Diffusion lammps cb935730c0b6

Merge branch 'master' into compute_rdf_dynamic
cb935730c0b6
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Authored by Axel Kohlmeyer <akohlmey@gmail.com> on Jul 13 2017, 21:02.

Description

Merge branch 'master' into compute_rdf_dynamic

Details

Committed

Axel Kohlmeyer <akohlmey@gmail.com>

Jul 13 2017, 21:02

Pushed

junge

Oct 19 2017, 09:53

Parents

rLAMMPS71ddcaf0b607: whitespace cleanup
rLAMMPS983eb0e80dab: Merge pull request #572 from junghans/data2xmovie

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Event Timeline

Axel Kohlmeyer <akohlmey@gmail.com> committed rLAMMPScb935730c0b6: Merge branch 'master' into compute_rdf_dynamic (authored by Axel Kohlmeyer <akohlmey@gmail.com>).Jul 13 2017, 21:02

Merged Changes

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

Commit	Author	Details	Committed
983eb0e80dab	sjplimp/GitHub	Merge pull request #572 from junghans/data2xmovie	Jul 13 2017
fc6c10c9a98a	sjplimp/GitHub	Merge pull request #571 from hasanmetin/reaxc-omp-credits-update	Jul 13 2017
a3a0c9b144c5	sjplimp/GitHub	Merge pull request #570 from akohlmey/collected-small-changes	Jul 13 2017
b64849d5748e	sjplimp/GitHub	Merge pull request #569 from ellio167/kim-install-py	Jul 13 2017
e58bcd8b4aa4	sjplimp/GitHub	Merge pull request #568 from akohlmey/fix_gcmc_parallel_workaround	Jul 13 2017
ef2f4980e9dd	sjplimp/GitHub	Merge pull request #566 from akohlmey/compute_rdf_dynamic	Jul 13 2017
d3a45f6d5057	sjplimp/GitHub	Merge pull request #560 from aershadinia/master	Jul 13 2017
de8d417aeccd	Axel Kohlmeyer	fix off-by-one memory allocation bug	Jul 13 2017
0af9203fdc99	Axel Kohlmeyer	remove useless and incorrect neighbor list request in fix qeq/comb/omp	Jul 13 2017
c24fca61f37a	Axel Kohlmeyer	fix possible uninitialized data access with pppm and pppm/disp	Jul 13 2017
01e848387ac8	Axel Kohlmeyer	avoid accessing uninitialized data when exiting LAMMPS early	Jul 13 2017
734729b0a4d5	Axel Kohlmeyer	avoid small memory leak with USER-REAXC + USER-OMP, spotted by GCC's address…	Jul 12 2017
a419c7c57c52	Axel Kohlmeyer	update src/.gitignore for fix wall*/ees sources	Jul 12 2017
69d97fa60cf0	Axel Kohlmeyer	fix enforce2d has to be defined after fixes with enforce2d_flag set	Jul 12 2017
a9ff593763c7	Axel Kohlmeyer	avoid segfault when calling enforce2d before langevin data has been initialized	Jul 12 2017
ddc96213255a	Axel Kohlmeyer	remove absolutely last reference to xmovie	Jul 12 2017
f717a70638f9	Christoph Junghans	tools/Makefile: remove remains of data2xmovie	Jul 12 2017
f7f4a24930ba	Axel Kohlmeyer	whitspace cleanup	Jul 11 2017
338fc2897073	Axel Kohlmeyer	combine citeme.log entry for pair reax/c/omp and fix qeq/reax/omp	Jul 11 2017
