!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_Olsson_2010_Au__MO_228280943430_000 Supported species : Au random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Au (Configuration in file "config-F-Au.xyz") ----------------------------------------------------------------------------------------------------- Energy = 112.45207738343937 Forces: 1 -6.81744356e+00 -2.05527854e+01 -2.34218606e+01 2 -7.90454612e+00 7.57624347e+00 -1.69560340e+01 3 8.57907984e+00 -1.77157649e+01 -4.16515764e+00 4 -1.37721392e+01 2.37133537e+01 1.12749709e+01 5 6.21382387e+00 -2.26636340e+01 -9.27080767e+00 6 1.01438411e+01 4.54858441e+00 -1.46345708e+01 7 1.74291901e+01 -4.47527505e+01 -3.12890200e+01 8 -3.47660455e+01 -2.91264302e+01 -3.84975503e+00 9 -2.25411868e+01 -4.71217677e+00 -2.13785712e+01 10 -1.17499496e+01 3.47758306e+01 -3.17963166e+01 11 -1.90907964e+01 -2.41614028e+01 2.18160295e+01 12 -1.32256343e+01 1.58014770e+01 -3.48790659e+00 13 1.08225266e+00 -1.42319545e+01 -6.47898707e+01 14 1.21472577e+01 1.28219961e+01 -8.42397639e+00 15 6.56531933e+01 4.73998243e+00 1.69207306e+00 16 9.98655408e+00 4.88240704e+01 1.64903710e+01 17 -2.42756719e+01 -1.62631107e+01 2.11765799e+00 18 9.31273955e+00 1.67299589e+01 -4.86060795e+00 19 5.04599027e+00 -2.08166289e+01 1.60062596e+01 20 -1.26926022e+01 6.75035901e+00 1.34978631e+01 21 -1.63386217e+01 -1.91410934e+01 1.21637897e+01 22 3.39372449e+01 2.48097301e+01 3.43506979e+01 23 6.33772399e+00 -3.43805212e+00 8.87466958e+00 24 3.96757348e+00 3.12873953e+00 1.12401209e+01 25 -2.47866875e+01 -1.79183229e+01 -1.21455448e+01 26 -7.96691315e+00 3.52331239e+01 -1.30051805e+01 27 1.67203151e+01 -4.10488668e+01 3.07013635e+01 28 -3.58440529e+01 3.46227994e+01 1.57458430e+01 29 -1.03155455e+01 -1.32226971e+01 1.82252031e+01 30 1.65113389e+01 1.99743446e+01 7.44162143e+00 31 2.40807762e+01 -7.95235190e+00 1.68686197e+01 32 1.49389413e+01 2.36674293e+01 2.49680268e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Au (Configuration in file "config-T-Au.xyz") ----------------------------------------------------------------------------------------------------- Energy = 112.45207738343937 Forces: 1 -6.81744356e+00 -2.05527854e+01 -2.34218606e+01 2 -7.90454612e+00 7.57624347e+00 -1.69560340e+01 3 8.57907984e+00 -1.77157649e+01 -4.16515764e+00 4 -1.37721392e+01 2.37133537e+01 1.12749709e+01 5 6.21382387e+00 -2.26636340e+01 -9.27080767e+00 6 1.01438411e+01 4.54858441e+00 -1.46345708e+01 7 1.74291901e+01 -4.47527505e+01 -3.12890200e+01 8 -3.47660455e+01 -2.91264302e+01 -3.84975503e+00 9 -2.25411868e+01 -4.71217677e+00 -2.13785712e+01 10 -1.17499496e+01 3.47758306e+01 -3.17963166e+01 11 -1.90907964e+01 -2.41614028e+01 2.18160295e+01 12 -1.32256343e+01 1.58014770e+01 -3.48790659e+00 13 1.08225266e+00 -1.42319545e+01 -6.47898707e+01 14 1.21472577e+01 1.28219961e+01 -8.42397639e+00 15 6.56531933e+01 4.73998243e+00 1.69207306e+00 16 9.98655408e+00 4.88240704e+01 1.64903710e+01 17 -2.42756719e+01 -1.62631107e+01 2.11765799e+00 18 9.31273955e+00 1.67299589e+01 -4.86060795e+00 19 5.04599027e+00 -2.08166289e+01 1.60062596e+01 20 -1.26926022e+01 6.75035901e+00 1.34978631e+01 21 -1.63386217e+01 -1.91410934e+01 1.21637897e+01 22 3.39372449e+01 2.48097301e+01 3.43506979e+01 23 6.33772399e+00 -3.43805212e+00 8.87466958e+00 24 3.96757348e+00 3.12873953e+00 1.12401209e+01 25 -2.47866875e+01 -1.79183229e+01 -1.21455448e+01 26 -7.96691315e+00 3.52331239e+01 -1.30051805e+01 27 1.67203151e+01 -4.10488668e+01 3.07013635e+01 28 -3.58440529e+01 3.46227994e+01 1.57458430e+01 29 -1.03155455e+01 -1.32226971e+01 1.82252031e+01 30 1.65113389e+01 1.99743446e+01 7.44162143e+00 31 2.40807762e+01 -7.95235190e+00 1.68686197e+01 32 1.49389413e+01 2.36674293e+01 2.49680268e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==60568== Memcheck, a