!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : Sim_LAMMPS_ReaxFF_KeithFantauzziJacob_2010_AuO__SM_974345878378_000 Supported species : Au O random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Au (Configuration in file "config-F-Au.xyz") ----------------------------------------------------------------------------------------------------- Energy = 368.5868170857606 Forces: 1 -1.35303430e+01 -2.25688251e+01 -2.43171035e+01 2 -8.94022547e+00 1.34645387e+01 -2.37873439e+01 3 1.47356609e+01 -4.00185016e+01 -1.54147902e+01 4 -3.13038252e+01 1.44356857e+01 4.87119955e-01 5 -3.39994447e+00 -3.72997334e+01 -1.31683324e+01 6 2.42146475e+01 1.30795344e+01 -2.61577908e+01 7 2.33251688e+01 -6.05086485e+01 -3.89347708e+01 8 -2.94081275e+01 -2.29443968e+01 -3.37741150e+00 9 -2.44575788e+01 -1.64888991e+01 -4.11359053e+01 10 -8.38717739e+00 4.49176260e+01 -4.55092541e+01 11 -1.00015963e+01 -2.89824980e+01 6.40428838e+00 12 -2.97051090e+01 3.82323195e+01 5.74394073e+00 13 -9.62597453e+00 -2.94196031e+01 -8.79674715e+01 14 2.30350129e+01 2.75732463e+01 -2.06782233e+01 15 7.96335719e+01 -1.83857185e+01 9.99246591e+00 16 7.22629042e+00 7.05729007e+01 2.50549379e+01 17 -4.45554005e+01 -2.88205785e+01 -5.94573237e+00 18 2.52388313e+01 2.94903102e+01 2.07149810e+01 19 1.62093359e+01 -2.45827526e+01 2.28503920e+01 20 -1.71564230e+01 1.96192595e+01 2.27072489e+01 21 -2.88907814e+01 -3.33303503e+01 9.07856821e+00 22 5.03149962e+01 4.40713503e+01 3.53390351e+01 23 3.01403405e+01 -1.79392448e+01 2.16481684e+01 24 -2.05038705e+01 1.90626105e+01 1.97068777e+01 25 -3.42698761e+01 -1.22138074e+01 1.73824738e+01 26 -1.20874838e+01 4.97868849e+01 -1.92533509e+01 27 2.00272131e+01 -6.73441569e+01 3.11853882e+01 28 -5.62611358e+01 4.61885306e+01 1.58877960e+01 29 -1.68745719e+01 -2.73318744e+01 2.21603846e+01 30 2.71321907e+01 3.75743214e+01 1.08153576e+01 31 3.82929250e+01 -1.57214588e+01 2.92459247e+01 32 1.98332594e+01 3.58319293e+01 3.92421316e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Au (Configuration in file "config-T-Au.xyz") ----------------------------------------------------------------------------------------------------- Energy = 368.5868170856668 Forces: 1 -1.35303430e+01 -2.25688251e+01 -2.43171035e+01 2 -8.94022547e+00 1.34645387e+01 -2.37873439e+01 3 1.47356609e+01 -4.00185016e+01 -1.54147902e+01 4 -3.13038252e+01 1.44356857e+01 4.87119955e-01 5 -3.39994447e+00 -3.72997334e+01 -1.31683324e+01 6 2.42146475e+01 1.30795344e+01 -2.61577908e+01 7 2.33251688e+01 -6.05086485e+01 -3.89347708e+01 8 -2.94081275e+01 -2.29443968e+01 -3.37741150e+00 9 -2.44575788e+01 -1.64888991e+01 -4.11359053e+01 10 -8.38717739e+00 4.49176260e+01 -4.55092541e+01 11 -1.00015963e+01 -2.89824980e+01 6.40428838e+00 12 -2.97051090e+01 3.82323195e+01 5.74394073e+00 13 -9.62597453e+00 -2.94196031e+01 -8.79674715e+01 14 2.30350129e+01 2.75732463e+01 -2.06782233e+01 15 7.96335719e+01 -1.83857185e+01 9.99246591e+00 16 7.22629042e+00 7.05729007e+01 2.50549379e+01 17 -4.45554005e+01 -2.88205785e+01 -5.94573237e+00 18 2.52388313e+01 2.94903102e+01 2.07149810e+01 19 1.62093359e+01 -2.45827526e+01 2.28503920e+01 20 -1.71564230e+01 1.96192595e+01 2.27072489e+01 21 -2.88907814e+01 -3.33303503e+01 9.07856821e+00 22 5.03149962e+01 4.40713503e+01 3.53390351e+01 23 3.01403405e+01 -1.79392448e+01 2.16481684e+01 24 -2.05038705e+01 1.90626105e+01 1.97068777e+01 25 -3.42698761e+01 -1.22138074e+01 1.73824738e+01 26 -1.20874838e+01 4.97868849e+01 -1.92533509e+01 27 2.00272131e+01 -6.73441569e+01 3.11853882e+01 28 -5.62611358e+01 4.61885306e+01 1.58877960e+01 29 -1.68745719e+01 -2.73318744e+01 2.21603846e+01 30 2.71321907e+01 3.75743214e+01 1.08153576e+01 31 3.82929250e+01 -1.57214588e+01 2.92459247e+01 32 1.98332594e+01 3.58319293e+01 3.92421316e+01 MONOATOMIC STRUCTURE (pbc=False)-- Species = O (Configuration in file "config-F-O.xyz") ----------------------------------------------------------------------------------------------------- Energy = 32.44665732981773 Forces: 1 -1.12954315e+00 -8.51592229e-01 -1.00629066e+00 2 -2.82589901e+00 2.16095856e+00 -1.86325415e+00 3 5.21523645e+00 -4.96300433e+00 5.43338765e+00 4 -3.85482437e+00 -9.99906361e-01 -1.00498591e+00 5 5.44684234e-01 -1.04365827e+00 -5.47064550e-01 6 1.32394477e+00 -1.93837044e+00 -2.55983746e-01 7 6.54453533e-01 2.54599735e+00 -7.54056873e-01 8 1.98745088e+00 -6.73543711e-01 -1.73561211e+00 9 1.85032650e+00 -6.09058503e-01 -6.37425456e-01 10 -2.46547769e+00 1.28336313e+00 -1.29367896e+00 11 2.56267282e-01 2.35457299e+00 -1.15726658e+00 12 -5.24522142e-01 3.98077581e-01 -1.99534168e+00 13 2.67065367e-01 -3.02763042e+00 -4.80797971e+00 14 -9.47549670e-03 1.13052574e-01 9.55015486e-01 15 5.44463224e+00 4.14525270e+00 -2.34024139e-02 16 -1.32167403e+00 1.63093068e+00 -1.81496026e-01 17 1.45979622e+00 4.46543106e-02 8.42788755e-01 18 -1.34444179e+00 -1.30523909e+00 -6.11812690e+00 19 -8.45903842e-02 -1.04405010e+00 -1.46682309e+00 20 -1.92250238e+00 7.42347928e-01 4.26139168e-03 21 -7.93808083e+00 -2.10248639e+00 -2.01042622e+00 22 2.58623642e+00 -3.79492797e+00 3.81272499e-02 23 1.44173322e+00 3.85923999e-01 -3.31090224e-01 24 1.67641346e+00 -5.19135121e+00 4.76504461e+00 25 -5.08365643e+00 -2.40116136e+00 1.66339076e+00 26 -2.19084891e+00 3.64574895e+00 9.13100991e-01 27 4.40284886e-01 7.59967461e+00 6.98744024e+00 28 -6.09386428e-01 8.19724492e-01 6.72331738e-02 29 -3.57891954e+00 -4.29743413e+00 2.23373883e+00 30 5.61640202e+00 1.58216110e+00 -5.85403785e-01 31 2.75861820e+00 3.36604433e+00 8.62272281e-01 32 1.36029690e+00 1.42492922e+00 3.00990763e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = O (Configuration in file "config-T-O.xyz") ----------------------------------------------------------------------------------------------------- Energy = 32.44665733042579 Forces: 1 -1.12954315e+00 -8.51592229e-01 -1.00629066e+00 2 -2.82589901e+00 2.16095856e+00 -1.86325415e+00 3 5.21523645e+00 -4.96300433e+00 5.43338765e+00 4 -3.85482437e+00 -9.99906361e-01 -1.00498591e+00 5 5.44684234e-01 -1.04365827e+00 -5.47064550e-01 6 1.32394477e+00 -1.93837044e+00 -2.55983746e-01 7 6.54453534e-01 2.54599735e+00 -7.54056873e-01 8 1.98745088e+00 -6.73543711e-01 -1.73561211e+00 9 1.85032650e+00 -6.09058503e-01 -6.37425457e-01 10 -2.46547769e+00 1.28336313e+00 -1.29367896e+00 11 2.56267282e-01 2.35457299e+00 -1.15726658e+00 12 -5.24522142e-01 3.98077581e-01 -1.99534168e+00 13 2.67065367e-01 -3.02763042e+00 -4.80797971e+00 14 -9.47549672e-03 1.13052575e-01 9.55015486e-01 15 5.44463224e+00 4.14525270e+00 -2.34024138e-02 16 -1.32167403e+00 1.63093068e+00 -1.81496026e-01 17 1.45979622e+00 4.46543106e-02 8.42788755e-01 18 -1.34444179e+00 -1.30523909e+00 -6.11812690e+00 19 -8.45903842e-02 -1.04405010e+00 -1.46682309e+00 20 -1.92250238e+00 7.42347928e-01 4.26139171e-03 21 -7.93808083e+00 -2.10248639e+00 -2.01042622e+00 22 2.58623642e+00 -3.79492797e+00 3.81272499e-02 23 1.44173322e+00 3.85923999e-01 -3.31090224e-01 24 1.67641346e+00 -5.19135121e+00 4.76504461e+00 25 -5.08365643e+00 -2.40116136e+00 1.66339076e+00 26 -2.19084891e+00 3.64574895e+00 9.13100992e-01 27 4.40284886e-01 7.59967461e+00 6.98744024e+00 28 -6.09386428e-01 8.19724492e-01 6.72331735e-02 29 -3.57891954e+00 -4.29743413e+00 2.23373883e+00 30 5.61640202e+00 1.58216110e+00 -5.85403785e-01 31 2.75861820e+00 3.36604433e+00 8.62272281e-01 32 1.36029690e+00 1.42492922e+00 3.00990763e+00 MIXED STRUCTURE (pbc=False)-- Species = Au O (Configuration in file "config-F-AuO.xyz") ----------------------------------------------------------------------------------------------------- Energy = 127.73123220050512 Forces: 1 -4.97614145e+00 -4.38282328e+00 -7.99566411e+00 2 1.89531317e+00 1.42509374e+00 -8.70007461e+00 3 3.56188790e+00 -6.29995963e+00 5.38833152e+00 4 -7.34077088e+00 4.70707032e+00 -8.65493673e+00 5 -2.25562997e-01 -3.25608950e+00 -4.88200091e+00 6 3.74575975e+00 -3.83249343e+00 -2.76401185e+00 7 3.91672886e+00 -2.44459118e+00 -1.74779054e+00 8 -9.44322131e+00 -3.11955789e+01 -9.26035822e+00 9 -2.32819805e+00 2.95220049e+00 -2.80202586e+00 10 -3.56767350e+01 1.21018971e+01 -2.30006779e+01 11 3.28976205e+00 -1.28746133e+00 -4.57440761e+00 12 -5.16753825e+00 7.77960658e+00 -3.25562420e+00 13 1.09318466e+01 -1.69474463e+01 -3.59376690e+01 14 1.31875397e+00 7.82117917e-02 -4.09684546e-01 15 2.64428834e+01 2.77237824e+00 -8.09623197e+00 16 1.29628274e+01 4.63756568e+01 -2.58260901e-02 17 -2.32866782e+00 -1.33164635e+01 8.63915039e+00 18 3.00386534e+00 -1.72719040e+00 -2.09434237e+00 19 2.19506602e+00 -4.18428407e+00 3.07963137e+00 20 -5.22079777e+00 1.76836683e+00 8.60888950e+00 21 9.92268846e-01 -5.77299407e+00 -5.57186630e-02 22 1.25841433e+01 -2.76531208e+00 -1.79956025e+00 23 4.00472600e+00 -1.17887564e+01 1.16917782e+01 24 -1.58705189e+00 -8.16593103e-01 6.25701276e+00 25 -3.61974413e+01 -8.81326166e+00 -1.75132022e+01 26 -9.75488261e+00 6.18810966e+01 -3.44921801e+00 27 9.71200147e+00 -3.70225463e+01 4.69218972e+01 28 -1.43239928e+01 1.50036450e+01 1.57668231e+01 29 1.36565754e+01 -2.51667332e+01 1.35147958e+01 30 8.67188293e+00 3.20668305e+01 -1.00241389e+01 31 7.51988992e+00 -1.26060893e+01 3.10621805e+01 32 4.16481981e+00 4.71461365e+00 6.11267412e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==76782== Memcheck, a memory error detector ==76782== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==76782== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==76782== Command: python runner2.py Sim_LAMMPS_ReaxFF_KeithFantauzziJacob_2010_AuO__SM_974345878378_000 ==76782== ==76943== Warning: invalid file descriptor 1048564 in syscall close() ==76943== Warning: invalid file descriptor 1048565 in syscall close() ==76943== Warning: invalid file descriptor 1048566 in syscall close() ==76943== Warning: invalid file descriptor 1048567 in syscall close() ==76943== Use --log-fd= to select an alternative log fd. ==76943== Warning: invalid file descriptor 1048568 in syscall close() ==76943== Warning: invalid file descriptor 1048569 in syscall close() ==76944== Warning: invalid file descriptor 1048564 in syscall close() ==76944== Warning: invalid file descriptor 1048565 in syscall close() ==76944== Warning: invalid file descriptor 1048566 in syscall close() ==76944== Warning: invalid file descriptor 1048567 in syscall close() ==76944== Use --log-fd= to select an alternative log fd. ==76944== Warning: invalid file descriptor 1048568 in syscall close() ==76944== Warning: invalid file descriptor 1048569 in syscall close() ==76945== Warning: invalid file descriptor 1048564 in syscall close() ==76945== Warning: invalid file descriptor 1048565 in syscall close() ==76945== Warning: invalid file descriptor 1048566 in syscall close() ==76945== Warning: invalid file descriptor 1048567 in syscall close() ==76945== Use --log-fd= to select