Diffusion lammps b12ad2cecf64

Merge branch 'integration' into vashishta-tabulation
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Authored by Axel Kohlmeyer <akohlmey@gmail.com> on Sep 1 2016, 14:25.

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Merge branch 'integration' into vashishta-tabulation

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Committed

Axel Kohlmeyer <akohlmey@gmail.com>

Sep 1 2016, 14:25

Pushed

junge

Oct 19 2017, 09:53

Parents

rLAMMPScdf06646efc4: Update documentation for tabulation in vashista pair style
rLAMMPSfb2c18ee8872: Merge pull request #17 from akohlmey/small-doc-fixes

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Axel Kohlmeyer <akohlmey@gmail.com> committed rLAMMPSb12ad2cecf64: Merge branch 'integration' into vashishta-tabulation (authored by Axel Kohlmeyer <akohlmey@gmail.com>).Sep 1 2016, 14:25

Merged Changes

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

Commit	Author	Details	Committed
fb2c18ee8872	sjplimp/GitHub	Merge pull request #17 from akohlmey/small-doc-fixes	Sep 1 2016
b5c758f22c60	Steve Plimpton	Merge branch 'goo' into integration	Sep 1 2016
de0036fafd07	Steve Plimpton	removing searchindex.js	Sep 1 2016
c3c9788dc72c	Axel Kohlmeyer	include autogenerated html code	Sep 1 2016
2abd5ad28ae2	Axel Kohlmeyer	Merge branch 'integration' into small-doc-fixes	Sep 1 2016
1c3302d1db6e	sjplimp/GitHub	Merge pull request #15 from rbberger/pylammps-improvements	Sep 1 2016
24409b61782b	Steve Plimpton	Merge branch 'error' into integration	Sep 1 2016
de21cb2cd596	Steve Plimpton	small changes to doc page	Sep 1 2016
639ab0fd3e37	Steve Plimpton	Merge branch 'core/cpp_exceptions' of https://github.com/rbberger/lammps into…	Sep 1 2016
6c65af710c01	Steve Plimpton	bad file?	Sep 1 2016
29e480ad666c	Axel Kohlmeyer	corrections for various compute something/chunk examples	Aug 31 2016
7c01ef57eeb0	Steve Plimpton	sync with SVN	Aug 31 2016
0316bb579be8	sjplimp/GitHub	Merge pull request #3 from akohlmey/fix-flow-gauss	Aug 31 2016
f89448d73c91	sjplimp/GitHub	Merge pull request #6 from akohlmey/manifold-doc-update	Aug 31 2016
ad879d97dbfe	Steve Plimpton	sync w/ SVN	Aug 31 2016
4051aedf2c78	Steve Plimpton	Merge branch 'small' into integration	Aug 31 2016
ec8b9e21dbb4	Steve Plimpton	sync with SVN	Aug 31 2016
1986eda4d5f1	Richard Berger	Remove no longer needed generated files in doc	Aug 31 2016
e71fafdd256c	Richard Berger	Use Google Custom Search API for searching in docs	Aug 31 2016
6cbdad7a97a7	Richard Berger	Add utility function to IPyLammps for embedding videos	Aug 30 2016
a08cf7a4b6a0	Richard Berger	Add verbose option in PyLammps methods	Aug 30 2016
