!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_DawLawsonBauschlicher_2011pot2_ZrB__MO_728716510644_000 Supported species : B Zr random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = B (Configuration in file "config-F-B.xyz") ----------------------------------------------------------------------------------------------------- Energy = -144.5544129925315 Forces: 1 4.33953796e+00 2.57790654e+00 1.59909033e+00 2 -2.81720436e+00 1.70522190e+00 4.03605862e+00 3 -2.36422388e+00 3.44204282e+00 -2.54437480e+00 4 4.97917957e+00 2.98964621e-01 2.64072012e-01 5 1.28905341e+00 3.12460747e+00 2.82804159e+00 6 -3.89511304e+00 -6.89787331e-01 4.21662725e+00 7 -2.07434648e+00 -4.93189767e+00 -9.50811386e+00 8 -2.16046828e-01 -3.68232303e+00 -3.66001282e+00 9 1.99209082e+00 -2.19141800e+00 3.13266433e+00 10 -1.62784476e+00 -2.50333744e+00 3.20964762e+00 11 -1.43812668e+00 -1.67364321e+00 -1.14157065e+00 12 3.14910339e+00 -1.83548497e+00 -1.86167364e+00 13 -2.98462158e+00 -9.44437003e-01 -3.69078485e+00 14 -4.68320027e+00 -2.69254222e+00 3.63484590e+00 15 2.87641737e+00 4.50397949e+00 1.28623867e+00 16 4.37135235e+00 1.16144503e+00 -7.63280085e-01 17 1.53025797e+00 1.80938919e+00 1.13303739e+00 18 -8.56027454e-01 1.33638335e+00 7.31770347e-01 19 1.05589821e+00 3.07470038e+00 -2.35904343e+00 20 3.28213694e+00 5.19449000e-02 -2.52714006e+00 21 -1.60041601e+00 2.90618562e+00 3.71178361e+00 22 2.93754567e+00 5.95574869e-01 8.50353786e+00 23 -5.38753804e+00 3.28179230e+00 -2.75977419e+00 24 3.22784568e+00 -3.24257883e+00 -3.79254098e+00 25 8.44898597e-01 1.74523342e-01 2.06004256e+00 26 -8.88656568e-01 -2.26463092e+00 5.04339652e-01 27 9.95894162e-02 -2.59806211e+00 -2.10648807e+00 28 1.27544610e+00 -8.48305615e-01 -2.85733796e+00 29 -5.51392307e-01 2.81815813e+00 6.23871121e-01 30 -3.47329285e+00 -2.34027438e+00 -5.59842071e-01 31 -1.23759264e+00 8.08939542e-01 7.68087460e-01 32 -1.15470971e+00 -1.23303677e+00 -2.11177887e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = B (Configuration in file "config-T-B.xyz") ----------------------------------------------------------------------------------------------------- Energy = -144.5544129925315 Forces: 1 4.33953796e+00 2.57790654e+00 1.59909033e+00 2 -2.81720436e+00 1.70522190e+00 4.03605862e+00 3 -2.36422388e+00 3.44204282e+00 -2.54437480e+00 4 4.97917957e+00 2.98964621e-01 2.64072012e-01 5 1.28905341e+00 3.12460747e+00 2.82804159e+00 6 -3.89511304e+00 -6.89787331e-01 4.21662725e+00 7 -2.07434648e+00 -4.93189767e+00 -9.50811386e+00 8 -2.16046828e-01 -3.68232303e+00 -3.66001282e+00 9 1.99209082e+00 -2.19141800e+00 3.13266433e+00 10 -1.62784476e+00 -2.50333744e+00 3.20964762e+00 11 -1.43812668e+00 -1.67364321e+00 -1.14157065e+00 12 3.14910339e+00 -1.83548497e+00 -1.86167364e+00 13 -2.98462158e+00 -9.44437003e-01 -3.69078485e+00 14 -4.68320027e+00 -2.69254222e+00 3.63484590e+00 15 2.87641737e+00 4.50397949e+00 1.28623867e+00 16 4.37135235e+00 1.16144503e+00 -7.63280085e-01 17 1.53025797e+00 1.80938919e+00 1.13303739e+00 18 -8.56027454e-01 1.33638335e+00 7.31770347e-01 19 1.05589821e+00 3.07470038e+00 -2.35904343e+00 20 3.28213694e+00 5.19449000e-02 -2.52714006e+00 21 -1.60041601e+00 