!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : SW_DingAndersen_1986_Ge__MO_775478537242_000 Supported species : Ge random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Ge (Configuration in file "config-F-Ge.xyz") ----------------------------------------------------------------------------------------------------- Energy = 1063.254072259134 Forces: 1 -3.94296973e+01 -3.34967738e+01 -3.77017242e+01 2 -2.13853273e+01 -9.32146023e+00 -9.88981591e+01 3 -2.56225574e+01 -9.38649352e+01 -1.60690960e+01 4 -8.41822355e+01 -7.45638723e+00 -7.62136495e+00 5 2.72478135e+01 -7.07116747e+01 -6.10331327e+01 6 4.30010802e+01 -1.64961305e+01 -5.92243283e+01 7 6.72760413e+01 -1.00010859e+02 -4.47383838e+01 8 7.07825553e+00 -6.37582834e+01 -5.03494015e+01 9 -5.22610635e+01 -4.38071597e+00 -7.65139373e+01 10 -3.20087237e+01 8.18106819e+01 -8.21146968e+01 11 -5.13154797e+01 3.41273179e+00 -1.82046666e+01 12 -6.95543408e+01 5.76173363e+01 -7.07922889e+00 13 3.39481117e+01 2.76158107e+00 -1.42046246e+02 14 5.32869503e+01 3.84932519e+01 -3.47310967e+01 15 1.35228870e+02 2.05355502e+01 -2.27570030e+01 16 2.39732281e+01 1.30178124e+02 5.07075032e+00 17 -6.21889384e+01 -3.50484270e+01 9.58685430e+00 18 -3.73914776e+01 -1.81370176e+01 4.06969835e+01 19 -3.03223543e+00 -4.51972676e+01 5.11764780e+01 20 -4.57203814e+01 -5.43208826e+00 4.34216065e+01 21 2.11874617e+01 -8.90411648e+01 3.57232132e+01 22 1.05061872e+02 -1.36072131e+01 3.70779516e+01 23 2.24414689e+01 -2.29199288e+01 3.66193456e+01 24 5.17667327e+00 -2.36718822e+01 8.99485753e+01 25 -1.10321310e+02 1.20074165e+01 2.02317619e+01 26 -3.51104687e+01 1.15178700e+02 3.03835877e+01 27 -2.30138763e+01 -1.30225161e+01 8.59132192e+01 28 -6.04727832e+01 4.53412186e+01 2.71853647e+01 29 1.66847304e+01 2.29801040e+01 6.25790129e+01 30 7.56949076e+01 6.78201089e+01 3.15268705e+01 31 7.79022731e+01 1.08216587e+01 7.82959213e+01 32 3.78211576e+01 5.66162610e+01 7.36449690e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ge (Configuration in file "config-T-Ge.xyz") ----------------------------------------------------------------------------------------------------- Energy = 1063.254072259134 Forces: 1 -3.94296973e+01 -3.34967738e+01 -3.77017242e+01 2 -2.13853273e+01 -9.32146023e+00 -9.88981591e+01 3 -2.56225574e+01 -9.38649352e+01 -1.60690960e+01 4 -8.41822355e+01 -7.45638723e+00 -7.62136495e+00 5 2.72478135e+01 -7.07116747e+01 -6.10331327e+01 6 4.30010802e+01 -1.64961305e+01 -5.92243283e+01 7 6.72760413e+01 -1.00010859e+02 -4.47383838e+01 8 7.07825553e+00 -6.37582834e+01 -5.03494015e+01 9 -5.22610635e+01 -4.38071597e+00 -7.65139373e+01 10 -3.20087237e+01 8.18106819e+01 -8.21146968e+01 11 -5.13154797e+01 3.41273179e+00 -1.82046666e+01 12 -6.95543408e+01 5.76173363e+01 -7.07922889e+00 13 3.39481117e+01 2.76158107e+00 -1.42046246e+02 14 5.32869503e+01 3.84932519e+01 -3.47310967e+01 15 1.35228870e+02 2.05355502e+01 -2.27570030e+01 16 2.39732281e+01 1.30178124e+02 5.07075032e+00 17 -6.21889384e+01 -3.50484270e+01 9.58685430e+00 18 -3.73914776e+01 -1.81370176e+01 4.06969835e+01 19 -3.03223543e+00 -4.51972676e+01 5.11764780e+01 20 -4.57203814e+01 -5.43208826e+00 4.34216065e+01 21 