Diffusion lammps 427161ef56aa

Merge branch 'master' into lammps-icms
427161ef56aa
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Authored by Axel Kohlmeyer <akohlmey@gmail.com> on Jan 9 2013, 13:09.

Description

Merge branch 'master' into lammps-icms

Resolved Conflicts:
src/MAKE/Makefile.openmpi
src/min_linesearch.cpp

Details

Committed

Axel Kohlmeyer <akohlmey@gmail.com>

Jan 9 2013, 13:09

Pushed

junge

Oct 6 2016, 16:49

Parents

rLAMMPS5d0835345b8a: Corrected some errors in the mathematical expressions
rLAMMPS21ba48544fb1: Merge branch 'master' into lammps-icms

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Axel Kohlmeyer <akohlmey@gmail.com> committed rLAMMPS427161ef56aa: Merge branch 'master' into lammps-icms (authored by Axel Kohlmeyer <akohlmey@gmail.com>).Jan 9 2013, 13:09

Merged Changes

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

Commit	Author	Details	Committed
5d0835345b8a	athomps	Corrected some errors in the mathematical expressions	Jan 9 2013
1d9c0274639b	athomps	Corrected some errors in the mathematical expressions	Jan 9 2013
9d9587cb963b	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9251 f3b2605a-c512-4ea7…	Jan 8 2013
405ed1733845	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9250 f3b2605a-c512-4ea7…	Jan 8 2013
1ec45d89fffc	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9249 f3b2605a-c512-4ea7…	Jan 8 2013
57d9d9c7c4e2	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9248 f3b2605a-c512-4ea7…	Jan 8 2013
18c211af658c	pscrozi	Updating MSM code to reflect changes allowing non-periodic boundaries.	Jan 8 2013
27c6f67b93d6	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9246 f3b2605a-c512-4ea7…	Jan 8 2013
46287db34f0d	pscrozi	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9245 f3b2605a-c512-4ea7…	Jan 8 2013
426ad1c55bd8	pscrozi	Updating kspace docs to reflect changes in MSM allowing non-periodic boundaries.	Jan 8 2013
7886b6f1d170	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9243 f3b2605a-c512-4ea7…	Jan 7 2013
71e58a480a1b	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9241 f3b2605a-c512-4ea7…	Jan 5 2013
b72f03d427a8	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9240 f3b2605a-c512-4ea7…	Jan 5 2013
9934c92093e6	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9239 f3b2605a-c512-4ea7…	Jan 5 2013
5ce40edc4c46	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9237 f3b2605a-c512-4ea7…	Jan 5 2013
15137c006528	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9236 f3b2605a-c512-4ea7…	Jan 5 2013
5a3ba8343aa8	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9235 f3b2605a-c512-4ea7…	Jan 5 2013
0fd35228c602	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9234 f3b2605a-c512-4ea7…	Jan 5 2013
a535ce285a0c	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9233 f3b2605a-c512-4ea7…	Jan 5 2013
c183aa664407	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9232 f3b2605a-c512-4ea7…	Jan 5 2013
0921544c24d4	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9230 f3b2605a-c512-4ea7…	Jan 4 2013
51d6ffe7953d	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9228 f3b2605a-c512-4ea7…	Jan 4 2013
9b87f881246e	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9227 f3b2605a-c512-4ea7…	Jan 4 2013
fe5de26b2347	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9226 f3b2605a-c512-4ea7…	Jan 4 2013
11a5f87d1ae1	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9225 f3b2605a-c512-4ea7…	Jan 4 2013
b684961fc9fb	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9224 f3b2605a-c512-4ea7…	Jan 4 2013
da22df7e32cd	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9223 f3b2605a-c512-4ea7…	Jan 4 2013
fa8c7b68fc42	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9222 f3b2605a-c512-4ea7…	Jan 4 2013
f2d187716cde	pscrozi	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9221 f3b2605a-c512-4ea7…	Jan 3 2013
5188afc7f083	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9219 f3b2605a-c512-4ea7…	Jan 3 2013
5c4099d1268d	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9217 f3b2605a-c512-4ea7…	Jan 3 2013
0c063777a949	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9214 f3b2605a-c512-4ea7…	Jan 3 2013
462efcafaa74	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9210 f3b2605a-c512-4ea7…	Jan 3 2013
7f95feb0e4ab	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9209 f3b2605a-c512-4ea7…	Jan 3 2013
2f87c0a14dbb	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9208 f3b2605a-c512-4ea7…	Jan 3 2013
da49b01f7647	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9206 f3b2605a-c512-4ea7…	Jan 3 2013
0147edb8eaab	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9205 f3b2605a-c512-4ea7…	Jan 3 2013
772e83406ddd	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9204 f3b2605a-c512-4ea7…	Jan 3 2013
91a1b21ad618	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9203 f3b2605a-c512-4ea7…	Jan 3 2013
bee86b9a2ad0	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9200 f3b2605a-c512-4ea7…	Jan 3 2013
cf4ed82081bc	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9199 f3b2605a-c512-4ea7…	Jan 3 2013
72aa99b5b3dd	athomps	Increased MIN_ALPHA_FAC for line forcezero	Jan 2 2013
fcc96239984a	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9195 f3b2605a-c512-4ea7…	Jan 2 2013
da634ab53290	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9194 f3b2605a-c512-4ea7…	Jan 2 2013
c3ed94c40c1a	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9193 f3b2605a-c512-4ea7…	Jan 2 2013
47fcc6f93b11	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9190 f3b2605a-c512-4ea7…	Jan 2 2013
f678e2afa9c4	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9189 f3b2605a-c512-4ea7…	Jan 2 2013
0a4cdacb6735	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9188 f3b2605a-c512-4ea7…	Jan 2 2013
8106d6ed04f9	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9187 f3b2605a-c512-4ea7…	Jan 2 2013
e4665335170e	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9186 f3b2605a-c512-4ea7…	Jan 2 2013

