!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_Ag__MO_505250810900_000 Supported species : Ag random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Ag (Configuration in file "config-F-Ag.xyz") ----------------------------------------------------------------------------------------------------- Energy = 225.0693738194362 Forces: 1 -8.79972746e+00 -1.63190337e+01 -1.68902641e+01 2 -1.59165232e+01 2.44729576e+01 -2.21040707e+01 3 -2.22503404e+00 -2.37162948e+01 -2.55003975e+00 4 -1.36746791e+01 7.69179448e+00 8.04860116e+00 5 2.31020914e+01 -3.65502560e+01 -8.15602079e+00 6 8.97117565e+00 2.00794928e+00 -1.41619436e+01 7 1.32736150e+01 -5.14552019e+01 -4.55278667e+01 8 -1.51044312e+01 -1.79064924e+01 -8.53497653e+00 9 -1.88298417e+01 -2.66744376e+01 -4.50907039e+01 10 -2.28379021e+00 3.83966331e+01 -3.90079660e+01 11 -7.01684096e+00 -2.64150115e+01 1.61634230e+01 12 -2.81983654e+01 3.74377746e+01 2.04712818e+01 13 -7.86688298e+00 -2.00218182e+01 -7.46907422e+01 14 1.57656604e+01 1.92573000e+01 -1.32726313e+01 15 6.69935371e+01 -7.68823014e+00 1.63025334e+01 16 8.40268528e+00 5.41575373e+01 2.38858341e+01 17 -2.20996828e+01 -1.08166464e+01 -7.87505218e+00 18 -1.15078785e+01 1.43928080e+01 1.10855800e+01 19 9.52626797e+00 -1.88957633e+01 1.48690670e+01 20 -1.02111320e+01 1.36333925e+01 1.21807016e+01 21 -1.66908859e+01 -2.38599994e+01 1.52396037e+01 22 3.65355512e+01 3.79642023e+01 3.61049616e+01 23 8.48180150e+00 -4.16141430e+00 1.38368824e+01 24 4.68783129e+00 1.02780755e+00 1.34461667e+01 25 -2.07773551e+01 -6.21457076e+00 1.45740877e+01 26 -1.32897436e+01 3.47670298e+01 -1.56717784e+01 27 1.57695744e+01 -5.32523657e+01 1.98205622e+01 28 -4.69866786e+01 3.84827245e+01 8.50992857e+00 29 -1.16726519e+01 -1.68158591e+01 1.32145532e+01 30 1.76960877e+01 2.62116018e+01 2.15130803e+00 31 2.85051962e+01 -1.62021890e+01 2.44048366e+01 32 1.54410496e+01 2.70640714e+01 2.92241433e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ag (Configuration in file "config-T-Ag.xyz") ----------------------------------------------------------------------------------------------------- Energy = 225.0693738194362 Forces: 1 -8.79972746e+00 -1.63190337e+01 -1.68902641e+01 2 -1.59165232e+01 2.44729576e+01 -2.21040707e+01 3 -2.22503404e+00 -2.37162948e+01 -2.55003975e+00 4 -1.36746791e+01 7.69179448e+00 8.04860116e+00 5 2.31020914e+01 -3.65502560e+01 -8.15602079e+00 6 8.97117565e+00 2.00794928e+00 -1.41619436e+01 7 1.32736150e+01 -5.14552019e+01 -4.55278667e+01 8 -1.51044312e+01 -1.79064924e+01 -8.53497653e+00 9 -1.88298417e+01 -2.66744376e+01 -4.50907039e+01 10 -2.28379021e+00 3.83966331e+01 -3.90079660e+01 11 -7.01684096e+00 -2.64150115e+01 1.61634230e+01 12 -2.81983654e+01 3.74377746e+01 2.04712818e+01 13 -7.86688298e+00 -2.00218182e+01 -7.46907422e+01 14 1.57656604e+01 1.92573000e+01 -1.32726313e+01 15 6.69935371e+01 -7.68823014e+00 1.63025334e+01 16 8.40268528e+00 5.41575373e+01 2.38858341e+01 17 -2.20996828e+01 -1.08166464e+01 -7.87505218e+00 18 -1.15078785e+01 1.43928080e+01 1.10855800e+01 19 9.52626797e+00 -1.88957633e+01 1.48690670e+01 20 -1.02111320e+01 1.36333925e+01 1.21807016e+01 21 -1.66908859e+01 -2.38599994e+01 1.52396037e+01 22 3.65355512e+01 3.79642023e+01 3.61049616e+01 23 8.48180150e+00 -4.16141430e+00 1.38368824e+01 24 4.68783129e+00 1.02780755e+00 1.34461667e+01 25 -2.07773551e+01 -6.21457076e+00 1.45740877e+01 26 -1.32897436e+01 3.47670298e+01 -1.56717784e+01 27 1.57695744e+01 -5.32523657e+01 1.98205622e+01 28 -4.69866786e+01 3.84827245e+01 8.50992857e+00 29 -1.16726519e+01 -1.68158591e+01 1.32145532e+01 30 1.76960877e+01 2.62116018e+01 2.15130803e+00 31 2.85051962e+01 -1.62021890e+01 2.44048366e+01 32 1.54410496e+01 2.70640714e+01 2.92241433e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==86213== Memcheck, a