!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_ZhouWadleyJohnson_2001_Cu__MO_380822813353_000 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 = -20.577083342616653 Forces: 1 -2.00136265e+00 -4.20296484e+00 -4.50478848e+00 2 -5.39537617e+00 7.48807914e+00 -6.18126839e+00 3 2.07966045e+00 -5.98893989e+00 -1.17488187e+00 4 -4.20341443e+00 3.28343102e+00 1.51513447e+00 5 6.48713476e+00 -1.08896831e+01 -1.40691162e+00 6 2.31127157e+00 9.32163464e-01 -3.89414626e+00 7 3.01141762e+00 -1.48546643e+01 -1.30957127e+01 8 -6.96327945e+00 -7.54992931e+00 2.38847377e+00 9 -7.43268695e+00 -1.65984883e+00 -7.68068811e+00 10 -3.77440803e+00 1.14950166e+01 -1.05309809e+01 11 -3.89061099e+00 -8.55338422e+00 7.52407582e+00 12 -4.58467492e+00 8.99197983e+00 -4.35809979e+00 13 -1.86798202e+00 -4.76305463e+00 -2.39492295e+01 14 3.96142220e+00 5.12071982e+00 -3.12977513e+00 15 2.10413325e+01 -9.79381754e-01 7.11625265e+00 16 2.95243151e+00 1.64479969e+01 7.90807347e+00 17 -8.95813539e+00 -5.53703297e+00 -1.97350007e+00 18 5.53527820e+00 7.33006737e+00 4.06598075e-01 19 2.99165898e+00 -6.53013592e+00 4.16341606e+00 20 -3.34243934e+00 4.13533538e+00 4.37317355e+00 21 -7.46380122e+00 -4.96903283e+00 3.04691648e+00 22 9.65711249e+00 1.21934067e+01 9.96421663e+00 23 2.35730180e+00 -5.96919050e-01 4.65907164e+00 24 1.88292444e+00 1.93768200e+00 2.31735559e+00 25 -4.80533773e+00 -7.64957406e+00 4.98334791e+00 26 -2.96801390e+00 1.05007419e+01 -4.64341118e+00 27 5.65897314e+00 -1.63250238e+01 6.49938126e+00 28 -1.35734763e+01 1.15467964e+01 2.69042860e+00 29 -4.46691475e+00 -8.02806809e+00 3.00681704e+00 30 4.48056262e+00 8.07761100e+00 -3.01218902e+00 31 7.01922978e+00 -7.86596112e+00 8.56440439e+00 32 4.26420220e+00 7.46257120e+00 8.40844562e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Cu (Configuration in file "config-T-Cu.xyz") ----------------------------------------------------------------------------------------------------- Energy = -20.577083342616653 Forces: 1 -2.00136265e+00 -4.20296484e+00 -4.50478848e+00 2 -5.39537617e+00 7.48807914e+00 -6.18126839e+00 3 2.07966045e+00 -5.98893989e+00 -1.17488187e+00 4 -4.20341443e+00 3.28343102e+00 1.51513447e+00 5 6.48713476e+00 -1.08896831e+01 -1.40691162e+00 6 2.31127157e+00 9.32163464e-01 -3.89414626e+00 7 3.01141762e+00 -1.48546643e+01 -1.30957127e+01 8 -6.96327945e+00 -7.54992931e+00 2.38847377e+00 9 -7.43268695e+00 -1.65984883e+00 -7.68068811e+00 10 -3.77440803e+00 1.14950166e+01 -1.05309809e+01 11 -3.89061099e+00 -8.55338422e+00 7.52407582e+00 12 -4.58467492e+00 8.99197983e+00 -4.35809979e+00 13 -1.86798202e+00 -4.76305463e+00 -2.39492295e+01 14 3.96142220e+00 5.12071982e+00 -3.12977513e+00 15 2.10413325e+01 -9.79381754e-01 7.11625265e+00 16 2.95243151e+00 1.64479969e+01 7.90807347e+00 17 -8.95813539e+00 -5.53703297e+00 -1.97350007e+00 18 5.53527820e+00 7.33006737e+00 4.06598075e-01 19 2.99165898e+00 -6.53013592e+00 4.16341606e+00 20 -3.34243934e+00 4.13533538e+00 4.37317355e+00 21 -7.46380122e+00 -4.96903283e+00 3.04691648e+00 22 9.65711249e+00 1.21934067e+01 9.96421663e+00 23 2.35730180e+00 -5.96919050e-01 4.65907164e+00 24 1.88292444e+00 1.93768200e+00 2.31735559e+00 25 -4.80533773e+00 -7.64957406e+00 4.98334791e+00 26 -2.96801390e+00 1.05007419e+01 -4.64341118e+00 27 5.65897314e+00 -1.63250238e+01 6.49938126e+00 28 -1.35734763e+01 1.15467964e+01 2.69042860e+00 29 -4.46691475e+00 -8.02806809e+00 3.00681704e+00 30 4.48056262e+00 8.07761100e+00 -3.01218902e+00 31 7.01922978e+00 -7.86596112e+00 8.56440439e+00 32 4.26420220e+00 7.46257120e+00 8.40844562e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==97944== Memcheck, a memory error detector ==97944== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==97944== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==97944== Command: python runner2.py EAM_Dynamo_ZhouWadleyJohnson_2001_Cu__MO_380822813353_000 ==97944== ==99343== Warning: invalid file descriptor 1048564 in syscall close() ==99343== Warning: invalid file descriptor 1048565 in syscall close() ==99343== Warning: invalid file descriptor 1048566 in syscall close() ==99343== Warning: invalid file descriptor 1048567 in syscall close() ==99343== Use --log-fd= to select an alternative log fd. ==99343== Warning: invalid file descriptor 1048568 in syscall close() ==99343== Warning: invalid file descriptor 1048569 in syscall close() ==99354== Warning: invalid file descriptor 1048564 in syscall close() ==99354== Warning: invalid file descriptor 1048565 in syscall close() ==99354== Warning: invalid file descriptor 1048566 in syscall close() ==99354== Warning: invalid file descriptor 1048567 in syscall close() ==99354== Use --log-fd= to select an alternative log fd. ==99354== Warning: invalid file descriptor 1048568 in syscall close() ==99354== Warning: invalid file descriptor 1048569 in syscall close() ==99517== Warning: invalid file descriptor 1048564 in syscall close() ==99517== Warning: invalid file descriptor 1048565 in syscall close() ==99517== Warning: invalid file descriptor 1048566 in syscall close() ==99517== Warning: invalid file descriptor 1048567 in syscall close() ==99517== Use --log-fd= to select an alternative log fd. ==99517== Warning: invalid file descriptor 1048568 in syscall close() ==99517== Warning: invalid file descriptor 1048569 in syscall close() ==99523== Warning: invalid file descriptor 1048564 in syscall close() ==99523== Warning: invalid file descriptor 1048565 in syscall close() ==99523== Warning: invalid file descriptor 1048566 in syscall close() ==99523== Warning: invalid file descriptor 1048567 in syscall close() ==99523== Use --log-fd= to select an alternative log fd. ==99523== Warning: invalid file descriptor 1048568 in syscall close() ==99523== Warning: invalid file descriptor 1048569 in syscall close() ==99531== Warning: invalid file descriptor 1048564 in syscall close() ==99531== Warning: invalid file descriptor 1048565 in syscall close() ==99531== Warning: invalid file descriptor 1048566 in syscall close() ==99531== Warning: invalid file descriptor 1048567 in syscall close() ==99531== Use --log-fd= to select an alternative log fd. ==99531== Warning: invalid file descriptor 1048568 in syscall close() ==99531== Warning: invalid file descriptor 1048569 in syscall close() ==99540== Warning: invalid file descriptor 1048564 in syscall close() ==99540== Warning: invalid file descriptor 1048565 in syscall close() ==99540== Warning: invalid file descriptor 1048566 in syscall close() ==99540== Warning: invalid file descriptor 1048567 in syscall close() ==99540== Use --log-fd= to select an alternative log fd. ==99540== Warning: invalid file descriptor 1048568 in syscall close() ==99540== Warning: invalid file descriptor 1048569 in syscall close() ==97944== ==97944== HEAP SUMMARY: ==97944== in use at exit: 1,718,292 bytes in 1,321 blocks ==97944== total heap usage: 31,120 allocs, 29,799 frees, 47,289,518 bytes allocated ==97944== ==97944== LEAK SUMMARY: ==97944== definitely lost: 0 bytes in 0 blocks ==97944== indirectly lost: 0 bytes in 0 blocks ==97944== possibly lost: 178,943 bytes in 97 blocks ==97944== still reachable: 1,539,349 bytes in 1,224 blocks ==97944== suppressed: 0 bytes in 0 blocks ==97944== Rerun with --leak-check=full to see details of leaked memory ==97944== ==97944== For counts of detected and suppressed errors, rerun with: -v ==97944== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16324 from 600) ================================================================================ 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.