!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_ZhouBarteltSills_2021_PdHHe__MO_865505436319_000 Supported species : H He Pd random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = H (Configuration in file "config-F-H.xyz") ----------------------------------------------------------------------------------------------------- Energy = 305.158748213216 Forces: 1 -1.57529301e+00 -2.10039189e+00 -2.98840509e+00 2 -2.69449073e+00 6.74482482e+00 -2.33400864e+00 3 5.34508054e-01 -1.88631961e+00 3.80838291e+00 4 -1.01445943e+00 3.06082430e+00 2.03327949e+00 5 4.89537095e+00 -5.86539659e+00 -1.45158011e+00 6 1.13600732e+00 9.33971018e-01 -2.02804210e+00 7 2.91582726e+00 -8.02926112e+00 -7.72379401e+00 8 -6.22977611e+00 1.57563527e-01 4.45581901e-01 9 -1.15470996e+00 -2.62208500e+00 -2.81277058e+00 10 -1.53775046e+00 3.30896368e+00 -4.32750512e+00 11 -1.58805794e+00 -3.71754064e+00 1.34370608e+00 12 -1.32622677e+00 2.16588297e+00 1.92042547e+00 13 -4.00769955e+00 -4.07128045e+00 -1.16631562e+01 14 2.15951876e+00 3.95652262e+00 -2.34900990e+00 15 9.64827079e+00 -3.57264889e+00 5.26990012e+00 16 1.26688989e+00 7.40882758e+00 5.01816373e+00 17 -2.28537463e+00 -1.36686963e+00 -2.19514000e+00 18 1.33065662e+00 3.21889236e+00 -9.19012648e-01 19 2.26625016e+00 -2.09669680e+00 2.01440556e+00 20 -6.72160965e-01 2.32069467e+00 1.20681317e+00 21 -5.61436115e+00 -2.01723534e+00 4.80114414e+00 22 4.23734296e+00 5.15157511e+00 4.21059473e+00 23 8.96108533e-01 1.36982704e-01 1.42948927e+00 24 -9.32599348e-02 -7.92311917e-01 4.68722899e-01 25 -2.56289888e+00 -3.43711425e+00 -2.28406460e+00 26 -9.51094757e-01 4.35998695e+00 -3.45598197e+00 27 5.26603457e+00 -1.03287108e+01 3.93071012e+00 28 -8.34316782e+00 8.13178961e+00 1.46833796e+00 29 -2.25073521e+00 -2.92825552e+00 1.15843772e+00 30 9.80599834e-01 2.58938206e+00 6.94129444e-01 31 4.03811338e+00 -2.12718579e+00 2.16136626e+00 32 2.33001823e+00 3.31262031e+00 3.14887997e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = H (Configuration in file "config-T-H.xyz") ----------------------------------------------------------------------------------------------------- Energy = 305.158748213216 Forces: 1 -1.57529301e+00 -2.10039189e+00 -2.98840509e+00 2 -2.69449073e+00 6.74482482e+00 -2.33400864e+00 3 5.34508054e-01 -1.88631961e+00 3.80838291e+00 4 -1.01445943e+00 3.06082430e+00 2.03327949e+00 5 4.89537095e+00 -5.86539659e+00 -1.45158011e+00 6 1.13600732e+00 9.33971018e-01 -2.02804210e+00 7 2.91582726e+00 -8.02926112e+00 -7.72379401e+00 8 -6.22977611e+00 1.57563527e-01 4.45581901e-01 9 -1.15470996e+00 -2.62208500e+00 -2.81277058e+00 10 -1.53775046e+00 3.30896368e+00 -4.32750512e+00 11 -1.58805794e+00 -3.71754064e+00 1.34370608e+00 12 -1.32622677e+00 2.16588297e+00 1.92042547e+00 13 -4.00769955e+00 -4.07128045e+00 -1.16631562e+01 14 2.15951876e+00 3.95652262e+00 -2.34900990e+00 15 9.64827079e+00 -3.57264889e+00 5.26990012e+00 16 1.26688989e+00 7.40882758e+00 5.01816373e+00 17 -2.28537463e+00 -1.36686963e+00 -2.19514000e+00 18 1.33065662e+00 3.21889236e+00 -9.19012648e-01 19 2.26625016e+00 -2.09669680e+00 2.01440556e+00 20 -6.72160965e-01 2.32069467e+00 1.20681317e+00 21 -5.61436115e+00 -2.01723534e+00 4.80114414e+00 22 4.23734296e+00 