Diffusion lammps 2f8eae4d354e

Merge remote-tracking branch 'upstream/lammps-icms' into user-vtk
2f8eae4d354e
Actions

Authored by Richard Berger <richard.berger@jku.at> on Jan 26 2016, 00:25.

Description

Merge remote-tracking branch 'upstream/lammps-icms' into user-vtk

Details

Committed

Richard Berger <richard.berger@jku.at>

Jan 26 2016, 00:25

Pushed

junge

Oct 6 2016, 16:49

Parents

rLAMMPS252f7bd3f8a8: Remove shared code with dump_custom
rLAMMPS32f22f2ff4ad: fix last minute typo

Branches

Unknown

Tags

Unknown

Event Timeline

Richard Berger <richard.berger@jku.at> committed rLAMMPS2f8eae4d354e: Merge remote-tracking branch 'upstream/lammps-icms' into user-vtk (authored by Richard Berger <richard.berger@jku.at>).Jan 26 2016, 00:25

Merged Changes

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

Commit	Author	Details	Committed
32f22f2ff4ad	Axel Kohlmeyer	fix last minute typo	Jan 25 2016
7f4c5276775f	Axel Kohlmeyer	Merge branch 'lammps-icms' of bitbucket.org:akohlmey/lammps-icms into lammps…	Jan 25 2016
05a1d98c042c	Axel Kohlmeyer	only allow fix adapt to control 2-d parameter arrays for pair parameters	Jan 25 2016
c3d483916547	Axel Kohlmeyer	Merge branch 'lammps-icms' into kim-fix-adapt-changes	Jan 25 2016
33759a8b187d	Axel Kohlmeyer	Merge branch 'lammps-icms' of bitbucket.org:akohlmey/lammps-icms into lammps…	Jan 24 2016
2aaf9f3d5937	Axel Kohlmeyer	Merge remote-tracking branch 'lammps-ro/master' into lammps-icms	Jan 23 2016
aca24423f4c7	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14485 f3b2605a-c512-4ea7…	Jan 23 2016
f593ffb67b98	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14484 f3b2605a-c512-4ea7…	Jan 23 2016
67d5513df13b	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14483 f3b2605a-c512-4ea7…	Jan 23 2016
b31f864e8341	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14482 f3b2605a-c512-4ea7…	Jan 23 2016
8b7e9fea4cb5	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14481 f3b2605a-c512-4ea7…	Jan 23 2016
3621171480f3	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14480 f3b2605a-c512-4ea7…	Jan 23 2016
5d99bf664efb	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14479 f3b2605a-c512-4ea7…	Jan 23 2016
7f049bb31b3d	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14478 f3b2605a-c512-4ea7…	Jan 23 2016
627561054c70	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14477 f3b2605a-c512-4ea7…	Jan 23 2016
d4a5571aaba9	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14476 f3b2605a-c512-4ea7…	Jan 23 2016
28d6cef69782	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14475 f3b2605a-c512-4ea7…	Jan 23 2016
79466c37d8e3	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14474 f3b2605a-c512-4ea7…	Jan 23 2016
ad1d7ffdc70a	athomps	Fixed another bug in edge_histo	Jan 23 2016
34785af4a6a0	stamoor	Fixing Kokkos bugs	Jan 23 2016
611bb37724ba	Axel Kohlmeyer	import changes to fix adapt posted by ryan elliot to lammps-users	Jan 22 2016
c8fb84783edb	stamoor	Fixing Kokkos bug	Jan 22 2016
e3e687f7b35e	athomps	Added peratom keyword	Jan 22 2016
05dd231d6734	Axel Kohlmeyer	fix broken download link	Jan 22 2016
666d63d81c9a	Axel Kohlmeyer	Merge remote-tracking branch 'lammps-ro/master' into lammps-icms	Jan 22 2016
56ef0d40fcbc	athomps	Added description of peratom keyword	Jan 22 2016
4da36d1c01a0	athomps	Added data output example	Jan 22 2016
eb105410ad06	stamoor	Fixing Kokkos bug	Jan 21 2016
eebf110e0250	athomps	Further tweaked the flangevin issue	Jan 21 2016
b833b5593398	Axel Kohlmeyer	Merge remote-tracking branch 'lammps-ro/master' into lammps-icms	Jan 21 2016
d13b2ecfc9f5	athomps	Added faces as local compute	Jan 21 2016
66a048bbb996	athomps	Added faces as local compute	Jan 21 2016
005f9d5ac5e8	athomps	Added faces as local compute	Jan 21 2016
fe10d8c87b00	athomps	Removed flangevin==NULL check	Jan 20 2016
f3b15cd4d165	Axel Kohlmeyer	Merge remote-tracking branch 'lammps-ro/master' into lammps-icms	Jan 20 2016
2e035a00f766	Axel Kohlmeyer	add documentation for ndx2group command	Jan 20 2016
6d4beaa7d86b	Axel Kohlmeyer	hack to make USER-INTEL compilable without OpenMP support	Jan 20 2016
7fb6016839d1	Axel Kohlmeyer	add ndx2group command that allows restoring groups from an index file	Jan 20 2016
dcec5c28c669	Axel Kohlmeyer	skip over deleted groups when printing the list of groups	Jan 20 2016
fa01d915e336	athomps	Changed behavior for non-periodic systems	Jan 20 2016
81d55a790498	athomps	Changed behavior for non-periodic systems	Jan 20 2016
a3c0f3e43e36	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14459 f3b2605a-c512-4ea7…	Jan 20 2016
7c810d619885	athomps	Added 2d example	Jan 19 2016
0d1c7af98b5a	athomps	Updated description of 2d and free surface cases	Jan 19 2016
f16130ab67ba	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14456 f3b2605a-c512-4ea7…	Jan 19 2016
b9913826d9f1	Axel Kohlmeyer	Merge remote-tracking branch 'lammps-ro/master' into lammps-icms	Jan 16 2016
f6f88c2f2804	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14455 f3b2605a-c512-4ea7…	Jan 15 2016
0d79f78f73b6	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14453 f3b2605a-c512-4ea7…	Jan 15 2016
b66f1e351e27	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14452 f3b2605a-c512-4ea7…	Jan 15 2016
fb0230aed29b	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14451 f3b2605a-c512-4ea7…	Jan 15 2016

