Merge branch 'development' into LSM

Docs/sphinx_doc/Inputs.rst

@@ -771,6 +771,30 @@ List of Parameters
 | | Rayleigh damping | | |
 +----------------------------------+-------------------+-------------------+-------------+
 
+In addition, custom forcings or tendencies may be defined on a problem-specific
+basis. This affords additional flexibility in defining the RHS source term as
+a function of time and/or height. Implementation entails modifying problem
+source code inside the Exec directory and overriding the ``update_*_sources()``
+function(s).
+
++--------------------------------------------+-------------------+-------------------+-------------+
+| Parameter | Definition | Acceptable | Default |
+| | | Values | |
++============================================+===================+===================+=============+
+| **erf.custom_forcing_uses_primitive_vars** | User-defined | true or false | false |
+| | source terms set | | |
+| | the tendency of | | |
+| | primitive | | |
+| | variables instead | | |
+| | of conserved | | |
+| | quantities | | |
+| | (rho*prim_var) | | |
++--------------------------------------------+-------------------+-------------------+-------------+
+| **erf.add_custom_rhotheta_forcing** | Apply the | true or false | false |
+| | user-defined | | |
+| | temperature source| | |
+| | term | | |
++--------------------------------------------+-------------------+-------------------+-------------+
 
 Initialization
 ==============

Exec/CMakeLists.txt

@@ -28,4 +28,5 @@ else ()
  add_subdirectory(DevTests/MiguelDev)
  add_subdirectory(DevTests/MetGrid)
  add_subdirectory(DevTests/LandSurfaceModel)
+ add_subdirectory(DevTests/TemperatureSource)
 endif()

Exec/DevTests/MetGrid/inputs

@@ -19,7 +19,7 @@ zlo.type = "NoSlipWall"
 zhi.type = "SlipWall"
 
 # TIME STEP CONTROL
-erf.fixed_dt  = 1.0 # fixed time step depending on grid resolution
+erf.fixed_dt = 0.5 # fixed time step depending on grid resolution
 
 erf.use_terrain = true
 erf.terrain_smoothing = 2
@@ -39,8 +39,8 @@ erf.check_int = 100 # number of timesteps between checkpoints
 
 # PLOTFILES
 erf.plot_file_1 = plt # prefix of plotfile name
-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
+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 
 
 # SOLVER CHOICE
 erf.alpha_T = 1.0
@@ -49,18 +49,17 @@ erf.use_gravity = true
 
 erf.molec_diff_type = "None"
 erf.les_type = "Smagorinsky"
-#erf.les_type = "Deardorff"
 erf.Cs = 0.1
 
-erf.moisture_model = "SAM"
+erf.moisture_model = "NullMoist"
 
 #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.metgrid_bdy_width = 5
+erf.metgrid_bdy_width = 7
 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"
+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"
 
 #There will be no OpenMP tiling
 fabarray.mfiter_tile_size = 1024 1024 1024

Exec/DevTests/MetGrid/inputs_fitch_flowmas

@@ -1,5 +1,5 @@
 # ------------------ INPUTS TO MAIN PROGRAM -------------------
-max_step = 100
+max_step = 1000
 
 amrex.fpe_trap_invalid = 1
 amrex.fpe_trap_zero = 1
@@ -19,7 +19,7 @@ zlo.type = "NoSlipWall"
 zhi.type = "SlipWall"
 
 # TIME STEP CONTROL
-erf.fixed_dt  = 1.0 # 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
@@ -34,12 +34,12 @@ 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
+erf.check_int = 25 # number of timesteps between checkpoints
 
 # PLOTFILES
 erf.plot_file_1 = plt # prefix of plotfile name
-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
+erf.plot_int_1 = 25 # 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
 
 # SOLVER CHOICE
 erf.alpha_T = 1.0
@@ -50,10 +50,10 @@ erf.molec_diff_type = "None"
 erf.les_type = "Smagorinsky"
 erf.Cs = 0.1
 
-erf.moisture_model = "Kessler"
+erf.moisture_model = "NullMoist"
 
 # INITIALIZATION WITH ATM DATA
-erf.metgrid_bdy_width = 5
+erf.metgrid_bdy_width = 7
 erf.metgrid_bdy_set_width = 1
 erf.init_type = "metgrid"
 erf.nc_init_file_0 = "met_em.d01.2015-04-01_00_00_00.nc" "met_em.d01.2015-04-01_08_00_00.nc"

Exec/DevTests/TemperatureSource/CMakeLists.txt

@@ -0,0 +1,12 @@
+set(erf_exe_name erf_abl_with_temperature_source)
+
+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/DevTests/TemperatureSource/GNUmakefile

@@ -0,0 +1,34 @@
+# 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_POISSON_SOLVE = TRUE
+
+# GNU Make
+Bpack := ./Make.package
+Blocs := .
+ERF_HOME := ../..
+ERF_PROBLEM_DIR = $(ERF_HOME)/Exec/DevTests/TemperatureSource
+include $(ERF_HOME)/Exec/Make.ERF

Exec/DevTests/TemperatureSource/Make.package

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

Exec/DevTests/TemperatureSource/README

@@ -0,0 +1 @@
+This is a copy of the ABL problem, but with update_rhotheta_sources defined

