!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_AcklandWoodingBacon_1995v2_Zr__MO_398441626455_000 Supported species : Zr random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Zr (Configuration in file "config-F-Zr.xyz") ----------------------------------------------------------------------------------------------------- Energy = 333.855164157456 Forces: 1 -1.22003623e+01 -4.07824574e+01 -3.13212397e+01 2 -8.17222317e+00 1.20055034e+01 -2.76811744e+01 3 2.98233102e+00 -3.56640920e+01 -1.90699376e+01 4 -2.60125020e+01 2.28104945e+01 2.84056435e+01 5 8.67170747e+00 -3.57563196e+01 -1.39531459e+01 6 2.04770191e+01 -6.72374996e-03 -2.34897135e+01 7 1.38578073e+01 -6.74609914e+01 -5.78119770e+01 8 -3.02232008e+01 -3.01122250e+01 2.51342118e+00 9 -1.02742160e+01 5.01882635e+00 -3.11482147e+01 10 -1.36647313e+01 2.60634999e+01 -4.01999347e+01 11 -1.07957879e+01 -2.45348057e+01 -1.23972969e+01 12 -2.50865544e+01 2.27724638e+01 6.25514682e-01 13 -2.34151778e+01 -8.97565261e+00 -9.29893763e+01 14 1.88020257e+01 1.81667237e+01 -1.41443324e+01 15 8.81612734e+01 1.41730281e+01 2.81081987e+01 16 1.39502810e+01 6.17827402e+01 2.61828882e+01 17 -3.32076519e+01 -1.49259026e+01 9.15074950e-01 18 5.57077400e+00 3.24434409e+01 -1.29434142e-01 19 5.61706956e-02 -3.32480115e+01 3.32349083e+01 20 -1.79928040e+01 4.76827087e+00 1.42495941e+01 21 -1.17161399e+01 -2.70242759e+01 1.80123683e+01 22 4.71962552e+01 4.46790636e+01 5.24825912e+01 23 1.08621452e+01 -7.63433113e+00 1.51230483e+01 24 5.24871994e+00 1.36452865e-01 2.27062031e+01 25 -5.34398477e+01 -1.15797528e+01 1.50974543e+00 26 2.09459045e+00 5.30713108e+01 -9.61163697e+00 27 3.25046625e+01 -6.52215058e+01 3.12053044e+01 28 -6.86588410e+01 6.06629923e+01 2.02309283e+01 29 -3.91814323e-01 -1.88566767e+01 1.47118779e+01 30 2.46773560e+01 2.99719732e+01 -5.21556470e+00 31 3.24119525e+01 -1.81273449e+01 3.31563534e+01 32 1.77267831e+01 3.13842843e+01 3.57893149e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Zr (Configuration in file "config-T-Zr.xyz") ----------------------------------------------------------------------------------------------------- Energy = 333.855164157456 Forces: 1 -1.22003623e+01 -4.07824574e+01 -3.13212397e+01 2 -8.17222317e+00 1.20055034e+01 -2.76811744e+01 3 2.98233102e+00 -3.56640920e+01 -1.90699376e+01 4 -2.60125020e+01 2.28104945e+01 2.84056435e+01 5 8.67170747e+00 -3.57563196e+01 -1.39531459e+01 6 2.04770191e+01 -6.72374996e-03 -2.34897135e+01 7 1.38578073e+01 -6.74609914e+01 -5.78119770e+01 8 -3.02232008e+01 -3.01122250e+01 2.51342118e+00 9 -1.02742160e+01 5.01882635e+00 -3.11482147e+01 10 -1.36647313e+01 2.60634999e+01 -4.01999347e+01 11 -1.07957879e+01 -2.45348057e+01 -1.23972969e+01 12 -2.50865544e+01 2.27724638e+01 6.25514682e-01 13 -2.34151778e+01 -8.97565261e+00 -9.29893763e+01 14 1.88020257e+01 1.81667237e+01 -1.41443324e+01 15 8.81612734e+01 1.41730281e+01 2.81081987e+01 16 1.39502810e+01 6.17827402e+01 2.61828882e+01 17 -3.32076519e+01 -1.49259026e+01 9.15074950e-01 18 5.57077400e+00 3.24434409e+01 -1.29434142e-01 19 5.61706956e-02 -3.32480115e+01 3.32349083e+01 20 -1.79928040e+01 4.76827087e+00 1.42495941e+01 21 -1.17161399e+01 -2.70242759e+01 1.80123683e+01 22 4.71962552e+01 4.46790636e+01 5.24825912e+01 23 1.08621452e+01 -7.63433113e+00 1.51230483e+01 24 5.24871994e+00 1.36452865e-01 2.27062031e+01 25 -5.34398477e+01 -1.15797528e+01 1.50974543e+00 26 2.09459045e+00 5.30713108e+01 -9.61163697e+00 27 3.25046625e+01 -6.52215058e+01 3.12053044e+01 28 -6.86588410e+01 6.06629923e+01 2.02309283e+01 29 -3.91814323e-01 -1.88566767e+01 1.47118779e+01 30 2.46773560e+01 2.99719732e+01 -5.21556470e+00 31 3.24119525e+01 -1.81273449e+01 3.31563534e+01 32 1.77267831e+01 3.13842843e+01 3.57893149e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==9910== Memcheck, a memory error detector ==9910== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==9910== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==9910== Command: python runner2.py EAM_Dynamo_AcklandWoodingBacon_1995v2_Zr__MO_398441626455_000 ==9910== ==11511== Warning: invalid file descriptor 1048564 in syscall close() ==11511== Warning: invalid file descriptor 1048565 in syscall close() ==11511== Warning: invalid file descriptor 1048566 in syscall close() ==11511== Warning: invalid file descriptor 1048567 in syscall close() ==11511== Use --log-fd= to select an alternative log fd. ==11511== Warning: invalid file descriptor 1048568 in syscall close() ==11511== Warning: invalid file descriptor 1048569 in syscall close() ==11518== Warning: invalid file descriptor 1048564 in syscall close() ==11518== Warning: invalid file descriptor 1048565 in syscall close() ==11518== Warning: invalid file descriptor 1048566 in syscall close() ==11518== Warning: invalid file descriptor 1048567 in syscall close() ==11518== Use --log-fd= to select an alternative log fd. ==11518== Warning: invalid file descriptor 1048568 in syscall close() ==11518== Warning: invalid file descriptor 1048569 in syscall close() ==11651== Warning: invalid file descriptor 1048564 in syscall close() ==11651== Warning: invalid file descriptor 1048565 in syscall close() ==11651== Warning: invalid file descriptor 1048566 in syscall close() ==11651== Warning: invalid file descriptor 1048567 in syscall close() ==11651== Use --log-fd= to select an alternative log fd. ==11651== Warning: invalid file descriptor 1048568 in syscall close() ==11651== Warning: invalid file descriptor 1048569 in syscall close() ==11652== Warning: invalid file descriptor 1048564 in syscall close() ==11652== Warning: invalid file descriptor 1048565 in syscall close() ==11652== Warning: invalid file descriptor 1048566 in syscall close() ==11652== Warning: invalid file descriptor 1048567 in syscall close() ==11652== Use --log-fd= to select an alternative log fd. ==11652== Warning: invalid file descriptor 1048568 in syscall close() ==11652== Warning: invalid file descriptor 1048569 in syscall close() ==11653== Warning: invalid file descriptor 1048564 in syscall close() ==11653== Warning: invalid file descriptor 1048565 in syscall close() ==11653== Warning: invalid file descriptor 1048566 in syscall close() ==11653== Warning: invalid file descriptor 1048567 in syscall close() ==11653== Use --log-fd= to select an alternative log fd. ==11653== Warning: invalid file descriptor 1048568 in syscall close() ==11653== Warning: invalid file descriptor 1048569 in syscall close() ==11654== Warning: invalid file descriptor 1048564 in syscall close() ==11654== Warning: invalid file descriptor 1048565 in syscall close() ==11654== Warning: invalid file descriptor 1048566 in syscall close() ==11654== Warning: invalid file descriptor 1048567 in syscall close() ==11654== Use --log-fd= to select an alternative log fd. ==11654== Warning: invalid file descriptor 1048568 in syscall close() ==11654== Warning: invalid file descriptor 1048569 in syscall close() ==9910== ==9910== HEAP SUMMARY: ==9910== in use at exit: 1,718,292 bytes in 1,321 blocks ==9910== total heap usage: 31,120 allocs, 29,799 frees, 47,288,936 bytes allocated ==9910== ==9910== LEAK SUMMARY: ==9910== definitely lost: 0 bytes in 0 blocks ==9910== indirectly lost: 0 bytes in 0 blocks ==9910== possibly lost: 178,943 bytes in 97 blocks ==9910== still reachable: 1,539,349 bytes in 1,224 blocks ==9910== suppressed: 0 bytes in 0 blocks ==9910== Rerun with --leak-check=full to see details of leaked memory ==9910== ==9910== For counts of detected and suppressed errors, rerun with: -v ==9910== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16350 from 600) ================================================================================ 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.