Diffusion lammps 20f8a8c219a7

Merge branch 'master' into github-tutorial-update
20f8a8c219a7
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Authored by Stefan Paquay <stefanpaquay@gmail.com> on Jan 9 2017, 14:38.

Description

Merge branch 'master' into github-tutorial-update

Details

Committed

Stefan Paquay <stefanpaquay@gmail.com>

Jan 9 2017, 14:38

Pushed

junge

Oct 19 2017, 09:53

Parents

rLAMMPSccd09e39676e: Updated images of succesful merge.
rLAMMPS51fa33a407c7: patch 6Jan17

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Stefan Paquay <stefanpaquay@gmail.com> committed rLAMMPS20f8a8c219a7: Merge branch 'master' into github-tutorial-update (authored by Stefan Paquay <stefanpaquay@gmail.com>).Jan 9 2017, 14:38

Merged Changes

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

Commit	Author	Details	Committed
51fa33a407c7	Steve Plimpton	patch 6Jan17	Jan 6 2017
142770cb2a69	Steve Plimpton	enable pppm/tip4p to work with triclinic	Jan 6 2017
63f202501b27	sjplimp/GitHub	Merge pull request #324 from ibaned/pair-table-kokkos-inherit	Jan 6 2017
83da5d3b5d6f	sjplimp/GitHub	Merge pull request #323 from akohlmey/pppm-cg-triclinic	Jan 6 2017
ebbf60b1120b	sjplimp/GitHub	Merge pull request #319 from andeplane/domain_bug	Jan 6 2017
12c4fa25e8b1	sjplimp/GitHub	Merge pull request #318 from andeplane/initialize_pointers	Jan 6 2017
3ac58452de6a	sjplimp/GitHub	Merge pull request #310 from EfremBraun/master	Jan 6 2017
9b348d567bd6	sjplimp/GitHub	Merge pull request #315 from Pakketeretet2/github-tutorial-update	Jan 6 2017
467377094aad	sjplimp/GitHub	Merge pull request #314 from stanmoore1/fix-momentum-kokkos	Jan 6 2017
5656e90b7882	sjplimp/GitHub	Merge pull request #313 from stanmoore1/kokkos_bugfixes	Jan 6 2017
41a6a3076e17	sjplimp/GitHub	Merge pull request #309 from giacomofiorin/colvars-2016-12-22	Jan 6 2017
d4e8d4738769	sjplimp/GitHub	Merge pull request #306 from timattox/USER-DPD_updates	Jan 6 2017
f6a819580c6b	Steve Plimpton	pair TIP4P bug fix for cutoffs >> box size	Jan 6 2017
9bf771207d7f	Dan Ibanez	make PairTable::allocate() virtual	Jan 6 2017
b9144d63325d	Dan Ibanez	Revert "move enum to pair.h"	Jan 6 2017
267f05e5ca0c	Dan Ibanez	protect PairTable dtor with copymode	Jan 5 2017
aebc8ea82671	Dan Ibanez	move enum to pair.h	Jan 5 2017
53a1de1d4081	Dan Ibanez/Dan Ibanez	fix several GPU memory bugs in pair_table_kokkos	Jan 5 2017
d059b5d3344f	Dan Ibanez/Dan Ibanez	fix crash in create_kokkos_tables	Jan 5 2017
7cff343680ce	Dan Ibanez	fix allocation regressions in PairTableKokkos	Jan 5 2017
a1ac86108494	Dan Ibanez	PairTableKokkos : public PairTable	Jan 5 2017
