!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_ZhouJohnsonWadley_2004NISTretabulation_CuAgAu__MO_318213562153_000 Supported species : Ag Au Cu random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Ag (Configuration in file "config-F-Ag.xyz") ----------------------------------------------------------------------------------------------------- Energy = 225.06937381943632 Forces: 1 -8.79972746e+00 -1.63190336e+01 -1.68902641e+01 2 -1.59165232e+01 2.44729576e+01 -2.21040707e+01 3 -2.22503404e+00 -2.37162948e+01 -2.55003975e+00 4 -1.36746791e+01 7.69179448e+00 8.04860116e+00 5 2.31020914e+01 -3.65502560e+01 -8.15602079e+00 6 8.97117565e+00 2.00794928e+00 -1.41619436e+01 7 1.32736150e+01 -5.14552019e+01 -4.55278667e+01 8 -1.51044312e+01 -1.79064924e+01 -8.53497653e+00 9 -1.88298417e+01 -2.66744376e+01 -4.50907039e+01 10 -2.28379021e+00 3.83966331e+01 -3.90079660e+01 11 -7.01684096e+00 -2.64150115e+01 1.61634230e+01 12 -2.81983654e+01 3.74377746e+01 2.04712818e+01 13 -7.86688298e+00 -2.00218182e+01 -7.46907422e+01 14 1.57656604e+01 1.92573000e+01 -1.32726313e+01 15 6.69935371e+01 -7.68823014e+00 1.63025334e+01 16 8.40268528e+00 5.41575373e+01 2.38858341e+01 17 -2.20996828e+01 -1.08166464e+01 -7.87505218e+00 18 -1.15078785e+01 1.43928080e+01 1.10855800e+01 19 9.52626797e+00 -1.88957633e+01 1.48690670e+01 20 -1.02111320e+01 1.36333925e+01 1.21807016e+01 21 -1.66908859e+01 -2.38599994e+01 1.52396037e+01 22 3.65355512e+01 3.79642023e+01 3.61049616e+01 23 8.48180150e+00 -4.16141430e+00 1.38368824e+01 24 4.68783129e+00 1.02780755e+00 1.34461667e+01 25 -2.07773551e+01 -6.21457076e+00 1.45740877e+01 26 -1.32897436e+01 3.47670298e+01 -1.56717784e+01 27 1.57695744e+01 -5.32523657e+01 1.98205622e+01 28 -4.69866786e+01 3.84827245e+01 8.50992857e+00 29 -1.16726519e+01 -1.68158591e+01 1.32145532e+01 30 1.76960877e+01 2.62116018e+01 2.15130803e+00 31 2.85051962e+01 -1.62021890e+01 2.44048366e+01 32 1.54410496e+01 2.70640714e+01 2.92241433e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ag (Configuration in file "config-T-Ag.xyz") ----------------------------------------------------------------------------------------------------- Energy = 225.06937381943632 Forces: 1 -8.79972746e+00 -1.63190336e+01 -1.68902641e+01 2 -1.59165232e+01 2.44729576e+01 -2.21040707e+01 3 -2.22503404e+00 -2.37162948e+01 -2.55003975e+00 4 -1.36746791e+01 7.69179448e+00 8.04860116e+00 5 2.31020914e+01 -3.65502560e+01 -8.15602079e+00 6 8.97117565e+00 2.00794928e+00 -1.41619436e+01 7 1.32736150e+01 -5.14552019e+01 -4.55278667e+01 8 -1.51044312e+01 -1.79064924e+01 -8.53497653e+00 9 -1.88298417e+01 -2.66744376e+01 -4.50907039e+01 10 -2.28379021e+00 3.83966331e+01 -3.90079660e+01 11 -7.01684096e+00 -2.64150115e+01 1.61634230e+01 12 -2.81983654e+01 3.74377746e+01 2.04712818e+01 13 -7.86688298e+00 -2.00218182e+01 -7.46907422e+01 14 1.57656604e+01 1.92573000e+01 -1.32726313e+01 15 6.69935371e+01 -7.68823014e+00 1.63025334e+01 16 8.40268528e+00 5.41575373e+01 2.38858341e+01 17 -2.20996828e+01 -1.08166464e+01 -7.87505218e+00 18 -1.15078785e+01 1.43928080e+01 1.10855800e+01 19 9.52626797e+00 -1.88957633e+01 1.48690670e+01 20 -1.02111320e+01 1.36333925e+01 1.21807016e+01 21 -1.66908859e+01 -2.38599994e+01 1.52396037e+01 22 3.65355512e+01 3.79642023e+01 