Merge branch 'development' into pbl-doc-update

erf-model · Nov 10, 2023 · cedc211 · cedc211
2 parents cb7f1f9 + fa25dc6
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diff --git a/CHANGES b/CHANGES
@@ -1,3 +1,16 @@
+#23.11
+
+  -- AMReX submodule set to 23.11 release hash (ae7b64b)
+
+  -- Bug fix with vertical grid stretching and MOST (#1275)
+
+  -- Bug fix with negative K_turb below surface and MYNN2.5 PBL model (#1271)
+
+  -- Correction to equation of state with moisture (#1263)
+
+  -- Generalized multi-level sponge zones. This allows for nudging of fine solution
+     towards coarse solution with complex box arrays. (#1233)
+
 # 23.10
 
   -- First release since JOSS paper. Too many key ERF PRs to summarize.

diff --git a/CMake/BuildERFExe.cmake b/CMake/BuildERFExe.cmake
@@ -45,7 +45,6 @@ function(build_erf_lib erf_lib_name)
 
   if(ERF_ENABLE_NETCDF)
     target_sources(${erf_lib_name} PRIVATE
-                   ${SRC_DIR}/IO/NCBuildFABs.cpp
                    ${SRC_DIR}/IO/NCInterface.cpp
                    ${SRC_DIR}/IO/NCPlotFile.cpp
                    ${SRC_DIR}/IO/NCCheckpoint.cpp
@@ -79,6 +78,7 @@ function(build_erf_lib erf_lib_name)
                    ${SRC_DIR}/Radiation/Aero_rad_props.cpp
                    ${SRC_DIR}/Radiation/Optics.cpp
                    ${SRC_DIR}/Radiation/Radiation.cpp
+                   ${SRC_DIR}/Radiation/Albedo.cpp
                    ${CMAKE_SOURCE_DIR}/Submodules/RRTMGP/cpp/examples/mo_load_coefficients.cpp
                    ${CMAKE_SOURCE_DIR}/Submodules/RRTMGP/cpp/extensions/fluxes_byband/mo_fluxes_byband_kernels.cpp
                   )
@@ -113,6 +113,7 @@ function(build_erf_lib erf_lib_name)
        ${SRC_DIR}/BoundaryConditions/BoundaryConditions_zvel.cpp
        ${SRC_DIR}/BoundaryConditions/BoundaryConditions_bndryreg.cpp
        ${SRC_DIR}/BoundaryConditions/BoundaryConditions_wrfbdy.cpp
+       ${SRC_DIR}/BoundaryConditions/BoundaryConditions_metgrid.cpp
        ${SRC_DIR}/BoundaryConditions/ERF_FillPatch.cpp
        ${SRC_DIR}/BoundaryConditions/ERF_FillPatcher.cpp
        ${SRC_DIR}/BoundaryConditions/ERF_PhysBCFunct.cpp
@@ -146,6 +147,7 @@ function(build_erf_lib erf_lib_name)
        ${SRC_DIR}/TimeIntegration/ERF_TimeStep.cpp
        ${SRC_DIR}/TimeIntegration/ERF_advance_dycore.cpp
        ${SRC_DIR}/TimeIntegration/ERF_advance_microphysics.cpp
+       ${SRC_DIR}/TimeIntegration/ERF_advance_radiation.cpp
        ${SRC_DIR}/TimeIntegration/ERF_make_buoyancy.cpp
        ${SRC_DIR}/TimeIntegration/ERF_make_condensation_source.cpp
        ${SRC_DIR}/TimeIntegration/ERF_make_fast_coeffs.cpp

diff --git a/Docs/sphinx_doc/Inputs.rst b/Docs/sphinx_doc/Inputs.rst
@@ -164,6 +164,61 @@ Examples of Usage
      level-1 grids will be created every 2 level-0 time steps, and new
      level-2 grids will be created every 2 level-1 time steps.
 
