Merge branch 'development' into pbl-doc-update

erf-model · Oct 3, 2023 · cb7f1f9 · cb7f1f9
2 parents 4400741 + 0598c89
commit cb7f1f9
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diff --git a/CHANGES b/CHANGES
@@ -0,0 +1,5 @@
+# 23.10
+
+  -- First release since JOSS paper. Too many key ERF PRs to summarize.
+
+  -- AMReX submodule set to 23.10 release hash (388738d)
diff --git a/Docs/sphinx_doc/GettingStarted.rst b/Docs/sphinx_doc/GettingStarted.rst
@@ -24,6 +24,9 @@ type:
 
              git clone --recursive https://github.com/erf-model/ERF.git
 
+.. include:: submodule.rst
+
+
 .. include:: building.rst
 
 

diff --git a/Docs/sphinx_doc/submodule.rst b/Docs/sphinx_doc/submodule.rst
@@ -0,0 +1,22 @@
+.. _Submodule:
+
+Git Submodules
+--------------
+
+When using the submodule to build, it is ideal to properly update and match what is in the repository. Depending on Git version, different commands and options to ensure these match. An example workflow is to run ``git pull`` to get the latest commit on your current branch, and then run ``git submodule update`` to explicitly update the submodule. This should work for all versions of ``git`` which support submodules.
+
+The following example demonstrates a shorter form that combines both commands and requires Git 2.14 or newer:
+
+    .. code:: shell
+              # Replaces your git pull to use both the updated code and the updated submodule
+              git pull --recurse-submodules
+The following example demonstrates setting defaults in the config file for the repository and requires Git 2.15 or newer:
+
+    .. code:: shell
+              # Set this once
+              git config submodule.recurse true
+              # When configured as true, this will use both the updated code and the updated submodule
+              git pull
+              # This option will override any configuration and not update the submodule
+              git pull --no-recurse-submodules
+These example also apply to ``git checkout``. For more details see _`Git Tools Submodules`: https://git-scm.com/book/en/v2/Git-Tools-Submodules
diff --git a/Source/BoundaryConditions/ABLMost.cpp b/Source/BoundaryConditions/ABLMost.cpp
@@ -20,35 +20,35 @@ ABLMost::update_fluxes (int lev,
     if (flux_type == FluxCalcType::MOENG) {
         if (theta_type == ThetaCalcType::HEAT_FLUX) {
             if (rough_type == RoughCalcType::CONSTANT) {
-                surface_flux most_flux(m_ma.get_zref(),surf_temp, surf_temp_flux);
+                surface_flux most_flux(m_ma.get_zref(), surf_temp_flux);
                 compute_fluxes(lev, max_iters, most_flux);
             } else if (rough_type == RoughCalcType::CHARNOCK) {
-                surface_flux_charnock most_flux(m_ma.get_zref(),surf_temp, surf_temp_flux, cnk_a);
+                surface_flux_charnock most_flux(m_ma.get_zref(), surf_temp_flux, cnk_a);
                 compute_fluxes(lev, max_iters, most_flux);
             } else {
-                surface_flux_mod_charnock most_flux(m_ma.get_zref(),surf_temp, surf_temp_flux, depth);
+                surface_flux_mod_charnock most_flux(m_ma.get_zref(), surf_temp_flux, depth);
                 compute_fluxes(lev, max_iters, most_flux);
             }
         } else if (theta_type == ThetaCalcType::SURFACE_TEMPERATURE) {
             if (rough_type == RoughCalcType::CONSTANT) {
-                surface_temp most_flux(m_ma.get_zref(),surf_temp, surf_temp_flux);
+                surface_temp most_flux(m_ma.get_zref(), surf_temp_flux);
                 compute_fluxes(lev, max_iters, most_flux);
             } else if (rough_type == RoughCalcType::CHARNOCK) {
-                surface_temp_charnock most_flux(m_ma.get_zref(),surf_temp, surf_temp_flux, cnk_a);
+                surface_temp_charnock most_flux(m_ma.get_zref(), surf_temp_flux, cnk_a);
                 compute_fluxes(lev, max_iters, most_flux);
             } else {
-                surface_temp_mod_charnock most_flux(m_ma.get_zref(),surf_temp, surf_temp_flux, depth);
+                surface_temp_mod_charnock most_flux(m_ma.get_zref(), surf_temp_flux, depth);
                 compute_fluxes(lev, max_iters, most_flux);
             }
         } else {
             if (rough_type == RoughCalcType::CONSTANT) {
-                adiabatic most_flux(m_ma.get_zref(),surf_temp, surf_temp_flux);
+                adiabatic most_flux(m_ma.get_zref(), surf_temp_flux);
                 compute_fluxes(lev, max_iters, most_flux);
             } else if (rough_type == RoughCalcType::CHARNOCK) {
-                adiabatic_charnock most_flux(m_ma.get_zref(),surf_temp, surf_temp_flux, cnk_a);
+                adiabatic_charnock most_flux(m_ma.get_zref(), surf_temp_flux, cnk_a);
                 compute_fluxes(lev, max_iters, most_flux);
             } else {
-                adiabatic_mod_charnock most_flux(m_ma.get_zref(),surf_temp, surf_temp_flux, depth);
+                adiabatic_mod_charnock most_flux(m_ma.get_zref(), surf_temp_flux, depth);
                 compute_fluxes(lev, max_iters, most_flux);
             }
         } // theta flux

