Diffusion lammps 8a0787104756

Merge remote-tracking branch 'lammps-ro/master' into lammps-icms
8a0787104756
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Authored by Axel Kohlmeyer <akohlmey@gmail.com> on Jan 29 2014, 13:08.

Description

Merge remote-tracking branch 'lammps-ro/master' into lammps-icms

Resolved Conflicts:
doc/Manual.txt
src/REPLICA/neb.h
src/USER-REAXC/fix_qeq_reax.cpp
src/read_data.h

Details

Committed

Axel Kohlmeyer <akohlmey@gmail.com>

Jan 29 2014, 13:08

Pushed

junge

Oct 6 2016, 16:49

Parents

rLAMMPS7f81b2f2ff7f: git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11371 f3b2605a-c512-4ea7…
rLAMMPSbea87398b383: update format strings for bond, dihedral and improper warnings that use tags

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Axel Kohlmeyer <akohlmey@gmail.com> committed rLAMMPS8a0787104756: Merge remote-tracking branch 'lammps-ro/master' into lammps-icms (authored by Axel Kohlmeyer <akohlmey@gmail.com>).Jan 29 2014, 13:08

Merged Changes

Commit	Author	Details	Committed
7f81b2f2ff7f	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11371 f3b2605a-c512-4ea7…	Jan 29 2014
8cc453078458	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11369 f3b2605a-c512-4ea7…	Jan 29 2014
0ba6a33cb0f6	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11368 f3b2605a-c512-4ea7…	Jan 29 2014
91bdb7f69053	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11367 f3b2605a-c512-4ea7…	Jan 29 2014
8431b8f71174	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11366 f3b2605a-c512-4ea7…	Jan 29 2014
6b5813f25700	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11365 f3b2605a-c512-4ea7…	Jan 29 2014
b9f719057825	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11364 f3b2605a-c512-4ea7…	Jan 29 2014
64138f3433a2	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11363 f3b2605a-c512-4ea7…	Jan 29 2014
1e28f6b2185c	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11362 f3b2605a-c512-4ea7…	Jan 29 2014
20631c3811de	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11361 f3b2605a-c512-4ea7…	Jan 28 2014
b5b9910dba11	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11360 f3b2605a-c512-4ea7…	Jan 28 2014
cafa5783095d	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11359 f3b2605a-c512-4ea7…	Jan 28 2014
a18390d61e70	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11358 f3b2605a-c512-4ea7…	Jan 28 2014
796c42ceb427	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11357 f3b2605a-c512-4ea7…	Jan 28 2014
a3d94884fc5b	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11356 f3b2605a-c512-4ea7…	Jan 28 2014
8e8151fe350e	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11355 f3b2605a-c512-4ea7…	Jan 28 2014
e3cdc315199e	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11354 f3b2605a-c512-4ea7…	Jan 28 2014
9cb5fbfb3df6	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11353 f3b2605a-c512-4ea7…	Jan 28 2014
1f0f8c82c799	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11352 f3b2605a-c512-4ea7…	Jan 28 2014
d2b514f35183	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11351 f3b2605a-c512-4ea7…	Jan 28 2014
763aa3ed68b2	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11350 f3b2605a-c512-4ea7…	Jan 28 2014
b0334176f540	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11349 f3b2605a-c512-4ea7…	Jan 28 2014
9f6290042ee8	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11348 f3b2605a-c512-4ea7…	Jan 28 2014

Changes (261)
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Very Large Commit

This commit is very large. Load each file individually.

