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395 Commits

Author SHA1 Message Date
julient31 7c3f619e13 Commit JT 042519 
- moved examples/SPIN/gneb/interpolate/ toward
tools/spin/interpolate/gneb
- added gneb in the command files in doc/src
- modified the error messages in neb_spin.h/cpp
 2019-04-25 09:18:33 -06:00
Axel Kohlmeyer 13cf357f66
document in README, that msi2lmp is now build alongside LAMMPS 2019-04-07 00:47:10 -04:00
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Axel Kohlmeyer f96f98241c replace outdated moltemplate distribution with README explaining how to install the latest version 2019-01-03 00:39:58 -05:00
Axel Kohlmeyer 980f7e3b36 Merge branch 'collected-small-changes' into collected-post-stable-patches 2018-12-16 20:41:02 -05:00
Axel Kohlmeyer 5508438ba1 make included Pizza.py code for reading dumps compatible with python 2.7 2018-12-16 18:30:44 -05:00
Axel Kohlmeyer e86b933862 remove meam and reax from documentation 2018-12-10 14:38:25 -05:00
Axel Kohlmeyer dedc6cf20c remove obsolete reax tools and rename pair_meam.txt to pair_meamc.txt 2018-12-10 14:16:08 -05:00
Axel Kohlmeyer 6f7b052e24
update comments and remove commented code 2018-11-19 16:38:25 -05:00
Diego Ugarte 9b401b6ed0 fix topology parsing 2018-11-20 06:22:32 +09:00
Axel Kohlmeyer ab8215a669 remove dead code 2018-11-09 01:09:31 -05:00
Axel Kohlmeyer fe04147ee0 fix typo 2018-11-09 01:09:22 -05:00
Axel Kohlmeyer 7ed6cab040 do not generate illegal dihedrals, e.g. from 3-membered rings 2018-11-05 20:35:43 -05:00
Axel Kohlmeyer 50fe209782 mention -*- cookie for switching emacs modes and clarify file pattern text 2018-07-31 10:24:36 +02:00
HaoZeke a00d7becc3
emacs: Major readme update and refactor 
Also update the license and switch to GPL v2 like lammps
 2018-07-30 20:51:28 +05:30
HaoZeke 2c9e96be11
emacs: Stop forcing filename patterns 2018-07-30 19:58:18 +05:30
HaoZeke 82fc3b99d9
emacs: Update mode file 
This is a squashed commit including the following changes:
1) Update mode header
2) Clean up white-space
3) Fix free variable warning
4) Add proper file ending stuff
5) Rename to keep conventional naming scheme
6) Updates to the readme
7) Update to conform to `package-lint` criteria
8) Add license header
9) Add in-file instructions
 2018-07-30 19:37:01 +05:30
Axel Kohlmeyer 7abc960d39 import moltemplate 2.8.6 from andrew jewett 2018-06-28 08:18:35 -04:00
Yossi Eliaz 9c3296aad2 Tools/Matlab: Allow to read LAMPPS output field 
Some output fields have attributes attached on the same
line. e.g. "ITEM: BOX BOUNDS pp pp pp". This patch replaced all
the strcmpi to strncmpi in order to limit the number of character
compared with LAMPPS outputs.

Signed-off-by: Yossi Eliaz <eliaz123@gmail.com>
 2018-03-12 13:45:13 -05:00
Axel Kohlmeyer 54dc73c771 correctly compute adjusted box lengths for triclinic boxes. code taken from topotools 2018-02-19 14:06:26 +01:00
Axel Kohlmeyer 7bd089aa6d fix typo 2018-02-19 14:05:50 +01:00
Evangelos Voyiatzis b220b647d4
Update error.cpp 
When compiling with g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18) an error occurs: 
error.cpp: In member function ‘void Error::generate_error(unsigned int, std::string, std::string)’:
error.cpp:146: error: ‘exit’ was not declared in this scope
The fix is to include the #include <cstdlib> where the exit() function is decleared in the error.cpp file
 2018-02-16 10:49:08 +01:00
Axel Kohlmeyer 9fd1e47968 ignore generated/copied files 2018-01-28 06:24:03 -05:00
Axel Kohlmeyer 6753977837 recreate 1ac7 input deck with up to date tools and LAMMPS binary. 2018-01-28 06:23:09 -05:00
Axel Kohlmeyer 031812b2bf recreate 1gb1 input deck with CMAP included. 2018-01-28 06:22:03 -05:00
Axel Kohlmeyer ba68548e38 clarify ch2lmp commands purpose in tools section 2018-01-28 06:19:33 -05:00
Dr. Nandor Tamaskovics 9b12984378 Small correction in image caption in Developer.dox.lammps 2018-01-17 14:46:44 +01:00
Dr. Nandor Tamaskovics 8d29f64236 Small character corrections to the file Developer.dox.lammps 2018-01-17 14:05:30 +01:00
Dr. Nandor Tamaskovics 86ed55599d The bash shell script doxygen.sh has been revised. 2018-01-16 17:28:58 +01:00
Dr. Nandor Tamaskovics 26d6f6d1f1 Tools for LAMMPS documentation with the "doxygen" documentation platform 
are provided.

