Refactor Harp (#105)

This is a large haul-over of refactoring RT. - Absorber moved to opacity module - Use factory classes - Remove custom Absorber enroll routines - Build Python wrapper APIs
chengcli · Nov 5, 2023 · ac51d80 · ac51d80
1 parent d92b8f9
commit ac51d80
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diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -292,24 +292,18 @@ jobs:
       - name: create build directory
         # Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make.
         # See https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html?highlight=cmake_build_type
-        run: cmake -DTASK=ktable_test -DACCOUNT=${{env.ACCOUNT}} -DTOKEN=${{secrets.ACCESS_TOKEN}} -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}} -B ${{github.workspace}}/build-netcdf
+        run: cmake -DTASK=ktable_earth -DACCOUNT=${{env.ACCOUNT}} -DTOKEN=${{secrets.ACCESS_TOKEN}} -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}} -B ${{github.workspace}}/build-netcdf
 
       - name: build
         # Build your program with the given configuration
         run: |
           cmake --build ${{github.workspace}}/build-netcdf --config ${{env.BUILD_TYPE}} -- -j2
 
       - name: test generating ktable
-        working-directory: ${{github.workspace}}/build-netcdf
+        working-directory: ${{github.workspace}}/build-netcdf/bin
         # Execute tests defined by the CMake configuration.
         # See https://cmake.org/cmake/help/latest/manual/ctest.1.html for more detail
-        run: |
-          cp ./bin/example_giants_ir.yaml .
-          python ./bin/run_ktable.py -i ./bin/example_giants_ir.inp
-
-      - name: test jupiter heating/cooling
-        working-directory: ${{github.workspace}}/build-netcdf
-        run: echo "Cheers!"
+        run: python ./run_ktable_simple.py
 
   straka-2d:
     if: github.event.pull_request.draft == false

diff --git a/cmake/ktable_test.cmake → cmake/ktable_earth.cmake b/cmake/ktable_test.cmake → cmake/ktable_earth.cmake
@@ -14,11 +14,8 @@ set_if_empty(NVAPOR 0)
 set_if_empty(NCLOUD 0)
 set_if_empty(NTRACER 2)
 
-# canoe task set(TASKLIST InversionTasks)
-
 # canoe configure
 set(CMAKE_INSTALL_PREFIX "$ENV{HOME}/opt/")
-set(USER_MODS ${CMAKE_SOURCE_DIR}/examples/giants_add_absorber)
 set(HYDROSTATIC ON)
 set(RFM ON)
 set(NETCDF ON)

