Enter a model name: === Verification check vc-memory-leak start (2025-07-09 15:05:02) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_FoilesBaskesDaw_1986Universal3_Pd__MO_786012902615_001 Supported species : Pd random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Pd (Configuration in file "config-F-Pd.xyz") ----------------------------------------------------------------------------------------------------- Energy = 131.2828125163628 Forces: 1 -1.19629488e+01 -2.44073183e+01 -2.78986600e+01 2 -8.36481836e+00 1.44605847e+01 -2.13665973e+01 3 1.23168988e+01 -2.12502270e+01 -2.67890237e-01 4 -1.80318978e+01 2.22247373e+01 1.40224453e+01 5 1.50805649e+01 -2.82485388e+01 -5.11278152e+00 6 8.98432944e+00 -4.59678051e+00 -1.29486173e+01 7 1.41679216e+01 -4.73241040e+01 -4.31739779e+01 8 -3.19210801e+01 -2.90126516e+01 -2.77896717e+00 9 -1.98045663e+01 -9.26289357e+00 -3.11137443e+01 10 -7.26392630e+00 3.56560699e+01 -3.51937244e+01 11 -1.57444166e+01 -2.40203882e+01 1.66794908e+01 12 -1.99700811e+01 2.11460136e+01 9.23959156e+00 13 -4.21019329e+00 -1.19144588e+01 -7.03546156e+01 14 1.23919134e+01 1.33126515e+01 -8.26342249e+00 15 7.05421297e+01 1.11390364e+01 1.44302789e+01 16 1.30067123e+01 5.33872208e+01 2.07133250e+01 17 -3.25737243e+01 -1.83215076e+01 -4.10947114e+00 18 1.27816380e+01 1.69482150e+01 -6.90780508e+00 19 1.03900725e+01 -2.49951143e+01 1.81074326e+01 20 -1.50585983e+01 1.11196374e+01 1.76259462e+01 21 -1.69692234e+01 -2.03525966e+01 1.39445576e+01 22 3.77306972e+01 2.88905697e+01 3.18366668e+01 23 6.01394322e+00 -3.85641530e+00 1.32252165e+01 24 7.74346951e+00 4.30313149e+00 1.26555007e+01 25 -2.39048051e+01 -7.67600002e+00 -3.85697743e+00 26 -1.03634479e+01 3.61647102e+01 -1.27935011e+01 27 1.30002656e+01 -4.23258783e+01 2.62208489e+01 28 -3.99757626e+01 3.41623218e+01 1.24166191e+01 29 -1.09858305e+01 -1.44458900e+01 1.73176348e+01 30 1.71075464e+01 2.49412986e+01 -8.72108450e+00 31 2.29968239e+01 -2.02190429e+01 2.78077085e+01 32 1.28503945e+01 2.43736073e+01 2.86185743e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Pd (Configuration in file "config-T-Pd.xyz") ----------------------------------------------------------------------------------------------------- Energy = 131.2828125163628 Forces: 1 -1.19629488e+01 -2.44073183e+01 -2.78986600e+01 2 -8.36481836e+00 1.44605847e+01 -2.13665973e+01 3 1.23168988e+01 -2.12502270e+01 -2.67890237e-01 4 -1.80318978e+01 2.22247373e+01 1.40224453e+01 5 1.50805649e+01 -2.82485388e+01 -5.11278152e+00 6 8.98432944e+00 -4.59678051e+00 -1.29486173e+01 7 1.41679216e+01 -4.73241040e+01 -4.31739779e+01 8 -3.19210801e+01 -2.90126516e+01 -2.77896717e+00 9 -1.98045663e+01 -9.26289357e+00 -3.11137443e+01 10 -7.26392630e+00 3.56560699e+01 -3.51937244e+01 11 -1.57444166e+01 -2.40203882e+01 1.66794908e+01 12 -1.99700811e+01 2.11460136e+01 9.23959156e+00 13 -4.21019329e+00 -1.19144588e+01 -7.03546156e+01 14 1.23919134e+01 1.33126515e+01 -8.26342249e+00 15 7.05421297e+01 1.11390364e+01 1.44302789e+01 16 1.30067123e+01 5.33872208e+01 2.07133250e+01 17 -3.25737243e+01 -1.83215076e+01 -4.10947114e+00 18 1.27816380e+01 1.69482150e+01 -6.90780508e+00 19 1.03900725e+01 -2.49951143e+01 1.81074326e+01 20 -1.50585983e+01 1.11196374e+01 1.76259462e+01 21 -1.69692234e+01 -2.03525966e+01 1.39445576e+01 22 3.77306972e+01 2.88905697e+01 3.18366668e+01 23 6.01394322e+00 -3.85641530e+00 1.32252165e+01 24 7.74346951e+00 4.30313149e+00 1.26555007e+01 25 -2.39048051e+01 -7.67600002e+00 -3.85697743e+00 26 -1.03634479e+01 3.61647102e+01 -1.27935011e+01 27 1.30002656e+01 -4.23258783e+01 2.62208489e+01 28 -3.99757626e+01 3.41623218e+01 1.24166191e+01 29 -1.09858305e+01 -1.44458900e+01 1.73176348e+01 30 1.71075464e+01 2.49412986e+01 -8.72108450e+00 31 2.29968239e+01 -2.02190429e+01 2.78077085e+01 32 1.28503945e+01 2.43736073e+01 2.86185743e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==4016302== Memcheck, a memory error detector ==4016302== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==4016302== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info ==4016302== Command: python runner2.py EAM_Dynamo_FoilesBaskesDaw_1986Universal3_Pd__MO_786012902615_001 ==4016302== ==4016302== Invalid read of size 8 ==4016302== at 0x40286A0: strncmp (strcmp.S:170) ==4016302== by 0x400668D: is_dst (dl-load.c:216) ==4016302== by 0x400810E: _dl_dst_count (dl-load.c:253) ==4016302== by 0x400810E: expand_dynamic_string_token (dl-load.c:395) ==4016302== by 0x40082B7: fillin_rpath.isra.0 (dl-load.c:483) ==4016302== by 0x4008602: decompose_rpath (dl-load.c:654) ==4016302== by 0x400A8C8: cache_rpath (dl-load.c:696) ==4016302== by 0x400A8C8: cache_rpath (dl-load.c:677) ==4016302== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==4016302== by 0x4003494: openaux (dl-deps.c:64) ==4016302== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==4016302== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==4016302== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==4016302== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==4016302== by 0x400DF99: dl_open_worker (dl-open.c:782) ==4016302== Address 0x56cc881 is 1 bytes inside a block of size 8 alloc'd ==4016302== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==4016302== by 0x40271DF: malloc (rtld-malloc.h:56) ==4016302== by 0x40271DF: strdup (strdup.c:42) ==4016302== by 0x4008594: decompose_rpath (dl-load.c:629) ==4016302== by 0x400A8C8: cache_rpath (dl-load.c:696) ==4016302== by 0x400A8C8: cache_rpath (dl-load.c:677) ==4016302== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==4016302== by 0x4003494: openaux (dl-deps.c:64) ==4016302== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==4016302== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==4016302== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==4016302== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==4016302== by 0x400DF99: dl_open_worker (dl-open.c:782) ==4016302== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==4016302== by 0x400E34D: _dl_open (dl-open.c:883) ==4016302== ==4016302== Invalid read of size 8 ==4016302== at 0x40286A8: strncmp (strcmp.S:172) ==4016302== by 0x400668D: is_dst (dl-load.c:216) ==4016302== by 0x400810E: _dl_dst_count (dl-load.c:253) ==4016302== by 0x400810E: expand_dynamic_string_token (dl-load.c:395) ==4016302== by 0x40082B7: fillin_rpath.isra.0 (dl-load.c:483) ==4016302== by 0x4008602: decompose_rpath (dl-load.c:654) ==4016302== by 0x400A8C8: cache_rpath (dl-load.c:696) ==4016302== by 0x400A8C8: cache_rpath (dl-load.c:677) ==4016302== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==4016302== by 0x4003494: openaux (dl-deps.c:64) ==4016302== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==4016302== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==4016302== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==4016302== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==4016302== by 0x400DF99: dl_open_worker (dl-open.c:782) ==4016302== Address 0x56cc889 is 1 bytes after a block of size 8 alloc'd ==4016302== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==4016302== by 0x40271DF: malloc (rtld-malloc.h:56) ==4016302== by 0x40271DF: strdup (strdup.c:42) ==4016302== by 0x4008594: decompose_rpath (dl-load.c:629) ==4016302== by 0x400A8C8: cache_rpath (dl-load.c:696) ==4016302== by 0x400A8C8: cache_rpath (dl-load.c:677) ==4016302== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==4016302== by 0x4003494: openaux (dl-deps.c:64) ==4016302== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==4016302== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==4016302== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==4016302== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==4016302== by 0x400DF99: dl_open_worker (dl-open.c:782) ==4016302== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==4016302== by 0x400E34D: _dl_open (dl-open.c:883) ==4016302== ==4016302== Invalid read of size 8 ==4016302== at 0x40286A0: strncmp (strcmp.S:170) ==4016302== by 0x400668D: is_dst (dl-load.c:216) ==4016302== by 0x4007F79: _dl_dst_substitute (dl-load.c:295) ==4016302== by 0x40082B7: fillin_rpath.isra.0 (dl-load.c:483) ==4016302== by 0x4008602: decompose_rpath (dl-load.c:654) ==4016302== by 0x400A8C8: cache_rpath (dl-load.c:696) ==4016302== by 0x400A8C8: cache_rpath (dl-load.c:677) ==4016302== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==4016302== by 