!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 and Daniel S. Karls ----------------------------------------------------------------------------------------------------- Results for KIM Model : Tersoff_LAMMPS_AlbeNordlundAverback_2002_PtC__MO_500121566391_004 Supported species : C Pt random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = C (Configuration in file "config-F-C.xyz") ----------------------------------------------------------------------------------------------------- Energy = 201.3317583064447 Forces: 1 -2.16919808e+00 -3.64983001e+01 -2.04878068e+01 2 -3.20086148e+01 1.82889228e+01 -3.24582466e+01 3 1.08111133e+01 -2.98179126e+01 -3.88121937e+01 4 -3.27548903e+01 3.33127556e+01 2.11200805e+01 5 3.15326168e+01 -5.52686299e+01 -1.39343747e+01 6 1.79255442e+01 -2.23343714e+01 -2.48111816e+01 7 7.89005867e+00 -6.28072461e+01 -7.69808380e+01 8 -3.28276771e+01 7.35050586e+00 1.02632396e+01 9 -2.21897788e+01 -2.64100599e+01 -6.77807139e+01 10 -1.03397061e+01 5.98178243e+01 -5.54179469e+01 11 -3.20448733e+01 -7.22153273e+01 -1.26025978e+01 12 -3.92659390e+01 4.06293055e+01 3.21618314e+01 13 -2.28819386e+01 -2.46103250e+01 -1.87264871e+02 14 3.36985679e+01 2.58150057e+01 -2.71171933e+01 15 1.11799043e+02 -9.79267923e+00 1.24471393e+01 16 -3.33849725e+01 1.22216767e+02 6.38987035e+01 17 -7.88317218e+01 -1.70212747e+01 -1.48058749e+01 18 6.48741408e+00 4.32864849e+01 -2.28519480e+01 19 4.32236062e+01 -4.11538772e+01 5.68059107e+01 20 -1.78477857e+01 1.90001866e+01 2.93984973e+01 21 -1.83099853e+01 -7.51328231e+01 5.23562124e+01 22 7.59845943e+01 6.04813443e+00 3.26400981e+01 23 1.57176782e+01 4.30780438e+00 2.94301961e+01 24 1.07834254e+01 1.21552495e+00 1.91496358e+01 25 -2.61984081e+01 -1.66846133e+01 -1.35336051e+01 26 3.75549926e+01 5.62192471e+01 -7.39757112e+00 27 3.16162477e+01 -6.86841886e+01 5.65392777e+01 28 -9.79634711e+01 6.21962435e+01 8.41207040e+00 29 -3.83069122e+01 -6.19323433e+00 1.04078885e+02 30 4.17715733e+01 4.99475237e+01 2.68894843e+01 31 5.48968899e+01 -5.47717683e+00 2.99733863e+01 32 5.63250715e+00 2.04498031e+01 3.06923155e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = C (Configuration in file "config-T-C.xyz") ----------------------------------------------------------------------------------------------------- Energy = 201.3317583064447 Forces: 1 -2.16919808e+00 -3.64983001e+01 -2.04878068e+01 2 -3.20086148e+01 1.82889228e+01 -3.24582466e+01 3 1.08111133e+01 -2.98179126e+01 -3.88121937e+01 4 -3.27548903e+01 3.33127556e+01 2.11200805e+01 5 3.15326168e+01 -5.52686299e+01 -1.39343747e+01 6 1.79255442e+01 -2.23343714e+01 -2.48111816e+01 7 7.89005867e+00 -6.28072461e+01 -7.69808380e+01 8 -3.28276771e+01 7.35050586e+00 1.02632396e+01 9 -2.21897788e+01 -2.64100599e+01 -6.77807139e+01 10 -1.03397061e+01 5.98178243e+01 -5.54179469e+01 11 -3.20448733e+01 -7.22153273e+01 -1.26025978e+01 12 -3.92659390e+01 4.06293055e+01 3.21618314e+01 13 -2.28819386e+01 -2.46103250e+01 -1.87264871e+02 14 3.36985679e+01 2.58150057e+01 -2.71171933e+01 15 1.11799043e+02 -9.79267923e+00 1.24471393e+01 16 -3.33849725e+01 1.22216767e+02 6.38987035e+01 17 -7.88317218e+01 -1.70212747e+01 -1.48058749e+01 18 6.48741408e+00 4.32864849e+01 -2.28519480e+01 