!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : EAM_Dynamo_ZopeMishin_2003_TiAl__MO_117656786760_005 Supported species : Al Ti random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Al (Configuration in file "config-F-Al.xyz") ----------------------------------------------------------------------------------------------------- Energy = -27.76186272629013 Forces: 1 -1.95102235e+00 -2.10367455e+00 -2.58474764e+00 2 -9.11778666e-01 1.82615433e+00 -4.42878314e+00 3 1.04169293e+00 -3.85492443e+00 2.39685208e-01 4 -3.60410402e+00 1.62802838e+00 1.10020841e+00 5 1.72868322e+00 -4.65210007e+00 -1.70390030e+00 6 2.13735692e+00 1.19157728e+00 -2.86000863e+00 7 2.26438493e+00 -5.69590869e+00 -3.64019368e+00 8 -2.58157331e+00 -1.48317624e+00 -1.22253431e-01 9 -4.21016633e+00 -1.94649450e+00 -5.46388593e+00 10 -2.26194055e-01 6.80741597e+00 -5.76808795e+00 11 -3.06451685e+00 -5.34254040e+00 3.00956732e+00 12 -4.85335713e+00 3.99260654e+00 1.42215607e+00 13 4.35882577e+00 -2.36008174e+00 -7.88017433e+00 14 1.50620664e+00 1.36039940e+00 -1.61009779e+00 15 6.52350190e+00 -8.02393243e-01 -3.02882034e+00 16 1.97884757e+00 7.83158175e+00 3.54283489e+00 17 -4.87295708e+00 -2.79864193e+00 -1.16118723e+00 18 1.44411728e+00 3.10726800e+00 -1.65853606e+00 19 1.22118972e+00 -4.86536165e+00 3.53999874e+00 20 -3.06528649e+00 2.45759298e+00 3.08063302e+00 21 -2.16638596e+00 -4.59034466e+00 8.74776452e-01 22 6.04507752e+00 3.21536982e+00 2.88000549e+00 23 1.83070930e+00 -8.43757254e-01 2.77002608e+00 24 8.60009609e-01 1.72533860e+00 3.48156091e+00 25 -4.57703937e+00 -3.11642224e+00 -1.15142717e+00 26 1.43727964e+00 6.22311225e+00 -2.22180172e+00 27 1.75383512e+00 -5.59125167e+00 4.96581859e+00 28 -5.80198240e+00 4.12926208e+00 2.99282550e+00 29 -2.95782871e+00 -2.40906294e+00 2.65386131e+00 30 3.44719721e+00 5.43477806e+00 4.22421385e-01 31 3.79912715e+00 -2.53667900e+00 4.45851657e+00 32 1.46615031e+00 4.06232977e+00 3.84900938e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Al (Configuration in file "config-T-Al.xyz") ----------------------------------------------------------------------------------------------------- Energy = -27.76186272629013 Forces: 1 -1.95102235e+00 -2.10367455e+00 -2.58474764e+00 2 -9.11778666e-01 1.82615433e+00 -4.42878314e+00 3 1.04169293e+00 -3.85492443e+00 2.39685208e-01 4 -3.60410402e+00 1.62802838e+00 1.10020841e+00 5 1.72868322e+00 -4.65210007e+00 -1.70390030e+00 6 2.13735692e+00 1.19157728e+00 -2.86000863e+00 7 2.26438493e+00 -5.69590869e+00 -3.64019368e+00 8 -2.58157331e+00 -1.48317624e+00 -1.22253431e-01 9 -4.21016633e+00 -1.94649450e+00 -5.46388593e+00 10 -2.26194055e-01 6.80741597e+00 -5.76808795e+00 11 -3.06451685e+00 -5.34254040e+00 3.00956732e+00 12 -4.85335713e+00 3.99260654e+00 1.42215607e+00 13 4.35882577e+00 -2.36008174e+00 -7.88017433e+00 14 1.50620664e+00 1.36039940e+00 -1.61009779e+00 15 6.52350190e+00 -8.02393243e-01 -3.02882034e+00 16 1.97884757e+00 7.83158175e+00 3.54283489e+00 17 -4.87295708e+00 -2.79864193e+00 -1.16118723e+00 18 1.44411728e+00 3.10726800e+00 -1.65853606e+00 19 1.22118972e+00 -4.86536165e+00 