9470a0eeb6
clarified doc pages for fix property/atom and read_data
2021-08-19 11:34:25 -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
a9ff9312d6
Merge remote-tracking branch 'origin/master' into varargs-log-error-functions
2021-04-28 18:13:31 -04:00
7b1b57aa9b
rename utils::fgets_trunc_nl() to utils::fgets_trunc()
2021-04-27 18:32:51 -04:00
15cff295c0
change read_data to use new utility function
2021-04-27 16:14:08 -04:00
18215ff3e7
Merge remote-tracking branch 'origin/master' into more-unit-tests
2021-04-26 14:48:14 -04:00
6b04ebd617
Merge branch 'master' into varargs-log-error-functions
2021-04-26 13:27:58 -04:00
e9e0bb71b6
Use varargs version of Error:all() and Error::one() where applicable
2021-04-25 21:30:51 -04:00
7e7a448a08
remove the old versions of the utility function and use the new
2021-04-24 21:33:36 -04:00
6943a3da35
must check if file is readable before changes to internal data
2021-04-24 07:12:45 -04:00
d2cdb318ab
apply new logmesg() overload to a bunch of cases.
2021-04-21 23:38:45 -04:00
b53822da46
provide Command base class in command.h for deriving command styles from
2021-04-13 17:47:00 -04:00
1ca38db9df
simplify and avoid temporary buffers when piping to/from gzip
2021-04-07 23:26:21 -04:00
2e86cb4176
for atom style template number of bonds does not depend on newton_bond
2021-03-30 15:33:11 -04:00
b9bc226e39
save style names alongside the classes when using read_data nocoeff
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this fixes #2673
2021-03-19 10:06:02 -04:00
42895ac6df
Merge pull request #2654 from akohlmey/collected-small-changes
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Collected small changes
2021-03-16 19:34:54 -04:00
5d5fc4a04d
simplify by using utils::strdup()
2021-03-16 08:56:52 -04:00
8c4918457f
consistently compare atom->molecular against enumerator constants
2021-03-14 01:25:22 -05:00
e6def05178
refactor parse_coeffs() function to avoid calling strtok()
2021-03-13 18:09:36 -05:00
882b221a17
rename arg,narg,maxarg to avoid shadowing in command() function
2021-03-13 17:35:49 -05:00
955da06aca
avoid segfaults with non-template atoms when reading data files
2020-10-26 23:02:24 -04:00
adf74b3a22
use https://lammps.sandia.gov based URLs consistently
2020-10-21 16:45:30 -04:00
c01ff34785
we must initialize the number of types with any "extra" values
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so far, the "extra" value will only be applied if the "types" line is
present in the header. if not, the "extra" value is ignored. now will
first apply this and then lets it be overwritten in case a "types" line
is present in the header.
2020-10-11 23:26:35 -04:00
0f6a34775c
Merge branch 'master' into symbolic-atom-constants
2020-09-15 17:44:31 -04:00
618b08dcfc
Merge branch 'master' into symbolic-atom-constants
2020-09-15 14:58:13 -04:00
326d9f398c
Merge branch 'master' into iss2345
2020-09-15 14:06:16 -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
16d2fef5ad
add check that shrinkwrap boundaries are not use when reading a data file while a MSM kspace style is defined
2020-09-12 11:06:20 -04:00
9d0c3bc665
replace some numeric constants in Atom and AtomVec classes with enumerators
2020-09-11 19:07:55 -04:00
c7c4297cfc
update include handling for commands
2020-09-03 00:51:58 -04:00
a4a1f7e848
more IWYU cleanup
2020-09-02 23:49:17 -04:00
96d8d12a88
replace calls to force->*numeric() with the corresponding utils::*numeric()
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this also removes the now obsolete functions from Force
2020-08-29 20:31:02 -04:00
feebdf9149
print complete read_data and special output to both screen and logfile
2020-07-22 07:23:33 -04:00
7918919d30
enable write_data for atom styles with bonus data
2020-07-06 17:30:45 -06:00
eafcc06670
secs -> seconds
2020-06-30 13:56:35 -04:00
e4a3a518f7
more use of fmtlib and std::string
2020-06-25 22:50:38 -04:00
4f804f58e3
Merge remote-tracking branch 'origin/master' into refactor-table-reading
2020-06-05 16:41:05 -04:00
7df387f7d5
Merge remote-tracking branch 'origin/master' into refactor-table-reading
2020-06-05 12:09:57 -04:00
f547d66104
Merge branch 'master' into more-fmtlib-and-string
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# Conflicts:
# src/write_restart.cpp
2020-06-05 11:13:44 -04:00
73c6171ad6
get rid of BIGINT_FORMAT and use utils::logmesg()
2020-06-05 08:19:45 -04:00
54a8b4e08b
more local buffers removed and file error status added.
2020-06-04 20:14:19 -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
ecd3652f61
update to current master
2020-04-30 11:57:17 -06:00
ac143dbdb7
capitalize comment
2020-01-21 17:57:12 -07:00
11f687c1fb
make comment string consistent
2020-01-21 17:56:00 -07:00
646dc83394
remove trailing whitespace
2020-01-21 15:46:28 -05:00
90ff2eb6c9
modified versions of creating atoms on subset of lattice, ditto for set type/fraction
2020-01-21 13:31:47 -07:00
4f6cb13592
added atom styles with bonus data, also a few USER packages
2019-11-27 16:03:50 -07:00
