Merge branch 'MFlowCode:master' into refactoring

Author: wilfonba

.github/workflows/doc.yml

@@ -30,17 +30,18 @@ jobs:
         git ls-remote "${{ secrets.DOC_PUSH_URL }}" -q
         code=$?
         if [ "$code" -ne "0" ]; then exit 0; fi
-        git config --global user.name  "MFC Action"
-        git config --global user.email "MFC Action"
+        git config --global user.name  'MFC Action'
+        git config --global user.email '<>'
         git clone "${{ secrets.DOC_PUSH_URL }}"
         cd "$(find . -name '*.github.io')"
         mv .github ..
         rm -rf $(pwd)/*
         mv ../.github       .
         mv ../install/doc/mfc/* .
         git add -A
-        git commit -m "${GITHUB_SHA::7}: $(date +%d/%m/%Y-%H:%M:%S)" || true
+        git commit -m "Docs @ ${GITHUB_SHA::7}" || true
         git push
 
 # DOC_PUSH_URL should be of the format:
-# - "https://${{ github.repository_owner }}:${{ TOKEN }}@github.com/${{ github.repository_owner }}/${{ github.repository_owner }}.github.io"
+# --> https://<username>:<token>@github.com/<username>/<repository>
+

CMakeLists.txt

@@ -216,7 +216,13 @@ if (MFC_BUILD_SIMULATION)
 
 
     if (MFC_WITH_OPEN_ACC)
-        find_package(OpenACC REQUIRED)
+        find_package(OpenACC)
+
+        # This should be equivalent to if (NOT OpenACC_FC_FOUND)
+        if (NOT TARGET OpenACC::OpenACC_Fortran)
+            message(FATAL_ERROR "OpenACC + Fortran is unsupported.")
+        endif()
+
         target_link_libraries(simulation PRIVATE OpenACC::OpenACC_Fortran)
 
 
@@ -315,26 +321,23 @@ macro(GEN_DOCS target name)
     set(DOXYGEN_PROJECT_NAME "${name}")
     set(DOXYGEN_INPUT        "${CMAKE_CURRENT_SOURCE_DIR}/src/${target}/ ${CMAKE_CURRENT_BINARY_DIR}/doxygen/${target}/")
 
-    file(
-        COPY        "${CMAKE_CURRENT_SOURCE_DIR}/doc/${target}"
-        DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doxygen"
-    )
+    file(COPY        "${CMAKE_CURRENT_SOURCE_DIR}/doc/${target}"
+         DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doxygen")
+
+    file(COPY        "${CMAKE_CURRENT_SOURCE_DIR}/doc/doxygen"
+         DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doxygen/${target}")
 
     configure_file(
         "${CMAKE_CURRENT_SOURCE_DIR}/doc/Doxyfile.in"
         "${CMAKE_CURRENT_BINARY_DIR}/doxygen/${target}/Doxyfile"
         @ONLY
     )
 
-    file(
-        COPY        "${CMAKE_CURRENT_SOURCE_DIR}/doc/res"
-        DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doxygen"
-    )
+    file(COPY        "${CMAKE_CURRENT_SOURCE_DIR}/doc/res"
+         DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doxygen")
 
-    file(
-        COPY        "${CMAKE_CURRENT_SOURCE_DIR}/doc/config.js"
-        DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doxygen"
-    )
+    file(COPY        "${CMAKE_CURRENT_SOURCE_DIR}/doc/config.js"
+         DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doxygen")
 
     add_custom_command(
         OUTPUT  "${CMAKE_CURRENT_BINARY_DIR}/doxygen/${target}/html/index.html"
@@ -382,7 +385,7 @@ if (MFC_BUILD_DOC)
     ExternalProject_Add(doxygen-awesome-css
         PREFIX            doxygen-awesome-css
         GIT_REPOSITORY    "https://github.com/jothepro/doxygen-awesome-css"
-        GIT_TAG           "a5efba07a3d4fd6317d95657b3095b97e134b791"
+        GIT_TAG           "8a34f701d3435309a21080f44fbd4a466979aa19"
         CONFIGURE_COMMAND ""
         BUILD_COMMAND     ""
         INSTALL_COMMAND   ""
@@ -398,6 +401,6 @@ if (MFC_BUILD_DOC)
     GEN_DOCS(post_process "MFC: Post-Process")
 
     # === === Generate Landing Page
-    GEN_DOCS(landing "MFC")
+    GEN_DOCS(documentation "MFC")
 
 endif()

README.md

@@ -1,4 +1,6 @@
-![MFC Banner](doc/res/banner.png)
+<p align="center">
+  <img src="doc/res/banner.png" alt="MFC Banner" width="500"/></center>
+</p>
 
 <p align="center">
   <a href="http://dx.doi.org/10.1016/j.cpc.2020.107396">
@@ -24,19 +26,25 @@
   </a>
 </p>
 
-Welcome to MFC! The MFC is a fully-documented parallel simulation software for multi-component, multi-phase, and bubbly flows.
+Welcome to the home of MFC!
+MFC simulates compressible multi-component and multi-phase flows, amongst other things. 
+It scales ideally to tens of thousands of GPUs.
+MFC is written in Fortran and makes use of metaprogramming to keep the codebase readable and compact.
+Please contact the developers, like [Spencer](mailto:[email protected]), if you have any questions.
+We have an active Slack channel to help ease in new MFC users and support development.
 
