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543 Commits

Author SHA1 Message Date
Axel Kohlmeyer 8359a4384a
more OpenMPI suppressions 2020-07-11 13:17:51 -04:00
Axel Kohlmeyer 4b2c1f5edd
some more OpenMPI suppressions 2020-07-11 13:16:25 -04:00
Axel Kohlmeyer 1df59c4b95
change lammps2pdb.pl to only ignore the first line of a data file. whitespace fixes 2020-07-05 23:36:00 -04:00
Richard Berger 0f094c2501
Add PyYAML to Fedora 32 container 2020-06-30 10:05:14 -04:00
Richard Berger af2e1bf7c6
Update Ubuntu 18.04 GPU container 2020-06-30 09:38:28 -04:00
Richard Berger 21462ede4b
Simplify tool: git only stores executable bit 2020-06-26 17:03:10 -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
Richard Berger f9a202288c
Add missing kmod package to AMD ROCm container 2020-06-26 13:09:16 -04:00
Axel Kohlmeyer bdb4cc561c
add update README files 2020-06-26 11:11:59 -04:00
Richard Berger e6b3611c2d
Update ROCm container to version 3.5 2020-06-25 19:05:28 -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
Richard Berger 95e79b2347
Keep file permissions while fixing whitespace issues 2020-06-16 07:19:19 -04:00
Richard Berger 943d252403
Change regex to detect more whitespace errors 2020-06-16 07:11:31 -04:00
Richard Berger 036b2bd82c
Add non-zero exit code on whitespace check failure 2020-06-16 07:06:37 -04:00
Richard Berger 61235308f1
Add non-zero exit code on permission check failure 2020-06-16 07:05:15 -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 9aee8d41bd
Merge branch 'master' into collected-small-changes 2020-06-15 12:12:45 -04:00
Richard Berger 49982e22bf
Add check for permissions 2020-06-13 09:54:12 -04:00
Axel Kohlmeyer e006286603
rather than forcing tcp communication for OpenMPI, we disable infiniband instead for better stability of tests 2020-06-13 01:40:53 -04:00
Richard Berger cf5fa3959c
Add first version of whitespace utility 2020-06-12 21:52:51 -04:00
Axel Kohlmeyer cf5c748fb4
Merge branch 'master' into feature-cnt 2020-06-12 05:53:17 -04:00
Axel Kohlmeyer 016629252d
a few more tweaks needed for centos8 and fedora32 2020-06-08 19:18:01 -04:00
Axel Kohlmeyer ac85071bc4
need one more step with ubuntu to allow enabling PPA repos 2020-06-08 16:08:03 -04:00
Axel Kohlmeyer 2668e3deb6
add manual installation of plumed library 2020-06-08 14:39:34 -04:00
Axel Kohlmeyer a9d1932032
update singularity definition files to include kim-api packages 2020-06-07 16:11:26 -04:00
Axel Kohlmeyer 5827f69da5
OpenMPI's "sm" transport layer has gone from some newer versions. use "tcp" as lowest common denominator 2020-05-19 20:25:53 -04:00
iafoss ed43c1e22b Merge branch 'master' into feature-cnt 2020-05-18 18:23:16 -04:00
iafoss e26be18b1e update 2020-05-18 17:28:48 -04:00
Axel Kohlmeyer eefeaf4d25
make OpenMPI only use shared memory comm by default and silence some warnings 2020-05-07 18:15:57 -04:00
Axel Kohlmeyer d7650e8e02
no need to include googletest libs, we download and compile internally 2020-05-07 17:02:04 -04:00
Axel Kohlmeyer 4dce25d89e
update some defitions files and also include hack to indicate image type in prompt 2020-05-06 15:07:02 -04:00
Axel Kohlmeyer db71b3b994
update singularity image defitions to include gtest and libyaml. drop f30 2020-05-06 00:02:04 -04:00
Richard Berger f9ba4b497f Use ccache on Ubuntu by default 2020-05-01 08:01:17 -04:00
Richard Berger d9e0bc5d94 Add missing packages for legacy build 2020-05-01 05:55:03 -04:00
Richard Berger 814f45d756 Add missing symlink 2020-04-30 18:25:25 -04:00
Axel Kohlmeyer 002c49737f
update definition for ubuntu20.04 2020-04-29 22:58:08 -04:00
Axel Kohlmeyer e97bf005cb
include hdf5 and netcdf in more images 2020-04-29 22:36:33 -04:00
Richard Berger aad8659788 Reduce CUDA footprint in containers 2020-04-29 20:02:25 -04:00
Richard Berger 633651fa56 Add valgrind, gdb to containers and clean caches 2020-04-29 17:32:19 -04:00
Richard Berger 8235c48f49 Avoid errors due to host Lmod in containers 
These changes ensure that environment variables that are automatically passed
to the container don't interfere with Lmod inside of the container. The previous
implementation would not take care of sticky packages from the outside and Lmod
would try to reload them.

