!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_ZhouJohnsonWadley_2004_Cu__MO_127245782811_005 Supported species : Cu random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Cu (Configuration in file "config-F-Cu.xyz") ----------------------------------------------------------------------------------------------------- Energy = 6.795338337914177 Forces: 1 -2.77353066e+00 -6.21870096e+00 -6.63369274e+00 2 -8.09475752e+00 1.22987529e+01 -8.20343988e+00 3 7.40159604e-01 -8.46283901e+00 -1.43465366e+00 4 -4.02915951e+00 3.86157210e+00 3.90681061e+00 5 1.01417008e+01 -1.63242732e+01 -1.67049392e+00 6 3.00559577e+00 1.63561694e+00 -5.19027994e+00 7 3.75756653e+00 -2.17885906e+01 -2.02370013e+01 8 -7.75390804e+00 -8.89398961e+00 9.60887426e-01 9 -9.87112636e+00 -5.65707475e+00 -1.45102944e+01 10 -3.41381260e+00 1.63257264e+01 -1.58514962e+01 11 -2.29266140e+00 -1.27364758e+01 1.03559956e+01 12 -7.83204614e+00 1.34799857e+01 7.00824990e-02 13 -3.82471526e+00 -7.33097255e+00 -3.35000758e+01 14 5.31218202e+00 7.01741620e+00 -4.36108860e+00 15 2.85006958e+01 -3.91592301e+00 9.22199455e+00 16 3.69510233e+00 2.18085927e+01 1.16410544e+01 17 -8.64421377e+00 -3.50652935e+00 -3.54101512e+00 18 -2.88508748e+00 7.77058694e+00 3.17884814e+00 19 4.60967316e+00 -6.80874330e+00 5.21514203e+00 20 -2.96303228e+00 6.22626099e+00 3.98507421e+00 21 -8.10432751e+00 -8.21286004e+00 6.24425699e+00 22 1.33236725e+01 1.85744149e+01 1.61214408e+01 23 2.33362407e+00 -6.97966188e-01 4.35289561e+00 24 1.90644903e+00 8.46184823e-01 3.76948331e+00 25 -5.40123538e+00 -7.96631253e+00 9.86204607e+00 26 -5.40084940e+00 1.34101890e+01 -7.63842281e+00 27 8.49750524e+00 -2.52575319e+01 6.93373950e+00 28 -2.04997045e+01 1.70194301e+01 2.63170024e+00 29 -6.07171084e+00 -9.75553187e+00 3.18156121e+00 30 6.07000187e+00 1.02423767e+01 3.28038612e-01 31 1.14139337e+01 -7.81251833e+00 9.44120680e+00 32 6.54801628e+00 1.08297267e+01 1.13696957e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Cu (Configuration in file "config-T-Cu.xyz") ----------------------------------------------------------------------------------------------------- Energy = 6.795338337914177 Forces: 1 -2.77353066e+00 -6.21870096e+00 -6.63369274e+00 2 -8.09475752e+00 1.22987529e+01 -8.20343988e+00 3 7.40159604e-01 -8.46283901e+00 -1.43465366e+00 4 -4.02915951e+00 3.86157210e+00 3.90681061e+00 5 1.01417008e+01 -1.63242732e+01 -1.67049392e+00 6 3.00559577e+00 1.63561694e+00 -5.19027994e+00 7 3.75756653e+00 -2.17885906e+01 -2.02370013e+01 8 -7.75390804e+00 -8.89398961e+00 9.60887426e-01 9 -9.87112636e+00 -5.65707475e+00 -1.45102944e+01 10 -3.41381260e+00 1.63257264e+01 -1.58514962e+01 11 -2.29266140e+00 -1.27364758e+01 1.03559956e+01 12 -7.83204614e+00 1.34799857e+01 7.00824990e-02 13 -3.82471526e+00 -7.33097255e+00 -3.35000758e+01 14 5.31218202e+00 7.01741620e+00 -4.36108860e+00 15 2.85006958e+01 -3.91592301e+00 9.22199455e+00 16 3.69510233e+00 2.18085927e+01 1.16410544e+01 17 -8.64421377e+00 -3.50652935e+00 -3.54101512e+00 18 -2.88508748e+00 7.77058694e+00 3.17884814e+00 19 4.60967316e+00 -6.80874330e+00 5.21514203e+00 20 -2.96303228e+00 6.22626099e+00 3.98507421e+00 21 -8.10432751e+00 -8.21286004e+00 6.24425699e+00 22 1.33236725e+01 1.85744149e+01 1.61214408e+01 23 2.33362407e+00 -6.97966188e-01 4.35289561e+00 24 1.90644903e+00 8.46184823e-01 3.76948331e+00 25 -5.40123538e+00 -7.96631253e+00 9.86204607e+00 26 -5.40084940e+00 1.34101890e+01 -7.63842281e+00 27 8.49750524e+00 -2.52575319e+01 6.93373950e+00 28 -2.04997045e+01 1.70194301e+01 2.63170024e+00 29 -6.07171084e+00 -9.75553187e+00 3.18156121e+00 30 6.07000187e+00 1.02423767e+01 3.28038612e-01 31 1.14139337e+01 -7.81251833e+00 9.44120680e+00 32 6.54801628e+00 1.08297267e+01 1.13696957e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==80075== Memcheck, a memory error detector ==80075== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==80075== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==80075== Command: python runner2.py EAM_Dynamo_ZhouJohnsonWadley_2004_Cu__MO_127245782811_005 ==80075== ==81257== Warning: invalid file descriptor 1048564 in syscall close() ==81257== Warning: invalid file descriptor 1048565 in syscall close() ==81257== Warning: invalid file descriptor 1048566 in syscall close() ==81257== Warning: invalid file descriptor 1048567 in syscall close() ==81257== Use --log-fd= to select an alternative log fd. ==81257== Warning: invalid file descriptor 1048568 in syscall close() ==81257== Warning: invalid file descriptor 1048569 in syscall close() ==81259== Warning: invalid file descriptor 1048564 in syscall close() ==81259== Warning: invalid file descriptor 1048565 in syscall close() ==81259== Warning: invalid file descriptor 1048566 in syscall close() ==81259== Warning: invalid file descriptor 1048567 in syscall close() ==81259== Use --log-fd= to select an alternative log fd. ==81259== Warning: invalid file descriptor 1048568 in syscall close() ==81259== Warning: invalid file descriptor 1048569 in syscall close() ==81265== Warning: invalid file descriptor 1048564 in syscall close() ==81265== Warning: invalid file descriptor 1048565 in syscall close() ==81265== Warning: invalid file descriptor 1048566 in syscall close() ==81265== Warning: invalid file descriptor 1048567 in syscall close() ==81265== Use --log-fd= to select an alternative log fd. ==81265== Warning: invalid file descriptor 1048568 in syscall close() ==81265== Warning: invalid file descriptor 1048569 in syscall close() ==81266== Warning: invalid file descriptor 1048564 in syscall close() ==81266== Warning: invalid file descriptor 1048565 in syscall close() ==81266== Warning: invalid file descriptor 1048566 in syscall close() ==81266== Warning: invalid file descriptor 1048567 in syscall close() ==81266== Use --log-fd= to select an alternative log fd. ==81266== Warning: invalid file descriptor 1048568 in syscall close() ==81266== Warning: invalid file descriptor 1048569 in syscall close() ==81267== Warning: invalid file descriptor 1048564 in syscall close() ==81267== Warning: invalid file descriptor 1048565 in syscall close() ==81267== Warning: invalid file descriptor 1048566 in syscall close() ==81267== Warning: invalid file descriptor 1048567 in syscall close() ==81267== Use --log-fd= to select an alternative log fd. ==81267== Warning: invalid file descriptor 1048568 in syscall close() ==81267== Warning: invalid file descriptor 1048569 in syscall close() ==81268== Warning: invalid file descriptor 1048564 in syscall close() ==81268== Warning: invalid file descriptor 1048565 in syscall close() ==81268== Warning: invalid file descriptor 1048566 in syscall close() ==81268== Warning: invalid file descriptor 1048567 in syscall close() ==81268== Use --log-fd= to select an alternative log fd. ==81268== Warning: invalid file descriptor 1048568 in syscall close() ==81268== Warning: invalid file descriptor 1048569 in syscall close() ==80075== ==80075== HEAP SUMMARY: ==80075== in use at exit: 1,718,292 bytes in 1,321 blocks ==80075== total heap usage: 31,120 allocs, 29,799 frees, 40,376,526 bytes allocated ==80075== ==80075== LEAK SUMMARY: ==80075== definitely lost: 0 bytes in 0 blocks ==80075== indirectly lost: 0 bytes in 0 blocks ==80075== possibly lost: 178,943 bytes in 97 blocks ==80075== still reachable: 1,539,349 bytes in 1,224 blocks ==80075== suppressed: 0 bytes in 0 blocks ==80075== Rerun with --leak-check=full to see details of leaked memory ==80075== ==80075== For counts of detected and suppressed errors, rerun with: -v ==80075== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16338 from 599) ================================================================================ 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.