c25ef8edb0
fix segfault: must not count bonds on atoms that are not in a molecule
2020-10-28 15:11:19 -04:00
94462bfb48
do not add langevin thermostat forces and torques if disabled, e.g. in 2d system.
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Note that fix rigid/small does not support the force or torque options and thus
the zeroing has to be done directly when computing the langevin data.
2020-10-28 10:41:20 -04:00
94f57d8849
rephrase paragraph about availability of the manual and add note about browser compatibility
2020-10-28 04:49:09 -04:00
9a3f935c9b
do not include polyfill.js anymore
2020-10-27 20:17:59 -04:00
5dc09ae3c0
increase timeout, properly handle timeouts, and fix symbol lookup in exception handling
2020-10-27 17:16:47 -04:00
5872b05e2f
Merge pull request #2447 from akohlmey/atom-style-template-fixes
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Fix bugs and update implementation of atom style template
2020-10-27 13:03:05 -04:00
b8e84d0070
Merge pull request #2442 from ProfessorMiller/master
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Create logic in parsing KIM Simulator Models to treat periodic vs. aperiodic simulations differently
2020-10-27 11:44:20 -04:00
3b267430ac
Merge pull request #2452 from jrgissing/bond_react-small-docs-updates
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Bond/react: docs clarifications
2020-10-27 11:03:46 -04:00
86f8b566f0
eliminate TABs
2020-10-27 00:39:52 -04:00
8976cf0230
Update data.spce
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The masses were assigned wrongly in the data file (although they eventually get overwritten in the in.gcmc.h2o script)
2020-10-27 00:35:51 -04:00
a3c887accb
update examples and include restart example, too.
2020-10-27 00:31:25 -04:00
6af2da7603
Correct path for icons and .desktop file
2020-10-26 23:56:55 -04:00
4a853cd838
Merge branch 'master' into atom-style-template-fixes
2020-10-26 23:56:48 -04:00
af483ca34f
small documentation update
2020-10-26 23:15:43 -04:00
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
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
39da827a2d
correct formatting style for keywords block
2020-10-23 02:24:11 -04:00
