!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_WilliamsMishinHamilton_2006_Ag__MO_131620013077_005 Supported species : Ag random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Ag (Configuration in file "config-F-Ag.xyz") ----------------------------------------------------------------------------------------------------- Energy = 195.30822155166376 Forces: 1 -7.72174221e+00 -1.67216810e+01 -1.43947267e+01 2 -5.59014268e+00 7.23724229e+00 -1.60199933e+01 3 5.51173130e+00 -1.56913911e+01 -2.85696781e+00 4 -1.46711888e+01 8.10855696e+00 6.85938594e+00 5 2.02289700e+00 -2.15819623e+01 -9.49821529e+00 6 1.28915238e+01 2.57425946e+00 -1.51896482e+01 7 1.30103478e+01 -2.58537092e+01 -1.40884739e+01 8 -1.09954124e+01 -1.07617967e+01 4.58639407e+00 9 -1.06593494e+01 -1.47908050e+01 -2.38453263e+01 10 1.27899021e+01 2.21251289e+01 -1.80382749e+01 11 1.80839984e+00 -1.33477444e+01 -9.36558561e+00 12 -2.42026856e+01 2.14185199e+01 1.05598923e+01 13 -8.98405977e+00 -5.48383734e+00 -4.02714425e+01 14 1.22771926e+01 1.50460211e+01 -1.26466570e+01 15 3.70568133e+01 -8.06706906e+00 5.13744702e+00 16 -1.40644053e+00 3.62932543e+01 2.98611435e+00 17 -2.37455716e+01 -1.47715531e+01 -5.48472711e+00 18 8.79221068e+00 1.03652431e+01 -1.85667993e+00 19 8.67568494e+00 -1.76878275e+01 1.51892361e+01 20 -1.29392843e+01 9.76914866e+00 1.52265307e+01 21 -1.19564704e+01 -1.50770600e+01 6.92384565e+00 22 2.23365767e+01 1.72218050e+01 1.24692233e+01 23 7.45910203e+00 -4.29809436e+00 1.26062924e+01 24 1.43070875e+00 -4.49416690e+00 1.14673643e+01 25 -2.96069252e+01 -1.92421513e+00 1.38808374e+01 26 -6.23809440e+00 2.92320700e+01 -5.88376647e+00 27 4.45562200e-01 -2.21159941e+01 1.65314391e+01 28 -2.35898570e+01 1.76347828e+01 7.67520782e+00 29 4.21105801e-01 -1.44321625e+01 8.08816132e+00 30 1.56264268e+01 1.76432971e+01 3.25283235e+00 31 2.08593811e+01 -7.09320951e+00 1.53966533e+01 32 8.89165744e+00 1.95249498e+01 2.06036276e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ag (Configuration in file "config-T-Ag.xyz") ----------------------------------------------------------------------------------------------------- Energy = 195.30822155166376 Forces: 1 -7.72174221e+00 -1.67216810e+01 -1.43947267e+01 2 -5.59014268e+00 7.23724229e+00 -1.60199933e+01 3 5.51173130e+00 -1.56913911e+01 -2.85696781e+00 4 -1.46711888e+01 8.10855696e+00 6.85938594e+00 5 2.02289700e+00 -2.15819623e+01 -9.49821529e+00 6 1.28915238e+01 2.57425946e+00 -1.51896482e+01 7 1.30103478e+01 -2.58537092e+01 -1.40884739e+01 8 -1.09954124e+01 -1.07617967e+01 4.58639407e+00 9 -1.06593494e+01 -1.47908050e+01 -2.38453263e+01 10 1.27899021e+01 2.21251289e+01 -1.80382749e+01 11 1.80839984e+00 -1.33477444e+01 -9.36558561e+00 12 -2.42026856e+01 2.14185199e+01 1.05598923e+01 13 -8.98405977e+00 -5.48383734e+00 -4.02714425e+01 14 1.22771926e+01 1.50460211e+01 -1.26466570e+01 15 3.70568133e+01 -8.06706906e+00 5.13744702e+00 16 -1.40644053e+00 3.62932543e+01 2.98611435e+00 17 -2.37455716e+01 -1.47715531e+01 -5.48472711e+00 18 8.79221068e+00 1.03652431e+01 -1.85667993e+00 19 8.67568494e+00 -1.76878275e+01 1.51892361e+01 20 -1.29392843e+01 9.76914866e+00 1.52265307e+01 21 -1.19564704e+01 -1.50770600e+01 6.92384565e+00 22 2.23365767e+01 1.72218050e+01 1.24692233e+01 23 7.45910203e+00 -4.29809436e+00 1.26062924e+01 24 1.43070875e+00 -4.49416690e+00 1.14673643e+01 25 -2.96069252e+01 -1.92421513e+00 1.38808374e+01 26 -6.23809440e+00 2.92320700e+01 -5.88376647e+00 27 4.45562200e-01 -2.21159941e+01 1.65314391e+01 28 -2.35898570e+01 1.76347828e+01 7.67520782e+00 29 4.21105801e-01 -1.44321625e+01 8.08816132e+00 30 1.56264268e+01 1.76432971e+01 3.25283235e+00 31 2.08593811e+01 -7.09320951e+00 1.53966533e+01 32 8.89165744e+00 1.95249498e+01 2.06036276e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==71339== Memcheck, a memory error detector ==71339== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==71339== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==71339== Command: python runner2.py EAM_Dynamo_WilliamsMishinHamilton_2006_Ag__MO_131620013077_005 ==71339== ==72506== Warning: invalid file descriptor 1048564 in syscall close() ==72506== Warning: invalid file descriptor 1048565 in syscall close() ==72506== Warning: invalid file descriptor 1048566 in syscall close() ==72506== Warning: invalid file descriptor 1048567 in syscall close() ==72506== Use --log-fd= to select an alternative log fd. ==72506== Warning: invalid file descriptor 1048568 in syscall close() ==72506== Warning: invalid file descriptor 1048569 in syscall close() ==72507== Warning: invalid file descriptor 1048564 in syscall close() ==72507== Warning: invalid file descriptor 1048565 in syscall close() ==72507== Warning: invalid file descriptor 1048566 in syscall close() ==72507== Warning: invalid file descriptor 1048567 in syscall close() ==72507== Use --log-fd= to select an alternative log fd. ==72507== Warning: invalid file descriptor 1048568 in syscall close() ==72507== Warning: invalid file descriptor 1048569 in syscall close() ==72509== Warning: invalid file descriptor 1048564 in syscall close() ==72509== Warning: invalid file descriptor 1048565 in syscall close() ==72509== Warning: invalid file descriptor 1048566 in syscall close() ==72509== Warning: invalid file descriptor 1048567 in syscall close() ==72509== Use --log-fd= to select an alternative log fd. ==72509== Warning: invalid file descriptor 1048568 in syscall close() ==72509== Warning: invalid file descriptor 1048569 in syscall close() ==72510== Warning: invalid file descriptor 1048564 in syscall close() ==72510== Warning: invalid file descriptor 1048565 in syscall close() ==72510== Warning: invalid file descriptor 1048566 in syscall close() ==72510== Warning: invalid file descriptor 1048567 in syscall close() ==72510== Use --log-fd= to select an alternative log fd. ==72510== Warning: invalid file descriptor 1048568 in syscall close() ==72510== Warning: invalid file descriptor 1048569 in syscall close() ==72511== Warning: invalid file descriptor 1048564 in syscall close() ==72511== Warning: invalid file descriptor 1048565 in syscall close() ==72511== Warning: invalid file descriptor 1048566 in syscall close() ==72511== Warning: invalid file descriptor 1048567 in syscall close() ==72511== Use --log-fd= to select an alternative log fd. ==72511== Warning: invalid file descriptor 1048568 in syscall close() ==72511== Warning: invalid file descriptor 1048569 in syscall close() ==72512== Warning: invalid file descriptor 1048564 in syscall close() ==72512== Warning: invalid file descriptor 1048565 in syscall close() ==72512== Warning: invalid file descriptor 1048566 in syscall close() ==72512== Warning: invalid file descriptor 1048567 in syscall close() ==72512== Use --log-fd= to select an alternative log fd. ==72512== Warning: invalid file descriptor 1048568 in syscall close() ==72512== Warning: invalid file descriptor 1048569 in syscall close() ==71339== ==71339== HEAP SUMMARY: ==71339== in use at exit: 1,718,292 bytes in 1,321 blocks ==71339== total heap usage: 31,120 allocs, 29,799 frees, 47,289,239 bytes allocated ==71339== ==71339== LEAK SUMMARY: ==71339== definitely lost: 0 bytes in 0 blocks ==71339== indirectly lost: 0 bytes in 0 blocks ==71339== possibly lost: 178,943 bytes in 97 blocks ==71339== still reachable: 1,539,349 bytes in 1,224 blocks ==71339== suppressed: 0 bytes in 0 blocks ==71339== Rerun with --leak-check=full to see details of leaked memory ==71339== ==71339== For counts of detected and suppressed errors, rerun with: -v ==71339== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16357 from 601) ================================================================================ 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.