b37cd14dd1
avoid superfluous calls to utils::strdup and improve error messages
2022-10-23 03:15:58 -04:00
a921a6bdc1
silence compiler warning about not copying the final null byte
2022-10-23 03:15:47 -04:00
51a0345941
Update fix_bond_react.rst
2022-10-23 03:15:35 -04:00
8d70960e2d
bond/react: create atoms error check
...
check that post-reaction template has 'Coords' section if it has 'CreateIDs' section
2022-10-23 03:15:12 -04:00
5661703b30
Update pair_threebody_table.cpp
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Correcting for hard coded ntheta = 79 in the extreme case that theta is exactly equal to 180.0 degrees.
2022-10-23 03:13:50 -04:00
bc30304f72
update plumed package version to 2.8.1
2022-10-22 23:01:47 -04:00
c76da483fb
must bootstrap centos 7 from dockerhub now
2022-10-22 22:59:52 -04:00
036a1e47d2
replace one more suffix
2022-10-22 22:28:35 -04:00
5430c3b592
add workaround for missing links to fortran functions in sphinx output
2022-10-21 19:01:31 -04:00
9b7cb8200c
small sphinx tweaks. require sphinx 5.2 or later.
2022-10-21 19:01:24 -04:00
550eedbb1f
make Linux behavior default for loading Python shared lib
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This adds portability to platforms like FreeBSD
2022-10-21 15:52:26 -04:00
3a058f278d
Python support in ML-IAP requires NumPy. Check for it if CMake supports it.
2022-10-21 15:50:08 -04:00
0f7f0b5f86
find cythonize executable on recent FreeBSD versions
2022-10-21 11:39:02 -04:00
3de7534b84
try to make more portable (in case this ever gets ported to windows)
2022-10-21 11:38:50 -04:00
7065462faf
add md5sums for plumed 2.7.5 and 2.8.1, update default version to 2.8.1
2022-10-21 11:38:40 -04:00
2e9d8e1ccb
preserve pair/only package setting during clear command
2022-10-19 14:50:27 -04:00
19b84f7cbd
delete atomfile variables when using the clear command
2022-10-19 14:44:10 -04:00
9b7c445a15
include non-buffered flag
2022-10-19 14:44:04 -04:00
91e56444ce
add CMake check that will refuse compilation of unit tests or skip tests
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This is mainly because the default compilers on RHEL/CentOS 7.x are
not sufficient to compile googletest. Also some Fortran module test
requires a working F90 module and others are more recent Fortran compiler.
2022-10-17 18:12:21 -04:00
9b3c8c36bd
update version
2022-10-14 21:35:16 -04:00
3403520967
Fix issue with KSpace slab correction energy with non-neutral systems
2022-10-11 16:37:45 -04:00
d8f969f1df
update python package requirements for building the manual
2022-09-30 20:18:05 -04:00
3487deccb6
update broken URLs
2022-09-27 08:03:11 -04:00
0926fc627d
step update counter
2022-09-25 09:04:45 -04:00
7999778d94
initialize sllod fixes consistently
2022-09-25 07:02:35 -04:00
b4ef4c1ff2
correct indentation
2022-09-25 07:02:35 -04:00
72b08e4b87
backport dump fixes from develop
2022-09-25 07:02:28 -04:00
faa64a84e8
bugfixes and updates to the DIELECTRIC package from upstream
2022-09-09 19:42:01 -04:00
32b67fff2b
print an error if the filename before '*' is too long for the regex matcher
2022-09-07 21:06:19 -04:00
f3dbf4122d
extend the length to which the regex matcher checks strings to 256 chars.
2022-09-07 20:47:16 -04:00
e25ac786da
must apply bond/angle offsets when determining shake bond/angle types
2022-09-05 10:52:06 -04:00
f30fba0061
support paths with blanks and avoid race condition when updating potentials
2022-09-02 21:33:30 -04:00
03f319604f
recover dump_modify every behavior
2022-08-31 17:26:09 -04:00
0782dab1ec
properly initialize result storage for per-chunk arrays
2022-08-29 13:04:40 -04:00
c43cce54ab
re-initialize neighbor lists at end to clear out the occasional list entry
2022-08-28 11:47:27 -04:00
281a368702
correct pair coeff mixing diagnostic for CLASS2 pair styles
2022-08-28 05:51:38 -04:00
f28d69b429
bugfix for writing data files with atom style dielectric
2022-08-19 16:18:38 -04:00
e674e0c927
correctly handle the case where there are no atoms in the fix group
2022-08-14 03:53:02 -04:00
eebabf99b8
adjust location of local ref targets for recent sphinx versions
2022-08-05 22:09:01 -04:00
23a19f4431
need new CSS hack to hide duplicate headers derived from the navigation bar
2022-08-05 21:46:38 -04:00
d618b0ffc0
Merge pull request #3324 from akohlmey/maintenance-2022-06-23
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First round of maintenance fixes for the stable release
2022-08-05 16:57:43 -04:00
ffc71b8733
energy is not an array
2022-08-05 08:23:23 -04:00
564df78698
fix typo
2022-08-05 08:22:59 -04:00
8db0b5ca39
fix index copy-n-paste error
2022-08-05 08:22:09 -04:00
79e26fe829
correct bond style bpm/rotational example
2022-08-05 03:24:29 -04:00
523d4b0242
correct issues in fix adapt and fix adapt/fep related to using fix STORE
2022-08-04 10:19:26 -04:00
fe39a3e581
Documentation updates for simulations including dipoles
2022-08-03 16:47:29 -04:00
081cc1f992
clarification on what constituets single, double, and triple quotes.
2022-08-03 01:51:43 -04:00
53c80c2c00
match pow(0,0) = 1.0 behavior in powint()
2022-07-31 18:52:08 -04:00
554b64a147
avoid deprecation warning and update PyPy package requirements
2022-07-30 17:37:35 -04:00
