Diffusion lammps 5c64815a2a39

Merge branch 'lammps-icms' into lammps-colvars
5c64815a2a39
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Authored by Axel Kohlmeyer <akohlmey@gmail.com> on Jun 24 2012, 02:06.

Description

Merge branch 'lammps-icms' into lammps-colvars

Details

Committed

Axel Kohlmeyer <akohlmey@gmail.com>

Jun 24 2012, 02:06

Pushed

junge

Oct 6 2016, 16:49

Parents

rLAMMPS47b02a0db346: delete unused variable
rLAMMPS2b8a2cecbe14: Merge branch 'lammps-icms' into lammps-colvars

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Axel Kohlmeyer <akohlmey@gmail.com> committed rLAMMPS5c64815a2a39: Merge branch 'lammps-icms' into lammps-colvars (authored by Axel Kohlmeyer <akohlmey@gmail.com>).Jun 24 2012, 02:06

Merged Changes

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

Commit	Author	Details	Committed
47b02a0db346	Axel Kohlmeyer	delete unused variable	Jun 24 2012
aa6c10fa9433	Axel Kohlmeyer	update fix qeq/comb with changes from upstream	Jun 24 2012
a47ece862eee	Axel Kohlmeyer	update multi-threaded neighbor list code with new upstream modules.	Jun 24 2012
a3e3a9d4558a	Axel Kohlmeyer	initialize variables in region command immediately	Jun 23 2012
de240b156546	Axel Kohlmeyer	update to sync with upstream (fix rigid support)	Jun 23 2012
4055b29e10e6	Axel Kohlmeyer	Merge branch 'master' into lammps-icms	Jun 23 2012
e7611d421f60	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8386 f3b2605a-c512-4ea7…	Jun 23 2012
8f68628a20f8	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8385 f3b2605a-c512-4ea7…	Jun 22 2012
6e511540f87f	Axel Kohlmeyer	Merge branch 'master' into lammps-icms	Jun 22 2012
b33ba405a3b1	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8382 f3b2605a-c512-4ea7…	Jun 22 2012
186fec68f324	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8381 f3b2605a-c512-4ea7…	Jun 22 2012
4f6d26042e33	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8379 f3b2605a-c512-4ea7…	Jun 22 2012
ab6544cd71f9	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8378 f3b2605a-c512-4ea7…	Jun 22 2012
45f8666346b3	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8377 f3b2605a-c512-4ea7…	Jun 22 2012
87fe07030be3	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8376 f3b2605a-c512-4ea7…	Jun 21 2012
c76a926406d5	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8374 f3b2605a-c512-4ea7…	Jun 21 2012
b3560bde9c3d	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8373 f3b2605a-c512-4ea7…	Jun 21 2012
ee874d1dff4a	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8371 f3b2605a-c512-4ea7…	Jun 21 2012
83416310f2d5	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8370 f3b2605a-c512-4ea7…	Jun 21 2012
79a7e57328ff	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8369 f3b2605a-c512-4ea7…	Jun 21 2012
63f63e456772	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8368 f3b2605a-c512-4ea7…	Jun 21 2012
dc17d7963573	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8367 f3b2605a-c512-4ea7…	Jun 21 2012
0030566ad843	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8366 f3b2605a-c512-4ea7…	Jun 21 2012
31bc11ee34db	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8365 f3b2605a-c512-4ea7…	Jun 21 2012
7398f3eca3d0	athomps	Removed energy_updte_freq from nonbond calculation	Jun 20 2012
e7b124f39600	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8362 f3b2605a-c512-4ea7…	Jun 20 2012
b247eeb103f5	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8361 f3b2605a-c512-4ea7…	Jun 20 2012
4baf5cec9930	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8360 f3b2605a-c512-4ea7…	Jun 20 2012
1c162a9e1b31	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8358 f3b2605a-c512-4ea7…	Jun 20 2012
7975177abdc9	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8357 f3b2605a-c512-4ea7…	Jun 20 2012
69f5fbf42194	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8356 f3b2605a-c512-4ea7…	Jun 20 2012
f3eb64fd0f7a	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8355 f3b2605a-c512-4ea7…	Jun 20 2012
0cd34fb8a2d9	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8354 f3b2605a-c512-4ea7…	Jun 20 2012
bf54b6b9ff9f	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8353 f3b2605a-c512-4ea7…	Jun 20 2012
a4fb2e6e1ef9	Axel Kohlmeyer	adjust input according to new syntax	Jun 20 2012
c1e0bec7f6d6	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8352 f3b2605a-c512-4ea7…	Jun 20 2012
f55e618e9e83	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8351 f3b2605a-c512-4ea7…	Jun 20 2012
e2d32549ab64	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8349 f3b2605a-c512-4ea7…	Jun 20 2012
7000d43d107a	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8348 f3b2605a-c512-4ea7…	Jun 20 2012
4441f9b5aafd	Axel Kohlmeyer	Merge branch 'master' into lammps-icms	Jun 20 2012
0296f2593f6a	Axel Kohlmeyer	fix long-standing typo.	Jun 20 2012
4fce93faf9ac	Axel Kohlmeyer	update inputs and reference log files for newer LAMMPS version	Jun 20 2012
b96c9934caef	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8347 f3b2605a-c512-4ea7…	Jun 19 2012
9733df592997	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8346 f3b2605a-c512-4ea7…	Jun 19 2012
7198c2aaca71	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8344 f3b2605a-c512-4ea7…	Jun 19 2012
dc9431dcb221	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8343 f3b2605a-c512-4ea7…	Jun 19 2012
7b55b61abb74	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8342 f3b2605a-c512-4ea7…	Jun 19 2012
d2882ddaa6d8	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8341 f3b2605a-c512-4ea7…	Jun 19 2012
0241b5ce29e3	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8340 f3b2605a-c512-4ea7…	Jun 19 2012
df9a09506336	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8339 f3b2605a-c512-4ea7…	Jun 19 2012

Changes (119)
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Very Large Commit

This commit is very large. Load each file individually.

