Paper2v2 updates

paper2_examples/README.md

@@ -1,10 +1,18 @@
-The code in this repository supplements a paper that is currently in production.
 
+# Computational Experiments to accompany the paper
 
-## Computational Experiments for the paper Analysis and Performance Evaluation of Adjoint-Guided Adaptive Mesh Refinement Using Clawpack
+###  "Analysis and Performance Evaluation of Adjoint-Guided Adaptive Mesh Refinement Using Clawpack" 
 
-The code in this repository supplements the paper (currently in production): "Analysis and Performance Evaluation of Adjoint-Guided Adaptive Mesh Refinement Using Clawpack."
+by Brisa N. Davis and Randall J. LeVeque
 
+This version goes with version 2 of the paper, currently submitted for publication.
+
+Check out the `paper2v1` branch for the version of the code that accompanies the original preprint https://arxiv.org/abs/1810.00927. 
+
+This version is updated in the following ways:
+ - It uses Clawpack v5.6.1, which has the adjoint flagging now built in.
+ - Example 1 from the original paper has been dropped from v2 of the paper, so the subdirectories have been renamed.
+
 The code is designed to work with the Clawpack 5 software. For more information visit 
 [the Clawpack webpage](http://www.clawpack.org/ ). 
 The Clawpack software is open source, and the code is openly available at 
@@ -18,10 +26,10 @@ the use of the adjoint method for guiding adaptive mesh refinement in Clawpack i
 
 * gfortran 5.0.0
 * python 2.7.10
-* clawpack 5.3.0 : [Clawpack](http://www.clawpack.org/ )
+* clawpack 5.6.1 : [Clawpack](http://www.clawpack.org/ )
 * git: to clone this repository
 
-Note: Clawpack 5.0 or higher is required, other versions of gfortran and python might work as well.
+Note: Later versions of Clawpack should work, other versions of gfortran and python might work as well.
 
 **Operating system.**
 
@@ -30,24 +38,24 @@ Note: Clawpack 5.0 or higher is required, other versions of gfortran and python
 
 ### Examples Included and Folder Organization
 
-* **acoustics_1d_ex1:** contains the code to run the first one-dimensional variable coefficients 
-linear acoustics equations example. 
+* **acoustics_1d_ex1_old:** contains the code to run the first one-dimensional variable coefficients 
+linear acoustics example from v1 of the paper, not used in v2 of the paper.
 The internal folder: **adjoint**, contains the code for the adjoint problem. 
 
-* **acoustics_1d_ex2:** contains the code to run the second one-dimensional variable coefficients 
-linear acoustics equations example. 
+* **acoustics_1d_example1:** contains the code to run the one-dimensional variable coefficients 
+linear acoustics example that is Example 1 in v2 of the paper. 
 The internal folder: **adjoint**, contains the code for the adjoint problem. 
 
-* **acoustics_2d_ex1:** contains the code to run the first two-dimensional variable coefficients 
-linear acoustics equations example. 
+* **acoustics_2d_example2:** contains the code to run the first two-dimensional variable coefficients 
+linear acoustics problem that is Example 2 in v2 of the paper.
 The internal folder: **adjoint**, contains the code for the adjoint problem. 
 
-* **acoustics_2d_ex2:** contains the code to run the second two-dimensional variable coefficients 
-linear acoustics equations example. 
+* **acoustics_2d_example3:** contains the code to run the second two-dimensional variable coefficients 
+linear acoustics problem that is Example 3 in v2 of the paper.
 The internal folder: **adjoint**, contains the code for the adjoint problem. 
 
 ### Running the Code
-* **Install Clawpack 5.3.0:**
+* **Install Clawpack 5.6.1:**
 - Go to: http://www.clawpack.org/installing.html#installation-instructions
 - Follow the download and installation intructions in the section: Install all Clawpack packages 
 - Follow the setup instructions in the section: Set environment variables.
@@ -60,9 +68,11 @@ The internal folder: **adjoint**, contains the code for the adjoint problem.
 - Create a copy of the adjoint repository by running the code:
 
 ```
-git://github.com/BrisaDavis/adjoint.git
+    git clone https://github.com/clawpack/adjoint.git
+    cd adjoint
+    git checkout paper2v2
 ```
 
 * **Run the code**
 
-* Go any of the folders and follow the instructions in the README.md in that folder.
+* Go any of the folders in `paper2_examples` and follow the instructions in the README.md in that folder.

