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14051 Commits

Author SHA1 Message Date
Axel Kohlmeyer 3e0cb9b463 rename examples to match usual naming conventions and add reference output. 2018-02-01 18:56:10 +01:00
Axel Kohlmeyer b70149e86a include added docpages in toctrees for sphinx 2018-02-01 18:50:25 +01:00
Axel Kohlmeyer 080ce422ae correct incorrect reference 2018-02-01 18:40:28 +01:00
Axel Kohlmeyer cc54848f7b adapt to current manual conventions 2018-02-01 18:40:17 +01:00
Christoph Junghans 3f967e3d84
cmake: add USER-MOFFF 2018-01-21 08:10:38 -07:00
Hendrik Heenen 5212e95787 added src/USER-MOFFF/README 2018-01-21 13:34:02 +01:00
Hendrik Heenen f7e2bf239f Added MOF-FF src, doc and example files 2018-01-21 11:40:48 +01:00
Steven J Plimpton 5e9d257ec2 patch 17Jan18 2018-01-17 13:00:48 -07:00
Steve Plimpton e1e6825eb2
Merge pull request #776 from numericalfreedom/lammps-tools-doxygen 
Small character corrections to the file Developer.dox.lammps
 2018-01-17 07:34:18 -07:00
Steve Plimpton 88a2f9fcc6
Merge pull request #775 from wmbrownIntel/user-intel-2018u1 
USER-INTEL: Adding compiler flag and small fix to tersoff/intel for 2…
 2018-01-17 07:34:08 -07:00
Steve Plimpton 480d7dd6ce
Merge pull request #774 from lammps/neigh-tweak 
small changes to recent PR to standardize with other npair styles
 2018-01-17 07:33:46 -07:00
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
Axel Kohlmeyer 1b91c0eab0 fix typo in docs resulting in broken link 2018-01-16 21:01:25 -05:00
Stan Moore 0c8af0704e Tweak to npair_halffull_newtoff.cpp 2018-01-16 16:43:25 -07:00
Steven J Plimpton f1901237be small changes to recent PR to standardize with other npair styles 2018-01-16 15:49:16 -07:00
Steve Plimpton 0cd864134d
Merge pull request #765 from stanmoore1/halffull_ghost 
Add ghost option to npair_halffull
 2018-01-16 15:39:07 -07:00
Steve Plimpton bf48f3e240
Merge pull request #758 from mkanski/ci-ReaxFF 
Modification of ReaxFF
 2018-01-16 13:04:20 -07:00
Steve Plimpton 23dda3d51b
Merge pull request #770 from numericalfreedom/lammps-tools-doxygen 
Tools for LAMMPS documentation for developers with the "doxygen" documentation platform
 2018-01-16 13:02:10 -07:00
Steve Plimpton 5d254855eb
Merge pull request #772 from akohlmey/improved-variable-error-reporting 
More improved variable error reporting
 2018-01-16 13:00:42 -07:00
Steve Plimpton 9a70f2d182
Merge pull request #773 from lammps/couple-simple 
update of COUPLE/simple examples
 2018-01-16 12:59:51 -07:00
Axel Kohlmeyer b95cf658c7 remove faulty line of code, left in by accident 2018-01-16 14:10:46 -05:00
Axel Kohlmeyer 709ce8a230 Merge branch 'neigh-identical-check' into couple-simple 
# Conflicts:
#	src/create_bonds.cpp
#	src/delete_atoms.cpp
 2018-01-16 14:09:21 -05:00
Axel Kohlmeyer 2ad823ffd4 correct check for identical requests 2018-01-16 14:08:18 -05:00
Axel Kohlmeyer 4c0cd5f1ad
add short bond cutoff warning also to USER-OMP 
This implements the warning about a total cutoff shorter than 2x bond cutoff also to the USER-OMP variant of reax/c
 2018-01-16 13:50:49 -05:00
Steven J Plimpton 8d37c89cb6 different bug fix for create_bonds, delete_atoms neigh list issue 2018-01-16 11:32:37 -07:00
Steven J Plimpton 21ff4407ab update of COUPLE/simple examples 2018-01-16 10:48:38 -07:00
Dr. Nandor Tamaskovics f2c0c4a7d1 Merge branch 'lammps-tools-doxygen' of https://github.com/numericalfreedom/lammps into lammps-tools-doxygen 2018-01-16 18:39:08 +01:00
Dr. Nandor Tamaskovics 1640066132 Merge remote-tracking branch 'lammps-origin/master' into lammps-tools-doxygen 2018-01-16 18:38:12 +01:00
Axel Kohlmeyer 3b1ec14a68
add a warning if the bonded cutoff is large 
This should print a warning when 2x the bonded interaction cutoff list larger then other cutoffs, as was the setting before the performance optimization with the change in 2690075405
 2018-01-16 12:01:47 -05:00
Axel Kohlmeyer 01cfb710ff propagate printing variable name with error deeper into the code 
this now covers a large set of cases where the variable name can be printed.
