changed docs to reflect geometry names.

    grids became patches and related changes.

doc/ClawPlotItem.rst

@@ -38,7 +38,7 @@ The following attributes can be set by the user:
     * '2d_contour' : two dimensional contour plot,
     * '2d_pcolor' : two dimensional pcolor plot,
     * '2d_schlieren' : two dimensional Schlieren plot,
-    * '2d_grid' : two dimensional plot of only the grids, no data
+    * '2d_edges' : two dimensional plot of only the cell and/or patch edges, no data
 
 .. attribute:: outdir : str or None
 
@@ -52,7 +52,7 @@ The following attributes can be set by the user:
      the Python convention that plot_var=0 corresponds to the first
      component).
 
-     If a function, then this function is applied to q on each grid to
+     If a function, then this function is applied to q on each patch to
      compute the variable var that is plotted.  The signature is
 
      * var = plot_var(current_data)
@@ -72,30 +72,30 @@ The following attributes can be set by the user:
 
         def afteritem(current_data):
 
-.. attribute:: aftergrid : str or function or None
+.. attribute:: afterpatch : str or function or None
 
      A string or function that is to be executed after plotting this item on
-     each grid. (There may be more than 1 grid in an AMR calculation.)
+     each patch. (There may be more than 1 patch in an AMR calculation.)
      If a string, this string is executed using *exec*.  If a
      function, it should be defined to have a single argument
      "data", [documentation to appear!] 
 
      For example::
 
-        def aftergrid(current_data):
+        def afterpatch(current_data):
             cd = current_data
-	    print "On grid number %s, xlower = %s, ylower = %s" \
-	          % (cd.gridno, cd.xlower, cd.ylower)
+	    print "On patch number %s, xlower = %s, ylower = %s" \
+	          % (cd.patchno, cd.xlower, cd.ylower)
 
-     would print out the grid number and lower left corner for each grid in
-     a 2d computation after the grid is plotted.
+     would print out the patch number and lower left corner for each patch in
+     a 2d computation after the patch is plotted.
 
 
 
 .. attribute:: MappedGrid : bool
 
-     If True, the grid mapping specified by the *mapc2p* attribute of the
-     underlying `ClawPlotData` object should be applied to the grid before
+     If True, the mapping specified by the *mapc2p* attribute of the
+     underlying `ClawPlotData` object should be applied to the patch before
      plotting.
 
 
@@ -200,16 +200,16 @@ Special attributes for plot_type = '1d_from_2d_data'
 Special attributes for all 2d plots,  plot_type = '2d...'
 ------------------------------------------------------------
 
-.. attribute:: gridlines_show : bool
+.. attribute:: celledges_show : bool
 
-     If True, draw the grid lines on the plot.  
-     The attribute 'amr_gridlines_show' should be used for AMR computations
-     to specify that gridlines should be shown on some levels and not
+     If True, draw the cell edges on the plot.  
+     The attribute 'amr_celledges_show' should be used for AMR computations
+     to specify that cell edges should be shown on some levels and not
      others. See :ref:`amr_attributes`.
 
-.. attribute:: gridedges_show : bool
+.. attribute:: patchedges_show : bool
 
-     If True, draw the edges of grids, mostly useful in AMR computations.
+     If True, draw the edges of patches, mostly useful in AMR computations.
 
 Special attributes for plot_type = '2d_contour'
 ------------------------------------------------------
@@ -247,9 +247,9 @@ Special attributes for plot_type = '2d_contour'
 
      to use black lines on Level 1, blue on Level 2, and red for all
      subsequent levels.  This is useful since with the matplotlib contour
-     plotter you will see both fine and course grid lines on top of one
+     plotter you will see both fine and coarse cell edges on top of one
      another in refined regions (Matplotlib lacks the required
-     hidden line removal to blank out the lines from coarser grids easily.
+     hidden line removal to blank out the lines from coarser patches easily.
      See also the next attributes.)
 
 .. attribute:: contour_show : boolean
@@ -261,7 +261,7 @@ Special attributes for plot_type = '2d_contour'
 .. attribute:: amr_contour_show : list or tuple of booleans
 
      Determines whether to show the contour lines on each AMR level.  Useful
-     if you only want to view the lines on the finest grids.
+     if you only want to view the lines on the finest patches.
 
 
 .. attribute:: contour_kwargs : dictionary
@@ -280,7 +280,7 @@ Special attributes for plot_type = '2d_pcolor'
      In general you should specify *pcolor_cmin* and *pcolor_cmax* to
      specify the range of q values over which the colormap applies.  If they 
      are not specified they will be chosen automatically and may vary from
-     frame to frame.  Also, if AMR is used, they may vary from grid to grid,
+     frame to frame.  Also, if AMR is used, they may vary from patch to patch,
      yielding very confusing plots.
 
 .. attribute:: pcolor_colorbar : bool
@@ -309,21 +309,21 @@ other hand::
     plotitem = plotaxes.new_plotitem(plot_type='2d_contour')
     plotitem.amr_contour_color = ['k', 'b']
 
-will result in contour lines on grids at level 1 being black and on grids of
-level 2 or higher being blue.  
+will result in contour lines on patches at level 1 being black and on
+patches of level 2 or higher being blue.  
 
 Note that if the list is shorter than the number of levels, the last element
 is used repeatedly.
 