2.11874617e+01 -8.90411648e+01 3.57232132e+01 22 1.05061872e+02 -1.36072131e+01 3.70779516e+01 23 2.24414689e+01 -2.29199288e+01 3.66193456e+01 24 5.17667327e+00 -2.36718822e+01 8.99485753e+01 25 -1.10321310e+02 1.20074165e+01 2.02317619e+01 26 -3.51104687e+01 1.15178700e+02 3.03835877e+01 27 -2.30138763e+01 -1.30225161e+01 8.59132192e+01 28 -6.04727832e+01 4.53412186e+01 2.71853647e+01 29 1.66847304e+01 2.29801040e+01 6.25790129e+01 30 7.56949076e+01 6.78201089e+01 3.15268705e+01 31 7.79022731e+01 1.08216587e+01 7.82959213e+01 32 3.78211576e+01 5.66162610e+01 7.36449690e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==3013705== Memcheck, a memory error detector ==3013705== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==3013705== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info ==3013705== Command: python runner2.py SW_DingAndersen_1986_Ge__MO_775478537242_000 ==3013705== ==3013705== Conditional jump or move depends on uninitialised value(s) ==3013705== at 0x699E487: NpyIter_GetInnerFixedStrideArray (in /usr/local/lib/python3.8/dist-packages/numpy/core/_multiarray_umath.cpython-38-x86_64-linux-gnu.so) ==3013705== by 0x6A9ACFC: execute_ufunc_loop (in /usr/local/lib/python3.8/dist-packages/numpy/core/_multiarray_umath.cpython-38-x86_64-linux-gnu.so) ==3013705== by 0x6AA3E77: ufunc_generic_fastcall (in /usr/local/lib/python3.8/dist-packages/numpy/core/_multiarray_umath.cpython-38-x86_64-linux-gnu.so) ==3013705== by 0x5D2C50: ??? (in /usr/bin/python3.8) ==3013705== by 0x5D2F14: PyObject_CallFunctionObjArgs (in /usr/bin/python3.8) ==3013705== by 0x69B0AC5: array_add (in /usr/local/lib/python3.8/dist-packages/numpy/core/_multiarray_umath.cpython-38-x86_64-linux-gnu.so) ==3013705== by 0x4E64CE: PyNumber_Add (in /usr/bin/python3.8) ==3013705== by 0x547A41: _PyEval_EvalFrameDefault (in /usr/bin/python3.8) ==3013705== by 0x5D5845: _PyFunction_Vectorcall (in /usr/bin/python3.8) ==3013705== by 0x547446: _PyEval_EvalFrameDefault (in /usr/bin/python3.8) ==3013705== by 0x545529: _PyEval_EvalCodeWithName (in /usr/bin/python3.8) ==3013705== by 0x5D5A22: _PyFunction_Vectorcall (in /usr/bin/python3.8) ==3013705== ==3013705== ==3013705== HEAP SUMMARY: ==3013705== in use at exit: 2,277,246 bytes in 1,710 blocks ==3013705== total heap usage: 57,736 allocs, 56,026 frees, 72,212,827 bytes allocated ==3013705== ==3013705== LEAK SUMMARY: ==3013705== definitely lost: 0 bytes in 0 blocks ==3013705== indirectly lost: 0 bytes in 0 blocks ==3013705== possibly lost: 188,754 bytes in 107 blocks ==3013705== still reachable: 2,088,460 bytes in 1,602 blocks ==3013705== of which reachable via heuristic: ==3013705== stdstring : 38 bytes in 1 blocks ==3013705== suppressed: 32 bytes in 1 blocks ==3013705== Rerun with --leak-check=full to see details of leaked memory ==3013705== ==3013705== Use --track-origins=yes to see where uninitialised values come from ==3013705== For lists of detected and suppressed errors, rerun with: -s ==3013705== ERROR SUMMARY: 7 errors from 1 contexts (suppressed: 18373 from 605) ================================================================================ 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.