!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : Sim_LAMMPS_MEAM_AsadiZaeemNouranian_2015_Cu__SM_239791545509_000 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 = -10.674951828456132 Forces: 1 -1.50142041e-01 -5.84841456e+00 -6.27925616e+00 2 -7.22762070e+00 8.77832341e+00 -2.24391823e+00 3 4.33253899e+00 -1.07453523e+01 -7.16011997e+00 4 -5.72180980e+00 4.87595981e+00 3.86528419e+00 5 6.50626774e+00 -1.20443369e+01 -5.52211191e-01 6 2.64262468e+00 2.96544248e+00 -2.24526484e+00 7 7.81693923e-01 -2.15320060e+01 -2.23149789e+01 8 -1.06296090e+01 -8.47024141e+00 -4.91138455e+00 9 -9.63794998e+00 -5.18357417e+00 -1.23179905e+01 10 -5.70337926e+00 1.61326946e+01 -1.45621664e+01 11 3.94677193e+00 -1.04784743e+01 1.03361154e+01 12 -6.93416305e+00 1.06211425e+01 2.99014958e+00 13 -4.58699303e+00 -9.38113256e+00 -2.67890009e+01 14 3.96182331e+00 6.14033675e+00 -4.54506247e+00 15 2.63391650e+01 -4.92837528e+00 1.18267611e+01 16 5.02372851e+00 1.53290538e+01 9.29157989e+00 17 -9.48986784e+00 -4.85584874e+00 -4.05341012e+00 18 2.46226348e+00 9.80370800e+00 4.96318631e+00 19 3.59937181e+00 -5.96474489e+00 5.43634837e+00 20 -3.13702659e+00 6.26303499e+00 4.43103936e+00 21 -1.32493815e+01 -9.51519433e+00 1.99208530e+00 22 1.90315642e+01 2.25082596e+01 1.87563031e+01 23 4.83594236e+00 -1.00901235e+00 6.12800306e+00 24 1.66241265e+00 5.85613281e-01 2.55055961e+00 25 -3.62259385e+00 -7.59202605e+00 -6.87508130e-01 26 -3.33763736e+00 8.60723932e+00 -8.85155497e+00 27 6.69456865e+00 -2.19910447e+01 2.70467840e+00 28 -2.02782671e+01 1.94086113e+01 1.24176561e+01 29 -6.31326982e+00 -5.08026163e+00 2.63622859e+00 30 5.42961516e+00 1.01584181e+01 -4.81299264e+00 31 6.92445707e+00 -9.76738469e+00 8.93646793e+00 32 5.84490153e+00 1.22095870e+01 1.30643738e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Cu (Configuration in file "config-T-Cu.xyz") ----------------------------------------------------------------------------------------------------- Energy = -10.674951828456132 Forces: 1 -1.50142041e-01 -5.84841456e+00 -6.27925616e+00 2 -7.22762070e+00 8.77832341e+00 -2.24391823e+00 3 4.33253899e+00 -1.07453523e+01 -7.16011997e+00 4 -5.72180980e+00 4.87595981e+00 3.86528419e+00 5 6.50626774e+00 -1.20443369e+01 -5.52211191e-01 6 2.64262468e+00 2.96544248e+00 -2.24526484e+00 7 7.81693923e-01 -2.15320060e+01 -2.23149789e+01 8 -1.06296090e+01 -8.47024141e+00 -4.91138455e+00 9 -9.63794998e+00 -5.18357417e+00 -1.23179905e+01 10 -5.70337926e+00 1.61326946e+01 -1.45621664e+01 11 3.94677193e+00 -1.04784743e+01 1.03361154e+01 12 -6.93416305e+00 1.06211425e+01 2.99014958e+00 13 -4.58699303e+00 -9.38113256e+00 -2.67890009e+01 14 3.96182331e+00 6.14033675e+00 -4.54506247e+00 15 2.63391650e+01 -4.92837528e+00 1.18267611e+01 16 5.02372851e+00 1.53290538e+01 9.29157989e+00 17 -9.48986784e+00 -4.85584874e+00 -4.05341012e+00 18 2.46226348e+00 9.80370800e+00 4.96318631e+00 19 3.59937181e+00 -5.96474489e+00 5.43634837e+00 20 -3.13702659e+00 6.26303499e+00 4.43103936e+00 21 -1.32493815e+01 -9.51519433e+00 1.99208530e+00 22 1.90315642e+01 2.25082596e+01 1.87563031e+01 23 4.83594236e+00 -1.00901235e+00 6.12800306e+00 24 1.66241265e+00 5.85613281e-01 2.55055961e+00 25 -3.62259385e+00 -7.59202605e+00 -6.87508130e-01 26 -3.33763736e+00 8.60723932e+00 -8.85155497e+00 27 6.69456865e+00 -2.19910447e+01 2.70467840e+00 28 -2.02782671e+01 1.94086113e+01 1.24176561e+01 29 -6.31326982e+00 -5.08026163e+00 2.63622859e+00 30 5.42961516e+00 1.01584181e+01 -4.81299264e+00 31 6.92445707e+00 -9.76738469e+00 8.93646793e+00 32 5.84490153e+00 1.22095870e+01 1.30643738e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==34635== Memcheck, a memory error detector ==34635== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==34635== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==34635== Command: python runner2.py Sim_LAMMPS_MEAM_AsadiZaeemNouranian_2015_Cu__SM_239791545509_000 ==34635== ==35950== Warning: invalid file descriptor 1048564 in syscall close() ==35950== Warning: invalid file descriptor 1048565 in syscall close() ==35950== Warning: invalid file descriptor 1048566 in syscall close() ==35950== Warning: invalid file descriptor 1048567 in syscall close() ==35950== Use --log-fd= to select an alternative log fd. ==35950== Warning: invalid