19 4.32236062e+01 -4.11538772e+01 5.68059107e+01 20 -1.78477857e+01 1.90001866e+01 2.93984973e+01 21 -1.83099853e+01 -7.51328231e+01 5.23562124e+01 22 7.59845943e+01 6.04813443e+00 3.26400981e+01 23 1.57176782e+01 4.30780438e+00 2.94301961e+01 24 1.07834254e+01 1.21552495e+00 1.91496358e+01 25 -2.61984081e+01 -1.66846133e+01 -1.35336051e+01 26 3.75549926e+01 5.62192471e+01 -7.39757112e+00 27 3.16162477e+01 -6.86841886e+01 5.65392777e+01 28 -9.79634711e+01 6.21962435e+01 8.41207040e+00 29 -3.83069122e+01 -6.19323433e+00 1.04078885e+02 30 4.17715733e+01 4.99475237e+01 2.68894843e+01 31 5.48968899e+01 -5.47717683e+00 2.99733863e+01 32 5.63250715e+00 2.04498031e+01 3.06923155e+01 MONOATOMIC STRUCTURE (pbc=False)-- Species = Pt (Configuration in file "config-F-Pt.xyz") ----------------------------------------------------------------------------------------------------- Energy = 468.6054253845185 Forces: 1 -4.78159006e+01 -6.57277813e+01 -2.44602243e+01 2 2.84975134e+01 6.70908711e+01 -3.15852816e+01 3 -4.57557595e+01 -7.38404470e+01 -6.24129017e+00 4 -3.18573456e+01 1.56372012e+01 3.75866920e+01 5 4.52667332e+01 -5.11629946e+01 -4.81221956e+01 6 3.37364155e+01 -3.53577123e+00 -3.42650415e+01 7 6.17472646e+01 -6.11149748e+01 -3.48670445e+01 8 3.98522201e+01 8.26843466e+01 -1.20310077e+02 9 -1.72254229e+01 2.37783013e+01 -2.42535364e+01 10 -2.23181798e+01 2.23664483e+01 -2.97249114e+01 11 -1.29243138e+01 -5.87042196e+01 -3.40363843e+01 12 -1.05877880e+02 7.82801587e+01 -1.39198053e+02 13 6.58724492e-01 -5.38548047e+01 -9.14267180e+01 14 2.61017544e+01 2.73741021e+01 -2.46267802e+01 15 1.26600950e+02 -5.38801438e+01 -1.16669968e+02 16 -2.54847928e+00 1.18366784e+02 3.41501849e+01 17 -3.37244420e+01 -2.71535565e+01 -5.16539314e+00 18 -1.13973540e+02 3.69052090e+01 8.04068368e+01 19 1.86672465e+01 -2.19680108e+01 1.82995851e+01 20 -1.99606073e+01 2.19421510e+01 1.65084691e+01 21 -2.13344045e+01 -1.01330600e+02 4.18615546e+01 22 7.94467430e+01 -3.48327826e+01 -6.00023987e+01 23 5.93085608e+01 -4.16163725e+01 9.03622736e+01 24 -2.30068864e+01 -3.26278088e+01 4.98079052e+01 25 -1.04916220e+02 -9.98523162e+01 4.33994886e+01 26 1.36280494e+02 9.58177420e+01 5.30638254e+01 27 -4.62683198e+01 -6.17601288e+01 5.40719186e+01 28 -3.35253738e+01 3.68867940e+01 4.04505466e+01 29 -1.27373832e+02 -6.02458265e+01 5.46841416e+01 30 6.05328926e+01 1.55032413e+02 7.95310348e+01 31 5.45271660e+01 5.50718529e+01 9.06171737e+01 32 3.91822293e+01 6.59741645e+01 4.01536679e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Pt (Configuration in file "config-T-Pt.xyz") ----------------------------------------------------------------------------------------------------- Energy = 468.6054253845185 Forces: 1 -4.78159006e+01 -6.57277813e+01 -2.44602243e+01 2 2.84975134e+01 6.70908711e+01 -3.15852816e+01 3 -4.57557595e+01 -7.38404470e+01 -6.24129017e+00 4 -3.18573456e+01 1.56372012e+01 3.75866920e+01 5 4.52667332e+01 -5.11629946e+01 -4.81221956e+01 6 3.37364155e+01 -3.53577123e+00 -3.42650415e+01 7 6.17472646e+01 -6.11149748e+01 -3.48670445e+01 8 3.98522201e+01 8.26843466e+01 -1.20310077e+02 9 -1.72254229e+01 2.37783013e+01 -2.42535364e+01 10 -2.23181798e+01 2.23664483e+01 -2.97249114e+01 11 -1.29243138e+01 -5.87042196e+01 -3.40363843e+01 12 -1.05877880e+02 7.82801587e+01 -1.39198053e+02 13 6.58724492e-01 -5.38548047e+01 -9.14267180e+01 14 2.61017544e+01 2.73741021e+01 -2.46267802e+01 15 1.26600950e+02 -5.38801438e+01 -1.16669968e+02 16 -2.54847928e+00 1.18366784e+02 3.41501849e+01 17 -3.37244420e+01 -2.71535565e+01 -5.16539314e+00 18 -1.13973540e+02 3.69052090e+01 8.04068368e+01 19 1.86672465e+01 -2.19680108e+01 1.82995851e+01 20 -1.99606073e+01 2.19421510e+01 1.65084691e+01 21 -2.13344045e+01 -1.01330600e+02 4.18615546e+01 22 7.94467430e+01 -3.48327826e+01 -6.00023987e+01 23 5.93085608e+01 -4.16163725e+01 9.03622736e+01 24 -2.30068864e+01 -3.26278088e+01 4.98079052e+01 25 -1.04916220e+02 -9.98523162e+01 4.33994886e+01 26 1.36280494e+02 9.58177420e+01 5.30638254e+01 27 -4.62683198e+01 -6.17601288e+01 5.40719186e+01 28 -3.35253738e+01 3.68867940e+01 4.04505466e+01 29 -1.27373832e+02 -6.02458265e+01 5.46841416e+01 30 6.05328926e+01 1.55032413e+02 7.95310348e+01 31 5.45271660e+01 5.50718529e+01 9.06171737e+01 32 3.91822293e+01 6.59741645e+01 4.01536679e+01 MIXED STRUCTURE (pbc=False)-- Species = C Pt (Configuration in file "config-F-CPt.xyz") ----------------------------------------------------------------------------------------------------- Energy = 157.19099328354227 Forces: 1 -9.52594394e+00 -3.60306044e+01 -3.30104058e+01 2 2.78340184e+01 7.11741274e+00 -4.31936648e+01 3 -2.50763034e+00 -2.31557508e+01 1.22909624e+01 4 -6.44135463e+01 -4.51588174e+01 5.05499330e+01 5 -2.23747664e+01 -7.89230714e+01 -8.82786897e+01 6 1.88351970e+01 -2.52556180e+01 -5.24112154e+01 7 5.85925595e+01 -7.31383240e+01 -1.58678658e+00 8 -8.15821067e+01 7.27477379e+01 5.11041156e+01 9 -6.21697028e+01 -1.19427557e+02 -1.82569060e+02 10 7.35439497e+01 5.49898670e+01 -7.30443109e+01 11 6.65777865e+01 9.06977032e-01 -8.39603836e+00 12 -7.48379071e+01 1.29008268e+02 1.92994275e+02 13 -2.41098073e+00 -2.26543945e+00 -8.55463068e+00 14 3.29897585e+00 1.52915540e+00 -1.15914461e+00 15 5.23839735e+01 6.07502579e+01 1.34330518e+01 16 1.48907768e+01 2.18598192e+01 -3.69472965e+01 17 -1.85856619e+01 -6.28383647e+00 -2.64685092e+01 18 2.28559500e+00 -2.22218108e+00 -1.78949730e+00 19 2.99952890e+01 -2.40143856e+01 3.39994285e+01 20 -1.65343754e+01 1.57692108e+01 8.21977741e+00 21 -6.04249094e-01 -2.30942202e+01 6.03743005e+00 22 2.47940405e+01 2.94394312e+01 3.16488994e+01 23 -1.55887992e+00 1.24086444e+00 -8.83443280e-01 24 6.20165092e+00 8.52332157e+00 3.24101954e+01 25 -2.83091427e+01 2.42545054e+01 3.92392745e+01 26 -1.67349382e+01 2.54901833e+01 3.08360054e+01 27 2.59055056e+01 -2.40594572e+01 1.61076595e+01 28 -2.78858982e+01 2.39048227e+01 6.93435755e+00 29 -9.56451489e-01 1.16164959e+00 8.58384597e+00 30 2.76424311e+01 1.10537236e+01 1.66169311e+01 31 1.00608653e+01 -1.58890691e+01 6.96967477e+00 32 -1.18504333e+01 9.17112423e+00 3.16876365e-01 MIXED STRUCTURE (pbc=True)-- Species = C Pt (Configuration in file "config-T-CPt.xyz") ----------------------------------------------------------------------------------------------------- Energy = 427.99882019402094 Forces: 1 -8.09507915e+01 2.62360395e+01 -1.60734110e+01 2 3.56916699e+01 1.14654799e+01 -4.29079207e+01 3 -1.70692986e+00 