!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : SW_BereSerra_2006_GaN__MO_861114678890_001 Supported species : Ga N random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Ga (Configuration in file "config-F-Ga.xyz") ----------------------------------------------------------------------------------------------------- Energy = 165.96510320586788 Forces: 1 -9.12719721e+00 -1.43469553e+01 -1.70804404e+01 2 -4.13740951e+00 6.67197950e+00 -2.15952055e+01 3 8.00819492e+00 -1.62486274e+01 1.05495622e+00 4 -1.80812096e+01 1.28320921e+01 5.45103634e+00 5 7.37243887e+00 -1.98357730e+01 -4.40444577e+00 6 1.24261108e+01 -4.66171939e+00 -1.51654014e+01 7 8.34284429e+00 -2.68884228e+01 -1.96428184e+01 8 -9.74890423e+00 -1.99694007e+01 -3.87146154e+00 9 -1.20066410e+01 -7.38451771e+00 -1.80988040e+01 10 -1.97528519e+00 2.26662689e+01 -2.88769284e+01 11 -2.40525814e+01 -2.07984921e+01 2.03919612e+00 12 -2.41659878e+01 1.44685231e+01 5.67292678e+00 13 7.12653710e+00 1.94100031e+00 -4.19011868e+01 14 9.35851883e+00 8.91792618e+00 -8.41854404e+00 15 4.31999802e+01 3.84146650e+00 -1.13963117e+01 16 9.27034333e+00 4.16330286e+01 -1.54110875e+00 17 -1.60601170e+01 -8.91135372e+00 3.39003084e+00 18 1.65479733e+00 -2.48306749e+00 -1.94774131e+00 19 3.00814025e-01 -1.58502403e+01 1.13428932e+01 20 -1.18505855e+01 3.20560471e+00 1.06107223e+01 21 -7.48645310e+00 -1.96011641e+01 5.80575906e+00 22 2.84315104e+01 8.35974477e+00 1.66455916e+01 23 6.28387108e+00 -2.67231291e+00 9.35206994e+00 24 4.42319377e+00 4.10911791e+00 1.37006429e+01 25 -2.18503754e+01 -2.48567102e+00 -7.09280870e+00 26 -7.50158612e+00 2.99651622e+01 9.67930384e+00 27 1.43018330e+00 -1.57030087e+01 2.50192117e+01 28 -2.17775213e+01 1.67275439e+01 1.13797663e+01 29 -3.61397892e+00 -1.07581899e+01 2.32486130e+01 30 2.11323517e+01 2.19296715e+01 3.31549337e+00 31 1.62042095e+01 -4.90703709e+00 2.34922136e+01 32 8.46993375e+00 1.62368236e+01 1.98327795e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ga (Configuration in file "config-T-Ga.xyz") ----------------------------------------------------------------------------------------------------- Energy = 165.96510320586788 Forces: 1 -9.12719721e+00 -1.43469553e+01 -1.70804404e+01 2 -4.13740951e+00 6.67197950e+00 -2.15952055e+01 3 8.00819492e+00 -1.62486274e+01 1.05495622e+00 4 -1.80812096e+01 1.28320921e+01 5.45103634e+00 5 7.37243887e+00 -1.98357730e+01 -4.40444577e+00 6 1.24261108e+01 -4.66171939e+00 -1.51654014e+01 7 8.34284429e+00 -2.68884228e+01 -1.96428184e+01 8 -9.74890423e+00 -1.99694007e+01 -3.87146154e+00 9 -1.20066410e+01 -7.38451771e+00 -1.80988040e+01 10 -1.97528519e+00 2.26662689e+01 -2.88769284e+01 11 -2.40525814e+01 -2.07984921e+01 2.03919612e+00 12 -2.41659878e+01 1.44685231e+01 5.67292678e+00 13 7.12653710e+00 1.94100031e+00 -4.19011868e+01 14 9.35851883e+00 8.91792618e+00 -8.41854404e+00 15 4.31999802e+01 3.84146650e+00 -1.13963117e+01 16 9.27034333e+00 4.16330286e+01 -1.54110875e+00 17 -1.60601170e+01 -8.91135372e+00 3.39003084e+00 18 1.65479733e+00 -2.48306749e+00 -1.94774131e+00 19 3.00814025e-01 -1.58502403e+01 1.13428932e+01 20 -1.18505855e+01 3.20560471e+00 1.06107223e+01 21 -7.48645310e+00 -1.96011641e+01 5.80575906e+00 22 2.84315104e+01 8.35974477e+00 1.66455916e+01 23 6.28387108e+00 -2.67231291e+00 9.35206994e+00 24 4.42319377e+00 4.10911791e+00 1.37006429e+01 25 -2.18503754e+01 -2.48567102e+00 -7.09280870e+00 26 -7.50158612e+00 2.99651622e+01 9.67930384e+00 27 1.43018330e+00 -1.57030087e+01 2.50192117e+01 28 -2.17775213e+01 1.67275439e+01 1.13797663e+01 29 -3.61397892e+00 -1.07581899e+01 2.32486130e+01 30 2.11323517e+01 2.19296715e+01 3.31549337e+00 31 1.62042095e+01 -4.90703709e+00 2.34922136e+01 32 8.46993375e+00 1.62368236e+01 1.98327795e+01 MONOATOMIC STRUCTURE (pbc=False)-- Species = N (Configuration in file "config-F-N.xyz") ----------------------------------------------------------------------------------------------------- Energy = -19.1481737730188 Forces: 1 2.82014563e+00 1.66098802e+00 2.06116494e+00 2 -1.92028252e+00 -1.92436476e+00 3.81045382e+00 3 -2.36213280e+00 2.67818300e+00 -3.00827136e+00 4 2.29550477e+00 -9.86089076e-01 -2.95729965e+00 5 2.28331447e+00 9.64729913e-01 1.33937702e+00 6 -9.65242207e-01 2.50971773e-01 2.21878366e+00 7 -1.44769092e+00 5.53483663e-01 -1.77109241e+00 8 -2.70200125e+00 2.70340256e+00 5.52097898e-01 9 2.79740267e-01 -1.14294939e+00 1.19640488e+00 10 8.28715789e-01 -1.39873587e+00 5.99926485e-01 11 1.09592373e+00 8.91764537e-01 -1.52598424e-01 12 2.00437876e+00 -1.01421623e+00 7.38214374e-01 13 3.61364509e-01 1.18589301e+00 1.13714455e+00 14 -1.62930071e+00 -1.12979045e+00 3.69485224e-01 15 -1.66140603e+00 -6.12095979e-01 4.71594795e-01 16 -6.65881793e-01 -2.92612945e+00 2.93321547e+00 17 4.29821228e-01 1.43812859e+00 1.17634729e+00 18 2.28543605e+00 -6.70818643e-01 -1.13235466e-01 19 1.34851933e+00 1.32913488e+00 -1.32238630e+00 20 9.16642656e-01 -1.43851424e+00 -2.26655022e+00 21 3.66986977e-01 2.94794399e+00 2.63711711e+00 22 -2.04397798e+00 -1.07633223e+00 2.04984130e+00 23 -1.35717906e+00 1.84052374e+00 -2.16682827e+00 24 2.40553646e-01 1.14598048e+00 -2.13250645e+00 25 1.24311074e+00 1.73866372e+00 1.41822050e+00 26 -7.65580771e-01 -2.49030836e+00 8.35529056e-01 27 1.63971845e+00 1.92092634e+00 -2.39337219e+00 28 1.84648273e+00 -1.42082344e+00 -2.41919850e+00 29 1.61507061e+00 7.56406478e-01 -2.99928391e-01 30 -2.26273685e+00 -1.98462293e+00 -1.31143079e+00 31 -3.59516119e+00 -1.78624300e-01 -2.45393689e+00 32 -5.22856264e-01 -3.61270935e+00 -7.76283055e-01 MONOATOMIC STRUCTURE (pbc=True)-- Species = N (Configuration in file "config-T-N.xyz") ----------------------------------------------------------------------------------------------------- Energy = -19.1481737730188 Forces: 1 2.82014563e+00 1.66098802e+00 2.06116494e+00 2 -1.92028252e+00 -1.92436476e+00 3.81045382e+00 3 -2.36213280e+00 2.67818300e+00 -3.00827136e+00 4 2.29550477e+00 -9.86089076e-01 -2.95729965e+00 5 2.28331447e+00 9.64729913e-01 1.33937702e+00 6 -9.65242207e-01 2.50971773e-01 2.21878366e+00 7 -1.44769092e+00 5.53483663e-01 -1.77109241e+00 8 -2.70200125e+00 2.70340256e+00 5.52097898e-01 9 2.79740267e-01 -1.14294939e+00 1.19640488e+00 10 8.28715789e-01 -1.39873587e+00 5.99926485e-01 11 1.09592373e+00 8.91764537e-01 -1.52598424e-01 12 2.00437876e+00 -1.01421623e+00 7.38214374e-01 