!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : Tersoff_LAMMPS_ZhangNguyen_2021_MoSe__MO_152208847456_001 Supported species : Mo Se random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Mo (Configuration in file "config-F-Mo.xyz") ----------------------------------------------------------------------------------------------------- Energy = 310.93794472069294 Forces: 1 -2.48014240e+01 -2.69206264e+01 -4.15811659e+01 2 -2.55956339e+01 3.77749758e+01 -2.72128011e+01 3 8.78304374e+00 -2.34314845e+01 3.02149692e+01 4 -2.02000991e+01 1.83219077e+01 1.44295099e+01 5 1.10857114e+01 -5.94422292e+01 -1.66551453e+01 6 3.62538253e+01 1.93530125e+01 -3.54559502e+01 7 1.42249961e+01 -1.16094095e+02 -9.96829687e+01 8 -6.52720159e+01 -6.35171848e+01 1.72504420e+01 9 -7.94016743e+00 -5.59257044e+01 -5.91247632e+01 10 -1.53249912e+01 4.22324458e+01 -6.04190671e+01 11 6.92790070e+01 -5.51977011e+01 -8.21876813e+01 12 -4.24627916e+01 6.75631320e+01 3.46912313e+01 13 -5.16614633e+01 -2.39373129e+01 -1.60521059e+02 14 2.37831849e+01 2.78333555e+01 -1.52572031e+01 15 1.52700338e+02 5.54691098e+00 5.31543717e+01 16 2.87919786e+01 1.01999582e+02 4.99661017e+01 17 -4.30977961e+01 -3.14315771e+01 -2.58962035e+01 18 2.67559725e+01 3.01402918e+01 -2.28137113e+01 19 2.64859231e+01 -4.15043967e+01 3.63196788e+01 20 -2.38407079e+01 2.64575722e+01 3.07050710e+01 21 -5.96921462e+01 -3.28954483e+01 1.37607339e+01 22 7.00308179e+01 1.00815220e+02 9.01534200e+01 23 2.35409455e+01 -3.82281620e+00 3.62625861e+01 24 1.59734431e+00 -4.61750753e+00 1.49060622e+01 25 -1.32020277e+02 6.96827164e+00 8.92864376e+01 26 -2.67676649e+01 6.99174836e+01 -2.54051122e+01 27 5.54851501e+01 -1.32891005e+02 3.28593129e+01 28 -1.13769803e+02 9.75260714e+01 1.05251984e+01 29 -9.40433530e+00 -4.47933739e+01 2.46081041e+01 30 2.51980818e+01 3.88456383e+01 3.27617699e+00 31 5.61168995e+01 -2.66322391e+01 3.80718805e+01 32 3.17380966e+01 5.17588310e+01 5.17715431e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Mo (Configuration in file "config-T-Mo.xyz") ----------------------------------------------------------------------------------------------------- Energy = 310.93794472069294 Forces: 1 -2.48014240e+01 -2.69206264e+01 -4.15811659e+01 2 -2.55956339e+01 3.77749758e+01 -2.72128011e+01 3 8.78304374e+00 -2.34314845e+01 3.02149692e+01 4 -2.02000991e+01 1.83219077e+01 1.44295099e+01 5 1.10857114e+01 -5.94422292e+01 -1.66551453e+01 6 3.62538253e+01 1.93530125e+01 -3.54559502e+01 7 1.42249961e+01 -1.16094095e+02 -9.96829687e+01 8 -6.52720159e+01 -6.35171848e+01 1.72504420e+01 9 -7.94016743e+00 -5.59257044e+01 -5.91247632e+01 10 -1.53249912e+01 4.22324458e+01 -6.04190671e+01 11 6.92790070e+01 -5.51977011e+01 -8.21876813e+01 12 -4.24627916e+01 6.75631320e+01 3.46912313e+01 13 -5.16614633e+01 -2.39373129e+01 -1.60521059e+02 14 2.37831849e+01 2.78333555e+01 -1.52572031e+01 15 1.52700338e+02 5.54691098e+00 5.31543717e+01 16 2.87919786e+01 1.01999582e+02 4.99661017e+01 17 -4.30977961e+01 -3.14315771e+01 -2.58962035e+01 18 2.67559725e+01 3.01402918e+01 -2.28137113e+01 19 2.64859231e+01 -4.15043967e+01 3.63196788e+01 20 -2.38407079e+01 2.64575722e+01 3.07050710e+01 21 -5.96921462e+01 -3.28954483e+01 1.37607339e+01 22 7.00308179e+01 1.00815220e+02 9.01534200e+01 23 2.35409455e+01 -3.82281620e+00 3.62625861e+01 24 1.59734431e+00 -4.61750753e+00 1.49060622e+01 25 -1.32020277e+02 6.96827164e+00 8.92864376e+01 26 -2.67676649e+01 6.99174836e+01 -2.54051122e+01 27 5.54851501e+01 -1.32891005e+02 3.28593129e+01 28 -1.13769803e+02 9.75260714e+01 1.05251984e+01 29 -9.40433530e+00 -4.47933739e+01 2.46081041e+01 30 2.51980818e+01 3.88456383e+01 3.27617699e+00 31 5.61168995e+01 -2.66322391e+01 3.80718805e+01 32 3.17380966e+01 5.17588310e+01 5.17715431e+01 MONOATOMIC STRUCTURE (pbc=False)-- Species = Se (Configuration in file "config-F-Se.xyz") ----------------------------------------------------------------------------------------------------- Energy = 85.10219299130505 Forces: 1 -1.20975096e+01 -1.53218992e+01 -1.43713332e+01 2 1.83534108e+01 -1.54172279e+01 -1.93195465e+01 3 1.40843480e+01 -4.89825960e+01 -1.74195940e+01 4 -3.58944013e+01 1.17817800e+01 -1.78028830e+01 5 -4.04206234e+01 -1.78639867e+01 -3.83454957e+01 6 2.77030747e+01 5.07027372e+00 -1.36688713e+01 7 4.26759108e+01 -1.50340835e+01 3.47863100e+01 8 2.30197182e+01 2.71057556e+01 -6.01481025e+01 9 -3.33061207e+01 1.03824373e+01 -2.15130555e+01 10 9.49583386e+00 1.00081368e+01 -1.28057770e+01 11 2.91037580e+01 2.62625771e+01 -1.47044444e+01 12 -1.33246038e+01 9.05964296e+00 8.01796818e+00 13 -1.43010739e+01 1.45683858e+01 -1.17855004e+01 14 1.02501439e+01 1.30283082e+01 -4.89308389e+00 15 4.46534590e+01 -1.98295620e+01 -1.37051100e+01 16 -2.15835361e+01 4.17220472e+01 -9.08699935e+00 17 -2.56986932e+01 -2.94296669e+01 1.06580654e+01 18 -2.98762794e+01 7.97435071e+00 4.91997119e+01 19 1.39237504e+01 -1.34258676e+01 5.07282335e+00 20 -1.58862031e+01 2.17877571e+01 1.62533684e+01 21 1.31003027e+01 -6.19376819e+01 4.55505120e+01 22 3.02185367e+01 2.47098354e+01 -3.33872343e+01 23 4.04001224e+00 -3.88994030e+01 3.60668102e+01 24 -1.67652418e+01 -8.48218727e+00 2.35775934e+01 25 -3.40956270e+01 1.18931575e+01 2.08603474e+01 26 3.94087992e+00 2.19614322e+01 -1.21384634e+01 27 7.45332508e+00 -1.46567871e+01 2.22078375e+01 28 -2.24346603e+01 1.24212255e+01 8.25305249e+00 29 -2.18480819e+00 8.84695574e+00 1.87376838e+01 30 9.81784323e+00 6.15756714e+00 -5.04965220e+00 31 2.20506030e+01 1.32820040e+00 1.09301887e+01 32 -6.01552876e+00 1.32111228e+01 9.97287383e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Se (Configuration in file "config-T-Se.xyz") ----------------------------------------------------------------------------------------------------- Energy = 85.10219299130505 Forces: 1 -1.20975096e+01 -1.53218992e+01 -1.43713332e+01 2 1.83534108e+01 -1.54172279e+01 -1.93195465e+01 3 1.40843480e+01 -4.89825960e+01 -1.74195940e+01 4 -3.58944013e+01 1.17817800e+01 -1.78028830e+01 5 -4.04206234e+01 -1.78639867e+01 -3.83454957e+01 6 2.77030747e+01 5.07027372e+00 -1.36688713e+01 7 4.26759108e+01 -1.50340835e+01 3.47863100e+01 8 2.30197182e+01 2.71057556e+01 -6.01481025e+01 9 -3.33061207e+01 1.03824373e+01 -2.15130555e+01 10 9.49583386e+00 1.00081368e+01 -1.28057770e+01 11 2.91037580e+01 2.62625771e+01 -1.47044444e+01 12 -1.33246038e+01 9.05964296e+00 