17bdb57bb469	Dan Ibanez	try PairTableKokkos : public PairTable	Jan 5 2017
4cfe122ac692	Dan Ibanez/Stan Moore	fix warning about enum comparisons	Jan 4 2017
b46629ee39f2	Stan Moore/GitHub	Merge pull request #5 from ibaned/kokkos-fixes	Jan 4 2017
42bbeb3f16cf	Anders Hafreager	NULLing pointers after delete	Jan 4 2017
a7c5905ca4ec	Dan Ibanez	prevent implicit dereference of s_CTEMP	Jan 3 2017
37d5567f6d8b	Anders Hafreager	Fixed bug in lamda_box_corners function	Jan 3 2017
b10d0c17eca3	Anders Hafreager	Initializing pointers in neighbor.cpp	Jan 3 2017
b0ebd3ef4e17	Efrem Braun/GitHub	Merge pull request #1 from akohlmey/pull-310	Dec 28 2016
94c4f8fe5f13	Axel Kohlmeyer	add authorship attribution	Dec 28 2016
aa146e9b383c	Efrem Braun	Moved fix_nvk to USER-MISC, updated documentation to reflect move	Dec 28 2016
eca9539f84f7	Stan Moore/Stan Gerald Moore (stamoor)	Disallowing full neighborlist for pair_tersoff_kokkos styles until a bugfix is…	Dec 28 2016
27172c4a553b	Stan Moore/Stan Gerald Moore (stamoor)	Fixing Kokkos bug when many atom types	Dec 28 2016
4f195254af35	Stan Moore/Stan Gerald Moore (stamoor)	Fixing bug with Kokkos and reading restart files	Dec 28 2016
9a0007a13f43	Dan Ibanez/Stan Gerald Moore (stamoor)	rename region_block_kokkos inside()	Dec 28 2016
994f36bc6f8b	Dan Ibanez/Stan Gerald Moore (stamoor)	silence "implicit dereference" warning	Dec 28 2016
b3557bfbf50f	Dan Ibanez/Stan Gerald Moore (stamoor)	add missing return in comm_tiled_kokkos	Dec 28 2016
371df8ea72d6	Dan Ibanez/Stan Gerald Moore (stamoor)	repair sync bugs in fix_momentum_kokkos	Dec 28 2016
06ae2804f6c2	Dan Ibanez/Stan Gerald Moore (stamoor)	ensure velocity is marked as modified before syncing	Dec 28 2016
68814d4fc818	Efrem Braun	Made documentation changes to fix nvk	Dec 28 2016
616ca1de0345	Efrem Braun	Fix nvk implemented.	Dec 28 2016
b0263e87bbaa	Giacomo Fiorin	Fix missing force with extended-Lagrangian mass	Dec 27 2016
925f42727f32	Giacomo Fiorin	Fix typo	Dec 27 2016
f553e230dbcb	Giacomo Fiorin	Update Colvars library to version 2016-12-22	Dec 27 2016
6ab716164b43	Giacomo Fiorin	Fix seg fault for gyration collective variable	Dec 27 2016
7a45c72b9735	Giacomo Fiorin	Allow extended Lagrangian on non-scalar collective variables	Dec 27 2016
634eb357d2a7	Axel Kohlmeyer	synchronize pppm/cg with pppm and remove block on triclinic	Dec 24 2016
a1036f2d74be	Tim Mattox	USER-DPD: bugfix for new PairExp6rx::polynomialScaling() function.	Dec 23 2016
c301d70333a9	Tim Mattox	USER-DPD: update example input and output (see commits 3faa57 and eff7238)	Dec 22 2016
781daad2a02d	Tim Mattox	USER-DPD: update documentation for changes in commit 3faa57	Dec 22 2016