691de01b3383	Richard Berger	Allow setting the position of atoms	Aug 30 2016
33a87a470a2b	Richard Berger	Return 2D vectors in 2D cases	Aug 30 2016
59dc83eadbde	Richard Berger	Fix resource leak	Aug 30 2016
a2ea263652c6	Axel Kohlmeyer	remove vector/array class members shadowing the base class	Aug 30 2016
493613b49549	Axel Kohlmeyer	avoid NaNs in MEAM	Aug 30 2016
021ade199a31	Axel Kohlmeyer	null-ing of pointers and a couple select integers for fix ave/chunk	Aug 30 2016
b7749ab21285	Axel Kohlmeyer	individual computes do not need to set vector/array to NULL. reordering fixes…	Aug 30 2016
554ac7dd12b6	Efrem Braun/Axel Kohlmeyer	Use MPI_Allreduce values instead of each processor's values	Aug 30 2016
ef86d1172963	Axel Kohlmeyer	Merge branch 'integration' into small-bugfixes	Aug 30 2016
62b7b69a87b0	Steve Plimpton	Merge branch 'init' into integration	Aug 30 2016
1c1c9c310146	Axel Kohlmeyer	use correct order when initializing arrays	Aug 29 2016
48ba812f0ada	Anders Hafreager/Axel Kohlmeyer	Fixed initialization of arrays in computes/fixes in MC package	Aug 29 2016
f9a21ae65496	Anders Hafreager/Axel Kohlmeyer	Fixed initialization of arrays in computes/fixes in MANYBODY package	Aug 29 2016
d6b9d0b9b6cd	Anders Hafreager/Axel Kohlmeyer	Fixed initialization of arrays in fixes	Aug 29 2016
36e085e393eb	Anders Hafreager/Axel Kohlmeyer	Fixed initialization of arrays in fixes	Aug 29 2016
425142ba2e73	Anders Hafreager/Axel Kohlmeyer	Fixed initialization of arrays in fixes	Aug 29 2016
07eb1d443b27	Anders Hafreager/Axel Kohlmeyer	Fixed initialization of arrays in fixes	Aug 29 2016
265cc14125e4	Anders Hafreager/Axel Kohlmeyer	Fixed initialization of arrays in fixes	Aug 29 2016
fd05a1325ee1	Anders Hafreager/Axel Kohlmeyer	Fixed initialization of arrays in fixes	Aug 29 2016
b5a562788bfa	Anders Hafreager/Axel Kohlmeyer	Fixed initialization of arrays in fixes	Aug 29 2016
2c7241bfe282	Anders Hafreager/Axel Kohlmeyer	Fixed initialization of arrays in fixes	Aug 29 2016
ee2f6ded2990	Anders Hafreager/Axel Kohlmeyer	Fixed initialization of arrays in fixes	Aug 29 2016
db077ef186c2	Anders Hafreager/Axel Kohlmeyer	Fixed initialization of arrays in fixes	Aug 29 2016
fc5db8a737be	Axel Kohlmeyer	fix off-by one bug when looking for bonds.	Aug 28 2016
56d0ab947412	Axel Kohlmeyer	updated doc build readme for current Fedora and RHEL/CentOS	Aug 28 2016
f8d6b979ec1a	Axel Kohlmeyer	Merge branch 'integration' into small-bugfixes	Aug 28 2016
4e03df2d197b	Axel Kohlmeyer	Merge branch 'integration' into fix-flow-gauss	Aug 28 2016
e1045851c035	Axel Kohlmeyer	incorporate bugfix and cleanup from lammps-icms and upstream	Aug 28 2016
f5a50c3cd1c8	Richard Berger	Added documentation about -DLAMMPS_EXCEPTIONS flag	Aug 28 2016

