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 1 ksteube 1811 2 jfenwick 3989 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 3 jfenwick 6651 % Copyright (c) 2003-2018 by The University of Queensland 4 jfenwick 3989 5 gross 625 % 6 ksteube 1811 % Primary Business: Queensland, Australia 7 jfenwick 6112 % Licensed under the Apache License, version 2.0 8 9 gross 625 % 10 jfenwick 3989 % Development until 2012 by Earth Systems Science Computational Center (ESSCC) 11 jfenwick 4657 % Development 2012-2013 by School of Earth Sciences 12 % Development from 2014 by Centre for Geoscience Computing (GeoComp) 13 jfenwick 3989 % 14 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 15 jgs 102 16 caltinay 5295 \chapter{The \finley Module}\label{chap:finley} 17 caltinay 3306 %\declaremodule{extension}{finley} 18 %\modulesynopsis{Solving linear, steady partial differential equations using finite elements} 19 jgs 102 20 jfenwick 5658 The \finley library allows the creation of domains for solving 21 linear, steady partial differential 22 caltinay 4891 equations\index{partial differential equations} (PDEs) or systems 23 caltinay 3330 of PDEs using isoparametrical finite elements\index{FEM!isoparametrical}. 24 It supports unstructured 1D, 2D and 3D meshes. 25 jfenwick 5658 The PDEs themselves are represented by the \LinearPDE class 26 of \escript. 27 \finley is parallelized under both \OPENMP and \MPI. 28 A more restricted form of this library ({\it dudley}) is described in 29 Section~\ref{sec:dudley}. 30 jgs 102 31 gross 993 \section{Formulation} 32 caltinay 3330 For a single PDE that has a solution with a single component the linear PDE is 33 defined in the following form: 34 gross 993 \begin{equation}\label{FINLEY.SINGLE.1} 35 \begin{array}{cl} & 36 \displaystyle{ 37 jfenwick 3295 \int_{\Omega} 38 A_{jl} \cdot v_{,j}u_{,l}+ B_{j} \cdot v_{,j} u+ C_{l} \cdot v u_{,l}+D \cdot vu \; d\Omega } \\ 39 + & \displaystyle{\int_{\Gamma} d \cdot vu \; d{\Gamma} } 40 + \displaystyle{\int_{\Gamma^{contact}} d^{contact} \cdot [v][u] \; d{\Gamma} } \\ 41 = & \displaystyle{\int_{\Omega} X_{j} \cdot v_{,j}+ Y \cdot v \; d\Omega }\\ 42 + & \displaystyle{\int_{\Gamma} y \cdot v \; d{\Gamma}} + 43 \displaystyle{\int_{\Gamma^{contact}} y^{contact}\cdot [v] \; d{\Gamma}} \\ 44 gross 993 \end{array} 45 \end{equation} 46 47 \section{Meshes} 48 gross 2793 \label{FINLEY MESHES} 49 jgs 102 50 caltinay 3330 \begin{figure} 51 \centerline{\includegraphics{FinleyMesh}} 52 \caption{Subdivision of an Ellipse into triangles order 1 (\finleyelement{Tri3})} 53 \label{FINLEY FIG 0} 54 \end{figure} 55 56 To understand the usage of \finley one needs to have an understanding of how 57 the finite element meshes\index{FEM!mesh} are defined. 58 \fig{FINLEY FIG 0} shows an example of the subdivision of an ellipse into 59 so-called elements\index{FEM!elements}\index{element}. 60 In this case, triangles have been used but other forms of subdivisions can be 61 constructed, e.g. quadrilaterals or, in the three-dimensional case, into 62 tetrahedra and hexahedra. The idea of the finite element method is to 63 approximate the solution by a function which is a polynomial of a certain order 64 and is continuous across its boundary to neighbour elements. 65 In the example of \fig{FINLEY FIG 0} a linear polynomial is used on each 66 triangle. As one can see, the triangulation is quite a poor approximation of 67 the ellipse. It can be improved by introducing a midpoint on each element edge 68 then positioning those nodes located on an edge expected to describe the 69 boundary, onto the boundary. 70 In this case the triangle gets a curved edge which requires a parameterization 71 of the triangle using a quadratic polynomial. 72 For this case, the solution is also approximated by a piecewise quadratic 73 polynomial (which explains the name isoparametrical elements), 74 see \Ref{Zienc,NumHand} for more details. 75 \finley also supports macro elements\index{macro elements}. 