Changeset 3099

Timestamp:

Jun 6, 2006, 1:27:24 PM (18 years ago)

Author:

howard

Message:

Amended glossary

File:

• documentation/user_manual/anuga_user_manual.tex (modified) (68 diffs)

documentation/user_manual/anuga_user_manual.tex

@@ -550 +550 @@
 
 \begin{itemize}
-    \item \textbf{Reflective boundary} Returns same \code{stage} as
+    \item \textbf{Reflective boundary}\label{def:reflective boundary} Returns same \code{stage} as
       as present in its neighbour volume but momentum vector
       reversed 180 degrees (reflected).
@@ -556 +556 @@
       momentum quantities assumed to be the second and third conserved
       quantities. A reflective boundary condition models a solid wall.
-    \item \textbf{Transmissive boundary} Returns same conserved quantities as
+    \item \textbf{Transmissive boundary}\label{def:transmissive boundary} Returns same conserved quantities as
       those present in its neighbour volume. This is one way of modelling
       outflow from a domain, but it should be used with caution if flow is
@@ -562 +562 @@
       may cause occasional spurious effects. If this occurs,
       consider using e.g. a Dirichlet boundary condition.
-    \item \textbf{[Dirichlet boundary} Specifies a fixed value at the
+    \item \textbf{[Dirichlet boundary}\label{def:dirichlet boundary} Specifies a fixed value at the
       boundary and assigns initial values to the $x$-momentum and $y$-momentum.
-    \item \textbf {Time boundary} Like a Dirichlet boundary but with behaviour
+    \item \textbf{Time boundary}\label{def:time boundary} Like a Dirichlet boundary but with behaviour
       varying with time.
 \end{itemize}
@@ -791 +791 @@
 In practice, the details of the polygons used are read from a
 separate file \file{project.py}. The resulting mesh is output to a
-\emph{meshfile}\index{meshfile}. This term is used to describe a
-file of a specific format used to store the data specifying a mesh.
-(There are in fact two possible formats for such a file: it can
-either be a binary file, with extension \code{.msh}, or an ASCII
-file, with extension \code{.tsh}. In the present case, the binary
-file format \code{.msh} is used. See Section \ref{sec:file formats}
-(page \pageref{sec:file formats}) for more on file formats.)
-\code{pmesh} assigns a name to the file by appending the extension
-\code{.msh} to the name specified in the input file
+\emph{meshfile}\index{meshfile}\label{def:meshfile}. This term is
+used to describe a file of a specific format used to store the data
+specifying a mesh. (There are in fact two possible formats for such
+a file: it can either be a binary file, with extension \code{.msh},
+or an ASCII file, with extension \code{.tsh}. In the present case,
+the binary file format \code{.msh} is used. See Section
+\ref{sec:file formats} (page \pageref{sec:file formats}) for more on
+file formats.) \code{pmesh} assigns a name to the file by appending
+the extension \code{.msh} to the name specified in the input file
 \file{project.py}. This name is stored in the variable
 \code{meshname}.
@@ -1031 +1031 @@
 
 Rather than using either of these forms, in this chapter we specify
-the location simply as \code{pmesh.mesh_interface}, in keeping with
+the location simply as \code{pmesh.mesh\_interface}, in keeping with
 the usage in the Python statement for importing the function,
 namely:
@@ -1085 +1085 @@
 
 This function allows a user to initiate the automatic creation of a
-mesh inside a specified polygon (input \code{bounding_polygon}). 
+mesh inside a specified polygon (input \code{bounding_polygon}).
 Among the parameters that can be
 set are the \emph{resolution} (maximal area for any triangle in the
@@ -1098 +1098 @@
 
 
-\begin{funcdesc} {add_region}{}
-
-\end{funcdesc}
-
-\begin{funcdesc} {add_hole}{}
-
-\end{funcdesc}
-
-
-\begin{funcdesc}  {add_region_from_polygon}{self, polygon, tags=None,
+\begin{funcdesc} {add\_region}{}
+
+\end{funcdesc}
+
+\begin{funcdesc} {add\_hole}{}
+
+\end{funcdesc}
+
+
+\begin{funcdesc}  {add\_region\_from\_polygon}{self, polygon, tags=None,
                                 max_triangle_area=None, geo_reference=None}
 Module: \module{pmesh.mesh}  Class: \class{Mesh}
@@ -1120 +1120 @@
 \end{funcdesc}
 
-\begin{funcdesc}  {add_hole_from_polygon}{self, polygon, tags=None,
+\begin{funcdesc}  {add\_hole\_from\_polygon}{self, polygon, tags=None,
     geo_reference=None}
 Module: \module{pmesh.mesh.Mesh}
@@ -1133 +1133 @@
 \end{funcdesc}
 
-\begin{funcdesc}  {generate_mesh}{self,
+\begin{funcdesc}  {generate\_mesh}{self,
                       maximum_triangle_area=None,
                       minimum_triangle_angle=28.0,
@@ -1146 +1146 @@
 
 
-\begin{funcdesc}  {export_mesh_file}{self,ofile}
+\begin{funcdesc}  {export\_mesh_file}{self,ofile}
 Module: \module{pmesh.mesh.Mesh}
 
@@ -1218 +1218 @@
     Module: \module{pyvolution.domain}
 
-    Returns the name assigned to the domain by \code{set_name}. If no name has been
+    Returns the name assigned to the domain by \code{set\_name}. If no name has been
     assigned, returns \code{`domain'}.
 \end{funcdesc}
@@ -1226 +1226 @@
 
     Specifies the directory used for data, assigning it to the pathname \code{name}. The default value, before
-    \code{set\_datadir} has been run, is the value \code{default_datadir}
+    \code{set\_datadir} has been run, is the value \code{default\_datadir}
     specified in \code{config.py}.
 
