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adaptiveConvectionDiffusionReaction_example.html
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adaptiveConvectionDiffusionReaction_example.html
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<div class="title">adaptiveConvectionDiffusionReaction_example.cpp </div> </div>
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<div class="textblock"><h1><a class="anchor" id="adaptiveConvectionDiffusionReaction_exampleAnnotated"></a>
Annotated source file</h1>
<p>Here is the full file <code>examples/adaptiveConvectionDiffusionReaction_example.cpp</code>. Clicking on a function or class name will lead you to its reference documentation.</p>
<div class="fragment"><div class="line"></div>
<div class="line"><span class="preprocessor"># include <<a class="code" href="gismo_8h.html">gismo.h</a>></span></div>
<div class="line"><span class="preprocessor"># include <<a class="code" href="gsAdaptiveRefUtils_8h.html">gsAssembler/gsAdaptiveRefUtils.h</a>></span></div>
<div class="line"></div>
<div class="line"><span class="keyword">using namespace </span>std;</div>
<div class="line"><span class="keyword">using namespace </span>gismo;</div>
<div class="line"></div>
<div class="line"><span class="keywordtype">int</span> <a class="code" href="example__shell2D_8cpp.html#a0ddf1224851353fc92bfbff6f499fa97">main</a>(<span class="keywordtype">int</span> argc, <span class="keywordtype">char</span> *argv[])</div>
<div class="line">{</div>
<div class="line"> <span class="keywordtype">bool</span> plot = <span class="keyword">false</span>;</div>
<div class="line"></div>
<div class="line"> <a class="code" href="classgismo_1_1gsCmdLine.html">gsCmdLine</a> cmd(<span class="stringliteral">"Example for solving a convection-diffusion problem."</span>);</div>
<div class="line"> cmd.addSwitch(<span class="stringliteral">"plot"</span>, <span class="stringliteral">"Create a ParaView visualization file with the solution"</span>, plot);</div>
<div class="line"> <span class="keywordflow">try</span> { cmd.getValues(argc,argv); } <span class="keywordflow">catch</span> (<span class="keywordtype">int</span> rv) { <span class="keywordflow">return</span> rv; }</div>
<div class="line"></div>
<div class="line"> <span class="comment">// --------------- specify exact solution and right-hand-side ---------------</span></div>
<div class="line"></div>
<div class="line"> <span class="comment">// Define exact solution (will be used for specifying Dirichlet boundary conditions</span></div>
<div class="line"> <span class="comment">//gsFunctionExpr<> g("if( y<-x/2-1/2, 1, 0 )", 2);</span></div>
<div class="line"> <a class="code" href="classgismo_1_1gsFunctionExpr.html">gsFunctionExpr<></a> g(<span class="stringliteral">"if( y>=0, if( x <=-1, 1, 0 ), 0 )"</span>, 2);</div>
<div class="line"> <span class="comment">// Define source function</span></div>
<div class="line"> <a class="code" href="classgismo_1_1gsFunctionExpr.html">gsFunctionExpr<></a> rhs(<span class="stringliteral">"0"</span>,2);</div>
<div class="line"></div>
<div class="line"> <span class="comment">// diffusion coefficient:</span></div>
<div class="line"> <a class="code" href="classgismo_1_1gsFunctionExpr.html">gsFunctionExpr<></a> coeff_diff(<span class="stringliteral">"0.000001"</span>,<span class="stringliteral">"0"</span>,<span class="stringliteral">"0"</span>,<span class="stringliteral">"0.000001"</span>,2);</div>
<div class="line"> <span class="comment">// convection coefficient:</span></div>
<div class="line"> <a class="code" href="classgismo_1_1gsFunctionExpr.html">gsFunctionExpr<></a> coeff_conv(<span class="stringliteral">"3/sqrt(13)"</span>,<span class="stringliteral">"-2/sqrt(13)"</span>,2);</div>
<div class="line"> <span class="comment">// reaction coefficient:</span></div>
<div class="line"> <a class="code" href="classgismo_1_1gsFunctionExpr.html">gsFunctionExpr<></a> coeff_reac(<span class="stringliteral">"0"</span>,2);</div>
<div class="line"></div>
<div class="line"> <span class="comment">// Print out source function and solution</span></div>
