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11400 Commits

Author SHA1 Message Date
Tim Mattox 559637f4bc USER-DPD Bugfix: reset_dt() is not called when I thought it should be called. 
Move the calculation of dtsqrt inside FixShardlow::initial_integrate()
 2016-10-11 16:11:29 -04:00
sjplimp fbf7df14b5 Merge pull request #212 from timattox/USER-DPD_fix_eos_atom_style_checks 
USER-DPD: Add atom_style compatibility checks in fix_eos_*.cpp files.
 2016-10-11 13:40:00 -06:00
sjplimp 6f1162927a Merge pull request #207 from timattox/USER-DPD_new_VV_for_DPD 
USER-DPD: add support for using VV with DPD
 2016-10-11 13:39:25 -06:00
sjplimp 803dc57bfa Merge pull request #214 from akohlmey/make-no-lib-no-mpiio 
make no-lib should also remove MPIIO and USER-LB packages
 2016-10-11 12:42:53 -06:00
sjplimp 3e8e2911cc Merge pull request #213 from akohlmey/improper-virial-bugfixes 
Improper virial bugfixes
 2016-10-11 12:42:08 -06:00
Steve Plimpton 04f5eadcf1 added LAST option to dump_modify thresh, more restart info printed out to screen 2016-10-11 12:39:52 -06:00
Axel Kohlmeyer b00b40bccd make no-lib should also remove MPIIO and USER-LB packages 2016-10-11 08:03:59 -04:00
Axel Kohlmeyer ef079ae4eb bugfix for AngleAngle term in CLASS2 impropers by Ivan A. Strelnikov, ICP RAS 
this closes #56
 2016-10-10 23:56:36 -04:00
Axel Kohlmeyer bb0bfd508b Merge branch 'master' into improper-virial-bugfixes 2016-10-10 23:55:36 -04:00
sjplimp e70d530c46 Merge pull request #203 from rbberger/txt2rst-external-link-fix 
txt2rst external link fix
 2016-10-10 13:59:27 -06:00
sjplimp ed8cc82713 Merge pull request #211 from akohlmey/add-respa-to-fix-flow-gauss 
Add respa support to fix flow/gauss
 2016-10-10 13:59:01 -06:00
sjplimp 27dac02466 Merge pull request #209 from akohlmey/static-double-deallocation-workaround 
workaround for double free issue when using USER-COLVARS with with lammps python wrapper and python package
 2016-10-10 13:58:16 -06:00
sjplimp 467bcad0a0 Merge pull request #204 from rbberger/fix-user-omp 
Migrate changes from GRANULAR to USER-OMP
 2016-10-10 13:57:37 -06:00
Tim Mattox a2b0840064 USER-DPD: Add atom_style compatibility checks in fix_eos_*.cpp files. 2016-10-10 13:40:33 -04:00
Axel Kohlmeyer 144e6a8091 whitespace cleanup 2016-10-10 09:40:09 -04:00
Steven Strong 72ac073412 edited documentation 
(cherry picked from commit eff14c74b0)
 2016-10-10 09:38:54 -04:00
Steven Strong 49c45ab03b edited documentation 
(cherry picked from commit fd560889c3)
 2016-10-10 09:38:53 -04:00
Steven Strong c2cd439944 first draft of documentation for respa 
(cherry picked from commit d7dcbcfbd9)
 2016-10-10 09:38:53 -04:00
Steven Strong e96ebb29bc adjusted default respa level to be outermost 
(cherry picked from commit 7fc4d46a41)
 2016-10-10 09:38:53 -04:00
Steven Strong 3ce178d43f now understand how respa works in lammps 
(cherry picked from commit c829027e83)
 2016-10-10 09:38:52 -04:00
Steven Strong 23781d6ec9 added respa to fix_flow_gauss, not fully understood yet 
(cherry picked from commit 8d9737b04d)
 2016-10-10 09:38:52 -04:00
Axel Kohlmeyer fca6d721c0 completed synchronization with non-threaded version 2016-10-10 09:16:21 -04:00
Axel Kohlmeyer dd192ca7ea whitespace cleanup 2016-10-10 09:15:42 -04:00
Axel Kohlmeyer 683689c808 revert to previous style conventions for size_t constants 2016-10-08 11:00:23 -04:00
Axel Kohlmeyer e01e90eb96 workaround for double free issue when using USER-COLVARS with lammps code loaded as shared library into a standalone executable 2016-10-08 10:45:22 -04:00
Tim Mattox 9507a786f0 USER-DPD: whitespace and indentation fixes 2016-10-07 15:59:47 -04:00
Tim Mattox 9789f047d7 USER-DPD: update the USER/dpd examples and their reference outputs 2016-10-07 15:55:35 -04:00
Tim Mattox e27ed6c94a USER-DPD: Added support to use VV integrator with USER-DPD if desired. 