@@ -1245 +1245 @@
 \end{funcdesc}
 
-\begin{funcdesc} {get_datadir}{}
+\begin{funcdesc} {get\_datadir}{}
     Module: \module{pyvolution.domain}
 
-    Returns the data directory set by \code{set_datadir} or,
-    if \code{set_datadir} has not
-    been run, returns the value \code{default_datadir} specified in
+    Returns the data directory set by \code{set\_datadir} or,
+    if \code{set\_datadir} has not
+    been run, returns the value \code{default\_datadir} specified in
     \code{config.py}.
 \end{funcdesc}
 
-\begin{funcdesc} {set_time}{time=0.0}
+\begin{funcdesc} {set\_time}{time=0.0}
     Module: \module{pyvolution.domain}
 
@@ -1261 +1261 @@
 \end{funcdesc}
 
-\begin{funcdesc} {set_default_order}{n}
+\begin{funcdesc} {set\_default\_order}{n}
     Sets the default (spatial) order to the value specified by
     \code{n}, which must be either 1 or 2. (Assigning any other value
@@ -1295 +1295 @@
     use_cache = False}
   Module: \module{pyvolution.domain}
-  (see also \module{pyvolution.quantity.set_values})
+  (see also \module{pyvolution.quantity.set\_values})
 
 This function is used to assign values to individual quantities for a
@@ -1309 +1309 @@
 \item a function (e.g.\ see the samples introduced in Chapter 2)
 \item an expression composed of other quantities and numbers, arrays, lists (for
-example, a linear combination of quantities, such as 
+example, a linear combination of quantities, such as
 \code{domain.set\_quantity('stage','elevation'+x))}
-\item the name of a file from which the data can be read. In this case, the optional argument attribute_name will select which attribute to use from the file. If left out, set_quantity will pick one. This is useful in cases where there is only one attribute.
-\item a geospatial dataset (See ?????). Optional argument attribute_name applies here as with files.
+\item the name of a file from which the data can be read. In this case, the optional argument attribute\_name will select which attribute to use from the file. If left out, set\_quantity will pick one. This is useful in cases where there is only one attribute.
+\item a geospatial dataset (See ?????). Optional argument attribute\_name applies here as with files.
 \end{itemize}
 
@@ -1331 +1331 @@
 Other optional arguments are
 \begin{itemize}
-\item \code{indices} which is a list of ids of triangles to which set_quantity should apply its assignment of values.
+\item \code{indices} which is a list of ids of triangles to which set\_quantity should apply its assignment of values.
 \item \code{location} determines which part of the triangles to assign to. Options are 'vertices' (default), 'edges', and 'centroids'.
 \end{itemize}
@@ -1346 +1346 @@
 %%%
 \anuga provides a number of predefined initial conditions to be used
-with \code{set_quantity}.
+with \code{set\_quantity}.
 
 \begin{funcdesc}{slump_tsunami}{length, depth, slope, width=None, thickness=None,
@@ -1367 +1367 @@
 
 %%%
-\begin{funcdesc}{file_function}{filename,
+\begin{funcdesc}{file\_function}{filename,
                   domain = None,
                   quantities = None,
@@ -1380 +1380 @@
 a callable object. \code{filename} could be a \code{sww} file.
 Returns interpolated values based on the input
-file using the underlying \code{interpolation_function}.
+file using the underlying \code{interpolation\_function}.
 
 \code{quantities} is either the name of a single quantity to be
@@ -1386 +1386 @@
 function will return a tuple of values---one for each quantity.
 
-\code{interpolation_points} is a list of absolute UTM coordinates
+\code{interpolation\_points} is a list of absolute UTM coordinates
 for points at which values are sought.
 
 The model time stored within the file function can be accessed using
-the method \code{f.get_time()}
+the method \code{f.get\_time()}
 \end{funcdesc}
 
@@ -1416 +1416 @@
 an array---or dictionary of arrays (used in conjunction with the
 optional argument \code{quantity\_names}) --- called
-\code{quantities}. The optional arguments \code{vertex_coordinates}
+\code{quantities}. The optional arguments \code{vertex\_coordinates}
 and \code{triangles} represent the spatial mesh associated with the
 quantity arrays. If omitted the function created by
@@ -1463 +1463 @@
 \end{funcdesc}
 
-\begin{funcdesc} {get_boundary_tags}{}
+\begin{funcdesc} {get\_boundary\_tags}{}
 Module: \module{pyvolution.mesh}
 
@@ -1472 +1472 @@
 \subsection{Predefined boundary conditions}
 
-\begin{classdesc}{Reflective_boundary}{Boundary}
+\begin{classdesc}{Reflective\_boundary}{Boundary}
 Module: \module{pyvolution.shallow\_water}
 
@@ -1483 +1483 @@
 
 %%%
-\begin{classdesc}{Transmissive_boundary}{domain = None}
+\begin{classdesc}{Transmissive\_boundary}{domain = None}
 Module: \module{pyvolution.generic\_boundary\_conditions}
 
@@ -1493 +1493 @@
 
 %%%
-\begin{classdesc}{Dirichlet_boundary}{conserved_quantities=None}
+\begin{classdesc}{Dirichlet\_boundary}{conserved_quantities=None}
 Module: \module{pyvolution.generic\_boundary\_conditions}
 
 A Dirichlet boundary returns constant values for each of conserved
-quantities. In the example of \code{Dirichlet\_boundary([0.2, 0.0, 0.0])}, 
-the \code{stage} value at the boundary is 0.2 and the \code{xmomentum} and 
+quantities. In the example of \code{Dirichlet\_boundary([0.2, 0.0, 0.0])},
+the \code{stage} value at the boundary is 0.2 and the \code{xmomentum} and
 \code{ymomentum} at the boundary are set to 0.0. The list must contain
 a value for each conserved quantity.
@@ -1504 +1504 @@
 
