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23069 Commits

Author SHA1 Message Date
Richard Berger a2b5c379f2
Update docs for COMPRESS styles 2020-09-01 12:17:08 -04:00
Richard Berger 3db1a6d690
Use PkgConfig to find Zstd 2020-09-01 11:14:36 -04:00
tomswinburne ae3a7d8901 minor changes to example 2020-09-01 17:02:24 +02:00
Richard Berger 8e0c4d764e
Change include for fmt 2020-09-01 10:58:13 -04:00
Axel Kohlmeyer 75b3bbd657
modernize 2020-09-01 10:09:34 -04:00
Axel Kohlmeyer 95aab99c2a
remove redundant entries 2020-09-01 09:57:44 -04:00
Axel Kohlmeyer 2802db4493
correct application of the BEGIN_CAPTURE macro 2020-09-01 09:41:26 -04:00
Anne Gunn 3b765956d2 Manually resolve merge conflict 
Merge branch 'iss1109' of https://github.com/eagunn/lammps into iss1109
 2020-09-01 06:31:35 -06:00
Anne Gunn 4f03acc560 Fix merge conflicts caused by code's do-si-do around Axel's additions 
to the utils namespace.
 2020-09-01 06:30:12 -06:00
Anne Gunn 2536f28e1a Per comments from Axel, continued the evolution of the output messages. 
- Converted Compute message with imputed value to fmt::format style.
- Condensed most error-> output messages to oneliners where fmt::format
is called within the call to the error method. For a couple, the
formatting string/value list were complex enough that I continued using
a temporary string variable to make the code easier to read.
 2020-09-01 05:49:29 -06:00
Anne Gunn 52748f57da Delete extraneous, unused file/folder that should never have gotten 
into the repo.
 2020-09-01 05:49:29 -06:00
Anne Gunn 9ef725ea52 Move destruction of splines data structure to FixBocs destructor 
from ComputePressure destructor.
 2020-09-01 05:49:29 -06:00
Anne Gunn e11a3c4799 Remove "test" example files. 2020-09-01 05:49:29 -06:00
Anne Gunn 4dca927693 Switch dynamically created arrays/matrices to use memory->create and 
->destroy, LAMMPS-standard for dynamic memory management.
 2020-09-01 05:49:29 -06:00
Anne Gunn fe89edc828 Remove c_str() calls from message strings. Message class now accepts 
actual strings.
 2020-09-01 05:49:29 -06:00
Anne Gunn 0aa66319fe Change the build_xxx_splines methods to accept a const reference parameter 
to the data vector rather than a vector parameter. Vectors are, as all
types are, passed by value in C++. Using a vector directly as a parameter
causes the data to be copied. Using a reference to the vector neatly
avoids that problem.

Also tucked fmt/format.h into its rightful place in the include list
since Axel says there's no absolute rule about it being an exception.
 2020-09-01 05:49:29 -06:00
Anne Gunn 076c834734 Manually reconciled conflict from: 
Corrected two issues in code identified by valgrind:
1) memory leaks (the subject of the original #1109) and
2) an invalid memory access (reading from beyond the end of an array).

Also:
- replaced several dynamically-allocated (calloc and free) local arrays with std::vector.
- reorganized include statements per new conventions, and
- updated messages to use strings and fmt.

Added folders and files used in manual testing and verification to examples folder.

No changes in analysis results are expected or intended. This is pure refactoring except for a bit of error message cleanup.
 2020-09-01 05:48:49 -06:00
Anne Gunn aa12f4f78a Per request from Axel, Revert revert one commit too far: 
"Per suggestion from Axel, reformat code to what I believe to be"

