jianmu
/
lammps
forked from lijiext/lammps
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
23,128 Commits 9 Branches 198 Tags 1.1 GiB
Commit Graph

23128 Commits

Author SHA1 Message Date
Giacomo Fiorin 85d36ad6c4 Condense export of debug macro 2020-09-16 17:28:28 -04:00
Giacomo Fiorin b99e005ca1 Update example output files 2020-09-09 18:26:34 -04:00
Giacomo Fiorin d43cb34c70 Support debugging flag for Colvars via CMake 2020-09-09 18:19:29 -04:00
Giacomo Fiorin 85c394453c Update Colvars to version 2020-07-07 
This update contains several fixes and small new features or usability
improvements.  Descriptions and authorship information can be accessed from
the pull requests listed below.

Skip the zero-step also when multiple run commands are executed in sequence (@giacomofiorin)
https://github.com/Colvars/colvars/pull/357

Do not accumulate data at step 0 (@giacomofiorin)
https://github.com/Colvars/colvars/pull/345

Support for symmetry permutations of atoms in RMSD (@jhenin)
https://github.com/Colvars/colvars/pull/344

Detect new grid parameters (@jhenin)
https://github.com/Colvars/colvars/pull/341

Only access the output streams in non-threaded regions (@giacomofiorin)
https://github.com/Colvars/colvars/pull/338

Fix incomplete setting of default colvarsRestartFrequency (@giacomofiorin)
https://github.com/Colvars/colvars/pull/334

Fix typo (@e-kwsm)
https://github.com/Colvars/colvars/pull/333

Convert the input keyword to lowercase in read_state_data_key (@HanatoK)
https://github.com/Colvars/colvars/pull/332