 %%%
-\begin{classdesc}{Time_boundary}{domain = None, f = None}
+\begin{classdesc}{Time\_boundary}{domain = None, f = None}
 Module: \module{pyvolution.generic\_boundary\_conditions}
 
@@ -1513 +1513 @@
 
 %%%
-\begin{classdesc}{File_boundary}{Boundary}
+\begin{classdesc}{File\_boundary}{Boundary}
 Module: \module{pyvolution.generic\_boundary\_conditions}
 
 This method may be used if the user wishes to apply a SWW file or
-a time series file to a boundary segment or segments. 
+a time series file to a boundary segment or segments.
 The boundary values are obtained from a file and interpolated to the
 appropriate segments for each conserved quantity.
@@ -1579 +1579 @@
 \subsection{Diagnostics}
 
-  \begin{funcdesc}{timestepping_statistics}{}
+  \begin{funcdesc}{timestepping\_statistics}{}
   Module: \module{pyvolution.domain}
 
@@ -1593 +1593 @@
 
 
-  \begin{funcdesc}{get_quantity}{name, location='vertices', indices = None}
+  \begin{funcdesc}{get\_quantity}{name, location='vertices', indices = None}
   Module: \module{pyvolution.domain}
   Allow access to individual quantities and their methods
@@ -1600 +1600 @@
 
 
-  \begin{funcdesc}{get_values}{location='vertices', indices = None}
+  \begin{funcdesc}{get\_values}{location='vertices', indices = None}
   Module: \module{pyvolution.quantity}
 
@@ -1608 +1608 @@
 
 
-  \begin{funcdesc}{get_integral}{}
+  \begin{funcdesc}{get\_integral}{}
   Module: \module{pyvolution.quantity}
 
@@ -1618 +1618 @@
 \section{Other}
 
-  \begin{funcdesc}{domain.create_quantity_from_expression}{???}
+  \begin{funcdesc}{domain.create\_quantity\_from\_expression}{???}
 
   Handy for creating derived quantities on-the-fly.
@@ -1625 +1625 @@
 
 
-  \begin{classdesc}{Geospatial_data}{data_points = None,
+  \begin{classdesc}{Geospatial\_data}{data_points = None,
                  attributes = None,
                  geo_reference = None,
                  default_attribute_name = None,
                  file_name = None}
-    Module: \module{geospatial_data.geo_spatial_data}
+    Module: \module{geospatial\_data.geo\_spatial\_data}
     Creates a georeferenced geospatial data object from either arrays or
     a file (pts or xya).
@@ -1636 +1636 @@
     Objects of this class can be used with \method{set\_quantity}.
 
-    FIXME (Ole): Describe methods such as get_attributes() etc
+    FIXME (Ole): Describe methods such as get\_attributes() etc
   \end{classdesc}
 
@@ -1778 +1778 @@
 
 The SWW format is used not only for output but also serves as input
-for functions such as \function{file_boundary} and
-\function{file_function}, described in Chapter \ref{ch:interface}.
+for functions such as \function{file\_boundary} and
+\function{file\_function}, described in Chapter \ref{ch:interface}.
 
 A TMS file is used to store time series data that is independent of
@@ -1791 +1791 @@
 be either a TSH file, which is an ASCII file, or an MSH file, which
 is a NetCDF file. A meshfile can be generated from the function
-\function{create_mesh_from_regions} (see Section
+\function{create\_mesh\_from\_regions} (see Section
 \ref{sec:meshgeneration}) and used to initialise a domain.
 
@@ -1815 +1815 @@
 attributes associated with a set of points.
 
-The format for an XYA file is:
+The format for an XYA file is:\\
 %\begin{verbatim}
 
@@ -1858 +1858 @@
 
 \begin{tabular}{l l}
-\code{ncols}      &   \code{753}
-\code{nrows}      &   \code{766}
-\code{xllcorner}  &   \code{314036.58727982}
-\code{yllcorner}  &   \code{6224951.2960092}
-\code{cellsize}   &   \code{100}
+\code{ncols}      &   \code{753}\\
+\code{nrows}      &   \code{766}\\
+\code{xllcorner}  &   \code{314036.58727982}\\
+\code{yllcorner}  & \code{6224951.2960092}\\
+\code{cellsize}   & \code{100}\\
 \code{NODATA_value} & \code{-9999}
 \end{tabular}
@@ -1903 +1903 @@
 
   Takes data from an SWW file \code{basename_in} and converts it to DEM format (ASC or
-  ERS) of a desired grid size \code{cellsize} in metres. 
-  The easting and northing values are used if the user wished to clip the output 
+  ERS) of a desired grid size \code{cellsize} in metres.
+  The easting and northing values are used if the user wished to clip the output
   file to a specified rectangular area. The \code{reduction} input refers to a function
   to reduce the quantities over all time step of the SWW file, example, maximum.
@@ -2019 +2019 @@
 
   If the function definition changes after a result has been cached, this will be
-  detected by examining the functions \code{bytecode (co_code, co_consts,
-  func_defaults, co_argcount)} and the function will be recomputed.
-
-  Options are set by means of the function \code{set_option(key, value)},
+  detected by examining the functions \code{bytecode (co\_code, co\_consts,
+  func\_defaults, co\_argcount)} and the function will be recomputed.
+
+  Options are set by means of the function \code{set\_option(key, value)},
   where \code{key} is a key associated with a
   Python dictionary \code{options}. This dictionary stores settings such as the name of
@@ -2034 +2034 @@
 
 
-   \textbf{USAGE:}
+   \textbf{USAGE:} \nopagebreak
 
     {\small \begin{verbatim}
@@ -2070 +2070 @@
 up/down arrows & increase/decrease speed\\
 
