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13525 Commits

Author SHA1 Message Date
Axel Kohlmeyer 388eab5eeb correctly initialize `thermo_virial` in fix poems and protect access to vflag_XXX by checking for evflag !=0 2017-09-17 20:49:41 -04:00
Axel Kohlmeyer a500048c9c remove bogus version of temper/npt command 2017-09-17 19:25:22 -04:00
Axel Kohlmeyer b4ecad7fbf remove another couple of purge items from long ago 2017-09-17 19:22:43 -04:00
Axel Kohlmeyer b5894e2190 automatically call 'make purge' before calling 'make package-update' or 'make package-overwrite' 2017-09-17 19:19:45 -04:00
Axel Kohlmeyer 6f1935ea40 correct embarrassing typo 
this always happens after too much exposure to fortran codes. :-(
 2017-09-15 21:58:47 -04:00
Steve Plimpton d101fe3e79 Merge pull request #649 from akohlmey/fix-virial-aidan 
Add support for selected fixes to optionally contribute to the virial
 2017-09-15 15:25:09 -06:00
Steve Plimpton 27f99534ec Merge pull request #654 from giacomofiorin/colvars-small-fix 
Fix small typo to calculation of accumulated work in Colvars
 2017-09-15 15:22:09 -06:00
Steve Plimpton 5f6937dadd Merge pull request #653 from jdevemy/master 
Bugfix for the limit keyword
 2017-09-15 15:21:53 -06:00
Steve Plimpton 3b39694f23 Merge pull request #628 from lammps/cmake_improvements 
CMake improvements
 2017-09-15 15:19:46 -06:00
Axel Kohlmeyer 99e5dc7104 add support for fix_modify virial yes to fix smd 2017-09-15 01:21:16 -04:00
Axel Kohlmeyer ccb67d8dc5 correct cut-n-paste errors in the documentation of fix_modify virial 2017-09-15 01:20:56 -04:00
Axel Kohlmeyer 2cd7cbd964 correct cut-n-paste error, add docs 2017-09-15 00:54:19 -04:00
Axel Kohlmeyer 8776b81033 add virial support to fix addforce 2017-09-15 00:46:18 -04:00
Giacomo Fiorin f1fce64ff9 Fix small typo to calculation of accumulated work in Colvars 2017-09-14 12:58:00 -04:00
Julien Devemy da7776f818 Bugfix for the limit keyword 2017-09-14 11:00:55 +02:00
Steve Plimpton f971cd6e45 Merge pull request #647 from rbberger/gpu_opencl_2 
Use OpenCL 2.x API in GPU package when supported
 2017-09-12 10:56:13 -06:00
Steve Plimpton 0cb3a3821f Merge pull request #644 from akohlmey/collected-small-fixes 
Collected small fixes for next patch
 2017-09-12 10:31:51 -06:00
Steve Plimpton e927794696 Merge pull request #643 from andeplane/gpu_opencl_compile_fix 
Fixed OpenCL compilation issues with __global keywords
 2017-09-12 10:31:22 -06:00
Axel Kohlmeyer e196a2b9e5 import changes to various fixes by aidan to include virial contributions 2017-09-11 22:24:06 -04:00
Axel Kohlmeyer cb19ef547e update src/.gitignore 2017-09-11 22:00:58 -04:00
Axel Kohlmeyer 95d8492853 the original fix qeq went away over 7 years ago, we don't need to purge it 2017-09-11 21:59:22 -04:00
Axel Kohlmeyer b3547a9eca add infrastructure for enabling fixes to contribute to the virial by aidan 2017-09-11 11:09:59 -04:00
Richard Berger 84b84c10db Use OpenCL 2.x API in GPU package when supported 2017-09-09 19:53:56 -04:00
Christoph Junghans 0be7f46750 cmake: added USER-MESO 2017-09-09 08:25:57 -06:00
Christoph Junghans 4738fedca3 Merge remote-tracking branch 'origin/master' into cmake_improvements 2017-09-09 08:22:30 -06:00
Christoph Junghans 1601433ca1 cmake: fix lib suffix 2017-09-09 07:05:51 -06:00
Christoph Junghans 3fdb6f10fa cmake: OpenCL is always found if required 2017-09-09 06:51:24 -06:00
Richard Berger ff18cff46b Merge branch 'cmake_pkg_libs' into cmake_improvements 2017-09-08 23:34:59 -04:00
Richard Berger 8a06a7bc6b Add OpenCL support to CMake build 2017-09-08 22:20:47 -04:00
Axel Kohlmeyer de8297ea19 recover ability to compile USER-INTEL without OpenMP enabled 2017-09-06 12:02:14 -04:00
Axel Kohlmeyer fe557cb882 fix typo in commands table 2017-09-06 11:35:52 -04:00
Steve Plimpton c80203cb01 Merge pull request #641 from lammps/doc-tweak 
small update to docs for new commands
 2017-09-06 08:52:51 -06:00
Steve Plimpton 4161868bcf Merge pull request #640 from ohenrich/user-cgdna 
USER-CGDNA - sequence-dependent stacking and h-bonding strength
 2017-09-06 08:52:05 -06:00
Steve Plimpton 9ca39c89a6 Merge pull request #639 from rbberger/python_interface_improvements 
Python interface improvements
 2017-09-06 08:51:27 -06:00
Steve Plimpton 99791ce01c Merge pull request #632 from timattox/USER-DPD_kokkos_merge 
Add Kokkos version of the USER-DPD package
 2017-09-06 08:50:43 -06:00
Tim Mattox 0248a7b98e remove duplicate listing of deleted USER-DPD files from Purge.list 2017-09-06 09:24:05 -05:00
Anders Hafreager dbc60d949f Fixed OpenCL compilation issues with __global keywords 2017-09-06 15:08:02 +02:00
Axel Kohlmeyer d886cc91f3 fix syntax error in fix saed/vtk docs example 
This addresses the issue reported on github
by @subhammridha closes thus clodes #642
 2017-09-05 17:45:56 -04:00
Axel Kohlmeyer 4c5d901e2b fix stupid typo (too much compiling of fortran codes...) 2017-09-05 16:45:03 -04:00
Axel Kohlmeyer c8f92c1a61 add a couple deleted files from USER-DPD to Purge.list 2017-09-05 16:42:58 -04:00
Axel Kohlmeyer dec1d7b2dc re-indent so that gcc no longer complains about inconsistent indentation 2017-09-05 16:41:19 -04:00
Axel Kohlmeyer 45602e58f9 fix another couple of typos 2017-09-05 12:48:28 -04:00
Axel Kohlmeyer cd72532fb9 fix typo 2017-09-05 12:47:34 -04:00
Steve Plimpton b170606052 Merge pull request #620 from amilumas/master 
Temper_NPT
 2017-09-05 10:08:55 -06:00
Steve Plimpton 65b295e826 Merge pull request #638 from jdevemy/master 
Mods for extra/special/per/atom and add toluene
 2017-09-05 10:05:49 -06:00
Steve Plimpton 89a0bc947f small update to docs for new commands 2017-09-05 10:04:20 -06:00
Oliver Henrich c8967a335f Included hyperlink to package 2017-09-05 11:45:32 +01:00
Oliver Henrich 2105145f55 More minor changes 2017-09-05 11:40:36 +01:00
Oliver Henrich f7715ab6ce Added comment about optimised damping coefficient for BD 2017-09-05 11:35:26 +01:00
Oliver Henrich 12fe614ddf Added sequence-dependent stacking and base-pairing strength 2017-09-05 10:48:38 +01:00