+
+Grid Stretching
+===============
+
+This automatically activates **erf.use_terrain**. By default, the
+problem-specific terrain is initialized to be flat at an elevation of z=0.
+These inputs are used to automatically generate the staggered z levels used to
+calculate the grid metric transformation. Alternatively, arbitrary z levels may
+be specified with the **erf.terrain_z_levels** parameter.
+
+.. _list-of-parameters-3:
+
+List of Parameters
+------------------
+
++-------------------------------+-----------------+-----------------+-------------+
+| Parameter                     | Definition      | Acceptable      | Default     |
+|                               |                 | Values          |             |
++===============================+=================+=================+=============+
+| **erf.grid_stretching_ratio** | scaling factor  | Real > 0        | 0 (no grid  |
+|                               | applied to      |                 | stretching) |
+|                               | delta z at each |                 |             |
+|                               | level           |                 |             |
++-------------------------------+-----------------+-----------------+-------------+
+| **erf.initial_dz**            | vertical grid   | Real > 0        | must be set |
+|                               | spacing for the |                 | if grid     |
+|                               | cell above the  |                 | stretching  |
+|                               | bottom surface  |                 | ratio is set|
++-------------------------------+-----------------+-----------------+-------------+
+| **erf.terrain_z_levels**      | nominal         | List of Real    | NONE        |
+|                               | staggered       |                 |             |
+|                               | z levels        |                 |             |
++-------------------------------+-----------------+-----------------+-------------+
+
+.. _notes-3:
+
+Notes
+-----
+
+- If both **erf.terrain_z_levels** and **erf.grid_stretching_ratio** are
+  specified, the simple grid stretching will be ignored.
+- The number of input **erf.terrain_z_levels** must be equal **amr.n_cell** in
+  the z direction + 1.
+
+.. _examples-of-usage-3:
+
+Examples of Usage
+-----------------
+
+-  **erf.grid_stretching_ratio** = 1.025
+
+-  | **erf.initial_dz** = 5.0
+   | the first cell center would be at z=2.5
+
+
 Regridding
 ==========
 
@@ -805,7 +860,7 @@ List of Parameters
 | **erf.use_terrain**         | use terrain-fitted |  true / false      | false      |
 |                             | coordinates?       |                    |            |
 +-----------------------------+--------------------+--------------------+------------+
-| **erf.terrain_type**        | static or moving?  |  0 / 1             | 0          |
+| **erf.terrain_type**        | static or moving?  |  Static / Moving   | Static     |
 +-----------------------------+--------------------+--------------------+------------+
 | **erf.terrain_smoothing**   | specify terrain    | 0,                 | 0          |
 |                             | following          | 1,                 |            |

diff --git a/Docs/sphinx_doc/Plotfiles.rst b/Docs/sphinx_doc/Plotfiles.rst
@@ -209,6 +209,22 @@ Output Options
 |                             |                  |
 |                             |                  |
 +-----------------------------+------------------+
+| **Kmv**                     | Vertical         |
+|                             | Eddy Diffusivity |
+|                             | of Momentum      |
++-----------------------------+------------------+
+| **Kmh**                     | Horizontal       |
+|                             | Eddy Diffusivity |
+|                             | of Momentum      |
++-----------------------------+------------------+
+| **Khv**                     | Vertical         |
+|                             | Eddy Diffusivity |
+|                             | of Heat          |
++-----------------------------+------------------+
+| **Khh**                     | Horizontal       |
+|                             | Eddy Diffusivity |
+|                             | of Heat          |
++-----------------------------+------------------+
 | **qt**                      | Nonprecipitating |
 |                             | water (qv + qc + |
 |                             | qi)              |

diff --git a/Docs/sphinx_doc/RegressionTests.rst b/Docs/sphinx_doc/RegressionTests.rst
@@ -45,7 +45,7 @@ The following problems are currently tested in the CI:
 | DensityCurrent_detJ2_MT       | 256 4 64 | Symmetry | Periodic | SlipWall   | None  | use_terrain = true    |
 |                               |          | Outflow  |          | SlipWall   |       | uses zlevels          |
 |                               |          | Outflow  |          | SlipWall   |       | detJ = 2 everywhere   |
-|                               |          |          |          |            |       | terrain_type = 1      |
+|                               |          |          |          |            |       | terrain_type = Moving |
 +-------------------------------+----------+----------+----------+------------+-------+-----------------------+
 | EkmanSpiral                   | 4 4 400  | Periodic | Periodic | NoSlipWall | Geo   | +Coriolis             |
 |                               |          |          |          | SlipWall   |       | +gravity              |

diff --git a/Docs/sphinx_doc/theory/WetEquations.rst b/Docs/sphinx_doc/theory/WetEquations.rst
@@ -38,7 +38,7 @@ The governing equations for this model are
   \frac{\partial \rho_d}{\partial t} &= - \nabla \cdot (\rho_d \mathbf{u})
 
