update docs (#1162)

* update docs * clean up code and add more variables to tag on * update amrex version
erf-model · Jul 16, 2023 · 7891c17 · 7891c17
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diff --git a/Docs/sphinx_doc/Inputs.rst b/Docs/sphinx_doc/Inputs.rst
@@ -112,8 +112,9 @@ List of Parameters
 |                           | subsequent      |                 |             |
 |                           | levels          |                 |             |
 +---------------------------+-----------------+-----------------+-------------+
-| **amr.regrid_int**        | how often to    | Integer > 0     | must be set |
-|                           | regrid          |                 |             |
+| **amr.regrid_int**        | how often to    | Integer > 0     | -1          |
+|                           | regrid          | (if negative,   |             |
+|                           |                 | no regridding)  |             |
 +---------------------------+-----------------+-----------------+-------------+
 | **amr.regrid_on_restart** | should we       | 0 or 1          | 0           |
 |                           | regrid          |                 |             |

diff --git a/Docs/sphinx_doc/MeshRefinement.rst b/Docs/sphinx_doc/MeshRefinement.rst
@@ -34,13 +34,13 @@ one level of refinement, where prob_lo_z and prob_hi_z are the vertical extents
           amr.max_level = 1
           amr.ref_ratio = 2
 
-          amr.refinement_indicators = box1 box2
+          erf.refinement_indicators = box1 box2
 
-          amr.box1.in_box_lo = .15 .25
-          amr.box1.in_box_hi = .35 .45
+          erf.box1.in_box_lo = .15 .25
+          erf.box1.in_box_hi = .35 .45
 
-          amr.box2.in_box_lo = .65 .75
-          amr.box2.in_box_hi = .85 .95
+          erf.box2.in_box_lo = .65 .75
+          erf.box2.in_box_hi = .85 .95
 
 In the example below, we refine the region ((.15,.25,prob_lo_z)(.35,.45,prob_hi_z))
 by two levels of factor 3 refinement. In this case, the refined region at level 1 will
@@ -51,10 +51,10 @@ be sufficient to enclose the refined region at level 2.
           amr.max_level = 2
           amr.ref_ratio = 3 3
 
-          amr.refinement_indicators = box1
+          erf.refinement_indicators = box1
 
-          amr.box1.in_box_lo = .15 .25
-          amr.box1.in_box_hi = .35 .45
+          erf.box1.in_box_lo = .15 .25
+          erf.box1.in_box_hi = .35 .45
 
 And in this final example, the region ((.15,.25,prob_lo_z)(.35,.45,prob_hi_z))
 will be refined by two levels of factor 3, but the larger region, ((.05,.05,prob_lo_z)(.75,.75,prob_hi_z))
@@ -65,14 +65,14 @@ will be refined by a single factor 3 refinement.
           amr.max_level = 2
           amr.ref_ratio = 3 3
 
-          amr.refinement_indicators = box1 box2
+          erf.refinement_indicators = box1 box2
 
-          amr.box1.in_box_lo = .15 .25
-          amr.box1.in_box_hi = .35 .45
+          erf.box1.in_box_lo = .15 .25
+          erf.box1.in_box_hi = .35 .45
 
-          amr.box2.in_box_lo = .05 .05
-          amr.box2.in_box_hi = .75 .75
-          amr.box2.max_level = 1
+          erf.box2.in_box_lo = .05 .05
+          erf.box2.in_box_hi = .75 .75
+          erf.box2.max_level = 1
 
 
 Dynamic Mesh Refinement
@@ -102,23 +102,23 @@ computed by dividing the variable named rhotheta by the variable named density.
 
