Add infrared opacity functionality (#45)

.gitignore

@@ -18,3 +18,6 @@ data/[^(CMakeLists)]*.txt
 
 # test file
 tests/Testing
+
+# netcdf
+*.nc

README.md

@@ -269,3 +269,8 @@ git restore <file>
 ```
 git config --global alias.co checkout
 ```
+- clean *ALL* untracked files (this will cause unrecoverable damage, make sure what you
+  are doing.
+```
+git clean -fd
+```

cmake/application.cmake

@@ -6,7 +6,7 @@ FetchContent_Declare(
   application
   # GIT_REPOSITORY https://github.com/chengcli/application/ GIT_TAG cli/flush)
   DOWNLOAD_EXTRACT_TIMESTAMP TRUE
-  URL https://github.com/chengcli/application/archive/refs/tags/v0.6.tar.gz)
+  URL https://github.com/chengcli/application/archive/refs/tags/v0.6.1.tar.gz)
 
 FetchContent_MakeAvailable(application)
 

cmake/athena.cmake

@@ -2,18 +2,18 @@ include(FetchContent)
 
 set(FETCHCONTENT_QUIET FALSE)
 
-set(decomposition_patch
+set(patch_command
     git apply ${CMAKE_CURRENT_SOURCE_DIR}/patches/19.decomposition.patch
     ${CMAKE_CURRENT_SOURCE_DIR}/patches/21.implicit_dt.patch)
 
 FetchContent_Declare(
   athenapp
   GIT_REPOSITORY https://github.com/chengcli/athenapp/
   GIT_TAG snap-mods
-  PATCH_COMMAND ${decomposition_patch}
+  PATCH_COMMAND ${patch_command}
   UPDATE_DISCONNECTED TRUE)
 # DOWNLOAD_EXTRACT_TIMESTAMP TRUE URL
-# https://github.com/chengcli/athenapp/archive/refs/tags/v0.5.tar.gz)
+# https://github.com/chengcli/athenapp/archive/refs/tags/v0.8.tar.gz)
 
 FetchContent_MakeAvailable(athenapp)
 

doc/README-fork.md

@@ -1,3 +1,4 @@
+# How to private fork [canoe](https://github.com/chengcli/canoe)
 The [canoe](https://github.com/chengcli/canoe) repository is public by default
 but Github does not allow the creation of private forks for public repositories.
 
@@ -31,7 +32,7 @@ For the [canoe](https://github.com/chengcli/canoe) repo, the specific commands a
     git push --mirror https://<username>@github.com/<username>/canoe-dev.git
     ```
 
- 1. Push the repository's Git Large File Storage objects to your mirror.
+ 1. Push the repository's Git Large File Storage objects to your fork.
     ```bash
     git lfs push --all https://<username>@github.com/<username>/canoe-dev.git
     ```
@@ -65,10 +66,38 @@ For the [canoe](https://github.com/chengcli/canoe) repo, the specific commands a
     ```bash
     git push origin <branch_name>
     ```
-    When you want to pull changes from `upstream`, do so on `upstream` and `rebase` on top of your work.
     ```bash
-    git fetch upstream
-    git rebase upstream/master
     ```
 
  1. Finally, resolve the conflicts if any.
+
+# How to fetch updates from upstream
+
+If `upstream` has updates without lfs object, you can simply pull changes
+from `upstream` by:
+```bash
+git fetch upstream
+git rebase upstream/master
+```
+When `upstream` has new lfs object, do these extra steps before fetch:
+
+ 1. Create another bare clone of [canoe](https://github.com/chengcli/canoe).
+     ```bash
+     git clone --bare https://github.com/chengcli/canoe.git
+     ```
+
+ 1. Pull in the updated Git Large File Storage objects.
+    ```bash
+    cd canoe.git
+    git lfs fetch --all
+    ```
+
+ 1. Push the repository's Git Large File Storage objects to your fork.
+    ```bash
+    git lfs push --all https://<username>@github.com/<username>/canoe-dev.git
+    ```
+Then, `fetch` and `rebase` will bring in the update from `upstream`
+```bash
+git fetch upstream
+git rebase upstream/master
+```