Moisture source term profiles for BOMEX (erf-model#1466)

* Moisture source term profiles for BOMEX

* Formatting fixes only.

* This starts but dies from touching uninitialized data.

* qv is updated in post, move the sources there.

---------

Co-authored-by: Chandru Dhandapani <chandru@x1000c5s2b1n1.hsn.cm.kestrel.hpc.nrel.gov>
Co-authored-by: AMLattanzi <AMLattanzi@lbl.gov>
Co-authored-by: Aaron M. Lattanzi <103702284+AMLattanzi@users.noreply.github.com>

Exec/DevTests/Bomex/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/Bomex/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/Bomex
+include $(ERF_HOME)/Exec/Make.ERF

Exec/DevTests/Bomex/Make.package

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

Exec/DevTests/Bomex/README

@@ -0,0 +1 @@
+This is a copy of the DEvtests/TemperatureSource problem, but with update_rhoQ1_sources added

Exec/DevTests/Bomex/input_SAM

@@ -0,0 +1,77 @@
+# ------------------  INPUTS TO MAIN PROGRAM  -------------------
+stop_time = 21600
+
+amrex.fpe_trap_invalid = 1
+
+fabarray.mfiter_tile_size = 1024 1024 1024
+
+# PROBLEM SIZE & GEOMETRY
+geometry.prob_extent =  6400     6400    3000
+amr.n_cell           =    64       64      75
+
+geometry.is_periodic = 1 1 0
+
+# MOST BOUNDARY (DEFAULT IS ADIABATIC FOR THETA)
+zlo.type      = "Most"
+
+erf.most.z0   = 0.000283
+erf.most.zref = 20.0
+erf.most.surf_temp_flux = 0.008
+
+zhi.type = "SlipWall"
+
+# TIME STEP CONTROL
+erf.fixed_dt           = 1.0 # 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       = 600        # number of timesteps between checkpoints
+
+# PLOTFILES
+erf.plot_file_1     = plt       # prefix of plotfile name
+erf.plot_int_1      = 60        # number of timesteps between plotfiles
+erf.plot_vars_1     = density rhotheta x_velocity y_velocity z_velocity pressure temp theta qt qp qv qc qi
+
+# SOLVER CHOICE
+erf.alpha_T = 0.0
+erf.alpha_C = 1.0
+erf.use_gravity = false
+
+erf.moisture_model  = "SAM"
+
+erf.molec_diff_type = "None"
+erf.les_type        = "Smagorinsky"
+erf.Cs              = 0.1
+
+erf.init_type = "input_sounding"
+erf.init_sounding_ideal = true
+
+erf.add_custom_rhotheta_forcing = true
+erf.add_custom_moisture_forcing = true
+erf.custom_forcing_uses_primitive_vars = false
+
+# Higher values of perturbations lead to instability
+# Instability seems to be coming from BC
+prob.U_0_Pert_Mag = 0.01
+prob.V_0_Pert_Mag = 0.01 
+prob.W_0_Pert_Mag = 0.0
+
+prob.pert_ref_height = 400.0
+prob.T_pert          = 0.1
+prob.qv_pert         = 0.025
+
+prob.advection_heating_rate   = -2.3148E-5
+prob.source_cutoff            = 1500.0
+prob.source_cutoff_transition = 3000.0
+
+prob.advection_moisture_rate   		    = -1.2E-8
+prob.moisture_source_cutoff            	= 300.0
+prob.moisture_source_cutoff_transition 	= 500.0

Exec/DevTests/Bomex/input_sounding

@@ -0,0 +1,7 @@
+1015. 298.7 17.0
+   0.0 298.700 17.00 -8.750 0.0
+ 520.0 298.700 16.30 -8.750 0.0
+ 700.0 299.394 15.25 -8.750 0.0
+1480.0 302.400 10.70 -7.346 0.0
+2000.0 308.200  4.20 -6.410 0.0
+3000.0 311.850  3.00 -4.610 0.0

Exec/DevTests/Bomex/prob.H

@@ -0,0 +1,106 @@
+#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
+
+  //==============================================
+  // USER-DEFINED INPUTS
+  // source terms
+  amrex::Real advection_heating_rate = 0.0;
+  amrex::Real restart_time = 9e9;
+  amrex::Real cutoff = 500.0;
+  amrex::Real cutoff_transition = 50.0;
+
+  amrex::Real advection_moisture_rate = 0.0;
+  amrex::Real moisture_cutoff = 500.0;
+  amrex::Real moisture_cutoff_transition = 50.0;
+  //==============================================
+
+  // 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;
+
+    void update_rhoqt_sources (
+        const amrex::Real& /*time*/,
+        amrex::Vector<amrex::Real>& qsrc,
+        amrex::Gpu::DeviceVector<amrex::Real>& d_qsrc,
+        const amrex::Geometry& geom,
+        std::unique_ptr<amrex::MultiFab>& z_phys_cc) override;
+
+protected:
+    std::string name () override { return "BOMEX"; }
+
+private:
+    ProbParm parms;
+    amrex::Vector<amrex::Real> zlevels;
+};
+
+#endif