Merge pull request #538 from akohlmey/collected-small-changes
4fc3f4f7e563
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Authored by sjplimp <sjplimp@sandia.gov> on Jun 22 2017, 15:52.

Description

Merge pull request #538 from akohlmey/collected-small-changes

Collected small changes and bugfixes

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Committed

GitHub <noreply@github.com>

Jun 22 2017, 15:52

Pushed

junge

Oct 19 2017, 09:53

Parents

rLAMMPS1a77135ed65b: whitespace cleanup in docs
rLAMMPSe69ef56f108e: Merge pull request #539 from lammps/neighsize

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GitHub <noreply@github.com> committed rLAMMPS4fc3f4f7e563: Merge pull request #538 from akohlmey/collected-small-changes (authored by sjplimp <sjplimp@sandia.gov>).Jun 22 2017, 15:52

Merged Changes

Commit	Author	Details	Committed
1a77135ed65b	Axel Kohlmeyer	whitespace cleanup in docs	Jun 21 2017
f45c7e1fb023	Axel Kohlmeyer	update fix ti/spring docs to reflect it is part of USER-MISC	Jun 21 2017
0cfe8980d4ca	Axel Kohlmeyer	dead code removal	Jun 21 2017
2988508cee98	Axel Kohlmeyer	correct indexing bug in pair style lj/long/tip4p/long	Jun 20 2017
15c596153aaa	Axel Kohlmeyer	remove dead code	Jun 20 2017
e13c94ed4f26	Axel Kohlmeyer	fix uninitialized variable bug spotted by coverity scan	Jun 20 2017
812f1a8fabd7	Axel Kohlmeyer	remove local variables shadowing global ones in BondsOMP()	Jun 20 2017
218bc92c82d5	Axel Kohlmeyer	make pre-processor defines for using libc's qsort() consistent	Jun 20 2017
ffa906de6ff6	Axel Kohlmeyer	add C++ format identifiers to .h files	Jun 20 2017
cccf72a21d6a	Axel Kohlmeyer	make certain class member list is initialized to NULL before assigned to a…	Jun 20 2017

