!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : hNN_WT_WenTadmor_2019Grx_C__MO_421038499185_000 Supported species : C random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = C (Configuration in file "config-F-C.xyz") ----------------------------------------------------------------------------------------------------- Energy = -109.45127959776566 Forces: 1 3.54324957e+00 4.36860616e+00 4.44441300e+00 2 1.30307844e+00 -3.56194881e+00 2.47198367e+00 3 -1.54673065e+00 3.68560752e+00 1.10453542e-01 4 1.60148037e+00 -2.80894149e+00 -2.24003554e+00 5 -5.53628871e-01 6.71168952e+00 2.19947030e+00 6 -3.74502632e+00 -2.20461309e+00 3.19993803e+00 7 -3.25816018e+00 5.27418564e+00 1.12849516e+00 8 2.06656736e+00 2.38353727e+00 1.24735767e+00 9 3.33326507e+00 2.62695317e+00 5.73141120e+00 10 -8.69704603e-01 -3.25431228e+00 4.38238806e+00 11 -2.42693215e+00 -4.04082864e-01 3.96309108e-01 12 3.10793234e+00 -4.25316920e+00 -1.42999470e+00 13 2.38841066e+00 8.66276523e-01 4.54461389e+00 14 -2.35593844e+00 -2.10912515e+00 2.03463679e+00 15 -4.68505653e+00 1.35533327e+00 1.29724725e+00 16 -1.89906608e+00 -2.70508689e+00 -3.16664458e+00 17 3.84928170e+00 2.60229743e+00 2.00291713e+00 18 1.24807784e+00 -1.94526481e+00 -3.31754193e+00 19 -1.88084110e+00 4.63444918e+00 -1.69631456e+00 20 2.94675003e+00 -3.07880199e+00 -3.48164350e+00 21 1.61744996e+00 1.81389219e+00 1.35079143e+00 22 -2.48141087e+00 -3.48254398e+00 -1.05595602e+00 23 -3.48363151e+00 2.38508759e+00 -3.99303962e+00 24 1.89380424e+00 -2.19199104e+00 -2.68339071e+00 25 4.04290014e+00 1.05185114e+00 -2.52422049e+00 26 4.42843852e+00 -4.74013463e+00 4.08504104e+00 27 -2.02151194e+00 2.96563611e+00 -2.69673543e+00 28 1.57771808e+00 -1.73527776e+00 -5.28927264e-01 29 2.66192789e+00 1.95725021e+00 -1.29305638e+00 30 -2.49987563e+00 -5.96051159e+00 -4.44647692e-01 31 -7.07708734e+00 3.11828698e+00 -4.43069779e+00 32 -8.25729987e-01 -3.36513434e+00 -5.64462106e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = C (Configuration in file "config-T-C.xyz") ----------------------------------------------------------------------------------------------------- Energy = -109.45127959776566 Forces: 1 3.54324957e+00 4.36860616e+00 4.44441300e+00 2 1.30307844e+00 -3.56194881e+00 2.47198367e+00 3 -1.54673065e+00 3.68560752e+00 1.10453542e-01 4 1.60148037e+00 -2.80894149e+00 -2.24003554e+00 5 -5.53628871e-01 6.71168952e+00 2.19947030e+00 6 -3.74502632e+00 -2.20461309e+00 3.19993803e+00 7 -3.25816018e+00 5.27418564e+00 1.12849516e+00 8 2.06656736e+00 2.38353727e+00 1.24735767e+00 9 3.33326507e+00 2.62695317e+00 5.73141120e+00 10 -8.69704603e-01 -3.25431228e+00 4.38238806e+00 11 -2.42693215e+00 -4.04082864e-01 3.96309108e-01 12 3.10793234e+00 -4.25316920e+00 -1.42999470e+00 13 2.38841066e+00 8.66276523e-01 4.54461389e+00 14 -2.35593844e+00 -2.10912515e+00 2.03463679e+00 15 -4.68505653e+00 1.35533327e+00 1.29724725e+00 16 -1.89906608e+00 -2.70508689e+00 -3.16664458e+00 17 3.84928170e+00 2.60229743e+00 2.00291713e+00 18 1.24807784e+00 -1.94526481e+00 -3.31754193e+00 19 -1.88084110e+00 4.63444918e+00 -1.69631456e+00 20 2.94675003e+00 -3.07880199e+00 -3.48164350e+00 21 1.61744996e+00 1.81389219e+00 1.35079143e+00 22 -2.48141087e+00 -3.48254398e+00 -1.05595602e+00 23 -3.48363151e+00 2.38508759e+00 -3.99303962e+00 24 1.89380424e+00 -2.19199104e+00 -2.68339071e+00 25 4.04290014e+00 1.05185114e+00 -2.52422049e+00 26 4.42843852e+00 -4.74013463e+00 4.08504104e+00 27 -2.02151194e+00 2.96563611e+00 -2.69673543e+00 28 1.57771808e+00 -1.73527776e+00 -5.28927264e-01 29 2.66192789e+00 1.95725021e+00 -1.29305638e+00 30 -2.49987563e+00 -5.96051159e+00 -4.44647692e-01 31 -7.07708734e+00 3.11828698e+00 -4.43069779e+00 32 -8.25729987e-01 -3.36513434e+00 -5.64462106e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==24126== Memcheck, a memory error detector ==24126== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==24126== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==24126== Command: python runner2.py hNN_WT_WenTadmor_2019Grx_C__MO_421038499185_000 ==24126== ==24148== Warning: invalid file descriptor 1048564 in syscall close() ==24148== Warning: invalid file descriptor 1048565 in syscall close() ==24148== Warning: invalid file descriptor 1048566 in syscall close() ==24148== Warning: invalid file descriptor 1048567 in syscall close() ==24148== Use --log-fd= to select an alternative log fd. ==24148== Warning: invalid file descriptor 1048568 in syscall close() ==24148== Warning: invalid file descriptor 1048569 in syscall close() ==24149== Warning: invalid file descriptor 1048564 in syscall close() ==24149== Warning: invalid file descriptor 1048565 in syscall close() ==24149== Warning: invalid file descriptor 1048566 in syscall close() ==24149== Warning: invalid file descriptor 1048567 in syscall close() ==24149== Use --log-fd= to select an alternative log fd. ==24149== Warning: invalid file descriptor 1048568 in syscall close() ==24149== Warning: invalid file descriptor 1048569 in syscall close() ==24150== Warning: invalid file descriptor 1048564 in syscall close() ==24150== Warning: invalid file descriptor 1048565 in syscall close() ==24150== Warning: invalid file descriptor 1048566 in syscall close() ==24150== Warning: invalid file descriptor 1048567 in syscall close() ==24150== Use --log-fd= to select an alternative log fd. ==24150== Warning: invalid file descriptor 1048568 in syscall close() ==24150== Warning: invalid file descriptor 1048569 in syscall close() ==24151== Warning: invalid file descriptor 1048564 in syscall close() ==24151== Warning: invalid file descriptor 1048565 in syscall close() ==24151== Warning: invalid file descriptor 1048566 in syscall close() ==24151== Warning: invalid file descriptor 1048567 in syscall close() ==24151== Use --log-fd= to select an alternative log fd. ==24151== Warning: invalid file descriptor 1048568 in syscall close() ==24151== Warning: invalid file descriptor 1048569 in syscall close() ==24151== Warning: invalid file descriptor 1048570 in syscall close() ==24152== Warning: invalid file descriptor 1048564 in syscall close() ==24152== Warning: invalid file descriptor 1048565 in syscall close() ==24152== Warning: invalid file descriptor 1048566 in syscall close() ==24152== Warning: invalid file descriptor 1048567 in syscall close() ==24152== Use --log-fd= to select an alternative log fd. ==24152== Warning: invalid file descriptor 1048568 in syscall close() ==24152== Warning: invalid file descriptor 1048569 in syscall close() ==24153== Warning: invalid file descriptor 1048564 in syscall close() ==24153== Warning: invalid file descriptor 1048565 in syscall close() ==24153== Warning: invalid file descriptor 1048566 in syscall close() ==24153== Warning: invalid file descriptor 1048567 in syscall close() ==24153== Use --log-fd= to select an alternative log fd. ==24153== Warning: invalid file descriptor 1048568 in syscall close() ==24153== Warning: invalid file descriptor 1048569 in syscall close() ==24126== ==24126== HEAP SUMMARY: ==24126== in use at exit: 1,720,123 bytes in 1,325 blocks ==24126== total heap usage: 34,241 allocs, 32,916 frees, 87,681,810 bytes allocated ==24126== ==24126== LEAK SUMMARY: ==24126== definitely lost: 0 bytes in 0 blocks ==24126== indirectly lost: 0 bytes in 0 blocks ==24126== possibly lost: 178,943 bytes in 97 blocks ==24126== still reachable: 1,541,180 bytes in 1,228 blocks ==24126== suppressed: 0 bytes in 0 blocks ==24126== Rerun with --leak-check=full to see details of leaked memory ==24126== ==24126== For counts of detected and suppressed errors, rerun with: -v ==24126== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 11243 from 585) ================================================================================ 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.