Merge branch 'master' into kokkos-vashishta
9ed5c4f0fa98
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Authored by Axel Kohlmeyer <akohlmey@gmail.com> on Nov 9 2016, 21:15.

Description

Merge branch 'master' into kokkos-vashishta

Details

Committed

Axel Kohlmeyer <akohlmey@gmail.com>

Nov 9 2016, 21:15

Pushed

junge

Oct 19 2017, 09:53

Parents

rLAMMPSd20b32092ec1: Building correct shortlists and removed rsq test in force loops
rLAMMPSa23b287a7aac: sync with SVN for creation of stable release

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Axel Kohlmeyer <akohlmey@gmail.com> committed rLAMMPS9ed5c4f0fa98: Merge branch 'master' into kokkos-vashishta (authored by Axel Kohlmeyer <akohlmey@gmail.com>).Nov 9 2016, 21:15

Merged Changes

This commit merges a very large number of changes. Only the first 50 are shown.

Commit	Author	Details	Committed
a23b287a7aac	Steve Plimpton	sync with SVN for creation of stable release	Nov 8 2016
31204aab6a1b	Steve Plimpton	sync with SVN	Nov 8 2016
77bbf03f0f85	sjplimp/GitHub	Merge pull request #252 from akohlmey/preinstalled-vs-scm	Nov 4 2016
7cff08ca0a88	sjplimp/GitHub	Merge pull request #249 from lammps/unstable	Nov 4 2016
f0131393e00a	sjplimp/GitHub	Merge pull request #248 from akohlmey/collected-small-fixes	Nov 4 2016
32e0a5834319	sjplimp/GitHub	Merge pull request #247 from akohlmey/bounds-error-with-code-line	Nov 4 2016
60908eeab424	sjplimp/GitHub	Merge pull request #246 from akohlmey/manybody-short-neighbor-list	Nov 4 2016
8214555b2977	sjplimp/GitHub	Merge pull request #244 from ketankhare/patch-2	Nov 4 2016
f48b71f46ba6	Steve Plimpton	added examples/threebody, fix reaxc/speceies/kk	Nov 4 2016
6cc4eb19af55	Axel Kohlmeyer	remove the misleading "(which it is by default)" from several doc files	Nov 4 2016
7d23a0737ef5	Axel Kohlmeyer	add thorough checking for valid arguments to -partition or -p	Nov 4 2016
02510ec3217c	Axel Kohlmeyer	add temporary force accumulation to local variables for vashishta styles	Nov 3 2016
33140e500493	Axel Kohlmeyer	accumulate forces in temporary local variables for tersoff	Nov 3 2016
639fb6f444a0	Axel Kohlmeyer	use local variables for more efficient force accumulation	Nov 2 2016
b156771721ee	Axel Kohlmeyer	build short neighbor list for sw on based on ij parameters only	Nov 2 2016
5d787f7f16c9	Axel Kohlmeyer	avoid tiny memory leak, when the restart command is specified multiple times	Nov 2 2016
c8f4b55588ac	Axel Kohlmeyer	avoid uninitialized data for using ewald/disp with lj only	Nov 1 2016
e13e4031cfd4	Axel Kohlmeyer	avoid memory leak in pppm/disp/omp	Nov 1 2016
782a3280807e	Axel Kohlmeyer	avoid memory leaks when using kspace solvers for lennard-jones	Nov 1 2016