		Path
V		bench/{log.28Jan14.chain.fixed.linux.1 ← log.30Jul13.chain.fixed.linux.1}
V		bench/{log.28Jan14.chain.fixed.linux.4 ← log.30Jul13.chain.fixed.linux.4}
V		bench/{log.28Jan14.chain.scaled.linux.4 ← log.30Jul13.chain.scaled.linux.4}
V		bench/{log.28Jan14.chute.fixed.linux.1 ← log.30Jul13.chute.fixed.linux.1}
V		bench/{log.28Jan14.chute.fixed.linux.4 ← log.30Jul13.chute.fixed.linux.4}
V		bench/{log.28Jan14.chute.scaled.linux.4 ← log.30Jul13.chute.scaled.linux.4}
V		bench/{log.28Jan14.eam.fixed.linux.1 ← log.30Jul13.eam.fixed.linux.1}
V		bench/{log.28Jan14.eam.fixed.linux.4 ← log.30Jul13.eam.fixed.linux.4}
V		bench/{log.28Jan14.eam.scaled.linux.4 ← log.30Jul13.eam.scaled.linux.4}
V		bench/{log.28Jan14.lj.fixed.linux.1 ← log.30Jul13.lj.fixed.linux.1}
V		bench/{log.28Jan14.lj.fixed.linux.4 ← log.30Jul13.lj.fixed.linux.4}
V		bench/{log.28Jan14.lj.scaled.linux.4 ← log.30Jul13.lj.scaled.linux.4}
V		bench/{log.28Jan14.rhodo.fixed.linux.1 ← log.30Jul13.rhodo.fixed.linux.1}
V		bench/{log.28Jan14.rhodo.fixed.linux.4 ← log.30Jul13.rhodo.fixed.linux.4}
V		bench/{log.28Jan14.rhodo.scaled.linux.4 ← log.30Jul13.rhodo.scaled.linux.4}
V		bench/{log.30Jul13.chain.fixed.linux.1 → log.28Jan14.chain.fixed.linux.1}
V		bench/{log.30Jul13.chain.fixed.linux.4 → log.28Jan14.chain.fixed.linux.4}
V		bench/{log.30Jul13.chain.scaled.linux.4 → log.28Jan14.chain.scaled.linux.4}
V		bench/{log.30Jul13.chute.fixed.linux.1 → log.28Jan14.chute.fixed.linux.1}
V		bench/{log.30Jul13.chute.fixed.linux.4 → log.28Jan14.chute.fixed.linux.4}
V		bench/{log.30Jul13.chute.scaled.linux.4 → log.28Jan14.chute.scaled.linux.4}
V		bench/{log.30Jul13.eam.fixed.linux.1 → log.28Jan14.eam.fixed.linux.1}
V		bench/{log.30Jul13.eam.fixed.linux.4 → log.28Jan14.eam.fixed.linux.4}
V		bench/{log.30Jul13.eam.scaled.linux.4 → log.28Jan14.eam.scaled.linux.4}
V		bench/{log.30Jul13.lj.fixed.linux.1 → log.28Jan14.lj.fixed.linux.1}
V		bench/{log.30Jul13.lj.fixed.linux.4 → log.28Jan14.lj.fixed.linux.4}
V		bench/{log.30Jul13.lj.scaled.linux.4 → log.28Jan14.lj.scaled.linux.4}
V		bench/{log.30Jul13.rhodo.fixed.linux.1 → log.28Jan14.rhodo.fixed.linux.1}
V		bench/{log.30Jul13.rhodo.fixed.linux.4 → log.28Jan14.rhodo.fixed.linux.4}
V		bench/{log.30Jul13.rhodo.scaled.linux.4 → log.28Jan14.rhodo.scaled.linux.4}
M		doc/Manual.html
M		doc/Manual.txt
M		doc/kspace_modify.html
M		doc/kspace_modify.txt
M		examples/pour/in.pour.2d.molecule
M		examples/reax/AB/in.AB
A	(dir)	examples/reax/AuO/
V		examples/reax/{AuO ← Au_O}/README
V		examples/reax/{AuO ← Au_O}/data.AuO