8.01796818e+00 13 -1.43010739e+01 1.45683858e+01 -1.17855004e+01 14 1.02501439e+01 1.30283082e+01 -4.89308389e+00 15 4.46534590e+01 -1.98295620e+01 -1.37051100e+01 16 -2.15835361e+01 4.17220472e+01 -9.08699935e+00 17 -2.56986932e+01 -2.94296669e+01 1.06580654e+01 18 -2.98762794e+01 7.97435071e+00 4.91997119e+01 19 1.39237504e+01 -1.34258676e+01 5.07282335e+00 20 -1.58862031e+01 2.17877571e+01 1.62533684e+01 21 1.31003027e+01 -6.19376819e+01 4.55505120e+01 22 3.02185367e+01 2.47098354e+01 -3.33872343e+01 23 4.04001224e+00 -3.88994030e+01 3.60668102e+01 24 -1.67652418e+01 -8.48218727e+00 2.35775934e+01 25 -3.40956270e+01 1.18931575e+01 2.08603474e+01 26 3.94087992e+00 2.19614322e+01 -1.21384634e+01 27 7.45332508e+00 -1.46567871e+01 2.22078375e+01 28 -2.24346603e+01 1.24212255e+01 8.25305249e+00 29 -2.18480819e+00 8.84695574e+00 1.87376838e+01 30 9.81784323e+00 6.15756714e+00 -5.04965220e+00 31 2.20506030e+01 1.32820040e+00 1.09301887e+01 32 -6.01552876e+00 1.32111228e+01 9.97287383e+00 MIXED STRUCTURE (pbc=False)-- Species = Mo Se (Configuration in file "config-F-MoSe.xyz") ----------------------------------------------------------------------------------------------------- Energy = 228.66346316707737 Forces: 1 -1.41127179e+01 -9.86387793e+00 -1.32805779e+01 2 -3.82913577e+01 -2.77003208e+01 -2.71815547e+01 3 -2.30910437e+01 -4.26415949e+01 -1.51984255e+00 4 -3.97208729e+01 -1.63763181e+01 -4.08335447e+01 5 1.77048480e+01 -3.07329166e+01 -3.60567309e+01 6 6.10758619e+01 -7.44944353e-01 -4.20504081e+01 7 3.09302129e+01 -4.81426333e+01 -1.67185277e+01 8 -3.07126009e+01 3.68330795e+01 2.22503156e+01 9 -3.53615416e+01 -2.65641349e+00 -3.57840947e+01 10 4.20200278e+01 3.31372623e+01 -7.85855167e+01 11 1.44389442e+01 -1.25102625e+01 4.05418518e+01 12 -7.08674735e+01 2.06308766e+01 5.17943984e+01 13 2.47780085e+01 5.02260869e+01 -4.12118970e+01 14 1.80833271e+01 1.46807097e+01 -2.15014818e+01 15 2.18618032e+01 -2.39706008e+01 -6.02160496e+00 16 -1.57862997e+01 2.94875801e+01 9.81299378e+00 17 -4.20159074e+01 -3.55073029e+01 -9.50745803e+00 18 3.45898500e+01 2.47533633e+01 2.28641375e+01 19 2.89071994e+01 -2.99054154e+01 2.58749820e+01 20 -3.12699321e+01 1.66781434e+01 1.92345150e+01 21 -1.23816049e+01 -6.20133170e+01 9.30571013e+00 22 3.56438525e+01 2.83237580e+01 8.18564133e+00 23 5.91030955e+01 -6.17884346e+01 3.72060082e+01 24 -4.19818589e+01 5.12750732e+01 2.98873924e+01 25 -2.26657455e+01 3.19900135e+01 2.46481465e+01 26 5.69270030e+01 2.28993617e+01 -5.19960023e+01 27 7.79871828e+00 1.32962877e+01 1.47206404e+01 28 -5.51689816e+01 -7.32212933e+00 6.61798156e+01 29 -2.94787700e+01 -9.63097560e+00 -1.79220695e+01 30 3.62861360e+01 3.23275201e+01 -2.12827937e+00 31 4.09867777e+01 -3.77643693e+01 3.64537131e+01 32 -2.82289575e+01 5.27327111e+01 2.33393292e+01 MIXED STRUCTURE (pbc=True)-- Species = Mo Se (Configuration in file "config-T-MoSe.xyz") ----------------------------------------------------------------------------------------------------- Energy = 398.8944944476858 Forces: 1 -2.33584825e+01 1.29721716e+01 3.35960689e+00 2 -2.79305518e+01 -3.95841160e+01 1.35585417e+01 3 -2.67417334e+01 -1.55207426e+00 1.25936661e+01 4 