Reorganize docs.

AMReX-Combustion · Sep 13, 2023 · cd68c2e · cd68c2e
1 parent 9f9afc5
commit cd68c2e
Show file tree

Hide file tree

Showing 87 changed files with 7 additions and 75 deletions.
diff --git a/Docs/CMakeLists.txt b/Docs/CMakeLists.txt
@@ -3,13 +3,13 @@ project(PeleLMeX-Docs NONE)
 list(APPEND CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake")
 
 find_package(Sphinx REQUIRED)
-#find_package(Doxygen)
 
 add_custom_target(sphinx ALL
-  COMMAND ${CMAKE_COMMAND} -E make_directory ${CMAKE_BINARY_DIR}/html
-  COMMAND ${CMAKE_COMMAND} -E copy_directory ${CMAKE_SOURCE_DIR}/source/landing
-                                             ${CMAKE_BINARY_DIR}/html
-  COMMAND ${SPHINX_EXECUTABLE} -M html "${CMAKE_SOURCE_DIR}/source/manual"
-                                       "${CMAKE_BINARY_DIR}/html/manual"
-                                       -c ${CMAKE_SOURCE_DIR}/source/manual
+  COMMAND ${CMAKE_COMMAND} -E make_directory ${CMAKE_CURRENT_BINARY_DIR}/html
+  COMMAND ${CMAKE_COMMAND} -E copy_directory ${CMAKE_CURRENT_SOURCE_DIR}/sphinx/landing
+                                             ${CMAKE_CURRENT_BINARY_DIR}/html
+  COMMAND ${SPHINX_EXECUTABLE} -M html "${CMAKE_CURRENT_SOURCE_DIR}/sphinx/manual"
+                                       "${CMAKE_CURRENT_BINARY_DIR}/html/manual"
+                                       -c ${CMAKE_CURRENT_SOURCE_DIR}/sphinx/manual
+                                       -W --keep-going -n
   )
diff --git a/Docs/Makefile b/Docs/Makefile
diff --git a/Docs/make.bat b/Docs/make.bat
diff --git a/Docs/requirements.txt b/Docs/requirements.txt
diff --git a/Docs/source/landing/.nojekyll → Docs/sphinx/landing/.nojekyll b/Docs/source/landing/.nojekyll → Docs/sphinx/landing/.nojekyll
diff --git a/Docs/source/landing/css/font-awesome.min.css → Docs/sphinx/landing/css/font-awesome.min.css b/Docs/source/landing/css/font-awesome.min.css → Docs/sphinx/landing/css/font-awesome.min.css
diff --git a/Docs/source/landing/css/skel.css → Docs/sphinx/landing/css/skel.css b/Docs/source/landing/css/skel.css → Docs/sphinx/landing/css/skel.css
diff --git a/Docs/source/landing/css/style-large.css → Docs/sphinx/landing/css/style-large.css b/Docs/source/landing/css/style-large.css → Docs/sphinx/landing/css/style-large.css
diff --git a/Docs/source/landing/css/style-medium.css → Docs/sphinx/landing/css/style-medium.css b/Docs/source/landing/css/style-medium.css → Docs/sphinx/landing/css/style-medium.css
diff --git a/Docs/source/landing/css/style-small.css → Docs/sphinx/landing/css/style-small.css b/Docs/source/landing/css/style-small.css → Docs/sphinx/landing/css/style-small.css
diff --git a/Docs/source/landing/css/style-xlarge.css → Docs/sphinx/landing/css/style-xlarge.css b/Docs/source/landing/css/style-xlarge.css → Docs/sphinx/landing/css/style-xlarge.css
diff --git a/Docs/source/landing/css/style-xsmall.css → Docs/sphinx/landing/css/style-xsmall.css b/Docs/source/landing/css/style-xsmall.css → Docs/sphinx/landing/css/style-xsmall.css
diff --git a/Docs/source/landing/css/style.css → Docs/sphinx/landing/css/style.css b/Docs/source/landing/css/style.css → Docs/sphinx/landing/css/style.css
diff --git a/Docs/source/landing/fonts/FontAwesome.otf → Docs/sphinx/landing/fonts/FontAwesome.otf b/Docs/source/landing/fonts/FontAwesome.otf → Docs/sphinx/landing/fonts/FontAwesome.otf
