2e6526b8f7
log labelmap reading from data file and improve error messages
2022-09-09 06:11:22 -04:00
3b6a06fcf5
small behavior tweaks for inputs without labelmap, add warnings about type offsets
2022-09-06 18:18:44 -04:00
a7d4d819ef
update error handling for read_data command
2022-09-04 16:15:13 -04:00
26e1b7c44d
add UTF-8 substitution and detection
2022-09-04 06:45:11 -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
50256d6bec
fix initialization issues
2022-09-03 10:48:36 -04:00
2eca1eecdc
initialize LabelMap class through constructor, properly wipe out old data
2022-09-03 10:39:55 -04:00
4b842d52e6
Merge branch 'develop' into type-labels
2022-08-22 10:45:48 -04:00
92c9614429
Merge branch 'develop' into refactor-find-xxx
...
# Conflicts:
# src/atom.h
# src/compute_centroid_stress_atom.cpp
2022-08-17 15:48:26 -04:00
f592e3184e
simplify Molecule::check_attributes()
2022-08-13 16:56:53 -04:00
a4faa3aced
modernize using get_fix_by_id()
2022-08-13 01:49:00 -04:00
363b80f85c
begin unfeaturing multiple label maps feature
2022-08-09 01:01:31 -04:00
f9717049b1
Merge branch 'develop' into type-labels
2022-08-08 17:16:50 -04:00
97fab45f7e
Merge branch 'develop' into amoeba-ak
2022-05-28 05:24:02 -04:00
f0f6660050
join lines
2022-05-26 12:15:27 -04:00
929734ce45
Merge remote-tracking branch 'github/develop' into amoeba-ak
...
# Conflicts:
# doc/src/Commands_pair.rst
# src/memory.h
2022-04-28 20:08:18 -04:00
13664a0185
add utility to print url with pointer to error message
2022-04-22 05:25:50 -04:00
f8f2b9542e
sync with current develop
2022-04-18 17:29:23 -06:00
200b4f13c7
use dynamic cast instead of c-style cast when casting from base type to derived class
2022-04-10 18:18:06 -04:00
39b316729b
use auto type when assigning from cast or using new
2022-04-10 18:16:36 -04:00
f3fa04ae0a
bugfix
2022-03-30 15:01:03 -04:00
999c880dfd
simplify parsing numbers and reduce usage of BIGINT_FORMAT
2022-03-30 07:12:25 -04:00
e13a70ad2f
Merge branch 'develop' into type-labels
2022-03-23 01:08:35 -04:00
bbe065e649
initial version of fix pitorsion
2022-03-09 15:37:19 -07:00
844ea0ab8e
UB testing
2022-03-08 15:37:16 -07:00
3bc91386a0
apply include statement updates suggested by running IWYU
2022-02-13 19:39:15 -05:00
4104353d7a
plug memory leak
2022-01-20 16:55:59 -05:00
9efa2369dd
join wrapped strings
2021-12-31 14:34:24 -05:00
c17a183816
do error checking already in read_data code
2021-12-31 14:34:09 -05:00
863de683ee
do not shadow "natoms" class member
2021-12-31 13:43:56 -05:00
83a978d69b
error messages
2021-12-07 23:32:14 -05:00
ee9ea4f80f
whitespace
2021-12-06 23:08:30 -05:00
76eb4f8057
Update the implementation & typelabels interface
...
Update the typelabels interface in the code and update the
LabelMap use based on class changes.
2021-11-28 18:55:55 -06:00
5bc399c22b
force unique labels in data file
...
note: not possible to create duplicate label in a second data file (if duplicate, assigns to existing label)
still need to enforce unique labels when using labelmap command
2021-11-07 01:01:41 -04:00
049895b3e4
correct merge conflict
2021-11-05 01:11:08 -04:00
8d4956046b
Merge branch 'develop' of https://github.com/lammps/lammps into lammps-develop
2021-11-04 21:20:29 -04:00
adf1beea74
add mechanism to check for known data file section names
...
using this mechanism we can reject custom section names that will
conflict with existing section names and thus avoid misleading errors.
apply this also to fix property atom, where the section name is
determined by the fix ID.
in addition, allow to specify NULL as section name, which will use
the fix ID.
2021-10-28 14:23:27 -04:00
85433e8bd1
use true/false instead of 1/0 detected and changed by clang-tidy
2021-10-20 12:41:02 -04:00
f4851e9103
change check for reset image flags to print messages only once per data file
2021-10-13 21:54:18 -04:00
6a9bb577cf
rename "zip" functions to "compress" functions. update related docs
2021-10-07 12:38:11 -04:00
ec1a55b35b
use platform code for reading/writing of compressed text file via a pipe
2021-10-06 15:04:48 -04:00
8b36061db4
replace MPI_Wtime() with platform::walltime()
2021-10-05 22:53:39 -04:00
37bfe3d0ce
integrate platform sub-namespace into source code and documentation
...
this updates function calls to functions that have been moved from
the utils namepsace or the Info class to platform::
2021-10-02 16:55:11 -04:00
67ae6eb7b6
Merge branch 'lammps:master' into type-labels
2021-09-30 09:44:18 -04:00
973cf017a9
do not call memset on a null pointer
2021-09-24 15:32:59 -04:00
f7bd07b3e6
whitespace
2021-09-18 17:03:03 -04:00
c63d6ce790
minor update
2021-09-15 07:07:48 -05:00
ee166cbe85
remove extra white space
2021-09-01 13:15:41 -05:00
edfac22f39
memory leak
2021-08-28 15:56:14 -04:00