5.15157511e+00 4.21059473e+00 23 8.96108533e-01 1.36982704e-01 1.42948927e+00 24 -9.32599348e-02 -7.92311917e-01 4.68722899e-01 25 -2.56289888e+00 -3.43711425e+00 -2.28406460e+00 26 -9.51094757e-01 4.35998695e+00 -3.45598197e+00 27 5.26603457e+00 -1.03287108e+01 3.93071012e+00 28 -8.34316782e+00 8.13178961e+00 1.46833796e+00 29 -2.25073521e+00 -2.92825552e+00 1.15843772e+00 30 9.80599834e-01 2.58938206e+00 6.94129444e-01 31 4.03811338e+00 -2.12718579e+00 2.16136626e+00 32 2.33001823e+00 3.31262031e+00 3.14887997e+00 MONOATOMIC STRUCTURE (pbc=False)-- Species = He (Configuration in file "config-F-He.xyz") ----------------------------------------------------------------------------------------------------- Energy = 22.718431380852234 Forces: 1 -6.95999952e-02 1.38709525e+00 1.08456070e+00 2 1.31661460e+00 2.06003051e-01 1.04389401e+00 3 -1.17183168e+00 1.44583230e+00 1.85306652e-01 4 6.31184357e+00 5.56418117e-02 -2.35229765e-01 5 -8.63228126e-01 5.03291114e+00 3.21360491e+00 6 -2.79348103e+00 1.06125133e+00 9.67596588e-01 7 -1.17266597e+00 2.77746837e-01 -9.11153740e-02 8 9.08429376e-01 -1.46519050e-01 -2.16660064e+00 9 1.10756850e+00 4.31239744e-01 3.12179418e+00 10 -1.73872534e-01 -5.92988726e-01 2.02230946e+00 11 -2.22914836e+00 -2.53994824e+00 1.47020330e+00 12 6.44323492e+00 -4.85285011e+00 -1.86483805e+00 13 -1.69397972e-01 -2.93570368e-01 6.08317675e+00 14 -9.99884032e-01 -2.42899599e+00 1.08982473e+00 15 -5.82192628e+00 6.37624509e-01 6.38945461e-01 16 -1.90812969e+00 -1.77964319e+00 -4.31581943e+00 17 2.47134477e+00 3.43677190e+00 -1.03797427e+00 18 -3.33134175e-02 -1.16887794e+00 1.18090784e+00 19 7.35506315e-01 1.42778096e+00 -1.10054587e+00 20 3.10943031e-01 -7.67625484e-01 -1.33303411e+00 21 -2.39276930e-02 2.17149526e+00 4.52944524e-01 22 -1.16396775e+00 1.95850015e+00 2.47844359e-01 23 -1.02404827e+00 9.39620743e-01 -6.35576211e-01 24 -7.00221748e-01 5.66672177e-01 -4.60725808e+00 25 -9.75683327e-01 2.82556870e-01 -2.63319033e+00 26 3.03034116e-01 8.57016896e-02 -5.79358329e-01 27 2.28397068e+00 -3.42397478e-01 1.12224239e-01 28 3.16662818e-02 -6.58990602e-03 -1.38200608e-01 29 3.33178994e+00 7.41817255e-01 2.64177891e+00 30 1.81455529e+00 -2.42126503e+00 4.45143233e+00 31 -7.20152835e+00 1.82053000e+00 -4.06483487e+00 32 1.12535483e+00 -6.62552145e+00 -5.20477302e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = He (Configuration in file "config-T-He.xyz") ----------------------------------------------------------------------------------------------------- Energy = 22.718431380852234 Forces: 1 -6.95999952e-02 1.38709525e+00 1.08456070e+00 2 1.31661460e+00 2.06003051e-01 1.04389401e+00 3 -1.17183168e+00 1.44583230e+00 1.85306652e-01 4 6.31184357e+00 5.56418117e-02 -2.35229765e-01 5 -8.63228126e-01 5.03291114e+00 3.21360491e+00 6 -2.79348103e+00 1.06125133e+00 9.67596588e-01 7 -1.17266597e+00 2.77746837e-01 -9.11153740e-02 8 9.08429376e-01 -1.46519050e-01 -2.16660064e+00 9 1.10756850e+00 4.31239744e-01 3.12179418e+00 10 -1.73872534e-01 -5.92988726e-01 2.02230946e+00 11 -2.22914836e+00 -2.53994824e+00 1.47020330e+00 12 6.44323492e+00 -4.85285011e+00 -1.86483805e+00 13 -1.69397972e-01 -2.93570368e-01 6.08317675e+00 14 -9.99884032e-01 -2.42899599e+00 1.08982473e+00 