   \frac{\partial (\rho_d \mathbf{u})}{\partial t} &= - \nabla \cdot (\rho_d \mathbf{u} \mathbf{u}) -
-          \frac{1}{1 + q_v + q_c}  \nabla p^\prime - \nabla \cdot \tau + \mathbf{F} + \delta_{i,3}\mathbf{B}
+          \frac{1}{1 + q_v + q_c} ( \nabla p^\prime  + \delta_{i,3}\mathbf{B} ) - \nabla \cdot \tau + \mathbf{F}
 
   \frac{\partial (\rho_d \theta_d)}{\partial t} &= - \nabla \cdot (\rho_d \mathbf{u} \theta_d)
                 + \nabla \cdot ( \rho_d \alpha_{T}\ \nabla \theta_d) + \frac{\theta_d L_v}{T_d C_{pd}} f_{cond}

diff --git a/Exec/ABL/inputs_most_pbl b/Exec/ABL/inputs_most_pbl
@@ -0,0 +1,65 @@
+# ------------------  INPUTS TO MAIN PROGRAM  -------------------
+max_step = 3000
+
+amrex.fpe_trap_invalid = 1
+
+fabarray.mfiter_tile_size = 1024 1024 1024
+
+# PROBLEM SIZE & GEOMETRY
+geometry.prob_extent =  1024    1024    1024
+amr.n_cell           =     4       4      64
+
+#erf.grid_stretching_ratio = 1.025
+#erf.initial_dz = 16.0
+
+geometry.is_periodic = 1 1 0
+
+# MOST BOUNDARY (DEFAULT IS ADIABATIC FOR THETA)
+zlo.type      = "Most"
+erf.most.z0   = 0.1
+erf.most.zref = 8.0
+
+zhi.type = "SlipWall"
+
+# TIME STEP CONTROL
+erf.fixed_dt           = 0.1  # fixed time step depending on grid resolution
+
+# DIAGNOSTICS & VERBOSITY
+erf.sum_interval   = 1       # timesteps between computing mass
+erf.v              = 1       # verbosity in ERF.cpp
+amr.v                = 1       # verbosity in Amr.cpp
+
+# REFINEMENT / REGRIDDING
+amr.max_level       = 0       # maximum level number allowed
+
+# CHECKPOINT FILES
+erf.check_file      = chk       # root name of checkpoint file
+erf.check_int       = -1        # number of timesteps between checkpoints
+
+# PLOTFILES
+erf.plot_file_1     = plt       # prefix of plotfile name
+erf.plot_int_1      = 100       # number of timesteps between plotfiles
+erf.plot_vars_1     = density rhoadv_0 x_velocity y_velocity z_velocity pressure temp theta
+
+# SOLVER CHOICE
+erf.alpha_T = 0.0
+erf.alpha_C = 1.0
+erf.use_gravity = false
+
+erf.molec_diff_type = "None"
+erf.les_type        = "Smagorinsky"
+erf.Cs              = 0.1
+
+erf.pbl_type        = "MYNN2.5"
+
+erf.init_type = "uniform"
+
+# PROBLEM PARAMETERS
+prob.rho_0 = 1.0
+prob.A_0 = 1.0
+
+prob.U_0 = 10.0
+prob.V_0 = 0.0
+prob.W_0 = 0.0
+prob.T_0 = 300.0
+
diff --git a/Exec/CMakeLists.txt b/Exec/CMakeLists.txt
@@ -14,6 +14,7 @@ else ()
   add_subdirectory(RegTests/EkmanSpiral_custom)
   add_subdirectory(RegTests/EkmanSpiral_ideal)
   add_subdirectory(RegTests/EkmanSpiral_input_sounding)
+  add_subdirectory(RegTests/GABLS1)
   add_subdirectory(RegTests/IsentropicVortex)
   add_subdirectory(RegTests/PoiseuilleFlow)
   add_subdirectory(RegTests/ScalarAdvDiff)
@@ -23,4 +24,5 @@ else ()
   add_subdirectory(DevTests/MovingTerrain)
   add_subdirectory(DevTests/ParticlesOverWoA)
   add_subdirectory(DevTests/MiguelDev)
+  add_subdirectory(DevTests/MetGrid)
 endif()
diff --git a/Exec/DevTests/MetGrid/CMakeLists.txt b/Exec/DevTests/MetGrid/CMakeLists.txt
@@ -0,0 +1,12 @@
+set(erf_exe_name erf_metgrid_dev)
+
+add_executable(${erf_exe_name} "")
+target_sources(${erf_exe_name}
+   PRIVATE
+     prob.cpp
+)
+
+target_include_directories(${erf_exe_name} PRIVATE ${CMAKE_CURRENT_SOURCE_DIR})
+
+include(${CMAKE_SOURCE_DIR}/CMake/BuildERFExe.cmake)
+build_erf_exe(${erf_exe_name})
diff --git a/Exec/DevTests/MetGrid/GNUmakefile b/Exec/DevTests/MetGrid/GNUmakefile
@@ -19,14 +19,19 @@ USE_HIP  = FALSE
 USE_SYCL = FALSE
 