Implement reflecting b.c. for ext Lagrangian (@jhenin)
https://github.com/Colvars/colvars/pull/329
 2020-09-09 18:19:21 -04:00
Axel Kohlmeyer d995ed0d87
Merge pull request #2344 from akohlmey/use-improved-sphinx-fortran 
Use modernized version of sphinx-fortran
 2020-09-04 18:46:34 -04:00
Axel Kohlmeyer 75a119d534
divert installation of sphinx-fortran to github branch with parallel read capable version 2020-09-04 17:40:26 -04:00
Axel Kohlmeyer e6592d2324
Merge pull request #2336 from akohlmey/collected-small-changes 
Collected small changes for the next patch release
 2020-09-04 15:22:31 -04:00
Axel Kohlmeyer ceed9284c1
Merge branch 'master' into collected-small-changes 2020-09-04 13:32:47 -04:00
Axel Kohlmeyer de777ce994
Merge pull request #2341 from akohlmey/doc-updates 
Revised links and related descriptions in the manual
 2020-09-04 13:29:58 -04:00
Axel Kohlmeyer 41a3e7c712
update a few links in the programmer guide 2020-09-04 11:59:04 -04:00
Axel Kohlmeyer 5c22d1197e
Merge branch 'master' into doc-updates 2020-09-04 11:50:28 -04:00
Axel Kohlmeyer d0d3cee28d
a few more cosmetic changes 2020-09-04 11:50:02 -04:00
Axel Kohlmeyer 90c13b1b14
update build files for plumed 2.6.1 release 2020-09-04 11:44:39 -04:00
Axel Kohlmeyer 2b1e4749dd
first chunk of revised updates to the manual addressing link issues. 2020-09-04 11:39:38 -04:00
Axel Kohlmeyer c8327e66b3
Merge pull request #2338 from akohlmey/include-cleanup 
Update list of included headers for latest updates of the convention
 2020-09-04 10:14:12 -04:00
Axel Kohlmeyer f19ce32bf5
a few more small tweaks 2020-09-04 09:42:11 -04:00
Axel Kohlmeyer 255bf2f8fd
update iwyu custom mapping file 2020-09-04 09:41:57 -04:00
Axel Kohlmeyer f541647d44
some more IWYU tweaks 2020-09-04 09:23:20 -04:00
Axel Kohlmeyer d6ba95bed6
minor tweaks 2020-09-04 08:05:59 -04:00
Axel Kohlmeyer 2d802411e9
remove pointless stringstream abuse 2020-09-04 08:03:53 -04:00
Axel Kohlmeyer 91a87b745f
final second round IWYU cleanup 2020-09-04 08:01:11 -04:00
Axel Kohlmeyer 63e5ca53ef
add iwyu mappings for gtest and gmock 2020-09-04 08:00:38 -04:00
Axel Kohlmeyer bb7447363c
more include cleanup and IWYU tweaks 2020-09-04 07:22:39 -04:00
Axel Kohlmeyer fc3d9fee5e
more USER-OMP updates 2020-09-04 01:32:52 -04:00
Axel Kohlmeyer d0691d0a5d
add mapping for Eigen3 includes 2020-09-04 01:32:15 -04:00
Axel Kohlmeyer 2e0af2fdce
some more second pass cleanup 2020-09-04 00:46:23 -04:00
Axel Kohlmeyer 508b49c976
add missing comma 2020-09-04 00:45:41 -04:00
Axel Kohlmeyer 87dfdb8723
add comments/warnings to docs of fix property/atom and fix store/state about restarting 2020-09-04 00:14:01 -04:00
Axel Kohlmeyer cb618e19d1
small tweak to address formal issues 2020-09-03 18:30:35 -04:00
Axel Kohlmeyer 18cea11100
Merge pull request #66 from junghans/include-cleanup 
cmake: use static iwyu-extra-map.imp
 2020-09-03 18:27:00 -04:00
Axel Kohlmeyer 5a7189e95f
update note for write_data command on missing coefficient data. 2020-09-03 18:24:12 -04:00
Axel Kohlmeyer ce78be864a
move date2num() convernience function from Universe class to utils namespace 2020-09-03 17:47:45 -04:00
Axel Kohlmeyer 390c6ba106
rechecking some corefiles with IWYU after the many updates 2020-09-03 15:28:07 -04:00
Christoph Junghans 93d0358ebc cmake: use static iwyu-extra-map.imp 2020-09-03 11:36:02 -06:00
Axel Kohlmeyer 05c7cfe59f
more include updates for USER-OMP 2020-09-03 11:16:32 -04:00
Axel Kohlmeyer f67bd8eb5d
more KOKKOS, USER-OMP, and USER-INTEL include file cleanup 2020-09-03 10:54:06 -04:00
Axel Kohlmeyer 27203304d6
USER-INTEL include handling cleanup 2020-09-03 09:47:48 -04:00
Axel Kohlmeyer 88ddfa4eb0
more IWYU cleanup in packages 2020-09-03 05:20:02 -04:00
Axel Kohlmeyer 55704368d0
include updates for commonly used packages 2020-09-03 01:45:05 -04:00
Axel Kohlmeyer c7c4297cfc
update include handling for commands 2020-09-03 00:51:58 -04:00
Axel Kohlmeyer c2cf19bdd4
fixes for file readers 2020-09-03 00:32:57 -04:00
Axel Kohlmeyer baa79bd1c4
add another iwyu-mapping entry 2020-09-03 00:22:28 -04:00
Axel Kohlmeyer 9925122cea
more IWYU updates 2020-09-03 00:22:09 -04:00
Axel Kohlmeyer a4a1f7e848
more IWYU cleanup 2020-09-02 23:49:17 -04:00
Axel Kohlmeyer 047c14d17c
tweak iwyu target. generate file with custom mappings 2020-09-02 23:41:16 -04:00
Axel Kohlmeyer 45f80f4f06
more include file updates found by iwyu 2020-09-02 22:52:22 -04:00
Axel Kohlmeyer 7b8fe97a88
remove trailing whitespace 2020-09-02 22:51:42 -04:00
Axel Kohlmeyer 71d111ccd9
get rid of 'using namespace std;' 2020-09-02 22:51:30 -04:00
Axel Kohlmeyer 203e42073a
fix compilation error 2020-09-02 22:51:14 -04:00
Axel Kohlmeyer f88f4cd60e
more include file updates 2020-09-02 21:44:04 -04:00