Commit Graph

4192 Commits

Author SHA1 Message Date
1b51efd6b8 Merge pull request #744 from akohlmey/doc-update
Documentation build updates
2018-01-08 09:15:02 -07:00
73c55ac4d1 Fix up docs after renaming 2017-12-15 14:06:16 -05:00
2a131d1416 Merge remote-tracking branch 'upstream/master' into fix_python_move 2017-12-15 13:56:54 -05:00
bcc5f49d0b Rename fix python to fix python/invoke 2017-12-15 13:53:04 -05:00
81a1c007ed correct file name for doc file 2017-12-07 16:39:41 -05:00
0b51e9b2ff add documentation for fix move/python 2017-12-07 16:36:36 -05:00
4b1bcaa1ae fix speelink in documentation files 2017-12-07 16:01:02 -05:00
ed8680d695 suspend support for sphinxcontrib.images
the sphinxcontrib.image extension was broken with sphinx 16.x.
however, sphinx 15.x breaks with newer version of the multiprocessor module.
so we suspend the thumbnail processing and lift the lock to sphinx 15.x

also, the number of parallel sphinx tasks is can be overridden with SPHINXEXTRA="-j #'.
default is to try use all local CPU cores.
2017-12-07 15:38:15 -05:00
3e99d1a83a Add pair yukawa/kk to Section_commands 2017-12-07 09:06:33 -07:00
bae45e2493 Merge pull request #737 from akohlmey/collected-bugfixes
Collected bugfixes and small updates for next patch
2017-12-07 08:23:06 -07:00
73d509f339 Merge pull request #735 from jaapkroe/extep
Add ExTeP pair style
2017-12-07 08:22:34 -07:00
e1189381e0 correct documentation for create_atoms rotate
This closes #736
2017-11-28 11:19:19 -05:00
5770a20e2c added ExTeP to USER-MISC 2017-11-27 21:16:51 +01:00
53c1558271 Updated docs for pair_yukawa 2017-11-17 14:21:54 -05:00
ec067bde36 fix cut-n-paste error in create_bond docs 2017-11-13 17:59:16 -05:00
f2dc764d1d Merge pull request #723 from lammps/replicate_bbox
Add bounding box to Replicate command
2017-11-13 09:01:38 -07:00
2e40c00995 add option to the print command to also print to the global universe screen and logfile 2017-11-07 10:00:57 -05:00
e337db4059 Replicate bbox from Chris Knight 2017-11-06 11:31:43 -07:00
09c61ca598 correct listing of USER-OMP variants of fix rigid styles 2017-11-06 13:29:59 -05:00
65b77230fd added missing "dihedral" in compute dihedral/local docs 2017-11-02 15:04:04 -04:00
f6658d10b7 fix incorrect create_atoms example for selecting created atoms with a variable 2017-10-30 23:33:26 -04:00
39df9f5d94 patch 23Oct17 2017-10-23 16:07:21 -06:00
2137be3219 update to doc pages for new coreshell pair styles 2017-10-21 15:50:27 -06:00
998aedc6c1 Merge pull request #670 from vishalkenchan/pair_style/coul_wolf_cs
add coul/wolf/cs and born/coul/wolf/cs pair styles for CORESHELL package
2017-10-20 16:09:33 -06:00
aaf5e87c84 Merge pull request #703 from akohlmey/custom-rigid-body-generation
Allow rigid body generation from custom properties
2017-10-20 14:08:15 -06:00
83c7d3a1d2 update fix rigid documentation 2017-10-20 14:18:50 -04:00
f479f02589 Fix a Colvars error that was hidden by the previous segfault 2017-10-20 13:41:31 -04:00
e284545c5b added some documentation and reference example 2017-10-20 12:03:22 +02:00
6e7504f153 Import segfault fix in Colvars module 2017-10-19 08:09:44 -04:00
f709a723cd cross ref fix deform and new fix nvt/uef 2017-10-18 15:26:15 -06:00
281b1dc375 small updates to recently added docs and rename of an example dir 2017-10-18 14:56:47 -06:00
e93f8f8889 Merge pull request #671 from danicholson/user-uef
USER-UEF package for extensional flow
2017-10-18 13:38:56 -06:00
35f2cfa0bf Merge pull request #669 from urpedersen/master
fix rhok - biasing long-range order
2017-10-18 13:31:15 -06:00
374d619769 add gromos bond style 2017-10-16 14:57:12 -04:00
3e89b270fd Update Colvars to version 2017-10-11
Notable features are the umbrella-integration based free energy estimator for
eABF, and the traditional thermodynamic integration estimator now available
for umbrella sampling, SMD, metadynamics.  Also included are several small fixes.

