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1107 Commits

Author SHA1 Message Date
Axel Kohlmeyer 79833f9b83
Merge pull request #2521 from rbberger/python_package 
Turn LAMMPS Python module into Python package
 2020-12-17 17:06:03 -05:00
Richard Berger bcb89a1d90
Honor DESTDIR for packaging 2020-12-17 12:13:06 -05:00
Axel Kohlmeyer f7e0bd45f3
Merge pull request #2520 from akohlmey/add-pgi-preset 
Add a CMake preset and some workarounds for using PGI (Nvidia) compilers with LAMMPS
 2020-12-16 21:30:04 -05:00
Yaser Afshar 47d18c9f90
Add KIM_EXTRA_UNITTESTS option 
Add KIM_EXTRA_UNITTESTS option which defaults to OFF
and can be enabled on request to add a corresponding
pre-processor define to do extra tests.
 2020-12-15 15:48:49 -06:00
Richard Berger aca2eefce5
Transform LAMMPS Python module into package 
- Moves lammps.py into its own package
- Imports entire module in __init__.py
- Changes both how legacy and CMake build systems install
- Added traditional setup.py for Python-only installation

Note: the CMake install target runs setup.py build and install
in a way that produces files in CMAKE_BINARY_DIR/python instead
of python/build. This is to maintain out-of-source compilation
support.
 2020-12-15 15:11:21 -05:00
Axel Kohlmeyer 65dc5c0351
work around PGI compiler issues 2020-12-15 14:32:18 -05:00
Axel Kohlmeyer f7dc7e3f3f
add preset for use with PGI compilers (tested with version 20.11) 2020-12-15 14:31:40 -05:00
Ryan S. Elliott 7f29c56c8f
update for kim-api-2.2.1 2020-12-14 00:03:59 -06:00
Axel Kohlmeyer cc222791a5
use variables to infer filenames from original .pyx source 2020-12-09 10:47:06 -05:00
Axel Kohlmeyer ddcd5a3c2e
small CMake tweaks and cleanups 2020-12-09 10:28:12 -05:00
Axel Kohlmeyer c4ee2f2e42
don't need Python interpreter for compiling the PYTHON package 2020-12-08 00:28:16 -05:00
Axel Kohlmeyer 5b6b327a5d
fix CMake errors 2020-12-08 00:04:54 -05:00
Axel Kohlmeyer 280c19cf32
rename CMake configuation variable to MLIAP_ENABLE_PYTHON to be more consistent with other packages 2020-12-07 17:46:54 -05:00
Axel Kohlmeyer 3f5a896aab
update build system to make it auto-adapt to include python support or not into MLIAP 2020-12-07 17:35:10 -05:00
Aidan Thompson 3c34bdfded Updated the build files 2020-12-03 19:04:53 -07:00
Aidan Thompson 664ed0f850 Merge remote-tracking branch 'origin/mliappy2' into mliappy3 2020-12-03 17:37:26 -07:00
Stan Moore 369197fd5e Update KOKKOS.cmake 2020-11-30 10:55:40 -07:00
Nicholas Lubbers 35f2c9bdf2 Several improvements to capabilities and build. 
- cmake fixed, no longer needs numpy headers.
- models can be loaded from an external interepreter.
 2020-11-26 12:40:28 -07:00
Ryan S. Elliott c247a4f709
More adjustments 2020-11-24 21:06:27 -06:00
Ryan S. Elliott 8faee10da5
Hack to work with preinstalled kim-api-2.1.3 2020-11-24 20:37:17 -06:00
Ryan S. Elliott c3e012c70c
KIM.cmake changes to support 2.1.3 kim-api too 2020-11-23 16:53:25 -06:00
Ryan S. Elliott 0f3b0eabd3
Adjust KIM.cmake to continue to work with kim-api < 2.2.0 2020-11-23 16:42:58 -06:00
Ryan S. Elliott 7ec7430c6e
Update KIM.cmake for kim-api-2.2.0 2020-11-19 13:29:16 -06:00
Axel Kohlmeyer 552dc7fba9
whitespace 2020-11-10 18:05:06 -05:00
Axel Kohlmeyer 2f3cbfed13
add CMake code to download and compile libyaml if not found locally 2020-11-10 17:58:26 -05:00
Nicholas Lubbers 7c1634e57f Squashed commit for MLIAPPY package 
Includes CMAKE install, doc updates, example files.
 2020-11-06 13:12:59 -07:00
Axel Kohlmeyer 9a3f935c9b
do not include polyfill.js anymore 2020-10-27 20:17:59 -04:00
Richard Berger 6af2da7603
Correct path for icons and .desktop file 2020-10-26 23:56:55 -04:00
Axel Kohlmeyer 4475a095ce
Merge pull request #2453 from rbberger/cmake_gitversion_fix 
Enable gathering of git info with git v1.8.3.1
 2020-10-26 18:45:52 -04:00
Richard Berger f7d9cf813f
Enable gathering of git info with git v1.8.3.1 
The -C flag wasn't supported back then. The workaround is to change the
working directory via CMake. This issue was detected while building on
CentOS 7.
