() ==30668== Warning: invalid file descriptor 1048564 in syscall close() ==30668== Warning: invalid file descriptor 1048565 in syscall close() ==30668== Warning: invalid file descriptor 1048566 in syscall close() ==30668== Warning: invalid file descriptor 1048567 in syscall close() ==30668== Use --log-fd= to select an alternative log fd. ==30668== Warning: invalid file descriptor 1048568 in syscall close() ==30668== Warning: invalid file descriptor 1048569 in syscall close() ==30669== Warning: invalid file descriptor 1048564 in syscall close() ==30669== Warning: invalid file descriptor 1048565 in syscall close() ==30669== Warning: invalid file descriptor 1048566 in syscall close() ==30669== Warning: invalid file descriptor 1048567 in syscall close() ==30669== Use --log-fd= to select an alternative log fd. ==30669== Warning: invalid file descriptor 1048568 in syscall close() ==30669== Warning: invalid file descriptor 1048569 in syscall close() ==30670== Warning: invalid file descriptor 1048564 in syscall close() ==30670== Warning: invalid file descriptor 1048565 in syscall close() ==30670== Warning: invalid file descriptor 1048566 in syscall close() ==30670== Warning: invalid file descriptor 1048567 in syscall close() ==30670== Use --log-fd= to select an alternative log fd. ==30670== Warning: invalid file descriptor 1048568 in syscall close() ==30670== Warning: invalid file descriptor 1048569 in syscall close() ==27732== ==27732== HEAP SUMMARY: ==27732== in use at exit: 1,780,719 bytes in 1,488 blocks ==27732== total heap usage: 28,631 allocs, 27,143 frees, 48,626,972 bytes allocated ==27732== ==27732== LEAK SUMMARY: ==27732== definitely lost: 0 bytes in 0 blocks ==27732== indirectly lost: 0 bytes in 0 blocks ==27732== possibly lost: 178,423 bytes in 96 blocks ==27732== still reachable: 1,602,296 bytes in 1,392 blocks ==27732== suppressed: 0 bytes in 0 blocks ==27732== Rerun with --leak-check=full to see details of leaked memory ==27732== ==27732== For counts of detected and suppressed errors, rerun with: -v ==27732== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16449 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.