Diffusion lammps c2ac3c93c316

Merge branch 'master' into lammps-icms
c2ac3c93c316
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Authored by Axel Kohlmeyer <akohlmey@gmail.com> on Nov 4 2010, 23:29.

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Merge branch 'master' into lammps-icms

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Committed

Axel Kohlmeyer <akohlmey@gmail.com>

Nov 4 2010, 23:29

Pushed

junge

Oct 6 2016, 16:49

Parents

rLAMMPS9225c4a45dff: Turned on kc2
rLAMMPS60a5ec92ac11: remove executable file permissions where useless.

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Axel Kohlmeyer <akohlmey@gmail.com> committed rLAMMPSc2ac3c93c316: Merge branch 'master' into lammps-icms (authored by Axel Kohlmeyer <akohlmey@gmail.com>).Nov 4 2010, 23:29

Merged Changes

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

Commit	Author	Details	Committed
9225c4a45dff	athomps	Turned on kc2	Nov 3 2010
bbdc8801bba6	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5211 f3b2605a-c512-4ea7…	Nov 2 2010
612a5fa21bca	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5208 f3b2605a-c512-4ea7…	Nov 2 2010
6654e997718d	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5207 f3b2605a-c512-4ea7…	Nov 2 2010
5c922f8426c2	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5206 f3b2605a-c512-4ea7…	Nov 2 2010
1b39008e5e3c	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5204 f3b2605a-c512-4ea7…	Nov 2 2010
4460d767e38d	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5203 f3b2605a-c512-4ea7…	Nov 2 2010
508ee5d6aaea	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5202 f3b2605a-c512-4ea7…	Nov 2 2010
453aba29e558	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5201 f3b2605a-c512-4ea7…	Nov 2 2010
b63b44e27417	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5200 f3b2605a-c512-4ea7…	Nov 2 2010
88e059498755	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5197 f3b2605a-c512-4ea7…	Nov 1 2010
16116d300d85	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5193 f3b2605a-c512-4ea7…	Oct 29 2010
ca670a5f77bc	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5191 f3b2605a-c512-4ea7…	Oct 29 2010
0aa371887b35	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5190 f3b2605a-c512-4ea7…	Oct 29 2010
9895060359a5	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5189 f3b2605a-c512-4ea7…	Oct 29 2010
25e2de1bf218	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5182 f3b2605a-c512-4ea7…	Oct 27 2010
ce8d4a318cfb	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5181 f3b2605a-c512-4ea7…	Oct 27 2010
820987761c07	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5180 f3b2605a-c512-4ea7…	Oct 27 2010
1c6e154327ec	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5179 f3b2605a-c512-4ea7…	Oct 27 2010
e1b42c7308db	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5177 f3b2605a-c512-4ea7…	Oct 27 2010
fcbd40ebf666	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5176 f3b2605a-c512-4ea7…	Oct 27 2010
3ab35d6073ff	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5175 f3b2605a-c512-4ea7…	Oct 27 2010
31a310e58888	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5174 f3b2605a-c512-4ea7…	Oct 27 2010
f2b88626a06c	athomps	Added check for qeq and option to turn off check	Oct 27 2010
df8655f6d5c1	athomps	Added check for qeq and option to turn off check	Oct 27 2010
701a14195032	athomps	Added fix qeq/reax check	Oct 27 2010
eb967e3b592a	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5170 f3b2605a-c512-4ea7…	Oct 27 2010
5c7cadb89af4	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5168 f3b2605a-c512-4ea7…	Oct 27 2010
1040f124cb06	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5167 f3b2605a-c512-4ea7…	Oct 27 2010
2eacfc04656f	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5166 f3b2605a-c512-4ea7…	Oct 27 2010
91dc344af39d	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5162 f3b2605a-c512-4ea7…	Oct 27 2010
32d8d22b8c86	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5161 f3b2605a-c512-4ea7…	Oct 27 2010
e1175cca27c8	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5157 f3b2605a-c512-4ea7…	Oct 26 2010
91746a0ad70c	athomps	Modified pair_styles reax and reax/c	Oct 26 2010
a2dba93f2c95	athomps	Modified pair_styles reax and reax/c	Oct 26 2010
8860ab54ecd9	athomps	Modified pair_styles reax and reax/c	Oct 26 2010
ca774da8266e	athomps	Modified pair_style reax/c	Oct 26 2010
ad75964dc2a6	athomps	Modified pair_styles reax and reax/c	Oct 26 2010
2712b6814e5d	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5150 f3b2605a-c512-4ea7…	Oct 26 2010
890d2a255ff4	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5149 f3b2605a-c512-4ea7…	Oct 26 2010
445ea55e74fc	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5145 f3b2605a-c512-4ea7…	Oct 26 2010
d2be0cb70a35	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5144 f3b2605a-c512-4ea7…	Oct 26 2010
bfd6a79fe67f	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5143 f3b2605a-c512-4ea7…	Oct 26 2010
c2723c7d2710	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5142 f3b2605a-c512-4ea7…	Oct 26 2010
2e39d108c2eb	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5141 f3b2605a-c512-4ea7…	Oct 26 2010
a35661e98963	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5139 f3b2605a-c512-4ea7…	Oct 25 2010
e58496a13880	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5138 f3b2605a-c512-4ea7…	Oct 25 2010
5f5fada72707	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5136 f3b2605a-c512-4ea7…	Oct 25 2010
186fd0ac29cd	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5134 f3b2605a-c512-4ea7…	Oct 25 2010
575837b83e5b	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5133 f3b2605a-c512-4ea7…	Oct 25 2010