diff --git a/...rce/landing/fonts/fontawesome-webfont.eot → ...inx/landing/fonts/fontawesome-webfont.eot b/...rce/landing/fonts/fontawesome-webfont.eot → ...inx/landing/fonts/fontawesome-webfont.eot
diff --git a/...rce/landing/fonts/fontawesome-webfont.svg → ...inx/landing/fonts/fontawesome-webfont.svg b/...rce/landing/fonts/fontawesome-webfont.svg → ...inx/landing/fonts/fontawesome-webfont.svg
diff --git a/...rce/landing/fonts/fontawesome-webfont.ttf → ...inx/landing/fonts/fontawesome-webfont.ttf b/...rce/landing/fonts/fontawesome-webfont.ttf → ...inx/landing/fonts/fontawesome-webfont.ttf
diff --git a/...ce/landing/fonts/fontawesome-webfont.woff → ...nx/landing/fonts/fontawesome-webfont.woff b/...ce/landing/fonts/fontawesome-webfont.woff → ...nx/landing/fonts/fontawesome-webfont.woff
diff --git a/Docs/source/landing/gallery.html → Docs/sphinx/landing/gallery.html b/Docs/source/landing/gallery.html → Docs/sphinx/landing/gallery.html
diff --git a/Docs/source/landing/help.html → Docs/sphinx/landing/help.html b/Docs/source/landing/help.html → Docs/sphinx/landing/help.html
diff --git a/...source/landing/images/CoverPistonBowl.png → ...sphinx/landing/images/CoverPistonBowl.png b/...source/landing/images/CoverPistonBowl.png → ...sphinx/landing/images/CoverPistonBowl.png
diff --git a/Docs/source/landing/images/PB_AMR.gif → Docs/sphinx/landing/images/PB_AMR.gif b/Docs/source/landing/images/PB_AMR.gif → Docs/sphinx/landing/images/PB_AMR.gif
diff --git a/Docs/source/landing/index.html → Docs/sphinx/landing/index.html b/Docs/source/landing/index.html → Docs/sphinx/landing/index.html
diff --git a/Docs/source/landing/js/html5shiv.js → Docs/sphinx/landing/js/html5shiv.js b/Docs/source/landing/js/html5shiv.js → Docs/sphinx/landing/js/html5shiv.js
diff --git a/Docs/source/landing/js/init.js → Docs/sphinx/landing/js/init.js b/Docs/source/landing/js/init.js → Docs/sphinx/landing/js/init.js
diff --git a/Docs/source/landing/js/jquery.min.js → Docs/sphinx/landing/js/jquery.min.js b/Docs/source/landing/js/jquery.min.js → Docs/sphinx/landing/js/jquery.min.js
diff --git a/Docs/source/landing/js/skel-layers.min.js → Docs/sphinx/landing/js/skel-layers.min.js b/Docs/source/landing/js/skel-layers.min.js → Docs/sphinx/landing/js/skel-layers.min.js
diff --git a/Docs/source/landing/js/skel.min.js → Docs/sphinx/landing/js/skel.min.js b/Docs/source/landing/js/skel.min.js → Docs/sphinx/landing/js/skel.min.js
diff --git a/Docs/source/landing/overview.html → Docs/sphinx/landing/overview.html b/Docs/source/landing/overview.html → Docs/sphinx/landing/overview.html
diff --git a/Docs/source/landing/web_icon.ico → Docs/sphinx/landing/web_icon.ico b/Docs/source/landing/web_icon.ico → Docs/sphinx/landing/web_icon.ico
diff --git a/Docs/source/manual/Implementation.rst → Docs/sphinx/manual/Implementation.rst b/Docs/source/manual/Implementation.rst → Docs/sphinx/manual/Implementation.rst
diff --git a/Docs/source/manual/LMeXControls.rst → Docs/sphinx/manual/LMeXControls.rst b/Docs/source/manual/LMeXControls.rst → Docs/sphinx/manual/LMeXControls.rst
diff --git a/Docs/source/manual/Model.rst → Docs/sphinx/manual/Model.rst b/Docs/source/manual/Model.rst → Docs/sphinx/manual/Model.rst
diff --git a/Docs/source/manual/Performances.rst → Docs/sphinx/manual/Performances.rst b/Docs/source/manual/Performances.rst → Docs/sphinx/manual/Performances.rst
