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1107 Commits

Author SHA1 Message Date
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
Axel Kohlmeyer 3f685c346f
add doxygen integration with conventional and cmake doc build 2020-08-24 17:58:37 -04:00
Axel Kohlmeyer 3c7d59401c
Merge pull request #2107 from junghans/offline_gtest 
cmake: allow to overwrite GTest URL for offline machines
 2020-08-21 10:57:08 -04:00
Axel Kohlmeyer 8e74d5ad02
Eigen3 is now hosted at GitLab. The bitbucket repo is gone. Update URLs and MD5s 2020-08-18 21:29:43 -04:00
Axel Kohlmeyer 265b7cf11c
use new dependency resolver in pip for the documentation build virtual environment 2020-08-11 14:11:44 -04:00
Axel Kohlmeyer d09d40af9d
make check for alternate linke more restrictive: also check for linker binary. 2020-08-03 11:36:02 -04:00
Axel Kohlmeyer d0b6ce8284
displace target link options (if supported by CMake version) 2020-07-29 17:46:24 -04:00
Axel Kohlmeyer 1f1767f5af
convert linker choice to (advanced) choice. only for Clang and GNU at the moment 2020-07-29 17:36:34 -04:00
Axel Kohlmeyer 4d9781f9b6
fix typo an reorder 2020-07-29 11:10:14 -04:00
Axel Kohlmeyer 1677b76b6c
try using faster alternatives to GNU ld when building (many) test executables 2020-07-28 20:56:32 -04:00
Axel Kohlmeyer 39cefc4eb3
Merge pull request #2241 from yafshar/cmake 
Update the deprecated property and fix the empty value on macOS
 2020-07-20 12:23:20 -04:00
Yaser Afshar 05c0b5d5ce Update the deprecated property and fix the empty value on macOS 
The `IMPORTED_LINK_INTERFACE_LIBRARIES` is deprecated and is
updated to `INTERFACE_LINK_LIBRARIES` instead.
On macOS `CMAKE_THREAD_LIBS_INIT` is empty since empty the thread
functions are provided by the system libraries. To avoid getting
`set_target_properties called with incorrect number of arguments` error
message, we put it inside double quotes.
 2020-07-18 15:12:31 -05:00
Axel Kohlmeyer c5698ac994
Merge branch 'collected-small-fixes' of github.com:rbberger/lammps into collected-small-changes 2020-07-17 14:03:17 -04:00
Axel Kohlmeyer 73a076daf3
don't set CMAKE_TUNE_FLAGS to anything by default 2020-07-15 16:19:48 -04:00
Axel Kohlmeyer aa82608142
print warning for unknown/unsupported CUDA versions 2020-07-15 11:28:33 -04:00
Axel Kohlmeyer a082895b90
update CMake script for GPU package to include handling of Arch 8.0 and CUDA 11 2020-07-15 11:08:06 -04:00
Richard Berger fadfb1b482
Allow changing CMAKE_CXX_EXTENSIONS option to resolve #2079 2020-07-03 12:41:49 -04:00
Axel Kohlmeyer 8929ba42cd
enable exceptions by default when testing is enabled, so we can test for failures 2020-07-02 09:50:15 -04:00
Axel Kohlmeyer 66271448ae
Merge pull request #2167 from Vsevak/master 
Update GPU CMake and Makefile scripts for ROCm v3.5
 2020-06-26 13:43:32 -04:00
Axel Kohlmeyer cd6de39319
whitespace 2020-06-25 15:35:25 -04:00
Axel Kohlmeyer a7d2b792a8
Merge branch 'master' into test-updates 2020-06-24 17:25:55 -04:00
Axel Kohlmeyer 3525d1f104
simplify suppression handling by creating a custom local file 2020-06-24 13:35:36 -04:00
Axel Kohlmeyer 57538fb91c
add leak sanitizer option 2020-06-24 13:34:47 -04:00
Axel Kohlmeyer 5ea9b1b38d
simplify detection and application of valgrind suppressions 2020-06-24 09:33:19 -04:00
Richard Berger 8cec13a038
Add memory checker support in CMake 
If ENABLE_TESTING is ON, you can now use memory checking tools to run the test
suite and check for memory leaks. By default CMake will try to find valgrind in
your path and set some default options.