Includes documentation and examples.
NOTE: VV requires very small timesteps under isoenergetic conditions.
Consider using fix_shardlow instead, since this VV support is
primarily for comparison purposes.
 2016-10-07 15:03:30 -04:00
Richard Berger 615a2da044 Migrate changes from GRANULAR to USER-OMP 2016-10-06 21:48:06 -04:00
Richard Berger 7f3a7c5cbe Fix broken link 2016-10-06 20:33:24 -04:00
Richard Berger e78b4267b7 Fix issue with external links containing anchors 2016-10-06 20:29:07 -04:00
sjplimp e9fed80928 Merge pull request #202 from akohlmey/doc-formatting-fixes 
collected documentation updates and corrections from LAMMPS-ICMS
 2016-10-06 15:49:44 -06:00
sjplimp 54fc194e5b Merge pull request #199 from akohlmey/small-changes 
Collected small changes and bugfixes
 2016-10-06 15:49:24 -06:00
Steve Plimpton b3d2fb91bb new fix wall/gran/region command, REBO bug fix, new example log files 2016-10-06 15:47:41 -06:00
Axel Kohlmeyer 19984c9bd1 Revert "bugfix for AngleAngle term in CLASS2 impropers by Ivan A. Strelnikov, ICP RAS" 
This reverts commit 83bcdb6a50.
 2016-10-06 17:23:10 -04:00
Axel Kohlmeyer f92618a33b Revert "bugfix for virial tally for improper style umbrella from Steven Vandenbrande (U Gent)" 
This reverts commit 4921dc18a0.
 2016-10-06 17:21:38 -04:00
Axel Kohlmeyer 887981cfaa bugfix for virial tally for improper style umbrella from Steven Vandenbrande (U Gent) 
this closes #182

(cherry picked from commit 4921dc18a0)
 2016-10-06 17:20:22 -04:00
Axel Kohlmeyer 0b5d71537a collected documentation updates and corrections from LAMMPS-ICMS 
fixes formatting issues due to tabs, permission issues and
a few typos and badly worded text.
 2016-10-06 15:48:18 -04:00
sjplimp c213457550 Merge pull request #197 from giacomofiorin/colvars_2016-10-05 
Colvars 2016-10-05
 2016-10-06 13:02:52 -06:00
sjplimp 0f45cd61a5 Merge pull request #196 from akohlmey/charmm-cmap-updates 
Some more cmap-related updates for ch2lmp
 2016-10-06 13:02:27 -06:00
Steve Plimpton 493873fb93 clean up doc src 2016-10-06 13:00:46 -06:00
Axel Kohlmeyer 60a031ebac Merge branch 'USER-DPD_pair_exp6_rx_mathfix' of https://github.com/timattox/lammps_USER-DPD into small-changes 
This closes #201
 2016-10-06 14:28:08 -04:00
Axel Kohlmeyer 27e76a70b9 Merge branch 'USER-DPD_hybrid_atom_bugfix' of https://github.com/timattox/lammps_USER-DPD into small-changes 
This closes #200
 2016-10-06 14:27:27 -04:00
Tim Mattox e1e9a5c126 USER-DPD: math corrections in pair_exp6_rx.cpp (by Jim Larentzos) 2016-10-06 13:49:47 -04:00
Tim Mattox d31121b18c USER-DPD: bugfix in unpack_comm_hybrid(); now works with hybrid atom style 2016-10-06 13:21:27 -04:00
Axel Kohlmeyer 0853cdbe6f update reference data files for updated/corrected clayff parameters 2016-10-06 11:47:08 -04:00
Axel Kohlmeyer 83bcdb6a50 bugfix for AngleAngle term in CLASS2 impropers by Ivan A. Strelnikov, ICP RAS 
this closes #56
 2016-10-06 11:27:18 -04:00
Axel Kohlmeyer 22ce671804 improved whitespace handling in msi2lmp for force fields and topologies 2016-10-06 11:16:59 -04:00
Axel Kohlmeyer 4921dc18a0 bugfix for virial tally for improper style umbrella from Steven Vandenbrande (U Gent) 
this closes #182
 2016-10-06 10:47:08 -04:00
Axel Kohlmeyer d133167bf6 Merge branch 'master' of https://github.com/albapa/lammps into small-changes 
USER-QUIP related improvements from github user albapa. This closes #198
 2016-10-06 09:32:50 -04:00