!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_Dynamo_OBrienBarrPrice_2018_PtAu__MO_946831081299_000 Supported species : Au Pt random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Au (Configuration in file "config-F-Au.xyz") ----------------------------------------------------------------------------------------------------- Energy = 629.0751335761844 Forces: 1 -4.05683235e+01 -4.29428759e+01 -6.40547927e+01 2 -3.35669736e+01 4.26703898e+01 -4.95220903e+01 3 1.26113028e+01 -4.27704330e+01 3.55704139e+01 4 -3.33387901e+01 3.47439702e+01 2.33519390e+01 5 3.76594648e+01 -7.62573757e+01 -2.89368847e+01 6 3.43807654e+01 1.36044211e+01 -4.01666630e+01 7 2.26604036e+01 -1.72491381e+02 -1.63130103e+02 8 -1.29381034e+02 -1.19823725e+02 1.70849987e+01 9 -7.37837240e+01 -1.26947354e+01 -7.55168711e+01 10 -3.94932716e+01 1.07433038e+02 -1.05904357e+02 11 -2.45154662e+01 -7.91232352e+01 7.94095516e+01 12 -4.33312019e+01 9.80604517e+01 -5.77711053e+01 13 -2.98795990e+01 -2.85117807e+01 -2.31043937e+02 14 3.36736936e+01 3.57273296e+01 -1.74163581e+01 15 2.43515590e+02 6.66883242e+01 7.81067560e+01 16 5.05702901e+01 1.32584186e+02 8.97793952e+01 17 -6.27132750e+01 -4.54859397e+01 -3.21454968e+01 18 3.17896755e+01 3.80116429e+01 -8.76553149e+00 19 2.57907672e+01 -6.13878237e+01 3.83503381e+01 20 -3.04139451e+01 3.61188910e+01 3.86221157e+01 21 -6.56539518e+01 -4.62978353e+01 4.36275689e+01 22 1.03239284e+02 1.45621674e+02 1.34203988e+02 23 1.94886189e+01 -1.03676539e+01 3.91049130e+01 24 1.93295618e+01 1.52999748e+01 2.45897952e+01 25 -3.25764310e+01 -8.70348107e+01 6.16486910e+01 26 -3.03683522e+01 9.10459976e+01 -4.82241250e+01 27 9.61036219e+01 -1.96234154e+02 5.55269063e+01 28 -1.74509290e+02 1.53343286e+02 2.53677255e+01 29 -4.06147420e+01 -5.95809860e+01 1.41137278e+01 30 4.01366649e+01 7.59820893e+01 -4.34939915e+01 31 6.93457032e+01 -7.93981201e+01 8.87543491e+01 32 4.44129633e+01 7.34671992e+01 7.88791339e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Au (Configuration in file "config-T-Au.xyz") ----------------------------------------------------------------------------------------------------- Energy = 629.0751335761844 Forces: 1 -4.05683235e+01 -4.29428759e+01 -6.40547927e+01 2 -3.35669736e+01 4.26703898e+01 -4.95220903e+01 3 1.26113028e+01 -4.27704330e+01 3.55704139e+01 4 -3.33387901e+01 3.47439702e+01 2.33519390e+01 5 3.76594648e+01 -7.62573757e+01 -2.89368847e+01 6 3.43807654e+01 1.36044211e+01 -4.01666630e+01 7 2.26604036e+01 -1.72491381e+02 -1.63130103e+02 8 -1.29381034e+02 -1.19823725e+02 1.70849987e+01 9 -7.37837240e+01 -1.26947354e+01 -7.55168711e+01 10 -3.94932716e+01 1.07433038e+02 -1.05904357e+02 11 -2.45154662e+01 -7.91232352e+01 7.94095516e+01 12 -4.33312019e+01 9.80604517e+01 -5.77711053e+01 13 -2.98795990e+01 -2.85117807e+01 -2.31043937e+02 14 3.36736936e+01 3.57273296e+01 -1.74163581e+01 