Merge remote-tracking branch 'upstream/development' into AWAKEN_Refactor

.codespell-ignore-words

@@ -4,4 +4,4 @@ inout
 parms
 pres
 rime
-wth
+wth

.codespellrc

@@ -1,3 +1,4 @@
 [codespell]
 skip = .git,*.ipynb,*.bib,*.ps,*.patch,*~,CHANGES,*/Submodules,*/tmp_build_dir,Cell_D_*
 ignore-words = .codespell-ignore-words
+uri-ignore-words-list = *

.github/workflows/macos.yml

@@ -31,7 +31,7 @@ jobs:
       run: |
         cmake \
           -B${{runner.workspace}}/ERF/build \
-          -DBUILD_SHARED_LIBS:BOOL=TRUE \
+          -DBUILD_SHARED_LIBS:BOOL=FALSE \
           -DCMAKE_CXX_COMPILER_LAUNCHER=$(which ccache) \
           -DCMAKE_BUILD_TYPE:STRING=Debug \
           -DCMAKE_CXX_COMPILER_LAUNCHER=ccache \

CHANGES

@@ -1,4 +1,17 @@
-#24.09
+# 24.10
+    -- Add WENO7 advection operators (#1858)
+
+    -- Multi-level inflow plane capability (#1851)
+
+    -- Fast integrator fill bug fix (#1853)
+
+    -- Refactor set/nudging with real BDYs (#1841)
+
+    -- First pass at GAD sources (#1839)
+
+    -- Anelastic with FFT option for Poisson eq (#1838)
+
+# 24.09
     -- AMReX submodule set to 24.09 release hash (74127d6)
 
     -- Arbitrary number of scalars similar to WRF chem (#1782)

CMake/BuildERFExe.cmake

@@ -18,15 +18,8 @@ function(build_erf_lib erf_lib_name)
   target_compile_definitions(${erf_lib_name} PUBLIC ERF_USE_MOISTURE)
 
   if(ERF_ENABLE_MULTIBLOCK)
-    target_sources(${erf_lib_name} PRIVATE
-                   ${SRC_DIR}/MultiBlock/ERF_MultiBlockContainer.cpp)
     target_compile_definitions(${erf_lib_name} PUBLIC ERF_USE_MULTIBLOCK)
-#    if(NOT ERF_MB_EXTERN)
-      target_sources(${erf_lib_name} PRIVATE
-                     ${SRC_DIR}/MultiBlock/ERF_MultiBlockContainer.cpp)
-      target_include_directories(${erf_lib_name} PRIVATE $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/Source/MultiBlock>)
-#    endif()
-   endif()
+  endif()
 
   if(ERF_ENABLE_WARM_NO_PRECIP)
     target_compile_definitions(${erf_lib_name} PUBLIC ERF_USE_WARM_NO_PRECIP)
@@ -91,10 +84,10 @@ function(build_erf_lib erf_lib_name)
                    ${CMAKE_SOURCE_DIR}/Submodules/RRTMGP/cpp/extensions/fluxes_byband/mo_fluxes_byband_kernels.cpp
                   )
 
-    # The interface code needs to know about the RRTMGP includes 
+    # The interface code needs to know about the RRTMGP includes
     target_compile_definitions(${erf_lib_name} PUBLIC ERF_USE_RRTMGP)
 
