lijiext
/
lammps
mirror of https://github.com/lammps/lammps.git
1
0
Fork 1
Code Issues Packages Projects Releases Wiki Activity
23,185 Commits 9 Branches 202 Tags 1.2 GiB
Commit Graph

23185 Commits

Author SHA1 Message Date
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
Axel Kohlmeyer 3c71d300e5
Merge pull request #2320 from akohlmey/programmer-guide 
Add programmer guide part 2
 2020-08-31 10:06:04 -04:00
Anne Gunn b72c1c0eda Per suggestion from Axel, reformat code to what I believe to be 
LAMMPS standards. I used the .clang-format file from the unit-test
folder but changed all spacing settings to 2 from 4.
 2020-08-31 06:31:48 -06:00
Anne Gunn 0c067700e6 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.
 2020-08-31 06:31:48 -06:00
Anne Gunn f0b304efcb Delete extraneous, unused file/folder that should never have gotten 
into the repo.
 2020-08-31 06:31:48 -06:00
Anne Gunn 69b42ea9ae Move destruction of splines data structure to FixBocs destructor 
from ComputePressure destructor.
 2020-08-31 06:31:48 -06:00
Anne Gunn a4790fdf00 Remove "test" example files. 2020-08-31 06:31:47 -06:00
Anne Gunn c75c3451f6 Switch dynamically created arrays/matrices to use memory->create and 
->destroy, LAMMPS-standard for dynamic memory management.
 2020-08-31 06:31:47 -06:00
Anne Gunn e8306a2535 Remove c_str() calls from message strings. Message class now accepts 
actual strings.
 2020-08-31 06:31:47 -06:00
Anne Gunn 3760ccd672 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.
 2020-08-31 06:31:47 -06:00
Anne Gunn b241294e84 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.
 2020-08-31 06:31:47 -06:00
Axel Kohlmeyer c7360fb808
include example use of PotentialFileReader class 2020-08-31 07:45:52 -04:00
Axel Kohlmeyer c84033677c
add documentation for potential file reader 2020-08-31 07:31:28 -04:00
Axel Kohlmeyer 33f2cbc713
add docs for TextFileReader class to developer guide 2020-08-31 06:57:16 -04:00
Axel Kohlmeyer 39a9974f3d
add ValueTokenizer example and use captions with code-blocks 2020-08-30 23:57:02 -04:00
Axel Kohlmeyer 569b6f95a3
no need to use ValueTokenizer. Make code more compact. 2020-08-30 23:32:17 -04:00
Axel Kohlmeyer e8e57b0628
remove doxygen tool folder and references to it in the input as it is no longer compatible and needed 2020-08-30 19:59:52 -04:00
Trung Nguyen ecb1f266b5 More updates 2020-08-30 15:10:29 -05:00
Trung Nguyen 7a5f193c02 Updated several Makefile's in lib/gpu for newer compute capabilities 2020-08-30 15:06:44 -05:00
Axel Kohlmeyer 4484699ab6
fix spelling 2020-08-30 15:52:42 -04:00
Axel Kohlmeyer 65d2ee7464
add work-in-progress marker to fortran library wrapper 2020-08-30 15:23:02 -04:00
Axel Kohlmeyer 199cfeba78
more tweaks. doxygen translation has no more warnings now. 2020-08-30 14:32:53 -04:00
Axel Kohlmeyer cd0cdf0b74
silence compiler warning 2020-08-30 14:28:29 -04:00
Axel Kohlmeyer f3ed1dea4d
minor tweaks 2020-08-30 14:28:19 -04:00
Axel Kohlmeyer 8d45b724a6
fix bug in conventional build makefile preventing the correct Install.py in the lib folder to be run 2020-08-30 14:12:53 -04:00
Axel Kohlmeyer 4b0999e167
complete documentation of tokenizer classes 2020-08-30 14:12:21 -04:00
Vsevak 5623009962 arch 3.0 is dropped in CUDA 11 2020-08-30 13:12:42 +03:00
Axel Kohlmeyer 96ee132e85
start documenting tokenizer classes 2020-08-30 01:50:37 -04:00
Axel Kohlmeyer 8d2c16ad66
remove trailing whitespace 2020-08-30 00:31:04 -04:00
Axel Kohlmeyer f123246189
minor doc updates 2020-08-30 00:25:01 -04:00
Axel Kohlmeyer ceeaf1e988
update and correct documentation for utils functions 2020-08-29 23:51:46 -04:00
Axel Kohlmeyer 9c404e02fd
update include file conventions 2020-08-29 22:56:37 -04:00
Axel Kohlmeyer 83a9e5e724
handle spelling issues with new doc text 2020-08-29 22:55:05 -04:00
Axel Kohlmeyer e51a5ad8f4
import doxygen docs for new utils functions 2020-08-29 22:46:25 -04:00
Axel Kohlmeyer 4396dbd9a3
move Force::open_potential() to utils::open_potential() 2020-08-29 22:37:14 -04:00