1ff34d4b13
avoid doxygen lookup ambiguity
2020-08-31 12:46:05 -04:00
67a5db03c7
Merge pull request #2326 from ndtrung81/gpu-update-makefiles
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update makefiles in lib/gpu for more recent architectures
2020-08-31 12:30:28 -04:00
0c7b9a7c63
update utils tester for API change in bound()/boundsbig()
2020-08-31 11:43:25 -04:00
dd03c7232a
Merge remote-tracking branch 'github/master' into move-convenience-functions
2020-08-31 11:41:18 -04:00
a4d3b21a43
Merge pull request #2322 from Vsevak/cmake_cuda
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Fix CMake building for CUDA 11
2020-08-31 11:33:52 -04:00
cf11945e21
get rid of utils::boundsbig() by making it a template function with two specializations
2020-08-31 11:25:43 -04:00
8034a83ee8
Merge pull request #2325 from akohlmey/fortran-interface
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New Fortran interface to LAMMPS
2020-08-31 10:27:10 -04:00
3c71d300e5
Merge pull request #2320 from akohlmey/programmer-guide
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Add programmer guide part 2
2020-08-31 10:06:04 -04:00
b72c1c0eda
Per suggestion from Axel, reformat code to what I believe to be
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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
0c067700e6
Per comments from Axel, continued the evolution of the output messages.
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- 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
f0b304efcb
Delete extraneous, unused file/folder that should never have gotten
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into the repo.
2020-08-31 06:31:48 -06:00
69b42ea9ae
Move destruction of splines data structure to FixBocs destructor
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from ComputePressure destructor.
2020-08-31 06:31:48 -06:00
a4790fdf00
Remove "test" example files.
2020-08-31 06:31:47 -06:00
c75c3451f6
Switch dynamically created arrays/matrices to use memory->create and
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->destroy, LAMMPS-standard for dynamic memory management.
2020-08-31 06:31:47 -06:00
e8306a2535
Remove c_str() calls from message strings. Message class now accepts
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actual strings.
2020-08-31 06:31:47 -06:00
3760ccd672
Change the build_xxx_splines methods to accept a const reference parameter
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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
b241294e84
Corrected two issues in code identified by valgrind:
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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
c7360fb808
include example use of PotentialFileReader class
2020-08-31 07:45:52 -04:00
c84033677c
add documentation for potential file reader
2020-08-31 07:31:28 -04:00
33f2cbc713
add docs for TextFileReader class to developer guide
2020-08-31 06:57:16 -04:00
39a9974f3d
add ValueTokenizer example and use captions with code-blocks
2020-08-30 23:57:02 -04:00
569b6f95a3
no need to use ValueTokenizer. Make code more compact.
2020-08-30 23:32:17 -04:00
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
ecb1f266b5
More updates
2020-08-30 15:10:29 -05:00
7a5f193c02
Updated several Makefile's in lib/gpu for newer compute capabilities
2020-08-30 15:06:44 -05:00
4484699ab6
fix spelling
2020-08-30 15:52:42 -04:00
65d2ee7464
add work-in-progress marker to fortran library wrapper
2020-08-30 15:23:02 -04:00
199cfeba78
more tweaks. doxygen translation has no more warnings now.
2020-08-30 14:32:53 -04:00
cd0cdf0b74
silence compiler warning
2020-08-30 14:28:29 -04:00
f3ed1dea4d
minor tweaks
2020-08-30 14:28:19 -04:00
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
4b0999e167
complete documentation of tokenizer classes
2020-08-30 14:12:21 -04:00
5623009962
arch 3.0 is dropped in CUDA 11
2020-08-30 13:12:42 +03:00
96ee132e85
start documenting tokenizer classes
2020-08-30 01:50:37 -04:00
8d2c16ad66
remove trailing whitespace
2020-08-30 00:31:04 -04:00
f123246189
minor doc updates
2020-08-30 00:25:01 -04:00
ceeaf1e988
update and correct documentation for utils functions
2020-08-29 23:51:46 -04:00
9c404e02fd
update include file conventions
2020-08-29 22:56:37 -04:00
83a9e5e724
handle spelling issues with new doc text
2020-08-29 22:55:05 -04:00
e51a5ad8f4
import doxygen docs for new utils functions
2020-08-29 22:46:25 -04:00
4396dbd9a3
move Force::open_potential() to utils::open_potential()
2020-08-29 22:37:14 -04:00
798226967f
Merge branch 'move-convenience-functions' of github.com:akohlmey/lammps into move-convenience-functions
2020-08-29 22:22:45 -04:00
6b7f4c500f
document changes to LAMMPS_POTENTIALS environment variable
2020-08-29 22:22:27 -04:00
5a22f4d7f2
support that LAMMPS_POTENTIALS is a real path variable with multiple entries, not just a single folder
2020-08-29 22:22:03 -04:00
b06ba74d18
support that LAMMPS_POTENTIALS is a real path variable with multiple entries, not just a single folder
2020-08-29 22:09:07 -04:00
05ff352021
add utils::open_potential() function to utils namespace
2020-08-29 22:08:16 -04:00
7413dc783e
add tokenizer tests for splitting path environment variables
2020-08-29 22:07:22 -04:00
8601e608ca
add unit tests for utils::bounds() and utils::boundsbig()
2020-08-29 22:00:07 -04:00
96d8d12a88
replace calls to force->*numeric() with the corresponding utils::*numeric()
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this also removes the now obsolete functions from Force
2020-08-29 20:31:02 -04:00
27b4e93bf5
silence compiler warnings
2020-08-29 18:32:21 -04:00
