!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_Polymorphic_BereSerra_2006_GaN__SM_518345582208_000 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 = 165.9651030478744 Forces: 1 -9.12720667e+00 -1.43469530e+01 -1.70804547e+01 2 -4.13741692e+00 6.67198605e+00 -2.15952057e+01 3 8.00820682e+00 -1.62486281e+01 1.05497408e+00 4 -1.80812125e+01 1.28320913e+01 5.45103738e+00 5 7.37244247e+00 -1.98357808e+01 -4.40444495e+00 6 1.24261090e+01 -4.66172080e+00 -1.51654013e+01 7 8.34281548e+00 -2.68883979e+01 -1.96428300e+01 8 -9.74887357e+00 -1.99694153e+01 -3.87147128e+00 9 -1.20066453e+01 -7.38452091e+00 -1.80988062e+01 10 -1.97526398e+00 2.26662725e+01 -2.88769414e+01 11 -2.40525718e+01 -2.07984810e+01 2.03919491e+00 12 -2.41660076e+01 1.44685195e+01 5.67293619e+00 13 7.12652366e+00 1.94099435e+00 -4.19012053e+01 14 9.35851105e+00 8.91791775e+00 -8.41854212e+00 15 4.31999893e+01 3.84146837e+00 -1.13962755e+01 16 9.27033930e+00 4.16330264e+01 -1.54109839e+00 17 -1.60601142e+01 -8.91135287e+00 3.39002987e+00 18 1.65479844e+00 -2.48307352e+00 -1.94773911e+00 19 3.00817341e-01 -1.58502317e+01 1.13428916e+01 20 -1.18505824e+01 3.20560365e+00 1.06107208e+01 21 -7.48645451e+00 -1.96011650e+01 5.80575692e+00 22 2.84315151e+01 8.35975317e+00 1.66456038e+01 23 6.28387216e+00 -2.67231390e+00 9.35207070e+00 24 4.42318427e+00 4.10911365e+00 1.37006402e+01 25 -2.18503817e+01 -2.48567542e+00 -7.09282056e+00 26 -7.50159799e+00 2.99651698e+01 9.67929957e+00 27 1.43018834e+00 -1.57030051e+01 2.50192205e+01 28 -2.17775164e+01 1.67275453e+01 1.13797685e+01 29 -3.61395753e+00 -1.07582007e+01 2.32486081e+01 30 2.11323535e+01 2.19296683e+01 3.31548729e+00 31 1.62041946e+01 -4.90703173e+00 2.34922076e+01 32 8.46994207e+00 1.62368175e+01 1.98327883e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ga (Configuration in file "config-T-Ga.xyz") ----------------------------------------------------------------------------------------------------- Energy = 165.9651030478744 Forces: 1 -9.12720667e+00 -1.43469530e+01 -1.70804547e+01 2 -4.13741692e+00 6.67198605e+00 -2.15952057e+01 3 8.00820682e+00 -1.62486281e+01 1.05497408e+00 4 -1.80812125e+01 1.28320913e+01 5.45103738e+00 5 7.37244247e+00 -1.98357808e+01 -4.40444495e+00 6 1.24261090e+01 -4.66172080e+00 -1.51654013e+01 7 8.34281548e+00 -2.68883979e+01 -1.96428300e+01 8 -9.74887357e+00 -1.99694153e+01 -3.87147128e+00 9 -1.20066453e+01 -7.38452091e+00 -1.80988062e+01 10 -1.97526398e+00 2.26662725e+01 -2.88769414e+01 11 -2.40525718e+01 -2.07984810e+01 2.03919491e+00 12 -2.41660076e+01 1.44685195e+01 5.67293619e+00 13 7.12652366e+00 1.94099435e+00 -4.19012053e+01 14 9.35851105e+00 8.91791775e+00 -8.41854212e+00 15 4.31999893e+01 3.84146837e+00 -1.13962755e+01 16 9.27033930e+00 4.16330264e+01 -1.54109839e+00 17 -1.60601142e+01 -8.91135287e+00 3.39002987e+00 18 1.65479844e+00 -2.48307352e+00 -1.94773911e+00 19 3.00817341e-01 -1.58502317e+01 1.13428916e+01 20 -1.18505824e+01 3.20560365e+00 1.06107208e+01 21 -7.48645451e+00 -1.96011650e+01 5.80575692e+00 22 2.84315151e+01 8.35975317e+00 1.66456038e+01 23 6.28387216e+00 -2.67231390e+00 9.35207070e+00 24 4.42318427e+00 4.10911365e+00 1.37006402e+01 25 -2.18503817e+01 -2.48567542e+00 -7.09282056e+00 26 -7.50159799e+00 2.99651698e+01 9.67929957e+00 27 1.43018834e+00 -1.57030051e+01 2.50192205e+01 28 -2.17775164e+01 1.67275453e+01 1.13797685e+01 29 -3.61395753e+00 -1.07582007e+01 2.32486081e+01 30 2.11323535e+01 2.19296683e+01 3.31548729e+00 31 1.62041946e+01 -4.90703173e+00 2.34922076e+01 32 8.46994207e+00 1.62368175e+01 1.98327883e+01 MONOATOMIC STRUCTURE (pbc=False)-- Species = N (Configuration in file "config-F-N.xyz") ----------------------------------------------------------------------------------------------------- Energy = -19.148173776947544 Forces: 1 2.82014635e+00 1.66098846e+00 2.06116540e+00 2 -1.92028296e+00 -1.92436448e+00 3.81045289e+00 3 -2.36213333e+00 2.67818246e+00 -3.00827109e+00 4 2.29550490e+00 -9.86089507e-01 -2.95729942e+00 5 2.28331424e+00 9.64729959e-01 1.33937683e+00 6 -9.65242184e-01 2.50971803e-01 2.21878367e+00 7 -1.44769070e+00 5.53483655e-01 -1.77109217e+00 8 -2.70200098e+00 2.70340226e+00 5.52098589e-01 9 2.79740149e-01 -1.14294925e+00 1.19640464e+00 10 8.28715733e-01 -1.39873596e+00 5.99926556e-01 11 1.09592380e+00 8.91766071e-01 -1.52598090e-01 12 2.00437883e+00 -1.01421622e+00 7.38214365e-01 13 3.61365013e-01 1.18589276e+00 1.13714432e+00 14 -1.62930096e+00 -1.12979060e+00 3.69485280e-01 15 -1.66140629e+00 -6.12095957e-01 4.71595015e-01 16 -6.65883082e-01 -2.92612976e+00 2.93321521e+00 17 4.29820984e-01 1.43812742e+00 1.17634644e+00 18 2.28543693e+00 -6.70819169e-01 -1.13236150e-01 19 1.34851924e+00 1.32913488e+00 -1.32238628e+00 20 9.16642870e-01 -1.43851696e+00 -2.26654646e+00 21 3.66986932e-01 2.94794363e+00 2.63711692e+00 22 -2.04397797e+00 -1.07633240e+00 2.04984137e+00 23 -1.35717906e+00 1.84052389e+00 -2.16682839e+00 24 2.40553490e-01 1.14598077e+00 -2.13250708e+00 25 1.24311005e+00 1.73864708e+00 1.41820133e+00 26 -7.65580489e-01 -2.49030849e+00 8.35528840e-01 27 1.63971872e+00 1.92092700e+00 -2.39337227e+00 28 1.84648310e+00 -1.42080299e+00 -2.41918196e+00 29 1.61507057e+00 7.56406121e-01 -2.99927920e-01 30 -2.26273663e+00 -1.98462313e+00 -1.31143059e+00 31 -3.59516099e+00 -1.78624323e-01 -2.45393675e+00 32 -5.22856276e-01 -3.61270905e+00 -7.76283033e-01 MONOATOMIC STRUCTURE (pbc=True)-- Species = N (Configuration in file "config-T-N.xyz") ----------------------------------------------------------------------------------------------------- Energy = -19.148173776947544 Forces: 1 2.82014635e+00 1.66098846e+00 2.06116540e+00 2 -1.92028296e+00 -1.92436448e+00 3.81045289e+00 3 -2.36213333e+00 2.67818246e+00 -3.00827109e+00 4 2.29550490e+00 -9.86089507e-01 -2.95729942e+00 5 2.28331424e+00 9.64729959e-01 1.33937683e+00 6 -9.65242184e-01 2.50971803e-01 2.21878367e+00 7 -1.44769070e+00 5.53483655e-01 -1.77109217e+00 8 -2.70200098e+00 2.70340226e+00 5.52098589e-01 9 2.79740149e-01 -1.14294925e+00 1.19640464e+00 10 8.28715733e-01 -1.39873596e+00 5.99926556e-01 11 1.09592380e+00 8.91766071e-01 -1.52598090e-01 12 2.00437883e+00 -1.01421622e+00 7.38214365e-01 13 3.61365013e-01 1.18589276e+00 1.13714432e+00 14 -1.62930096e+00 -1.12979060e+00 3.69485280e-01 15 -1.66140629e+00 -6.12095957e-01 4.71595015e-01 16 -6.65883082e-01 -2.92612976e+00 2.93321521e+00 17 4.29820984e-01 1.43812742e+00 1.17634644e+00 18 2.28543693e+00 -6.70819169e-01 -1.13236150e-01 19 1.34851924e+00 1.32913488e+00 -1.32238628e+00 20 9.16642870e-01 -1.43851696e+00 -2.26654646e+00 21 3.66986932e-01 2.94794363e+00 2.63711692e+00 22 -2.04397797e+00 -1.07633240e+00 2.04984137e+00 23 -1.35717906e+00 1.84052389e+00 -2.16682839e+00 24 2.40553490e-01 1.14598077e+00 -2.13250708e+00 25 1.24311005e+00 1.73864708e+00 1.41820133e+00 26 -7.65580489e-01 -2.49030849e+00 8.35528840e-01 27 1.63971872e+00 1.92092700e+00 -2.39337227e+00 28 1.84648310e+00 -1.42080299e+00 -2.41918196e+00 29 1.61507057e+00 7.56406121e-01 -2.99927920e-01 30 -2.26273663e+00 -1.98462313e+00 -1.31143059e+00 31 -3.59516099e+00 -1.78624323e-01 -2.45393675e+00 32 -5.22856276e-01 -3.61270905e+00 -7.76283033e-01 MIXED STRUCTURE (pbc=False)-- Species = Ga N (Configuration in file "config-F-GaN.xyz") ----------------------------------------------------------------------------------------------------- Energy = 99.72009322003952 Forces: 1 -1.13710245e+01 -6.46657229e+00 -1.36937202e+01 2 -4.72196468e-01 1.62726605e+01 -1.32237192e+01 3 5.93510182e+00 -3.07136098e+01 -9.77297575e+00 4 -4.03209220e+01 1.02623142e+01 -1.48346201e+01 5 1.65500222e+01 -1.38241428e+01 -8.01525510e+00 6 1.05948929e+01 -9.83570290e+00 -8.40081758e+00 7 5.40896205e+00 -4.47497267e+00 -3.59539856e+00 8 6.30914049e+00 3.34214019e+00 -2.16762026e+00 9 -5.26200451e+00 1.25763702e-01 -9.81948854e+00 10 -8.39442823e+00 7.63072015e+00 -1.33541985e+01 11 -1.22857755e+01 -2.66345419e+01 -5.07975039e+00 12 -1.89109049e+01 1.16700157e+01 -9.29679788e+00 13 -5.02484223e+00 -9.78032022e+00 -3.11662156e+01 14 8.13457044e+00 6.80084213e+00 -6.69826835e+00 15 3.33120379e+01 -4.82445602e-01 8.70532209e+00 16 1.43006251e+01 4.69761982e+01 -1.34386839e+00 17 -2.81950478e+01 -3.70229798e+01 1.07709915e+01 18 1.29649455e+01 1.19223739e+01 -4.60654263e+00 19 -4.40210921e+00 -1.49106057e+01 2.38750516e+01 20 -1.23069400e+01 3.60046098e+00 1.54243378e+01 21 8.06235362e+00 -2.59791714e+01 -5.72176856e+00 22 2.10555956e+01 3.31007644e+01 -1.68900292e+01 23 9.31337677e+00 -3.13259910e+01 2.34600536e+01 24 3.97261381e+00 8.28003819e+00 2.63214967e+01 25 -2.99365302e+01 1.30977735e+01 1.55250215e+01 26 -6.61732463e+00 3.69289025e+01 7.90322769e+00 27 -5.89808872e+00 -3.29685268e+00 2.23724130e+01 28 -1.07925298e+00 4.24783471e-01 2.35767811e+00 29 2.33507482e+01 -6.91268718e+00 6.32475008e+00 30 1.63554452e+00 3.27151043e-01 4.70250693e+00 31 3.20607139e-03 -9.33458846e-02 -1.19538720e+00 32 9.57365488e+00 1.09910390e+01 1.11335913e+01 MIXED STRUCTURE (pbc=True)-- Species = Ga N (Configuration in file "config-T-GaN.xyz") ----------------------------------------------------------------------------------------------------- Energy = 171.36726565745803 Forces: 1 -9.45143931e+00 -1.67974277e+01 -1.48303162e+01 2 -7.04525064e+00 2.77047128e+01 7.09098972e+00 3 4.01210974e+00 -7.06062037e+00 -9.11190976e+00 4 -1.77623699e+01 6.73989818e+00 -4.20738503e+00 5 2.67975475e+01 -1.59907312e+01 1.47716037e+01 6 -3.23439870e+00 -6.27415968e+00 -8.39590550e+00 7 -7.65273209e+00 -1.52962149e+01 -5.48604303e+00 8 4.72276102e+00 3.74433714e+00 -1.38937623e+00 9 8.69352403e+00 5.30056628e+00 -2.13628103e+01 10 -1.57621725e+01 -2.57995657e+00 -1.86705324e+01 11 -1.20253348e+01 -2.79206487e+01 -5.02143794e+00 12 -1.53952359e+01 8.29403454e+00 -1.18500067e+01 13 -5.95799285e+00 -7.24711448e+00 -2.68205881e+01 14 9.94228020e+00 9.75054185e+00 -1.07897839e+01 15 9.11735462e+00 1.81738627e+00 5.32254739e+00 16 1.96464573e+01 3.25548963e+01 5.23823562e+00 17 -1.71134720e+01 -3.26456115e+01 1.16274377e+01 18 1.69113283e+01 1.45461573e+01 -5.78673281e+00 19 -2.22093046e+01 -1.72232879e+01 9.91017711e+00 20 -5.19340390e-01 1.00102716e+01 2.02179268e+01 21 1.45427332e+01 -1.16972544e+01 -8.55928919e+00 22 -1.47156804e+00 3.68419263e+01 -1.33325315e+01 23 4.89588626e+00 -3.66044523e+01 1.88022073e+01 24 1.29448853e+01 2.14447940e+01 -1.57277366e+00 25 -1.42817687e+01 1.10497630e+01 1.84620754e+01 26 -2.58440321e+00 1.31011942e+01 8.58366372e+00 27 -7.57772194e+00 -3.80462293e+00 1.99695247e+01 28 -1.45507108e+00 1.91611444e+00 7.31249939e+00 29 2.34861492e+01 -6.94206489e+00 6.08261778e+00 30 -6.07742478e+00 5.92565015e+00 9.55684363e+00 31 -9.58368223e-02 1.93643328e+00 -8.78779411e-01 32 1.19598216e+01 -4.59451000e+00 5.11785161e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==73610== Memcheck, a memory error detector ==73610== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==73610== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==73610== Command: python runner2.py Sim_LAMMPS_Polymorphic_BereSerra_2006_GaN__SM_518345582208_000 ==73610== ==73610== Conditional jump or move depends on uninitialised value(s) ==73610== at 0x4FCBE77: __wcsnlen_avx2 (strlen-avx2.S:261) ==73610== by 0x4EF9EC1: wcsrtombs (wcsrtombs.c:104) ==73610== by 0x4E7FB20: wcstombs (wcstombs.c:34) ==73610== by 0x54744F: ??? (in /usr/bin/python3.6) ==73610== by 0x6332BD: _Py_stat (in /usr/bin/python3.6) ==73610== by 0x5BA510: ??? (in /usr/bin/python3.6) ==73610== by 0x551760: ??? (in /usr/bin/python3.6) ==73610== by 0x5AA69B: _PyObject_FastCallKeywords (in /usr/bin/python3.6) ==73610== by 0x50AB52: ??? (in /usr/bin/python3.6) ==73610== by 0x50C548: _PyEval_EvalFrameDefault (in /usr/bin/python3.6) ==73610== by 0x509CE7: ??? (in /usr/bin/python3.6) ==73610== by 0x50AA1C: ??? (in /usr/bin/python3.6) ==73610== ==73610== Conditional jump or move depends on uninitialised value(s) ==73610== at 0x4E63408: internal_utf8_loop (loop.c:298) ==73610== by 0x4E63408: __gconv_transform_internal_utf8 (skeleton.c:609) ==73610== by 0x4EF9EF4: wcsrtombs (wcsrtombs.c:110) ==73610== by 0x4E7FB20: wcstombs (wcstombs.c:34) ==73610== by 0x54744F: ??? (in /usr/bin/python3.6) ==73610== by 0x6332BD: _Py_stat (in /usr/bin/python3.6) ==73610== by 0x5BA510: ??? (in /usr/bin/python3.6) ==73610== by 0x551760: ??? (in /usr/bin/python3.6) ==73610== by 0x5AA69B: _PyObject_FastCallKeywords (in /usr/bin/python3.6) ==73610== by 0x50AB52: ??? (in /usr/bin/python3.6) ==73610== by 0x50C548: _PyEval_EvalFrameDefault (in /usr/bin/python3.6) ==73610== by 0x509CE7: ??? (in /usr/bin/python3.6) ==73610== by 0x50AA1C: ??? (in /usr/bin/python3.6) ==73610== ==73610== Conditional jump or move depends on uninitialised value(s) ==73610== at 0x4E63411: internal_utf8_loop (loop.c:303) ==73610== by 0x4E63411: __gconv_transform_internal_utf8 (skeleton.c:609) ==73610== by 