Merge develop.

.codespell-ignore-words

@@ -4,4 +4,5 @@ inout
 parms
 pres
 rime
-wth
+TE
+wth

.github/workflows/docs.yml

@@ -24,10 +24,10 @@ jobs:
         run: |
           ./Docs/BuildDocs.sh
 
-      - name: Check links
-        run: |
-          cd Docs/sphinx_doc
-          make SPHINXOPTS="-v -W --keep-going" NO_DOXYGEN=TRUE linkcheck
+#     - name: Check links
+#       run: |
+#         cd Docs/sphinx_doc
+#         make SPHINXOPTS="-v -W --keep-going" NO_DOXYGEN=TRUE linkcheck
 
       - name: Deploy to Webpage
         if: github.event_name == 'push' && github.repository == 'erf-model/ERF' && github.ref == 'refs/heads/development'

Build/cmake_with_fft.sh

@@ -0,0 +1,17 @@
+
+# Example CMake config script for an OSX laptop with OpenMPI
+
+cmake -DCMAKE_INSTALL_PREFIX:PATH=./install \
+      -DCMAKE_CXX_COMPILER:STRING=mpicxx \
+      -DCMAKE_C_COMPILER:STRING=mpicc \
+      -DCMAKE_Fortran_COMPILER:STRING=mpifort \
+      -DMPIEXEC_PREFLAGS:STRING=--oversubscribe \
+      -DCMAKE_BUILD_TYPE:STRING=Release \
+      -DERF_DIM:STRING=3 \
+      -DERF_ENABLE_MPI:BOOL=ON \
+      -DERF_ENABLE_TESTS:BOOL=ON \
+      -DERF_ENABLE_FCOMPARE:BOOL=ON \
+      -DERF_ENABLE_DOCUMENTATION:BOOL=OFF \
+      -DERF_ENABLE_FFT:BOOL=ON \
+      -DCMAKE_EXPORT_COMPILE_COMMANDS:BOOL=ON \
+      .. && make -j8

CMake/BuildERFExe.cmake

@@ -42,11 +42,18 @@ function(build_erf_lib erf_lib_name)
                    ${SRC_DIR}/EB/ERF_eb_cylinder.cpp
                    ${SRC_DIR}/EB/ERF_eb_regular.cpp
                    ${SRC_DIR}/EB/ERF_initEB.cpp
-                   ${SRC_DIR}/EB/ERF_writeEBsurface.cpp)
+                   ${SRC_DIR}/EB/ERF_writeEBsurface.cpp 
+                   ${SRC_DIR}/LinearSolvers/ERF_solve_with_EB_mlmg.cpp)
     target_include_directories(${erf_lib_name} PUBLIC $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/Source/EB>)
     target_compile_definitions(${erf_lib_name} PUBLIC ERF_USE_EB)
   endif()
 
+  if(ERF_ENABLE_FFT)
+    target_sources(${erf_lib_name} PRIVATE
+                   ${SRC_DIR}/LinearSolvers/ERF_solve_with_fft.cpp)
+    target_compile_definitions(${erf_lib_name} PUBLIC ERF_USE_FFT)
+  endif()
+
   if(ERF_ENABLE_NETCDF)
     target_sources(${erf_lib_name} PRIVATE
                    ${SRC_DIR}/IO/ERF_NCInterface.cpp
@@ -96,10 +103,6 @@ function(build_erf_lib erf_lib_name)
                               )
   endif()
 