-left/right arrows & direction in time \emph{(when running)}\\ & step through simulation \emph{(when stopped)}\\
+left/right arrows & direction in time \emph{(when running)}\\
+& step through simulation \emph{(when stopped)}\\
 
 left mouse button & rotate\\
@@ -2088 +2089 @@
 Options:\\  \nopagebreak
 \begin{tabular}{ll}
-  \code{--display <type>} & \code{MONITOR | POWERWALL | REALITY_CENTER |}\\
-                                    & \code{HEAD_MOUNTED_DISPLAY}\\
+  \code{--display <type>} & \code{MONITOR | POWERWALL | REALITY\_CENTER |}\\
+                                    & \code{HEAD\_MOUNTED\_DISPLAY}\\
   \code{--rgba} & Request a RGBA colour buffer visual\\
   \code{--stencil} & Request a stencil buffer visual\\
   \code{--stereo} & Use default stereo mode which is \code{ANAGLYPHIC} if not \\
                                     & overridden by environmental variable\\
-  \code{--stereo <mode>} & \code{ANAGLYPHIC | QUAD_BUFFER | HORIZONTAL_SPLIT |}\\
-                                    & \code{VERTICAL_SPLIT | LEFT_EYE | RIGHT_EYE |}\\
+  \code{--stereo <mode>} & \code{ANAGLYPHIC | QUAD\_BUFFER | HORIZONTAL\_SPLIT |}\\
+                                    & \code{VERTICAL\_SPLIT | LEFT\_EYE | RIGHT\_EYE |}\\
                                      & \code{ON | OFF} \\
   \code{-alphamax <float 0-1>} & Maximum transparency clamp value\\
   \code{-alphamin <float 0-1>} & Transparency value at \code{hmin}\\
+\end{tabular}
+
+\begin{tabular}{ll}
   \code{-cullangle <float angle 0-90>} & Cull triangles steeper than this value\\
   \code{-help} & Display this information\\
   \code{-hmax <float>} & Height above which transparency is set to
                                      \code{alphamax}\\
+\end{tabular}
+
+\begin{tabular}{ll}
+
   \code{-hmin <float>} & Height below which transparency is set to
                                      zero\\
+\end{tabular}
+
+\begin{tabular}{ll}
   \code{-lightpos <float>,<float>,<float>} & $x,y,z$ of bedslope directional light ($z$ is
                                      up, default is overhead)\\
+\end{tabular}
+
+\begin{tabular}{ll}
   \code{-loop}  & Repeated (looped) playback of \code{.swm} files\\
+
+\end{tabular}
+
+\begin{tabular}{ll}
   \code{-movie <dirname>} & Save numbered images to named directory and
                                      quit\\
+
   \code{-nosky} & Omit background sky\\
+
+
   \code{-scale <float>} & Vertical scale factor\\
   \code{-texture <file>} & Image to use for bedslope topography\\
@@ -2123 +2144 @@
   \refmodindex{utilities.polygon}
 
-  \begin{classdesc}{Polygon_function}{regions, default = 0.0, geo_reference = None}
+  \begin{classdesc}{Polygon\_function}{regions, default = 0.0, geo_reference = None}
   Module: \code{utilities.polygon}
 
@@ -2141 +2162 @@
   \end{classdesc}
 
-  \begin{funcdesc}{read_polygon}{filename}
+  \begin{funcdesc}{read\_polygon}{filename}
   Module: \code{utilities.polygon}
 
@@ -2149 +2170 @@
   \end{funcdesc}
 
-  \begin{funcdesc}{populate_polygon}{polygon, number_of_points, seed = None, exclude = None}
+  \begin{funcdesc}{populate\_polygon}{polygon, number_of_points, seed = None, exclude = None}
   Module: \code{utilities.polygon}
 
@@ -2156 +2177 @@
   \end{funcdesc}
 
-  \begin{funcdesc}{point_in_polygon}{polygon, delta=1e-8}
+  \begin{funcdesc}{point\_in\_polygon}{polygon, delta=1e-8}
   Module: \code{utilities.polygon}
 
@@ -2164 +2185 @@
   \end{funcdesc}
 
-  \begin{funcdesc}{inside_polygon}{points, polygon, closed = True, verbose = False}
+  \begin{funcdesc}{inside\_polygon}{points, polygon, closed = True, verbose = False}
   Module: \code{utilities.polygon}
 
@@ -2175 +2196 @@
   \end{funcdesc}
 
-  \begin{funcdesc}{outside_polygon}{points, polygon, closed = True, verbose = False}
+  \begin{funcdesc}{outside\_polygon}{points, polygon, closed = True, verbose = False}
   Module: \code{utilities.polygon}
 
-  Exactly like \code{inside_polygon}, but with the words `inside' and `outside' interchanged.
+  Exactly like \code{inside\_polygon}, but with the words `inside' and `outside' interchanged.
   \end{funcdesc}
 
-  \begin{funcdesc}{is_inside_polygon}{point, polygon, closed=True, verbose=False}
+  \begin{funcdesc}{is\_inside\_polygon}{point, polygon, closed=True, verbose=False}
   Module: \code{utilities.polygon}
 
@@ -2189 +2210 @@
   \end{funcdesc}
 
-  \begin{funcdesc}{is_outside_polygon}{point, polygon, closed=True, verbose=False}
+  \begin{funcdesc}{is\_outside\_polygon}{point, polygon, closed=True, verbose=False}
   Module: \code{utilities.polygon}
 
-  Exactly like \code{is_outside_polygon}, but with the words `inside' and `outside' interchanged.
+  Exactly like \code{is\_outside\_polygon}, but with the words `inside' and `outside' interchanged.
   \end{funcdesc}
 
-  \begin{funcdesc}{point_on_line}{x, y, x0, y0, x1, y1}
+  \begin{funcdesc}{point\_on\_line}{x, y, x0, y0, x1, y1}
   Module: \code{utilities.polygon}
 
