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371 Commits

Author SHA1 Message Date
Axel Kohlmeyer 22288e06b7
Merge branch 'master' into fix-compiler-warnings 2019-10-25 14:07:50 -04:00
Richard Berger 648799ef5e Add PowerTools repo for CentOS8 Singularity definition 
Some packages were moved into a PowerTools repo in RHEL8/CentOS8.
 2019-10-22 11:22:34 -04:00
Axel Kohlmeyer 054766a380
include info about ready-to-use images uploaded to the singularity library 2019-10-21 14:54:30 +02:00
Axel Kohlmeyer 5200d60dd3
update singularity definition files 2019-10-21 11:29:08 +02:00
Axel Kohlmeyer b4b071ee60
modernize fortran code in eam_database to replace features no longer allowed in fortran 2018 2019-10-21 03:12:17 -04:00
Axel Kohlmeyer 27d3d44297
step version number, year, and changelog to reflect fixed bug. 2019-10-17 09:30:08 -04:00
Axel Kohlmeyer 645df22eb9
fix incorrect order of commandline flags in example 2019-10-15 16:36:50 +02:00
Axel Kohlmeyer e4bbfc992b
Singularity definition files for compiling LAMMPS 2019-10-15 16:22:08 +02:00
Axel Kohlmeyer d4dbc32ba2
Merge pull request #1672 from akohlmey/dump-with-unit 
Add ITEM: UNITS line to native text format dumps
 2019-09-19 10:31:13 -04:00
Axel Kohlmeyer eab66f27fd
Merge pull request #1681 from akohlmey/collected-small-fixes 
Collected small changes for next patch release
 2019-09-19 10:27:54 -04:00
Axel Kohlmeyer c26c8aca4f
get rid of (evil) tabs and trailing whitespace in bundled Pizza.py components 2019-09-19 07:34:27 -04:00
Axel Kohlmeyer 28b634f20d
some more whitespace cleanup 2019-09-17 16:10:32 -04:00
Axel Kohlmeyer fd63b08f99
Merge branch 'reorder_remd_traj' of github.com:tanmoy7989/lammps into reorder_remd_traj 
# Conflicts:
#	tools/replica/reorder_remd_traj.py
 2019-09-17 16:09:13 -04:00
Axel Kohlmeyer 636a8aaef9
whitespace cleanup, mention pip install --user 2019-09-17 16:06:12 -04:00
Axel Kohlmeyer 4bbe4c73aa
whitespace cleanup 2019-09-10 09:38:44 -04:00
tanmoy.7989 91a1971977 added a line to tools/README and fixed the alphabetical ordering in docs 2019-09-09 02:04:59 -07:00
tanmoy.7989 f41a1f8303 vectorized in parts and made changes as suggested by evoyiatzis 2019-09-08 10:43:22 -07:00
tanmoy.7989 bbb0f5740e link to data.peptide was deleted by me by mistake. Now that it's re-added, I revoked (un-necessary) changes I made since to the in.peptide input script 2019-09-06 11:18:33 -07:00
Axel Kohlmeyer 82423ff4e0
re-add link to data.peptide file, which got deleted somehow 2019-09-06 13:25:31 -04:00
tanmoy.7989 4fdece59a5 (a)fixed bz2 import, (b)linked to data.peptide in examples/peptide, (c)added a runlog 2019-09-05 21:19:57 -07:00
tanmoy.7989 21699b89e0 python tool to reorder replica traj 2019-09-04 15:26:10 -07:00
Axel Kohlmeyer fd55d7d367
update list of known LAMMPS keywords 2019-06-11 11:15:04 -04:00
Axel Kohlmeyer 3d5db63381
minor cleanup 2019-06-11 10:36:04 -04:00
Vishnu V. Krishnan 239dfe163c
Simplify vim-files 
Resolves #1500
 2019-06-08 17:11:20 +05:30
julient31 11f223416c Commit JT 051319 
- added a cubic anisotropy in fix_precession_spin
- added associated doc and examples
- corrected neb/spin commands in doc/src/
- added tools/spin/ description
 2019-05-13 16:59:39 -06:00
Axel Kohlmeyer 0fac0e18d1
no need for libm or GSL to compile the interpolate code 2019-04-27 17:50:12 -04:00
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