it also is complete for the current code, since no more default arguments are required
 2018-01-16 11:31:20 -05:00
Axel Kohlmeyer 3de39c70c1 print variable name with errors only for known variables. 
this makes errors for "anonymous" evaluations (if statement, immediate variables) less confusing.
 2018-01-16 11:29:48 -05:00
Dr. Nandor Tamaskovics 86ed55599d The bash shell script doxygen.sh has been revised. 2018-01-16 17:28:58 +01:00
Steve Plimpton e798cdf31f
Merge pull request #771 from stanmoore1/reax_example 
Add ReaxFF Example
 2018-01-16 09:05:36 -07:00
Steve Plimpton 97dd812647
Merge pull request #769 from rbberger/cmake_compilation_fixes 
CMake compilation fixes
 2018-01-16 09:04:04 -07:00
Steve Plimpton e07a6d1e34
Merge pull request #768 from akohlmey/collected-doc-fixes 
collected documentation fixes
 2018-01-16 09:03:45 -07:00
Steve Plimpton 6e37272c9d
Merge pull request #764 from akohlmey/improved-variable-error-reporting 
Improved error messages when defining or evaluating variables
 2018-01-16 09:02:20 -07:00
Steve Plimpton 6bd6e62767
Merge pull request #763 from stanmoore1/kk_neighlist 
Enhance Kokkos Neighbor lists
 2018-01-16 09:01:15 -07:00
Steve Plimpton 57dd6c78c1
Merge pull request #761 from stanmoore1/kk_snap 
Kokkos version of Pair SNAP and ZBL
 2018-01-16 09:00:52 -07:00
Steve Plimpton 9e413bf57a
Merge pull request #760 from akohlmey/info-coeffs 
New "coeffs" keyword added to "info" command
 2018-01-16 09:00:34 -07:00
Stan Moore b374813104 Add reax example 2018-01-16 08:50:30 -07:00
Michael Brown 07ddb5e62c USER-INTEL: Adding compiler flag and small fix to tersoff/intel for 2018u1 compilers. 2018-01-15 23:54:48 -08:00
Stan Moore 72b479d42e Add missing return value in pair_snap_kokkos 2018-01-15 11:01:07 -07:00
Axel Kohlmeyer c8b5d83cc7 mention tool/doxygen folder in tools section and refer to README file 2018-01-15 10:43:30 -05:00
smoore a5998179bf Fix issues with Kokkos skip lists 2018-01-15 08:23:39 -07:00
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 f37f4f0041 support more cases where the variable name is reported on errors 2018-01-14 17:56:03 -05:00
Richard Berger d2983caad4 CMake: limit visibility of COLVARS lepton library headers 2018-01-14 18:01:19 +01:00
Richard Berger 2b7c233791 Simplify change to CMake build for USER-COLVARS 2018-01-14 08:44:50 +01:00
smoore 9e35e76b8c Fix issues in Kokkos npair_halffull and npair_skip 2018-01-13 21:32:59 -07:00