@@ -2203 +2224 @@
   \end{funcdesc}
 
-  \begin{funcdesc}{separate_points_by_polygon}{points, polygon, closed = True, verbose = False}
-    \indexedcode{separate_points_by_polygon}
+  \begin{funcdesc}{separate\_points\_by\_polygon}{points, polygon, closed = True, verbose = False}
+    \indexedcode{separate\_points\_by\_polygon}
   Module: \code{utilities.polygon}
 
   \end{funcdesc}
 
-  \begin{funcdesc}{polygon_area}{polygon}
+  \begin{funcdesc}{polygon\_area}{polygon}
   Module: \code{utilities.polygon}
 
@@ -2215 +2236 @@
   \end{funcdesc}
 
-  \begin{funcdesc}{plot_polygons}{polygons, figname, verbose = False}
+  \begin{funcdesc}{plot\_polygons}{polygons, figname, verbose = False}
   Module: \code{utilities.polygon}
 
-  Plots each polygon contained in input polygon list, e.g. 
+  Plots each polygon contained in input polygon list, e.g.
  \code{polygons = [poly1, poly2, poly3]} where \code{poly1 = [[x11,y11],[x12,y12],[x13,y13]]}
  etc.  Each polygon is closed for plotting purposes and subsequent plot saved to \code{figname}.
@@ -2225 +2246 @@
   \end{funcdesc}
 
-\section{coordinate_transforms}
-
-\section{geospatial_data}
+\section{coordinate\_transforms}
+
+\section{geospatial\_data}
 
 This describes a class that represents arbitrary point data in UTM
@@ -2238 +2259 @@
 
 
-\begin{classdesc}{Geospatial_data}
+\begin{classdesc}{Geospatial\_data}
   {data_points = None,
     attributes = None,
@@ -2244 +2265 @@
     default_attribute_name = None,
     file_name = None}
-Module: \code{geospatial_data}
+Module: \code{geospatial\_data}
 
 This class is used to store a set of data points and associated
@@ -2251 +2272 @@
 
 The data points are specified either by reading them from a NetCDF
-or XYA file, identified through the parameter \code{file_name}, or
+or XYA file, identified through the parameter \code{file\_name}, or
 by providing their \code{x}- and \code{y}-coordinates in metres,
 either as a sequence of 2-tuples of floats or as an $M \times 2$
 Numeric array of floats, where $M$ is the number of points.
 Coordinates are interpreted relative to the origin specified by the
-object \code{geo_reference}, which contains data indicating the UTM
-zone, easting and northing. If \code{geo_reference} is not
+object \code{geo\_reference}, which contains data indicating the UTM
+zone, easting and northing. If \code{geo\_reference} is not
 specified, a default is used.
 
@@ -2264 +2285 @@
 keys are the attribute names and whose values are lists or arrays of
 length $M$. One of the attributes may be specified as the default
-attribute, by assigning its name to \code{default_attribute_name}.
+attribute, by assigning its name to \code{default\_attribute\_name}.
 If no value is specified, the default attribute is taken to be the
 first one.
@@ -2270 +2291 @@
 
 
-\begin{funcdesc}{import_points_file}{delimiter = None, verbose = False}
-
-\end{funcdesc}
-
-
-\begin{funcdesc}{export_points_file}{ofile, absolute=False}
-
-\end{funcdesc}
-
-
-\begin{funcdesc}{get_data_points}{absolute = True}
-
-\end{funcdesc}
-
-
-\begin{funcdesc}{set_attributes}{attributes}
-
-\end{funcdesc}
-
-
-\begin{funcdesc}{get_attributes}{attribute_name = None}
-
-\end{funcdesc}
-
-
-\begin{funcdesc}{get_all_attributes}{}
-
-\end{funcdesc}
-
-
-\begin{funcdesc}{set_default_attribute_name}{default_attribute_name}
-
-\end{funcdesc}
-
-
-\begin{funcdesc}{set_geo_reference}{geo_reference}
-
-\end{funcdesc}
-
-
-\begin{funcdesc}{__add__}
+\begin{funcdesc}{import\_points\_file}{delimiter = None, verbose = False}
+
+\end{funcdesc}
+
+
+\begin{funcdesc}{export\_points\_file}{ofile, absolute=False}
+
+\end{funcdesc}
+
+
+\begin{funcdesc}{get\_data\_points}{absolute = True}
+
+\end{funcdesc}
+
+
+\begin{funcdesc}{set\_attributes}{attributes}
+
+\end{funcdesc}
+
+
+\begin{funcdesc}{get\_attributes}{attribute_name = None}
+
+\end{funcdesc}
+
+
+\begin{funcdesc}{get\_all\_attributes}{}
+
+\end{funcdesc}
+
+
+\begin{funcdesc}{set\_default\_attribute\_name}{default_attribute_name}
+
+\end{funcdesc}
+
+
+\begin{funcdesc}{set\_geo\_reference}{geo_reference}
+
+\end{funcdesc}
+
+
+\begin{funcdesc}{add}{}
 
 \end{funcdesc}
@@ -2317 +2338 @@
 \section{pmesh GUI}
 
-\section{alpha_shape}
+\section{alpha\_shape}
 An \emph{alpha shape} is a shape created from a set of points in the
 plane, according to an algorithm. This shape is intended to capture
@@ -2335 +2356 @@
 associated with instances of this class.
 