This reverts commit b72c1c0eda.
 2020-09-01 05:10:44 -06:00
tomswinburne fbffcf3321 spelling 2020-09-01 11:34:11 +02:00
tomswinburne c18eccad39 force -> utils:: 2020-09-01 11:25:25 +02:00
tomswinburne 2f182b4606 force-> -> utils:: 2020-09-01 11:24:06 +02:00
tomswinburne c6de769696 Merge branch 'master' of github.com:tomswinburne/lammps 2020-09-01 11:12:29 +02:00
tomswinburne ac080228dc whitespace style fix 2020-09-01 11:12:05 +02:00
TD Swinburne (Tom) 0541996919
Merge branch 'master' into master 2020-09-01 10:59:03 +02:00
tomswinburne d601acd0ca merge 2020-09-01 10:57:43 +02:00
tomswinburne 2eb6a8a8a4 update python interface 2020-09-01 10:55:45 +02:00
tomswinburne db9de111be updated python interface 2020-09-01 10:54:18 +02:00
Richard Berger fe833e6c87
Add missing #ifdef 2020-08-31 19:49:17 -04:00
Richard Berger 0925fc822d
Make Zstd support optional 2020-08-31 18:21:58 -04:00
Richard Berger 3865de8705
Add lost line 2020-08-31 16:43:06 -04:00
Richard Berger 2effd2f707
Merge remote-tracking branch 'origin/master' into zstd_support 2020-08-31 15:38:56 -04:00
Richard Berger c5a2e50bf5
Add Zstd variants of dump local and xyz 2020-08-31 15:38:20 -04:00
Richard Berger a0f82a4b18
Add compression_level parameter to dump xyz/gz and local/gz 2020-08-31 15:00:57 -04:00
Richard Berger 443a817152
Add tests for dump local/gz and xyz/gz 2020-08-31 14:54:10 -04:00
Axel Kohlmeyer 24f5807623
Merge pull request #2319 from akohlmey/move-convenience-functions 
Move some more convenience functions to utils namespace
 2020-08-31 14:29:42 -04:00
Richard Berger 99b83333c9
Add dump cfg/zstd 2020-08-31 14:20:52 -04:00
Richard Berger a922355e19
Add compression_level parameter to dump cfg/gz 2020-08-31 14:20:36 -04:00
Axel Kohlmeyer 54ed23448b
instantiate bounds() also with long long to make windows happy. 2020-08-31 14:14:51 -04:00
Richard Berger 5faca3aef0
Add tests for dump cfg/gz 2020-08-31 13:36:42 -04:00
Axel Kohlmeyer 675cf20e93
Merge remote-tracking branch 'github/master' into move-convenience-functions 2020-08-31 12:58:21 -04:00
Axel Kohlmeyer 22ccde1d13
modernize utils::bounds() implementation and remove duplicate definition. 2020-08-31 12:58:00 -04:00
Axel Kohlmeyer 9a4ec23c7f
Merge pull request #2327 from akohlmey/remove-doxygen-tool 
Remove doxygen tool folder and references to it in the manual
 2020-08-31 12:49:24 -04:00
Axel Kohlmeyer 7fca3b7a65
revert accidental change 2020-08-31 12:46:22 -04:00
Axel Kohlmeyer 1ff34d4b13
avoid doxygen lookup ambiguity 2020-08-31 12:46:05 -04:00
Axel Kohlmeyer 67a5db03c7
Merge pull request #2326 from ndtrung81/gpu-update-makefiles 
update makefiles in lib/gpu for more recent architectures
 2020-08-31 12:30:28 -04:00
Axel Kohlmeyer 0c7b9a7c63
update utils tester for API change in bound()/boundsbig() 2020-08-31 11:43:25 -04:00
Axel Kohlmeyer dd03c7232a
Merge remote-tracking branch 'github/master' into move-convenience-functions 2020-08-31 11:41:18 -04:00
Axel Kohlmeyer a4d3b21a43
Merge pull request #2322 from Vsevak/cmake_cuda 
Fix CMake building for CUDA 11
 2020-08-31 11:33:52 -04:00
Axel Kohlmeyer cf11945e21
get rid of utils::boundsbig() by making it a template function with two specializations 2020-08-31 11:25:43 -04:00
Axel Kohlmeyer 8034a83ee8
Merge pull request #2325 from akohlmey/fortran-interface 
New Fortran interface to LAMMPS
 2020-08-31 10:27:10 -04:00