3.61049616e+01 23 8.48180150e+00 -4.16141430e+00 1.38368824e+01 24 4.68783129e+00 1.02780755e+00 1.34461667e+01 25 -2.07773551e+01 -6.21457076e+00 1.45740877e+01 26 -1.32897436e+01 3.47670298e+01 -1.56717784e+01 27 1.57695744e+01 -5.32523657e+01 1.98205622e+01 28 -4.69866786e+01 3.84827245e+01 8.50992857e+00 29 -1.16726519e+01 -1.68158591e+01 1.32145532e+01 30 1.76960877e+01 2.62116018e+01 2.15130803e+00 31 2.85051962e+01 -1.62021890e+01 2.44048366e+01 32 1.54410496e+01 2.70640714e+01 2.92241433e+01 MONOATOMIC STRUCTURE (pbc=False)-- Species = Au (Configuration in file "config-F-Au.xyz") ----------------------------------------------------------------------------------------------------- Energy = 199.39063661675024 Forces: 1 -9.79438730e+00 -1.34686467e+01 -1.50439805e+01 2 -1.01967407e+01 -2.20675300e+01 -6.11364781e+01 3 1.73751032e+01 -5.16516176e+01 -2.49966436e+01 4 -4.63108737e+01 3.37888282e+01 -3.39623094e+01 5 -9.55480964e+00 -2.26467522e+01 -2.44528176e+01 6 4.18265345e+01 -2.02598536e+01 -3.06214743e+01 7 1.91790445e+01 -1.34161347e+01 4.92418610e+00 8 2.73531798e+01 -2.56898910e+01 1.25075339e+01 9 -1.00780919e+01 3.36073327e+00 -1.09901012e+01 10 -8.18507691e+00 9.23587142e+00 -1.90497599e+01 11 -3.60761079e+01 3.65128595e+01 1.40177028e+01 12 -1.10773453e+01 1.55428880e+01 -5.51721180e+00 13 -4.86353341e+01 1.50602503e+01 -7.70469223e+01 14 9.60824923e+00 1.24433814e+01 -1.08407347e+01 15 7.56333829e+01 1.53616343e+01 5.36949274e+01 16 3.35789465e+00 2.83915410e+01 -2.67747616e+01 17 -4.96231688e+01 -6.60528026e+01 3.63725227e+01 18 2.57089464e+01 4.29694100e+01 -3.04784153e-01 19 8.05900548e+00 -3.63464342e+01 4.46022367e+01 20 -3.29972367e+01 1.33286948e+01 2.33118495e+01 21 -3.07403015e+00 -2.85951874e+01 -5.75580653e+00 22 3.07967328e+01 1.08639028e+01 -1.64624648e+01 23 3.02320323e+01 -3.50239212e+01 2.44621398e+01 24 -2.38764620e+01 2.09265111e+01 2.77671585e+01 25 -1.43906083e+01 3.68584771e+00 8.31829316e+00 26 -2.38501133e+01 2.05001395e+01 2.95932109e+01 27 1.10224928e+01 -7.89588592e+00 1.11805786e+01 28 -1.43249350e+01 1.61452267e+01 4.01999634e+00 29 8.91837053e+00 1.34472369e+01 3.49263652e+01 30 3.10924569e+01 1.70657710e+01 1.98606748e+01 31 1.65064377e+01 2.88664221e+00 6.11881476e+00 32 -4.62454187e+00 1.15972869e+01 7.27805953e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Au (Configuration in file "config-T-Au.xyz") ----------------------------------------------------------------------------------------------------- Energy = 199.39063661675024 Forces: 1 -9.79438730e+00 -1.34686467e+01 -1.50439805e+01 2 -1.01967407e+01 -2.20675300e+01 -6.11364781e+01 3 1.73751032e+01 -5.16516176e+01 -2.49966436e+01 4 -4.63108737e+01 3.37888282e+01 -3.39623094e+01 5 -9.55480964e+00 -2.26467522e+01 -2.44528176e+01 6 4.18265345e+01 -2.02598536e+01 -3.06214743e+01 7 1.91790445e+01 -1.34161347e+01 4.92418610e+00 8 2.73531798e+01 -2.56898910e+01 1.25075339e+01 9 -1.00780919e+01 3.36073327e+00 -1.09901012e+01 10 -8.18507691e+00 9.23587142e+00 -1.90497599e+01 11 -3.60761079e+01 3.65128595e+01 1.40177028e+01 12 -1.10773453e+01 1.55428880e+01 -5.51721180e+00 13 -4.86353341e+01 1.50602503e+01 -7.70469223e+01 14 9.60824923e+00 1.24433814e+01 -1.08407347e+01 15 7.56333829e+01 1.53616343e+01 5.36949274e+01 16 