67c2352015
actually assume type labels don't start with number
2021-01-22 21:47:48 -05:00
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
93c33ac4f4
type label support for molecule files
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replace types directly for molecule files
2021-01-12 17:52:55 -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
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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
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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
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()
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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
c2b557233e
Update value parsing in Molecule
2020-06-09 12:12:52 -04:00
7df387f7d5
Merge remote-tracking branch 'origin/master' into refactor-table-reading
2020-06-05 12:09:57 -04:00
54a8b4e08b
more local buffers removed and file error status added.
2020-06-04 20:14:19 -04:00
62ee8d41f3
get rid of local buffers and snprinf()
2020-06-04 16:41:24 -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
1fd956a696
fix bug when allocating and freeing newly added data structures
2020-03-19 00:51:14 -04:00
71582c99ca
rearrange pointer variables to a more logical location, quell compiler warning and initialize all pointer
2020-03-18 22:51:16 -04:00
43a6c13f01
change 'groups' to 'fragments'
2020-03-10 21:11:34 -06:00
337cee7b49
add groups to molecule templates
2020-03-06 22:51:42 -07:00
21e4d92507
another memory correction
2020-03-06 22:49:23 -07:00
b55a6b0fd1
memory correction
2020-03-03 23:28:27 -07:00
90bfa6b783
add molecule IDs to molecule templates
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for when more than one molecule per file
2020-03-02 00:53:19 -07:00
256531a29a
put implementation header first for all remaining main folder source files
2019-07-03 19:34:13 -04:00
96744c4933
more include file cleanup
2019-06-30 15:53:17 -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
