Add user-defined ("custom") temperature sources (#1407)

* Implement stub for update_rhotheta_sources

* Initialize sources and add calls to update function

* Copy to device in update function

* Pass source pointer to slow RHS update functions

* Add custom source term within the RHS update

* Make a copy of the ABL problem

* Override Problem::update_rhotheta_sources()

* Fix sign error

* Add test problem inputs

* Add missing file

* Add option to have source terms correspond to prim vars

* Document custom forcing

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

@@ -27,4 +27,5 @@ else ()
   add_subdirectory(DevTests/ParticlesOverWoA)
   add_subdirectory(DevTests/MiguelDev)
   add_subdirectory(DevTests/MetGrid)
+  add_subdirectory(DevTests/TemperatureSource)
 endif()

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