Enter a model name: === Verification check vc-memory-leak start (2022-11-30 10:16:29) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_LiuOhotnickyAdams_1997_AlMg__MO_559870613549_000 Supported species : Al Mg random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Al (Configuration in file "config-F-Al.xyz") ----------------------------------------------------------------------------------------------------- Energy = -65.751740028305 Forces: 1 -1.33221294e+00 -1.12663460e+00 -2.13581863e+00 2 -1.09610679e+00 2.22087960e+00 -9.47033463e-01 3 1.81004205e+00 -8.19700331e-01 2.01114771e+00 4 -9.95294587e-01 1.49324390e+00 1.62027735e+00 5 1.11273039e+00 -2.36791910e+00 5.13056012e-02 6 6.37807492e-01 1.39643460e+00 -7.09774256e-01 7 1.57208331e+00 -5.85946643e+00 -5.46435026e+00 8 -3.97342221e+00 -2.54510958e+00 -7.50107444e-01 9 -1.94258969e+00 -1.97505004e+00 -2.94490234e+00 10 -1.05821519e+00 3.53532250e+00 -3.92371089e+00 11 -6.04628994e-01 -2.82508920e+00 3.78066131e+00 12 -7.90968976e-01 1.90314789e+00 1.14101160e+00 13 -1.39172744e+00 -3.19193068e+00 -7.79516228e+00 14 7.08625863e-01 1.39903013e+00 -5.52537139e-01 15 7.24772578e+00 -9.60847933e-01 2.40507482e+00 16 1.72851012e+00 5.54742656e+00 3.03645935e+00 17 -1.62524334e+00 -1.10777064e+00 -1.90400839e+00 18 7.28852601e-01 2.71441847e+00 -2.67300270e+00 19 1.25337601e+00 -2.35417862e+00 2.04277848e+00 20 -4.52451021e-01 1.72205960e+00 9.84886604e-01 21 -2.98747534e+00 -2.12465180e+00 5.37860508e-01 22 2.76572372e+00 5.30267435e+00 4.28831255e+00 23 6.78560872e-01 -2.48409857e-01 8.10667342e-01 24 2.22648074e-01 1.78926011e+00 1.52178597e+00 25 -1.78244520e+00 -1.81845811e+00 2.52863411e-01 26 -1.83269400e+00 3.45475880e+00 -2.13197692e+00 27 2.70360195e+00 -7.13104409e+00 1.56572760e+00 28 -4.05846915e+00 3.82822139e+00 4.57761932e-01 29 -2.45278576e+00 -2.34806203e+00 1.35817932e+00 30 9.70125602e-01 2.97586420e+00 -9.58335354e-01 31 2.70327565e+00 -3.12768509e+00 2.66338270e+00 32 1.53304115e+00 2.64926602e+00 2.36057591e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Al (Configuration in file "config-T-Al.xyz") ----------------------------------------------------------------------------------------------------- Energy = -65.751740028305 Forces: 1 -1.33221294e+00 -1.12663460e+00 -2.13581863e+00 2 -1.09610679e+00 2.22087960e+00 -9.47033463e-01 3 1.81004205e+00 -8.19700331e-01 2.01114771e+00 4 -9.95294587e-01 1.49324390e+00 1.62027735e+00 5 1.11273039e+00 -2.36791910e+00 5.13056012e-02 6 6.37807492e-01 1.39643460e+00 -7.09774256e-01 7 1.57208331e+00 -5.85946643e+00 -5.46435026e+00 8 -3.97342221e+00 -2.54510958e+00 -7.50107444e-01 9 -1.94258969e+00 -1.97505004e+00 -2.94490234e+00 10 -1.05821519e+00 3.53532250e+00 -3.92371089e+00 11 -6.04628994e-01 -2.82508920e+00 3.78066131e+00 12 -7.90968976e-01 1.90314789e+00 1.14101160e+00 13 -1.39172744e+00 -3.19193068e+00 -7.79516228e+00 14 7.08625863e-01 1.39903013e+00 -5.52537139e-01 15 7.24772578e+00 -9.60847933e-01 2.40507482e+00 16 1.72851012e+00 5.54742656e+00 3.03645935e+00 17 -1.62524334e+00 -1.10777064e+00 -1.90400839e+00 18 7.28852601e-01 2.71441847e+00 -2.67300270e+00 19 1.25337601e+00 -2.35417862e+00 2.04277848e+00 20 -4.52451021e-01 1.72205960e+00 9.84886604e-01 21 -2.98747534e+00 -2.12465180e+00 5.37860508e-01 22 2.76572372e+00 5.30267435e+00 4.28831255e+00 23 6.78560872e-01 -2.48409857e-01 8.10667342e-01 24 2.22648074e-01 1.78926011e+00 1.52178597e+00 25 -1.78244520e+00 -1.81845811e+00 2.52863411e-01 26 -1.83269400e+00 3.45475880e+00 -2.13197692e+00 27 2.70360195e+00 -7.13104409e+00 1.56572760e+00 28 -4.05846915e+00 3.82822139e+00 4.57761932e-01 29 -2.45278576e+00 -2.34806203e+00 1.35817932e+00 