-\begin{classdesc}{Alpha_Shape}{points, alpha = None}
-Module: \code{alpha_shape}
+\begin{classdesc}{Alpha\_Shape}{points, alpha = None}
+Module: \code{alpha\_shape}
 
 To instantiate this class the user supplies the points from which
 the alpha shape is to be created (in the form of a list of 2-tuples
 \code{[[x1, y1],[x2, y2]}\ldots\code{]}, assigned to the parameter
-\code{points}) and, optionally, a value for the parameter $\alpha$.
-The alpha shape is then computed and details of the required
-boundary may be retrieved as attributes of the class instance.
+\code{points}) and, optionally, a value for the parameter
+\code{alpha}. The alpha shape is then computed and details of the
+required boundary may be retrieved as attributes of the class
+instance.
 \end{classdesc}
 
 
-\begin{funcdesc}{alpha_shape_via_files}{point_file, boundary_file, alpha= None}
-Module: \code{alpha_shape}
+\begin{funcdesc}{alpha\_shape\_via\_files}{point_file, boundary_file, alpha= None}
+Module: \code{alpha\_shape}
 
 This function reads points from the specified file
-\code{point_file}, computes the associated alpha shape (either using
-the specified value for \code{alpha} or, if no value is specified,
-automatically setting it to a value judged to be optimal} and
-outputs the boundary to a file named \code{boundary_file}. This
+\code{point\_file}, computes the associated alpha shape (either
+using the specified value for \code{alpha} or, if no value is
+specified, automatically setting it to a value judged to be optimal)
+and outputs the boundary to a file named \code{boundary\_file}. This
 output file lists the coordinates \code{x, y} of each point in the
 boundary, using one line per point.
@@ -2360 +2382 @@
 
 
-\begin{funcdesc}{set_boundary_type}{self,raw_boundary=True,
+\begin{funcdesc}{set\_boundary\_type}{self,raw_boundary=True,
                           remove_holes=False,
                           smooth_indents=False,
                           expand_pinch=False,
                           boundary_points_fraction=0.2}
-Module: \code{alpha_shape}
+Module: \code{alpha\_shape}
 
 This function sets flags that govern the operation of the algorithm
-that computes the boundary, 
-        raw_boundary    Return raw boundary i.e. the regular edges of the
-                        alpha shape.
-        remove_holes    filter to remove small holes
-                        (small is defined by  boundary_points_fraction )
-        smooth_indents  remove sharp triangular indents in boundary
-        expand_pinch    test for pinch-off and correct
-                           i.e. a boundary vertex with more than two edges.
-\end{funcdesc}
-
-\section{utilities/numerical_tools}
-
-\begin{tabular}{|l l|}  \hline
+that computes the boundary, as follows:
+
+        Set \code{raw\_boundary = True} to return raw boundary, i.e. the regular edges of the
+                        alpha shape.\\
+        Set \code{remove\_holes = True} to remove small holes
+                        (`small' is defined by
+                        \code{boundary\_points\_fraction})\\
+        Set \code{smooth\_indents = True} to remove sharp triangular indents in
+        boundary\\
+        Set \code{expand\_pinch = True} to test for pinch-off and
+        correct, i.e. to prevent a boundary vertex having more than two edges.
+\end{funcdesc}
+
+\section{Numerical Tools}
+
+The following table describes some useful numerical functions that
+may be found in the module \module{utilities.numerical\_tools}:
+
+\begin{tabular}{|p{8cm} p{8cm}|}  \hline
 \code{angle(v1, v2=None)} & Angle between two-dimensional vectors
-\code{v1} and \code{v2}, in range $0$ to $2\pi$. If \code{v2} is
-omitted it is taken as the unit vector in the $x$-direction.\\
-
-\code{normal_vector(v)} & Normal vector to \code{v}\\
-
-\code{mean(x)} & Mean value of a vector\\
+\code{v1} and \code{v2}, or between \code{v1} and the $x$-axis if
+\code{v2} is \code{None}. Value is in range $0$ to $2\pi$. \\
+
+\code{normal\_vector(v)} & Normal vector to \code{v}.\\
+
+\code{mean(x)} & Mean value of a vector \code{x}.\\
 
 \code{cov(x, y=None)} & Covariance of vectors \code{x} and \code{y}.
-If y is None, returns \code{cov(x, x)}\\
+If \code{y} is \code{None}, returns \code{cov(x, x)}.\\
 
 \code{err(x, y=0, n=2, relative=True)} & Relative error of
 $\parallel$\code{x}$-$\code{y}$\parallel$ to
 $\parallel$\code{y}$\parallel$ (2-norm if \code{n} = 2 or Max norm
-if \code{n} = None). If denominator evaluates to zero or if \code{y}
+if \code{n} = \code{None}). If denominator evaluates to zero or if
+\code{y}
 is omitted, absolute error is returned.\\
 
-\code{norm(x)} & 2-norm of \code{x}\\
+\code{norm(x)} & 2-norm of \code{x}.\\
 
 \code{corr(x, y=None)} & Correlation of \code{x} and \code{y}. If
 \code{y} is \code{None} returns autocorrelation of \code{x}.\\
 
-\code{ensure_numeric(A, typecode = None)} & Ensure that sequence is
+\code{ensure\_numeric(A, typecode = None)} & Ensure that sequence is
 a Numeric array. If \code{A} is already a Numeric array it will be
 returned unaltered. Otherwise, an attempt is made to convert it to a
-Numeric array. This function is necessary as \code{array(A)} can
-cause memory overflow.\\
+Numeric array. (Needed because \code{array(A)} can
+cause memory overflow.)\\
 
 \code{histogram(a, bins, relative=False)} & Standard histogram. If
@@ -2413 +2442 @@
 the total and thus represent frequencies rather than counts.\\
 
-\code{create_bins(data, number_of_bins = None)} & Safely create bins
-for use with histogram. If data contains only one point or is
-constant, one bin will be created. If \code{number_of_bins} is
-omitted, 10 bins will be created.\\  \hline
+\code{create\_bins(data, number\_of\_bins = None)} & Safely create
+bins for use with histogram. If \code{data} contains only one point
+or is constant, one bin will be created. If \code{number\_of\_bins}
+is omitted, 10 bins will be created.\\  \hline
 
 \end{tabular}
-
-
-\begin{itemize}
-  \item \indexedcode{ensure_numeric}
-  \item \indexedcode{mean}
-  \item
-\end{itemize}
 
 
@@ -2481 +2503 @@
 
 \subsubsection{Can I start the simulation at an arbitrary time?}
-Yes, using \code{domain.set_time()} you can specify an arbitrary starting time.
-This is for example useful in conjunction with a file_boundary, which may start hours before anything hits the model boundary. By assigning a later time for the model to start, computational resources aren't wasted.
+Yes, using \code{domain.set\_time()} you can specify an arbitrary
+starting time. This is for example useful in conjunction with a
+file\_boundary, which may start hours before anything hits the model
+boundary. By assigning a later time for the model to start,
+computational resources aren't wasted.
 