13 3.61364509e-01 1.18589301e+00 1.13714455e+00 14 -1.62930071e+00 -1.12979045e+00 3.69485224e-01 15 -1.66140603e+00 -6.12095979e-01 4.71594795e-01 16 -6.65881793e-01 -2.92612945e+00 2.93321547e+00 17 4.29821228e-01 1.43812859e+00 1.17634729e+00 18 2.28543605e+00 -6.70818643e-01 -1.13235466e-01 19 1.34851933e+00 1.32913488e+00 -1.32238630e+00 20 9.16642656e-01 -1.43851424e+00 -2.26655022e+00 21 3.66986977e-01 2.94794399e+00 2.63711711e+00 22 -2.04397798e+00 -1.07633223e+00 2.04984130e+00 23 -1.35717906e+00 1.84052374e+00 -2.16682827e+00 24 2.40553646e-01 1.14598048e+00 -2.13250645e+00 25 1.24311074e+00 1.73866372e+00 1.41822050e+00 26 -7.65580771e-01 -2.49030836e+00 8.35529056e-01 27 1.63971845e+00 1.92092634e+00 -2.39337219e+00 28 1.84648273e+00 -1.42082344e+00 -2.41919850e+00 29 1.61507061e+00 7.56406478e-01 -2.99928391e-01 30 -2.26273685e+00 -1.98462293e+00 -1.31143079e+00 31 -3.59516119e+00 -1.78624300e-01 -2.45393689e+00 32 -5.22856264e-01 -3.61270935e+00 -7.76283055e-01 MIXED STRUCTURE (pbc=False)-- Species = Ga N (Configuration in file "config-F-GaN.xyz") ----------------------------------------------------------------------------------------------------- Energy = 99.72009342606349 Forces: 1 -1.13710088e+01 -6.46656612e+00 -1.36936973e+01 2 -4.72206438e-01 1.62726369e+01 -1.32236942e+01 3 5.93508387e+00 -3.07135732e+01 -9.77301115e+00 4 -4.03208936e+01 1.02622994e+01 -1.48346108e+01 5 1.65500301e+01 -1.38241390e+01 -8.01525688e+00 6 1.05948858e+01 -9.83570210e+00 -8.40081813e+00 7 5.40896295e+00 -4.47497039e+00 -3.59540184e+00 8 6.30913026e+00 3.34211779e+00 -2.16760956e+00 9 -5.26200285e+00 1.25770726e-01 -9.81949506e+00 10 -8.39443406e+00 7.63072000e+00 -1.33542049e+01 11 -1.22858719e+01 -2.66345360e+01 -5.07966717e+00 12 -1.89109141e+01 1.16700055e+01 -9.29680642e+00 13 -5.02478808e+00 -9.78031599e+00 -3.11662533e+01 14 8.13457973e+00 6.80084524e+00 -6.69827713e+00 15 3.33120514e+01 -4.82450096e-01 8.70532327e+00 16 1.43006179e+01 4.69762022e+01 -1.34387228e+00 17 -2.81950623e+01 -3.70229893e+01 1.07709697e+01 18 1.29649205e+01 1.19223967e+01 -4.60656722e+00 19 -4.40209641e+00 -1.49106055e+01 2.38750796e+01 20 -1.23069429e+01 3.60046694e+00 1.54243479e+01 21 8.06235685e+00 -2.59791591e+01 -5.72178121e+00 22 2.10555962e+01 3.31007706e+01 -1.68900308e+01 23 9.31337795e+00 -3.13259934e+01 2.34600547e+01 24 3.97260226e+00 8.28004756e+00 2.63214927e+01 25 -2.99364915e+01 1.30977576e+01 1.55249933e+01 26 -6.61731040e+00 3.69289002e+01 7.90322545e+00 27 -5.89808340e+00 -3.29687505e+00 2.23724186e+01 28 -1.07925142e+00 4.24786124e-01 2.35767822e+00 29 2.33507607e+01 -6.91268997e+00 6.32477043e+00 30 1.63553837e+00 3.27150528e-01 4.70250237e+00 31 3.20239583e-03 -9.33464730e-02 -1.19538889e+00 32 9.57366102e+00 1.09910377e+01 1.11335881e+01 MIXED STRUCTURE (pbc=True)-- Species = Ga N (Configuration in file "config-T-GaN.xyz") ----------------------------------------------------------------------------------------------------- Energy = 171.36726600863273 Forces: 1 -9.45141062e+00 -1.67974282e+01 -1.48302878e+01 2 -7.04524854e+00 2.77046763e+01 7.09100182e+00 3 4.01208448e+00 -7.06057374e+00 -9.11195565e+00 