diff --git a/Source/BoundaryConditions/MOSTStress.H b/Source/BoundaryConditions/MOSTStress.H
@@ -15,7 +15,6 @@ public:
     amrex::Real kappa{KAPPA};        ///< von Karman constant
     amrex::Real gravity{CONST_GRAV}; ///< Acceleration due to gravity (m/s^2)
     amrex::Real surf_temp_flux{0.0}; ///< Heat flux
-    amrex::Real surf_temp;           ///< Surface temperature
     amrex::Real Cnk_a{0.0185};       ///< Standard Charnock constant https://doi.org/10.1175/JAMC-D-17-0137.1
     amrex::Real Cnk_b1{1.0/30.0};    ///< Modified Charnock Eq (4) https://doi.org/10.1175/JAMC-D-17-0137.1
     amrex::Real Cnk_b2{1260.0};      ///< Modified Charnock Eq (4) https://doi.org/10.1175/JAMC-D-17-0137.1
@@ -70,11 +69,9 @@ private:
 struct adiabatic
 {
     adiabatic (amrex::Real zref,
-               amrex::Real temp,
                amrex::Real flux)
     {
         mdata.zref = zref;
-        mdata.surf_temp = temp;
         mdata.surf_temp_flux = flux;
     }
 
@@ -110,12 +107,10 @@ private:
 struct adiabatic_charnock
 {
     adiabatic_charnock (amrex::Real zref,
-                        amrex::Real temp,
                         amrex::Real flux,
                         amrex::Real cnk_a)
     {
         mdata.zref = zref;
-        mdata.surf_temp = temp;
         mdata.surf_temp_flux = flux;
         mdata.Cnk_a = cnk_a;
     }
@@ -164,12 +159,10 @@ private:
 struct adiabatic_mod_charnock
 {
     adiabatic_mod_charnock (amrex::Real zref,
-                            amrex::Real temp,
                             amrex::Real flux,
                             amrex::Real depth)
     {
         mdata.zref = zref;
-        mdata.surf_temp = temp;
         mdata.surf_temp_flux = flux;
         mdata.Cnk_d = depth;
         mdata.Cnk_b = mdata.Cnk_b1 * std::log(mdata.Cnk_b2 / mdata.Cnk_d);
@@ -219,11 +212,9 @@ private:
 struct surface_flux
 {
     surface_flux (amrex::Real zref,
-                  amrex::Real temp,
                   amrex::Real flux)
     {
         mdata.zref = zref;
-        mdata.surf_temp = temp;
         mdata.surf_temp_flux = flux;
     }
 
@@ -279,12 +270,10 @@ private:
 struct surface_flux_charnock
 {
     surface_flux_charnock (amrex::Real zref,
-                           amrex::Real temp,
                            amrex::Real flux,
                            amrex::Real cnk_a)
     {
         mdata.zref = zref;
-        mdata.surf_temp = temp;
         mdata.surf_temp_flux = flux;
         mdata.Cnk_a = cnk_a;
     }
@@ -339,17 +328,15 @@ private:
 