76 For these elements a piecewise linear approximation is used on an element which 77 is further subdivided (in the case of \finley halved). 78 As such, these elements do not provide more than a further mesh refinement but 79 should be used in the case of incompressible flows, see \class{StokesProblemCartesian}. 80 For these problems a linear approximation of the pressure across the element is 81 used (use the \ReducedSolutionFS) while the refined element is used to 82 approximate velocity. So a macro element provides a continuous pressure 83 approximation together with a velocity approximation on a refined mesh. 84 This approach is necessary to make sure that the incompressible flow has a 85 unique solution. 86 87 jgs 102 The union of all elements defines the domain of the PDE. 88 caltinay 3330 Each element is defined by the nodes used to describe its shape. 89 In \fig{FINLEY FIG 0} the element, which has type \finleyelement{Tri3}, with 90 element reference number $19$\index{element!reference number} is defined by the 91 nodes with reference numbers $9$, $11$ and $0$\index{node!reference number}. 92 Notice that the order is counterclockwise. 93 The coefficients of the PDE are evaluated at integration nodes with each 94 individual element. 95 For quadrilateral elements a Gauss quadrature scheme is used. 96 In the case of triangular elements a modified form is applied. 97 The boundary of the domain is also subdivided into elements\index{element!face}. 98 In \fig{FINLEY FIG 0} line elements with two nodes are used. 99 The elements are also defined by their describing nodes, e.g. the face element 100 with reference number $20$, which has type \finleyelement{Line2}, is defined by 101 the nodes with the reference numbers $11$ and $0$. 102 Again the order is crucial, if moving from the first to second node the domain 103 has to lie on the left hand side (in the case of a two-dimensional surface 104 element the domain has to lie on the left hand side when moving 105 counterclockwise). If the gradient on the surface of the domain is to be 106 calculated rich face elements need to be used. Rich elements on a face are 107 identical to interior elements but with a modified order of nodes such that the 108 'first' face of the element aligns with the surface of the domain. 109 In \fig{FINLEY FIG 0} elements of the type \finleyelement{Tri3Face} are used. 110 The face element reference number $20$ as a rich face element is defined by the 111 nodes with reference numbers $11$, $0$ and $9$. 112 Notice that the face element $20$ is identical to the interior element $19$ 113 except that, in this case, the order of the node is different to align the first 114 edge of the triangle (which is the edge starting with the first node) with the 115 boundary of the domain. 116 jgs 102 117 caltinay 3330 Be aware that face elements and elements in the interior of the domain must 118 match, i.e. a face element must be the face of an interior element or, in case 119 of a rich face element, it must be identical to an interior element. 120 If no face elements are specified \finley implicitly assumes homogeneous 121 natural boundary conditions\index{natural boundary conditions!homogeneous}, 122 i.e. \var{d}=$0$ and \var{y}=$0$, on the entire boundary of the domain. 123 For inhomogeneous natural boundary conditions\index{natural boundary conditions!inhomogeneous}, 124 caltinay 3293 the boundary must be described by face elements. 125 jgs 102 126 caltinay 3330 \begin{figure} 127 \centerline{\includegraphics{FinleyContact}} 128 \caption{Mesh around a contact region (\finleyelement{Rec4})} 129 \label{FINLEY FIG 01} 130 \end{figure} 131 jgs 102 132 caltinay 3330 If discontinuities of the PDE solution are considered, contact 133 elements\index{element!contact}\index{contact conditions} are introduced to 134 describe the contact region $\Gamma^{contact}$ even if $d^{contact}$ and 135 $y^{contact}$ are zero. 136 \fig{FINLEY FIG 01} shows a simple example of a mesh of rectangular elements 137 around a contact region $\Gamma^{contact}$\index{element!contact}. 