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11320 Commits

Author SHA1 Message Date
Axel Kohlmeyer 411ecca8df plug memory leak 2016-10-14 07:27:14 -04:00
sjplimp d11363c7eb Merge pull request #220 from rbberger/fix-doc-makefile 
Allow building non-html doc targets without Python3 and virtualenv
 2016-10-13 17:00:23 -06:00
sjplimp 5aefb2a882 Merge pull request #219 from akohlmey/python-no-double-load 
do not require the LAMMPS shared library when loading the python wrapper from inside LAMMPS
 2016-10-13 16:58:35 -06:00
sjplimp 40f2310a2a Merge pull request #218 from timattox/USER-DPD_fix_rx_init_bugfix 
USER-DPD fix_rx initialization bugfix
 2016-10-13 16:56:19 -06:00
Steve Plimpton 2c8a7a318a bug fix for fix GCMC w/ fix shake, enhance of fix wall/gran/region with restarting 2016-10-13 16:55:53 -06:00
Richard Berger 95cca1bd9f Allow building other targets without Python3 and virtualenv 2016-10-13 11:40:44 -04:00
Axel Kohlmeyer 0b426dadc1 do not require the LAMMPS shared library when loading the python wrapper from inside LAMMPS 
Thanks to Giacomo Fiorin for figuring this out with NAMD/Colvars.
This requires linking with -Xlinker -export-dynamic or equivalent,
which is the default when using python-config to provide linker flags.
We will fall back to loading the DSO in case the initial load fails.
 2016-10-12 18:36:38 -04:00
Tim Mattox fcb5271026 USER-DPD: Initialize the dpdThetaLocal array consistently in fix_rx 2016-10-12 15:56:45 -04:00
Tim Mattox 4958e114ba USER-DPD bugfix: Properly initialize the local temperature averaging array. 2016-10-12 15:46:46 -04:00
Steve Plimpton 63e71cd45b patch to add DPD-VV 2016-10-12 07:35:47 -06:00
sjplimp 4a5d9eaae2 Merge pull request #217 from akohlmey/small-fixes 
Collected small changes and bugfixes
 2016-10-12 07:32:08 -06:00
sjplimp 4e3a55047f Merge pull request #215 from timattox/USER-DPD_bugfix_for_dtsqrt 
USER-DPD Bugfix: reset_dt() is not called when I thought it should be called.
 2016-10-12 07:30:10 -06:00
Axel Kohlmeyer f8a26dd158 update Timer::force_timeout() to trigger at next loop iteration 2016-10-12 07:26:03 -04:00
Axel Kohlmeyer c24bf512f3 update #include statements for system includes 2016-10-12 00:00:53 -04:00
Axel Kohlmeyer 6b4ab0a390 update .gitignore 2016-10-12 00:00:21 -04:00
Axel Kohlmeyer adc98e07df whitespace cleanup in USER-DPD 2016-10-11 23:58:36 -04:00
Axel Kohlmeyer 39a22039e9 correct broken link 2016-10-11 23:57:40 -04:00
Axel Kohlmeyer b75860048b updates for recent changes to the manual 2016-10-11 23:50:45 -04:00
Steve Plimpton 0eb7fbf34d tweaks to new USER-DPD docs 2016-10-11 15:43:59 -06:00
Tim Mattox 2f07a627a2 Forgot to remove my call to reset_dt() 2016-10-11 16:30:41 -04:00
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