Below is a list of relevant commits in the Colvars repository since the last update.

321d06a 2017-10-10 Add macros to manage colvarscript commands [Giacomo Fiorin]
26c3bec 2017-10-09 Document coming availability of Lepton in LAMMPS [Giacomo Fiorin]
cc8f249 2017-10-04 Clarify that SMP depends on code build [Giacomo Fiorin]
0b2ffac 2017-10-04 Summarize colvar definition options, clarify some details [Giacomo Fiorin]
28002e0 2017-10-01 Separate writing of restart file from other output (e.g. PMFs) [Giacomo Fiorin]
92f7c1d 2017-10-01 Deprecate colvarsTrajAppend [Giacomo Fiorin]
12a707f 2017-09-26 Accurate Jacobian calculation for RMSD variants [Jérôme Hénin]
fe389c9 2017-09-21 Allow subtractAppliedForce with extended-L again [Jérôme Hénin]
c050ce0 2017-09-18 Silence compiler warnings, remove Tabs [Giacomo Fiorin]
cb41905 2017-01-11 Add base class for TI estimator in other biases than ABF [Giacomo Fiorin]
a1bc676 2017-09-14 Avoid writing to unopened traj file [Jérôme Hénin]
b58d8cd 2017-09-08 Function to check for overlapping groups [Jérôme Hénin]
1e5efec 2017-09-07 Check for overlapping groups in coordNum [Jérôme Hénin]
03a61a4 2017-04-06 Add UI-based estimator [fhh2626]
ae43754 2017-08-17 Fix outputCenters parsing [Josh Vermaas]
1619e0e 2017-08-14 Delete static feature arrays in cvm destructor [Jérôme Hénin]
2017-10-13 13:45:10 -04:00
a1f5693fe0 Merge pull request #681 from lammps/dump-modify
remove dependence of dump modify 'at' and 'append'
2017-10-09 08:29:12 -06:00
b6187173e6 Merge branch 'master' into HEAD 2017-10-07 12:35:51 -06:00
88a33edb50 Merge pull request #680 from lammps/map-yes
add atom_modify map yes, also timers to create_atoms and replicate
2017-10-06 17:43:52 -06:00
6820db99e2 avoid merge conflict 2017-10-06 14:41:38 -04:00
e91e505fb3 remove dependence of dump modify 'at' and 'append' 2017-10-06 09:44:29 -06:00
f7cbdcf995 Merge pull request #673 from pastewka/17_dump_nc2
Multi file support for NetCDF dump style
2017-10-06 09:14:12 -06:00
352a20fc1c DOC: Updated doc to separate description of 'append' and 'at' keywords. 2017-10-06 16:38:15 +02:00
05847a0e87 Merge branch 'master' into user-intel-update 2017-10-06 10:18:38 -04:00
15853a0e38 Merge pull request #676 from stanmoore1/kokkos_reverse_comm
Add Kokkos threaded reverse communication
2017-10-05 17:08:49 -06:00
214c0cfb2b add atom_modify map yes, also timers to create_atoms and replicate 2017-10-05 16:44:24 -06:00
ca032f21fb Add Kokkos threaded reverse comm option 2017-10-03 10:14:24 -06:00
1bb7af9ef9 integrate fix rhok into the LAMMPS source code management and documentation system 2017-10-03 10:45:08 -04:00
5e89269631 Minor adjustments to intel makefiles and documentation based on the reversed
preprocessor logic and default memory align. Removing knl_coprocessor makefile.
2017-10-02 23:41:14 -07:00
11eed234f0 include dump cfg/uef in commands toctree 2017-10-03 00:14:34 -04:00
af1fc45db0 added citation to doc 2017-10-03 00:04:52 -04:00