138 The contact region is described by the elements $4$, $3$ and $6$. 139 Their element type is \finleyelement{Line2_Contact}. 140 The nodes $9$, $12$, $6$ and $5$ define contact element $4$, where the 141 coordinates of nodes $12$ and $5$ and nodes $4$ and $6$ are identical, with the 142 idea that nodes $12$ and $9$ are located above and nodes $5$ and $6$ below the 143 contact region. 144 Again, the order of the nodes within an element is crucial. 145 There is also the option of using rich elements if the gradient is to be 146 calculated on the contact region. Similarly to the rich face elements these 147 are constructed from two interior elements by reordering the nodes such that 148 the 'first' face of the element above and the 'first' face of the element below 149 the contact regions line up. The rich version of element $4$ is of type 150 \finleyelement{Rec4Face_Contact} and is defined by the nodes $9$, $12$, $16$, 151 $18$, $6$, $5$, $0$ and $2$. 152 \tab{FINLEY TAB 1} shows the interior element types and the corresponding 153 element types to be used on the face and contacts. 154 \fig{FINLEY.FIG:1}, \fig{FINLEY.FIG:2} and \fig{FINLEY.FIG:4} show the ordering 155 of the nodes within an element. 156 gross 2748 157 jgs 102 \begin{table} 158 caltinay 3293 \centering 159 \begin{tabular}{l|llll} 160 caltinay 3330 \textbf{interior}&\textbf{face}&\textbf{rich face}&\textbf{contact}&\textbf{rich contact}\\ 161 caltinay 3293 \hline 162 \finleyelement{Line2} & \finleyelement{Point1} & \finleyelement{Line2Face} & \finleyelement{Point1_Contact} & \finleyelement{Line2Face_Contact}\\ 163 \finleyelement{Line3} & \finleyelement{Point1} & \finleyelement{Line3Face} & \finleyelement{Point1_Contact} & \finleyelement{Line3Face_Contact}\\ 164 \finleyelement{Tri3} & \finleyelement{Line2} & \finleyelement{Tri3Face} & \finleyelement{Line2_Contact} & \finleyelement{Tri3Face_Contact}\\ 165 \finleyelement{Tri6} & \finleyelement{Line3} & \finleyelement{Tri6Face} & \finleyelement{Line3_Contact} & \finleyelement{Tri6Face_Contact}\\ 166 \finleyelement{Rec4} & \finleyelement{Line2} & \finleyelement{Rec4Face} & \finleyelement{Line2_Contact} & \finleyelement{Rec4Face_Contact}\\ 167 \finleyelement{Rec8} & \finleyelement{Line3} & \finleyelement{Rec8Face} & \finleyelement{Line3_Contact} & \finleyelement{Rec8Face_Contact}\\ 168 \finleyelement{Rec9} & \finleyelement{Line3} & \finleyelement{Rec9Face} & \finleyelement{Line3_Contact} & \finleyelement{Rec9Face_Contact}\\ 169 \finleyelement{Tet4} & \finleyelement{Tri6} & \finleyelement{Tet4Face} & \finleyelement{Tri6_Contact} & \finleyelement{Tet4Face_Contact}\\ 170 \finleyelement{Tet10} & \finleyelement{Tri9} & \finleyelement{Tet10Face} & \finleyelement{Tri9_Contact} & \finleyelement{Tet10Face_Contact}\\ 171 \finleyelement{Hex8} & \finleyelement{Rec4} & \finleyelement{Hex8Face} & \finleyelement{Rec4_Contact} & \finleyelement{Hex8Face_Contact}\\ 172 \finleyelement{Hex20} & \finleyelement{Rec8} & \finleyelement{Hex20Face} & \finleyelement{Rec8_Contact} & \finleyelement{Hex20Face_Contact}\\ 173 caltinay 3330 \finleyelement{Hex27} & \finleyelement{Rec9} & N/A & N/A & N/A\\ 174 \finleyelement{Hex27Macro} & \finleyelement{Rec9Macro} & N/A & N/A & N/A\\ 175 \finleyelement{Tet10Macro} & \finleyelement{Tri6Macro} & N/A & N/A & N/A\\ 176 \finleyelement{Rec9Macro} & \finleyelement{Line3Macro} & N/A & N/A & N/A\\ 177 \finleyelement{Tri6Macro} & \finleyelement{Line3Macro} & N/A & N/A & N/A\\ 178 caltinay 3293 \end{tabular} 179 caltinay 3330 \caption{Finley elements and corresponding elements to be used on domain faces 180 and contacts. 181 The rich types have to be used if the gradient of the function is to be 182 calculated on faces and contacts, respectively.} 183 jgs 102 \label{FINLEY TAB 1} 184 \end{table} 185 186 The native \finley file format is defined as follows. 