 
 /**
- * Surface flux with charnock roughness
+ * Surface flux with modified charnock roughness
  */
 struct surface_flux_mod_charnock
 {
     surface_flux_mod_charnock (amrex::Real zref,
-                               amrex::Real temp,
                                amrex::Real flux,
                                amrex::Real depth)
     {
         mdata.zref = zref;
-        mdata.surf_temp = temp;
         mdata.surf_temp_flux = flux;
         mdata.Cnk_d = depth;
         mdata.Cnk_b = mdata.Cnk_b1 * std::log(mdata.Cnk_b2 / mdata.Cnk_d);
@@ -410,11 +397,9 @@ private:
 struct surface_temp
 {
     surface_temp (amrex::Real zref,
-                  amrex::Real temp,
                   amrex::Real flux)
     {
         mdata.zref = zref;
-        mdata.surf_temp = temp;
         mdata.surf_temp_flux = flux;
     }
 
@@ -467,17 +452,15 @@ private:
 
 
 /**
- * Surface temperature with constant roughness
+ * Surface temperature with charnock roughness
  */
 struct surface_temp_charnock
 {
     surface_temp_charnock (amrex::Real zref,
-                           amrex::Real temp,
                            amrex::Real flux,
                            amrex::Real cnk_a)
     {
         mdata.zref = zref;
-        mdata.surf_temp = temp;
         mdata.surf_temp_flux = flux;
         mdata.Cnk_a = cnk_a;
     }
@@ -534,17 +517,15 @@ private:
 
 
 /**
- * Surface temperature with constant roughness
+ * Surface temperature with modified charnock roughness
  */
 struct surface_temp_mod_charnock
 {
     surface_temp_mod_charnock (amrex::Real zref,
-                               amrex::Real temp,
                                amrex::Real flux,
                                amrex::Real depth)
     {
         mdata.zref = zref;
-        mdata.surf_temp = temp;
         mdata.surf_temp_flux = flux;
         mdata.Cnk_d = depth;
         mdata.Cnk_b = mdata.Cnk_b1 * std::log(mdata.Cnk_b2 / mdata.Cnk_d);
@@ -606,7 +587,7 @@ private:
  */
 struct moeng_flux
 {
-    moeng_flux(int l_zlo,
+    moeng_flux (int l_zlo,
                amrex::Real l_dz)
       :  zlo(l_zlo), dz(l_dz) {}
 
@@ -809,7 +790,7 @@ private:
  */
 struct donelan_flux
 {
-    donelan_flux(int l_zlo,
+    donelan_flux (int l_zlo,
                amrex::Real l_dz)
       :  zlo(l_zlo), dz(l_dz) {}
 

diff --git a/Source/ERF_Constants.H b/Source/ERF_Constants.H
@@ -1,5 +1,5 @@
-#ifndef _CONSTANTS_H_
-#define _CONSTANTS_H_
+#ifndef ERF_CONSTANTS_H_
+#define ERF_CONSTANTS_H_
 
 #include <AMReX_REAL.H>
 

diff --git a/Source/IndexDefines.H b/Source/IndexDefines.H
@@ -35,8 +35,8 @@
   #define PrimQt_comp    (RhoQt_comp-1)
   #define PrimQp_comp    (RhoQp_comp-1)
 #elif defined(ERF_USE_WARM_NO_PRECIP)
-  #define PrimQv_comp    RhoQv_comp-1
-  #define PrimQc_comp    RhoQc_comp-1
+  #define PrimQv_comp    (RhoQv_comp-1)
+  #define PrimQc_comp    (RhoQc_comp-1)
 #endif
 #define NUM_PRIM         (NVAR-1)
 

diff --git a/Source/Microphysics/Cloud.cpp b/Source/Microphysics/Cloud.cpp
@@ -8,7 +8,7 @@ using namespace amrex;
 /**
  * Compute Cloud-related Microphysics quantities.
  */
-void Microphysics::Cloud() {
+void Microphysics::Cloud () {
 