15 -5.82192628e+00 6.37624509e-01 6.38945461e-01 16 -1.90812969e+00 -1.77964319e+00 -4.31581943e+00 17 2.47134477e+00 3.43677190e+00 -1.03797427e+00 18 -3.33134175e-02 -1.16887794e+00 1.18090784e+00 19 7.35506315e-01 1.42778096e+00 -1.10054587e+00 20 3.10943031e-01 -7.67625484e-01 -1.33303411e+00 21 -2.39276930e-02 2.17149526e+00 4.52944524e-01 22 -1.16396775e+00 1.95850015e+00 2.47844359e-01 23 -1.02404827e+00 9.39620743e-01 -6.35576211e-01 24 -7.00221748e-01 5.66672177e-01 -4.60725808e+00 25 -9.75683327e-01 2.82556870e-01 -2.63319033e+00 26 3.03034116e-01 8.57016896e-02 -5.79358329e-01 27 2.28397068e+00 -3.42397478e-01 1.12224239e-01 28 3.16662818e-02 -6.58990602e-03 -1.38200608e-01 29 3.33178994e+00 7.41817255e-01 2.64177891e+00 30 1.81455529e+00 -2.42126503e+00 4.45143233e+00 31 -7.20152835e+00 1.82053000e+00 -4.06483487e+00 32 1.12535483e+00 -6.62552145e+00 -5.20477302e+00 MONOATOMIC STRUCTURE (pbc=False)-- Species = Pd (Configuration in file "config-F-Pd.xyz") ----------------------------------------------------------------------------------------------------- Energy = 389.90585850548604 Forces: 1 -1.78087626e+00 -2.80458465e+00 -3.32813681e+00 2 -4.49433167e+00 -1.56217838e+00 -4.45321496e+00 3 -1.46338496e+00 -6.28210271e+00 -3.82457414e+00 4 -6.83772589e+00 2.64402423e+00 -1.77827872e+00 5 -6.44497656e-01 -4.96200542e+00 -4.18077278e+00 6 6.58137850e+00 -1.97290674e+00 -5.73611629e+00 7 6.11236913e+00 -6.76641428e+00 -2.42402354e+00 8 -1.89050896e+00 1.40342337e+00 -1.63397404e+00 9 -6.12653562e+00 -2.88337159e+00 -4.49541370e+00 10 1.95993914e+00 6.05175212e+00 -8.46386807e+00 11 7.05235703e-01 -4.80831623e+00 -1.05242412e+00 12 -7.43667663e+00 6.73761920e+00 1.83923172e+00 13 8.75938375e-03 4.76961220e+00 -4.87369384e+00 14 3.54545877e+00 2.22972693e+00 -3.93614967e+00 15 6.11145492e+00 2.36434339e+00 2.34248569e+00 16 1.73906136e+00 4.72490634e+00 1.38322362e+00 17 -3.96340300e+00 -4.72516024e+00 -1.10721326e+00 18 4.98611703e-01 -1.55210900e+00 1.36939052e+00 19 1.23241189e+00 -4.73256565e+00 5.01740895e+00 20 -5.96686444e+00 1.75610294e+00 5.61990398e+00 21 1.14949714e+00 -5.84232533e+00 2.54813788e+00 22 6.61694132e+00 1.24447695e+00 5.31887590e+00 23 1.11174655e+00 -8.94463766e-01 1.86288888e+00 24 2.84598922e+00 -3.72418770e+00 4.43353405e+00 25 -9.26509448e+00 -1.32939963e+00 -1.53956336e+00 26 1.10471732e-01 7.42272130e+00 1.61034886e+00 27 3.16179179e-01 -8.30388723e-01 7.71889961e+00 28 -3.48241501e+00 5.19043962e+00 4.33772130e+00 29 4.33350128e+00 1.22786465e+00 8.45551071e-01 30 4.65544607e+00 2.67681954e+00 -7.11396507e-01 31 2.31506624e+00 3.61634806e-01 1.35186806e+00 32 1.40279533e+00 4.86701246e+00 5.93934371e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Pd (Configuration in file "config-T-Pd.xyz") ----------------------------------------------------------------------------------------------------- Energy = 389.90585850548604 Forces: 1 -1.78087626e+00 -2.80458465e+00 -3.32813681e+00 2 -4.49433167e+00 -1.56217838e+00 -4.45321496e+00 3 -1.46338496e+00 -6.28210271e+00 -3.82457414e+00 4 -6.83772589e+00 2.64402423e+00 -1.77827872e+00 5 -6.44497656e-01 -4.96200542e+00 -4.18077278e+00 6 6.58137850e+00 -1.97290674e+00 -5.73611629e+00 7 