a0c4fac428
assume type labels begin with letter
2021-01-19 22:56:06 -05:00
739dc46fab
type labels: restart support
2021-01-19 21:52:22 -05:00
e138cf2476
add labelmap command
2021-01-15 21:46:40 -05:00
d7fb74f0be
multi-data-file support for bond, angles, diheddral, impropers
2021-01-11 16:00:37 -05:00
03b697a6e0
labels: introduce framework for multiple data files
...
subsequent data files merge types with first
starting with support for selected atom types sections, will attach small example to PR
2021-01-08 23:22:19 -05:00
73968fb4d8
prepare for multiple data files
...
not yet tested
2021-01-07 20:15:25 -05:00
48e1d202fe
refactor to use read_data local lmap
...
also add errors to enforce order of read_data sections
2021-01-07 10:37:24 -05:00
fef2d178e4
use vector<string> for type label arrays
2020-12-17 14:21:42 -05:00
bc32dfb480
refactor into label_map class
2020-12-16 23:07:58 -05:00
a0911b7563
read_data: add bond, etc. label sections
2020-12-16 17:00:05 -05:00
af1e96c6df
generalize read typelabel function
...
will greatly reduce code # of lines
2020-12-16 12:43:17 -05:00
e4c7ec6933
read_data: add atomtypelabels section
...
type labels for atoms
2020-12-16 12:26:31 -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
...
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
...
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()
...
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
...
# 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
...
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
b6b022b610
whitespace cleanup: remove trailing blanks
2019-11-03 11:03:39 -05:00
a50d57bceb
Merge branch 'master' into improve-include-consistency
...
# Conflicts:
# src/utils.cpp
2019-07-19 17:57:58 -04:00
1de00aaab0
improve parsing of data file header
...
the header lines are now checked using regular expressions
instead of strstr() which allows for stricter checking, but
also is more forgiving in terms of extra or different whitespace
return value of sscanf() calls is checked and on failure LAMMPS errors out
2019-07-19 11:16:41 -04:00
ce6fa0118a
continuing to clean up include file lists
2019-07-04 08:39:17 -04:00
256531a29a
put implementation header first for all remaining main folder source files
2019-07-03 19:34:13 -04:00
55116db8fb
avoid segfault and print more meaningful error message with empty lines in coeff sections
2019-05-20 14:15:04 -04:00
3f9d59294e
replace STL map with atom->map in special, better code comments
2019-03-26 11:01:37 -04:00
9912c44413
rendevous comm option for special bonds and fix rigid/small
2019-03-26 11:01:33 -04:00
d890848412
add a check for consistent bonus data
2019-02-17 15:03:59 -05:00