30 9.70125602e-01 2.97586420e+00 -9.58335354e-01 31 2.70327565e+00 -3.12768509e+00 2.66338270e+00 32 1.53304115e+00 2.64926602e+00 2.36057591e+00 MONOATOMIC STRUCTURE (pbc=False)-- Species = Mg (Configuration in file "config-F-Mg.xyz") ----------------------------------------------------------------------------------------------------- Energy = -14.889074295363113 Forces: 1 -1.38729737e+00 -1.82126091e+00 -1.74206904e+00 2 1.78264831e+00 -1.34802731e+00 -4.27890646e+00 3 5.51777745e-01 -2.04450340e+00 4.07356930e-01 4 -3.87503828e+00 5.09264156e-01 2.23624281e+00 5 -8.46801596e-01 -1.33509731e+00 -1.74224715e+00 6 1.92499317e+00 5.82106139e-01 -2.53336206e+00 7 1.85815011e+00 -1.89968044e+00 3.12804044e-01 8 7.64341040e-01 -2.97899467e+00 4.50842953e-01 9 -1.94064483e+00 6.10544043e-01 -1.47233486e+00 10 -7.66122106e-01 2.10586024e+00 -1.31560804e+00 11 -2.68665866e+00 3.47443795e+00 -9.35368039e-02 12 -1.18715202e+00 8.30011031e-01 3.02009593e-01 13 7.81575134e-01 -1.18948737e+00 -4.42026535e+00 14 1.87956092e+00 1.42322304e+00 -1.95269740e+00 15 3.53409588e+00 2.49891646e-01 1.52792378e+00 16 -1.06468366e+00 2.94387926e+00 1.77338969e+00 17 -1.11980364e+00 -6.51715484e-01 2.24005436e-02 18 5.03920652e-01 -2.68540527e+00 6.27163173e-01 19 1.39922511e-02 -2.11825707e+00 1.02982322e+00 20 -2.82127800e+00 -1.36074716e+00 2.23313385e+00 21 -1.70334637e+00 -2.49012215e+00 6.78934045e-01 22 2.72587061e+00 1.30440531e+00 -3.87241450e-01 23 6.81655581e-01 -8.95447057e-01 8.79147341e-01 24 9.48073054e-01 8.50582745e-01 1.99141904e+00 25 -3.37417354e+00 1.18144203e+00 -1.50847030e+00 26 8.04639804e-01 2.20377027e+00 -2.23362121e-01 27 8.56237134e-01 6.88711349e-01 2.16525483e+00 28 -6.11042199e-01 5.97063342e-01 7.13503396e-01 29 1.19431825e+00 9.19989242e-01 2.28939510e+00 30 1.36911792e+00 1.93399880e+00 -9.44775962e-01 31 8.96495172e-01 -1.23462842e+00 1.86146458e+00 32 3.12579507e-01 1.64419343e+00 1.11266811e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Mg (Configuration in file "config-T-Mg.xyz") ----------------------------------------------------------------------------------------------------- Energy = -14.889074295363113 Forces: 1 -1.38729737e+00 -1.82126091e+00 -1.74206904e+00 2 1.78264831e+00 -1.34802731e+00 -4.27890646e+00 3 5.51777745e-01 -2.04450340e+00 4.07356930e-01 4 -3.87503828e+00 5.09264156e-01 2.23624281e+00 5 -8.46801596e-01 -1.33509731e+00 -1.74224715e+00 6 1.92499317e+00 5.82106139e-01 -2.53336206e+00 7 1.85815011e+00 -1.89968044e+00 3.12804044e-01 8 7.64341040e-01 -2.97899467e+00 4.50842953e-01 9 -1.94064483e+00 6.10544043e-01 -1.47233486e+00 10 -7.66122106e-01 2.10586024e+00 -1.31560804e+00 11 -2.68665866e+00 3.47443795e+00 -9.35368039e-02 12 -1.18715202e+00 8.30011031e-01 3.02009593e-01 13 7.81575134e-01 -1.18948737e+00 -4.42026535e+00 14 1.87956092e+00 1.42322304e+00 -1.95269740e+00 15 3.53409588e+00 2.49891646e-01 1.52792378e+00 16 -1.06468366e+00 2.94387926e+00 1.77338969e+00 17 -1.11980364e+00 -6.51715484e-01 2.24005436e-02 18 5.03920652e-01 -2.68540527e+00 6.27163173e-01 19 1.39922511e-02 -2.11825707e+00 1.02982322e+00 20 -2.82127800e+00 -1.36074716e+00 2.23313385e+00 21 -1.70334637e+00 -2.49012215e+00 6.78934045e-01 22 2.72587061e+00 1.30440531e+00 -3.87241450e-01 23 6.81655581e-01 -8.95447057e-01 8.79147341e-01 24 9.48073054e-01 8.50582745e-01 1.99141904e+00 25 -3.37417354e+00 1.18144203e+00 -1.50847030e+00 26 8.04639804e-01 2.20377027e+00 -2.23362121e-01 27 8.56237134e-01 6.88711349e-01 2.16525483e+00 28 -6.11042199e-01 5.97063342e-01 7.13503396e-01 29 1.19431825e+00 9.19989242e-01 2.28939510e+00 30 1.36911792e+00 1.93399880e+00 -9.44775962e-01 31 8.96495172e-01 -1.23462842e+00 