Diffusion lammps 8e91a7e6cd40

Merge branch 'lammps-icms' into unified-timer
8e91a7e6cd40
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Authored by Axel Kohlmeyer <akohlmey@gmail.com> on Jul 26 2013, 14:52.

Description

Merge branch 'lammps-icms' into unified-timer

Details

Committed

Axel Kohlmeyer <akohlmey@gmail.com>

Jul 26 2013, 14:52

Pushed

junge

Oct 6 2016, 16:49

Parents

rLAMMPS8358adc96414: modify_cuda depends on style_computeh and its .d needs to be updated
rLAMMPSe131e2a141a4: make sure everything compiles again

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Axel Kohlmeyer <akohlmey@gmail.com> committed rLAMMPS8e91a7e6cd40: Merge branch 'lammps-icms' into unified-timer (authored by Axel Kohlmeyer <akohlmey@gmail.com>).Jul 26 2013, 14:52

Merged Changes

Commit	Author	Details	Committed
8358adc96414	Axel Kohlmeyer	modify_cuda depends on style_computeh and its .d needs to be updated	Jul 26 2013
60e58c44cf1f	Axel Kohlmeyer	Merge remote branch 'lammps-ro/master' into lammps-icms	Jul 26 2013
434c695e3927	Axel Kohlmeyer	re-instate Makefile.lammps	Jul 26 2013
e6f6722365f3	Axel Kohlmeyer	make USER-CUDA compile with current LAMMPS-ICMS	Jul 26 2013
d3b876aff90d	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10398 f3b2605a-c512-4ea7…	Jul 26 2013
921d24c0f89d	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10397 f3b2605a-c512-4ea7…	Jul 26 2013
7d3d8b5b9d52	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10395 f3b2605a-c512-4ea7…	Jul 26 2013
026a04e4f11a	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10394 f3b2605a-c512-4ea7…	Jul 26 2013
43a8d254fae5	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10393 f3b2605a-c512-4ea7…	Jul 26 2013
609842916cc0	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10392 f3b2605a-c512-4ea7…	Jul 26 2013
6cc90ecca273	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10391 f3b2605a-c512-4ea7…	Jul 26 2013
745ced23a7c9	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10389 f3b2605a-c512-4ea7…	Jul 26 2013
2ef83a744220	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10388 f3b2605a-c512-4ea7…	Jul 26 2013
38305bf20c31	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10387 f3b2605a-c512-4ea7…	Jul 26 2013
da8124b43be4	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10386 f3b2605a-c512-4ea7…	Jul 26 2013
489dceb7e659	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10385 f3b2605a-c512-4ea7…	Jul 26 2013
4bde9638de3e	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10384 f3b2605a-c512-4ea7…	Jul 26 2013
b3ce5149ac19	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10381 f3b2605a-c512-4ea7…	Jul 26 2013
e5b54caa95eb	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10380 f3b2605a-c512-4ea7…	Jul 26 2013
d348e525e8ef	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10378 f3b2605a-c512-4ea7…	Jul 26 2013
7b3106594435	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10377 f3b2605a-c512-4ea7…	Jul 26 2013
ddb9f3f4ecd4	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10375 f3b2605a-c512-4ea7…	Jul 26 2013
476c0a0a309d	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10374 f3b2605a-c512-4ea7…	Jul 26 2013
5642cae07bb7	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10372 f3b2605a-c512-4ea7…	Jul 26 2013
ea122c8016ab	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10371 f3b2605a-c512-4ea7…	Jul 26 2013
a66131ef179f	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10370 f3b2605a-c512-4ea7…	Jul 26 2013
f6b6aeb0dc24	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10369 f3b2605a-c512-4ea7…	Jul 26 2013
2bbf3f1ef74e	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10368 f3b2605a-c512-4ea7…	Jul 26 2013
28a774a70b3a	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10367 f3b2605a-c512-4ea7…	Jul 26 2013
87b941f25069	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10366 f3b2605a-c512-4ea7…	Jul 26 2013
dea3df948edd	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10365 f3b2605a-c512-4ea7…	Jul 26 2013
a26ee56443e6	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10364 f3b2605a-c512-4ea7…	Jul 26 2013
be3847ff317e	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10363 f3b2605a-c512-4ea7…	Jul 26 2013
de94416d0282	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10361 f3b2605a-c512-4ea7…	Jul 25 2013
6715450f0625	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10360 f3b2605a-c512-4ea7…	Jul 25 2013
fadc25d704ef	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10359 f3b2605a-c512-4ea7…	Jul 25 2013
9f07d255bf46	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10358 f3b2605a-c512-4ea7…	Jul 25 2013
dcc4d8a01b0e	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10356 f3b2605a-c512-4ea7…	Jul 25 2013
1b02a37d2f4d	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10355 f3b2605a-c512-4ea7…	Jul 25 2013
2efedae09ef8	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10354 f3b2605a-c512-4ea7…	Jul 25 2013
3503b9c82845	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10353 f3b2605a-c512-4ea7…	Jul 25 2013
28dcb90c7b87	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10352 f3b2605a-c512-4ea7…	Jul 25 2013
328cbc4db9cc	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10351 f3b2605a-c512-4ea7…	Jul 25 2013
48510d047be7	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10350 f3b2605a-c512-4ea7…	Jul 25 2013
856f78e50a84	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10349 f3b2605a-c512-4ea7…	Jul 25 2013
f25feed9ff91	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10348 f3b2605a-c512-4ea7…	Jul 25 2013
b6f3dad06e19	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10347 f3b2605a-c512-4ea7…	Jul 25 2013
971b4e98dff6	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10346 f3b2605a-c512-4ea7…	Jul 25 2013