e81ae21dbd3a	Axel Kohlmeyer	do not access uninitialized data for ewald/disp and pppm/disp	Nov 1 2016
7fdd6e280771	Axel Kohlmeyer	remove work repetitions for 'the'	Nov 1 2016
2e0d304c7eeb	Axel Kohlmeyer	remove word repetitions for 'a'	Nov 1 2016
c4b86a25a71a	Axel Kohlmeyer	Merge branch 'master' into manybody-short-neighbor-list	Oct 28 2016
218e121b41d7	Axel Kohlmeyer	Merge branch 'master' into bounds-error-with-code-line	Oct 28 2016
93d393aa691a	Axel Kohlmeyer	permission cleanup in tools folder	Oct 28 2016
4216be49f3ce	Axel Kohlmeyer	Merge branch 'master' into collected-small-fixes	Oct 28 2016
c3a1e72183cc	Axel Kohlmeyer	Version 27 Oct 2016	Oct 27 2016
f9a9e27f5a9a	Axel Kohlmeyer	add error location propagation to atom->set_mass() and atom->check_mass()	Oct 26 2016
35753b8f089e	Axel Kohlmeyer	add error location propagation to force->bounds() and force->boundsbig()	Oct 26 2016
f028a9a9678d	Axel Kohlmeyer	region cylinder is compatible with open_faces[2], so do not disallow it.	Oct 26 2016
ef9f7c818e1a	Axel Kohlmeyer	fix off-by-one bug in buffer re-allocator	Oct 26 2016
8e61bed2d855	Axel Kohlmeyer	add USER-OMP variant of manybody short neighbor list	Oct 26 2016
3267b345904e	Axel Kohlmeyer	simplify short neighbor list implementation. remove unneeded class member	Oct 26 2016
0a417b4016f3	Axel Kohlmeyer	add short neighbor list support to pair style tersoff	Oct 26 2016
399c0af150e3	Axel Kohlmeyer	consistent short neighbor list for vashishta and vashishta/table	Oct 26 2016
e8b3f79690d5	Axel Kohlmeyer	fully tested multi-element compatible short neighbor list for Stillinger-Weber	Oct 26 2016
7f3f5e8c380b	ketankhare/GitHub	Clean whitespace	Oct 25 2016
f350500e69cf	ketankhare/GitHub	Enable write_data	Oct 25 2016
d7c77a419d1f	ketankhare/GitHub	Enable write_data for dihedral_fourier	Oct 25 2016
d2da0fabb43c	Axel Kohlmeyer	Version 20 Oct 2016	Oct 19 2016
13ce1037f23d	Axel Kohlmeyer	Version 18 Oct 2016	Oct 18 2016
fa984b2c3bbd	Axel Kohlmeyer	Version 13 Oct 2016	Oct 14 2016
8540a9f038dd	Axel Kohlmeyer	Version 11 Oct 2016	Oct 11 2016
13b6eb1bae6c	Axel Kohlmeyer	Version 6 Oct 2016	Oct 7 2016
d80a9def1772	Axel Kohlmeyer	Version 5 Oct 2016	Oct 6 2016
be4734bdce03	Axel Kohlmeyer	Version 30 Sep 2016	Sep 30 2016
2551619b074d	Axel Kohlmeyer	Version 29 Sep 2016	Sep 29 2016
d8bf149edc56	Axel Kohlmeyer	Version 28 Sep 2016	Sep 29 2016
473b12ded42a	Axel Kohlmeyer	Version 26 Sep 2016	Sep 29 2016
27c31495907a	Axel Kohlmeyer	Version 21 Sep 2016	Sep 29 2016

Changes (343)
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This commit is very large. Load each file individually.