V		examples/reax/{AuO ← Au_O}/ffield.reax.AuO
V		examples/reax/{AuO ← Au_O}/in.AuO
V		examples/reax/{AuO ← Au_O}/lmp_control
V		examples/reax/{AuO ← Au_O}/log.reaxc.auo.18Feb11.linux.1
V		examples/reax/{AuO ← Au_O}/log.reaxc.auo.18Feb11.linux.4
V		examples/reax/{AuO ← Au_O}/param.qeq
D		examples/reax/Au_O
V		examples/reax/{Au_O → AuO}/README
V		examples/reax/{Au_O → AuO}/data.AuO
V		examples/reax/{Au_O → AuO}/ffield.reax.AuO
V		examples/reax/{Au_O → AuO}/in.AuO
V		examples/reax/{Au_O → AuO}/lmp_control
V		examples/reax/{Au_O → AuO}/log.reaxc.auo.18Feb11.linux.1
V		examples/reax/{Au_O → AuO}/log.reaxc.auo.18Feb11.linux.4
V		examples/reax/{Au_O → AuO}/param.qeq
A	(dir)	examples/reax/FC/
V		examples/reax/{FC ← Fluorographene}/README
V		examples/reax/{FC ← Fluorographene}/data.FC
V		examples/reax/{FC ← Fluorographene}/dumpnpt.xyz
V		examples/reax/{FC ← Fluorographene}/ffield.reax.FC
V		examples/reax/{FC ← Fluorographene}/in.FC
V		examples/reax/{FC ← Fluorographene}/log.FC
A		examples/reax/FC/log.cite
A		examples/reax/FC/log.lammps
A	(dir)	examples/reax/FeOH3/
V		examples/reax/{FeOH3 ← Fe_O_H}/README
V		examples/reax/{FeOH3 ← Fe_O_H}/data.FeOH3
V		examples/reax/{FeOH3 ← Fe_O_H}/ffield.reax.Fe_O_C_H
V		examples/reax/{FeOH3 ← Fe_O_H}/in.FeOH3
V		examples/reax/{FeOH3 ← Fe_O_H}/lmp_control
V		examples/reax/{FeOH3 ← Fe_O_H}/log.reaxc.feoh.18Feb11.linux.1
V		examples/reax/{FeOH3 ← Fe_O_H}/log.reaxc.feoh.18Feb11.linux.4
V		examples/reax/{FeOH3 ← Fe_O_H}/param.qeq
D		examples/reax/Fe_O_H
V		examples/reax/{Fe_O_H → FeOH3}/README
V		examples/reax/{Fe_O_H → FeOH3}/data.FeOH3
V		examples/reax/{Fe_O_H → FeOH3}/ffield.reax.Fe_O_C_H
V		examples/reax/{Fe_O_H → FeOH3}/in.FeOH3
V		examples/reax/{Fe_O_H → FeOH3}/lmp_control
V		examples/reax/{Fe_O_H → FeOH3}/log.reaxc.feoh.18Feb11.linux.1
V		examples/reax/{Fe_O_H → FeOH3}/log.reaxc.feoh.18Feb11.linux.4
V		examples/reax/{Fe_O_H → FeOH3}/param.qeq
D		examples/reax/Fluorographene
V		examples/reax/{Fluorographene → FC}/README
V		examples/reax/{Fluorographene → FC}/data.FC
V		examples/reax/{Fluorographene → FC}/dumpnpt.xyz
V		examples/reax/{Fluorographene → FC}/ffield.reax.FC
V		examples/reax/{Fluorographene → FC}/in.FC
V		examples/reax/{Fluorographene → FC}/log.FC
M		examples/reax/RDX/in.RDX
A	(dir)	examples/reax/VOH/
V		examples/reax/{VOH ← V_O_H}/README
V		examples/reax/{VOH ← V_O_H}/data.VOH
V		examples/reax/{VOH ← V_O_H}/ffield.reax.V_O_C_H
V		examples/reax/{VOH ← V_O_H}/in.VOH
V		examples/reax/{VOH ← V_O_H}/lmp_control
V		examples/reax/{VOH ← V_O_H}/log.reaxc.voh.18Feb11.linux.1
