diff --git a/extensions/base_problems/LinearElasticity.h b/extensions/base_problems/LinearElasticity.h
index f757b82eb2a4c6264a460696a327d221739924db..7db74f0f3258f27ebee47a366960670c07165251 100644
--- a/extensions/base_problems/LinearElasticity.h
+++ b/extensions/base_problems/LinearElasticity.h
@@ -37,8 +37,6 @@ public: // methods
// === getting/setting methods ===
-protected: // methods
-
virtual void fillOperators();
virtual void fillBoundaryConditions();
diff --git a/extensions/demo/CMakeLists.txt b/extensions/demo/CMakeLists.txt
new file mode 100644
index 0000000000000000000000000000000000000000..074280e7a7696d784a9efc0acf00ec8b9eda67b1
--- /dev/null
+++ b/extensions/demo/CMakeLists.txt
@@ -0,0 +1,57 @@
+project("amdis_demo")
+cmake_minimum_required(VERSION 2.8)
+
+#find_package(AMDIS REQUIRED COMPONENTS umfpack )
+find_package(AMDIS REQUIRED)
+
+if(AMDIS_FOUND)
+ message("amdis was found\n")
+ include(${AMDIS_USE_FILE})
+ SET(BASIS_LIBS ${AMDIS_LIBRARIES})
+endif(AMDIS_FOUND)
+
+
+# set(elliptBase src/elliptBaseProblem.cc)
+# add_executable("elliptBase" ${elliptBase})
+# target_link_libraries("elliptBase" ${BASIS_LIBS})
+#
+# set(elliptImplicit src/elliptImplicit.cc)
+# add_executable("elliptImplicit" ${elliptImplicit})
+# target_link_libraries("elliptImplicit" ${BASIS_LIBS})
+#
+# set(cahn_hilliard src/cahn_hilliard.cc)
+# add_executable("cahn_hilliard" ${cahn_hilliard})
+# target_link_libraries("cahn_hilliard" ${BASIS_LIBS})
+#
+# set(pfc src/pfc.cc)
+# add_executable("pfc" ${pfc})
+# target_link_libraries("pfc" ${BASIS_LIBS})
+#
+# set(drivenCavity src/chns/drivenCavity.cc)
+# add_executable("drivenCavity" ${drivenCavity})
+# target_link_libraries("drivenCavity" ${BASIS_LIBS})
+#
+# include_directories(/home/spraetor/projects/src/common)
+# set(navierStokes src/navierStokes.cc)
+# add_executable("navierStokes" ${navierStokes})
+# target_link_libraries("navierStokes" ${BASIS_LIBS})
+#
+# set(navierStokesDd src/navierStokes_diffuseDomain.cc)
+# add_executable("navierStokesDd" ${navierStokesDd})
+# target_link_libraries("navierStokesDd" ${BASIS_LIBS})
+#
+# set(linearElasticityDd src/linearElasticity.cc)
+# add_executable("linearElasticityDd" ${linearElasticityDd})
+# target_link_libraries("linearElasticityDd" ${BASIS_LIBS})
+
+ set(fsi src/fsi_explicit/fluidStructureInteraction.cc)
+ add_executable("fsi" ${fsi})
+ target_link_libraries("fsi" ${BASIS_LIBS})
+
+# set(ddFsi src/diffuseDomainFsi.cc)
+# add_executable("ddFsi" ${ddFsi})
+# target_link_libraries("ddFsi" ${BASIS_LIBS})
+
+
+#create the output dir
+# file(MAKE_DIRECTORY output)
diff --git a/extensions/demo/fsi b/extensions/demo/fsi
new file mode 100755
index 0000000000000000000000000000000000000000..c2afb5ade420e28ebb1f6ba916b943a2d3443b34
Binary files /dev/null and b/extensions/demo/fsi differ
diff --git a/extensions/demo/init/fsi.dat.2d b/extensions/demo/init/fsi.dat.2d
new file mode 100644
index 0000000000000000000000000000000000000000..6e882951062dd3e2750dcc8bd363d19bc6fb4d85
--- /dev/null
+++ b/extensions/demo/init/fsi.dat.2d
@@ -0,0 +1,168 @@
+dimension of world: 2
+
+% ====================== VARIABLES ========================
+output_folder: output
+output_postfix: _fsi
+
+% ====================== MESH =============================
+mesh->H: 0.4 %0.41
+mesh->L: 2.4 %2.5
+
+
+obstacle->num vertices: 4
+obstacle->vertex[0]: [0.16, 0.12]
+obstacle->vertex[1]: [0.16, 0.24]
+obstacle->vertex[2]: [0.28, 0.24]
+obstacle->vertex[3]: [0.28, 0.12]
+
+flag->num vertices: 4
+flag->vertex[0]: [0.28, 0.20]
+flag->vertex[1]: [0.64, 0.20]
+flag->vertex[2]: [0.64, 0.16]
+flag->vertex[3]: [0.28, 0.16]
+
+connection->num vertices: 4
+connection->vertex[0]: [0.26, 0.20]
+connection->vertex[1]: [0.30, 0.20]
+connection->vertex[2]: [0.30, 0.16]
+connection->vertex[3]: [0.26, 0.16]
+
+obstacle->P: 0.2
+
+mesh->refinement->initial level: 4
+mesh->refinement->level on interface: 6
+mesh->refinement->level in inner domain: 4
+mesh->refinement->level in outer domain: 0
+mesh->refinement->interface width: 0.01
+mesh->refinement->fade out width: 0.1
+
+% ====================== MESH =============================
+mesh1->macro file name: macro/obstacle_in_channel.2d
+mesh1->global refinements: 0
+mesh1->check: 1
+
+mesh2->macro file name: macro/channel.2d
+mesh2->global refinements: 0
+mesh2->check: 1
+
+% ====================== INCLUDES =========================
+polynomial-degree: 1
+mesh_name: mesh2
+#include "init/navierStokes_TaylorHood.inc.2d"
+
+% =========== ELASTICITY_PROBLEM 1 ================================
+
+% --------------- PROBLEM-SPACES ----------------------------------
+elasticity->obstacle->space->components: 2*${dimension of world}
+
+elasticity->obstacle->space->polynomial degree[0]: ${polynomial-degree}
+elasticity->obstacle->space->polynomial degree[1]: ${polynomial-degree}
+elasticity->obstacle->space->polynomial degree[2]: ${polynomial-degree}
+elasticity->obstacle->space->polynomial degree[3]: ${polynomial-degree}
+elasticity->obstacle->space->polynomial degree[4]: ${polynomial-degree}
+elasticity->obstacle->space->polynomial degree[5]: ${polynomial-degree}