        New directory: tools/doxygen

        New file:      tools/doxygen/Developer.dox.lammps
        New file:      tools/doxygen/Doxyfile.lammps
        New file:      tools/doxygen/doxygen.sh
        New file:      tools/doxygen/README

The Developer.dox.lammps file contains a slightly revised version of the
Developer.pdf file adopted to the LAMMPS "doxygen" documentation.

The Doxyfile.lammps file is a first proposal for a LAMMPS "doxygen"
documentation flavor and can be adjusted to specific requirements.

The "doxygen.sh" shell script generates the LAMMPS "doxygen"
documentation.

Detailed instructions can be found in the README file.
 2018-01-15 15:42:31 +01:00
Axel Kohlmeyer 4c71beb024 cleanup/simplification of compilation for fix phonon analysis tool "phana" 
- include the used tricubic functions directly as static functions
- silence compiler warnings
- define f2c.h imported data types directly or use C equivalents
- since the direct LAPACK API was called and not cLAPACK, declare LAPACK interface and depend only on LAPACK
- add proper dependencies
- disable automatic minor version number generation. step version manually.
- comment out optional spglib functionality by default
 2017-09-30 12:12:15 -04:00
Julien Devemy a5b65c1af4 Mods for extra/special/per/atom and add toluene 2017-08-31 15:03:04 +02:00
Axel Kohlmeyer de0fdbed6c moltemplate bugfix update 2017-08-24 07:12:45 -04:00
Axel Kohlmeyer 12150ffa73 add moltemplate version 2017-8-22 2017-08-23 07:54:56 -04:00
Axel Kohlmeyer 57aafba7c3 remove old moltemplate version 2017-08-23 07:54:05 -04:00
Axel Kohlmeyer 60e14f1490 add comment to msi2lmp README about symmetry limitations 2017-08-14 08:54:26 -04:00
Christoph Junghans f717a70638 tools/Makefile: remove remains of data2xmovie 
data2xmovie was removed in e110d6961a
 2017-07-11 16:16:03 -06:00
Axel Kohlmeyer dec36e9bfe fix typos and remove trailing whitespace 2017-04-17 17:40:57 -04:00
Axel Kohlmeyer dd90c860ee refactor msi2lmp documentation to emphasize lack of active development 
- put a note into the manual
- reorder contents of the README file
- request for information should be sent to lammps-users
- add list of known missing features
 2017-04-17 17:40:21 -04:00
Steve Plimpton dcede304df changes for next patch, 2d disc options for spheres, fix external upgrade, bug fixes for fix ave/chunk for density calcs, Aidan doc page citation deconvolution 2017-03-21 08:56:37 -06:00
Axel Kohlmeyer 82d952ae0e mention NumPy dependency instead of Numeric for python tools 2017-03-20 17:26:19 -04:00
Axel Kohlmeyer 47d6451d03 fix compilation for pymol_asphere tool 2017-03-20 17:18:24 -04:00
Axel Kohlmeyer e110d6961a remove obsolete tools and files 2017-03-20 17:17:35 -04:00
Axel Kohlmeyer a42b0b7dcb update colvars abf integrate tool from git repo 2017-03-20 17:04:16 -04:00
Axel Kohlmeyer 03828b5836 adapt binary2txt.cpp source to current coding conventions 2017-03-20 16:57:32 -04:00
Axel Kohlmeyer ecf17621aa more permission fixes 2017-03-20 16:25:06 -04:00
Axel Kohlmeyer f0c6ed004d remove xmovie 2017-03-20 16:24:38 -04:00
Richard Berger 08baaa9d8e Fix more typos in tools 2017-03-07 01:00:25 -05:00
Richard Berger dd76ac5010 Fix typos in tools folder 2017-03-05 21:18:01 -05:00
Richard Berger e261bef7bb Spelling fixes in source files 2017-03-05 18:30:39 -05:00
Agilio Padua 27aca14094 Updated polarizer.py to use coul/long/cs 2017-02-04 15:02:08 +01:00
Axel Kohlmeyer 34cb4027df make formatting comment consistent 2017-01-11 07:46:07 -05:00
Axel Kohlmeyer 7ddb6670c0 fix typo 2016-11-30 00:12:35 -05:00
Axel Kohlmeyer 9e9d9d5aa5 update bundled version of moltemplate to v1.40 2016-11-21 11:34:42 -05:00
Axel Kohlmeyer 93d393aa69 permission cleanup in tools folder 2016-10-28 10:48:35 -04:00
sjplimp 54fc194e5b Merge pull request #199 from akohlmey/small-changes 
Collected small changes and bugfixes
 2016-10-06 15:49:24 -06:00
Axel Kohlmeyer 0853cdbe6f update reference data files for updated/corrected clayff parameters 2016-10-06 11:47:08 -04:00
Axel Kohlmeyer 22ce671804 improved whitespace handling in msi2lmp for force fields and topologies 2016-10-06 11:16:59 -04:00
Axel Kohlmeyer d7d321a512 some more updates to the README file to reflect the inclusion of the CMAP example and renamed file names 2016-10-05 18:41:45 -04:00
Axel Kohlmeyer 326fdf2cf1 added 1GB1 example from Robert Latour and update 1AC7 example files 2016-10-05 18:20:09 -04:00
Axel Kohlmeyer f32819dd10 added tweak to write out the command line used for the conversion to the beginning of the LAMMPS input 2016-10-05 18:13:46 -04:00
Axel Kohlmeyer c07a01c661 import updated README file for charmm2lammps.pl with CMAP support 2016-10-05 18:11:52 -04:00
Axel Kohlmeyer 6e719f2d94 remove trailing whitespace 2016-10-03 07:07:28 -04:00
Axel Kohlmeyer 45d2cc2895 permission update for ch2lmp tool folder 2016-10-03 07:03:42 -04:00
Axel Kohlmeyer 690f91300b rebuild charmm2lammps example output files with updated tools 2016-10-03 06:58:51 -04:00
Axel Kohlmeyer 3b94627dfe properly handle -nohints flag, make -cmap flag take version as option. step version number 2016-10-03 06:52:30 -04:00
Axel Kohlmeyer c2e11dffa2 import updated charmm2lammps.pl script from Rober Latour 2016-10-02 20:33:20 -04:00
