CH_coding.xml

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<chapter id="Chapter-Coding">
  <title>Writing &oof2; Extensions</title>
  <para>
    This chapter describes the contents of the source files for &oof2;
    extensions.  It begins with an overview of some import
    classes. <xref linkend="Chapter-Extending"/> describes how to
    assemble the source files into a loadable extension module.
  </para>
  
  <section id="Section-Coding-Directory-Structure">
    <title>Source Directory Layout</title>
    <para>
      The &oof2; source code is divided into four main directories:
      <itemizedlist>
        <listitem>
          <simpara>
            <filename>SRC/common</filename>: &micros; and general
            infrastructure.
          </simpara>
        </listitem>
        <listitem>
          <simpara>
            <filename>SRC/engine</filename>: &skels;, &meshes;,
            &properties;, &materials;, and anything else related to the
            finite element machinery.
          </simpara>
        </listitem>
        <listitem>
          <simpara>
            <filename>SRC/image</filename>: &images;.
          </simpara>
        </listitem>
        <listitem>
          <simpara>
            <filename>SRC/orientationmap</filename>: <link
            linkend="Section-Concepts-Microstructure-OrientationMap">orientation
            maps</link>. 
          </simpara>
        </listitem>
      </itemizedlist>
      Most of these directories have a subdirectory called
      <filename>IO</filename> for files related to user interactions
      (menus and such).  Inside <filename>IO</filename> a directory
      called <filename>GUI</filename> holds the gtk-specific code for
      the graphical user interface.  It's not always obvious what
      belongs in <filename>IO</filename> and what doesn't, so we
      regretted making that distinction, and the most recent
      subdirectory, <filename>SRC/orientationmap</filename>, skips
      <filename>IO</filename> and just contains
      <filename>GUI</filename> directly.
    </para>
    <para>
      As a general rule, files in <filename>SRC/common</filename>
      don't include or import any files in any other
      subdirectories. Files in <filename>SRC/engine</filename>,
      <filename>SRC/image</filename>, and
      <filename>SRC/orientationmap</filename> include or import
      code from <filename>SRC/common</filename> but from nowhere else.
      Similarly, all of the code in any <filename>GUI</filename>
      directory refers to code in the directories above it, but
      nothing in the directories above refers to anything in
      <filename>GUI</filename>.  This ensures that the program will
      work correctly when not using the GUI.<footnote><simpara>The
      only exception to these rules is that the code for starting the
      GUI and loading the various modules, in
      <filename>SRC/common/oof.py</filename>, needs to be able to
      initialize the other modules.</simpara></footnote>
    </para>
    <para>
      Additional directories within <filename>SRC</filename> don't
      have <filename>IO</filename> or <filename>GUI</filename>
      subdirectories.  They are
      <itemizedlist>
        <listitem>
          <simpara>
            <filename>EXTENSIONS</filename>:  Source code for
            internal extensions.
          </simpara>
        </listitem>
        <listitem>
          <simpara>
            <filename>Eigen</filename> and
            <filename>unsupported</filename>: a copy of the <ulink
            url="https://eigen.tuxfamily.org/"
            role="external">Eigen</ulink> library and its unsupported
            extensions.
          </simpara>
        </listitem>
        <listitem>
          <simpara>
            <filename>tutorials</filename>: the &oof2; <link
            linkend="MenuItem-OOF.Help.Tutorials">tutorials</link>.
          </simpara>
        </listitem>
      </itemizedlist>
      Of these, only <filename>EXTENSIONS</filename> is important to
      extension authors, probably.
    </para>
  </section>
  <section id="Section-Coding-Package">
    <title>Python Package Layout</title>
    <para>
      The Python package structure mimics the directory layout
      described in <xref
      linkend="Section-Coding-Directory-Structure"/>.  The top-level
      package is <code>ooflib</code>, and within it are packages
      called <code>common</code>, <code>engine</code>,
      <code>image</code>, and <code>orientationmap</code>. When &oof2;
      is started, it modifies the Python path so that the
      <code>ooflib</code> package can be found.
    </para>
    <para>
      Python modules created by <ulink url="http://www.swig.org"
      role="external">swig</ulink>, however, are installed into the
      package <code>ooflib.SWIG</code>.  Within
      <code>ooflib.SWIG</code> are packages named <code>common</code>,
      <code>engine</code>, <code>image</code>, and
      <code>orientationmap</code>.
    </para>
    <para>
      For example, the Python code defining the
      <classname>Microstructure</classname>
      <filename>SRC/common/microstructure.py</filename> can be
      imported into another Python file with
      <programlisting>
from ooflib.common import microstructure </programlisting>
      and the C++ underpinnings of the class, defined in
      <filename>SRC/common/cmicrostructure.C</filename> and wrapped by
      <filename>SRC/common/cmicrostructure.swg</filename>, can be
      imported with
      <programlisting>
from ooflib.SWIG.common import cmicrostructure </programlisting>
    </para>
  </section>

  <!-- =========================================================== -->
  
  <section id="Section-Coding-AddFields">
    <title>Adding New Fields, Fluxes, and Equations</title>
    <para>
      New &Fields;, &Fluxes;, and &Equations; can be
      added with just a few lines of Python code.  The &oof2;
      &Field;, &Flux;, and &Equation; classes represent
      <emphasis>global</emphasis> objects &mdash; there is only one
      instance of the <varname>Temperature</varname> field, for
      example, although the field may be defined on more than one
      &mesh;, or on none at all.  Creating a &Field;,
      &Flux;, or &Equation; object makes it available for
      use in a &mesh;, and records some information about it, such as
      its name and dimension.
    </para>
    <para>
      When a new material &Property; is created, it indicates which
      &Fields;, &Fluxes; and &Equations; it uses.  The &Field;,
      &Flux;, and &Equation; classes themselves are not explicitly
      tied to any particular &Properties;. See <xref
      linkend="Section-Coding-Material"/> for the details.
    </para>
    <para>
      &oof2; predefines some &Fields;, &Fluxes;, and
      &Equations; in <filename>SRC/engine/problem.py</filename>.
      Refer to that file for examples.
    </para>
    <para>
      The &Field; subclasses defined in
      <code>ooflib.SWIG.engine.field</code> are:
      <itemizedlist spacing="compact">
	    <listitem>
	      <simpara>
	        <xref linkend="Class-ScalarField"/>:
	        <foreignphrase>e.g,</foreignphrase>, Temperature, Density
	      </simpara>
	    </listitem>
	    <listitem>
	      <simpara>
	        <xref linkend="Class-TwoVectorField"/>:
	        <foreignphrase>e.g,</foreignphrase> Displacement,
	        Polarization
	      </simpara>
	    </listitem>
      </itemizedlist>
      These classes actually define <xref
      linkend="Class-CompoundField"/>s, which represent the <link
      linkend="Section-Concepts-Mesh-3D">in-plane</link> part of a
      &Field; along with its out of plane components, and the time
      derivatives of its in-plane and out-of-plane components.
    </para>
    <para>
      To create a &Field;, &Flux;, or &Equation;,
      simply call the derived class's Python
      constructor.<footnote><para> &Fields;, &Fluxes;, and
      &Equations; are C++ classes, but they should only be
      instantiated by calling their swigged Python
      constructors. </para></footnote> For example:
      <programlisting>
from ooflib.SWIG.engine import field
Temperature = field.ScalarField("Temperature") </programlisting>
    </para>
    <para>
      New &Fields; should only be created by calling <xref
      linkend="Class-CompoundField"/> constructors in Python. This
      will create four new Python variables whose names are the name
      of the &Field;, the name of the field suffixed with
      <quote>_z</quote> for the out-of-plane field, and the name
      suffixed with <quote>_t</quote> and <quote>_tz</quote> for the
      time derivative and its out-of-plane part.  These variables live
      in the main &oof2; namespace, which is the one in which <link
      linkend="Section-ScriptGUI">text mode</link>, <link
      linkend="MenuItem-OOF.File.Load.Script">scripts</link> and <link
      linkend="Section-Windows-Console">Console Window</link> commands
      are executed.
    </para>
    <para>
      Code outside of the main &oof2; namespace can gain access to the
      new &Fields; with the <xref linkend="Function-getField"/>
      function.  Within the script that created the &Field;, the
      &Field; can of course be referred to via a local variable
      referring to the new object:
      <programlisting>
<emphasis role="bold">gee</emphasis> = field.TwoVectorField("<emphasis role="bold">gee</emphasis>")</programlisting>
      It is acceptable for the local variable name to be the same as
      the global variable name.
    </para>
    
