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
41a3eccd1c
apply utils::logical() to more commands
2021-09-21 07:48:50 -04:00
7d92d665e8
use explicit scoping when virtual dispatch is not available.
2021-09-15 16:08:17 -04:00
42a3a7d10f
Merge branch 'master' into collected-small-changes
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# Conflicts:
# src/fix_property_atom.cpp
2021-08-26 21:14:23 -04:00
ab8c9851b2
change style to styles to remove override of fix->style string
2021-08-26 15:20:52 -06:00
dfc03bd107
avoid 32bit integer overflow on 64-bit storage sizes
2021-08-24 15:49:41 -04:00
1a81a94dfb
fix up whitespace issues (remove tabs, trailing whitespace)
2021-08-20 15:00:19 -04:00
c53875421b
fix read_data bug
2021-08-18 22:50:42 -04:00
b942c4d122
fix data corruption bug affecting write_data
2021-08-18 22:31:46 -04:00
d9f3745eff
pretty
2021-08-18 20:26:01 -04:00
546c9a109e
fix uninitialized data bug
2021-08-18 20:25:49 -04:00
0a99d338f2
update argument parsing
2021-08-18 14:35:02 -04:00
e08c4abb4b
whitespace fixes
2021-08-18 13:06:00 -04:00
c50abed92b
recover compilation
2021-08-18 12:59:31 -04:00
2bf9fa91db
more changes to merge with current master
2021-08-17 14:03:58 -06:00
e6af1eecb8
resolved merge conflicts with master
2021-08-17 11:55:33 -06:00
09c19a936b
update URLs in source code and manual
2021-05-24 14:18:20 -04:00
d1941392d3
disable clang-format for all existing .cpp files (for now)
2021-05-05 23:53:38 -04:00
e9e0bb71b6
Use varargs version of Error:all() and Error::one() where applicable
2021-04-25 21:30:51 -04:00
4b076e01be
silence compiler warning
2021-03-22 21:36:33 -04:00
a6e6f43d55
write a comment to the custom data file section with the column assignment
2021-03-14 15:36:09 -04:00
3642dcfedb
use ValueTokenizer for parsing fix property/atom sections of data files
2021-03-14 15:35:12 -04:00
826c618aa9
replace a few more cases of atoi()/atof() with utils::*numeric() functions
2021-02-21 15:09:50 -05:00
cf427bcad8
apply utils::strdup() in a few more cases
2021-02-04 17:52:32 -05:00
4e791ac4f7
replace 'strstr(xxx,"x_") == xxx' with utils::strmatch("^x_")
2021-02-04 15:20:43 -05:00
0b14770468
merge with current master
2021-01-11 16:13:33 -07:00
adf74b3a22
use https://lammps.sandia.gov based URLs consistently
2020-10-21 16:45:30 -04:00
0f6a34775c
Merge branch 'master' into symbolic-atom-constants
2020-09-15 17:44:31 -04:00
93a0d4c096
fix up some comments
2020-09-12 14:26:34 -04:00
f1ef7d85a8
T2345: Replace instances of NULL with nullptr
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The following changes have been applied to src and lib folders:
regex replace: ([^"_])NULL ⇒ \1nullptr (8968 chgs in src, 1153 in lib)
Manually find/change: (void \*) nullptr ⇒ nullptr (1 case)
regex find: ".*?nullptr.*?"
Manually ~14 cases back to "NULL" in src, ~2 in lib
regex finds a few false positive where nullptr appears between two
strings in a function call
2020-09-12 09:34:38 -06:00
9d0c3bc665
replace some numeric constants in Atom and AtomVec classes with enumerators
2020-09-11 19:07:55 -04:00
d1442b0538
enable per-atom custom arrays in addition to vectors
2020-09-04 11:33:49 -06:00
6113169a47
IWYU based include statement cleanup
2020-09-02 17:39:34 -04:00
e3beec8b95
revert permission change and replace 'b/c' with 'because'
2020-08-10 11:37:52 -04:00
41904f7946
Added cautionary comments
2020-08-08 09:15:56 -06:00
7df387f7d5
Merge remote-tracking branch 'origin/master' into refactor-table-reading
2020-06-05 12:09:57 -04:00
2777d37a61
remove local buffers and snprintf() for file open error messages.
2020-06-04 13:30:44 -04:00
9291d2a9d7
Simplify count_words, add trim_and_count_words
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The original count_words function (before it was put into utils::) also trimmed
comments. For compatibility this behaviour was retained at first. However, due
to the name the trimming is not immediatly apparent and many times not
wanted.
Therefore, this commit replaces count_words with an implementation that
just does what it says. If a comment should be trimmed there is a
trim_comment function. For convenience, a trim_and_count_words function was
added and is now used where the old behaviour was needed.
2020-06-04 11:13:37 -04:00
4a2d3e95cb
Replace Atom::count_words with utils::count_words
2020-05-20 15:53:19 -04:00
7967cb1133
put implementation header first to avoid issues with mpi.h and lmptype.h with OpenMPI
2019-07-03 06:16:16 -04:00
31cbccda85
continue cleaning up include file lists
2019-06-29 09:37:44 -04:00
ca04e8f31c
use snprintf() in a bunch of cases to avoid overflowing fixed size buffers with unchecked strings
2018-09-06 02:57:53 -04:00
71bc72ec13
formatting: add additional space to avoid bad syntax highlights
2018-08-27 22:13:43 -04:00
e9bc939098
Fix more unused parameter warnings ( #1076 )
2018-08-23 12:22:44 -06:00
e4071d7f46
replace C-style include files with their C++ equivalents
2018-04-27 18:00:24 -04:00
415a55bc3e
Fix bug in fix_property_atom
2018-01-17 10:41:56 -07:00
d5f8f36442
Change to fix_property_atom to allow virtual override of grow_arrays() function
2016-12-15 15:48:09 -07:00
958e3e6a80
sync with Git
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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15520 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-08-29 23:49:20 +00:00
e135e3ee79
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15188 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-06-17 18:29:08 +00:00
b29c07bd76
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14914 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-04-30 18:10:54 +00:00