+
+elasticity->obstacle->space->dim: ${dimension of world}
+elasticity->obstacle->space->mesh: mesh1
+
+% --------------- SOLVER ----------------------------------
+elasticity->obstacle->space->solver: umfpack
+elasticity->obstacle->space->solver->symmetric strategy: 0
+elasticity->obstacle->space->solver->tolerance: 1.e-8
+elasticity->obstacle->space->solver->info: 1
+
+% --------------- OUTPUT ----------------------------------
+elasticity->obstacle->displacement->output->filename: ${output_folder}/displacement${output_postfix}_
+elasticity->obstacle->displacement->output->ParaView animation: 1
+elasticity->obstacle->displacement->output->ParaView vector format: 1
+elasticity->obstacle->displacement->output->write vector as 3d vector: 1
+elasticity->obstacle->displacement->output->write every i-th timestep: 1
+elasticity->obstacle->displacement->output->append index: 1
+elasticity->obstacle->displacement->output->index length: 9
+elasticity->obstacle->displacement->output->index decimals: 7
+
+elasticity->obstacle->space->output->filename: ${output_folder}/elasticity${output_postfix}_
+elasticity->obstacle->space->output->ParaView animation: 1
+elasticity->obstacle->space->output->ParaView format: 1
+elasticity->obstacle->space->output->write every i-th timestep: 1
+elasticity->obstacle->space->output->append index: 1
+elasticity->obstacle->space->output->index length: 9
+elasticity->obstacle->space->output->index decimals: 7
+
+% =========== ELASTICITY_PROBLEM 2 ================================
+
+% --------------- PROBLEM-SPACES ----------------------------------
+elasticity->fluid->space->components: ${dimension of world}
+
+elasticity->fluid->space->polynomial degree[0]: ${polynomial-degree}
+elasticity->fluid->space->polynomial degree[1]: ${polynomial-degree}
+elasticity->fluid->space->polynomial degree[2]: ${polynomial-degree}
+
+elasticity->fluid->space->dim: ${dimension of world}
+elasticity->fluid->space->mesh: mesh2
+
+% --------------- SOLVER ----------------------------------
+elasticity->fluid->space->solver: umfpack
+elasticity->fluid->space->solver->symmetric strategy: 0
+elasticity->fluid->space->solver->tolerance: 1.e-8
+elasticity->fluid->space->solver->info: 1
+
+% ====================== MAIN_PROBLEM ==============
+
+main->dim: ${dimension of world}
+main->solver: umfpack
+
+% ====================== USER_PARAMETER - NS ==============
+
+% glycerine
+ns->viscosity: 1.13*1.e-3
+ns->density: 1.26*1.e3
+
+ns->theta: 0.5
+%ns->force: [0.0, 9.81] % gravitational force [m/s^2]
+
+ns->force dirichlet bc: 0
+
+ns->Um: 1.5
+ns->beta: 1
+ns->alpha: 2.7
+
+ns->initial velocity: 0
+ns->initial velocity value: 0.0
+ns->laplace operator: 1 % 0... div(nu*grad(u)), 1... div(0.5*nu*(grad(u)+grad(u)^T)) [sehr langsam]
+ns->non-linear term: 2 % 0... u^old*grad(u_i^old), 1... u'*grad(u_i^old), 2... u^old*grad(u'_i)
+
+% ====================== USER_PARAMETER - NS ==============
+
+% polypropylene
+elasticity->obstacle->mu: 317*1.e6
+elasticity->obstacle->lambda: 1.6637*1.e9
+elasticity->obstacle->rho: 1.1*1.e3
+
+elasticity->obstacle->beta: 1
+elasticity->obstacle->alpha: 2.7
+
+% polypropylene
+elasticity->fluid->mu: 700
+elasticity->fluid->lambda: 1200
+elasticity->fluid->rho: 1
+
+elasticity->fluid->beta: 1
+elasticity->fluid->alpha: 2.7
+
+% ====================== TIMESTEPS ========================
+adapt->max iteration: 1
+adapt->max timestep iteration: 1
+adapt->max time iteration: 1
+
+adapt->timestep: 1.e-5
+adapt->max timestep: 1e+10
+adapt->min timestep: 1e-6
+adapt->start time: 0.0
+adapt->end time: 25
+
+% ====================== ESTIMATORS =======================
+adapt->strategy: 0 % 0=explicit, 1=implicit
+
+WAIT: 1
+
diff --git a/extensions/demo/init/navierStokes_TaylorHood.inc.2d b/extensions/demo/init/navierStokes_TaylorHood.inc.2d
new file mode 100644
index 0000000000000000000000000000000000000000..868aff11896b70ce32132f9e3bdbce792d290398
--- /dev/null
+++ b/extensions/demo/init/navierStokes_TaylorHood.inc.2d
@@ -0,0 +1,65 @@
+
+ns->space->mesh: ${mesh_name}
+
+% ============ USER_PARAMETERS - NS =================================
+ns->viscosity: 1
+ns->beta: 1
+ns->sigma: 0.072
+ns->beta: 1
+ns->exponent: 2
+ns->theta: 0.5
+%ns->force: [0.0, -9.81] % gravitational force
+
+ns->viscosity1: 1
+ns->viscosity2: ${ns->viscosity1}/1000
+
+ns->force dirichlet bc: 0
+ns->poisson problem pertubation: 0 % 1..applySingularPertubation, 2..applySingularDBC, 0..nothing
+ns->simple algorithm: 1
+ns->calculate pressure: 0
+ns->initial velocity: 3
+ns->initial velocity value: 0.1
+ns->laplace operator: 1 % 0... div(nu*grad(u)), 1... div(0.5*nu*(grad(u)+grad(u)^T)) [sehr langsam]
+ns->non-linear term: 2 % 0... u^old*grad(u_i^old), 1... u'*grad(u_i^old), 2... u^old*grad(u'_i)
+
+% =========== OUTPUT ==============================================
+
+ns->velocity->output->filename: ${output_folder}/velocity${output_postfix}_
+ns->space->output[2]->filename: ${output_folder}/pressure${output_postfix}_
+
+% ============= PROBLEM-SPACES ==================================
+ns->space->components: 3
