!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : EAM_IMD_BrommerBoissieuEuchner_2009_MgZn__MO_710767216198_003 Supported species : Mg Zn random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Mg (Configuration in file "config-F-Mg.xyz") ----------------------------------------------------------------------------------------------------- Energy = 196.9370237524336 Forces: 1 -1.29857972e+03 -2.39314563e+03 -2.76829050e+03 2 -1.22550307e+03 1.28348565e+03 -1.75983415e+03 3 1.54992856e+03 -3.02925180e+03 -1.40127015e+03 4 -1.51553727e+03 1.87889841e+03 1.21496394e+03 5 2.05759621e+02 -3.46823452e+03 -1.43508548e+03 6 1.49374111e+03 1.42858702e+03 -1.76508475e+03 7 3.63995217e+03 -3.89736143e+03 -1.32774829e+03 8 -2.96477679e+03 -2.83539407e+03 -1.59752610e+03 9 -3.17004546e+03 -2.57160991e+03 -4.87485091e+03 10 -5.78621035e+02 6.09781409e+03 -4.13847446e+03 11 -2.15786508e+03 -3.94869840e+03 3.66034084e+03 12 -2.82960797e+03 4.02036705e+03 1.19506193e+03 13 1.72785572e+03 -3.07633379e+03 -6.00647616e+03 14 2.59231275e+03 3.35122038e+03 -2.19044198e+03 15 6.72600488e+03 -3.37166673e+03 -9.71750782e+02 16 3.78542210e+02 6.93665563e+03 6.70879507e+02 17 -4.66917095e+03 -2.32066256e+03 -1.65076435e+03 18 7.18158830e+02 3.15482182e+03 1.35789264e+03 19 1.84852129e+03 -4.03761252e+03 2.14509412e+03 20 -1.44820295e+03 2.88063690e+03 2.14221394e+03 21 -3.71427726e+03 -2.68525076e+03 1.20577072e+03 22 4.20292607e+03 3.06748599e+03 1.29362329e+03 23 1.20791584e+03 -5.55241904e+02 2.69069600e+03 24 2.08626551e+03 2.66581489e+02 1.21676577e+03 25 -2.90731682e+03 -3.00176975e+03 7.81877722e+02 26 -1.79950928e+03 5.93079935e+03 -2.94600038e+03 27 -6.59685473e+02 -3.29646481e+03 3.18778761e+03 28 -3.17695826e+03 2.38234874e+03 1.98412033e+03 29 -2.00427885e+03 -3.46212527e+03 2.14064154e+03 30 2.44857887e+03 3.81422896e+03 1.02331227e+03 31 4.03064700e+03 -2.51298631e+03 2.72256082e+03 32 1.26282581e+03 3.96987869e+03 4.19999544e+03 MONOATOMIC STRUCTURE (pbc=True)-- Species = Mg (Configuration in file "config-T-Mg.xyz") ----------------------------------------------------------------------------------------------------- Energy = 196.9370237524336 Forces: 1 -1.29857972e+03 -2.39314563e+03 -2.76829050e+03 2 -1.22550307e+03 1.28348565e+03 -1.75983415e+03 3 1.54992856e+03 -3.02925180e+03 -1.40127015e+03 4 -1.51553727e+03 1.87889841e+03 1.21496394e+03 5 2.05759621e+02 -3.46823452e+03 -1.43508548e+03 6 1.49374111e+03 1.42858702e+03 -1.76508475e+03 7 3.63995217e+03 -3.89736143e+03 -1.32774829e+03 8 -2.96477679e+03 -2.83539407e+03 -1.59752610e+03 9 -3.17004546e+03 -2.57160991e+03 -4.87485091e+03 10 -5.78621035e+02 6.09781409e+03 -4.13847446e+03 11 -2.15786508e+03 -3.94869840e+03 