Changes (166)
Show All Changes

Very Large Commit

This commit is very large. Load each file individually.

				Path
	M			doc/Manual.html
	M			doc/Manual.txt
	M			doc/Section_commands.html
	M			doc/Section_commands.txt
	M			doc/Section_start.txt
	M			doc/atom_style.html
	M			doc/atom_style.txt
	M			doc/body.html
	M			doc/body.txt
	M			doc/compute.html
	M			doc/compute.txt
	M			doc/compute_chunk_atom.html
	M			doc/compute_chunk_atom.txt
	M			doc/compute_msd.html
	M			doc/compute_msd.txt
	M			doc/compute_msd_chunk.html
	M			doc/compute_msd_chunk.txt
	M			doc/compute_saed.html
	M			doc/compute_saed.txt
	M			doc/compute_voronoi_atom.html
	M			doc/compute_voronoi_atom.txt
	M			doc/compute_xrd.html
	M			doc/compute_xrd.txt
	M			doc/delete_bonds.html
	M			doc/delete_bonds.txt
	M			doc/displace_atoms.html
	M			doc/displace_atoms.txt
	M			doc/dump_image.html
	M			doc/dump_image.txt
	M			doc/fix_move.html
	M			doc/fix_move.txt
	M			doc/fix_nh.html
	M			doc/fix_nh.txt
	M			doc/fix_nve_sphere.html
	M			doc/fix_nve_sphere.txt
	M			doc/fix_qeq.html
	M			doc/fix_qeq.txt
	M			doc/fix_store_state.html
	M			doc/fix_store_state.txt
	M			doc/group2ndx.txt
	M			doc/pair_beck.html
	M			doc/pair_beck.txt
	M			doc/pair_line_lj.html
	M			doc/pair_line_lj.txt
	M			doc/pair_tri_lj.html
	M			doc/pair_tri_lj.txt
	M			doc/searchindex.js
	M			doc/set.html
	M			doc/set.txt
	M			examples/ASPHERE/line/in.line
	M			examples/ASPHERE/line/in.line.srd
	M			examples/USER/phonon/1-1D-mono/in.Ana
	V			examples/USER/smtbq/{log.smtbq.Al → log.smtbq.Al.g++.1}
	V			examples/USER/smtbq/{log.smtbq.Al.g++.1 ← log.smtbq.Al}
	A			examples/USER/smtbq/log.smtbq.Al.g++.4
	P			examples/USER/smtbq/log.smtbq.Al2O3 Deleted after being copied to multiple locations: examples/USER/smtbq/log.smtbq.Al2O3.g++.1 examples/USER/smtbq/log.smtbq.Al2O3.g++.4
	P			examples/USER/smtbq/log.smtbq.Al2O3.g++.1 Copied from examples/USER/smtbq/log.smtbq.Al2O3
	V			examples/USER/smtbq/{log.smtbq.Al2O3.g++.4 ← log.smtbq.Al2O3}
	P			examples/USER/smtbq/log.smtbq.TiO2 Deleted after being copied to multiple locations: examples/USER/smtbq/log.smtbq.TiO2.g++.1 examples/USER/smtbq/log.smtbq.TiO2.g++.4
	P			examples/USER/smtbq/log.smtbq.TiO2.g++.1 Copied from examples/USER/smtbq/log.smtbq.TiO2
	V			examples/USER/smtbq/{log.smtbq.TiO2.g++.4 ← log.smtbq.TiO2}
	M			examples/qeq/in.qeq.buck
	A			examples/voronoi/in.voronoi.2d
	A			examples/voronoi/in.voronoi.data
	M			extra_cleanup.sh
	M			src/ASPHERE/pair_line_lj.cpp
	M			src/ASPHERE/pair_line_lj.h
	M			src/ASPHERE/pair_tri_lj.cpp
	M			src/BODY/body_nparticle.cpp
	M			src/BODY/body_nparticle.h
	M			src/CORESHELL/compute_temp_cs.cpp
	M			src/GRANULAR/fix_pour.cpp
	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/KOKKOS/atom_vec_atomic_kokkos.cpp