Changes (149)
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This commit is very large. Load each file individually.

		Path
A		doc/Eqs/fix_gld1.jpg
A		doc/Eqs/fix_gld1.tex
M		doc/Manual.html
M		doc/Manual.txt
M		doc/Section_commands.html
M		doc/Section_commands.txt
M		doc/Section_modify.html
M		doc/Section_modify.txt
M		doc/Section_tools.html
M		doc/Section_tools.txt
M		doc/atom_style.html
M		doc/atom_style.txt
M		doc/compute_property_atom.html
M		doc/compute_property_atom.txt
M		doc/compute_ti.html
M		doc/compute_ti.txt
M		doc/compute_voronoi_atom.html
M		doc/compute_voronoi_atom.txt
M		doc/fix_deposit.html
M		doc/fix_deposit.txt
M		doc/fix_efield.html
M		doc/fix_efield.txt
M		doc/fix_evaporate.html
M		doc/fix_evaporate.txt
A		doc/fix_gld.html
A		doc/fix_gld.txt
M		doc/fix_orient_fcc.html
M		doc/fix_orient_fcc.txt
A		doc/fix_property_atom.html
A		doc/fix_property_atom.txt
M		doc/fix_thermal_conductivity.html
M		doc/fix_thermal_conductivity.txt
M		doc/fix_ttm.html
M		doc/fix_ttm.txt
M		doc/fix_viscosity.html
M		doc/fix_viscosity.txt
M		doc/pair_kim.html
M		doc/pair_kim.txt
M		doc/read_data.html
M		doc/read_data.txt
M		doc/set.html
M		doc/set.txt
M		doc/variable.html
M		doc/variable.txt
M		examples/README
A		examples/kim/log.kim.lj.12Jul12.mac_mpi.1
A		examples/kim/log.kim.lj.12Jul12.mac_mpi.4
A		examples/kim/log.kim.lj.lmp.12Jul12.mac_mpi.1
A		examples/kim/log.kim.lj.lmp.12Jul12.mac_mpi.4
A	(dir)	examples/voronoi/
A		examples/voronoi/in.voronoi
M		lib/cuda/Makefile.common
M		lib/cuda/Makefile.defaults
A		lib/cuda/Makefile.lammps
M		src/DIPOLE/atom_vec_dipole.cpp
M		src/KIM/Makefile.lammps
M		src/KIM/pair_kim.cpp
M		src/KIM/pair_kim.h
A	(dir)	src/MISC/
V		src/{MISC ← }/compute_msd_nongauss.cpp
V		src/{MISC ← }/compute_msd_nongauss.h
V		src/{MISC ← }/compute_ti.cpp
V		src/{MISC ← }/compute_ti.h
V		src/{MISC ← }/fix_deposit.cpp
V		src/{MISC ← }/fix_deposit.h
V		src/{MISC ← }/fix_efield.cpp
V		src/{MISC ← }/fix_efield.h
V		src/{MISC ← }/fix_evaporate.cpp
P		src/MISC/fix_evaporate.h Copied from src/fix_evaporate.h
A		src/MISC/fix_gld.cpp
V		src/{MISC/fix_gld.h ← fix_evaporate.h}
V		src/{MISC ← }/fix_orient_fcc.cpp
V		src/{MISC ← }/fix_orient_fcc.h
V		src/{MISC ← }/fix_thermal_conductivity.cpp
V		src/{MISC ← }/fix_thermal_conductivity.h
