Implement new AMReX tagging format (#1243)

The refinement scheme from AMReX-Codes/amrex#1166 is implemented. Rather than using the Fortran tagging namelist, applications may use the inputs file. The scheme looks like:
```
amr.refinement_indicators = dens temp

amr.refine.dens.max_level = 1
amr.refine.dens.value_greater = 2.0
amr.refine.dens.field_name = Density

amr.refine.temp.max_level = 2
amr.refine.temp.value_less = 1.0
amr.refine.temp.field_name = Temp
```
amr.refinement_indicators is a list of user-defined names for refinement schemes. For each defined name, amr.refine.<name> accepts predefined fields describing when to tag. In the current implementation, these are max_level (maximum level to refine to), start_time (when to start tagging), end_time (when to stop tagging), value_greater (value above which we refine), and value_less (value below which to refine), and field_name (name of the string defining the field in the code). If a refinement indicator is added, either value_greater or value_less must be provided. (In the future we will support other refinement schemes such as gradients.)

A wdmerger setup is converted to the new scheme as a test.

CHANGES.md

@@ -1,5 +1,30 @@
 # 20.10
 
+   * A new refinement scheme using the inputs file rather than the Fortran
+     tagging namelist has been added. (#1243) As an example, consider:
+
+     ```
+     amr.refinement_indicators = dens temp
+
+     amr.refine.dens.max_level = 1
+     amr.refine.dens.value_greater = 2.0
+     amr.refine.dens.field_name = Density
+
+     amr.refine.temp.max_level = 2
+     amr.refine.temp.value_less = 1.0
+     amr.refine.temp.field_name = Temp
+     ```
+
+     `amr.refinement_indicators` is a list of user-defined names for refinement
+     schemes. For each defined name, amr.refine.<name> accepts predefined fields
+     describing when to tag. In the current implementation, these are `max_level`
+     (maximum level to refine to), `start_time` (when to start tagging), `end_time`
+     (when to stop tagging), `value_greater` (value above which we refine),
+     `value_less` (value below which to refine), and `field_name` (name of the
+     string defining the field in the code). If a refinement indicator is added,
+     either `value_greater` or `value_less` must be provided. (In the future we
+     will support other refinement schemes such as gradients.)
+
    * Automatic problem parameter configuration is now available to every
      problem by placing a _prob_params file in your problem directory.
      Examples can be found in most of the problems in Castro/Exec, and you

Docs/source/AMR.rst

@@ -179,6 +179,30 @@ problem_tagging_3d.f90 to our work directory and set it up as follows:
 
     end subroutine set_problem_tags
 
+We also provide a mechanism for defining a limited set of refinement
+schemes from the inputs file; for example,
+
+::
+
+   amr.refinement_indicators = dens temp
+
+   amr.refine.dens.max_level = 1
+   amr.refine.dens.value_greater = 2.0
+   amr.refine.dens.field_name = Density
+
+   amr.refine.temp.max_level = 2
+   amr.refine.temp.value_less = 1.0
+   amr.refine.temp.field_name = Temp
+
+``amr.refinement_indicators`` is a list of user-defined names for refinement
+schemes. For each defined name, ``amr.refine.<name>`` accepts predefined fields
+describing when to tag. These are ``max_level`` (maximum level to refine to),
+``start_time`` (when to start tagging), ``end_time`` (when to stop tagging),
+``value_greater`` (value above which we refine), ``value_less`` (value below
+which to refine), and ``field_name`` (name of the string defining the field
+in the code). If a refinement indicator is added, either ``value_greater`` or
+``value_less`` must be provided.
+
 .. _sec:amr_synchronization:
 
 Synchronization Algorithm

Exec/science/wdmerger/tests/wdmerger_3D/inputs_test_wdmerger_3D

@@ -45,6 +45,12 @@ amr.n_cell = 96 96 96                              # Number of cells on the coar
 amr.max_level = 1                                  # Maximum level number allowed
 amr.ref_ratio = 2
 
