Merge branch 'revisions'

CMakeLists.txt

@@ -33,7 +33,7 @@ if( CMAKE_BUILD_TYPE STREQUAL "Debug")
     set( LIBRARY_OUTPUT_PATH ${PROJECT_SOURCE_DIR}/Debug/lib )
     set( EXECUTABLE_OUTPUT_PATH ${PROJECT_SOURCE_DIR}/Debug/bin )
     set( debugExt -dbg )
-    set( CXX_FLAGS "${CXXFLAGS} -g ")
+    set( CMAKE_CXX_FLAGS "${CXXFLAGS} -g ")
     #AddCompilerFlag( "-g" )
 else()
     set( PROJECT_BUILD_PATH ${PROJECT_SOURCE_DIR}/Release/src )

ChangeLog

+
+        * tnlBoundaryConditionsSetter was implemented 
+           - it allows to set boundary conditions to given function
+           - in explicit solvers, it must be called explicitly now after calling tnlExplicitUpdater
+
 2015-12-25 Tomas Oberhuber  <tomas.oberhuber@fjfi.cvut.cz>
         * significant changes in grids
             - the central structure is now grid entity rather than grid itself

TODO

+TODO:
+ - implementovat tnlMixedGridBoundaryConditions, kde by se pro kazdou stranu gridu definoval jiny zvlastni typ
+   okrajovych podminek
+ - dalo by se tim resit i skladani zpetnych a doprednych diferenci u nelinearni difuze, kdy je potreba napr. dopredne diference
+   vycislit i na leve a dolni hranici 2D gridu
+
+TODO:
+ - implementovat tuple pro snazsi a snad efektoivnejsi prenos dat na GPU
+ - nebylo by nutne definovat pomocne datove structury pro traverser
+ - data by se na hostu preskupila do souvisleho bloku dat a ten se prenesl najednou
+
+
 TODO:
  - zavest namespaces
 
@@ -21,9 +33,6 @@ TODO: Mesh
  * prejmenovat Tagy v topologies na Topology zrejme
  * zrusit tnlStorageTraits
 
-TODO: v tnlMeshResolver se provadi preklad pro vsechny mozne sablonove parametry => prorezat
-
-TODO: napsat FunctionDiscretizer pro jednotne rozhrani RightHandSide
 
 TODO: implementace maticovych resicu
       * Gaussova eliminace

build

@@ -93,6 +93,11 @@ ${CMAKE} ${ROOT_DIR} \
          -DINSTANTIATE_INT=${INSTANTIATE_INT} \
          -DINSTANTIATE_LONG_INT=${INSTANTIATE_LONG_INT}
 
+if test $? != 0; then
+    echo "Error: cmake exited with error code."
+    exit 1
+fi
+
 if test ${CMAKE_ONLY} = "yes";
 then
     exit 1
@@ -101,10 +106,18 @@ fi
 echo "Building ${BUILD} $TARGET using $BUILD_JOBS processors ..."
 
 make -j${BUILD_JOBS} ${VERBOSE}
+if test $? != 0; then
+    echo "Error: Build process failed."
+    exit 1
+fi
+
 
 if test WITH_TESTS = "yes";
 then
     make -j${BUILD_JOBS} test
+    if test $? != 0; then
+        echo "Error: Some test did not pass successfuly."
+    fi
 fi
 
 exit 0

examples/CMakeLists.txt

 add_subdirectory( heat-equation )
 add_subdirectory( navier-stokes )
+#add_subdirectory( mean-curvature-flow )

examples/heat-equation/tnl-heat-equation-eoc.h

@@ -67,7 +67,7 @@ class heatEquationSetter
       typedef tnlTestFunction< MeshType::meshDimensions, Real, Device > TestFunction;
       typedef tnlHeatEquationEocRhs< ExactOperator, TestFunction > RightHandSide;
       typedef tnlStaticVector < MeshType::meshDimensions, Real > Vertex;
-      typedef tnlDirichletBoundaryConditions< MeshType, TestFunction, Real, Index > BoundaryConditions;
+      typedef tnlDirichletBoundaryConditions< MeshType, TestFunction, Dimensions, Real, Index > BoundaryConditions;
       typedef tnlHeatEquationEocProblem< MeshType, BoundaryConditions, RightHandSide, ApproximateOperator > Solver;
       SolverStarter solverStarter;
       return solverStarter.template run< Solver >( parameters );