+
+ns->space->polynomial degree[0]: ${polynomial-degree}+1
+ns->space->polynomial degree[1]: ${polynomial-degree}+1
+ns->space->polynomial degree[2]: ${polynomial-degree}
+
+ns->space->dim: 2
+
+% ================== SOLVER ======================================
+ns->space->solver: umfpack
+ns->space->solver->symmetric strategy: 0
+ns->space->solver->ell: 3
+ns->space->solver->max iteration: 500
+ns->space->solver->restart: 10 % only used for GMRES
+ns->space->solver->tolerance: 10 %1.e-8
+ns->space->solver->info: 1
+ns->space->solver->left precon: ilu
+
+% =================== OUTPUT =========================================
+ns->velocity->output->ParaView animation: 1
+ns->velocity->output->ParaView vector format: 1
+ns->velocity->output->write vector as 3d vector: 1
+ns->velocity->output->write every i-th timestep: 1
+%ns->velocity->output->compression: gzip
+ns->velocity->output->append index: 1
+ns->velocity->output->index length: 9
+ns->velocity->output->index decimals: 7
+
+ns->space->output[2]->ParaView animation: 0
+ns->space->output[2]->ParaView format: 0
+ns->space->output[2]->write every i-th timestep: 1
+%ns->space->output[2]->compression: gzip
+ns->space->output[2]->append index: 1
+ns->space->output[2]->index length: 9
+ns->space->output[2]->index decimals: 7
diff --git a/extensions/demo/init/reinit.inc.2d b/extensions/demo/init/reinit.inc.2d
new file mode 100644
index 0000000000000000000000000000000000000000..4d7d822ea427b31fcc1ae530635259e800a8e4ca
--- /dev/null
+++ b/extensions/demo/init/reinit.inc.2d
@@ -0,0 +1,5 @@
+reinit->tolerance: 1.e-4
+reinit->maximal number of iteration steps: 100
+reinit->Gauss-Seidel iteration: 1
+reinit->infinity value: 1.e8
+reinit->boundary initialization: 3
diff --git a/extensions/demo/macro/channel.2d b/extensions/demo/macro/channel.2d
new file mode 100644
index 0000000000000000000000000000000000000000..18ed55f59afaebe384858e47507dc7775efd3630
--- /dev/null
+++ b/extensions/demo/macro/channel.2d
@@ -0,0 +1,8247 @@
+DIM: 2
+DIM_OF_WORLD: 2
+
+number of elements: 2328
+number of vertices: 1249
+
+vertex coordinates:
+0 0
+0.04 0
+0.08 0
+0.12 0
+0.16 0
+0.2 0
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diff --git a/extensions/demo/macro/macro.square.2d b/extensions/demo/macro/macro.square.2d
new file mode 100644
index 0000000000000000000000000000000000000000..7d310bfbb624959589f9fa057df7154400383bed
--- /dev/null
+++ b/extensions/demo/macro/macro.square.2d
@@ -0,0 +1,47 @@
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+
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diff --git a/extensions/demo/macro/obstacle_in_channel.2d b/extensions/demo/macro/obstacle_in_channel.2d
new file mode 100644
index 0000000000000000000000000000000000000000..cb5acbd02a4adbb6aeea219de6017d17a11221d1
--- /dev/null
+++ b/extensions/demo/macro/obstacle_in_channel.2d
@@ -0,0 +1,282 @@
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+0.48 0.2
+0.52 0.2
+0.56 0.2
+0.6 0.2
+0.64 0.2
+0.16 0.24
+0.2 0.24
+0.24 0.24
+0.28 0.24
+0.18 0.14
+0.22 0.14
+0.26 0.14
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+0.34 0.18
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+0.42 0.18
+0.46 0.18
+0.5 0.18
+0.54 0.18
+0.58 0.18
+0.62 0.18
+0.18 0.22
+0.22 0.22
+0.26 0.22
+
+element vertices:
+0 1 34
+1 5 34
+5 4 34
+4 0 34
+1 2 35
+2 6 35
+6 5 35
+5 1 35
+2 3 36
+3 7 36
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+12 13 45
+13 26 45
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+13 14 46
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+27 14 47
+15 16 48
+16 29 48
+29 28 48
+28 15 48
+17 18 49
+18 31 49
+31 30 49
+30 17 49
+18 19 50
+19 32 50
+32 31 50
+31 18 50
+19 20 51
+20 33 51
+33 32 51
+32 19 51
+
+element boundaries:
+0 0 10
+0 0 0
+0 0 0
+0 0 10
+0 0 10
+0 0 0
+0 0 0
+0 0 0
+0 0 10
+0 0 10
+0 0 0
+0 0 0
+0 0 0
+0 0 0
+0 0 0
+0 0 10
+0 0 0
+0 0 0
+0 0 0
+0 0 0
+0 0 0
+0 0 0
+0 0 0
+0 0 0
+0 0 1
+0 0 0
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+0 0 1
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+0 0 1
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+0 0 0
+0 0 1
+0 0 0
+0 0 1
+0 0 0
+0 0 1
+0 0 0
+0 0 1
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+0 0 0
+0 0 1
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+0 0 1
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+0 0 1
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+0 0 1
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+0 0 1
+0 0 0
+0 0 1
+0 0 0
+0 0 1
+0 0 1
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+0 0 10
+0 0 10
+0 0 0
+0 0 0
+0 0 10
+0 0 0
+0 0 0
+0 0 10
+0 0 10
+0 0 0
+
+element neighbours:
+1 3 -1
+2 0 7
+3 1 12
+0 2 -1
+5 7 -1
+6 4 11
+7 5 16
+4 6 1
+9 11 -1
+10 8 -1
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+15 13 60
+12 14 -1
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+19 17 64
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+23 21 68
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+25 27 -1
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+46 44 51