-    target_include_directories(${erf_lib_name} SYSTEM PUBLIC 
+    target_include_directories(${erf_lib_name} SYSTEM PUBLIC
                                ${CMAKE_SOURCE_DIR}/Submodules/RRTMGP/cpp/extensions/fluxes_byband
                                ${CMAKE_SOURCE_DIR}/Submodules/RRTMGP/cpp/extensions/cloud_optics
                                ${CMAKE_SOURCE_DIR}/Submodules/RRTMGP/cpp/examples
@@ -122,6 +115,7 @@ function(build_erf_lib erf_lib_name)
        ${SRC_DIR}/BoundaryConditions/ERF_BoundaryConditions_xvel.cpp
        ${SRC_DIR}/BoundaryConditions/ERF_BoundaryConditions_yvel.cpp
        ${SRC_DIR}/BoundaryConditions/ERF_BoundaryConditions_zvel.cpp
+       ${SRC_DIR}/BoundaryConditions/ERF_BoundaryConditions_basestate.cpp
        ${SRC_DIR}/BoundaryConditions/ERF_BoundaryConditions_bndryreg.cpp
        ${SRC_DIR}/BoundaryConditions/ERF_BoundaryConditions_realbdy.cpp
        ${SRC_DIR}/BoundaryConditions/ERF_FillPatch.cpp
@@ -136,15 +130,18 @@ function(build_erf_lib erf_lib_name)
        ${SRC_DIR}/Diffusion/ERF_ComputeStrain_N.cpp
        ${SRC_DIR}/Diffusion/ERF_ComputeStrain_T.cpp
        ${SRC_DIR}/Diffusion/ERF_ComputeTurbulentViscosity.cpp
+       ${SRC_DIR}/Initialization/ERF_init_bcs.cpp
        ${SRC_DIR}/Initialization/ERF_init_custom.cpp
        ${SRC_DIR}/Initialization/ERF_init_from_hse.cpp
        ${SRC_DIR}/Initialization/ERF_init_from_input_sounding.cpp
        ${SRC_DIR}/Initialization/ERF_init_from_wrfinput.cpp
        ${SRC_DIR}/Initialization/ERF_init_from_metgrid.cpp
+       ${SRC_DIR}/Initialization/ERF_init_geowind.cpp
+       ${SRC_DIR}/Initialization/ERF_init_rayleigh.cpp
+       ${SRC_DIR}/Initialization/ERF_init_sponge.cpp
        ${SRC_DIR}/Initialization/ERF_init_uniform.cpp
        ${SRC_DIR}/Initialization/ERF_init1d.cpp
        ${SRC_DIR}/Initialization/ERF_init_TurbPert.cpp
-       ${SRC_DIR}/Initialization/ERF_input_sponge.cpp
        ${SRC_DIR}/IO/ERF_Checkpoint.cpp
        ${SRC_DIR}/IO/ERF_ReadBndryPlanes.cpp
        ${SRC_DIR}/IO/ERF_WriteBndryPlanes.cpp
@@ -157,7 +154,7 @@ function(build_erf_lib erf_lib_name)
        ${SRC_DIR}/PBL/ERF_ComputeDiffusivityMYNN25.cpp
        ${SRC_DIR}/PBL/ERF_ComputeDiffusivityYSU.cpp
        ${SRC_DIR}/SourceTerms/ERF_ApplySpongeZoneBCs.cpp
-       ${SRC_DIR}/SourceTerms/ERF_ApplySpongeZoneBCs_ReadFromFile.cpp	  
+       ${SRC_DIR}/SourceTerms/ERF_ApplySpongeZoneBCs_ReadFromFile.cpp
        ${SRC_DIR}/SourceTerms/ERF_make_buoyancy.cpp
        ${SRC_DIR}/SourceTerms/ERF_add_thin_body_sources.cpp
        ${SRC_DIR}/SourceTerms/ERF_make_mom_sources.cpp
@@ -201,13 +198,6 @@ function(build_erf_lib erf_lib_name)
        ${SRC_DIR}/LandSurfaceModel/MM5/ERF_MM5.cpp
   )
 
-  if(NOT "${erf_exe_name}" STREQUAL "erf_unit_tests")
-    target_sources(${erf_lib_name}
-       PRIVATE
-         ${SRC_DIR}/main.cpp
-    )
-  endif()
-
   include(AMReXBuildInfo)
   generate_buildinfo(${erf_lib_name} ${CMAKE_SOURCE_DIR})
 if (${ERF_USE_INTERNAL_AMREX})
@@ -246,7 +236,7 @@ endif()
   target_include_directories(${erf_lib_name} PUBLIC $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/Source/Microphysics>)
   target_include_directories(${erf_lib_name} PUBLIC $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/Source/Microphysics/Null>)
   target_include_directories(${erf_lib_name} PUBLIC $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/Source/Microphysics/SAM>)
-  target_include_directories(${erf_lib_name} PUBLIC $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/Source/Microphysics/Kessler>) 
+  target_include_directories(${erf_lib_name} PUBLIC $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/Source/Microphysics/Kessler>)
   target_include_directories(${erf_lib_name} PUBLIC $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/Source/WindFarmParametrization>)
   target_include_directories(${erf_lib_name} PUBLIC $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/Source/WindFarmParametrization/Null>)
   target_include_directories(${erf_lib_name} PUBLIC $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/Source/WindFarmParametrization/Fitch>)
@@ -257,7 +247,7 @@ endif()
   target_include_directories(${erf_lib_name} PUBLIC $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/Source/LandSurfaceModel/Null>)
   target_include_directories(${erf_lib_name} PUBLIC $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/Source/LandSurfaceModel/SLM>)
   target_include_directories(${erf_lib_name} PUBLIC $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/Source/LandSurfaceModel/MM5>)
-    
+
   if(ERF_ENABLE_RRTMGP)
      target_link_libraries(${erf_lib_name} PUBLIC yakl)
      target_link_libraries(${erf_lib_name} PUBLIC rrtmgp)
@@ -292,15 +282,17 @@ function(build_erf_exe erf_exe_name)
 
   set(SRC_DIR ${CMAKE_SOURCE_DIR}/Source)
 