6.34234779e+00 -4.88392656e+00 -5.56386192e+01 5 1.58349617e+01 -1.07703673e+01 -3.31474726e+01 6 2.04745822e+01 -9.74663456e+00 -3.95009031e+01 7 1.59352501e+01 -2.42802541e+01 3.02058812e+00 8 -3.05274651e+01 3.78433906e+01 2.05898667e+01 9 -2.14300133e+01 3.23599796e+01 1.12894880e+00 10 6.01233351e+01 -1.33707841e+01 -5.20395234e+01 11 1.50332549e+01 -1.21788354e+01 4.23786809e+01 12 -4.71791079e+01 -1.30579750e+00 6.46975737e+01 13 3.64544046e+01 5.22716029e+01 -1.34883037e+01 14 -4.32273714e+00 -1.21298931e+01 -4.28054096e+01 15 1.36947758e+01 -2.36823424e+01 -7.43586185e+00 16 -7.31505105e+00 -1.49472463e+01 1.21898317e+01 17 5.63825095e+00 -4.86809048e+01 3.61951165e+00 18 3.42733006e+01 2.33175741e+01 2.39278412e+01 19 4.75904218e+01 9.04390385e+00 -1.41968537e+01 20 -2.84088250e+01 -3.15046630e-01 -2.61594982e+01 21 -1.23137321e+01 -3.94927107e+01 5.14876956e+00 22 -5.09471310e+01 4.50303725e+01 1.75961038e+01 23 6.03838320e+01 -4.60498340e+01 3.34465901e+01 24 -3.80786686e+01 4.98131176e+01 1.17993591e+01 25 5.38006626e+00 3.40060027e+01 2.57909958e+01 26 6.19847992e+01 -8.15394195e+00 -5.76212652e+01 27 3.16920535e-01 2.99870763e+01 -3.75819004e+01 28 -7.06718228e+01 -2.79347461e+01 4.18582604e+01 29 -2.90506672e+01 -9.46899644e+00 -1.66337812e+01 30 1.70050206e+01 3.51441837e+01 -1.37776666e+00 31 3.54982946e+01 -3.57044485e+01 3.17349274e+01 32 -3.36878299e+01 2.24435255e+01 2.91874954e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==1819526== Memcheck, a memory error detector ==1819526== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==1819526== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info ==1819526== Command: python runner2.py Tersoff_LAMMPS_ZhangNguyen_2021_MoSe__MO_152208847456_001 ==1819526== ==1820811== Warning: invalid file descriptor 1024 in syscall close() ==1820811== Warning: invalid file descriptor 1025 in syscall close() ==1820811== Warning: invalid file descriptor 1026 in syscall close() ==1820811== Warning: invalid file descriptor 1027 in syscall close() ==1820811== Use --log-fd= to select an alternative log fd. ==1820811== Warning: invalid file descriptor 1028 in syscall close() ==1820811== Warning: invalid file descriptor 1029 in syscall close() ==1819526== ==1819526== HEAP SUMMARY: ==1819526== in use at exit: 2,257,703 bytes in 1,703 blocks ==1819526== total heap usage: 88,560 allocs, 86,857 frees, 67,563,815 bytes allocated ==1819526== ==1819526== LEAK SUMMARY: ==1819526== definitely lost: 0 bytes in 0 blocks ==1819526== indirectly lost: 0 bytes in 0 blocks ==1819526== possibly lost: 180,827 bytes in 103 blocks ==1819526== still reachable: 2,076,844 bytes in 1,599 blocks ==1819526== of which reachable via heuristic: ==1819526== stdstring : 38 bytes in 1 blocks ==1819526== suppressed: 32 bytes in 1 blocks ==1819526== Rerun with --leak-check=full to see details of leaked memory ==1819526== ==1819526== For lists of detected and suppressed errors, rerun with: -s ==1819526== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 8029 from 557) ================================================================================ 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.