a4faa3aced
modernize using get_fix_by_id()
2022-08-13 01:49:00 -04:00
97fab45f7e
Merge branch 'develop' into amoeba-ak
2022-05-28 05:24:02 -04:00
f0f6660050
join lines
2022-05-26 12:15:27 -04:00
929734ce45
Merge remote-tracking branch 'github/develop' into amoeba-ak
...
# Conflicts:
# doc/src/Commands_pair.rst
# src/memory.h
2022-04-28 20:08:18 -04:00
13664a0185
add utility to print url with pointer to error message
2022-04-22 05:25:50 -04:00
f8f2b9542e
sync with current develop
2022-04-18 17:29:23 -06:00
200b4f13c7
use dynamic cast instead of c-style cast when casting from base type to derived class
2022-04-10 18:18:06 -04:00
39b316729b
use auto type when assigning from cast or using new
2022-04-10 18:16:36 -04:00
f3fa04ae0a
bugfix
2022-03-30 15:01:03 -04:00
999c880dfd
simplify parsing numbers and reduce usage of BIGINT_FORMAT
2022-03-30 07:12:25 -04:00
bbe065e649
initial version of fix pitorsion
2022-03-09 15:37:19 -07:00
844ea0ab8e
UB testing
2022-03-08 15:37:16 -07:00
3bc91386a0
apply include statement updates suggested by running IWYU
2022-02-13 19:39:15 -05:00
4104353d7a
plug memory leak
2022-01-20 16:55:59 -05:00
9efa2369dd
join wrapped strings
2021-12-31 14:34:24 -05:00
c17a183816
do error checking already in read_data code
2021-12-31 14:34:09 -05:00
863de683ee
do not shadow "natoms" class member
2021-12-31 13:43:56 -05:00
adf1beea74
add mechanism to check for known data file section names
...
using this mechanism we can reject custom section names that will
conflict with existing section names and thus avoid misleading errors.
apply this also to fix property atom, where the section name is
determined by the fix ID.
in addition, allow to specify NULL as section name, which will use
the fix ID.
2021-10-28 14:23:27 -04:00
85433e8bd1
use true/false instead of 1/0 detected and changed by clang-tidy
2021-10-20 12:41:02 -04:00
f4851e9103
change check for reset image flags to print messages only once per data file
2021-10-13 21:54:18 -04:00
6a9bb577cf
rename "zip" functions to "compress" functions. update related docs
2021-10-07 12:38:11 -04:00
ec1a55b35b
use platform code for reading/writing of compressed text file via a pipe
2021-10-06 15:04:48 -04:00
8b36061db4
replace MPI_Wtime() with platform::walltime()
2021-10-05 22:53:39 -04:00
37bfe3d0ce
integrate platform sub-namespace into source code and documentation
...
this updates function calls to functions that have been moved from
the utils namepsace or the Info class to platform::
2021-10-02 16:55:11 -04:00
973cf017a9
do not call memset on a null pointer
2021-09-24 15:32:59 -04:00
9470a0eeb6
clarified doc pages for fix property/atom and read_data
2021-08-19 11:34:25 -06:00
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
a9ff9312d6
Merge remote-tracking branch 'origin/master' into varargs-log-error-functions
2021-04-28 18:13:31 -04:00
7b1b57aa9b
rename utils::fgets_trunc_nl() to utils::fgets_trunc()
2021-04-27 18:32:51 -04:00
15cff295c0
change read_data to use new utility function
2021-04-27 16:14:08 -04:00
18215ff3e7
Merge remote-tracking branch 'origin/master' into more-unit-tests
2021-04-26 14:48:14 -04:00
6b04ebd617
Merge branch 'master' into varargs-log-error-functions
2021-04-26 13:27:58 -04:00
e9e0bb71b6
Use varargs version of Error:all() and Error::one() where applicable
2021-04-25 21:30:51 -04:00
7e7a448a08
remove the old versions of the utility function and use the new
2021-04-24 21:33:36 -04:00
6943a3da35
must check if file is readable before changes to internal data
2021-04-24 07:12:45 -04:00
d2cdb318ab
apply new logmesg() overload to a bunch of cases.
2021-04-21 23:38:45 -04:00
b53822da46
provide Command base class in command.h for deriving command styles from
2021-04-13 17:47:00 -04:00
1ca38db9df
simplify and avoid temporary buffers when piping to/from gzip
2021-04-07 23:26:21 -04:00
2e86cb4176
for atom style template number of bonds does not depend on newton_bond
2021-03-30 15:33:11 -04:00
b9bc226e39
save style names alongside the classes when using read_data nocoeff
...
this fixes #2673
2021-03-19 10:06:02 -04:00
42895ac6df
Merge pull request #2654 from akohlmey/collected-small-changes
...
Collected small changes
2021-03-16 19:34:54 -04:00
5d5fc4a04d
simplify by using utils::strdup()
2021-03-16 08:56:52 -04:00
8c4918457f
consistently compare atom->molecular against enumerator constants
2021-03-14 01:25:22 -05:00
e6def05178
refactor parse_coeffs() function to avoid calling strtok()
2021-03-13 18:09:36 -05:00
882b221a17
rename arg,narg,maxarg to avoid shadowing in command() function
2021-03-13 17:35:49 -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