diff --git a/doc/README-tips.md b/doc/README-tips.md
@@ -8,6 +8,14 @@ git reset <file>
 ```
 git restore <file>
 ```
+- undo a "git rebase"
+```
+git reset --hard ORIG_HEAD
+```
+- hard reset to remote
+```
+git reset --hard origin/main
+```
 - aliasing a git command
 ```
 git config --global alias.co checkout

diff --git a/examples/2018-Li-harp/CMakeLists.txt b/examples/2018-Li-harp/CMakeLists.txt
@@ -1,33 +1,15 @@
+# =============================================
+# Examples published in Li et al. (2018), JQSRT
+# =============================================
+
 string(TOLOWER ${CMAKE_BUILD_TYPE} buildl)
 string(TOUPPER ${CMAKE_BUILD_TYPE} buildu)
 
 # 1. Compile giants_re.cpp
 
-set(namel giants_re)
-
-add_executable(${namel}.${buildl} ${namel}_pgen.cpp ${namel}_mods.cpp
-  ${CMAKE_BINARY_DIR}/main_${TASK}.cpp)
-
-set_target_properties(
-    ${namel}.${buildl}
-    PROPERTIES
-    RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/bin"
-    COMPILE_FLAGS ${CMAKE_CXX_FLAGS_${buildu}}
-    )
-
-target_link_libraries(${namel}.${buildl}
-    ${CANOE_LIBRARY_${buildu}}
-    )
-
-target_include_directories(${namel}.${buildl}
-    PRIVATE
-    ${CMAKE_BINARY_DIR}
-    ${CANOE_INCLUDE_DIR}
-    ${EIGEN3_INCLUDE_DIR}
-    )
-
-# 1. Copy input file to run directory
+setup_problem(giants_re)
 
+# 2. Copy input file to run directory
 file(GLOB inputs *.inp *.toml *.yaml)
 foreach(input ${inputs})
   file(COPY ${input} DESTINATION ${CMAKE_BINARY_DIR}/bin)

diff --git a/examples/2018-Li-harp/giants_ir.yaml b/examples/2018-Li-harp/giants_ir.yaml
@@ -1,5 +1,3 @@
-category: infrared
-
 opacity-sources:
   - name: H2-H2-CIA
     long-name: "Hydrogen-Hydrogen collisional absorption"
@@ -28,6 +26,7 @@ opacity-sources:
 bands: [B1, B2, B3, B4, B5, B6, B7, B8, B9, B10]
 
 B1:
+  grid-type: regular
   rt-solver: Disort
   unit: cm-1
   wavenumber-range: [10., 200.]

diff --git a/examples/2018-Li-harp/giants_re_pgen.cpp → examples/2018-Li-harp/giants_re.cpp b/examples/2018-Li-harp/giants_re_pgen.cpp → examples/2018-Li-harp/giants_re.cpp
diff --git a/examples/2018-Li-harp/giants_re_mods.cpp b/examples/2018-Li-harp/giants_re_mods.cpp
diff --git a/examples/2020-Li-polar-vortex/CMakeLists.txt b/examples/2020-Li-polar-vortex/CMakeLists.txt
@@ -1,37 +1,10 @@
-string(TOLOWER ${CMAKE_BUILD_TYPE} buildl)
-string(TOUPPER ${CMAKE_BUILD_TYPE} buildu)
-
-# 1. Compile straka.cpp
-
-#set(namel straka)
-
-foreach(namel shallow_xy polar_vortex)
-  find_package(Boost REQUIRED)
-
-  add_executable(${namel}.${buildl} ${namel}.cpp
-    ${CMAKE_BINARY_DIR}/main_${TASK}.cpp)
-
-  set_target_properties(
-      ${namel}.${buildl}
-      PROPERTIES
-      RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/bin"
-      COMPILE_FLAGS ${CMAKE_CXX_FLAGS_${buildu}}
-      )
-
-  target_link_libraries(${namel}.${buildl}
-      ${CANOE_LIBRARY_${buildu}}
-      )
-
-  target_include_directories(${namel}.${buildl}
-      PRIVATE
-      ${CMAKE_BINARY_DIR}
-      ${CANOE_INCLUDE_DIR}
-      ${MPI_CXX_INCLUDE_PATH}
-      ${NETCDF_INCLUDES}
-      ${PNETCDF_INCLUDE_DIR}
-      )
-endforeach()
+# ============================================
+# Examples published in Li et al. (2022), PNAS
+# ============================================
 
+# 1. Compile shallow_xy and polar_vortex
+setup_problem(shallow_xy)
+setup_problem(polar_vortex)
 
 # 1. Copy input file to run directory
 

diff --git a/examples/2023-Chen-exo3/CMakeLists.txt b/examples/2023-Chen-exo3/CMakeLists.txt
@@ -1,39 +1,11 @@
-string(TOLOWER ${CMAKE_BUILD_TYPE} buildl)
-string(TOUPPER ${CMAKE_BUILD_TYPE} buildu)
+# ===============================================
+# Examples published in Cheng et al. (2023), ApJS
+# ===============================================
 
 # 1. Compile dam_break.cpp
+setup_problem(dam_break)
 
-foreach(namel dam_break)
-  add_executable(${namel}.${buildl} ${namel}.cpp
-    ${CMAKE_BINARY_DIR}/main_${TASK}.cpp)
-
-  set_target_properties(
-      ${namel}.${buildl}
-      PROPERTIES
-      RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/bin"
-      COMPILE_FLAGS ${CMAKE_CXX_FLAGS_${buildu}}
-      )
-
-  target_link_libraries(${namel}.${buildl}
-      ${CANOE_LIBRARY_${buildu}}
-      ${NETCDF_LIBRARIES}
-      ${PNETCDF_LIBRARY}
-      ${MPI_CXX_LIBRARIES}
-      )
-
-  target_include_directories(${namel}.${buildl}
-      PRIVATE
-      ${CMAKE_BINARY_DIR}
-      ${CANOE_INCLUDE_DIR}
-      ${MPI_CXX_INCLUDE_PATH}
-      ${NETCDF_INCLUDES}
-      ${PNETCDF_INCLUDE_DIR}
-      )
-endforeach()
-
-
-# 1. Copy input file to run directory
-
+# 2. Copy input file to run directory
 file(GLOB inputs *.inp *.dat)
 foreach(input ${inputs})
     file(COPY ${input} DESTINATION ${CMAKE_BINARY_DIR}/bin)

diff --git a/examples/2023-Li-saturn-vla/CMakeLists.txt b/examples/2023-Li-saturn-vla/CMakeLists.txt
@@ -1,37 +1,11 @@
-string(TOLOWER ${CMAKE_BUILD_TYPE} buildl)
-string(TOUPPER ${CMAKE_BUILD_TYPE} buildu)
+# ========================================================
+# Examples published in Li et al. (2019), Science Advances
+# ========================================================
 
-# 1. Compile juno.cpp
-
-set(namel saturn_radio)
-
-add_executable(${namel}.${buildl} ${namel}.cpp
-  ${CMAKE_BINARY_DIR}/main_${TASK}.cpp)
-
-set_target_properties(
-    ${namel}.${buildl}
-    PROPERTIES
-    RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/bin"
-    COMPILE_FLAGS ${CMAKE_CXX_FLAGS_${buildu}}
-    )
-
-target_link_libraries(${namel}.${buildl}
-    ${ATHENAPP_LIBRARY_${buildu}}
-    ${CANOE_LIBRARY_${buildu}}
-    ${NETCDF_LIBRARIES}
-    ${CPPDISORT_LIBRARY_${buildu}}
-    )
-
-target_include_directories(${namel}.${buildl}
-    PRIVATE
-    ${CMAKE_BINARY_DIR}
-    ${CANOE_INCLUDE_DIR}
-    ${EIGEN3_INCLUDE_DIR}
-    ${MPI_CXX_INCLUDE_PATH}
-    )
-
-# 1. Copy input file to run directory
+# 1. Compile saturn_radio.cpp
+setup_problem(saturn_radio)
 
+# 2. Copy input file to run directory
 file(GLOB inputs *.inp *.yaml)
 foreach(input ${inputs})
     file(COPY ${input} DESTINATION ${CMAKE_BINARY_DIR}/bin)