Diffusion lammps 5fbf034e55e4

Merge branch 'lammps-icms' of bitbucket.org:akohlmey/lammps-icms into lammps…
5fbf034e55e4
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Authored by Axel Kohlmeyer <akohlmey@gmail.com> on Nov 6 2013, 20:49.

Description

Merge branch 'lammps-icms' of bitbucket.org:akohlmey/lammps-icms into lammps-icms

Details

Committed

Axel Kohlmeyer <akohlmey@gmail.com>

Nov 6 2013, 20:49

Pushed

junge

Oct 6 2016, 16:49

Parents

rLAMMPSb4ab2b2261ac: fix typo in previous bugfix noticed by bart vorselaars
rLAMMPS1fbe63d33328: explicitly include headers that were implicit for now

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Axel Kohlmeyer <akohlmey@gmail.com> committed rLAMMPS5fbf034e55e4: Merge branch 'lammps-icms' of bitbucket.org:akohlmey/lammps-icms into lammps… (authored by Axel Kohlmeyer <akohlmey@gmail.com>).Nov 6 2013, 20:49

Merged Changes

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

Commit	Author	Details	Committed
b4ab2b2261ac	Axel Kohlmeyer	fix typo in previous bugfix noticed by bart vorselaars	Nov 6 2013
fa036de2993d	Axel Kohlmeyer	Merge remote branch 'lammps-ro/master' into lammps-icms	Nov 6 2013
767784895d26	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10983 f3b2605a-c512-4ea7…	Nov 5 2013
c44a7a267340	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10982 f3b2605a-c512-4ea7…	Nov 5 2013
c90a68646c56	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10980 f3b2605a-c512-4ea7…	Nov 5 2013
91913c8b8dde	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10979 f3b2605a-c512-4ea7…	Nov 5 2013
51331821987d	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10978 f3b2605a-c512-4ea7…	Nov 5 2013
9f6f931565fa	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10977 f3b2605a-c512-4ea7…	Nov 5 2013
7f04aae7ed62	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10975 f3b2605a-c512-4ea7…	Nov 5 2013
3cbbe1490247	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10974 f3b2605a-c512-4ea7…	Nov 5 2013
b1b39a15c460	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10973 f3b2605a-c512-4ea7…	Nov 5 2013
772af4afd00f	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10972 f3b2605a-c512-4ea7…	Nov 5 2013
5725a9cfd8be	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10971 f3b2605a-c512-4ea7…	Nov 5 2013
0a6129594435	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10970 f3b2605a-c512-4ea7…	Nov 5 2013
7e26c6085fce	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10969 f3b2605a-c512-4ea7…	Nov 5 2013
4d4698f0998b	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10968 f3b2605a-c512-4ea7…	Nov 5 2013
b927375ca421	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10967 f3b2605a-c512-4ea7…	Nov 5 2013
3237d21989d2	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10966 f3b2605a-c512-4ea7…	Nov 5 2013
4900a9922891	Axel Kohlmeyer	recover adjustment to altered FFT3d API	Nov 5 2013
dc1278ee51e6	Axel Kohlmeyer	Merge remote branch 'lammps-ro/master' into lammps-icms	Nov 5 2013
661c056cdb2e	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10965 f3b2605a-c512-4ea7…	Nov 4 2013
8777a53f1a60	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10963 f3b2605a-c512-4ea7…	Nov 4 2013
83d209b7f89b	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10962 f3b2605a-c512-4ea7…	Nov 4 2013
ff824424cbbb	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10960 f3b2605a-c512-4ea7…	Nov 4 2013
83c5f05e64b5	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10959 f3b2605a-c512-4ea7…	Nov 4 2013
0d9e811cbb87	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10958 f3b2605a-c512-4ea7…	Nov 4 2013
b0064e507cdf	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10957 f3b2605a-c512-4ea7…	Nov 4 2013
90a2bccf8379	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10956 f3b2605a-c512-4ea7…	Nov 4 2013
fb24b5ad83be	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10955 f3b2605a-c512-4ea7…	Nov 4 2013
315cc6011e70	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10954 f3b2605a-c512-4ea7…	Nov 4 2013
343928a9f1fd	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10953 f3b2605a-c512-4ea7…	Nov 4 2013
a3c23107159a	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10950 f3b2605a-c512-4ea7…	Nov 4 2013
63b1d81230eb	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10949 f3b2605a-c512-4ea7…	Nov 4 2013
d592b4689e92	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10948 f3b2605a-c512-4ea7…	Nov 4 2013
52779f898fa2	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10947 f3b2605a-c512-4ea7…	Nov 4 2013
5e6680916b94	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10946 f3b2605a-c512-4ea7…	Nov 4 2013
ed9d5b6dc43f	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10945 f3b2605a-c512-4ea7…	Nov 4 2013
6afeb95e53eb	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10944 f3b2605a-c512-4ea7…	Nov 4 2013
bbc2b231ba53	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10943 f3b2605a-c512-4ea7…	Nov 4 2013
d1d32497ae66	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10942 f3b2605a-c512-4ea7…	Nov 4 2013
6eac9cb9bc4f	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10941 f3b2605a-c512-4ea7…	Nov 4 2013
bbeddc892238	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10940 f3b2605a-c512-4ea7…	Nov 4 2013
0b7666f338a5	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10937 f3b2605a-c512-4ea7…	Nov 4 2013
0c047f2ce868	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10936 f3b2605a-c512-4ea7…	Nov 4 2013
5f9001a59de0	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10935 f3b2605a-c512-4ea7…	Nov 4 2013
519dd71a0bac	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10934 f3b2605a-c512-4ea7…	Nov 4 2013
53b308a66110	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10933 f3b2605a-c512-4ea7…	Nov 4 2013
2353a9d74c05	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10932 f3b2605a-c512-4ea7…	Nov 4 2013
1dc726ef168d	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10931 f3b2605a-c512-4ea7…	Nov 4 2013
3b6c9afb095b	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10928 f3b2605a-c512-4ea7…	Nov 4 2013