1.86146458e+00 32 3.12579507e-01 1.64419343e+00 1.11266811e+00 MIXED STRUCTURE (pbc=False)-- Species = Al Mg (Configuration in file "config-F-AlMg.xyz") ----------------------------------------------------------------------------------------------------- Energy = -43.8767829802474 Forces: 1 -3.40495558e-01 -1.33315819e+00 -1.43955439e+00 2 -2.51413729e+00 1.32312046e+00 -2.65220567e+00 3 2.02639404e+00 -3.15512852e+00 -1.41190420e+00 4 -2.80657921e+00 2.75887761e+00 2.93781835e-01 5 4.99349125e-01 -2.09665705e+00 -6.28201706e-01 6 3.15124282e-01 1.60910422e+00 -1.14874457e+00 7 5.57782913e-01 -1.23186956e+00 1.92771562e+00 8 4.02595311e+00 -3.45079994e+00 1.79147934e+00 9 -5.76524688e-01 -6.20598333e-01 -6.52241732e-01 10 -7.81737134e-01 1.60684271e+00 -1.27751676e+00 11 -3.57904062e+00 3.39764410e+00 9.63726973e-01 12 9.26516106e-02 8.30096366e-02 1.04718544e+00 13 1.46423670e+00 -5.87006402e-01 -1.85716985e+00 14 1.23640085e-01 2.88314061e-01 -1.82259594e-01 15 8.31451834e-01 -1.20509347e+00 -5.91215388e-01 16 4.88525517e-01 9.64806809e-01 2.82127813e-01 17 -4.53770662e+00 -2.73381324e+00 -1.79118348e+00 18 2.65647212e+00 4.88883408e+00 5.44062355e-02 19 2.73418940e+00 -3.54797122e+00 3.76289701e+00 20 -2.23221534e+00 2.42447061e+00 1.78970647e+00 21 1.31688694e+00 -1.51479078e+00 -7.14143486e-01 22 5.19900969e-01 1.38562610e+00 -4.82761505e-01 23 6.84570826e-01 -9.55051111e-01 4.53191244e-01 24 -5.31717360e-01 2.01059796e+00 6.79412867e-01 25 -1.37645659e+00 -3.52964884e-01 -9.12605128e-01 26 -4.52100792e+00 3.65090994e+00 -4.66218469e+00 27 2.09964268e+00 -3.96764777e+00 2.41350194e+00 28 -2.53599464e+00 2.65896628e+00 6.42386366e-01 29 2.66980571e+00 -4.56898264e+00 9.59559414e-02 30 4.82611830e-01 2.27368531e+00 -5.23975583e-02 31 -3.12297024e-01 -1.14526063e+00 9.47403594e-01 32 3.05672031e+00 1.14198384e+00 3.31141101e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==1443529== Memcheck, a memory error detector ==1443529== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==1443529== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info ==1443529== Command: python runner2.py EAM_Dynamo_LiuOhotnickyAdams_1997_AlMg__MO_559870613549_000 ==1443529== ==1445023== Warning: invalid file descriptor 1024 in syscall close() ==1445023== Warning: invalid file descriptor 1025 in syscall close() ==1445023== Warning: invalid file descriptor 1026 in syscall close() ==1445023== Warning: invalid file descriptor 1027 in syscall close() ==1445023== Use --log-fd= to select an alternative log fd. ==1445023== Warning: invalid file descriptor 1028 in syscall close() ==1445023== Warning: invalid file descriptor 1029 in syscall close() ==1443529== ==1443529== HEAP SUMMARY: ==1443529== in use at exit: 2,257,799 bytes in 1,705 blocks ==1443529== total heap usage: 92,557 allocs, 90,852 frees, 88,162,893 bytes allocated ==1443529== ==1443529== LEAK SUMMARY: ==1443529== definitely lost: 0 bytes in 0 blocks ==1443529== indirectly lost: 0 bytes in 0 blocks ==1443529== possibly lost: 180,827 bytes in 103 blocks ==1443529== still reachable: 2,076,940 bytes in 1,601 blocks ==1443529== of which reachable via heuristic: ==1443529== stdstring : 38 bytes in 1 blocks ==1443529== suppressed: 32 bytes in 1 blocks ==1443529== Rerun with --leak-check=full to see details of leaked memory ==1443529== ==1443529== For lists of detected and suppressed errors, rerun with: -s ==1443529== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 8120 from 563) ================================================================================ 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. === Verification check vc-memory-leak end (2022-11-30 10:17:05) ===