187 caltinay 3330 Each node \var{i} has \var{dim} spatial coordinates \var{Node[i]}, a reference 188 number \var{Node_ref[i]}, a degree of freedom \var{Node_DOF[i]} and a tag 189 \var{Node_tag[i]}. 190 In most cases \var{Node_DOF[i]}=\var{Node_ref[i]} however, for periodic 191 boundary conditions, \var{Node_DOF[i]} is chosen differently, see example below. 192 The tag can be used to mark nodes sharing the same properties. 193 Element \var{i} is defined by the \var{Element_numNodes} nodes 194 \var{Element_Nodes[i]} which is a list of node reference numbers. 195 The order of these is crucial. Each element has a reference number 196 \var{Element_ref[i]} and a tag \var{Element_tag[i]}. 197 The tag can be used to mark elements sharing the same properties. 198 For instance elements above a contact region are marked with tag $2$ and 199 elements below a contact region are marked with tag $1$. 200 \var{Element_Type} and \var{Element_Num} give the element type and the number 201 of elements in the mesh. 202 Analogue notations are used for face and contact elements. 203 The following \PYTHON script prints the mesh definition in the \finley file 204 format: 205 jgs 102 \begin{python} 206 caltinay 3330 print("%s\n"%mesh_name) 207 # node coordinates: 208 print("%dD-nodes %d\n"%(dim, numNodes)) 209 for i in range(numNodes): 210 print("%d %d %d"%(Node_ref[i], Node_DOF[i], Node_tag[i])) 211 for j in range(dim): print(" %e"%Node[i][j]) 212 print("\n") 213 # interior elements 214 print("%s %d\n"%(Element_Type, Element_Num)) 215 for i in range(Element_Num): 216 print("%d %d"%(Element_ref[i], Element_tag[i])) 217 for j in range(Element_numNodes): print(" %d"%Element_Nodes[i][j]) 218 print("\n") 219 # face elements 220 print("%s %d\n"%(FaceElement_Type, FaceElement_Num)) 221 for i in range(FaceElement_Num): 222 print("%d %d"%(FaceElement_ref[i], FaceElement_tag[i])) 223 for j in range(FaceElement_numNodes): print(" %d"%FaceElement_Nodes[i][j]) 224 print("\n") 225 # contact elements 226 print("%s %d\n"%(ContactElement_Type, ContactElement_Num)) 227 for i in range(ContactElement_Num): 228 print("%d %d"%(ContactElement_ref[i], ContactElement_tag[i])) 229 jfenwick 6678 for j in range(ContactElement_numNodes): 230 print(" %d"%ContactElement_Nodes[i][j]) 231 caltinay 3330 print("\n") 232 # point sources (not supported yet) 233 print("Point1 0") 234 jgs 102 \end{python} 235 236 The following example of a mesh file defines the mesh shown in \fig{FINLEY FIG 01}: 237 \begin{verbatim} 238 Example 1 239 2D Nodes 16 240 0 0 0 0. 0. 241 2 2 0 0.33 0. 242 3 3 0 0.66 0. 243 7 4 0 1. 0. 244 5 5 0 0. 0.5 245 6 6 0 0.33 0.5 246 8 8 0 0.66 0.5 247 10 10 0 1.0 0.5 248 12 12 0 0. 0.5 249 9 9 0 0.33 0.5 250 13 13 0 0.66 0.5 251 15 15 0 1.0 0.5 252 16 16 0 0. 1.0 253 18 18 0 0.33 1.0 254 19 19 0 0.66 1.0 255 20 20 0 1.0 1.0 256 Rec4 6 257 0 1 0 2 6 5 258 1 1 2 3 8 6 259 2 1 3 7 10 8 260 5 2 12 9 18 16 261 7 2 13 19 18 9 262 10 2 20 19 13 15 263 Line2 0 264 Line2_Contact 3 265 4 0 9 12 6 5 266 3 0 13 9 8 6 267 6 0 15 13 10 8 268 Point1 0 269 \end{verbatim} 270 Notice that the order in which the nodes and elements are given is arbitrary. 271 caltinay 3330 In the case that rich contact elements are used the contact element section 272 gets the form 273 jgs 102 \begin{verbatim} 274 Rec4Face_Contact 3 275 4 0 9 12 16 18 6 5 0 2 276 3 0 13 9 18 19 8 6 2 3 277 6 0 15 13 19 20 10 8 3 7 278 \end{verbatim} 279 caltinay 3330 Periodic boundary conditions\index{boundary conditions!periodic} can be 280 introduced by altering \var{Node_DOF}. 281 It allows identification of nodes even if they have different physical locations. 282 For instance, to enforce periodic boundary conditions at the face $x_0=0$ and 283 $x_0=1$ one identifies the degrees of freedom for nodes $0$, $5$, $12$ and $16$ 284 with the degrees of freedom for $7$, $10$, $15$ and $20$, respectively. 285 The node section of the \finley mesh now reads: 286 jgs 102 \begin{verbatim} 287 2D Nodes 16 288 0 0 0 0. 