Diffusion lammps 72e5f537c8d0

Merge pull request #576 from akohlmey/sanitizer-changes
72e5f537c8d0
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Authored by sjplimp <sjplimp@sandia.gov> on Jul 20 2017, 20:03.

Description

Merge pull request #576 from akohlmey/sanitizer-changes

Collected changes for issues detected by gcc -fsanitize

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Committed

GitHub <noreply@github.com>

Jul 20 2017, 20:03

Pushed

junge

Oct 19 2017, 09:53

Parents

rLAMMPS8499e72cdc91: updates to USER-REAXC code in USER-OMP from Chris Knight. addresses issues with…
rLAMMPScc9b3864bff6: Merge pull request #577 from v0i0/airebo-kim-difference

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GitHub <noreply@github.com> committed rLAMMPS72e5f537c8d0: Merge pull request #576 from akohlmey/sanitizer-changes (authored by sjplimp <sjplimp@sandia.gov>).Jul 20 2017, 20:03

Merged Changes

Commit	Author	Details	Committed
8499e72cdc91	Axel Kohlmeyer	updates to USER-REAXC code in USER-OMP from Chris Knight. addresses issues with…	Jul 20 2017
148364949e21	Axel Kohlmeyer	fix memory corruption issue in fix reax/c/species	Jul 18 2017
4ad952899922	Axel Kohlmeyer	safer handling of memory management for lists in reax/c	Jul 18 2017
358915d16ee7	Axel Kohlmeyer	avoid division by zero in peri pair styles	Jul 18 2017
d9186c8fde6d	Axel Kohlmeyer	Revert "use neighbor list exclusions instead of a zero cutoff"	Jul 18 2017
bc5186bc30e1	Axel Kohlmeyer	fix unitialized pointer issue in USER-OMP with pppm/disp	Jul 18 2017
c083d5d6f3f8	Axel Kohlmeyer	fix memory leak in list of neighbor list requests	Jul 18 2017
c3a2ed0d1b30	Axel Kohlmeyer	plug small memory leak in USER-OMP variants of pppm kspace styles	Jul 18 2017
23033404b0a4	Axel Kohlmeyer	skip table consistency check for bitmapped tables	Jul 18 2017
992ce797010d	Axel Kohlmeyer	add sanity checks to EAM potential file reader subroutine	Jul 16 2017
4ec07422f07c	Axel Kohlmeyer	avoid division by zero when using cutoff 0.0 with pair_modify shift yes	Jul 15 2017
3f297382ac1f	Axel Kohlmeyer	Revert "do not allow pairwise cutoffs <= 0.0. avoids undefined behavior and…	Jul 15 2017
bbb4d63db980	Axel Kohlmeyer	use neighbor list exclusions instead of a zero cutoff	Jul 14 2017
1c92eecea7fc	Axel Kohlmeyer	move updated gauss_flow example to the correct folder	Jul 14 2017
a04711b21f06	Axel Kohlmeyer	do not allow pairwise cutoffs <= 0.0. avoids undefined behavior and division by…	Jul 14 2017
e084d4dad633	Axel Kohlmeyer	print warnings in Pair::init() only on MPI rank 0	Jul 14 2017
522bc13d6786	Axel Kohlmeyer	avoid casts to the wrong derived class, which upsets code analysis tools. seems…	Jul 14 2017
14f1d646ad76	Axel Kohlmeyer	provide working examples for all four peridynamics models and reference outputs	Jul 14 2017
3b1134c1649a	Axel Kohlmeyer	correct formatting error in peridynamics pair style docs	Jul 14 2017
4d4c03a1e4f5	Axel Kohlmeyer	restore gaussian flow example that was lost. tweak input to make it usable for…	Jul 14 2017
8a1db83b7306	Axel Kohlmeyer	silence static code analysis warning	Jul 14 2017
de45a46529f9	Axel Kohlmeyer	Merge branch 'compute_rdf_dynamic' into sanitizer-changes	Jul 13 2017
32ca58bdf23c	Axel Kohlmeyer	whitespace cleanup	Jul 13 2017
111786e92e0f	Axel Kohlmeyer	avoid trying to free NULL pointers and reallocate storage for OpenMP, when not…	Jul 13 2017
132cee984051	Axel Kohlmeyer	protect warning printf()s to be only printed on rank 0	Jul 13 2017
609c8b1e8774	Axel Kohlmeyer	add flag to reax/c system struct to signaling, whether OpenMP is active	Jul 13 2017
cb935730c0b6	Axel Kohlmeyer	Merge branch 'master' into compute_rdf_dynamic	Jul 13 2017
71ddcaf0b607	Axel Kohlmeyer	whitespace cleanup	Jul 7 2017

