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23069 Commits

Author SHA1 Message Date
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
Axel Kohlmeyer 798226967f
Merge branch 'move-convenience-functions' of github.com:akohlmey/lammps into move-convenience-functions 2020-08-29 22:22:45 -04:00
Axel Kohlmeyer 6b7f4c500f
document changes to LAMMPS_POTENTIALS environment variable 2020-08-29 22:22:27 -04:00
Axel Kohlmeyer 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
Axel Kohlmeyer 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
Axel Kohlmeyer 05ff352021
add utils::open_potential() function to utils namespace 2020-08-29 22:08:16 -04:00
Axel Kohlmeyer 7413dc783e
add tokenizer tests for splitting path environment variables 2020-08-29 22:07:22 -04:00
Axel Kohlmeyer 8601e608ca
add unit tests for utils::bounds() and utils::boundsbig() 2020-08-29 22:00:07 -04:00
Axel Kohlmeyer 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
Axel Kohlmeyer 27b4e93bf5
silence compiler warnings 2020-08-29 18:32:21 -04:00
Axel Kohlmeyer 741a1d1fc9
move Input::expand_args() to utils::expand_args() 2020-08-29 18:32:10 -04:00
Axel Kohlmeyer fcd0b9f78f
move Force::bounds() and Force::boundsbig() to utils. 2020-08-29 18:23:03 -04:00
Axel Kohlmeyer 60dfb6f77f
still need to disable variable tracking to silence unwanted warnings on ubuntu 2020-08-28 22:03:27 -04:00
Axel Kohlmeyer 31c91a8928
fix typo 2020-08-28 21:22:06 -04:00
Axel Kohlmeyer cec18b6aef
add docs for the new fortran interface 2020-08-28 20:57:19 -04:00
Axel Kohlmeyer e44707d5e1
add unittest support for the fortran interface to LAMMPS 2020-08-28 20:56:52 -04:00
Axel Kohlmeyer 3e92647abb
add new "official" fortran interface to LAMMPS in new folder "fortran" 2020-08-28 20:56:15 -04:00