Skip to content
Permalink
Browse files

Merge branch 'doc' into develop

  • Loading branch information...
jbakosi committed Jun 12, 2019
2 parents a8bd531 + e67c9fd commit 26f5ea284425251dbefd0662e78cc1baf11144f8
Showing with 164 additions and 120 deletions.
  1. +57 −0 doc/images/README.md
  2. +0 −7 doc/pages/17-workflow.dox
  3. +0 −30 doc/pages/98-logo.dox
  4. +1 −1 doc/pages/{001-build.dox → build.dox}
  5. 0 doc/pages/{11-concurrency.dox → concurrency.dox}
  6. 0 doc/pages/{07-coverage.dox → coverage.dox}
  7. 0 doc/pages/{10-diffeq.dox → diffeq.dox}
  8. +0 −1 doc/pages/directories.dox
  9. 0 doc/pages/{06-fileconv.dox → fileconv.dox}
  10. +1 −1 doc/pages/{12-git-submodules-subtrees.dox → git-submodules-subtrees.dox}
  11. +1 −0 doc/pages/{02-inciter.dox → inciter.dox}
  12. 0 doc/pages/{18-inciter_design.dox → inciter_design.dox}
  13. 0 doc/pages/{21-inciter_newpde.dox → inciter_newpde.dox}
  14. 0 doc/pages/{21b-inciter_newpde_configuremultimat.c.dox → inciter_newpde_configuremultimat.c.dox}
  15. 0 doc/pages/{21a-inciter_newpde_configuremultimat.h.dox → inciter_newpde_configuremultimat.h.dox}
  16. 0 doc/pages/{21e-inciter_newpde_dg.h.dox → inciter_newpde_dg.h.dox}
  17. 0 doc/pages/{21c-inciter_newpde_dgmultimat.h.dox → inciter_newpde_dgmultimat.h.dox}
  18. 0 doc/pages/{21d-inciter_newpde_dgveleq.h.dox → inciter_newpde_dgveleq.h.dox}
  19. 0 doc/pages/{21h-inciter_newpde_problem.h.dox → inciter_newpde_problem.h.dox}
  20. 0 doc/pages/{21f-inciter_newpde_userdefined.h.dox → inciter_newpde_userdefined.h.dox}
  21. 0 doc/pages/{21g-inciter_newpde_vorticalflow.h.dox → inciter_newpde_vorticalflow.h.dox}
  22. 0 doc/pages/{20-inciter_newscheme.dox → inciter_newscheme.dox}
  23. 0 doc/pages/{20a-inciter_newscheme_alecg.ci.dox → inciter_newscheme_alecg.ci.dox}
  24. 0 doc/pages/{20d-inciter_newscheme_class.dox → inciter_newscheme_class.dox}
  25. 0 doc/pages/{20c-inciter_newscheme_header.dox → inciter_newscheme_header.dox}
  26. 0 doc/pages/{20b-inciter_newscheme_nowarning.dox → inciter_newscheme_nowarning.dox}
  27. 0 doc/pages/{19-inciter_performance.dox → inciter_performance.dox}
  28. 0 doc/pages/{09-inhomogeneity.dox → inhomogeneity.dox}
  29. 0 doc/pages/{13-io.dox → io.dox}
  30. 0 doc/pages/{08-layout.dox → layout.dox}
  31. +7 −12 doc/pages/{99-licenses.dox → licenses.dox}
  32. +8 −50 doc/pages/mainpage.dox
  33. 0 doc/pages/{05-meshconv.dox → meshconv.dox}
  34. +1 −1 doc/pages/{06-papers.dox → papers.dox}
  35. +58 −0 doc/pages/resources.dox
  36. 0 doc/pages/{14-rngs_input.dox → rngs_input.dox}
  37. +4 −0 doc/pages/{03-rngtest.dox → rngtest.dox}
  38. 0 doc/pages/{15-rngtest_design.dox → rngtest_design.dox}
  39. 0 doc/pages/{16-statistics_output.dox → statistics_output.dox}
  40. 0 doc/pages/{04-unittest.dox → unittest.dox}
  41. +1 −0 doc/pages/{01-walker.dox → walker.dox}
  42. +5 −8 doc/pages/{00-why.dox → why.dox}
  43. +10 −6 doc/quinoa.doxy
  44. +7 −2 src/CMakeLists.txt
  45. +3 −1 tools/recent_mods.sh
@@ -0,0 +1,57 @@
# How to generate logos

