01a32b67b0
add minimal unit test program for molecule files
2021-03-02 11:07:03 -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
ca8b268ad5
new convencience function for checking valid IDs (includes unit tests)
2021-03-02 11:02:09 -05:00
0f63f07ce5
Merge pull request #2634 from evoyiatzis/master
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Small extension of extract method in Buckingham pair styles
2021-03-01 09:03:49 -05:00
7e3ca726b1
Merge pull request #2635 from ssande7/fix_nh_extract_bug
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[BUGFIX] Correct return values for FixNH::extract()
2021-03-01 08:49:12 -05:00
0ae38fb2ea
Fix return values of extract for pressure variables
2021-03-01 09:48:31 +10:00
a57311ce3a
whitespace fixes
2021-02-28 12:03:50 -05:00
30d15b9b22
test for extract parameters in unit tests
2021-02-28 11:59:17 -05:00
4e7df729ae
Update fix_adapt_fep.rst
2021-02-28 11:41:28 +01:00
97718fa957
Update fix_adapt.rst
2021-02-28 11:40:43 +01:00
39422dff94
Update compute_fep.rst
2021-02-28 11:39:02 +01:00
2f764edadc
Addition of extract method in PairBuckCoulCut cpp
2021-02-28 11:30:12 +01:00
947fa67531
Addition of extract method in BuckCoulCut
2021-02-28 11:25:49 +01:00
b622416417
Extent extract method of PairBuckCoulMSM
2021-02-28 11:21:38 +01:00
6ff8fc093e
Extent extract method of BuckCoulLong
2021-02-28 11:20:31 +01:00
9efc83195a
Merge pull request #2624 from rbberger/collected_small_changes
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Collection of small changes
2021-02-26 20:38:47 -05:00
1521c7a370
Merge pull request #2625 from yafshar/kim_citation
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Updating the kim citation report to lammps conventions
2021-02-26 20:38:28 -05:00
ad7f14936e
Merge pull request #2627 from jrgissing/bond/react-performance-improvement
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Bond/react performance improvement
2021-02-26 20:38:01 -05:00
2ab9c34e52
Merge pull request #2631 from rbberger/python_additions
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Add LAMMPS output readers to Python package
2021-02-26 20:27:52 -05:00
15c5aa9bc1
Merge pull request #2633 from evan-charmworks/utils-regex-context
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Make regex code in utils thread-safe
2021-02-26 20:22:12 -05:00
a89f0f332d
Make regex code in utils thread-safe
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regex_context_t is only 520 bytes on platforms with 8-byte pointers,
which is reasonable to allocate on the stack instead of as a global in
a userland program.
2021-02-26 15:24:08 -06:00
f69768d919
one more change
2021-02-26 15:58:26 -05:00
09e33fd342
fix bugs found by or avoid warnings from coverity scan
2021-02-26 15:55:20 -05:00
099dcedb7f
correct docs
2021-02-26 15:54:20 -05:00
3042e28297
try to catch format errors from fmtlib
2021-02-26 14:08:38 -05:00
335a6308d0
update kim query example log file
2021-02-26 13:04:29 -06:00
e88c124da6
add extra cases for query unit test
2021-02-26 12:47:43 -06:00
820cd83713
use utils::strmatch instead of strchr
2021-02-26 12:47:21 -06:00
bb13ce4349
silence compiler warning
2021-02-26 11:35:26 -05:00
9503a089ef
adapt kim_init code to use the utils::strfind() and drop using std::regex
2021-02-26 11:20:06 -05:00
272b89688e
Merge branch 'master' into kim_citation
2021-02-26 10:51:15 -05:00
aea0ceac03
Merge pull request #2632 from akohlmey/utils-regex-update
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Add new utils::strfind() function and update mini-regex code
2021-02-26 10:50:34 -05:00
9017d46235
Merge pull request #2629 from akohlmey/citeme-use-hash
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Use a 64-bit hash in the CiteMe class to identify unique citations
2021-02-26 10:49:58 -05:00
e7c829e31e
use correct data type for storing hashes
2021-02-26 09:49:06 -05:00
dfae88cf13
address spelling issues
2021-02-25 23:11:41 -05:00
533b406d77
add docs for utils::strfind()
2021-02-25 23:11:25 -05:00
cfc86f7a2d
add unit tests for new utils::strfind() function
2021-02-25 23:05:48 -05:00
92d892aa2d
add new utility function utils::strfind()
2021-02-25 23:03:17 -05:00
a9467e830e
update regex code in utils to state of git repo of 2021-02-25
2021-02-25 23:02:46 -05:00
8e63f1ebf5
detect and abort if inconsistent body data for rounded polygon/polyhedra was provided
2021-02-25 18:26:20 -05:00
37086c391f
use std::hash instead of a local crc32 implementation.
2021-02-25 18:15:09 -05:00
f92089298d
Fix bug in AvgChunkReader and add docs
2021-02-25 16:56:19 -05:00
69245cb294
add unit tests for citeme class crc32 checks of unique citations
2021-02-25 15:52:38 -05:00
3d96d0a674
Fix wrong group name output in fix ave/chunk
2021-02-25 15:34:29 -05:00
977ba9ff66
Add LogFile and AvgChunkFile readers
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Implements changes proposed in #144
2021-02-25 15:32:53 -05:00
0ad39757e2
Cleaning up legacy C-style string processing
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Most of the C-style strcmp in the code are replaced with string for
simpler/safer/readable alternatives,
2021-02-25 13:55:24 -06:00
be81376426
use crc32 checksum instead of pointer addresses as unique id for citations
2021-02-25 14:45:17 -05:00