0x4003494: openaux (dl-deps.c:64) ==4016302== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==4016302== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==4016302== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==4016302== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==4016302== by 0x400DF99: dl_open_worker (dl-open.c:782) ==4016302== Address 0x56cc881 is 1 bytes inside a block of size 8 alloc'd ==4016302== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==4016302== by 0x40271DF: malloc (rtld-malloc.h:56) ==4016302== by 0x40271DF: strdup (strdup.c:42) ==4016302== by 0x4008594: decompose_rpath (dl-load.c:629) ==4016302== by 0x400A8C8: cache_rpath (dl-load.c:696) ==4016302== by 0x400A8C8: cache_rpath (dl-load.c:677) ==4016302== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==4016302== by 0x4003494: openaux (dl-deps.c:64) ==4016302== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==4016302== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==4016302== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==4016302== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==4016302== by 0x400DF99: dl_open_worker (dl-open.c:782) ==4016302== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==4016302== by 0x400E34D: _dl_open (dl-open.c:883) ==4016302== ==4016302== Invalid read of size 8 ==4016302== at 0x40286A8: strncmp (strcmp.S:172) ==4016302== by 0x400668D: is_dst (dl-load.c:216) ==4016302== by 0x4007F79: _dl_dst_substitute (dl-load.c:295) ==4016302== by 0x40082B7: fillin_rpath.isra.0 (dl-load.c:483) ==4016302== by 0x4008602: decompose_rpath (dl-load.c:654) ==4016302== by 0x400A8C8: cache_rpath (dl-load.c:696) ==4016302== by 0x400A8C8: cache_rpath (dl-load.c:677) ==4016302== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==4016302== by 0x4003494: openaux (dl-deps.c:64) ==4016302== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==4016302== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==4016302== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==4016302== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==4016302== by 0x400DF99: dl_open_worker (dl-open.c:782) ==4016302== Address 0x56cc889 is 1 bytes after a block of size 8 alloc'd ==4016302== at 0x4848899: malloc (in /usr/libexec/valgrind/vgpreload_memcheck-amd64-linux.so) ==4016302== by 0x40271DF: malloc (rtld-malloc.h:56) ==4016302== by 0x40271DF: strdup (strdup.c:42) ==4016302== by 0x4008594: decompose_rpath (dl-load.c:629) ==4016302== by 0x400A8C8: cache_rpath (dl-load.c:696) ==4016302== by 0x400A8C8: cache_rpath (dl-load.c:677) ==4016302== by 0x400A8C8: _dl_map_object (dl-load.c:2117) ==4016302== by 0x4003494: openaux (dl-deps.c:64) ==4016302== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==4016302== by 0x4003C7B: _dl_map_object_deps (dl-deps.c:248) ==4016302== by 0x400EA0E: dl_open_worker_begin (dl-open.c:592) ==4016302== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==4016302== by 0x400DF99: dl_open_worker (dl-open.c:782) ==4016302== by 0x4B08A97: _dl_catch_exception (dl-error-skeleton.c:208) ==4016302== by 0x400E34D: _dl_open (dl-open.c:883) ==4016302== ==4016302== ==4016302== HEAP SUMMARY: ==4016302== in use at exit: 3,734,006 bytes in 5,931 blocks ==4016302== total heap usage: 83,541 allocs, 77,610 frees, 287,773,592 bytes allocated ==4016302== ==4016302== LEAK SUMMARY: ==4016302== definitely lost: 0 bytes in 0 blocks ==4016302== indirectly lost: 0 bytes in 0 blocks ==4016302== possibly lost: 158,559 bytes in 109 blocks ==4016302== still reachable: 3,575,447 bytes in 5,822 blocks ==4016302== of which reachable via heuristic: ==4016302== stdstring : 4,256 bytes in 48 blocks ==4016302== suppressed: 0 bytes in 0 blocks ==4016302== Rerun with --leak-check=full to see details of leaked memory ==4016302== ==4016302== For lists of detected and suppressed errors, rerun with: -s ==4016302== ERROR SUMMARY: 8 errors from 4 contexts (suppressed: 0 from 0) ================================================================================ 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. === Verification check vc-memory-leak end (2025-07-09 15:05:46) ===