1eebdcbd03
fix obvious bugs
2020-09-22 05:34:29 -04:00
b876f451f8
make compiler choice overridable
2020-09-22 05:34:12 -04:00
f186eb7005
be more selective about which elements not to display
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we only want to skip the redundant User-Documentation and Programmer-Documentation captions
2020-09-21 22:41:19 -04:00
54aacc47ea
add section about citing LAMMPS
2020-09-21 22:40:36 -04:00
cc8b042abf
cmake: export LAMMPS_LIB_NO_MPI for serial version
2020-09-21 12:54:56 -06:00
fbcb888ec0
cmake: do not install install mpi.h
2020-09-21 12:41:34 -06:00
51b900b043
Merge remote-tracking branch 'origin/master' into cmake_install_fix
2020-09-21 12:39:51 -06:00
36fdba32e7
Merge pull request #2382 from junghans/cmake_install_fix_2
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cmake: install missing utils.h
2020-09-21 13:29:29 -04:00
7eab154786
one-line bug when checking for molecule fragments
2020-09-21 11:01:04 -04:00
a1407de09d
have make yes/no package terminate with error status for non-existing packages
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this closes #2387
2020-09-21 07:09:13 -04:00
c7c7d2f474
Merge pull request #2377 from akohlmey/move-version-to-lammps
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Move the members `version` and `num_ver` form Universe class to LAMMPS class
2020-09-21 02:10:08 -04:00
29a7d598ac
update formatting style to be more consistent
2020-09-21 02:04:58 -04:00
0a11cc5eb9
make code valgrind clean
2020-09-21 01:55:07 -04:00
486131f4c5
fix segmentation fault bug in USER-PTM. closes #2386
2020-09-21 01:54:36 -04:00
0951fea738
Merge branch 'collected-small-changes' of github.com:akohlmey/lammps into collected-small-changes
2020-09-20 19:20:42 -04:00
acb5fd2ebf
Simplify GenerateBinaryHeader utility
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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
7d07d04989
Use correct library for unit test if LAMMPS_MACHINE_NAME is set
2020-09-20 17:52:24 -04:00
54b9e60dd0
reformat
2020-09-20 14:06:40 -04:00
4cbf821af3
modernize example
2020-09-20 14:03:13 -04:00
774bffe623
relax result precision requirement somewhat
2020-09-20 13:57:04 -04:00
f2bb835e23
cmake: install missing utils.h
2020-09-20 10:44:54 -06:00
dfd447f570
Add missing tools for PDF index build to containers
2020-09-19 23:07:24 -04:00
61ce73273b
Add missing -u flag for unbuffered PyLammps tests
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Addresses issue #2380
2020-09-19 23:07:13 -04:00
92f8398bed
check more thoroughly for prerequisites to translate the PDF manual. update doc/README
2020-09-19 18:16:52 -04:00
705a9a0a8b
cmake: do not install mpi.h without library
2020-09-19 15:12:36 -06:00
f72fb7290b
fix links
2020-09-19 16:28:20 -04:00
67aeb7a5e5
Merge branch 'move-version-to-lammps' into collected-small-changes
2020-09-19 16:17:01 -04:00
6b0346c299
try use unencrypted download or using wget if normal download of polyfill.js fails
2020-09-19 16:14:08 -04:00
c91ee210e4
simplify variable lookup in set command
2020-09-19 16:04:09 -04:00
9c0808e95a
update unit tests for move of version string location
2020-09-19 15:00:03 -04:00
4c51a8ae57
move version and num_ver from Universe to LAMMPS and make num_ver an int
2020-09-19 11:37:08 -04:00
89506efd23
document Pointers class and LAMMPS_NS namespace
2020-09-19 11:16:44 -04:00
73c65d43e1
update list of main folders and descriptions
2020-09-19 02:53:36 -04:00
9030c987e6
tweak formatting and style setting to have the desired structure and layout
2020-09-19 00:54:54 -04:00
6dda562501
skip over uninitialized and internal variables. correctly identify all kinds of boolean values
2020-09-18 23:40:31 -04:00
9cdde97863
correct test logic
2020-09-18 22:37:54 -04:00
5ce6259632
correct reference to function
2020-09-18 22:35:56 -04:00
56d9222156
Merge pull request #2374 from akohlmey/next_patch_version
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Step version strings for the next patch release
2020-09-18 21:45:34 -04:00
897a7d0ed4
only try to broadcast if we have a proper communicator
2020-09-18 21:17:31 -04:00
f5fda95da6
Merge branch 'master' into next_patch_version
2020-09-18 21:15:12 -04:00
094a1bea91
Merge pull request #2369 from akohlmey/collected-small-changes
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Collected small changes and fixes for the next patch release
2020-09-18 20:20:41 -04:00
51957a6219
fix merge conflict
2020-09-18 19:49:36 -04:00
a0afb9b554
Merge branch 'master' into collected-small-changes
2020-09-18 18:38:47 -04:00
7580176020
Merge pull request #2376 from giacomofiorin/colvars-update
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Update Colvars to version 2020-09-17
2020-09-18 18:38:17 -04:00
b520a6287b
Revert parts of "Restore PDF index"
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We need to update the container image(s) for building the
pdf documentation on ci.lammps.org by adding `latexmk`
and `xindy` before we can re-enable this change to the makefile.
This partially reverts commit 3c3b76a781
2020-09-18 18:37:26 -04:00
494498df03
update docs on building the PDF version of the manual
2020-09-18 18:27:23 -04:00
906e000e4c
Merge pull request #2368 from jrgissing/bond/react-update_all_charges_default
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Bond/react update all charges by default
2020-09-18 18:17:54 -04:00
33a2857b33
Fix whitespace
2020-09-18 17:56:12 -04:00
3c3b76a781
Restore PDF index
2020-09-18 17:51:51 -04:00
07c9298558
Fix some broken internal hyperlinks in Colvars PDF
2020-09-18 17:24:12 -04:00
