!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : Morse_Shifted_Glyde_1970_Ne__MO_169434419764_002 Supported species : Ne random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Ne (Configuration in file "config-F-Ne.xyz") ----------------------------------------------------------------------------------------------------- Energy = 34.40654739209448 Forces: 1 -1.94275276e+00 -2.07109529e+00 -3.11213280e+00 2 -1.69569268e+00 2.06336728e+00 -2.40542795e+00 3 6.30061246e-01 -2.02853632e+00 1.77723512e+00 4 -1.56101477e+00 1.70488402e+00 1.16645915e+00 5 1.82402630e+00 -3.73003517e+00 -1.40198003e+00 6 1.66883514e+00 6.65591297e-01 -1.97692522e+00 7 1.18280124e+00 -8.56880065e+00 -8.00832062e+00 8 -6.57607744e+00 -6.22936576e+00 8.94839237e-01 9 -3.65902486e+00 -6.47924690e-01 -3.70343242e+00 10 -2.04634202e+00 5.38454478e+00 -5.29689033e+00 11 -1.45829196e+00 -4.05898722e+00 4.01708774e+00 12 -2.08421668e+00 4.78850053e+00 -2.84521100e+00 13 -1.43982613e+00 -1.42481424e+00 -1.18665386e+01 14 1.70608050e+00 1.82256497e+00 -8.69145107e-01 15 1.24363855e+01 3.34916975e+00 3.93283719e+00 16 2.53859120e+00 6.88589211e+00 4.53352331e+00 17 -3.02480589e+00 -2.18751841e+00 -1.61385929e+00 18 1.57563370e+00 1.87191393e+00 -4.18515301e-01 19 1.28560232e+00 -2.95798677e+00 1.83053915e+00 20 -1.43046874e+00 1.79309308e+00 1.84435626e+00 21 -3.32650555e+00 -2.22816603e+00 2.16364578e+00 22 5.07322229e+00 7.16983187e+00 6.62773099e+00 23 9.29606301e-01 -4.90520681e-01 1.92528831e+00 24 9.43627068e-01 7.61242505e-01 1.12020497e+00 25 -1.63599724e+00 -4.32817897e+00 3.04749010e+00 26 -1.57592987e+00 4.58289269e+00 -2.37829677e+00 27 4.65485370e+00 -9.70607434e+00 2.76780735e+00 28 -8.50288498e+00 7.47140991e+00 1.20489574e+00 29 -2.06660715e+00 -3.05459037e+00 9.04963430e-01 30 1.93800887e+00 3.71947048e+00 -2.12738017e+00 31 3.41310189e+00 -3.93587352e+00 4.37419857e+00 32 2.22600149e+00 3.61409920e+00 3.89095318e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ne (Configuration in file "config-T-Ne.xyz") ----------------------------------------------------------------------------------------------------- Energy = 34.40654739209448 Forces: 1 -1.94275276e+00 -2.07109529e+00 -3.11213280e+00 2 -1.69569268e+00 2.06336728e+00 -2.40542795e+00 3 6.30061246e-01 -2.02853632e+00 1.77723512e+00 4 -1.56101477e+00 1.70488402e+00 1.16645915e+00 5 1.82402630e+00 -3.73003517e+00 -1.40198003e+00 6 1.66883514e+00 6.65591297e-01 -1.97692522e+00 7 1.18280124e+00 -8.56880065e+00 -8.00832062e+00 8 -6.57607744e+00 -6.22936576e+00 8.94839237e-01 9 -3.65902486e+00 -6.47924690e-01 -3.70343242e+00 10 -2.04634202e+00 5.38454478e+00 -5.29689033e+00 11 -1.45829196e+00 -4.05898722e+00 4.01708774e+00 12 -2.08421668e+00 4.78850053e+00 -2.84521100e+00 13 -1.43982613e+00 -1.42481424e+00 -1.18665386e+01 14 1.70608050e+00 1.82256497e+00 -8.69145107e-01 15 1.24363855e+01 3.34916975e+00 3.93283719e+00 16 2.53859120e+00 6.88589211e+00 4.53352331e+00 17 -3.02480589e+00 -2.18751841e+00 -1.61385929e+00 18 1.57563370e+00 1.87191393e+00 -4.18515301e-01 19 1.28560232e+00 -2.95798677e+00 1.83053915e+00 20 -1.43046874e+00 1.79309308e+00 1.84435626e+00 21 -3.32650555e+00 -2.22816603e+00 2.16364578e+00 22 5.07322229e+00 7.16983187e+00 6.62773099e+00 23 9.29606301e-01 -4.90520681e-01 1.92528831e+00 24 9.43627068e-01 7.61242505e-01 1.12020497e+00 25 -1.63599724e+00 -4.32817897e+00 3.04749010e+00 26 -1.57592987e+00 4.58289269e+00 -2.37829677e+00 27 4.65485370e+00 -9.70607434e+00 2.76780735e+00 28 -8.50288498e+00 7.47140991e+00 1.20489574e+00 29 -2.06660715e+00 -3.05459037e+00 9.04963430e-01 30 1.93800887e+00 3.71947048e+00 -2.12738017e+00 31 3.41310189e+00 -3.93587352e+00 4.37419857e+00 32 2.22600149e+00 3.61409920e+00 3.89095318e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==71484== Memcheck, a memory error detector ==71484== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==71484== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==71484== Command: python runner2.py Morse_Shifted_Glyde_1970_Ne__MO_169434419764_002 ==71484== ==73709== Warning: invalid file descriptor 1048564 in syscall close() ==73709== Warning: invalid file descriptor 1048565 in syscall close() ==73709== Warning: invalid file descriptor 1048566 in syscall close() ==73709== Warning: invalid file descriptor 1048567 in syscall close() ==73709== Use --log-fd= to select an alternative log fd. ==73709== Warning: invalid file descriptor 1048568 in syscall close() ==73709== Warning: invalid file descriptor 1048569 in syscall close() ==73710== Warning: invalid file descriptor 1048564 in syscall close() ==73710== Warning: invalid file descriptor 1048565 in syscall close() ==73710== Warning: invalid file descriptor 1048566 in syscall close() ==73710== Warning: invalid file descriptor 1048567 in syscall close() ==73710== Use --log-fd= to select an alternative log fd. ==73710== Warning: invalid file descriptor 1048568 in syscall close() ==73710== Warning: invalid file descriptor 1048569 in syscall close() ==73711== Warning: invalid file descriptor 1048564 in syscall close() ==73711== Warning: invalid file descriptor 1048565 in syscall close() ==73711== Warning: invalid file descriptor 1048566 in syscall close() ==73711== Warning: invalid file descriptor 1048567 in syscall close() ==73711== Use --log-fd= to select an alternative log fd. ==73711== Warning: invalid file descriptor 1048568 in syscall close() ==73711== Warning: invalid file descriptor 1048569 in syscall close() ==73712== Warning: invalid file descriptor 1048564 in syscall close() ==73712== Warning: invalid file descriptor 1048565 in syscall close() ==73712== Warning: invalid file descriptor 1048566 in syscall close() ==73712== Warning: invalid file descriptor 1048567 in syscall close() ==73712== Use --log-fd= to select an alternative log fd. ==73712== Warning: invalid file descriptor 1048568 in syscall close() ==73712== Warning: invalid file descriptor 1048569 in syscall close() ==73713== Warning: invalid file descriptor 1048564 in syscall close() ==73713== Warning: invalid file descriptor 1048565 in syscall close() ==73713== Warning: invalid file descriptor 1048566 in syscall close() ==73713== Warning: invalid file descriptor 1048567 in syscall close() ==73713== Use --log-fd= to select an alternative log fd. ==73713== Warning: invalid file descriptor 1048568 in syscall close() ==73713== Warning: invalid file descriptor 1048569 in syscall close() ==73714== Warning: invalid file descriptor 1048564 in syscall close() ==73714== Warning: invalid file descriptor 1048565 in syscall close() ==73714== Warning: invalid file descriptor 1048566 in syscall close() ==73714== Warning: invalid file descriptor 1048567 in syscall close() ==73714== Use --log-fd= to select an alternative log fd. ==73714== Warning: invalid file descriptor 1048568 in syscall close() ==73714== Warning: invalid file descriptor 1048569 in syscall close() ==71484== ==71484== HEAP SUMMARY: ==71484== in use at exit: 1,718,292 bytes in 1,321 blocks ==71484== total heap usage: 31,396 allocs, 30,075 frees, 38,293,059 bytes allocated ==71484== ==71484== LEAK SUMMARY: ==71484== definitely lost: 0 bytes in 0 blocks ==71484== indirectly lost: 0 bytes in 0 blocks ==71484== possibly lost: 178,943 bytes in 97 blocks ==71484== still reachable: 1,539,349 bytes in 1,224 blocks ==71484== suppressed: 0 bytes in 0 blocks ==71484== Rerun with --leak-check=full to see details of leaked memory ==71484== ==71484== For counts of detected and suppressed errors, rerun with: -v ==71484== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 11245 from 589) ================================================================================ 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.