    <para>
      The &Flux; subclasses defined in
      <code>ooflib.SWIG.engine.flux</code> are:
      <itemizedlist spacing="compact">
	<listitem>
	  <simpara>
	    <xref linkend="Class-VectorFlux"/>:
	    <foreignphrase>e.g,</foreignphrase> Mass Current, Heat
	    Flow
	  </simpara>
	</listitem>
	<listitem>
	  <simpara>
	    <xref linkend="Class-SymmetricTensorFlux"/>:
	    <foreignphrase>e.g,</foreignphrase> Stress
	  </simpara>
	</listitem>
      </itemizedlist>
    </para>
    <para>
      The &Equation; subclasses defined in
      <code>ooflib.SWIG.engine.equation</code> are:
      <itemizedlist spacing="compact">
	<listitem>
	  <simpara>
	    <xref linkend="Class-DivergenceEquation"/>: any
	    equation of the form <quote>divergence of a &Flux; =
	    external force</quote>.
	  </simpara>
	</listitem>
	<listitem>
	  <simpara>
	    <xref linkend="Class-PlaneFluxEquation"/>: any equation
	    that constrains the out-of-plane components of a &Flux;.
	  </simpara>
	</listitem>
      </itemizedlist>
      The &Equation; constructors each take a name, a &Flux;, and a
      dimension.   The &Flux; is the
      &Flux; that the &Equation; operates on, and the dimension is an
      integer specifying how many components the equation has.  (The
      divergence of a vector &Flux; has one component, and the divergence
      of a tensor flux has three components.  A
      <classname>PlaneFluxEquation</classname> has as many components
      as there are out-of-plane components of the associated &Flux;.)
    </para>
    <para>
      Like the <xref linkend="Class-Field"/> classes,
      <xref linkend="Class-Flux"/>es and
      <xref linkend="Class-Equation"/>s can be retrieved by name in the
      main &oof2; namespace.  They can also be retrieved by the
      <xref linkend="Function-getFlux"/> and
      <xref linkend="Function-getEquation"/> functions in either C++ or
      Python.  Unlike <xref linkend="Class-Field"/>s, they have no
      auxiliary out-of-plane or time derivative parts.
    </para>
    <para>
      As an example, the following code fully defines the quantities
      necessary to solve the static heat conductivity problem (except
      for the thermal conductivity &material; &property;, which is
      discussed <link linkend="Section-Coding-Material">later</link>).

      <programlisting>
from ooflib.SWIG.engine.field import ScalarField
from ooflib.SWIG.engine.flux import VectorFlux
from ooflib.SWIG.engine.equation import DivergenceEquation, PlaneFluxEquation

Temperature = ScalarField('Temperature')
Heat_Flux = VectorFlux('Heat_Flux')
HeatBalanceEqn = DivergenceEquation('Heat_Eqn', Heat_Flux, 1)
HeatOutOfPlane = PlaneFluxEquation('Plane_Heat_Flux', Heat_Flux, 1) </programlisting>

      Note that all of these quantities are already defined in &oof2;
      (in <filename>SRC/engine/problem.py</filename> to be exact) so
      don't redefine them.  This is just an example of how you might
      define new &Fields; and &Equations;.
    </para>
  </section><!-- Adding New Fields, Fluxes, and Equations -->


  <!-- ========================================================== -->

  <section id="Section-Coding-Indices">
    <title>Indices and Iterators</title>
    <para>
      Before proceeding, it's necessary to take a diversion on the
      topic of indices and iterators.
    </para>
    <para>
      It is often necessary to refer to the components of &Fields;,
      &Fluxes;, &Equations;, and &OutputVal;s.  &oof2;'s
      <filename>fieldindex</filename> module provides a generic
      mechanism for doing this, so that it's possible to loop over all
      of the components of an object without even having to know how
      many indices are required to specify a component.  It takes two
      indices to specify a tensor component, one for a vector, and
      zero for a scalar, but all three cases can be handled
      identically.
    </para>
    <para>
      The basic machinery contains:
      <itemizedlist>
        <listitem>
          <para>
            The &FieldIndex; base class, which designates a component
            of a &Field; or other object.  <!-- There are different
            subclasses for different kinds of objects (scalars,
            vectors, tensors, <foreignphrase>etc</foreignphrase>). -->
          </para>
        </listitem>
        <listitem>
          <para>
            A &Components; base class, which is a container that can
            be iterated over to obtain the &FieldIndexes;.  <!-- There are
            different subclasses for different kinds of objects, and
            for different ways of iterating over them (in-plane,
            out-of-plane, <foreignphrase>etc</foreignphrase>).  Each
            indexable class (&Field;, &Flux;,
            <foreignphrase>etc</foreignphrase>) has a virtual function
            that returns the appropriate type of &Components;. -->
          </para>
        </listitem>
        <listitem>
          <para>
            A &ComponentIterator; base class that is used for
            iterating over the &Components;.  <!-- Different subclasses of
            &ComponentIterator;s iterate over different types of
            &Components;. -->
          </para>
        </listitem>
        <listitem>
          <para>
            Generic wrapper classes, &IndexP; and
            &ComponentIteratorP;, that wrap pointers to &FieldIndex;
            and &ComponentIterator;.
          </para>
        </listitem>
      </itemizedlist>
    </para>
    <para>
      The base class for indices is &FieldIndex;. There are subclasses
      of &FieldIndex; for different kinds of &Fields;, &Fluxes;,
      &Equations;, and &OutputVal;s.  (From now on we'll talk about
      &Fields;, but everything also applies to &Fluxes;, &Equations;
      and &OutputVal;s, unless explicitly stated otherwise.)  To
      handle the polymorphism, generic C++ code doesn't use the
      &FieldIndex; classes directly.  Instead it uses a wrapper class,
      &IndexP;, which is a light-weight object that contains a pointer
      (hence the <quote>P</quote> in the name) to a &FieldIndex;.  The
      wrapper frees the user from having to know the actual class
      being used.  It provides access to its &FieldIndex; and its
      virtual functions, and deallocates it when it goes out of scope.
    </para>
    <para>
      Note that &IndexP; does not do reference
      counting. When an &IndexP; is destructed,
      its &FieldIndex; is destructed as well.
      When an &IndexP; is copied, the original
      &FieldIndex; is copied as well.
    </para>
    <para>
      For looping over the indices of a &Field;, there are
      &Components; and &ComponentIterator; class hierarchies.  Each
      type of &Field; has a <link
      linkend="Class-Field-components"><function>components()</function></link>
      method that returns a &Components; pointer.  The &Components; classes
      are conceptually containers for &FieldIndexes;.  The instances
      of the &Components; subclasses are static immutable objects.
    </para>
    <para>
      In C++, &Components; objects have
      <function>begin()</function> and <function>end()</function>
      methods that return &ComponentIterator;
      objects, allowing them to work like STL iterators for looping
      over indexes.  For example, you can print the indices of the
      components of the Temperature and Displacement &Fields; like this:

      <programlisting>
Field *temperature = Field::getField("Temperature");
Components* comps = temperature->components();
for(ComponentIteratorP ip = comps->begin(); ip!=comps->end(); ++ip)
  std::cerr &lt;&lt; *ip &lt;&lt; std::endl;

Field *displacement = Field::getField("Displacement");
Components* comps = displacement->components();
for(ComponentIteratorP ip = comps->begin(); ip!=comps->end(); ++ip)
  std::cerr &lt;&lt; *ip &lt;&lt; std::endl; </programlisting>

      or, more compactly, using range based for loops like this:

      <programlisting>
for(IndexP i : *Field::getField("Temperature")->components())
   std::cerr &lt;&lt; i &lt;&lt; std::endl;

for(IndexP i : *Field::getField("Displacement")->components())
   std::cerr &lt;&lt; i &lt;&lt; std::endl; </programlisting>

      both of which print
   <literallayout class="monospaced">
IndexP(ScalarFieldIndex())    <lineannotation>[The single component of Temperature]</lineannotation>
IndexP(VectorFieldIndex(0))   <lineannotation>[The first component of Displacement]</lineannotation>
IndexP(VectorFieldIndex(1))   <lineannotation>[The second component of Displacement]</lineannotation></literallayout>
   </para>
   <para>
     In Python, the <function>components()</function>
     methods return generator functions that serve the same purpose.
     For example, in Python you can print the indices of the
     components of the temperature and displacement &Fields; like
     this:
     <programlisting>
for i in Temperature.components():
   print(i)
for i in Displacement.components():
   print(i) </programlisting>

     which prints
     <literallayout class="monospaced">
ScalarFieldIndex()     <lineannotation>[The single component of Temperature]</lineannotation>
VectorFieldIndex(0)    <lineannotation>[The first component of Displacement]</lineannotation>
VectorFieldIndex(1)    <lineannotation>[The second component of Displacement]</lineannotation></literallayout>