-  if(ERF_ENABLE_HDF5)
-    target_compile_definitions(${erf_lib_name} PUBLIC ERF_USE_HDF5)
-  endif()
-
   target_sources(${erf_lib_name}
      PRIVATE
        ${SRC_DIR}/ERF_Derive.cpp
@@ -166,6 +169,7 @@ function(build_erf_lib erf_lib_name)
        ${SRC_DIR}/SourceTerms/ERF_make_sources.cpp
        ${SRC_DIR}/SourceTerms/ERF_moist_set_rhs.cpp
        ${SRC_DIR}/SourceTerms/ERF_NumericalDiffusion.cpp
+       ${SRC_DIR}/SourceTerms/ERF_ForestDrag.cpp
        ${SRC_DIR}/TimeIntegration/ERF_ComputeTimestep.cpp
        ${SRC_DIR}/TimeIntegration/ERF_Advance.cpp
        ${SRC_DIR}/TimeIntegration/ERF_TimeStep.cpp
@@ -183,8 +187,12 @@ function(build_erf_lib erf_lib_name)
        ${SRC_DIR}/Utils/ERF_AverageDown.cpp
        ${SRC_DIR}/Utils/ERF_ChopGrids.cpp
        ${SRC_DIR}/Utils/ERF_MomentumToVelocity.cpp
-       ${SRC_DIR}/Utils/ERF_PoissonSolve.cpp
-       ${SRC_DIR}/Utils/ERF_PoissonSolve_tb.cpp
+       ${SRC_DIR}/LinearSolvers/ERF_PoissonSolve.cpp
+       ${SRC_DIR}/LinearSolvers/ERF_PoissonSolve_tb.cpp
+       ${SRC_DIR}/LinearSolvers/ERF_compute_divergence.cpp
+       ${SRC_DIR}/LinearSolvers/ERF_solve_with_gmres.cpp
+       ${SRC_DIR}/LinearSolvers/ERF_solve_with_mlmg.cpp
+       ${SRC_DIR}/LinearSolvers/ERF_TerrainPoisson.cpp
        ${SRC_DIR}/Utils/ERF_TerrainMetrics.cpp
        ${SRC_DIR}/Utils/ERF_VelocityToMomentum.cpp
        ${SRC_DIR}/Utils/ERF_InteriorGhostCells.cpp
@@ -236,6 +244,7 @@ endif()
   target_include_directories(${erf_lib_name} PUBLIC $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/Source/Diffusion>)
   target_include_directories(${erf_lib_name} PUBLIC $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/Source/Initialization>)
   target_include_directories(${erf_lib_name} PUBLIC $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/Source/IO>)
+  target_include_directories(${erf_lib_name} PUBLIC $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/Source/LinearSolvers>)
   target_include_directories(${erf_lib_name} PUBLIC $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/Source/PBL>)
   target_include_directories(${erf_lib_name} PUBLIC $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/Source/SourceTerms>)
   target_include_directories(${erf_lib_name} PUBLIC $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/Source/TimeIntegration>)

CMake/SetAmrexOptions.cmake

@@ -36,6 +36,11 @@ if(ERF_ENABLE_PARTICLES)
   set(AMReX_PARTICLES ON)
 endif()
 
+set(AMReX_FFT OFF)
+if(ERF_ENABLE_FFT)
+  set(AMReX_FFT ON)
+endif()
+
 set(AMReX_EB OFF)
 if(ERF_ENABLE_EB)
   set(AMReX_EB ON)

CMakeLists.txt

@@ -245,7 +245,7 @@ target_link_libraries(erf_api PUBLIC erf_srclib)
 add_library(${PROJECT_NAME}::erf_api ALIAS erf_srclib)
 