3.35789465e+00 2.83915410e+01 -2.67747616e+01 17 -4.96231688e+01 -6.60528026e+01 3.63725227e+01 18 2.57089464e+01 4.29694100e+01 -3.04784153e-01 19 8.05900548e+00 -3.63464342e+01 4.46022367e+01 20 -3.29972367e+01 1.33286948e+01 2.33118495e+01 21 -3.07403015e+00 -2.85951874e+01 -5.75580653e+00 22 3.07967328e+01 1.08639028e+01 -1.64624648e+01 23 3.02320323e+01 -3.50239212e+01 2.44621398e+01 24 -2.38764620e+01 2.09265111e+01 2.77671585e+01 25 -1.43906083e+01 3.68584771e+00 8.31829316e+00 26 -2.38501133e+01 2.05001395e+01 2.95932109e+01 27 1.10224928e+01 -7.89588592e+00 1.11805786e+01 28 -1.43249350e+01 1.61452267e+01 4.01999634e+00 29 8.91837053e+00 1.34472369e+01 3.49263652e+01 30 3.10924569e+01 1.70657710e+01 1.98606748e+01 31 1.65064377e+01 2.88664221e+00 6.11881476e+00 32 -4.62454187e+00 1.15972869e+01 7.27805953e+00 MONOATOMIC STRUCTURE (pbc=False)-- Species = Cu (Configuration in file "config-F-Cu.xyz") ----------------------------------------------------------------------------------------------------- Energy = 0.28797836278989575 Forces: 1 -7.75353382e-01 -9.23020520e-01 -7.20547066e-01 2 -1.06777069e+01 -2.49566706e+00 -1.12547436e+01 3 -1.19424129e+01 -1.46439773e+01 2.27733091e+00 4 -9.70263173e+00 1.72332327e+00 -1.06570956e+01 5 -2.82473998e+00 -6.99430612e+00 -1.17877794e+01 6 9.39649693e+00 6.26426557e+00 -1.21374024e+01 7 7.55836706e+00 -1.29182985e+01 1.27956733e+01 8 1.28389090e+01 7.46949013e+00 8.46139308e+00 9 -8.54750165e+00 -1.41358439e+01 -1.03365773e+01 10 2.98199627e+00 9.32388812e+00 -1.23599493e+01 11 -1.21042346e+01 1.99226131e+00 -4.34988898e+00 12 -6.68610817e+00 1.08719909e+01 1.06435795e+01 13 1.40378093e+00 3.89707465e+00 -8.52697649e+00 14 2.69350668e+00 4.90244676e+00 -2.43411067e+00 15 9.72608697e+00 -2.45616054e+00 -2.70198785e+00 16 7.16615436e+00 1.79491953e+01 -4.75126033e+00 17 -4.26716732e+00 -8.90346888e+00 2.41285540e+00 18 1.22241660e+01 -6.93270933e+00 3.18077114e+00 19 -1.44051153e+01 -1.27911848e+01 1.24893983e+01 20 -1.16297341e+01 -1.13485163e+01 1.06637364e+01 21 7.65717597e+00 -5.73742776e+00 -1.28659506e+01 22 4.22932007e+00 1.34301993e+00 2.62164142e+00 23 5.95413726e+00 -2.23855318e+00 5.50008015e+00 24 1.09917881e+01 5.85877664e+00 5.11523377e+00 25 -1.27628761e+01 1.34384174e+01 -3.07886389e+00 26 1.54211864e+00 4.33201164e+00 -2.02360388e+00 27 4.15069826e+00 1.46555460e+01 5.15121468e+00 28 -3.89630881e+00 1.26016164e+00 3.82990424e+00 29 -8.12693158e+00 -1.88749233e+01 1.33243281e+01 30 1.97808394e+01 1.43877383e+01 -4.54274299e+00 31 9.92662374e+00 -1.16891112e+01 7.38611326e+00 32 -1.18733432e+01 1.34135610e+01 8.67622671e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Cu (Configuration in file "config-T-Cu.xyz") ----------------------------------------------------------------------------------------------------- Energy = 0.28797836278989575 Forces: 1 -7.75353382e-01 -9.23020520e-01 -7.20547066e-01 2 -1.06777069e+01 -2.49566706e+00 -1.12547436e+01 3 -1.19424129e+01 -1.46439773e+01 2.27733091e+00 4 -9.70263173e+00 1.72332327e+00 -1.06570956e+01 5 -2.82473998e+00 -6.99430612e+00 -1.17877794e+01 6 9.39649693e+00 6.26426557e+00 -1.21374024e+01 7 7.55836706e+00 -1.29182985e+01 1.27956733e+01 8 1.28389090e+01 7.46949013e+00 8.46139308e+00 9 -8.54750165e+00 -1.41358439e+01 -1.03365773e+01 10 2.98199627e+00 9.32388812e+00 -1.23599493e+01 11 -1.21042346e+01 1.99226131e+00 -4.34988898e+00 12 -6.68610817e+00 1.08719909e+01 1.06435795e+01 13 1.40378093e+00 3.89707465e+00 -8.52697649e+00 14 2.69350668e+00 4.90244676e+00 -2.43411067e+00 15 9.72608697e+00 -2.45616054e+00 -2.70198785e+00 16 7.16615436e+00 1.79491953e+01 -4.75126033e+00 17 -4.26716732e+00 -8.90346888e+00 2.41285540e+00 18 1.22241660e+01 -6.93270933e+00 3.18077114e+00 19 -1.44051153e+01 -1.27911848e+01 1.24893983e+01 20 -1.16297341e+01 -1.13485163e+01 1.06637364e+01 21 7.65717597e+00 -5.73742776e+00 -1.28659506e+01 22 4.22932007e+00 1.34301993e+00 2.62164142e+00 23 5.95413726e+00 -2.23855318e+00 5.50008015e+00 24 1.09917881e+01 5.85877664e+00 5.11523377e+00 25 -1.27628761e+01 1.34384174e+01 -3.07886389e+00 26 1.54211864e+00 4.33201164e+00 -2.02360388e+00 27 4.15069826e+00 1.46555460e+01 5.15121468e+00 28 -3.89630881e+00 1.26016164e+00 3.82990424e+00 29 -8.12693158e+00 -1.88749233e+01 1.33243281e+01 30 1.97808394e+01 1.43877383e+01 -4.54274299e+00 31 9.92662374e+00 -1.16891112e+01 7.38611326e+00 32 -1.18733432e+01 1.34135610e+01 8.67622671e+00 MIXED STRUCTURE (pbc=False)-- Species = Ag Au Cu (Configuration in file "config-F-AgAuCu.xyz") ----------------------------------------------------------------------------------------------------- Energy = 172.05451405624234 Forces: 1 -2.65592066e+01 -3.23545431e+01 -4.53823956e+01 2 -1.59843484e+01 2.48531668e+01 -3.87580337e+01 3 2.86937931e+01 -5.81782846e+01 1.33401294e+01 4 -4.84607413e+01 4.47177343e+01 1.32081229e+01 5 9.33462223e+00 -2.88665653e+01 -1.84274792e+01 6 1.32416331e+01 1.80991859e+01 -2.64728272e+01 7 1.77846382e+01 -3.00295154e+01 2.33007490e+01 8 2.16475605e+01 -6.71126216e+00 8.72281064e+00 9 -8.41317409e+00 -1.95953674e+00 -1.42107277e+01 10 -8.10473300e+00 2.63935706e+01 -1.25727763e+01 11 -2.17607880e+01 7.24610213e+00 -1.47834059e+01 12 -1.03520783e+01 1.38570116e+01 8.52553622e+00 13 1.51362824e+01 -9.62325669e+00 -1.77497900e+01 14 3.79956226e+00 9.14262246e+00 -7.23017986e+00 15 1.69652049e+01 -1.60600734e+01 -1.38502930e+01 16 -1.70173512e+00 1.75333006e+01 -1.09646534e+01 17 -3.92673667e+01 -2.43434210e+01 -3.96764048e+00 18 1.43420532e+01 3.51432195e+01 7.67666103e+00 19 4.16480686e+00 -3.86299137e+01 2.87262959e+01 20 -2.04790869e+01 9.13381063e+00 1.70895204e+01 21 1.45013772e+01 -1.55161279e+01 -4.36287162e-01 22 8.37681484e+00 5.25061025e+00 -1.83888698e-01 23 5.77766959e+00 -6.67210400e+00 4.85432947e+00 24 1.62719621e+01 1.81584745e+01 1.59740505e+01 25 -1.73828749e+01 -3.87363987e+00 -4.05666641e+00 26 -4.62607703e+01 3.93789408e+01 -4.07390429e+01 27 1.98357622e+01 -5.55196447e+01 3.89362774e+01 28 -4.52571262e+01 4.79957901e+01 8.78599747e+00 29 3.82823106e+01 -4.70433282e+01 1.04292625e+01 30 2.02442925e+01 2.83929997e+01 1.51768669e+01 31 6.06306233e+00 -5.31739635e+00 1.12266608e+01 32 3.55206217e+01 3.54020732e+01 4.38128170e+01 MIXED STRUCTURE (pbc=True)-- Species = Ag Au Cu (Configuration in file "config-T-AgAuCu.xyz") ----------------------------------------------------------------------------------------------------- Energy = 312.0435678806379 Forces: 1 -5.47125081e+00 -2.74573536e+01 -4.27305689e+01 2 -1.71284756e+01 2.82802877e+01 -1.72124062e+01 3 3.68515155e+01 -3.32034414e+01 2.17956606e+01 4 -2.54550932e+01 5.10867729e+01 2.63116175e+01 5 1.13499267e+01 -2.35422002e+01 -4.51321912e+00 6 -2.19510605e+01 3.22965351e+01 -1.61788017e+01 7 -4.81618204e+00 -1.83994237e+01 4.18878838e+01 8 2.06780030e+01 -5.48302546e+00 1.04925039e+01 9 -1.15338228e+00 1.23574735e-01 1.55682791e+01 10 -4.22369582e+00 1.11329435e+01 5.39492461e+00 11 -2.14428392e+01 7.34245722e+00 -1.45249655e+01 12 -5.88492409e+00 -1.29171000e+01 2.07611762e+01 13 2.12518511e+01 -1.17469634e+01 -3.88651385e+00 14 -7.98517401e+00 -1.03096949e+01 -1.07791172e+01 15 -3.80356209e-01 -1.87288112e+01 -9.36556533e+00 16 5.95786407e-01 2.49694633e+00 -1.30531483e+01 17 -3.15254516e+01 -2.37722350e+01 -7.54701574e+00 18 1.45632035e+01 3.54008224e+01 7.70688101e+00 19 1.29944980e+00 -1.70164160e+01 1.64618128e+01 20 -3.30895743e+00 1.28876873e+01 -1.39872682e+01 21 1.54199440e+01 -9.85172708e-01 5.26213929e-01 22 -2.18942462e+00 8.10616318e+00 -6.38115359e-02 23 -5.75257687e+00 -1.36291973e+01 -1.10043495e+01 24 2.15218942e+01 2.42770307e+01 -1.31505106e+01 25 -6.64651833e+00 -6.71526594e+00 -5.91673076e+00 26 -4.55919570e+01 3.30834658e+01 -4.26223245e+01 27 2.78330366e+01 -6.11739044e+01 6.72885216e+00 28 -4.18003901e+01 5.06880320e+01 -4.43491327e+00 29 3.86975415e+01 -4.72641362e+01 9.63273913e+00 30 1.21448693e+01 2.71456326e+01 1.77372607e+01 31 -1.91213093e+01 -1.10397534e+01 -3.80674013e-01 32 4.96219973e+01 1.90357434e+01 3.03460989e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==1304775== Memcheck, a memory error detector ==1304775== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==1304775== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info ==1304775== Command: python runner2.py EAM_Dynamo_ZhouJohnsonWadley_2004NISTretabulation_CuAgAu__MO_318213562153_000 ==1304775== ==1306170== Warning: invalid file descriptor 1024 in syscall close() ==1306170== Warning: invalid file descriptor 1025 in syscall close() ==1306170== Warning: invalid file descriptor 1026 in syscall close() ==1306170== Warning: invalid file descriptor 1027 in syscall close() ==1306170== Use --log-fd= to select an alternative log fd. ==1306170== Warning: invalid file descriptor 1028 in syscall close() ==1306170== Warning: invalid file descriptor 1029 in syscall close() ==1304775== ==1304775== HEAP SUMMARY: ==1304775== in use at exit: 2,257,767 bytes in 1,704 blocks ==1304775== total heap usage: 102,163 allocs, 100,459 frees, 129,738,999 bytes allocated ==1304775== ==1304775== LEAK SUMMARY: ==1304775== definitely lost: 0 bytes in 0 blocks ==1304775== indirectly lost: 0 bytes in 0 blocks ==1304775== possibly lost: 180,827 bytes in 103 blocks ==1304775== still reachable: 2,076,908 bytes in 1,600 blocks ==1304775== of which reachable via heuristic: ==1304775== stdstring : 38 bytes in 1 blocks ==1304775== suppressed: 32 bytes in 1 blocks ==1304775== Rerun with --leak-check=full to see details of leaked memory ==1304775== ==1304775== For lists of detected and suppressed errors, rerun with: -s ==1304775== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 8138 from 561) ================================================================================ 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.