00557e00a4
Add AtomState struct and ASSERT helpers
2020-11-13 12:35:25 -05:00
26a8d875e9
whitespace fix
2020-10-29 14:52:22 -04:00
f2b9db0de4
update atom style tester to test replicate for atom style template
2020-10-29 06:21:54 -04:00
c7b39283b1
need to transfer molecule templates when using "replicate"
2020-10-29 05:58:39 -04:00
584943fc92
Merge pull request #2458 from akohlmey/next_lammps_version
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Step version string for next LAMMPS release
2020-10-28 19:53:36 -04:00
00ef63049a
Merge pull request #2456 from akohlmey/final-changes-for-stable
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Final changes for stable release
2020-10-28 18:46:51 -04:00
f55c24ff96
Merge pull request #2455 from stanmoore1/relax_NaN
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Add non-numeric pressure check to fix box/relax
2020-10-28 17:37:42 -04:00
4f9ec11311
Merge pull request #2448 from akohlmey/fix-read-dump-issues
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Fix a couple issues related to read dump
2020-10-28 17:15:26 -04:00
bf87c0dc56
add (incomplete) unit test for atom style template
2020-10-28 15:43:36 -04:00
9f1526c66d
cannot currently use replicate command with atom style template
2020-10-28 15:42:50 -04:00
c25ef8edb0
fix segfault: must not count bonds on atoms that are not in a molecule
2020-10-28 15:11:19 -04:00
72f4650b52
Merge pull request #2460 from stanmoore1/kk_bugfix
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Kokkos bugfix for pair forward comm
2020-10-28 12:46:46 -04:00
99c99e86e0
Kokkos bugfix for pair forward comm
2020-10-28 09:15:49 -06:00
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
d2c6c89ccc
step version string for next LAMMPS release
2020-10-28 08:09:23 -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
6f66f5b23b
Add non-numeric pressure check to fix box/relax
2020-10-27 13:55:50 -06:00
e38dcb9302
Merge branch 'master' into fix-read-dump-issues
2020-10-27 13:06:52 -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