Exec/DevTests/TemperatureSource/input_sounding

@@ -0,0 +1,3 @@
+1000.0 300.0 0.0
+ 0.0 300.0 0.0 10.0 0.0
+1000.0 300.0 0.0 10.0 0.0

Exec/DevTests/TemperatureSource/neutral_column.i

@@ -0,0 +1,50 @@
+# ------------------ INPUTS TO MAIN PROGRAM -------------------
+stop_time = 999.9
+max_step = 20
+
+amrex.fpe_trap_invalid = 1
+
+fabarray.mfiter_tile_size = 1024 1024 1024
+
+# PROBLEM SIZE & GEOMETRY
+geometry.prob_extent = 40. 40. 640.
+amr.n_cell = 4 4 64
+
+geometry.is_periodic = 1 1 0
+
+zlo.type = "SlipWall"
+zhi.type = "SlipWall"
+
+# INITIALIZATION
+erf.init_type = input_sounding
+erf.init_sounding_ideal = true
+
+# TIME STEP CONTROL
+erf.fixed_dt = 0.1
+
+# DIAGNOSTICS & VERBOSITY
+amr.v = 1 # verbosity in Amr.cpp
+erf.v = 1 # verbosity in ERF.cpp -- needs to be 1 to write out data_log files
+erf.sum_interval = 1 # timesteps between computing mass
+
+# 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 = 5 # number of timesteps between plotfiles (DEBUG)
+erf.plot_vars_1 = density x_velocity y_velocity z_velocity pressure theta
+
+# SOLVER CHOICES
+erf.use_gravity = true
+erf.use_coriolis = false
+
+erf.molec_diff_type = "None"
+erf.les_type = "None"
+
+erf.add_custom_rhotheta_forcing = true
+erf.custom_forcing_uses_primitive_vars = true

Exec/DevTests/TemperatureSource/prob.H

@@ -0,0 +1,85 @@
+#ifndef _PROB_H_
+#define _PROB_H_
+
+#include <string>
+
+#include "AMReX_REAL.H"
+
+#include "prob_common.H"
+
+struct ProbParm : ProbParmDefaults {
+ amrex::Real rho_0 = 0.0;
+ amrex::Real T_0 = 0.0;
+ amrex::Real A_0 = 1.0;
+ amrex::Real QKE_0 = 0.1;
+
+ amrex::Real U_0 = 0.0;
+ amrex::Real V_0 = 0.0;
+ amrex::Real W_0 = 0.0;
+
+ // random initial perturbations (legacy code)
+ amrex::Real U_0_Pert_Mag = 0.0;
+ amrex::Real V_0_Pert_Mag = 0.0;
+ amrex::Real W_0_Pert_Mag = 0.0;
+ amrex::Real T_0_Pert_Mag = 0.0; // perturbation to rho*Theta
+
+ // divergence-free initial perturbations
+ amrex::Real pert_deltaU = 0.0;
+ amrex::Real pert_deltaV = 0.0;
+ amrex::Real pert_periods_U = 5.0;
+ amrex::Real pert_periods_V = 5.0;
+ amrex::Real pert_ref_height = 100.0;
+
+ // rayleigh damping
+ amrex::Real dampcoef = 0.2; // inverse time scale [1/s]
+ amrex::Real zdamp = 500.0; // damping depth [m] from model top
+
+ // helper vars
+ amrex::Real aval;
+ amrex::Real bval;
+ amrex::Real ufac;
+ amrex::Real vfac;
+}; // namespace ProbParm
+
+class Problem : public ProblemBase
+{
+public:
+ Problem(const amrex::Real* problo, const amrex::Real* probhi);
+
+#include "Prob/init_constant_density_hse.H"
+#include "Prob/init_rayleigh_damping.H"
+
+ void init_custom_pert (
+ const amrex::Box& bx,
+ const amrex::Box& xbx,
+ const amrex::Box& ybx,
+ const amrex::Box& zbx,
+ amrex::Array4<amrex::Real > const& state,
+ amrex::Array4<amrex::Real > const& x_vel,
+ amrex::Array4<amrex::Real > const& y_vel,
+ amrex::Array4<amrex::Real > const& z_vel,
+ amrex::Array4<amrex::Real > const& r_hse,
+ amrex::Array4<amrex::Real > const& p_hse,
+ amrex::Array4<amrex::Real const> const& z_nd,
+ amrex::Array4<amrex::Real const> const& z_cc,
+ amrex::GeometryData const& geomdata,
+ amrex::Array4<amrex::Real const> const& mf_m,
+ amrex::Array4<amrex::Real const> const& mf_u,
+ amrex::Array4<amrex::Real const> const& mf_v,
+ const SolverChoice& sc) override;
+
+ void update_rhotheta_sources (
+ const amrex::Real& time,
+ amrex::Vector<amrex::Real>& src,
+ amrex::Gpu::DeviceVector<amrex::Real>& d_src,
+ const amrex::Geometry& geom,
+ std::unique_ptr<amrex::MultiFab>& z_phys_cc) override;
+
+protected:
+ std::string name() override { return "ABL"; }
+
+private:
+ ProbParm parms;
+};
+
+#endif