Changes (194)

				Path
	M			doc/src/Manual.txt
	M			doc/src/PDF/colvars-refman-lammps.pdf
	M			doc/src/Section_commands.txt
	M			doc/src/fix_colvars.txt
	M			doc/src/fix_eos_table_rx.txt
	M			doc/src/fix_momentum.txt
	A			doc/src/fix_nvk.txt
	M			doc/src/fixes.txt
	M			doc/src/lammps.book
	M			doc/src/pair_exp6_rx.txt
	M			doc/src/pair_multi_lucy_rx.txt
	M			doc/src/pair_table_rx.txt
	M			examples/USER/dpd/dpde-vv/log.dpde-vv.reference
	M			examples/USER/dpd/dpdrx-shardlow/in.dpdrx-shardlow
	M			examples/USER/dpd/dpdrx-shardlow/log.dpdrx-shardlow.reference
	A			lib/colvars/Makefile.colvars
	M			lib/colvars/colvar.cpp
	M			lib/colvars/colvar.h
	M			lib/colvars/colvaratoms.cpp
	M			lib/colvars/colvaratoms.h
	M			lib/colvars/colvarbias.cpp
	M			lib/colvars/colvarbias.h
	M			lib/colvars/colvarbias_abf.cpp
	M			lib/colvars/colvarbias_abf.h
	M			lib/colvars/colvarbias_alb.cpp
	M			lib/colvars/colvarbias_alb.h
	M			lib/colvars/colvarbias_histogram.cpp
	M			lib/colvars/colvarbias_histogram.h
	M			lib/colvars/colvarbias_meta.cpp
	M			lib/colvars/colvarbias_meta.h
	M			lib/colvars/colvarbias_restraint.cpp
	M			lib/colvars/colvarbias_restraint.h
	M			lib/colvars/colvarcomp.cpp
	M			lib/colvars/colvarcomp.h
	M			lib/colvars/colvarcomp_angles.cpp
	M			lib/colvars/colvarcomp_coordnums.cpp
	M			lib/colvars/colvarcomp_distances.cpp
	M			lib/colvars/colvarcomp_protein.cpp
	M			lib/colvars/colvarcomp_rotations.cpp
	M			lib/colvars/colvardeps.cpp
	M			lib/colvars/colvardeps.h
	M			lib/colvars/colvargrid.cpp
	M			lib/colvars/colvargrid.h
	M			lib/colvars/colvarmodule.cpp
	M			lib/colvars/colvarmodule.h
	M			lib/colvars/colvarparse.cpp
	M			lib/colvars/colvarparse.h
	M			lib/colvars/colvarproxy.h
	M			lib/colvars/colvarscript.cpp
	M			lib/colvars/colvarscript.h
	M			lib/colvars/colvartypes.cpp
	M			lib/colvars/colvartypes.h
	M			lib/colvars/colvarvalue.cpp
	M			lib/colvars/colvarvalue.h
	M			src/.gitignore
	M			src/KOKKOS/Install.sh
	M			src/KOKKOS/atom_vec_angle_kokkos.cpp
	M			src/KOKKOS/atom_vec_atomic_kokkos.cpp
	M			src/KOKKOS/atom_vec_bond_kokkos.cpp
	M			src/KOKKOS/atom_vec_charge_kokkos.cpp
	M			src/KOKKOS/atom_vec_full_kokkos.cpp
	M			src/KOKKOS/atom_vec_molecular_kokkos.cpp
	M			src/KOKKOS/comm_tiled_kokkos.cpp
	M			src/KOKKOS/compute_temp_kokkos.h
	M			src/KOKKOS/domain_kokkos.h
	A			src/KOKKOS/fix_momentum_kokkos.cpp
	P			src/KOKKOS/fix_momentum_kokkos.h Copied from src/fix_momentum.h
	M			src/KOKKOS/fix_setforce_kokkos.h
	A			src/KOKKOS/kokkos_few.h
	M			src/KOKKOS/kokkos_type.h
	M			src/KOKKOS/modify_kokkos.cpp
	M			src/KOKKOS/modify_kokkos.h
	M			src/KOKKOS/pair_buck_coul_cut_kokkos.h
	M			src/KOKKOS/pair_buck_coul_long_kokkos.h
	M			src/KOKKOS/pair_buck_kokkos.h
	M			src/KOKKOS/pair_coul_cut_kokkos.h
	M			src/KOKKOS/pair_coul_debye_kokkos.h
	M			src/KOKKOS/pair_coul_long_kokkos.h
	M			src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp
	M			src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.h
	M			src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp
	M			src/KOKKOS/pair_lj_charmm_coul_charmm_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_class2_coul_cut_kokkos.cpp
	M			src/KOKKOS/pair_lj_class2_coul_cut_kokkos.h
	M			src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp
	M			src/KOKKOS/pair_lj_class2_coul_long_kokkos.h
	M			src/KOKKOS/pair_lj_class2_kokkos.cpp
	M			src/KOKKOS/pair_lj_class2_kokkos.h
	M			src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp
	M			src/KOKKOS/pair_lj_cut_coul_cut_kokkos.h
	M			src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp
	M			src/KOKKOS/pair_lj_cut_coul_debye_kokkos.h
	M			src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp
	M			src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.h
	M			src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp
	M			src/KOKKOS/pair_lj_cut_coul_long_kokkos.h
	M			src/KOKKOS/pair_lj_cut_kokkos.cpp
	M			src/KOKKOS/pair_lj_cut_kokkos.h
	M			src/KOKKOS/pair_lj_expand_kokkos.cpp
	M			src/KOKKOS/pair_lj_expand_kokkos.h
	M			src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp
	M			src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.h
	M			src/KOKKOS/pair_lj_gromacs_kokkos.cpp
	M			src/KOKKOS/pair_lj_gromacs_kokkos.h
	M			src/KOKKOS/pair_lj_sdk_kokkos.cpp
	M			src/KOKKOS/pair_lj_sdk_kokkos.h
	M			src/KOKKOS/pair_table_kokkos.cpp
	M			src/KOKKOS/pair_table_kokkos.h
	M			src/KOKKOS/pair_tersoff_kokkos.cpp
	M			src/KOKKOS/pair_tersoff_kokkos.h
	M			src/KOKKOS/pair_tersoff_mod_kokkos.cpp
	M			src/KOKKOS/pair_tersoff_mod_kokkos.h
	M			src/KOKKOS/pair_tersoff_zbl_kokkos.cpp
	M			src/KOKKOS/pair_tersoff_zbl_kokkos.h
	M			src/KOKKOS/region_block_kokkos.cpp
	M			src/KOKKOS/region_block_kokkos.h
	M			src/KSPACE/pair_lj_cut_tip4p_long.cpp
	M			src/KSPACE/pair_lj_long_tip4p_long.cpp
	M			src/KSPACE/pair_tip4p_long.cpp
	M			src/KSPACE/pppm.cpp
	M			src/KSPACE/pppm_cg.cpp
	M			src/KSPACE/pppm_disp_tip4p.cpp
	M			src/KSPACE/pppm_tip4p.cpp
	M			src/KSPACE/pppm_tip4p.h
	A			src/MAKE/MACHINES/Makefile.white
	M			src/MOLECULE/fix_cmap.cpp
	M			src/MOLECULE/fix_cmap.h
	M			src/MOLECULE/pair_lj_cut_tip4p_cut.cpp
	M			src/MOLECULE/pair_tip4p_cut.cpp
	M			src/OPT/pair_lj_cut_tip4p_long_opt.cpp
	M			src/QEQ/fix_qeq.cpp
	M			src/QEQ/fix_qeq.h
	M			src/REPLICA/compute_event_displace.cpp
	M			src/REPLICA/fix_neb.cpp
	M			src/USER-ATC/fix_atc.cpp
	M			src/USER-ATC/fix_atc.h
	M			src/USER-COLVARS/README
	M			src/USER-COLVARS/colvarproxy_lammps.cpp
	M			src/USER-COLVARS/colvarproxy_lammps.h
	M			src/USER-COLVARS/fix_colvars.cpp
	M			src/USER-COLVARS/fix_colvars.h
	M			src/USER-COLVARS/group_ndx.cpp
	M			src/USER-COLVARS/group_ndx.h
	M			src/USER-COLVARS/ndx_group.cpp
	M			src/USER-COLVARS/ndx_group.h
	M			src/USER-DPD/fix_eos_table_rx.cpp
	M			src/USER-DPD/fix_eos_table_rx.h
	M			src/USER-DPD/fix_rx.cpp
	M			src/USER-DPD/fix_shardlow.cpp
	M			src/USER-DPD/fix_shardlow.h
	M			src/USER-DPD/pair_exp6_rx.cpp
	M			src/USER-DPD/pair_exp6_rx.h
	M			src/USER-DPD/pair_multi_lucy_rx.cpp
	M			src/USER-DPD/pair_multi_lucy_rx.h
	M			src/USER-DPD/pair_table_rx.cpp
	M			src/USER-DPD/pair_table_rx.h
	M			src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp
	M			src/USER-FEP/pair_tip4p_long_soft.cpp
	M			src/USER-INTEL/fix_intel.cpp
	M			src/USER-INTEL/fix_intel.h
	M			src/USER-MISC/README
	A			src/USER-MISC/fix_nvk.cpp
	P			src/USER-MISC/fix_nvk.h Copied from src/fix_momentum.h
	M			src/USER-OMP/pair_lj_cut_tip4p_cut_omp.cpp
	M			src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp
	M			src/USER-OMP/pair_lj_cut_tip4p_long_soft_omp.cpp
	M			src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp
	M			src/USER-OMP/pair_tip4p_cut_omp.cpp
	M			src/USER-OMP/pair_tip4p_long_omp.cpp
	M			src/USER-OMP/pair_tip4p_long_soft_omp.cpp
	M			src/USER-OMP/pppm_disp_tip4p_omp.cpp
	M			src/USER-OMP/pppm_tip4p_omp.cpp
	M			src/USER-REAXC/fix_qeq_reax.cpp
	M			src/USER-REAXC/fix_qeq_reax.h
	M			src/atom.cpp
	M			src/domain.cpp
	M			src/domain.h
	M			src/finish.cpp
	M			src/fix.h
	P			src/fix_momentum.h Copied to multiple locations: src/KOKKOS/fix_momentum_kokkos.h src/USER-MISC/fix_nvk.h
	M			src/fix_restrain.cpp
	M			src/force.cpp
	M			src/min.cpp
	M			src/modify.cpp
	M			src/modify.h
	M			src/neighbor.cpp
	M			src/pair_table.cpp
	M			src/pair_table.h
	M			src/respa.cpp
	M			src/run.cpp
	M			src/verlet.cpp
	M			src/version.h