!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : ThreeBodyCluster_KP_KaxirasPandey_1988_Si__MO_072486242437_000 Supported species : Si random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Si (Configuration in file "config-F-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 37.30022948328294 Forces: 1 -3.60627305e+00 -8.96699307e+00 -1.16660857e+01 2 -5.28746288e+00 -5.65017922e-01 -1.17824558e+01 3 -3.50799949e-01 -1.39887578e+01 -6.05534175e+00 4 -1.06566073e+01 6.46237081e+00 3.98896807e+00 5 1.96101789e+00 -1.05573464e+01 -5.76285417e+00 6 6.69466147e+00 6.15249923e-01 -6.12540150e+00 7 5.68320629e+00 -1.25861898e+01 -1.15406006e+01 8 -5.59007960e-01 -1.10835848e+01 -6.32504260e-01 9 -1.02350848e+01 -1.07771797e+00 -1.13378554e+01 10 -6.17179941e+00 1.71998717e+01 -1.52908740e+01 11 -9.49505340e+00 -7.02001860e+00 -6.30797677e-01 12 -1.04177536e+01 9.47669823e+00 -4.29413688e-01 13 5.66971712e+00 1.08061084e+00 -2.19146469e+01 14 6.91560651e+00 6.47483520e+00 -5.73719366e+00 15 2.19706893e+01 -5.38026336e-01 1.79508335e+00 16 5.20174221e+00 1.83974500e+01 6.00625825e+00 17 -1.39213280e+01 -8.82691453e+00 -1.96291331e+00 18 4.53161807e+00 3.48399150e+00 8.08711493e-01 19 3.85400437e+00 -1.06259272e+01 1.26079259e+01 20 -7.64468673e+00 5.85447923e+00 9.17478566e+00 21 -4.43437632e+00 -1.48555983e+01 7.57199703e+00 22 1.66852597e+01 9.84922611e+00 8.39018773e+00 23 2.97816553e+00 -1.85431515e+00 6.77431449e+00 24 1.77949416e+00 -5.94157454e+00 1.08909306e+01 25 -1.03834313e+01 -8.67636742e-01 5.70013716e+00 26 -6.75747771e+00 1.57780681e+01 -6.05475731e+00 27 -1.00154910e+01 -9.98179559e+00 1.41531017e+01 28 -1.03450576e+01 5.04914214e+00 4.92617481e+00 29 4.52748327e+00 2.44812645e-01 3.13045798e+00 30 1.06423908e+01 7.81125508e+00 -2.54158595e+00 31 1.28104029e+01 -2.79857564e+00 9.17674469e+00 32 8.37623138e+00 1.43579286e+01 1.43695028e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Si (Configuration in file "config-T-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 37.30022948328294 Forces: 1 -3.60627305e+00 -8.96699307e+00 -1.16660857e+01 2 -5.28746288e+00 -5.65017922e-01 -1.17824558e+01 3 -3.50799949e-01 -1.39887578e+01 -6.05534175e+00 4 -1.06566073e+01 6.46237081e+00 3.98896807e+00 5 1.96101789e+00 -1.05573464e+01 -5.76285417e+00 6 6.69466147e+00 6.15249923e-01 -6.12540150e+00 7 5.68320629e+00 -1.25861898e+01 -1.15406006e+01 8 -5.59007960e-01 -1.10835848e+01 -6.32504260e-01 9 -1.02350848e+01 -1.07771797e+00 -1.13378554e+01 10 -6.17179941e+00 1.71998717e+01 -1.52908740e+01 11 -9.49505340e+00 -7.02001860e+00 -6.30797677e-01 12 -1.04177536e+01 9.47669823e+00 -4.29413688e-01 13 5.66971712e+00 1.08061084e+00 -2.19146469e+01 14 6.91560651e+00 6.47483520e+00 -5.73719366e+00 15 2.19706893e+01 -5.38026336e-01 1.79508335e+00 16 5.20174221e+00 1.83974500e+01 6.00625825e+00 17 -1.39213280e+01 -8.82691453e+00 -1.96291331e+00 18 4.53161807e+00 3.48399150e+00 8.08711493e-01 19 3.85400437e+00 -1.06259272e+01 1.26079259e+01 20 -7.64468673e+00 5.85447923e+00 9.17478566e+00 21 -4.43437632e+00 -1.48555983e+01 7.57199703e+00 22 1.66852597e+01 9.84922611e+00 8.39018773e+00 23 2.97816553e+00 -1.85431515e+00 6.77431449e+00 24 1.77949416e+00 -5.94157454e+00 1.08909306e+01 25 -1.03834313e+01 -8.67636742e-01 5.70013716e+00 26 -6.75747771e+00 1.57780681e+01 -6.05475731e+00 27 -1.00154910e+01 -9.98179559e+00 1.41531017e+01 28 -1.03450576e+01 5.04914214e+00 4.92617481e+00 29 4.52748327e+00 2.44812645e-01 3.13045798e+00 30 1.06423908e+01 7.81125508e+00 -2.54158595e+00 31 1.28104029e+01 -2.79857564e+00 9.17674469e+00 32 8.37623138e+00 1.43579286e+01 1.43695028e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==22328== Memcheck, a memory error detector ==22328== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==22328== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==22328== Command: python runner2.py ThreeBodyCluster_KP_KaxirasPandey_1988_Si__MO_072486242437_000 ==22328== ==23427== Warning: invalid file descriptor 1048564 in syscall close() ==23427== Warning: invalid file descriptor 1048565 in syscall close() ==23427== Warning: invalid file descriptor 1048566 in syscall close() ==23427== Warning: invalid file descriptor 1048567 in syscall close() ==23427== Use --log-fd= to select an alternative log fd. ==23427== Warning: invalid file descriptor 1048568 in syscall close() ==23427== Warning: invalid file descriptor 1048569 in syscall close() ==23428== Warning: invalid file descriptor 1048564 in syscall close() ==23428== Warning: invalid file descriptor 1048565 in syscall close() ==23428== Warning: invalid file descriptor 1048566 in syscall close() ==23428== Warning: invalid file descriptor 1048567 in syscall close() ==23428== Use --log-fd= to select an alternative log fd. ==23428== Warning: invalid file descriptor 1048568 in syscall close() ==23428== Warning: invalid file descriptor 1048569 in syscall close() ==23430== Warning: invalid file descriptor 1048564 in syscall close() ==23430== Warning: invalid file descriptor 1048565 in syscall close() ==23430== Warning: invalid file descriptor 1048566 in syscall close() ==23430== Warning: invalid file descriptor 1048567 in syscall close() ==23430== Use --log-fd= to select an alternative log fd. ==23430== Warning: invalid file descriptor 1048568 in syscall close() ==23430== Warning: invalid file descriptor 1048569 in syscall close() ==23431== Warning: invalid file descriptor 1048564 in syscall close() ==23431== Warning: invalid file descriptor 1048565 in syscall close() ==23431== Warning: invalid file descriptor 1048566 in syscall close() ==23431== Warning: invalid file descriptor 1048567 in syscall close() ==23431== Use --log-fd= to select an alternative log fd. ==23431== Warning: invalid file descriptor 1048568 in syscall close() ==23431== Warning: invalid file descriptor 1048569 in syscall close() ==23432== Warning: invalid file descriptor 1048564 in syscall close() ==23432== Warning: invalid file descriptor 1048565 in syscall close() ==23432== Warning: invalid file descriptor 1048566 in syscall close() ==23432== Warning: invalid file descriptor 1048567 in syscall close() ==23432== Use --log-fd= to select an alternative log fd. ==23432== Warning: invalid file descriptor 1048568 in syscall close() ==23432== Warning: invalid file descriptor 1048569 in syscall close() ==23433== Warning: invalid file descriptor 1048564 in syscall close() ==23433== Warning: invalid file descriptor 1048565 in syscall close() ==23433== Warning: invalid file descriptor 1048566 in syscall close() ==23433== Warning: invalid file descriptor 1048567 in syscall close() ==23433== Use --log-fd= to select an alternative log fd. ==23433== Warning: invalid file descriptor 1048568 in syscall close() ==23433== Warning: invalid file descriptor 1048569 in syscall close() ==22328== ==22328== HEAP SUMMARY: ==22328== in use at exit: 1,718,292 bytes in 1,321 blocks ==22328== total heap usage: 30,943 allocs, 29,622 frees, 38,073,412 bytes allocated ==22328== ==22328== LEAK SUMMARY: ==22328== definitely lost: 0 bytes in 0 blocks ==22328== indirectly lost: 0 bytes in 0 blocks ==22328== possibly lost: 178,943 bytes in 97 blocks ==22328== still reachable: 1,539,349 bytes in 1,224 blocks ==22328== suppressed: 0 bytes in 0 blocks ==22328== Rerun with --leak-check=full to see details of leaked memory ==22328== ==22328== For counts of detected and suppressed errors, rerun with: -v ==22328== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16372 from 604) ================================================================================ 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.