Add python wrapper for juno_mwr

.github/workflows/main.yml

@@ -705,5 +705,5 @@ jobs:
         run: python3 combine.py -o test
 
       - name: Test
-        working-directory: ${{github.workspace}}/examples/2023-jupiter-mwr-eq
+        working-directory: ${{github.workspace}}/examples/2024-CLi-juno-mwr
         run: echo "cheers"

CMakeLists.txt

@@ -20,8 +20,16 @@ else()
   message(STATUS "")
 endif()
 
+# load all modules
 LIST(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake/modules/)
 
+# load all macros
+FILE(GLOB _macro_files "${CMAKE_SOURCE_DIR}/cmake/macros/*.cmake")
+FOREACH(_file ${_macro_files})
+  MESSAGE(STATUS "Include ${_file}")
+  INCLUDE(${_file})
+ENDFOREACH()
+
 ## 1. set up compiler flags ##
 message(STATUS "1. Set up project compiler flags ...")
 message(STATUS "Include ${CMAKE_SOURCE_DIR}/cmake/compilers.cmake")
@@ -35,10 +43,10 @@ message(STATUS "Load custom task = ${TASK}")
 if (NOT ${TASK} STREQUAL "")
   if (EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/cmake/examples/${TASK}.cmake)
     message(STATUS "Load custom setting - ${TASK} -")
-    message(STATUS "Include ${CMAKE_CURRENT_SOURCE_DIR}/cmake/${TASK}.cmake")
+    message(STATUS "Include ${CMAKE_CURRENT_SOURCE_DIR}/cmake/examples/${TASK}.cmake")
     include(${CMAKE_CURRENT_SOURCE_DIR}/cmake/examples/${TASK}.cmake)
   else()
-    message(FATAL_ERROR "Cannot find custom file cmake/${TASK}.cmake")
+    message(FATAL_ERROR "Cannot find custom file cmake/examples/${TASK}.cmake")
   endif()
   set(TASK ${TASK} CACHE STRING "Custom task to be performed")
 else()
@@ -70,24 +78,17 @@ add_subdirectory(src)
 add_subdirectory(tools)
 add_subdirectory(data)
 
-## 5. set up python binding ##
-if (PYTHON_BINDINGS)
-  add_subdirectory(python)
-endif()
-
-## 6. set up unit tests and examples
+## 5. set up examples and tests
 message(STATUS "6. Set up unit tests")
 
-# load all macros
-FILE(GLOB _macro_files "${CMAKE_SOURCE_DIR}/cmake/macros/*.cmake")
-FOREACH(_file ${_macro_files})
-  MESSAGE(STATUS "Include ${_file}")
-  INCLUDE(${_file})
-ENDFOREACH()
-
 add_subdirectory(examples)
 add_subdirectory(tests)
 
+## 6. set up python binding ##
+if (PYTHON_BINDINGS)
+  add_subdirectory(python)
+endif()
+
 ## 7. add uninstall targets ##
 configure_file(
     "${CMAKE_CURRENT_SOURCE_DIR}/cmake/cmake_uninstall.cmake.in"

cmake/examples/juno.cmake

@@ -19,5 +19,6 @@ set_if_empty(NTRACER 2)
 # canoe configure
 set(HYDROSTATIC ON)
 set(NETCDF ON)
-set(FITS ON)
+# set(FITS ON)
 set(RadianceSolver lambert)
+set(PYTHON_BINDINGS ON)

cmake/macros/macro_set_if_empty.cmake

@@ -0,0 +1,9 @@
+# A small macro used for set a variable if it is empty
+#
+# Usage: set_if_empty(name)
+
+macro(set_if_empty _variable)
+  if("${${_variable}}" STREQUAL "")
+    set(${_variable} ${ARGN})
+  endif()
+endmacro()

cmake/parameters.cmake

@@ -1,11 +1,5 @@
 # define default parameters
 
-macro(SET_IF_EMPTY _variable)
-  if("${${_variable}}" STREQUAL "")
-    set(${_variable} ${ARGN})
-  endif()
-endmacro()
-
 list(APPEND CMAKE_PREFIX_PATH "/usr/include/mpich-x84_64" "/usr/lib64/mpich/")
 
 # populate the default values

examples/2024-CLi-earth-rt/run_ktable_earth.py

@@ -4,8 +4,8 @@
 sys.path.append("../python")
 sys.path.append(".")
 
