Refactor initialization routines, problem definition (erf-model#1232)

* Minor cleanup + update comments * Update .gitignore * Additional clarifying comments and minor cleanup * Make sure base state is set prior to calling init_custom * Move common includes into prob_common.H * Add common includes for erf_init_dens_hse and erf_init_rayleigh * Restore final call to initHSE in order to pass reg tests for now * Implement ProblemBase class, refactor all problems - ProblemBase provides stubs for erf_init_dens_hse, init_custom_prob, init_custom_terrain, and erf_init_rayleigh - Each problem in Exec implements a derived class, overriding these functions - The ERF constructor instantiates the derived class * Add init_isentropic_hse[_terrain] functions to ProblemBase - add new prob_common.cpp source file - cleanup prob_common.H - cleanup all prob.cpp that had copies of these functions * Rearrange function declarations for consistency * Add ProbParmDefaults struct * Implement additional recipes for erf_init_dens_hse for variable density, with and without terrain * Add T_0 to the ProbParmDefaults; make consistent the usage of T_0 (ref potential temperature) * Implement init_custom(lev) which calls new prob->init_state() init_state() will set the background field to a uniform field based on parms.rho_0 and parms.T_0 and should only be called in the absence of any other initialization type -- NOTE: this **will break the r-tests** because the prob.cpp source files have not been updated to guarantee that the background field is not double-counted! * Rename init_custom_prob() --> init_custom_pert() for clarity * Implement init_type="uniform" for backwards compatibility * Add missing source/header files * Implement default initialization based on HSE * Whitespace * Remove redundant initHSE call verified that there is no change in rtests * Add virtual destructor and comment unused vars. * Update DensityCurrent* gold data * Update MovingTerrain* gold data * Update TaylorGreen* gold data * Fixes for GPU * Cleanup prob source files * Move ProblemBase member functions to HSE_utils namespace because member functions (e.g., init_isentropic_hse) cannot be called from inside a device lambda --------- Co-authored-by: Aaron M. Lattanzi <[email protected]> Co-authored-by: AMLattanzi <[email protected]> Co-authored-by: Ann Almgren <[email protected]>
ewquon · Sep 8, 2023 · 049f84f · 049f84f
1 parent 6f05140
commit 049f84f
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diff --git a/.gitignore b/.gitignore
@@ -8,6 +8,7 @@
 
 # Log files
 datlog
+log.*
 
 # Ignore everything in Build except the cmake script
 /Build/*
@@ -21,6 +22,9 @@ datlog
 !/Build/cmake_with_poisson.sh
 !/Build/cmake_with_warm_no_precip.sh
 
+# Temporary files
+*/Testing/Temporary
+.*.swp
 
 /Exec/WORK/*
 ic.txt
@@ -35,3 +39,4 @@ cmake_build*
 cmake*ser*
 cmake*par*
 .idea
+*.ipynb
diff --git a/CMake/BuildERFExe.cmake b/CMake/BuildERFExe.cmake
@@ -128,9 +128,11 @@ function(build_erf_lib erf_lib_name)
        ${SRC_DIR}/Diffusion/NumericalDiffusion.cpp
        ${SRC_DIR}/Diffusion/PBLModels.cpp
        ${SRC_DIR}/Initialization/ERF_init_custom.cpp
+       ${SRC_DIR}/Initialization/ERF_init_from_hse.cpp
        ${SRC_DIR}/Initialization/ERF_init_from_input_sounding.cpp
        ${SRC_DIR}/Initialization/ERF_init_from_wrfinput.cpp
        ${SRC_DIR}/Initialization/ERF_init_from_metgrid.cpp
+       ${SRC_DIR}/Initialization/ERF_init_uniform.cpp
        ${SRC_DIR}/Initialization/ERF_init1d.cpp
        ${SRC_DIR}/IO/Checkpoint.cpp
        ${SRC_DIR}/IO/ERF_ReadBndryPlanes.cpp

diff --git a/Exec/ABL/inputs.read b/Exec/ABL/inputs.read
@@ -53,6 +53,8 @@ erf.molec_diff_type = "None"
 erf.les_type        = "Smagorinsky"
 erf.Cs              = 0.1
 