examples/mean-curvature-flow/CMakeLists.txt

+set( tnl_mean_curvature_flow_SOURCES     
+     tnl-mean-curvature-flow.cpp
+     tnl-mean-curvature-flow-eoc.cpp
+     tnl-mean-curvature-flow.cu
+     tnl-mean-curvature-flow-eoc.cu )
+               
+IF( BUILD_CUDA )
+   CUDA_ADD_EXECUTABLE(tnl-mean-curvature-flow${debugExt} tnl-mean-curvature-flow.cu)
+   CUDA_ADD_EXECUTABLE(tnl-mean-curvature-flow-eoc-test${debugExt} tnl-mean-curvature-flow-eoc.cu)
+   target_link_libraries (tnl-mean-curvature-flow${debugExt} tnl${debugExt}-${tnlVersion}  ${CUSPARSE_LIBRARY} )
+   target_link_libraries (tnl-mean-curvature-flow-eoc-test${debugExt} tnl${debugExt}-${tnlVersion}  ${CUSPARSE_LIBRARY} )
+ELSE(  BUILD_CUDA )               
+   ADD_EXECUTABLE(tnl-mean-curvature-flow${debugExt} tnl-mean-curvature-flow.cpp)     
+   ADD_EXECUTABLE(tnl-mean-curvature-flow-eoc-test${debugExt} tnl-mean-curvature-flow-eoc.cpp)   
+   target_link_libraries (tnl-mean-curvature-flow${debugExt} tnl${debugExt}-${tnlVersion} )
+   target_link_libraries (tnl-mean-curvature-flow-eoc-test${debugExt} tnl${debugExt}-${tnlVersion} )
+ENDIF( BUILD_CUDA )
+
+INSTALL( TARGETS tnl-mean-curvature-flow${debugExt}
+                 tnl-mean-curvature-flow-eoc-test${debugExt}
+         RUNTIME DESTINATION bin
+         PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE )
+        
+INSTALL( FILES tnl-run-mean-curvature-flow-eoc-test
+               tnl-run-mean-curvature-flow
+               tnl-run-mean-curvature-flow-contour-video
+               tnl-run-mean-curvature-flow-videos
+               ${tnl_mean_curvature_flow_SOURCES}
+         DESTINATION share/tnl-${tnlVersion}/examples/mean-curvature-flow )
\ No newline at end of file

examples/mean-curvature-flow/Makefile

+TNL_VERSION=0.1
+TNL_INSTALL_DIR=${HOME}/local/lib
+TNL_INCLUDE_DIR=${HOME}/local/include/tnl-${TNL_VERSION}
+
+TARGET = mean-curvature-flow-eoc
+INSTALL_DIR = ${HOME}/local
+CXX = g++
+CUDA_CXX = nvcc
+CXX_FLAGS = -std=gnu++0x -I$(TNL_INCLUDE_DIR)   -O0 -g
+LD_FLAGS = -L$(TNL_INSTALL_DIR) -ltnl-dbg-0.1
+
+SOURCES = tnl-mean-curvature-flow-eoc.cpp
+HEADERS = 
+OBJECTS = tnl-mean-curvature-flow-eoc.o
+DIST = $(SOURCES) Makefile
+
+all: $(TARGET)
+clean: 
+	rm -f $(OBJECTS)	
+
+dist: $(DIST)
+	tar zcvf $(TARGET).tgz $(DIST) 
+
+install: $(TARGET)
+	cp $(TARGET) $(INSTALL_DIR)/bin
+	cp $(INSTALL_DIR)/share/tnl-0.1/examples/mean-curvature-flow
+
+uninstall: $(TARGET)
+	rm -f $(INSTALL_DIR)/bin/$(TARGET) 
+	rm -f $(INSTALL_DIR)/share/tnl-0.1/examples/mean-curvature-flow
+
+$(TARGET): $(OBJECTS)
+	$(CXX) -o $(TARGET) $(OBJECTS) $(LD_FLAGS)
+
+%.o: %.cpp $(HEADERS)
+	$(CXX) -c -o $@ $(CXX_FLAGS) $<

examples/mean-curvature-flow/tnl-mean-curvature-flow-eoc.cpp

+/***************************************************************************
+                          tnl-mean-curvature-flow-eoc.cpp  -  description
+                             -------------------
+    begin                : Dec 29, 2015
+    copyright            : (C) 2015 by oberhuber
+    email                : tomas.oberhuber@fjfi.cvut.cz
+ ***************************************************************************/
+
+/***************************************************************************
+ *                                                                         *
+ *   This program is free software; you can redistribute it and/or modify  *
+ *   it under the terms of the GNU General Public License as published by  *
+ *   the Free Software Foundation; either version 2 of the License, or     *
+ *   (at your option) any later version.                                   *
+ *                                                                         *
+ ***************************************************************************/
+
+#include "tnl-mean-curvature-flow-eoc.h"
+
+