sjplimp 8a6e5ed3ce git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15637 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-09-23 22:59:43 +00:00
sjplimp 863a3d3319 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15163 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-06-14 13:59:39 +00:00
sjplimp d7c5025530 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15068 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-05-31 13:58:37 +00:00
sjplimp bfa988207e git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14448 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2016-01-15 15:39:44 +00:00
sjplimp 074d5962c8 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14367 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2015-12-15 15:59:11 +00:00
sjplimp 5f802f86b5 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14366 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2015-12-15 15:59:01 +00:00
sjplimp b857237fef git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14269 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2015-11-19 15:34:38 +00:00
sjplimp 0aa77408f8 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14219 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2015-10-30 19:46:30 +00:00
sjplimp 01e0beda67 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14218 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2015-10-30 19:44:45 +00:00
sjplimp 2ed7d366a6 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14057 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2015-09-24 20:16:09 +00:00
sjplimp 16eed7a053 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13902 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2015-08-19 14:39:33 +00:00
sjplimp 7be9bc38a2 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13900 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2015-08-19 14:33:40 +00:00
sjplimp 24bf97204b git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13881 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2015-08-14 14:56:57 +00:00
sjplimp d7e358c359 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13833 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2015-08-04 20:56:54 +00:00
sjplimp b0dec93ffb git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13826 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2015-08-04 18:54:11 +00:00
sjplimp 57ed470003 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13825 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2015-08-04 18:48:13 +00:00
sjplimp d58afbcc48 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13730 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2015-07-27 14:58:04 +00:00
sjplimp dce226f164 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13410 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2015-04-14 14:18:40 +00:00
sjplimp d510bb54ef git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12924 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2015-01-09 17:04:59 +00:00
sjplimp b92650b918 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12922 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2015-01-09 16:58:58 +00:00
sjplimp b2e008ee04 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12771 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2014-11-24 17:12:48 +00:00
sjplimp 997f7a8845 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12769 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2014-11-24 17:02:36 +00:00
sjplimp 3a10de35be git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12750 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2014-11-20 16:08:15 +00:00
sjplimp 89c7a5df32 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12504 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2014-09-12 14:13:43 +00:00
sjplimp 7e3fd44a0b git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12303 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2014-08-13 14:04:13 +00:00
sjplimp 0553f4af2b git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12168 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2014-07-02 14:30:06 +00:00
sjplimp 4e3bc9d059 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12053 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2014-05-30 13:48:37 +00:00
sjplimp 474a7279e2 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11995 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2014-05-15 13:23:10 +00:00
sjplimp db78f042ef git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11955 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2014-05-09 15:34:57 +00:00
sjplimp 4a1807d397 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11915 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2014-05-06 15:15:48 +00:00
sjplimp acae56ce82 git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11914 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2014-05-06 15:15:35 +00:00
sjplimp 6883b645fa git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11898 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2014-05-02 19:17:28 +00:00
sjplimp 9a0d1c765b git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11897 f3b2605a-c512-4ea7-a41b-209d697bcdaa 2014-05-02 19:17:02 +00:00