V		examples/reax/{VOH ← V_O_H}/log.reaxc.voh.18Feb11.linux.4
V		examples/reax/{VOH ← V_O_H}/param.qeq
D		examples/reax/V_O_H
V		examples/reax/{V_O_H → VOH}/README
V		examples/reax/{V_O_H → VOH}/data.VOH
V		examples/reax/{V_O_H → VOH}/ffield.reax.V_O_C_H
V		examples/reax/{V_O_H → VOH}/in.VOH
V		examples/reax/{V_O_H → VOH}/lmp_control
V		examples/reax/{V_O_H → VOH}/log.reaxc.voh.18Feb11.linux.1
V		examples/reax/{V_O_H → VOH}/log.reaxc.voh.18Feb11.linux.4
V		examples/reax/{V_O_H → VOH}/param.qeq
A	(dir)	examples/reax/ZnOH2/
V		examples/reax/{ZnOH2 ← Zn_O_H}/README
V		examples/reax/{ZnOH2 ← Zn_O_H}/data.ZnOH2
V		examples/reax/{ZnOH2 ← Zn_O_H}/ffield.reax.ZnOH
V		examples/reax/{ZnOH2 ← Zn_O_H}/in.ZnOH2
V		examples/reax/{ZnOH2 ← Zn_O_H}/lmp_control
V		examples/reax/{ZnOH2 ← Zn_O_H}/log.reaxc.znoh.18Feb11.linux.1
V		examples/reax/{ZnOH2 ← Zn_O_H}/log.reaxc.znoh.18Feb11.linux.4
V		examples/reax/{ZnOH2 ← Zn_O_H}/param.qeq
D		examples/reax/Zn_O_H
V		examples/reax/{Zn_O_H → ZnOH2}/README
V		examples/reax/{Zn_O_H → ZnOH2}/data.ZnOH2
V		examples/reax/{Zn_O_H → ZnOH2}/ffield.reax.ZnOH
V		examples/reax/{Zn_O_H → ZnOH2}/in.ZnOH2
V		examples/reax/{Zn_O_H → ZnOH2}/lmp_control
V		examples/reax/{Zn_O_H → ZnOH2}/log.reaxc.znoh.18Feb11.linux.1
V		examples/reax/{Zn_O_H → ZnOH2}/log.reaxc.znoh.18Feb11.linux.4
V		examples/reax/{Zn_O_H → ZnOH2}/param.qeq
M		lib/gpu/Makefile.linux
M		lib/gpu/Makefile.linux.double
M		lib/gpu/Makefile.linux_opencl
M		src/CLASS2/dihedral_class2.h
M		src/CLASS2/improper_class2.h
M		src/DIPOLE/atom_vec_dipole.h
M		src/DIPOLE/pair_lj_long_dipole_long.h
M		src/GPU/fix_gpu.h
M		src/GPU/pair_lj_gromacs_gpu.h
M		src/GPU/pair_sw_gpu.h
P		src/GRANULAR/fix_pour.h Copied from src/read_data.h
M		src/KIM/pair_kim.h
M		src/KSPACE/ewald.h
M		src/KSPACE/ewald_disp.cpp
M		src/KSPACE/ewald_disp.h
M		src/KSPACE/fix_tune_kspace.h
M		src/KSPACE/msm.h
M		src/KSPACE/pair_buck_long_coul_long.h
M		src/KSPACE/pair_lj_long_coul_long.h
M		src/KSPACE/pppm.h
M		src/KSPACE/pppm_disp.h
M		src/KSPACE/pppm_old.h
M		src/MANYBODY/fix_qeq_comb.h
M		src/MANYBODY/pair_airebo.h
M		src/MANYBODY/pair_comb.h
M		src/MANYBODY/pair_comb3.h
M		src/MANYBODY/pair_lcbop.h
M		src/MANYBODY/pair_nb3b_harmonic.h
M		src/MANYBODY/pair_tersoff_mod.h
M		src/MC/fix_bond_swap.h
M		src/MC/fix_gcmc.cpp
M		src/MC/fix_gcmc.h
M		src/MISC/fix_deposit.h
M		src/MISC/fix_efield.h
M		src/MISC/fix_gld.h
M		src/MISC/fix_ttm.h
P		src/MISC/pair_nm_cut.h Copied from src/create_atoms.h
M		src/MISC/pair_nm_cut_coul_cut.h
M		src/MISC/pair_nm_cut_coul_long.h