0. 289 2 2 0 0.33 0. 290 3 3 0 0.66 0. 291 7 0 0 1. 0. 292 5 5 0 0. 0.5 293 6 6 0 0.33 0.5 294 8 8 0 0.66 0.5 295 10 5 0 1.0 0.5 296 12 12 0 0. 0.5 297 9 9 0 0.33 0.5 298 13 13 0 0.66 0.5 299 15 12 0 1.0 0.5 300 16 16 0 0. 1.0 301 18 18 0 0.33 1.0 302 19 19 0 0.66 1.0 303 20 16 0 1.0 1.0 304 \end{verbatim} 305 306 jfenwick 1955 \clearpage 307 \input{finleyelements} 308 \clearpage 309 jgs 102 310 caltinay 3330 \section{Macro Elements} 311 \label{SEC FINLEY MACRO} 312 313 gross 2793 \begin{figure}[th] 314 \begin{center} 315 caltinay 3330 \includegraphics{FinleyMacroLeg}\\ 316 \subfigure[Triangle]{\label{FINLEY MACRO TRI}\includegraphics{FinleyMacroTri}}\quad 317 \subfigure[Quadrilateral]{\label{FINLEY MACRO REC}\includegraphics{FinleyMacroRec}} 318 gross 2793 \end{center} 319 caltinay 3330 \caption{Macro elements in \finley} 320 gross 2793 \end{figure} 321 322 caltinay 3330 \finley supports the usage of macro elements\index{macro elements} which can be 323 used to achieve LBB compliance when solving incompressible fluid flow problems. 324 LBB compliance is required to get a problem which has a unique solution for 325 pressure and velocity. For macro elements the pressure and velocity are 326 approximated by a polynomial of order 1 but the velocity approximation bases on 327 a refinement of the elements. The nodes of a triangle and quadrilateral element 328 are shown in Figures~\ref{FINLEY MACRO TRI} and~\ref{FINLEY MACRO REC}, 329 respectively. In essence, the velocity uses the same nodes like a quadratic 330 polynomial approximation but replaces the quadratic polynomial by piecewise 331 linear polynomials. In fact, this is the way \finley defines the macro elements. 332 In particular \finley uses the same local ordering of the nodes for the macro 333 element as for the corresponding quadratic element. Another interpretation is 334 that one uses a linear approximation of the velocity together with a linear 335 approximation of the pressure but on elements created by combining elements to 336 macro elements. Notice that the macro elements still use quadratic 337 interpolation to represent the element and domain boundary. 338 However, if elements have linear boundaries a macro element approximation for 339 the velocity is equivalent to using a linear approximation on a mesh which is 340 created through a one-step global refinement. 341 Typically macro elements are only required to use when an incompressible fluid 342 flow problem is solved, e.g. the Stokes problem in \Sec{STOKES PROBLEM}. 343 Please see \Sec{FINLEY MESHES} for more details on the supported macro elements. 344 jgs 102 345 caltinay 3330 \section{Linear Solvers in \SolverOptions} 346 gross 2748 347 caltinay 3330 Table~\ref{TAB FINLEY SOLVER OPTIONS 1} and 348 Table~\ref{TAB FINLEY SOLVER OPTIONS 2} show the solvers and preconditioners 349 supported by \finley through the \PASO library. 350 Currently direct solvers are not supported under \MPI. 351 By default, \finley uses the iterative solvers \PCG for symmetric and \BiCGStab 352 for non-symmetric problems. 353 If the direct solver is selected, which can be useful when solving very 354 ill-posed equations, \finley uses the \MKL\footnote{If the stiffness matrix is 355 non-regular \MKL may return without a proper error code. If you observe 356 suspicious solutions when using \MKL, this may be caused by a non-invertible 357 operator.