15 2.43515590e+02 6.66883242e+01 7.81067560e+01 16 5.05702901e+01 1.32584186e+02 8.97793952e+01 17 -6.27132750e+01 -4.54859397e+01 -3.21454968e+01 18 3.17896755e+01 3.80116429e+01 -8.76553149e+00 19 2.57907672e+01 -6.13878237e+01 3.83503381e+01 20 -3.04139451e+01 3.61188910e+01 3.86221157e+01 21 -6.56539518e+01 -4.62978353e+01 4.36275689e+01 22 1.03239284e+02 1.45621674e+02 1.34203988e+02 23 1.94886189e+01 -1.03676539e+01 3.91049130e+01 24 1.93295618e+01 1.52999748e+01 2.45897952e+01 25 -3.25764310e+01 -8.70348107e+01 6.16486910e+01 26 -3.03683522e+01 9.10459976e+01 -4.82241250e+01 27 9.61036219e+01 -1.96234154e+02 5.55269063e+01 28 -1.74509290e+02 1.53343286e+02 2.53677255e+01 29 -4.06147420e+01 -5.95809860e+01 1.41137278e+01 30 4.01366649e+01 7.59820893e+01 -4.34939915e+01 31 6.93457032e+01 -7.93981201e+01 8.87543491e+01 32 4.44129633e+01 7.34671992e+01 7.88791339e+01 MONOATOMIC STRUCTURE (pbc=False)-- Species = Pt (Configuration in file "config-F-Pt.xyz") ----------------------------------------------------------------------------------------------------- Energy = -113.8887012055536 Forces: 1 -1.44526755e+00 -2.49947030e+00 -2.87195066e+00 2 3.14529009e+00 -2.85725619e+00 -7.35794313e+00 3 1.98936762e+00 -8.32253324e+00 -3.14355593e+00 4 -7.35804138e+00 2.39720210e+00 1.15765320e+00 5 1.26021013e+00 -2.47053120e+00 -2.42239301e+00 6 3.21888769e+00 -1.97916531e+00 -2.44342130e+00 7 2.70565705e+00 -2.82121347e+00 -1.58869970e+00 8 2.13260129e+00 1.52626722e+00 -6.70417034e+00 9 -7.91255279e+00 2.23913347e+00 -5.12725889e+00 10 -1.48917608e+00 5.73762857e+00 -7.77409182e+00 11 2.22787884e+00 -2.02375199e+00 2.76310415e+00 12 -3.81609453e+00 3.23269710e+00 2.04171144e-01 13 -3.21696531e+00 -1.50109258e+00 -5.86507533e+00 14 3.51175155e+00 3.51080830e+00 -1.61840106e+00 15 6.13009782e+00 2.71392152e+00 -1.05594530e+00 16 4.69736921e+00 5.93921656e+00 1.40695335e+00 17 -5.11832967e+00 -4.45233411e+00 2.61200571e+00 18 -2.96548881e-02 -3.80795172e+00 3.48130234e+00 19 2.02294490e+00 -3.53496168e+00 3.29905714e+00 20 -4.24658835e+00 5.72221487e-01 3.53061751e+00 21 -1.08922188e+00 -7.56745196e+00 2.26113149e+00 22 9.55220299e+00 -1.30460342e+00 2.18065037e+00 23 2.02206860e+00 -2.33041485e+00 2.36518396e+00 24 -3.54003751e+00 -3.51251877e+00 6.68263232e+00 25 -1.07715833e+01 2.66282625e+00 -8.56587527e-01 26 -3.04979768e+00 7.69818305e+00 2.35713294e+00 27 1.10531937e+00 7.95242594e-01 8.70331727e+00 28 -9.30506039e-01 1.26570203e+00 5.51545426e-01 29 4.69026798e-01 1.71360057e+00 -1.62761686e+00 30 4.11956084e+00 3.13428068e+00 -1.52783895e+00 31 4.86991617e+00 2.27899139e+00 3.15998064e+00 32 -1.16633396e+00 3.56732791e+00 5.26851082e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Pt (Configuration in file "config-T-Pt.xyz") ----------------------------------------------------------------------------------------------------- Energy = -113.8887012055536 Forces: 1 -1.44526755e+00 -2.49947030e+00 -2.87195066e+00 2 3.14529009e+00 -2.85725619e+00 -7.35794313e+00 3 1.98936762e+00 -8.32253324e+00 -3.14355593e+00 4 -7.35804138e+00 2.39720210e+00 1.15765320e+00 5 1.26021013e+00 -2.47053120e+00 -2.42239301e+00 6 3.21888769e+00 -1.97916531e+00 -2.44342130e+00 7 2.70565705e+00 -2.82121347e+00 -1.58869970e+00 8 2.13260129e+00 1.52626722e+00 -6.70417034e+00 9 -7.91255279e+00 2.23913347e+00 -5.12725889e+00 10 -1.48917608e+00 5.73762857e+00 -7.77409182e+00 11 2.22787884e+00 -2.02375199e+00 2.76310415e+00 12 -3.81609453e+00 3.23269710e+00 2.04171144e-01 13 -3.21696531e+00 -1.50109258e+00 -5.86507533e+00 14 3.51175155e+00 3.51080830e+00 -1.61840106e+00 15 6.13009782e+00 2.71392152e+00 -1.05594530e+00 16 4.69736921e+00 5.93921656e+00 1.40695335e+00 17 -5.11832967e+00 -4.45233411e+00 2.61200571e+00 18 -2.96548881e-02 -3.80795172e+00 3.48130234e+00 19 2.02294490e+00 -3.53496168e+00 3.29905714e+00 20 -4.24658835e+00 5.72221487e-01 3.53061751e+00 21 -1.08922188e+00 -7.56745196e+00 2.26113149e+00 22 9.55220299e+00 -1.30460342e+00 2.18065037e+00 23 2.02206860e+00 -2.33041485e+00 2.36518396e+00 24 -3.54003751e+00 -3.51251877e+00 6.68263232e+00 25 -1.07715833e+01 2.66282625e+00 -8.56587527e-01 26 -3.04979768e+00 7.69818305e+00 2.35713294e+00 27 1.10531937e+00 7.95242594e-01 8.70331727e+00 28 -9.30506039e-01 1.26570203e+00 5.51545426e-01 29 4.69026798e-01 1.71360057e+00 -1.62761686e+00 30 4.11956084e+00 3.13428068e+00 -1.52783895e+00 31 4.86991617e+00 2.27899139e+00 3.15998064e+00 32 -1.16633396e+00 3.56732791e+00 5.26851082e+00 MIXED STRUCTURE (pbc=False)-- Species = Au Pt (Configuration in file "config-F-AuPt.xyz") ----------------------------------------------------------------------------------------------------- Energy = 65.25406214962877 Forces: 1 -3.25460724e+01 -3.95798976e+01 -2.23606594e+01 2 4.20904377e+01 4.13977960e+01 -4.33228721e+01 3 -3.98273140e+01 -5.35395767e+01 2.61846545e+01 4 -3.60183947e+01 6.93932067e+00 3.17351308e+01 5 1.77296094e+01 -1.09642764e+01 -3.15167098e+01 6 1.01222684e+01 2.77293764e+01 -3.16978776e+01 7 7.71174804e+00 -3.20662481e+01 2.72050864e+01 8 2.69420923e+01 7.31054431e+01 -2.27223178e+01 9 -2.42735031e+01 -1.26040118e+01 -2.25210151e+01 10 2.02178783e+01 2.23996495e+01 -2.06481508e+01 11 3.53109546e+01 -1.56834846e+01 9.09845187e+00 12 -3.49460838e+01 2.29069992e+01 1.39447205e+01 13 -1.02000359e+01 -5.05397258e+00 -6.62514797e+00 14 5.99422523e+00 2.73056691e+01 -2.13034733e+01 15 9.74188016e+00 -2.15069077e+01 2.20359300e+01 16 -7.50008389e-01 3.65033786e+00 4.61914227e-01 17 -3.15918824e+01 -3.86850243e+01 -1.85705348e+01 18 2.50889132e+01 1.24179601e+01 -2.72246818e+01 19 1.84968152e+01 -2.73514491e+01 2.37299412e+01 20 -3.09416165e+01 1.68268274e+01 2.34065375e+01 21 9.88442843e+00 -4.81529476e+01 