 ::
 
-          amr.refinement_indicators = hi_rho lo_theta advdiff
+          erf.refinement_indicators = hi_rho lo_theta advdiff
 
-          amr.hi_rho.max_level = 3
-          amr.hi_rho.value_greater = 1. 2.
-          amr.hi_rho.field_name = density
+          erf.hi_rho.max_level = 3
+          erf.hi_rho.value_greater = 1. 2.
+          erf.hi_rho.field_name = density
 
-          amr.lo_theta.max_level = 1
-          amr.lo_theta.value_less = 300
-          amr.lo_theta.field_name = rhotheta
-          amr.lo_theta.in_box_lo = .25 .25 .25
-          amr.lo_theta.in_box_hi = .75 .75 .75
+          erf.lo_theta.max_level = 1
+          erf.lo_theta.value_less = 300
+          erf.lo_theta.field_name = rhotheta
+          erf.lo_theta.in_box_lo = .25 .25 .25
+          erf.lo_theta.in_box_hi = .75 .75 .75
 
-          amr.advdiff.max_level = 2
-          amr.advdiff.adjacent_difference_greater = 0.01
-          amr.advdiff.field_name = rhoadv_0
-          amr.advdiff.start_time = 0.001
-          amr.advdiff.end_time = 0.002
+          erf.advdiff.max_level = 2
+          erf.advdiff.adjacent_difference_greater = 0.01
+          erf.advdiff.field_name = rhoadv_0
+          erf.advdiff.start_time = 0.001
+          erf.advdiff.end_time = 0.002
 
 Coupling Types
 --------------

diff --git a/Exec/inputs.mesh_refinement b/Exec/inputs.mesh_refinement
@@ -9,6 +9,6 @@ amr.regrid_int      = 2 2 2 2     # how often to regrid
 amr.n_error_buf     = 2 2 2 2     # number of buffer cells in error est
 
 # How to specify a region for static refinement
-amr.refinement_indicators = box1
-amr.box1.in_box_lo = .15 .25
-amr.box1.in_box_hi = .55 .65
+erf.refinement_indicators = box1
+erf.box1.in_box_lo = .15 .25
+erf.box1.in_box_hi = .55 .65
diff --git a/Source/ERF.H b/Source/ERF.H
@@ -203,8 +203,10 @@ public:
                          amrex::Real dt, amrex::Real time,
                          amrex::InterpFaceRegister* ifr);
 
+#if defined(ERF_USE_MOISTURE)
     void advance_microphysics (int lev, amrex::MultiFab& cons_in,
                                const amrex::Real& dt_advance);
+#endif
 
     amrex::MultiFab& build_fine_mask (int lev);
 

diff --git a/Source/ERF_Tagging.cpp b/Source/ERF_Tagging.cpp
@@ -20,17 +20,32 @@ ERF::ErrorEst (int level, TagBoxArray& tags, Real time, int /*ngrow*/)
     {
         std::unique_ptr<MultiFab> mf;
 
-        // This allows dynamic refinement based on the value of the scalar
-        if (ref_tags[j].Field() == "scalar") {
+        // This allows dynamic refinement based on the value of the density
+        if (ref_tags[j].Field() == "density")
+        {
+            mf = std::make_unique<MultiFab>(grids[level], dmap[level], 1, 0);
+            MultiFab::Copy(*mf,vars_new[level][Vars::cons],Rho_comp,0,1,0);
+
+        // This allows dynamic refinement based on the value of the scalar/pressure/theta
+        } else if ( (ref_tags[j].Field() == "scalar"  ) ||
+                    (ref_tags[j].Field() == "pressure") ||
+                    (ref_tags[j].Field() == "theta"   ) )
+        {
             mf = std::make_unique<MultiFab>(grids[level], dmap[level], 1, 0);
             for (MFIter mfi(*mf, TilingIfNotGPU()); mfi.isValid(); ++mfi)
             {
                 const Box& bx = mfi.tilebox();
                 auto& dfab = (*mf)[mfi];
                 auto& sfab = vars_new[level][Vars::cons][mfi];
-                derived::erf_derscalar(bx, dfab, 0, 1, sfab, Geom(level), time, nullptr, level);
+                if (ref_tags[j].Field() == "scalar") {
+                    derived::erf_derscalar(bx, dfab, 0, 1, sfab, Geom(level), time, nullptr, level);
+                } else if (ref_tags[j].Field() == "pressure") {
+                    derived::erf_derpres(bx, dfab, 0, 1, sfab, Geom(level), time, nullptr, level);
+                } else if (ref_tags[j].Field() == "theta") {
+                    derived::erf_dertheta(bx, dfab, 0, 1, sfab, Geom(level), time, nullptr, level);
+                }
             } // mfi
-        } // scalar
+        }
 