<div class="line"> <a class="code" href="gsDebug_8h.html#af6177e1e282640c3cb9175565f84a432">gsInfo</a><<<span class="stringliteral">"Source function "</span> << rhs << <span class="stringliteral">"\n"</span>;</div>
<div class="line"> <a class="code" href="gsDebug_8h.html#af6177e1e282640c3cb9175565f84a432">gsInfo</a><<<span class="stringliteral">"Dirichlet boundary conditions "</span> << g << <span class="stringliteral">"\n\n"</span>;</div>
<div class="line"></div>
<div class="line"></div>
<div class="line"> <span class="comment">// --------------- read geometry from file ---------------</span></div>
<div class="line"></div>
<div class="line"> <span class="comment">// Read geometry from file</span></div>
<div class="line"><span class="comment"></span> <span class="comment">// Read xml and create gsMultiPatch</span></div>
<div class="line"> <span class="keywordtype">string</span> fileSrc( <span class="stringliteral">"planar/lshape2d_3patches_thb.xml"</span> );</div>
<div class="line"> <a class="code" href="classgismo_1_1gsMultiPatch.html">gsMultiPatch<real_t></a> patches;</div>
<div class="line"> <a class="code" href="classgismo_1_1gsReadFile.html">gsReadFile<real_t></a>( fileSrc, patches);</div>
<div class="line"> <a class="code" href="gsDebug_8h.html#af6177e1e282640c3cb9175565f84a432">gsInfo</a> << <span class="stringliteral">"The domain is a "</span><< patches <<<span class="stringliteral">"\n"</span>;</div>
<div class="line"></div>
<div class="line"> <span class="comment">// Get all interfaces and boundaries:</span></div>
<div class="line"> patches.computeTopology();</div>
<div class="line"></div>
<div class="line"> <span class="comment">// --------------- add bonudary conditions ---------------</span></div>
<div class="line"><span class="comment"></span> <a class="code" href="classgismo_1_1gsBoundaryConditions.html">gsBoundaryConditions<></a> bcInfo;</div>
<div class="line"></div>
<div class="line"> <span class="comment">// For simplicity, set Dirichlet boundary conditions</span></div>
<div class="line"> <span class="comment">// given by exact solution g on all boundaries:</span></div>
<div class="line"> <span class="keywordflow">for</span> ( <a class="code" href="classgismo_1_1gsMultiPatch.html">gsMultiPatch<>::const_biterator</a></div>
<div class="line"> bit = patches.bBegin(); bit != patches.bEnd(); ++bit)</div>
<div class="line"> {</div>
<div class="line"> bcInfo.<a class="code" href="classgismo_1_1gsBoundaryConditions.html#a1dd0c4f4cdae8082d37db999fc3932d2">addCondition</a>( *bit, <a class="code" href="structgismo_1_1condition__type.html#a7aead736a07eaf25623ad7bfa1f0ee2da1b4f535d1f53363637f933002efc2b4b">condition_type::dirichlet</a>, &g );</div>
<div class="line"> }</div>
<div class="line"></div>
<div class="line"> <span class="comment">// --------------- define Pde ---------------</span></div>
<div class="line"><span class="comment"></span> <a class="code" href="classgismo_1_1gsConvDiffRePde.html">gsConvDiffRePde<real_t></a> cdrPde(patches, bcInfo, & coeff_diff,& coeff_conv, & coeff_reac, & rhs);</div>
<div class="line"></div>
<div class="line"></div>
<div class="line"> <span class="comment">// --------------- set up basis ---------------</span></div>
<div class="line"></div>
<div class="line"> <span class="comment">// Copy basis from the geometry</span></div>
<div class="line"> <a class="code" href="classgismo_1_1gsMultiBasis.html">gsMultiBasis<></a> bases( patches );</div>
<div class="line"></div>
<div class="line"></div>
<div class="line"> <span class="comment">// Number of initial uniform refinement steps:</span></div>
<div class="line"> <span class="keywordtype">int</span> numInitUniformRefine = 2;</div>
<div class="line"></div>
<div class="line"> <span class="keywordflow">for</span> (<span class="keywordtype">int</span> i = 0; i < numInitUniformRefine; ++i)</div>
<div class="line"> bases.uniformRefine();</div>
<div class="line"></div>
<div class="line"></div>
<div class="line"> <span class="comment">// --------------- set up adaptive refinement loop ---------------</span></div>
<div class="line"></div>
<div class="line"> <span class="comment">// Number of refinement loops to be done</span></div>
<div class="line"> <span class="keywordtype">int</span> numRefinementLoops = 3;</div>