3.53999874e+00 20 -3.06528649e+00 2.45759298e+00 3.08063302e+00 21 -2.16638596e+00 -4.59034466e+00 8.74776452e-01 22 6.04507752e+00 3.21536982e+00 2.88000549e+00 23 1.83070930e+00 -8.43757254e-01 2.77002608e+00 24 8.60009609e-01 1.72533860e+00 3.48156091e+00 25 -4.57703937e+00 -3.11642224e+00 -1.15142717e+00 26 1.43727964e+00 6.22311225e+00 -2.22180172e+00 27 1.75383512e+00 -5.59125167e+00 4.96581859e+00 28 -5.80198240e+00 4.12926208e+00 2.99282550e+00 29 -2.95782871e+00 -2.40906294e+00 2.65386131e+00 30 3.44719721e+00 5.43477806e+00 4.22421385e-01 31 3.79912715e+00 -2.53667900e+00 4.45851657e+00 32 1.46615031e+00 4.06232977e+00 3.84900938e+00 MONOATOMIC STRUCTURE (pbc=False)-- Species = Ti (Configuration in file "config-F-Ti.xyz") ----------------------------------------------------------------------------------------------------- Energy = 49.469305722230565 Forces: 1 -5.32958692e+00 -7.23097207e+00 -8.45263557e+00 2 -7.65603487e+00 -3.88515521e+00 -2.83650106e+01 3 8.98720198e+00 -2.67581950e+01 -1.40259644e+01 4 -2.40529105e+01 2.34893049e+01 -1.90438549e+01 5 -2.58479397e+00 -1.12629140e+01 -1.23633845e+01 6 1.43633317e+01 -8.06429669e+00 -1.49905646e+01 7 1.87289200e+01 -5.01924383e+00 -9.08848823e+00 8 1.66180146e+01 -9.82479167e+00 8.44203786e+00 9 -4.45792685e+00 -9.03047685e-01 -4.47201689e+00 10 -1.22187637e+00 4.41009562e+00 -6.84629221e+00 11 -3.12068343e+01 1.23528921e+01 5.56990275e+00 12 -7.34262096e+00 5.59195467e+00 -2.12112971e+00 13 -5.79057005e+00 9.15315919e+00 -3.47851852e+01 14 3.61539429e+00 4.50821850e+00 -4.41819231e+00 15 2.47295243e+01 9.51526266e+00 1.94857444e+01 16 1.43104478e+01 1.44674259e+01 -1.35604054e+01 17 -2.72363779e+01 -3.82043337e+01 2.12607347e+01 18 1.95556616e+01 2.53933512e+01 -4.23925688e+00 19 8.77438397e+00 -2.28634972e+01 2.45429293e+01 20 -1.97199181e+01 7.23602025e+00 1.44628725e+01 21 -1.03275049e+01 -1.51606859e+01 1.24160154e+01 22 1.55687462e+01 9.94827901e+00 -1.05783311e+01 23 1.39078798e+01 -2.35024338e+01 1.02138003e+01 24 -1.61803031e+01 1.48228011e+01 1.37075878e+01 25 -8.37488517e+00 1.48570488e+00 -3.17408412e+00 26 -1.22532800e+01 1.13560567e+01 1.83932322e+01 27 1.12301443e+01 -7.72052173e+00 7.60127261e+00 28 -9.84314166e+00 1.21089521e+01 3.28333460e+00 29 1.24852730e+01 6.05870758e+00 2.27175810e+01 30 1.34816195e+01 6.09106985e+00 -1.06064612e+01 31 1.23403828e+01 -5.37545286e+00 5.17173934e+00 32 -1.51183603e+01 7.78628501e+00 1.38624732e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ti (Configuration in file "config-T-Ti.xyz") ----------------------------------------------------------------------------------------------------- Energy = 49.469305722230565 Forces: 1 -5.32958692e+00 -7.23097207e+00 -8.45263557e+00 2 -7.65603487e+00 -3.88515521e+00 -2.83650106e+01 3 8.98720198e+00 -2.67581950e+01 -1.40259644e+01 4 -2.40529105e+01 2.34893049e+01 -1.90438549e+01 5 -2.58479397e+00 -1.12629140e+01 -1.23633845e+01 6 1.43633317e+01 -8.06429669e+00 -1.49905646e+01 7 1.87289200e+01 -5.01924383e+00 -9.08848823e+00 8 1.66180146e+01 -9.82479167e+00 8.44203786e+00 9 -4.45792685e+00 -9.03047685e-01 -4.47201689e+00 10 -1.22187637e+00 4.41009562e+00 -6.84629221e+00 11 -3.12068343e+01 1.23528921e+01 5.56990275e+00 12 -7.34262096e+00 5.59195467e+00 -2.12112971e+00 13 -5.79057005e+00 9.15315919e+00 -3.47851852e+01 14 3.61539429e+00 4.50821850e+00 -4.41819231e+00 15 2.47295243e+01 9.51526266e+00 1.94857444e+01 16 1.43104478e+01 1.44674259e+01 -1.35604054e+01 17 -2.72363779e+01 -3.82043337e+01 2.12607347e+01 18 1.95556616e+01 2.53933512e+01 -4.23925688e+00 19 8.77438397e+00 -2.28634972e+01 2.45429293e+01 20 -1.97199181e+01 7.23602025e+00 1.44628725e+01 21 -1.03275049e+01 -1.51606859e+01 1.24160154e+01 22 1.55687462e+01 9.94827901e+00 -1.05783311e+01 23 1.39078798e+01 -2.35024338e+01 1.02138003e+01 24 -1.61803031e+01 1.48228011e+01 1.37075878e+01 25 -8.37488517e+00 1.48570488e+00 -3.17408412e+00 26 -1.22532800e+01 1.13560567e+01 1.83932322e+01 27 1.12301443e+01 -7.72052173e+00 7.60127261e+00 28 -9.84314166e+00 1.21089521e+01 3.28333460e+00 29 1.24852730e+01 6.05870758e+00 2.27175810e+01 30 1.34816195e+01 6.09106985e+00 -1.06064612e+01 31 1.23403828e+01 -5.37545286e+00 5.17173934e+00 32 -1.51183603e+01 7.78628501e+00 1.38624732e+01 MIXED STRUCTURE (pbc=False)-- Species = Al Ti (Configuration in file "config-F-AlTi.xyz") ----------------------------------------------------------------------------------------------------- Energy = 612.393473811033 Forces: 1 -6.40103243e+01 -7.69645231e+00 -7.39867237e+01 2 -1.19611947e+02 4.21584023e+02 -4.30034500e+02 3 1.17578114e+02 -4.15509474e+02 4.40097307e+02 4 -1.13154058e+02 -1.16805841e+02 -9.18525163e+00 5 5.78760381e+01 -9.73451409e+01 -5.27015375e+01 6 6.20260768e+01 2.89225369e+01 -6.34322180e+01 7 5.07222431e+01 -6.26078810e+01 1.01463758e+01 8 -5.10554598e+01 4.12610144e+01 4.71110665e+01 9 -5.01124340e+01 6.54794242e+01 -1.34202402e+02 10 -8.81164952e+00 8.21253861e+01 -5.52412658e+01 11 6.95377929e+01 -1.35671162e+02 3.22794247e+01 12 -1.02429738e+02 6.72753206e+01 -6.96511490e+00 13 -2.19675350e+01 -5.49219346e+01 -4.46309053e+01 14 3.82386475e+01 4.15802574e+01 -5.11607801e+01 15 7.24267771e+01 -5.73900738e+01 4.20381435e+01 16 -5.88416531e+01 1.07631448e+02 7.00282567e+00 17 -1.94623567e+01 -2.86697391e+01 -5.93615316e+00 18 5.91328560e+01 -1.34933020e+01 5.23498674e+01 19 1.91475551e+00 -9.74420284e+00 6.70054626e+00 20 -8.22200395e+00 4.13207061e-01 1.17755812e+01 21 -2.65211902e+01 -5.84434602e+01 -5.79023365e+01 22 4.71691244e+01 2.64936438e+01 -4.48033863e+01 23 1.99560981e+01 -2.55041915e+01 2.79910401e+01 24 -4.06567617e+01 -8.57342707e+01 1.81682745e+02 25 -1.73519874e+01 1.60124400e+01 5.48739756e+01 26 3.77876022e+01 4.64237734e+01 -3.55166185e+01 27 -1.83875395e+02 -5.14517777e+01 2.92999998e+02 28 -5.80955155e+01 5.07648042e+01 8.15467919e+01 29 1.15262503e+02 3.51979187e+01 -2.67801473e+02 30 8.47400425e+01 1.76737179e+01 3.04522348e+01 31 5.47843349e+01 6.67876040e+01 1.90028491e+01 32 5.50270025e+01 1.05362384e+02 -4.55010653e+00 MIXED STRUCTURE (pbc=True)-- Species = Al Ti (Configuration in file "config-T-AlTi.xyz") ----------------------------------------------------------------------------------------------------- Energy = 905.3094307302277 Forces: 1 -2.85037975e+01 -1.41104560e+01 -7.59065718e+01 2 -1.19256727e+02 4.20800675e+02 -4.21619442e+02 3 1.05550583e+02 -3.68042077e+02 4.63364206e+02 4 -9.82333955e+01 -1.15686683e+02 -1.14027030e+01 5 1.61541469e+02 9.57883533e+01 -1.77683883e+01 6 2.52112657e+01 7.01901932e+00 -3.77394093e+01 7 2.74784273e+01 -5.65408983e+01 1.91600378e+01 8 -5.02499619e+01 3.92429947e+01 4.64314326e+01 9 1.73818487e+01 5.73444895e+01 -1.39520979e+02 10 -9.45729714e+01 -1.10556390e+02 -9.57023525e+01 11 6.60419278e+01 -1.35691548e+02 3.42331471e+01 12 -4.79617634e+01 7.82577047e+01 5.36407541e+00 13 -7.90563032e+01 -5.53816988e+01 4.33804292e+01 14 8.23019547e+00 1.73549884e+02 8.33162759e+01 15 1.21470191e+01 -6.62770878e+01 5.88840223e+01 16 -5.14697133e+01 7.53605807e+01 2.47861948e+01 17 -5.52839902e-01 -3.17326033e+01 -5.78408396e+00 18 5.80843450e+01 -1.34946518e+01 5.27972786e+01 19 -3.44506622e+00 1.28489271e+00 -1.17943652e+01 20 1.46347220e+00 6.31636433e+00 9.18723775e-01 21 -3.22476081e+01 -4.74207822e+01 -5.55920945e+01 22 2.32269938e+01 3.63091136e+01 -3.53708253e+01 23 5.63124305e+00 -2.69822147e+01 1.60966391e+01 24 -4.05855127e+01 -8.69928564e+01 1.72925429e+02 25 -1.51586363e+01 1.64196379e+01 5.58134122e+01 26 3.94510555e+01 3.91680069e+01 -3.26293284e+01 27 -1.87245892e+02 -5.99823793e+01 2.68743128e+02 28 -5.52586292e+01 4.23194476e+01 6.99381181e+01 29 1.14644024e+02 3.56470908e+01 -2.66765112e+02 30 8.61456362e+01 7.72474317e+00 3.28409061e+01 31 1.00791598e+02 -4.57220999e+01 -2.28250777e+02 32 5.07777127e+01 1.02061429e+02 -1.31470223e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==2015== Memcheck, a memory error detector ==2015== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==2015== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==2015== Command: python runner2.py EAM_Dynamo_ZopeMishin_2003_TiAl__MO_117656786760_005 ==2015== ==3291== Warning: invalid file descriptor 1048564 in syscall close() ==3291== Warning: invalid file descriptor 1048565 in syscall close() ==3291== Warning: invalid file descriptor 1048566 in syscall close() ==3291== Warning: invalid file descriptor 1048567 in syscall close() ==3291== Use --log-fd= to select an alternative log fd. ==3291== Warning: invalid file descriptor 1048568 in syscall close() ==3291== Warning: invalid file descriptor 1048569 in syscall close() ==3299== Warning: invalid file descriptor 1048564 in syscall close() ==3299== Warning: invalid file descriptor 1048565 in syscall close() ==3299== Warning: invalid file descriptor 1048566 in syscall close() ==3299== Warning: invalid file descriptor 1048567 in syscall close() ==3299== Use --log-fd= to select an alternative log fd. ==3299== Warning: invalid file descriptor 1048568 in syscall close() ==3299== Warning: invalid file descriptor 1048569 in syscall close() ==3524== Warning: invalid file descriptor 1048564 in syscall close() ==3524== Warning: invalid file descriptor 1048565 in syscall close() ==3524== Warning: invalid file descriptor 1048566 in syscall