2.90618562e+00 3.71178361e+00 22 2.93754567e+00 5.95574869e-01 8.50353786e+00 23 -5.38753804e+00 3.28179230e+00 -2.75977419e+00 24 3.22784568e+00 -3.24257883e+00 -3.79254098e+00 25 8.44898597e-01 1.74523342e-01 2.06004256e+00 26 -8.88656568e-01 -2.26463092e+00 5.04339652e-01 27 9.95894162e-02 -2.59806211e+00 -2.10648807e+00 28 1.27544610e+00 -8.48305615e-01 -2.85733796e+00 29 -5.51392307e-01 2.81815813e+00 6.23871121e-01 30 -3.47329285e+00 -2.34027438e+00 -5.59842071e-01 31 -1.23759264e+00 8.08939542e-01 7.68087460e-01 32 -1.15470971e+00 -1.23303677e+00 -2.11177887e+00 MONOATOMIC STRUCTURE (pbc=False)-- Species = Zr (Configuration in file "config-F-Zr.xyz") ----------------------------------------------------------------------------------------------------- Energy = 658.047288832201 Forces: 1 -3.04785312e+01 -1.18149106e+01 -2.60781324e+01 2 -6.02783237e+01 -8.13011326e+00 -1.02295881e+02 3 -6.06913694e+01 -5.94060423e+01 6.22973430e+01 4 -4.90281331e+01 -1.77579058e+01 3.13409459e+00 5 3.32587044e+01 -9.39930207e+01 -1.31257165e+02 6 8.87218619e+01 -4.06925028e+01 -7.44824056e+01 7 7.87349102e+01 -5.99510754e+01 2.31928886e+01 8 -4.56593781e+00 3.12256813e+01 9.01315356e+01 9 -4.24573726e+01 -3.25223887e+01 -6.06360732e+01 10 2.72823860e+01 2.66080496e+01 -3.27814058e+01 11 7.45046657e+00 6.13185458e+01 4.02393123e+01 12 -3.21037665e+01 5.11036399e+01 3.76451949e+01 13 -7.16859062e+01 7.41462504e+01 -9.46855637e+01 14 2.21119783e+01 3.62228544e+01 -1.96877442e+01 15 9.51264902e+01 4.02883115e+01 9.26249440e+01 16 -2.50310172e-01 2.93707439e+01 -2.53333091e+01 17 -2.30576538e+01 -2.95452355e+01 1.22319745e+01 18 -5.83317374e+01 -1.88718870e+01 -2.14345879e+01 19 -4.46371971e+01 -4.90284032e+01 5.54805425e+01 20 -2.92417547e+01 -3.17122767e+01 4.60234555e+01 21 3.34159841e+01 -6.63702141e+01 -3.65985264e+01 22 5.20943845e+01 2.87209789e+01 -5.39538380e+01 23 6.60687686e+01 -7.72793149e+01 5.90128932e+01 24 -3.65110594e+01 3.85895488e+01 7.78287097e+01 25 -9.76003003e+01 -8.65724929e+01 -6.78839683e+01 26 8.05813327e+01 9.19506831e+01 -9.84704466e+01 27 -2.35194672e+01 -1.75761101e+01 1.30385105e+02 28 -7.39500054e+01 1.04997181e+02 1.44613645e+02 29 8.56405571e+01 2.39171067e+01 -7.52004267e+01 30 4.57240787e+01 2.62940436e+01 -2.99625534e+01 31 2.64393054e+01 -7.39656917e+00 2.64251431e+01 32 -4.26238255e+00 4.38668441e+01 4.94752457e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Zr (Configuration in file "config-T-Zr.xyz") ----------------------------------------------------------------------------------------------------- Energy = 658.047288832201 Forces: 1 -3.04785312e+01 -1.18149106e+01 -2.60781324e+01 2 -6.02783237e+01 -8.13011326e+00 -1.02295881e+02 3 -6.06913694e+01 -5.94060423e+01 6.22973430e+01 4 -4.90281331e+01 -1.77579058e+01 3.13409459e+00 5 3.32587044e+01 -9.39930207e+01 -1.31257165e+02 6 8.87218619e+01 -4.06925028e+01 -7.44824056e+01 7 7.87349102e+01 -5.99510754e+01 2.31928886e+01 8 -4.56593781e+00 3.12256813e+01 9.01315356e+01 9 -4.24573726e+01 -3.25223887e+01 -6.06360732e+01 10 2.72823860e+01 2.66080496e+01 -3.27814058e+01 11 7.45046657e+00 6.13185458e+01 4.02393123e+01 12 -3.21037665e+01 5.11036399e+01 