 # Debugging
-DEBUG = FALSE
+#DEBUG = FALSE
 DEBUG = TRUE
 
 TEST = TRUE
 USE_ASSERTION = TRUE
 
 USE_NETCDF = TRUE
 
+#USE_MOISTURE = FALSE
+USE_MOISTURE = TRUE
+
+#USE_WARM_NO_PRECIP = TRUE
+
 # GNU Make
 Bpack := ./Make.package
 Blocs := .

diff --git a/Exec/DevTests/MetGrid/inputs b/Exec/DevTests/MetGrid/inputs
@@ -1,11 +1,13 @@
 # ------------------  INPUTS TO MAIN PROGRAM  -------------------
-max_step = 1
+max_step = 100
 
 amrex.fpe_trap_invalid = 1
+amrex.fpe_trap_zero = 1
+amrex.fpe_trap_overflow = 1
 
 # PROBLEM SIZE & GEOMETRY
-geometry.prob_extent =  10600 5000 5000
-amr.n_cell           =   140 80 60
+geometry.prob_extent =  28000 16000 8000
+amr.n_cell           =   140 80 100
 
 geometry.is_periodic = 0 0 0
 
@@ -17,9 +19,10 @@ zlo.type = "NoSlipWall"
 zhi.type = "SlipWall"
 
 # TIME STEP CONTROL
-erf.fixed_dt           = 0.1  # fixed time step depending on grid resolution
+erf.fixed_dt           = 1.0  # fixed time step depending on grid resolution
 
 erf.use_terrain = true
+erf.terrain_smoothing = 2
 
 # DIAGNOSTICS & VERBOSITY
 erf.sum_interval   = -1       # timesteps between computing mass
@@ -36,22 +39,26 @@ erf.check_int       = 100        # number of timesteps between checkpoints
 
 # PLOTFILES
 erf.plot_file_1     = plt        # prefix of plotfile name
-erf.plot_int_1      = 10         # number of timesteps between plotfiles
-erf.plot_vars_1     = density rhoadv_0 x_velocity y_velocity z_velocity pressure temp theta z_phys
+erf.plot_int_1      = 1          # number of timesteps between plotfiles
+erf.plot_vars_1     = qv Rhoqv density dens_hse rhoadv_0 x_velocity y_velocity z_velocity pressure temp theta z_phys mapfac pres_hse pert_pres KE QKE
 