close() ==3524== Warning: invalid file descriptor 1048567 in syscall close() ==3524== Use --log-fd= to select an alternative log fd. ==3524== Warning: invalid file descriptor 1048568 in syscall close() ==3524== Warning: invalid file descriptor 1048569 in syscall close() ==3529== Warning: invalid file descriptor 1048564 in syscall close() ==3529== Warning: invalid file descriptor 1048565 in syscall close() ==3529== Warning: invalid file descriptor 1048566 in syscall close() ==3529== Warning: invalid file descriptor 1048567 in syscall close() ==3529== Use --log-fd= to select an alternative log fd. ==3529== Warning: invalid file descriptor 1048568 in syscall close() ==3529== Warning: invalid file descriptor 1048569 in syscall close() ==3534== Warning: invalid file descriptor 1048564 in syscall close() ==3534== Warning: invalid file descriptor 1048565 in syscall close() ==3534== Warning: invalid file descriptor 1048566 in syscall close() ==3534== Warning: invalid file descriptor 1048567 in syscall close() ==3534== Use --log-fd= to select an alternative log fd. ==3534== Warning: invalid file descriptor 1048568 in syscall close() ==3534== Warning: invalid file descriptor 1048569 in syscall close() ==3541== Warning: invalid file descriptor 1048564 in syscall close() ==3541== Warning: invalid file descriptor 1048565 in syscall close() ==3541== Warning: invalid file descriptor 1048566 in syscall close() ==3541== Warning: invalid file descriptor 1048567 in syscall close() ==3541== Use --log-fd= to select an alternative log fd. ==3541== Warning: invalid file descriptor 1048568 in syscall close() ==3541== Warning: invalid file descriptor 1048569 in syscall close() ==3732== Warning: invalid file descriptor 1048564 in syscall close() ==3732== Warning: invalid file descriptor 1048565 in syscall close() ==3732== Warning: invalid file descriptor 1048566 in syscall close() ==3732== Warning: invalid file descriptor 1048567 in syscall close() ==3732== Use --log-fd= to select an alternative log fd. ==3732== Warning: invalid file descriptor 1048568 in syscall close() ==3732== Warning: invalid file descriptor 1048569 in syscall close() ==3734== Warning: invalid file descriptor 1048564 in syscall close() ==3734== Warning: invalid file descriptor 1048565 in syscall close() ==3734== Warning: invalid file descriptor 1048566 in syscall close() ==3734== Warning: invalid file descriptor 1048567 in syscall close() ==3734== Use --log-fd= to select an alternative log fd. ==3734== Warning: invalid file descriptor 1048568 in syscall close() ==3734== Warning: invalid file descriptor 1048569 in syscall close() ==3736== Warning: invalid file descriptor 1048564 in syscall close() ==3736== Warning: invalid file descriptor 1048565 in syscall close() ==3736== Warning: invalid file descriptor 1048566 in syscall close() ==3736== Warning: invalid file descriptor 1048567 in syscall close() ==3736== Use --log-fd= to select an alternative log fd. ==3736== Warning: invalid file descriptor 1048568 in syscall close() ==3736== Warning: invalid file descriptor 1048569 in syscall close() ==3738== Warning: invalid file descriptor 1048564 in syscall close() ==3738== Warning: invalid file descriptor 1048565 in syscall close() ==3738== Warning: invalid file descriptor 1048566 in syscall close() ==3738== Warning: invalid file descriptor 1048567 in syscall close() ==3738== Use --log-fd= to select an alternative log fd. ==3738== Warning: invalid file descriptor 1048568 in syscall close() ==3738== Warning: invalid file descriptor 1048569 in syscall close() ==3809== Warning: invalid file descriptor 1048564 in syscall close() ==3809== Warning: invalid file descriptor 1048565 in syscall close() ==3809== Warning: invalid file descriptor 1048566 in syscall close() ==3809== Warning: invalid file descriptor 1048567 in syscall close() ==3809== Use --log-fd= to select an alternative log fd. ==3809== Warning: invalid file descriptor 1048568 in syscall close() ==3809== Warning: invalid file descriptor 1048569 in syscall close() ==3810== Warning: invalid file descriptor 1048564 in syscall close() ==3810== Warning: invalid file descriptor 1048565 in syscall close() ==3810== Warning: invalid file descriptor 1048566 in syscall close() ==3810== Warning: invalid file descriptor 1048567 in syscall close() ==3810== Use --log-fd= to select an alternative log fd. ==3810== Warning: invalid file descriptor 1048568 in syscall close() ==3810== Warning: invalid file descriptor 1048569 in syscall close() ==3811== Warning: invalid file descriptor 1048564 in syscall close() ==3811== Warning: invalid file descriptor 1048565 in syscall close() ==3811== Warning: invalid file descriptor 1048566 in syscall close() ==3811== Warning: invalid file descriptor 1048567 in syscall close() ==3811== Use --log-fd= to select an alternative log fd. ==3811== Warning: invalid file descriptor 1048568 in syscall close() ==3811== Warning: invalid file descriptor 1048569 in syscall close() ==3812== Warning: invalid file descriptor 1048564 in syscall close() ==3812== Warning: invalid file descriptor 1048565 in syscall close() ==3812== Warning: invalid file descriptor 1048566 in syscall close() ==3812== Warning: invalid file descriptor 1048567 in syscall close() ==3812== Use --log-fd= to select an alternative log fd. ==3812== Warning: invalid file descriptor 1048568 in syscall close() ==3812== Warning: invalid file descriptor 1048569 in syscall close() ==2015== ==2015== HEAP SUMMARY: ==2015== in use at exit: 1,719,294 bytes in 1,331 blocks ==2015== total heap usage: 49,252 allocs, 47,921 frees, 110,760,721 bytes allocated ==2015== ==2015== LEAK SUMMARY: ==2015== definitely lost: 0 bytes in 0 blocks ==2015== indirectly lost: 0 bytes in 0 blocks ==2015== possibly lost: 178,943 bytes in 97 blocks ==2015== still reachable: 1,540,351 bytes in 1,234 blocks ==2015== suppressed: 0 bytes in 0 blocks ==2015== Rerun with --leak-check=full to see details of leaked memory ==2015== ==2015== For counts of detected and suppressed errors, rerun with: -v ==2015== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 11352 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" Grade: P Comment: No memory leak detected.