3.76451949e+01 13 -7.16859062e+01 7.41462504e+01 -9.46855637e+01 14 2.21119783e+01 3.62228544e+01 -1.96877442e+01 15 9.51264902e+01 4.02883115e+01 9.26249440e+01 16 -2.50310172e-01 2.93707439e+01 -2.53333091e+01 17 -2.30576538e+01 -2.95452355e+01 1.22319745e+01 18 -5.83317374e+01 -1.88718870e+01 -2.14345879e+01 19 -4.46371971e+01 -4.90284032e+01 5.54805425e+01 20 -2.92417547e+01 -3.17122767e+01 4.60234555e+01 21 3.34159841e+01 -6.63702141e+01 -3.65985264e+01 22 5.20943845e+01 2.87209789e+01 -5.39538380e+01 23 6.60687686e+01 -7.72793149e+01 5.90128932e+01 24 -3.65110594e+01 3.85895488e+01 7.78287097e+01 25 -9.76003003e+01 -8.65724929e+01 -6.78839683e+01 26 8.05813327e+01 9.19506831e+01 -9.84704466e+01 27 -2.35194672e+01 -1.75761101e+01 1.30385105e+02 28 -7.39500054e+01 1.04997181e+02 1.44613645e+02 29 8.56405571e+01 2.39171067e+01 -7.52004267e+01 30 4.57240787e+01 2.62940436e+01 -2.99625534e+01 31 2.64393054e+01 -7.39656917e+00 2.64251431e+01 32 -4.26238255e+00 4.38668441e+01 4.94752457e+01 MIXED STRUCTURE (pbc=False)-- Species = B Zr (Configuration in file "config-F-BZr.xyz") ----------------------------------------------------------------------------------------------------- Energy = 58.787356862528505 Forces: 1 -2.80110545e+01 -3.25441262e+01 5.67459727e+00 2 1.86705003e+01 2.43262955e+01 -2.89379465e+01 3 -6.60334504e+00 -5.80807798e+00 1.89897206e+01 4 -2.69887288e+00 3.67694352e+00 -1.21504855e+00 5 -2.18305591e+01 -3.83174976e+01 -2.19917682e+01 6 3.41677578e+01 2.73647868e+01 -5.65804958e+01 7 3.10949874e+01 -3.55151924e+01 3.75638412e+01 8 1.78648783e+00 -1.39854943e+01 6.02427401e+00 9 -1.53961724e+01 1.07333036e+01 1.95267917e-01 10 -3.28214414e+01 4.43197469e+01 -3.91062037e+01 11 -5.99375036e+01 -2.47186655e+01 -7.73634653e+00 12 -8.63159383e+00 6.30920070e+00 5.82125114e+00 13 2.64649926e+01 -2.38044091e+01 -4.13037058e+01 14 8.13313983e+00 1.62078920e+01 -6.79082765e+00 15 3.01852942e+01 1.52597406e+01 2.58991009e+01 16 5.87175523e+00 1.95609356e+01 9.66359275e+00 17 -5.55756286e+01 -4.27478847e+01 -3.80998302e+01 18 1.36284486e+01 1.73917084e+01 -1.29656861e+01 19 3.89294791e+01 -2.54372234e+01 3.79831171e+01 20 -1.01731225e+01 2.88186490e+01 1.94787403e+01 21 -1.45848428e+01 -1.65236802e+00 6.90759626e+00 22 1.39417482e+01 4.89915187e+00 -1.56292374e+01 23 1.29713949e+01 -1.81772751e+01 1.04953247e+01 24 -1.88245578e+01 9.80445850e+00 2.51268682e+01 25 -9.65023600e+00 3.29055111e+00 8.45882161e+00 26 -2.60549094e+01 1.33254502e+01 -1.04953365e+01 27 -6.13331925e+00 -1.09148858e+01 6.81016105e-02 28 -6.85121720e+00 3.98881087e+00 1.44317369e+00 29 5.39783301e+01 -1.06055629e+01 2.33320493e+01 30 4.47056995e+00 -4.66625150e+00 1.68836857e+00 31 1.00343929e+01 1.10490144e+01 -3.43725782e+00 32 1.94490973e+01 2.85682749e+01 3.94758836e+01 MIXED STRUCTURE (pbc=True)-- Species = B Zr (Configuration in file "config-T-BZr.xyz") ----------------------------------------------------------------------------------------------------- Energy = 172.7695928325724 Forces: 1 -2.10211765e+01 -3.19159689e+01 5.05728783e+00 2 1.77561731e+01 4.07476677e+01 5.45203512e+00 3 -6.47625765e+00 -7.30562850e+00 2.02727831e+01 4 2.22818608e+01 