!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_Wen_2021_FeH__MO_634187028437_000 Supported species : Fe H 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 = 1.9001582622174533 Forces: 1 -6.67015338e+00 -5.62688958e+00 -1.07267723e+01 2 -1.01833121e+01 1.72899648e+01 -7.41404945e+00 3 9.97502990e+00 -9.68028071e+00 1.07944869e+00 4 -6.45306546e+00 8.50548549e+00 3.70205232e+00 5 1.21993852e+01 -2.04414441e+01 1.82762894e+00 6 2.47762386e+00 1.26460060e+00 -3.44253626e+00 7 3.55538635e+00 -3.17123752e+01 -3.60873281e+01 8 -1.70581663e+01 -1.28187768e+01 -1.06408480e+01 9 -1.05158661e+01 -7.68821709e+00 -1.79062550e+01 10 -5.55677599e+00 1.79042334e+01 -1.98186600e+01 11 -4.35469828e+00 -1.48250158e+01 1.59549652e+01 12 -7.60058891e+00 1.03500518e+01 8.15255203e+00 13 -1.01670889e+01 -1.43611023e+01 -4.61036538e+01 14 5.46757518e+00 7.14051913e+00 -4.47677280e+00 15 4.07202639e+01 -2.49022978e+00 1.57404789e+01 16 4.97093958e+00 2.84867979e+01 1.81095685e+01 17 -1.43711785e+01 -9.56937602e+00 -5.77465354e+00 18 6.96579749e+00 1.04930931e+01 -3.11477443e+00 19 4.40192258e+00 -9.00159430e+00 8.14727404e+00 20 -3.35215920e+00 8.29651335e+00 1.06825395e+01 21 -1.55470727e+01 -1.06275952e+01 6.71193926e+00 22 2.40903636e+01 2.38426595e+01 2.56117036e+01 23 8.16340963e+00 -3.85371007e+00 9.05451870e+00 24 -5.57302535e+00 7.41188621e-01 4.96690647e+00 25 -8.41954423e+00 -8.25176225e+00 -8.61350565e+00 26 -4.46690483e+00 1.54612654e+01 -9.64958222e+00 27 2.17967931e+01 -3.73319362e+01 1.59271862e+01 28 -3.34796406e+01 3.16561740e+01 4.44960781e+00 29 -8.97936259e+00 1.09013099e+00 1.21242652e+01 30 5.68965313e+00 9.96166744e+00 -1.79875057e+00 31 1.43429859e+01 -6.11106923e+00 1.11059943e+01 32 7.93147385e+00 1.19070291e+01 1.22195127e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Fe (Configuration in file "config-T-Fe.xyz") ----------------------------------------------------------------------------------------------------- Energy = 1.9001582622174533 Forces: 1 -6.67015338e+00 -5.62688958e+00 -1.07267723e+01 2 -1.01833121e+01 1.72899648e+01 -7.41404945e+00 3 9.97502990e+00 -9.68028071e+00 1.07944869e+00 4 -6.45306546e+00 8.50548549e+00 3.70205232e+00 5 1.21993852e+01 -2.04414441e+01 1.82762894e+00 6 2.47762386e+00 1.26460060e+00 -3.44253626e+00 7 3.55538635e+00 -3.17123752e+01 -3.60873281e+01 8 -1.70581663e+01 -1.28187768e+01 -1.06408480e+01 9 -1.05158661e+01 -7.68821709e+00 -1.79062550e+01 10 -5.55677599e+00 1.79042334e+01 -1.98186600e+01 11 -4.35469828e+00 -1.48250158e+01 1.59549652e+01 12 -7.60058891e+00 1.03500518e+01 8.15255203e+00 13 -1.01670889e+01 -1.43611023e+01 -4.61036538e+01 14 5.46757518e+00 7.14051913e+00 -4.47677280e+00 15 4.07202639e+01 -2.49022978e+00 1.57404789e+01 16 4.97093958e+00 2.84867979e+01 1.81095685e+01 17 -1.43711785e+01 -9.56937602e+00 -5.77465354e+00 18 6.96579749e+00 1.04930931e+01 -3.11477443e+00 19 4.40192258e+00 -9.00159430e+00 8.14727404e+00 20 -3.35215920e+00 8.29651335e+00 1.06825395e+01 21 -1.55470727e+01 -1.06275952e+01 6.71193926e+00 22 2.40903636e+01 2.38426595e+01 2.56117036e+01 23 