} solver package. If \MKL is not available \UMFPACK is used. 358 If \UMFPACK is not available a suitable iterative solver from \PASO is used. 359 gross 2748 360 gross 2558 \begin{table} 361 caltinay 3330 \centering 362 jfenwick 2651 {\scriptsize 363 gross 2558 \begin{tabular}{l||c|c|c|c|c|c|c|c} 364 gross 3379 \member{setSolverMethod} & \member{DIRECT}& \member{PCG} & \member{GMRES} & \member{TFQMR} & \member{MINRES} & \member{PRES20} & \member{BICGSTAB} & lumping \\ 365 gross 2558 \hline 366 \hline 367 \member{setReordering} & $\checkmark$ & & & & & &\\ 368 \hline \member{setRestart} & & & $\checkmark$ & & & $20$ & \\ 369 \hline\member{setTruncation} & & & $\checkmark$ & & & $5$ & \\ 370 \hline\member{setIterMax} & & $\checkmark$& $\checkmark$ & $\checkmark$& $\checkmark$& $\checkmark$ & $\checkmark$ \\ 371 \hline\member{setTolerance} & & $\checkmark$& $\checkmark$ & $\checkmark$& $\checkmark$& $\checkmark$ & $\checkmark$ \\ 372 \hline\member{setAbsoluteTolerance} & & $\checkmark$& $\checkmark$ & $\checkmark$& $\checkmark$& $\checkmark$ & $\checkmark$ \\ 373 gross 2573 \hline\member{setReordering} & $\checkmark$ & & & & & & & \\ 374 gross 2558 \end{tabular} 375 } 376 caltinay 3330 \caption{Solvers available for \finley and the \PASO package and the relevant 377 options in \class{SolverOptions}. 378 \MKL supports \member{MINIMUM_FILL_IN}\index{linear solver!minimum fill-in ordering}\index{minimum fill-in ordering} 379 and \member{NESTED_DISSECTION}\index{linear solver!nested dissection ordering}\index{nested dissection} 380 caltinay 3293 reordering. 381 Currently the \UMFPACK interface does not support any reordering. 382 caltinay 3330 \label{TAB FINLEY SOLVER OPTIONS 1}} 383 caltinay 3293 \end{table} 384 gross 2558 385 \begin{table} 386 jfenwick 3616 \begin{center} 387 gross 2558 {\scriptsize 388 gross 3439 \begin{tabular}{l||c|c|c|c|c|c|c} 389 caltinay 3330 \member{NO_PRECONDITIONER}& 390 \member{AMG}& 391 \member{JACOBI}& 392 caltinay 3293 \member{GAUSS_SEIDEL}& 393 gross 2558 \member{REC_ILU}& 394 caltinay 3330 \member{RILU}& 395 \member{ILU0}& 396 \member{DIRECT}\\ 397 gross 2558 \hline 398 gross 3439 status:& $\checkmark$ &$\checkmark$&$\checkmark$&$\checkmark$&later&$\checkmark$&later\\ 399 gross 2558 \hline 400 caltinay 3330 \hline 401 gross 3439 \member{setLevelMax}&$\checkmark$& & & & & &\\ 402 caltinay 3330 \hline 403 gross 3439 \member{setCoarseningThreshold}&$\checkmark$& & & & & &\\ 404 caltinay 3330 \hline 405 gross 3439 \member{setMinCoarseMatrixSize}&$\checkmark$& & & & & &\\ 406 caltinay 3330 \hline 407 gross 3439 \member{setMinCoarseMatrixSparsity}&$\checkmark$& & & & & &\\ 408 gross 3353 \hline 409 gross 3439 \member{setNumSweeps}& &$\checkmark$&$\checkmark$& & & &\\ 410 caltinay 3330 \hline 411 gross 3439 \member{setNumPreSweeps}&$\checkmark$& & & & & &\\ 412 caltinay 3330 \hline 413 gross 3439 \member{setNumPostSweeps}&$\checkmark$& & & & & &\\ 414 caltinay 3330 \hline 415 gross 3439 \member{setDiagonalDominanceThreshold}&$\checkmark$& & & & & &\\ 416 gross 3402 \hline 417 gross 3439 \member{setAMGInterpolation}&$\checkmark$& & & & & &\\ 418 \hline 419 \member{setRelaxationFactor}& & & & &$\checkmark$& &\\ 420 gross 2558 \end{tabular} 421 } 422 caltinay 3330 \caption{Preconditioners available for \finley and the \PASO package and the 423 relevant options in \class{SolverOptions}. 424 \label{TAB FINLEY SOLVER OPTIONS 2}} 425 jfenwick 3616 \end{center} 426 gross 2558 \end{table} 427 428 gross 2793 \section{Functions} 429 gross 2690 \begin{funcdesc}{ReadMesh}{fileName \optional{, \optional{integrationOrder=-1}, optimize=True}} 430 caltinay 3330 creates a \Domain object from the FEM mesh defined in file \var{fileName}. 431 The file must be in the \finley file format. 432 If \var{integrationOrder} is positive, a numerical integration scheme is chosen 433 which is accurate on each element up to a polynomial of degree 434 \var{integrationOrder}\index{integration order}. 435 Otherwise an appropriate integration order is chosen independently. 436 By default the labeling of mesh nodes and element distribution is optimized. 437 Set \var{optimize=False} to switch off relabeling and redistribution. 438 gross 2690 \end{funcdesc} 439 440 gross 3625 \begin{funcdesc}{ReadGmsh}{fileName, numDim, \optional{, \optional{integrationOrder=-1}, optimize=True\optional{, useMacroElements=False}}} 441 creates a \Domain object from the FEM mesh defined in file \var{fileName} for 442 a domain of dimension \var{numDim}. 443 caltinay 3330 The file must be in the \gmshextern file format. 