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16419 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 2b5073fb90
Merge pull request #1311 from akohlmey/correct-delete-callback 
Correct calls to atom->delete_callback()
 2019-02-01 17:25:25 +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 bc2eeaf22a remove extraneous atom->delete_callback() 2019-01-31 19:10:14 -05:00
Axel Kohlmeyer 5c927d484e add missing atom->delete_callback() 2019-01-31 19:09:59 -05:00
Axel Kohlmeyer 8ee1fefe19 add pointer to README and Manual to help. 2019-01-31 18:46:43 -05:00
Axel Kohlmeyer 763dda64af update lib/gpu/README to current state 2019-01-31 18:45:17 -05:00
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 f28ab59695 output bounding box info for regions, if present 2019-01-31 18:12:56 -05:00
Axel Kohlmeyer 2e60e461a0 must convert regions bounding box to lattice coordinates before checking to reduce lattice creation range 2019-01-31 18:12:37 -05:00
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 cdb07f9f06
Merge pull request #1310 from akohlmey/reaxc-with-qeq-shielded 
Support using fix qeq/shielded with pair style reax/c
 2019-01-31 22:57:31 +01:00
Axel Kohlmeyer 0cce3387bb
Merge pull request #1285 from Adrian-Diaz/4D-grow-memory 
Added 4D memory grow routine
 2019-01-31 17:32:45 +01:00
Axel Kohlmeyer a93d8dda3c add example input and logfiles for using fix qeq/shielded with pair style reax/c 2019-01-31 14:14:29 +01:00
Axel Kohlmeyer 327ca344ff make fix qeq/shielded fully compatible with pair style reax/c as a replacement for fix qeq/reax 2019-01-31 13:49:05 +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 ae6fb92478 whitespace cleanup 2019-01-31 12:02:43 +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 8338969af5 bugfix for create_atoms region optimization 2019-01-31 11:46:03 +01:00
Axel Kohlmeyer ef5c327f74 Merge branch 'master' into collected-small-changes 2019-01-31 11:45:15 +01:00
Axel Kohlmeyer 06d5c1d62f
Merge pull request #1279 from akohlmey/create-atoms-bounding-box 
Optimize performance of create_atoms for large boxes and small regions
 2019-01-31 09:39:55 +01:00
Axel Kohlmeyer 0e1c6082b0
Merge pull request #1309 from PabloPiaggi/pair_entropy 
compute entropy/atom - enhancement/optimization
 2019-01-31 09:36:44 +01:00
Axel Kohlmeyer a59a385d6e fix storage size for internal compute ids in fix plumed 2019-01-31 02:55:37 -05:00
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 1d6bf1ea7d add overlooked entry to Purge.list 2019-01-30 18:05:10 +01:00
PabloPiaggi ccdfde4978 Update example log file 2019-01-30 15:16:35 +01:00
PabloPiaggi 136e247cd8 compute entropy/atom - Use NL with ghost atoms only with avg yes 2019-01-30 14:59:23 +01:00
Axel Kohlmeyer 8cc593fe6b
Merge pull request #1308 from agiliopadua/master 
Fix in extract() method of pair_thole
 2019-01-30 08:12:30 +01:00
Agilio Padua f7bb48102f Fix in extract() method of pair_thole 2019-01-29 18:03:12 +01:00
Axel Kohlmeyer bad6c8aa35 Patch release 30 January 2019 2019-01-29 13:37:50 +01:00
Axel Kohlmeyer 1465352454 some cleanups and small bugfixes to conform better with python conventions 2019-01-28 17:37:05 -05:00
Axel Kohlmeyer 0cae619320 increase portability by using python modules instead of subprocesses 2019-01-28 15:54:19 -05:00
Axel Kohlmeyer b7ab017a76 improve portability by using shutil.copyfile, os.path.join, and make -C 2019-01-28 17:44:46 +01:00
Axel Kohlmeyer 4fcfa4987a fix typo 2019-01-28 14:56:47 +01:00
Axel Kohlmeyer 53f600ea35 use enable all available plumed modules when using download/compile mode 2019-01-26 09:55:48 -05:00
Axel Kohlmeyer 8c323a7056 fix issue in USER-PLUMED due to incorrectly copying strings 2019-01-26 05:58:41 -05:00
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 fb30d2d078
Merge pull request #1303 from pastewka/19_dump_nc1 
ENH: Output computes/fixes of with arbitrary number of columns to NetCDF
 2019-01-25 10:42:46 +01:00
Axel Kohlmeyer 1927659fb1 fix cut-n-paste bug in extract_setting() method 2019-01-24 17:55:37 +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