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4955 Commits

Author SHA1 Message Date
efetis 7c1fb847f4 Slight tweak to sed in doc/Makefile 2019-02-06 18:00:23 -08:00
efetis 4fe6528ed4 Add support for Sphinx+PDF+MathJax 2019-02-06 17:14:50 -08:00
Axel Kohlmeyer d6eaf73db1
Merge pull request #1307 from akohlmey/next-patch-release 
Patch release 1 February 2019
 2019-02-01 20:22:18 +01:00
Axel Kohlmeyer f2a977884c
Merge pull request #1290 from akohlmey/python-script-portability 
Use argparse module in for Install.py scripts in lib and further portability and consistency enhancements. Some lint removal as well.
 2019-02-01 01:18:40 +01:00
Axel Kohlmeyer a9f8b17cbd
Merge pull request #1282 from akohlmey/collected-small-changes 
Collected small changes and bugfixes for the next patch release
 2019-02-01 00:24:15 +01:00
Axel Kohlmeyer d6a918f4fd
Merge pull request #1270 from akohlmey/get-moltemplate-from-web 
Replace bundled moltemplate distribution with installation instructions only
 2019-01-31 22:58:31 +01:00
Axel Kohlmeyer 7606529f03
Merge pull request #1302 from akohlmey/combined-user-fep-soft-updates 
Combined USER-FEP related updates
 2019-01-31 22:57:51 +01:00
Axel Kohlmeyer c5256624e8 document coul/streitz and reax/c keywords to extract qeq parameters from pair styles 2019-01-31 13:48:06 +01:00
Axel Kohlmeyer 14ab0ec459 remove references to pre-installed packages as this was changed with the 22 August 2018 version 2019-01-31 12:02:22 +01:00
Axel Kohlmeyer ef5c327f74 Merge branch 'master' into collected-small-changes 2019-01-31 11:45:15 +01:00
Axel Kohlmeyer d2846404bd update development workflow description to state of latest discussions 2019-01-31 02:55:11 -05:00
Axel Kohlmeyer ee5f39d895 Patch release 1 February 2019 2019-01-30 16:16:32 -05:00
Axel Kohlmeyer bad6c8aa35 Patch release 30 January 2019 2019-01-29 13:37:50 +01:00
Axel Kohlmeyer 21dac57c7c fix typo 2019-01-26 05:16:38 -05:00
Axel Kohlmeyer 6c72d15c31 Merge branch 'core_soft' of https://github.com/agiliopadua/lammps into combined-user-fep-soft-updates 
Resolved Conflicts:
	doc/src/Commands_pair.txt
	doc/src/pair_fep_soft.txt
	doc/src/pair_style.txt
	doc/src/pairs.txt
 2019-01-25 16:25:19 +01:00
Agilio Padua f2aab01e96 Approximation in tail correction better explained 2019-01-25 15:04:52 +01:00
Axel Kohlmeyer 272ff1dbdf link class2 soft-core pair styles from pair style overviews 2019-01-24 11:20:12 -05:00
Agilio Padua 06c8a67247 Updated broken links to pair_fep_soft 2019-01-24 17:10:39 +01:00
Axel Kohlmeyer 1e3cc7784b update false positives list for spell checking 2019-01-24 11:06:22 -05:00
Axel Kohlmeyer e83600eee3 make naming of extract-able parameters consistent across similar pair styles (a/b/cparm -> a/b/c) 2019-01-24 10:54:17 -05:00
Axel Kohlmeyer 5c09732dc3 file spelling 2019-01-24 10:49:47 -05:00
Axel Kohlmeyer 82905dc62d correctly spell "through" 2019-01-24 10:29:51 -05:00
Axel Kohlmeyer 89a3f60289 replace references to pair_lj_soft with pair_fep_soft in docs 2019-01-24 15:49:46 +01:00
Axel Kohlmeyer a6ecd3d08c Merge branch 'core_soft' of https://github.com/agiliopadua/lammps into combined-user-fep-soft-updates 
Resolved Conflicts:
	doc/src/compute_fep.txt