+erf.init_type = "uniform"
+
 # PROBLEM PARAMETERS
 prob.rho_0 = 1.0
 prob.A_0 = 1.0

diff --git a/Exec/ABL/inputs.write b/Exec/ABL/inputs.write
@@ -46,6 +46,8 @@ erf.molec_diff_type = "None"
 erf.les_type        = "Smagorinsky"
 erf.Cs              = 0.1
 
+erf.init_type = "uniform"
+
 # PROBLEM PARAMETERS
 prob.rho_0 = 1.0
 prob.A_0 = 1.0

diff --git a/Exec/ABL/inputs_deardorff b/Exec/ABL/inputs_deardorff
@@ -45,6 +45,8 @@ erf.Ck       = 0.1
 erf.sigma_k  = 1.0
 erf.Ce       = 0.1
 
+erf.init_type = "uniform"
+
 # PROBLEM PARAMETERS
 prob.rho_0 = 1.0
 prob.A_0 = 1.0

diff --git a/Exec/ABL/inputs_deardorff_msf b/Exec/ABL/inputs_deardorff_msf
@@ -50,6 +50,8 @@ erf.Ck       = 0.1
 erf.sigma_k  = 1.0
 erf.Ce       = 0.1
 
+erf.init_type = "uniform"
+
 # PROBLEM PARAMETERS
 prob.rho_0 = 1.0
 prob.A_0 = 1.0

diff --git a/Exec/ABL/inputs_deardorff_no_msf b/Exec/ABL/inputs_deardorff_no_msf
@@ -49,6 +49,8 @@ erf.Ck       = 0.1
 erf.sigma_k  = 1.0
 erf.Ce       = 0.1
 
+erf.init_type = "uniform"
+
 # PROBLEM PARAMETERS
 prob.rho_0 = 1.0
 prob.A_0 = 1.0

diff --git a/Exec/ABL/inputs_ml_most b/Exec/ABL/inputs_ml_most
@@ -46,6 +46,8 @@ erf.use_gravity = false
 erf.les_type = "Smagorinsky"
 erf.Cs       = 0.1
 
+erf.init_type = "uniform"
+
 # PROBLEM PARAMETERS
 prob.rho_0 = 1.0
 prob.A_0   = 1.0

diff --git a/Exec/ABL/inputs_most b/Exec/ABL/inputs_most
@@ -47,6 +47,8 @@ erf.molec_diff_type = "None"
 erf.les_type        = "Smagorinsky"
 erf.Cs              = 0.1
 
+erf.init_type = "uniform"
+
 # PROBLEM PARAMETERS
 prob.rho_0 = 1.0
 prob.A_0 = 1.0

diff --git a/Exec/ABL/inputs_most_msf b/Exec/ABL/inputs_most_msf
@@ -60,6 +60,8 @@ erf.dycore_vert_adv_type     = "Upwind_3rd"
 erf.dryscal_horiz_adv_type   = "Upwind_3rd"
 erf.dryscal_vert_adv_type    = "Upwind_3rd"
 
+erf.init_type = "uniform"
+
 # PROBLEM PARAMETERS
 prob.rho_0 = 1.0
 prob.A_0 = 1.0

diff --git a/Exec/ABL/inputs_most_no_msf b/Exec/ABL/inputs_most_no_msf
@@ -58,6 +58,8 @@ erf.dycore_vert_adv_type     = "Upwind_3rd"
 erf.dryscal_horiz_adv_type   = "Upwind_3rd"
 erf.dryscal_vert_adv_type    = "Upwind_3rd"
 
+erf.init_type = "uniform"
+
 # PROBLEM PARAMETERS
 prob.rho_0 = 1.0
 prob.A_0 = 1.0

diff --git a/Exec/ABL/inputs_most_test b/Exec/ABL/inputs_most_test
@@ -61,6 +61,8 @@ erf.les_type = "Smagorinsky"
 #erf.pbl_type = "MYNN2.5"
 erf.Cs       = 0.1
 
