!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 ----------------------------------------------------------------------------------------------------- Results for KIM Model : EAM_Dynamo_AdamsFoilesWolfer_1989Universal6_Pd__MO_169076431435_000 Supported species : Pd random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Pd (Configuration in file "config-F-Pd.xyz") ----------------------------------------------------------------------------------------------------- Energy = 141.98386501044448 Forces: 1 -1.22094714e+01 -2.45038094e+01 -2.82604412e+01 2 -8.23368770e+00 1.46658582e+01 -2.14622516e+01 3 1.29210808e+01 -2.15952007e+01 -9.33882087e-02 4 -1.82026304e+01 2.25492063e+01 1.42702172e+01 5 1.52280739e+01 -2.83561179e+01 -5.15447127e+00 6 9.19502563e+00 -4.75402506e+00 -1.33357380e+01 7 1.45549826e+01 -4.70117767e+01 -4.27938916e+01 8 -3.23448042e+01 -2.88995539e+01 -2.59801741e+00 9 -2.00565770e+01 -9.71729072e+00 -3.17450668e+01 10 -6.93640368e+00 3.61833092e+01 -3.54890308e+01 11 -1.56480035e+01 -2.45864306e+01 1.71884880e+01 12 -2.04036947e+01 2.16912285e+01 9.65076972e+00 13 -4.14237685e+00 -1.22331180e+01 -7.01214571e+01 14 1.28377370e+01 1.38569363e+01 -8.53630139e+00 15 7.02689470e+01 1.07704832e+01 1.43464580e+01 16 1.29809172e+01 5.36713857e+01 2.07714707e+01 17 -3.33525990e+01 -1.87265968e+01 -4.50625478e+00 18 1.34362808e+01 1.77014717e+01 -7.48345912e+00 19 1.08108842e+01 -2.58604391e+01 1.84275071e+01 20 -1.55331609e+01 1.18412238e+01 1.82185132e+01 21 -1.76665901e+01 -2.06793892e+01 1.37655755e+01 22 3.78359092e+01 2.89382230e+01 3.10665810e+01 23 6.31189870e+00 -3.95515514e+00 1.38800092e+01 24 8.03446026e+00 4.80602430e+00 1.28050757e+01 25 -2.42021568e+01 -8.12656644e+00 -4.05649737e+00 26 -1.03362340e+01 3.65968499e+01 -1.32695758e+01 27 1.25757521e+01 -4.23892506e+01 2.64767815e+01 28 -3.97429697e+01 3.39256261e+01 1.26638108e+01 29 -1.14159475e+01 -1.51031077e+01 1.72842616e+01 30 1.73715473e+01 2.54433243e+01 -9.07483118e+00 31 2.32279238e+01 -2.08875579e+01 2.80978312e+01 32 1.28358868e+01 2.47442353e+01 2.90673231e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Pd (Configuration in file "config-T-Pd.xyz") ----------------------------------------------------------------------------------------------------- Energy = 141.98386501044448 Forces: 1 -1.22094714e+01 -2.45038094e+01 -2.82604412e+01 2 -8.23368770e+00 1.46658582e+01 -2.14622516e+01 3 1.29210808e+01 -2.15952007e+01 -9.33882087e-02 4 -1.82026304e+01 2.25492063e+01 1.42702172e+01 5 1.52280739e+01 -2.83561179e+01 -5.15447127e+00 6 9.19502563e+00 -4.75402506e+00 -1.33357380e+01 7 1.45549826e+01 -4.70117767e+01 -4.27938916e+01 8 -3.23448042e+01 -2.88995539e+01 -2.59801741e+00 9 -2.00565770e+01 -9.71729072e+00 -3.17450668e+01 10 -6.93640368e+00 3.61833092e+01 -3.54890308e+01 11 -1.56480035e+01 -2.45864306e+01 1.71884880e+01 12 -2.04036947e+01 2.16912285e+01 9.65076972e+00 13 -4.14237685e+00 -1.22331180e+01 -7.01214571e+01 14 1.28377370e+01 1.38569363e+01 -8.53630139e+00 15 7.02689470e+01 1.07704832e+01 1.43464580e+01 16 1.29809172e+01 5.36713857e+01 2.07714707e+01 17 -3.33525990e+01 -1.87265968e+01 -4.50625478e+00 18 1.34362808e+01 1.77014717e+01 -7.48345912e+00 19 1.08108842e+01 -2.58604391e+01 1.84275071e+01 20 -1.55331609e+01 1.18412238e+01 1.82185132e+01 21 -1.76665901e+01 -2.06793892e+01 1.37655755e+01 22 3.78359092e+01 2.89382230e+01 3.10665810e+01 23 6.31189870e+00 -3.95515514e+00 1.38800092e+01 24 8.03446026e+00 4.80602430e+00 1.28050757e+01 25 -2.42021568e+01 -8.12656644e+00 -4.05649737e+00 26 -1.03362340e+01 3.65968499e+01 -1.32695758e+01 27 1.25757521e+01 -4.23892506e+01 2.64767815e+01 28 -3.97429697e+01 3.39256261e+01 1.26638108e+01 29 -1.14159475e+01 -1.51031077e+01 1.72842616e+01 30 1.73715473e+01 2.54433243e+01 -9.07483118e+00 31 2.32279238e+01 -2.08875579e+01 2.80978312e+01 32 1.28358868e+01 2.47442353e+01 2.90673231e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==14120== Memcheck, a