diff --git a/Docs/source/manual/Troubleshooting.rst → Docs/sphinx/manual/Troubleshooting.rst b/Docs/source/manual/Troubleshooting.rst → Docs/sphinx/manual/Troubleshooting.rst
diff --git a/Docs/source/manual/Tutorials.rst → Docs/sphinx/manual/Tutorials.rst b/Docs/source/manual/Tutorials.rst → Docs/sphinx/manual/Tutorials.rst
diff --git a/Docs/source/manual/Tutorials_BFSFlame.rst → Docs/sphinx/manual/Tutorials_BFSFlame.rst b/Docs/source/manual/Tutorials_BFSFlame.rst → Docs/sphinx/manual/Tutorials_BFSFlame.rst
diff --git a/Docs/source/manual/Tutorials_FlameSheet.rst → Docs/sphinx/manual/Tutorials_FlameSheet.rst b/Docs/source/manual/Tutorials_FlameSheet.rst → Docs/sphinx/manual/Tutorials_FlameSheet.rst
diff --git a/Docs/source/manual/Tutorials_FlowPastCyl.rst → Docs/sphinx/manual/Tutorials_FlowPastCyl.rst b/Docs/source/manual/Tutorials_FlowPastCyl.rst → Docs/sphinx/manual/Tutorials_FlowPastCyl.rst
diff --git a/Docs/source/manual/Tutorials_TripleFlame.rst → Docs/sphinx/manual/Tutorials_TripleFlame.rst b/Docs/source/manual/Tutorials_TripleFlame.rst → Docs/sphinx/manual/Tutorials_TripleFlame.rst
diff --git a/Docs/source/manual/Validation.rst → Docs/sphinx/manual/Validation.rst b/Docs/source/manual/Validation.rst → Docs/sphinx/manual/Validation.rst
diff --git a/...anual/_static/swirlH2Fast_OH_vort_256.png → ...anual/_static/swirlH2Fast_OH_vort_256.png b/...anual/_static/swirlH2Fast_OH_vort_256.png → ...anual/_static/swirlH2Fast_OH_vort_256.png
diff --git a/Docs/source/manual/_static/theme.css → Docs/sphinx/manual/_static/theme.css b/Docs/source/manual/_static/theme.css → Docs/sphinx/manual/_static/theme.css
diff --git a/Docs/source/manual/conf.py → Docs/sphinx/manual/conf.py b/Docs/source/manual/conf.py → Docs/sphinx/manual/conf.py
diff --git a/...anual/images/model/PeleLMeX_Algorithm.png → ...anual/images/model/PeleLMeX_Algorithm.png b/...anual/images/model/PeleLMeX_Algorithm.png → ...anual/images/model/PeleLMeX_Algorithm.png
diff --git a/...nual/images/model/PeleLMeX_Subcycling.png → ...nual/images/model/PeleLMeX_Subcycling.png b/...nual/images/model/PeleLMeX_Subcycling.png → ...nual/images/model/PeleLMeX_Subcycling.png
diff --git a/...formances/PMF/SingleNodePMFComparison.png → ...formances/PMF/SingleNodePMFComparison.png b/...formances/PMF/SingleNodePMFComparison.png → ...formances/PMF/SingleNodePMFComparison.png
diff --git a/...erformances/PMF/SingleNodePMF_Crusher.png → ...erformances/PMF/SingleNodePMF_Crusher.png b/...erformances/PMF/SingleNodePMF_Crusher.png → ...erformances/PMF/SingleNodePMF_Crusher.png
diff --git a/...ges/performances/PMF/SingleNodePMF_PM.png → ...ges/performances/PMF/SingleNodePMF_PM.png b/...ges/performances/PMF/SingleNodePMF_PM.png → ...ges/performances/PMF/SingleNodePMF_PM.png
diff --git a/...performances/PMF/SingleNodePMF_Summit.png → ...performances/PMF/SingleNodePMF_Summit.png b/...performances/PMF/SingleNodePMF_Summit.png → ...performances/PMF/SingleNodePMF_Summit.png
diff --git a/...performances/PMF/WeakScalingFSCrusher.png → ...performances/PMF/WeakScalingFSCrusher.png b/...performances/PMF/WeakScalingFSCrusher.png → ...performances/PMF/WeakScalingFSCrusher.png
diff --git a/...manual/images/tutorials/BFS_1200steps.png → ...manual/images/tutorials/BFS_1200steps.png b/...manual/images/tutorials/BFS_1200steps.png → ...manual/images/tutorials/BFS_1200steps.png
diff --git a/.../manual/images/tutorials/BFS_250steps.png → .../manual/images/tutorials/BFS_250steps.png b/.../manual/images/tutorials/BFS_250steps.png → .../manual/images/tutorials/BFS_250steps.png