+erf.init_type = "uniform"
+
 # PROBLEM PARAMETERS
 prob.rho_0 = 1.0
 prob.A_0   = 1.0

diff --git a/Exec/ABL/inputs_numdiff b/Exec/ABL/inputs_numdiff
@@ -48,6 +48,8 @@ erf.Ce       = 0.1
 erf.use_NumDiff  = true
 erf.NumDiffCoeff = 0.5
 
+erf.init_type = "uniform"
+
 # PROBLEM PARAMETERS
 prob.rho_0 = 1.0
 prob.A_0   = 1.0

diff --git a/Exec/ABL/inputs_omp b/Exec/ABL/inputs_omp
@@ -51,6 +51,8 @@ erf.Ck       = 0.1
 erf.sigma_k  = 1.0
 erf.Ce       = 0.1
 
+erf.init_type = "uniform"
+
 # PROBLEM PARAMETERS
 prob.rho_0 = 1.0
 prob.A_0 = 1.0

diff --git a/Exec/ABL/inputs_sample b/Exec/ABL/inputs_sample
@@ -51,6 +51,8 @@ erf.molec_diff_type = "None"
 erf.les_type        = "Smagorinsky"
 erf.Cs              = 0.1
 
+erf.init_type = "uniform"
+
 # PROBLEM PARAMETERS
 prob.rho_0 = 1.0
 prob.A_0 = 1.0

diff --git a/Exec/ABL/inputs_smagorinsky b/Exec/ABL/inputs_smagorinsky
@@ -43,6 +43,8 @@ erf.molec_diff_type = "None"
 erf.les_type        = "Smagorinsky"
 erf.Cs              = 0.1
 
+erf.init_type = "uniform"
+
 # PROBLEM PARAMETERS
 prob.rho_0 = 1.0
 prob.A_0 = 1.0

diff --git a/Exec/ABL/inputs_smagorinsky_msf b/Exec/ABL/inputs_smagorinsky_msf
@@ -47,6 +47,8 @@ erf.dynamicViscosity = 1.0
 erf.les_type        = "Smagorinsky"
 erf.Cs              = 0.1
 
+erf.init_type = "uniform"
+
 # PROBLEM PARAMETERS
 prob.rho_0 = 1.0
 prob.A_0 = 1.0

diff --git a/Exec/ABL/inputs_smagorinsky_no_msf b/Exec/ABL/inputs_smagorinsky_no_msf
@@ -46,6 +46,8 @@ erf.dynamicViscosity = 1.0
 erf.les_type        = "Smagorinsky"
 erf.Cs              = 0.1
 
+erf.init_type = "uniform"
+
 # PROBLEM PARAMETERS
 prob.rho_0 = 1.0
 prob.A_0 = 1.0

diff --git a/Exec/ABL/prob.H b/Exec/ABL/prob.H
@@ -1,13 +1,17 @@
 #ifndef _PROB_H_
 #define _PROB_H_
 
-#include <AMReX_REAL.H>
+#include <string>
 
-struct ProbParm {
-  amrex::Real rho_0   = 0.0;
-  amrex::Real Theta_0 = 0.0;
-  amrex::Real A_0     = 1.0;
-  amrex::Real QKE_0   = 0.1;
+#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;
@@ -37,6 +41,51 @@ struct ProbParm {
   amrex::Real vfac;
 }; // namespace ProbParm
 
-extern ProbParm parms;
+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,
+#if defined(ERF_USE_MOISTURE)
+        amrex::Array4<amrex::Real      > const& qv,
+        amrex::Array4<amrex::Real      > const& qc,
+        amrex::Array4<amrex::Real      > const& qi,
+#elif defined(ERF_USE_WARM_NO_PRECIP)
+        amrex::Array4<amrex::Real      > const& qv,
+        amrex::Array4<amrex::Real      > const& qc,
+#endif
+        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 init_custom_terrain (
+        const amrex::Geometry& geom,
+        amrex::MultiFab& z_phys_nd,
+        const amrex::Real& time) override;
+
+protected:
+    std::string name() override { return "ABL"; }
+
+private:
+    ProbParm parms;
+};
 
 #endif