To customize this behavior use the MEMORYCHECK_COMMAND and
MEMORYCHECK_COMMAND_OPTIONS variables. To run tests with the memory checker,
use the MemCheck action in ctest:

Run entire test suite:

ctest -T MemCheck

Run single test:

ctest -T MemCheck -R TESTNAME

Run test in verbose mode:

ctest -V -T MemCheck -R TESTNAME
 2020-06-23 13:35:59 -04:00
Axel Kohlmeyer 2e48ea8680
include MLIAP package in cross-compiler builds 2020-06-23 07:11:30 -04:00
Axel Kohlmeyer ac48f2dd67
add a hard dependency of MLIAP on SNAP 2020-06-22 13:30:43 -04:00
Axel Kohlmeyer 233b56105a
Merge branch 'master' into mliap 2020-06-22 11:24:49 -04:00
Axel Kohlmeyer 75114afc0e
integrate MLIAP package into CMake procedure 2020-06-22 11:24:44 -04:00
Vsevak 723b9e6760 Try to keep compatibility with deprecated ROCm hcc compiler 2020-06-20 15:17:54 +03:00
Axel Kohlmeyer 8f4e18ba3a
change logic of selecting and allowing sanitizer options to be compatible with unsupported compilers 2020-06-19 11:30:38 -04:00
Axel Kohlmeyer e934f7bac3
try to work around linker issues with older CMake versions and using coverage or sanitizers 2020-06-19 00:20:20 -04:00
Vsevak 2ea5d9956a find_package is unnecessary for rocprim 2020-06-19 00:01:03 +03:00
Axel Kohlmeyer b866ea68f6
make sanitizers an explicit cmake option (again) so we can set the flags properly 2020-06-18 11:46:42 -04:00
Axel Kohlmeyer d6ca98cb44
don't validate compiler flags provided with CMAKE_TUNE_FLAGS anymore 
closes #2084
 2020-06-17 23:47:55 -04:00
Vsevak d3baa414d2 Fix cmake for GPU ROCm 3.5 backend 2020-06-17 23:33:16 +03:00
Axel Kohlmeyer 2d52a09d08
patch the source code to the ScaFaCoS lib with a proper fix instead of working around it with compiler flags 2020-06-17 13:01:29 -04:00
Axel Kohlmeyer 34e46cc336
add workaround to USER-SCAFACOS package CMake script for linker error in FMM with GNU gcc 10.0 2020-06-17 07:41:00 -04:00
Axel Kohlmeyer fd8cfed86d
fix typo 2020-06-15 17:33:50 -04:00
Axel Kohlmeyer 14c22a004a
Merge branch 'master' into use-clang-format-demo 
# Conflicts:
#	unittest/force-styles/pair_style.cpp
#	unittest/utils/test_utils.cpp
 2020-06-15 16:14:13 -04:00
Axel Kohlmeyer 4a3d9afb54
Merge pull request #2154 from rbberger/coding_standard 
Add utilities for checking code
 2020-06-15 15:32:35 -04:00
Axel Kohlmeyer 0ca7270668
re-enable USER-MESONT package for MinGW cross compilation 2020-06-15 13:47:16 -04:00
Axel Kohlmeyer 0199e369fa
work around race condition and minimizing download attemps for transparently downloaded potential files 2020-06-15 13:46:54 -04:00
Axel Kohlmeyer 9aee8d41bd
Merge branch 'master' into collected-small-changes 2020-06-15 12:12:45 -04:00
Richard Berger e840fa23f1
Add format-tests target 2020-06-15 11:21:43 -04:00
Axel Kohlmeyer 57eab1f785
USER-MESONT fails to download with Win64 for some strange reason. disabling from mingw preset for now 2020-06-15 11:12:55 -04:00
Axel Kohlmeyer b5ee87697a
workaround for GNU Fortran 10 and later when compiling downloaded ScaFaCoS lib 2020-06-15 10:59:32 -04:00