 2020-10-26 17:26:46 -04:00
Axel Kohlmeyer c51d2a286a
call resource compiler to include icon files into LAMMPS shell on Windows 2020-10-23 20:06:21 -04:00
Axel Kohlmeyer 8854e7b8de
Add desktop integration for LAMMPS shell 2020-10-23 00:20:15 -04:00
Axel Kohlmeyer 1b358603c2
simplify 2020-10-20 18:52:53 -04:00
Axel Kohlmeyer 7297ed3115
apply stack-protector fix required by newer versions of MinGW, e.g. on Fedora 33 2020-10-19 21:59:27 -04:00
Axel Kohlmeyer eab5d68a09
move SWIG support to tools/swig folder 2020-10-18 08:19:20 -04:00
Axel Kohlmeyer fcbbc51a33
add minimally tested swig wrapper for Lua, Perl5, Python, and Tcl 2020-10-17 23:51:36 -04:00
Axel Kohlmeyer 234f27514f
avoid CMake failure when reporting packages without any of them enabled 2020-10-14 14:59:24 -04:00
Axel Kohlmeyer 00e1edfae9
add a preset for selecting gcc compilers (for cases where they are not the default) 2020-10-14 04:51:34 -04:00
Axel Kohlmeyer 338b05d9dd
set only build type specific compiler flags, so using -DCMAKE_CXX_FLAGS will work as expected 2020-10-13 12:00:03 -04:00
Axel Kohlmeyer 60a296fea8
small tweaks 2020-10-12 23:51:00 -04:00
Axel Kohlmeyer 9bdae2b5c0
move installed packages summary to a different location further down in the output 2020-10-12 18:04:19 -04:00
Axel Kohlmeyer 1d7fa39bc2
don't print a message for each generated style/package header file 2020-10-12 17:10:38 -04:00
Axel Kohlmeyer a97e632bb0
make enabled packages report more compact 2020-10-12 17:10:04 -04:00
Axel Kohlmeyer ec4eab5061
CMake change requested by @junghans 2020-10-12 15:21:08 -04:00
Axel Kohlmeyer 97964604c6
no point in trying a static link of executables 2020-10-09 13:29:13 -04:00
Axel Kohlmeyer 74e1d0f8cf
move Tools compilation script code from CMakeLists.txt to separate Tools.cmake file 2020-10-09 11:15:00 -04:00
Axel Kohlmeyer eb3992a69a
enable static linkage for executables when cross-compiling with MinGW 2020-10-09 02:26:46 -04:00
Axel Kohlmeyer 4f4bc427ae
implement LAMMPS_LIB_NO_MPI to LAMMPS_LIB_MPI change 2020-10-08 21:50:15 -04:00
Axel Kohlmeyer fb1dab6098
Merge branch 'master' into collected-small-fixes 2020-10-06 18:00:33 -04:00
Axel Kohlmeyer bd206dca10
simplify based on suggestions from @junghans 2020-10-05 11:44:19 -04:00
Axel Kohlmeyer b6d333535c
correct variable name 2020-10-05 11:43:43 -04:00
Axel Kohlmeyer 3e74e03bbb
update all_on/all_off presets to really include all packages 2020-10-04 16:46:29 -04:00
Axel Kohlmeyer ffcd905bf1
complete LAMMPS shell docs interation. Warn if exceptions are missing but don't fail 2020-10-04 14:03:34 -04:00
Axel Kohlmeyer 7f3db6f8e3
improve wording 2020-10-03 22:04:54 -04:00
Axel Kohlmeyer 4e8feff52c
add support for building the LAMMPS shell in CMake 2020-10-03 22:01:57 -04:00
Axel Kohlmeyer a9b27caf17
Merge branch 'master' into progguide-axel 2020-09-30 19:57:20 -04:00
Axel Kohlmeyer d84300a3ac
do not fail when looking for gzip or ffmpeg executables when cross compiling to windows 2020-09-30 00:05:15 -04:00
Axel Kohlmeyer fdbdd26585
include intel fortran compiler into intel cmake preset 2020-09-26 22:30:21 -04:00
Axel Kohlmeyer 28812b1ea7
Merge pull request #2381 from akohlmey/collected-small-changes 
Collected small changes
 2020-09-24 16:17:28 -04:00
Christoph Junghans cc8b042abf cmake: export LAMMPS_LIB_NO_MPI for serial version 2020-09-21 12:54:56 -06:00
Christoph Junghans fbcb888ec0 cmake: do not install install mpi.h 2020-09-21 12:41:34 -06:00
Christoph Junghans 51b900b043 Merge remote-tracking branch 'origin/master' into cmake_install_fix 2020-09-21 12:39:51 -06:00
Richard Berger acb5fd2ebf
Simplify GenerateBinaryHeader utility 
The function implementation was incomplete for handling the case
of multiple files. It would generate wrong C code in case more than
one files were specified. Since we don't have this use case, it's
safe to only leave the single input file implementation.