3.66034084e+03 12 -2.82960797e+03 4.02036705e+03 1.19506193e+03 13 1.72785572e+03 -3.07633379e+03 -6.00647616e+03 14 2.59231275e+03 3.35122038e+03 -2.19044198e+03 15 6.72600488e+03 -3.37166673e+03 -9.71750782e+02 16 3.78542210e+02 6.93665563e+03 6.70879507e+02 17 -4.66917095e+03 -2.32066256e+03 -1.65076435e+03 18 7.18158830e+02 3.15482182e+03 1.35789264e+03 19 1.84852129e+03 -4.03761252e+03 2.14509412e+03 20 -1.44820295e+03 2.88063690e+03 2.14221394e+03 21 -3.71427726e+03 -2.68525076e+03 1.20577072e+03 22 4.20292607e+03 3.06748599e+03 1.29362329e+03 23 1.20791584e+03 -5.55241904e+02 2.69069600e+03 24 2.08626551e+03 2.66581489e+02 1.21676577e+03 25 -2.90731682e+03 -3.00176975e+03 7.81877722e+02 26 -1.79950928e+03 5.93079935e+03 -2.94600038e+03 27 -6.59685473e+02 -3.29646481e+03 3.18778761e+03 28 -3.17695826e+03 2.38234874e+03 1.98412033e+03 29 -2.00427885e+03 -3.46212527e+03 2.14064154e+03 30 2.44857887e+03 3.81422896e+03 1.02331227e+03 31 4.03064700e+03 -2.51298631e+03 2.72256082e+03 32 1.26282581e+03 3.96987869e+03 4.19999544e+03 MONOATOMIC STRUCTURE (pbc=False)-- Species = Zn (Configuration in file "config-F-Zn.xyz") ----------------------------------------------------------------------------------------------------- Energy = 247.60852284868474 Forces: 1 -1.55165402e+03 -1.94258021e+03 -2.93940161e+01 2 2.38921022e+03 4.85269737e+02 -9.57220505e+02 3 -7.34906972e+02 -2.99139340e+02 -3.77655044e+02 4 -2.41421346e+03 -1.52266067e+03 1.16478363e+03 5 -4.02230032e+02 -9.95825307e+02 -7.82907260e+02 6 2.85115100e+03 -7.26693709e+02 -2.62411871e+03 7 1.58341097e+03 -4.49072718e+02 -1.08601620e+03 8 -2.17267471e+03 9.25198779e+02 1.27067409e+03 9 -1.23537736e+03 1.09425930e+03 -8.67905137e+02 10 -1.23045972e+03 1.80900680e+03 -2.73189707e+02 11 2.44945475e+03 1.14019785e+03 -9.07237422e+01 12 -1.04265816e+03 9.64139029e+02 -1.13053623e+03 13 -4.69502065e+01 -1.60432992e+03 -1.73037288e+03 14 1.36576748e+03 1.84212425e+03 -2.98464855e+03 15 2.82115931e+03 -2.17915320e+03 2.83664974e+03 16 -3.05152117e+03 3.14148212e+03 2.51982440e+02 17 -2.77736862e+01 -1.43565833e+01 1.85504556e+01 18 -6.07891495e+02 1.95291145e+02 -1.72812614e+03 19 4.61587293e+00 -1.25146834e+03 9.35172399e+02 20 -8.08965044e+02 -1.19778408e+03 1.35913287e+03 21 -2.66028121e+03 -2.90542120e+03 1.09615047e+03 22 3.63662088e+03 8.28511600e+02 -3.23230186e+03 23 6.71450490e+02 -1.48081854e+03 2.02688794e+03 24 -2.33000779e+03 -1.63783700e+03 2.63783593e+03 25 -7.68398202e+02 -1.11000537e+03 -2.11135805e+03 26 8.96071779e+02 1.03385495e+03 -5.50664801e+02 27 1.06499810e+03 -6.63239507e+02 1.12382493e+03 28 -1.99896033e+03 2.99458704e+03 2.32640104e+03 29 -1.74482678e+03 -1.67286169e+03 -1.08975548e+03 30 