8.16340963e+00 -3.85371007e+00 9.05451870e+00 24 -5.57302535e+00 7.41188621e-01 4.96690647e+00 25 -8.41954423e+00 -8.25176225e+00 -8.61350565e+00 26 -4.46690483e+00 1.54612654e+01 -9.64958222e+00 27 2.17967931e+01 -3.73319362e+01 1.59271862e+01 28 -3.34796406e+01 3.16561740e+01 4.44960781e+00 29 -8.97936259e+00 1.09013099e+00 1.21242652e+01 30 5.68965313e+00 9.96166744e+00 -1.79875057e+00 31 1.43429859e+01 -6.11106923e+00 1.11059943e+01 32 7.93147385e+00 1.19070291e+01 1.22195127e+01 MONOATOMIC STRUCTURE (pbc=False)-- Species = H (Configuration in file "config-F-H.xyz") ----------------------------------------------------------------------------------------------------- Energy = -19.488418689735127 Forces: 1 -1.96237280e-01 -1.71227124e-01 -2.05602537e-01 2 -3.43137891e+00 3.66622144e+00 1.17253340e+00 3 -9.42914162e-01 1.76087496e+00 7.20663504e-01 4 2.57999287e+00 -2.50557862e+00 2.87922725e+00 5 2.30425852e+00 2.07934364e+00 3.35187540e+00 6 -3.37952722e+00 -1.47227621e+00 4.45193843e+00 7 -3.70857613e+00 3.98656766e+00 -3.18656156e+00 8 4.07568858e+00 -1.90457993e+00 -1.10537315e+00 9 3.46045946e+00 -2.74811873e+00 6.98570985e-02 10 9.30768013e-01 4.12395271e-01 3.37657846e+00 11 7.19905020e-01 -3.53161218e+00 2.03218274e+00 12 1.64325630e+00 -7.16063342e-02 -1.08443084e+00 13 4.20925653e+00 1.69745338e+00 2.29712205e+00 14 -4.53112821e+00 -4.14271165e+00 3.03596205e+00 15 -1.58599319e+00 1.97551963e+00 9.92648735e-01 16 8.96736382e-01 -1.36467338e+00 -3.81456664e+00 17 2.13590577e+00 3.98172923e+00 7.46586081e-01 18 -8.13806657e-01 4.16163834e+00 -6.02726047e-01 19 -1.71376921e+00 3.18817787e+00 -1.81084148e+00 20 3.79120698e+00 -3.84274795e+00 -2.80925507e+00 21 3.03388073e+00 1.88291701e+00 2.49172394e+00 22 -4.59984462e+00 2.57511455e+00 -1.86702876e+00 23 -4.11513046e+00 2.76563017e+00 -2.06133830e+00 24 8.12205776e-01 -2.32643285e+00 -2.74451061e+00 25 4.26838031e+00 3.22434253e+00 2.83485359e+00 26 -2.33680309e+00 -2.99250399e+00 1.99203018e+00 27 5.69349616e-01 4.02740852e-01 -3.64771709e+00 28 9.71616544e-01 -1.49239558e+00 -2.50137712e+00 29 6.89242886e-01 -3.33416173e+00 3.39010598e-01 30 -1.77710512e+00 -3.00973778e+00 -2.84651086e+00 31 -2.06580064e+00 -1.45028397e+00 -1.31096029e+00 32 -1.89409540e+00 -1.40001855e+00 -1.18599315e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = H (Configuration in file "config-T-H.xyz") ----------------------------------------------------------------------------------------------------- Energy = -19.488418689735127 Forces: 1 -1.96237280e-01 -1.71227124e-01 -2.05602537e-01 2 -3.43137891e+00 3.66622144e+00 1.17253340e+00 3 -9.42914162e-01 1.76087496e+00 7.20663504e-01 4 2.57999287e+00 -2.50557862e+00 2.87922725e+00 5 2.30425852e+00 2.07934364e+00 3.35187540e+00 6 -3.37952722e+00 -1.47227621e+00 4.45193843e+00 7 -3.70857613e+00 3.98656766e+00 -3.18656156e+00 8 4.07568858e+00 -1.90457993e+00 -1.10537315e+00 9 3.46045946e+00 -2.74811873e+00 6.98570985e-02 10 9.30768013e-01 4.12395271e-01 3.37657846e+00 11 7.19905020e-01 -3.53161218e+00 2.03218274e+00 12 1.64325630e+00 -7.16063342e-02 -1.08443084e+00 