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11340 Commits

Author SHA1 Message Date
Axel Kohlmeyer 7b7cb297e6 add mixing for pair styles gauss and gauss/cut contributed by andrew jewett. also add support for write_data. 2016-10-18 22:26:47 -04:00
Steve Plimpton 2106dce2b3 new fix halt command, other sundry small bug fixes 2016-10-18 13:11:40 -06:00
sjplimp 713b2af067 Merge pull request #221 from akohlmey/collected-bugfixes 
Collected bugfixes and small changes
 2016-10-18 12:58:25 -06:00
Axel Kohlmeyer a752966eef Merge branch 'collected-bugfixes' of github.com:akohlmey/lammps into collected-bugfixes 2016-10-18 14:07:05 -04:00
Axel Kohlmeyer 1f7693faf2 fix typo 2016-10-18 14:06:43 -04:00
Axel Kohlmeyer 2c5ea9fc61 reapply changes to the timer class that got lost somehow 2016-10-18 14:05:08 -04:00
Axel Kohlmeyer 3e88fb5355 Merge branch 'master' into collected-bugfixes 2016-10-18 13:54:15 -04:00
Steve Plimpton 6eadd45c45 Merge branch 'halt2' 2016-10-18 11:16:44 -06:00
Steve Plimpton 003581c6a8 final changes to fix halt 2016-10-18 11:16:28 -06:00
Axel Kohlmeyer 1f1c87235a add support for "error continue" option, which resets the timer timeout setting after a soft exit 2016-10-18 12:21:27 -04:00
Axel Kohlmeyer 394c3bb504 add Timer::reset_timeout() API, that allows restoring the previous timeout setting after a forced timeout 2016-10-18 12:20:49 -04:00
Steve Plimpton 954d536826 added bondmax method to fix halt 2016-10-18 09:27:01 -06:00
Axel Kohlmeyer e4ff8128f1 fix typo 
(cherry picked from commit c65fb0e311)
 2016-10-16 12:29:53 -04:00
Axel Kohlmeyer e7825ba21a import fix halt prototype code with corrections for soft exit 2016-10-15 07:30:07 -04:00
Axel Kohlmeyer e77e1f6b8e replace complex solution to implement a soft exit with simpler one 2016-10-14 19:40:51 -04:00
Axel Kohlmeyer 909ec2c096 remove unused class members 2016-10-14 12:04:32 -04:00
Axel Kohlmeyer f67975fd8a apply proper initialization and remove redundant variable declaration 2016-10-14 07:37:06 -04:00
Axel Kohlmeyer deceb9d5c6 remove assignment without effect 2016-10-14 07:31:52 -04:00
Axel Kohlmeyer c9c66ca0bd replace unsafe code 2016-10-14 07:28:25 -04:00
Axel Kohlmeyer d07703efff re-apply bugfix from two years ago 2016-10-14 07:27:40 -04:00
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