!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_BonnyCastinBullens_2013_FeW__MO_737567242631_000 Supported species : Fe W random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Fe (Configuration in file "config-F-Fe.xyz") ----------------------------------------------------------------------------------------------------- Energy = -12.95272051977955 Forces: 1 -5.87390505e+00 -4.84725584e+00 -8.96036531e+00 2 -9.51453664e+00 1.81155168e+01 -5.95879083e+00 3 9.44585508e+00 -8.06745995e+00 -1.11574291e+00 4 -6.44851549e+00 4.99687439e+00 2.42348447e+00 5 1.12301562e+01 -1.88081719e+01 1.99660501e+00 6 2.20036414e+00 1.52072897e+00 -2.88523803e+00 7 1.54555860e+00 -2.80440210e+01 -3.27455228e+01 8 -1.10151711e+01 -8.67682853e+00 -9.12130990e+00 9 -2.83012154e+00 -4.89971014e+00 -8.22294561e+00 10 -6.36218390e+00 8.28876469e+00 -1.44713706e+01 11 -1.92942481e+00 -7.84689189e+00 -5.03094529e-03 12 -5.78101278e+00 1.08945057e+01 1.76584798e+00 13 -1.40928841e+01 -1.23163327e+01 -3.86032105e+01 14 6.99241990e+00 1.16790911e+01 -8.64130726e+00 15 3.02632570e+01 -1.30592957e+01 1.62195600e+01 16 1.62651103e+00 2.22182786e+01 1.75475705e+01 17 -1.61418815e+01 -2.23090250e+00 -5.73058553e+00 18 1.58347484e+00 4.25906315e+00 2.13663464e+00 19 1.37563803e+01 -1.00153907e+01 1.04492599e+01 20 -5.48634829e+00 9.23915736e+00 3.89304480e+00 21 -1.12801483e+01 -9.97084690e+00 8.01847653e+00 22 2.00728561e+01 2.29259782e+01 2.27547088e+01 23 9.70757114e+00 -5.27105871e+00 5.26362631e+00 24 -8.39078336e+00 6.29691079e+00 3.76629100e+00 25 -8.58804679e+00 -6.52143864e+00 6.14567984e+00 26 1.43759992e+00 1.20868384e+01 -7.17963245e+00 27 2.19335343e+01 -3.65076645e+01 7.82346708e+00 28 -3.21540754e+01 2.72412502e+01 3.55139704e+00 29 -7.45086726e+00 2.08132702e+00 9.99799198e+00 30 5.71752038e+00 9.73752321e+00 5.72126280e+00 31 1.03391007e+01 -4.54757038e+00 6.76153373e+00 32 5.48774660e+00 1.00490313e+01 7.40461028e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Fe (Configuration in file "config-T-Fe.xyz") ----------------------------------------------------------------------------------------------------- Energy = -12.95272051977955 Forces: 1 -5.87390505e+00 -4.84725584e+00 -8.96036531e+00 2 -9.51453664e+00 1.81155168e+01 -5.95879083e+00 3 9.44585508e+00 -8.06745995e+00 -1.11574291e+00 4 -6.44851549e+00 4.99687439e+00 2.42348447e+00 5 1.12301562e+01 -1.88081719e+01 1.99660501e+00 6 2.20036414e+00 1.52072897e+00 -2.88523803e+00 7 1.54555860e+00 -2.80440210e+01 -3.27455228e+01 8 -1.10151711e+01 -8.67682853e+00 -9.12130990e+00 9 -2.83012154e+00 -4.89971014e+00 -8.22294561e+00 10 -6.36218390e+00 8.28876469e+00 -1.44713706e+01 11 -1.92942481e+00 -7.84689189e+00 -5.03094529e-03 12 -5.78101278e+00 1.08945057e+01 1.76584798e+00 13 -1.40928841e+01 -1.23163327e+01 -3.86032105e+01 14 6.99241990e+00 1.16790911e+01 -8.64130726e+00 15 3.02632570e+01 -1.30592957e+01 1.62195600e+01 16 1.62651103e+00 2.22182786e+01 1.75475705e+01 17 -1.61418815e+01 -2.23090250e+00 -5.73058553e+00 18 1.58347484e+00 4.25906315e+00 2.13663464e+00 19 1.37563803e+01 -1.00153907e+01 1.04492599e+01 20 -5.48634829e+00 9.23915736e+00 3.89304480e+00 21 -1.12801483e+01 -9.97084690e+00 8.01847653e+00 22 2.00728561e+01 2.29259782e+01 2.27547088e+01 23 9.70757114e+00 -5.27105871e+00 5.26362631e+00 24 -8.39078336e+00 6.29691079e+00 3.76629100e+00 25 -8.58804679e+00 -6.52143864e+00 6.14567984e+00 26 1.43759992e+00 1.20868384e+01 -7.17963245e+00 27 2.19335343e+01 -3.65076645e+01 7.82346708e+00 28 -3.21540754e+01 2.72412502e+01 3.55139704e+00 29 -7.45086726e+00 2.08132702e+00 9.99799198e+00 30 5.71752038e+00 9.73752321e+00 5.72126280e+00 31 1.03391007e+01 -4.54757038e+00 6.76153373e+00 32 5.48774660e+00 1.00490313e+01 7.40461028e+00 MONOATOMIC STRUCTURE (pbc=False)-- Species = W (Configuration in file "config-F-W.xyz") ----------------------------------------------------------------------------------------------------- Energy = 930.4543650305048 Forces: 1 -7.85863490e+01 -6.55683228e+01 -1.07939598e+02 2 3.55361870e+01 7.35005801e+00 -1.79797394e+02 3 1.38034805e+02 -2.16372489e+02 5.18440857e+01 4 -2.09884506e+02 1.34624084e+02 1.10531786e+02 5 -4.87939426e+00 -3.78579241e+01 -5.05718108e+01 6 4.29456224e+01 7.77784444e+01 -8.40005078e+01 7 1.37089760e+02 -1.08151738e+02 -8.67775150e+01 8 9.74598762e+01 -4.81766224e+00 -2.77851947e+01 9 -1.30171506e+02 -3.21952706e+02 -2.60792179e+02 10 5.78900550e+01 1.49665196e+02 -1.15631020e+02 11 -2.14381822e+02 7.65742226e+01 -1.85970468e+02 12 -8.69509546e+01 3.15741272e+02 2.96015969e+02 13 1.00176945e+02 -4.61113330e+01 -7.50194584e+01 14 4.12635146e+01 3.35801767e+01 -6.51115870e+01 15 4.51818434e+01 -7.16751940e+01 1.75904773e+00 16 -2.72943925e+01 7.32512141e+01 -1.83219426e+01 17 -1.11049807e+02 -4.90257515e+01 -5.62200406e+01 18 -3.74016781e+01 -1.77515855e+02 -1.16550940e+01 19 8.77247155e+01 -5.21722963e+01 1.15859390e+02 20 -1.63755962e+02 -8.49462440e+00 1.53541366e+02 21 -2.15379405e+02 -1.91160396e+02 1.16931760e+02 22 2.35248116e+02 1.29858144e+02 -1.45732405e+02 23 6.65369193e+01 -1.37405164e+02 1.00220905e+02 24 -1.59136936e+02 6.45456772e+01 2.05954048e+02 25 -1.36146512e+02 -4.60474786e+01 -8.58431035e+01 26 3.37667711e+01 1.25679932e+02 1.55613595e+01 27 1.15654962e+02 -3.82454723e+01 1.19827021e+02 28 -9.26463030e+01 1.00689043e+02 4.63292151e+01 29 3.24693726e+02 1.77292005e+02 1.30533779e+02 30 1.05528505e+02 3.85950896e+01 -3.70848747e+01 31 7.57775771e+01 2.68111851e+01 3.01894660e+01 32 -7.28443716e+01 4.05386625e+01 9.91549938e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = W (Configuration in file "config-T-W.xyz") ----------------------------------------------------------------------------------------------------- Energy = 930.4543650305048 Forces: 1 -7.85863490e+01 -6.55683228e+01 -1.07939598e+02 2 3.55361870e+01 7.35005801e+00 -1.79797394e+02 3 1.38034805e+02 -2.16372489e+02 5.18440857e+01 4 -2.09884506e+02 1.34624084e+02 1.10531786e+02 5 -4.87939426e+00 -3.78579241e+01 -5.05718108e+01 6 4.29456224e+01 7.77784444e+01 -8.40005078e+01 7 1.37089760e+02 -1.08151738e+02 -8.67775150e+01 8 9.74598762e+01 -4.81766224e+00 -2.77851947e+01 9 -1.30171506e+02 -3.21952706e+02 -2.60792179e+02 10 5.78900550e+01 1.49665196e+02 -1.15631020e+02 11 -2.14381822e+02 7.65742226e+01 -1.85970468e+02 12 -8.69509546e+01 3.15741272e+02 