Diffusion lammps 96ccc7976d2b

Merge remote-tracking branch 'lammps-ro/master' into lammps-icms
96ccc7976d2b
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Authored by Axel Kohlmeyer <akohlmey@gmail.com> on Feb 4 2014, 13:14.

Description

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

Resolved Conflicts:
doc/Manual.html
doc/Manual.txt

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Committed

Axel Kohlmeyer <akohlmey@gmail.com>

Feb 4 2014, 13:14

Pushed

junge

Oct 6 2016, 16:49

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rLAMMPSb7d55ca48407: git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11467 f3b2605a-c512-4ea7…
rLAMMPS6f99bf9132da: fix a few more cases of incorrect markup

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Axel Kohlmeyer <akohlmey@gmail.com> committed rLAMMPS96ccc7976d2b: Merge remote-tracking branch 'lammps-ro/master' into lammps-icms (authored by Axel Kohlmeyer <akohlmey@gmail.com>).Feb 4 2014, 13:14

Merged Changes

Commit	Author	Details	Committed
b7d55ca48407	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11467 f3b2605a-c512-4ea7…	Feb 4 2014
a1b640205f2e	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11466 f3b2605a-c512-4ea7…	Feb 4 2014
f474d7d106b8	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11464 f3b2605a-c512-4ea7…	Feb 4 2014
fc5f92579dec	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11463 f3b2605a-c512-4ea7…	Feb 4 2014
45bcc8660215	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11461 f3b2605a-c512-4ea7…	Feb 4 2014
8688b7b430e6	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11460 f3b2605a-c512-4ea7…	Feb 4 2014
298e177acbdd	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11459 f3b2605a-c512-4ea7…	Feb 4 2014
e3979f61439e	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11458 f3b2605a-c512-4ea7…	Feb 4 2014
495c5a09b32d	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11457 f3b2605a-c512-4ea7…	Feb 4 2014
743cf8b837ad	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11456 f3b2605a-c512-4ea7…	Feb 4 2014
76e47e855be7	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11455 f3b2605a-c512-4ea7…	Feb 4 2014
53509fac9f5f	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11452 f3b2605a-c512-4ea7…	Feb 3 2014
036f4f8dbfe9	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11450 f3b2605a-c512-4ea7…	Feb 1 2014
d5d663a10511	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11449 f3b2605a-c512-4ea7…	Feb 1 2014
19e47c5264ec	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11448 f3b2605a-c512-4ea7…	Feb 1 2014
a16612ffbee5	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11447 f3b2605a-c512-4ea7…	Feb 1 2014
09f02ddf7cb0	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11446 f3b2605a-c512-4ea7…	Feb 1 2014
532dd7c50003	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11444 f3b2605a-c512-4ea7…	Feb 1 2014
47632aab2296	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11443 f3b2605a-c512-4ea7…	Feb 1 2014
9be41fa46b79	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11442 f3b2605a-c512-4ea7…	Feb 1 2014
634881f8ceca	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11441 f3b2605a-c512-4ea7…	Feb 1 2014
7bf0ad314c6e	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11440 f3b2605a-c512-4ea7…	Feb 1 2014
8031ade7de10	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11439 f3b2605a-c512-4ea7…	Feb 1 2014
e9f63600bef4	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11437 f3b2605a-c512-4ea7…	Feb 1 2014
c137068c4700	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11436 f3b2605a-c512-4ea7…	Feb 1 2014
f6d1f6822ce1	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11435 f3b2605a-c512-4ea7…	Feb 1 2014
ceb4da003907	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11434 f3b2605a-c512-4ea7…	Feb 1 2014
57b7ebbef002	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11433 f3b2605a-c512-4ea7…	Feb 1 2014

