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chengcli · Nov 5, 2023 · 73bef6b · 73bef6b
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Showing 10 changed files with 39 additions and 331 deletions.
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)

diff --git a/examples/2023-Li-saturn-vla/radio_channels.yaml b/examples/2023-Li-saturn-vla/radio_channels.yaml
@@ -1,68 +1,66 @@
 name: Saturn radio channel opacity file
 
 opacity-sources:
-  - name: radio-CIA
+  - name: CIA
+    class: radio-CIA
     long-name: "Hydrogen/Helium collisional induced absorption"
     parameters: {xHe: 0.135, xCH4: 2.04E-3, mix: 0.}
 
-  - name: radio-NH3
+  - name: NH3
+    class: radio-NH3
     long-name: "Ammonia line absorption"
     model: Hanley09
     dependent-species: [vapor.NH3, vapor.H2O]
     parameters: {xHe: 0.135, power: 0.}
 
-  - name: radio-H2O
+  - name: H2O
+    class: radio-H2O
     long-name: "H2O line absorption"
     model: Karpowicz
     dependent-species: [vapor.H2O]
     parameters: {xHe: 0.135, scale: 0.}
 
-  - name: radio-Electron
+  - name: Electron
+    class: radio-Electron
     long-name: "Electron absorption"
     model: AppletonHartree
     dependent-species: [tracer.e-]
 
 bands: [CH1, CH2, CH3, CH4, CH5, CH6]
 
 CH1:
-  type: radio
   rt-solver: Lambert
   unit: GHz
-  wavenumber-range: [0.6, 0.6]
+  frequency-range: [0.6, 0.6]
   opacity: [CIA, NH3, H2O, Electron]
   paramters: {alpha: 0.0}
 
 CH2:
-  type: radio
   rt-solver: Lambert
   unit: GHz
-  wavenumber-range: [1.25, 1.25]
+  frequency-range: [1.25, 1.25]
   opacity: [CIA, NH3, H2O]
 
 CH3:
-  type: radio
   rt-solver: Lambert
   unit: GHz
-  wavenumber-range: [2.6, 2.6]
+  frequency-range: [2.6, 2.6]
   opacity: [CIA, NH3, H2O]
 
 CH4:
-  type: radio
   rt-solver: Lambert
   unit: GHz
-  wavenumber-range: [5.2, 5.2]
+  frequency-range: [5.2, 5.2]
   opacity: [CIA, NH3, H2O]
 
 CH5:
-  type: radio
   rt-solver: Lambert
   unit: GHz
-  wavenumber-range: [10., 10.]
+  frequency-range: [10., 10.]
   opacity: [CIA, NH3, H2O]
 
 CH6:
-  type: radio
   rt-solver: Lambert
   unit: GHz
-  wavenumber-range: [22., 22.]
+  frequency-range: [22., 22.]
   opacity: [CIA, NH3, H2O]
diff --git a/examples/CMakeLists.txt b/examples/CMakeLists.txt
@@ -6,7 +6,7 @@ if(${HYDROSTATIC})
   #add_subdirectory(1d-rad-jupiter)
   add_subdirectory(2023-jupiter-mwr-eq)
   add_subdirectory(2023-Li-saturn-vla)
-  add_subdirectory(2023-Li-uranus)
+  #add_subdirectory(2023-Li-uranus)
   add_subdirectory(2018-Li-harp)
   if(${EQUATION_OF_STATE} STREQUAL "shallow_yz")
     add_subdirectory(2023-Chen-exo3)
@@ -16,6 +16,6 @@ else()
     add_subdirectory(2020-Li-polar-vortex)
   else()
     add_subdirectory(2019-Li-snap)
-    add_subdirectory(2024-Li-plume)
+    #add_subdirectory(2024-Li-plume)
   endif()
 endif()
diff --git a/python/CMakeLists.txt b/python/CMakeLists.txt
@@ -45,5 +45,4 @@ endmacro()
 add_python_module(pyathena)
 add_python_module(pycanoe)
 add_python_module(pyharp)
-add_python_module(pyopacity)
 add_python_module(utilities)
diff --git a/python/pyopacity.cpp b/python/pyopacity.cpp
diff --git a/src/opacity/absorber_factory.cpp b/src/opacity/absorber_factory.cpp
@@ -102,17 +102,17 @@ AbsorberPtr AbsorberFactory::createAbsorberPartial(std::string name,
     ab = std::make_shared<FreedmanSimple>();
   } else if (type == "freedman_mean") {
     ab = std::make_shared<FreedmanSimple>();
-  } else if (type == "JunoMWR-NH3") {
+  } else if (type == "radio-NH3") {
     ab = std::make_shared<gp::MwrAbsorberNH3>();
-  } else if (type == "JunoMWR-H2O") {
+  } else if (type == "radio-H2O") {
     ab = std::make_shared<gp::MwrAbsorberH2O>();
-  } else if (type == "JunoMWR-H2S") {
+  } else if (type == "radio-H2S") {
     ab = std::make_shared<gp::MwrAbsorberH2S>();
-  } else if (type == "JunoMWR-PH3") {
+  } else if (type == "radio-PH3") {
     ab = std::make_shared<gp::MwrAbsorberPH3>();
-  } else if (type == "JunoMWR-CIA") {
+  } else if (type == "radio-CIA") {
     ab = std::make_shared<gp::MwrAbsorberCIA>();
-  } else if (type == "JunoMWR-Electron") {
+  } else if (type == "radio-Electron") {
     ab = std::make_shared<gp::MwrAbsorberElectron>();
   } else {
     throw NotFoundError("createAbsorberPartial", "Class = " + type);