562296bdb7
Updated link to preprint article
2018-11-06 19:44:35 +00:00
91c4ef6f64
Merge pull request #1189 from jrgissing/bond/react-custom_group
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Bond/react custom group support
2018-11-06 10:32:06 -05:00
f46d6a4312
Merge pull request #1192 from julient31/master
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update reference for SPIN package
2018-11-06 10:26:27 -05:00
cb828e9579
update reference
2018-11-06 07:48:47 +01:00
ed77701e56
Merge pull request #31 from lammps/master
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rebase
2018-11-05 20:25:38 -07:00
7ed6cab040
do not generate illegal dihedrals, e.g. from 3-membered rings
2018-11-05 20:35:43 -05:00
81e79ec884
Have KIM use LAMMPS specified compilers
2018-11-05 15:39:10 -06:00
4a4147e0e4
Remove hard-coded compiler versions for KIM in CMake
2018-11-05 11:15:07 -06:00
29ae88e309
Update docs for KIM
2018-11-05 09:37:35 -06:00
dd61ded311
Update cmake build to work with cmake-based KIM
2018-11-05 09:31:21 -06:00
ce7f76de1d
cmake: switch plumed to full static mode
2018-11-05 07:39:23 -07:00
58d2f0cc57
cmake: fix linking again plumed
2018-11-05 05:55:31 -07:00
ab7aa9dfda
correction to fix group property doc
2018-11-05 00:49:33 -07:00
6d1ea2d0b1
broke smooth restarts at some point. fixed
2018-11-05 00:46:53 -07:00
9ed6f2fc43
Adjust lib/kim install script and settings
2018-11-04 20:10:04 -06:00
a3ca177d20
various small changes and reformatting
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- add memory usage estimator
- test against varying number of atoms
- test against non-consecutive atom tags
- test for 32-bit overflow in number of atoms
- test for 32-bit overflow in timestep
- reduce tail correction error to warning
- more LAMMPS style formatting of the source code
- remove trailing whitespace
- avoid leaking memory from allocated arrays for masses/charges/tags
2018-11-04 19:52:10 -05:00
a3c0fe7726
Added check on fix modify for PLUMED to ensures that virial is calculated for group all
2018-11-04 11:43:07 +00:00
a051d61e1f
Added functionality to support fix modify for fix plumed
2018-11-04 11:24:01 +00:00
8cb665f013
Added functionality to throw error when time step changes and PLUMED is being used
2018-11-04 10:21:28 +00:00
cb8c51e353
Got rid of some of the hard-coded units in the plumed interface
2018-11-03 18:13:28 +00:00
a37d718ed1
update bond/react examples
2018-11-03 12:01:00 -06:00
f7aa01d74a
bond/react: convert group-ID to group-ID-prefix
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enables consistent syntax when using custom groups
2018-11-03 11:57:46 -06:00
badfdd7433
download only the plumed-src package and include further tweaks to be compatible with plumed 2.5b
2018-11-03 00:21:10 -04:00
ac11d66d5a
provide reference logfiles and move generated files to reference folder
2018-11-02 23:28:09 -04:00
18216de084
correctly check for fixes that maintain their own pressure compute
2018-11-02 23:21:09 -04:00
3cb2291a5a
need to include comm.h now
2018-11-02 22:52:51 -04:00
54c52c3bdf
adjust compilation settings to link in plumed library statically and all its dependencies
2018-11-02 22:52:36 -04:00
df3390e224
update formatting to closer match LAMMPS' programming style
2018-11-02 21:33:30 -04:00
d185b34b19
reformat to closer match LAMMPS programming style
2018-11-02 21:19:53 -04:00
30518a993b
add LAMMPS header
2018-11-02 21:14:36 -04:00
b7e507a258
fix typo and reformat
2018-11-02 21:08:45 -04:00
ea9746f26d
insert fix plumed docs into manual generation
2018-11-02 21:08:32 -04:00
2635f7d160
Merge pull request #1190 from giacomofiorin/colvars-update
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Update Colvars library to version 2018-10-16
2018-11-02 20:11:28 -04:00
85a5cab663
Update Colvars library to version 2018-10-16
2018-11-02 17:45:20 -04:00
b1c50e3bbe
Added plumed documentation in a txt file
2018-11-02 19:50:49 +00:00
b0938b70d5
Merge branch 'master' into kim-v2-update
2018-11-01 19:41:13 -05:00
8dd3bce7c5
Update to C KIM_API bindings
2018-11-01 19:33:52 -05:00
0c7c344e19
additional molecule templates sanity-check
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thanks to Sagar Patil for report
2018-11-01 01:26:12 -06:00
b67e54dd7d
reciprocal 'related commands'
2018-11-01 01:09:52 -06:00
5821a5ecc8
bond/react: custom group with stabilization option
2018-11-01 01:04:45 -06:00
20b9c7fd79
Merge pull request #30 from lammps/master
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rebase
2018-10-31 20:15:45 -06:00
a66d4c7451
Merge pull request #1186 from akohlmey/various-small-fixes
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Various small fixes
2018-10-31 12:13:38 -04:00
7514838700
put LAMMPS sources folder first in list of include directories
2018-10-31 04:18:08 -04:00
1fccb391a6
Merge pull request #1185 from jrgissing/bond/react-update_edges-option
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Bond/react: update edges option
2018-10-31 00:43:07 -04:00
688945a0ef
silence compiler warnings about initialization order and unused args
2018-10-31 00:34:58 -04:00
50b99c8450
silence compiler warnings about unused arguments
2018-10-31 00:19:06 -04:00
446b05ebc1
silence warning about initialization order
2018-10-31 00:17:17 -04:00
2a5cd1d31e
remove debug output
2018-10-31 00:16:44 -04:00
3faecc4d28
add option to update all atoms' atomic charges
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option to update all atomic charges, even when edge atoms are defined
2018-10-30 22:11:52 -06:00
762a4b97ac
Revert "pair_kim - no need to comm vatom() values"
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This reverts commit 9962f941e6
2018-10-30 21:54:59 -05:00
