7a8afb6eef
add fragment count to molecule file output
2021-08-19 20:10:26 -04:00
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
d2cdb318ab
apply new logmesg() overload to a bunch of cases.
2021-04-21 23:38:45 -04:00
f455869de3
update a few more error messages
2021-03-03 13:43:54 -05:00
4af4c0a99b
parsing is done on all MPI ranks, so we better use error->all() instead of error->one()
2021-03-03 08:43:51 -05:00
2db78823a0
open() method not really needed.
2021-03-03 08:43:23 -05:00
f02b0cf09b
review error messages for Coords, Types, Molecules, and Fragments sections
2021-03-03 08:24:21 -05:00
7ddb0c7014
clarify some more error messages
2021-03-02 22:26:23 -05:00
92ff812e9d
simplify
2021-03-02 15:53:33 -05:00
d6dbdfdbe6
detect and warn about unknown header keywords (instead of error out on an empty line)
2021-03-02 15:53:17 -05:00
eecc85659d
add missing line
2021-03-02 12:43:06 -05:00
60694b2a94
better error check and error message when looking for section headers
2021-03-02 11:59:54 -05:00
371ee63c2c
begin refactor of parsing of sections
2021-03-02 11:06:24 -05:00
e941d0fd4a
simplify parsing of keywords
2021-03-02 11:05:18 -05:00
2d96a01bb2
use trim functions in utils to remove whitespace and comments
2021-03-02 11:03:51 -05:00
e09f4b6e7a
simplify checking for valid molecule ID
2021-03-02 11:03:17 -05:00
db2eefae5c
consistently allow comments in molecule file section headers
2021-01-11 16:12:31 -05:00
51a20175c9
more code formatting consistency changes for loops and conditionals
2020-12-30 09:47:45 -05:00
af0df870f4
Fix bug introduced by uninitialized moloffset
2020-11-24 13:55:10 -05:00
8b9f2e0539
molecule: add atom ID completeness check
2020-11-14 15:51:26 -05:00
8e3a556461
Merge pull request #109 from lammps/master
...
rebase
2020-11-14 13:52:16 -05:00
d09eb491f8
molecule: add iatom < 0 check
2020-11-11 13:00:10 -05:00
731072cfb8
handle case of molecule template atoms not included in shake
2020-10-26 18:49:59 -04:00
bb2e616c5f
molecule: use user-provided IDs in molecule files
2020-10-24 12:56:02 -04:00
00e4e23456
only check for type overflows if a box has been created.
2020-10-23 21:51:10 -04:00
c62ddaa4a2
remove pre-box check so that atom style template can work
2020-10-23 21:10:41 -04:00
adf74b3a22
use https://lammps.sandia.gov based URLs consistently
2020-10-21 16:45:30 -04:00
28812b1ea7
Merge pull request #2381 from akohlmey/collected-small-changes
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Collected small changes
2020-09-24 16:17:28 -04:00
b6d98707ec
molecule: revert overzealous error checking
2020-09-23 11:23:10 -04:00
1be766c8cd
molecule fragment: let's add more checks
2020-09-23 10:37:33 -04:00
ed3975054a
fix typo
2020-09-23 10:30:19 -04:00
e29f838121
also add error checks
2020-09-23 10:28:48 -04:00
88b8461e0f
the right molecule fragment fix
2020-09-23 10:19:38 -04:00
7eab154786
one-line bug when checking for molecule fragments
2020-09-21 11:01:04 -04:00
29a7d598ac
update formatting style to be more consistent
2020-09-21 02:04:58 -04:00
62a63d0cd8
silence compiler warnings
2020-09-17 10:27:06 -04:00
f5998692d0
Merge branch 'master' into math_eigen
2020-09-15 21:37:05 -04:00
0f6a34775c
Merge branch 'master' into symbolic-atom-constants
2020-09-15 17:44:31 -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
9d0c3bc665
replace some numeric constants in Atom and AtomVec classes with enumerators
2020-09-11 19:07:55 -04:00
eb6f7f9740
Merge branch 'master' into math_eigen
2020-09-06 10:59:20 -07:00
57f82abae3
updated all code in LAMMPS to use the open-source "math_eigen.h" instead of "math_extra.h". Code in "lib" now uses its own abbreviated local version of the "math_eigen.h" file (which is named "jacobi_pd.h"), since it is not clear how code from "lib/" can access the code in "src/"
2020-09-05 01:39:27 -07:00
390c6ba106
rechecking some corefiles with IWYU after the many updates
2020-09-03 15:28:07 -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
27b4e93bf5
silence compiler warnings
2020-08-29 18:32:21 -04:00
2fd654f4fd
silence compiler warnings about unused variables
2020-08-22 15:06:00 -04:00
c9dc5d90d2
Merge remote-tracking branch 'origin/master' into refactor-reading
2020-07-17 23:08:26 -04:00
f2a4d12f7e
more output simplification with fmtlib, std::string, and utils::logmesg()
2020-06-25 23:48:17 -04:00