examples/mean-curvature-flow/tnl-mean-curvature-flow-eoc.cu

+/***************************************************************************
+                          tnl-mean-curvature-flow-eoc.cu  -  description
+                             -------------------
+    begin                : Dec 29, 2015
+    copyright            : (C) 2015 by oberhuber
+    email                : tomas.oberhuber@fjfi.cvut.cz
+ ***************************************************************************/
+
+/***************************************************************************
+ *                                                                         *
+ *   This program is free software; you can redistribute it and/or modify  *
+ *   it under the terms of the GNU General Public License as published by  *
+ *   the Free Software Foundation; either version 2 of the License, or     *
+ *   (at your option) any later version.                                   *
+ *                                                                         *
+ ***************************************************************************/
+
+#include "tnl-mean-curvature-flow-eoc.h"
+
+

examples/mean-curvature-flow/tnl-mean-curvature-flow-eoc.h

+/***************************************************************************
+                          tnl-heat-equation-eoc.h  -  description
+                             -------------------
+    begin                : Nov 29, 2014
+    copyright            : (C) 2014 by oberhuber
+    email                : tomas.oberhuber@fjfi.cvut.cz
+ ***************************************************************************/
+
+/***************************************************************************
+ *                                                                         *
+ *   This program is free software; you can redistribute it and/or modify  *
+ *   it under the terms of the GNU General Public License as published by  *
+ *   the Free Software Foundation; either version 2 of the License, or     *
+ *   (at your option) any later version.                                   *
+ *                                                                         *
+ ***************************************************************************/
+
+#ifndef TNL_MEAN_CURVATURE_FLOW_EOC_H_
+#define TNL_MEAN_CURVATURE_FLOW_EOC_H_
+
+#include <solvers/tnlSolver.h>
+#include <solvers/tnlFastBuildConfigTag.h>
+#include <solvers/tnlBuildConfigTags.h>
+#include <functions/tnlTestFunction.h>
+#include <operators/tnlDirichletBoundaryConditions.h>
+#include <operators/tnlNeumannBoundaryConditions.h>
+#include <problems/tnlMeanCurvatureFlowEocRhs.h>
+#include <problems/tnlMeanCurvatureFlowEocProblem.h>
+#include <operators/diffusion/tnlExactNonlinearDiffusion.h>
+#include <operators/diffusion/tnlNonlinearDiffusion.h>
+#include <operators/operator-Q/tnlOneSideDiffOperatorQ.h>
+#include <operators/operator-Q/tnlFiniteVolumeOperatorQ.h>
+#include <operators/diffusion/tnlExactNonlinearDiffusion.h>
+#include <operators/diffusion/nonlinear-diffusion-operators/tnlOneSideDiffNonlinearOperator.h>
+#include <operators/diffusion/nonlinear-diffusion-operators/tnlFiniteVolumeNonlinearOperator.h>
+#include <operators/geometric/tnlExactGradientNorm.h>
+
+//typedef tnlDefaultConfigTag BuildConfig;
+typedef tnlFastBuildConfig BuildConfig;
+
+template< typename ConfigTag >
+class meanCurvatureFlowEocConfig
+{
+   public:
+      static void configSetup( tnlConfigDescription& config )
+      {
+         config.addDelimiter( "Mean Curvature Flow EOC settings:" );         
+         config.addEntry< tnlString >( "numerical-scheme", "Numerical scheme for the solution approximation.", "fvm" );
+            config.addEntryEnum< tnlString >( "fdm" );
+            config.addEntryEnum< tnlString >( "fvm" );
+
+         config.addEntry< double >( "eps", "This sets a eps in operator Q.", 1.0 );
+         config.addDelimiter( "Tests setting::" );         
+         tnlTestFunction< 3, double >::configSetup( config );
+      }
+};
+
+template< typename Real,
+          typename Device,
+          typename Index,
+          typename MeshType,
+          typename ConfigTag,
+          typename SolverStarter >
+class meanCurvatureFlowEocSetter
+{
+   public:
+
+   typedef Real RealType;
+   typedef Device DeviceType;
+   typedef Index IndexType;
+
+   typedef typename MeshType::VertexType Vertex;
+   enum { Dimensions = MeshType::meshDimensions };
+
+   static bool run( const tnlParameterContainer& parameters )
+   {
+
+      typedef tnlFiniteVolumeOperatorQ<MeshType, Real, Index, 0> OperatorQ;
+      typedef tnlFiniteVolumeNonlinearOperator<MeshType, OperatorQ, Real, Index > NonlinearOperator;
+      typedef tnlNonlinearDiffusion< MeshType, NonlinearOperator, Real, Index > ApproximateOperator;
+      typedef tnlExactNonlinearDiffusion< tnlExactGradientNorm< Dimensions >, Dimensions > ExactOperator;
+      typedef tnlTestFunction< MeshType::meshDimensions, Real, Device > TestFunction;
+      typedef tnlMeanCurvatureFlowEocRhs< ExactOperator, TestFunction, Dimensions > RightHandSide;
+      typedef tnlStaticVector < MeshType::meshDimensions, Real > Vertex;
+      typedef tnlDirichletBoundaryConditions< MeshType, TestFunction, Dimensions, Real, Index > BoundaryConditions;
+      typedef tnlMeanCurvatureFlowEocProblem< MeshType, BoundaryConditions, RightHandSide, ApproximateOperator > Solver;
+      SolverStarter solverStarter;
+      return solverStarter.template run< Solver >( parameters );
+   };
+};
+
+int main( int argc, char* argv[] )
+{
+   tnlSolver< meanCurvatureFlowEocSetter, meanCurvatureFlowEocConfig, BuildConfig > solver;
+   if( ! solver. run( argc, argv ) )
+      return EXIT_FAILURE;
+   return EXIT_SUCCESS;
+}
+
+#endif /* TNL_MEAN_CURVATURE_FLOW_EOC_H_ */