5a1e020bf01c	H. Metin Aktulga	updated the credits and citations for pair style reaxc/omp and qeq/reax/omp	Jul 11 2017
c8939d8df6da	Axel Kohlmeyer	clarify explanation of body style molecule in rigid fixes	Jul 11 2017
e30c5fc9560c	Ryan S. Elliott	Fixed shebang and renamed to lib/kim/Install.py	Jul 11 2017
c29e8fba9bd0	Ryan S. Elliott	Updated lib/kim/README file to go along with new install.py	Jul 11 2017
8d592f4b9e43	Ryan S. Elliott	Finalized code for lib/kim/install.py	Jul 10 2017
c9a0d38a3eff	Axel Kohlmeyer	mention restriction for use with fix shake or fix rigid in fix gcmc docs	Jul 10 2017
b5e9e90bb66d	Axel Kohlmeyer	white space cleanup	Jul 10 2017
92395e9bb412	Axel Kohlmeyer	disallow MC moves with fix rigid and fix shake active. update examples and add…	Jul 10 2017
b0be8b24eac9	Ryan S. Elliott	Further work on lib/kim/install.py	Jul 6 2017
16fc2d6fe179	Ryan S. Elliott	Add install.py and update config for kim lib	Jul 6 2017
7193fffe0d1c	Axel Kohlmeyer	make example input / output conform with LAMMPS conventions (no dump files, no…	Jul 6 2017
23925b3a57fc	Axel Kohlmeyer	update fix wall/ees and wall/region/ees file to conform more to common…	Jul 6 2017
423e3b6389dc	Axel Kohlmeyer	integrate fix wall/ees and wall/region/ees into doc system	Jul 6 2017
8be6d5bfd841	Abdoreza Ershadinia/GitHub	Merged two doc files	Jul 6 2017
a62eb43791da	Abdoreza Ershadinia/GitHub	Delete "fix_wall_region_ees.txt"	Jul 6 2017
33be51af5432	Abdoreza Ershadinia/GitHub	Deleted "fix wall/region/ees" doc file	Jul 6 2017
47649ff50f3a	Abdo	some edits to make examples more illustrative.	Jul 6 2017
d451dbb1a079	Axel Kohlmeyer	adjust EES wall input example to print out some thermodynamic info that can be…	Jul 5 2017
6eddc1a2ee77	Axel Kohlmeyer	coding style and whitespace cleanup to match LAMMPS style	Jul 5 2017
9fa4588eb720	Abdoreza Ershadinia/GitHub	fixed a typo	Jul 5 2017
f5440a777b7d	Abdo	Merge branch 'master' of https://github.com/aershadinia/lammps hello	Jul 5 2017
92831f185b3f	Abdo	Merge branch 'master' of https://github.com/aershadinia/lammps	Jul 5 2017
8e279d4ec84e	Abdo	Examples moved	Jul 5 2017
cbd8f997548f	Abdoreza Ershadinia/GitHub	Restrictions Added	Jul 5 2017
b720f391637b	Abdoreza Ershadinia/GitHub	Restrictions Added	Jul 5 2017
e0521f27b42d	Abdoreza Ershadinia/GitHub	Added reference to example directory.	Jul 5 2017
5eb5391b20c7	Abdoreza Ershadinia/GitHub	Add reference to example	Jul 5 2017
d3b8e688c972	Abdo	Files Added to MISC	Jul 5 2017
67d474df2a5d	Abdo	deleteing USER-EES	Jul 5 2017
8f37285b056a	Abdoreza Ershadinia/GitHub	UPLOAD examples	Mar 16 2017
ef72145540a5	Abdoreza Ershadinia/GitHub	Readme for examples	Mar 16 2017

Changes (76)

