Diffusion lammps be4734bdce03

Version 30 Sep 2016
be4734bdce03
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Authored by Axel Kohlmeyer <akohlmey@gmail.com> on Sep 30 2016, 17:57.

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Version 30 Sep 2016

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Committed

Axel Kohlmeyer <akohlmey@gmail.com>

Sep 30 2016, 17:57

Pushed

junge

Oct 19 2017, 09:53

Parents

rLAMMPS2551619b074d: Version 29 Sep 2016
rLAMMPSe2c7acabac53: Merge pull request #187 from akohlmey/colvars-update-2016-09-30

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Axel Kohlmeyer <akohlmey@gmail.com> committed rLAMMPSbe4734bdce03: Version 30 Sep 2016 (authored by Axel Kohlmeyer <akohlmey@gmail.com>).Sep 30 2016, 17:57

Merged Changes

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

Commit	Author	Details	Committed
e2c7acabac53	sjplimp/GitHub	Merge pull request #187 from akohlmey/colvars-update-2016-09-30	Sep 30 2016
91edee25302a	sjplimp/GitHub	Merge pull request #186 from akohlmey/small-bugfixes	Sep 30 2016
b9d0f96a1923	Steve Plimpton	change purge target in Makefile, also fixed one issue with Make.py	Sep 30 2016
5bb85b482d71	Axel Kohlmeyer	remove unused variable	Sep 30 2016
d4b074d85b68	Axel Kohlmeyer	enable dynamic groups for fix dt/reset	Sep 30 2016
6d200061ca64	Axel Kohlmeyer	update colvars library to version 2016-09-30	Sep 30 2016
cb7bd2799e7e	Axel Kohlmeyer	flag header as C++ to emacs	Sep 30 2016
4337f2c240d7	Axel Kohlmeyer	include charmm22 and charmm36 cmap files and include date added signature	Sep 30 2016
0eeb24073051	Axel Kohlmeyer	whitespace cleanup, fix bug in looking for empty strings, improve read…	Sep 30 2016
c88acc961340	Axel Kohlmeyer	make reader for target geometry file more resilient	Sep 30 2016
f7b5afee82a1	sjplimp/GitHub	Merge pull request #184 from akohlmey/dynamic-groups-for-respa	Sep 29 2016
a315dcda9b84	Axel Kohlmeyer	remove dead code	Sep 29 2016
f6c77c3aba63	Axel Kohlmeyer	support dynamic groups with run style respa	Sep 29 2016
5b2becd09b97	Axel Kohlmeyer	Merge branch 'integration' into new-master	Sep 29 2016
78a22be93ffd	sjplimp	sync Make.py and fix addforce change with GHub	Sep 29 2016
596b260f5d48	sjplimp/GitHub	Merge pull request #45 from akohlmey/small-bugfixes	Sep 29 2016
189825489c73	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15673 f3b2605a-c512-4ea7…	Sep 29 2016
bdd0f665cabf	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15672 f3b2605a-c512-4ea7…	Sep 29 2016
6897cc803f19	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15671 f3b2605a-c512-4ea7…	Sep 29 2016
f511c177c694	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15670 f3b2605a-c512-4ea7…	Sep 28 2016
1ec3987b313f	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15669 f3b2605a-c512-4ea7…	Sep 28 2016
8c1d0031c999	Axel Kohlmeyer	correct typo in Make.py	Sep 28 2016
45e50b46c3c6	sjplimp	sync with GH	Sep 27 2016
1adf3858a9bf	Axel Kohlmeyer	correct bug and synchronize fix addforce respa level init with other fixes	Sep 27 2016
f82e0c53b634	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15666 f3b2605a-c512-4ea7…	Sep 27 2016
1fbddc97d114	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15665 f3b2605a-c512-4ea7…	Sep 27 2016
1cfa49f03d6f	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15664 f3b2605a-c512-4ea7…	Sep 27 2016
3486b7d503fb	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15663 f3b2605a-c512-4ea7…	Sep 27 2016
6fedf8d89965	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15662 f3b2605a-c512-4ea7…	Sep 27 2016
56b0856e2feb	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15661 f3b2605a-c512-4ea7…	Sep 27 2016
f9c204972474	Axel Kohlmeyer	need to ignore new fix cmap sources	Sep 27 2016
e1c6b6b7d153	Axel Kohlmeyer	correctly handle exceptions raised from subprocess module	Sep 27 2016
3333e4b47562	athomps	Put snap before zbl to get more helpful error message	Sep 27 2016
2ae966c26f78	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15657 f3b2605a-c512-4ea7…	Sep 27 2016
d1b8ffd92409	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15656 f3b2605a-c512-4ea7…	Sep 27 2016
b66039b8bbca	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15653 f3b2605a-c512-4ea7…	Sep 27 2016
995ecea5ed41	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15652 f3b2605a-c512-4ea7…	Sep 27 2016
43633180ebe3	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15651 f3b2605a-c512-4ea7…	Sep 27 2016
b68e9547617c	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15650 f3b2605a-c512-4ea7…	Sep 27 2016
2b88050a1feb	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15649 f3b2605a-c512-4ea7…	Sep 27 2016
063307c71ca4	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15648 f3b2605a-c512-4ea7…	Sep 27 2016
f280bd32a669	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15647 f3b2605a-c512-4ea7…	Sep 27 2016
53eac4431d50	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15646 f3b2605a-c512-4ea7…	Sep 27 2016
fb64ae612f94	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15645 f3b2605a-c512-4ea7…	Sep 26 2016
5769c1018967	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15643 f3b2605a-c512-4ea7…	Sep 26 2016
7453a4f55f21	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15642 f3b2605a-c512-4ea7…	Sep 26 2016
50d59454d239	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15640 f3b2605a-c512-4ea7…	Sep 24 2016
24ff008a0f14	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15639 f3b2605a-c512-4ea7…	Sep 24 2016
da480bd4d4eb	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15638 f3b2605a-c512-4ea7…	Sep 24 2016
8a6e5ed3ced4	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15637 f3b2605a-c512-4ea7…	Sep 24 2016