Changes (298)
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This commit is very large. Load each file individually.

		Path
M		README
A		doc/Eqs/angle_cosine_periodic.jpg
A		doc/Eqs/angle_cosine_periodic.tex
A		doc/Eqs/dreiding_hbond.jpg
M		doc/Eqs/fix_wall_colloid.jpg
M		doc/Eqs/fix_wall_colloid.tex
A		doc/Eqs/improper_umbrella.jpg
A		doc/Eqs/improper_umbrella.tex
A		doc/Eqs/pair_hbond_dreiding.jpg
A		doc/Eqs/pair_hbond_dreiding.tex
A		doc/Eqs/umbrella.jpg
A		doc/JPG/screenshot1.jpg
A		doc/JPG/screenshot1_small.jpg
M		doc/Manual.html
M		doc/Manual.txt
M		doc/Section_commands.html
M		doc/Section_commands.txt
M		doc/Section_errors.html
M		doc/Section_errors.txt
M		doc/Section_history.html
M		doc/Section_history.txt
M		doc/Section_howto.html
M		doc/Section_howto.txt
M		doc/Section_intro.html
M		doc/Section_intro.txt
M		doc/Section_modify.html
M		doc/Section_modify.txt
A		doc/Section_python.html
A		doc/Section_python.txt
M		doc/Section_start.html
M		doc/Section_start.txt
M		doc/angle_coeff.html
M		doc/angle_coeff.txt
A		doc/angle_cosine_periodic.html
A		doc/angle_cosine_periodic.txt
M		doc/angle_style.html
M		doc/angle_style.txt
M		doc/compute.html
M		doc/compute.txt
A		doc/compute_atom_molecule.html
A		doc/compute_atom_molecule.txt
M		doc/compute_com_molecule.html
M		doc/compute_com_molecule.txt
M		doc/compute_gyration_molecule.html
M		doc/compute_gyration_molecule.txt
M		doc/compute_msd_molecule.html
M		doc/compute_msd_molecule.txt
A		doc/compute_pair.html
A		doc/compute_pair.txt
M		doc/compute_property_molecule.html
M		doc/compute_property_molecule.txt
A		doc/compute_ti.html
A		doc/compute_ti.txt
M		doc/fix.html
M		doc/fix.txt
M		doc/fix_adapt.html
M		doc/fix_adapt.txt
M		doc/fix_ave_spatial.html
M		doc/fix_ave_spatial.txt
M		doc/fix_indent.html
M		doc/fix_indent.txt
M		doc/fix_press_berendsen.html
M		doc/fix_press_berendsen.txt
A		doc/fix_qeq_reax.html
A		doc/fix_qeq_reax.txt
M		doc/fix_srd.html
M		doc/fix_srd.txt
M		doc/fix_wall.html
M		doc/fix_wall.txt
P		doc/fix_wall_reflect.html Copied to doc/fix_wall_srd.html
P		doc/fix_wall_reflect.txt Copied to doc/fix_wall_srd.txt
P		doc/fix_wall_srd.html Copied from doc/fix_wall_reflect.html
P		doc/fix_wall_srd.txt Copied from doc/fix_wall_reflect.txt
M		doc/improper_coeff.html
M		doc/improper_coeff.txt
M		doc/improper_style.html
M		doc/improper_style.txt
A		doc/improper_umbrella.html
A		doc/improper_umbrella.txt
M		doc/pair_coeff.html