memory error detector ==60568== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==60568== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==60568== Command: python runner2.py EAM_Dynamo_Olsson_2010_Au__MO_228280943430_000 ==60568== ==61671== Warning: invalid file descriptor 1048564 in syscall close() ==61671== Warning: invalid file descriptor 1048565 in syscall close() ==61671== Warning: invalid file descriptor 1048566 in syscall close() ==61671== Warning: invalid file descriptor 1048567 in syscall close() ==61671== Use --log-fd= to select an alternative log fd. ==61671== Warning: invalid file descriptor 1048568 in syscall close() ==61671== Warning: invalid file descriptor 1048569 in syscall close() ==61672== Warning: invalid file descriptor 1048564 in syscall close() ==61672== Warning: invalid file descriptor 1048565 in syscall close() ==61672== Warning: invalid file descriptor 1048566 in syscall close() ==61672== Warning: invalid file descriptor 1048567 in syscall close() ==61672== Use --log-fd= to select an alternative log fd. ==61672== Warning: invalid file descriptor 1048568 in syscall close() ==61672== Warning: invalid file descriptor 1048569 in syscall close() ==61732== Warning: invalid file descriptor 1048564 in syscall close() ==61732== Warning: invalid file descriptor 1048565 in syscall close() ==61732== Warning: invalid file descriptor 1048566 in syscall close() ==61732== Warning: invalid file descriptor 1048567 in syscall close() ==61732== Use --log-fd= to select an alternative log fd. ==61732== Warning: invalid file descriptor 1048568 in syscall close() ==61732== Warning: invalid file descriptor 1048569 in syscall close() ==61733== Warning: invalid file descriptor 1048564 in syscall close() ==61733== Warning: invalid file descriptor 1048565 in syscall close() ==61733== Warning: invalid file descriptor 1048566 in syscall close() ==61733== Warning: invalid file descriptor 1048567 in syscall close() ==61733== Use --log-fd= to select an alternative log fd. ==61733== Warning: invalid file descriptor 1048568 in syscall close() ==61733== Warning: invalid file descriptor 1048569 in syscall close() ==61734== Warning: invalid file descriptor 1048564 in syscall close() ==61734== Warning: invalid file descriptor 1048565 in syscall close() ==61734== Warning: invalid file descriptor 1048566 in syscall close() ==61734== Warning: invalid file descriptor 1048567 in syscall close() ==61734== Use --log-fd= to select an alternative log fd. ==61734== Warning: invalid file descriptor 1048568 in syscall close() ==61734== Warning: invalid file descriptor 1048569 in syscall close() ==61738== Warning: invalid file descriptor 1048564 in syscall close() ==61738== Warning: invalid file descriptor 1048565 in syscall close() ==61738== Warning: invalid file descriptor 1048566 in syscall close() ==61738== Warning: invalid file descriptor 1048567 in syscall close() ==61738== Use --log-fd= to select an alternative log fd. ==61738== Warning: invalid file descriptor 1048568 in syscall close() ==61738== Warning: invalid file descriptor 1048569 in syscall close() ==60568== ==60568== HEAP SUMMARY: ==60568== in use at exit: 1,718,308 bytes in 1,321 blocks ==60568== total heap usage: 32,186 allocs, 30,865 frees, 49,563,511 bytes allocated ==60568== ==60568== LEAK SUMMARY: ==60568== definitely lost: 0 bytes in 0 blocks ==60568== indirectly lost: 0 bytes in 0 blocks ==60568== possibly lost: 178,943 bytes in 97 blocks ==60568== still reachable: 1,539,365 bytes in 1,224 blocks ==60568== suppressed: 0 bytes in 0 blocks ==60568== Rerun with --leak-check=full to see details of leaked memory ==60568== ==60568== For counts of detected and suppressed errors, rerun with: -v ==60568== 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.