Changes (120)
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Very Large Commit

This commit is very large. Load each file individually.

		Path
A		doc/Eqs/eff_ECP1.jpg
A		doc/Eqs/eff_ECP1.tex
A		doc/Eqs/eff_ECP2.jpg
A		doc/Eqs/eff_ECP2.tex
M		doc/Eqs/pair_gromacs.jpg
M		doc/Eqs/pair_gromacs.tex
M		doc/fix_adapt.html
M		doc/fix_adapt.txt
M		doc/fix_addforce.html
M		doc/fix_addforce.txt
M		doc/fix_append_atoms.html
M		doc/fix_append_atoms.txt
M		doc/fix_external.html
M		doc/fix_external.txt
M		doc/fix_heat.html
M		doc/fix_heat.txt
M		doc/kspace_modify.html
M		doc/kspace_modify.txt
M		doc/kspace_style.html
M		doc/kspace_style.txt
M		doc/pair_eff.html
M		doc/pair_eff.txt
M		doc/pair_gromacs.html
M		doc/pair_gromacs.txt
M		doc/pair_hbond_dreiding.html
M		doc/pair_hbond_dreiding.txt
M		doc/read_data.html
M		doc/read_data.txt
M		examples/COUPLE/lammps_quest/Makefile.g++
M		examples/COUPLE/lammps_quest/README
M		examples/COUPLE/lammps_quest/in.lammps
M		examples/COUPLE/lammps_quest/lmpqst.cpp
M		examples/USER/eff/Auger-Adamantane/in.adamantane_ionized.nve
M		examples/USER/eff/Be-solid/in.Be-solid.spe
M		examples/USER/eff/ECP/Si2H6/data.Si2H6
M		examples/USER/eff/ECP/Si2H6/in.Si2H6
A	(dir)	examples/USER/eff/ECP/SiC/
A	(dir)	examples/USER/eff/ECP/SiC/bulk/
A		examples/USER/eff/ECP/SiC/bulk/data.SiC
A		examples/USER/eff/ECP/SiC/bulk/in.SiC
M		examples/USER/eff/ECP/SiH4/data.SiH4
M		examples/USER/eff/ECP/SiH4/in.SiH4
M		examples/USER/eff/ECP/SiH4/in.SiH4.ang
M		examples/USER/eff/H/in.h_atom.spe.ang
M		examples/USER/eff/H/in.h_atom.spe.bohr
M		examples/USER/eff/H2/in.h2
M		examples/USER/eff/H_plasma/in.h2bulk.npt
M		examples/USER/eff/H_plasma/in.h2bulk.nve
M		examples/USER/eff/H_plasma/in.h2bulk.nve.ang
M		examples/USER/eff/Li-dendritic/in.Li-dendritic.min
M		examples/USER/eff/Li-dendritic/in.Li-dendritic.nvt
M		examples/USER/eff/Li-solid/in.Li.ang
M		examples/USER/eff/Li-solid/in.Li.bohr
M		examples/USER/eff/fixed-core/CH4/in.CH4fc.ang