M		doc/pair_coeff.txt
M		doc/pair_gauss.html
M		doc/pair_gauss.txt
A		doc/pair_hbond_dreiding.html
A		doc/pair_hbond_dreiding.txt
M		doc/pair_hybrid.html
M		doc/pair_hybrid.txt
M		doc/pair_reax.html
M		doc/pair_reax.txt
A		doc/pair_reax_c.html
A		doc/pair_reax_c.txt
M		doc/pair_style.html
M		doc/pair_style.txt
M		doc/read_restart.html
M		doc/read_restart.txt
M		doc/region.html
M		doc/region.txt
M		doc/special_bonds.html
M		doc/special_bonds.txt
M		doc/variable.html
M		doc/variable.txt
M		examples/micelle/in.micelle
M		examples/neb/in.neb.hop1
M		examples/neb/in.neb.hop2
A		examples/reax/control.reax_c.tatb
M		examples/reax/ffield.reax
M		examples/reax/in.reax.rdx
M		examples/reax/in.reax.tatb
A		examples/reax/in.reax_c.rdx
A		examples/reax/in.reax_c.tatb
M		potentials/README.reax
M		potentials/ffield.reax.cho
A	(dir)	python/
A		python/README
A	(dir)	python/examples/
A		python/examples/demo.py
A		python/examples/gui.py
A		python/examples/in.demo
A		python/examples/in.gui
A		python/examples/in.plot
A		python/examples/in.simple
A		python/examples/in.trivial
A		python/examples/in.viz
A		python/examples/log.lammps
A	(dir)	python/examples/pizza/
A		python/examples/pizza/dump.py
A		python/examples/pizza/gl.py
A		python/examples/pizza/gnu.py
A		python/examples/pizza/vizinfo.py
A		python/examples/plot.py
A		python/examples/simple.py
A		python/examples/trivial.py
A		python/examples/viz.py
A		python/examples/vizplotgui.py
A		python/lammps.py
A		python/setup.py
A		python/setup_serial.py
M		src/CLASS2/pair_lj_class2_coul_long.cpp
M		src/CLASS2/pair_lj_class2_coul_long.h
M		src/COLLOID/fix_wall_colloid.cpp
M		src/COLLOID/pair_colloid.cpp
M		src/COLLOID/pair_lubricate.cpp
M		src/COLLOID/pair_lubricate.h
M		src/GRANULAR/atom_vec_granular.cpp
M		src/KSPACE/ewald.cpp
M		src/KSPACE/pair_born_coul_long.cpp
M		src/KSPACE/pair_born_coul_long.h
M		src/KSPACE/pair_buck_coul_long.cpp
P		src/KSPACE/pair_buck_coul_long.h Copied to src/USER-REAXC/pair_reax_c.h
M		src/KSPACE/pair_coul_long.cpp
M		src/KSPACE/pair_coul_long.h
M		src/KSPACE/pair_lj_charmm_coul_long.cpp
M		src/KSPACE/pair_lj_charmm_coul_long.h
M		src/KSPACE/pair_lj_cut_coul_long.cpp
M		src/KSPACE/pair_lj_cut_coul_long.h
M		src/KSPACE/pair_lj_cut_coul_long_tip4p.cpp
M		src/KSPACE/pair_lj_cut_coul_long_tip4p.h
M		src/KSPACE/pppm.cpp
M		src/MAKE/Makefile.mac_mpi
M		src/MANYBODY/pair_airebo.cpp
M		src/MEAM/pair_meam.cpp
M		src/MOLECULE/Install.sh