Changes (120)
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		Path
M		doc/Eqs/pair_comb1.jpg
M		doc/Eqs/pair_comb2.jpg
M		doc/Eqs/pair_comb2.tex
M		doc/Manual.html
M		doc/Manual.txt
M		doc/Section_commands.html
M		doc/Section_commands.txt
M		doc/compute_damage_atom.html
M		doc/compute_damage_atom.txt
A		doc/compute_dilatation.html
A		doc/compute_dilatation.txt
A		doc/compute_plasticity.html
A		doc/compute_plasticity.txt
M		doc/compute_vacf.html
M		doc/compute_vacf.txt
M		doc/fix_ave_time.html
M		doc/fix_ave_time.txt
A		doc/fix_vector.html
A		doc/fix_vector.txt
M		doc/pair_comb.html
M		doc/pair_comb.txt
M		doc/pair_peri.html
M		doc/pair_peri.txt
M		examples/KAPPA/in.heat
M		examples/KAPPA/in.heatflux
M		examples/comb/data.comb3-OHCCu
M		examples/comb/in.comb3
M		potentials/ffield.comb3
M		potentials/lib.comb3
M		src/MANYBODY/pair_comb3.cpp
M		src/MANYBODY/pair_comb3.h
P		src/PERI/compute_damage_atom.cpp Copied to multiple locations: src/PERI/compute_dilatation_atom.cpp src/PERI/compute_plasticity_atom.cpp
P		src/PERI/compute_dilatation_atom.cpp Copied from src/PERI/compute_damage_atom.cpp
A		src/PERI/compute_dilatation_atom.h
P		src/PERI/compute_plasticity_atom.cpp Copied from src/PERI/compute_damage_atom.cpp
A		src/PERI/compute_plasticity_atom.h
M		src/PERI/fix_peri_neigh.cpp
M		src/PERI/fix_peri_neigh.h
P		src/PERI/pair_peri_eps.cpp Copied from src/PERI/pair_peri_ves.cpp
P		src/PERI/pair_peri_eps.h Copied from src/PERI/pair_peri_ves.h
M		src/PERI/pair_peri_lps.cpp
M		src/PERI/pair_peri_lps.h
P		src/PERI/pair_peri_ves.cpp Copied to src/PERI/pair_peri_eps.cpp
P		src/PERI/pair_peri_ves.h Copied to src/PERI/pair_peri_eps.h
M		src/fix_ave_time.cpp
A		src/fix_vector.cpp
A		src/fix_vector.h
M		src/version.h
M		tools/moltemplate/common/amber/amberparm2lt.sh
M		tools/moltemplate/common/amber/amberparm_pair_to_lt.py
M		tools/moltemplate/common/gaff.lt
M		tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py
M		tools/moltemplate/examples/CG_biomolecules/membrane+protein/run.in.npt
M		tools/moltemplate/examples/CG_biomolecules/membrane+protein/run.in.nvt
M		tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/calc_table/calc_table.py
M		tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/system.lt
M		tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py
M		tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/README.sh
M		tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/run.in.min
M		tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/run.in.nvt
M		tools/moltemplate/examples/CG_misc/translocation/run.in.nvt
M		tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/run.in.npt
M		tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/run.in.nvt
A		tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/WARNING.TXT
A	(dir)	tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/
A		tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/README.TXT
A		tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/README_run.sh
P		tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/README_setup.sh Copied from tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/README_setup.sh
A		tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/README_visualize.txt
A		tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/WARNING.TXT
A	(dir)	tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/images/
A		tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/images/hexadecane_12x12x2_t=0_LR.jpg
A		tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/images/hexadecane_12x12x2_t=10ps_npt_LR.jpg
A		tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/images/hexadecane_LR.jpg
A	(dir)	tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/moltemplate_files/
A		tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/moltemplate_files/ch2group.lt
A		tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/moltemplate_files/ch3group.lt
A		tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/moltemplate_files/hexadecane.lt
A		tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/moltemplate_files/system.lt
A		tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/run.in.npt
A		tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/run.in.nvt
P		tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/README_setup.sh Copied to tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/README_setup.sh
M		tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/moltemplate_files/system.lt
M		tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/run.in.npt
M		tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/run.in.nvt
A		tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/cnt.lt
A	(dir)	tools/moltemplate/examples/all_atom_examples/hexadecane/
A		tools/moltemplate/examples/all_atom_examples/hexadecane/README.TXT
A		tools/moltemplate/examples/all_atom_examples/hexadecane/README_run.sh
A		tools/moltemplate/examples/all_atom_examples/hexadecane/README_setup.sh
A		tools/moltemplate/examples/all_atom_examples/hexadecane/README_visualize.txt
A		tools/moltemplate/examples/all_atom_examples/hexadecane/WARNING.TXT
A	(dir)	tools/moltemplate/examples/all_atom_examples/hexadecane/images/
A		tools/moltemplate/examples/all_atom_examples/hexadecane/images/hexadecane_12x12x2_t=0_LR.jpg
A		tools/moltemplate/examples/all_atom_examples/hexadecane/images/hexadecane_12x12x2_t=10ps_npt_LR.jpg
A		tools/moltemplate/examples/all_atom_examples/hexadecane/images/hexadecane_LR.jpg
A	(dir)	tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/
A		tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/alkanes.lt
A		tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/ch2group.lt
A		tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/ch3group.lt
A		tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/hexadecane.lt
A		tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/system.lt
A		tools/moltemplate/examples/all_atom_examples/hexadecane/run.in.npt
A		tools/moltemplate/examples/all_atom_examples/hexadecane/run.in.nvt
M		tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/nanotube.lt
M		tools/moltemplate/examples/all_atom_examples/nanotube+water/run.in.npt
M		tools/moltemplate/examples/all_atom_examples/nanotube+water/run.in.nvt
P		tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.npt Copied from tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.npt
P		tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.nvt Copied from tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.nvt
P		tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.npt Copied to tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.npt
P		tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.nvt Copied to tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.nvt
M		tools/moltemplate/src/dump2data.py
M		tools/moltemplate/src/lttree.py
M		tools/moltemplate/src/lttree_check.py
M		tools/moltemplate/src/moltemplate.sh
M		tools/moltemplate/src/nbody_by_type.py
D		tools/moltemplate/src/nbody_by_type_lib_old.py
M		tools/moltemplate/src/postprocess_input_script.py
M		tools/moltemplate/src/raw2data.py
M		tools/moltemplate/src/ttree.py