3a0b49b5bf
Merge branch 'develop' into type-labels
2022-09-06 19:16:07 -04:00
55f97e5fbc
whitespace
2022-09-06 19:15:18 -04:00
1d986280ce
rename variable special function to retrieve types for labels to label2type()
2022-09-06 18:56:00 -04:00
3b6a06fcf5
small behavior tweaks for inputs without labelmap, add warnings about type offsets
2022-09-06 18:18:44 -04:00
1a5a509c1d
add typelabel support for Shake Bond Types section in molecule files
2022-09-05 10:28:00 -04:00
4f3f2412fb
replace Input::readtype() with utils::expand_type()
2022-09-05 06:16:18 -04:00
75e897b2fe
new utility function "utils::expand_type" to convert type labels to numeric strings
2022-09-05 05:45:31 -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
c376d72158
update parsing for Types section in molecule files
2022-09-04 17:52:31 -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
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
fa1584cc17
add "labelmap clear" command, update docs
2022-09-03 12:38:07 -04:00
e7916a7e18
improve error message
2022-09-03 11:47:06 -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
6c8750c041
Merge branch 'develop' into collected-small-changes
2022-09-02 16:41:14 -04:00
ff10b2bc26
modernize accessors and error handling in fixes box/relax and spring/chunk
2022-09-02 05:42:35 -04:00
9b41d28947
Merge branch 'develop' into type-labels
...
# Conflicts:
# doc/src/dihedral_coeff.rst
2022-09-01 21:09:04 -04:00
b0f58bd7c4
select array dimension so they cannot be overflown
2022-09-01 16:03:56 -04:00
ea254d9105
remove bogus else branch
2022-09-01 16:03:23 -04:00
d503e441ff
modernize accessor handling
2022-09-01 16:03:02 -04:00
7bba3c516f
avoid excess string copy in auto loops
2022-09-01 16:02:32 -04:00
e0e4be1872
alternate workaround for hipcc/dpcpp fmtlib issue from upstream
2022-09-01 14:18:05 -04:00
6a745f40ea
make bugfix compatible with using a variable for dump_modify every
2022-08-31 17:19:44 -04:00
673eeff581
recover dump_modify every behavior
2022-08-31 14:39:46 -04:00
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
4e1a346f5a
changed SWITCH parameter in pair_mesocnt for better energy conservation
2022-08-31 12:34:35 +01:00
d874976222
Merge branch 'develop' into collected-small-changes
2022-08-30 14:59:07 -04:00
46fa86a1e0
modernize and fix memory leak
2022-08-30 14:33:23 -04:00
4c64a2f2a1
fix out-of-range memory access in sort function
2022-08-30 14:27:28 -04:00
3c52be6a44
prevent clang-format from messing up Style macros
2022-08-30 13:20:59 -04:00
227d794876
update MD5HASH for automatic download of updated potential file
2022-08-30 12:53:20 -04:00
