Add option to write a smallplotfile as in AmrLevel. A user defined

Docs/sphinx_documentation/source/InputsPlotFiles.rst

@@ -26,11 +26,19 @@ as whether the EB geometry should be written out.
 +---------------------+-----------------------------------------------------------------------+-------------+-----------+
 
 The following inputs must be preceded by "amr" and control what variables will be written in plotfiles.
+By default, incflo plotfiles contain the velocity, pressure gradient, density, tracer, velocity magnitude, vorticity,
+and if using EB, volume fraction.
 
 +---------------------+-----------------------------------------------------------------------+-------------+-----------+
 |                     | Description                                                           |   Type      | Default   |
 +=====================+=======================================================================+=============+===========+
-| plt_ccse_regtest    | Save all variables to plot file (overrides all other IO flags)        |    Int      | 0         |
+| plotVariables       | Space separated list of variable names. **Takes precedent over all**  |  String     | see above |
+|                     | **other plotfile options**. Plotfile will contain only this list,     |             |           |
+|                     | e.g. "amr.plotVariables = velx density" will result in plotfiles      |             |           |
+|                     | containing only the x-component of the velocity and the density.      |             |           |
++---------------------+-----------------------------------------------------------------------+-------------+-----------+
+| plt_ccse_regtest    | Collection of variables for regression test plotfiles (will get       |    Int      | 0         |
+|                     | overwritten by plotVariables or plt_* flags)                          |             |           |
 +---------------------+-----------------------------------------------------------------------+-------------+-----------+
 | plt_velx            | Save x-velocity to plot file                                          |    Int      | 1         |
 +---------------------+-----------------------------------------------------------------------+-------------+-----------+
@@ -62,3 +70,24 @@ The following inputs must be preceded by "amr" and control what variables will b
 +---------------------+-----------------------------------------------------------------------+-------------+-----------+
 | plt_vfrac           | Save EB volume fraction to plot file                                  |    Int      | 1         |
 +---------------------+-----------------------------------------------------------------------+-------------+-----------+
+
+incflo provides the option to write a user defined selection of variables to a "smallplotfile" at an interval that is
+different than that of the full plotfile.
+The following inputs must be preceded by "amr" and control frequency and naming of smallplotfile generation.
+
++--------------------------+-----------------------------------------------------------------------+-------------+-----------+
+|                          | Description                                                           |   Type      | Default   |
++==========================+=======================================================================+=============+===========+
+| smallplot_int            | Frequency of smallplotfile output;                                    |    Int      | -1        |
+|                          | if -1 then no plotfiles will be written at this frequency             |             |           |
+| smallplot_per_approx     | Time period of smallplotfile output (approximate); does not modify dt |    Real     | -1        |
+|                          | if -1 then no smallplotfiles will be written at this frequency        |             |           |
++--------------------------+-----------------------------------------------------------------------+-------------+-----------+
++--------------------------+-----------------------------------------------------------------------+-------------+-----------+
+| smallplotfile_on_restart | Write smallplotfile when restarting (only used if smallplot_int>0)    |    Bool     | False     |
++--------------------------+-----------------------------------------------------------------------+-------------+-----------+
+| smallplot_file           | Prefix to use for smallplotfile output                                |  String     | smallplt  |
++--------------------------+-----------------------------------------------------------------------+-------------+-----------+
++--------------------------+-----------------------------------------------------------------------+-------------+-----------+
+| smallplotVariables       | Space separated list of variable names.                               |  String     | none      |
++--------------------------+-----------------------------------------------------------------------+-------------+-----------+

src/incflo.H

@@ -569,33 +569,29 @@ private:
     amrex::Vector<amrex::Real> tag_region_lo;
     amrex::Vector<amrex::Real> tag_region_hi;
 
-    // Flags for saving fluid data in plot files
-    int m_plt_velx        = 1;
-    int m_plt_vely        = 1;
-    int m_plt_velz        = 1;
-    int m_plt_gpx         = 1;
-    int m_plt_gpy         = 1;
-    int m_plt_gpz         = 1;
-    int m_plt_rho         = 1;
-    int m_plt_tracer      = 1;
-    int m_plt_p           = 0;
-    int m_plt_macphi      = 0;
-    int m_plt_eta         = 0;
-    int m_plt_magvel      = 1;
-    int m_plt_vort        = 1;
-    int m_plt_forcing     = 0;
-    int m_plt_strainrate  = 0;
-    int m_plt_divu        = 0;
-    int m_plt_vfrac       = 1;
-    int m_plt_error_u     = 0;
-    int m_plt_error_v     = 0;
-    int m_plt_error_w     = 0;
-    int m_plt_error_p     = 0;
-    int m_plt_error_mac_p = 0;
+    // Specify fluid data in plot files
+    amrex::Vector<std::string> m_plotVars =
+#if (AMREX_SPACEDIM == 3)
+        {"velx","vely","velz","gpx","gpy","gpz","density","tracer","magvel","vort","vfrac"};
+#else
+        {"velx","vely","gpx","gpy","density","tracer","magvel","vort","vfrac"};
+#endif
 