M		examples/USER/eff/fixed-core/CH4/in.CH4fc.bohr
M		examples/USER/eff/fixed-core/CH4/in.CH4fc.spe.ang
M		examples/USER/eff/fixed-core/CH4/in.CH4fc.spe.bohr
A		lib/gpu/Makefile.xk7
M		lib/gpu/lal_base_ellipsoid.cpp
M		lib/gpu/lal_preprocessor.h
M		lib/gpu/lal_yukawa.cu
M		src/CLASS2/dihedral_class2.cpp
M		src/DIPOLE/atom_vec_dipole.cpp
M		src/GPU/gpu_extra.h
M		src/GPU/pppm_gpu.cpp
M		src/GPU/pppm_gpu.h
M		src/KSPACE/ewald.cpp
M		src/KSPACE/msm.cpp
M		src/KSPACE/msm.h
M		src/KSPACE/pair_lj_long_coul_long.cpp
M		src/MAKE/Makefile.openmpi
M		src/MOLECULE/pair_hbond_dreiding_lj.cpp
M		src/MOLECULE/pair_hbond_dreiding_morse.cpp
M		src/Makefile.lib
M		src/Makefile.shlib
M		src/SHOCK/fix_append_atoms.cpp
M		src/SHOCK/fix_append_atoms.h
M		src/USER-EFF/atom_vec_electron.cpp
M		src/USER-EFF/pair_eff_cut.cpp
M		src/USER-EFF/pair_eff_cut.h
M		src/USER-EFF/pair_eff_inline.h
M		src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp
M		src/atom.cpp
M		src/atom.h
M		src/domain.cpp
M		src/fix.h
M		src/fix_adapt.cpp
M		src/fix_external.cpp
M		src/fix_external.h
M		src/fix_heat.cpp
M		src/fix_heat.h
M		src/fix_print.cpp
M		src/fix_print.h
M		src/fix_store_state.cpp
M		src/fix_tmd.cpp
M		src/input.cpp
M		src/input.h
M		src/kspace.cpp
M		src/min.cpp
M		src/min_linesearch.cpp
M		src/modify.cpp
M		src/modify.h
M		src/pair_lj_expand.cpp
M		src/pair_lj_expand.h
M		src/respa.cpp
M		src/thermo.cpp
M		src/verlet.cpp
M		src/version.h
M		tools/eff/lmp2xyz.py
M		tools/moltemplate/src/extract_lammps_data.py
M		tools/moltemplate/src/ltemplify.py
M		tools/moltemplate/src/lttree.py
M		tools/moltemplate/src/lttree_check.py
A		tools/moltemplate/src/lttree_postprocess.py
M		tools/moltemplate/src/moltemplate.sh
M		tools/moltemplate/src/nbody_graph_search.py
M		tools/moltemplate/src/postprocess_input_script.py
M		tools/moltemplate/src/ttree.py
M		tools/moltemplate/src/ttree_lex.py
M		tools/moltemplate/src/ttree_render.py