0x4EF9EF4: wcsrtombs (wcsrtombs.c:110) ==73610== by 0x4E7FB20: wcstombs (wcstombs.c:34) ==73610== by 0x54744F: ??? (in /usr/bin/python3.6) ==73610== by 0x6332BD: _Py_stat (in /usr/bin/python3.6) ==73610== by 0x5BA510: ??? (in /usr/bin/python3.6) ==73610== by 0x551760: ??? (in /usr/bin/python3.6) ==73610== by 0x5AA69B: _PyObject_FastCallKeywords (in /usr/bin/python3.6) ==73610== by 0x50AB52: ??? (in /usr/bin/python3.6) ==73610== by 0x50C548: _PyEval_EvalFrameDefault (in /usr/bin/python3.6) ==73610== by 0x509CE7: ??? (in /usr/bin/python3.6) ==73610== by 0x50AA1C: ??? (in /usr/bin/python3.6) ==73610== ==73610== Conditional jump or move depends on uninitialised value(s) ==73610== at 0x4E63458: internal_utf8_loop (loop.c:298) ==73610== by 0x4E63458: __gconv_transform_internal_utf8 (skeleton.c:609) ==73610== by 0x4EF9EF4: wcsrtombs (wcsrtombs.c:110) ==73610== by 0x4E7FB20: wcstombs (wcstombs.c:34) ==73610== by 0x54744F: ??? (in /usr/bin/python3.6) ==73610== by 0x6332BD: _Py_stat (in /usr/bin/python3.6) ==73610== by 0x5BA510: ??? (in /usr/bin/python3.6) ==73610== by 0x551760: ??? (in /usr/bin/python3.6) ==73610== by 0x5AA69B: _PyObject_FastCallKeywords (in /usr/bin/python3.6) ==73610== by 0x50AB52: ??? (in /usr/bin/python3.6) ==73610== by 0x50C548: _PyEval_EvalFrameDefault (in /usr/bin/python3.6) ==73610== by 0x509CE7: ??? (in /usr/bin/python3.6) ==73610== by 0x50AA1C: ??? (in /usr/bin/python3.6) ==73610== ==73610== Conditional jump or move depends on uninitialised value(s) ==73610== at 0x4FCBCEC: __wcsnlen_avx2 (strlen-avx2.S:103) ==73610== by 0x4EF9EC1: wcsrtombs (wcsrtombs.c:104) ==73610== by 0x4E7FB20: wcstombs (wcstombs.c:34) ==73610== by 0x54744F: ??? (in /usr/bin/python3.6) ==73610== by 0x547730: PyUnicode_FSConverter (in /usr/bin/python3.6) ==73610== by 0x4CABB1: ??? (in /usr/bin/python3.6) ==73610== by 0x551760: ??? (in /usr/bin/python3.6) ==73610== by 0x5AA69B: _PyObject_FastCallKeywords (in /usr/bin/python3.6) ==73610== by 0x50AB52: ??? (in /usr/bin/python3.6) ==73610== by 0x50C548: _PyEval_EvalFrameDefault (in /usr/bin/python3.6) ==73610== by 0x509CE7: ??? (in /usr/bin/python3.6) ==73610== by 0x50AA1C: ??? (in /usr/bin/python3.6) ==73610== ==73610== ==73610== HEAP SUMMARY: ==73610== in use at exit: 10,699,735 bytes in 2,511 blocks ==73610== total heap usage: 53,576 allocs, 51,065 frees, 91,030,884 bytes allocated ==73610== ==73610== LEAK SUMMARY: ==73610== definitely lost: 8,040 bytes in 67 blocks ==73610== indirectly lost: 7,401,688 bytes in 526 blocks ==73610== possibly lost: 292,969 bytes in 104 blocks ==73610== still reachable: 2,997,038 bytes in 1,814 blocks ==73610== suppressed: 0 bytes in 0 blocks ==73610== Rerun with --leak-check=full to see details of leaked memory ==73610== ==73610== For counts of detected and suppressed errors, rerun with: -v ==73610== Use --track-origins=yes to see where uninitialised values come from ==73610== ERROR SUMMARY: 6672 errors from 5 contexts (suppressed: 15457 from 619) ================================================================================ 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" (Search for the word "lost" in the file to identify memory leaks.) Grade: F Comment: Memory leak detected.