!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_PunYamakovMishin_2013_AlCo__MO_678952612413_000 Supported species : Al Co 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 = 15.748816483952284 Forces: 1 -3.32162199e+00 -2.71300023e+00 -3.36275383e+00 2 1.54871207e+00 -1.27660982e+00 -6.91169765e+00 3 2.36517606e+00 -6.00636464e+00 5.90553202e-01 4 -6.54962087e+00 2.23910015e+00 -1.91217463e-01 5 -1.06656256e+00 -4.38847396e+00 -3.37430556e+00 6 3.91511222e+00 1.32338239e+00 -3.92406613e+00 7 3.38281527e+00 -3.63218127e+00 -2.44533702e-01 8 -1.00222258e+00 -2.00451364e+00 1.11383409e+00 9 -4.44345893e+00 -3.71816170e-01 -5.60228727e+00 10 5.99657894e-01 6.29311272e+00 -4.91647929e+00 11 -2.64053314e+00 -2.60777589e+00 -4.18957555e-01 12 -5.78210754e+00 4.78440302e+00 1.07239430e+00 13 2.13438604e+00 -1.63800197e+00 -7.32135649e+00 14 4.45056715e+00 3.92477590e+00 -4.84225819e+00 15 6.95307838e+00 -1.92040836e+00 -6.87301117e-01 16 -2.10717474e+00 8.77559510e+00 -6.59957539e-01 17 -5.81740313e+00 -4.53392588e+00 1.98383034e-01 18 1.68181027e+00 5.03823555e-01 -5.29389044e-01 19 2.36383466e+00 -5.91260672e+00 3.58786943e+00 20 -4.53291514e+00 2.10375186e+00 5.28772038e+00 21 -2.22324160e+00 -4.54991930e+00 8.40256659e-01 22 5.67890564e+00 1.04095799e+00 5.70112364e-01 23 2.61351873e+00 -1.90940832e+00 4.18526229e+00 24 9.64954235e-01 -8.50093998e-01 4.75954576e+00 25 -6.20728022e+00 -1.12678807e+00 -7.12281380e-01 26 5.08469748e-01 7.22825913e+00 -1.14053229e+00 27 -1.09940743e+00 -1.37664178e+00 6.09638427e+00 28 -4.54190987e+00 3.00072388e+00 3.47790985e+00 29 3.69218618e-01 -3.17290396e+00 1.97507436e+00 30 5.34550452e+00 5.09108759e+00 1.76371820e+00 31 4.76341002e+00 -9.09565054e-01 4.24297631e+00 32 1.69632823e+00 4.59202574e+00 5.07737999e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Al (Configuration in file "config-T-Al.xyz") ----------------------------------------------------------------------------------------------------- Energy = 15.748816483952284 Forces: 1 -3.32162199e+00 -2.71300023e+00 -3.36275383e+00 2 1.54871207e+00 -1.27660982e+00 -6.91169765e+00 3 2.36517606e+00 -6.00636464e+00 5.90553202e-01 4 -6.54962087e+00 2.23910015e+00 -1.91217463e-01 5 -1.06656256e+00 -4.38847396e+00 -3.37430556e+00 6 3.91511222e+00 1.32338239e+00 -3.92406613e+00 7 3.38281527e+00 -3.63218127e+00 -2.44533702e-01 8 -1.00222258e+00 -2.00451364e+00 1.11383409e+00 9 -4.44345893e+00 -3.71816170e-01 -5.60228727e+00 10 5.99657894e-01 6.29311272e+00 -4.91647929e+00 11 -2.64053314e+00 -2.60777589e+00 -4.18957555e-01 12 -5.78210754e+00 4.78440302e+00 1.07239430e+00 13 2.13438604e+00 -1.63800197e+00 -7.32135649e+00 14 4.45056715e+00 3.92477590e+00 -4.84225819e+00 15 6.95307838e+00 -1.92040836e+00 -6.87301117e-01 16 -2.10717474e+00 8.77559510e+00 -6.59957539e-01 17 -5.81740313e+00 -4.53392588e+00 1.98383034e-01 18 1.68181027e+00 5.03823555e-01 -5.29389044e-01 19 2.36383466e+00 -5.91260672e+00 3.58786943e+00 20 -4.53291514e+00 2.10375186e+00 5.28772038e+00 21 -2.22324160e+00 -4.54991930e+00 8.40256659e-01 22 5.67890564e+00 1.04095799e+00 5.70112364e-01 23 2.61351873e+00 -1.90940832e+00 4.18526229e+00 24 9.64954235e-01 -8.50093998e-01 4.75954576e+00 25 -6.20728022e+00 -1.12678807e+00 -7.12281380e-01 26 5.08469748e-01 7.22825913e+00 -1.14053229e+00 27 -1.09940743e+00 -1.37664178e+00 6.09638427e+00 28 -4.54190987e+00 3.00072388e+00 3.47790985e+00 29 3.69218618e-01 -3.17290396e+00 1.97507436e+00 30 5.34550452e+00 5.09108759e+00 1.76371820e+00 31 4.76341002e+00 -9.09565054e-01 4.24297631e+00 32 1.69632823e+00 4.59202574e+00 5.07737999e+00 MONOATOMIC STRUCTURE (pbc=False)-- Species = Co (Configuration in file "config-F-Co.xyz") ----------------------------------------------------------------------------------------------------- Energy = 1456.0317966828768 Forces: 1 -3.63983422e+01 -1.16324659e+02 -1.21564129e+02 2 1.93466316e+02 -9.21612052e+01 -8.11902413e+01 3 3.53778501e+01 -6.58561780e+01 -2.06228513e+01 4 -7.78416724e+01 7.80622464e+01 1.32210026e+02 5 -5.84262896e+02 -2.03686379e+02 -6.82780395e+02 6 6.06983392e+02 2.42990439e+02 -8.09884700e+02 7 1.28684658e+03 -9.26253794e+02 6.11509181e+02 8 -1.29191089e+03 8.38255076e+02 8.57377847e+02 9 -1.49771316e+02 1.08547288e+02 -2.48393746e+01 10 -1.63667951e+02 2.93050473e+01 -1.14262394e+02 11 1.07422487e+03 1.81331519e+02 -8.70072315e+02 12 -1.01344656e+01 1.97171134e+01 1.03176326e+00 13 -9.51586634e+02 -2.72883654e+03 -3.22276610e+02 14 1.44575651e+03 1.79738814e+03 -9.02235077e+02 15 3.30686357e+01 2.25024865e+01 -2.38565489e+00 16 -3.50054412e+02 9.57911165e+02 1.31428510e+03 17 -3.20990767e+01 -3.20649419e+01 1.42407660e+01 18 2.55635175e+01 3.37178777e+01 3.86375284e+01 19 2.94019735e+00 -3.94194254e+00 5.30872081e+00 20 -7.26667924e+00 -6.35149235e+00 7.64920994e-01 21 -7.76577907e+00 -3.31769625e+01 -3.55891804e+01 22 8.20812884e+02 1.89996781e+02 -7.83129669e+02 23 2.15243367e+01 -1.40227267e+01 1.85750280e+01 24 -8.36213214e+02 -2.40849762e+02 7.85790746e+02 25 -1.06951945e+03 -1.37007961e+02 9.31278148e+02 26 1.87145939e+02 -5.84476892e+01 -4.11687948e+02 27 1.13831659e+02 -3.44258063e+02 6.24225706e+01 28 -3.30435690e+02 4.21708622e+02 3.36156781e+02 29 -7.37696941e+00 -3.70453191e+01 -2.80065045e+01 30 1.32536813e+01 2.40096866e+01 -1.90257757e+01 31 2.20490377e+01 5.85815566e+01 6.71858933e+01 32 2.34600379e+01 3.62605748e+01 5.27777977e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Co (Configuration in file "config-T-Co.xyz") ----------------------------------------------------------------------------------------------------- Energy = 1456.0317966828768 Forces: 1 -3.63983422e+01 -1.16324659e+02 -1.21564129e+02 2 1.93466316e+02 -9.21612052e+01 -8.11902413e+01 3 3.53778501e+01 -6.58561780e+01 -2.06228513e+01 4 -7.78416724e+01 7.80622464e+01 1.32210026e+02 5 -5.84262896e+02 -2.03686379e+02 -6.82780395e+02 6 6.06983392e+02 2.42990439e+02 -8.09884700e+02 7 1.28684658e+03 -9.26253794e+02 6.11509181e+02 8 -1.29191089e+03 8.38255076e+02 8.57377847e+02 9 -1.49771316e+02 1.08547288e+02 -2.48393746e+01 10 -1.63667951e+02 2.93050473e+01 -1.14262394e+02 11 1.07422487e+03 1.81331519e+02 -8.70072315e+02 12 -1.01344656e+01 1.97171134e+01 1.03176326e+00 13 -9.51586634e+02 -2.72883654e+03 -3.22276610e+02 14 1.44575651e+03 1.79738814e+03 -9.02235077e+02 15 3.30686357e+01 2.25024865e+01 -2.38565489e+00 16 -3.50054412e+02 9.57911165e+02 1.31428510e+03 17 -3.20990767e+01 -3.20649419e+01 1.42407660e+01 18 2.55635175e+01 3.37178777e+01 3.86375284e+01 19 2.94019735e+00 -3.94194254e+00 5.30872081e+00 20 -7.26667924e+00 -6.35149235e+00 7.64920994e-01 21 -7.76577907e+00 -3.31769625e+01 -3.55891804e+01 22 8.20812884e+02 1.89996781e+02 -7.83129669e+02 23 2.15243367e+01 -1.40227267e+01 1.85750280e+01 24 -8.36213214e+02 -2.40849762e+02 7.85790746e+02 25 -1.06951945e+03 -1.37007961e+02 9.31278148e+02 26 1.87145939e+02 -5.84476892e+01 -4.11687948e+02 27 1.13831659e+02 -3.44258063e+02 6.24225706e+01 28 -3.30435690e+02 4.21708622e+02 3.36156781e+02 29 -7.37696941e+00 -3.70453191e+01 -2.80065045e+01 30 1.32536813e+01 2.40096866e+01 -1.90257757e+01 31 2.20490377e+01 5.85815566e+01 6.71858933e+01 32 2.34600379e+01 3.62605748e+01 5.27777977e+01 MIXED STRUCTURE (pbc=False)-- Species = Al Co (Configuration in file "config-F-AlCo.xyz") ----------------------------------------------------------------------------------------------------- Energy = 1659.267343453613 Forces: 1 6.66132956e+00 -7.70289879e+01 -1.28999088e+02 2 -2.30762902e+02 1.43424818e+02 -7.38619121e+01 3 3.84161874e+02 -6.81154122e+02 -2.26076090e+02 4 -7.28964262e+02 8.96155388e+02 -2.24703803e+02 5 -7.02436151e+01 -2.53906710e+02 -2.23543229e+02 6 2.51263180e+02 5.41965581e+02 -4.31804426e+02 7 2.68229571e+02 -4.96997951e+02 3.55698195e+02 8 -2.09241512e+00 8.37362729e+02 -5.22846298e+02 9 -1.22796006e+02 -1.97801206e+02 -1.93633854e+02 10 2.89018561e+02 1.67078760e+02 -2.61445461e+02 11 4.81800295e+02 -4.00161877e+02 -1.72412336e+02 12 -9.03875019e+02 3.36125342e+02 5.40214411e+01 13 -8.96571369e+01 -9.85390559e+01 -1.21324216e+01 14 1.90898095e+02 5.62536653e+02 -3.90900643e+02 15 -6.91500019e+01 -4.60377562e+02 3.71624836e+02 16 -1.57767304e+01 4.27434578e+01 -3.15292960e+01 17 7.22532208e+01 -4.91446737e+02 3.10895531e+02 18 2.87876706e+02 -3.94604827e+02 -4.62534382e+02 19 2.63728898e+02 -2.79080154e+02 3.68510205e+00 20 -5.83987092e+02 3.87616631e+02 4.67392460e+02 21 -3.31702914e+01 -6.89195624e+02 8.41543990e+02 22 3.05334299e+02 9.41716163e+02 -8.94055088e+02 23 5.51750129e+01 -1.23644101e+03 8.31242923e+02 24 -2.97660830e+02 3.20720479e+02 9.07511759e+01 25 -2.48331394e+02 5.84093013e+01 9.20321410e+01 26 3.82597616e+02 1.35112189e+02 4.04297521e+02 27 1.30179041e+02 4.03996254e+02 3.82606679e+02 28 -5.32396397e+00 2.12364353e+00 7.10121770e+00 29 -2.61840340e+01 -1.89907386e+02 -1.14658426e+02 30 3.40792535e+01 4.63096880e+01 -7.27090143e+00 31 2.23665113e+02 -1.89838641e+02 1.64137586e+01 32 -1.98946372e+02 3.13084771e+02 1.43100684e+02 MIXED STRUCTURE (pbc=True)-- Species = Al Co (Configuration in file "config-T-AlCo.xyz") ----------------------------------------------------------------------------------------------------- Energy = 1643.1803994500006 Forces: 1 -1.89937113e+01 -4.05449247e+01 -1.08720933e+02 2 -2.18360208e+02 1.40937413e+02 -5.44170525e+01 3 3.83554731e+02 -6.34261629e+02 -2.08063331e+02 4 -7.25389320e+02 8.95253907e+02 -2.27417735e+02 5 -6.99716490e+01 -2.60871031e+02 -2.12192587e+02 6 3.03668528e+02 5.40527668e+02 -3.54903409e+02 