744e615dbb
Revamping public methods for history, adding support for bond react
2021-12-13 17:35:53 -07:00
5ead32f886
more debugging and features
2021-12-10 11:13:06 -07:00
d4149e9139
bug fixes to make a series of test inputs run correctly
2021-12-08 16:44:51 -07:00
26492b13d5
logic for dumps every steps and time delta
2021-12-07 13:46:36 -07:00
1afdd3c011
new output vars for dumps
2021-12-07 09:16:19 -07:00
15f1c2d960
Fix inaccurate error message
2021-11-18 08:50:09 -07:00
94b11964f8
Write dump header after sort to fix incorrect atom count for multiproc
2021-11-18 08:32:41 -07:00
5616336d5e
Allow sorting with reorderflag for more than 2 billion atoms
2021-11-18 07:59:45 -07:00
136c15a8ba
Allow dump sort to work with more than 2 billion atoms
2021-11-04 19:59:48 -06:00
5b40e4cb38
new accessor APIs for fixes and computes in Modify plus a few applications
2021-10-16 06:00:28 -04:00
6a9bb577cf
rename "zip" functions to "compress" functions. update related docs
2021-10-07 12:38:11 -04:00
6c7b42a190
small tweaks and fixes for compiling with MSVC++
2021-10-06 15:24:59 -04:00
ec1a55b35b
use platform code for reading/writing of compressed text file via a pipe
2021-10-06 15:04:48 -04:00
41a3eccd1c
apply utils::logical() to more commands
2021-09-21 07:48:50 -04:00
6fea5dd316
avoid creating empty per atom position arrays for enforcing pbc for dumps
2021-08-26 16:16:30 -04:00
80f28e7fa9
fixing merge conflicts, update to master
2021-06-02 12:33:37 -06:00
09c19a936b
update URLs in source code and manual
2021-05-24 14:18:20 -04:00
d939a16d3b
Completing pair and fix
2021-05-14 17:26:51 -06:00
d1941392d3
disable clang-format for all existing .cpp files (for now)
2021-05-05 23:53:38 -04:00
1ca38db9df
simplify and avoid temporary buffers when piping to/from gzip
2021-04-07 23:26:21 -04:00
1f50557b38
Adopt utils::strdup in dump styles
2021-03-19 15:34:43 -04:00
e2e6639013
add typecast to avoid (unlikely but possible) integer overflows.
...
this will silence a lot of static code analysis warnings
2021-02-02 17:27:04 -05:00
adf74b3a22
use https://lammps.sandia.gov based URLs consistently
2020-10-21 16:45:30 -04:00
cebf6d33ba
Merge pull request #2358 from eagunn/iss2345
...
Replace instances of NULL with nullptr
2020-09-15 17:41:24 -04:00
0183e999c9
consistently return "memory_usage" as double.
2020-09-15 01:59:58 -04:00
93a0d4c096
fix up some comments
2020-09-12 14:26:34 -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
485a169ef2
move merge sort to utils namespace
2020-09-06 17:38:53 -04:00
6113169a47
IWYU based include statement cleanup
2020-09-02 17:39:34 -04:00
31bd76efa5
Merge remote-tracking branch 'origin/master' into zstd_support
2020-09-01 12:58:41 -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
0d8454ac25
First version of Zstd dump atom
2020-08-25 23:27:42 -04:00
01214de6bd
add support for adding an ITEM: TIME output to some dump files
2019-09-30 11:03:22 -04:00
e413aaf217
add support for optionally including unit information in standard dump files
2019-09-12 14:37:42 -04:00
7967cb1133
put implementation header first to avoid issues with mpi.h and lmptype.h with OpenMPI
2019-07-03 06:16:16 -04:00
31cbccda85
continue cleaning up include file lists
2019-06-29 09:37:44 -04:00
a20d58312d
add missing convesion to fractional coordinates and back for enforced PBC dumps of triclinic cells
2019-03-25 12:25:50 -04:00
e9bc939098
Fix more unused parameter warnings ( #1076 )
2018-08-23 12:22:44 -06:00
f65b06de0e
dump_modify maxfiles tweak
2018-05-11 15:54:16 -06:00
075598b405
port dump_modify maxfiles option to COMPRESS and MPIIO package
2018-05-10 23:44:27 -04:00
7780d92823
implement 'dump_modify maxfiles' feature as discussed
2018-05-10 23:25:26 -04:00
e4071d7f46
replace C-style include files with their C++ equivalents
2018-04-27 18:00:24 -04:00
a19e8fb269
Merge branch 'master' into resetids
2018-03-30 09:15:24 -06:00
5fd17670b1
new reset_ids command and dump_modify delay option
2018-03-28 11:31:35 -06:00
2aef3a0e96
new dump_modify refresh and compute displace/atom refresh commands for incremental dump files
2018-03-27 14:37:04 -06:00
8d384b9149
whitespace cleanup
2017-10-02 15:03:48 -04:00
d2610d9e7c
minor changes to NEB doc pages and examples
2017-06-20 08:19:23 -06:00
c1b0b1b3f9
restore old qsort() based code and add preprocessor directives to switch
...
-DLMP_USE_LIBC_QSORT will use qsort() from libc to sort (requires static/global variables).
-DLMP_USE_MERGE_SORT will use a plain merge sort. slightly slower for expensive comparisons.
-DLMP_USE_HYBRID_SORT will use hybrid merge sort. faster than merge sort (no static/global variables)
2017-06-16 18:17:48 -04:00
8500a197ae
whitespace cleanup
2017-06-14 23:13:10 -04:00
1f17e8ebbb
remove need for static class member variables in Dump and Irregular
...
The dump and irregular classes were using qsort() from the C-library
for sorting lists through custom comparison functions, which required
access to additional data, which was passed via static class variables,
i.e. globals. This collides with having multiple LAMMPS instances in
the same address space.
the calls to qsort() are replaced with a custom merge sort, which passes
a void pointer to the comparison functions, which can contain any kind
of desired information, e.g. a class handle or a list
2017-06-14 23:10:53 -04:00
