Data Sampler for Plane/Line Output (#1897)

* Super rough but it plotted a line.

* Need to test on multi-proc.

* codespell fix.

* Plot T and Wsp and clean up the realBox location.

* Bump AMReX hash.

Docs/sphinx_doc/Inputs.rst

@@ -718,6 +718,74 @@ The requested output files have the following columns:
   #. SGS turbulence dissipation, :math:`\epsilon` (m2/s3)
 
 
+Data Sampling Outputs
+==================
+
+Data along query lines or planes may be output during the simulation if
+``erf.do_line_sampling = true`` or  ``erf.do_plane_sampling = true``, respectively.
+The potential temperature and wind-speed will be written to native ``plt_line/plane``
+at the step frequency dictated by ``erf.sampler_interval = <int>``. For line sampling,
+users must prescribe ``sample_line_lo`` and ``sample_line_hi`` inputs which are 3 integer
+values corresponding to the (i,j,k) indices at the beginning and end of the line.
+Additionally, users must specify ``sample_line_dir`` to prescribed the direction of
+the line. The same inputs are used for the plane sampling except that ``sample_plane_lo/hi``
+must be the physical locations of the plane corners. This output functionality has
+not been implemented for terrain.
+
+.. _list-of-parameters-10b:
+
+
+List of Parameters
+------------------
+
++-------------------------------+------------------+----------------+----------------+
+| Parameter                     | Definition       | Acceptable     | Default        |
+|                               |                  | Values         |                |
++===============================+==================+================+================+
+| **erf.sampler_interval**      | Output           | Integer        | -1             |
+|                               | frequency        |                |                |
++-------------------------------+------------------+----------------+----------------+
+| **erf.do_line_sampling**      | Flag to do line  | Boolean        | false          |
+|                               | sampling         |                |                |
+|                               |                  |                |                |
++-------------------------------+------------------+----------------+----------------+
+| **erf.do_plane_sampling**     | Flag to do plane | Boolean        | false          |
+|                               | sampling         |                |                |
+|                               |                  |                |                |
++-------------------------------+------------------+----------------+----------------+
+| **erf.sample_line_dir**       | Directionality   | Integer        | None           |
+|                               | of the line      |                |                |
++-------------------------------+------------------+----------------+----------------+
+| **erf.sample_plane_dir**      | Directionality   | Integer        | None           |
+|                               | of the plane     |                |                |
++-------------------------------+------------------+----------------+----------------+
+| **erf.sample_line_lo/hi**     | Bounding (i,j,k) | 3 Integers per | None           |
+|                               | on the line(s)   | line           |                |
++-------------------------------+------------------+----------------+----------------+
+| **erf.sample_plane_lo/hi**    | Bounding point   | 3 Reals per    | None           |
+|                               | on the plane(s)  | plane          |                |
++-------------------------------+------------------+----------------+----------------+
+
+.. _examples-of-usage-10b:
+
+Example of Usage
+-----------------
+
+::
+
+   erf.sampler_interval = 1                  # Write plt files every step
+
+   erf.do_line_sampling = true               # Do line sampling
+   erf.sample_line_lo   = 5 32  5 10   32 5  # Lo points for two lines
+   erf.sample_line_hi   = 5 32 25 1000 32 5  # Hi points for two lines
+   erf.sample_line_dir  = 2 0                # One line in z and one in x
+
+   erf.do_plane_sampling = true              # Do plane sampling
+   erf.sample_plane_lo   =  48.0  48.0  32.0 # Lo points for one plane
+   erf.sample_plane_hi   = 320.0 320.0  32.0 # Hi points for one plane
+   erf.sample_plane_dir  = 2                 # One plane with z normal
+
+
 Advection Schemes
 =================
 