diff --git a/.../manual/images/tutorials/BFS_500steps.png → .../manual/images/tutorials/BFS_500steps.png b/.../manual/images/tutorials/BFS_500steps.png → .../manual/images/tutorials/BFS_500steps.png
diff --git a/...nual/images/tutorials/BFS_CondAverage.png → ...nual/images/tutorials/BFS_CondAverage.png b/...nual/images/tutorials/BFS_CondAverage.png → ...nual/images/tutorials/BFS_CondAverage.png
diff --git a/...e/manual/images/tutorials/BFS_InitSol.png → ...x/manual/images/tutorials/BFS_InitSol.png b/...e/manual/images/tutorials/BFS_InitSol.png → ...x/manual/images/tutorials/BFS_InitSol.png
diff --git a/...nual/images/tutorials/BFS_SetupSketch.png → ...nual/images/tutorials/BFS_SetupSketch.png b/...nual/images/tutorials/BFS_SetupSketch.png → ...nual/images/tutorials/BFS_SetupSketch.png
diff --git a/...nual/images/tutorials/FPC_Coarse_25ms.png → ...nual/images/tutorials/FPC_Coarse_25ms.png b/...nual/images/tutorials/FPC_Coarse_25ms.png → ...nual/images/tutorials/FPC_Coarse_25ms.png
diff --git a/...nual/images/tutorials/FPC_SetupSketch.png → ...nual/images/tutorials/FPC_SetupSketch.png b/...nual/images/tutorials/FPC_SetupSketch.png → ...nual/images/tutorials/FPC_SetupSketch.png
diff --git a/...l/images/tutorials/FPC_VorticityFinal.png → ...l/images/tutorials/FPC_VorticityFinal.png b/...l/images/tutorials/FPC_VorticityFinal.png → ...l/images/tutorials/FPC_VorticityFinal.png
diff --git a/...e/manual/images/tutorials/FS_120steps.png → ...x/manual/images/tutorials/FS_120steps.png b/...e/manual/images/tutorials/FS_120steps.png → ...x/manual/images/tutorials/FS_120steps.png
diff --git a/...ce/manual/images/tutorials/FS_50steps.png → ...nx/manual/images/tutorials/FS_50steps.png b/...ce/manual/images/tutorials/FS_50steps.png → ...nx/manual/images/tutorials/FS_50steps.png
diff --git a/...al/images/tutorials/FS_InitSolDefault.png → ...al/images/tutorials/FS_InitSolDefault.png b/...al/images/tutorials/FS_InitSolDefault.png → ...al/images/tutorials/FS_InitSolDefault.png
diff --git a/...ual/images/tutorials/FS_InitSolTweaks.png → ...ual/images/tutorials/FS_InitSolTweaks.png b/...ual/images/tutorials/FS_InitSolTweaks.png → ...ual/images/tutorials/FS_InitSolTweaks.png
diff --git a/...manual/images/tutorials/TF_ACcomplete.png → ...manual/images/tutorials/TF_ACcomplete.png b/...manual/images/tutorials/TF_ACcomplete.png → ...manual/images/tutorials/TF_ACcomplete.png
diff --git a/.../manual/images/tutorials/TF_ACcontrol.png → .../manual/images/tutorials/TF_ACcontrol.png b/.../manual/images/tutorials/TF_ACcontrol.png → .../manual/images/tutorials/TF_ACcontrol.png
diff --git a/...ual/images/tutorials/TF_CoarseDetails.png → ...ual/images/tutorials/TF_CoarseDetails.png b/...ual/images/tutorials/TF_CoarseDetails.png → ...ual/images/tutorials/TF_CoarseDetails.png
diff --git a/...manual/images/tutorials/TF_InitialSol.png → ...manual/images/tutorials/TF_InitialSol.png b/...manual/images/tutorials/TF_InitialSol.png → ...manual/images/tutorials/TF_InitialSol.png
diff --git a/...urce/manual/images/tutorials/TF_Intro.png → ...hinx/manual/images/tutorials/TF_Intro.png b/...urce/manual/images/tutorials/TF_Intro.png → ...hinx/manual/images/tutorials/TF_Intro.png
diff --git a/...anual/images/tutorials/TF_SetupSketch.png → ...anual/images/tutorials/TF_SetupSketch.png b/...anual/images/tutorials/TF_SetupSketch.png → ...anual/images/tutorials/TF_SetupSketch.png