,::,` `.
.;;;'';;;: ;;#
;;;@+ +;;; ;;;;;, ;;;;. ;;;;;, ;;;; ;;;; `;;;;;;: ;;;
:;;@` :;;' .;;;@, ,;@, ,;;;@: .;;;' .;+;. ;;;@#:';;; ;;;;'
;;;# ;;;: ;;;' ;: ;;;' ;;;;; ;# ;;;@ ;;; ;+;;'
.;;+ ;;;# ;;;' ;: ;;;' ;#;;;` ;# ;;@ `;;+ .;#;;;.
;;;# :;;' ;;;' ;: ;;;' ;# ;;; ;# ;;;@ ;;; ;# ;;;+
;;;# .;;; ;;;' ;: ;;;' ;# ,;;; ;# ;;;# ;;;: ;@ ;;;
;;;# .;;' ;;;' ;: ;;;' ;# ;;;; ;# ;;;' ;;;+ ;', ;;;@
;;;+ ,;;+ ;;;' ;: ;;;' ;# ;;;' ;# ;;;' ;;;' ;':::;;;;
`;;; ;;;@ ;;;' ;: ;;;' ;# ;;;';# ;;;@ ;;;:,;+++++;;;'
;;;; ;;;@ ;;;# .;. ;;;' ;# ;;;;# `;;+ ;;# ;# ;;;'
.;;; :;;@ ,;;+ ;+ ;;;' ;# ;;;# ;;; ;;;@ ;@ ;;;.
';;; ;;;@, ;;;;``.;;@ ;;;' ;+ .;;# ;;; :;;@ ;;; ;;;+
:;;;;;;;+@` ';;;;;'@ ;;;;;, ;;;; ;;+ +;;;;;;#@ ;;;;. .;;;;;;
.;;#@' `#@@@: ;::::; ;:::: ;@ '@@@+ ;:::; ;::::::
:;;;;;;.
.;@+@';;;;;;'
` '#''@`
## Quinoa ASCII art logo
The Quinoa ASCII art logo, displayed above, has been generated at
http://picascii.com, based on the [Xfig](http://mcj.sourceforge.net/) image,
[doc/images/quinoa.fig](https://github.com/quinoacomputing/quinoa/blob/master/doc/images/quinoa.fig)
displayed at https://quinoacomputing.org.
## ASCII art logos of executable names
The ASCII art logos of the _executable_ names, e.g., at
https://quinoacomputing.org/inciter_main.html, have been generated at
http://patorjk.com/software/taag using the default settings:
- Font: _Graffiti_
- Character width: _default_
- Character height: _default_
## ASCII art logos in SVG format
The ASCII art logos in SVG format, to display them on HTML pages, e.g., at
https://quinoacomputing.org/inciter_main.html, have been generated by
[LaTeX](https://www.latex-project.org/), using
[doc/txt2pdf](https://github.com/quinoacomputing/quinoa/tree/master/doc/txt2pdf),
yielding a PDF which then was converted to SVG using
[pdf2svg](http://www.cityinthesky.co.uk/opensource/pdf2svg/) as
cd doc/txt2pdf/
make pdf
pdf2svg txt2pdf.pdf <executable>.svg
## Quinoa hex color codes
- <span style="color:#1d3564">blue: 1d3564</span>
- <span style="color:#c96a00">dark orange: c96a00</span>
- <span style="color:#e6851c">light orange: ce6861c</span>

This file was deleted.

This file was deleted.

@@ -1,5 +1,5 @@
/*!
@page build How to build
@page build Build

@tableofcontents{xml}

File renamed without changes.
File renamed without changes.
File renamed without changes.
@@ -1,5 +1,4 @@
/*!
\page files Files

@dir src
@brief Root of the source tree
File renamed without changes.
@@ -1,5 +1,5 @@
/*!
\page git_submodules_subtrees Third-party libraries and external tools using git submodules and subtrees
\page git_submodules_subtrees Modules

Quinoa uses git _submodules_ as well as git _subtrees_ to pull in third-party
libraries (TPLs) and auxiliary tools. This allows easy update to a TPL's (or
@@ -31,6 +31,7 @@ codes, to large problems on large computers using Charm++'s automatic load
balancing capabilities.

@section inciter_pages Related pages
- @ref papers_inciter "Publications"
- @ref inciter_performance "Performance"
- @ref inciter_design "Software design"
- @ref inciter_newscheme "How to add a new scheme"
File renamed without changes.
File renamed without changes.
File renamed without changes.
File renamed without changes.
File renamed without changes.
File renamed without changes.
File renamed without changes.
File renamed without changes.
File renamed without changes.
File renamed without changes.
File renamed without changes.
File renamed without changes.
File renamed without changes.
File renamed without changes.
File renamed without changes.
@@ -1,19 +1,18 @@
/*!
\page licenses Third-party libraries, compilers, and tools
\page licenses Third-party

@tableofcontents{xml}

This page collects links to full verbatim texts of the licenses of all third-party
libraries (TPLs), and the list of compilers and tools used by Quinoa.