	M			src/KOKKOS/atom_vec_charge_kokkos.cpp
	M			src/KOKKOS/pair_kokkos.h
	M			src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp
	M			src/KOKKOS/pair_lj_charmm_coul_long_kokkos.h
	M			src/KOKKOS/pair_lj_cut_kokkos.cpp
	M			src/KOKKOS/pair_lj_cut_kokkos.h
	M			src/MANYBODY/pair_comb.cpp
	M			src/MANYBODY/pair_comb.h
	M			src/MANYBODY/pair_comb3.cpp
	M			src/MANYBODY/pair_comb3.h
	M			src/MISC/fix_deposit.cpp
	M			src/Makefile
	M			src/Purge.list
	M			src/QEQ/fix_qeq.cpp
	M			src/QEQ/fix_qeq.h
	A			src/QEQ/fix_qeq_fire.cpp
	P			src/QEQ/fix_qeq_fire.h Copied from src/fix_store.h
	M			src/REPLICA/tad.cpp
	A			src/USER-COLVARS/ndx_group.cpp
	P			src/USER-COLVARS/ndx_group.h Copied from src/fix_store.h
	M			src/USER-FEP/fix_adapt_fep.cpp
	M			src/USER-INTEL/intel_preprocess.h
	M			src/USER-INTEL/pair_tersoff_intel.cpp
	M			src/USER-INTEL/pair_tersoff_intel.h
	D			src/USER-OMP/pair_line_lj_omp.cpp
	D			src/USER-OMP/pair_line_lj_omp.h
	D			src/USER-OMP/pair_tri_lj_omp.cpp
	D			src/USER-OMP/pair_tri_lj_omp.h
	M			src/USER-SMTBQ/pair_smtbq.cpp
	M			src/VORONOI/compute_voronoi_atom.cpp
	M			src/VORONOI/compute_voronoi_atom.h
	M			src/atom.cpp
	M			src/atom_vec_body.cpp
	M			src/atom_vec_body.h
	M			src/atom_vec_line.cpp
	M			src/atom_vec_line.h
	M			src/atom_vec_tri.cpp
	M			src/atom_vec_tri.h
	M			src/body.h
	M			src/compute_chunk_atom.cpp
	M			src/compute_chunk_atom.h
	M			src/compute_displace_atom.cpp
	M			src/compute_msd.cpp
	M			src/compute_msd_chunk.cpp
	M			src/compute_msd_chunk.h
	M			src/compute_vacf.cpp
	M			src/create_atoms.cpp
	M			src/displace_atoms.cpp
	M			src/dump_image.cpp
	M			src/dump_image.h
	M			src/fix_adapt.cpp
	M			src/fix_adapt.h
	M			src/fix_langevin.cpp
	M			src/fix_langevin.h
	M			src/fix_move.cpp
	M			src/fix_move.h
	M			src/fix_nh.cpp
	M			src/fix_nh.h
	M			src/fix_nh_sphere.cpp
	M			src/fix_nh_sphere.h
	M			src/fix_nve_sphere.cpp
	M			src/fix_property_atom.cpp
	M			src/fix_shear_history.h
	M			src/fix_store.cpp
	P			src/fix_store.h Copied to multiple locations: src/QEQ/fix_qeq_fire.h src/USER-COLVARS/ndx_group.h
	M			src/fix_store_state.cpp
	M			src/fix_store_state.h
	M			src/force.cpp
	M			src/force.h
	M			src/info.cpp
	M			src/math_extra.cpp
	M			src/math_extra.h
	M			src/min.cpp
	M			src/molecule.cpp
	M			src/molecule.h
	M			src/pair.h
	M			src/pair_hybrid.cpp
	M			src/pair_hybrid.h
	M			src/read_data.cpp
	M			src/respa.cpp
	M			src/set.cpp
	M			src/variable.cpp
	M			src/verlet.cpp
	M			src/version.h
	M			tools/ch2lmp/charmm2lammps.pl
	A			tools/msi2lmp/test/pmma-poly-class2c.car
	A			tools/msi2lmp/test/pmma-poly-class2c.mdf
	A			tools/msi2lmp/test/reference/pmma-poly-class2c.data
	A			tools/msi2lmp/test/reference/pmma-poly-class2c.data2
	M			tools/msi2lmp/test/runtests.sh