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+48 50 45
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+54 52 59
+55 53 -1
+52 54 49
+57 59 -1
+58 56 -1
+59 57 -1
+56 58 53
+61 63 14
+62 60 67
+63 61 -1
+60 62 -1
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+66 64 71
+67 65 -1
+64 66 61
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+70 68 -1
+71 69 -1
+68 70 65
+
diff --git a/extensions/demo/src/fsi_explicit/ElasticityNavierStokes.h b/extensions/demo/src/fsi_explicit/ElasticityNavierStokes.h
new file mode 100644
index 0000000000000000000000000000000000000000..9c120acb06878b58ebceda5e116ab5fc1254b12a
--- /dev/null
+++ b/extensions/demo/src/fsi_explicit/ElasticityNavierStokes.h
@@ -0,0 +1,305 @@
+/** \file ElasticityNavierStokes.h */
+
+#ifndef ELASTICITY_NAVIER_STOKES_H
+#define ELASTICITY_NAVIER_STOKES_H
+
+// coupling structures
+#include "CouplingIterationInterface.h"
+#include "CouplingTimeInterface.h"
+#include "CouplingProblemStat.h"
+
+// structures for local refinement
+#include "Refinement.h"
+#include "MeshFunction_Level.h"
+
+#include "NavierStokesPhase_TaylorHood.h"
+#include "LinearElasticity.h"
+#include "navierStokes.h"
+#include "SignedDistFunctors.h"
+#include "PhaseFieldConvert.h"
+
+using namespace AMDiS;
+
+/**
+ * \ingroup Problem
+ *
+ * \brief
+ */
+template<typename Elasticity_Type1 = LinearElasticity,
+ typename Elasticity_Type2 = StandardBaseProblem,
+ typename NS_Type = NavierStokesPhase_TaylorHood>
+class ElasticityNavierStokes : public CouplingIterationInterface,
+ public CouplingTimeInterface,
+ public CouplingProblemStat
+{
+public:
+
+ ElasticityNavierStokes(std::string name_, Elasticity_Type1 *elastProb_, Elasticity_Type2 *elastProb2_, NS_Type *nsProb_)
+ : CouplingProblemStat(name_),
+ elastProb(elastProb_),
+ elastProb2(elastProb2_),
+ nsProb(nsProb_),
+ refFunction1(NULL),
+ refFunction2(NULL),
+ refinement1(NULL),
+ refinement2(NULL)
+ {
+ dow = Global::getGeo(WORLD);
+ }
+
+
+ ~ElasticityNavierStokes() {
+ if (refFunction1 != NULL)
+ delete refFunction1;
+ if (refinement1 != NULL)
+ delete refinement1;
+ if (refFunction2 != NULL)
+ delete refFunction2;
+ if (refinement2 != NULL)
+ delete refinement2;
+
+ for (int i = 0; i < Global::getGeo(WORLD); i++) {
+ delete parametricCoords1[i];
+ delete parametricCoords2[i];
+ }
+
+ delete parametric1;
+ delete parametric2;
+ }
+
+
+ /**
+ * Add the problems to the iterationInterface, timeInterface and couplingProblemStat.
+ * As a consequence all problem can be initialized one after another and in the
+ * adaption loop they are solved in rotation.
+ * At the end the problems are filled with operators and coupling operators as well as
+ * boundary conditions are added.
+ *
+ * In the adaption loop the problems are solved the same order as they are added to the
+ * iterationInterface in this method. This order can be changed manually in the oneIteration
+ * method.
+ **/
+ void initialize(AdaptInfo *adaptInfo)
+ {
+ for (size_t i = 0; i < elastProb->getNumProblems(); i++)
+ addProblem(elastProb->getProblem(i));
+ for (size_t i = 0; i < elastProb2->getNumProblems(); i++)
+ addProblem(elastProb2->getProblem(i));
+ for (size_t i = 0; i < nsProb->getNumProblems(); i++)
+ addProblem(nsProb->getProblem(i));
+
+ addIterationInterface(elastProb);
+ addIterationInterface(elastProb2);
+ addIterationInterface(nsProb);
+
+ addTimeInterface(elastProb);
+ addTimeInterface(elastProb2);
+ addTimeInterface(nsProb);
+
+// CouplingProblemStat::initialize(INIT_ALL | INIT_EXACT_SOLUTION);
+ nsProb->initialize(INIT_ALL);
+ elastProb->initialize(INIT_ALL);
+ elastProb2->initialize(INIT_ALL);
+ dim = elastProb->getMesh()->getDim();
+
+ initData();
+ elastProb->initData();
+ elastProb2->initData();
+ nsProb->initData();
+ fillCouplingBoundaryConditions();
+
+ elastProb->fillOperators();
+ elastProb2->fillOperators();
+ nsProb->fillOperators();
+
+ elastProb->fillBoundaryConditions();
+ elastProb2->fillBoundaryConditions();
+ nsProb->fillBoundaryConditions();
+ }
+
+
+ void initData()
+ { MSG("initData()\n");
+
+ // ===== create coords vector =====
+ for (int i = 0; i < Global::getGeo(WORLD); i++) {
+ parametricCoords1[i] = new DOFVector<double>(elastProb->getFeSpace(0),
+ "parametric1 coords "+boost::lexical_cast<std::string>(i));
+ parametricCoords2[i] = new DOFVector<double>(elastProb2->getFeSpace(0),
+ "parametric2 coords "+boost::lexical_cast<std::string>(i));
+ }
+
+ // ===== create parametric object =====
+ parametric1 = new ParametricFirstOrder(¶metricCoords1);
+ parametric2 = new ParametricFirstOrder(¶metricCoords2);
+ }
+
+
+ void fillCouplingBoundaryConditions()
+ { MSG("fillCouplingBoundaryConditions()\n");
+ elastProb->setNormalStress(nsProb->getNormalStress());
+ elastProb2->setDeformation(elastProb->getDeformation());
+ nsProb->setDeformationVelocity(elastProb->getDeformationVelocity());
+ }
+
+
+ /**
+ * Solves the initial problems.Before this is done the mesh is refined by the Refinement-class
+ * This provides local refinement functions for phaseField-refinement or signed-distance-refinement.
+ * See MeshFunction_Level.h for some details.