V		src/{MISC ← }/fix_ttm.cpp
V		src/{MISC ← }/fix_ttm.h
V		src/{MISC ← }/fix_viscosity.cpp
V		src/{MISC ← }/fix_viscosity.h
M		src/MOLECULE/atom_vec_angle.cpp
M		src/MOLECULE/atom_vec_bond.cpp
M		src/MOLECULE/atom_vec_full.cpp
M		src/MOLECULE/atom_vec_molecular.cpp
M		src/Make.sh
M		src/Makefile
M		src/PERI/atom_vec_peri.cpp
M		src/RIGID/fix_rigid_small.cpp
M		src/USER-AWPMD/atom_vec_wavepacket.cpp
M		src/USER-CUDA/fix_nh_cuda.cpp
M		src/USER-CUDA/verlet_cuda.cpp
M		src/USER-EFF/atom_vec_electron.cpp
M		src/USER-SPH/atom_vec_meso.cpp
M		src/VORONOI/README
M		src/VORONOI/compute_voronoi_atom.cpp
M		src/VORONOI/compute_voronoi_atom.h
M		src/atom.cpp
M		src/atom.h
M		src/atom_vec_atomic.cpp
M		src/atom_vec_body.cpp
M		src/atom_vec_charge.cpp
M		src/atom_vec_ellipsoid.cpp
M		src/atom_vec_hybrid.cpp
M		src/atom_vec_line.cpp
M		src/atom_vec_sphere.cpp
M		src/atom_vec_tri.cpp
M		src/comm.cpp
V		src/{ → MISC}/compute_msd_nongauss.cpp
V		src/{ → MISC}/compute_msd_nongauss.h
M		src/compute_property_atom.cpp
M		src/compute_property_atom.h
V		src/{ → MISC}/compute_ti.cpp
V		src/{ → MISC}/compute_ti.h
M		src/fix.cpp
M		src/fix.h
V		src/{ → MISC}/fix_deposit.cpp
V		src/{ → MISC}/fix_deposit.h
V		src/{ → MISC}/fix_efield.cpp
V		src/{ → MISC}/fix_efield.h
V		src/{ → MISC}/fix_evaporate.cpp
P		src/fix_evaporate.h Deleted after being copied to multiple locations: src/MISC/fix_evaporate.h src/MISC/fix_gld.h
V		src/{ → MISC}/fix_orient_fcc.cpp
V		src/{ → MISC}/fix_orient_fcc.h
A		src/fix_property_atom.cpp
A		src/fix_property_atom.h
V		src/{ → MISC}/fix_thermal_conductivity.cpp
V		src/{ → MISC}/fix_thermal_conductivity.h
V		src/{ → MISC}/fix_ttm.cpp
V		src/{ → MISC}/fix_ttm.h
V		src/{ → MISC}/fix_viscosity.cpp
V		src/{ → MISC}/fix_viscosity.h
M		src/modify.cpp
M		src/read_data.cpp
M		src/read_data.h
M		src/replicate.cpp
M		src/set.cpp
M		src/set.h
M		src/variable.cpp
M		src/version.h
M		tools/moltemplate/moltemplate_manual.pdf
M		tools/moltemplate/src/lttree.py
M		tools/moltemplate/src/moltemplate.sh
M		tools/moltemplate/src/nbody_by_type.py
M		tools/moltemplate/src/nbody_graph_search.py
M		tools/moltemplate/src/ttree.py
M		tools/moltemplate/src/ttree_lex.py
A	(dir)	tools/polybond/
A		tools/polybond/Manual.pdf
A		tools/polybond/README
A		tools/polybond/lmpsdata.py