!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : EAM_Dynamo_HanZepedaAckland_2003_V__MO_411020944797_000 Supported species : V random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = V (Configuration in file "config-F-V.xyz") ----------------------------------------------------------------------------------------------------- Energy = 4.716237186338494 Forces: 1 -6.25578603e+00 -5.96595550e+00 -9.49412144e+00 2 -3.43567788e+00 1.03567125e+01 -8.15889874e+00 3 1.59523538e+00 -8.95109493e+00 5.39605948e+00 4 -6.56983708e+00 5.54180677e+00 2.40229797e+00 5 5.11678077e+00 -1.22150741e+01 -6.76877949e+00 6 5.90627607e+00 3.58450939e+00 -5.49294021e+00 7 1.21814014e+01 -2.23970188e+01 -2.51395527e+01 8 -1.31276178e+01 -3.12785254e+00 -8.49728073e+00 9 -9.49618762e+00 -1.00218172e+01 -1.60930300e+01 10 6.51232167e+00 1.51633348e+01 -1.21762471e+01 11 -2.48374670e+00 -1.23289012e+01 3.56980112e+00 12 -1.33217834e+01 1.25742759e+01 7.44936100e+00 13 -1.09284773e+01 -1.26330989e+01 -3.71942874e+01 14 6.59891404e+00 7.63171050e+00 -5.28462910e+00 15 3.33080688e+01 -5.29078189e+00 1.21745186e+01 16 -9.35230964e-01 2.64400662e+01 8.53824861e+00 17 -9.79064744e+00 -6.61821739e+00 3.59477744e-01 18 2.00055926e+00 7.49804240e+00 -1.17153746e+00 19 2.08876423e+00 -1.04610116e+01 6.59404874e+00 20 -6.15596713e+00 4.77302658e+00 5.51809857e+00 21 -1.27192999e+01 -1.62288409e+01 1.44327569e+01 22 2.27881679e+01 1.25542731e+01 1.09541116e+01 23 7.81186647e+00 -4.07810768e+00 6.24603964e+00 24 -3.07832633e+00 6.96049886e+00 8.68067367e+00 25 -1.13286388e+01 -4.58070917e+00 2.49047242e+00 26 -3.20904500e+00 1.67245236e+01 -7.27980794e+00 27 1.87910195e+01 -3.21555685e+01 1.02206014e+01 28 -2.92334390e+01 2.44408727e+01 4.84499586e+00 29 -6.17164617e+00 9.45583988e-01 1.24923853e+01 30 9.39604478e+00 1.51180976e+01 -6.44761595e+00 31 9.30428364e+00 -1.36703388e+01 1.42616888e+01 32 4.84165064e+00 1.04170543e+01 1.25730908e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = V (Configuration in file "config-T-V.xyz") ----------------------------------------------------------------------------------------------------- Energy = 4.716237186338494 Forces: 1 -6.25578603e+00 -5.96595550e+00 -9.49412144e+00 2 -3.43567788e+00 1.03567125e+01 -8.15889874e+00 3 1.59523538e+00 -8.95109493e+00 5.39605948e+00 4 -6.56983708e+00 5.54180677e+00 2.40229797e+00 5 5.11678077e+00 -1.22150741e+01 -6.76877949e+00 6 5.90627607e+00 3.58450939e+00 -5.49294021e+00 7 1.21814014e+01 -2.23970188e+01 -2.51395527e+01 8 -1.31276178e+01 -3.12785254e+00 -8.49728073e+00 9 -9.49618762e+00 -1.00218172e+01 -1.60930300e+01 10 6.51232167e+00 1.51633348e+01 -1.21762471e+01 11 -2.48374670e+00 -1.23289012e+01 3.56980112e+00 12 -1.33217834e+01 1.25742759e+01 7.44936100e+00 13 -1.09284773e+01 -1.26330989e+01 -3.71942874e+01 14 6.59891404e+00 7.63171050e+00 -5.28462910e+00 15 3.33080688e+01 -5.29078189e+00 1.21745186e+01 16 -9.35230964e-01 2.64400662e+01 8.53824861e+00 17 -9.79064744e+00 -6.61821739e+00 3.59477744e-01 18 2.00055926e+00 7.49804240e+00 -1.17153746e+00 19 2.08876423e+00 -1.04610116e+01 6.59404874e+00 20 -6.15596713e+00 4.77302658e+00 5.51809857e+00 21 -1.27192999e+01 -1.62288409e+01 1.44327569e+01 22 2.27881679e+01 1.25542731e+01 1.09541116e+01 23 7.81186647e+00 -4.07810768e+00 6.24603964e+00 24 -3.07832633e+00 6.96049886e+00 8.68067367e+00 25 -1.13286388e+01 -4.58070917e+00 2.49047242e+00 26 -3.20904500e+00 1.67245236e+01 -7.27980794e+00 27 1.87910195e+01 -3.21555685e+01 1.02206014e+01 28 -2.92334390e+01 2.44408727e+01 4.84499586e+00 29 -6.17164617e+00 9.45583988e-01 1.24923853e+01 30 9.39604478e+00 1.51180976e+01 -6.44761595e+00 31 9.30428364e+00 -1.36703388e+01 1.42616888e+01 32 4.84165064e+00 1.04170543e+01 1.25730908e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==32433== Memcheck, a memory error detector ==32433== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==32433== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==32433== Command: python runner2.py EAM_Dynamo_HanZepedaAckland_2003_V__MO_411020944797_000 ==32433== ==33556== Warning: invalid file descriptor 1048564 in syscall close() ==33556== Warning: invalid file descriptor 1048565 in syscall close() ==33556== Warning: invalid file descriptor 1048566 in syscall close() ==33556== Warning: invalid file descriptor 1048567 in syscall close() ==33556== Use --log-fd= to select an alternative log fd. ==33556== Warning: invalid file descriptor 1048568 in syscall close() ==33556== Warning: invalid file descriptor 1048569 in syscall close() ==33557== Warning: invalid file descriptor 1048564 in syscall close() ==33557== Warning: invalid file descriptor 1048565 in syscall close() ==33557== Warning: invalid file descriptor 1048566 in syscall close() ==33557== Warning: invalid file descriptor 1048567 in syscall close() ==33557== Use --log-fd= to select an alternative log fd. ==33557== Warning: invalid file descriptor 1048568 in syscall close() ==33557== Warning: invalid file descriptor 1048569 in syscall close() ==33582== Warning: invalid file descriptor 1048564 in syscall close() ==33582== Warning: invalid file descriptor 1048565 in syscall close() ==33582== Warning: invalid file descriptor 1048566 in syscall close() ==33582== Warning: invalid file descriptor 1048567 in syscall close() ==33582== Use --log-fd= to select an alternative log fd. ==33582== Warning: invalid file descriptor 1048568 in syscall close() ==33582== Warning: invalid file descriptor 1048569 in syscall close() ==33583== Warning: invalid file descriptor 1048564 in syscall close() ==33583== Warning: invalid file descriptor 1048565 in syscall close() ==33583== Warning: invalid file descriptor 1048566 in syscall close() ==33583== Warning: invalid file descriptor 1048567 in syscall close() ==33583== Use --log-fd= to select an alternative log fd. ==33583== Warning: invalid file descriptor 1048568 in syscall close() ==33583== Warning: invalid file descriptor 1048569 in syscall close() ==33590== Warning: invalid file descriptor 1048564 in syscall close() ==33590== Warning: invalid file descriptor 1048565 in syscall close() ==33590== Warning: invalid file descriptor 1048566 in syscall close() ==33590== Warning: invalid file descriptor 1048567 in syscall close() ==33590== Use --log-fd= to select an alternative log fd. ==33590== Warning: invalid file descriptor 1048568 in syscall close() ==33590== Warning: invalid file descriptor 1048569 in syscall close() ==33592== Warning: invalid file descriptor 1048564 in syscall close() ==33592== Warning: invalid file descriptor 1048565 in syscall close() ==33592== Warning: invalid file descriptor 1048566 in syscall close() ==33592== Warning: invalid file descriptor 1048567 in syscall close() ==33592== Use --log-fd= to select an alternative log fd. ==33592== Warning: invalid file descriptor 1048568 in syscall close() ==33592== Warning: invalid file descriptor 1048569 in syscall close() ==32433== ==32433== HEAP SUMMARY: ==32433== in use at exit: 1,718,308 bytes in 1,321 blocks ==32433== total heap usage: 31,217 allocs, 29,896 frees, 47,298,400 bytes allocated ==32433== ==32433== LEAK SUMMARY: ==32433== definitely lost: 0 bytes in 0 blocks ==32433== indirectly lost: 0 bytes in 0 blocks ==32433== possibly lost: 178,943 bytes in 97 blocks ==32433== still reachable: 1,539,365 bytes in 1,224 blocks ==32433== suppressed: 0 bytes in 0 blocks ==32433== Rerun with --leak-check=full to see details of leaked memory ==32433== ==32433== For counts of detected and suppressed errors, rerun with: -v ==32433== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16330 from 612) ================================================================================ 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.