    </para>
    <para>
      In some cases it's necessary to restrict iteration to either the
      <link linkend="Section-Concepts-Mesh-3D">in-plane or
      out-of-plane components</link> of a &Field; or &Flux; (but not
      an &Equation;).  In those cases, the
      <methodname>components()</methodname> method takes an argument
      of the &Planarity; class.  If no argument is provided, as in the
      examples above, the default planarity is
      <varname>ALL_INDICES</varname>.  See <link
      linkend="Class-Field-components"><function>Field::components</function></link>,
      <link
      linkend="Class-Field-oop-components"><function>Field::outOfPlaneComponents</function></link>,
      <link
      linkend="Class-Flux-components"><function>Flux::components</function></link>,
      and <link
      linkend="Class-Flux-oop-components"><function>Flux::outOfPlaneComponents</function></link>
      for examples and some important details.
    </para>

  </section>                    <!-- Indices and Iterators -->
  
  <section id="Section-Coding-Conjugates">
    <title>Conjugate Pairs</title>
    <para>
      Finite element problems which lead to a symmetric stiffness
      matrix can be solved efficiently by the <link
      linkend="RegisteredClass-ConjugateGradient">conjugate
      gradient</link> method. &oof2; needs to be told how to construct
      a symmetric matrix, though.
    </para>
    <para>
      Consider a simple elasticity problem.  The degrees of freedom
      are the components of the displacement at each node of the mesh.
      The equations are the components of the force balance at each
      node.  In the stiffness matrix, degrees of freedom correspond to
      columns and equations correspond to rows.  The matrix will be
      symmetric if the columns and rows are ordered so that the force
      component and node of the
      <emphasis>n</emphasis><superscript>th</superscript> row are the
      same as the displacement component and node of the
      <emphasis>n</emphasis><superscript>th</superscript> column.
    </para>
    <para>
      In general, this correspondence is <emphasis>not</emphasis>
      trivial.  If the stress in the example above came from material
      properties other than elasticity, the matrix would not
      necessarily be symmetric.  Including thermal expansion can make
      an elasticity problem asymmetric.
    </para>
    <para>
      The function <link
      linkend="Function-conjugatePair"><function>conjugatePair()</function></link>
      in the <code>ooflib.SWIG.engine.conjugate</code> module
      establishes the correspondence between &Field; and &Equation;
      components that is necessary to build a symmetric matrix.  After
      <link linkend="Section-Coding-AddFields">creating</link>
      &Fields; and &Equations;, call
      <function>conjugatePair</function> like this:

      <programlisting>
from ooflib.SWIG.engine.conjugate import conjugatePair
conjugatePair(proptype, equation, eqncomp, field, fieldcomp) </programlisting>

      where <varname>proptype</varname> is the <link
      linkend="para-propertyType"><classname>PropertyType</classname></link>
      of the &property; that will be symmetrized by this conjugacy
      pair; <varname>equation</varname> is an &Equation; object;
      <varname>field</varname> is a &Field; object, and
      <varname>eqncomp</varname> and <varname>fieldcomp</varname> are
      either &FieldIndex; objects or iterable containers of them.  For
      example, the following code establishes the correspondence
      between the <emphasis>x</emphasis> and <emphasis>y</emphasis>
      components of the displacement field and the force balance
      equation (<code>import</code> statements have been omitted for
      conciseness):

      <programlisting>
equation = getEquation('Force_Balance')
field = getField('Displacement')
conjugatePair("Elasticity",
              equation, equation.components(),
              field, field.components()) </programlisting>

      See <link
      linkend="Function-conjugatePair"><function>conjugatePair()</function></link>
      for some important details about making sure that the &Equation;
      and &Field; components are in the same order.
    </para>
    <para>
      Calling <function>conjugatePair</function> is necessary but not
      sufficient for &oof2; to create symmetric stiffness matrices.
      The &properties; that contribute to the stiffness matrix must
      also support symmetry.  This is discussed in <xref
      linkend="Section-Coding-Material"/>.
    </para>
    <para>
      It is not required that <function>conjugatePair</function> be
      called on all defined fields and equations, but failing to do so
      will make the <link
      linkend="RegisteredClass-ConjugateGradient">conjugate
      gradient</link> solver unavailable for problems involving these
      fields and equations.
    </para>
    <para>
      It is also not necessary to call the
      <function>conjugatePair</function> for the predefined fields in
      &oof2;, since conjugacy is predefined for these fields and
      equations in <filename>SRC/engine/problem.py</filename>.
    </para>
  </section><!-- Conjugate Pairs -->