examples/mean-curvature-flow/tnl-mean-curvature-flow.cpp

+/***************************************************************************
+                          tnl-mean-cudvature-flow.cpp  -  description
+                             -------------------
+    begin                : Dec 29, 2015
+    copyright            : (C) 2015 by Tomas Oberhuber
+    email                : tomas.oberhuber@fjfi.cvut.cz
+ ***************************************************************************/
+
+/***************************************************************************
+ *                                                                         *
+ *   This program is free software; you can redistribute it and/or modify  *
+ *   it under the terms of the GNU General Public License as published by  *
+ *   the Free Software Foundation; either version 2 of the License, or     *
+ *   (at your option) any later version.                                   *
+ *                                                                         *
+ ***************************************************************************/
+
+#include "tnl-mean-curvature-flow.h"

examples/mean-curvature-flow/tnl-mean-curvature-flow.cu

+/***************************************************************************
+                          tnl-mean-curvature-flow.cu  -  description
+                             -------------------
+    begin                : Dec 29, 2015
+    copyright            : (C) 2015 by Tomas Oberhuber
+    email                : tomas.oberhuber@fjfi.cvut.cz
+ ***************************************************************************/
+
+/***************************************************************************
+ *                                                                         *
+ *   This program is free software; you can redistribute it and/or modify  *
+ *   it under the terms of the GNU General Public License as published by  *
+ *   the Free Software Foundation; either version 2 of the License, or     *
+ *   (at your option) any later version.                                   *
+ *                                                                         *
+ ***************************************************************************/
+
+#include "tnl-mean-curvature-flow.h"