Changes (104)
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		Path
M		doc/src/pair_peri.txt
M		examples/USER/misc/flow_gauss/README
M		examples/USER/misc/flow_gauss/in.GD
A		examples/USER/misc/flow_gauss/log.6Jul17.GD.g++.1
A		examples/USER/misc/flow_gauss/log.6Jul17.GD.g++.4
A	(dir)	examples/USER/misc/flow_gauss/output-files/
A		examples/USER/misc/flow_gauss/output-files/GD.out
A		examples/USER/misc/flow_gauss/output-files/Vy_profile
A		examples/USER/misc/flow_gauss/output-files/x_profiles
P		examples/peri/in.peri Deleted after being copied to multiple locations: examples/peri/in.peri-pmb examples/peri/in.peri.eps examples/peri/in.peri.lps examples/peri/in.peri.pmb examples/peri/in.peri.ves
P		examples/peri/in.peri-pmb Copied from examples/peri/in.peri
P		examples/peri/in.peri.eps Copied from examples/peri/in.peri
P		examples/peri/in.peri.lps Copied from examples/peri/in.peri
P		examples/peri/in.peri.pmb Copied from examples/peri/in.peri
V		examples/peri/{in.peri.ves ← in.peri}
V		examples/peri/{log.5Oct16.peri.g++.1 → log.6Jul17.peri.pmb.g++.1}
V		examples/peri/{log.5Oct16.peri.g++.4 → log.6Jul17.peri.pmb.g++.4}
A		examples/peri/log.6Jul17.peri.eps.g++.1
A		examples/peri/log.6Jul17.peri.eps.g++.4
A		examples/peri/log.6Jul17.peri.lps.g++.1
A		examples/peri/log.6Jul17.peri.lps.g++.4
V		examples/peri/{log.6Jul17.peri.pmb.g++.1 ← log.5Oct16.peri.g++.1}
V		examples/peri/{log.6Jul17.peri.pmb.g++.4 ← log.5Oct16.peri.g++.4}
A		examples/peri/log.6Jul17.peri.ves.g++.1
A		examples/peri/log.6Jul17.peri.ves.g++.4
M		src/ASPHERE/pair_gayberne.cpp
M		src/ASPHERE/pair_resquared.cpp
M		src/CLASS2/pair_lj_class2.cpp
M		src/CLASS2/pair_lj_class2_coul_cut.cpp
M		src/CLASS2/pair_lj_class2_coul_long.cpp
M		src/COLLOID/pair_colloid.cpp
M		src/COLLOID/pair_yukawa_colloid.cpp
M		src/DIPOLE/pair_lj_cut_dipole_cut.cpp
M		src/DIPOLE/pair_lj_cut_dipole_long.cpp
M		src/DIPOLE/pair_lj_long_dipole_long.cpp
M		src/KSPACE/pair_born_coul_long.cpp
M		src/KSPACE/pair_buck_coul_long.cpp
M		src/KSPACE/pair_buck_long_coul_long.cpp
M		src/KSPACE/pair_lj_cut_coul_long.cpp
M		src/KSPACE/pair_lj_long_coul_long.cpp
M		src/MANYBODY/pair_airebo.cpp
M		src/MANYBODY/pair_eam.cpp
M		src/MANYBODY/pair_eam_alloy.cpp
M		src/MANYBODY/pair_eam_fs.cpp
M		src/MISC/pair_nm_cut.cpp
M		src/MISC/pair_nm_cut_coul_cut.cpp
M		src/MISC/pair_nm_cut_coul_long.cpp
M		src/MOLECULE/pair_lj_cut_tip4p_cut.cpp
M		src/PERI/fix_peri_neigh.cpp
M		src/PERI/pair_peri_eps.cpp
M		src/PERI/pair_peri_lps.cpp
M		src/USER-CGSDK/pair_lj_sdk.cpp
M		src/USER-CGSDK/pair_lj_sdk_coul_long.cpp
M		src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp
M		src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp
M		src/USER-FEP/pair_lj_cut_coul_long_soft.cpp
M		src/USER-FEP/pair_lj_cut_soft.cpp
M		src/USER-MISC/pair_buck_mdf.cpp
M		src/USER-MISC/pair_coul_diel.cpp
M		src/USER-MISC/pair_gauss_cut.cpp
M		src/USER-MISC/pair_kolmogorov_crespi_z.cpp
M		src/USER-MISC/pair_list.cpp
M		src/USER-OMP/pair_peri_lps_omp.cpp
M		src/USER-OMP/pair_reaxc_omp.cpp
M		src/USER-OMP/pppm_cg_omp.cpp
M		src/USER-OMP/pppm_cg_omp.h
M		src/USER-OMP/pppm_disp_omp.cpp
M		src/USER-OMP/pppm_disp_omp.h
M		src/USER-OMP/pppm_disp_tip4p_omp.cpp
M		src/USER-OMP/pppm_disp_tip4p_omp.h
M		src/USER-OMP/pppm_omp.cpp
M		src/USER-OMP/pppm_omp.h
M		src/USER-OMP/pppm_tip4p_omp.cpp
M		src/USER-OMP/pppm_tip4p_omp.h
M		src/USER-OMP/reaxc_bonds_omp.cpp
M		src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp
M		src/USER-OMP/reaxc_init_md_omp.cpp
M		src/USER-OMP/reaxc_multi_body_omp.cpp
M		src/USER-OMP/reaxc_nonbonded_omp.cpp
M		src/USER-OMP/reaxc_torsion_angles_omp.cpp
M		src/USER-OMP/reaxc_valence_angles_omp.cpp
M		src/USER-OMP/thr_data.cpp
M		src/USER-REAXC/fix_reaxc_species.cpp
M		src/USER-REAXC/pair_reaxc.cpp
M		src/USER-REAXC/reaxc_allocate.cpp
M		src/USER-REAXC/reaxc_ffield.cpp
M		src/USER-REAXC/reaxc_list.cpp
M		src/USER-REAXC/reaxc_types.h
M		src/compute_rdf.cpp
M		src/neighbor.cpp
M		src/pair.cpp
M		src/pair_born.cpp
M		src/pair_born_coul_dsf.cpp
M		src/pair_born_coul_wolf.cpp
M		src/pair_buck.cpp
M		src/pair_buck_coul_cut.cpp
M		src/pair_lj96_cut.cpp
M		src/pair_lj_cut.cpp
M		src/pair_lj_cut_coul_cut.cpp
M		src/pair_lj_cut_coul_dsf.cpp
M		src/pair_lj_expand.cpp
M		src/pair_mie_cut.cpp
M		src/pair_table.cpp
M		src/pair_yukawa.cpp