Note that Lmod defines the 'module' bash function, which doesn't propagate to
the final shell when using 'singularity shell'. If the 'module' command is needed
a login shell needs to be launched:

$ singularity exec <CONTAINER> bash -l
 2020-04-29 17:01:55 -04:00
Richard Berger 82b1fc717f Add missing python36 and hdf5-devel to CentOS containers 2020-04-29 16:46:22 -04:00
Axel Kohlmeyer 867088dbd8
add packages to also allow a regular build not just cross-compilation 2020-04-28 01:12:31 -04:00
Axel Kohlmeyer edd708dbce
fix command ordering issues with gpu image build 2020-04-27 17:17:33 -04:00
Axel Kohlmeyer 7b79b31018
remove latex support from accelerator image definitions 2020-04-27 15:17:45 -04:00
Axel Kohlmeyer 1aaf3ee03f
add new combined container for compiling with GPU support. 2020-04-27 15:14:02 -04:00
Axel Kohlmeyer 9f923c51f8
update singularity definition files for ubuntu variants to enable more LAMMPS build options and features 2020-04-21 12:07:34 -04:00
Axel Kohlmeyer 17fdf976b0
must force non-interactive setup 2020-04-12 01:35:41 -04:00
Axel Kohlmeyer fa0cc2c217
update singularity definition files 2020-04-11 21:36:08 -04:00
Richard Berger 98fcf83180 Checkout specific hipCUB version 2020-04-10 15:31:06 -04:00
Richard Berger e7a8de0368 Add container with both ROCm and CUDA 2020-04-09 13:28:56 -04:00
Axel Kohlmeyer e53e443e21
add singularity description file for Ubuntu 20.04 LTS 2020-04-02 21:52:20 -04:00
Axel Kohlmeyer c8481e620d
set C locale 2020-04-02 19:41:00 -04:00
Axel Kohlmeyer d4fbeccb2b
add latex support 2020-04-02 19:40:29 -04:00
Axel Kohlmeyer 2ef4c4166d
update container definitions for building documentation 2020-04-02 17:48:17 -04:00
Axel Kohlmeyer a9dad3d46c
test for PDFLaTeX and update README 2020-04-02 14:31:47 -04:00
Axel Kohlmeyer 9397e11c6f
fix issue in README file 2020-04-02 13:29:37 -04:00
Axel Kohlmeyer 2de7e90e58
add Fedora 30 definition and update README file 2020-04-01 20:21:30 -04:00
Axel Kohlmeyer 927b1b05e5
ignore singularity container files in the entire repo 2020-04-01 20:08:00 -04:00
Richard Berger 0cf48c37e1 Add NVIDIA Singularity container 2020-04-01 17:41:40 -04:00
Richard Berger 03988a9048 Add ROCm Singularity container 2020-04-01 17:29:07 -04:00
Richard Berger ccdf010ef0 Add Intel OpenCL Singularity container 2020-04-01 17:08:40 -04:00
Richard Berger dbdce3946b Update/Sync singularity container definition for Ubuntu 18.04 2020-04-01 16:35:00 -04:00
iafoss a8fc2005d4
Merge branch 'master' into feature-cnt 2020-03-20 14:35:57 -04:00
iafoss 53ccc4c607 fix code related issues 2020-03-20 14:21:24 -04:00
Axel Kohlmeyer 2714fad178
Merge branch 'master' into collected-small-changes 
# Conflicts:
#	doc/src/Build_development.rst
 2020-03-18 20:59:16 -04:00
Eisuke Kawashima ca1e1e2dff
Convert British spelling to American 2020-03-18 23:09:23 +09:00
Axel Kohlmeyer 5109b7f1b1
correct incorrect spelling correction 2020-03-17 20:45:52 -04:00
Axel Kohlmeyer 1d8e9ca014
include gcc sanitizer libraries 2020-03-17 18:53:28 -04:00
Axel Kohlmeyer 6f6855e831
do not advertise multiple targets in cmbuild wrapper 2020-03-17 15:57:33 -04:00
Axel Kohlmeyer 5779731da3
provide cmbuild wrapper script for cmake. document it and add some improvements to CMake build docs 2020-03-17 13:04:38 -04:00
Eisuke Kawashima 649a8cc01a
Fix typo 2020-03-14 13:57:48 +09:00
iafoss 0204bf286b CNT package 
The tubular potential model (TPM) force field for Carbon Nanotubes (CNTs) package.