 # Collect all headers and make them installable with the target
-set(ERF_INCLUDES "Source/ERF.H;Source/ERF_Constants.H;Source/WindFarmParametrization/SimpleActuatorDisk/ERF_SimpleAD.H;Source/WindFarmParametrization/EWP/ERF_EWP.H;Source/WindFarmParametrization/Null/ERF_NullWindFarm.H;Source/WindFarmParametrization/ERF_WindFarm.H;Source/WindFarmParametrization/Fitch/ERF_Fitch.H;Source/BoundaryConditions/ERF_PhysBCFunct.H;Source/BoundaryConditions/ERF_MOSTAverage.H;Source/BoundaryConditions/ERF_MOSTRoughness.H;Source/BoundaryConditions/ERF_ABLMost.H;Source/BoundaryConditions/ERF_FillPatcher.H;Source/BoundaryConditions/ERF_MOSTStress.H;Source/BoundaryConditions/ERF_TimeInterpolatedData.H;Source/Utils/ERF_Interpolation.H;Source/Utils/ERF_TileNoZ.H;Source/Utils/ERF_PlaneAverage.H;Source/Utils/ERF_Interpolation_WENO.H;Source/Utils/ERF_DirectionSelector.H;Source/Utils/ERF_ParFunctions.H;Source/Utils/ERF_Wstar.H;Source/Utils/ERF_Microphysics_Utils.H;Source/Utils/ERF_Sat_methods.H;Source/Utils/ERF_Interpolation_1D.H;Source/Utils/ERF_Interpolation_UPW.H;Source/Utils/ERF_TerrainMetrics.H;Source/Utils/ERF_Interpolation_WENO_Z.H;Source/Utils/ERF_Thetav.H;Source/Utils/ERF_Water_vapor_saturation.H;Source/Utils/ERF_Utils.H;Source/Utils/ERF_Orbit.H;Source/Utils/ERF_EOS.H;Source/Utils/ERF_HSE_utils.H;Source/EB/ERF_TerrainIF.H;Source/EB/ERF_FlowerIF.H;Source/EB/ERF_eb_if.H;Source/Particles/ERFPC.H;Source/Particles/ERF_ParticleData.H;Source/Prob/ERF_init_density_hse_dry.H;Source/Prob/ERF_init_rayleigh_damping.H;Source/Prob/ERF_init_constant_density_hse.H;Source/ERF_prob_common.H;Source/ERF_Derive.H;Source/Radiation/ERF_Mam4_constituents.H;Source/Radiation/ERF_Mam4_aero.H;Source/Radiation/ERF_Optics.H;Source/Radiation/ERF_Modal_aero_wateruptake.H;Source/Radiation/ERF_Cloud_rad_props.H;Source/Radiation/ERF_Phys_prop.H;Source/Radiation/ERF_Radiation.H;Source/Radiation/ERF_Albedo.H;Source/Radiation/ERF_Parameterizations.H;Source/Radiation/ERF_Rad_constants.H;Source/Radiation/ERF_Aero_rad_props.H;Source/Radiation/ERF_m2005_effradius.H;Source/Radiation/ERF_Linear_interpolate.H;Source/Radiation/ERF_Slingo.H;Source/Radiation/ERF_Rrtmgp.H;Source/Radiation/ERF_Ebert_curry.H;Source/SourceTerms/ERF_NumericalDiffusion.H;Source/SourceTerms/ERF_Src_headers.H;Source/IO/ERF_SampleData.H;Source/IO/ERF_NCInterface.H;Source/IO/ERF_NCWpsFile.H;Source/IO/ERF_NCPlotFile.H;Source/IO/ERF_ReadBndryPlanes.H;Source/IO/ERF_WriteBndryPlanes.H;Source/PBL/ERF_MYNNStruct.H;Source/PBL/ERF_PBLModels.H;Source/PBL/ERF_PBLHeight.H;Source/TimeIntegration/ERF_TI_substep_fun.H;Source/TimeIntegration/ERF_TI_slow_headers.H;Source/TimeIntegration/ERF_TI_slow_rhs_fun.H;Source/TimeIntegration/ERF_TI_fast_headers.H;Source/TimeIntegration/ERF_TI_utils.H;Source/TimeIntegration/ERF_MRI.H;Source/TimeIntegration/ERF_TI_no_substep_fun.H;Source/LandSurfaceModel/Null/ERF_NullSurf.H;Source/LandSurfaceModel/ERF_LandSurface.H;Source/LandSurfaceModel/MM5/ERF_MM5.H;Source/LandSurfaceModel/SLM/ERF_SLM.H;Source/ERF_IndexDefines.H;Source/Advection/ERF_AdvectionSrcForMom_N.H;Source/Advection/ERF_AdvectionSrcForScalars.H;Source/Advection/ERF_AdvectionSrcForMom_T.H;Source/Advection/ERF_Advection.H;Source/MultiBlock/ERF_MultiBlockContainer.H;Source/Initialization/ERF_Metgrid_utils.H;Source/Diffusion/ERF_EddyViscosity.H;Source/Diffusion/ERF_Diffusion.H;Source/Microphysics/Null/ERF_NullMoistLagrangian.H;Source/Microphysics/Null/ERF_NullMoist.H;Source/Microphysics/ERF_Microphysics.H;Source/Microphysics/ERF_LagrangianMicrophysics.H;Source/Microphysics/ERF_EulerianMicrophysics.H;Source/Microphysics/Kessler/ERF_Kessler.H;Source/Microphysics/SAM/ERF_SAM.H;Source/DataStructs/ERF_InputSpongeData.H;Source/DataStructs/ERF_TurbPertStruct.H;Source/DataStructs/ERF_SpongeStruct.H;Source/DataStructs/ERF_AdvStruct.H;Source/DataStructs/ERF_DataStruct.H;Source/DataStructs/ERF_InputSoundingData.H;Source/DataStructs/ERF_DiffStruct.H;Source/DataStructs/ERF_TurbStruct.H")