		Path
A		doc/src/Eqs/fix_wall_ees.jpg
A		doc/src/Eqs/fix_wall_ees.tex
A		doc/src/JPG/fix_wall_ees_image.jpg
M		doc/src/Section_commands.txt
M		doc/src/fix_gcmc.txt
M		doc/src/fix_rigid.txt
A		doc/src/fix_wall_ees.txt
M		doc/src/fixes.txt
M		doc/src/lammps.book
M		examples/README
A	(dir)	examples/USER/misc/ees/
A		examples/USER/misc/ees/Data_region
A		examples/USER/misc/ees/Data_wall
A		examples/USER/misc/ees/README
A		examples/USER/misc/ees/in.fix_wall
A		examples/USER/misc/ees/in.fix_wall_region
A		examples/USER/misc/ees/log.23Jun17.fix_wall.g++.1
A		examples/USER/misc/ees/log.23Jun17.fix_wall.g++.4
A		examples/USER/misc/ees/log.23Jun17.fix_wall_region.g++.1
A		examples/USER/misc/ees/log.23Jun17.fix_wall_region.g++.4
A		examples/gcmc/H2O.txt
P		examples/gcmc/in.gcmc.co2 Copied to examples/gcmc/in.gcmc.h2o
P		examples/gcmc/in.gcmc.h2o Copied from examples/gcmc/in.gcmc.co2
V		examples/gcmc/{log.24Mar17.gcmc.co2.g++.1 → log.6Jul17.gcmc.co2.g++.1}
D		examples/gcmc/log.24Mar17.gcmc.co2.g++.4
V		examples/gcmc/{log.24Mar17.gcmc.lj.g++.1 → log.6Jul17.gcmc.lj.g++.1}
V		examples/gcmc/{log.24Mar17.gcmc.lj.g++.4 → log.6Jul17.gcmc.lj.g++.4}
V		examples/gcmc/{log.6Jul17.gcmc.co2.g++.1 ← log.24Mar17.gcmc.co2.g++.1}
A		examples/gcmc/log.6Jul17.gcmc.co2.g++.4
A		examples/gcmc/log.6Jul17.gcmc.h2o.g++.1
A		examples/gcmc/log.6Jul17.gcmc.h2o.g++.4
V		examples/gcmc/{log.6Jul17.gcmc.lj.g++.1 ← log.24Mar17.gcmc.lj.g++.1}
V		examples/gcmc/{log.6Jul17.gcmc.lj.g++.4 ← log.24Mar17.gcmc.lj.g++.4}
A		lib/kim/.gitignore
A		lib/kim/Install.py
M		lib/kim/Makefile.lammps
M		lib/kim/README
M		src/.gitignore
M		src/KSPACE/pppm.cpp
M		src/KSPACE/pppm_disp.cpp
M		src/MC/fix_gcmc.cpp
M		src/RIGID/fix_rigid.cpp
M		src/RIGID/fix_rigid_small.cpp
M		src/USER-MISC/README
A		src/USER-MISC/fix_wall_ees.cpp
A		src/USER-MISC/fix_wall_ees.h
A		src/USER-MISC/fix_wall_region_ees.cpp
A		src/USER-MISC/fix_wall_region_ees.h
M		src/USER-OMP/fix_nphug_omp.cpp
M		src/USER-OMP/fix_qeq_comb_omp.cpp
M		src/USER-OMP/fix_qeq_reax_omp.cpp
M		src/USER-OMP/fix_qeq_reax_omp.h
M		src/USER-OMP/pair_reaxc_omp.cpp
M		src/USER-OMP/pair_reaxc_omp.h
M		src/USER-OMP/reaxc_bond_orders_omp.cpp
M		src/USER-OMP/reaxc_bond_orders_omp.h
M		src/USER-OMP/reaxc_bonds_omp.cpp
M		src/USER-OMP/reaxc_bonds_omp.h
M		src/USER-OMP/reaxc_forces_omp.cpp
M		src/USER-OMP/reaxc_forces_omp.h
M		src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp
M		src/USER-OMP/reaxc_hydrogen_bonds_omp.h
M		src/USER-OMP/reaxc_init_md_omp.cpp
M		src/USER-OMP/reaxc_init_md_omp.h
M		src/USER-OMP/reaxc_multi_body_omp.cpp
M		src/USER-OMP/reaxc_multi_body_omp.h
M		src/USER-OMP/reaxc_nonbonded_omp.cpp
M		src/USER-OMP/reaxc_nonbonded_omp.h
M		src/USER-OMP/reaxc_torsion_angles_omp.cpp
M		src/USER-OMP/reaxc_torsion_angles_omp.h
M		src/USER-OMP/reaxc_valence_angles_omp.cpp
M		src/USER-OMP/reaxc_valence_angles_omp.h
M		src/USER-REAXC/reaxc_allocate.cpp
M		src/comm_brick.cpp
M		src/fix_enforce2d.cpp
M		tools/Makefile