Changes (121)
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This commit is very large. Load each file individually.

				Path
	M			doc/Makefile
	M			doc/README.md
	M			doc/html/.gitignore
	M			doc/html/Section_howto.html
	M			doc/html/Section_start.html
	M			doc/html/compute_angmom_chunk.html
	M			doc/html/compute_com_chunk.html
	M			doc/html/compute_dipole_chunk.html
	M			doc/html/compute_inertia_chunk.html
	M			doc/html/compute_msd_chunk.html
	M			doc/html/compute_omega_chunk.html
	M			doc/html/compute_property_chunk.html
	M			doc/html/compute_torque_chunk.html
	M			doc/html/compute_vcm_chunk.html
	M			doc/html/fix_nve_manifold_rattle.html
	M			doc/html/fix_nvt_manifold_rattle.html
	D			doc/html/searchindex.js
	M			doc/src/Section_howto.txt
	M			doc/src/Section_start.txt
	M			doc/src/compute_angmom_chunk.txt
	M			doc/src/compute_com_chunk.txt
	M			doc/src/compute_dipole_chunk.txt
	M			doc/src/compute_inertia_chunk.txt
	M			doc/src/compute_msd_chunk.txt
	M			doc/src/compute_omega_chunk.txt
	M			doc/src/compute_property_chunk.txt
	M			doc/src/compute_torque_chunk.txt
	M			doc/src/compute_vcm_chunk.txt
	M			doc/src/fix_nve_manifold_rattle.txt
	M			doc/src/fix_nvt_manifold_rattle.txt
	M			doc/utils/sphinx-config/_themes/lammps_theme/search.html
	M			lib/kokkos/Makefile.kokkos
	M			lib/meam/meam_setup_done.F
	M			python/lammps.py
	M			src/BODY/compute_body_local.h
	M			src/KOKKOS/pair_reax_c_kokkos.cpp
	M			src/MANYBODY/fix_qeq_comb.cpp
	M			src/MC/fix_atom_swap.cpp
	M			src/MC/fix_bond_break.cpp
	M			src/MC/fix_bond_create.cpp
	M			src/MC/fix_bond_swap.cpp
	M			src/MC/fix_gcmc.cpp
	M			src/MC/fix_tfmc.cpp
	M			src/RIGID/compute_rigid_local.h
	M			src/USER-MISC/fix_flow_gauss.cpp
	M			src/USER-REAXC/compute_spec_atom.h
	M			src/atom.cpp
	M			src/compute_angle_local.cpp
	M			src/compute_angle_local.h
	M			src/compute_bond_local.cpp
	M			src/compute_bond_local.h
	M			src/compute_chunk_atom.cpp
	M			src/compute_cna_atom.cpp
	M			src/compute_dihedral_local.cpp
	M			src/compute_dihedral_local.h
	M			src/compute_displace_atom.cpp
	M			src/compute_improper_local.cpp
	M			src/compute_improper_local.h
	M			src/compute_omega_chunk.cpp
	M			src/compute_pair_local.cpp
	M			src/compute_pair_local.h
	M			src/compute_property_atom.cpp
	M			src/compute_property_atom.h
	M			src/compute_property_local.cpp
	M			src/compute_property_local.h
	M			src/create_box.cpp
	M			src/error.cpp
	M			src/error.h
	M			src/fix.cpp
	M			src/fix_adapt.cpp
	M			src/fix_addforce.cpp
	M			src/fix_ave_atom.cpp
	M			src/fix_ave_chunk.cpp
	M			src/fix_ave_correlate.cpp
	M			src/fix_ave_histo.cpp
	M			src/fix_ave_time.cpp
	M			src/fix_aveforce.cpp
	M			src/fix_balance.cpp
	M			src/fix_box_relax.cpp
	M			src/fix_controller.cpp
	M			src/fix_deform.cpp
	M			src/fix_enforce2d.cpp
	M			src/fix_external.cpp
	M			src/fix_gravity.cpp
	M			src/fix_group.cpp
	M			src/fix_heat.cpp
	M			src/fix_indent.cpp
	M			src/fix_langevin.cpp
	M			src/fix_minimize.cpp
	M			src/fix_move.cpp
	M			src/fix_nh.cpp
	M			src/fix_press_berendsen.cpp
	M			src/fix_print.cpp
	M			src/fix_property_atom.cpp
	M			src/fix_read_restart.cpp
	M			src/fix_respa.cpp
	M			src/fix_restrain.cpp
	M			src/fix_setforce.cpp
	M			src/fix_shear_history.cpp
	M			src/fix_spring.cpp
	M			src/fix_spring_chunk.cpp
	M			src/fix_spring_self.cpp
	M			src/fix_store.cpp
	M			src/fix_store_force.cpp
	M			src/fix_store_state.cpp
	M			src/fix_temp_berendsen.cpp
	M			src/fix_temp_csld.cpp
	M			src/fix_temp_csvr.cpp
	M			src/fix_temp_rescale.cpp
	M			src/fix_tmd.cpp
	M			src/fix_vector.cpp
	M			src/fix_viscous.cpp
	M			src/fix_wall.cpp
	M			src/fix_wall_reflect.cpp
	M			src/fix_wall_region.cpp
	M			src/library.cpp
	M			src/library.h
	M			src/main.cpp
	M			src/math_extra.h
	M			src/modify.cpp
	M			src/variable.cpp