+set(ERF_INCLUDES "Source/ERF.H;Source/ERF_Constants.H;Source/WindFarmParametrization/SimpleActuatorDisk/ERF_SimpleAD.H;Source/WindFarmParametrization/EWP/ERF_EWP.H;Source/WindFarmParametrization/Null/ERF_NullWindFarm.H;Source/WindFarmParametrization/ERF_WindFarm.H;Source/WindFarmParametrization/Fitch/ERF_Fitch.H;Source/BoundaryConditions/ERF_PhysBCFunct.H;Source/BoundaryConditions/ERF_MOSTAverage.H;Source/BoundaryConditions/ERF_MOSTRoughness.H;Source/BoundaryConditions/ERF_ABLMost.H;Source/BoundaryConditions/ERF_FillPatcher.H;Source/BoundaryConditions/ERF_MOSTStress.H;Source/BoundaryConditions/ERF_TimeInterpolatedData.H;Source/Utils/ERF_Interpolation.H;Source/Utils/ERF_TileNoZ.H;Source/Utils/ERF_PlaneAverage.H;Source/Utils/ERF_Interpolation_WENO.H;Source/Utils/ERF_DirectionSelector.H;Source/Utils/ERF_ParFunctions.H;Source/Utils/ERF_Wstar.H;Source/Utils/ERF_Microphysics_Utils.H;Source/Utils/ERF_Sat_methods.H;Source/Utils/ERF_Interpolation_1D.H;Source/Utils/ERF_Interpolation_UPW.H;Source/Utils/ERF_TerrainMetrics.H;Source/Utils/ERF_Interpolation_WENO_Z.H;Source/Utils/ERF_Thetav.H;Source/Utils/ERF_Water_vapor_saturation.H;Source/Utils/ERF_Utils.H;Source/Utils/ERF_Orbit.H;Source/Utils/ERF_EOS.H;Source/Utils/ERF_HSE_utils.H;Source/EB/ERF_TerrainIF.H;Source/EB/ERF_FlowerIF.H;Source/EB/ERF_eb_if.H;Source/Particles/ERFPC.H;Source/Particles/ERF_ParticleData.H;Source/Prob/ERF_init_density_hse_dry.H;Source/Prob/ERF_init_rayleigh_damping.H;Source/Prob/ERF_init_constant_density_hse.H;Source/ERF_prob_common.H;Source/ERF_Derive.H;Source/Radiation/ERF_Mam4_constituents.H;Source/Radiation/ERF_Mam4_aero.H;Source/Radiation/ERF_Optics.H;Source/Radiation/ERF_Modal_aero_wateruptake.H;Source/Radiation/ERF_Cloud_rad_props.H;Source/Radiation/ERF_Phys_prop.H;Source/Radiation/ERF_Radiation.H;Source/Radiation/ERF_Albedo.H;Source/Radiation/ERF_Parameterizations.H;Source/Radiation/ERF_Rad_constants.H;Source/Radiation/ERF_Aero_rad_props.H;Source/Radiation/ERF_m2005_effradius.H;Source/Radiation/ERF_Linear_interpolate.H;Source/Radiation/ERF_Slingo.H;Source/Radiation/ERF_Rrtmgp.H;Source/Radiation/ERF_Ebert_curry.H;Source/SourceTerms/ERF_NumericalDiffusion.H;Source/SourceTerms/ERF_Src_headers.H;Source/IO/ERF_SampleData.H;Source/IO/ERF_NCInterface.H;Source/IO/ERF_NCWpsFile.H;Source/IO/ERF_NCPlotFile.H;Source/IO/ERF_ReadBndryPlanes.H;Source/IO/ERF_WriteBndryPlanes.H;Source/PBL/ERF_MYNNStruct.H;Source/PBL/ERF_PBLModels.H;Source/PBL/ERF_PBLHeight.H;Source/TimeIntegration/ERF_TI_substep_fun.H;Source/TimeIntegration/ERF_TI_slow_headers.H;Source/TimeIntegration/ERF_TI_slow_rhs_fun.H;Source/TimeIntegration/ERF_TI_fast_headers.H;Source/TimeIntegration/ERF_TI_utils.H;Source/TimeIntegration/ERF_MRI.H;Source/TimeIntegration/ERF_TI_no_substep_fun.H;Source/LandSurfaceModel/Null/ERF_NullSurf.H;Source/LandSurfaceModel/ERF_LandSurface.H;Source/LandSurfaceModel/MM5/ERF_MM5.H;Source/LandSurfaceModel/SLM/ERF_SLM.H;Source/ERF_IndexDefines.H;Source/Advection/ERF_AdvectionSrcForMom_N.H;Source/Advection/ERF_AdvectionSrcForScalars.H;Source/Advection/ERF_AdvectionSrcForMom_T.H;Source/Advection/ERF_Advection.H;Source/MultiBlock/ERF_MultiBlockContainer.H;Source/Initialization/ERF_Metgrid_utils.H;Source/Diffusion/ERF_EddyViscosity.H;Source/Diffusion/ERF_Diffusion.H;Source/Microphysics/Null/ERF_NullMoistLagrangian.H;Source/Microphysics/Null/ERF_NullMoist.H;Source/Microphysics/ERF_Microphysics.H;Source/Microphysics/ERF_LagrangianMicrophysics.H;Source/Microphysics/ERF_EulerianMicrophysics.H;Source/Microphysics/Kessler/ERF_Kessler.H;Source/Microphysics/SAM/ERF_SAM.H;Source/DataStructs/ERF_InputSpongeData.H;Source/DataStructs/ERF_TurbPertStruct.H;Source/DataStructs/ERF_SpongeStruct.H;Source/DataStructs/ERF_AdvStruct.H;Source/DataStructs/ERF_DataStruct.H;Source/DataStructs/ERF_InputSoundingData.H;Source/DataStructs/ERF_DiffStruct.H;Source/DataStructs/ERF_TurbStruct.H ERF_TerrainPoisson.H ERF_FFT_TerrainPrecond.H")
 set_target_properties(
   erf_srclib PROPERTIES PUBLIC_HEADER "${ERF_INCLUDES}")
 

