d64bbb99bf
add examples for demonstrating the use of atom style template
2020-10-26 23:10:45 -04:00
955da06aca
avoid segfaults with non-template atoms when reading data files
2020-10-26 23:02:24 -04:00
8975c7e316
relax checks to avoid segfaults and accept non-template atoms
2020-10-26 23:01:58 -04:00
efd31fbb60
fix up placement of polyfill loader layout.html and load it only for internet explorer
2020-10-26 21:03:05 -04:00
731072cfb8
handle case of molecule template atoms not included in shake
2020-10-26 18:49:59 -04:00
f70775bd52
cannot determine communication without a box
2020-10-26 18:49:30 -04:00
656b7eac8b
correctly report number of constrained bonds and angles
2020-10-26 18:49:09 -04:00
4475a095ce
Merge pull request #2453 from rbberger/cmake_gitversion_fix
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Enable gathering of git info with git v1.8.3.1
2020-10-26 18:45:52 -04:00
f7d9cf813f
Enable gathering of git info with git v1.8.3.1
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The -C flag wasn't supported back then. The workaround is to change the
working directory via CMake. This issue was detected while building on
CentOS 7.
2020-10-26 17:26:46 -04:00
d84bb54019
do not enforce atom types in molecule files for atom style template.
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types are only needed when creating atoms and presence is tested then.
2020-10-26 17:26:18 -04:00
ba97141d45
restore and correct read_data docs for atom style template
2020-10-26 17:25:16 -04:00
6554547b41
Merge pull request #2444 from stanmoore1/kk_global_dof
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Add support for extra global DOFs to Kokkos minimize
2020-10-26 17:07:27 -04:00
65e93cbaab
decrement/increment molindex and atomindex to have 1-based indices in files and 0-based internally
2020-10-26 17:06:27 -04:00
d9646472c3
Revert "support choosing the molecule index from the set of molecules in a template"
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This reverts commit 186359caa9
2020-10-26 15:46:58 -04:00
f9b45faa76
Merge pull request #2445 from akohlmey/lammps-shell-desktop
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Add desktop integration for LAMMPS shell
2020-10-26 15:41:25 -04:00
406d6e27ce
bond/react: clarify how reactions are searched for
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thanks to Ben Jensen (NASA Langley)
2020-10-26 11:22:35 -04:00
5159d255a7
update bundled fmtlib to version 7.1.0
2020-10-26 11:02:09 -04:00
b67950e130
update email
2020-10-24 13:54:27 -04:00
c2a852ddef
clarify exactly what is used to identify reaction site
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thanks to Øystein Gullbrekken for the suggestion
2020-10-24 13:46:28 -04:00
9c129d3a34
update output of read_restart to make read_data and signify if atom style template is used
2020-10-24 01:05:11 -04:00
186359caa9
support choosing the molecule index from the set of molecules in a template
2020-10-24 00:45:41 -04:00
13450606c6
update read_data docs with actual format for atom style template
2020-10-24 00:45:06 -04:00
4a6517fd51
for atom style template only write out the number of types
2020-10-23 21:51:55 -04:00
00e4e23456
only check for type overflows if a box has been created.
2020-10-23 21:51:10 -04:00
9e0062a9ef
we have a new map style when using atom style template
2020-10-23 21:50:38 -04:00
23e2a4af00
use symbolic constant
2020-10-23 21:50:18 -04:00
3bf081745d
add missing velocity comm ids
2020-10-23 21:50:04 -04:00
c62ddaa4a2
remove pre-box check so that atom style template can work
2020-10-23 21:10:41 -04:00
b4f1779b62
reformat with clang-format
2020-10-23 21:04:45 -04:00
1382559dbe
adapt behavior of lammps-shell when passing filename without -in/-i flag
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To better handle the case of file association. We now split the path into
a directory and basename string and change the current working directory
to that directory and read the file with the basename.
This simplifies the .desktop file and makes the LAMMPS shell behave as
expected on Windows, too.
2020-10-23 20:42:24 -04:00
b931501711
add utils::path_dirname() to complement utils::path_basename()
2020-10-23 20:40:18 -04:00
c51d2a286a
call resource compiler to include icon files into LAMMPS shell on Windows
2020-10-23 20:06:21 -04:00
5c98eeec1b
remove strtok dependency
2020-10-23 11:25:35 -04:00
ceaaf149eb
Whitespace cleanup
2020-10-23 08:53:53 -06:00
9543ff02c6
Fix memory issue
2020-10-23 08:49:53 -06:00
30c050fda7
Add missing global DOF calls
2020-10-23 08:36:48 -06:00
e3ecb6ccc4
must nullify "readers" array, so there is no crash when deleting it later
2020-10-23 04:21:15 -04:00
114f039a68
must not check for compatible dump frequency when using write_dump
2020-10-23 04:20:40 -04:00
39da827a2d
correct formatting style for keywords block
2020-10-23 02:24:11 -04:00
aa15f221d4
add missing "boff" keyword
2020-10-23 02:21:58 -04:00
3242cd5d31
mention desktop file and icons in README
2020-10-23 00:29:48 -04:00
8854e7b8de
Add desktop integration for LAMMPS shell
2020-10-23 00:20:15 -04:00
c29474c533
Merge pull request #2443 from akohlmey/next_lammps_version
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Step version strings for next release
2020-10-22 18:11:33 -04:00
ef048cad55
Add extra global DOFs for Kokkos minimize
2020-10-22 16:03:42 -06:00
c7a10050c2
Merge pull request #2439 from akohlmey/collected-small-changes
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Collected small changes for the next release
2020-10-22 17:23:49 -04:00
9bc3ccd49a
fix misplaced "#endif"
2020-10-22 15:45:24 -04:00
5ff0dbb431
step version strings for next patch release (and stable release candidate)
2020-10-22 15:36:58 -04:00
fcd442d751
simplify code. print warnings only on MPI rank 0. update parameter names
2020-10-22 15:35:45 -04:00
cfbeaad112
updates to kim_interactions to generalize interpretor for smspec.edn (logic to allow variants for aperiodic vs periodic simulations
2020-10-22 15:05:07 -04:00
68b533d1b8
correct order of functions
2020-10-22 14:59:55 -04:00