+ **/
+ void solveInitialProblem(AdaptInfo *adaptInfo)
+ { MSG("solveInitialProblem()\n");
+
+
+
+ size_t nVertices = 0;
+ WorldVector<double> c,c2;
+ Parameters::get("obstacle->num vertices",nVertices);
+ std::vector<WorldVector<double> > v(nVertices,c);
+ for (size_t i = 0; i < nVertices; i++)
+ Parameters::get("obstacle->vertex["+boost::lexical_cast<std::string>(i)+"]",v[i]);
+ v.push_back(v[0]);
+
+ obstacle = new Polygon(v);
+
+ Parameters::get("flag->num vertices",nVertices);
+ std::vector<WorldVector<double> > v2(nVertices,c);
+ for (size_t i = 0; i < nVertices; i++)
+ Parameters::get("flag->vertex["+boost::lexical_cast<std::string>(i)+"]",v2[i]);
+ v2.push_back(v2[0]);
+
+ flag = new Polygon(v2);
+
+ Parameters::get("connection->num vertices",nVertices);
+ std::vector<WorldVector<double> > v3(nVertices,c);
+ for (size_t i = 0; i < nVertices; i++)
+ Parameters::get("connection->vertex["+boost::lexical_cast<std::string>(i)+"]",v3[i]);
+ v3.push_back(v3[0]);
+
+ signedDistFct = new MinWrapper(new Polygon(v2), new MinWrapper(obstacle,flag));
+
+ refFunction1 = new SignedDistRefinement(elastProb->getMesh());
+ refinement1 = new RefinementLevelCoords2(
+ elastProb->getFeSpace(0),
+ refFunction1,
+ signedDistFct);
+
+ refFunction2 = new SignedDistRefinement(elastProb2->getMesh());
+ refinement2 = new RefinementLevelCoords2(
+ elastProb2->getFeSpace(0),
+ refFunction2,
+ signedDistFct);
+
+ // initial refinement
+ refinement1->refine(10);
+ refinement2->refine(10);
+ flag->refine(10);
+
+ // solve all initial problems of the problems added to the CouplingTimeInterface
+ CouplingTimeInterface::solveInitialProblem(adaptInfo);
+
+ DOFVector<WorldVector<double> > coords1(parametricCoords1[0]->getFeSpace(), "coords");
+ parametricCoords1[0]->getFeSpace()->getMesh()->getDofIndexCoords(parametricCoords1[0]->getFeSpace(), coords1);
+ DOFVector<WorldVector<double> > coords2(parametricCoords2[0]->getFeSpace(), "coords");
+ parametricCoords2[0]->getFeSpace()->getMesh()->getDofIndexCoords(parametricCoords2[0]->getFeSpace(), coords2);
+ for (int i = 0; i < Global::getGeo(WORLD); i++) {
+ transformDOF(&coords1, parametricCoords1[i], new Component(i));
+ transformDOF(&coords2, parametricCoords2[i], new Component(i));
+ }
+
+ // ===== enable parametric traverse =====
+ elastProb->getMesh()->setParametric(parametric1);
+ elastProb2->getMesh()->setParametric(parametric2);
+ }
+
+
+ /**
+ * Called at the end of each timestep.
+ * If the phase-field has changed the mesh is updated by the refinement-method
+ **/
+ void closeTimestep(AdaptInfo *adaptInfo)
+ { MSG("closeTimestep()\n");
+
+ CouplingTimeInterface::closeTimestep(adaptInfo);
+
+ flag->move(elastProb->getDeformation());
+ updateMesh(elastProb->getDeformation(), parametricCoords1, parametric1);
+ updateMesh(elastProb2->getDeformation(), parametricCoords2, parametric2);
+// refinement1->refine(5);
+// refinement2->refine(5);
+ }
+
+ void updateMesh(DOFVector<WorldVector<double> >* vec, WorldVector<DOFVector<double>*>& parametricCoords, ParametricFirstOrder* parametric)
+ {
+ FUNCNAME("ParametricSphere::buildAfterCoarsen()");
+ MSG("calculation of parametric coordinates\n");
+ const FiniteElemSpace* feSpace = vec->getFeSpace();
+ int dim = feSpace->getMesh()->getDim();
+ int dow = Global::getGeo(WORLD);
+ WorldVector<double> newCoords;
+
+ DegreeOfFreedom dof;
+ WorldVector<double> x;
+
+ const BasisFunction *basFcts = feSpace->getBasisFcts();
+ int numBasFcts = basFcts->getNumber();
+ std::vector<DegreeOfFreedom> localIndices(numBasFcts);
+ DOFAdmin *admin = feSpace->getAdmin();
+
+ // ===== disable parametric traverse =====
+ feSpace->getMesh()->setParametric(NULL);
+
+ std::map<DegreeOfFreedom, bool> visited;
+
+ TraverseStack stack;
+ ElInfo *elInfo = stack.traverseFirst(feSpace->getMesh(), -1,
+ Mesh::CALL_LEAF_EL | Mesh::FILL_COORDS);
+ while (elInfo) {
+ basFcts->getLocalIndices(elInfo->getElement(), admin, localIndices);
+ for (int i = 0; i < dim + 1; i++) {
+ dof = localIndices[i];
+ newCoords = (*vec)[dof];
+ if (!visited[dof]) {
+ for (int j = 0; j < dow; j++)
+ (*(parametricCoords[j]))[dof] += newCoords[j];
+
+ visited[dof] = true;
+ }
+ }
+ elInfo = stack.traverseNext(elInfo);
+ }
+
+ // ===== enable parametric traverse =====
+ feSpace->getMesh()->setParametric(parametric);
+ }
+
+protected:
+
+ Elasticity_Type1 *elastProb; // LinearElasticity baseProblem
+ Elasticity_Type2 *elastProb2; // LinearElasticity baseProblem
+ NS_Type *nsProb; // Navier-Stokes baseProblem
+
+ /// DOFVector storing parametric coordinates.
+ WorldVector<DOFVector<double>*> parametricCoords1;
+ WorldVector<DOFVector<double>*> parametricCoords2;
+
+ /// Parametrizes vertex coordinates while mesh traversal.