 If both attributes *contour_color* and *amr_contour_color* are set, 
 only *amr_contour_color* is used.
 
-A common use is to show grid lines only on coarse levels, not on finer
+A common use is to show cell edges only on coarse levels, not on finer
 levels, e.g.::
 
-    plotitem.amr_gridlines_show = [1,1,0]
+    plotitem.amr_celledges_show = [1,1,0]
 
-will result in gridlines being shown only on levels 1 and 2, not on finer
+will result in celledges being shown only on levels 1 and 2, not on finer
 levels.
 
 

doc/README.txt

@@ -1 +1,7 @@
 This directory is for documentation.
+
+To make the documentation in this directory, run
+  make htmls
+in the doc directory of the doc repository, after insuring that
+  visclaw_doc
+is a link to this directory.

doc/current_data.rst

@@ -18,7 +18,7 @@ Call back functions include:
 
  * *beforeframe* and *afterframe* attributes of :ref:`ClawPlotData` 
  * *afteraxes* attribute of :ref:`ClawPlotAxes` 
- * *afteritem*, *aftergrid*, *plot_var*, *map2d_to_1d* attributes of :ref:`ClawPlotItem` 
+ * *afteritem*, *afterpatch*, *plot_var*, *map2d_to_1d* attributes of :ref:`ClawPlotItem` 
 
 
 All of these functions are designed to take a single argument
@@ -48,22 +48,22 @@ current context, e.g. in a *beforeframe* function.
 
    The current frame number
 
-.. attribute:: grid : 
+.. attribute:: patch : 
 
-   Object of :class:`pyclaw.solution.grid` with data for the last grid
+   Object of :class:`pyclaw.solution.patch` with data for the last patch
    plotted.
 
-.. attribute:: gridno : 
+.. attribute:: patchno : 
 
-   Grid number of this grid, of interest only in AMR calculations.
+   Grid number of this patch, of interest only in AMR calculations.
 
 .. attribute:: q : 
 
     q array for current frame, so for example the in a scalar 2d problem the
     value in the (i,j) cell would be *current_data.q[i,j,0]* (remember that
     Python always indexes starting at 0).
 
-    In an AMR calculation q will be from the last grid plotted.  
+    In an AMR calculation q will be from the last patch plotted.  
 
 .. attribute:: aux : 
 
@@ -74,7 +74,7 @@ current context, e.g. in a *beforeframe* function.
 
     If fort.a files are not found then current_data.aux will be None.
 
-    In an AMR calculation aux will be from the last grid plotted.  
+    In an AMR calculation aux will be from the last patch plotted.  
 
 .. attribute:: var : 
 
@@ -84,9 +84,9 @@ current context, e.g. in a *beforeframe* function.
 
 .. attribute:: level : 
 
-   For AMR computations, where *current_data.grid* is for the last grid plotted,
-   *current_data.level* is the AMR level of this grid.  Particularly useful
-   in `aftergrid` functions.
+   For AMR computations, where *current_data.patch* is for the last patch plotted,
+   *current_data.level* is the AMR level of this patch.  Particularly useful
+   in `afterpatch` functions.
 
 .. attribute:: t : 
 
@@ -102,11 +102,11 @@ current context, e.g. in a *beforeframe* function.
 
 .. attribute:: xlower :
 
-    left edge of current grid.
+    left edge of current patch.
 
 .. attribute:: ylower :
 
-    left edge of current grid in y (only in 2d).
+    left edge of current patch in y (only in 2d).
 
 
 

doc/plotting.rst

@@ -34,7 +34,7 @@ The advantages of using the Python options are:
    open source visualization tools such as `VisIt
    <https://wci.llnl.gov/codes/visit>`_ (developed at Lawrence Livermore
    National Laboratory) are much better for dealing
-   with large data sets, AMR grids, etc.  VisIt has Python bindings and 
+   with large data sets, AMR meshes, etc.  VisIt has Python bindings and 
    we are currently extending our tools to work with VisIt.  If you are
    already a VisIt user, note that VisIt has a Claw reader that can be used to
    import data from Clawpack, see `Application Toolkit Formats

doc/plotting_faq.rst

@@ -43,7 +43,7 @@ If plot_var is a function then this function is applied to applied to
 :ref:`current_data` and should return the array of values to be plotted.
 For an example, see :ref:`plotexample-acou-1d-6`.
 
-Sometimes you want to plot something other than the solution on the grid, 
+Sometimes you want to plot something other than the solution on the patch, 
 for example to add another feature to a plot of the solution. This can be
 done via an ``afteraxes`` command, for example, which is called after all
 items have been plotted on the current axes.  See :ref:`ClawPlotAxes` for

doc/setplot.rst

@@ -38,8 +38,8 @@ Overview
 The approach outlined below may seem more complicated than necessary, and it
 would be if all you ever want to do is plot one set of data at each output
 time.  However, when adaptive mesh refinement is used each frame of data may
-contain several grids and so creating the desired plot requires looping over
-all grids.  This is done by the plotting utilities described in :ref:`plotting`,
+contain several patches and so creating the desired plot requires looping over
+all patches.  This is done by the plotting utilities described in :ref:`plotting`,
 but for this to work it is necessary to specify what plot(s) are desired.
 
 Most example directories contain a file setplot.py that contains a