+  if(NOT "${erf_exe_name}" STREQUAL "erf_unit_tests")
+  target_sources(${erf_exe_name}
+     PRIVATE
+       ${SRC_DIR}/main.cpp
+  )
+  endif()
+
   target_link_libraries(${erf_exe_name}  PUBLIC ${erf_lib_name})
   include(${CMAKE_SOURCE_DIR}/CMake/SetERFCompileFlags.cmake)
   set_erf_compile_flags(${erf_exe_name})
 
-  target_sources(${erf_exe_name}
-     PRIVATE
-       ${SRC_DIR}/Initialization/ERF_init_bcs.cpp
-
-  )
   if(ERF_ENABLE_CUDA)
     set(pctargets "${erf_exe_name}")
     foreach(tgt IN LISTS pctargets)

Docs/sphinx_doc/Discretizations.rst

@@ -204,7 +204,7 @@ Sauer, J. A., & Muñoz-Esparza, D. (2020). The FastEddy® resident-GPU accelerat
 
 WENO Methods
 ------------
-Additionally, weighted essentially non-oscillatory (WENO) schemes are available for :math:`3rd` and :math:`5th` order interpolation. The general formulation is as follows:
+Additionally, weighted essentially non-oscillatory (WENO) schemes are available for :math:`3rd`, :math:`5th`, and :math:`7th` order interpolation. The general formulation is as follows:
 
 .. math::
 
@@ -237,8 +237,11 @@ With the WENO5 scheme, one has :math:`N=3, \; \omega_{1} = 1/10, \; \omega_{2} =
    q_{m + \frac{1}{2}}^{(3)} = \frac{1}{3} q_{m} + \frac{5}{6} q_{m+1} - \frac{1}{6} q_{m+2}
    \end{array}
 
-By default, the WENO3 scheme will be employed for moisture variables if the code is compiled with moisture support.
-However, users may utilize the WENO scheme for dry scalar variables as well.   The scheme for each type is specified by
+Details for the WENO7 scheme are provided in `Shu, C.W. (1997)`_.
+By default, the WENO3 scheme will be employed for moisture variables if the code is compiled with moisture support. However, users may
+utilize the WENO scheme for dry scalar variables as well.   The scheme for each type is specified by
+
+.. _`Shu, C.W. (1997)`: https://www3.nd.edu/~zxu2/acms60790S13/Shu-WENO-notes.pdf
 
 ::
 
@@ -247,7 +250,9 @@ However, users may utilize the WENO scheme for dry scalar variables as well.   T
    erf.moistscal_horiz_adv_type =
    erf.moistscal_vert_adv_type  =
 
-Ref: Muñoz-Esparza, D., Sauer, J. A., Jensen, A. A., Xue, L., & Grabowski, W. W. (2022). The FastEddy® resident-GPU accelerated large-eddy simulation framework: Moist dynamics extension, validation and sensitivities of modeling non-precipitating shallow cumulus clouds. Journal of Advances in Modeling Earth Systems, 14, e2021MS002904.
+Ref: Muñoz-Esparza, D., Sauer, J. A., Jensen, A. A., Xue, L., & Grabowski, W. W. (2022). The FastEddy® resident-GPU accelerated large-eddy
+simulation framework: Moist dynamics extension, validation and sensitivities of modeling non-precipitating shallow cumulus clouds.
+Journal of Advances in Modeling Earth Systems, 14, e2021MS002904.
 `doi:10.1029/2021MS002904 <https://onlinelibrary.wiley.com/doi/10.1029/2021MS002904>`_
 
 Momentum, Thermal, and Scalar Diffusion Contribution to DNS

Docs/sphinx_doc/Inputs.rst

@@ -771,7 +771,7 @@ and "Centered_6th".
 The allowed advection types for the dry and moist scalars are
 "Centered_2nd", "Upwind_3rd", "Blended_3rd4th", "Centered_4th", "Upwind_5th", "Blended_5th6th",
 "Centered_6th" and in addition,
-"WENO3", "WENOZ3", "WENOMZQ3", "WENO5", and "WENOZ5."
+"WENO3", "WENOZ3", "WENOMZQ3", "WENO5", "WENOZ5", "WENO7", and "WENOZ7."
 
 Note: if using WENO schemes, the horizontal and vertical advection types must be set to
 the same string.