  <section id="Section-Coding-Material">
    <title>Adding New Material Properties</title>
    <para>
      New &material; &properties; are the most complicated kind of
      &oof2; extension.  Just to make it simpler, there are two ways
      of doing it.  &properties; can be written in C++ or they can be
      written in Python.  Python &properties; are a bit easier to
      write and install, but will run significantly more slowly.  It
      may be convenient to develop new &properties; in Python and
      translate them to C++ after the bugs have been worked out.
    </para>
    <para>
      Whether a &property; is written in C++ or Python, the same code
      elements must be present.  Not all of them are necessary for
      every &property;.  It is safe simply to omit the unnecessary
      ones.
    </para>
    <para>
      A &property; consists of a class definition and a <link
      linkend="Class-PropertyRegistration"><classname>PropertyRegistration</classname></link>
      object.  The registration contains metadata about the &property;
      and allows it to be found in the user interface.  The class
      must be a subclass of one of these intermediate base classes:
      <itemizedlist>
        <listitem>
          <para>
            A <xref linkend="Class-FluxProperty"/> contributes to a
            &flux;.  For example, <xref
            linkend="Property-Mechanical-Elasticity-Isotropic"/>
            contributes to <xref linkend="Flux-Stress"/>. 
          </para>
        </listitem>
        <listitem>
          <para>
            An <xref linkend="Class-EqnProperty"/> contributes
            directly to an &equation;.  For example, <xref
            linkend="Property-Mechanical-MassDensity-ConstantMassDensity"/>
            provides the mass times acceleration term in the <xref
            linkend="Equation-Force_Balance"/> equation.
          </para>
        </listitem>
        <listitem>
          <para>
            An <xref linkend="Class-AuxProperty"/> is neither of the
            above, but can be used indirectly by other &Properties;.
            For example, <xref linkend="Property-Orientation"/> is
            used by all anisotropic &Properties;.  <xref
            linkend="Property-Color"/> is used to display &materials;.
          </para>
        </listitem>
      </itemizedlist>
      See the documentation for each intermediate class for the
      details.
    </para>
    <para>
      &property; classes perform the following types of tasks (the
      links below each task lead to detailed documentation, see the
      pages for the classes for the full list of methods):
      <itemizedlist>
	    <listitem>
	      <para>
            <anchor id="para-propertyType"/>
	        <emphasis>Identification.</emphasis> &properties; have
	        names by which they are identified in the user interface.
	        They also have a <emphasis>propertyType</emphasis>.  A
	        <varname>propertyType</varname> is a string that
	        identifies the &property;'s physical role.  Each
	        &material; instance can have at most one &property; of
	        each <varname>propertyType</varname>.  For example, all
	        &properties; that provide an elastic modulus have the type
	        <literal>'Elasticity'</literal>, and all thermal expansion
	        &properties; have the type
	        <literal>'ThermalExpansion'</literal>.  Authors of new
	        types of &property; should invent new
	        <varname>propertyType</varname> strings.  Authors of new
	        versions of a preexisting &property; should examine the
	        existing <link
	        linkend="Class-PropertyRegistration"><classname>PropertyRegistrations</classname></link>
	        and reuse the same <varname>propertyType</varname>.
	      </para>
	      <itemizedlist spacing="compact">
	        <listitem>
	          <simpara>
		        <link linkend="Class-PropertyRegistration"><classname>PropertyRegistration</classname></link>
	          </simpara>
	        </listitem>
	        <listitem>
	          <simpara><link
	          linkend="Class-Property-Constructors"><classname>Property</classname>
	          constructor</link></simpara>
	        </listitem>
	      </itemizedlist>
	    </listitem>
	    <listitem>
	      <para>
	        <emphasis>Cross Referencing.</emphasis> Sometimes a
	        &property; needs to use data from other &properties; in
	        the same &material;.  For example, any anisotropic
	        &property; will need to find out its &material;'s <link
	        linkend="MenuItem-OOF.Property.Parametrize.Orientation"><classname>Orientation</classname></link>. Cross
	        referencing allows a &property; to use
	        <classname>propertyType</classname> information to locate
	        other &properties;.  This is done after a &material; is
	        constructed but before it is used for numerical
	        computations.
	      </para>
	      <itemizedlist spacing="compact">
	        <listitem>
	          <simpara><link
		                   linkend="Class-Property-cross_reference"><code>Property::cross_reference</code></link></simpara>
	        </listitem>
	      </itemizedlist>
	    </listitem>
	    <listitem>
	      <para>
            <anchor id="para-precomputation"/>
	        <emphasis>Precomputation.</emphasis> When constructing the
	        finite element stiffness matrix, the &oof2; program loops
	        over all &elems; and asks their &materials; to ask their
	        &properties; to make their contributions to the matrix at
            each Gauss point.
	        For efficiency, &properties; may want to precompute some
	        quantities before this process begins.  There are three
	        possible precomputation points: before looping over
            &elems;, before looping over &nodes;, and before looping
            over Gauss points (to integrate shape functions):
	      </para>
	      <itemizedlist spacing="compact">
	        <listitem>
	          <simpara>
		        <link
		        linkend="Class-Property-precompute"><code>Property::precompute</code></link>
	          </simpara>
	        </listitem>
	        <listitem>
	          <simpara>
		        <link
		        linkend="Class-Property-begin_element"><code>Property::begin_element</code></link>
	          </simpara>
	        </listitem>
	        <listitem>
	          <simpara>
		        <link
                    linkend="Class-FluxProperty-begin_point"><code>FluxProperty::begin_point</code></link>
                and <link linkend="Class-EqnProperty-begin_point"><code>EqnProperty::begin_point</code></link>
	          </simpara>
	        </listitem>
	      </itemizedlist>
	    </listitem>
	    <listitem>
	      <para>
            <anchor id="para-computation"/>
	        <emphasis>Computation.</emphasis> &properties; can make
	        contributions to the finite element stiffness matrix in
            various ways: and
	        to the right-hand side vector of external
	        <quote>forces</quote>.  There are various ways of doing
            this, applicable in different situations:
	      </para>
	      <itemizedlist spacing="compact">
	        <listitem>
	          <simpara>
		        <link
		        linkend="Class-FluxProperty-flux_matrix"><code>FluxProperty::flux_matrix</code></link>
	          </simpara>
	        </listitem>
	        <listitem>
	          <simpara>
		        <link
		        linkend="Class-FluxProperty-flux_offset"><code>FluxProperty::flux_offset</code></link>
	          </simpara>
	        </listitem>
            <listitem>
              <simpara>
                <link
                    linkend="Class-FluxProperty-flux_value"><code>FluxProperty::flux_value</code></link>
              </simpara>
            </listitem>
            <listitem>
              <simpara>
                <link
                    linkend="Class-FluxProperty-static_flux_value"><code>FluxProperty::static_flux_value</code></link>
              </simpara>
            </listitem>
          </itemizedlist>
          <para>
            A &property; can make contributions to the force vector
            and other quantities (such as mass or damping terms) that
            appear in the equations but aren't part of a &flux;:
          </para>
          <itemizedlist>
            <listitem>
              <simpara>
                <link linkend="Class-EqnProperty-force_deriv_matrix"><code>EqnProperty::force_deriv_matrix</code></link>
              </simpara>
            </listitem>
            <listitem>
              <simpara>
                <link linkend="Class-EqnProperty-force_value"><code>EqnProperty::force_value</code></link>
              </simpara>
            </listitem>
            <listitem>
              <simpara>
                <link linkend="Class-EqnProperty-time_deriv_matrices"><code>EqnProperty::time_deriv_matrices</code></link>
              </simpara>
            </listitem>
	      </itemizedlist>

          <para>
	        There are also a few functions that &properties; may
	        define that influence the way they're used or the way a
	        computation is done:
          </para>
	      <itemizedlist spacing="compact">
	        <listitem>
		      <simpara>
		        <link
		        linkend="Class-Property-is_symmetric"><code>Property::is_symmetric</code></link>
		      </simpara>
	        </listitem>
	        <listitem>
		      <simpara>
		        <link
		        linkend="Class-PhysicalProperty-integration_order"><code>PhysicalProperty::integration_order</code></link>
		      </simpara>
	        </listitem>
	      </itemizedlist>
	    </listitem>
	    <listitem>
	      <para>
	        <emphasis>Postcomputation.</emphasis> This is just like
	        <link linkend="para-precomputation">precomputation</link>,
	        but later.  It can be done after the <link
	        linkend="para-computation">computation</link> on each
	        Gauss point, each <classname>GaussPoint</classname>, each
	        &elem;, or after a full solution has been obtained.
	      </para>
	      <itemizedlist spacing="compact">
	        <listitem>
		      <simpara>
		        <link
                    linkend="Class-FluxProperty-end_point"><code>FluxProperty::end_point</code></link>
                and
                <link linkend="Class-EqnProperty-end_point"><code>EqnProperty::end_point</code></link>
		      </simpara>
	        </listitem>
	        <listitem>
	          <simpara>
		        <link
		        linkend="Class-Property-end_element"><code>Property::end_element</code></link>
	          </simpara>
	        </listitem>
	        <listitem>
	          <simpara>
		        <link
		        linkend="Class-Property-post_process"><code>Property::post_process</code></link>
	          </simpara>
	        </listitem>
	      </itemizedlist>
	    </listitem>
	    <listitem>
	      <para>
	        <emphasis>Outputs.</emphasis> Many <link
	        linkend="Section-Concepts-Outputs">output</link>
	        quantities, such as &field; invariants, are defined
	        without reference to &properties;, but there are also many
	        outputs, such as energy densities, that depend upon a
	        &property; in one way or another, and rely upon the
	        &property;'s code.  See <xref
	        linkend="Section-Coding-Output"/> to learn how to add new
	        outputs.
	      </para>
	      <itemizedlist spacing="compact">
	        <listitem>
	          <simpara>
		        <link linkend="Class-Property-output"><code>Property::output</code></link>
	          </simpara>
	        </listitem>
	      </itemizedlist>
	    </listitem>
      </itemizedlist>
    </para>
  </section>                   <!-- Adding New Material Properties -->