Changes (243)
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This commit is very large. Load each file individually.

		Path
A		doc/Eqs/fix_ti_rs_force.jpg
A		doc/Eqs/fix_ti_rs_force.tex
A		doc/Eqs/fix_ti_rs_function_1.jpg
A		doc/Eqs/fix_ti_rs_function_1.tex
A		doc/Eqs/fix_ti_rs_function_2.jpg
A		doc/Eqs/fix_ti_rs_function_2.tex
A		doc/Eqs/fix_ti_rs_function_3.jpg
A		doc/Eqs/fix_ti_rs_function_3.tex
A		doc/Eqs/fix_ti_spring_force.jpg
A		doc/Eqs/fix_ti_spring_force.tex
A		doc/Eqs/fix_ti_spring_function_1.jpg
A		doc/Eqs/fix_ti_spring_function_1.tex
A		doc/Eqs/fix_ti_spring_function_2.jpg
A		doc/Eqs/fix_ti_spring_function_2.tex
M		doc/Eqs/pair_comb1.jpg
M		doc/Eqs/pair_comb1.tex
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/Section_start.html
M		doc/Section_start.txt
M		doc/compute_msd.html
M		doc/compute_msd.txt
M		doc/compute_ti.html
M		doc/compute_ti.txt
M		doc/dump.html
M		doc/dump.txt
M		doc/dump_image.html
M		doc/dump_image.txt
M		doc/dump_modify.html
M		doc/dump_modify.txt
M		doc/fix_append_atoms.html
M		doc/fix_append_atoms.txt
M		doc/fix_langevin.html
M		doc/fix_langevin.txt
M		doc/fix_phonon.html
M		doc/fix_phonon.txt
A		doc/fix_ti_rs.html
A		doc/fix_ti_rs.txt
A		doc/fix_ti_spring.html
A		doc/fix_ti_spring.txt
M		doc/pair_comb.html
M		doc/pair_comb.txt
M		doc/write_dump.html
M		doc/write_dump.txt
M		examples/COUPLE/simple/simple.c
A	(dir)	examples/USER/misc/ti/
A		examples/USER/misc/ti/in.ti_rs
A		examples/USER/misc/ti/in.ti_spring
A		examples/comb/data.comb3-OHCCu
A		examples/comb/ffield.comb3
A		examples/comb/in.comb3
A		examples/comb/lib.comb3
A		examples/comb/log.comb3.4Nov13.linux.1
A		examples/comb/log.comb3.4Nov13.linux.4
M		potentials/README
A		potentials/ffield.comb3
A		potentials/lib.comb3
M		src/MANYBODY/fix_qeq_comb.cpp
M		src/MANYBODY/fix_qeq_comb.h
A		src/MANYBODY/pair_comb3.cpp
A		src/MANYBODY/pair_comb3.h
M		src/USER-MISC/README
A		src/USER-MISC/fix_ti_rs.cpp
A		src/USER-MISC/fix_ti_rs.h
A		src/USER-MISC/fix_ti_spring.cpp
A		src/USER-MISC/fix_ti_spring.h
M		src/USER-PHONON/fix_phonon.cpp
M		src/USER-PHONON/fix_phonon.h
M		src/USER-REAXC/reaxc_control.cpp
M		src/atom.cpp
A		src/compute_vacf.cpp
A		src/compute_vacf.h
M		src/dump_cfg.cpp
M		src/dump_cfg.h
M		src/dump_custom.cpp
M		src/dump_image.cpp
M		src/dump_image.h
M		src/dump_movie.cpp
M		src/neigh_list.cpp
M		src/neighbor.cpp
M		src/special.cpp
M		src/variable.cpp
M		src/version.h
M		src/write_dump.cpp
M		tools/amber2lmp/README
M		tools/amber2lmp/amber2lammps.py
A	(dir)	tools/moltemplate/common/amber/
A		tools/moltemplate/common/amber/README.TXT
A		tools/moltemplate/common/amber/amberparm2lt.sh
A		tools/moltemplate/common/amber/amberparm_angle_to_lt.py
A		tools/moltemplate/common/amber/amberparm_bond_to_lt.py
A		tools/moltemplate/common/amber/amberparm_dihedral_to_lt.py
A		tools/moltemplate/common/amber/amberparm_improper_to_lt.py
A		tools/moltemplate/common/amber/amberparm_mass_to_lt.py
A		tools/moltemplate/common/amber/amberparm_pair_to_lt.py
A		tools/moltemplate/common/gaff.lt
M		tools/moltemplate/common/spce.lt
V		tools/moltemplate/common/{tip3p_1983.lt ← tip3p_attempts/tip3pcharmm.lt}
V		tools/moltemplate/common/{tip3p_2004.lt ← tip3p_attempts/tip3p2004.lt}
D		tools/moltemplate/common/tip3p_attempts
D		tools/moltemplate/common/tip3p_attempts/README.TXT
V		tools/moltemplate/common/{tip3p_attempts/tip3p2004.lt → tip3p_2004.lt}
V		tools/moltemplate/common/{tip3p_attempts/tip3pcharmm.lt → tip3p_1983.lt}