+amr.refinement_indicators = temperature
+
+amr.refine.temperature.max_level = 4
+amr.refine.temperature.value_greater = 2.e8
+amr.refine.temperature.field_name = Temp
+
 amr.max_grid_size = 32                             # Maximum grid size at each level
 amr.blocking_factor = 16                           # Grid sizes must be a multiple of this
 

Exec/science/wdmerger/tests/wdmerger_3D/probin_test_wdmerger_3D

@@ -28,8 +28,6 @@
 /
 
 &tagging 
-  max_temperr_lev    = 4
-  temperr            = 2.d8
 /
 
 &sponge

Source/driver/Castro.H

@@ -1180,6 +1180,11 @@ public:
     static amrex::Vector<int> upass_map;
     static amrex::Vector<int> qpass_map;
 
+///
+/// Vector storing list of custom error tags.
+///
+    static amrex::Vector<amrex::AMRErrorTag> custom_error_tags;
+
 ///
 /// This MultiFab is on the coarser level.  This is useful for the coarser level
 ///     to mask out the finer level.  We only build this when it is needed.

Source/driver/Castro.cpp

@@ -74,6 +74,8 @@ Vector<std::string> Castro::source_names;
 Vector<int> Castro::upass_map;
 Vector<int> Castro::qpass_map;
 
+Vector<AMRErrorTag> Castro::custom_error_tags;
+
 #ifdef TRUE_SDC
 int          Castro::SDC_NODES;
 Vector<Real> Castro::dt_sdc;
@@ -469,6 +471,54 @@ Castro::read_params ()
 
     compute_new_dt_on_regrid = 1;
 
+    // Read in custom refinement scheme.
+
+    Vector<std::string> refinement_indicators;
+    ppa.queryarr("refinement_indicators", refinement_indicators, 0, ppa.countval("refinement_indicators"));
+
+    for (int i = 0; i < refinement_indicators.size(); ++i)
+    {
+        std::string ref_prefix = "amr.refine." + refinement_indicators[i];
+
+        ParmParse ppr(ref_prefix);
+
+        AMRErrorTagInfo info;
+
+        if (ppr.countval("start_time") > 0) {
+            Real min_time;
+            ppr.get("start_time", min_time);
+            info.SetMinTime(min_time);
+        }
+        if (ppr.countval("end_time") > 0) {
+            Real max_time;
+            ppr.get("end_time", max_time);
+            info.SetMaxTime(max_time);
+        }
+        if (ppr.countval("max_level") > 0) {
+            int max_level;
+            ppr.get("max_level", max_level);
+            info.SetMaxLevel(max_level);
+        }
+
+        if (ppr.countval("value_greater") > 0) {
+            Real value;
+            ppr.get("value_greater", value);
+            std::string field;
+            ppr.get("field_name", field);
+            custom_error_tags.push_back(AMRErrorTag(value, AMRErrorTag::GREATER, field, info));
+        }
+        else if (ppr.countval("value_less") > 0) {
+            Real value;
+            ppr.get("value_less", value);
+            std::string field;
+            ppr.get("field_name", field);
+            custom_error_tags.push_back(AMRErrorTag(value, AMRErrorTag::LESS, field, info));
+        }
+        else {
+            amrex::Abort("Unrecognized refinement indicator for " + refinement_indicators[i]);
+        }
+    }
+
 }
 
 Castro::Castro ()
@@ -3176,6 +3226,16 @@ Castro::errorEst (TagBoxArray& tags,
         apply_tagging_func(tags, ltime, j);
     }
 
+    // Apply each of the custom tagging criteria.
+
+    for (int j = 0; j < custom_error_tags.size(); j++) {
+        std::unique_ptr<MultiFab> mf;
+        if (custom_error_tags[j].Field() != std::string()) {
+            mf = derive(custom_error_tags[j].Field(), time, custom_error_tags[j].NGrow());
+        }
+        custom_error_tags[j](tags, mf.get(), TagBox::CLEAR, TagBox::SET, time, level, geom);
+    }
+
     // Now we'll tag any user-specified zones using the full state array.
 
     apply_problem_tags(tags, ltime);