 \subsubsection{Can I change values for any quantity during the simulation?}
-Yes, using \code{domain.set_quantity()} inside the domain.evolve loop you
-can change values of any quantity. This is for example useful if you wish to
-let the system settle for a while before assigning an initial condition. Another example would be changing the values for elevation to model e.g. erosion.
+Yes, using \code{domain.set\_quantity()} inside the domain.evolve
+loop you can change values of any quantity. This is for example
+useful if you wish to let the system settle for a while before
+assigning an initial condition. Another example would be changing
+the values for elevation to model e.g. erosion.
 
 \subsubsection{Can I change boundary conditions during the simulation?}
@@ -2499 +2526 @@
 
 \subsubsection{How do I use a DEM in my simulation?}
-You use \code{dem2pts} to convert your DEM to the required .pts format. This .pts file is then called 
+You use \code{dem2pts} to convert your DEM to the required .pts format. This .pts file is then called
 when setting the elevation data to the mesh in \code{domain.set_quantity}
 
 \subsubsection{What sort of DEM resolution should I use?}
-Try and work with the \emph{best} you have available. Onshore DEMs are typically available in 25m, 100m and 250m grids. Note, offshore data is often sparse,
-or non-existant.
+Try and work with the \emph{best} you have available. Onshore DEMs
+are typically available in 25m, 100m and 250m grids. Note, offshore
+data is often sparse, or non-existent.
 
 \subsubsection{What sort of mesh resolution should I use?}
@@ -2528 +2556 @@
 
 \subsubsection{How do I know which boundary tags are available?}
-The method \code{domain.get_boundary_tags()} will return a list of
-available tags for use with \code{domain.set_boundary_condition()}.
+The method \code{domain.get\_boundary\_tags()} will return a list of
+available tags for use with
+\code{domain.set\_boundary\_condition()}.
 
 
@@ -2537 +2566 @@
 \chapter{Glossary}
 
-\begin{tabular}{|l p{10cm}| c|}  \hline
+\begin{tabular}{|lp{10cm}|c|}  \hline
+%\begin{tabular}{|llll|}  \hline
     \emph{Term} & \emph{Definition} & \emph{Page}\\  \hline
 
@@ -2543 +2573 @@
     GA) & \pageref{def:anuga}\\
 
-    \indexedbold{domain} & The domain of a function is the set of all input values to the
-    function.&\\
-
-    \indexedbold{Dirichlet boundary} & A Dirichlet boundary condition imposed on a differential equation
- which specifies the values the solution is to take on the boundary of the
- domain.&\\
-
-    \indexedbold{elevation} & refers to bathymetry and topography&\\
-
     \indexedbold{bathymetry} & offshore elevation &\\
 
-    \indexedbold{topography} & onshore elevation &\\
+    \indexedbold{conserved quantity} & conserved (stage, x and y
+    momentum) & \\
+
+%    \indexedbold{domain} & The domain of a function is the set of all input values to the
+%    function.&\\
+
+    \indexedbold{Digital Elevation Model (DEM)} & DEMs are digital files consisting of points of elevations,
+sampled systematically at equally spaced intervals.& \\
+
+    \indexedbold{Dirichlet boundary} & A boundary condition imposed on a differential equation
+ that specifies the values the solution is to take on the boundary of the
+ domain. & \pageref{def:dirichlet boundary}\\
+
+    \indexedbold{edge} & A triangular cell within the computational mesh can be depicted
+    as a set of vertices joined by lines (the edges). & \\
+
+    \indexedbold{elevation} & refers to bathymetry and topography &\\
 
     \indexedbold{evolution} & integration of the shallow water wave equations
     over time &\\
 
