!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_LiuAdams_1998_AlMg__MO_019873715786_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 = 84.87627804952577 Forces: 1 -5.79149304e+00 -6.87900314e+00 -7.14681529e+00 2 -1.62243808e+00 2.15066864e+00 -1.08811680e+01 3 3.28929954e+00 -1.05142283e+01 -1.54389710e+00 4 -9.40346008e+00 1.67894555e-01 3.73817391e+00 5 -1.81143008e+00 -1.28242751e+01 -9.08094252e+00 6 9.63887380e+00 3.04877085e+00 -1.19718712e+01 7 1.01236962e+01 -1.14124588e+01 9.72951260e-01 8 -3.97651879e+00 -4.62691510e+00 1.94446115e+00 9 -7.91296513e+00 -3.13392972e+00 -1.57318061e+01 10 1.48585952e+00 1.39475376e+01 -1.16069363e+01 11 -3.81697576e+00 -7.08086798e+00 3.67554769e+00 12 -1.23359031e+01 1.24718064e+01 3.86518691e+00 13 -1.88897617e-01 -3.00476428e+00 -1.74395170e+01 14 1.17503544e+01 1.05921965e+01 -9.47620358e+00 15 1.62187462e+01 -5.28646923e+00 3.60554919e-01 16 -8.43034143e-01 1.75031255e+01 2.66835359e+00 17 -1.57268794e+01 -8.07482069e+00 -3.91545176e+00 18 2.99606994e+00 7.76512052e+00 -1.73405549e-01 19 6.05797602e+00 -1.30132790e+01 1.00091253e+01 20 -7.88831730e+00 8.08229048e+00 8.81647360e+00 21 -5.97315613e+00 -1.14943887e+01 2.39996045e+00 22 1.33655075e+01 6.93667099e+00 2.32824983e+00 23 5.94000328e+00 -4.49644721e+00 8.72315504e+00 24 -1.48013189e+00 1.49249306e+00 7.35744228e+00 25 -1.22886987e+01 -5.02193509e+00 3.68013204e+00 26 1.04967682e+00 1.68931912e+01 -6.34153855e+00 27 -2.15509792e+00 -9.72085672e+00 1.00015689e+01 28 -9.42817177e+00 5.87236339e+00 5.60226887e+00 29 -3.20916979e+00 -8.48468990e+00 6.21405526e+00 30 1.01695698e+01 1.26674392e+01 1.92039467e-01 31 1.09463358e+01 -5.54510834e+00 9.28009140e+00 32 2.82076970e+00 1.10228684e+01 1.34797611e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Al (Configuration in file "config-T-Al.xyz") ----------------------------------------------------------------------------------------------------- Energy = 84.87627804952577 Forces: 1 -5.79149304e+00 -6.87900314e+00 -7.14681529e+00 2 -1.62243808e+00 2.15066864e+00 -1.08811680e+01 3 3.28929954e+00 -1.05142283e+01 -1.54389710e+00 4 -9.40346008e+00 1.67894555e-01 3.73817391e+00 5 -1.81143008e+00 -1.28242751e+01 -9.08094252e+00 6 9.63887380e+00 3.04877085e+00 -1.19718712e+01 7 1.01236962e+01 -1.14124588e+01 9.72951260e-01 8 -3.97651879e+00 -4.62691510e+00 1.94446115e+00 9 -7.91296513e+00 -3.13392972e+00 -1.57318061e+01 10 1.48585952e+00 1.39475376e+01 -1.16069363e+01 11 -3.81697576e+00 -7.08086798e+00 3.67554769e+00 12 -1.23359031e+01 1.24718064e+01 3.86518691e+00 13 -1.88897617e-01 -3.00476428e+00 -1.74395170e+01 14 1.17503544e+01 1.05921965e+01 -9.47620358e+00 15 1.62187462e+01 -5.28646923e+00 3.60554919e-01 16 -8.43034143e-01 1.75031255e+01 2.66835359e+00 17 -1.57268794e+01 -8.07482069e+00 -3.91545176e+00 18 2.99606994e+00 7.76512052e+00 -1.73405549e-01 19 6.05797602e+00 -1.30132790e+01 1.00091253e+01 20 -7.88831730e+00 8.08229048e+00 8.81647360e+00 21 -5.97315613e+00 -1.14943887e+01 2.39996045e+00 22 1.33655075e+01 6.93667099e+00 2.32824983e+00 23 5.94000328e+00 -4.49644721e+00 8.72315504e+00 24 -1.48013189e+00 1.49249306e+00 7.35744228e+00 25 -1.22886987e+01 -5.02193509e+00 3.68013204e+00 26 1.04967682e+00 1.68931912e+01 -6.34153855e+00 27 -2.15509792e+00 -9.72085672e+00 1.00015689e+01 28 -9.42817177e+00 5.87236339e+00 5.60226887e+00 