@section licenses_tpl_vs_tool TPLs and external tools
An important distinction between @ref tpl_licenses and @ref tools_web is that
TPLs are libraries whose source we directly use, e.g., via include files and/or
(static and dynamic) linking, while from a tool we do not include source code
nor link its object files, only build it and use it as a separate (external)
executable.

An important distinction between TPLs and tools is that TPLs are libraries whose
source we directly use, e.g., via include files and/or (static and dynamic)
linking, while from a tool we do not include source code nor link its object
files, only build it and use it as a separate (external) executable.

\section tpl_licenses Third-party libraries
\section tpl_licenses Third-party libraries (TPLs)

\subsection charm_license The Charm++ Parallel Programming System
- Required
@@ -182,8 +181,6 @@ files, only build it and use it as a separate (external) executable.
- Web: https://github.com/edouarda/brigand
- License: @subpage brigand_license_page

<hr>

\section compiler_web Compilers

\subsection clang_web Clang C++ compiler
@@ -198,8 +195,6 @@ files, only build it and use it as a separate (external) executable.
\subsection cray_web Cray C++ compiler
- Web: https://pubs.cray.com/content/S-2179/8.7/cray-c-and-c++-reference-manual

<hr>

\section tools_web Tools

\subsection doxygen_web Doxygen for design, theory, and software API documentation
@@ -20,7 +20,7 @@ Our ultimate goal is to simulate large and complex engineering multiphysics
problems with a production-quality code that is extensible and maintainable,
using hardware resources efficiently, even for problems with _a priori_
unknown, heterogeneous, and dynamic load distribution. Read more at our @ref
why page.
why "Philosophy" page.

@m_class{m-note m-default m-landing-news}

@@ -93,10 +93,13 @@ container](https://hub.docker.com/r/quinoacomputing/quinoa). See also
- https://quinoacomputing.github.io/examples.html
- https://github.com/quinoacomputing/quinoa-examples

For larger problems and computers, however, you should build from source.
For larger problems and computers, however, you should @ref build "build" from source.

@section mainpage_build Build

The simplest way to build from source is to perform the following steps. For
other ways to build, see the page on @ref build "building Quinoa".

- Install prerequisites: _Debian/Ubuntu linux_ (line 1: required, line 2: recommended)

apt-get install cmake gfortran gcc g++ openmpi-bin libopenmpi-dev
@@ -116,8 +119,7 @@ For larger problems and computers, however, you should build from source.
@note The above will use 8 CPU cores to compile the code and run the tests.
You might need to adjust this to get optimal performance.

All executables will be under `build/Main/`. For more information on how to
build, see the page on @ref build.
All executables will be under `build/Main/`.

We roughly follow the development model described
[here](http://nvie.com/posts/a-successful-git-branching-model). As a
@@ -145,57 +147,13 @@ git clone --recurse-submodules --branch=develop https://github.com/quinoacomputi
└── README.md - This file, rendered at github.com/quinoacomputing/quinoa
@endverbatim

@section mainpage_contributing Contribute

Contributions and collaborators are welcome. Contact us via
[GitHub](https://github.com/quinoacomputing/quinoa),
[Email](mailto:quinoa@lanl.gov) or
[Gitter](https://gitter.im/quinoacomputing/quinoa).

@section mainpage_authors Authors

(in chronological order of contribution)

1. [Jozsef Bakosi](https://github.com/jbakosi)
2. [Francisco Gonzalez](https://github.com/franjgonzalez)
3. [Brandon Rogers](https://github.com/brog2610)
4. [Christoph Junghans](https://github.com/junghans)
5. [Robert Pavel](https://github.com/rspavel)
6. [Aditya Pakki](https://github.com/adityapakki)
7. [Bob Bird](https://github.com/rfbird)
8. [Aditya Pandare](https://github.com/adityakpandare)
9. [Weizhao Li](https://github.com/WeizhaoLi2018)

@section mainpage_resources Resources

- Source --- https://github.com/quinoacomputing/quinoa
- Releases --- https://github.com/quinoacomputing/quinoa/releases
- Contributing --- https://www.clahub.com/agreements/quinoacomputing/quinoa
- License --- https://github.com/quinoacomputing/quinoa/blob/master/LICENSE
- Third-party libraries and licenses --- https://quinoacomputing.github.io/licenses.html
- Documentation --- https://quinoacomputing.github.io
- Web --- https://quinoacomputing.github.io
- Email --- mailto:quinoa@lanl.gov
- Gitter --- https://gitter.im/quinoacomputing/quinoa
- Philosophy --- https://quinoacomputing.github.io/why
- Papers --- https://quinoacomputing.github.io/papers
- Roadmap --- https://github.com/quinoacomputing/quinoa/issues
- Doxygen --- https://quinoacomputing.github.io
- Coverage --- https://quinoacomputing.github.io/coverage
- Codecov --- https://codecov.io/gh/quinoacomputing/quinoa/commits
- Sonarqube --- https://sonarqube.com/organizations/quinoacomputing
- Docker --- https://hub.docker.com/r/quinoacomputing/quinoa
- Azure --- https://dev.azure.com/quinoacomputing/Quinoa
- Analytics --- http://www.openhub.net/p/quinoacomputing
- Practices --- https://bestpractices.coreinfrastructure.org/projects/2120
- Cite --- https://zenodo.org/badge/latestdoi/38454430