				Path
	M			bench-accel/bench_gb/data.gb
	M			bench-accel/bench_gb/in.gb
	M			bench-accel/bench_gb/log.gb.1
	M			bench-accel/bench_gb/log.gb.4
	M			bench-accel/bench_granular/log.granular.1
	M			bench-accel/bench_granular/log.granular.4
	M			bench-accel/bench_spce/in.spce
	M			bench-accel/bench_spce/log.spce.1
	M			bench-accel/bench_spce/log.spce.4
	M			doc/Section_commands.html
	M			doc/Section_commands.txt
	M			doc/Section_errors.html
	M			doc/Section_errors.txt
	M			doc/Section_start.html
	M			doc/Section_start.txt
	M			doc/balance.html
	M			doc/balance.txt
	M			doc/fix_ave_correlate.html
	M			doc/fix_ave_correlate.txt
	M			doc/fix_ave_histo.html
	M			doc/fix_ave_histo.txt
	M			doc/fix_ave_spatial.html
	M			doc/fix_ave_spatial.txt
	M			doc/fix_ave_time.html
	M			doc/fix_ave_time.txt
	A			doc/fix_balance.html
	A			doc/fix_balance.txt
	M			doc/fix_rigid.html
	M			doc/fix_rigid.txt
	M			doc/read_dump.html
	M			doc/read_dump.txt
	M			doc/rerun.html
	M			doc/rerun.txt
	M			examples/rerun/in.rerun
	M			lib/README
	D			lib/kim
	D			lib/kim/Makefile.lammps
	D			lib/kim/README
	D			lib/molfile
	D			lib/molfile/Makefile.lammps
	D			lib/molfile/README
	M			src/GPU/Install.sh
	M			src/GRANULAR/pair_gran_hertz_history.cpp
	M			src/GRANULAR/pair_gran_hooke.cpp
	M			src/GRANULAR/pair_gran_hooke_history.cpp
	M			src/GRANULAR/pair_gran_hooke_history.h
	M			src/KIM/Install.sh
	A			src/KIM/Makefile.lammps
	M			src/MANYBODY/fix_qeq_comb.cpp
	M			src/MANYBODY/fix_qeq_comb.h
	M			src/MEAM/Install.sh
	M			src/MOLECULE/dihedral_helix.cpp
	M			src/POEMS/Install.sh
	M			src/REAX/Install.sh
	M			src/REPLICA/prd.cpp
	M			src/USER-ATC/Install.sh
	M			src/USER-AWPMD/Install.sh
	M			src/USER-CG-CMM/Package.sh
	M			src/USER-COLVARS/Install.sh
	M			src/USER-CUDA/Install.sh
	M			src/USER-MOLFILE/Install.sh
	A			src/USER-MOLFILE/Makefile.lammps
	M			src/USER-MOLFILE/README
	M			src/USER-OMP/fix_qeq_comb_omp.cpp
	M			src/USER-OMP/neigh_full_omp.cpp
	M			src/USER-OMP/neigh_half_bin_omp.cpp
	M			src/USER-OMP/neigh_half_nsq_omp.cpp
	M			src/USER-OMP/pair_gran_hertz_history_omp.cpp
	M			src/USER-OMP/pair_gran_hooke_history_omp.cpp
	M			src/USER-OMP/pair_gran_hooke_omp.cpp
	M			src/USER-REAXC/fix_qeq_reax.cpp
	M			src/USER-REAXC/fix_reaxc_bonds.cpp
	M			src/USER-REAXC/fix_reaxc_bonds.h
	M			src/USER-REAXC/pair_reax_c.cpp
	M			src/USER-REAXC/reaxc_nonbonded.cpp
	M			src/accelerator_omp.h
	M			src/balance.cpp
	M			src/balance.h
	M			src/compute_angle_local.cpp
	M			src/compute_atom_molecule.cpp
	M			src/compute_bond_local.cpp
	M			src/compute_dihedral_local.cpp
	M			src/compute_gyration.cpp
	M			src/compute_gyration_molecule.cpp
	M			src/compute_improper_local.cpp
	M			src/compute_property_local.cpp
	M			src/create_atoms.cpp
	M			src/fix_ave_correlate.cpp
	M			src/fix_ave_correlate.h
	M			src/fix_ave_histo.cpp
	M			src/fix_ave_histo.h
	M			src/fix_ave_spatial.cpp
	M			src/fix_ave_spatial.h
	M			src/fix_ave_time.cpp
	M			src/fix_ave_time.h
	A			src/fix_balance.cpp
	A			src/fix_balance.h
	M			src/fix_rigid.cpp
	M			src/fix_rigid.h
	M			src/irregular.cpp
	M			src/irregular.h
	M			src/modify.cpp
	M			src/neigh_full.cpp
	M			src/neigh_half_bin.cpp
	M			src/neigh_half_nsq.cpp
	M			src/neigh_stencil.cpp
	M			src/neighbor.cpp
	M			src/neighbor.h
	M			src/pair_lj_cut.cpp
	M			src/read_dump.cpp
	M			src/reader.cpp
	M			src/reader_xyz.cpp
	M			src/region.cpp
	M			src/region.h
	M			src/rerun.cpp
	M			src/variable.cpp
	M			src/velocity.h
	M			src/version.h
	M			tools/vim/lammps.vim