444 If \var{integrationOrder} is positive, a numerical integration scheme is chosen 445 which is accurate on each element up to a polynomial of degree 446 \var{integrationOrder}\index{integration order}. 447 Otherwise an appropriate integration order is chosen independently. 448 By default the labeling of mesh nodes and element distribution is optimized. 449 Set \var{optimize=False} to switch off relabeling and redistribution. 450 If \var{useMacroElements} is set, second order elements are interpreted as 451 macro elements\index{macro elements}. 452 jgs 102 \end{funcdesc} 453 454 gross 2748 \begin{funcdesc}{MakeDomain}{design\optional{, integrationOrder=-1\optional{, optimizeLabeling=True\optional{, useMacroElements=False}}}} 455 caltinay 3330 creates a \finley \Domain from a \pycad \class{Design} object using \gmshextern. 456 gross 2748 The \class{Design} \var{design} defines the geometry. 457 caltinay 3330 If \var{integrationOrder} is positive, a numerical integration scheme is chosen 458 which is accurate on each element up to a polynomial of degree 459 \var{integrationOrder}\index{integration order}. 460 Otherwise an appropriate integration order is chosen independently. 461 Set \var{optimizeLabeling=False} to switch off relabeling and redistribution 462 (not recommended). 463 If \var{useMacroElements} is set, macro elements\index{macro elements} are used. 464 Currently \function{MakeDomain} does not support \MPI. 465 gross 2748 \end{funcdesc} 466 gross 2690 467 gross 2417 \begin{funcdesc}{load}{fileName} 468 caltinay 3330 recovers a \Domain object from a dump file \var{fileName} created by the 469 \function{dump} method of a \Domain object. 470 gross 2417 \end{funcdesc} 471 472 jgs 102 \begin{funcdesc}{Rectangle}{n0,n1,order=1,l0=1.,l1=1., integrationOrder=-1, \\ 473 gross 3904 periodic0=\False, periodic1=\False, useElementsOnFace=\False, optimize=\False} 474 caltinay 3330 generates a \Domain object representing a two-dimensional rectangle between 475 $(0,0)$ and $(l0,l1)$ with orthogonal edges. 476 The rectangle is filled with \var{n0} elements along the $x_0$-axis and 477 caltinay 3293 \var{n1} elements along the $x_1$-axis. 478 caltinay 3330 For \var{order}=1 and \var{order}=2, elements of type \finleyelement{Rec4} and 479 caltinay 3293 \finleyelement{Rec8} are used, respectively. 480 caltinay 3330 In the case of \var{useElementsOnFace}=\False, \finleyelement{Line2} and 481 caltinay 3293 \finleyelement{Line3} are used to subdivide the edges of the rectangle, respectively. 482 caltinay 3330 If \var{order}=-1, \finleyelement{Rec8Macro} and \finleyelement{Line3Macro}\index{macro elements} 483 are used. This option should be used when solving incompressible fluid flow 484 problems, e.g. \class{StokesProblemCartesian}. 485 In the case of \var{useElementsOnFace}=\True (this option should be used if 486 gradients are calculated on domain faces), \finleyelement{Rec4Face} and 487 caltinay 3293 \finleyelement{Rec8Face} are used on the edges, respectively. 488 caltinay 3330 If \var{integrationOrder} is positive, a numerical integration scheme is chosen 489 which is accurate on each element up to a polynomial of degree 490 \var{integrationOrder}\index{integration order}. 491 Otherwise an appropriate integration order is chosen independently. 492 If \var{periodic0}=\True, periodic boundary conditions\index{periodic boundary conditions} 493 along the $x_0$-direction are enforced. 494 That means for any solution of a PDE solved by \finley the values on the line 495 $x_0=0$ will be identical to the values on $x_0=\var{l0}$. 496 Correspondingly, \var{periodic1}=\True sets periodic boundary conditions in the 497 $x_1$-direction. 