Axel Kohlmeyer b3a99f3165
add and document new "download" preset 2020-06-14 19:50:14 -04:00
Axel Kohlmeyer 9b0213f1ab
small CMake tweaks from progguide branch 2020-06-13 12:03:50 -04:00
Richard Berger 49982e22bf
Add check for permissions 2020-06-13 09:54:12 -04:00
Richard Berger fcd3e9a3f9
Make quiet Python 3 check 2020-06-13 08:40:27 -04:00
Axel Kohlmeyer ec6d3586ce
require at least python 3.5 for building docs and import CMake improvements from progguide branch 2020-06-13 01:20:24 -04:00
Richard Berger cf5fa3959c
Add first version of whitespace utility 2020-06-12 21:52:51 -04:00
Axel Kohlmeyer b246c96056
remove duplicate package name 2020-06-12 06:36:44 -04:00
Axel Kohlmeyer d61d8899ff
Merge branch 'fetch-potentials' into feature-cnt 2020-06-12 05:54:45 -04:00
Axel Kohlmeyer cf5c748fb4
Merge branch 'master' into feature-cnt 2020-06-12 05:53:17 -04:00
Axel Kohlmeyer b9303378ac
move pair style mesocnt from USER-MISC to (upcoming) USER-MESONT package 
the remaining documentation and README files will be updated once USER-MESONT is integrated
 2020-06-11 17:41:19 -04:00
Axel Kohlmeyer 1a1cc99144
use correct expression for source folder. small output tweak. 2020-06-10 12:41:20 -04:00
Axel Kohlmeyer 6891fa2610
update a few URLs to use https: instead of http: 2020-06-10 12:34:09 -04:00
Axel Kohlmeyer f36a84bdd3
add CMake support for fetching external potential files 2020-06-10 12:29:48 -04:00
Richard Berger e47d48eed8
Change output message and use list(APPEND) 2020-06-09 12:10:35 -04:00
Richard Berger 954f728225
Always set CMAKE_LIBRARY_PATH if environment variable LIBRARY_PATH is set 
This resolves issues such as CUDA_CUDA_LIBRARY NOTFOUND if LIBRARY_PATH is
set to the CUDA stubs folder, but ignored by CMake.
 2020-06-09 11:30:54 -04:00
Axel Kohlmeyer 78f030a07a
test for *cubin.h files in lib/gpu that conflict with cmake compilation 2020-06-09 07:32:49 -04:00
Axel Kohlmeyer 2a4bd9ef53
small tweaks and documentation update to coverage cleaning targets 2020-05-29 08:33:34 -04:00
Axel Kohlmeyer 30020594df
add custom target to remove/reset collected coverage data 2020-05-29 08:23:25 -04:00
Richard Berger 0c503ab122
Move coverage html into folder 2020-05-29 08:23:08 -04:00
Christoph Junghans 042cfc521b cmake: allow to overwrite GTest URL for offline machines 2020-05-24 19:38:19 -06:00
iafoss 4868f5fdfc update 2020-05-20 22:04:00 -04:00
Axel Kohlmeyer 8691579def
Merge pull request #2098 from lammps/unittest 
Add first part of an integrated unit test framework
 2020-05-20 15:44:52 -04:00
Axel Kohlmeyer 58ca1dcf8e
Merge pull request #2094 from akohlmey/collected-small-changes 
Collected small changes and bug fixes for the next patch release
 2020-05-20 14:33:34 -04:00
iafoss 35f7aa810d update 2020-05-20 00:33:36 -04:00
iafoss bddd6d5e84 update 2020-05-19 23:19:49 -04:00
Axel Kohlmeyer c04a71a239
add unit test framework for pair, bond, angle styles from progguide branch 2020-05-19 22:24:31 -04:00
Axel Kohlmeyer 48a9e0d732
consolidate setting CMake policy CMP0074 into main cmake file 2020-05-19 15:20:41 -04:00
