# Diff of /trunk/doc/user/finley.tex

revision 993 by gross, Fri Feb 23 06:39:38 2007 UTC revision 1388 by trankine, Fri Jan 11 07:45:58 2008 UTC
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5  %               \url{http://www.access.edu.au  %
6  %         Primary Business: Queensland, Australia.  %           Copyright 2003-2007 by ACceSS MNRF
7  %   Licensed under the Open Software License version 3.0  %       Copyright 2007 by University of Queensland
9    %                http://esscc.uq.edu.au
10    %        Primary Business: Queensland, Australia
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17    \chapter{ The Module \finley}

\chapter{ The module \finley}
18   \label{CHAPTER ON FINLEY}   \label{CHAPTER ON FINLEY}
19
20  \begin{figure}  \begin{figure}
# Line 81  to second node the domain has to lie on Line 86  to second node the domain has to lie on
86  the domain has to lie on the left hand side when moving counterclockwise). If the gradient on the  the domain has to lie on the left hand side when moving counterclockwise). If the gradient on the
87  surface of the domain is to be calculated rich face elements face to be used. Rich elements on a face  surface of the domain is to be calculated rich face elements face to be used. Rich elements on a face
88  are identical to interior elements but with a modified order of nodes such that the 'first' face of the element aligns  are identical to interior elements but with a modified order of nodes such that the 'first' face of the element aligns
89  with the surface of the domian. In \fig{FINLEY FIG 0}  with the surface of the domain. In \fig{FINLEY FIG 0}
90  elements of the type \finleyelement{Tri3Face} are used.  elements of the type \finleyelement{Tri3Face} are used.
91  The face element reference number $20$ as a rich face element is defined by the nodes  The face element reference number $20$ as a rich face element is defined by the nodes
92  with reference numbers $11$, $0$ and $9$. Notice that the face element $20$ is identical to the  with reference numbers $11$, $0$ and $9$. Notice that the face element $20$ is identical to the
# Line 132  the nodes within an element. Line 137  the nodes within an element.
137  \linev{\finleyelement{Hex20}}{\finleyelement{Rec8}}{\finleyelement{Hex20Face}}{\finleyelement{Rec8_Contact}}{\finleyelement{Hex20Face_Contact}}  \linev{\finleyelement{Hex20}}{\finleyelement{Rec8}}{\finleyelement{Hex20Face}}{\finleyelement{Rec8_Contact}}{\finleyelement{Hex20Face_Contact}}
138  \end{tablev}  \end{tablev}
139  \caption{Finley elements and corresponding elements to be used on domain faces and contacts.  \caption{Finley elements and corresponding elements to be used on domain faces and contacts.
140  The rich types have to be used if the gradient of function is to be calculated on faces and contacts, resepctively.}  The rich types have to be used if the gradient of function is to be calculated on faces and contacts, respectively.}
141  \label{FINLEY TAB 1}  \label{FINLEY TAB 1}
142  \end{table}  \end{table}
143
# Line 176  for i in range(ContactElement_Num): Line 181  for i in range(ContactElement_Num):
181     for j in range(ContactElement_numNodes): print " %d"%ContactElement_Nodes[i][j]     for j in range(ContactElement_numNodes): print " %d"%ContactElement_Nodes[i][j]
182     print "\n"     print "\n"
183  # point sources (not supported yet)  # point sources (not supported yet)
184  write("Point1 0",face_element_typ,numFaceElements)  write("Point1 0",face_element_type,numFaceElements)
185  \end{python}  \end{python}
186
187  The following example of a mesh file defines the mesh shown in \fig{FINLEY FIG 01}:  The following example of a mesh file defines the mesh shown in \fig{FINLEY FIG 01}:
# Line 252  $7$, $10$, $15$ and $20$, respectively. Line 257  $7$, $10$, $15$ and $20$, respectively.
257
258  \subsection{Linear Solvers in \LinearPDE}  \subsection{Linear Solvers in \LinearPDE}
259  Currently \finley supports the linear solvers \PCG, \GMRES, \PRESTWENTY and \BiCGStab.  Currently \finley supports the linear solvers \PCG, \GMRES, \PRESTWENTY and \BiCGStab.
260  For \GMRES the options \var{trancation} and \var{restart} of the \method{getSolution} can be  For \GMRES the options \var{truncation} and \var{restart} of the \method{getSolution} can be
261  used to control the trunction and restart during iteration. Default values are  used to control the truncation and restart during iteration. Default values are
262  \var{truncation}=5 and \var{restart}=20.  \var{truncation}=5 and \var{restart}=20.
263  The default solver is \BiCGStab  but if the symmetry flag is set \PCG is the default solver.  The default solver is \BiCGStab  but if the symmetry flag is set \PCG is the default solver.
264  \finley supports the solver options \var{iter_max} which specifies the maximum number of iterations steps,  \finley supports the solver options \var{iter_max} which specifies the maximum number of iterations steps,
# Line 262  In some installations \finley supports t Line 267  In some installations \finley supports t
267  solver options \var{reordering}=\constant{util.NO_REORDERING},  solver options \var{reordering}=\constant{util.NO_REORDERING},
268  \constant{util.MINIMUM_FILL_IN} or \constant{util.NESTED_DISSECTION} (default is \constant{util.NO_REORDERING}),  \constant{util.MINIMUM_FILL_IN} or \constant{util.NESTED_DISSECTION} (default is \constant{util.NO_REORDERING}),
269  \var{drop_tolerance} specifying the threshold for values to be dropped in the  \var{drop_tolerance} specifying the threshold for values to be dropped in the
270  incomplete elimation process (default is 0.01) and \var{drop_storage} specifying the maximum increase  incomplete elimination process (default is 0.01) and \var{drop_storage} specifying the maximum increase
271  in storage allowed in the  in storage allowed in the
272  incomplete elimation process (default is 1.20).  incomplete elimination process (default is 1.20).
273
274  \subsection{Functions}  \subsection{Functions}
275  \begin{funcdesc}{Mesh}{fileName,integrationOrder=-1}  \begin{funcdesc}{Mesh}{fileName,integrationOrder=-1}
# Line 276  degree \var{integrationOrder} \index{int Line 281  degree \var{integrationOrder} \index{int
281  an appropriate integration order is chosen independently.  an appropriate integration order is chosen independently.
282  \end{funcdesc}  \end{funcdesc}
283
\begin{funcdesc}{Interval}{n0,order=1,l0=1.,integrationOrder=-1, \\
periodic0=\False,useElementsOnFace=\False}
Generates a \Domain object representing a interval $[0,l0]$. The interval is filled with
\var{n0} elements.
For \var{order}=1 and \var{order}=2
\finleyelement{Line2} and
\finleyelement{Line3} are used, respectively.
In the case of \var{useElementsOnFace}=\False,
\finleyelement{Point1} are used to describe the boundary points.
In the case of \var{useElementsOnFace}=\True (this option should be used if gradients
are calculated on domain faces),
\finleyelement{Line2} and
\finleyelement{Line3} are used on both ends of the interval.
If \var{integrationOrder} is positive, a numerical integration scheme
chosen which is accurate on each element up to a polynomial of
degree \var{integrationOrder} \index{integration order}. Otherwise
an appropriate integration order is chosen independently. If
\var{periodic0}=\True, periodic boundary conditions \index{periodic boundary conditions}
along the $x_0$-directions are enforced. That means when for any solution of a PDE solved by \finley
the value at $x_0=0$ will be identical to the values at $x_0=\var{l0}$.
\end{funcdesc}