  <section id="Section-Coding-Output">
    <title>Adding New Outputs</title>
    <para>
      <classname>Outputs</classname> in &oof2; are operations
      performed on &mesh; data.  The results can be sent to the <link
      linkend="Chapter-Graphics">graphics window</link> and displayed
      in a <link
      linkend="RegisteredClass-FilledContourDisplay">contour
      plot</link>, or analyzed on the <link
      linkend="Section-Tasks-Analysis">Analysis Page</link>.
    </para>
    <para>
      The outputs that the user sees come in three flavors:
      <itemizedlist spacing="compact">
	<listitem>
	  <para>
	    <emphasis>Scalar</emphasis> outputs are just numbers, to
	    be plotted or analyzed.
	  </para>
	</listitem>
	<listitem>
	  <para>
	    <emphasis>Aggregate</emphasis> outputs are quantities like
	    &Fields; and &Fluxes; that can't be plotted directly
	    (because they generally have too many components) but can
	    still be analyzed.
	  </para>
	</listitem>
	<listitem>
	  <para>
	    <emphasis>Position</emphasis> outputs are two dimensional
	    vectors that determine where scalar outputs are displayed
	    in contour plots.
	  </para>
	</listitem>
      </itemizedlist>
    </para>
    <para>
      Under the hood, the scalar, aggregate, and position outputs are
      built by combining <link
      linkend="Class-Output"><classname>Output</classname></link>
      objects.  Each <classname>Output</classname> object performs a
      simple operation on a set of input values and creates a set of
      output values.  Simple <classname>Outputs</classname> are
      chained together, with the output of one connected to the input
      of another, to create more complicated
      <classname>Outputs</classname>.  (One
      <classname>Output</classname> object can be used in many
      different Output chains.)  Only those
      <classname>Outputs</classname> that are <link
	linkend="Function-definePositionOutput">registered</link> with
      the GUI are directly available to the user.
    </para>
    <para>
      <classname>Outputs</classname> have parameters which govern
      their behavior.  <classname>Output</classname> parameters use
      the same <link
      linkend="Class-Parameter"><classname>Parameter</classname></link>
      classes that are used in
      <link
          linkend="Class-OOFMenuItem"><classname>OOFMenuItems</classname></link>
      and 
      <link
      linkend="Class-PropertyRegistration"><classname>PropertyRegistrations</classname></link>.
    </para>
    <para>
      &oof2; includes predefined <classname>Outputs</classname> that
      can be used by themselves or combined with new
      <classname>Outputs</classname>.  The predefined
      <classname>Outputs</classname> can evaluate the components and
      invariants of &Fields; and &Fluxes; and compute energies and
      strains.  For the details, consult the source code in
      <filename>SRC/engine/IO/outputClones.py</filename> and
      <filename>SRC/engine/IO/outputDefs.py</filename>.
    </para>
    <para>
      Creating a new <classname>Output</classname> involves the
      following steps:
      <itemizedlist spacing="compact">
	<listitem>
	  <para>
	    Write a callback function.  This is what does the actual
	    computation.  See <xref linkend="Class-Output"/> for the details.
	  </para>
	</listitem>
	<listitem>
	  <para>
	    Invoke the <classname>Output</classname> <link
	    linkend="Class-Output-constructor">constructor</link>,
	    specifying the type of the <classname>Output</classname>,
	    the types of its inputs (if any), its parameters (if any),
	    and its callback function.
	  </para>
	</listitem>
	<listitem>
	  <para>
	    Connect the <classname>Output</classname> to its inputs,
	    if any, by calling <link
	    linkend="Class-Output-connect"><methodname>Output.connect</methodname></link>.
	  </para>
	</listitem>
	<listitem>
	  <para>
	    Set parameters in the inputs, if desired.
	    <classname>Parameters</classname> which have fixed values
	    in the <classname>Output</classname> definition will
	    <emphasis>not</emphasis> be settable by the user.  To make
	    a <classname>Parameter</classname> settable by the user,
	    leave its value alone (or set it to
	    <literal>None</literal>).  Use <link
	    linkend="Class-Output-findParam"><methodname>Output.findParam</methodname></link>
	    or <link
	    linkend="Class-Output-resolveAlias"><methodname>Output.resolveAlias</methodname></link>
	    to gain access to an <classname>Output</classname>'s
	    parameters, or those of its connected inputs.
	  </para>
	</listitem>
	<listitem>
	  <para>
	    If any of the inputs have parameters that are
	    <emphasis>not</emphasis> specified in advance, these need to
	    be given aliases so that they can be used in scripts and the
	    GUI.  See <link
	    linkend="Class-Output-aliasParam"><methodname>Output.aliasParam</methodname></link>
	    for the details.
	  </para>
	</listitem>
	<listitem>
	  <para>
	    If the <classname>Output</classname> is to appear as an
	    option in the GUI, it must be registered by calling <link
	    linkend="Function-definePositionOutput"><function>definePositionOutput</function></link>,
	    <link
	    linkend="Function-definePositionOutput"><function>defineScalarOutput</function></link>,
	    or <link
	    linkend="Function-definePositionOutput"><function>defineAggregateOutput</function></link>.
	  </para>
	</listitem>
      </itemizedlist>
    </para>
    <section id="Section-Coding-Output-Examples">
      <title>Examples</title>
      <para>
	Here are a few example <classname>Output</classname>
	definitions, extracted from the &oof2; source code.  The
	examples illustrate all of the important features of the
	<classname>Output</classname> class.
      </para>
      <section id="Section-Coding-Output-Example1">
	<title>Evaluating a Field</title>
	<para>
	  The first example returns <classname>Field</classname>
	  values as <link
	  linkend="Class-OutputVal"><classname>OutputVal</classname></link>
	  instances.  It's copied<footnote>
	    <para>
	      Ok, we lied. The example is copied from an
	      <emphasis>old</emphasis> version of the source code.
	      The given example is very inefficient because the
	      <code>+=</code> inside the loop is continuously
	      reallocating and copying the <varname>ans</varname>
	      list.  See the actual code in
	      <filename>SRC/engine/IO/outputClones.py</filename> for a
	      more efficient but less obvious scheme.
	    </para>
	  </footnote>
 from
	  <filename>SRC/engine/IO/outputClones.py</filename>.
	</para>

	<programlisting>
def _field(mesh, elements, coords, field): <co id="example1-callback"/>
    ans = [] <co id="example1-ans"/>
    for element, ecoords in zip(elements, coords): <co id="example1-zip"/>
        ans += element.outputFields(mesh, field, ecoords) <co id="example1-eoF"/>
    return ans

FieldOutput = output.Output(
    name = "field", <co id="example1-name"/>
    callback = _field, <co id="example1-callback2"/>
    otype = outputval.<link linkend="Class-OutputVal">OutputValPtr</link>, <co id="example1-otype"/>
    params = [meshparameters.<link linkend="Class-FieldParameter">FieldParameter</link>("field", outofplane=1)], <co id="example1-param"/>
    ) </programlisting>

	<calloutlist>
	  <callout arearefs="example1-callback">
	    <para>
	      This is the callback function.  All callbacks have
	      <varname>mesh</varname>, <varname>elements</varname>,
	      and <varname>coords</varname> arguments.
	      <varname>elements</varname> is a list of the mesh <link
	      linkend="Class-Element"><classname>Elements</classname></link>
	      within which the output is to be computed.
	      <varname>coords</varname> is a list of lists of <link
	      linkend="Class-MasterCoord"><classname>MasterCoords</classname></link>
	      specifying the computation points within each
	      <classname>Element</classname>.
	    </para>
	    <para>
	      Any additional callback arguments are either inputs or
	      parameters, with names determined by the input and
	      parameter lists in the <classname>Output</classname>
	      constructor.  Here <varname>field</varname> is a
	      <classname>Parameter</classname> value.
	    </para>
	  </callout>
	  <callout arearefs="example1-ans">
	    <para>
	      The result of the computation is a
	      <emphasis>flat</emphasis> list of <link
	      linkend="Class-OutputVal"><classname>OutputVal</classname></link>
	      objects, one for each coordinate in
	      <varname>coords</varname>.
	    </para>
	  </callout>
	  <callout arearefs="example1-zip">
	    <para>
	      The <code>zip</code> call here matches up each
	      <classname>Element</classname> to the list of
	      coordinates at which the output should be evaluated
	      within the <classname>Element</classname>.
	      <varname>element</varname> is an
	      <classname>Element</classname>, and
	      <varname>ecoords</varname> is a list of <link
	      linkend="Class-MasterCoord"><classname>MasterCoords</classname></link>.
	    </para>
	  </callout>
	  <callout arearefs="example1-eoF">
	    <para>
	      <methodname>Element:outputFields</methodname>
	      returns a list of <classname>OutputVals</classname>
	      containing <classname>Field</classname> values at the
	      specified points within the given
	      <classname>Element</classname>.  The list is appended to
	      results already obtained.
	    </para>
	  </callout>
	<callout arearefs="example1-name">
	    <para>
	      This specifies the name of the
	      <classname>Output</classname>. It will be used to when
	      setting parameters and connecting this
	      <classname>Output</classname> to others.  It will
	      <emphasis>not</emphasis> be used in scripts or the user
	      interface.
	    </para>
	  </callout>
	  <callout arearefs="example1-callback2">
	    <para>
	      This is just the name of the callback function defined above.
	    </para>
	  </callout>
	  <callout arearefs="example1-otype">
	    <para>
	      This specifies the type of the quantities computed by
	      this <classname>Output</classname>.<footnote>
		<para>
		  Note that the type is
		  <classname>OutputValPtr</classname>, not
		  <classname>OutputVal</classname>.  That's because
		  <classname>OutputVal</classname> is a swigged C++
		  class.  <application>swig</application> creates two
		  Python classes for each C++ class.  One, with a name
		  ending in <literal>Ptr</literal>
		  (<foreignphrase>e.g,</foreignphrase>
		  <classname>OutputValPtr</classname>) is a pointer
		  (of sorts) to the C++ object, and is used to refer
		  to an object that was created in C++.  The other
		  Python class has no <literal>Ptr</literal> suffix
		  (<foreignphrase>e.g,</foreignphrase>
		  <classname>OutputVal</classname>) and is used when
		  an object was created directly in Python.  In the
		  <varname>FieldOutput</varname> callback,
		  <methodname>Element::outputFields</methodname>
		  returns <classname>OutputVals</classname> created by
		  the C++ code.
		</para>
		<para>
		  In general, in <varname>otype</varname>
		  specifications, it's safe to use the
		  <literal>Ptr</literal> form of a swigged class if
		  you're not sure which is correct.  The type checking
		  mechanism allows subclasses of the given type.
		  <literal>Ptr</literal> will always work because the
		  non-<literal>Ptr</literal> version of a class is
		  derived from the <literal>Ptr</literal> version.
		</para>
	      </footnote>
	    </para>
	  </callout>
	  <callout arearefs="example1-param">
	    <para>
	      This states that the <classname>Output</classname> has
	      one parameter, named <literal>field</literal>, whose
	      value is a <link
	      linkend="Class-Field"><classname>Field</classname></link>.
	    </para>
	  </callout>
	</calloutlist>
	<para>
	  To make the <varname>FieldOutput</varname> available in
	  scripts and the GUI,
	  <filename>SRC/engine/IO/outputDefs.py</filename> contains
	  the following lines:
	</para>
	