-from pyharp import radiation_band
-from utilities import load_configure, find_resource
+from canoe.harp import radiation_band
+from canoe import load_configure, find_resource
 from numpy import *
 from rfmlib import *
 
@@ -44,7 +44,7 @@ def create_rfm_atmosphere(nlyr: int) -> dict:
 
     band = radiation_band(band_name, info)
 
-    nspec = band.get_num_spec_grids()
+    nspec = band.get_num_specgrids()
     wmin, wmax = band.get_range()
     wres = (wmax - wmin) / (nspec - 1)
 

examples/2023-jupiter-mwr-eq/CMakeLists.txt → examples/2024-CLi-juno-mwr/CMakeLists.txt

@@ -5,8 +5,13 @@
 # 1. Compile juno_mwr.cpp
 setup_problem(juno_mwr)
 
+# PGEN variable will be used in python bindings
+set(PGEN ${CMAKE_CURRENT_SOURCE_DIR}/juno_mwr
+  CACHE INTERNAL "Path to the source file for problem generator")
+
 # 4. Copy input file to run directory
-file(GLOB inputs *.inp *.yaml)
+file(GLOB inputs *.inp *.yaml *.py)
 foreach(input ${inputs})
-    file(COPY ${input} DESTINATION ${CMAKE_BINARY_DIR}/bin)
+  # softlink inp files
+  execute_process(COMMAND ln -sf ${input} ${CMAKE_BINARY_DIR}/bin/${inp})
 endforeach()

examples/2023-jupiter-mwr-eq/juno_mwr.cpp → examples/2024-CLi-juno-mwr/juno_mwr.cpp

@@ -55,7 +55,7 @@
 #include <opacity/Giants/microwave/mwr_absorbers.hpp>
 
 // inversion
-#include <inversion/profile_inversion.hpp>
+// #include <inversion/profile_inversion.hpp>
 
 // special includes
 #include "juno_mwr_specs.hpp"

examples/2023-jupiter-mwr-eq/juno_mwr.inp → examples/2024-CLi-juno-mwr/juno_mwr.inp

@@ -91,7 +91,7 @@ Ttriple2    = 195.4
 Ptriple2    = 6060.
 
 <radiation>
-radiation_config = mwr_channels.yaml
+radiation_config = juno_mwr.yaml
 outdir      = (0,) (15,) (30,) (45,)
 
 #<inversion>

examples/2024-CLi-juno-mwr/run_juno_mwr.py

@@ -0,0 +1,64 @@
+#! /usr/bin/env python3
+import sys, os
+
+sys.path.append("../python")
+sys.path.append(".")
+
+from canoe import def_species, load_configure
+from canoe.snap import def_thermo
+from canoe.athena import Mesh, ParameterInput
+from typing import Tuple
+
+# from canoe.snap import air_parcel
+
+
+def construct_atmosphere(
+    nlyr: int = 100,
+    comp: dict = {},
+    plim: Tuple[float, float] = [0.1e5, 100.0e5],
+    zlim: Tuple[float, float] = [0.0, 10.0e3],
+    T0: float = 169.0,
+    P0: float = 1.0e5,
+    Tmin: float = 100.0,
+) -> Mesh:
+    mb = Mesh(nlyr)
+
+    air = air_parcel(comp)
+    dlnp = (log(plim[1]) - log(plim[0])) / nlyr
+
+    mb.set_layer(0, air)
+    for i in range(1, nlyr):
+        atm_extrapolate(air, -dlnp / 2.0, method="dry_adiabat")
+        mb.set_layer(i, air)
+
+    return mb
+
+
+def modify_atmosphere(
+    mb: Mesh,
+    comp: dict = {},
+    plim: Tuple[float, float] = [0.1e5, 100.0e5],
+    zlim: Tuple[float, float] = [0.0, 10.0e3],
+    T0: float = 169.0,
+    P0: float = 1.0e5,
+) -> Mesh:
+    pass
+
+
+if __name__ == "__main__":
+    pin = ParameterInput()
+    pin.load_from_file("juno_mwr.inp")
+
+    vapors = pin.get_string("species", "vapor").split(", ")
+    clouds = pin.get_string("species", "cloud").split(", ")
+    tracers = pin.get_string("species", "tracer").split(", ")
+
+    def_species(vapors=vapors, clouds=clouds, tracers=tracers)
+    def_thermo(pin)
+
+    config = load_configure("juno_mwr.yaml")
+
+    print(pin.get_real("problem", "qH2O.ppmv"))
+
+    mesh = Mesh(pin)
+    mesh.initialize(pin)

examples/2024-FDing-jupiter-rt/run_disort_jup.py

@@ -4,8 +4,8 @@
 sys.path.append("../python")
 sys.path.append(".")
 
