demos for extensions added

extensions/base_problems/LinearElasticity.h

@@ -37,8 +37,6 @@ public: // methods
 
   // === getting/setting methods ===
 
-protected: // methods
-
   virtual void fillOperators();
   virtual void fillBoundaryConditions();
 

extensions/demo/CMakeLists.txt

+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)

extensions/demo/init/fsi.dat.2d

+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
+

extensions/demo/init/navierStokes_TaylorHood.inc.2d

+
+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

extensions/demo/init/reinit.inc.2d

+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

extensions/demo/macro/macro.square.2d

+DIM: 2
+DIM_OF_WORLD: 2
+
+number of elements: 8
+number of vertices: 9
+
+vertex coordinates:
+-1 -1 
+0 -1 
+1 -1 
+-1 0 
+0 0 
+1 0 
+-1 1 
+0 1 
+1 1 
+
+element vertices:
+0 4 3
+4 0 1
+1 5 4
+5 1 2
+3 7 6
+7 3 4
+4 8 7
+8 4 5
+
+element boundaries:
+0 1 0
+3 0 0
+0 0 0
+3 2 0
+4 1 0
+0 0 0
+4 0 0
+0 2 0
+
+element neighbours:
+5 -1 1
+-1 2 0
+7 1 3
+-1 -1 2
+-1 -1 5
+0 6 4
+-1 5 7
+2 -1 6
+

extensions/demo/macro/obstacle_in_channel.2d

+DIM: 2
+DIM_OF_WORLD: 2
+
+number of elements: 72
+number of vertices: 52
+
+vertex coordinates:
+0.16 0.12 
+0.2 0.12 
+0.24 0.12 
+0.28 0.12 
+0.16 0.16 
+0.2 0.16 
+0.24 0.16 
+0.28 0.16 
+0.32 0.16 
+0.36 0.16 
+0.4 0.16 
+0.44 0.16 
+0.48 0.16 
+0.52 0.16 
+0.56 0.16 
+0.6 0.16 
+0.64 0.16 
+0.16 0.2 
+0.2 0.2 
+0.24 0.2 
+0.28 0.2 
+0.32 0.2 
+0.36 0.2 
+0.4 0.2 
+0.44 0.2 
+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 
+0.18 0.18 
+0.22 0.18 
+0.26 0.18 
+0.3 0.18 
+0.34 0.18 
+0.38 0.18 
+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
+7 6 36
+6 2 36
+4 5 37
+5 18 37
+18 17 37
+17 4 37
+5 6 38
+6 19 38
+19 18 38
+18 5 38
+6 7 39
+7 20 39
+20 19 39
+19 6 39
+7 8 40
+8 21 40
+21 20 40
+20 7 40
+8 9 41
+9 22 41
+22 21 41
+21 8 41
+9 10 42
+10 23 42
+23 22 42
+22 9 42
+10 11 43
+11 24 43
+24 23 43
+23 10 43
+11 12 44
+12 25 44
+25 24 44
+24 11 44
+12 13 45
+13 26 45
+26 25 45
+25 12 45
+13 14 46
+14 27 46
+27 26 46
+26 13 46
+14 15 47
+15 28 47
+28 27 47
+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
+0 0 1
+0 0 0
+0 0 1
+0 0 0
+0 0 1
+0 0 0
+0 0 1
+0 0 0
+0 0 1
+0 0 0
+0 0 1
+0 0 0
+0 0 1
+0 0 0
+0 0 1
+0 0 0
+0 0 1
+0 0 0
+0 0 1
+0 0 0
+0 0 1
+0 0 0
+0 0 1
+0 0 0
+0 0 1
+0 0 0
+0 0 1
+0 0 0
+0 0 1
+0 0 0
+0 0 1
+0 0 1
+0 0 1
+0 0 0
+0 0 0
+0 0 0
+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
+11 9 20
+8 10 5
+13 15 2
+14 12 19
+15 13 60
+12 14 -1
+17 19 6
+18 16 23
+19 17 64
+16 18 13
+21 23 10
+22 20 27
+23 21 68
+20 22 17
+25 27 -1
+26 24 31
+27 25 -1
+24 26 21
+29 31 -1
+30 28 35
+31 29 -1
+28 30 25
+33 35 -1
+34 32 39
+35 33 -1
+32 34 29
+37 39 -1
+38 36 43
+39 37 -1
+36 38 33
+41 43 -1
+42 40 47
+43 41 -1
+40 42 37
+45 47 -1
+46 44 51
+47 45 -1
+44 46 41
+49 51 -1
+50 48 55
+51 49 -1
+48 50 45
+53 55 -1
+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
+65 67 18
+66 64 71
+67 65 -1
+64 66 61
+69 71 22
+70 68 -1
+71 69 -1
+68 70 65
+

extensions/demo/src/fsi_explicit/ElasticityNavierStokes.h

+/** \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"