29 -3.20916979e+00 -8.48468990e+00 6.21405526e+00 30 1.01695698e+01 1.26674392e+01 1.92039467e-01 31 1.09463358e+01 -5.54510834e+00 9.28009140e+00 32 2.82076970e+00 1.10228684e+01 1.34797611e+01 MONOATOMIC STRUCTURE (pbc=False)-- Species = Mg (Configuration in file "config-F-Mg.xyz") ----------------------------------------------------------------------------------------------------- Energy = 116.37745542741492 Forces: 1 -4.50703516e+00 -5.34377074e+00 -6.48816195e+00 2 6.20644842e-01 -1.43731329e+00 -9.36171916e+00 3 2.47639696e-01 -1.01493591e+01 -2.11325197e+00 4 -1.08130668e+01 1.52644542e+00 1.19146193e+00 5 8.28811245e-01 -7.20182760e+00 -7.86803222e+00 6 7.89587623e+00 2.55882067e-02 -7.70394045e+00 7 8.91760313e+00 -8.79103993e+00 -1.88443803e+00 8 -8.44295151e-01 5.95913768e-01 -1.75040253e+00 9 -1.00592295e+01 -1.24730205e+00 -8.69119446e+00 10 4.00864863e-01 1.00098656e+01 -1.00330285e+01 11 -3.17503275e-01 -3.35028776e+00 1.59463344e+00 12 -1.12978099e+01 9.05042780e+00 1.97771651e-01 13 2.90078372e+00 -1.36474975e+00 -1.04795280e+01 14 6.38699537e+00 4.76883604e+00 -4.66868865e+00 15 1.06330809e+01 1.86626871e+00 -1.14422357e+00 16 3.54112075e+00 1.11391938e+01 9.89460617e-01 17 -8.86713150e+00 -1.04998572e+01 9.10341050e-02 18 -3.10126165e-01 2.05228150e+00 -1.74938878e+00 19 2.30465095e+00 -8.50559103e+00 9.26689052e+00 20 -9.62033112e+00 8.27934736e-01 8.59031598e+00 21 -1.85049981e-01 -1.22411647e+01 1.43418094e+00 22 1.01794189e+01 4.54375565e-01 1.66959870e-01 23 5.45772502e+00 -6.04669403e+00 5.26866331e+00 24 -2.71739561e-01 -2.44019807e+00 1.18072357e+01 25 -1.11725659e+01 -1.58401654e+00 -2.38874782e-02 26 -3.15174164e-01 1.13563478e+01 3.34724699e+00 27 -1.13568116e+00 2.17812727e+00 1.20303177e+01 28 -4.30650927e+00 4.94428780e+00 4.68183469e+00 29 -1.16875671e+00 1.96942841e+00 -1.43607964e+00 30 7.72351533e+00 8.72857752e+00 -1.30227014e+00 31 8.71204891e+00 1.80233745e-01 8.03461753e+00 32 -1.55877457e+00 8.52903793e+00 8.00561051e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Mg (Configuration in file "config-T-Mg.xyz") ----------------------------------------------------------------------------------------------------- Energy = 116.37745542741492 Forces: 1 -4.50703516e+00 -5.34377074e+00 -6.48816195e+00 2 6.20644842e-01 -1.43731329e+00 -9.36171916e+00 3 2.47639696e-01 -1.01493591e+01 -2.11325197e+00 4 -1.08130668e+01 1.52644542e+00 1.19146193e+00 5 8.28811245e-01 -7.20182760e+00 -7.86803222e+00 6 7.89587623e+00 2.55882067e-02 -7.70394045e+00 7 8.91760313e+00 -8.79103993e+00 -1.88443803e+00 8 -8.44295151e-01 5.95913768e-01 -1.75040253e+00 9 -1.00592295e+01 -1.24730205e+00 -8.69119446e+00 10 4.00864863e-01 1.00098656e+01 -1.00330285e+01 11 -3.17503275e-01 -3.35028776e+00 1.59463344e+00 12 -1.12978099e+01 9.05042780e+00 1.97771651e-01 13 2.90078372e+00 -1.36474975e+00 -1.04795280e+01 14 6.38699537e+00 4.76883604e+00 -4.66868865e+00 15 1.06330809e+01 1.86626871e+00 -1.14422357e+00 16 3.54112075e+00 1.11391938e+01 9.89460617e-01 17 -8.86713150e+00 -1.04998572e+01 9.10341050e-02 18 -3.10126165e-01 2.05228150e+00 -1.74938878e+00 19 2.30465095e+00 -8.50559103e+00 9.26689052e+00 20 -9.62033112e+00 8.27934736e-01 8.59031598e+00 21 -1.85049981e-01 -1.22411647e+01 1.43418094e+00 22 1.01794189e+01 4.54375565e-01 1.66959870e-01 23 5.45772502e+00 -6.04669403e+00 5.26866331e+00 