file descriptor 1048568 in syscall close() ==35950== Warning: invalid file descriptor 1048569 in syscall close() ==35958== Warning: invalid file descriptor 1048564 in syscall close() ==35958== Warning: invalid file descriptor 1048565 in syscall close() ==35958== Warning: invalid file descriptor 1048566 in syscall close() ==35958== Warning: invalid file descriptor 1048567 in syscall close() ==35958== Use --log-fd= to select an alternative log fd. ==35958== Warning: invalid file descriptor 1048568 in syscall close() ==35958== Warning: invalid file descriptor 1048569 in syscall close() ==35962== Warning: invalid file descriptor 1048564 in syscall close() ==35962== Warning: invalid file descriptor 1048565 in syscall close() ==35962== Warning: invalid file descriptor 1048566 in syscall close() ==35962== Warning: invalid file descriptor 1048567 in syscall close() ==35962== Use --log-fd= to select an alternative log fd. ==35962== Warning: invalid file descriptor 1048568 in syscall close() ==35962== Warning: invalid file descriptor 1048569 in syscall close() ==35964== Warning: invalid file descriptor 1048564 in syscall close() ==35964== Warning: invalid file descriptor 1048565 in syscall close() ==35964== Warning: invalid file descriptor 1048566 in syscall close() ==35964== Warning: invalid file descriptor 1048567 in syscall close() ==35964== Use --log-fd= to select an alternative log fd. ==35964== Warning: invalid file descriptor 1048568 in syscall close() ==35964== Warning: invalid file descriptor 1048569 in syscall close() ==35967== Warning: invalid file descriptor 1048564 in syscall close() ==35967== Warning: invalid file descriptor 1048565 in syscall close() ==35967== Warning: invalid file descriptor 1048566 in syscall close() ==35967== Warning: invalid file descriptor 1048567 in syscall close() ==35967== Use --log-fd= to select an alternative log fd. ==35967== Warning: invalid file descriptor 1048568 in syscall close() ==35967== Warning: invalid file descriptor 1048569 in syscall close() ==35969== Warning: invalid file descriptor 1048564 in syscall close() ==35969== Warning: invalid file descriptor 1048565 in syscall close() ==35969== Warning: invalid file descriptor 1048566 in syscall close() ==35969== Warning: invalid file descriptor 1048567 in syscall close() ==35969== Use --log-fd= to select an alternative log fd. ==35969== Warning: invalid file descriptor 1048568 in syscall close() ==35969== Warning: invalid file descriptor 1048569 in syscall close() ==35971== Warning: invalid file descriptor 1048564 in syscall close() ==35971== Warning: invalid file descriptor 1048565 in syscall close() ==35971== Warning: invalid file descriptor 1048566 in syscall close() ==35971== Warning: invalid file descriptor 1048567 in syscall close() ==35971== Use --log-fd= to select an alternative log fd. ==35971== Warning: invalid file descriptor 1048568 in syscall close() ==35971== Warning: invalid file descriptor 1048569 in syscall close() ==35972== Warning: invalid file descriptor 1048564 in syscall close() ==35972== Warning: invalid file descriptor 1048565 in syscall close() ==35972== Warning: invalid file descriptor 1048566 in syscall close() ==35972== Warning: invalid file descriptor 1048567 in syscall close() ==35972== Use --log-fd= to select an alternative log fd. ==35972== Warning: invalid file descriptor 1048568 in syscall close() ==35972== Warning: invalid file descriptor 1048569 in syscall close() ==34635== ==34635== HEAP SUMMARY: ==34635== in use at exit: 1,780,719 bytes in 1,488 blocks ==34635== total heap usage: 28,639 allocs, 27,151 frees, 48,637,811 bytes allocated ==34635== ==34635== LEAK SUMMARY: ==34635== definitely lost: 0 bytes in 0 blocks ==34635== indirectly lost: 0 bytes in 0 blocks ==34635== possibly lost: 178,423 bytes in 96 blocks ==34635== still reachable: 1,602,296 bytes in 1,392 blocks ==34635== suppressed: 0 bytes in 0 blocks ==34635== Rerun with --leak-check=full to see details of leaked memory ==34635== ==34635== For counts of detected and suppressed errors, rerun with: -v ==34635== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16438 from 620) ================================================================================ 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.