06f6434b38
when creating or replacing a fix or compute, return pointer to new instance
2021-08-06 13:39:02 -04:00
5861577a72
use temporary vector container to avoid explicit delete[]
2021-08-06 13:39:02 -04:00
912a1fc561
Merge pull request #2865 from rbberger/python_update
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Python package update
2021-08-06 13:37:14 -04:00
eece77eecf
Merge pull request #2866 from Colvars/colvars-update
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Update Colvars to version 2021-08-06 (silence Coverity Scan warnings)
2021-08-06 11:20:46 -04:00
eb52f7c290
Update Colvars to version 2021-08-06 (silence Coverity Scan warnings)
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Also include PDF copy of the manual forgotten in previous PR.
2021-08-06 10:32:37 -04:00
b9fa4e1db2
avoid memory leaks on specifying keywords multiple times
2021-08-06 10:22:31 -04:00
f3a03d6a84
Catch ValueError instead of base exception
2021-08-06 10:21:40 -04:00
53b94ac94d
Allow fix python/move to load class from __main__
2021-08-05 18:10:19 -04:00
980b817f3f
Allow python pair style to load class from __main__
2021-08-05 18:03:05 -04:00
5045595ad8
Merge pull request #2861 from akohlmey/fix-valgrind-issues
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Address issues flagged by running unit tests with valgrind and sanitizer instrumentation
2021-08-05 16:07:57 -04:00
3fc97e9466
Merge branch 'fix-valgrind-issues' of github.com:akohlmey/lammps into fix-valgrind-issues
2021-08-05 12:20:33 -04:00
5295bb5109
fix refactoring bugs
2021-08-05 12:20:20 -04:00
177e60830e
Merge branch 'master' into fix-valgrind-issues
2021-08-05 12:11:59 -04:00
c23dc22a3e
Merge pull request #2862 from akohlmey/intel-set_ntypes-consistent
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Make ForceConst::set_ntypes() more robust and fix related bug in pair style sw/intel
2021-08-05 11:50:50 -04:00
50c476b6af
Merge pull request #2863 from Colvars/colvars-update
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Update Colvars library to version 2021-08-03
2021-08-05 11:16:51 -04:00
9a60ab0c23
correctly insert atoms/molecules any nfreq timesteps even with multiple run
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this changes the computation of "next_reneighbor" so that it is based
on "nfirst" which is set during the constructor of the class.
This still maintains the property that the first deposit attempt is not
done during setup, but on the next step.
2021-08-04 21:32:10 -04:00
bc6dfdb656
update readme
2021-08-04 17:44:56 -04:00
08a727d510
make some class members temporaries since they don't need to persist
2021-08-04 17:19:23 -04:00
2e7b3081a1
fix bug enumerating output when using python invoke with multiple functions
2021-08-04 17:07:16 -04:00
bb9c0630f8
suppressions for readline function calls from lammps-shell
2021-08-04 17:06:02 -04:00
0ea6406bb9
Merge branch 'fix-valgrind-issues' of github.com:akohlmey/lammps into fix-valgrind-issues
2021-08-04 12:25:12 -04:00
c4442206d4
add special case for heredocs in utils::split_words() to avoid segfaults
2021-08-04 12:03:34 -04:00
7068f3e77b
add a few more test cases for testing utils::split_words()
2021-08-04 12:02:55 -04:00
2a9be42758
Update Colvars to version 2021-08-03
2021-08-03 18:03:18 -04:00
0938bc8999
update docs for hybrid style updates
2021-08-02 21:53:31 -04:00
c1c31c6b04
may not call memmove() on a null pointer, even if 'n' is 0.
2021-08-02 21:35:25 -04:00
04c7e7543e
use friend statement instead of (incorrect) cast to give access to protected class member
2021-08-02 21:34:30 -04:00
37ca6a8e0b
make handling of reference to Memory class in ForceConst class more robust
2021-08-02 15:50:44 -04:00
b7be9415de
fix segfault with pair style sw/intel
2021-08-02 15:49:26 -04:00
53050a0429
add suppressions for FlexiBLAS on Fedora
2021-08-02 15:45:32 -04:00
a3bfcc68ef
add libgomp suppression for newer GCC
2021-08-02 15:45:15 -04:00
848db31a77
reformat with clang-format
2021-08-02 15:25:01 -04:00
8aa39a6c40
make compatible with CLASS2
2021-08-02 15:23:16 -04:00
45858be1b6
avoid uninitialized data access for hybrid styles with OPENMP
2021-08-02 15:22:21 -04:00
50e8d7c36b
Merge pull request #2859 from akohlmey/next_patch_release
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Step version strings for next patch release
2021-07-30 16:40:10 -04:00
29eee29241
Merge pull request #2860 from evoyiatzis/patch-1
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fixing compute gyration/shape indexing bug
2021-07-30 15:45:51 -04:00
db4fcd7537
update package dependency
2021-07-30 15:24:23 -04:00
75214f1eeb
Merge pull request #2857 from akohlmey/update-formatted-output
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Modernize formatted output and string handling in packages
2021-07-30 12:50:25 -04:00
82936b1e4f
fixing indexing bug
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The gyration_tensor[4] element as computed by "compute gyration" corresponds to the xz component of the gyration tensor and the gyration_tensor[5] to the yz component. The code assumed that gyration_tensor[4] corresponds to the yz component and the gyration_tensor[5] to the xz.
2021-07-30 18:14:44 +02:00
f5b82ea3ef
Merge pull request #2856 from akohlmey/collected-small-changes
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Collected small changes and fixes
2021-07-30 11:36:40 -04:00
5f401da462
correct bug in derived CG-DNA FENE bond classes and optimize code
2021-07-30 10:48:15 -04:00
9dc662973e
step version strings for next patch release
2021-07-29 21:18:03 -04:00
d211bbc0d6
expand ArgInfo class unit tests
2021-07-29 20:58:02 -04:00
cb32bb972b
fix bugs in ArgInfo class
2021-07-29 20:57:42 -04:00
6b20da7549
update lammps shell test to use a fix that is always available
2021-07-29 17:48:35 -04:00
4710b7bc9e
modernize and simplify code to find best matching restart file
2021-07-29 17:25:42 -04:00
5cdf55937d
move pair style tracker to a better location
2021-07-29 17:17:06 -04:00
ca2abd22be
remove unused file
2021-07-29 17:08:16 -04:00
a80829bd79
avoid compilation error
2021-07-29 16:14:52 -04:00
a6d66c3518
update .gitignore
2021-07-29 16:07:23 -04:00
