Diffusion lammps b826d2958ef1

Merge branch 'lammps-icms' into lammps-colvars
b826d2958ef1
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Authored by Axel Kohlmeyer <akohlmey@gmail.com> on Jan 14 2013, 12:22.

Description

Merge branch 'lammps-icms' into lammps-colvars

Details

Committed

Axel Kohlmeyer <akohlmey@gmail.com>

Jan 14 2013, 12:22

Pushed

junge

Oct 6 2016, 16:49

Parents

rLAMMPSbf7d8848022d: used double precision FFT for MSM support
rLAMMPSc58b5f4d1b87: import from colvars svn repo

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Axel Kohlmeyer <akohlmey@gmail.com> committed rLAMMPSb826d2958ef1: Merge branch 'lammps-icms' into lammps-colvars (authored by Axel Kohlmeyer <akohlmey@gmail.com>).Jan 14 2013, 12:22

Merged Changes

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

Commit	Author	Details	Committed
bf7d8848022d	Axel Kohlmeyer	used double precision FFT for MSM support	Jan 14 2013
5bcb632d2960	Axel Kohlmeyer	add test for MSM	Jan 14 2013
25092cfc299d	Axel Kohlmeyer	Merge branch 'master' into lammps-icms	Jan 14 2013
1087ef306e59	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9267 f3b2605a-c512-4ea7…	Jan 12 2013
93e3045cfc38	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9266 f3b2605a-c512-4ea7…	Jan 12 2013
1fbdf607572d	pscrozi	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9265 f3b2605a-c512-4ea7…	Jan 12 2013
2bd231c5637e	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9264 f3b2605a-c512-4ea7…	Jan 11 2013
4277a7d8e6e7	pscrozi	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9263 f3b2605a-c512-4ea7…	Jan 11 2013
fafd420f351b	pscrozi	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9262 f3b2605a-c512-4ea7…	Jan 11 2013
a6eb6e4f8486	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9261 f3b2605a-c512-4ea7…	Jan 11 2013
bad59e0fca35	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9260 f3b2605a-c512-4ea7…	Jan 11 2013
37849c807e75	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9259 f3b2605a-c512-4ea7…	Jan 11 2013
e66eccef5f4a	pscrozi	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9258 f3b2605a-c512-4ea7…	Jan 10 2013
20150c50a8dc	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9257 f3b2605a-c512-4ea7…	Jan 10 2013
ec624ab44689	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9256 f3b2605a-c512-4ea7…	Jan 9 2013
feefdd97ea5c	pscrozi	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9255 f3b2605a-c512-4ea7…	Jan 9 2013
4fac34ed3e23	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9254 f3b2605a-c512-4ea7…	Jan 9 2013
427161ef56aa	Axel Kohlmeyer	Merge branch 'master' into lammps-icms	Jan 9 2013
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

Changes (141)
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Very Large Commit

This commit is very large. Load each file individually.

		Path
A	(dir)	bench-accel/bench_msm/
A		bench-accel/bench_msm/data.msm
A		bench-accel/bench_msm/in.msm
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_bond_swap.html
M		doc/fix_bond_swap.txt
M		doc/fix_external.html
M		doc/fix_external.txt
M		doc/fix_heat.html
M		doc/fix_heat.txt
M		doc/fix_wall_region.html
M		doc/fix_wall_region.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/MAKE/Makefile.openmpi-omp
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/RIGID/fix_rigid.cpp
M		src/RIGID/fix_rigid_nh.cpp
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/comm.cpp
M		src/domain.cpp
M		src/dump_custom.cpp
M		src/fix.h
M		src/fix_adapt.cpp
M		src/fix_deform.cpp
M		src/fix_external.cpp
M		src/fix_external.h
M		src/fix_heat.cpp
M		src/fix_heat.h
M		src/fix_langevin.cpp
M		src/fix_nh.cpp
M		src/fix_press_berendsen.cpp
M		src/fix_print.cpp
M		src/fix_print.h
M		src/fix_restrain.cpp
M		src/fix_store_state.cpp
M		src/fix_temp_berendsen.cpp
M		src/fix_temp_rescale.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_dpd_tstat.cpp
M		src/pair_lj_expand.cpp
M		src/pair_lj_expand.h
M		src/respa.cpp
M		src/thermo.cpp
M		src/variable.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