-Documentation is available on [our website](https://mflowcode.github.io/) and in markdown format at [doc/landing/readme.md](doc/landing/readme.md).
+MFC has both API and high-level documentation. 
+It is available on [the website](https://mflowcode.github.io/) and in markdown format at [doc/documentation/readme.md](doc/documentation/readme.md).
 
-The paper that describes the MFC's capabilities:
+If you use MFC, consider citing it:
 * <a href="https://doi.org/10.1016/j.cpc.2020.107396">
     S. H. Bryngelson, K. Schmidmayer, V. Coralic, K. Maeda, J. Meng, T. Colonius (2021) Computer Physics Communications 4655, 107396
 </a>
 
 ```
 @article{Bryngelson_2021,
   title = {MFC: An open-source high-order multi-component, multi-phase, and multi-scale compressible flow solver},
-  author = {Spencer H. Bryngelson and Kevin Schmidmayer and Vedran Coralic and Jomela C. Meng and Kazuki Maeda and  Tim Colonius},
+  author = {Spencer H. Bryngelson and Kevin Schmidmayer and Vedran Coralic and Jomela C. Meng and Kazuki Maeda and Tim Colonius},
   journal = {Computer Physics Communications},
   doi = {10.1016/j.cpc.2020.107396},
   year = 2021,
@@ -53,5 +61,5 @@ MFC is under the MIT license (see [LICENSE](LICENSE) file for full text).
 
 <p align="justify">
    MFC development was supported by multiple current and past grants from the US Office of Naval Research (ONR), the US National Institute of Health (NIH), and the US National Science Foundation (NSF).
-  MFC computations utilize the Extreme Science and Engineering Discovery Environment (XSEDE), under allocations TG-CTS120005 (PI Colonius) and TG-PHY210084 (PI Bryngelson) and OLCF Summit under allocation CFD154 (PI Bryngelson).
+  MFC computations utilize the Extreme Science and Engineering Discovery Environment (XSEDE, now ACCESS), under allocations TG-CTS120005 (PI Colonius) and TG-PHY210084 (PI Bryngelson) and OLCF Summit under allocation CFD154 (PI Bryngelson).
 </p>

doc/Doxyfile.in

@@ -38,7 +38,7 @@ PROJECT_NAME           = "@DOXYGEN_PROJECT_NAME@"
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = 4.0.0
+PROJECT_NUMBER         =
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a
@@ -1166,7 +1166,7 @@ HTML_FILE_EXTENSION    = .html
 # of the possible markers and block names see the documentation.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_HEADER            =
+HTML_HEADER            = doxygen/header.html
 
 # The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each
 # generated HTML page. If the tag is left blank doxygen will generate a standard
@@ -1176,7 +1176,7 @@ HTML_HEADER            =
 # that doxygen normally uses.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_FOOTER            =
+HTML_FOOTER            = doxygen/footer.html
 
 # The HTML_STYLESHEET tag can be used to specify a user-defined cascading style
 # sheet that is used by each HTML page. It can be used to fine-tune the look of
@@ -1211,7 +1211,7 @@ HTML_EXTRA_STYLESHEET  = @DOXYGEN_HTML_EXTRA_STYLESHEET@
 # files will be copied as-is; there are no commands or markers available.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_EXTRA_FILES       =
+HTML_EXTRA_FILES       = 
 
 # The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen
 # will adjust the colors in the style sheet and background images according to

doc/landing/CODE_OF_CONDUCT.md renamed to doc/documentation/CODE_OF_CONDUCT.md

@@ -81,9 +81,9 @@ Ph.D. Disserations:
     V. Coralic (2014) Ph.D. thesis, California Institute of Technology
   </a>
 
-### User Configuration (`defaults.yaml`)
+### User Configuration
 
-The `mfc.sh` script used in the previous section is configured through the file named `defaults.yaml`.
+The [mfc.sh](https://github.com/MFlowCode/MFC/blob/master/mfc.sh) script used in the previous section is configured through the [defaults.yaml](https://github.com/MFlowCode/MFC/blob/master/defaults.yaml) file.
 
 ## Development
 
@@ -112,7 +112,7 @@ You can append `-DMFC_MEMORY_DUMP` to `release-gpu`'s Fortran compiler options i
 ## License
 
 Copyright 2022.
-MFC is under the MIT license (see [LICENSE](LICENSE) file for full text).
+MFC is under the MIT license (see [LICENSE](https://github.com/MFlowCode/MFC/blob/master/LICENSE) file for full text).
 
 ## Acknowledgements