-#ifdef INCFLO_USE_PARTICLES
-    int m_plt_particle_count = 0;
+    // smallplotfile allows users to output certain variables at a different frequency.
+    // Off by default.
+    int m_smallplot_int = -1;
+    amrex::Real m_smallplot_per_approx = -1.0;
+    // No smallplot_per_exact because it requires changing the timestep
+    int m_last_smallplt = -1;
+    bool m_smallplotfile_on_restart = false;
+
+    std::string m_smallplot_file{"smallplt"};
 
+    // Require user to choose smallplotfile variables
+    amrex::Vector<std::string> m_smallplotVars;
+
+
+#ifdef INCFLO_USE_PARTICLES
     // Particle container with all particle species
     ParticleData particleData;
 
@@ -887,7 +883,9 @@ private:
     void copy_from_old_to_new_tracer   (int lev, amrex::IntVect const& ng = amrex::IntVect{0});
 
     void Advance ();
-    bool writeNow ();
+    bool writeNow () { return writeNow(m_plot_int, m_plot_per_approx, m_plot_per_exact); }
+    bool writeNow (int a_plot_int, amrex::Real a_plot_per_approx,
+                   amrex::Real a_plot_per_exact);
 
     ///////////////////////////////////////////////////////////////////////////
     //
@@ -963,6 +961,8 @@ private:
     void WriteJobInfo (const std::string& path) const;
     void WriteCheckPointFile () const;
     void WritePlotFile ();
+    void WritePlotVariables (amrex::Vector<std::string> vars, const std::string& plotfilename);
+    virtual void WriteSmallPlotFile ();
     void ReadCheckpointFile ();
 };
 

src/incflo.cpp

@@ -96,6 +96,11 @@ void incflo::InitData ()
             WritePlotFile();
             m_last_plt = 0;
         }
+        if (m_smallplot_int > 0 || m_smallplot_per_approx > 0)
+        {
+            WriteSmallPlotFile();
+            m_last_smallplt = 0;
+        }
         if (m_KE_int > 0)
         {
             amrex::Abort("xxxxx m_KE_int todo");
@@ -116,6 +121,11 @@ void incflo::InitData ()
             WritePlotFile();
             m_last_plt = 0;
         }
+        if (m_smallplotfile_on_restart)
+        {
+            WriteSmallPlotFile();
+            m_last_smallplt = 0;
+        }
     }
 
 #ifdef AMREX_USE_EB
@@ -166,6 +176,11 @@ void incflo::Evolve()
             WritePlotFile();
             m_last_plt = m_nstep;
         }
+        if (writeNow(m_smallplot_int, m_smallplot_per_approx, -1.))
+        {
+            WriteSmallPlotFile();
+            m_last_smallplt = m_nstep;
+        }
 
         if(m_check_int > 0 && (m_nstep % m_check_int == 0))
         {
@@ -278,28 +293,28 @@ void incflo::MakeNewLevelFromScratch (int lev, Real time, const BoxArray& new_gr
 }
 
 bool
-incflo::writeNow()
+incflo::writeNow(int a_plot_int, Real a_plot_per_approx, Real a_plot_per_exact)
 {
     bool write_now = false;
 
-    if ( ( m_plot_int > 0 && (m_nstep % m_plot_int == 0) ) ||
-         (m_plot_per_exact  > 0 && (std::abs(std::remainder(m_cur_time, m_plot_per_exact)) < 1.e-12) ) ) {
+    if ( ( a_plot_int > 0 && (m_nstep % a_plot_int == 0) ) ||
+         (a_plot_per_exact  > 0 && (std::abs(std::remainder(m_cur_time, a_plot_per_exact)) < 1.e-12) ) ) {
         write_now = true;
-    } else if (m_plot_per_approx > 0.0) {
-        // Check to see if we've crossed a m_plot_per_approx interval by comparing
+    } else if (a_plot_per_approx > 0.0) {
+        // Check to see if we've crossed a a_plot_per_approx interval by comparing
         // the number of intervals that have elapsed for both the current
         // time and the time at the beginning of this timestep.
 
-        int num_per_old = static_cast<int>(std::round((m_cur_time-m_dt) / m_plot_per_approx));
-        int num_per_new = static_cast<int>(std::round((m_cur_time     ) / m_plot_per_approx));
+        int num_per_old = static_cast<int>(std::round((m_cur_time-m_dt) / a_plot_per_approx));
+        int num_per_new = static_cast<int>(std::round((m_cur_time     ) / a_plot_per_approx));
 
         // Before using these, however, we must test for the case where we're
         // within machine epsilon of the next interval. In that case, increment
-        // the counter, because we have indeed reached the next m_plot_per_approx interval
+        // the counter, because we have indeed reached the next a_plot_per_approx interval
         // at this point.
 
         const Real eps = std::numeric_limits<Real>::epsilon() * Real(10.0) * std::abs(m_cur_time);
-        const Real next_plot_time = (num_per_old + 1) * m_plot_per_approx;
+        const Real next_plot_time = (num_per_old + 1) * a_plot_per_approx;
 
         if ((num_per_new == num_per_old) && std::abs(m_cur_time - next_plot_time) <= eps)
         {