+ ParametricFirstOrder *parametric1;
+ ParametricFirstOrder *parametric2;
+
+ Polygon* flag;
+ Polygon* obstacle;
+ AbstractFunction<double, WorldVector<double> >* signedDistFct;
+
+ SignedDistRefinement* refFunction1;
+ SignedDistRefinement* refFunction2;
+ RefinementLevelCoords2* refinement1;
+ RefinementLevelCoords2* refinement2;
+
+ unsigned dim; // dimension of the mesh
+ unsigned dow; // dimension of the world
+};
+
+
+#endif // CAHN_HILLIARD_NAVIER_STOKES_H
diff --git a/extensions/demo/src/fsi_explicit/fluidStructureInteraction.cc b/extensions/demo/src/fsi_explicit/fluidStructureInteraction.cc
new file mode 100644
index 0000000000000000000000000000000000000000..e8fba211a89baef3e742e1413d208ceb6803a7ef
--- /dev/null
+++ b/extensions/demo/src/fsi_explicit/fluidStructureInteraction.cc
@@ -0,0 +1,465 @@
+#include "AMDiS.h"
+#include "NavierStokesPhase_TaylorHood.h"
+#include "LinearElasticity.h"
+
+#include "ElasticityNavierStokes.h"
+#include "navierStokes.h"
+// #include "time/ExtendedRosenbrockAdaptInstationary.h"
+#include "Refinement.h"
+#include "MeshFunction_Level.h"
+#include "PhaseFieldConvert.h"
+#include "kdtree_nanoflann_dof.h"
+#include "Views.h"
+
+#include "boost/date_time/posix_time/posix_time.hpp"
+
+using namespace AMDiS;
+using namespace boost::posix_time;
+
+struct NormalStress : TertiaryAbstractFunction<double, WorldVector<double>, WorldVector<double>, WorldVector<double> >
+{
+ NormalStress(int comp_, double viscosity_) : comp(comp_), viscosity(viscosity_) {}
+
+ double operator()(const WorldVector<double>& normal, const WorldVector<double>& grdU0, const WorldVector<double>& grdU1) const
+ {
+ if (comp == 0)
+ return viscosity * (2.0*grdU0[0]*normal[0] + (grdU1[0] + grdU0[1])*normal[1]);
+ else
+ return viscosity * (2.0*grdU1[1]*normal[1] + (grdU1[0] + grdU0[1])*normal[0]);
+ }
+private:
+ int comp;
+ double viscosity;
+};
+
+struct NormalStressP : TertiaryAbstractFunction<double, WorldVector<double>, double, double>
+{
+ NormalStressP(int comp_) : comp(comp_) {}
+
+ double operator()(const WorldVector<double>& normal, const double& stress, const double& p) const
+ {
+ return stress-p*normal[comp];
+ }
+private:
+ int comp;
+};
+
+
+struct VectorBC : AbstractFunction<double, WorldVector<double> >
+{
+ VectorBC(int comp_, DOFVector<WorldVector<double> >* velocity_)
+ : AbstractFunction<double, WorldVector<double> >(4),
+ comp(comp_),
+ velocity(velocity_) {
+ TEST_EXIT(velocity != NULL)("pointer auf DOFVector<WorldVector> ist NULL\n");
+ }
+
+ double operator()(const WorldVector<double>& x) const
+ {
+ WorldVector<double> p = x;
+ WorldVector<double> localVel = evalAtPoint<WorldVector<double> >(*velocity, p);
+ return localVel[comp];
+ }
+private:
+ int comp;
+ DOFVector<WorldVector<double> >* velocity;
+};
+
+///_______________________________________________________________________________________________________________________
+
+class Elasticity_Obstacle : public LinearElasticity
+{
+public:
+ typedef LinearElasticity super;
+
+public:
+ Elasticity_Obstacle(std::string name_) : super(name_), stress(NULL) {}
+
+ ~Elasticity_Obstacle()
+ {
+ delete deformation;
+ delete deformationVelocity;
+ }
+
+ void initData()
+ {
+ super::initData();
+ dim = getMesh()->getDim();
+
+ stress = new DOFVector<WorldVector<double> >(getFeSpace(0), "stress");
+ deformation = new DOFVector<WorldVector<double> >(getFeSpace(0), "deformation");
+ deformationVelocity = new DOFVector<WorldVector<double> >(getFeSpace(dow), "deformation_velocity");
+ }
+
+ DOFVector<WorldVector<double> >* getDeformation()
+ {
+ return deformation;
+ }
+
+ DOFVector<WorldVector<double> >* getDeformationVelocity()
+ {
+ return deformationVelocity;
+ }
+
+ void setNormalStress(DOFVector<WorldVector<double> >* stress_)
+ {
+ boundaryStress = stress_;
+ }
+
+ void transferInitialSolution(AdaptInfo* adaptInfo)
+ {
+ super::transferInitialSolution(adaptInfo);
+ calcDeformation();
+ calcDeformationVelocity();
+ }
+
+ void initTimestep(AdaptInfo* adaptInfo)
+ {
+ super::initTimestep(adaptInfo);
+ TEST_EXIT(boundaryStress != NULL)("NULL-Pointer problem!\n");
+ interpol_coords(*boundaryStress, *stress);
+ }
+
+ void closeTimestep(AdaptInfo* adaptInfo)
+ {
+ super::closeTimestep(adaptInfo);
+ calcDeformation();
+ calcDeformationVelocity();
+ }
+
+ void fillBoundaryConditions()
+ {
+// super::fillBoundaryConditions();
+
+ AbstractFunction<double, WorldVector<double> > *zero = new AMDiS::Const<double, WorldVector<double> >(0.0);
+ double zeroValue = 0.0;
+
+ // +--+
+ // | | 10
+ // 1| +==========
+ // | |
+ // +--+
+
+ for (int i = 0; i < dow; i++) {
+ prob->addDirichletBC(1, i, i, zero);
+ prob->addNeumannBC(10, i, i, new VectorBC(i, stress));
+ }
+ }
+
+private:
+ DOFVector<WorldVector<double> >* deformation;
+ DOFVector<WorldVector<double> >* deformationVelocity;
+ DOFVector<WorldVector<double> >* stress;
+ DOFVector<WorldVector<double> >* boundaryStress;
+
+ void calcDeformation()
+ {
+ if (dow == 1)
+ transformDOF(prob->getSolution()->getDOFVector(0), deformation, new AMDiS::Vec1WorldVec<double>);