2.96015969e+02 13 1.00176945e+02 -4.61113330e+01 -7.50194584e+01 14 4.12635146e+01 3.35801767e+01 -6.51115870e+01 15 4.51818434e+01 -7.16751940e+01 1.75904773e+00 16 -2.72943925e+01 7.32512141e+01 -1.83219426e+01 17 -1.11049807e+02 -4.90257515e+01 -5.62200406e+01 18 -3.74016781e+01 -1.77515855e+02 -1.16550940e+01 19 8.77247155e+01 -5.21722963e+01 1.15859390e+02 20 -1.63755962e+02 -8.49462440e+00 1.53541366e+02 21 -2.15379405e+02 -1.91160396e+02 1.16931760e+02 22 2.35248116e+02 1.29858144e+02 -1.45732405e+02 23 6.65369193e+01 -1.37405164e+02 1.00220905e+02 24 -1.59136936e+02 6.45456772e+01 2.05954048e+02 25 -1.36146512e+02 -4.60474786e+01 -8.58431035e+01 26 3.37667711e+01 1.25679932e+02 1.55613595e+01 27 1.15654962e+02 -3.82454723e+01 1.19827021e+02 28 -9.26463030e+01 1.00689043e+02 4.63292151e+01 29 3.24693726e+02 1.77292005e+02 1.30533779e+02 30 1.05528505e+02 3.85950896e+01 -3.70848747e+01 31 7.57775771e+01 2.68111851e+01 3.01894660e+01 32 -7.28443716e+01 4.05386625e+01 9.91549938e+01 MIXED STRUCTURE (pbc=False)-- Species = Fe W (Configuration in file "config-F-FeW.xyz") ----------------------------------------------------------------------------------------------------- Energy = 695.4647858392343 Forces: 1 -2.75588902e+01 -1.77325005e+01 -6.51834219e+01 2 -1.38622267e+01 -6.24595719e+01 -9.05725078e+01 3 4.04480648e+01 -7.46684443e+01 2.00106190e+00 4 -1.59623892e+02 -3.07793983e+01 -6.09763561e+01 5 -1.11822262e+02 -6.12375399e+01 -1.06687873e+02 6 3.71142580e+01 1.01136544e+02 -7.70183178e+01 7 1.23797732e+02 -1.12204739e+02 1.08997490e+02 8 1.06966666e+01 -4.92468635e+01 -3.00903832e+01 9 -3.32364437e+01 1.03493357e+01 -4.08446919e+01 10 -1.40418544e+01 2.14068893e+01 -2.86476965e+01 11 -5.87444742e+01 9.73836329e+01 1.53435754e+02 12 -2.44295916e+02 -8.57193189e+00 -2.24590556e+02 13 1.16304905e+02 4.94318819e+00 -1.26175800e+02 14 1.66853359e+02 2.56187495e+00 -1.99940372e+02 15 4.68856233e+01 -1.01421414e+01 -5.40381967e+00 16 -1.55015217e+02 7.00597639e+01 1.76145947e+02 17 -1.18788578e+02 -1.23900604e+02 2.07317770e+01 18 1.51625046e+02 1.06826810e+02 2.56522652e+01 19 5.11253850e+00 -1.42256574e+01 2.58673386e+01 20 -3.36576912e+01 1.99494911e+01 4.98512737e+01 21 -1.10974766e+02 -6.19335348e+01 -9.78431985e+01 22 1.15181252e+02 9.18258419e+01 -6.16026439e+01 23 8.20572808e+01 -1.09055101e+02 1.97335549e+02 24 1.25135959e+01 -1.69719927e+02 2.47087660e+02 25 -4.82143632e+01 8.39991275e+00 3.21162691e+01 26 2.70728772e+02 8.86804789e+01 1.78859968e+02 27 -1.57758334e+02 -1.66921823e+02 7.30056964e+01 28 -8.53071711e+01 4.98497767e+01 5.98982574e+01 29 -4.00191940e+01 1.17439005e+02 -2.49078945e+02 30 9.45963172e+01 9.21713001e+01 -3.05266125e+01 31 3.66742280e+01 -1.40509295e+01 5.12445096e+01 32 1.02331636e+02 2.03866863e+02 9.29523775e+01 MIXED STRUCTURE (pbc=True)-- Species = Fe W (Configuration in file "config-T-FeW.xyz") ----------------------------------------------------------------------------------------------------- Energy = 785.0200791087693 Forces: 1 -2.48699795e+01 -1.60777716e+01 -6.33531949e+01 2 -1.30759022e+01 -6.95776730e+01 -7.82564874e+01 3 3.86635222e+01 -5.61289146e+01 -8.80268772e+00 4 -9.67514560e+01 -1.36312199e+01 -7.15533238e+01 5 -1.34585323e+02 2.88745315e+01 -1.13193534e+02 6 2.14231577e+01 1.02014447e+02 -8.72589435e+01 7 1.24032011e+02 -8.28325278e+01 1.21772649e+02 8 1.05192095e+01 -4.89762769e+01 -3.10558386e+01 9 -2.55584635e+01 3.49225352e-02 -2.04390196e+01 10 -2.41632662e+01 1.96357089e+01 -2.53935721e+00 11 -6.04571457e+01 9.78937415e+01 1.52277320e+02 12 -2.43398100e+02 -1.13375561e+01 -2.26540670e+02 13 1.22511152e+02 -2.10324807e+00 -1.08438888e+02 14 1.88812213e+02 -3.46411694e+01 -1.85379629e+02 15 3.69218129e+01 -4.17058379e+00 -6.37717471e+00 16 -1.73817555e+02 -2.14966115e+01 1.96954569e+02 17 -6.89934895e+01 -1.32820203e+02 1.82258193e+01 18 1.53202005e+02 1.05973704e+02 2.62118908e+01 19 3.47214655e+00 2.26745561e+00 1.73426522e+01 20 -2.24408346e+00 2.30522677e+01 7.27477623e+01 21 -1.20660421e+02 -2.00664941e+01 -9.01431429e+01 22 1.85573737e+01 1.08429022e+02 -6.72307011e+01 23 7.39767396e+01 -8.71053334e+01 1.92574110e+02 24 1.31093220e+01 -1.67016782e+02 2.42264679e+02 25 -3.19226645e+01 1.66100471e+01 2.76253905e+01 26 2.73667201e+02 5.63669246e+01 1.83605645e+02 27 -1.61817112e+02 -1.62507106e+02 4.49818844e+01 28 -6.36364352e+01 4.93856159e+01 5.44411594e+01 29 -3.88209190e+01 1.18178840e+02 -2.47477688e+02 30 9.06402635e+01 5.02218623e+01 -4.86467345e+01 31 1.80692291e+01 -3.46592598e+01 4.71465945e+01 32 9.71949575e+01 1.86209640e+02 5.85148878e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==4159476== Memcheck, a memory error detector ==4159476== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==4159476== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info ==4159476== Command: python runner2.py EAM_Dynamo_BonnyCastinBullens_2013_FeW__MO_737567242631_000 ==4159476== ==4161062== Warning: invalid file descriptor 1024 in syscall close() ==4161062== Warning: invalid file descriptor 1025 in syscall close() ==4161062== Warning: invalid file descriptor 1026 in syscall close() ==4161062== Warning: invalid file descriptor 1027 in syscall close() ==4161062== Use --log-fd= to select an alternative log fd. ==4161062== Warning: invalid file descriptor 1028 in syscall close() ==4161062== Warning: invalid file descriptor 1029 in syscall close() ==4159476== ==4159476== HEAP SUMMARY: ==4159476== in use at exit: 2,257,767 bytes in 1,704 blocks ==4159476== total heap usage: 82,856 allocs, 81,152 frees, 120,541,890 bytes allocated ==4159476== ==4159476== LEAK SUMMARY: ==4159476== definitely lost: 0 bytes in 0 blocks ==4159476== indirectly lost: 0 bytes in 0 blocks ==4159476== possibly lost: 180,827 bytes in 103 blocks ==4159476== still reachable: 2,076,908 bytes in 1,600 blocks ==4159476== of which reachable via heuristic: ==4159476== stdstring : 38 bytes in 1 blocks ==4159476== suppressed: 32 bytes in 1 blocks ==4159476== Rerun with --leak-check=full to see details of leaked memory ==4159476== ==4159476== For lists of detected and suppressed errors, rerun with: -s ==4159476== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 7979 from 559) ================================================================================ 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.