!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_LenoskySadighAlonso_2000_Si__SM_622320990752_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 = 245.52807681901214 Forces: 1 -1.14920862e+01 -1.59855232e+01 -2.71756812e+01 2 -1.90051363e+01 1.47319934e+01 -2.38795468e+01 3 9.35622254e+00 -3.03283289e+01 -1.39967822e+01 4 -1.96182686e+01 1.23054303e+01 7.02046492e+00 5 1.53837936e+01 -3.16270119e+01 -5.45477184e+00 6 1.12263938e+01 -2.10507917e+00 -2.02736546e+01 7 2.58562240e+01 -7.34031907e+01 -5.28005715e+01 8 -3.08574664e+01 -5.02232547e+01 -2.94460203e+01 9 -2.20577977e+01 -2.55036120e+01 -3.77906198e+01 10 -5.00916010e+01 5.65878533e+01 -7.59864823e+01 11 -5.39995816e+01 -5.20650150e+01 -6.14938520e+01 12 -3.44819809e+01 2.91459072e+01 1.70194134e+01 13 2.89952659e+01 -7.28944609e+01 -1.21100243e+02 14 1.56297500e+01 9.56894615e+00 -9.14879331e+00 15 9.90048819e+01 1.01099535e+01 -9.20275583e-01 16 6.24922028e+01 1.27278539e+02 5.21081656e+01 17 -4.94760448e+01 -1.95134464e+01 -5.33408899e+00 18 1.29820896e+01 1.76288749e+01 -8.39129616e+00 19 2.02805045e+01 -4.03319043e+01 4.04423893e+01 20 -2.24240366e+01 1.60161442e+01 2.09969137e+01 21 -1.94085344e+01 -3.04344946e+01 2.70610857e+01 22 5.93196535e+01 3.24430091e+01 4.59706242e+01 23 8.20162573e+00 -5.83171984e+00 1.36442646e+01 24 1.46528542e+00 -8.34582763e+00 2.36722339e+01 25 -7.32383041e+01 -1.03919132e+01 2.53896465e+01 26 -4.18196228e+01 1.04180207e+02 4.59225360e+01 27 7.48683791e+00 -4.19398821e+01 2.81738067e+01 28 -4.14646534e+01 3.59044960e+01 9.76682060e+00 29 2.63640611e+01 -7.83200224e+00 5.58894173e+01 30 2.56244871e+01 3.32637696e+01 -5.22326262e+00 31 4.36744748e+01 -2.46720552e+01 4.52626592e+01 32 1.60913603e+01 4.42635985e+01 4.00755002e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Si (Configuration in file "config-T-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 245.52807681901214 Forces: 1 -1.14920862e+01 -1.59855232e+01 -2.71756812e+01 2 -1.90051363e+01 1.47319934e+01 -2.38795468e+01 3 9.35622254e+00 -3.03283289e+01 -1.39967822e+01 4 -1.96182686e+01 1.23054303e+01 7.02046492e+00 5 1.53837936e+01 -3.16270119e+01 -5.45477184e+00 6 1.12263938e+01 -2.10507917e+00 -2.02736546e+01 7 2.58562240e+01 -7.34031907e+01 -5.28005715e+01 8 -3.08574664e+01 -5.02232547e+01 -2.94460203e+01 9 -2.20577977e+01 -2.55036120e+01 -3.77906198e+01 10 -5.00916010e+01 5.65878533e+01 -7.59864823e+01 11 -5.39995816e+01 -5.20650150e+01 -6.14938520e+01 12 -3.44819809e+01 2.91459072e+01 1.70194134e+01 13 2.89952659e+01 -7.28944609e+01 -1.21100243e+02 14 1.56297500e+01 9.56894615e+00 -9.14879331e+00 15 9.90048819e+01 1.01099535e+01 -9.20275583e-01 16 6.24922028e+01 1.27278539e+02 5.21081656e+01 17 -4.94760448e+01 -1.95134464e+01 -5.33408899e+00 18 1.29820896e+01 1.76288749e+01 -8.39129616e+00 19 2.02805045e+01 -4.03319043e+01 4.04423893e+01 20 -2.24240366e+01 1.60161442e+01 2.09969137e+01 21 -1.94085344e+01 -3.04344946e+01 2.70610857e+01 22 5.93196535e+01 3.24430091e+01 4.59706242e+01 23 8.20162573e+00 -5.83171984e+00 1.36442646e+01 24 1.46528542e+00 -8.34582763e+00 2.36722339e+01 25 -7.32383041e+01 -1.03919132e+01 2.53896465e+01 26 -4.18196228e+01 1.04180207e+02 4.59225360e+01 27 7.48683791e+00 -4.19398821e+01 2.81738067e+01 28 -4.14646534e+01 3.59044960e+01 9.76682060e+00 29 2.63640611e+01 -7.83200224e+00 5.58894173e+01 30 2.56244871e+01 3.32637696e+01 -5.22326262e+00 31 4.36744748e+01 -2.46720552e+01 4.52626592e+01 32 1.60913603e+01 4.42635985e+01 4.00755002e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==61097== Memcheck, a memory error detector ==61097== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==61097== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==61097== Command: python runner2.py Sim_LAMMPS_MEAM_LenoskySadighAlonso_2000_Si__SM_622320990752_000 ==61097== ==61233== Warning: invalid file descriptor 1048564 in syscall close() ==61233== Warning: invalid file descriptor 1048565 in syscall close() ==61233== Warning: invalid file descriptor 1048566 in syscall close() ==61233== Warning: invalid file descriptor 1048567 in syscall close() ==61233== Use --log-fd= to select an alternative log fd. ==61233== Warning: invalid file descriptor 1048568 in syscall close() ==61233== Warning: invalid file descriptor 1048569 in syscall close() ==61234== Warning: invalid file descriptor 1048564 in syscall close() ==61234== Warning: invalid file descriptor 1048565 in syscall close() ==61234== Warning: invalid file descriptor 1048566 in syscall close() ==61234== Warning: invalid file descriptor 1048567 in syscall close() ==61234== Use --log-fd= to select an alternative log fd. ==61234== Warning: invalid file descriptor 1048568 in syscall close() ==61234== Warning: invalid file descriptor 1048569 in syscall close() ==61235== Warning: invalid file descriptor 1048564 in syscall close() ==61235== Warning: invalid file descriptor 1048565 in syscall close() ==61235== Warning: invalid file descriptor 1048566 in syscall close() ==61235== Warning: invalid file descriptor 1048567 in syscall close() ==61235== Use --log-fd= to select an alternative log fd. ==61235== Warning: invalid file descriptor 1048568 in syscall close() ==61235== Warning: invalid file descriptor 1048569 in syscall close() ==61237== Warning: invalid file descriptor 1048564 in syscall close() ==61237== Warning: invalid file descriptor 1048565 in syscall close() ==61237== Warning: invalid file descriptor 1048566 in syscall close() ==61237== Warning: invalid file descriptor 1048567 in syscall close() ==61237== Use --log-fd= to select an alternative log fd. ==61237== Warning: invalid file descriptor 1048568 in syscall close() ==61237== Warning: invalid file descriptor 1048569 in syscall close() ==61241== Warning: invalid file descriptor 1048564 in syscall close() ==61241== Warning: invalid file descriptor 1048565 in syscall close() ==61241== Warning: invalid file descriptor 1048566 in syscall close() ==61241== Warning: invalid file descriptor 1048567 in syscall close() ==61241== Use --log-fd= to select an alternative log fd. ==61241== Warning: invalid file descriptor 1048568 in syscall close() ==61241== Warning: invalid file descriptor 1048569 in syscall close() ==61243== Warning: invalid file descriptor 1048564 in syscall close() ==61243== Warning: invalid file descriptor 1048565 in syscall close() ==61243== Warning: invalid file descriptor 1048566 in syscall close() ==61243== Warning: invalid file descriptor 1048567 in syscall close() ==61243== Use --log-fd= to select an alternative log fd. ==61243== Warning: invalid file descriptor 1048568 in syscall close() ==61243== Warning: invalid file descriptor 1048569 in syscall close() ==61245== Warning: invalid file descriptor 1048564 in syscall close() ==61245== Warning: invalid file descriptor 1048565 in syscall close() ==61245== Warning: invalid file descriptor 1048566 in syscall close() ==61245== Warning: invalid file descriptor 1048567 in syscall close() ==61245== Use --log-fd= to select an alternative log fd. ==61245== Warning: invalid file descriptor 1048568 in syscall close() ==61245== Warning: invalid file descriptor 1048569 in syscall close() ==61246== Warning: invalid file descriptor 1048564 in syscall close() ==61246== Warning: invalid file descriptor 1048565 in syscall close() ==61246== Warning: invalid file descriptor 1048566 in syscall close() ==61246== Warning: invalid file descriptor 1048567 in syscall close() ==61246== Use --log-fd= to select an alternative log fd. ==61246== Warning: invalid file descriptor 1048568 in syscall close() ==61246== Warning: invalid file descriptor 1048569 in syscall close() ==61097== ==61097== HEAP SUMMARY: ==61097== in use at exit: 1,780,719 bytes in 1,488 blocks ==61097== total heap usage: 28,449 allocs, 26,961 frees, 42,740,038 bytes allocated ==61097== ==61097== LEAK SUMMARY: ==61097== definitely lost: 0 bytes in 0 blocks ==61097== indirectly lost: 0 bytes in 0 blocks ==61097== possibly lost: 178,423 bytes in 96 blocks ==61097== still reachable: 1,602,296 bytes in 1,392 blocks ==61097== suppressed: 0 bytes in 0 blocks ==61097== Rerun with --leak-check=full to see details of leaked memory ==61097== ==61097== For counts of detected and suppressed errors, rerun with: -v ==61097== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16448 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.