13 4.20925653e+00 1.69745338e+00 2.29712205e+00 14 -4.53112821e+00 -4.14271165e+00 3.03596205e+00 15 -1.58599319e+00 1.97551963e+00 9.92648735e-01 16 8.96736382e-01 -1.36467338e+00 -3.81456664e+00 17 2.13590577e+00 3.98172923e+00 7.46586081e-01 18 -8.13806657e-01 4.16163834e+00 -6.02726047e-01 19 -1.71376921e+00 3.18817787e+00 -1.81084148e+00 20 3.79120698e+00 -3.84274795e+00 -2.80925507e+00 21 3.03388073e+00 1.88291701e+00 2.49172394e+00 22 -4.59984462e+00 2.57511455e+00 -1.86702876e+00 23 -4.11513046e+00 2.76563017e+00 -2.06133830e+00 24 8.12205776e-01 -2.32643285e+00 -2.74451061e+00 25 4.26838031e+00 3.22434253e+00 2.83485359e+00 26 -2.33680309e+00 -2.99250399e+00 1.99203018e+00 27 5.69349616e-01 4.02740852e-01 -3.64771709e+00 28 9.71616544e-01 -1.49239558e+00 -2.50137712e+00 29 6.89242886e-01 -3.33416173e+00 3.39010598e-01 30 -1.77710512e+00 -3.00973778e+00 -2.84651086e+00 31 -2.06580064e+00 -1.45028397e+00 -1.31096029e+00 32 -1.89409540e+00 -1.40001855e+00 -1.18599315e+00 MIXED STRUCTURE (pbc=False)-- Species = Fe H (Configuration in file "config-F-FeH.xyz") ----------------------------------------------------------------------------------------------------- Energy = -46.457593130668606 Forces: 1 2.04248128e+00 1.76008564e+00 1.51697500e+00 2 -8.77306901e-01 -5.74492498e-01 -2.61337033e-01 3 9.49771097e-01 -4.01635738e+00 -4.98495581e+00 4 -2.12382359e+00 1.48421064e+00 -1.37225503e+00 5 -5.12568141e+00 -1.22868537e-01 -2.51016431e+00 6 4.08815954e+00 1.62916736e+00 -2.34752897e+00 7 3.14709542e+00 -4.75827238e+00 4.87514481e+00 8 4.76270185e+00 -2.33137851e+00 -2.51702740e+00 9 -3.43760318e+00 -4.69819040e+00 -3.48377395e+00 10 3.76473010e+00 3.44831578e+00 -6.82769886e+00 11 -7.91604682e+00 -1.90286018e+00 -1.70942223e+01 12 -5.95453945e+00 3.61454299e+00 5.56034043e+00 13 -7.20013012e+00 -6.50511179e+00 -5.03858550e+00 14 2.23985404e+01 5.33652805e+00 -1.66526837e+01 15 1.43102539e-01 4.91495512e-02 -2.33203808e-01 16 -1.33594543e+01 8.30000730e+00 1.74981860e+01 17 -6.01612597e-01 -1.02224412e+00 2.87801274e+00 18 1.61576706e+00 -1.03290521e+01 7.47553596e+00 19 8.10073554e-02 1.95671518e+00 -1.71223557e+00 20 -1.26453045e+01 -2.04149912e+01 1.32532825e+01 21 7.79841817e-01 -7.08018177e-01 1.26810680e+00 22 1.65532279e+00 -1.15994690e+00 3.27821728e+00 23 -9.31579411e-01 1.88743659e+00 -9.26264058e-01 24 9.18811723e-02 -1.03503179e+00 -4.65694853e-01 25 -9.23700488e+00 8.91385524e+00 -5.53469792e+00 26 -8.03711097e+00 1.88718981e+01 1.46336498e+01 27 1.50991789e+01 1.21910741e+01 -2.01545084e+00 28 8.74195624e-01 -1.30329535e+00 -1.72467089e+00 29 1.87709074e+01 -6.26372628e+00 7.59553965e+00 30 -1.08525651e+00 -2.46964417e+00 6.51628228e-01 31 -6.62386566e-01 7.89517732e-01 -2.63393532e+00 32 -1.06984314e+00 -6.17022473e-01 -2.14823302e+00 MIXED STRUCTURE (pbc=True)-- Species = Fe H (Configuration in file "config-T-FeH.xyz") ----------------------------------------------------------------------------------------------------- Energy = -49.48735444375654 Forces: 1 -5.16343077e-01 -1.92490678e-01 -4.86308013e-01 2 -4.24524023e-01 