Docs/sphinx_doc/AMReX.rst

@@ -0,0 +1,18 @@
+
+ .. role:: cpp(code)
+    :language: c++
+
+.. _subsec:AMReX:
+
+AMReX
+==============
+
+ERF is built on AMReX, a C++--based software framework that supports the development of structured mesh algorithms for solving systems of partial differential equations, with options for adaptive mesh refinement, on machines from laptops to exascale architectures. AMReX was developed in the U.S. Department of Energy’s Exascale Computing Project and is now a member project of the High Performance Software Foundation under the umbrella of the Linux Foundation.
+
+AMReX uses an MPI+X model of hierarchical parallelism where blocks of data are distributed across MPI ranks (typically across multiple nodes).  Fine-grained parallelism at the node level (X) is achieved using
+OpenMP for CPU-only machines, or CUDA, HIP or SYCL for NVIDIA, AMD or Intel GPUs, respectively. AMReX provides extensive support for kernel launching on GPU accelerators (using ParallelFor looping constructs and C++ lambda functions) and the effective use of various memory types, including managed, device, and pinned. Architecture-specific aspects of the software for GPUs are highly localized within the code, and essentially hidden from the application developer or user.
+
+In addition to portability across architectures, AMReX provides data structures and iterators that define, allocate and efficiently operate on distributed multi-dimensional arrays.
+Data is defined on disjoint logically rectangular regions of the domain known as patches (or grids or boxes); we note that unlike WRF, AMReX (and therefore ERF) does not require one patch per MPI rank, thus allowing much more general domain decomposition. Common operations, such as parallel communication and reduction operations, as well as interpolation and averaging operators between levels of refinement, are provided by the AMReX framework.
+
+Finally, ERF currently leverages, or plans to leverage, AMReX capabilities for effective load balancing, adaptive mesh refinement, memory management, asynchronous I/O, Lagrangian particles with particle-mesh interactions, and linear solvers.