memory error detector ==86213== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==86213== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==86213== Command: python runner2.py EAM_Dynamo_ZhouWadleyJohnson_2001NISTretabulation_Ag__MO_505250810900_000 ==86213== ==87040== Warning: invalid file descriptor 1048564 in syscall close() ==87040== Warning: invalid file descriptor 1048565 in syscall close() ==87040== Warning: invalid file descriptor 1048566 in syscall close() ==87040== Warning: invalid file descriptor 1048567 in syscall close() ==87040== Use --log-fd= to select an alternative log fd. ==87040== Warning: invalid file descriptor 1048568 in syscall close() ==87040== Warning: invalid file descriptor 1048569 in syscall close() ==87045== Warning: invalid file descriptor 1048564 in syscall close() ==87045== Warning: invalid file descriptor 1048565 in syscall close() ==87045== Warning: invalid file descriptor 1048566 in syscall close() ==87045== Warning: invalid file descriptor 1048567 in syscall close() ==87045== Use --log-fd= to select an alternative log fd. ==87045== Warning: invalid file descriptor 1048568 in syscall close() ==87045== Warning: invalid file descriptor 1048569 in syscall close() ==87151== Warning: invalid file descriptor 1048564 in syscall close() ==87151== Warning: invalid file descriptor 1048565 in syscall close() ==87151== Warning: invalid file descriptor 1048566 in syscall close() ==87151== Warning: invalid file descriptor 1048567 in syscall close() ==87151== Use --log-fd= to select an alternative log fd. ==87151== Warning: invalid file descriptor 1048568 in syscall close() ==87151== Warning: invalid file descriptor 1048569 in syscall close() ==87159== Warning: invalid file descriptor 1048564 in syscall close() ==87159== Warning: invalid file descriptor 1048565 in syscall close() ==87159== Warning: invalid file descriptor 1048566 in syscall close() ==87159== Warning: invalid file descriptor 1048567 in syscall close() ==87159== Use --log-fd= to select an alternative log fd. ==87159== Warning: invalid file descriptor 1048568 in syscall close() ==87159== Warning: invalid file descriptor 1048569 in syscall close() ==87164== Warning: invalid file descriptor 1048564 in syscall close() ==87164== Warning: invalid file descriptor 1048565 in syscall close() ==87164== Warning: invalid file descriptor 1048566 in syscall close() ==87164== Warning: invalid file descriptor 1048567 in syscall close() ==87164== Use --log-fd= to select an alternative log fd. ==87164== Warning: invalid file descriptor 1048568 in syscall close() ==87164== Warning: invalid file descriptor 1048569 in syscall close() ==87170== Warning: invalid file descriptor 1048564 in syscall close() ==87170== Warning: invalid file descriptor 1048565 in syscall close() ==87170== Warning: invalid file descriptor 1048566 in syscall close() ==87170== Warning: invalid file descriptor 1048567 in syscall close() ==87170== Use --log-fd= to select an alternative log fd. ==87170== Warning: invalid file descriptor 1048568 in syscall close() ==87170== Warning: invalid file descriptor 1048569 in syscall close() ==86213== ==86213== HEAP SUMMARY: ==86213== in use at exit: 1,718,292 bytes in 1,321 blocks ==86213== total heap usage: 31,120 allocs, 29,799 frees, 40,378,575 bytes allocated ==86213== ==86213== LEAK SUMMARY: ==86213== definitely lost: 0 bytes in 0 blocks ==86213== indirectly lost: 0 bytes in 0 blocks ==86213== possibly lost: 178,943 bytes in 97 blocks ==86213== still reachable: 1,539,349 bytes in 1,224 blocks ==86213== suppressed: 0 bytes in 0 blocks ==86213== Rerun with --leak-check=full to see details of leaked memory ==86213== ==86213== For counts of detected and suppressed errors, rerun with: -v ==86213== 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.