Exec/ABL/inputs_DataSampler

@@ -0,0 +1,74 @@
+# ------------------  INPUTS TO MAIN PROGRAM  -------------------
+max_step = 4000
+
+amrex.fpe_trap_invalid = 1
+
+fabarray.mfiter_tile_size = 1024 1024 1024
+
+# PROBLEM SIZE & GEOMETRY
+geometry.prob_extent =  1024     1024    1024
+amr.n_cell           =    64      64     64
+
+geometry.is_periodic = 1 1 0
+
+zlo.type = "NoSlipWall"
+zhi.type = "SlipWall"
+
+# TIME STEP CONTROL
+erf.fixed_dt           = 0.1  # fixed time step depending on grid resolution
+
+# DIAGNOSTICS & VERBOSITY
+erf.sum_interval   = 1       # timesteps between computing mass
+erf.v              = 1       # verbosity in ERF.cpp
+amr.v              = 1       # verbosity in Amr.cpp
+
+erf.data_log = my_data_file
+
+erf.sampler_interval = 1
+erf.do_line_sampling = true
+erf.sample_line_lo   = 5 32  5 10   32 5
+erf.sample_line_hi   = 5 32 25 1000 32 5
+erf.sample_line_dir  = 2 0
+
+erf.do_plane_sampling = true
+erf.sample_plane_lo   =  48.0  48.0  32.0
+erf.sample_plane_hi   = 320.0 320.0  32.0 
+erf.sample_plane_dir  = 2
+
+# REFINEMENT / REGRIDDING
+amr.max_level       = 0       # maximum level number allowed
+
+# CHECKPOINT FILES
+erf.check_file      = chk        # root name of checkpoint file
+erf.check_int       = 100        # number of timesteps between checkpoints
+
+# PLOTFILES
+erf.plot_file_1     = plt        # prefix of plotfile name
+erf.plot_int_1      = 10         # number of timesteps between plotfiles
+erf.plot_vars_1     = density rhoadv_0 x_velocity y_velocity z_velocity pressure temp theta
+
+# SOLVER CHOICE
+erf.alpha_T = 0.0
+erf.alpha_C = 1.0
+erf.use_gravity = false
+
+erf.molec_diff_type = "None"
+erf.les_type        = "Smagorinsky"
+erf.Cs              = 0.1
+
+erf.init_type = "uniform"
+
+# PROBLEM PARAMETERS
+prob.rho_0 = 1.0
+prob.A_0 = 1.0
+
+prob.U_0 = 10.0
+prob.V_0 = 0.0
+prob.W_0 = 0.0
+prob.T_0 = 300.0
+
+# Higher values of perturbations lead to instability
+# Instability seems to be coming from BC
+prob.U_0_Pert_Mag = 0.08
+prob.V_0_Pert_Mag = 0.08 #
+prob.W_0_Pert_Mag = 0.0

Source/ERF.H

@@ -44,6 +44,7 @@
 #include <ERF_MRI.H>
 #include <ERF_PhysBCFunct.H>
 #include <ERF_FillPatcher.H>
+#include <ERF_SampleData.H>
 
 #ifdef ERF_USE_PARTICLES
 #include "ERF_ParticleData.H"
@@ -1263,6 +1264,11 @@ private:
         amrex::ParallelDescriptor::Barrier("ERF::setRecordSampleLineInfo");
     }
 
+    // Data sampler for line and plane output
+    int sampler_interval = -1;
+    amrex::Real sampler_per = -1.0;
+    std::unique_ptr<SampleData> data_sampler = nullptr;
+
     amrex::Vector<std::unique_ptr<std::fstream> > datalog;
     amrex::Vector<std::string> datalogname;
 

Source/ERF.cpp

@@ -538,6 +538,12 @@ ERF::post_timestep (int nstep, Real time, Real dt_lev0)
       }
     }
 
+    // Write plane/line sampler data
+    if (is_it_time_for_action(nstep, time, dt_lev0, sampler_interval, sampler_per) && (data_sampler) ) {
+        data_sampler->get_sample_data(geom, vars_new);
+        data_sampler->write_sample_data(t_new, istep, ref_ratio, geom);
+    }
+
     // Moving terrain
     if ( solverChoice.use_terrain &&  (solverChoice.terrain_type == TerrainType::Moving) )
     {
@@ -1167,6 +1173,11 @@ ERF::InitData_post ()
 
     }
 
+    // Create object to do line and plane sampling if needed
+    bool do_line = false; bool do_plane = false;
+    pp.query("do_line_sampling",do_line); pp.query("do_plane_sampling",do_plane);
+    if (do_line || do_plane) { data_sampler = std::make_unique<SampleData>(do_line, do_plane); }
+
 #ifdef ERF_USE_EB
     bool write_eb_surface = false;
     pp.query("write_eb_surface", write_eb_surface);
@@ -1495,6 +1506,10 @@ ERF::ReadParameters ()
         pp.query("column_loc_y", column_loc_y);
         pp.query("column_file_name", column_file_name);
 
+        // Sampler output frequency
+        pp.query("sampler_per", sampler_per);
+        pp.query("sampler_interval", sampler_interval);
+
         // Specify information about outputting planes of data
         pp.query("output_bndry_planes", output_bndry_planes);
         pp.query("bndry_output_planes_interval", bndry_output_planes_interval);