+ else if (dow == 2)
+ transformDOF(prob->getSolution()->getDOFVector(0), prob->getSolution()->getDOFVector(1), deformation, new AMDiS::Vec2WorldVec<double>);
+ else if (dow == 3)
+ transformDOF(prob->getSolution()->getDOFVector(0), prob->getSolution()->getDOFVector(1), prob->getSolution()->getDOFVector(2), deformation, new AMDiS::Vec3WorldVec<double>);
+ }
+
+ void calcDeformationVelocity()
+ {
+ if (dow == 1)
+ transformDOF(prob->getSolution()->getDOFVector(dow), deformationVelocity, new AMDiS::Vec1WorldVec<double>);
+ else if (dow == 2)
+ transformDOF(prob->getSolution()->getDOFVector(dow), prob->getSolution()->getDOFVector(dow+1), deformationVelocity, new AMDiS::Vec2WorldVec<double>);
+ else if (dow == 3)
+ transformDOF(prob->getSolution()->getDOFVector(dow), prob->getSolution()->getDOFVector(dow+1), prob->getSolution()->getDOFVector(dow+2), deformationVelocity, new AMDiS::Vec3WorldVec<double>);
+ }
+};
+
+///_______________________________________________________________________________________________________________________
+
+class Elasticity_Fluid : public StandardBaseProblem
+{
+public:
+ typedef StandardBaseProblem super;
+
+public:
+ Elasticity_Fluid(std::string name_) : super(name_), boundaryDeformation(NULL) {}
+
+ ~Elasticity_Fluid()
+ {
+ delete deformation;
+ }
+
+ void initData()
+ {
+ super::initData();
+ dim = getMesh()->getDim();
+
+ deformation = new DOFVector<WorldVector<double> >(getFeSpace(0), "deformation");
+ }
+
+ DOFVector<WorldVector<double> >* getDeformation()
+ {
+ return deformation;
+ }
+
+ void setDeformation(DOFVector<WorldVector<double> >* deformation_)
+ {
+ boundaryDeformation = deformation_;
+ }
+
+ void transferInitialSolution(AdaptInfo* adaptInfo)
+ {
+ super::transferInitialSolution(adaptInfo);
+ calcDeformation();
+ }
+
+ void initTimestep(AdaptInfo* adaptInfo)
+ {
+ super::initTimestep(adaptInfo);
+ TEST_EXIT(boundaryDeformation != NULL)("NULL-Pointer problem!\n");
+ interpol_coords(*boundaryDeformation, *deformation);
+ }
+
+ void closeTimestep(AdaptInfo* adaptInfo)
+ {
+ super::closeTimestep(adaptInfo);
+ calcDeformation();
+ }
+
+ void fillOperators()
+ {
+ // ===== create matrix operator =====
+ for (size_t i = 0; i < dow; i++) {
+ Operator *matrixOperator = new Operator(getFeSpace());
+ matrixOperator->addTerm(new Simple_SOT);
+ prob->addMatrixOperator(matrixOperator, i, i);
+ }
+ }
+
+ void fillBoundaryConditions()
+ {
+ super::fillBoundaryConditions();
+
+ AbstractFunction<double, WorldVector<double> > *zero = new AMDiS::Const<double, WorldVector<double> >(0.0);
+ double zeroValue = 0.0;
+
+ // +--+
+ // | | 10
+ // 1| +==========
+ // | |
+ // +--+
+
+ for (int i = 0; i < dow; i++) {
+ prob->addDirichletBC(1, i, i, zero);
+ prob->addDirichletBC(2, i, i, zero);
+ prob->addDirichletBC(3, i, i, zero);
+ prob->addDirichletBC(4, i, i, zero);
+ prob->addDirichletBC(5, i, i, zero);
+ prob->addDirichletBC(10, i, i, new VectorBC(i, deformation));
+ }
+ }
+
+private:
+ DOFVector<WorldVector<double> >* deformation;
+ DOFVector<WorldVector<double> >* boundaryDeformation;
+
+ void calcDeformation()
+ {
+ if (dow == 1)
+ transformDOF(prob->getSolution()->getDOFVector(0), deformation, new AMDiS::Vec1WorldVec<double>);
+ else if (dow == 2)
+ transformDOF(prob->getSolution()->getDOFVector(0), prob->getSolution()->getDOFVector(1), deformation, new AMDiS::Vec2WorldVec<double>);
+ else if (dow == 3)
+ transformDOF(prob->getSolution()->getDOFVector(0), prob->getSolution()->getDOFVector(1), prob->getSolution()->getDOFVector(2), deformation, new AMDiS::Vec3WorldVec<double>);
+ }
+};
+
+///_______________________________________________________________________________________________________________________
+
+class NS_Channel : public NavierStokes_TaylorHood
+{
+public:
+ typedef NavierStokes_TaylorHood super;
+
+public:
+ NS_Channel(std::string name_) : super(name_), boundaryVelocity(NULL) {}
+
+ ~NS_Channel()
+ {
+ delete inflowBC;
+ }
+
+ void initData()
+ {
+ super::initData();
+ stress = new DOFVector<WorldVector<double> >(getFeSpace(0), "stress");
+ dim = getMesh()->getDim();
+ }
+
+ void solveInitialProblem(AdaptInfo* adaptInfo)
+ {
+ super::solveInitialProblem(adaptInfo);
+
+ inflowBC->setTimePtr(adaptInfo->getTimePtr());
+ }
+
+ DOFVector<WorldVector<double> >* getNormalStress()
+ {
+ return stress;
+ }
+
+ void setDeformationVelocity(DOFVector<WorldVector<double> >* deformationVel_)
+ {
+ boundaryVelocity = deformationVel_;
+ }
+
+ void initTimestep(AdaptInfo* adaptInfo)
+ {
+ super::initTimestep(adaptInfo);
+ TEST_EXIT(boundaryVelocity != NULL)("NULL-Pointer problem!\n");
+ interpol_coords(*boundaryVelocity, *velocity);
+ }
+
+ void closeTimestep(AdaptInfo* adaptInfo)
+ {
+ super::closeTimestep(adaptInfo);
+ calcNormalStress();
+ }
+
+ void fillBoundaryConditions()
+ {
+
+ // +------ 5 ------+
+ // | |
+ // 2 # <--1 3
+ // | |
+ // +------ 4 ------+
+
+ AbstractFunction<double, WorldVector<double> > *zero = new AMDiS::Const<double, WorldVector<double> >(0.0);
+
+
+ /// at rigid wall: no-slip boundary condition