 # SOLVER CHOICE
-erf.alpha_T = 0.0
+erf.alpha_T = 1.0
 erf.alpha_C = 1.0
 erf.use_gravity = true
 
 erf.molec_diff_type = "None"
 erf.les_type        = "Smagorinsky"
+#erf.les_type        = "Deardorff"
 erf.Cs              = 0.1
 
+#erf.terrain_z_levels = 0 130 354 583 816 1054 1549 2068 2615 3193 3803 4450 5142 5892 6709 7603 8591 9702 10967 12442 14230 16610 18711 20752 22133 23960 26579 28493 31236 33699 36068 40000
+
 # INITIALIZATION WITH ATM DATA
-erf.init_type    = "metgrid"
-erf.nc_init_file_0 = "met_em_d01.nc"
-#erf.nc_bdy_file = ""
+erf.metgrid_bdy_width = 5
+erf.metgrid_bdy_set_width = 1
+erf.init_type      = "metgrid"
+erf.nc_init_file_0 = "met_em.d01.2022-06-18_00:00:00.nc" "met_em.d01.2022-06-18_06:00:00.nc" "met_em.d01.2022-06-18_12:00:00.nc" "met_em.d01.2022-06-18_18:00:00.nc"
 
 #There will be no OpenMP tiling
 fabarray.mfiter_tile_size = 1024 1024 1024
diff --git a/Exec/DevTests/MetGrid/prob.H b/Exec/DevTests/MetGrid/prob.H
@@ -12,7 +12,7 @@ struct ProbParm : ProbParmDefaults {
 class Problem : public ProblemBase
 {
 public:
-    Problem();
+    Problem(const amrex::Real* problo, const amrex::Real* probhi);
 
 protected:
     std::string name() override { return "Metgrid"; }

diff --git a/Exec/DevTests/MetGrid/prob.cpp b/Exec/DevTests/MetGrid/prob.cpp
@@ -8,5 +8,5 @@ amrex_probinit(const amrex_real* problo, const amrex_real* probhi)
     return std::make_unique<Problem>(problo, probhi);
 }
 
-Problem::Problem()
+Problem::Problem(const amrex::Real* problo, const amrex::Real* probhi)
 {}
diff --git a/Exec/DevTests/MiguelDev/inputs b/Exec/DevTests/MiguelDev/inputs
@@ -18,6 +18,7 @@ zlo.type = "Most" # "Most" # "NoSlipWall"
 #erf.most.time_average      = false
 erf.most.z0                = 0.001
 erf.most.zref              = 15.0 # >=dz/2
+erf.most.surf_temp_flux    = 0.05
 #erf.most.surf_temp         = 303.0
 zhi.type = "SlipWall"
 
@@ -38,7 +39,7 @@ erf.check_file      = chk        # root name of checkpoint file
 erf.check_int       =-100        # number of timesteps between checkpoints
 
 # PLOTFILES
-erf.plotfile_type   = netcdf
+#erf.plotfile_type   = netcdf
 erf.plot_file_1     = plt        # prefix of plotfile name
 erf.plot_int_1      = 100        # number of timesteps between plotfiles
 erf.plot_vars_1     = density rhotheta rhoQKE x_velocity y_velocity z_velocity pressure temp theta QKE pres_hse

diff --git a/Exec/DevTests/MovingTerrain/inputs b/Exec/DevTests/MovingTerrain/inputs
@@ -19,8 +19,8 @@ zlo.type = "SlipWall"
 zhi.type = "SlipWall"
 
 # TERRRAIN GRID TYPE
-erf.use_terrain = 1         # enable terrain stencils
-erf.terrain_type = 1        # moving terrain
+erf.use_terrain  = true     # enable terrain stencils
+erf.terrain_type = Moving   # moving terrain
 erf.terrain_smoothing = 2   # Sullivan 2004 approach
 
 # FOR NO SUBSTEPPING

diff --git a/Exec/LLJ/GNUmakefile b/Exec/LLJ/GNUmakefile
@@ -25,7 +25,7 @@ TEST = TRUE
 USE_ASSERTION = TRUE
 
 USE_NETCDF  = TRUE
-USE_HDF5    = TRUE
+#USE_HDF5    = TRUE
 
 # GNU Make
 Bpack := ./Make.package