M		src/MOLECULE/angle_table.h
M		src/MOLECULE/atom_vec_angle.h
M		src/MOLECULE/atom_vec_bond.h
M		src/MOLECULE/atom_vec_full.h
M		src/MOLECULE/atom_vec_molecular.h
M		src/MOLECULE/atom_vec_template.cpp
M		src/MOLECULE/atom_vec_template.h
M		src/MOLECULE/bond_fene.h
M		src/MOLECULE/bond_fene_expand.h
M		src/MOLECULE/bond_quartic.h
M		src/MOLECULE/bond_table.h
M		src/MOLECULE/dihedral_charmm.h
M		src/MOLECULE/dihedral_harmonic.h
M		src/MOLECULE/dihedral_helix.h
M		src/MOLECULE/dihedral_multi_harmonic.h
M		src/MOLECULE/dihedral_opls.h
M		src/MOLECULE/improper_cvff.h
M		src/MOLECULE/improper_harmonic.h
M		src/MOLECULE/improper_umbrella.h
M		src/MOLECULE/pair_lj_cut_tip4p_cut.h
M		src/MOLECULE/pair_tip4p_cut.h
M		src/MPIIO/dump_atom_mpiio.h
M		src/MPIIO/dump_custom_mpiio.h
M		src/MPIIO/dump_xyz_mpiio.h
M		src/MPIIO/restart_mpiio.h
M		src/PERI/atom_vec_peri.h
M		src/PERI/pair_peri_pmb.h
M		src/POEMS/fix_poems.cpp
M		src/POEMS/fix_poems.h
M		src/REPLICA/neb.h
M		src/REPLICA/prd.h
M		src/REPLICA/verlet_split.h
M		src/RIGID/compute_erotate_rigid.h
M		src/RIGID/compute_ke_rigid.h
M		src/RIGID/fix_rigid.h
M		src/RIGID/fix_rigid_small.h
M		src/RIGID/fix_shake.h
M		src/SHOCK/fix_append_atoms.h
M		src/SRD/fix_srd.h
M		src/USER-REAXC/fix_qeq_reax.cpp
M		src/USER-REAXC/reaxc_io_tools.cpp
M		src/VORONOI/compute_voronoi_atom.h
M		src/XTC/xdr_compat.h
M		src/atom.cpp
M		src/atom.h
M		src/atom_vec_atomic.h
M		src/atom_vec_body.h
M		src/atom_vec_charge.h
M		src/atom_vec_ellipsoid.h
M		src/atom_vec_hybrid.h
M		src/atom_vec_line.h
M		src/atom_vec_sphere.h
M		src/atom_vec_tri.h
M		src/citeme.h
M		src/compute.h
M		src/compute_property_atom.h
M		src/compute_property_local.h
M		src/compute_vacf.h
M		src/create_atoms.cpp
P		src/create_atoms.h Copied to src/MISC/pair_nm_cut.h
M		src/create_box.h
M		src/domain.h
M		src/dump.h
M		src/dump_cfg.h
M		src/dump_custom.h
M		src/dump_image.h
M		src/dump_movie.h
M		src/fix_ave_spatial.h
M		src/fix_nve_limit.h
M		src/fix_property_atom.h
M		src/fix_restrain.h
M		src/fix_shear_history.h
M		src/fix_store.h
M		src/image.h
M		src/input.h
M		src/kspace.h
M		src/lammps.h
M		src/molecule.h
M		src/neigh_bond.h
M		src/output.h
M		src/pair_table.h
M		src/read_data.cpp
P		src/read_data.h Copied to src/GRANULAR/fix_pour.h
M		src/read_dump.h
M		src/read_restart.cpp
M		src/read_restart.h
M		src/region_intersect.h
M		src/replicate.cpp
M		src/replicate.h
M		src/respa.h
M		src/set.h
M		src/variable.h
M		src/velocity.h
M		src/version.h
M		src/write_data.h
M		src/write_dump.h
M		src/write_restart.h