Axel Kohlmeyer 16db223d03
update test for whether to set CMake policy CMP0074 is needed. 2020-05-19 11:53:47 -04:00
iafoss ed43c1e22b Merge branch 'master' into feature-cnt 2020-05-18 18:23:16 -04:00
Axel Kohlmeyer 93fe33553a
need to set CMake policy CMP0074 to NEW behavior also for finding TBB Malloc 2020-05-18 17:50:28 -04:00
iafoss e26be18b1e update 2020-05-18 17:28:48 -04:00
Christoph Junghans 6f0a56c176 cmake: fftw is now a private dep 2020-05-15 13:42:51 -06:00
Axel Kohlmeyer e36d2ce3e6
Do not use -ffast-math by default. Too large a chance of miscompiled code. 2020-05-14 20:48:43 -04:00
Richard Berger cbd4ce5130
Use absolute path to LAMMPS_DIR for collecting git info 2020-05-08 16:04:55 -04:00
Axel Kohlmeyer 3b77546eb9
Merge pull request #2069 from junghans/latte_v1.2.2 
latte: bump to v1.2.2
 2020-05-07 14:27:19 -04:00
Axel Kohlmeyer 5fa7e138ea
Merge pull request #2070 from junghans/kokkos_v3.1.01 
cmake: bump kokkos to v3.1.01
 2020-05-07 14:16:56 -04:00
Christoph Junghans 66994562e6 cmake: bump kokkos to v3.1.01 2020-05-05 11:46:09 -06:00
Christoph Junghans fe62e1dbc9 latte: bump to v1.2.2 2020-05-05 10:51:11 -06:00
Axel Kohlmeyer fc7b1dc4fd
Merge branch 'cmake_enable_chain.x' of github.com:junghans/lammps into cmake_enable_chain.x 2020-05-05 11:27:40 -04:00
Axel Kohlmeyer b933538dfa
tweak tbbmalloc search path for intel 19.1 compiler 2020-05-05 11:27:19 -04:00
Christoph Junghans 8a114fca97 cmake: include where it is used 2020-05-05 08:53:49 -06:00
Axel Kohlmeyer 9708b58939
check for fortran instead of directly enabling it 2020-05-05 10:41:18 -04:00
Axel Kohlmeyer bcd50646b4
don't enable fortran if the generator does not support it. 2020-05-05 10:23:04 -04:00
Christoph Junghans b5af7da2c6 cmake: enable Fortran before checking for the compiler 2020-05-05 07:10:42 -06:00
Axel Kohlmeyer 71ab9dc02b
Merge pull request #2049 from rbberger/singularity_container_update 
Singularity container update
 2020-05-04 17:27:54 -04:00
Axel Kohlmeyer 61284891ee
add a few more packages to the "most" preset 2020-05-03 05:04:07 -04:00
Axel Kohlmeyer f1e1644fe1
fix typo that resulted in LAPACK not being properly linked with USER-ATC 2020-05-03 04:55:25 -04:00
Axel Kohlmeyer d811fd0da7
skip building chain.x, if no Fortran compiler is available 2020-05-03 04:23:52 -04:00
Axel Kohlmeyer fdb4ba51da
add patch to VORONOI package external build so it will compile with BSD make 2020-05-03 04:04:02 -04:00
Axel Kohlmeyer f5be3ccab4
add the check for MPI in USER-ATC at the correct location 2020-05-03 03:06:41 -04:00
Axel Kohlmeyer 863b50501c
port MPI stubs workaround to USER-ATC 2020-05-03 02:49:52 -04:00
Axel Kohlmeyer 696308a760
set cmake policy to honor HDF5_ROOT and NETCDF_ROOT. search for parallel NetCDF only with parallel builds 2020-04-29 22:39:33 -04:00
Christoph Junghans 1adda03202 cmake: only install shared lib and friends 2020-04-29 18:06:33 -06:00
Christoph Junghans 600d357155 cmake: disable installing of static libs 2020-04-29 16:26:56 -06:00