		Path
M		doc/src/Manual.txt
M		doc/src/Section_howto.txt
M		doc/src/Section_start.txt
M		doc/src/angle_charmm.txt
M		doc/src/angle_cosine.txt
M		doc/src/angle_cosine_delta.txt
M		doc/src/angle_cosine_periodic.txt
M		doc/src/angle_cosine_squared.txt
M		doc/src/angle_harmonic.txt
M		doc/src/angle_hybrid.txt
M		doc/src/angle_table.txt
M		doc/src/bond_fene.txt
M		doc/src/bond_fene_expand.txt
M		doc/src/bond_harmonic.txt
M		doc/src/bond_hybrid.txt
M		doc/src/bond_morse.txt
M		doc/src/bond_nonlinear.txt
M		doc/src/bond_quartic.txt
M		doc/src/bond_table.txt
M		doc/src/compute_centro_atom.txt
M		doc/src/compute_chunk_atom.txt
M		doc/src/compute_stress_atom.txt
M		doc/src/compute_temp_profile.txt
M		doc/src/dihedral_charmm.txt
M		doc/src/dihedral_harmonic.txt
M		doc/src/dihedral_helix.txt
M		doc/src/dihedral_hybrid.txt
M		doc/src/dihedral_multi_harmonic.txt
M		doc/src/dihedral_opls.txt
M		doc/src/dihedral_table.txt
M		doc/src/dump_modify.txt
M		doc/src/fix_cmap.txt
M		doc/src/fix_deform.txt
M		doc/src/fix_langevin.txt
M		doc/src/fix_lb_fluid.txt
M		doc/src/fix_reax_bonds.txt
M		doc/src/fix_reaxc_species.txt
M		doc/src/fix_rx.txt
M		doc/src/fix_smd_adjust_dt.txt
M		doc/src/fix_srd.txt
M		doc/src/fix_ttm.txt
M		doc/src/improper_cvff.txt
M		doc/src/improper_harmonic.txt
M		doc/src/improper_hybrid.txt
M		doc/src/improper_style.txt
M		doc/src/improper_umbrella.txt
M		doc/src/neb.txt
M		doc/src/next.txt
M		doc/src/pair_adp.txt
M		doc/src/pair_airebo.txt
M		doc/src/pair_bop.txt
M		doc/src/pair_born.txt
M		doc/src/pair_buck.txt
M		doc/src/pair_comb.txt
M		doc/src/pair_coul.txt
M		doc/src/pair_eam.txt
M		doc/src/pair_eim.txt
M		doc/src/pair_lcbop.txt
M		doc/src/pair_nb3b_harmonic.txt
M		doc/src/pair_polymorphic.txt
M		doc/src/pair_snap.txt
M		doc/src/pair_srp.txt
M		doc/src/pair_sw.txt
M		doc/src/pair_tersoff.txt
M		doc/src/pair_tersoff_mod.txt
M		doc/src/pair_tersoff_zbl.txt
M		doc/src/pair_vashishta.txt
M		doc/src/prd.txt
M		doc/src/python.txt
M		doc/src/read_dump.txt
M		doc/src/suffix.txt
M		doc/src/tad.txt
M		doc/src/tutorial_drude.txt
A	(dir)	examples/threebody/
A		examples/threebody/BNC.tersoff
P		examples/threebody/CdTeZnSeHgS0.sw Copied from potentials/CdTeZnSeHgS0.sw
A		examples/threebody/InP.vashishta
A		examples/threebody/Si.sw
A		examples/threebody/in.threebody
M		potentials/CdTe.sw
P		potentials/CdTeZnSeHgS0.sw Copied to examples/threebody/CdTeZnSeHgS0.sw
M		src/ASPHERE/pair_gayberne.cpp
M		src/ASPHERE/pair_line_lj.cpp
M		src/ASPHERE/pair_resquared.cpp
M		src/ASPHERE/pair_tri_lj.cpp
M		src/BODY/pair_body.cpp
M		src/CLASS2/angle_class2.cpp
M		src/CLASS2/bond_class2.cpp