D		tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/for_visualization
D		tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/for_visualization/psf_file_created_by_topotools
D		tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/for_visualization/psf_file_created_by_topotools/system.psf
M		tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README.TXT
A	(dir)	tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/
V		tools/moltemplate/examples/CG_biomolecules/{vesicle_Brannigan2005+Bellesia2010 ← vesicle_PACKMOL}/README.TXT
V		tools/moltemplate/examples/CG_biomolecules/{vesicle_Brannigan2005+Bellesia2010 ← vesicle_PACKMOL}/README_run.sh
V		tools/moltemplate/examples/CG_biomolecules/{vesicle_Brannigan2005+Bellesia2010 ← vesicle_PACKMOL}/README_setup.sh
P		tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/README_visualize.txt Copied from tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/README_visualize.txt
A	(dir)	tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/images/
A		tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/images/vesicle_membrane+protein_L.jpg
A	(dir)	tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/
V		tools/moltemplate/examples/CG_biomolecules/{vesicle_Brannigan2005+Bellesia2010 ← vesicle_PACKMOL}/moltemplate_files/1beadProtSci2010.lt
V		tools/moltemplate/examples/CG_biomolecules/{vesicle_Brannigan2005+Bellesia2010 ← vesicle_PACKMOL}/moltemplate_files/1beadProtSci2010_variations.lt
V		tools/moltemplate/examples/CG_biomolecules/{vesicle_Brannigan2005+Bellesia2010 ← vesicle_PACKMOL}/moltemplate_files/CGLipidBr2005.lt
V		tools/moltemplate/examples/CG_biomolecules/{vesicle_Brannigan2005+Bellesia2010 ← vesicle_PACKMOL}/moltemplate_files/README.sh
V	(dir)	tools/moltemplate/examples/CG_biomolecules/{vesicle_Brannigan2005+Bellesia2010/moltemplate_files/calc_table/ ← vesicle_PACKMOL/moltemplate_files/calc_table}
V		tools/moltemplate/examples/CG_biomolecules/{vesicle_Brannigan2005+Bellesia2010 ← vesicle_PACKMOL}/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py
V	(dir)	tools/moltemplate/examples/CG_biomolecules/{vesicle_Brannigan2005+Bellesia2010/moltemplate_files/calc_table/version_charmm_cutoff/ ← vesicle_PACKMOL/moltemplate_files/calc_table/version_charmm_cutoff}
V		tools/moltemplate/examples/CG_biomolecules/{vesicle_Brannigan2005+Bellesia2010 ← vesicle_PACKMOL}/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py
V		tools/moltemplate/examples/CG_biomolecules/{vesicle_Brannigan2005+Bellesia2010 ← vesicle_PACKMOL}/moltemplate_files/system.lt
V		tools/moltemplate/examples/CG_biomolecules/{vesicle_Brannigan2005+Bellesia2010 ← vesicle_PACKMOL}/moltemplate_files/table_int.dat
A	(dir)	tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/
V		tools/moltemplate/examples/CG_biomolecules/{vesicle_Brannigan2005+Bellesia2010 ← vesicle_PACKMOL}/packmol_files/DLPC.xyz
V		tools/moltemplate/examples/CG_biomolecules/{vesicle_Brannigan2005+Bellesia2010 ← vesicle_PACKMOL}/packmol_files/DPPC.xyz
V		tools/moltemplate/examples/CG_biomolecules/{vesicle_Brannigan2005+Bellesia2010 ← vesicle_PACKMOL}/packmol_files/README.sh
V		tools/moltemplate/examples/CG_biomolecules/{vesicle_Brannigan2005+Bellesia2010 ← vesicle_PACKMOL}/packmol_files/protein.xyz
V		tools/moltemplate/examples/CG_biomolecules/{vesicle_Brannigan2005+Bellesia2010 ← vesicle_PACKMOL}/packmol_files/step1_proteins.inp