	<programlisting>
from ooflib.common.IO import output
from ooflib.engine.IO import outputClones
output.defineAggregateOutput('Field:Value', outputClones.FieldOutput) </programlisting>
      
	<para>
	  <link
	  linkend="Function-definePositionOutput"><function>defineAggregateOutput</function></link>
	  states that this <classname>Output</classname> computes an
	  aggregate object (such as all of the components of a
	  <classname>Field</classname> or <varname>Flux</varname>), as
	  opposed to a scalar object.
	  <literal>'Field:Value'</literal> categorizes the output
	  &mdash; the GUI will refer to it as the
	  <literal>Value</literal> item in the
	  <literal>Field</literal> menu.
	</para>
      </section><!-- example 1 -->
      <section id="Section-Coding-Output-Example2">
	<title>Connecting Inputs</title>
	<para>
	  Note that the <classname>FieldOutput</classname> has no
	  inputs!  It reads its data from the mesh, not from any other
	  <classname>Output</classname>.  The next example,
	  <varname>ComponentOutput</varname>, has both a parameter and
	  an input, but doesn't read data from the mesh.
	</para>

      <programlisting>
def _component(mesh, elements, coords, field, component): <co id="example2-callback"/>
    if field: <co id="example2-if"/>
        comp = field[0].getIndex(component) <co id="example2-convert"/>
        return [f[comp] for f in field] <co id="example2-extract"/>
    return []
        
import types

ComponentOutput = output.Output(
    name = "component",
    callback = _component,
    otype = types.FloatType, <co id="example2-otype"/>
    inputs = [outputval.<link linkend="Class-OutputValParameter">OutputValParameter</link>('field')], <co id="example2-input"/>
    params = [meshparameters.<link
       linkend="Class-FieldIndexParameter">FieldIndexParameter</link>('component')] <co id="example2-param"/>
    ) </programlisting>

	<calloutlist>
	  <callout arearefs="example2-callback">
	    <para>
	      The callback here has the usual required
	      <varname>mesh</varname>, <varname>elements</varname>,
	      and <varname>coords</varname> arguments, although it
	      doesn't use them.  <varname>field</varname> is an input
	      list of <link
	      linkend="Class-OutputVal"><classname>OutputVal</classname></link>
	      objects, and <varname>component</varname> is a parameter
	      value.
	  </para>
	  </callout>
	  <callout arearefs="example2-if">
	    <para>
	      It's possible that the list of values could be empty.
	      The next line assumes that it's not empty, so we have to
	      check.
	    </para>
	  </callout>
	  <callout arearefs="example2-convert">
	    <para>
	      The <varname>component</varname> is passed in in a
	      user-friendly string form (such as <literal>'x'</literal> or
	      <literal>'yz'</literal>).  This line asks the <link
	      linkend="Class-OutputVal"><classname>OutputVal</classname></link>
	      class to convert the string into a computer-friendly
	      &FieldIndex; object.  (<code>field[0]</code> is used just
	      because it's an <classname>OutputVal</classname> of the
	      correct type. Its actual value isn't important here.)
	      Different kinds of <classname>OutputVal</classname>
	      interpret the strings differently.
	    </para>
	  </callout>
	  <callout arearefs="example2-extract">
	    <para>
	      This computes and returns a list of components of the
	      input <link
	      linkend="Class-OutputVal"><classname>OutputVal</classname></link>
	      objects.
	    </para>
	  </callout>
	  <callout arearefs="example2-otype">
	    <para>
	      Components of an <link
	      linkend="Class-OutputVal"><classname>OutputVal</classname></link>
	      are floating point numbers, so the output type of
	      <varname>ComponentOutput</varname> is
	      <literal>FloatType</literal>.
	    </para>
	  </callout>
	  <callout arearefs="example2-input">
	    <para>
	      Inputs are specified by a list of <link
	      linkend="Class-Parameter"><classname>Parameters</classname></link>,
	      although they don't actually have values the same way
	      that <classname>Parameters</classname> do.  The input
	      <classname>Parameter</classname> specifies the name and
	      type of the input.  In this case, the input is called
	      <literal>'field'</literal> and is a list of
	      <classname>OutputVals</classname> (or
	      <classname>OutputValPtrs</classname>).
	    </para>
	  </callout>
	  <callout arearefs="example2-param">
	    <para>
	      The <classname>Output</classname> has a single
	      parameter, named <literal>'component'</literal>, whose
	      value is a string representation of a component index.
	    </para>
	  </callout>
	</calloutlist>
	<para>
	  Note that despite the name of its input,
	  <literal>'field'</literal>, the
	  <varname>ComponentOutput</varname> can extract components
	  from any kind of <classname>OutputVal</classname>, not only
	  ones containing <classname>Fields</classname>.  The built-in
	  &oof2; outputs use <classname>ComponentOutput</classname> on
	  <classname>Fields</classname>,
	  <classname>Fluxes</classname>, and other multicomponent
	  quantities.
	</para>
	<para>
	  The <varname>FieldOutput</varname> and
	  <varname>ComponentOutput</varname> can be combined into a
	  <varname>FieldCompOutput</varname>, which extracts a given
	  component of a given <classname>Field</classname>, by using
	  <methodname>Output.connect</methodname>.  First, a copy of
	  the <varname>ComponentOutput</varname> is made, giving it a
	  new name at the same time:<footnote>
	    <para>
	      It's also possible to change the
	      <classname>Output</classname>'s <varname>tip</varname>
	      and <varname>discussion</varname> strings, which have
	      been omitted here.
	    </para>
	  </footnote>
	</para>
      
      <programlisting>
FieldCompOutput = ComponentOutput.clone(name="field component") </programlisting>

	<para>
	  <varname>FieldOutput</varname> is connected to the input
	  named <literal>'field'</literal> of the
	  <varname>FieldCompOutput</varname>:
	</para>

      <programlisting>
FieldCompOutput.connect("field", FieldOutput) </programlisting>

	<para>
	  <methodname>connect</methodname> automatically makes a copy
	  of its argument, so we don't have to worry about cloning
	  <varname>FieldOutput</varname> here.
	</para>
      </section><!-- Connecting inputs -->
      <section id="Section-Coding-Output-Example2.5">
	<title>Managing Output Parameters</title>
	<para>
	  At this stage, <varname>FieldCompOutput</varname> has two
	  parameters and no inputs.  (The one input of the original
	  <varname>ComponentOutput</varname> has been filled by the
	  <varname>FieldOutput</varname> that was connected to it.)
	  The original <varname>FieldOutput</varname> parameter, named
	  <varname>'field'</varname>, and the
	  <varname>ComponentOutput</varname> parameter, named
	  <literal>'component'</literal>, still remain.
	  <literal>'component'</literal> is a direct parameter of
	  <varname>FieldCompOutput</varname>.  It can be accessed by
	  the <link
	  linkend="Class-Output-findParam"><methodname>findParam</methodname></link>
	  method, <foreignphrase>e.g</foreignphrase>:

	  <programlisting>
FieldCompOutput.findParam('component').value = 'x' </programlisting>

	  Setting a parameter's value like this gives it a permanent
	  value, as far as <classname>Outputs</classname> are
	  concerned.  The user will not be able to change the value,
	  and the field-component <classname>Output</classname> has
	  been changed into an field-x-component
	  <classname>Output</classname>.
	</para>
	<para>
	  The <literal>'field'</literal> parameter of the original
	  <varname>FieldOutput</varname> can be accessed in a similar,
	  but not identical way.  The
	  <varname>FieldCompOutput</varname> has no parameter called
	  <literal>'field'</literal>, so we can't use
	  <code>FieldCompOutput.findParam('field')</code>, and the
	  original <varname>FieldOutput</varname> has been cloned, so
	  its <literal>'field'</literal> parameter isn't the same one
	  that <varname>FieldCompOutput</varname> uses.  The parameter
	  can be accessed by specifying both the name of the input and
	  the parameter in the call to
	  <methodname>findParam</methodname>:

