!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_EtesamiAsadi_2018_Cu__SM_316120381362_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 = 21.25431115263969 Forces: 1 -1.28399149e+01 -2.10926223e+01 -3.81909720e+01 2 -4.62223700e+00 8.10188038e+00 -5.64393425e+00 3 3.64594506e+01 -2.53878473e+01 2.03148270e+01 4 -2.75308821e+01 4.38432483e+01 1.75329861e+01 5 3.38097723e+00 -1.23181102e+01 -4.83206927e-01 6 4.13013809e+00 4.33455955e+00 -3.96251636e+00 7 -2.11113260e+00 -6.15418769e+01 -5.99740218e+01 8 -7.43494730e+00 -2.42437993e+01 -7.43951736e+00 9 -1.10232449e+00 -2.01376168e+01 -1.96160291e+01 10 -6.74644659e+00 1.30013108e+01 -1.74819538e+01 11 -8.41869661e+00 -1.34613361e+01 1.01804357e+00 12 -9.92270410e+00 2.01020981e+01 1.83470915e+01 13 -1.25399885e+01 -1.09093489e+01 -4.52973834e+01 14 4.67564147e+00 7.56360807e+00 -5.26182979e+00 15 4.25829185e+01 -1.40286610e+01 9.76511346e+00 16 5.02083268e+00 2.98710047e+01 1.23929265e+01 17 -1.13504567e+01 -5.08040321e+00 -6.92694277e+00 18 -8.94721292e+00 5.60288940e+00 -2.10455224e+01 19 8.29582542e+00 -1.33807943e+01 8.75372035e+00 20 -7.10292000e+00 1.01468123e+01 5.70823805e+00 21 -6.89583048e+00 -8.47985835e+00 -2.46971691e+00 22 1.59728129e+01 6.17684655e+01 5.73001761e+01 23 3.63832647e+00 -1.05575024e+00 5.93628531e+00 24 1.36805951e+01 3.76221312e+00 2.02860917e+01 25 -3.97932780e+00 6.03932475e-01 5.43683749e+00 26 -3.79837244e+00 9.01846176e+00 -8.83285167e+00 27 3.79561226e+01 -5.06210064e+01 5.78255347e+00 28 -4.88897371e+01 4.20295082e+01 3.67231988e+00 29 -8.37310077e+00 2.48158804e+00 3.10897146e+01 30 6.27014397e+00 1.27885256e+01 1.01717013e+01 31 5.62636947e+00 -4.29623233e+00 3.43527311e-01 32 4.91607802e+00 1.10151574e+01 8.77424476e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Cu (Configuration in file "config-T-Cu.xyz") ----------------------------------------------------------------------------------------------------- Energy = 21.25431115263969 Forces: 1 -1.28399149e+01 -2.10926223e+01 -3.81909720e+01 2 -4.62223700e+00 8.10188038e+00 -5.64393425e+00 3 3.64594506e+01 -2.53878473e+01 2.03148270e+01 4 -2.75308821e+01 4.38432483e+01 1.75329861e+01 5 3.38097723e+00 -1.23181102e+01 -4.83206927e-01 6 4.13013809e+00 4.33455955e+00 -3.96251636e+00 7 -2.11113260e+00 -6.15418769e+01 -5.99740218e+01 8 -7.43494730e+00 -2.42437993e+01 -7.43951736e+00 9 -1.10232449e+00 -2.01376168e+01 -1.96160291e+01 10 -6.74644659e+00 1.30013108e+01 -1.74819538e+01 11 -8.41869661e+00 -1.34613361e+01 1.01804357e+00 12 -9.92270410e+00 2.01020981e+01 1.83470915e+01 13 -1.25399885e+01 -1.09093489e+01 -4.52973834e+01 14 4.67564147e+00 7.56360807e+00 -5.26182979e+00 15 4.25829185e+01 -1.40286610e+01 9.76511346e+00 16 5.02083268e+00 2.98710047e+01 1.23929265e+01 17 -1.13504567e+01 -5.08040321e+00 -6.92694277e+00 18 -8.94721292e+00 5.60288940e+00 -2.10455224e+01 19 8.29582542e+00 -1.33807943e+01 8.75372035e+00 20 -7.10292000e+00 1.01468123e+01 5.70823805e+00 21 -6.89583048e+00 -8.47985835e+00 -2.46971691e+00 22 1.59728129e+01 6.17684655e+01 5.73001761e+01 23 3.63832647e+00 -1.05575024e+00 5.93628531e+00 24 1.36805951e+01 3.76221312e+00 2.02860917e+01 25 -3.97932780e+00 6.03932475e-01 5.43683749e+00 26 -3.79837244e+00 9.01846176e+00 -8.83285167e+00 27 3.79561226e+01 -5.06210064e+01 5.78255347e+00 28 -4.88897371e+01 4.20295082e+01 3.67231988e+00 29 -8.37310077e+00 2.48158804e+00 3.10897146e+01 30 6.27014397e+00 1.27885256e+01 1.01717013e+01 31 5.62636947e+00 -4.29623233e+00 3.43527311e-01 32 4.91607802e+00 1.10151574e+01 8.77424476e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==38952== Memcheck, a memory error detector ==38952== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==38952== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==38952== Command: python runner2.py Sim_LAMMPS_MEAM_EtesamiAsadi_2018_Cu__SM_316120381362_000 ==38952== ==40308== Warning: invalid file descriptor 1048564 in syscall close() ==40308== Warning: invalid file descriptor 1048565 in syscall close() ==40308== Warning: invalid file descriptor 1048566 in syscall close() ==40308== Warning: invalid file descriptor 1048567 in syscall close() ==40308== Use --log-fd= to select an alternative log fd. ==40308== Warning: invalid file descriptor 