1.45210695e+00 3.37629122e+01 4 -1.36132872e+01 -5.45554362e+01 5.19767446e+01 5 -6.30490446e+00 -4.71576444e+01 -1.01106785e+02 6 1.23660942e+01 -3.20729877e+01 -6.94272904e+01 7 3.95357588e+01 -4.30736801e+00 -3.37534066e+01 8 -8.34516056e+01 7.72442437e+01 5.43019516e+01 9 4.99092062e+01 -1.08697579e+02 -2.29642697e+02 10 1.28994566e+02 -2.76517009e+01 -6.77457070e+01 11 8.94346890e+01 4.94467126e-02 -3.07163502e+00 12 -2.37667849e+01 1.28909327e+02 2.02849177e+02 13 -3.20563687e+00 -7.89155623e+00 -7.12256163e+00 14 -4.03051209e+01 1.73602496e+01 -2.19150484e+01 15 -1.15893839e+02 3.64931497e+01 8.34285082e+01 16 8.85432777e+00 -2.24238191e+01 -1.61928477e+01 17 -1.85281846e+01 -4.52280759e+00 -2.56506143e+01 18 2.46134806e+00 9.87357983e+00 -2.96003869e+00 19 4.78148867e+01 3.03006169e+00 1.65438536e+00 20 -2.28821530e+01 2.28639444e+01 4.47826779e+00 21 -2.38021494e+00 -1.91136005e+01 7.66160944e+00 22 1.97153479e+01 3.99581166e+01 3.78650528e+01 23 4.13801688e-02 3.20331202e+00 1.33136458e+00 24 5.55030643e+00 1.47273174e+01 2.38486375e+01 25 -2.17803927e+01 1.90733120e+01 4.53068005e+01 26 -1.36748150e+01 -2.58952814e+00 2.63740912e+01 27 3.33576883e+01 -2.48487556e+01 8.54512736e+00 28 5.37874208e+01 7.40122736e+01 -1.93225713e+01 29 -3.04769881e+00 -1.76572248e+00 8.25939392e+00 30 1.04039446e+01 -6.49027823e+01 6.72365496e+01 31 -7.43407640e+01 -7.12758280e+01 -3.03511368e+00 32 -1.20855116e+01 7.82515527e+00 1.04707505e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==1819521== Memcheck, a memory error detector ==1819521== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==1819521== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info ==1819521== Command: python runner2.py Tersoff_LAMMPS_AlbeNordlundAverback_2002_PtC__MO_500121566391_004 ==1819521== ==1820804== Warning: invalid file descriptor 1024 in syscall close() ==1820804== Warning: invalid file descriptor 1025 in syscall close() ==1820804== Warning: invalid file descriptor 1026 in syscall close() ==1820804== Warning: invalid file descriptor 1027 in syscall close() ==1820804== Use --log-fd= to select an alternative log fd. ==1820804== Warning: invalid file descriptor 1028 in syscall close() ==1820804== Warning: invalid file descriptor 1029 in syscall close() ==1819521== ==1819521== HEAP SUMMARY: ==1819521== in use at exit: 2,259,591 bytes in 1,705 blocks ==1819521== total heap usage: 89,485 allocs, 87,780 frees, 66,974,140 bytes allocated ==1819521== ==1819521== LEAK SUMMARY: ==1819521== definitely lost: 0 bytes in 0 blocks ==1819521== indirectly lost: 0 bytes in 0 blocks ==1819521== possibly lost: 180,827 bytes in 103 blocks ==1819521== still reachable: 2,078,732 bytes in 1,601 blocks ==1819521== of which reachable via heuristic: ==1819521== stdstring : 38 bytes in 1 blocks ==1819521== suppressed: 32 bytes in 1 blocks ==1819521== Rerun with --leak-check=full to see details of leaked memory ==1819521== ==1819521== For lists of detected and suppressed errors, rerun with: -s ==1819521== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 8114 from 573) ================================================================================ 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.