         // This is sufficient for static refinement (where we don't need mf filled first)
         ref_tags[j](tags,mf.get(),clearval,tagval,time,level,geom[level]);

diff --git a/Source/TimeIntegration/ERF_advance_microphysics.cpp b/Source/TimeIntegration/ERF_advance_microphysics.cpp
@@ -2,11 +2,11 @@
 
 using namespace amrex;
 
+#if defined(ERF_USE_MOISTURE)
 void ERF::advance_microphysics(int lev,
                                MultiFab& cons,
                                const Real& dt_advance)
 {
-#if defined(ERF_USE_MOISTURE)
     micro.Init(cons, qmoist[lev],
                grids_to_evolve[lev],
                Geom(lev),
@@ -19,5 +19,5 @@ void ERF::advance_microphysics(int lev,
     micro.MicroPrecipFall();
 
     micro.Update(cons, qmoist[lev]);
-#endif
 }
+#endif
diff --git a/Source/TimeIntegration/ERF_slow_rhs_post.cpp b/Source/TimeIntegration/ERF_slow_rhs_post.cpp
@@ -18,7 +18,6 @@ using namespace amrex;
  *
  * @param[in]  level level of resolution
  * @param[in]  dt    slow time step
- * @param[in]  grids_to_evolve the region in the domain excluding the relaxation and specified zones
  * @param[out]  S_rhs RHS computed here
  * @param[in]  S_old solution at start of time step
  * @param[in]  S_new solution at end of current RK stage
@@ -48,7 +47,6 @@ using namespace amrex;
 
 void erf_slow_rhs_post (int /*level*/,
                         Real dt,
-                        BoxArray& grids_to_evolve,
                         Vector<MultiFab>& S_rhs,
                         Vector<MultiFab>& S_old,
                         Vector<MultiFab>& S_new,

diff --git a/Source/TimeIntegration/TI_headers.H b/Source/TimeIntegration/TI_headers.H
@@ -65,7 +65,6 @@ void erf_slow_rhs_pre (int level, int nrk,
  */
 void erf_slow_rhs_post (int level,
                        amrex::Real dt,
-                       amrex::BoxArray& grids_to_evolve,
                        amrex::Vector<amrex::MultiFab>& S_rhs,
                        amrex::Vector<amrex::MultiFab>& S_old,
                        amrex::Vector<amrex::MultiFab>& S_new,

diff --git a/Source/TimeIntegration/TI_slow_rhs_fun.H b/Source/TimeIntegration/TI_slow_rhs_fun.H
@@ -267,7 +267,7 @@
 
         // Moving terrain
         if ( solverChoice.use_terrain && (solverChoice.terrain_type == 1) ) {
-            erf_slow_rhs_post(level, slow_dt, grids_to_evolve[level],
+            erf_slow_rhs_post(level, slow_dt,
                               S_rhs, S_old, S_new, S_data, S_prim, S_scratch,
                               xvel_new, yvel_new, zvel_new,
                               source, SmnSmn, eddyDiffs,
@@ -282,7 +282,7 @@
 #endif
                               incompressible);
         } else {
-            erf_slow_rhs_post(level, slow_dt, grids_to_evolve[level],
+            erf_slow_rhs_post(level, slow_dt,
                               S_rhs, S_old, S_new, S_data, S_prim, S_scratch,
                               xvel_new, yvel_new, zvel_new,
                               source, SmnSmn, eddyDiffs,

diff --git a/Submodules/AMReX b/Submodules/AMReX