memory error detector ==14120== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==14120== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==14120== Command: python runner2.py EAM_Dynamo_AdamsFoilesWolfer_1989Universal6_Pd__MO_169076431435_000 ==14120== ==15654== Warning: invalid file descriptor 1048564 in syscall close() ==15654== Warning: invalid file descriptor 1048565 in syscall close() ==15654== Warning: invalid file descriptor 1048566 in syscall close() ==15654== Warning: invalid file descriptor 1048567 in syscall close() ==15654== Use --log-fd= to select an alternative log fd. ==15654== Warning: invalid file descriptor 1048568 in syscall close() ==15654== Warning: invalid file descriptor 1048569 in syscall close() ==15660== Warning: invalid file descriptor 1048564 in syscall close() ==15660== Warning: invalid file descriptor 1048565 in syscall close() ==15660== Warning: invalid file descriptor 1048566 in syscall close() ==15660== Warning: invalid file descriptor 1048567 in syscall close() ==15660== Use --log-fd= to select an alternative log fd. ==15660== Warning: invalid file descriptor 1048568 in syscall close() ==15660== Warning: invalid file descriptor 1048569 in syscall close() ==15738== Warning: invalid file descriptor 1048564 in syscall close() ==15738== Warning: invalid file descriptor 1048565 in syscall close() ==15738== Warning: invalid file descriptor 1048566 in syscall close() ==15738== Warning: invalid file descriptor 1048567 in syscall close() ==15738== Use --log-fd= to select an alternative log fd. ==15738== Warning: invalid file descriptor 1048568 in syscall close() ==15738== Warning: invalid file descriptor 1048569 in syscall close() ==15744== Warning: invalid file descriptor 1048564 in syscall close() ==15744== Warning: invalid file descriptor 1048565 in syscall close() ==15744== Warning: invalid file descriptor 1048566 in syscall close() ==15744== Warning: invalid file descriptor 1048567 in syscall close() ==15744== Use --log-fd= to select an alternative log fd. ==15744== Warning: invalid file descriptor 1048568 in syscall close() ==15744== Warning: invalid file descriptor 1048569 in syscall close() ==15750== Warning: invalid file descriptor 1048564 in syscall close() ==15750== Warning: invalid file descriptor 1048565 in syscall close() ==15750== Warning: invalid file descriptor 1048566 in syscall close() ==15750== Warning: invalid file descriptor 1048567 in syscall close() ==15750== Use --log-fd= to select an alternative log fd. ==15750== Warning: invalid file descriptor 1048568 in syscall close() ==15750== Warning: invalid file descriptor 1048569 in syscall close() ==15757== Warning: invalid file descriptor 1048564 in syscall close() ==15757== Warning: invalid file descriptor 1048565 in syscall close() ==15757== Warning: invalid file descriptor 1048566 in syscall close() ==15757== Warning: invalid file descriptor 1048567 in syscall close() ==15757== Use --log-fd= to select an alternative log fd. ==15757== Warning: invalid file descriptor 1048568 in syscall close() ==15757== Warning: invalid file descriptor 1048569 in syscall close() ==14120== ==14120== HEAP SUMMARY: ==14120== in use at exit: 1,718,308 bytes in 1,321 blocks ==14120== total heap usage: 31,220 allocs, 29,899 frees, 39,119,124 bytes allocated ==14120== ==14120== LEAK SUMMARY: ==14120== definitely lost: 0 bytes in 0 blocks ==14120== indirectly lost: 0 bytes in 0 blocks ==14120== possibly lost: 178,943 bytes in 97 blocks ==14120== still reachable: 1,539,365 bytes in 1,224 blocks ==14120== suppressed: 0 bytes in 0 blocks ==14120== Rerun with --leak-check=full to see details of leaked memory ==14120== ==14120== For counts of detected and suppressed errors, rerun with: -v ==14120== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16372 from 612) ================================================================================ 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.