V		tools/moltemplate/examples/CG_biomolecules/{vesicle_Brannigan2005+Bellesia2010 ← vesicle_PACKMOL}/packmol_files/step2_innerlayer.inp
V		tools/moltemplate/examples/CG_biomolecules/{vesicle_Brannigan2005+Bellesia2010 ← vesicle_PACKMOL}/packmol_files/step3_outerlayer.inp
V		tools/moltemplate/examples/CG_biomolecules/{vesicle_Brannigan2005+Bellesia2010 ← vesicle_PACKMOL}/run.in.min
V		tools/moltemplate/examples/CG_biomolecules/{vesicle_Brannigan2005+Bellesia2010 ← vesicle_PACKMOL}/run.in.nvt
D		tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL
V		tools/moltemplate/examples/CG_biomolecules/{vesicle_PACKMOL → vesicle_Brannigan2005+Bellesia2010}/README.TXT
V		tools/moltemplate/examples/CG_biomolecules/{vesicle_PACKMOL → vesicle_Brannigan2005+Bellesia2010}/README_run.sh
V		tools/moltemplate/examples/CG_biomolecules/{vesicle_PACKMOL → vesicle_Brannigan2005+Bellesia2010}/README_setup.sh
P		tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/README_visualize.txt Deleted after being copied to multiple locations: tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/README_visualize.txt tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/README_visualize.txt
D		tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/images
D		tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/images/vesicle_hole_blackbk_LR.jpg
D		tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/moltemplate_files
V		tools/moltemplate/examples/CG_biomolecules/{vesicle_PACKMOL → vesicle_Brannigan2005+Bellesia2010}/moltemplate_files/1beadProtSci2010.lt
V		tools/moltemplate/examples/CG_biomolecules/{vesicle_PACKMOL → vesicle_Brannigan2005+Bellesia2010}/moltemplate_files/1beadProtSci2010_variations.lt
V		tools/moltemplate/examples/CG_biomolecules/{vesicle_PACKMOL → vesicle_Brannigan2005+Bellesia2010}/moltemplate_files/CGLipidBr2005.lt
V		tools/moltemplate/examples/CG_biomolecules/{vesicle_PACKMOL → vesicle_Brannigan2005+Bellesia2010}/moltemplate_files/README.sh
V	(dir)	tools/moltemplate/examples/CG_biomolecules/{vesicle_PACKMOL/moltemplate_files/calc_table/ → vesicle_Brannigan2005+Bellesia2010/moltemplate_files/calc_table}
V		tools/moltemplate/examples/CG_biomolecules/{vesicle_PACKMOL → vesicle_Brannigan2005+Bellesia2010}/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py
V	(dir)	tools/moltemplate/examples/CG_biomolecules/{vesicle_PACKMOL/moltemplate_files/calc_table/version_charmm_cutoff/ → vesicle_Brannigan2005+Bellesia2010/moltemplate_files/calc_table/version_charmm_cutoff}
V		tools/moltemplate/examples/CG_biomolecules/{vesicle_PACKMOL → vesicle_Brannigan2005+Bellesia2010}/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py
V		tools/moltemplate/examples/CG_biomolecules/{vesicle_PACKMOL → vesicle_Brannigan2005+Bellesia2010}/moltemplate_files/system.lt
V		tools/moltemplate/examples/CG_biomolecules/{vesicle_PACKMOL → vesicle_Brannigan2005+Bellesia2010}/moltemplate_files/table_int.dat
D		tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/packmol_files
V		tools/moltemplate/examples/CG_biomolecules/{vesicle_PACKMOL → vesicle_Brannigan2005+Bellesia2010}/packmol_files/DLPC.xyz
V		tools/moltemplate/examples/CG_biomolecules/{vesicle_PACKMOL → vesicle_Brannigan2005+Bellesia2010}/packmol_files/DPPC.xyz
V		tools/moltemplate/examples/CG_biomolecules/{vesicle_PACKMOL → vesicle_Brannigan2005+Bellesia2010}/packmol_files/README.sh
V		tools/moltemplate/examples/CG_biomolecules/{vesicle_PACKMOL → vesicle_Brannigan2005+Bellesia2010}/packmol_files/protein.xyz