7 2.66765674e+02 -4.93294359e+02 3.56561391e+02 8 -2.60254318e+00 8.35872346e+02 -5.22416657e+02 9 -1.05181444e+02 -2.15483413e+02 -1.78940217e+02 10 3.33345301e+02 7.81584823e+01 -2.53260613e+02 11 4.80627814e+02 -4.00828607e+02 -1.73332276e+02 12 -8.97249236e+02 3.33544384e+02 5.79863997e+01 13 -1.22042173e+02 -9.72112771e+01 3.22529481e+01 14 1.97158198e+02 5.75617563e+02 -3.62171341e+02 15 -7.44845560e+01 -4.61727658e+02 3.71289994e+02 16 -1.55524400e+01 3.87459498e+01 -3.26778111e+01 17 1.18021251e+02 -4.66573744e+02 3.12850022e+02 18 2.87516033e+02 -3.95353635e+02 -4.62297892e+02 19 2.86301449e+02 -2.43815810e+02 -6.45777047e+00 20 -5.83769044e+02 4.03056022e+02 4.38164817e+02 21 -3.49077243e+01 -6.84985261e+02 8.42964395e+02 22 2.07545728e+02 9.84427186e+02 -8.89425926e+02 23 5.38209886e+01 -1.23482674e+03 8.29892941e+02 24 -3.48836429e+02 3.25784608e+02 3.02441214e+00 25 -2.45372084e+02 5.87052904e+01 9.19459431e+01 26 4.22562292e+02 5.98353156e+01 3.99429704e+02 27 1.30977392e+02 4.04155987e+02 3.81505632e+02 28 -4.42064944e+01 -1.85491660e+01 -3.39059844e+01 29 -2.60365772e+01 -1.90662756e+02 -1.14005486e+02 30 3.24042682e+01 4.34221295e+01 -6.89902092e+00 31 2.49647245e+02 -1.89561376e+02 -2.99906473e+01 32 -2.20961259e+02 3.10507137e+02 1.13628089e+02 ================================================================================ VALGRIND OUTPUT ================================================================================ ==1397795== Memcheck, a memory error detector ==1397795== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==1397795== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info ==1397795== Command: python runner2.py EAM_Dynamo_PunYamakovMishin_2013_AlCo__MO_678952612413_000 ==1397795== ==1399141== Warning: invalid file descriptor 1024 in syscall close() ==1399141== Warning: invalid file descriptor 1025 in syscall close() ==1399141== Warning: invalid file descriptor 1026 in syscall close() ==1399141== Warning: invalid file descriptor 1027 in syscall close() ==1399141== Use --log-fd= to select an alternative log fd. ==1399141== Warning: invalid file descriptor 1028 in syscall close() ==1399141== Warning: invalid file descriptor 1029 in syscall close() ==1397795== ==1397795== HEAP SUMMARY: ==1397795== in use at exit: 2,257,751 bytes in 1,704 blocks ==1397795== total heap usage: 82,937 allocs, 81,233 frees, 173,127,558 bytes allocated ==1397795== ==1397795== LEAK SUMMARY: ==1397795== definitely lost: 0 bytes in 0 blocks ==1397795== indirectly lost: 0 bytes in 0 blocks ==1397795== possibly lost: 180,827 bytes in 103 blocks ==1397795== still reachable: 2,076,892 bytes in 1,600 blocks ==1397795== of which reachable via heuristic: ==1397795== stdstring : 38 bytes in 1 blocks ==1397795== suppressed: 32 bytes in 1 blocks ==1397795== Rerun with --leak-check=full to see details of leaked memory ==1397795== ==1397795== For lists of detected and suppressed errors, rerun with: -s ==1397795== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 7878 from 555) ================================================================================ 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.