24 -2.71739561e-01 -2.44019807e+00 1.18072357e+01 25 -1.11725659e+01 -1.58401654e+00 -2.38874782e-02 26 -3.15174164e-01 1.13563478e+01 3.34724699e+00 27 -1.13568116e+00 2.17812727e+00 1.20303177e+01 28 -4.30650927e+00 4.94428780e+00 4.68183469e+00 29 -1.16875671e+00 1.96942841e+00 -1.43607964e+00 30 7.72351533e+00 8.72857752e+00 -1.30227014e+00 31 8.71204891e+00 1.80233745e-01 8.03461753e+00 32 -1.55877457e+00 8.52903793e+00 8.00561051e+00 MIXED STRUCTURE (pbc=False)-- Species = Al Mg (Configuration in file "config-F-AlMg.xyz") ----------------------------------------------------------------------------------------------------- Energy = 111.97442495938112 Forces: 1 -9.30506878e+00 -9.08281740e+00 -8.74640424e+00 2 1.69592612e+00 2.57665613e+00 -1.65935750e+01 3 1.38722875e+00 -1.33383579e+01 2.42215286e+00 4 -1.28447761e+01 -9.41161193e-01 2.34607254e+00 5 6.13142603e-01 -9.41255968e+00 -9.63268155e+00 6 1.05209667e+01 1.28004828e+00 -1.10385856e+01 7 1.04443725e+01 -1.01906111e+01 -3.03986228e-01 8 -7.27740481e-01 -1.62680540e+00 -1.53501901e+00 9 -1.07023224e+01 8.72040741e-02 -9.19273569e+00 10 -8.31672039e-01 1.09135361e+01 -1.13516995e+01 11 2.07927301e+00 -2.49533341e+00 -5.40699073e-01 12 -9.88149733e+00 1.01737157e+01 -8.67451271e-01 13 1.50035455e+00 4.13865015e-01 -1.26376567e+01 14 7.42950270e+00 4.34474904e+00 -4.33138234e+00 15 1.15293858e+01 8.21420754e-01 -7.02185347e-01 16 2.09203260e+00 1.20054255e+01 -1.52317992e-01 17 -1.06755428e+01 -1.14381065e+01 -1.60887849e+00 18 1.50292506e+00 2.20855566e+00 -1.38151697e-01 19 5.51664177e-01 -1.09287818e+01 1.01204159e+01 20 -1.20164367e+01 1.55046761e+00 1.06735063e+01 21 -1.96300700e+00 -1.54932762e+01 -2.54196737e+00 22 1.36426859e+01 1.01130648e+00 1.77630828e+00 23 6.97142864e+00 -7.14746575e+00 7.86461395e+00 24 6.07573912e-01 1.80490106e+00 1.46929460e+01 25 -1.65566094e+01 -2.10022890e+00 3.00949204e+00 26 1.78401356e+00 1.54489993e+01 3.22215049e+00 27 -3.02600337e-01 9.35812654e-01 1.32749519e+01 28 -6.22413817e+00 6.01672731e+00 5.51603564e+00 29 1.67446974e+00 2.80189271e+00 7.25964668e-01 30 7.01145639e+00 1.01659280e+01 2.04930481e+00 31 7.87007801e+00 1.24226720e+00 7.73563915e+00 32 1.12293080e+00 8.39202666e+00 6.48582267e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==36811== Memcheck, a memory error detector ==36811== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==36811== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==36811== Command: python runner2.py EAM_Dynamo_LiuAdams_1998_AlMg__MO_019873715786_000 ==36811== ==38562== Warning: invalid file descriptor 1048564 in syscall close() ==38562== Warning: invalid file descriptor 1048565 in syscall close() ==38562== Warning: invalid file descriptor 1048566 in syscall close() ==38562== Warning: invalid file descriptor 1048567 in syscall close() ==38562== Use --log-fd= to select an alternative log fd. ==38562== Warning: invalid file descriptor 1048568 in syscall close() ==38562== Warning: invalid file descriptor 1048569 in syscall close() ==38563== Warning: invalid file descriptor 1048564 in syscall close() ==38563== Warning: invalid file descriptor 1048565 in syscall close() ==38563== Warning: invalid file descriptor 1048566 in syscall close() ==38563== Warning: invalid file descriptor 1048567 in syscall close() ==38563== Use --log-fd= to select