1048568 in syscall close() ==40308== Warning: invalid file descriptor 1048569 in syscall close() ==40314== Warning: invalid file descriptor 1048564 in syscall close() ==40314== Warning: invalid file descriptor 1048565 in syscall close() ==40314== Warning: invalid file descriptor 1048566 in syscall close() ==40314== Warning: invalid file descriptor 1048567 in syscall close() ==40314== Use --log-fd= to select an alternative log fd. ==40314== Warning: invalid file descriptor 1048568 in syscall close() ==40314== Warning: invalid file descriptor 1048569 in syscall close() ==40319== Warning: invalid file descriptor 1048564 in syscall close() ==40319== Warning: invalid file descriptor 1048565 in syscall close() ==40319== Warning: invalid file descriptor 1048566 in syscall close() ==40319== Warning: invalid file descriptor 1048567 in syscall close() ==40319== Use --log-fd= to select an alternative log fd. ==40319== Warning: invalid file descriptor 1048568 in syscall close() ==40319== Warning: invalid file descriptor 1048569 in syscall close() ==40329== Warning: invalid file descriptor 1048564 in syscall close() ==40329== Warning: invalid file descriptor 1048565 in syscall close() ==40329== Warning: invalid file descriptor 1048566 in syscall close() ==40329== Warning: invalid file descriptor 1048567 in syscall close() ==40329== Use --log-fd= to select an alternative log fd. ==40329== Warning: invalid file descriptor 1048568 in syscall close() ==40329== Warning: invalid file descriptor 1048569 in syscall close() ==40342== Warning: invalid file descriptor 1048564 in syscall close() ==40342== Warning: invalid file descriptor 1048565 in syscall close() ==40342== Warning: invalid file descriptor 1048566 in syscall close() ==40342== Warning: invalid file descriptor 1048567 in syscall close() ==40342== Use --log-fd= to select an alternative log fd. ==40342== Warning: invalid file descriptor 1048568 in syscall close() ==40342== Warning: invalid file descriptor 1048569 in syscall close() ==40348== Warning: invalid file descriptor 1048564 in syscall close() ==40348== Warning: invalid file descriptor 1048565 in syscall close() ==40348== Warning: invalid file descriptor 1048566 in syscall close() ==40348== Warning: invalid file descriptor 1048567 in syscall close() ==40348== Use --log-fd= to select an alternative log fd. ==40348== Warning: invalid file descriptor 1048568 in syscall close() ==40348== Warning: invalid file descriptor 1048569 in syscall close() ==40353== Warning: invalid file descriptor 1048564 in syscall close() ==40353== Warning: invalid file descriptor 1048565 in syscall close() ==40353== Warning: invalid file descriptor 1048566 in syscall close() ==40353== Warning: invalid file descriptor 1048567 in syscall close() ==40353== Use --log-fd= to select an alternative log fd. ==40353== Warning: invalid file descriptor 1048568 in syscall close() ==40353== Warning: invalid file descriptor 1048569 in syscall close() ==40354== Warning: invalid file descriptor 1048564 in syscall close() ==40354== Warning: invalid file descriptor 1048565 in syscall close() ==40354== Warning: invalid file descriptor 1048566 in syscall close() ==40354== Warning: invalid file descriptor 1048567 in syscall close() ==40354== Use --log-fd= to select an alternative log fd. ==40354== Warning: invalid file descriptor 1048568 in syscall close() ==40354== Warning: invalid file descriptor 1048569 in syscall close() ==38952== ==38952== HEAP SUMMARY: ==38952== in use at exit: 1,780,635 bytes in 1,488 blocks ==38952== total heap usage: 28,635 allocs, 27,147 frees, 48,635,823 bytes allocated ==38952== ==38952== LEAK SUMMARY: ==38952== definitely lost: 0 bytes in 0 blocks ==38952== indirectly lost: 0 bytes in 0 blocks ==38952== possibly lost: 178,423 bytes in 96 blocks ==38952== still reachable: 1,602,212 bytes in 1,392 blocks ==38952== suppressed: 0 bytes in 0 blocks ==38952== Rerun with --leak-check=full to see details of leaked memory ==38952== ==38952== For counts of detected and suppressed errors, rerun with: -v ==38952== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16411 from 607) ================================================================================ 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.