<div class="line"></div>
<div class="line"> <span class="comment">// Specify cell-marking strategy...</span></div>
<div class="line"> MarkingStrategy adaptRefCrit = PUCA;</div>
<div class="line"> <span class="comment">//MarkingStrategy adaptRefCrit = GARU;</span></div>
<div class="line"> <span class="comment">//MarkingStrategy adaptRefCrit = errorFraction;</span></div>
<div class="line"></div>
<div class="line"> <span class="comment">// ... and parameter.</span></div>
<div class="line"> <span class="keyword">const</span> real_t adaptRefParam = 0.7;</div>
<div class="line"></div>
<div class="line"></div>
<div class="line"></div>
<div class="line"> <span class="comment">// Construct assembler</span></div>
<div class="line"> <a class="code" href="classgismo_1_1gsCDRAssembler.html">gsCDRAssembler<real_t></a> cdrAss( cdrPde, bases);</div>
<div class="line"> <span class="comment">// Set stabilization flag to 1 = SUPG</span></div>
<div class="line"> cdrAss.options().setInt(<span class="stringliteral">"Stabilization"</span>, <a class="code" href="structgismo_1_1stabilizerCDR.html#abed946c62f140eb7ff2ac742e6ad9497a9f15fee699801b2a7f2da012c89424a6">stabilizerCDR::SUPG</a>);</div>
<div class="line"> <span class="comment">// Compute Dirichlet values by L2-projection</span></div>
<div class="line"> <span class="comment">// Caution: Interpolation does not work for locally refined (T)HB-splines!</span></div>
<div class="line"> cdrAss.options().setInt(<span class="stringliteral">"DirichletValues"</span>,dirichlet::l2Projection);</div>
<div class="line"></div>
<div class="line"> <span class="comment">// --------------- adaptive refinement loop ---------------</span></div>
<div class="line"></div>
<div class="line"> <span class="keywordflow">for</span>( <span class="keywordtype">int</span> refLoop = 0; refLoop <= numRefinementLoops; refLoop++)</div>
<div class="line"> {</div>
<div class="line"> <a class="code" href="gsDebug_8h.html#af6177e1e282640c3cb9175565f84a432">gsInfo</a> << <span class="stringliteral">"====== Loop "</span> << refLoop << <span class="stringliteral">" of "</span></div>
<div class="line"> <<numRefinementLoops<< <span class="stringliteral">" ======"</span> << <span class="stringliteral">"\n"</span>;</div>
<div class="line"></div>
<div class="line"> <span class="comment">// --------------- solving ---------------</span></div>
<div class="line"></div>
<div class="line"> <span class="comment">// Generate system matrix and load vector</span></div>
<div class="line"> cdrAss.assemble();</div>
<div class="line"></div>
<div class="line"> <span class="comment">// Solve the system</span></div>
<div class="line"> <a class="code" href="classgismo_1_1gsMatrix.html">gsMatrix<real_t></a> solVector =</div>
<div class="line"> gsSparseSolver<>::BiCGSTABILUT( cdrAss.matrix() ).solve( cdrAss.rhs() );</div>
<div class="line"></div>
<div class="line"> <span class="comment">// Construct the solution as a scalar field</span></div>
<div class="line"> <a class="code" href="classgismo_1_1gsField.html">gsField<></a> solField;</div>
<div class="line"> solField = cdrAss.constructSolution(solVector);</div>
<div class="line"></div>
<div class="line"> <span class="comment">// --------------- error estimation/computation ---------------</span></div>
<div class="line"></div>
<div class="line"> <span class="comment">// Compute the H1-seminorm of the computed solution</span></div>
<div class="line"> <span class="comment">// ( which is, at least, equivalent to the energy norm in this example )</span></div>
<div class="line"> <span class="comment">// using the known exact solution.</span></div>
<div class="line"> <a class="code" href="classgismo_1_1gsExprEvaluator.html">gsExprEvaluator<></a> ev;</div>
<div class="line"> ev.<a class="code" href="classgismo_1_1gsExprEvaluator.html#a0ec66d534b5822bf6f68607c69af9c33">setIntegrationElements</a>(cdrAss.multiBasis());</div>
<div class="line"> gsExprEvaluator<>::geometryMap Gm = ev.<a class="code" href="classgismo_1_1gsExprEvaluator.html#acd8fe15286df0845bdce1e8689908304">getMap</a>(patches);</div>