diff --git a/.../manual/images/tutorials/TF_Transient.gif → .../manual/images/tutorials/TF_Transient.gif b/.../manual/images/tutorials/TF_Transient.gif → .../manual/images/tutorials/TF_Transient.gif
diff --git a/...ns/EBChannelFlow/Uplus_Re180_DNS_LMeX.png → ...ns/EBChannelFlow/Uplus_Re180_DNS_LMeX.png b/...ns/EBChannelFlow/Uplus_Re180_DNS_LMeX.png → ...ns/EBChannelFlow/Uplus_Re180_DNS_LMeX.png
diff --git a/...ns/EBChannelFlow/Uplus_Re395_LES_LMeX.png → ...ns/EBChannelFlow/Uplus_Re395_LES_LMeX.png b/...ns/EBChannelFlow/Uplus_Re395_LES_LMeX.png → ...ns/EBChannelFlow/Uplus_Re395_LES_LMeX.png
diff --git a/...ns/EBChannelFlow/Uplus_Re934_LES_LMeX.png → ...ns/EBChannelFlow/Uplus_Re934_LES_LMeX.png b/...ns/EBChannelFlow/Uplus_Re934_LES_LMeX.png → ...ns/EBChannelFlow/Uplus_Re934_LES_LMeX.png
diff --git a/...ChannelFlow/VelRMSplus_Re180_DNS_LMeX.png → ...ChannelFlow/VelRMSplus_Re180_DNS_LMeX.png b/...ChannelFlow/VelRMSplus_Re180_DNS_LMeX.png → ...ChannelFlow/VelRMSplus_Re180_DNS_LMeX.png
diff --git a/...ChannelFlow/VelRMSplus_Re395_LES_LMeX.png → ...ChannelFlow/VelRMSplus_Re395_LES_LMeX.png b/...ChannelFlow/VelRMSplus_Re395_LES_LMeX.png → ...ChannelFlow/VelRMSplus_Re395_LES_LMeX.png
diff --git a/...ChannelFlow/VelRMSplus_Re934_LES_LMeX.png → ...ChannelFlow/VelRMSplus_Re934_LES_LMeX.png b/...ChannelFlow/VelRMSplus_Re934_LES_LMeX.png → ...ChannelFlow/VelRMSplus_Re934_LES_LMeX.png
diff --git a/...ons/EBChannelFlow/nu_t_Re934_LES_LMeX.png → ...ons/EBChannelFlow/nu_t_Re934_LES_LMeX.png b/...ons/EBChannelFlow/nu_t_Re934_LES_LMeX.png → ...ons/EBChannelFlow/nu_t_Re934_LES_LMeX.png
diff --git a/...ns/Poiseuille3D/PoiseuilleConvergence.png → ...ns/Poiseuille3D/PoiseuilleConvergence.png b/...ns/Poiseuille3D/PoiseuilleConvergence.png → ...ns/Poiseuille3D/PoiseuilleConvergence.png
diff --git a/...ations/Poiseuille3D/PoiseuilleVelProf.png → ...ations/Poiseuille3D/PoiseuilleVelProf.png b/...ations/Poiseuille3D/PoiseuilleVelProf.png → ...ations/Poiseuille3D/PoiseuilleVelProf.png
diff --git a/...tions/PremixedFlame/LMeX_DRM19_Phi0p9.png → ...tions/PremixedFlame/LMeX_DRM19_Phi0p9.png b/...tions/PremixedFlame/LMeX_DRM19_Phi0p9.png → ...tions/PremixedFlame/LMeX_DRM19_Phi0p9.png
diff --git a/...tions/PremixedFlame/LMeX_FinevsCoarse.png → ...tions/PremixedFlame/LMeX_FinevsCoarse.png b/...tions/PremixedFlame/LMeX_FinevsCoarse.png → ...tions/PremixedFlame/LMeX_FinevsCoarse.png
diff --git a/...s/validations/TaylorGreen/Dissipation.png → ...s/validations/TaylorGreen/Dissipation.png b/...s/validations/TaylorGreen/Dissipation.png → ...s/validations/TaylorGreen/Dissipation.png
diff --git a/...ges/validations/TaylorGreen/Enstrophy.png → ...ges/validations/TaylorGreen/Enstrophy.png b/...ges/validations/TaylorGreen/Enstrophy.png → ...ges/validations/TaylorGreen/Enstrophy.png
diff --git a/...ions/TaylorGreen/Enstrophy_AllSchemes.png → ...ions/TaylorGreen/Enstrophy_AllSchemes.png b/...ions/TaylorGreen/Enstrophy_AllSchemes.png → ...ions/TaylorGreen/Enstrophy_AllSchemes.png
diff --git a/...ges/validations/TaylorGreen/KinEnergy.png → ...ges/validations/TaylorGreen/KinEnergy.png b/...ges/validations/TaylorGreen/KinEnergy.png → ...ges/validations/TaylorGreen/KinEnergy.png
diff --git a/Docs/source/manual/index.rst → Docs/sphinx/manual/index.rst b/Docs/source/manual/index.rst → Docs/sphinx/manual/index.rst