+ for (size_t i = 0; i < dow; i++) {
+ getProblem(0)->addDirichletBC(1, i, i, zero);
+ getProblem(0)->addDirichletBC(10, i, i, new VectorBC(i, velocity));
+ getProblem(0)->addDirichletBC(4, i, i, zero);
+ getProblem(0)->addDirichletBC(5, i, i, zero);
+ }
+
+ double H = 4.1;
+ double Um = 1.5;
+ Parameters::get("mesh->H",H);
+ Parameters::get("ns->Um",Um);
+ inflowBC = new InflowBC(H,Um);
+
+ /// at left wall: prescribed velocity
+ getProblem(0)->addDirichletBC(2, 0, 0, inflowBC);
+ getProblem(0)->addDirichletBC(2, 1, 1, zero);
+ getProblem(0)->addDirichletBC(3, 1, 1, zero);
+ }
+
+private:
+ DOFVector<WorldVector<double> >* stress;
+ DOFVector<WorldVector<double> >* boundaryVelocity;
+
+ void calcNormalStress(BoundaryType boundaryType = 1)
+ {
+ const FiniteElemSpace* feSpace = getFeSpace(0);
+ Mesh* mesh = feSpace->getMesh();
+
+ WorldVector<DOFVector<WorldVector<double> >*> grdU;
+ for (size_t i = 0; i < dow; i++) {
+ grdU[i] = new DOFVector<WorldVector<double> >(getFeSpace(i), "grdU_i");
+ getSolution()->getDOFVector(i)->getRecoveryGradient(grdU[i]);
+ }
+
+ WorldVector<double> normal;
+
+ std::map<DegreeOfFreedom, double> volume;
+
+ const BasisFunction *basFcts = feSpace->getBasisFcts();
+ int nBasisFcts = basFcts->getNumber();
+ DimVec<double> bary(dim, DEFAULT_VALUE, (1.0 / (dim + 1.0)));
+
+ TraverseStack stack;
+ ElInfo *elInfo = stack.traverseFirst(mesh, -1,
+ Mesh::CALL_LEAF_EL | Mesh::FILL_BOUND | Mesh::FILL_DET | Mesh::FILL_COORDS);
+
+ mtl::dense_vector<double> localUh(nBasisFcts);
+ std::vector<DegreeOfFreedom> localIndices(nBasisFcts);
+
+ while (elInfo) {
+ for (int face = 0; face < dim + 1; face++) {
+ if (elInfo->getBoundary(face) == boundaryType) {
+ elInfo->getNormal(face, normal);
+ double det = elInfo->getDet();
+ basFcts->getLocalIndices(elInfo->getElement(), feSpace->getAdmin(), localIndices);
+
+ for (int i = 0; i < nBasisFcts; i++) {
+ double p = (*getSolution()->getDOFVector(dow))[localIndices[i]];
+
+ for (int j = 0; j < Global::getGeo(WORLD); j++) {
+ double tmp = NormalStress(j, viscosity)(normal, (*grdU[0])[localIndices[i]], (*grdU[1])[localIndices[i]]);
+ double result = NormalStressP(j)(normal, tmp, p);
+ (*stress)[localIndices[i]][j] += result * det;
+ }
+ volume[localIndices[i]] += det;
+ }
+ }
+ }
+
+ elInfo = stack.traverseNext(elInfo);
+ }
+
+ std::map<DegreeOfFreedom, double>::iterator volIt;
+
+ for (volIt = volume.begin(); volIt != volume.end(); ++volIt) {
+ for (int j = 0; j < Global::getGeo(WORLD); j++) {
+ (*stress)[volIt->first][j] *= 1.0 / volIt->second;
+ }
+ }
+
+ for (size_t i = 0; i < dow; i++)
+ delete grdU[i];
+ }
+
+// Polygon* obstacle;
+ InflowBC* inflowBC;
+
+};
+
+
+int main(int argc, char** argv)
+{ FUNCNAME("main");
+
+ AMDiS::init(argc, argv);
+
+ NS_Channel nsProb("ns");
+ Elasticity_Obstacle elastProb("elasticity->obstacle");
+ Elasticity_Fluid elastProb2("elasticity->fluid");
+
+ ElasticityNavierStokes<Elasticity_Obstacle, Elasticity_Fluid, NS_Channel> mainProb("main", &elastProb, &elastProb2, &nsProb);
+
+ // Adapt-Infos
+ AdaptInfo adaptInfo("adapt", 7);
+ mainProb.initialize(&adaptInfo);
+
+ // adaption loop - solve ch-prob and ns-prob
+ AdaptInstationary adaptInstat("adapt", mainProb, adaptInfo, mainProb, adaptInfo);
+
+ // scale Mesh
+ double H = 4.1, L = 25.0;
+ Parameters::get("mesh->H",H);
+ Parameters::get("mesh->L",L);
+// WorldVector<double> scale; scale[0] = L; scale[1] = H;
+// Helpers::scaleMesh(nsProb.getMesh(), scale);
+
+ ptime start_time = microsec_clock::local_time();
+ int error_code = adaptInstat.adapt();
+ time_duration td = microsec_clock::local_time()-start_time;
+
+ MSG("elapsed time= %d sec\n", td.total_seconds());
+
+ AMDiS::finalize();
+
+ return error_code;
+};
diff --git a/extensions/demo/src/fsi_explicit/navierStokes.h b/extensions/demo/src/fsi_explicit/navierStokes.h
new file mode 100644
index 0000000000000000000000000000000000000000..5e1750459d7c2a2822716e92290b10b77e3c3e40
--- /dev/null
+++ b/extensions/demo/src/fsi_explicit/navierStokes.h
@@ -0,0 +1,43 @@
+/** \file navierStokes.h */
+
+#ifndef NAVIER_STOKES_H
+#define NAVIER_STOKES_H
+
+#include "AMDiS.h"
+#include "GeometryTools.h"
+
+struct InflowBC : AbstractFunction<double, WorldVector<double> >
+{
+ InflowBC(double H_=4.1, double Um_=1.5) : H(H_), Um(Um_) {}
+ double operator()(const WorldVector<double> &x) const {
+ double vel = 4.0 * Um * x[1] * (H - x[1]) / sqr(H);
+ return (*time < 2.0 ? vel*(1.0 - cos(m_pi * (*time)/2.0))/2.0 : vel);
+ }
+
+ void setTimePtr(double* time_)
+ {
+ time = time_;
+ }
+
+protected:
+ double H;
+ double Um;
+ double* time;
+};
+
+
+struct MinWrapper : AbstractFunction<double, WorldVector<double> >
+{
+ MinWrapper(AbstractFunction<double, WorldVector<double> >* dist1_, AbstractFunction<double, WorldVector<double> >* dist2_)
+ : dist1(dist1_), dist2(dist2_) {}
+
+ double operator()(const WorldVector<double>& x) const
+ {
+ return std::min((*dist1)(x), (*dist2)(x));
+ }
+private:
+ AbstractFunction<double, WorldVector<double> >* dist1;
+ AbstractFunction<double, WorldVector<double> >* dist2;
+};
+
+#endif