498 If \var{optimize}=\True mesh node relabeling will be attempted to reduce the 499 computation and also ParMETIS will be used to improve the mesh partition if 500 running on multiple CPUs with \MPI. 501 jgs 102 \end{funcdesc} 502 503 jfenwick 3301 \begin{funcdesc}{Brick}{n0,n1,n2,order=1,l0=1.,l1=1.,l2=1., integrationOrder=-1, 504 jduplessis 5677 periodic0=\False, periodic1=\False, \\ periodic2=\False, useElementsOnFace=\False,useFullElementOrder=\False, optimize=\False} 505 caltinay 3330 generates a \Domain object representing a three-dimensional brick between 506 jgs 102 $(0,0,0)$ and $(l0,l1,l2)$ with orthogonal faces. The brick is filled with 507 caltinay 3293 \var{n0} elements along the $x_0$-axis, 508 \var{n1} elements along the $x_1$-axis and 509 \var{n2} elements along the $x_2$-axis. 510 caltinay 3330 For \var{order}=1 and \var{order}=2, elements of type \finleyelement{Hex8} and 511 caltinay 3293 \finleyelement{Hex20} are used, respectively. 512 caltinay 3330 In the case of \var{useElementsOnFace}=\False, \finleyelement{Rec4} and 513 caltinay 3293 \finleyelement{Rec8} are used to subdivide the faces of the brick, respectively. 514 caltinay 3330 In the case of \var{useElementsOnFace}=\True (this option should be used if 515 gradients are calculated on domain faces), \finleyelement{Hex8Face} and 516 caltinay 3293 \finleyelement{Hex20Face} are used on the brick faces, respectively. 517 caltinay 3330 If \var{order}=-1, \finleyelement{Hex20Macro} and \finleyelement{Rec8Macro}\index{macro elements} 518 are used. This option should be used when solving incompressible fluid flow 519 problems, e.g. \class{StokesProblemCartesian}. 520 If \var{integrationOrder} is positive, a numerical integration scheme is chosen 521 which is accurate on each element up to a polynomial of degree 522 \var{integrationOrder}\index{integration order}. 523 Otherwise an appropriate integration order is chosen independently. 524 If \var{periodic0}=\True, periodic boundary conditions\index{periodic boundary conditions} 525 along the $x_0$-direction are enforced. 526 That means for any solution of a PDE solved by \finley the values on the plane 527 $x_0=0$ will be identical to the values on $x_0=\var{l0}$. 528 Correspondingly, \var{periodic1}=\True and \var{periodic2}=\True sets periodic 529 boundary conditions in the $x_1$-direction and $x_2$-direction, respectively. 530 If \var{optimize}=\True mesh node relabeling will be attempted to reduce the 531 computation and also ParMETIS will be used to improve the mesh partition if 532 running on multiple CPUs with \MPI. 533 jgs 102 \end{funcdesc} 534 535 gross 3567 \begin{funcdesc}{GlueFaces}{meshList, tolerance=1.e-13} 536 caltinay 3330 generates a new \Domain object from the list \var{meshList} of \finley meshes. 537 Nodes in face elements whose difference of coordinates is less than 538 \var{tolerance} times the diameter of the domain are merged. 539 The corresponding face elements are removed from the mesh. 540 gross 3567 \function{GlueFaces} is not supported under \MPI with more than one rank. 541 jgs 102 \end{funcdesc} 542 543 gross 3567 \begin{funcdesc}{JoinFaces}{meshList, tolerance=1.e-13} 544 caltinay 3330 generates a new \Domain object from the list \var{meshList} of \finley meshes. 545 Face elements whose node coordinates differ by less than \var{tolerance} times 546 the diameter of the domain are combined to form a contact element\index{element!contact}. 547 caltinay 3293 The corresponding face elements are removed from the mesh. 548 gross 3567 \function{JoinFaces} is not supported under \MPI with more than one rank. 549 caltinay 3330 \end{funcdesc} 550 jgs 102 551 jfenwick 5658 \section{\dudley} 552 \label{sec:dudley} 553 The {\it dudley} library is a restricted version of {\it finley}. 554 So in many ways it can be used as a drop-in'' replacement. 555 Dudley domains are simpler in that only triangular (2D), tetrahedral (3D) and line elements are supported. 556 Note, this also means that dudley does not support: 557 \begin{itemize} 558 \item dirac delta functions 559 \item contact elements 560 \item macro elements 561 \end{itemize} 562

## Properties

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svn:keywords Author Date Id Revision