!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_SamolyukBelandStocks_2016_NiPd__MO_532072268679_000 Supported species : Ni Pd random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Ni (Configuration in file "config-F-Ni.xyz") ----------------------------------------------------------------------------------------------------- Energy = -28.264191697364055 Forces: 1 -6.53768784e+00 -5.61532432e+00 -9.35550255e+00 2 -4.73931976e+00 8.00942065e+00 -4.70468225e+00 3 5.97573278e+00 -5.12798392e+00 5.59425357e+00 4 -5.05986738e+00 5.41959141e+00 4.74868456e+00 5 2.01607474e+00 -1.25388737e+01 -1.15884515e+00 6 6.47636829e+00 6.29660411e+00 -5.91678113e+00 7 3.22830004e+00 -2.65393631e+01 -2.30932756e+01 8 -1.36568846e+01 -9.18217879e+00 -3.68785031e+00 9 -9.17035378e+00 -6.51736782e+00 -1.41110408e+01 10 -4.46853269e+00 1.59774955e+01 -1.56086729e+01 11 -4.17197079e+00 -1.25773400e+01 1.22992519e+01 12 -4.95077110e+00 8.80184113e+00 3.65020295e+00 13 -6.03832518e+00 -1.15088163e+01 -3.44264284e+01 14 5.11256943e+00 7.54555722e+00 -4.25670550e+00 15 3.08627695e+01 -6.63175075e+00 8.08744435e+00 16 4.32329992e+00 2.36267392e+01 1.19254829e+01 17 -8.38963816e+00 -4.66604207e+00 -6.27800920e+00 18 3.39434737e+00 4.83349813e+00 -1.59942043e+00 19 9.22647360e+00 -9.82985358e+00 5.73211509e+00 20 -5.74813627e+00 9.12095788e+00 5.73503915e+00 21 -1.44789722e+01 -6.96833639e+00 1.96137860e+00 22 1.63069332e+01 2.08709632e+01 2.11310121e+01 23 5.57400086e+00 1.41611896e-02 8.26175037e+00 24 -7.84578331e-01 -2.11721578e+00 2.23996572e+00 25 -6.91285643e+00 -5.97153407e+00 6.23170077e-01 26 -5.98984011e+00 1.50438135e+01 -7.94373062e+00 27 1.26246463e+01 -2.86986779e+01 7.35255508e+00 28 -2.24719001e+01 2.01143138e+01 3.88362860e+00 29 -6.61731395e+00 -6.19730931e+00 6.74653723e+00 30 4.65197508e+00 9.82069354e+00 3.25327158e+00 31 1.33291324e+01 -6.05037890e+00 7.88354908e+00 32 7.08432526e+00 1.12426963e+01 1.10316520e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ni (Configuration in file "config-T-Ni.xyz") ----------------------------------------------------------------------------------------------------- Energy = -28.264191697364055 Forces: 1 -6.53768784e+00 -5.61532432e+00 -9.35550255e+00 2 -4.73931976e+00 8.00942065e+00 -4.70468225e+00 3 5.97573278e+00 -5.12798392e+00 5.59425357e+00 4 -5.05986738e+00 5.41959141e+00 4.74868456e+00 5 2.01607474e+00 -1.25388737e+01 -1.15884515e+00 6 6.47636829e+00 6.29660411e+00 -5.91678113e+00 7 3.22830004e+00 -2.65393631e+01 -2.30932756e+01 8 -1.36568846e+01 -9.18217879e+00 -3.68785031e+00 9 -9.17035378e+00 -6.51736782e+00 -1.41110408e+01 10 -4.46853269e+00 1.59774955e+01 -1.56086729e+01 11 -4.17197079e+00 -1.25773400e+01 1.22992519e+01 12 -4.95077110e+00 8.80184113e+00 3.65020295e+00 13 -6.03832518e+00 -1.15088163e+01 -3.44264284e+01 14 5.11256943e+00 7.54555722e+00 -4.25670550e+00 15 3.08627695e+01 -6.63175075e+00 8.08744435e+00 16 4.32329992e+00 2.36267392e+01 1.19254829e+01 17 -8.38963816e+00 -4.66604207e+00 -6.27800920e+00 18 3.39434737e+00 4.83349813e+00 -1.59942043e+00 19 9.22647360e+00 -9.82985358e+00 5.73211509e+00 20 -5.74813627e+00 9.12095788e+00 5.73503915e+00 21 -1.44789722e+01 -6.96833639e+00 1.96137860e+00 22 1.63069332e+01 2.08709632e+01 2.11310121e+01 23 5.57400086e+00 1.41611896e-02 8.26175037e+00 24 -7.84578331e-01 -2.11721578e+00 2.23996572e+00 25 -6.91285643e+00 -5.97153407e+00 6.23170077e-01 26 -5.98984011e+00 1.50438135e+01 -7.94373062e+00 27 1.26246463e+01 -2.86986779e+01 7.35255508e+00 28 -2.24719001e+01 2.01143138e+01 3.88362860e+00 29 -6.61731395e+00 -6.19730931e+00 6.74653723e+00 30 4.65197508e+00 9.82069354e+00 3.25327158e+00 31 1.33291324e+01 -6.05037890e+00 7.88354908e+00 32 7.08432526e+00 1.12426963e+01 1.10316520e+01 MONOATOMIC STRUCTURE (pbc=False)-- Species = Pd (Configuration in file "config-F-Pd.xyz") ----------------------------------------------------------------------------------------------------- Energy = 179.0725294132186 Forces: 1 -1.16369912e+01 -2.99588482e+01 -2.58879850e+01 2 -2.61508104e+01 1.71958672e+01 -5.29558247e+01 3 -1.87980000e+01 -4.38439808e+01 2.63398657e+01 4 -1.99489171e+01 1.71696043e+01 2.46330691e+01 5 1.49000617e+01 -2.87994060e+01 -3.10731064e+01 6 1.85750313e+01 2.23286553e+01 -2.06460685e+01 7 9.05319361e+00 -2.09688655e+01 1.42502959e+01 8 4.97172303e+01 -1.15176130e+01 7.34579134e+00 9 -1.26604574e+01 -1.33914674e+01 -2.76411797e+01 10 1.00120855e+01 1.44880043e+01 -1.62987217e+01 11 -4.57403593e+01 2.58238348e+01 1.36210336e+01 12 -2.68515545e+01 3.24143810e+01 -8.30626153e+00 13 -8.63341047e-01 -1.65096762e+01 -8.43984031e+01 14 2.72869698e+01 2.10016980e+01 -3.48297332e+01 15 5.30162557e+01 -5.64110266e+01 3.15983301e+01 16 -2.97661251e+01 7.88308868e+01 2.25488280e+01 17 -1.80804928e+01 -6.89485357e+00 -7.43495266e+00 18 -1.60294685e+01 8.09055149e-01 4.17657450e+00 19 5.67784548e+00 -2.43679560e+01 2.68137437e+01 20 -4.27847153e+01 -1.49415992e+01 1.28067843e+01 21 8.61954238e+00 -3.17081210e+01 1.07922825e+01 22 2.85685269e+01 -8.82558395e+00 -1.50891091e+01 23 4.88177324e+00 -5.46323155e+00 5.48884067e+00 24 2.46768869e+01 -5.83833562e+01 2.71382262e+01 25 -5.15013185e+01 -3.77686060e+01 2.32529133e+01 26 4.18838379e+01 4.98804003e+01 1.18647987e+01 27 -2.42815484e+01 4.94096770e+01 2.51695087e+01 28 -4.00449791e+00 7.22153957e+00 9.81059175e+00 29 2.73648178e+00 1.07805301e+01 -3.13072133e+01 30 1.68507320e+01 1.66099281e+01 1.19675022e+01 31 3.97580837e+01 9.31890353e+00 3.00080783e+01 32 -7.11594083e+00 3.64712258e+01 1.62415004e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Pd (Configuration in file "config-T-Pd.xyz") ----------------------------------------------------------------------------------------------------- Energy = 179.0725294132186 Forces: 1 -1.16369912e+01 -2.99588482e+01 -2.58879850e+01 2 -2.61508104e+01 1.71958672e+01 -5.29558247e+01 3 -1.87980000e+01 -4.38439808e+01 2.63398657e+01 4 -1.99489171e+01 1.71696043e+01 2.46330691e+01 5 1.49000617e+01 -2.87994060e+01 -3.10731064e+01 6 1.85750313e+01 2.23286553e+01 -2.06460685e+01 7 9.05319361e+00 -2.09688655e+01 1.42502959e+01 8 4.97172303e+01 -1.15176130e+01 7.34579134e+00 9 -1.26604574e+01 -1.33914674e+01 -2.76411797e+01 10 1.00120855e+01 1.44880043e+01 -1.62987217e+01 11 -4.57403593e+01 2.58238348e+01 1.36210336e+01 12 -2.68515545e+01 3.24143810e+01 -8.30626153e+00 13 -8.63341047e-01 -1.65096762e+01 -8.43984031e+01 14 2.72869698e+01 2.10016980e+01 -3.48297332e+01 15 5.30162557e+01 -5.64110266e+01 3.15983301e+01 16 -2.97661251e+01 7.88308868e+01 2.25488280e+01 17 -1.80804928e+01 -6.89485357e+00 -7.43495266e+00 18 -1.60294685e+01 8.09055149e-01 4.17657450e+00 19 5.67784548e+00 -2.43679560e+01 2.68137437e+01 20 -4.27847153e+01 -1.49415992e+01 1.28067843e+01 21 8.61954238e+00 -3.17081210e+01 1.07922825e+01 22 2.85685269e+01 -8.82558395e+00 -1.50891091e+01 23 4.88177324e+00 -5.46323155e+00 5.48884067e+00 24 2.46768869e+01 -5.83833562e+01 2.71382262e+01 25 -5.15013185e+01 -3.77686060e+01 2.32529133e+01 26 4.18838379e+01 4.98804003e+01 1.18647987e+01 27 -2.42815484e+01 4.94096770e+01 2.51695087e+01 28 -4.00449791e+00 7.22153957e+00 9.81059175e+00 29 2.73648178e+00 1.07805301e+01 -3.13072133e+01 30 1.68507320e+01 1.66099281e+01 1.19675022e+01 31 3.97580837e+01 9.31890353e+00 3.00080783e+01 32 -7.11594083e+00 3.64712258e+01 1.62415004e+01 MIXED STRUCTURE (pbc=False)-- Species = Ni Pd (Configuration in file "config-F-NiPd.xyz") ----------------------------------------------------------------------------------------------------- Energy = 138.68811756980068 Forces: 1 -1.19770874e+01 -1.60390127e+01 -2.18057254e+01 2 -1.16922202e+01 -1.24379594e-01 -3.69249573e+01 3 9.14777274e+00 -4.01393781e+01 -1.36711689e+01 4 -5.19817281e+01 3.86013140e+01 -3.39181348e+01 5 9.87081104e+00 -9.77999777e+00 -1.60862347e+01 6 2.69726044e+01 -2.03869439e+01 -1.80865909e+01 7 4.75759729e+00 -1.07324642e+01 -8.13378584e-01 8 5.66775795e+01 -5.98494402e-01 -1.55681390e+01 9 -1.17579654e+01 -6.80271671e-02 -8.14757312e+00 10 1.05615424e+01 7.64276700e+00 -1.85013537e+01 11 -1.09255367e+01 1.24076849e+01 -1.34843901e+01 12 -2.16175445e+01 9.74198801e+00 9.82038595e+00 13 -1.48031709e+01 2.58441925e+01 -2.55879606e+01 14 2.12055154e+01 1.03474420e+01 -1.33644085e+01 15 1.13210183e+01 4.90505143e+00 6.10582513e+00 16 -7.43911784e+00 1.62285123e+01 6.37153916e+00 17 -6.03042271e+01 -5.23455397e+01 2.31197214e+01 18 -6.50673739e+00 3.90089598e+01 5.94348842e+01 19 1.42465148e+01 -2.68439130e+01 3.95427069e+01 20 -2.90588980e+01 -1.79698860e+01 2.50929118e+01 21 2.10589135e+01 -4.89241223e+01 -7.24739900e+00 22 5.60491280e+01 4.06289533e+01 -7.36993961e+01 23 3.49276452e+01 -5.52406173e+01 3.70215041e+01 24 -6.21263948e+01 2.46324315e+01 6.91348392e+01 25 -1.37611574e+01 1.15012793e+01 -2.01619976e+01 26 -9.54732377e+00 2.55293101e+01 1.51825606e+01 27 2.20530653e+01 1.18461480e+01 9.39478571e+00 28 -6.35084400e+00 1.36793167e+01 9.21822853e+00 29 1.63128934e+01 -1.35250206e+01 1.33983191e+01 30 7.26652565e+00 7.71835376e+00 1.03440641e+00 31 3.08742260e+00 5.28617299e+00 6.46611779e+00 32 4.33340393e+00 7.16791917e+00 6.73007247e+00 MIXED STRUCTURE (pbc=True)-- Species = Ni Pd (Configuration in file "config-T-NiPd.xyz") ----------------------------------------------------------------------------------------------------- Energy = 247.73210999273022 Forces: 1 -3.20753718e+01 5.61821820e+00 -1.19173178e+01 2 -6.82594818e+00 -5.31948538e+00 -1.91919800e+01 3 1.77716644e+01 -2.25673876e+01 -5.96238146e+00 4 -4.23984723e+01 4.13710641e+01 -3.27106595e+01 5 2.36517209e+01 8.35099202e+00 -3.79256465e+00 6 2.18798857e+01 -1.90040515e+01 -4.17954539e+00 7 -1.00462915e+01 -8.05992002e+00 -1.38148129e+00 8 5.57927003e+01 7.15046177e-01 -1.40194976e+01 9 -5.30304901e+00 2.21624204e+00 -2.60614715e+00 10 1.21891200e+01 -3.82162462e+01 2.92834482e+00 11 -1.08388319e+01 1.19910653e+01 -1.31449728e+01 12 -1.80632310e+01 -2.04528124e+01 1.91224725e+00 13 -8.85453971e+00 2.40734502e+01 -1.36702595e+01 14 1.97006921e+01 9.78487734e+00 -1.28793980e+01 15 1.53096844e+00 6.32104372e+00 1.04182504e+01 16 -4.25811249e+00 1.06984892e+01 7.28836076e+00 17 -4.59220321e+01 -3.61065640e+01 3.21029942e+01 18 -5.51503149e+00 4.07261215e+01 5.89311098e+01 19 3.04614088e+00 5.14813319e+00 1.50488799e+01 20 -1.88419574e+01 -8.87843234e+00 8.63018166e+00 21 2.19740849e+01 -4.38103235e+01 -9.13568971e+00 22 4.25949610e+01 4.10719984e+01 -7.42191300e+01 23 2.14249746e+01 -5.80606265e+01 3.63457926e+01 24 -6.52373803e+01 2.47303555e+01 5.61849463e+01 25 -2.02307989e+00 1.24624080e+01 -2.36145617e+01 26 -8.07436413e+00 1.71806541e+01 1.39368581e+01 27 1.55237247e+01 1.54915199e+01 -1.10272500e+01 28 -3.89263979e+00 1.06406782e+01 1.14679360e+00 29 1.62786068e+01 -1.36127790e+01 1.33776930e+01 30 -5.58993196e+00 7.79011106e-01 2.08320145e+00 31 -1.51214081e+01 6.83026634e+00 2.63441127e+00 32 3.55224281e+01 -2.21130061e+01 -9.51722859e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==1396813== Memcheck, a memory error detector ==1396813== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==1396813== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info ==1396813== Command: python runner2.py EAM_Dynamo_SamolyukBelandStocks_2016_NiPd__MO_532072268679_000 ==1396813== ==1398771== Warning: invalid file descriptor 1024 in syscall close() ==1398771== Warning: invalid file descriptor 1025 in syscall close() ==1398771== Warning: invalid file descriptor 1026 in syscall close() ==1398771== Warning: invalid file descriptor 1027 in syscall close() ==1398771== Use --log-fd= to select an alternative log fd. ==1398771== Warning: invalid file descriptor 1028 in syscall close() ==1398771== Warning: invalid file descriptor 1029 in syscall close() ==1396813== ==1396813== HEAP SUMMARY: ==1396813== in use at exit: 2,257,767 bytes in 1,704 blocks ==1396813== total heap usage: 82,867 allocs, 81,163 frees, 135,399,974 bytes allocated ==1396813== ==1396813== LEAK SUMMARY: ==1396813== definitely lost: 0 bytes in 0 blocks ==1396813== indirectly lost: 0 bytes in 0 blocks ==1396813== possibly lost: 180,827 bytes in 103 blocks ==1396813== still reachable: 2,076,908 bytes in 1,600 blocks ==1396813== of which reachable via heuristic: ==1396813== stdstring : 38 bytes in 1 blocks ==1396813== suppressed: 32 bytes in 1 blocks ==1396813== Rerun with --leak-check=full to see details of leaked memory ==1396813== ==1396813== For lists of detected and suppressed errors, rerun with: -s ==1396813== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 8024 from 567) ================================================================================ 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.