an alternative log fd. ==76945== Warning: invalid file descriptor 1048568 in syscall close() ==76945== Warning: invalid file descriptor 1048569 in syscall close() ==76946== Warning: invalid file descriptor 1048564 in syscall close() ==76946== Warning: invalid file descriptor 1048565 in syscall close() ==76946== Warning: invalid file descriptor 1048566 in syscall close() ==76946== Warning: invalid file descriptor 1048567 in syscall close() ==76946== Use --log-fd= to select an alternative log fd. ==76946== Warning: invalid file descriptor 1048568 in syscall close() ==76946== Warning: invalid file descriptor 1048569 in syscall close() ==76947== Warning: invalid file descriptor 1048564 in syscall close() ==76947== Warning: invalid file descriptor 1048565 in syscall close() ==76947== Warning: invalid file descriptor 1048566 in syscall close() ==76947== Warning: invalid file descriptor 1048567 in syscall close() ==76947== Use --log-fd= to select an alternative log fd. ==76947== Warning: invalid file descriptor 1048568 in syscall close() ==76947== Warning: invalid file descriptor 1048569 in syscall close() ==76948== Warning: invalid file descriptor 1048564 in syscall close() ==76948== Warning: invalid file descriptor 1048565 in syscall close() ==76948== Warning: invalid file descriptor 1048566 in syscall close() ==76948== Warning: invalid file descriptor 1048567 in syscall close() ==76948== Use --log-fd= to select an alternative log fd. ==76948== Warning: invalid file descriptor 1048568 in syscall close() ==76948== Warning: invalid file descriptor 1048569 in syscall close() ==76949== Warning: invalid file descriptor 1048564 in syscall close() ==76949== Warning: invalid file descriptor 1048565 in syscall close() ==76949== Warning: invalid file descriptor 1048566 in syscall close() ==76949== Warning: invalid file descriptor 1048567 in syscall close() ==76949== Use --log-fd= to select an alternative log fd. ==76949== Warning: invalid file descriptor 1048568 in syscall close() ==76949== Warning: invalid file descriptor 1048569 in syscall close() ==76951== Warning: invalid file descriptor 1048564 in syscall close() ==76951== Warning: invalid file descriptor 1048565 in syscall close() ==76951== Warning: invalid file descriptor 1048566 in syscall close() ==76951== Warning: invalid file descriptor 1048567 in syscall close() ==76951== Use --log-fd= to select an alternative log fd. ==76951== Warning: invalid file descriptor 1048568 in syscall close() ==76951== Warning: invalid file descriptor 1048569 in syscall close() ==77002== Warning: invalid file descriptor 1048564 in syscall close() ==77002== Warning: invalid file descriptor 1048565 in syscall close() ==77002== Warning: invalid file descriptor 1048566 in syscall close() ==77002== Warning: invalid file descriptor 1048567 in syscall close() ==77002== Use --log-fd= to select an alternative log fd. ==77002== Warning: invalid file descriptor 1048568 in syscall close() ==77002== Warning: invalid file descriptor 1048569 in syscall close() ==77004== Warning: invalid file descriptor 1048564 in syscall close() ==77004== Warning: invalid file descriptor 1048565 in syscall close() ==77004== Warning: invalid file descriptor 1048566 in syscall close() ==77004== Warning: invalid file descriptor 1048567 in syscall close() ==77004== Use --log-fd= to select an alternative log fd. ==77004== Warning: invalid file descriptor 1048568 in syscall close() ==77004== Warning: invalid file descriptor 1048569 in syscall close() ==77006== Warning: invalid file descriptor 1048564 in syscall close() ==77006== Warning: invalid file descriptor 1048565 in syscall close() ==77006== Warning: invalid file descriptor 1048566 in syscall close() ==77006== Warning: invalid file descriptor 1048567 in syscall close() ==77006== Use --log-fd= to select an alternative log fd. ==77006== Warning: invalid file descriptor 1048568 in syscall close() ==77006== Warning: invalid file descriptor 1048569 in syscall close() ==77008== Warning: invalid file descriptor 1048564 in syscall close() ==77008== Warning: invalid file descriptor 1048565 in syscall close() ==77008== Warning: invalid file descriptor 1048566 in syscall close() ==77008== Warning: invalid file descriptor 1048567 in syscall close() ==77008== Use --log-fd= to select an alternative log fd. ==77008== Warning: invalid file descriptor 1048568 in syscall close() ==77008== Warning: invalid file descriptor 1048569 in syscall close() ==77022== Warning: invalid file descriptor 1048564 in syscall close() ==77022== Warning: invalid file descriptor 1048565 in syscall close() ==77022== Warning: invalid file descriptor 1048566 in syscall close() ==77022== Warning: invalid file descriptor 1048567 in syscall close() ==77022== Use --log-fd= to select an alternative log fd. ==77022== Warning: invalid file descriptor 1048568 in syscall close() ==77022== Warning: invalid file descriptor 1048569 in syscall close() ==77023== Warning: invalid file descriptor 1048564 in syscall close() ==77023== Warning: invalid file descriptor 1048565 in syscall close() ==77023== Warning: invalid file descriptor 1048566 in syscall close() ==77023== Warning: invalid file descriptor 1048567 in syscall close() ==77023== Use --log-fd= to select an alternative log fd. ==77023== Warning: invalid file descriptor 1048568 in syscall close() ==77023== Warning: invalid file descriptor 1048569 in syscall close() ==77025== Warning: invalid file descriptor 1048564 in syscall close() ==77025== Warning: invalid file descriptor 1048565 in syscall close() ==77025== Warning: invalid file descriptor 1048566 in syscall close() ==77025== Warning: invalid file descriptor 1048567 in syscall close() ==77025== Use --log-fd= to select an alternative log fd. ==77025== Warning: invalid file descriptor 1048568 in syscall close() ==77025== Warning: invalid file descriptor 1048569 in syscall close() ==77026== Warning: invalid file descriptor 1048564 in syscall close() ==77026== Warning: invalid file descriptor 1048565 in syscall close() ==77026== Warning: invalid file descriptor 1048566 in syscall close() ==77026== Warning: invalid file descriptor 1048567 in syscall close() ==77026== Use --log-fd= to select an alternative log fd. ==77026== Warning: invalid file descriptor 1048568 in syscall close() ==77026== Warning: invalid file descriptor 1048569 in syscall close() ==76782== ==76782== HEAP SUMMARY: ==76782== in use at exit: 1,780,791 bytes in 1,489 blocks ==76782== total heap usage: 50,362 allocs, 48,873 frees, 117,261,273 bytes allocated ==76782== ==76782== LEAK SUMMARY: ==76782== definitely lost: 0 bytes in 0 blocks ==76782== indirectly lost: 0 bytes in 0 blocks ==76782== possibly lost: 178,943 bytes in 97 blocks ==76782== still reachable: 1,601,848 bytes in 1,392 blocks ==76782== suppressed: 0 bytes in 0 blocks ==76782== Rerun with --leak-check=full to see details of leaked memory ==76782== ==76782== For counts of detected and suppressed errors, rerun with: -v ==76782== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16553 from 628) ================================================================================ 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.