A		src/MOLECULE/angle_cosine_periodic.cpp
P		src/MOLECULE/angle_cosine_periodic.h Copied from src/pair_buck.h
M		src/MOLECULE/dihedral_charmm.cpp
A		src/MOLECULE/improper_umbrella.cpp
P		src/MOLECULE/improper_umbrella.h Copied from src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.h
A		src/MOLECULE/pair_hbond_dreiding_lj.cpp
A		src/MOLECULE/pair_hbond_dreiding_lj.h
A		src/MOLECULE/pair_hbond_dreiding_morse.cpp
P		src/MOLECULE/pair_hbond_dreiding_morse.h Copied from src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.h
M		src/MOLECULE/pair_lj_charmm_coul_charmm.cpp
M		src/MOLECULE/pair_lj_charmm_coul_charmm.h
M		src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.cpp
P		src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.h Copied to multiple locations: src/MOLECULE/improper_umbrella.h src/MOLECULE/pair_hbond_dreiding_morse.h
M		src/Makefile
M		src/Makefile.lib
M		src/REAX/pair_reax.cpp
M		src/REAX/pair_reax.h
M		src/REPLICA/fix_neb.cpp
P		src/REPLICA/fix_neb.h Copied to src/SRD/fix_wall_srd.h
M		src/REPLICA/neb.cpp
M		src/SRD/Install.sh
M		src/SRD/fix_srd.cpp
M		src/SRD/fix_srd.h
A		src/SRD/fix_wall_srd.cpp
P		src/SRD/fix_wall_srd.h Copied from src/REPLICA/fix_neb.h
M		src/STUBS/mpi.c
M		src/STUBS/mpi.h
M		src/USER-CG-CMM/pair_cg_cmm_coul_long.cpp
M		src/USER-CG-CMM/pair_cg_cmm_coul_long.h
M		src/USER-EWALDN/ewald_n.cpp
M		src/USER-EWALDN/pair_buck_coul.cpp
M		src/USER-EWALDN/pair_buck_coul.h
M		src/USER-EWALDN/pair_lj_coul.cpp
M		src/USER-EWALDN/pair_lj_coul.h
A	(dir)	src/USER-REAXC/
A		src/USER-REAXC/Install.sh
A		src/USER-REAXC/README
A		src/USER-REAXC/fix_qeq_reax.cpp
A		src/USER-REAXC/fix_qeq_reax.h
A		src/USER-REAXC/fix_reax_c.cpp
P		src/USER-REAXC/fix_reax_c.h Copied from src/fix_adapt.h
A		src/USER-REAXC/pair_reax_c.cpp
P		src/USER-REAXC/pair_reax_c.h Copied from src/KSPACE/pair_buck_coul_long.h
A		src/USER-REAXC/reaxc_allocate.cpp
A		src/USER-REAXC/reaxc_allocate.h
A		src/USER-REAXC/reaxc_basic_comm.cpp
A		src/USER-REAXC/reaxc_basic_comm.h
A		src/USER-REAXC/reaxc_bond_orders.cpp
A		src/USER-REAXC/reaxc_bond_orders.h
A		src/USER-REAXC/reaxc_bonds.cpp
A		src/USER-REAXC/reaxc_bonds.h
A		src/USER-REAXC/reaxc_control.cpp
A		src/USER-REAXC/reaxc_control.h
A		src/USER-REAXC/reaxc_defs.h
A		src/USER-REAXC/reaxc_ffield.cpp
A		src/USER-REAXC/reaxc_ffield.h
A		src/USER-REAXC/reaxc_forces.cpp
A		src/USER-REAXC/reaxc_forces.h
A		src/USER-REAXC/reaxc_hydrogen_bonds.cpp
