!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : ThreeBodyBondOrder_WR_WangRockett_1991_Si__MO_081872846741_000 Supported species : Si random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Si (Configuration in file "config-F-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 253.7514727661312 Forces: 1 -1.59308078e+01 -2.01752848e+01 -2.24183455e+01 2 -8.99698807e+00 8.95677949e+00 -2.96622749e+01 3 1.29464457e+00 -2.34450030e+01 1.69124409e+01 4 -1.82758645e+01 1.66391737e+01 9.45433479e+00 5 1.67616170e+01 -3.02734328e+01 -1.77315077e+01 6 1.30465436e+01 6.13942609e+00 -1.90453894e+01 7 1.89637703e+01 -5.92340540e+01 -4.39675946e+01 8 -4.99491113e+01 -4.63450168e+01 -9.32277649e+00 9 -3.18789572e+01 -1.24163118e+00 -3.44365395e+01 10 -1.65217364e+01 4.72308477e+01 -4.14920147e+01 11 -2.03358211e+01 -2.72441654e+01 2.43926710e+01 12 -1.80781907e+01 2.05947933e+01 -8.49866500e+00 13 9.63831210e-01 -1.62764575e+01 -8.19510113e+01 14 1.75132135e+01 1.69479090e+01 -1.13332238e+01 15 8.85296602e+01 7.99573843e+00 2.02541561e+00 16 1.29621701e+01 6.39235824e+01 2.18819100e+01 17 -2.68422896e+01 -2.24110500e+01 -6.45384435e+00 18 1.42389371e+01 1.69373522e+01 -1.21273560e+01 19 6.70251770e+00 -2.95405916e+01 1.93521120e+01 20 -1.59227236e+01 1.18480192e+01 2.06082213e+01 21 -2.54648621e+01 -2.99699115e+01 1.48055679e+01 22 4.39897486e+01 3.37150200e+01 4.61798267e+01 23 1.15017820e+01 -6.32949766e+00 1.36542679e+01 24 3.06629512e+00 6.84031042e+00 1.91508345e+01 25 -3.57307218e+01 -2.34162724e+01 -1.06222689e+01 26 -1.02401541e+01 4.74004111e+01 -1.77015152e+01 27 2.20074652e+01 -5.81766020e+01 4.03084489e+01 28 -5.09055369e+01 4.88233838e+01 2.23726950e+01 29 -1.12420113e+01 -1.17605035e+01 2.17314008e+01 30 2.40445568e+01 3.18544887e+01 1.29647515e+01 31 3.78217039e+01 -7.96702201e+00 2.60211468e+01 32 2.29073193e+01 2.79592609e+01 3.49482816e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Si (Configuration in file "config-T-Si.xyz") ----------------------------------------------------------------------------------------------------- Energy = 253.7514727661312 Forces: 1 -1.59308078e+01 -2.01752848e+01 -2.24183455e+01 2 -8.99698807e+00 8.95677949e+00 -2.96622749e+01 3 1.29464457e+00 -2.34450030e+01 1.69124409e+01 4 -1.82758645e+01 1.66391737e+01 9.45433479e+00 5 1.67616170e+01 -3.02734328e+01 -1.77315077e+01 6 1.30465436e+01 6.13942609e+00 -1.90453894e+01 7 1.89637703e+01 -5.92340540e+01 -4.39675946e+01 8 -4.99491113e+01 -4.63450168e+01 -9.32277649e+00 9 -3.18789572e+01 -1.24163118e+00 -3.44365395e+01 10 -1.65217364e+01 4.72308477e+01 -4.14920147e+01 11 -2.03358211e+01 -2.72441654e+01 2.43926710e+01 12 -1.80781907e+01 2.05947933e+01 -8.49866500e+00 13 9.63831210e-01 -1.62764575e+01 -8.19510113e+01 14 1.75132135e+01 1.69479090e+01 -1.13332238e+01 15 8.85296602e+01 7.99573843e+00 2.02541561e+00 16 1.29621701e+01 6.39235824e+01 2.18819100e+01 17 -2.68422896e+01 -2.24110500e+01 -6.45384435e+00 18 1.42389371e+01 1.69373522e+01 -1.21273560e+01 19 6.70251770e+00 -2.95405916e+01 1.93521120e+01 20 -1.59227236e+01 1.18480192e+01 2.06082213e+01 21 -2.54648621e+01 -2.99699115e+01 1.48055679e+01 22 4.39897486e+01 3.37150200e+01 4.61798267e+01 23 1.15017820e+01 -6.32949766e+00 1.36542679e+01 24 3.06629512e+00 6.84031042e+00 1.91508345e+01 25 -3.57307218e+01 -2.34162724e+01 -1.06222689e+01 26 -1.02401541e+01 4.74004111e+01 -1.77015152e+01 27 2.20074652e+01 -5.81766020e+01 4.03084489e+01 28 -5.09055369e+01 4.88233838e+01 2.23726950e+01 29 -1.12420113e+01 -1.17605035e+01 2.17314008e+01 30 2.40445568e+01 3.18544887e+01 1.29647515e+01 31 3.78217039e+01 -7.96702201e+00 2.60211468e+01 32 2.29073193e+01 2.79592609e+01 3.49482816e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==18855== Memcheck, a memory error detector ==18855== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==18855== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==18855== Command: python runner2.py ThreeBodyBondOrder_WR_WangRockett_1991_Si__MO_081872846741_000 ==18855== ==20807== Warning: invalid file descriptor 1048564 in syscall close() ==20807== Warning: invalid file descriptor 1048565 in syscall close() ==20807== Warning: invalid file descriptor 1048566 in syscall close() ==20807== Warning: invalid file descriptor 1048567 in syscall close() ==20807== Use --log-fd= to select an alternative log fd. ==20807== Warning: invalid file descriptor 1048568 in syscall close() ==20807== Warning: invalid file descriptor 1048569 in syscall close() ==20812== Warning: invalid file descriptor 1048564 in syscall close() ==20812== Warning: invalid file descriptor 1048565 in syscall close() ==20812== Warning: invalid file descriptor 1048566 in syscall close() ==20812== Warning: invalid file descriptor 1048567 in syscall close() ==20812== Use --log-fd= to select an alternative log fd. ==20812== Warning: invalid file descriptor 1048568 in syscall close() ==20812== Warning: invalid file descriptor 1048569 in syscall close() ==20909== Warning: invalid file descriptor 1048564 in syscall close() ==20909== Warning: invalid file descriptor 1048565 in syscall close() ==20909== Warning: invalid file descriptor 1048566 in syscall close() ==20909== Warning: invalid file descriptor 1048567 in syscall close() ==20909== Use --log-fd= to select an alternative log fd. ==20909== Warning: invalid file descriptor 1048568 in syscall close() ==20909== Warning: invalid file descriptor 1048569 in syscall close() ==20916== Warning: invalid file descriptor 1048564 in syscall close() ==20916== Warning: invalid file descriptor 1048565 in syscall close() ==20916== Warning: invalid file descriptor 1048566 in syscall close() ==20916== Warning: invalid file descriptor 1048567 in syscall close() ==20916== Use --log-fd= to select an alternative log fd. ==20916== Warning: invalid file descriptor 1048568 in syscall close() ==20916== Warning: invalid file descriptor 1048569 in syscall close() ==20923== Warning: invalid file descriptor 1048564 in syscall close() ==20923== Warning: invalid file descriptor 1048565 in syscall close() ==20923== Warning: invalid file descriptor 1048566 in syscall close() ==20923== Warning: invalid file descriptor 1048567 in syscall close() ==20923== Use --log-fd= to select an alternative log fd. ==20923== Warning: invalid file descriptor 1048568 in syscall close() ==20923== Warning: invalid file descriptor 1048569 in syscall close() ==20929== Warning: invalid file descriptor 1048564 in syscall close() ==20929== Warning: invalid file descriptor 1048565 in syscall close() ==20929== Warning: invalid file descriptor 1048566 in syscall close() ==20929== Warning: invalid file descriptor 1048567 in syscall close() ==20929== Use --log-fd= to select an alternative log fd. ==20929== Warning: invalid file descriptor 1048568 in syscall close() ==20929== Warning: invalid file descriptor 1048569 in syscall close() ==18855== ==18855== HEAP SUMMARY: ==18855== in use at exit: 1,718,308 bytes in 1,321 blocks ==18855== total heap usage: 31,148 allocs, 29,827 frees, 38,094,362 bytes allocated ==18855== ==18855== LEAK SUMMARY: ==18855== definitely lost: 0 bytes in 0 blocks ==18855== indirectly lost: 0 bytes in 0 blocks ==18855== possibly lost: 178,943 bytes in 97 blocks ==18855== still reachable: 1,539,365 bytes in 1,224 blocks ==18855== suppressed: 0 bytes in 0 blocks ==18855== Rerun with --leak-check=full to see details of leaked memory ==18855== ==18855== For counts of detected and suppressed errors, rerun with: -v ==18855== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16361 from 604) ================================================================================ 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.