M		src/CLASS2/dihedral_class2.cpp
M		src/CLASS2/improper_class2.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_brownian.cpp
M		src/COLLOID/pair_colloid.cpp
M		src/COLLOID/pair_lubricate.cpp
M		src/COLLOID/pair_lubricateU.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/GPU/pair_eam_alloy_gpu.cpp
M		src/GPU/pair_eam_fs_gpu.cpp
M		src/GRANULAR/pair_gran_hooke_history.cpp
M		src/KIM/pair_kim.cpp
M		src/KOKKOS/fix_qeq_reax_kokkos.cpp
M		src/KOKKOS/fix_qeq_reax_kokkos.h
M		src/KOKKOS/fix_reaxc_species_kokkos.cpp
M		src/KOKKOS/fix_wall_reflect_kokkos.h
M		src/KOKKOS/neigh_full_kokkos.h
M		src/KOKKOS/neigh_list_kokkos.cpp
M		src/KOKKOS/neigh_list_kokkos.h
M		src/KOKKOS/pair_eam_alloy_kokkos.cpp
M		src/KOKKOS/pair_eam_fs_kokkos.cpp
M		src/KOKKOS/pair_reax_c_kokkos.h
M		src/KOKKOS/pair_sw_kokkos.cpp
M		src/KOKKOS/pair_sw_kokkos.h
M		src/KOKKOS/pair_table_kokkos.cpp
M		src/KOKKOS/pair_tersoff_kokkos.cpp
M		src/KOKKOS/pair_tersoff_kokkos.h
M		src/KOKKOS/pair_tersoff_mod_kokkos.cpp
M		src/KOKKOS/pair_tersoff_mod_kokkos.h
M		src/KOKKOS/pair_tersoff_zbl_kokkos.cpp
M		src/KOKKOS/pair_tersoff_zbl_kokkos.h
M		src/KSPACE/ewald_disp.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_coul_long.cpp
M		src/KSPACE/pair_lj_charmm_coul_long.cpp
M		src/KSPACE/pair_lj_cut_coul_long.cpp
M		src/KSPACE/pair_lj_long_coul_long.cpp
M		src/KSPACE/pppm_disp.cpp
M		src/MAKE/OPTIONS/Makefile.kokkos_phi
M		src/MANYBODY/pair_adp.cpp
M		src/MANYBODY/pair_eam.cpp
M		src/MANYBODY/pair_eam_alloy.cpp
M		src/MANYBODY/pair_eam_fs.cpp
M		src/MANYBODY/pair_eim.cpp
M		src/MANYBODY/pair_sw.cpp
M		src/MANYBODY/pair_sw.h
M		src/MANYBODY/pair_tersoff.cpp
M		src/MANYBODY/pair_tersoff.h
M		src/MANYBODY/pair_vashishta.cpp
M		src/MANYBODY/pair_vashishta.h
M		src/MANYBODY/pair_vashishta_table.cpp
M		src/MANYBODY/pair_vashishta_table.h
M		src/MC/pair_dsmc.cpp
M		src/MEAM/pair_meam.cpp
M		src/MISC/compute_ti.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/angle_charmm.cpp
M		src/MOLECULE/angle_cosine.cpp
M		src/MOLECULE/angle_cosine_periodic.cpp
M		src/MOLECULE/angle_cosine_squared.cpp
M		src/MOLECULE/angle_harmonic.cpp
M		src/MOLECULE/angle_table.cpp
M		src/MOLECULE/bond_fene.cpp
M		src/MOLECULE/bond_fene_expand.cpp
M		src/MOLECULE/bond_harmonic.cpp
M		src/MOLECULE/bond_morse.cpp
M		src/MOLECULE/bond_nonlinear.cpp
M		src/MOLECULE/bond_quartic.cpp
M		src/MOLECULE/bond_table.cpp
M		src/MOLECULE/dihedral_charmm.cpp
M		src/MOLECULE/dihedral_harmonic.cpp
M		src/MOLECULE/dihedral_helix.cpp
M		src/MOLECULE/dihedral_multi_harmonic.cpp
M		src/MOLECULE/dihedral_opls.cpp