paper2_examples/acoustics_1d_ex2/Makefile → paper2_examples/acoustics_1d_ex1_old/Makefile

@@ -31,8 +31,8 @@ FFLAGS ?=
 # package sources for this program:
 # ---------------------------------
 
-AMRLIB = $(CLAW)/amrclaw/src/1d_adjoint
-include $(AMRLIB)/Makefile.adjoint_amr_1d
+AMRLIB = $(CLAW)/amrclaw/src/1d
+include $(AMRLIB)/Makefile.amr_1d
 
 # ---------------------------------------
 # package sources specifically to exclude

paper2_examples/acoustics_1d_ex2/setaux.f → paper2_examples/acoustics_1d_ex1_old/setaux.f

@@ -22,10 +22,15 @@ subroutine setaux(mbc,mx,xlower,dx,maux,aux)
       common /comaux/ Zl, cl, Zr, cr
       double precision Zl, cl, Zr, cr
 
-      integer i,ii
+      integer i
       double precision xcell
 
       do i=1-mbc,mx+mbc
+
+         if (aux(1,i) .eq. NEEDS_TO_BE_SET) then
+            aux(innerprod_index,i) = 0.d0
+         endif
+
          xcell = xlower + (i-0.5d0)*dx
          if (xcell .lt. 0.0d0) then
             aux(1,i) = Zl
@@ -36,10 +41,5 @@ subroutine setaux(mbc,mx,xlower,dx,maux,aux)
          endif
       enddo
 
-      ! Initialize innerproduct to zero.
-      do ii=1-mbc,mx+mbc
-          aux(innerprod_index,ii) = 0.d0
-      enddo
-
       return
       end

