!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_Ta__MO_130046220009_005 Supported species : Ta random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Ta (Configuration in file "config-F-Ta.xyz") ----------------------------------------------------------------------------------------------------- Energy = 12.262090500075413 Forces: 1 -6.40193922e+00 -1.26364508e+01 -1.31357225e+01 2 -1.37975597e+01 2.24813273e+01 -1.64867930e+01 3 -2.50308101e+00 -2.04884028e+01 -2.38629493e+00 4 -1.13218710e+01 5.17063881e+00 6.13453791e+00 5 2.02461779e+01 -2.93281157e+01 -7.05461938e+00 6 6.69863349e+00 1.29019896e+00 -1.24302468e+01 7 1.38251813e+01 -4.59551666e+01 -4.01204929e+01 8 -2.98177019e+01 -2.99757617e+01 -1.16161616e+01 9 -1.32745118e+01 -2.03917296e+01 -3.23645958e+01 10 -3.70321727e+00 2.83400209e+01 -3.20002617e+01 11 -5.76428780e+00 -2.00837894e+01 1.74531807e+00 12 -2.17010112e+01 2.96722593e+01 1.42563245e+01 13 -5.99214085e+00 -1.46523506e+01 -5.94044249e+01 14 1.11536646e+01 1.07468814e+01 -5.64109167e+00 15 6.75303401e+01 1.73519587e+01 5.45755665e+00 16 1.57507752e+01 4.58531119e+01 1.87585753e+01 17 -1.76795902e+01 -8.55613913e+00 -6.10466364e+00 18 -1.38458611e+01 1.06848326e+01 1.30815886e+01 19 7.77359805e+00 -1.50915268e+01 1.25753227e+01 20 -7.70031007e+00 1.10619320e+01 8.78332581e+00 21 -1.43548284e+01 -2.13652619e+01 1.41027412e+01 22 3.36212554e+01 2.92310331e+01 3.57150941e+01 23 5.61431464e+00 -2.84150202e+00 1.04627877e+01 24 4.02942295e+00 7.35553185e-01 1.11684516e+01 25 -2.32797856e+01 -6.56958135e+00 1.75682305e+01 26 -1.18150608e+01 3.16513381e+01 -1.23778165e+01 27 1.16597947e+01 -4.54103913e+01 1.79170126e+01 28 -3.75611995e+01 3.10579055e+01 6.49375668e+00 29 -7.80230738e+00 -9.37734852e+00 1.54264997e+01 30 1.31918789e+01 1.79046985e+01 -3.70363277e+00 31 2.40920919e+01 -1.43750546e+01 2.05190031e+01 32 1.31291354e+01 2.38648827e+01 2.46606913e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ta (Configuration in file "config-T-Ta.xyz") ----------------------------------------------------------------------------------------------------- Energy = 12.262090500075413 Forces: 1 -6.40193922e+00 -1.26364508e+01 -1.31357225e+01 2 -1.37975597e+01 2.24813273e+01 -1.64867930e+01 3 -2.50308101e+00 -2.04884028e+01 -2.38629493e+00 4 -1.13218710e+01 5.17063881e+00 6.13453791e+00 5 2.02461779e+01 -2.93281157e+01 -7.05461938e+00 6 6.69863349e+00 1.29019896e+00 -1.24302468e+01 7 1.38251813e+01 -4.59551666e+01 -4.01204929e+01 8 -2.98177019e+01 -2.99757617e+01 -1.16161616e+01 9 -1.32745118e+01 -2.03917296e+01 -3.23645958e+01 10 -3.70321727e+00 2.83400209e+01 -3.20002617e+01 11 -5.76428780e+00 -2.00837894e+01 1.74531807e+00 12 -2.17010112e+01 2.96722593e+01 1.42563245e+01 13 -5.99214085e+00 -1.46523506e+01 -5.94044249e+01 14 1.11536646e+01 1.07468814e+01 -5.64109167e+00 15 6.75303401e+01 1.73519587e+01 5.45755665e+00 16 1.57507752e+01 4.58531119e+01 1.87585753e+01 17 -1.76795902e+01 -8.55613913e+00 -6.10466364e+00 18 -1.38458611e+01 1.06848326e+01 1.30815886e+01 19 7.77359805e+00 -1.50915268e+01 1.25753227e+01 20 -7.70031007e+00 1.10619320e+01 8.78332581e+00 21 -1.43548284e+01 -2.13652619e+01 1.41027412e+01 22 3.36212554e+01 2.92310331e+01 3.57150941e+01 23 5.61431464e+00 -2.84150202e+00 1.04627877e+01 24 4.02942295e+00 7.35553185e-01 1.11684516e+01 25 -2.32797856e+01 -6.56958135e+00 1.75682305e+01 26 -1.18150608e+01 3.16513381e+01 -1.23778165e+01 27 1.16597947e+01 -4.54103913e+01 1.79170126e+01 28 -3.75611995e+01 3.10579055e+01 6.49375668e+00 29 -7.80230738e+00 -9.37734852e+00 1.54264997e+01 30 1.31918789e+01 1.79046985e+01 -3.70363277e+00 31 2.40920919e+01 -1.43750546e+01 2.05190031e+01 32 1.31291354e+01 2.38648827e+01 2.46606913e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==83826== Memcheck, a memory error detector ==83826== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==83826== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==83826== Command: python runner2.py EAM_Dynamo_ZhouJohnsonWadley_2004_Ta__MO_130046220009_005 ==83826== ==85798== Warning: invalid file descriptor 1048564 in syscall close() ==85798== Warning: invalid file descriptor 1048565 in syscall close() ==85798== Warning: invalid file descriptor 1048566 in syscall close() ==85798== Warning: invalid file descriptor 1048567 in syscall close() ==85798== Use --log-fd= to select an alternative log fd. ==85798== Warning: invalid file descriptor 1048568 in syscall close() ==85798== Warning: invalid file descriptor 1048569 in syscall close() ==85805== Warning: invalid file descriptor 1048564 in syscall close() ==85805== Warning: invalid file descriptor 1048565 in syscall close() ==85805== Warning: invalid file descriptor 1048566 in syscall close() ==85805== Warning: invalid file descriptor 1048567 in syscall close() ==85805== Use --log-fd= to select an alternative log fd. ==85805== Warning: invalid file descriptor 1048568 in syscall close() ==85805== Warning: invalid file descriptor 1048569 in syscall close() ==85904== Warning: invalid file descriptor 1048564 in syscall close() ==85904== Warning: invalid file descriptor 1048565 in syscall close() ==85904== Warning: invalid file descriptor 1048566 in syscall close() ==85904== Warning: invalid file descriptor 1048567 in syscall close() ==85904== Use --log-fd= to select an alternative log fd. ==85904== Warning: invalid file descriptor 1048568 in syscall close() ==85904== Warning: invalid file descriptor 1048569 in syscall close() ==85905== Warning: invalid file descriptor 1048564 in syscall close() ==85905== Warning: invalid file descriptor 1048565 in syscall close() ==85905== Warning: invalid file descriptor 1048566 in syscall close() ==85905== Warning: invalid file descriptor 1048567 in syscall close() ==85905== Use --log-fd= to select an alternative log fd. ==85905== Warning: invalid file descriptor 1048568 in syscall close() ==85905== Warning: invalid file descriptor 1048569 in syscall close() ==85915== Warning: invalid file descriptor 1048564 in syscall close() ==85915== Warning: invalid file descriptor 1048565 in syscall close() ==85915== Warning: invalid file descriptor 1048566 in syscall close() ==85915== Warning: invalid file descriptor 1048567 in syscall close() ==85915== Use --log-fd= to select an alternative log fd. ==85915== Warning: invalid file descriptor 1048568 in syscall close() ==85915== Warning: invalid file descriptor 1048569 in syscall close() ==85920== Warning: invalid file descriptor 1048564 in syscall close() ==85920== Warning: invalid file descriptor 1048565 in syscall close() ==85920== Warning: invalid file descriptor 1048566 in syscall close() ==85920== Warning: invalid file descriptor 1048567 in syscall close() ==85920== Use --log-fd= to select an alternative log fd. ==85920== Warning: invalid file descriptor 1048568 in syscall close() ==85920== Warning: invalid file descriptor 1048569 in syscall close() ==83826== ==83826== HEAP SUMMARY: ==83826== in use at exit: 1,718,308 bytes in 1,321 blocks ==83826== total heap usage: 32,186 allocs, 30,865 frees, 42,652,860 bytes allocated ==83826== ==83826== LEAK SUMMARY: ==83826== definitely lost: 0 bytes in 0 blocks ==83826== indirectly lost: 0 bytes in 0 blocks ==83826== possibly lost: 178,943 bytes in 97 blocks ==83826== still reachable: 1,539,365 bytes in 1,224 blocks ==83826== suppressed: 0 bytes in 0 blocks ==83826== Rerun with --leak-check=full to see details of leaked memory ==83826== ==83826== For counts of detected and suppressed errors, rerun with: -v ==83826== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16341 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.