Changes (147)
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				Path
	M			doc/src/Section_commands.txt
	M			doc/src/Section_howto.txt
	M			doc/src/Section_packages.txt
	M			doc/src/Section_python.txt
	M			doc/src/accelerate_intel.txt
	M			doc/src/bond_oxdna.txt
	M			doc/src/compute_cnp_atom.txt
	M			doc/src/dump_vtk.txt
	M			doc/src/fix_box_relax.txt
	M			doc/src/fix_eos_table_rx.txt
	M			doc/src/fix_filter_corotate.txt
	M			doc/src/fix_gcmc.txt
	M			doc/src/fix_grem.txt
	M			doc/src/fix_ipi.txt
	M			doc/src/fix_mscg.txt
	M			doc/src/fix_nve_dot.txt
	M			doc/src/fix_nve_dotc_langevin.txt
	M			doc/src/fix_nvk.txt
	M			doc/src/fix_spring.txt
	M			doc/src/fix_ti_spring.txt
	M			doc/src/neb.txt
	M			doc/src/pair_agni.txt
	M			doc/src/pair_buck.txt
	M			doc/src/pair_exp6_rx.txt
	M			doc/src/pair_kolmogorov_crespi_z.txt
	M			doc/src/pair_multi_lucy_rx.txt
	M			doc/src/pair_oxdna.txt
	M			doc/src/pair_oxdna2.txt
	M			doc/src/pair_table_rx.txt
	M			doc/src/python.txt
	M			doc/src/tutorial_github.txt
	M			doc/src/tutorial_pylammps.txt
	M			src/CORESHELL/compute_temp_cs.h
	M			src/CORESHELL/pair_born_coul_long_cs.h
	M			src/CORESHELL/pair_buck_coul_long_cs.h
	M			src/GPU/pair_lj_cubic_gpu.h
	M			src/GPU/pair_tersoff_gpu.h
	M			src/GPU/pair_tersoff_mod_gpu.h
	M			src/GPU/pair_tersoff_zbl_gpu.h
	M			src/GPU/pair_zbl_gpu.h
	M			src/KOKKOS/pair_buck_kokkos.h
	M			src/KOKKOS/pair_sw_kokkos.h
	M			src/KOKKOS/pair_vashishta_kokkos.h
	M			src/KSPACE/pair_lj_long_tip4p_long.cpp
	M			src/MANYBODY/pair_airebo.cpp
	M			src/MANYBODY/pair_bop.h
	M			src/MANYBODY/pair_polymorphic.h
	M			src/MANYBODY/pair_vashishta_table.h
	M			src/MC/fix_atom_swap.h
	M			src/MC/fix_gcmc.h
	M			src/MC/fix_tfmc.h
	M			src/RIGID/fix_ehex.h
	M			src/USER-CGDNA/mf_oxdna.h
	M			src/USER-CGDNA/pair_oxdna2_coaxstk.h
	M			src/USER-CGDNA/pair_oxdna2_dh.h
	M			src/USER-CGDNA/pair_oxdna2_excv.h
	M			src/USER-CGDNA/pair_oxdna2_stk.h
	M			src/USER-CGDNA/pair_oxdna_coaxstk.h
	M			src/USER-CGDNA/pair_oxdna_excv.h
	M			src/USER-CGDNA/pair_oxdna_hbond.h
	M			src/USER-CGDNA/pair_oxdna_stk.h
	M			src/USER-CGDNA/pair_oxdna_xstk.h
	M			src/USER-DIFFRACTION/compute_saed.h
	M			src/USER-DIFFRACTION/compute_saed_consts.h
	M			src/USER-DIFFRACTION/compute_xrd.h
	M			src/USER-DIFFRACTION/compute_xrd_consts.h
	M			src/USER-DIFFRACTION/fix_saed_vtk.h
	M			src/USER-DPD/fix_dpd_energy.h
	M			src/USER-DPD/fix_rx.h
	M			src/USER-DPD/pair_exp6_rx.h
	M			src/USER-DPD/pair_multi_lucy_rx.h
	M			src/USER-DPD/pair_table_rx.h
	M			src/USER-MANIFOLD/fix_nve_manifold_rattle.h
	M			src/USER-MANIFOLD/fix_nvt_manifold_rattle.h
	M			src/USER-MANIFOLD/manifold.h
	M			src/USER-MANIFOLD/manifold_factory.h
	M			src/USER-MANIFOLD/manifold_gaussian_bump.h
	M			src/USER-MISC/compute_cnp_atom.cpp
	M			src/USER-MISC/fix_filter_corotate.h
	M			src/USER-MISC/fix_ti_spring.h
	M			src/USER-MISC/fix_ttm_mod.h
	M			src/USER-MISC/improper_distance.h
	M			src/USER-MISC/pair_buck_mdf.h
	M			src/USER-MISC/pair_edip_multi.h
	M			src/USER-MISC/pair_kolmogorov_crespi_z.h
	M			src/USER-MISC/pair_lennard_mdf.h
	M			src/USER-MISC/pair_lj_mdf.h
	M			src/USER-MISC/pair_meam_spline.h
	M			src/USER-MISC/pair_momb.h
	M			src/USER-NETCDF/dump_netcdf.h
	M			src/USER-NETCDF/dump_netcdf_mpiio.h
	M			src/USER-OMP/fix_qeq_reax_omp.h
	M			src/USER-OMP/pair_airebo_omp.cpp
	M			src/USER-OMP/pair_reaxc_omp.cpp
	M			src/USER-OMP/pair_reaxc_omp.h
	M			src/USER-OMP/reaxc_bond_orders_omp.cpp
	M			src/USER-OMP/reaxc_bonds_omp.cpp
	M			src/USER-OMP/reaxc_forces_omp.cpp
	M			src/USER-OMP/reaxc_multi_body_omp.cpp
	M			src/USER-OMP/reaxc_nonbonded_omp.cpp
	M			src/USER-QTB/fix_qbmsst.h
	M			src/USER-QTB/fix_qtb.h
	M			src/USER-QUIP/pair_quip.h
	M			src/USER-REAXC/fix_reaxc_species.cpp
	M			src/USER-SMD/atom_vec_smd.h
	M			src/USER-SMD/compute_smd_contact_radius.h
	M			src/USER-SMD/compute_smd_damage.h
	M			src/USER-SMD/compute_smd_hourglass_error.h
	M			src/USER-SMD/compute_smd_internal_energy.h
	M			src/USER-SMD/compute_smd_plastic_strain.h
	M			src/USER-SMD/compute_smd_plastic_strain_rate.h
	M			src/USER-SMD/compute_smd_rho.h
	M			src/USER-SMD/compute_smd_tlsph_defgrad.h
	M			src/USER-SMD/compute_smd_tlsph_dt.h
	M			src/USER-SMD/compute_smd_tlsph_num_neighs.h
	M			src/USER-SMD/compute_smd_tlsph_shape.h
	M			src/USER-SMD/compute_smd_tlsph_strain.h
	M			src/USER-SMD/compute_smd_tlsph_strain_rate.h
	M			src/USER-SMD/compute_smd_tlsph_stress.h
	M			src/USER-SMD/compute_smd_triangle_mesh_vertices.h
	M			src/USER-SMD/compute_smd_ulsph_effm.h
	M			src/USER-SMD/compute_smd_ulsph_num_neighs.h
	M			src/USER-SMD/compute_smd_ulsph_strain.h
	M			src/USER-SMD/compute_smd_ulsph_strain_rate.h
	M			src/USER-SMD/compute_smd_ulsph_stress.h
	M			src/USER-SMD/compute_smd_vol.h
	M			src/USER-SMD/fix_smd_adjust_dt.h
	M			src/USER-SMD/fix_smd_integrate_tlsph.h
	M			src/USER-SMD/fix_smd_integrate_ulsph.h
	M			src/USER-SMD/fix_smd_move_triangulated_surface.h
	M			src/USER-SMD/fix_smd_setvel.h
	M			src/USER-SMD/fix_smd_tlsph_reference_configuration.h
	M			src/USER-SMD/fix_smd_wall_surface.h
	M			src/USER-SMD/pair_smd_hertz.h
	M			src/USER-SMD/pair_smd_tlsph.h
	M			src/USER-SMD/pair_smd_triangulated_surface.h
	M			src/USER-SMD/pair_smd_ulsph.h
	M			src/USER-SMD/smd_kernels.h
	M			src/USER-SMD/smd_material_models.h
	M			src/USER-SMD/smd_math.h
	M			src/USER-SMTBQ/pair_smtbq.h
	M			src/USER-TALLY/compute_heat_flux_tally.cpp
	M			src/USER-VTK/dump_vtk.h
	M			src/compute_cna_atom.cpp
	M			src/dump.h
	M			src/irregular.h
	M			src/pair_coul_streitz.h