284  \begin{funcdesc}{Rectangle}{n0,n1,order=1,l0=1.,l1=1., integrationOrder=-1, \\  \begin{funcdesc}{Rectangle}{n0,n1,order=1,l0=1.,l1=1., integrationOrder=-1, \\
285    periodic0=\False,periodic1=\False,useElementsOnFace=\False}    periodic0=\False,periodic1=\False,useElementsOnFace=\False}
286  Generates a \Domain object representing a two dimensional rectangle between  Generates a \Domain object representing a two dimensional rectangle between
# Line 355  in $x_1$-direction and $x_2$-direction, Line 338  in $x_1$-direction and $x_2$-direction,
338  \end{funcdesc}  \end{funcdesc}
339
340  \begin{funcdesc}{GlueFaces}{meshList,safetyFactor=0.2,tolerance=1.e-13}  \begin{funcdesc}{GlueFaces}{meshList,safetyFactor=0.2,tolerance=1.e-13}
341  Generates a new \Domain object from the list \var{mehList} of \finley meshes.  Generates a new \Domain object from the list \var{meshList} of \finley meshes.
342  Nodes in face elements whose difference of coordinates is less then \var{tolerance} times the  Nodes in face elements whose difference of coordinates is less then \var{tolerance} times the
343  diameter of the domain are merged. The corresponding face elements are removed from the mesh.    diameter of the domain are merged. The corresponding face elements are removed from the mesh.
344
# Line 363  TODO: explain \var{safetyFactor} and sho Line 346  TODO: explain \var{safetyFactor} and sho
346  \end{funcdesc}  \end{funcdesc}
347
348  \begin{funcdesc}{JoinFaces}{meshList,safetyFactor=0.2,tolerance=1.e-13}  \begin{funcdesc}{JoinFaces}{meshList,safetyFactor=0.2,tolerance=1.e-13}
349  Generates a new \Domain object from the list \var{mehList} of \finley meshes.  Generates a new \Domain object from the list \var{meshList} of \finley meshes.
350  Face elements whose nodes coordinates have difference is less then \var{tolerance} times the  Face elements whose nodes coordinates have difference is less then \var{tolerance} times the
351  diameter of the domain are combined to form a contact element \index{element!contact}  diameter of the domain are combined to form a contact element \index{element!contact}
352  The corresponding face elements are removed from the mesh.    The corresponding face elements are removed from the mesh.

Legend:
 Removed from v.993 changed lines Added in v.1388