	  <programlisting>
FieldCompOutput.findParam('field:field').value = Displacement </programlisting>

	  Here the first <literal>field</literal> is the name of the
	  input, and the second is the name of the parameter of that
	  input.
	</para>
	<para>
	  Assuming that we want the user to be able to choose the
	  <classname>Field</classname> <emphasis>and</emphasis> the
	  component, we don't actually want to use
	  <methodname>findParam</methodname> and set the parameter
	  values.  However, we don't want the user to see an ugly name
	  like <literal>'field:field'</literal>.  For one thing,
	  parameter names are used as Python variable names in
	  scripts, and Python variable names can't contain colons.
	  The function <link
	  linkend="Class-Output-aliasParam"><methodname>Output.aliasParam</methodname></link>
	  assigns a new name to an <classname>Output</classname>
	  parameter, like this:
	  
	  <programlisting>
FieldCompOutput.aliasParam('field:field', 'field') </programlisting>

	  Now <varname>FieldCompOutput</varname> has a parameter
	  called <literal>'field'</literal> instead of
	  <literal>'field:field'</literal>.  Note that there's no
	  conflict between the aliased parameter named
	  <literal>'field'</literal> and the input named
	  <literal>'field'</literal>.  The confusion is always
	  resolved by the context.
	</para>
	<para>
	  <link
	  linkend="Class-Output-findParam"><methodname>Output.findParam</methodname></link>
	  never considers aliases, so the call
	  <code>FieldCompOutput.findParam('field')</code> will fail
	  (it will raise a <code>KeyError</code> exception).  To
	  retrieve an aliased parameter, use <link
	  linkend="Class-Output-resolveAlias"><methodname>Output.resolveAlias</methodname></link>
	  instead.  If <methodname>resolveAlias</methodname> can't
	  find an alias, it looks for a parameter, so the following
	  three function calls are equivalent:

	  <programlisting>
param = FieldCompOutput.resolveAlias('field')
param = FieldCompOutput.resolveAlias('field:field')
param = FieldCompOutput.findParam('field:field') </programlisting>
	</para>

	<para>
	  Aliases are only known to the <classname>Outputs</classname>
	  that create them.  In the example above, the
	  <varname>FieldOutput</varname> containing the original
	  <literal>'field'</literal> parameter doesn't know that it's
	  been aliased.  However, if
	  <varname>FieldCompOutput</varname> were to be used as an
	  input to another <classname>Output</classname>, like this:

	  <programlisting>
SomeOtherOutput.connect('otherinput', FieldCompOutput) </programlisting>

	  then the <varname>'field'</varname> parameter could be
	  accessed by

	  <programlisting>
param = SomeOtherOutput.resolveAlias('otherinput:field') </programlisting>

	  using the alias still stored in
	  <varname>FieldCompOutput</varname>.
	</para>
      </section><!-- Managing Output Parameters -->
      <section id="Section-Coding-Output-Example3">
	<title>Handling Multiple Parameters and Inputs</title>
	<para>
	  The examples above all use at most one parameter and one
	  input. <classname>Outputs</classname> can have as many
	  parameters and inputs as they like.  The
	  <varname>PointSumOutput</varname> from
	  <filename>SRC/engine/IO/outputClones.py</filename> is used
	  to add the Displacement to the original position of a node.
	  It's actually a little more general than that &mdash; it
	  takes two input streams which are lists of <link
	  linkend="Class-Coord"><classname>Coord</classname></link>
	  or <link linkend="Class-Point"><classname>Point</classname></link>
	  objects, multiplies them by scalar factors, and adds them
	  together.
	</para>

	<programlisting>
from ooflib.SWIG.common import coord
from ooflib.common import primitives
from ooflib.common.IO import output
from ooflib.common.IO import parameter

def _pointSum(mesh, elements, coords, point1, point2, a, b): <co id="example3-callback"/>
    ans = [a*f+b*s for f,s in zip(point1, point2)] <co id="example3-zip"/>
    return ans

PointSumOutput = output.Output(
    name="point sum",
    callback=_pointSum,
    otype=(coord.Coord, primitives.Point), <co id="example3-otype"/>
    inputs=[coord.CoordParameter("point1"), coord.CoordParameter("point2")], <co id="example3-input"/>
    params=[parameter.FloatParameter("a", default=1.0), <co id="example3-param"/>
            parameter.FloatParameter("b", default=1.0)]
    ) </programlisting>
	
	<calloutlist>
	  <callout arearefs="example3-callback">
	    <para>
	      The callback arguments include the usual
	      <varname>mesh</varname>, <varname>elements</varname>,
	      and <varname>coords</varname>, although they're not used
	      here.  <varname>point1</varname> and
	      <varname>point2</varname> are the names of the inputs,
	      and <varname>a</varname> and <varname>b</varname> are
	      the names of the parameters.
	    </para>
	  </callout>
	  <callout arearefs="example3-zip">
	    <para>
	      This line does all the work.  It can be written in such
	      a simple way because inputs are flat lists of data.
	    </para>
	  </callout>
	  <callout arearefs="example3-otype">
	    <para>
	      Because the input (see <xref linkend="example3-input"/>)
	      accepts either <classname>Coords</classname> or
	      <classname>Points</classname>, the output can be either
	      <classname>Coords</classname> or
	      <classname>Points</classname>.<footnote
		id="footnote-CoordPoint">
		<para>
		  The <classname>Coord</classname> and
		  <classname>Point</classname> classes are equivalent,
		  except that <classname>Coord</classname> is a
		  swigged C++ class, and <classname>Point</classname>
		  is a pure Python class. There are circumstances in
		  which the overhead of calling C++ from Python makes
		  using a Python class more efficient.
		</para>
	      </footnote>
	    </para>
	  </callout>
	  <callout arearefs="example3-input">
	    <para>
	      There are two inputs, named <literal>point1</literal>
	      and <literal>point2</literal>.  The <link
	      linkend="Class-CoordParameter"><classname>CoordParameter</classname></link>
	      class accepts either a <classname>Coord</classname> or a
	      <classname>Point</classname>.<footnoteref
	      linkend="footnote-CoordPoint"/>
	    </para>
	  </callout>
	  <callout arearefs="example3-param">
	    <para>
	      The two parameters, named <literal>'a'</literal> and
	      <literal>'b'</literal> have been given default values of
	      <literal>1.0</literal>, which is the value that will be
	      displayed in the GUI if the variable hasn't been set
	      yet.
	    </para>
	  </callout>
	</calloutlist>
	<para>
	  The <varname>PointSumOutput</varname> is used in
	  <filename>SRC/engine/IO/outputDefs.py</filename> to add the
	  displacement to the node position.  The displacement values
	  come from <varname>displacementOutput</varname> and the
	  position values come from <varname>posOutput</varname>,
	  which won't be explicitly discussed here.  The connection
	  looks like this:
	</para>
	
	<programlisting>
enhancedPosition = outputClones.PointSumOutput.clone(
    name='enhanced position',
    params=dict(b=1), <co id="example3-params2"/>
    tip='Exaggerated displacement field.') <co id="example3-tip"/>
enhancedPosition.connect('point1', displacementOutput) <co id="example3-connect"/>
enhancedPosition.connect('point2', outputClones.posOutput) <coref linkend="example3-connect"/>
enhancedPosition.aliasParam('a', 'factor', default=1.0, <co id="example3-alias"/>
                            tip='Displacement multiplier.') </programlisting>