+    \indexedbold{finite volume method} & The method evaluates the terms in the shallow water
+    wave equation as fluxes at the surfaces of each finite volume. Because the
+    flux entering a given volume is identical to that leaving the adjacent volume,
+    these methods are conservative. Another advantage of the finite volume method is
+    that it is easily formulated to allow for unstructured meshes. The method is used
+    in many computational fluid dynamics packages. & \\
+
     \indexedbold{forcing term} & &\\
-
-    \indexedbold{IDLE} & Development environment shipped with
-    Python &\\
-
-    \indexedbold{Manning friction coefficient} & &\\
-
-    \indexedbold{mesh} & Triangulation of domain &\\
-
-    \indexedbold{meshfile} & [generic word for either .tsh or
-    .msh file] & \\
-
-    \indexedbold{points file} & [generic word for either .pts or
-    .xya file] & \\
-
-    \indexedbold{grid} & evenly spaced mesh & \\
-
-    \indexedbold{NetCDF} & &\\
-
-    \indexedbold{conserved quantity} & conserved (stage, x and y
-    momentum) & \\
-
-    \indexedbold{reflective boundary} & &\\
-
-    \indexedbold{stage} & &\\
-
-%    \indexedbold{try this}
-
-    \indexedbold{swollen} & visualisation tool &\\
-
-    \indexedbold{time boundary} & defined in the manual (flog from
-    there)&\\
-
-    \indexedbold{transmissive boundary} & defined in the manual (flog from
-    there)&\\
-
-    \indexedbold{xmomentum} & conserved quantity (note, two-dimensional SWW equations say only x and y and NOT
-    z) &\\
-
-    \indexedbold{ymomentum}  & conserved quantity & \\
-
-
-
-    \indexedbold{resolution} &  The maximal area of a triangular cell in a
-    mesh & \\
-
-    \indexedbold{polygon} & A sequence of points in the plane. (Arbitrary polygons can be created
-    in this way.)
-    \anuga represents a polygon in one of two ways. One way is to represent it as a
-    list whose members are either Python tuples
-    or Python lists of length 2. The unit square, for example, would be represented by the
-    list
-    [ [0,0], [1,0], [1,1], [0,1] ]. The alternative is to represent it as an
-    $N \times 2$ Numeric array, where $N$ is the number of points.
-
-    NOTE: More can be read in the module utilities/polygon.py .... &
-    \\  \hline
-
-    \end{tabular}
-
-    \begin{tabular}{|l p{10cm}|c|}   \hline
-
-    \emph{Term} & \emph{Definition} & \emph{Page}\\  \hline
-    \indexedbold{easting} & A rectangular (x,y) coordinate measurement of distance east from a north-south reference line,
-usually a meridian used as the axis of origin within a map zone or
-projection. Easting is a UTM (Universal Transverse Mercator)
-Coordinate. & \\
-
-    \indexedbold{northing} & A rectangular (x,y) coordinate measurement of distance north from a north-south reference line,
-usually a meridian used as the axis of origin within a map zone or
-projection. Northing is a UTM (Universal Transverse Mercator)
-Coordinate. & \\
-
-
-    \indexedbold{latitude} & The angular distance on a mericlear north and south of the equator, expressed in degrees and
-    minutes. & \\
-
-    \indexedbold{longitude} & The angular distance east or west, between the meridian of a particular place on Earth and that of the
-Prime Meridian (located in Greenwich, England) expressed in degrees
-or time.& \\
-
-    \indexedbold{edge} & A triangular cell within the computational mesh can be depicted as a set of vertices joined by lines (the
-    edges). & \\
-
-    \indexedbold{vertex} & A point at which edges meet. & \\
-
-    \indexedbold{finite volume} & The method evaluates the terms in the shallow water wave equation as fluxes at the surfaces of each
-finite volume. Because the flux entering a given volume is identical
-to that leaving the adjacent volume, these methods are conservative.
-Another advantage of the finite volume method is that it is easily
-formulated to allow for unstructured meshes. The method is used in
-many computational fluid dynamics packages. & \\
-
 
     \indexedbold{flux} & the amount of flow through the volume per unit
     time & \\
 
-    \indexedbold{Digital Elevation Model (DEM)} & DEMs are digital files consisting of points of elevations,
-sampled systematically at equally spaced intervals.& \\  \hline
-
-
-\end{tabular}
+    \indexedbold{grid} & Evenly spaced mesh & \\
+
+    \indexedbold{latitude} & The angular distance on a mericlear north and south of the
+    equator, expressed in degrees and minutes. & \\
+
+    \indexedbold{longitude} & The angular distance east or west, between the meridian
+    of a particular place on Earth and that of the Prime Meridian (located in Greenwich,
+    England) expressed in degrees or time.& \\
+
+    \indexedbold{Manning friction coefficient} & &\\
+
+    \indexedbold{mesh} & Triangulation of domain &\\
+
+    \indexedbold{meshfile} & A TSH or MSH file & \pageref{def:meshfile}\\
+
+    \indexedbold{NetCDF} & &\\
+
+    \indexedbold{northing} & A rectangular (x,y) coordinate measurement of distance
+    north from a north-south reference line, usually a meridian used as the axis of
+    origin within a map zone or projection. Northing is a UTM (Universal Transverse
+    Mercator) coordinate. & \\
+
+    \indexedbold{points file} & A PTS or XYA file & \\  \hline
+
+    \end{tabular}
+
+    \begin{tabular}{|lp{10cm}|c|}  \hline
+
+    \indexedbold{polygon} & A sequence of points in the plane. \anuga represents a polygon
+    either as a list consisting of Python tuples or lists of length 2 or as an $N \times 2$
+    Numeric array, where $N$ is the number of points.
+
+    The unit square, for example, would be represented either as
+    \code{[ [0,0], [1,0], [1,1], [0,1] ]} or as \code{array( [0,0], [1,0], [1,1],
+    [0,1] )}.
+
+    NOTE: For details refer to the module \module{utilities/polygon.py}. &
+    \\     \indexedbold{resolution} &  The maximal area of a triangular cell in a
+    mesh & \\
+
+
+    \indexedbold{reflective boundary} & Models a solid wall. Returns same conserved
+    quantities as those present in the neighbouring volume but reflected. Specific to the
+    shallow water equation as it works with the momentum quantities assumed to be the
+    second and third conserved quantities. & \pageref{def:reflective boundary}\\
+
+    \indexedbold{stage} & &\\
+
+%    \indexedbold{try this}
+
+    \indexedbold{swollen} & visualisation tool used with \anuga & \pageref{sec:swollen}\\
+
+    \indexedbold{time boundary} & Returns values for the conserved
+quantities as a function of time. The user must specify
+the domain to get access to the model time. & \pageref{def:time boundary}\\
+
+    \indexedbold{topography} & onshore elevation &\\
+
+    \indexedbold{transmissive boundary} & & \pageref{def:transmissive boundary}\\
+
+    \indexedbold{vertex} & A point at which edges meet. & \\
+
+    \indexedbold{xmomentum} & conserved quantity (note, two-dimensional SWW equations say
+    only \code{x} and \code{y} and NOT \code{z}) &\\
+
+    \indexedbold{ymomentum}  & conserved quantity & \\  \hline
+
+    \end{tabular}
+
 
 %The \code{\e appendix} markup need not be repeated for additional