V		tools/moltemplate/examples/CG_biomolecules/{vesicle_PACKMOL → vesicle_Brannigan2005+Bellesia2010}/packmol_files/step1_proteins.inp
V		tools/moltemplate/examples/CG_biomolecules/{vesicle_PACKMOL → vesicle_Brannigan2005+Bellesia2010}/packmol_files/step2_innerlayer.inp
V		tools/moltemplate/examples/CG_biomolecules/{vesicle_PACKMOL → vesicle_Brannigan2005+Bellesia2010}/packmol_files/step3_outerlayer.inp
V		tools/moltemplate/examples/CG_biomolecules/{vesicle_PACKMOL → vesicle_Brannigan2005+Bellesia2010}/run.in.min
V		tools/moltemplate/examples/CG_biomolecules/{vesicle_PACKMOL → vesicle_Brannigan2005+Bellesia2010}/run.in.nvt
M		tools/moltemplate/examples/CG_misc/2bead_heteropolymer/images/for_visualization/psf_file_created_by_topotools/system.psf
M		tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/2bead.lt
D		tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/2bead_angles.lt
A		tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/2bead_forcefield.lt
M		tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/peptide.lt
D		tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/simplified_version_one_residue
D		tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/simplified_version_one_residue/2bead_simple.lt
M		tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/system.lt
D		tools/moltemplate/examples/CG_misc/translocation/images/for_visualization
D		tools/moltemplate/examples/CG_misc/translocation/images/for_visualization/psf_file_created_by_topotools
D		tools/moltemplate/examples/CG_misc/translocation/images/for_visualization/psf_file_created_by_topotools/system.psf
A		tools/moltemplate/examples/CG_misc/translocation/images/polymer_LR.jpg
A		tools/moltemplate/examples/CG_misc/translocation/images/solvent_LR.jpg
A		tools/moltemplate/examples/CG_misc/translocation/images/walls_LR.jpg
M		tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/monomer.lt
A	(dir)	tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/
A	(dir)	tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/
A		tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/README.TXT
A		tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/README_run.sh
A		tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/README_setup.sh
V		tools/moltemplate/examples/{all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane ← CG_biomolecules/vesicle_PACKMOL}/README_visualize.txt
A	(dir)	tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/images/
A		tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/images/isobutane.jpg
A		tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/images/water+isobutane_t=0_LR.jpg
A		tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/images/water+isobutane_t=840ps_LR.jpg
A		tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/images/water.jpg
A	(dir)	tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/moltemplate_files/
A		tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/moltemplate_files/isobutane.lt
A		tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/moltemplate_files/system.lt
P		tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/run.in.npt Copied from tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.npt
P		tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/run.in.nvt Copied from tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.nvt
M		tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_FIRST.TXT
V		tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/{README_run_lammps.sh → README_step3_run_lammps.sh}