3.01488293e-01 -8.47266282e-01 3 2.79456587e+00 -3.70247594e+00 -5.07212068e+00 4 -3.13249801e+00 3.25221167e+00 -1.02629592e+00 5 -3.83415258e+00 1.28127567e+01 -8.07538733e+00 6 3.57547050e+00 7.61336130e-01 -3.53732045e+00 7 5.24523135e+00 1.48426087e+00 7.55422983e+00 8 5.03733857e+00 -2.05674587e+00 -2.15779077e+00 9 -3.36201794e+00 -3.65311695e+00 -3.33475108e+00 10 -1.76222172e+00 -1.56203169e+00 -9.42358144e+00 11 -7.82525415e+00 -1.78852970e+00 -1.69064606e+01 12 -4.01673773e+00 3.01081034e+00 6.54821354e+00 13 -7.19387538e+00 -6.29728091e+00 -6.29955426e+00 14 2.37494866e+01 1.69300428e+00 -2.14491065e+01 15 4.49831004e-01 -3.27883996e-01 2.69965275e-02 16 -1.43697929e+01 -1.24003396e+00 2.28675306e+01 17 -2.04085282e+00 -2.48836743e+00 4.09342495e+00 18 1.82489931e+00 -9.22488464e+00 7.54170547e+00 19 2.05089498e-01 -9.37934540e-02 -1.57149258e-02 20 -1.28863367e+01 -2.19010987e+01 1.35121371e+01 21 1.62807315e+00 -1.09732068e+00 7.46936710e-01 22 1.57140943e+00 -1.19156559e+00 2.39067476e+00 23 2.70932456e-01 -7.42633777e-02 -6.05057662e-01 24 -6.58446624e-01 -1.64519014e-01 1.25751767e+00 25 -9.70541240e+00 9.43598002e+00 -5.89912645e+00 26 -8.33443996e+00 1.94672677e+01 1.39761900e+01 27 1.54931083e+01 1.24485377e+01 -2.67470480e+00 28 -2.52864060e-01 -7.50136811e-01 -3.09037205e-01 29 1.81667294e+01 -7.13013810e+00 7.16966178e+00 30 4.43163988e-01 4.64454509e-01 -9.36191413e-02 31 3.87101650e-01 -3.52891421e-01 1.07554120e-01 32 -5.26660985e-01 1.57460795e-01 4.20430299e-01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==1290== Memcheck, a memory error detector ==1290== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==1290== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info ==1290== Command: python runner2.py EAM_Dynamo_Wen_2021_FeH__MO_634187028437_000 ==1290== ==1858== Warning: invalid file descriptor 4096 in syscall close() ==1858== Warning: invalid file descriptor 4097 in syscall close() ==1858== Warning: invalid file descriptor 4098 in syscall close() ==1858== Warning: invalid file descriptor 4099 in syscall close() ==1858== Use --log-fd= to select an alternative log fd. ==1858== Warning: invalid file descriptor 4100 in syscall close() ==1858== Warning: invalid file descriptor 4101 in syscall close() ==1290== ==1290== HEAP SUMMARY: ==1290== in use at exit: 2,203,207 bytes in 1,644 blocks ==1290== total heap usage: 86,322 allocs, 84,678 frees, 172,604,942 bytes allocated ==1290== ==1290== LEAK SUMMARY: ==1290== definitely lost: 0 bytes in 0 blocks ==1290== indirectly lost: 0 bytes in 0 blocks ==1290== possibly lost: 198,622 bytes in 101 blocks ==1290== still reachable: 2,004,553 bytes in 1,542 blocks ==1290== suppressed: 32 bytes in 1 blocks ==1290== Rerun with --leak-check=full to see details of leaked memory ==1290== ==1290== For lists of detected and suppressed errors, rerun with: -s ==1290== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 9130 from 550) ================================================================================ 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.