Closes issue #2294
 2020-09-20 18:24:43 -04:00
Christoph Junghans f2bb835e23 cmake: install missing utils.h 2020-09-20 10:44:54 -06:00
Christoph Junghans 705a9a0a8b cmake: do not install mpi.h without library 2020-09-19 15:12:36 -06:00
Axel Kohlmeyer 51957a6219
fix merge conflict 2020-09-18 19:49:36 -04:00
Axel Kohlmeyer e1397b9a88
Merge branch 'master' into collected-small-changes 2020-09-18 16:11:47 -04:00
Giacomo Fiorin 3275419872 Allow Colvars to include headers from the LAMMPS source directory 2020-09-17 14:37:26 -04:00
Richard Berger 706a898163
Merge remote-tracking branch 'origin/master' into python_interface_guide 2020-09-17 12:08:12 -04:00
Axel Kohlmeyer e839fe0d30
Merge branch 'master' into collected-small-changes 2020-09-16 23:53:29 -04:00
Axel Kohlmeyer b96512171c
set -DCOLVARS_LAMMPS when compiling colvars library 2020-09-16 23:52:06 -04:00
Axel Kohlmeyer 4e304177a1
Merge pull request #2356 from giacomofiorin/colvars-update 
Update Colvars to version 2020-07-07
 2020-09-16 23:37:02 -04:00
Giacomo Fiorin 85d36ad6c4 Condense export of debug macro 2020-09-16 17:28:28 -04:00
Richard Berger cb253b2b1a
Add HTML report option for Python 2020-09-11 14:03:13 -04:00
Richard Berger 377163d940
Add target to generate Python coverage XML 2020-09-11 11:36:22 -04:00
Giacomo Fiorin d43cb34c70 Support debugging flag for Colvars via CMake 2020-09-09 18:19:29 -04:00
Christoph Junghans 8fb13f4fd1 cmake: make doc more consistent 2020-09-08 09:43:21 -06:00
Christoph Junghans 09b8b117fc cmake: consistent usage of find variable 2020-09-08 09:35:45 -06:00
Axel Kohlmeyer ceed9284c1
Merge branch 'master' into collected-small-changes 2020-09-04 13:32:47 -04:00
Axel Kohlmeyer 90c13b1b14
update build files for plumed 2.6.1 release 2020-09-04 11:44:39 -04:00
Axel Kohlmeyer 255bf2f8fd
update iwyu custom mapping file 2020-09-04 09:41:57 -04:00
Axel Kohlmeyer 63e5ca53ef
add iwyu mappings for gtest and gmock 2020-09-04 08:00:38 -04:00
Axel Kohlmeyer d0691d0a5d
add mapping for Eigen3 includes 2020-09-04 01:32:15 -04:00
Axel Kohlmeyer 508b49c976
add missing comma 2020-09-04 00:45:41 -04:00
Christoph Junghans 93d0358ebc cmake: use static iwyu-extra-map.imp 2020-09-03 11:36:02 -06:00
Axel Kohlmeyer baa79bd1c4
add another iwyu-mapping entry 2020-09-03 00:22:28 -04:00
Axel Kohlmeyer 047c14d17c
tweak iwyu target. generate file with custom mappings 2020-09-02 23:41:16 -04:00
Axel Kohlmeyer 4ba6a4f958
have clang-style output for easier parsing in compilation mode in emacs 2020-09-02 21:43:20 -04:00
Axel Kohlmeyer 4a10111ced
add iwyu target to CMake configuration 2020-09-02 18:42:19 -04:00
Axel Kohlmeyer a4380a548d
make more readable 2020-09-02 11:11:48 -04:00
Richard Berger 60b98f6b91
Require libzstd>=1.4 for Zstd dump styles 2020-09-01 13:52:56 -04:00
Richard Berger 31bd76efa5
Merge remote-tracking branch 'origin/master' into zstd_support 2020-09-01 12:58:41 -04:00
Richard Berger 3db1a6d690
Use PkgConfig to find Zstd 2020-09-01 11:14:36 -04:00
Richard Berger 0925fc822d
Make Zstd support optional 2020-08-31 18:21:58 -04:00
Vsevak 5623009962 arch 3.0 is dropped in CUDA 11 2020-08-30 13:12:42 +03:00
Axel Kohlmeyer d00807ee9a
Merge pull request #2311 from stanmoore1/kk_update_3.2 
Update Kokkos library in LAMMPS to v3.2
 2020-08-26 15:35:25 -04:00
Christoph Junghans d40b658644 cmake: update kokkos version/checksum 2020-08-26 10:05:14 -06:00
Richard Berger 0d8454ac25
First version of Zstd dump atom 2020-08-25 23:27:42 -04:00
Richard Berger 3a638440a4
Add missing PDF folder 2020-08-25 16:12:09 -04:00
Richard Berger df8fb26272
Refactor changes to documentation build 
- Added CMake variables for readability
- Moved Mathjax files to _static to avoid special copy logic
- Moved JPG/lammps-logo.png to _static to avoid special copy logic
- Removed dead CMake code
 2020-08-25 13:41:31 -04:00