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
5d254855eb
Merge pull request #772 from akohlmey/improved-variable-error-reporting
...
More improved variable error reporting
2018-01-16 13:00:42 -07:00
9a70f2d182
Merge pull request #773 from lammps/couple-simple
...
update of COUPLE/simple examples
2018-01-16 12:59:51 -07:00
b95cf658c7
remove faulty line of code, left in by accident
2018-01-16 14:10:46 -05:00
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
2ad823ffd4
correct check for identical requests
2018-01-16 14:08:18 -05:00
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
8d37c89cb6
different bug fix for create_bonds, delete_atoms neigh list issue
2018-01-16 11:32:37 -07:00
21ff4407ab
update of COUPLE/simple examples
2018-01-16 10:48:38 -07:00
f2c0c4a7d1
Merge branch 'lammps-tools-doxygen' of https://github.com/numericalfreedom/lammps into lammps-tools-doxygen
2018-01-16 18:39:08 +01:00
1640066132
Merge remote-tracking branch 'lammps-origin/master' into lammps-tools-doxygen
2018-01-16 18:38:12 +01:00
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
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
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
86ed55599d
The bash shell script doxygen.sh has been revised.
2018-01-16 17:28:58 +01:00
e798cdf31f
Merge pull request #771 from stanmoore1/reax_example
...
Add ReaxFF Example
2018-01-16 09:05:36 -07:00
97dd812647
Merge pull request #769 from rbberger/cmake_compilation_fixes
...
CMake compilation fixes
2018-01-16 09:04:04 -07:00
e07a6d1e34
Merge pull request #768 from akohlmey/collected-doc-fixes
...
collected documentation fixes
2018-01-16 09:03:45 -07:00
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
6bd6e62767
Merge pull request #763 from stanmoore1/kk_neighlist
...
Enhance Kokkos Neighbor lists
2018-01-16 09:01:15 -07:00
57dd6c78c1
Merge pull request #761 from stanmoore1/kk_snap
...
Kokkos version of Pair SNAP and ZBL
2018-01-16 09:00:52 -07:00
9e413bf57a
Merge pull request #760 from akohlmey/info-coeffs
...
New "coeffs" keyword added to "info" command
2018-01-16 09:00:34 -07:00
b374813104
Add reax example
2018-01-16 08:50:30 -07:00
07ddb5e62c
USER-INTEL: Adding compiler flag and small fix to tersoff/intel for 2018u1 compilers.
2018-01-15 23:54:48 -08:00
72b479d42e
Add missing return value in pair_snap_kokkos
2018-01-15 11:01:07 -07:00
c8b5d83cc7
mention tool/doxygen folder in tools section and refer to README file
2018-01-15 10:43:30 -05:00
a5998179bf
Fix issues with Kokkos skip lists
2018-01-15 08:23:39 -07:00
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
f37f4f0041
support more cases where the variable name is reported on errors
2018-01-14 17:56:03 -05:00
d2983caad4
CMake: limit visibility of COLVARS lepton library headers
2018-01-14 18:01:19 +01:00
2b7c233791
Simplify change to CMake build for USER-COLVARS
2018-01-14 08:44:50 +01:00
9e35e76b8c
Fix issues in Kokkos npair_halffull and npair_skip
2018-01-13 21:32:59 -07:00
7a78875911
Fix issues in Kokkos pair snap and zbl
2018-01-13 21:31:11 -07:00
1cfc3118cc
CMake: remove BUILD_SHARED_LIBS requirement from PYTHON package
2018-01-13 22:17:23 +01:00
23e8fb0542
Update CMake build for USER-COLVARS
2018-01-13 21:57:24 +01:00
72eb2dab52
Add missing math.h header
2018-01-13 20:41:05 +01:00
f6075c9d2c
One last tweak to npair_halffull_newtoff.cpp
2018-01-12 16:12:57 -07:00
24f1889b02
Only include ghosts for newton off, since this style exists as a standalone build, but the newton on method doesn't
2018-01-12 16:10:42 -07:00
dea8d592da
Optimize npair_halffull styles; the number of i atoms, whether owned or ghost, must match between the child half list and parent full list
2018-01-12 15:51:54 -07:00
52d3e98f3b
Fix issue in npair_skip_kokkos
2018-01-12 15:45:24 -07:00
6e3acce3be
Relax restriction in neighbor.cpp
2018-01-12 15:44:11 -07:00
1ec54827d6
Add Kokkos halffull neighbor list capability
2018-01-12 15:41:59 -07:00
61ebf6265a
address some formatting/markup issues reported by Nandor Tamaskovics
2018-01-12 12:50:02 -05:00
190cc78034
add dummy doc files for not-yet-implemented features
2018-01-12 12:29:03 -05:00
5863f115dd
correctly escape 'a_ ' text, which is not a reference unlike 'a_b '
2018-01-12 12:26:50 -05:00
75d259f5ee
improve PDF reader compatibility for the created PDF file.
2018-01-12 12:00:53 -05:00
3b1b9a2cbf
replace non-ASCII quotation marks with ASCII equivalent
2018-01-12 11:30:27 -05:00
17b6a4c3cd
Added more permanent citation
2018-01-12 11:47:35 +01:00
1c10c78684
Add ghost option to npair_halffull
2018-01-11 15:15:04 -07:00
26917280be
state name of the affected variable in error messages where possible
2018-01-11 15:01:08 -05:00