4.17359202e+01 22 2.30237597e+01 3.22316066e+01 -4.58336284e+01 23 1.16249581e+01 -6.35754808e+01 3.48829547e+01 24 -2.97350500e+01 1.68942216e+01 1.77911782e+01 25 -2.26317641e+01 3.86987222e+00 -3.69901939e-02 26 8.49934884e+00 7.65475735e+00 5.08018299e+00 27 6.53156313e+00 2.60075749e+01 3.06113155e+01 28 -7.05444737e+00 3.92032370e+00 6.72272407e+00 29 3.54658865e+00 -2.05535152e+00 -1.94399382e+01 30 5.73262992e+00 6.10118979e+00 1.41655167e+00 31 1.42882954e+01 1.02332819e+01 7.81329510e+00 32 -2.06222203e+00 9.22642147e+00 9.96750796e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==90007== Memcheck, a memory error detector ==90007== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==90007== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==90007== Command: python runner2.py EAM_Dynamo_OBrienBarrPrice_2018_PtAu__MO_946831081299_000 ==90007== ==90007== Conditional jump or move depends on uninitialised value(s) ==90007== at 0x4FCBE77: __wcsnlen_avx2 (strlen-avx2.S:261) ==90007== by 0x4EF9EC1: wcsrtombs (wcsrtombs.c:104) ==90007== by 0x4E7FB20: wcstombs (wcstombs.c:34) ==90007== by 0x547A3F: ??? (in /usr/bin/python3.6) ==90007== by 0x63345D: _Py_stat (in /usr/bin/python3.6) ==90007== by 0x5BA640: ??? (in /usr/bin/python3.6) ==90007== by 0x551B80: ??? (in /usr/bin/python3.6) ==90007== by 0x5AA6EB: _PyObject_FastCallKeywords (in /usr/bin/python3.6) ==90007== by 0x50ABB2: ??? (in /usr/bin/python3.6) ==90007== by 0x50C5B8: _PyEval_EvalFrameDefault (in /usr/bin/python3.6) ==90007== by 0x509D47: ??? (in /usr/bin/python3.6) ==90007== by 0x50AA7C: ??? (in /usr/bin/python3.6) ==90007== ==90007== Conditional jump or move depends on uninitialised value(s) ==90007== at 0x4E63408: internal_utf8_loop (loop.c:298) ==90007== by 0x4E63408: __gconv_transform_internal_utf8 (skeleton.c:609) ==90007== by 0x4EF9EF4: wcsrtombs (wcsrtombs.c:110) ==90007== by 0x4E7FB20: wcstombs (wcstombs.c:34) ==90007== by 0x547A3F: ??? (in /usr/bin/python3.6) ==90007== by 0x63345D: _Py_stat (in /usr/bin/python3.6) ==90007== by 0x5BA640: ??? (in /usr/bin/python3.6) ==90007== by 0x551B80: ??? (in /usr/bin/python3.6) ==90007== by 0x5AA6EB: _PyObject_FastCallKeywords (in /usr/bin/python3.6) ==90007== by 0x50ABB2: ??? (in /usr/bin/python3.6) ==90007== by 0x50C5B8: _PyEval_EvalFrameDefault (in /usr/bin/python3.6) ==90007== by 0x509D47: ??? (in /usr/bin/python3.6) ==90007== by 0x50AA7C: ??? (in /usr/bin/python3.6) ==90007== ==90007== Conditional jump or move depends on uninitialised value(s) ==90007== at 0x4E63411: internal_utf8_loop (loop.c:303) ==90007== by 0x4E63411: __gconv_transform_internal_utf8 (skeleton.c:609) ==90007== by 0x4EF9EF4: wcsrtombs (wcsrtombs.c:110) ==90007== by 0x4E7FB20: wcstombs (wcstombs.c:34) ==90007== by 0x547A3F: ??? (in /usr/bin/python3.6) ==90007== by 0x63345D: _Py_stat (in /usr/bin/python3.6) ==90007== by 0x5BA640: ??? (in /usr/bin/python3.6) ==90007== by 0x551B80: ??? (in /usr/bin/python3.6) ==90007== by 0x5AA6EB: _PyObject_FastCallKeywords (in /usr/bin/python3.6) ==90007== by 0x50ABB2: ??? (in /usr/bin/python3.6) ==90007== by 0x50C5B8: _PyEval_EvalFrameDefault (in /usr/bin/python3.6) ==90007== by 0x509D47: ??? (in /usr/bin/python3.6) ==90007== by 0x50AA7C: ??? (in /usr/bin/python3.6) ==90007== ==90007== Conditional jump or move depends on uninitialised value(s) ==90007== at 0x4E63458: internal_utf8_loop (loop.c:298) ==90007== by 0x4E63458: __gconv_transform_internal_utf8 (skeleton.c:609) ==90007== by 0x4EF9EF4: wcsrtombs (wcsrtombs.c:110) ==90007== by 0x4E7FB20: wcstombs (wcstombs.c:34) ==90007== by 0x547A3F: ??? (in /usr/bin/python3.6) ==90007== by 0x63345D: _Py_stat (in /usr/bin/python3.6) ==90007== by 0x5BA640: ??? (in /usr/bin/python3.6) ==90007== by 0x551B80: ??? (in /usr/bin/python3.6) ==90007== by 0x5AA6EB: _PyObject_FastCallKeywords (in /usr/bin/python3.6) ==90007== by 0x50ABB2: ??? (in /usr/bin/python3.6) ==90007== by 0x50C5B8: _PyEval_EvalFrameDefault (in /usr/bin/python3.6) ==90007== by 0x509D47: ??? (in /usr/bin/python3.6) ==90007== by 0x50AA7C: ??? (in /usr/bin/python3.6) ==90007== ==90007== Conditional jump or move depends on uninitialised value(s) ==90007== at 0x4FCBCEC: __wcsnlen_avx2 (strlen-avx2.S:103) ==90007== by 0x4EF9EC1: wcsrtombs (wcsrtombs.c:104) ==90007== by 0x4E7FB20: wcstombs (wcstombs.c:34) ==90007== by 0x547A3F: ??? (in /usr/bin/python3.6) ==90007== by 0x547D20: PyUnicode_FSConverter (in /usr/bin/python3.6) ==90007== by 0x4C51E6: ??? (in /usr/bin/python3.6) ==90007== by 0x4F8388: ??? (in /usr/bin/python3.6) ==90007== by 0x4FBD83: ??? (in /usr/bin/python3.6) ==90007== by 0x4FC914: _PyArg_ParseStack_SizeT (in /usr/bin/python3.6) ==90007== by 0x4C6C88: ??? (in /usr/bin/python3.6) ==90007== by 0x50A9D9: ??? (in /usr/bin/python3.6) ==90007== by 0x50C5B8: _PyEval_EvalFrameDefault (in /usr/bin/python3.6) ==90007== ==90007== ==90007== HEAP SUMMARY: ==90007== in use at exit: 2,764,995 bytes in 1,647 blocks ==90007== total heap usage: 55,202 allocs, 53,555 frees, 120,185,963 bytes allocated ==90007== ==90007== LEAK SUMMARY: ==90007== definitely lost: 0 bytes in 0 blocks ==90007== indirectly lost: 0 bytes in 0 blocks ==90007== possibly lost: 146,155 bytes in 87 blocks ==90007== still reachable: 2,618,840 bytes in 1,560 blocks ==90007== suppressed: 0 bytes in 0 blocks ==90007== Rerun with --leak-check=full to see details of leaked memory ==90007== ==90007== For counts of detected and suppressed errors, rerun with: -v ==90007== Use --track-origins=yes to see where uninitialised values come from ==90007== ERROR SUMMARY: 6672 errors from 5 contexts (suppressed: 12403 from 654) ================================================================================ 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.