paper2_examples/acoustics_1d_ex1_old/setplot.py

@@ -0,0 +1,165 @@
+
+""" 
+Set up the plot figures, axes, and items to be done for each frame.
+
+This module is imported by the plotting routines and then the
+function setplot is called to set the plot parameters.
+
+""" 
+
+from __future__ import absolute_import
+from __future__ import print_function
+
+amr_color = ['g','b','r','c','k']
+amr_marker = ['x','s','o','^','.']
+amr_linestyle = ['-','-','-','-','-']
+amr_plotstyle = [ma+li for ma,li in zip(amr_marker,amr_linestyle)]
+print('amr_plotstyle = ',amr_plotstyle)
+#amr_plotstyle = ['x-','s-','o-','^-','.-']
+
+#--------------------------
+def setplot(plotdata=None):
+#--------------------------
+
+    """ 
+    Specify what is to be plotted at each frame.
+    Input:  plotdata, an instance of clawpack.visclaw.data.ClawPlotData.
+    Output: a modified version of plotdata.
+
+    """ 
+
+
+    if plotdata is None:
+        from clawpack.visclaw.data import ClawPlotData
+        plotdata = ClawPlotData()
+
+    plotdata.clearfigures()  # clear any old figures,axes,items data
+
+    def draw_interface_add_legend(current_data):
+        from pylab import plot
+        plot([0., 0.], [-1000., 1000.], 'k--')
+        try:
+            from clawpack.visclaw import legend_tools
+            labels = ['Level 1','Level 2', 'Level 3', 'Level 4', 'Level 5']
+            legend_tools.add_legend(labels, colors=amr_color,
+                        markers=amr_marker, linestyles=amr_linestyle,
+                        loc='upper left')
+        except:
+            pass
+
+    def draw_interface_add_legend_innerprod(current_data):
+        from pylab import plot
+        plot([0., 0.], [-1000., 1000.], 'k--')
+        try:
+            from clawpack.visclaw import legend_tools
+            labels = ['Level 3','Level 4']
+            legend_tools.add_legend(labels, colors=['r','c'],
+                                    markers=['o','^'], linestyles=['',''],
+                                    loc='upper left')
+        except:
+            pass
+
+
+    # Figure for q[0]
+    plotfigure = plotdata.new_plotfigure(name='Pressure and Velocity', figno=1)
+    plotfigure.kwargs = {'figsize': (8,8)}
+    # Set up for axes in this figure:
+    plotaxes = plotfigure.new_plotaxes()
+    plotaxes.axescmd = 'subplot(2,1,1)'   # top figure
+    plotaxes.xlimits = [-12,12]
+    plotaxes.ylimits = [-.5,1.1]
+    plotaxes.title = 'Pressure'
+    plotaxes.afteraxes = draw_interface_add_legend
+
+    # Set up for item on these axes:
+    plotitem = plotaxes.new_plotitem(plot_type='1d_plot')
+    plotitem.plot_var = 0
+    plotitem.amr_color = amr_color
+    plotitem.amr_plotstyle = amr_plotstyle
+    plotitem.amr_data_show = [1,1,1]
+    plotitem.amr_kwargs = [{'markersize':5},{'markersize':4},{'markersize':3}]
+
+    # Figure for q[1]
+
+    # Set up for axes in this figure:
+    plotaxes = plotfigure.new_plotaxes()
+    plotaxes.axescmd = 'subplot(2,1,2)'   # bottom figure
+    plotaxes.xlimits = [-12,12]
+    plotaxes.ylimits = [-.5,1.1]
+    plotaxes.title = 'Velocity'
+    plotaxes.afteraxes = draw_interface_add_legend
+
+    # Set up for item on these axes:
+    plotitem = plotaxes.new_plotitem(plot_type='1d_plot')
+    plotitem.plot_var = 1
+    plotitem.amr_color = amr_color
+    plotitem.amr_plotstyle = amr_plotstyle
+    plotitem.amr_data_show = [1,1,1]
+    plotitem.amr_kwargs = [{'markersize':5},{'markersize':4},{'markersize':3}]
+
+    # Figure for inner product, q[2]
+
+    plotfigure = plotdata.new_plotfigure(name='Inner Product', figno=10)
+
+    # Set up for axes in this figure:
+    plotaxes = plotfigure.new_plotaxes()
+    plotaxes.xlimits = [-12,12]
+    plotaxes.ylimits = [-0.1,1]         # use when taking inner product with forward solution
+    #plotaxes.ylimits = [-0.01,0.02]    # use when taking inner product with Richardson error
+    plotaxes.title = 'Inner Product'
+    plotaxes.afteraxes = draw_interface_add_legend_innerprod
+
+    # Set up for item on these axes:
+    plotitem = plotaxes.new_plotitem(plot_type='1d')
+    plotitem.plot_var = plot_innerprod
+    plotitem.amr_color = amr_color
+    plotitem.amr_plotstyle = amr_plotstyle
+    plotitem.amr_data_show = [0,0,1,1,0]
+    plotitem.show = True       # show on plot?
+
+
+    #-----------------------------------------
+    # Figures for gauges
+    #-----------------------------------------
+    plotfigure = plotdata.new_plotfigure(name='q', figno=300, \
+                                         type='each_gauge')
+    plotfigure.clf_each_gauge = True
+    plotfigure.kwargs = {'figsize': (10,10)}
+
+    plotaxes = plotfigure.new_plotaxes()
+    plotaxes.axescmd = 'subplot(211)'
+    plotaxes.xlimits = 'auto'
+    plotaxes.ylimits = 'auto'
+    plotaxes.title = 'Pressure'
+    plotitem = plotaxes.new_plotitem(plot_type='1d_plot')
+    plotitem.plot_var = 0
+    plotitem.plotstyle = 'b-'
+
+    plotaxes = plotfigure.new_plotaxes()
+    plotaxes.axescmd = 'subplot(212)'
+    plotaxes.xlimits = 'auto'
+    plotaxes.ylimits = 'auto'
+    plotaxes.title = 'Velocity'
+    plotitem = plotaxes.new_plotitem(plot_type='1d_plot')
+    plotitem.plot_var = 1
+    plotitem.plotstyle = 'b-'
+
+    # Parameters used only when creating html and/or latex hardcopy
+    # e.g., via clawpack.visclaw.frametools.printframes:
+
+    plotdata.printfigs = True                # print figures
+    plotdata.print_format = 'png'            # file format
+    plotdata.print_framenos = 'all'          # list of frames to print
+    plotdata.print_fignos = 'all'            # list of figures to print
+    plotdata.html = True                     # create html files of plots?
+    plotdata.html_homelink = '../README.html'
+    plotdata.latex = True                    # create latex file of plots?
+    plotdata.latex_figsperline = 2           # layout of plots
+    plotdata.latex_framesperline = 1         # layout of plots
+    plotdata.latex_makepdf = False           # also run pdflatex?
+
+    return plotdata
+
+def plot_innerprod(current_data):
+    return current_data.aux[2,:]
+