 2020-02-06 16:50:38 -05:00
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
Axel Kohlmeyer 031812b2bf recreate 1gb1 input deck with CMAP included. 2018-01-28 06:22:03 -05:00
Axel Kohlmeyer ba68548e38 clarify ch2lmp commands purpose in tools section 2018-01-28 06:19:33 -05:00
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
Dr. Nandor Tamaskovics 86ed55599d The bash shell script doxygen.sh has been revised. 2018-01-16 17:28:58 +01:00
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 4c71beb024 cleanup/simplification of compilation for fix phonon analysis tool "phana" 
- include the used tricubic functions directly as static functions
- silence compiler warnings
- define f2c.h imported data types directly or use C equivalents
- since the direct LAPACK API was called and not cLAPACK, declare LAPACK interface and depend only on LAPACK
- add proper dependencies
- disable automatic minor version number generation. step version manually.
- comment out optional spglib functionality by default
 2017-09-30 12:12:15 -04:00
Julien Devemy a5b65c1af4 Mods for extra/special/per/atom and add toluene 2017-08-31 15:03:04 +02:00
Axel Kohlmeyer de0fdbed6c moltemplate bugfix update 2017-08-24 07:12:45 -04:00
Axel Kohlmeyer 12150ffa73 add moltemplate version 2017-8-22 2017-08-23 07:54:56 -04:00
Axel Kohlmeyer 57aafba7c3 remove old moltemplate version 2017-08-23 07:54:05 -04:00
Axel Kohlmeyer 60e14f1490 add comment to msi2lmp README about symmetry limitations 2017-08-14 08:54:26 -04:00
Christoph Junghans f717a70638 tools/Makefile: remove remains of data2xmovie 
data2xmovie was removed in e110d6961a
 2017-07-11 16:16:03 -06:00
Axel Kohlmeyer dec36e9bfe fix typos and remove trailing whitespace 2017-04-17 17:40:57 -04:00
Axel Kohlmeyer dd90c860ee refactor msi2lmp documentation to emphasize lack of active development 
- put a note into the manual
- reorder contents of the README file
- request for information should be sent to lammps-users
- add list of known missing features
 2017-04-17 17:40:21 -04:00
Steve Plimpton dcede304df changes for next patch, 2d disc options for spheres, fix external upgrade, bug fixes for fix ave/chunk for density calcs, Aidan doc page citation deconvolution 2017-03-21 08:56:37 -06:00
Axel Kohlmeyer 82d952ae0e mention NumPy dependency instead of Numeric for python tools 2017-03-20 17:26:19 -04:00
Axel Kohlmeyer 47d6451d03 fix compilation for pymol_asphere tool 2017-03-20 17:18:24 -04:00
Axel Kohlmeyer e110d6961a remove obsolete tools and files 2017-03-20 17:17:35 -04:00
Axel Kohlmeyer a42b0b7dcb update colvars abf integrate tool from git repo 2017-03-20 17:04:16 -04:00
Axel Kohlmeyer 03828b5836 adapt binary2txt.cpp source to current coding conventions 2017-03-20 16:57:32 -04:00
Axel Kohlmeyer ecf17621aa more permission fixes 2017-03-20 16:25:06 -04:00
Axel Kohlmeyer f0c6ed004d remove xmovie 2017-03-20 16:24:38 -04:00
Richard Berger 08baaa9d8e Fix more typos in tools 2017-03-07 01:00:25 -05:00
Richard Berger dd76ac5010 Fix typos in tools folder 2017-03-05 21:18:01 -05:00
Richard Berger e261bef7bb Spelling fixes in source files 2017-03-05 18:30:39 -05:00
Agilio Padua 27aca14094 Updated polarizer.py to use coul/long/cs 2017-02-04 15:02:08 +01:00
Axel Kohlmeyer 34cb4027df make formatting comment consistent 2017-01-11 07:46:07 -05:00