1.43148388e+03 1.05848102e+03 3.65907580e+02 31 4.27716342e+03 1.90330463e+03 2.18412626e+03 32 -6.12807814e+02 2.23753911e+03 2.04881455e+03 MONOATOMIC STRUCTURE (pbc=True)-- Species = Zn (Configuration in file "config-T-Zn.xyz") ----------------------------------------------------------------------------------------------------- Energy = 247.60852284868474 Forces: 1 -1.55165402e+03 -1.94258021e+03 -2.93940161e+01 2 2.38921022e+03 4.85269737e+02 -9.57220505e+02 3 -7.34906972e+02 -2.99139340e+02 -3.77655044e+02 4 -2.41421346e+03 -1.52266067e+03 1.16478363e+03 5 -4.02230032e+02 -9.95825307e+02 -7.82907260e+02 6 2.85115100e+03 -7.26693709e+02 -2.62411871e+03 7 1.58341097e+03 -4.49072718e+02 -1.08601620e+03 8 -2.17267471e+03 9.25198779e+02 1.27067409e+03 9 -1.23537736e+03 1.09425930e+03 -8.67905137e+02 10 -1.23045972e+03 1.80900680e+03 -2.73189707e+02 11 2.44945475e+03 1.14019785e+03 -9.07237422e+01 12 -1.04265816e+03 9.64139029e+02 -1.13053623e+03 13 -4.69502065e+01 -1.60432992e+03 -1.73037288e+03 14 1.36576748e+03 1.84212425e+03 -2.98464855e+03 15 2.82115931e+03 -2.17915320e+03 2.83664974e+03 16 -3.05152117e+03 3.14148212e+03 2.51982440e+02 17 -2.77736862e+01 -1.43565833e+01 1.85504556e+01 18 -6.07891495e+02 1.95291145e+02 -1.72812614e+03 19 4.61587293e+00 -1.25146834e+03 9.35172399e+02 20 -8.08965044e+02 -1.19778408e+03 1.35913287e+03 21 -2.66028121e+03 -2.90542120e+03 1.09615047e+03 22 3.63662088e+03 8.28511600e+02 -3.23230186e+03 23 6.71450490e+02 -1.48081854e+03 2.02688794e+03 24 -2.33000779e+03 -1.63783700e+03 2.63783593e+03 25 -7.68398202e+02 -1.11000537e+03 -2.11135805e+03 26 8.96071779e+02 1.03385495e+03 -5.50664801e+02 27 1.06499810e+03 -6.63239507e+02 1.12382493e+03 28 -1.99896033e+03 2.99458704e+03 2.32640104e+03 29 -1.74482678e+03 -1.67286169e+03 -1.08975548e+03 30 1.43148388e+03 1.05848102e+03 3.65907580e+02 31 4.27716342e+03 1.90330463e+03 2.18412626e+03 32 -6.12807814e+02 2.23753911e+03 2.04881455e+03 MIXED STRUCTURE (pbc=False)-- Species = Mg Zn (Configuration in file "config-F-MgZn.xyz") ----------------------------------------------------------------------------------------------------- Energy = 205.53832244991293 Forces: 1 -1.21600107e+03 -4.00741826e+03 -4.32030786e+03 2 3.43306040e+03 -1.85000344e+03 -6.69416415e+03 3 2.42114328e+03 -6.98717679e+03 -1.49090156e+03 4 -8.88591579e+03 2.00034910e+03 3.24988400e+03 5 1.20099596e+03 -2.15019853e+03 -2.49893545e+03 6 2.96167226e+03 -3.57688467e+03 -3.69011120e+03 7 4.42115870e+03 -5.84471137e+03 -1.92424685e+03 8 -2.10953635e+03 1.45764070e+03 -5.35319146e+03 9 -4.33378490e+03 2.58901980e+03 -3.38881194e+03 10 1.00453422e+03 2.23101735e+03 -2.33501327e+03 11 3.12967051e+02 3.65177798e+03 7.99546570e+02 12 -1.13038432e+03 4.76789017e+03 -1.99980225e+03 13 -4.39903101e+03 1.06994430e+03 -5.24262335e+03 14 3.74590019e+03 3.15060662e+03 -6.17289462e+03 15 7.11071386e+03 4.41081285e+01 6.31543864e+03 16 -3.31517134e+03 5.36874939e+03 1.00012882e+03 17 -7.75482718e+03 -6.78375849e+03 -1.27609365e+03 18 5.58630759e+03 3.08303743e+03 -2.19768282e+03 19 4.92760415e+03 -6.64666882e+03 4.98456019e+03 20 -9.94776316e+03 1.53548331e+03 6.25361591e+03 21 -1.87564154e+03 -7.54606969e+03 1.64850855e+03 22 6.05308920e+03 3.61404817e+03 -2.33589923e+03 23 1.27412484e+03 -3.22913880e+03 3.60117096e+03 24 3.54592042e+03 5.97991600e+02 4.93860899e+03 25 -5.35041332e+03 -5.74487474e+02 3.80660491e+03 26 -4.51387470e+03 6.44252115e+03 -2.62667598e+03 27 -1.58184801e+03 3.14451485e+03 5.77000377e+03 28 -1.27202595e+03 2.10008690e+02 1.10918123e+03 29 3.04576601e+03 -2.83861499e+03 9.42513240e+02 30 3.21492219e+03 3.82946321e+03 -2.64142646e+03 31 1.60894438e+03 -3.60417374e+02 5.33832553e+03 32 1.81739395e+03 3.60737675e+03 6.43069078e+03 MIXED STRUCTURE (pbc=True)-- Species = Mg Zn (Configuration in file "config-T-MgZn.xyz") ----------------------------------------------------------------------------------------------------- Energy = 234.88378379356578 Forces: 1 -1.14420532e+03 -3.55658272e+03 -4.35774731e+03 2 3.21371679e+03 -2.44853751e+03 -5.00465076e+03 3 2.44741376e+03 -5.04199825e+03 -1.34083156e+03 4 -6.60729639e+03 2.33918345e+03 4.10715229e+03 5 1.35814764e+03 -7.05322794e+02 -1.92568289e+03 6 8.82350388e+02 -4.57683010e+03 -3.29002526e+03 7 5.01277132e+03 -3.65015100e+03 -1.01530072e+03 8 -2.14570350e+03 1.47643188e+03 -5.30477438e+03 9 -2.31696230e+03 2.31111603e+03 -2.58072695e+03 10 2.02357450e+03 1.58572266e+03 -4.78106027e+02 11 3.42050385e+02 3.62388985e+03 8.27890184e+02 12 -1.31063684e+02 4.48134225e+03 -1.73711881e+03 13 -4.44638101e+03 1.04110825e+03 -5.00503177e+03 14 3.58635451e+03 2.63235460e+03 -6.36653039e+03 15 3.43780878e+03 -6.07438364e+02 6.02862105e+03 16 -4.19305166e+03 -9.69482216e+02 -2.40670906e+01 17 -7.05536266e+03 -4.77858876e+03 -2.99704432e+03 18 5.60330383e+03 3.08331549e+03 -2.21892538e+03 19 3.98767622e+03 -5.63983486e+03 3.81164596e+03 20 -8.61981730e+03 1.05520648e+03 6.38291080e+03 21 -1.68067913e+03 -5.07137968e+03 3.31626467e+03 22 4.32514733e+03 3.69443601e+03 -2.77277194e+03 23 1.14199467e+03 -1.69811027e+03 3.92268207e+03 24 3.55052691e+03 7.06314441e+02 4.76787853e+03 25 -3.04135347e+03 -1.35217239e+03 3.90766915e+03 26 -4.47876488e+03 5.96031500e+03 -2.86915920e+03 27 -9.84153106e+02 3.73571693e+03 3.91281381e+03 28 1.12355257e+03 -2.82135898e+02 1.89781415e+03 29 3.03630856e+03 -2.85534252e+03 9.23427400e+02 30 1.35494491e+02 3.03150716e+03 -4.42612838e+03 31 -4.57172417e+02 -4.19288906e+02 3.57353890e+03 32 2.09377418e+03 2.89523576e+03 6.33431416e+03 ================================================================================ VALGRIND OUTPUT ================================================================================ ==94248== Memcheck, a memory error detector ==94248== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==94248== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==94248== Command: python runner2.py EAM_IMD_BrommerBoissieuEuchner_2009_MgZn__MO_710767216198_003 ==94248== ==94248== Conditional jump or move depends on uninitialised value(s) ==94248== at 0x4FCBE77: __wcsnlen_avx2 (strlen-avx2.S:261) ==94248== by 0x4EF9EC1: wcsrtombs (wcsrtombs.c:104) ==94248== by 0x4E7FB20: wcstombs (wcstombs.c:34) ==94248== by 0x547A3F: ??? (in /usr/bin/python3.6) ==94248== by 0x63345D: _Py_stat (in /usr/bin/python3.6) ==94248== by 0x5BA640: ??? (in /usr/bin/python3.6) ==94248== by 0x551B80: ??? (in /usr/bin/python3.6) ==94248== by 0x5AA6EB: _PyObject_FastCallKeywords (in /usr/bin/python3.6) ==94248== by 0x50ABB2: ??? (in /usr/bin/python3.6) ==94248== by 0x50C5B8: _PyEval_EvalFrameDefault (in /usr/bin/python3.6) ==94248== by 0x509D47: ??? (in /usr/bin/python3.6) ==94248== by 0x50AA7C: ??? (in /usr/bin/python3.6) ==94248== ==94248== Conditional jump or move depends on uninitialised value(s) ==94248== at 0x4E63408: internal_utf8_loop (loop.c:298) ==94248== by 0x4E63408: __gconv_transform_internal_utf8 (skeleton.c:609) ==94248== by 0x4EF9EF4: wcsrtombs (wcsrtombs.c:110) ==94248== by 0x4E7FB20: wcstombs (wcstombs.c:34) ==94248== by 0x547A3F: ??? (in /usr/bin/python3.6) ==94248== by 0x63345D: _Py_stat (in /usr/bin/python3.6) ==94248== by 0x5BA640: ??? (in /usr/bin/python3.6) ==94248== by 0x551B80: ??? (in /usr/bin/python3.6) ==94248== by 0x5AA6EB: _PyObject_FastCallKeywords (in /usr/bin/python3.6) ==94248== by 0x50ABB2: ??? (in /usr/bin/python3.6) ==94248== by 0x50C5B8: _PyEval_EvalFrameDefault (in /usr/bin/python3.6) ==94248== by 0x509D47: ??? (in /usr/bin/python3.6) ==94248== by 0x50AA7C: ??? (in /usr/bin/python3.6) ==94248== ==94248== Conditional jump or move depends on uninitialised value(s) ==94248== at 0x4E63411: internal_utf8_loop (loop.c:303) ==94248== by 0x4E63411: __gconv_transform_internal_utf8 (skeleton.c:609) ==94248== by 0x4EF9EF4: wcsrtombs (wcsrtombs.c:110) ==94248== by 0x4E7FB20: wcstombs (wcstombs.c:34) ==94248== by 0x547A3F: ??? (in /usr/bin/python3.6) ==94248== by 0x63345D: _Py_stat (in /usr/bin/python3.6) ==94248== by 0x5BA640: ??? (in /usr/bin/python3.6) ==94248== by 0x551B80: ??? (in /usr/bin/python3.6) ==94248== by 0x5AA6EB: _PyObject_FastCallKeywords (in /usr/bin/python3.6) ==94248== by 