   constexpr Real an   = 1.0/(tbgmax-tbgmin);
   constexpr Real bn   = tbgmin*an;

diff --git a/Source/Microphysics/Diagnose.cpp b/Source/Microphysics/Diagnose.cpp
@@ -4,7 +4,7 @@
  * Computes diagnostic quantities like cloud ice/liquid and precipitation ice/liquid
  * from the existing Microphysics variables.
  */
-void Microphysics::Diagnose() {
+void Microphysics::Diagnose () {
 
   auto qt   = mic_fab_vars[MicVar::qt];
   auto qp   = mic_fab_vars[MicVar::qp];
@@ -44,7 +44,7 @@ void Microphysics::Diagnose() {
 /**
  * Wrapper for the PrecipFall, Cloud, Precipitation, and Diagnostics routines.
  */
-void Microphysics::Proc() {
+void Microphysics::Proc () {
 
     MicroPrecipFall();
 

diff --git a/Source/Microphysics/IceFall.cpp b/Source/Microphysics/IceFall.cpp
@@ -8,7 +8,7 @@ using namespace amrex;
 /**
  * Computes contributions to Microphysics and thermodynamic variables from falling cloud ice in each column.
  */
-void Microphysics::IceFall() {
+void Microphysics::IceFall () {
 
   Real dz  = m_geom.CellSize(2);
   Real dtn = dt;

diff --git a/Source/Microphysics/Init.cpp b/Source/Microphysics/Init.cpp
@@ -19,10 +19,10 @@ using namespace amrex;
  * @param[in] geom Geometry associated with these MultiFabs and grids
  * @param[in] dt_advance Timestep for the advance
  */
-void Microphysics::Init(const MultiFab& cons_in, MultiFab& qmoist,
-                        const BoxArray& grids_to_evolve,
-                        const Geometry& geom,
-                        const Real& dt_advance)
+void Microphysics::Init (const MultiFab& cons_in, MultiFab& qmoist,
+                         const BoxArray& grids_to_evolve,
+                         const Geometry& geom,
+                         const Real& dt_advance)
  {
   m_geom = geom;
   m_gtoe = grids_to_evolve;

diff --git a/Source/Microphysics/Microphysics.H b/Source/Microphysics/Microphysics.H
@@ -55,10 +55,10 @@ class Microphysics {
 
  public:
   // constructor
-  Microphysics() {}
+  Microphysics () {}
 
   // Set up for first time
-  void define(SolverChoice& sc)
+  void define (SolverChoice& sc)
   {
       docloud = sc.do_cloud;
       doprecip = sc.do_precip;
@@ -70,39 +70,39 @@ class Microphysics {
   }
 
   // destructor
-  ~Microphysics() = default;
+  ~Microphysics () = default;
 
   // cloud physics
-  void Cloud();
+  void Cloud ();
 
   // ice physics
-  void IceFall();
+  void IceFall ();
 
   // precip
-  void Precip();
+  void Precip ();
 
   // precip fall
-  void PrecipFall(int hydro_type);
+  void PrecipFall (int hydro_type);
 
   // micro interface for precip fall
-  void MicroPrecipFall();
+  void MicroPrecipFall ();
 
   // init
-  void Init(const amrex::MultiFab& cons_in,
-            amrex::MultiFab& qmoist,
-            const amrex::BoxArray& grids_to_evolve,
-            const amrex::Geometry& geom,
-            const amrex::Real& dt_advance);
+  void Init (const amrex::MultiFab& cons_in,
+             amrex::MultiFab& qmoist,
+             const amrex::BoxArray& grids_to_evolve,
+             const amrex::Geometry& geom,
+             const amrex::Real& dt_advance);
 
   // update ERF variables
-  void Update(amrex::MultiFab& cons_in,
-              amrex::MultiFab& qmoist);
+  void Update (amrex::MultiFab& cons_in,
+               amrex::MultiFab& qmoist);
 
   // diagnose
-  void Diagnose();
+  void Diagnose ();
 
   // process microphysics
-  void Proc();
+  void Proc ();
 
  private:
   // geometry