75e897b2fe
new utility function "utils::expand_type" to convert type labels to numeric strings
2022-09-05 05:45:31 -04:00
e1960bbb9a
streamline type label howto and remove discussions of not yet available features
2022-09-04 22:52:31 -04:00
e0b6ae77d3
update parser for bonded topology data
2022-09-04 22:13:23 -04:00
fc738ea239
type offsets are only applied to numeric types
2022-09-04 22:12:59 -04:00
53d82056ce
add molecule file tests with type labels
2022-09-04 21:09:43 -04:00
c376d72158
update parsing for Types section in molecule files
2022-09-04 17:52:31 -04:00
f956530f0d
add labelmap tests for bonds/angles/dihedrals/impropers
2022-09-04 17:51:06 -04:00
c7ab8e160a
fix logic bug
2022-09-04 17:43:20 -04:00
a7d4d819ef
update error handling for read_data command
2022-09-04 16:15:13 -04:00
14871facf2
accept type labels in Masses section of data file
2022-09-04 07:08:16 -04:00
8ad949a995
avoid extra char * to std::string conversion
2022-09-04 07:07:55 -04:00
26e1b7c44d
add UTF-8 substitution and detection
2022-09-04 06:45:11 -04:00
34104bbbe9
enable clang-format
2022-09-04 05:40:19 -04:00
3dc7b7e0b3
update parsers for bond topology data in data files
2022-09-04 05:27:29 -04:00
ad8a931fe4
revise/refacor Type Label section parsing and Atoms section parsing
...
- do not ignore numeric type in Type Label sections
- refuse invalid numeric types that will overflow arrays
- check for duplicate numeric type entries or non-unique labels
- better error messages
- use Tokenizer class instead of sscanf()
2022-09-04 01:01:36 -04:00
389c87ab7e
apply utils::is_type() to labelmap command
2022-09-03 23:26:56 -04:00
ca6222c12b
implement utils::is_type() convenience function
2022-09-03 23:18:44 -04:00
81b0cec887
improve death tests
2022-09-03 20:26:38 -04:00
7ecfb77e8d
implement "labelmap write" command
2022-09-03 19:52:07 -04:00
bb45137b1a
small tweaks to support type labels with single and double quotes. add tests
2022-09-03 19:04:24 -04:00
b143f87d10
bugfix
2022-09-03 18:12:22 -04:00
d43051d07c
allow '#' character in type labels. support also when reading Atoms section
2022-09-03 16:48:39 -04:00
8d9adeef16
clarify comments
2022-09-03 14:13:38 -04:00
fa1584cc17
add "labelmap clear" command, update docs
2022-09-03 12:38:07 -04:00
849b41f67a
more basic tests
2022-09-03 11:47:16 -04:00
e7916a7e18
improve error message
2022-09-03 11:47:06 -04:00
e43a8ac8c3
add basic unit tests for labelmap command
2022-09-03 11:14:01 -04:00
5772547a68
improve input error handling
2022-09-03 11:13:47 -04:00
50256d6bec
fix initialization issues
2022-09-03 10:48:36 -04:00
2307436b76
improve flow of control and remove redundant checks
2022-09-03 10:40:17 -04:00
2eca1eecdc
initialize LabelMap class through constructor, properly wipe out old data
2022-09-03 10:39:55 -04:00
fc67df3b5f
fix memory management bug
2022-09-03 10:38:31 -04:00
b60f144705
more formatting/typesetting consistency
2022-09-03 04:17:22 -04:00
b4eb3e8156
support paths with blanks and avoid race condition when updating potentials
2022-09-03 03:56:58 -04:00
9b41d28947
Merge branch 'develop' into type-labels
...
# Conflicts:
# doc/src/dihedral_coeff.rst
2022-09-01 21:09:04 -04:00
8315f9996b
Merge pull request #3425 from lammps/coverity
...
Add coverity workflow
2022-09-01 18:17:03 -04:00
2a8d4d6cf4
also allow to trigger the coverity workflow manually
2022-09-01 16:10:30 -04:00
cfee2078f1
Add coverity workflow
2022-09-01 12:05:30 -06:00
22f7255e1d
Merge pull request #3421 from phankl/mesocnt_stable
...
Major update to mesocnt styles
2022-08-31 11:54:22 -04:00
0c23ba71df
update md5hash for updated potential
2022-08-31 11:25:48 -04:00
0cc6ad8318
cosmetic. silence compiler warnings. remove dead code.
2022-08-31 11:25:35 -04:00
a288507934
corrected friction description
2022-08-31 15:37:30 +01:00
a85fbd83f4
mentioned interpolation range dependence of potential on delta1/2 values in doc
2022-08-31 15:11:01 +01:00
2bded3da5e
repeatable example
2022-08-31 12:42:47 +01:00
4e1a346f5a
changed SWITCH parameter in pair_mesocnt for better energy conservation
2022-08-31 12:34:35 +01:00
30191462f5
added change and add dates to doc
2022-08-31 12:33:22 +01:00
85965f01ce
spelling
2022-08-30 14:44:01 -04:00
46fa86a1e0
modernize and fix memory leak
2022-08-30 14:33:23 -04:00
e6088e73d7
make runs more reproducible and apply LAMMPS conventions
2022-08-30 14:28:17 -04:00
4c64a2f2a1
fix out-of-range memory access in sort function
2022-08-30 14:27:28 -04:00