0x50ABB2: ??? (in /usr/bin/python3.6) ==94248== by 0x50C5B8: _PyEval_EvalFrameDefault (in /usr/bin/python3.6) ==94248== by 0x509D47: ??? (in /usr/bin/python3.6) ==94248== by 0x50AA7C: ??? (in /usr/bin/python3.6) ==94248== ==94248== Conditional jump or move depends on uninitialised value(s) ==94248== at 0x4E63458: internal_utf8_loop (loop.c:298) ==94248== by 0x4E63458: __gconv_transform_internal_utf8 (skeleton.c:609) ==94248== by 0x4EF9EF4: wcsrtombs (wcsrtombs.c:110) ==94248== by 0x4E7FB20: wcstombs (wcstombs.c:34) ==94248== by 0x547A3F: ??? (in /usr/bin/python3.6) ==94248== by 0x63345D: _Py_stat (in /usr/bin/python3.6) ==94248== by 0x5BA640: ??? (in /usr/bin/python3.6) ==94248== by 0x551B80: ??? (in /usr/bin/python3.6) ==94248== by 0x5AA6EB: _PyObject_FastCallKeywords (in /usr/bin/python3.6) ==94248== by 0x50ABB2: ??? (in /usr/bin/python3.6) ==94248== by 0x50C5B8: _PyEval_EvalFrameDefault (in /usr/bin/python3.6) ==94248== by 0x509D47: ??? (in /usr/bin/python3.6) ==94248== by 0x50AA7C: ??? (in /usr/bin/python3.6) ==94248== ==94248== Conditional jump or move depends on uninitialised value(s) ==94248== at 0x4FCBCEC: __wcsnlen_avx2 (strlen-avx2.S:103) ==94248== by 0x4EF9EC1: wcsrtombs (wcsrtombs.c:104) ==94248== by 0x4E7FB20: wcstombs (wcstombs.c:34) ==94248== by 0x547A3F: ??? (in /usr/bin/python3.6) ==94248== by 0x547D20: PyUnicode_FSConverter (in /usr/bin/python3.6) ==94248== by 0x4C51E6: ??? (in /usr/bin/python3.6) ==94248== by 0x4F8388: ??? (in /usr/bin/python3.6) ==94248== by 0x4FBD83: ??? (in /usr/bin/python3.6) ==94248== by 0x4FC914: _PyArg_ParseStack_SizeT (in /usr/bin/python3.6) ==94248== by 0x4C6C88: ??? (in /usr/bin/python3.6) ==94248== by 0x50A9D9: ??? (in /usr/bin/python3.6) ==94248== by 0x50C5B8: _PyEval_EvalFrameDefault (in /usr/bin/python3.6) ==94248== ==94248== ==94248== HEAP SUMMARY: ==94248== in use at exit: 2,770,515 bytes in 1,657 blocks ==94248== total heap usage: 92,448 allocs, 90,791 frees, 97,180,915 bytes allocated ==94248== ==94248== LEAK SUMMARY: ==94248== definitely lost: 0 bytes in 0 blocks ==94248== indirectly lost: 0 bytes in 0 blocks ==94248== possibly lost: 146,155 bytes in 87 blocks ==94248== still reachable: 2,624,360 bytes in 1,570 blocks ==94248== suppressed: 0 bytes in 0 blocks ==94248== Rerun with --leak-check=full to see details of leaked memory ==94248== ==94248== For counts of detected and suppressed errors, rerun with: -v ==94248== Use --track-origins=yes to see where uninitialised values come from ==94248== ERROR SUMMARY: 6672 errors from 5 contexts (suppressed: 12433 from 658) ================================================================================ 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.