Changes (46)

				Path
	M			doc/src/PDF/colvars-refman-lammps.pdf
	M			doc/src/fix_colvars.txt
	P			examples/cmap/charmm22.cmap Copied to potentials/charmm22.cmap
	M			examples/tad/README
	M			lib/colvars/colvar.cpp
	M			lib/colvars/colvar.h
	M			lib/colvars/colvarbias_histogram.cpp
	M			lib/colvars/colvarbias_meta.cpp
	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/colvardeps.cpp
	M			lib/colvars/colvardeps.h
	M			lib/colvars/colvargrid.h
	M			lib/colvars/colvarmodule.cpp
	M			lib/colvars/colvarmodule.h
	M			lib/colvars/colvarscript.cpp
	M			lib/colvars/colvartypes.h
	M			lib/kokkos/config/configure_compton_cpu.sh
	M			lib/kokkos/config/configure_compton_mic.sh
	M			lib/kokkos/config/configure_kokkos.sh
	M			lib/kokkos/config/configure_kokkos_nvidia.sh
	M			lib/kokkos/config/configure_shannon.sh
	P			potentials/charmm22.cmap Copied from examples/cmap/charmm22.cmap
	A			potentials/charmm36.cmap
	M			src/.gitignore
	A			src/KOKKOS/comm_tiled_kokkos.cpp
	A			src/KOKKOS/comm_tiled_kokkos.h
	M			src/KOKKOS/neighbor_kokkos.cpp
	M			src/MOLECULE/fix_cmap.cpp
	M			src/MOLECULE/fix_cmap.h
	M			src/Make.py
	M			src/Makefile
	M			src/REPLICA/prd.cpp
	M			src/USER-REAXC/pair_reax_c.cpp
	M			src/comm_tiled.cpp
	M			src/comm_tiled.h
	M			src/fix_addforce.cpp
	M			src/fix_dt_reset.cpp
	M			src/fix_group.cpp
	M			src/fix_group.h
	M			src/fix_tmd.cpp