Docs/sphinx_doc/BoundaryConditions.rst

@@ -7,6 +7,14 @@
 Domain Boundary Conditions
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
+Lateral boundary conditions in ERF can be specified for idealized simulations as periodic, inflow, outflow, or open. More realistic conditions include the use of time-varying values read in from external files, such as the wrfbdy files generated by the WRF Preprocessing System (WPS).
+ERF also has the option to run precursor simulations, save planes of data at specified times, and later read boundary data from those files analogously to how data from the wrfbdy are used.
+
+The bottom surface boundary condition can be specified as a simple wall or by using Monin-Obukhov similarity theory (MOST).
+When utilizing MOST, the surface roughness, :math:`z_0`, may be specified as a constant, read from a file,
+or dynamically computed from the Charnock or shallow water formulation.
+Time-varying sea surface temperatures may also be employed in conjunction with MOST.
+
 Ideal Domain BCs
 ----------------------
 
@@ -201,43 +209,6 @@ current RK stage, :math:`\psi^{BDY}` is temporal interpolation of the observatio
 is a constant that ensure the exponential blending function obtains a value of 0.01 at the last relaxation cell,
 and :math:`n` is the minimum number of grid points from a lateral boundary.
 
-Sponge zone domain BCs
-----------------------
-
-ERF provides the capability to apply sponge zones at the boundaries to prevent spurious reflections that otherwise occur at the domain boundaries if standard extrapolation boundary condition is used. The sponge zone is implemented as a source term in the governing equations, which are active in a volumteric region at the boundaries that is specified by the user in the inputs file. Currently the target condition to which the sponge zones should be forced towards is to be specified by the user in the inputs file.
-
-.. math::
-
-   \frac{dQ}{dt} = \mathrm{RHS} - A\xi^n(Q-Q_\mathrm{target})
-
-where RHS are the other right-hand side terms. The parameters to be set by the user are -- `A` is the sponge amplitude, `n` is the sponge strength and the :math:`Q_\mathrm{target}` -- the target solution in the sponge. :math:`\xi` is a linear coordinate that is 0 at the beginning of the sponge and 1 at the end. An example of the sponge inputs can be found in ``Exec/RegTests/Terrain2d_Cylinder`` and is given below. This list of inputs specifies sponge zones in the inlet and outlet of the domain in the x-direction and the outlet of the domain in the z-direction. The `start` and `end` parameters specify the starting and ending of the sponge zones. At the inlet, the sponge starts at :math:`x=0` and at the outlet the sponge ends at :math:`x=L` -- the end of the domain. The sponge amplitude `A` has to be adjust
-ed in a problem-specific manner. The density and the :math:`x, y, z` velocities to be used in the sponge zones have to be specified in the inputs list.
-
-::
-
-          erf.sponge_strength = 10000.0
-          erf.use_xlo_sponge_damping = true
-          erf.xlo_sponge_end = 4.0
-          erf.use_xhi_sponge_damping = true
-          erf.xhi_sponge_start = 26.0
-          erf.use_zhi_sponge_damping = true
-          erf.zhi_sponge_start = 8.0
-
-          erf.sponge_density = 1.2
-          erf.sponge_x_velocity = 10.0
-          erf.sponge_y_velocity = 0.0
-          erf.sponge_z_velocity = 0.0
-
-Another way of specifying sponge zones is by providing the sponge zone data as a text file input. This is currently implemented only for forcing :math:`x` and :math:`y` velocities in the sponge zones.
-The sponge data is input as a text file with 3 columns containing :math:`z, u, v` values. An example can be found in ``Exec/SpongeTest`` and a sample inputs list for using this feature is given below. This list specifies a sponge zone in the inlet in the x-direction. The :math:`u` and :math:`v` velocity forcing in the sponge zones will be read in from the text file -- `input_sponge_file.txt`.
-
-::
-
-          erf.sponge_type = "input_sponge"
-          erf.input_sponge_file = "input_sponge_file.txt"
-          erf.sponge_strength = 1000.0
-          erf.use_xlo_sponge_damping = true
-          erf.xlo_sponge_end = 4.0
 
 Inflow turbulence generation
 ---------------------------

Docs/sphinx_doc/Checkpoint.rst

@@ -14,6 +14,10 @@ uses the native AMReX format for reading and writing checkpoints.
 In the inputs file, the following options control the generation of
 checkpoint files (which are really directories):
 
+The computational cost associated with reading and writing checkpoint files is
+typically negligible relative to the overall cost of the simulation;  in a recent performance
+study the cost of writing a checkpoint file was roughly a percent of the cost of a single timestep.
+
 Writing the Checkpoint "Files"
 ==============================