M		src/MOLECULE/improper_cvff.cpp
M		src/MOLECULE/improper_harmonic.cpp
M		src/MOLECULE/improper_umbrella.cpp
M		src/MOLECULE/pair_hbond_dreiding_lj.cpp
M		src/MOLECULE/pair_hbond_dreiding_morse.cpp
M		src/MOLECULE/pair_lj_charmm_coul_charmm.cpp
M		src/MOLECULE/pair_lj_cut_tip4p_cut.cpp
M		src/MOLECULE/pair_tip4p_cut.cpp
M		src/PERI/pair_peri_eps.cpp
M		src/PERI/pair_peri_lps.cpp
M		src/PERI/pair_peri_pmb.cpp
M		src/PERI/pair_peri_ves.cpp
M		src/REPLICA/prd.cpp
M		src/RIGID/fix_rigid.cpp
M		src/RIGID/fix_shake.cpp
M		src/USER-AWPMD/pair_awpmd_cut.cpp
M		src/USER-CG-CMM/angle_sdk.cpp
M		src/USER-CG-CMM/pair_lj_sdk.cpp
M		src/USER-CG-CMM/pair_lj_sdk_coul_long.cpp
M		src/USER-DPD/pair_dpd_fdt.cpp
M		src/USER-DPD/pair_dpd_fdt_energy.cpp
M		src/USER-DPD/pair_exp6_rx.cpp
M		src/USER-DPD/pair_multi_lucy.cpp
M		src/USER-DPD/pair_multi_lucy_rx.cpp
M		src/USER-DPD/pair_table_rx.cpp
M		src/USER-DRUDE/pair_lj_cut_thole_long.cpp
M		src/USER-DRUDE/pair_thole.cpp
M		src/USER-EFF/pair_eff_cut.cpp
M		src/USER-FEP/compute_fep.cpp
M		src/USER-FEP/fix_adapt_fep.cpp
M		src/USER-FEP/pair_coul_cut_soft.cpp
M		src/USER-FEP/pair_coul_long_soft.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-FEP/pair_morse_soft.cpp
M		src/USER-LB/fix_lb_rigid_pc_sphere.cpp
M		src/USER-MGPT/pair_mgpt.cpp
M		src/USER-MISC/angle_cosine_shift.cpp
M		src/USER-MISC/angle_cosine_shift_exp.cpp
M		src/USER-MISC/angle_dipole.cpp
M		src/USER-MISC/angle_fourier.cpp
M		src/USER-MISC/angle_fourier_simple.cpp
M		src/USER-MISC/angle_quartic.cpp
M		src/USER-MISC/bond_harmonic_shift.cpp
M		src/USER-MISC/bond_harmonic_shift_cut.cpp
M		src/USER-MISC/dihedral_cosine_shift_exp.cpp
M		src/USER-MISC/dihedral_fourier.cpp
M		src/USER-MISC/dihedral_fourier.h
M		src/USER-MISC/dihedral_nharmonic.cpp
M		src/USER-MISC/dihedral_quadratic.cpp
M		src/USER-MISC/dihedral_spherical.cpp
M		src/USER-MISC/dihedral_table.cpp
M		src/USER-MISC/fix_addtorque.cpp
M		src/USER-MISC/improper_cossq.cpp
M		src/USER-MISC/improper_distance.cpp
M		src/USER-MISC/improper_fourier.cpp
M		src/USER-MISC/improper_ring.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_lennard_mdf.cpp
M		src/USER-MISC/pair_list.cpp
M		src/USER-MISC/pair_lj_mdf.cpp
M		src/USER-MISC/pair_lj_sf.cpp
M		src/USER-MISC/pair_lj_sf_dipole_sf.cpp
M		src/USER-MISC/pair_morse_smooth_linear.cpp
M		src/USER-MISC/pair_srp.cpp
M		src/USER-OMP/pair_eam_alloy_omp.cpp
M		src/USER-OMP/pair_eam_fs_omp.cpp
M		src/USER-OMP/pair_sw_omp.cpp
M		src/USER-OMP/pair_tersoff_omp.cpp
M		src/USER-OMP/pair_vashishta_omp.cpp
M		src/USER-OMP/pair_vashishta_table_omp.cpp
M		src/USER-OMP/pppm_disp_omp.cpp