A		src/USER-REAXC/reaxc_hydrogen_bonds.h
A		src/USER-REAXC/reaxc_init_md.cpp
A		src/USER-REAXC/reaxc_init_md.h
A		src/USER-REAXC/reaxc_io_tools.cpp
A		src/USER-REAXC/reaxc_io_tools.h
A		src/USER-REAXC/reaxc_list.cpp
A		src/USER-REAXC/reaxc_list.h
A		src/USER-REAXC/reaxc_lookup.cpp
A		src/USER-REAXC/reaxc_lookup.h
A		src/USER-REAXC/reaxc_multi_body.cpp
A		src/USER-REAXC/reaxc_multi_body.h
A		src/USER-REAXC/reaxc_nonbonded.cpp
A		src/USER-REAXC/reaxc_nonbonded.h
A		src/USER-REAXC/reaxc_reset_tools.cpp
A		src/USER-REAXC/reaxc_reset_tools.h
A		src/USER-REAXC/reaxc_system_props.cpp
A		src/USER-REAXC/reaxc_system_props.h
A		src/USER-REAXC/reaxc_tool_box.cpp
A		src/USER-REAXC/reaxc_tool_box.h
A		src/USER-REAXC/reaxc_torsion_angles.cpp
A		src/USER-REAXC/reaxc_torsion_angles.h
A		src/USER-REAXC/reaxc_traj.cpp
A		src/USER-REAXC/reaxc_traj.h
A		src/USER-REAXC/reaxc_types.h
A		src/USER-REAXC/reaxc_valence_angles.cpp
A		src/USER-REAXC/reaxc_valence_angles.h
A		src/USER-REAXC/reaxc_vector.cpp
A		src/USER-REAXC/reaxc_vector.h
A		src/compute_atom_molecule.cpp
P		src/compute_atom_molecule.h Copied from src/compute_property_molecule.h
A		src/compute_pair.cpp
P		src/compute_pair.h Copied from src/fix_adapt.h
M		src/compute_pe.cpp
M		src/compute_property_molecule.cpp
P		src/compute_property_molecule.h Copied to src/compute_atom_molecule.h
A		src/compute_ti.cpp
P		src/compute_ti.h Copied from src/fix_adapt.h
M		src/finish.cpp
M		src/fix.cpp
M		src/fix.h
M		src/fix_adapt.cpp
P		src/fix_adapt.h Copied to multiple locations: src/USER-REAXC/fix_reax_c.h src/compute_pair.h src/compute_ti.h
M		src/fix_ave_spatial.cpp
M		src/fix_ave_spatial.h
M		src/fix_store_state.cpp
M		src/force.cpp
M		src/kspace.cpp
M		src/kspace.h
M		src/library.cpp
M		src/library.h
M		src/modify.cpp
M		src/modify.h
M		src/pair.cpp
M		src/pair.h
M		src/pair_born.cpp
M		src/pair_born.h
M		src/pair_buck.cpp
P		src/pair_buck.h Copied to multiple locations: src/MOLECULE/angle_cosine_periodic.h src/pair_gauss.h
M		src/pair_coul_cut.cpp
M		src/pair_coul_cut.h
M		src/pair_gauss.cpp
P		src/pair_gauss.h Copied from src/pair_buck.h
M		src/pair_hybrid.cpp
M		src/pair_hybrid.h
M		src/pair_lj_cut.cpp
M		src/pair_lj_cut.h
M		src/pair_soft.cpp
M		src/pair_soft.h
M		src/pair_table.cpp
M		src/pair_table.h
M		src/region.cpp
M		src/region.h
M		src/region_block.cpp
M		src/respa.cpp
M		src/verlet.cpp
M		src/verlet.h
M		src/version.h