V		tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/{README_run_ltemplify.sh → README_step1_run_ltemplify.sh}
V		tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/{README_run_moltemplate.sh → README_step2_run_moltemplate.sh}
V		tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/{README_step1_run_ltemplify.sh ← README_run_ltemplify.sh}
V		tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/{README_step2_run_moltemplate.sh ← README_run_moltemplate.sh}
V		tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/{README_step3_run_lammps.sh ← README_run_lammps.sh}
M		tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/graphene.lt
M		tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/spce.lt
M		tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/system.lt
A		tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/.0
M		tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/spce.lt
M		tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.npt
M		tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.nvt
M		tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/spce.lt
P		tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.npt Copied to tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/run.in.npt
P		tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.nvt Copied to tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/run.in.nvt
M		tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/pyramids.lt
A		tools/moltemplate/src/bonds_by_type.py
A		tools/moltemplate/src/dump2data.py
M		tools/moltemplate/src/ltemplify.py
M		tools/moltemplate/src/lttree.py
M		tools/moltemplate/src/lttree_check.py
M		tools/moltemplate/src/lttree_styles.py
M		tools/moltemplate/src/moltemplate.sh
P		tools/moltemplate/src/nbody_Impropers.py Copied to multiple locations: tools/moltemplate/src/nbody_alternate_symmetry/nbody_ImpropersIJIKILswapJK.py tools/moltemplate/src/nbody_alternate_symmetry/nbody_ImpropersIJIKILswapJKL.py tools/moltemplate/src/nbody_alternate_symmetry/nbody_ImpropersJIJKJLswapJK.py
A	(dir)	tools/moltemplate/src/nbody_alternate_symmetry/
A		tools/moltemplate/src/nbody_alternate_symmetry/nbody_Dihedrals_nosym.py
A		tools/moltemplate/src/nbody_alternate_symmetry/nbody_ImpropersIJIKILnoswap.py
P		tools/moltemplate/src/nbody_alternate_symmetry/nbody_ImpropersIJIKILswapJK.py Copied from tools/moltemplate/src/nbody_Impropers.py
P		tools/moltemplate/src/nbody_alternate_symmetry/nbody_ImpropersIJIKILswapJKL.py Copied from tools/moltemplate/src/nbody_Impropers.py
A		tools/moltemplate/src/nbody_alternate_symmetry/nbody_ImpropersJIJKJLnoswap.py
A		tools/moltemplate/src/nbody_alternate_symmetry/nbody_ImpropersJIJKJLswapIK.py
A		tools/moltemplate/src/nbody_alternate_symmetry/nbody_ImpropersJIJKJLswapIKL.py
P		tools/moltemplate/src/nbody_alternate_symmetry/nbody_ImpropersJIJKJLswapJK.py Copied from tools/moltemplate/src/nbody_Impropers.py
M		tools/moltemplate/src/nbody_by_type.py
P		tools/moltemplate/src/nbody_by_type_lib.py Copied to tools/moltemplate/src/nbody_by_type_lib_old.py
P		tools/moltemplate/src/nbody_by_type_lib_old.py Copied from tools/moltemplate/src/nbody_by_type_lib.py
M		tools/moltemplate/src/pdbsort.py
M		tools/moltemplate/src/postprocess_input_script.py
A		tools/moltemplate/src/raw2data.py
M		tools/moltemplate/src/ttree.py
M		tools/moltemplate/src/ttree_lex.py
M		tools/msi2lmp/README
D		tools/msi2lmp/TriclinicModification.pdf