<div class="line"> <a class="code" href="classgismo_1_1expr_1_1gsFeVariable.html">gsExprEvaluator<>::variable</a> is = ev.<a class="code" href="classgismo_1_1gsExprEvaluator.html#ac146357502c87ba4fe61a7fddf63c86d">getVariable</a>(solField.fields());</div>
<div class="line"> <span class="keyword">auto</span> ms = ev.<a class="code" href="classgismo_1_1gsExprEvaluator.html#ac146357502c87ba4fe61a7fddf63c86d">getVariable</a>(g, Gm);</div>
<div class="line"></div>
<div class="line"> <span class="comment">// Get the element-wise norms.</span></div>
<div class="line"> ev.<a class="code" href="classgismo_1_1gsExprEvaluator.html#a465bfc4ca998bdb2717d09465a3bfb4e">integralElWise</a>( ( igrad(is,Gm) - igrad(ms)).sqNorm()*<a class="code" href="namespacegismo_1_1expr.html#a85b75566d500893f259a628742efab75">meas</a>(Gm) );</div>
<div class="line"> <span class="keyword">const</span> std::vector<real_t> & eltErrs = ev.<a class="code" href="classgismo_1_1gsExprEvaluator.html#ab5ebf25dee71a277f71609d3a8729187">elementwise</a>();</div>
<div class="line"></div>
<div class="line"> <span class="comment">// --------------- adaptive refinement ---------------</span></div>
<div class="line"></div>
<div class="line"> <span class="comment">// Mark elements for refinement, based on the computed local errors and</span></div>
<div class="line"> <span class="comment">// the refinement-criterion and -parameter.</span></div>
<div class="line"> std::vector<bool> elMarked( eltErrs.size() );</div>
<div class="line"> <a class="code" href="group__Assembler.html#ga861ca4dbe178e7304a67686409577f7a">gsMarkElementsForRef</a>( eltErrs, adaptRefCrit, adaptRefParam, elMarked);</div>
<div class="line"> <a class="code" href="gsDebug_8h.html#af6177e1e282640c3cb9175565f84a432">gsInfo</a> <<<span class="stringliteral">"Marked "</span><< std::count(elMarked.begin(), elMarked.end(), <span class="keyword">true</span>) <<<span class="stringliteral">" elements.\n"</span>;</div>
<div class="line"></div>
<div class="line"> <span class="comment">// Refine the marked elements with a 1-ring of cells around marked elements</span></div>
<div class="line"> <a class="code" href="group__Assembler.html#gaadde8fcd91d5e1fdf65f1921de7e97d1">gsRefineMarkedElements</a>( cdrAss.multiBasis(), elMarked, 1 );</div>
<div class="line"></div>
<div class="line"></div>
<div class="line"> <span class="comment">// Call repair interfaces to make sure that the new meshes</span></div>
<div class="line"> <span class="comment">// match along patch interfaces.</span></div>
<div class="line"> cdrAss.multiBasis().repairInterfaces( patches.interfaces() );</div>
<div class="line"></div>
<div class="line"> cdrAss.refresh();</div>
<div class="line"></div>
<div class="line"> <span class="comment">// Export the final solution</span></div>
<div class="line"> <span class="keywordflow">if</span>( plot && refLoop == numRefinementLoops )</div>
<div class="line"> {</div>
<div class="line"> <span class="comment">// Write the computed solution to paraview files</span></div>
<div class="line"> gsWriteParaview<>( solField, <span class="stringliteral">"adaptRef"</span>, 1000, <span class="keyword">true</span>);</div>
<div class="line"> }</div>
<div class="line"></div>
<div class="line"> }</div>
<div class="line"></div>
<div class="line"> <span class="keywordflow">if</span>( plot )</div>
<div class="line"> {</div>
<div class="line"> <span class="comment">// Run paraview</span></div>
<div class="line"> <a class="code" href="classgismo_1_1gsFileManager.html#a0f725eecb78d3bc1f482326cb9e85eee">gsFileManager::open</a>(<span class="stringliteral">"adaptRef.pvd"</span>);</div>
<div class="line"> }</div>
<div class="line"> <span class="keywordflow">else</span></div>
<div class="line"> {</div>
<div class="line"> <a class="code" href="gsDebug_8h.html#af6177e1e282640c3cb9175565f84a432">gsInfo</a><<<span class="stringliteral">"Done. No output created, re-run with --plot to get a ParaView "</span></div>
<div class="line"> <span class="stringliteral">"file containing Plotting image data.\n"</span>;</div>
<div class="line"> }</div>
<div class="line"> <span class="keywordflow">return</span> EXIT_SUCCESS;</div>
<div class="line"></div>
<div class="line">}<span class="comment">// end main</span></div>
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