4 -1.77623545e+01 6.73989476e+00 -4.20739795e+00 5 2.67975598e+01 -1.59907227e+01 1.47716064e+01 6 -3.23436338e+00 -6.27414043e+00 -8.39587742e+00 7 -7.65274522e+00 -1.52962183e+01 -5.48605264e+00 8 4.72275062e+00 3.74431357e+00 -1.38936455e+00 9 8.69349061e+00 5.30055967e+00 -2.13628172e+01 10 -1.57621812e+01 -2.57995511e+00 -1.86705395e+01 11 -1.20254321e+01 -2.79206422e+01 -5.02135292e+00 12 -1.53952320e+01 8.29403264e+00 -1.18500096e+01 13 -5.95793822e+00 -7.24710850e+00 -2.68206222e+01 14 9.94228967e+00 9.75054830e+00 -1.07897989e+01 15 9.11736252e+00 1.81736263e+00 5.32254455e+00 16 1.96464497e+01 3.25548991e+01 5.23823060e+00 17 -1.71134870e+01 -3.26456240e+01 1.16274058e+01 18 1.69113003e+01 1.45461811e+01 -5.78675945e+00 19 -2.22092873e+01 -1.72232785e+01 9.91021051e+00 20 -5.19343880e-01 1.00102781e+01 2.02179410e+01 21 1.45427359e+01 -1.16972348e+01 -8.55930725e+00 22 -1.47156740e+00 3.68419360e+01 -1.33325378e+01 23 4.89588909e+00 -3.66044557e+01 1.88022108e+01 24 1.29448544e+01 2.14447994e+01 -1.57276046e+00 25 -1.42817353e+01 1.10497503e+01 1.84620405e+01 26 -2.58438037e+00 1.31011910e+01 8.58366632e+00 27 -7.57771641e+00 -3.80465162e+00 1.99695300e+01 28 -1.45506888e+00 1.91611688e+00 7.31249930e+00 29 2.34861615e+01 -6.94206685e+00 6.08263864e+00 30 -6.07742954e+00 5.92564554e+00 9.55684109e+00 31 -9.58401782e-02 1.93643242e+00 -8.78776168e-01 32 1.19598334e+01 -4.59451720e+00 5.11785010e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==2442193== Memcheck, a memory error detector ==2442193== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==2442193== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info ==2442193== Command: python runner2.py SW_BereSerra_2006_GaN__MO_861114678890_001 ==2442193== ==2442912== Warning: invalid file descriptor 1024 in syscall close() ==2442912== Warning: invalid file descriptor 1025 in syscall close() ==2442912== Warning: invalid file descriptor 1026 in syscall close() ==2442912== Warning: invalid file descriptor 1027 in syscall close() ==2442912== Use --log-fd= to select an alternative log fd. ==2442912== Warning: invalid file descriptor 1028 in syscall close() ==2442912== Warning: invalid file descriptor 1029 in syscall close() ==2442193== ==2442193== HEAP SUMMARY: ==2442193== in use at exit: 2,259,687 bytes in 1,706 blocks ==2442193== total heap usage: 84,727 allocs, 83,021 frees, 66,511,984 bytes allocated ==2442193== ==2442193== LEAK SUMMARY: ==2442193== definitely lost: 0 bytes in 0 blocks ==2442193== indirectly lost: 0 bytes in 0 blocks ==2442193== possibly lost: 180,827 bytes in 103 blocks ==2442193== still reachable: 2,078,828 bytes in 1,602 blocks ==2442193== of which reachable via heuristic: ==2442193== stdstring : 38 bytes in 1 blocks ==2442193== suppressed: 32 bytes in 1 blocks ==2442193== Rerun with --leak-check=full to see details of leaked memory ==2442193== ==2442193== For lists of detected and suppressed errors, rerun with: -s ==2442193== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 8096 from 564) ================================================================================ 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.