an alternative log fd. ==38563== Warning: invalid file descriptor 1048568 in syscall close() ==38563== Warning: invalid file descriptor 1048569 in syscall close() ==38568== Warning: invalid file descriptor 1048564 in syscall close() ==38568== Warning: invalid file descriptor 1048565 in syscall close() ==38568== Warning: invalid file descriptor 1048566 in syscall close() ==38568== Warning: invalid file descriptor 1048567 in syscall close() ==38568== Use --log-fd= to select an alternative log fd. ==38568== Warning: invalid file descriptor 1048568 in syscall close() ==38568== Warning: invalid file descriptor 1048569 in syscall close() ==38569== Warning: invalid file descriptor 1048564 in syscall close() ==38569== Warning: invalid file descriptor 1048565 in syscall close() ==38569== Warning: invalid file descriptor 1048566 in syscall close() ==38569== Warning: invalid file descriptor 1048567 in syscall close() ==38569== Use --log-fd= to select an alternative log fd. ==38569== Warning: invalid file descriptor 1048568 in syscall close() ==38569== Warning: invalid file descriptor 1048569 in syscall close() ==38570== Warning: invalid file descriptor 1048564 in syscall close() ==38570== Warning: invalid file descriptor 1048565 in syscall close() ==38570== Warning: invalid file descriptor 1048566 in syscall close() ==38570== Warning: invalid file descriptor 1048567 in syscall close() ==38570== Use --log-fd= to select an alternative log fd. ==38570== Warning: invalid file descriptor 1048568 in syscall close() ==38570== Warning: invalid file descriptor 1048569 in syscall close() ==38571== Warning: invalid file descriptor 1048564 in syscall close() ==38571== Warning: invalid file descriptor 1048565 in syscall close() ==38571== Warning: invalid file descriptor 1048566 in syscall close() ==38571== Warning: invalid file descriptor 1048567 in syscall close() ==38571== Use --log-fd= to select an alternative log fd. ==38571== Warning: invalid file descriptor 1048568 in syscall close() ==38571== Warning: invalid file descriptor 1048569 in syscall close() ==38581== Warning: invalid file descriptor 1048564 in syscall close() ==38581== Warning: invalid file descriptor 1048565 in syscall close() ==38581== Warning: invalid file descriptor 1048566 in syscall close() ==38581== Warning: invalid file descriptor 1048567 in syscall close() ==38581== Use --log-fd= to select an alternative log fd. ==38581== Warning: invalid file descriptor 1048568 in syscall close() ==38581== Warning: invalid file descriptor 1048569 in syscall close() ==38582== Warning: invalid file descriptor 1048564 in syscall close() ==38582== Warning: invalid file descriptor 1048565 in syscall close() ==38582== Warning: invalid file descriptor 1048566 in syscall close() ==38582== Warning: invalid file descriptor 1048567 in syscall close() ==38582== Use --log-fd= to select an alternative log fd. ==38582== Warning: invalid file descriptor 1048568 in syscall close() ==38582== Warning: invalid file descriptor 1048569 in syscall close() ==38583== Warning: invalid file descriptor 1048564 in syscall close() ==38583== Warning: invalid file descriptor 1048565 in syscall close() ==38583== Warning: invalid file descriptor 1048566 in syscall close() ==38583== Warning: invalid file descriptor 1048567 in syscall close() ==38583== Use --log-fd= to select an alternative