f2a4d12f7e
more output simplification with fmtlib, std::string, and utils::logmesg()
2020-06-25 23:48:17 -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
acd20512f0
require that box is defined before molecule command is issued
2018-06-15 17:40:14 -04:00
95e259fe71
also include consistent type checks
2018-05-26 15:18:26 -06:00
69a9f1bf94
molecule templates sanity checks
2018-05-26 15:03:24 -06:00
c83fedf100
replace variable length array in Molecule class with new/delete
2018-05-04 21:41:23 -04:00
e4071d7f46
replace C-style include files with their C++ equivalents
2018-04-27 18:00:24 -04:00
afd39eb9b8
correctly represent, that the molecule summary refers to the largest type number and not the number of types
2018-02-11 16:17:24 +01:00
f7a0a6eb70
Merge pull request #622 from akohlmey/collected-small-fixes
...
Collected small fixes
2017-08-23 14:12:45 -06:00
d1a0c040c9
add initializers for nmatch/nwant variables in molecule file parser
2017-08-20 23:28:13 -04:00
d671a04274
whitespace cleanup
2017-08-18 14:24:09 -04:00
bf7cff73d4
allocate the temporary special array on the heap and not the stack (it may get too big quickly) and clear the array before use.
2017-08-18 14:23:48 -04:00
9e85b3178a
molecule maxspecial value corrected when specials autogenerated
2017-08-17 21:39:25 -06:00
2a7d2dee36
add more strict checking of data when parsing molecule files to detect format errors
2017-08-10 14:49:51 -04:00
d0470799ac
consistently check for all per-atom-type masses being set only when per-atom masses are not set
...
rather than placing an if statement around every incidence of calling atom->check_mass() to ensure it is only called when per atom masses are not set, we place that check _inside_ Atom::check_mass(). This avoids unexpected error messages.
2017-06-28 06:26:21 -04:00
3a054d1a82
Fix more typos in src files
2017-03-07 00:55:01 -05:00
45f2e86dd6
NULLed ptrs in files
2016-11-07 16:07:37 +01:00
f9a9e27f5a
add error location propagation to atom->set_mass() and atom->check_mass()
2016-10-26 16:01:40 -04:00
db36c8bcc3
stop with error, if molecule command requires special bond auto-generation before box is defined
2016-10-21 14:51:09 -04:00
5881c6da6f
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15304 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-07-13 22:55:25 +00:00
6367c3700b
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15302 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-07-13 22:36:46 +00:00
cdc9712261
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15270 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-07-07 14:39:49 +00:00
0f3e4182e8
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15109 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-06-06 23:21:39 +00:00
10ad7e3475
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14909 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-04-30 18:03:40 +00:00
468ef144d4
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14602 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-02-15 16:10:43 +00:00
70aa37e4c8
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14589 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-02-15 15:26:57 +00:00
7ae65d4dcf
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14417 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2016-01-11 22:00:02 +00:00
4c19f60606
Fixed uninitialized variable for multiple molecule in set
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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14249 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-11-11 23:37:31 +00:00
354e20f431
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14220 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-10-30 20:04:06 +00:00
b229c719d0
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14163 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-10-22 21:48:05 +00:00
047be536bc
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13983 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-09-02 20:39:55 +00:00
3841dd58ca
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13931 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-08-21 22:55:12 +00:00
f851538729
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13748 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-07-28 14:37:39 +00:00
54ad69177c
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13696 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-07-23 15:47:57 +00:00
5a21de608e
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13609 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-07-16 21:21:40 +00:00
d2d6d38369
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13359 f3b2605a-c512-4ea7-a41b-209d697bcdaa
2015-04-01 21:42:42 +00:00
