!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : EMT_Asap_Standard_JacobsenStoltzeNorskov_1996_Cu__MO_396616545191_001 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 = 7.914786019564755 Forces: 1 -4.50441708e+00 -7.78775591e+00 -8.22137185e+00 2 -5.50015283e+00 1.07658664e+01 -3.29403908e+00 3 6.71461420e+00 -9.11219826e+00 -4.64537790e+00 4 -9.19627900e+00 3.40835570e+00 4.96729638e+00 5 2.11684377e+00 -1.49992564e+01 6.24600487e-02 6 7.06782530e+00 6.55119769e+00 -5.05579374e+00 7 3.21451724e+00 -2.81409167e+01 -2.81179478e+01 8 -1.50361956e+01 -8.13548649e+00 -5.95074022e+00 9 -7.95557499e+00 -7.21552263e+00 -1.63356075e+01 10 -4.34242001e+00 1.19666836e+01 -1.50590767e+01 11 1.16881664e+01 -4.58150236e+00 7.36620849e+00 12 -8.62588814e+00 1.08560157e+01 7.20101281e+00 13 -1.37811470e+01 -1.46791042e+01 -3.27593181e+01 14 5.75039330e+00 8.09187762e+00 -4.64041824e+00 15 3.17745794e+01 -4.76860398e+00 1.19000520e+01 16 3.17240403e+00 1.98114355e+01 1.41511279e+01 17 -1.21313324e+01 -5.70392961e+00 -4.69289753e+00 18 3.65211892e+00 1.03653637e+01 9.43699674e-01 19 3.49290562e+00 -1.30107193e+01 6.11500650e+00 20 -4.34612436e+00 7.30824354e+00 6.14539582e+00 21 -1.12892665e+01 -8.00024968e+00 7.79107967e+00 22 1.79777760e+01 2.53103354e+01 2.00210912e+01 23 2.57207613e+00 -1.51640953e+00 7.41685518e+00 24 5.48344995e+00 6.37761091e+00 4.74535756e+00 25 -1.36139742e+01 -1.03418324e+01 -1.23289994e+01 26 -4.49296239e+00 1.53339025e+01 -1.02255097e+01 27 2.11731528e+01 -3.25954871e+01 1.50948122e+01 28 -2.75147407e+01 2.86639748e+01 9.10825239e+00 29 -8.61599765e+00 -6.63854530e+00 6.03007954e+00 30 5.46538899e+00 1.11444886e+01 -1.20409999e+00 31 1.23101488e+01 -1.07535694e+01 1.11393565e+01 32 7.32011198e+00 1.20257377e+01 1.23320538e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Cu (Configuration in file "config-T-Cu.xyz") ----------------------------------------------------------------------------------------------------- Energy = 7.914786019564755 Forces: 1 -4.50441708e+00 -7.78775591e+00 -8.22137185e+00 2 -5.50015283e+00 1.07658664e+01 -3.29403908e+00 3 6.71461420e+00 -9.11219826e+00 -4.64537790e+00 4 -9.19627900e+00 3.40835570e+00 4.96729638e+00 5 2.11684377e+00 -1.49992564e+01 6.24600487e-02 6 7.06782530e+00 6.55119769e+00 -5.05579374e+00 7 3.21451724e+00 -2.81409167e+01 -2.81179478e+01 8 -1.50361956e+01 -8.13548649e+00 -5.95074022e+00 9 -7.95557499e+00 -7.21552263e+00 -1.63356075e+01 10 -4.34242001e+00 1.19666836e+01 -1.50590767e+01 11 1.16881664e+01 -4.58150236e+00 7.36620849e+00 12 -8.62588814e+00 1.08560157e+01 7.20101281e+00 13 -1.37811470e+01 -1.46791042e+01 -3.27593181e+01 14 5.75039330e+00 8.09187762e+00 -4.64041824e+00 15 3.17745794e+01 -4.76860398e+00 1.19000520e+01 16 3.17240403e+00 1.98114355e+01 1.41511279e+01 17 -1.21313324e+01 -5.70392961e+00 -4.69289753e+00 18 3.65211892e+00 1.03653637e+01 9.43699674e-01 19 3.49290562e+00 -1.30107193e+01 6.11500650e+00 20 -4.34612436e+00 7.30824354e+00 6.14539582e+00 21 -1.12892665e+01 -8.00024968e+00 7.79107967e+00 22 1.79777760e+01 2.53103354e+01 2.00210912e+01 23 2.57207613e+00 -1.51640953e+00 7.41685518e+00 24 5.48344995e+00 6.37761091e+00 4.74535756e+00 25 -1.36139742e+01 -1.03418324e+01 -1.23289994e+01 26 -4.49296239e+00 1.53339025e+01 -1.02255097e+01 27 2.11731528e+01 -3.25954871e+01 1.50948122e+01 28 -2.75147407e+01 2.86639748e+01 9.10825239e+00 29 -8.61599765e+00 -6.63854530e+00 6.03007954e+00 30 5.46538899e+00 1.11444886e+01 -1.20409999e+00 31 1.23101488e+01 -1.07535694e+01 1.11393565e+01 32 7.32011198e+00 1.20257377e+01 1.23320538e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==21552== Memcheck, a memory error detector ==21552== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==21552== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==21552== Command: python runner2.py EMT_Asap_Standard_JacobsenStoltzeNorskov_1996_Cu__MO_396616545191_001 ==21552== ==23681== Warning: invalid file descriptor 1048564 in syscall close() ==23681== Warning: invalid file descriptor 1048565 in syscall close() ==23681== Warning: invalid file descriptor 1048566 in syscall close() ==23681== Warning: invalid file descriptor 1048567 in syscall close() ==23681== Use --log-fd= to select an alternative log fd. ==23681== Warning: invalid file descriptor 1048568 in syscall close() ==23681== Warning: invalid file descriptor 1048569 in syscall close() ==23704== Warning: invalid file descriptor 1048564 in syscall close() ==23704== Warning: invalid file descriptor 1048565 in syscall close() ==23704== Warning: invalid file descriptor 1048566 in syscall close() ==23704== Warning: invalid file descriptor 1048567 in syscall close() ==23704== Use --log-fd= to select an alternative log fd. ==23704== Warning: invalid file descriptor 1048568 in syscall close() ==23704== Warning: invalid file descriptor 1048569 in syscall close() ==23847== Warning: invalid file descriptor 1048564 in syscall close() ==23847== Warning: invalid file descriptor 1048565 in syscall close() ==23847== Warning: invalid file descriptor 1048566 in syscall close() ==23847== Warning: invalid file descriptor 1048567 in syscall close() ==23847== Use --log-fd= to select an alternative log fd. ==23847== Warning: invalid file descriptor 1048568 in syscall close() ==23847== Warning: invalid file descriptor 1048569 in syscall close() ==23860== Warning: invalid file descriptor 1048564 in syscall close() ==23860== Warning: invalid file descriptor 1048565 in syscall close() ==23860== Warning: invalid file descriptor 1048566 in syscall close() ==23860== Warning: invalid file descriptor 1048567 in syscall close() ==23860== Use --log-fd= to select an alternative log fd. ==23860== Warning: invalid file descriptor 1048568 in syscall close() ==23860== Warning: invalid file descriptor 1048569 in syscall close() ==23870== Warning: invalid file descriptor 1048564 in syscall close() ==23870== Warning: invalid file descriptor 1048565 in syscall close() ==23870== Warning: invalid file descriptor 1048566 in syscall close() ==23870== Warning: invalid file descriptor 1048567 in syscall close() ==23870== Use --log-fd= to select an alternative log fd. ==23870== Warning: invalid file descriptor 1048568 in syscall close() ==23870== Warning: invalid file descriptor 1048569 in syscall close() ==23879== Warning: invalid file descriptor 1048564 in syscall close() ==23879== Warning: invalid file descriptor 1048565 in syscall close() ==23879== Warning: invalid file descriptor 1048566 in syscall close() ==23879== Warning: invalid file descriptor 1048567 in syscall close() ==23879== Use --log-fd= to select an alternative log fd. ==23879== Warning: invalid file descriptor 1048568 in syscall close() ==23879== Warning: invalid file descriptor 1048569 in syscall close() ==21552== ==21552== HEAP SUMMARY: ==21552== in use at exit: 1,718,308 bytes in 1,321 blocks ==21552== total heap usage: 31,041 allocs, 29,720 frees, 39,201,119 bytes allocated ==21552== ==21552== LEAK SUMMARY: ==21552== definitely lost: 0 bytes in 0 blocks ==21552== indirectly lost: 0 bytes in 0 blocks ==21552== possibly lost: 178,943 bytes in 97 blocks ==21552== still reachable: 1,539,365 bytes in 1,224 blocks ==21552== suppressed: 0 bytes in 0 blocks ==21552== Rerun with --leak-check=full to see details of leaked memory ==21552== ==21552== For counts of detected and suppressed errors, rerun with: -v ==21552== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16343 from 613) ================================================================================ 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.