	doc/src/fix_adapt_fep.txt
 2019-01-24 15:41:41 +01:00
Axel Kohlmeyer 1be589fb33 Merge branch 'patch-2' of https://github.com/evoyiatzis/lammps into combined-user-fep-soft-updates 2019-01-24 15:35:52 +01:00
Axel Kohlmeyer 4464f62c8f another permission fix 2019-01-24 08:20:24 -05:00
Axel Kohlmeyer 985913bce2
Merge pull request #1297 from stevenvdb/add-user-yaff 
Add USER-YAFF package for MOF simulations with QuickFF
 2019-01-24 11:05:55 +01:00
Axel Kohlmeyer f88c5e147a
Merge pull request #1298 from jrgissing/bond/react-distance_constraints 
Bond/react: add reaction constraints support
 2019-01-24 10:55:22 +01:00
Axel Kohlmeyer 48542f1832 permission update for some bundled PDF files 2019-01-24 04:51:55 -05:00
Agilio Padua 0bfb34389b Consolidated doc of soft-core pair styles 2019-01-23 20:56:54 +01:00
Agilio Padua 012d5a55bf Consolidated doc for soft pair styles 2019-01-23 12:02:23 +00:00
jrgissing fbee21f495 distance constraint: clarify use case in docs 2019-01-22 23:22:51 -07:00
jrgissing 7a10ac2019 bond/react:reaction_constraints 
introduce a distance constraint between any two reaction-site atoms, in order for reaction to occur
 2019-01-22 23:14:58 -07:00
Evangelos Voyiatzis a5248090fa
Update fix_adapt.txt 2019-01-22 19:46:35 +01:00
Evangelos Voyiatzis ade023861d
Update compute_fep.txt 2019-01-22 19:42:52 +01:00
Evangelos Voyiatzis 24bede9fff
Update fix_adapt_fep.txt 2019-01-22 19:37:58 +01:00
Axel Kohlmeyer dd3dbfaee2 restore aphabetical order of improper styles 2019-01-22 12:26:51 -05:00
Steven Vandenbrande ca31147d00 Fix USER-YAFF documentation issues 2019-01-22 14:58:38 +01:00
Oliver Henrich 7ec6e4b262 Merge branch 'master' into user-cgdna 2019-01-22 13:06:42 +00:00
Oliver Henrich 874e4fdafc Corrected required input angular velocity -> momentum 2019-01-22 13:05:15 +00:00
Steven Vandenbrande 794bf5084c Implementation and documentation for USER-YAFF package 2019-01-22 10:09:10 +01:00
Evangelos Voyiatzis e789715d92
Update fix_adapt_fep.txt 2019-01-21 23:12:34 +01:00
Evangelos Voyiatzis cab3380b55
Updating the list of potentials in fix_adapt_fep.txt 
There are several potentials that contain the method extract() but they are not included in the "fix adapt" and "fix adapt/fep"
A small update of the list is attempted here. The same potentials might be added to the documentation of fix_adapt if it is useful.
 2019-01-20 13:35:40 +01:00
Axel Kohlmeyer 1e1f754d0c make gpu library Install.py use argparse module 2019-01-14 12:52:21 -05:00
jrgissing b0af54ac37 bond/react:limit reaction occurrences 2019-01-13 00:07:03 -07:00
Steve Plimpton 0cc9a445e8 add parallel dump file info to rerun doc page 2019-01-04 17:09:11 -07:00
Axel Kohlmeyer c26b2078ee
Merge pull request #1271 from akohlmey/next-patch-release 
Patch release 4 January 2019
 2019-01-03 22:28:55 -05:00
Axel Kohlmeyer 7323179de3 rename pair style lebedeva to lebedeva/z to be consistent with kolmolgorov/crespi/z 2019-01-03 17:30:16 -05:00
Axel Kohlmeyer 19e12aada5 Patch release 4 January 2019 2019-01-03 13:44:18 -05:00
Axel Kohlmeyer f96f98241c replace outdated moltemplate distribution with README explaining how to install the latest version 2019-01-03 00:39:58 -05:00