@section mainpage_license License

Quinoa is certified [Open
Source](http://www.opensource.org/docs/definition.html) software. It may be
used for any purpose, including commercial purposes, at absolutely no cost. It
is distributed under the terms of the 3-clause BSD license listed below.
is distributed under the terms of the 3-clause BSD license listed below. See
also @ref resources_legal.

@include LICENSE

File renamed without changes.
@@ -1,5 +1,5 @@
/*!
\page papers Papers
\page papers Publications

This page collects peer-reviewed journal papers related to the algorithms
implemented in Quinoa. The papers are grouped by executables.
@@ -0,0 +1,58 @@
/*!
\page resources Resources

@section resources_code Code

- Source code --- https://github.com/quinoacomputing/quinoa
- Documentation --- https://quinoacomputing.org
- GitHub organization --- https://github.com/quinoacomputing

@section resources_releases Releases

- Source tarballs --- https://github.com/quinoacomputing/quinoa/releases
- Docker containers with pre-built executables --- https://hub.docker.com/r/quinoacomputing/quinoa

@section resources_legal Legal

- License --- https://github.com/quinoacomputing/quinoa/blob/master/LICENSE
- Third-party libraries and licenses --- https://quinoacomputing.org/licenses.html

@section resources_contributing Contributing

- Contributing / Roadmap --- @ref contributing

@section resources_quality Code quality

- GCov --- https://quinoacomputing.org/coverage
- Codecov --- https://codecov.io/gh/quinoacomputing/quinoa/commits
- Sonarqube --- https://sonarqube.com/organizations/quinoacomputing
- Azure --- https://dev.azure.com/quinoacomputing/Quinoa
- Analytics --- http://www.openhub.net/p/quinoacomputing
- Practices --- https://bestpractices.coreinfrastructure.org/projects/2120

@section resources_cite Cite

- Journal papers --- @ref papers
- Software --- https://zenodo.org/badge/latestdoi/38454430

@section resources_contact Contact

- Chat --- https://quinoa.zulipchat.com
- Email list --- https://quinoa.groups.io
- LANL-team email --- mailto:quinoa@lanl.gov

@section resources_authors Authors

@m_class{m-note m-default m-text-center}

[Jozsef Bakosi](https://github.com/jbakosi) -
[Bob Bird](https://github.com/rfbird) -
[Francisco Gonzalez](https://github.com/franjgonzalez) -
[Christoph Junghans](https://github.com/junghans) -
[Weizhao Li](https://github.com/WeizhaoLi2018) -
[Aditya Pakki](https://github.com/adityapakki) -
[Aditya Pandare](https://github.com/adityakpandare) -
[Robert Pavel](https://github.com/rspavel) -
[Brandon Rogers](https://github.com/brog2610)

*/
File renamed without changes.
@@ -31,4 +31,8 @@ rngtest_design page.

@section rngtest_ex Examples
\subpage rngtest_examples

@section rngtest_pages Related pages
- @ref rngtest_design
- @ref rngs_input
*/
File renamed without changes.
File renamed without changes.
File renamed without changes.
@@ -230,6 +230,7 @@ beta variables are mass-fractions. For more details on the beta SDE, see
\subpage walker_examples

@section walker_pages Related pages
- @ref papers_walker "Publications"
- @ref diffeq
- @ref concurrency
- @ref inhomogeneity
@@ -1,8 +1,8 @@
/*!
\page why Philosophy
\page why Why

This page describes our core software engineering values and explains why we are
motivated to work on this project. Here is the TL;DR version:
This page describes our philosophy and our core software engineering values and
explains why we are motivated to work on this project.

@m_div{m-col-t-4 m-right-t}
<img src="quinoa.svg"/>
@@ -33,11 +33,8 @@ We strive to
intertwining physics, algorithms, and complex load balancing code, to ensure
sustainability.

If you agree and would like to contribute to
or use these tools, contact us via
[GitHub](https://github.com/quinoacomputing/quinoa),
[Email](mailto:quinoa@lanl.gov) or
[Gitter](https://gitter.im/quinoacomputing/quinoa), and join us!
If you agree and would like to use or contribute to these tools, @ref
resources_contact "contact us", and join us!

@m_div{m-col-t-6 m-col-m-3 m-right-t}
<img src="kattekrab-Mainframe_noshadow.svg"/>

0 comments on commit 26f5ea2

Please sign in to comment.
You can’t perform that action at this time.