log fd. ==38583== Warning: invalid file descriptor 1048568 in syscall close() ==38583== Warning: invalid file descriptor 1048569 in syscall close() ==38584== Warning: invalid file descriptor 1048564 in syscall close() ==38584== Warning: invalid file descriptor 1048565 in syscall close() ==38584== Warning: invalid file descriptor 1048566 in syscall close() ==38584== Warning: invalid file descriptor 1048567 in syscall close() ==38584== Use --log-fd= to select an alternative log fd. ==38584== Warning: invalid file descriptor 1048568 in syscall close() ==38584== Warning: invalid file descriptor 1048569 in syscall close() ==38587== Warning: invalid file descriptor 1048564 in syscall close() ==38587== Warning: invalid file descriptor 1048565 in syscall close() ==38587== Warning: invalid file descriptor 1048566 in syscall close() ==38587== Warning: invalid file descriptor 1048567 in syscall close() ==38587== Use --log-fd= to select an alternative log fd. ==38587== Warning: invalid file descriptor 1048568 in syscall close() ==38587== Warning: invalid file descriptor 1048569 in syscall close() ==38589== Warning: invalid file descriptor 1048564 in syscall close() ==38589== Warning: invalid file descriptor 1048565 in syscall close() ==38589== Warning: invalid file descriptor 1048566 in syscall close() ==38589== Warning: invalid file descriptor 1048567 in syscall close() ==38589== Use --log-fd= to select an alternative log fd. ==38589== Warning: invalid file descriptor 1048568 in syscall close() ==38589== Warning: invalid file descriptor 1048569 in syscall close() ==38591== Warning: invalid file descriptor 1048564 in syscall close() ==38591== Warning: invalid file descriptor 1048565 in syscall close() ==38591== Warning: invalid file descriptor 1048566 in syscall close() ==38591== Warning: invalid file descriptor 1048567 in syscall close() ==38591== Use --log-fd= to select an alternative log fd. ==38591== Warning: invalid file descriptor 1048568 in syscall close() ==38591== Warning: invalid file descriptor 1048569 in syscall close() ==38593== Warning: invalid file descriptor 1048564 in syscall close() ==38593== Warning: invalid file descriptor 1048565 in syscall close() ==38593== Warning: invalid file descriptor 1048566 in syscall close() ==38593== Warning: invalid file descriptor 1048567 in syscall close() ==38593== Use --log-fd= to select an alternative log fd. ==38593== Warning: invalid file descriptor 1048568 in syscall close() ==38593== Warning: invalid file descriptor 1048569 in syscall close() ==36811== ==36811== HEAP SUMMARY: ==36811== in use at exit: 1,719,294 bytes in 1,331 blocks ==36811== total heap usage: 45,360 allocs, 44,029 frees, 49,045,299 bytes allocated ==36811== ==36811== LEAK SUMMARY: ==36811== definitely lost: 0 bytes in 0 blocks ==36811== indirectly lost: 0 bytes in 0 blocks ==36811== possibly lost: 178,943 bytes in 97 blocks ==36811== still reachable: 1,540,351 bytes in 1,234 blocks ==36811== suppressed: 0 bytes in 0 blocks ==36811== Rerun with --leak-check=full to see details of leaked memory ==36811== ==36811== For counts of detected and suppressed errors, rerun with: -v ==36811== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 11328 from 594) ================================================================================ 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.