Merge branch 'development' into ysu-pbl-moreprog

CMake/BuildERFExe.cmake

@@ -142,6 +142,7 @@ function(build_erf_lib erf_lib_name)
        ${SRC_DIR}/Initialization/ERF_init_from_metgrid.cpp
        ${SRC_DIR}/Initialization/ERF_init_uniform.cpp
        ${SRC_DIR}/Initialization/ERF_init1d.cpp
+       ${SRC_DIR}/Initialization/ERF_input_sponge.cpp
        ${SRC_DIR}/IO/Checkpoint.cpp
        ${SRC_DIR}/IO/ERF_ReadBndryPlanes.cpp
        ${SRC_DIR}/IO/ERF_WriteBndryPlanes.cpp
@@ -152,6 +153,7 @@ function(build_erf_lib erf_lib_name)
        ${SRC_DIR}/IO/writeJobInfo.cpp
        ${SRC_DIR}/IO/console_io.cpp
        ${SRC_DIR}/SourceTerms/ERF_ApplySpongeZoneBCs.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
@@ -174,7 +176,8 @@ function(build_erf_lib erf_lib_name)
        ${SRC_DIR}/Utils/MomentumToVelocity.cpp
        ${SRC_DIR}/Utils/TerrainMetrics.cpp
        ${SRC_DIR}/Utils/VelocityToMomentum.cpp
-       ${SRC_DIR}/Utils/InteriorGhostCells.cpp 
+       ${SRC_DIR}/Utils/InteriorGhostCells.cpp
+       ${SRC_DIR}/Utils/Time_Avg_Vel.cpp
        ${SRC_DIR}/Microphysics/SAM/Init_SAM.cpp
        ${SRC_DIR}/Microphysics/SAM/Cloud_SAM.cpp
        ${SRC_DIR}/Microphysics/SAM/IceFall.cpp

Docs/sphinx_doc/BoundaryConditions.rst

@@ -198,7 +198,8 @@ ERF provides the capability to apply sponge zones at the boundaries to prevent s
 
    \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. `\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``.
+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.
 
 ::
 
@@ -214,3 +215,14 @@ where RHS are the other right-hand side terms. The parameters to be set by the u
           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

Docs/sphinx_doc/Plotfiles.rst

@@ -108,7 +108,9 @@ PlotFile Outputs
 ================
 
 Plotfiles can include the quantities of several simulation parameters as output.
-They are summarized in the list below.
+They are summarized in the list below. Note that temporally averaged quantities
+(e.g., ``u_t_avg, v_t_avg, w_t_avg, umag_t_avg``) require the user to enable the
+storage of the time averaged variables with ``erf.time_avg_vel = true``.
 
 Output Options
 --------------
@@ -201,18 +203,34 @@ Output Options
 |                             |                  |
 |                             |                  |
 +-----------------------------+------------------+
-| **vorticity_x*              | x-component of   |
+| **vorticity_x**             | x-component of   |
 |                             | vorticity        |
 |                             |                  |
 +-----------------------------+------------------+
-| **vorticity_y*              | y-component of   |
+| **vorticity_y**             | y-component of   |
 |                             | vorticity        |
 |                             |                  |
 +-----------------------------+------------------+
-| **vorticity_z*              | z-component of   |
+| **vorticity_z**             | z-component of   |
 |                             | vorticity        |
 |                             |                  |
 +-----------------------------+------------------+
+| **u_t_avg**                 | time average of  |
+|                             | x-component of   |
+|                             | velocity         |
++-----------------------------+------------------+
+| **v_t_avg**                 | time average of  |
+|                             | y-component of   |
+|                             | velocity         |
++-----------------------------+------------------+
+| **w_t_avg**                 | time average of  |
+|                             | z-component of   |
+|                             | velocity         |
++-----------------------------+------------------+
+| **umag_t_avg**              | time average of  |
+|                             | velocity mag     |
+|                             |                  |
++-----------------------------+------------------+
 | **rhoadv_0**                | Conserved scalar |
 |                             |                  |
 |                             |                  |
@@ -233,6 +251,14 @@ Output Options
 |                             |                  |
 |                             |                  |
 +-----------------------------+------------------+
+| **lat_m**                   | Latitude at mass |
+|                             | points           |
+|                             |                  |
++-----------------------------+------------------+
+| **lon_m**                   | Longitude at     |
+|                             | mass points      |
+|                             |                  |
++-----------------------------+------------------+
 | **Kmv**                     | Vertical         |
 |                             | Eddy Diffusivity |
 |                             | of Momentum      |

Exec/ABL/inputs_vel_avg

@@ -0,0 +1,65 @@
+# ------------------  INPUTS TO MAIN PROGRAM  -------------------
+max_step = 4000
+
+amrex.fpe_trap_invalid = 1
+
+fabarray.mfiter_tile_size = 1024 1024 1024
+
+# PROBLEM SIZE & GEOMETRY
+geometry.prob_extent =  1024     1024    1024
+amr.n_cell           =    64      64     64
+
+geometry.is_periodic = 1 1 0
+
+zlo.type = "NoSlipWall"
+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       = 100        # number of timesteps between checkpoints
+
+# PLOTFILES
+erf.time_avg_vel      = true
+erf.plot_file_1       = plt       # prefix of plotfile name
+erf.plot_int_1        = 10        # number of timesteps between plotfiles
+erf.plot_vars_1       = density rhoKE rhoadv_0 x_velocity y_velocity z_velocity pressure temp theta u_t_avg v_t_avg w_t_avg umag_t_avg
+
+# SOLVER CHOICE
+erf.alpha_T = 0.0
+erf.alpha_C = 1.0
+erf.use_gravity = false
+
+erf.molec_diff_type = "None"
+erf.les_type = "Deardorff"
+erf.Ck       = 0.1
+erf.sigma_k  = 1.0
+erf.Ce       = 0.1
+
+erf.init_type = "uniform"
+erf.KE_0 = 0.1 # for Deardorff
+
+# 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
+
+# Higher values of perturbations lead to instability
+# Instability seems to be coming from BC
+prob.U_0_Pert_Mag = 0.08
+prob.V_0_Pert_Mag = 0.08 #
+prob.W_0_Pert_Mag = 0.0