M		src/USER-OMP/pppm_disp_omp.h
M		src/USER-SMD/pair_smd_hertz.cpp
M		src/USER-SMD/pair_smd_triangulated_surface.cpp
M		src/USER-SPH/pair_sph_heatconduction.cpp
M		src/USER-SPH/pair_sph_idealgas.cpp
M		src/USER-SPH/pair_sph_lj.cpp
M		src/USER-SPH/pair_sph_rhosum.cpp
M		src/USER-SPH/pair_sph_taitwater.cpp
M		src/USER-SPH/pair_sph_taitwater_morris.cpp
M		src/accelerator_kokkos.h
M		src/angle_hybrid.cpp
M		src/angle_zero.cpp
M		src/atom.cpp
M		src/atom.h
M		src/bond_hybrid.cpp
M		src/bond_zero.cpp
M		src/comm.cpp
M		src/compute_coord_atom.cpp
M		src/compute_rdf.cpp
M		src/delete_bonds.cpp
M		src/dihedral_hybrid.cpp
M		src/dihedral_zero.cpp
M		src/dump_image.cpp
M		src/fix_adapt.cpp
M		src/force.cpp
M		src/force.h
M		src/improper_hybrid.cpp
M		src/improper_zero.cpp
M		src/input.cpp
M		src/molecule.cpp
M		src/output.cpp
M		src/pair.cpp
M		src/pair_beck.cpp
M		src/pair_born.cpp
M		src/pair_born_coul_wolf.cpp
M		src/pair_buck.cpp
M		src/pair_buck_coul_cut.cpp
M		src/pair_coul_cut.cpp
M		src/pair_coul_dsf.cpp
M		src/pair_coul_wolf.cpp
M		src/pair_dpd.cpp
M		src/pair_dpd_tstat.cpp
M		src/pair_gauss.cpp
M		src/pair_hybrid.cpp
M		src/pair_hybrid_overlay.cpp
M		src/pair_lj96_cut.cpp
M		src/pair_lj_cubic.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_lj_gromacs.cpp
M		src/pair_lj_gromacs_coul_gromacs.cpp
M		src/pair_lj_smooth.cpp
M		src/pair_lj_smooth_linear.cpp
M		src/pair_mie_cut.cpp
M		src/pair_morse.cpp
M		src/pair_soft.cpp
M		src/pair_table.cpp
M		src/pair_yukawa.cpp
M		src/pair_zbl.cpp
M		src/pair_zero.cpp
M		src/read_data.cpp
M		src/region_cylinder.cpp
M		src/set.cpp
M		src/universe.cpp
M		src/variable.cpp
M		src/velocity.cpp
M		src/version.h
M		tools/pymol_asphere/src/cartesian.cpp
M		tools/pymol_asphere/src/cartesian.h
M		tools/pymol_asphere/src/colors.cpp
M		tools/pymol_asphere/src/colors.h
M		tools/pymol_asphere/src/commandline.cpp
M		tools/pymol_asphere/src/commandline.h
M		tools/pymol_asphere/src/error.cpp
M		tools/pymol_asphere/src/error.h
M		tools/pymol_asphere/src/glsurface.cpp
M		tools/pymol_asphere/src/glsurface.h
M		tools/pymol_asphere/src/m_constants.h
M		tools/pymol_asphere/src/misc.cpp
M		tools/pymol_asphere/src/misc.h
M		tools/pymol_asphere/src/miscm.cpp
M		tools/pymol_asphere/src/miscm.h
M		tools/pymol_asphere/src/spherical.cpp
M		tools/pymol_asphere/src/spherical.h
M		tools/xmovie/control.c
M		tools/xmovie/dummy.c
M		tools/xmovie/hpsort.c
M		tools/xmovie/read.c
M		tools/xmovie/resource.h
M		tools/xmovie/scene.c
M		tools/xmovie/toascii.c
M		tools/xmovie/tobinary.c
M		tools/xmovie/version.c
M		tools/xmovie/xmovie.c
M		tools/xmovie/xmovie.h