Commit Graph

716 Commits

Author SHA1 Message Date
e337db4059 Replicate bbox from Chris Knight 2017-11-06 11:31:43 -07:00
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
466fde6443 update documentation for the reversal in the INTEL_MKL_RNG define 2017-10-02 21:20:26 -04:00
92d9b361fc include USER-UEF styles in PDF version of manual 2017-10-02 17:39:59 -04:00
cf24dd0265 Adding pair style dpd/intel and dihedral style fourier/intel
Adding raw performance numbers for Skylake xeon server.
Fixes for using older Intel compilers and compiling without OpenMP.
Fix adding in hooks for using USER-INTEL w/ minimization.
2017-10-02 04:53:17 -07:00
a7b0d1f521 DOC: Corrected syntax for appending at certain frame (NetCDF only) 2017-10-01 14:40:19 +02:00
da7be99cc4 DOC: Added multi file example. 2017-10-01 14:28:20 +02:00
2a06b75af8 doc revisions 2017-09-29 15:36:41 -04:00
c66ddf9ac0 Update fix_rhok.txt 2017-09-29 08:03:02 +02:00
480b087c93 doc edits, README, and citeme 2017-09-28 18:31:51 -04:00
0029583463 doc edits i missed in earlier commit 2017-09-28 17:46:39 -04:00
80898b8695 first draft of doc done 2017-09-28 17:42:02 -04:00
855b6000ef initial commit. doc is in the works 2017-09-28 16:34:18 -04:00
10d1741e7f Update fix_rhok.txt 2017-09-28 18:38:25 +02:00
d11733d3a0 typo in equation 2017-09-28 18:28:46 +02:00
75b3f34a58 Update documentation 2017-09-28 18:16:06 +02:00
fe80c57bde more documentation 2017-09-28 17:01:12 +02:00
e49f0e396b Create fix_rhok.txt 2017-09-28 16:24:26 +02:00
37e55a825b Create fix_rhok.txt 2017-09-28 16:20:03 +02:00
de45fa6e71 correct bogus links in LATTE docs 2017-09-26 18:25:37 -04:00
bfdc4acb8b add missing entry for pdf version of manual 2017-09-26 16:53:36 -04:00
fd3ecd0481 fix typo in formatting 2017-09-26 16:52:24 -04:00