Exec/DevTests/MetGrid/inputs

@@ -44,7 +44,7 @@ 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 dens_hse rhoadv_0 x_velocity y_velocity z_velocity pressure temp theta z_phys mapfac pres_hse pert_pres 
+erf.plot_vars_1     = lat_m lon_m density dens_hse rhoadv_0 x_velocity y_velocity z_velocity pressure temp theta z_phys mapfac pres_hse pert_pres 
 
 # SOLVER CHOICE
 erf.alpha_T = 1.0

Exec/EWP/CMakeLists.txt

@@ -0,0 +1,12 @@
+set(erf_exe_name erf_fitch)
+
+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})

Exec/EWP/GNUmakefile

@@ -0,0 +1,37 @@
+# AMReX
+COMP = gnu
+PRECISION = DOUBLE
+
+# Profiling
+PROFILE       = FALSE
+TINY_PROFILE  = TRUE
+COMM_PROFILE  = FALSE
+TRACE_PROFILE = FALSE
+MEM_PROFILE   = FALSE
+USE_GPROF     = FALSE
+
+# Performance
+USE_MPI  = TRUE
+USE_OMP  = FALSE
+
+USE_CUDA = FALSE
+USE_HIP  = FALSE
+USE_SYCL = FALSE
+
+# Debugging
+DEBUG = FALSE
+
+TEST = TRUE
+USE_ASSERTION = TRUE
+
+USE_WINDFARM = TRUE
+
+
+#USE_POISSON_SOLVE = TRUE
+
+# GNU Make
+Bpack := ./Make.package
+Blocs := .
+ERF_HOME := ../..
+ERF_PROBLEM_DIR = $(ERF_HOME)/Exec/EWP
+include $(ERF_HOME)/Exec/Make.ERF

Exec/EWP/Make.package

@@ -0,0 +1,2 @@
+CEXE_headers += prob.H
+CEXE_sources += prob.cpp

Exec/EWP/README

@@ -0,0 +1,6 @@
+This problem setup is for simulation of the Atmospheric Boundary Layer (ABL)
+using one of two turbulence schemes (Smagorinsky or Deardorff) and the bottom
+boundary condition possibly specified by Monin Obukhov Similarity Theory (MOST).
+
+This version of the ABL problem initializes the data using a hydrostatic profile
+with random perturbations in velocity and potential temperature.

Exec/EWP/inputs_EWP_WindFarm

@@ -0,0 +1,78 @@
+# ------------------  INPUTS TO MAIN PROGRAM  -------------------
+max_step = 100000
+
+amrex.fpe_trap_invalid = 1
+
+fabarray.mfiter_tile_size = 1024 1024 1024
+
+# PROBLEM SIZE & GEOMETRY
+erf.latitude_lo      =   35.0
+erf.longitude_lo     = -100.0
+geometry.prob_extent =  200150   202637  1000
+amr.n_cell           =   50     50       40
+
+#erf.grid_stretching_ratio = 1.025
+#erf.initial_dz = 16.0
+
+geometry.is_periodic = 0 0 0
+
+# MOST BOUNDARY (DEFAULT IS ADIABATIC FOR THETA)
+#zlo.type      = "MOST"
+#erf.most.z0   = 0.1
+#erf.most.zref = 8.0
+
+zlo.type = "SlipWall"
+zhi.type = "SlipWall"
+xlo.type = "Outflow"
+xhi.type = "Outflow"
+ylo.type = "Outflow"
+yhi.type = "Outflow"
+
+# TIME STEP CONTROL
+erf.use_native_mri = 1
+erf.fixed_dt       = 0.25  # fixed time step depending on grid resolution
+#erf.fixed_fast_dt  = 0.0025
+
+# 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       = 10000        # number of timesteps between checkpoints
+#erf.restart         = chk02000
+
+# PLOTFILES
+erf.plot_file_1     = plt       # prefix of plotfile name
+erf.plot_int_1      = 1000       # number of timesteps between plotfiles
+erf.plot_vars_1     = density rhoadv_0 x_velocity y_velocity z_velocity pressure temp theta QKE num_turb vorticity
+
+# SOLVER CHOICE
+erf.alpha_T = 0.0
+erf.alpha_C = 1.0
+erf.use_gravity = false
+
+erf.molec_diff_type = "ConstantAlpha"
+erf.les_type        = "None"
+erf.Cs              = 1.5
+erf.dynamicViscosity = 100.0
+
+erf.pbl_type        = "None"
+
+erf.init_type = "uniform"
+
+erf.windfarm_type = "EWP"
+
+# PROBLEM PARAMETERS
+prob.rho_0 = 1.0
+prob.A_0 = 1.0
+
+prob.U_0 = 10.0
+prob.V_0 = 10.0
+prob.W_0 = 0.0
+prob.T_0 = 300.0
+