-from pyharp import radiation_band, subscribe_species
-from utilities import load_configure
+from canoe import def_species, load_configure
+from canoe.harp import radiation_band
 from numpy import linspace, ones, exp
 from netCDF4 import Dataset
 from pylab import *
@@ -35,11 +35,7 @@ def create_atmosphere(nlyr: int) -> dict:
 
 
 if __name__ == "__main__":
-    subscribe_species(
-        {
-            "vapor": ["H2O", "NH3"],
-        }
-    )
+    def_species(vapors=["H2O", "NH3"])
 
     config = load_configure("jupiter_rt.yaml")
     band = radiation_band("B1", config, load_opacity=True)

examples/2024-FDing-jupiter-rt/run_ktable_jup.py

@@ -4,8 +4,8 @@
 sys.path.append("../python")
 sys.path.append(".")
 
-from pyharp import radiation_band, subscribe_species
-from utilities import load_configure, find_resource
+from canoe import def_species, load_configure, find_resource
+from canoe.harp import radiation_band
 from netCDF4 import Dataset
 from numpy import *
 from rfmlib import *
@@ -40,16 +40,12 @@ def create_rfm_atmosphere(nlyr: int) -> dict:
 
 if __name__ == "__main__":
     hitran_file = find_resource("HITRAN2020.par")
-    subscribe_species(
-        {
-            "vapor": ["H2O", "NH3"],
-        }
-    )
+    def_species(vapors=["H2O", "NH3"])
 
     config = load_configure("jupiter_rt.yaml")
     band = radiation_band("B1", config)
 
-    nspec = band.get_num_spec_grids()
+    nspec = band.get_num_specgrids()
     wmin, wmax = band.get_range()
     wres = (wmax - wmin) / (nspec - 1)
 

examples/CMakeLists.txt

@@ -15,7 +15,7 @@ else()
 endif()
 
 if (${TASK} STREQUAL "juno")
-  add_subdirectory(2023-jupiter-mwr-eq)
+  add_subdirectory(2024-CLi-juno-mwr)
 endif()
 
 if (${TASK} STREQUAL "saturn_radio")

python/CMakeLists.txt

@@ -14,39 +14,41 @@ execute_process(
     OUTPUT_STRIP_TRAILING_WHITESPACE
 )
 
-macro(add_python_module namel)
-  # set module targets
-  pybind11_add_module(${namel} MODULE ${namel}.cpp)
-
-  target_include_directories(${namel}
-    PRIVATE
-    ${CMAKE_BINARY_DIR}
-    ${CPPDISORT_INCLUDE_DIR}
-    ${CANOE_INCLUDE_DIR}
-    ${PYTHON_INCLUDE_DIR}
-    ${PYBIND11_INCLUDE_DIR}
-    ${MPI_CXX_INCLUDE_PATH}
-    )
-
-  target_link_libraries(${namel} PRIVATE
-    search_path
-    ${CANOE_LIBRARY_${buildu}}
-    )
-
-  set_target_properties(${namel}
-    PROPERTIES
-    PREFIX "${PYTHON_MODULE_PREFIX}"
-    SUFFIX "${PYTHON_MODULE_EXTENSION}")
-
-  # softlink library
-  execute_process(
-    COMMAND ln -sf ${CMAKE_BINARY_DIR}/python/${namel}${PYTHON_MODULE_EXTENSION}
-    ${CMAKE_BINARY_DIR}/lib/${namel}${PYTHON_MODULE_EXTENSION}
-    )
-endmacro()
-
-# add python modules
-add_python_module(pyathena)
-add_python_module(pycanoe)
-add_python_module(pyharp)
-add_python_module(utilities)
+set(namel canoe)
+set_if_empty(PGEN empty)
+
+# set module targets
+pybind11_add_module(${namel} MODULE
+  pyathena.cpp
+  pycanoe.cpp
+  pyharp.cpp
+  pysnap.cpp
+  pyutils.cpp
+  ${PGEN}.cpp
+  )
+
+target_include_directories(${namel}
+  PRIVATE
+  ${CMAKE_BINARY_DIR}
+  ${CPPDISORT_INCLUDE_DIR}
+  ${CANOE_INCLUDE_DIR}
+  ${PYTHON_INCLUDE_DIR}
+  ${PYBIND11_INCLUDE_DIR}
+  ${MPI_CXX_INCLUDE_PATH}
+  )
+
+target_link_libraries(${namel} PRIVATE
+  search_path
+  ${CANOE_LIBRARY_${buildu}}
+  )
+
+set_target_properties(${namel}
+  PROPERTIES
+  PREFIX "${PYTHON_MODULE_PREFIX}"
+  SUFFIX "${PYTHON_MODULE_EXTENSION}")
+
+# softlink library
+execute_process(
+  COMMAND ln -sf ${CMAKE_BINARY_DIR}/python/${namel}${PYTHON_MODULE_EXTENSION}
+  ${CMAKE_BINARY_DIR}/lib/${namel}${PYTHON_MODULE_EXTENSION}
+  )

python/empty.cpp

@@ -0,0 +1 @@
+//! This is a placeholder file for the default pgen file.