	<calloutlist>
	  <callout arearefs="example3-params2">
	    <para>
	      Parameters can be set when cloning an
	      <classname>Output</classname>.  The
	      <varname>params</varname> argument is a
	      dictionary.<footnote>
		<para>
		  The parameter dictionary can also be written as
		  <code>params={'b' : 1}</code>.  This form would be
		  required if a full parameter name containing colons
		  were being used, <foreignphrase>e.g</foreignphrase>
		  <code>params={'input:b' : 1}</code>, because the
		  <function>dict</function> form requires that the
		  keywords be legal Python variable names.
		</para>
	      </footnote>
	      The dictionary keys are the names (or aliases) of the
	      parameters to be set.  Parameters set in this way remain
	      set.  The user will not have a chance to modify them.
	    </para>
	  </callout>
	  <callout arearefs="example3-tip">
	    <para>
	      Most of the examples have omitted the optional
	      <varname>tip</varname> argument.  When creating or
	      cloning <classname>Outputs</classname>, it's possible to
	      specify a <varname>tip</varname> string, which will
	      appear as a help string in the GUI, and a
	      <varname>discussion</varname> string, which will appear
	      in the manual.
	    </para>
	  </callout>
	  <callout arearefs="example3-connect">
	    <para>
	      These lines connect the preexisting
	      <varname>displacementOutput</varname> and
	      <varname>posOutput</varname>
	      <classname>Outputs</classname> to the inputs of the
	      <varname>PointSumOutput</varname> clone.
	    </para>
	  </callout>
	  <callout arearefs="example3-alias">
	    <para>
	      This line shows that <methodname>aliasParam</methodname>
	      can be used to change the name of a local parameter, as
	      well as parameters in the inputs.  Here the
	      non-descriptive parameter <literal>'a'</literal> is
	      renamed <literal>'factor'</literal> and given a default
	      value<footnote>
		<para>
		  The default value setting is redundant in this case,
		  because the default value of <literal>'a'</literal>
		  was already set to 1 when
		  <varname>PointSumOutput</varname> was created.
		</para>
	      </footnote>
	      and a <varname>tip</varname> string.
	    </para>
	  </callout>
	</calloutlist>
	<para>
	  At this point, the <varname>enhancedPosition</varname>
	  <classname>Output</classname> has one parameter,
	  <literal>'factor'</literal>, and no inputs.  It produces a
	  list of node positions, with displacement exaggerated by the
	  given amount.  The <varname>actualPosition</varname>
	  <classname>Output</classname> is now simply created by
	  cloning <varname>enhancedPosition</varname> and setting the
	  enhancement factor to 1.0:
	</para>

	<programlisting>
actualPosition = enhancedPosition.clone(
    name='actual position',
    params=dict(factor=1.0),
    tip='Displaced position.') </programlisting>

	<para>
	  Finally, both <varname>enhancedPosition</varname> and
	  <varname>actualPosition</varname> are made available in the
	  GUI by calling <link
	  linkend="Function-definePositionOutput"><function>definePositionOutput</function></link>:
	</para>

	<programlisting>
output.definePositionOutput('actual', actualPosition)
output.definePositionOutput('enhanced', enhancedPosition) </programlisting>

      </section><!-- Multiple Parameters and Inputs -->
    </section><!-- Output Examples -->

    <section id="Section-Coding-PropertyOutputs">
      <title><classname>PropertyOutputs</classname></title>
      <para>
	Output quantities that need to use information from the
	material <link
	linkend="Class-Property"><classname>Properties</classname></link>
	of the &mesh; are treated differently because they need to
	hook into existing <classname>Property</classname> instances
	and because many different <classname>Properties</classname>
	may contribute to any given <classname>Output</classname>.
	Outputs such as this are defined by creating an instance of a
	<link
	linkend="Class-PropertyOutputRegistration"><classname>PropertyOutputRegistration</classname></link>
	subclass, and listing the name of the subclass in a
	<classname>Property</classname>'s <link
	linkend="Class-PropertyRegistration"><classname>PropertyRegistration</classname></link>
	<varname>outputs</varname> list.  The
	<classname>PropertyOutputRegistration</classname> will
	automatically create <link
	linkend="Class-Output"><classname>Output</classname></link>
	objects.  When these <classname>Outputs</classname> are
	evaluated, the <classname>Property</classname>'s <link
	linkend="Class-Property-output"><methodname>output</methodname></link>
	function will be called, with a <link
	linkend="Class-PropertyOutput"><classname>PropertyOutput</classname></link>
	object as one of its arguments.
	<classname>Property::output</classname> can use the
	<classname>PropertyOutput</classname> object to find out which
	output is being computed, and to access the output's parameters.
      </para>
      <para>
	Clear?  Here's an example, illustrating the
	<literal>Energy</literal> output and how it's computed by the
	<classname>Elasticity</classname> property.  Some of the code
	has been slightly simplified for brevity, but the source files
	have been indicated for anyone interested in all the details.
      </para>
      <para>
	First, an <link
	  linkend="Section-Enums"><classname>Enum</classname></link>
	class is created to distinguish the different types of energy
	(in <filename>SRC/engine/IO/outputDefs.py</filename>):

      <programlisting>
from ooflib.common import enum

class EnergyType(enum.EnumClass("Total", "Elastic", ...)):
   pass </programlisting>

	The same file then defines a <link
	linkend="Class-PropertyOutputRegistration"><classname>ScalarPropertyOutputRegistration</classname></link>,
	because energy is a scalar quantity:

	<programlisting>
from ooflib.SWIG.engine.IO import propertyoutput

propertyoutput.ScalarPropertyOutputRegistration(
   "Energy",
   parameters=[enum.EnumParameter("etype", EnergyType, default="Total")]
) </programlisting>

	The string <literal>"Energy"</literal> is the name by which the
	output will be known both in the user interface and in the
	<classname>Property</classname> code.  The parameter name
	<literal>"etype"</literal> will also appear in the user interface
	and the code.  It's important that the parameter does
	<emphasis>not</emphasis> have an assigned value!  The Output
	mechanism assumes that parameters with values are not going to be
	set by the user.  Instead, the parameter has its
	<varname>default</varname> set, which provides an initial value to
	be displayed in the GUI, without actually fixing the
	<classname>Parameter</classname>'s value.
      </para>
      <para>
	Note that the output registration does
	<emphasis>not</emphasis> contain any information about what
	<literal>Energy</literal> is, or how it's computed.  That's
	the <classname>Properties</classname>' job.
	<classname>Elasticity</classname>'s
	<methodname>output</methodname> function looks like this (in
	<filename>SRC/engine/property/elasticity/elasticity.C</filename>):

	<programlisting>
void Elasticity::output(const FEMesh *mesh,
			const Element *element,
			const PropertyOutput *output,
			const MasterPosition &amp;pos,
			OutputVal *data)
  const 
{
  const std::string &amp;outputname = output->name();
  if(outputname == "Energy") {
    std::string etype = output->getEnumParam("etype");
    if(etype == "Total" || etype == "Elastic") {
      ScalarOutputVal *edata = dynamic_cast&lt;ScalarOutputVal*>(data);
      SymmMatrix strain(3);
      const Cijkl modulus = cijkl(mesh, element, pos);
      findGeometricStrain(mesh, element, pos, strain);
      SymmMatrix stress(modulus*strain);
      double e = 0;
      for(int i=0; i&lt;3; i++) {
	e += stress(i,i)*strain(i,i);
	int j = (i+1)%3;
	e += 2*stress(i,j)*strain(i,j);
      }
      *edata += 0.5*e;
    }
  }
} </programlisting>

	See the <link
	linkend="Class-Property-output"><methodname>Property::output</methodname></link>
	discussion for another example, with annotations.
      </para>
      <para>
	Finally, the <literal>Elasticity</literal> <link
	linkend="Class-PropertyRegistration"><classname>PropertyRegistration</classname></link>
	needs to indicate that <literal>"Energy"</literal> is one of
	the outputs that it can compute.  There are many types of
	elasticity, and each has its own registration.  Here's the one
	for isotropic elasticity, from
	<filename>SRC/engine/property/elasticity/iso/iso.spy</filename>:

	<programlisting>
from ooflib.engine import propertyregistration

propertyregistration.PropertyRegistration(
    name = "Mechanical:Elasticity:Isotropic",
    subclass = IsoElasticityProp,
    ...
    outputs=["Energy"],
    ...) </programlisting>

	<classname>IsoElasticityProp</classname> is a subclass of
	<classname>Elasticity</classname>, so because
	<classname>PropertyRegistration</classname> indicates that
	<classname>IsoElasticityProp</classname> can compute
	<literal>"Energy"</literal>, when a &material; contains
	<classname>IsoElasticityProp</classname>,
	<methodname>Elasticity::output</methodname> will be called to
	compute it.
      </para>
      <para>
	Property outputs can never use other
	<classname>Outputs</classname> as inputs, but they can, in
	principle, be used as inputs for other
	<classname>Outputs</classname>.  However, there's no machinery
	to make this easy to do, yet.
      </para>
    </section>                  <!-- PropertyOutputs -->
    
  </section>                    <!-- Adding New Outputs -->

</chapter>

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