1.49389754e+01 2.09773203e+00 5 -5.12503489e+01 -3.97255456e+00 3.05159009e+00 6 2.28321356e+01 4.96700991e+01 -2.95108824e+01 7 2.51077834e+00 -3.65880821e+01 4.15357474e+01 8 1.06924450e+00 -1.33981317e+01 6.48300114e+00 9 -8.22525336e+00 1.00019567e+01 -6.77599067e+00 10 -2.09291765e+01 3.30427376e+01 -9.14942477e-02 11 -5.84137924e+01 -2.51465229e+01 -6.76186662e+00 12 -7.99340757e+00 9.04876564e+00 5.36556314e+00 13 2.72528692e+01 -2.45434814e+01 -2.67588225e+01 14 2.36422616e+01 -4.50587703e+01 9.16562330e+00 15 1.80203610e+01 1.70480264e+01 2.83915201e+01 16 6.88516799e+00 1.81344346e+01 1.25299998e+01 17 -2.65814234e+01 -3.08244892e+01 -5.13131612e+01 18 1.45904272e+01 1.80461255e+01 -1.42002801e+01 19 4.37674464e+01 -1.89365761e+01 2.64265232e+00 20 -1.35528385e+01 3.19356510e+01 1.49608685e+01 21 -1.34947518e+01 -5.02771459e+00 6.51203780e+00 22 1.13862738e+01 6.20583223e+00 -1.50284122e+01 23 -2.20059595e+00 -5.72619711e+00 -3.03767481e+01 24 -1.87180788e+01 1.08834864e+01 6.74278741e+00 25 -8.10186549e+00 3.54139115e+00 1.01005524e+01 26 -2.57107093e+01 1.18064886e+01 -1.08982460e+01 27 -7.69553757e+00 -1.45889084e+01 -4.99150538e+00 28 -1.64902958e+01 -2.36501793e+01 -1.48981894e+01 29 5.41798110e+01 -1.07908746e+01 2.27516005e+01 30 3.43387948e-01 -3.21025331e+00 -4.24729150e+00 31 1.41744680e+01 1.02863483e+01 -3.08909731e+00 32 2.61628430e+01 1.53463467e+01 1.58286057e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==1819515== Memcheck, a memory error detector ==1819515== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==1819515== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info ==1819515== Command: python runner2.py Tersoff_LAMMPS_DawLawsonBauschlicher_2011pot2_ZrB__MO_728716510644_000 ==1819515== ==1820802== Warning: invalid file descriptor 1024 in syscall close() ==1820802== Warning: invalid file descriptor 1025 in syscall close() ==1820802== Warning: invalid file descriptor 1026 in syscall close() ==1820802== Warning: invalid file descriptor 1027 in syscall close() ==1820802== Use --log-fd= to select an alternative log fd. ==1820802== Warning: invalid file descriptor 1028 in syscall close() ==1820802== Warning: invalid file descriptor 1029 in syscall close() ==1819515== ==1819515== HEAP SUMMARY: ==1819515== in use at exit: 2,257,719 bytes in 1,703 blocks ==1819515== total heap usage: 88,713 allocs, 87,010 frees, 68,382,422 bytes allocated ==1819515== ==1819515== LEAK SUMMARY: ==1819515== definitely lost: 0 bytes in 0 blocks ==1819515== indirectly lost: 0 bytes in 0 blocks ==1819515== possibly lost: 180,827 bytes in 103 blocks ==1819515== still reachable: 2,076,860 bytes in 1,599 blocks ==1819515== of which reachable via heuristic: ==1819515== stdstring : 38 bytes in 1 blocks ==1819515== suppressed: 32 bytes in 1 blocks ==1819515== Rerun with --leak-check=full to see details of leaked memory ==1819515== ==1819515== For lists of detected and suppressed errors, rerun with: -s ==1819515== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 8151 from 583) ================================================================================ 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.