!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_2001NISTretabulation_Mo__MO_230319944007_000 Supported species : Mo random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Mo (Configuration in file "config-F-Mo.xyz") ----------------------------------------------------------------------------------------------------- Energy = 183.58124679882212 Forces: 1 -1.01702349e+01 -1.97959495e+01 -2.07430128e+01 2 -2.02937221e+01 3.25551605e+01 -2.72145125e+01 3 -3.45504102e+00 -2.96874060e+01 -2.98227833e+00 4 -1.59500301e+01 9.26077158e+00 1.06582433e+01 5 2.97697972e+01 -4.53914665e+01 -9.64265125e+00 6 1.09084879e+01 3.39421437e+00 -1.74540095e+01 7 1.63199777e+01 -6.55355908e+01 -5.95810632e+01 8 -2.04708698e+01 -2.17155846e+01 -1.04899568e+01 9 -2.39128385e+01 -3.47758642e+01 -5.76904454e+01 10 -2.68929442e+00 4.83477240e+01 -4.96897553e+01 11 -9.45627825e+00 -3.56355616e+01 2.10895729e+01 12 -3.58208213e+01 4.80148431e+01 2.65520631e+01 13 -1.03377969e+01 -2.70612895e+01 -9.57545740e+01 14 1.92590293e+01 2.30213400e+01 -1.60739995e+01 15 8.60780525e+01 -9.90324721e+00 2.12935522e+01 16 1.08656019e+01 6.97568541e+01 3.17985754e+01 17 -2.71131326e+01 -1.28466818e+01 -9.94488879e+00 18 -1.43848640e+01 2.00449247e+01 1.40723651e+01 19 1.28340643e+01 -2.31634741e+01 1.88879680e+01 20 -1.24743510e+01 1.73569287e+01 1.42515081e+01 21 -2.21213656e+01 -2.98888044e+01 2.00869131e+01 22 4.67831331e+01 4.96633651e+01 4.65800314e+01 23 9.51438654e+00 -4.78884624e+00 1.71069982e+01 24 5.60103277e+00 1.56010183e+00 1.56562090e+01 25 -2.56117609e+01 -8.90790907e+00 1.89594120e+01 26 -1.63312715e+01 4.33775810e+01 -2.07971508e+01 27 2.03030835e+01 -6.95155634e+01 2.47873100e+01 28 -5.99261377e+01 4.89989008e+01 1.02502512e+01 29 -1.50247204e+01 -2.20874090e+01 1.68496914e+01 30 2.20819281e+01 3.26620271e+01 2.15703620e+00 31 3.55384935e+01 -2.18771159e+01 3.01408447e+01 32 1.96874627e+01 3.45630267e+01 3.68797525e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Mo (Configuration in file "config-T-Mo.xyz") ----------------------------------------------------------------------------------------------------- Energy = 183.58124679882212 Forces: 1 -1.01702349e+01 -1.97959495e+01 -2.07430128e+01 2 -2.02937221e+01 3.25551605e+01 -2.72145125e+01 3 -3.45504102e+00 -2.96874060e+01 -2.98227833e+00 4 -1.59500301e+01 9.26077158e+00 1.06582433e+01 5 2.97697972e+01 -4.53914665e+01 -9.64265125e+00 6 1.09084879e+01 3.39421437e+00 -1.74540095e+01 7 1.63199777e+01 -6.55355908e+01 -5.95810632e+01 8 -2.04708698e+01 -2.17155846e+01 -1.04899568e+01 9 -2.39128385e+01 -3.47758642e+01 -5.76904454e+01 10 -2.68929442e+00 4.83477240e+01 -4.96897553e+01 11 -9.45627825e+00 -3.56355616e+01 2.10895729e+01 12 -3.58208213e+01 4.80148431e+01 2.65520631e+01 13 -1.03377969e+01 -2.70612895e+01 -9.57545740e+01 14 1.92590293e+01 2.30213400e+01 -1.60739995e+01 15 8.60780525e+01 -9.90324721e+00 2.12935522e+01 16 1.08656019e+01 6.97568541e+01 3.17985754e+01 17 -2.71131326e+01 -1.28466818e+01 -9.94488879e+00 18 -1.43848640e+01 2.00449247e+01 1.40723651e+01 19 1.28340643e+01 -2.31634741e+01 1.88879680e+01 20 -1.24743510e+01 1.73569287e+01 1.42515081e+01 21 -2.21213656e+01 -2.98888044e+01 2.00869131e+01 22 4.67831331e+01 4.96633651e+01 4.65800314e+01 23 9.51438654e+00 -4.78884624e+00 1.71069982e+01 24 5.60103277e+00 1.56010183e+00 1.56562090e+01 25 -2.56117609e+01 -8.90790907e+00 1.89594120e+01 26 -1.63312715e+01 4.33775810e+01 -2.07971508e+01 27 2.03030835e+01 -6.95155634e+01 2.47873100e+01 28 -5.99261377e+01 4.89989008e+01 1.02502512e+01 29 -1.50247204e+01 -2.20874090e+01 1.68496914e+01 30 2.20819281e+01 3.26620271e+01 2.15703620e+00 31 3.55384935e+01 -2.18771159e+01 3.01408447e+01 32 1.96874627e+01 3.45630267e+01 3.68797525e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==91152== Memcheck, a memory error detector ==91152== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==91152== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==91152== Command: python runner2.py EAM_Dynamo_ZhouWadleyJohnson_2001NISTretabulation_Mo__MO_230319944007_000 ==91152== ==92357== Warning: invalid file descriptor 1048564 in syscall close() ==92357== Warning: invalid file descriptor 1048565 in syscall close() ==92357== Warning: invalid file descriptor 1048566 in syscall close() ==92357== Warning: invalid file descriptor 1048567 in syscall close() ==92357== Use --log-fd= to select an alternative log fd. ==92357== Warning: invalid file descriptor 1048568 in syscall close() ==92357== Warning: invalid file descriptor 1048569 in syscall close() ==92359== Warning: invalid file descriptor 1048564 in syscall close() ==92359== Warning: invalid file descriptor 1048565 in syscall close() ==92359== Warning: invalid file descriptor 1048566 in syscall close() ==92359== Warning: invalid file descriptor 1048567 in syscall close() ==92359== Use --log-fd= to select an alternative log fd. ==92359== Warning: invalid file descriptor 1048568 in syscall close() ==92359== Warning: invalid file descriptor 1048569 in syscall close() ==92373== Warning: invalid file descriptor 1048564 in syscall close() ==92373== Warning: invalid file descriptor 1048565 in syscall close() ==92373== Warning: invalid file descriptor 1048566 in syscall close() ==92373== Warning: invalid file descriptor 1048567 in syscall close() ==92373== Use --log-fd= to select an alternative log fd. ==92373== Warning: invalid file descriptor 1048568 in syscall close() ==92373== Warning: invalid file descriptor 1048569 in syscall close() ==92375== Warning: invalid file descriptor 1048564 in syscall close() ==92375== Warning: invalid file descriptor 1048565 in syscall close() ==92375== Warning: invalid file descriptor 1048566 in syscall close() ==92375== Warning: invalid file descriptor 1048567 in syscall close() ==92375== Use --log-fd= to select an alternative log fd. ==92375== Warning: invalid file descriptor 1048568 in syscall close() ==92375== Warning: invalid file descriptor 1048569 in syscall close() ==92389== Warning: invalid file descriptor 1048564 in syscall close() ==92389== Warning: invalid file descriptor 1048565 in syscall close() ==92389== Warning: invalid file descriptor 1048566 in syscall close() ==92389== Warning: invalid file descriptor 1048567 in syscall close() ==92389== Use --log-fd= to select an alternative log fd. ==92389== Warning: invalid file descriptor 1048568 in syscall close() ==92389== Warning: invalid file descriptor 1048569 in syscall close() ==92397== Warning: invalid file descriptor 1048564 in syscall close() ==92397== Warning: invalid file descriptor 1048565 in syscall close() ==92397== Warning: invalid file descriptor 1048566 in syscall close() ==92397== Warning: invalid file descriptor 1048567 in syscall close() ==92397== Use --log-fd= to select an alternative log fd. ==92397== Warning: invalid file descriptor 1048568 in syscall close() ==92397== Warning: invalid file descriptor 1048569 in syscall close() ==91152== ==91152== HEAP SUMMARY: ==91152== in use at exit: 1,718,292 bytes in 1,321 blocks ==91152== total heap usage: 31,120 allocs, 29,799 frees, 40,378,567 bytes allocated ==91152== ==91152== LEAK SUMMARY: ==91152== definitely lost: 0 bytes in 0 blocks ==91152== indirectly lost: 0 bytes in 0 blocks ==91152== possibly lost: 178,943 bytes in 97 blocks ==91152== still reachable: 1,539,349 bytes in 1,224 blocks ==91152== suppressed: 0 bytes in 0 blocks ==91152== Rerun with --leak-check=full to see details of leaked memory ==91152== ==91152== For counts of detected and suppressed errors, rerun with: -v ==91152== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 13369 from 596) ================================================================================ 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.