6.11236913e+00 -6.76641428e+00 -2.42402354e+00 8 -1.89050896e+00 1.40342337e+00 -1.63397404e+00 9 -6.12653562e+00 -2.88337159e+00 -4.49541370e+00 10 1.95993914e+00 6.05175212e+00 -8.46386807e+00 11 7.05235703e-01 -4.80831623e+00 -1.05242412e+00 12 -7.43667663e+00 6.73761920e+00 1.83923172e+00 13 8.75938375e-03 4.76961220e+00 -4.87369384e+00 14 3.54545877e+00 2.22972693e+00 -3.93614967e+00 15 6.11145492e+00 2.36434339e+00 2.34248569e+00 16 1.73906136e+00 4.72490634e+00 1.38322362e+00 17 -3.96340300e+00 -4.72516024e+00 -1.10721326e+00 18 4.98611703e-01 -1.55210900e+00 1.36939052e+00 19 1.23241189e+00 -4.73256565e+00 5.01740895e+00 20 -5.96686444e+00 1.75610294e+00 5.61990398e+00 21 1.14949714e+00 -5.84232533e+00 2.54813788e+00 22 6.61694132e+00 1.24447695e+00 5.31887590e+00 23 1.11174655e+00 -8.94463766e-01 1.86288888e+00 24 2.84598922e+00 -3.72418770e+00 4.43353405e+00 25 -9.26509448e+00 -1.32939963e+00 -1.53956336e+00 26 1.10471732e-01 7.42272130e+00 1.61034886e+00 27 3.16179179e-01 -8.30388723e-01 7.71889961e+00 28 -3.48241501e+00 5.19043962e+00 4.33772130e+00 29 4.33350128e+00 1.22786465e+00 8.45551071e-01 30 4.65544607e+00 2.67681954e+00 -7.11396507e-01 31 2.31506624e+00 3.61634806e-01 1.35186806e+00 32 1.40279533e+00 4.86701246e+00 5.93934371e+00 MIXED STRUCTURE (pbc=False)-- Species = H He Pd (Configuration in file "config-F-HHePd.xyz") ----------------------------------------------------------------------------------------------------- Energy = 231.65413804343143 Forces: 1 -3.57699614e-02 -3.96229038e-01 -3.52047484e-01 2 2.43861635e+00 2.65073377e+00 -1.74758684e+00 3 3.20757337e+00 -1.40033680e+00 2.35460113e+00 4 -2.86757370e+00 2.64303361e+00 2.52265713e+00 5 1.69876429e-02 -2.90323169e-02 -1.65415096e-01 6 7.92909649e-02 -2.15382473e-02 -5.25260814e-03 7 -1.30642513e+00 2.24278021e-01 4.34890756e-01 8 6.52851892e-01 8.21133649e-02 -8.21225352e-01 9 -1.00284829e+00 -1.08891271e+00 -8.21462867e-01 10 2.19767891e+00 3.85170617e+00 -8.24907655e+00 11 4.11769589e+00 -9.88723241e+00 7.17398470e-01 12 -1.00551730e+01 2.73884132e+00 2.83526659e+00 13 7.42840694e-01 -4.11854586e-01 -4.86365740e-01 14 1.10045911e-01 -1.56000743e-02 2.77895978e-02 15 4.76844995e-01 8.64971598e-01 -2.30358733e+00 16 1.10167048e+00 2.82757285e-01 -6.48427617e-02 17 -1.86280956e+00 1.84652794e+00 -1.45869053e+00 18 -6.38781417e-01 -1.85583216e+00 -4.95080672e+00 19 3.25746264e+00 1.89063610e+00 1.59028600e+00 20 -6.04349347e+00 -4.50969220e+00 6.45225961e-01 21 1.13078273e-01 -2.50219190e+00 -1.93327235e+00 22 -5.95768855e-01 -1.54793146e+00 3.27315326e+00 23 9.11632981e-01 -6.47335781e-01 2.33415357e-01 24 1.02516811e-01 -9.07208277e-02 5.19622160e-01 25 2.67935205e+00 -1.10285961e+00 -1.00382800e+00 26 2.89607798e+00 1.85136312e+00 5.67713281e+00 27 3.78307921e+00 5.02976847e+00 3.12887897e+00 28 -5.52169675e-01 7.37670282e-01 7.48715406e-01 29 -3.85709123e+00 -2.13457851e-01 7.46676761e-01 30 -3.96651499e-01 -6.67399372e-01 3.29590298e-01 31 -2.12380846e-01 1.27909358e+00 -1.66906880e+00 32 5.41639573e-01 4.14662691e-01 2.47228383e-01 MIXED STRUCTURE (pbc=True)-- Species = H He Pd (Configuration in file "config-T-HHePd.xyz") ----------------------------------------------------------------------------------------------------- Energy = 218.5254247538426 Forces: 1 -1.79081493e+00 1.18851100e+00 3.72809516e-02 2 1.64420009e+00 3.45886739e+00 -3.75300635e+00 3 2.37760707e+00 -3.33359409e+00 2.29609858e+00 4 -2.51121443e+00 2.68429369e+00 1.98021711e+00 5 3.42544115e+00 2.64256577e+00 1.09325693e+00 6 -3.80514455e+00 -1.38761911e+00 3.14643540e-02 7 -1.08641629e+00 -6.77188456e-01 1.13150661e-01 8 2.35480169e+00 -5.64142608e-01 -3.41107023e+00 9 -2.60982481e+00 -2.06566639e+00 -1.34965683e-01 10 2.23853047e+00 6.39571024e+00 -7.07169894e+00 11 3.66245790e+00 -9.56685984e+00 1.13779175e+00 12 -1.05636301e+01 4.11359176e+00 4.38915044e+00 13 2.91991036e+00 -2.31285585e+00 3.89301822e-01 14 -1.28883629e+00 -8.66327693e-03 -5.69661255e-02 15 1.30700818e+00 1.43739466e+00 -2.54205343e+00 16 1.06643738e+00 1.27615788e+00 -8.62926340e-01 17 -1.40232674e+00 1.81500142e-01 -1.51925698e+00 18 -1.25841703e+00 -1.99127999e+00 -4.79431025e+00 19 2.79695969e+00 4.62870891e-01 1.39669382e+00 20 -9.08544057e-01 -6.69667846e+00 1.10202106e-01 21 1.99807458e+00 -6.07172016e-01 -1.91293543e+00 22 3.89809336e-01 -1.49832803e+00 3.87357239e+00 23 1.24406139e+00 -2.37732807e+00 -1.10615883e+00 24 1.43455221e+00 -7.83828377e-01 3.02119962e+00 25 4.52005031e+00 -2.81255456e+00 -5.79869031e-02 26 -7.84493245e-02 1.41635581e+00 6.40417822e+00 27 3.72429432e+00 3.33014881e+00 1.67694698e+00 28 -5.17540934e-01 7.89136918e-01 2.08039894e-01 29 -3.80105744e+00 1.33257765e-02 8.56787319e-01 30 -2.25005661e+00 2.17406479e+00 4.92043825e-01 31 -3.76038909e+00 4.69099748e+00 -2.90792843e+00 32 5.28466525e-01 4.28266130e-01 6.23887168e-01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==1946== Memcheck, a memory error detector ==1946== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==1946== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info ==1946== Command: python runner2.py EAM_Dynamo_ZhouBarteltSills_2021_PdHHe__MO_865505436319_000 ==1946== ==2688== Warning: invalid file descriptor 4096 in syscall close() ==2688== Warning: invalid file descriptor 4097 in syscall close() ==2688== Warning: invalid file descriptor 4098 in syscall close() ==2688== Warning: invalid file descriptor 4099 in syscall close() ==2688== Use --log-fd= to select an alternative log fd. ==2688== Warning: invalid file descriptor 4100 in syscall close() ==2688== Warning: invalid file descriptor 4101 in syscall close() ==1946== ==1946== HEAP SUMMARY: ==1946== in use at exit: 2,203,239 bytes in 1,645 blocks ==1946== total heap usage: 108,557 allocs, 106,912 frees, 164,044,942 bytes allocated ==1946== ==1946== LEAK SUMMARY: ==1946== definitely lost: 0 bytes in 0 blocks ==1946== indirectly lost: 0 bytes in 0 blocks ==1946== possibly lost: 198,622 bytes in 101 blocks ==1946== still reachable: 2,004,585 bytes in 1,543 blocks ==1946== suppressed: 32 bytes in 1 blocks ==1946== Rerun with --leak-check=full to see details of leaked memory ==1946== ==1946== For lists of detected and suppressed errors, rerun with: -s ==1946== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 9270 from 575) ================================================================================ 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.