examples/mean-curvature-flow/tnl-mean-curvature-flow.h

+/***************************************************************************
+                          tnl-heat-equation.h  -  description
+                             -------------------
+    begin                : Nov 29, 2014
+    copyright            : (C) 2014 by oberhuber
+    email                : tomas.oberhuber@fjfi.cvut.cz
+ ***************************************************************************/
+
+/***************************************************************************
+ *                                                                         *
+ *   This program is free software; you can redistribute it and/or modify  *
+ *   it under the terms of the GNU General Public License as published by  *
+ *   the Free Software Foundation; either version 2 of the License, or     *
+ *   (at your option) any later version.                                   *
+ *                                                                         *
+ ***************************************************************************/
+
+#ifndef TNL_MEAN_CURVATIVE_FLOW_H_
+#define TNL_MEAN_CURVATIVE_FLOW_H_
+
+#include <solvers/tnlSolver.h>
+#include <solvers/tnlFastBuildConfigTag.h>
+#include <operators/diffusion/tnlLinearDiffusion.h>
+#include <operators/tnlDirichletBoundaryConditions.h>
+#include <operators/tnlNeumannBoundaryConditions.h>
+#include <functions/tnlConstantFunction.h>
+#include <problems/tnlMeanCurvatureFlowProblem.h>
+#include <operators/diffusion/tnlOneSidedNonlinearDiffusion.h>
+#include <operators/operator-Q/tnlOneSideDiffOperatorQ.h>
+#include <operators/operator-Q/tnlFiniteVolumeOperatorQ.h>
+#include <operators/diffusion/nonlinear-diffusion-operators/tnlFiniteVolumeNonlinearOperator.h>
+#include <functions/tnlMeshFunction.h>
+
+//typedef tnlDefaultConfigTag BuildConfig;
+typedef tnlFastBuildConfig BuildConfig;
+
+template< typename ConfigTag >
+class meanCurvatureFlowConfig
+{
+   public:
+      static void configSetup( tnlConfigDescription& config )
+      {
+         config.addDelimiter( "Mean Curvature Flow settings:" );
+         config.addEntry< tnlString >( "numerical-scheme", "Numerical scheme for the solution approximation.", "fvm" );
+            config.addEntryEnum< tnlString >( "fdm" );
+            config.addEntryEnum< tnlString >( "fvm" );
+         config.addEntry< tnlString >( "boundary-conditions-type", "Choose the boundary conditions type.", "dirichlet");
+            config.addEntryEnum< tnlString >( "dirichlet" );
+            config.addEntryEnum< tnlString >( "neumann" );
+
+         config.addEntry< tnlString >( "boundary-conditions-file", "File with the values of the boundary conditions.", "boundary.tnl" );
+         config.addEntry< double >( "boundary-conditions-constant", "This sets a value in case of the constant boundary conditions." );
+         config.addEntry< tnlString >( "initial-condition", "File with the initial condition.", "initial.tnl");
+	      config.addEntry< double >( "right-hand-side-constant", "This sets a value in case of the constant right hand side.", 0.0 );
+	      config.addEntry< double >( "eps", "This sets a eps in operator Q.", 1.0 );
+      };
+};
+
+template< typename Real,
+          typename Device,
+          typename Index,
+          typename MeshType,
+          typename ConfigTag,
+          typename SolverStarter >
+class meanCurvatureFlowSetter
+{
+   public:
+
+   typedef Real RealType;
+   typedef Device DeviceType;
+   typedef Index IndexType;
+
+   typedef typename MeshType::VertexType Vertex;
+   enum { Dimensions = MeshType::meshDimensions };
+
+   static bool run( const tnlParameterContainer& parameters )
+   {
+      return setNumericalScheme( parameters );
+   }
+   
+   static bool setNumericalScheme( const tnlParameterContainer& parameters )
+   {
+      const tnlString& numericalScheme = parameters.getParameter< tnlString >( "numerical-scheme" );
+      if( numericalScheme == "fdm" )
+      {
+         typedef tnlOneSideDiffOperatorQ<MeshType, Real, Index > QOperator;
+         typedef tnlOneSideNonlinearDiffusion<MeshType, QOperator, Real, Index > NonlinearOperator;         
+         return setBoundaryConditions< NonlinearOperator, QOperator >( parameters );
+      }
+      if( numericalScheme == "fvm" )
+      {
+         typedef tnlFiniteVolumeOperatorQ<MeshType, Real, Index, 0> QOperator;
+         typedef tnlFiniteVolumeNonlinearOperator<MeshType, QOperator, Real, Index > NonlinearOperator;         
+         return setBoundaryConditions< NonlinearOperator, QOperator >( parameters );
+      }
+      return false;
+   }
+   
+   template< typename NonlinearOperator,
+             typename QOperator >
+   static bool setBoundaryConditions( const tnlParameterContainer& parameters )
+   {
+      typedef tnlOneSidedNonlinearDiffusion< MeshType, NonlinearOperator, Real, Index > ApproximateOperator;
+      typedef tnlConstantFunction< Dimensions, Real > RightHandSide;
+      typedef tnlStaticVector< MeshType::meshDimensions, Real > Vertex;
+
+      tnlString boundaryConditionsType = parameters.getParameter< tnlString >( "boundary-conditions-type" );
+      if( parameters.checkParameter( "boundary-conditions-constant" ) )
+      {
+         typedef tnlConstantFunction< Dimensions, Real > ConstantFunction;
+         if( boundaryConditionsType == "dirichlet" )
+         {
+            typedef tnlDirichletBoundaryConditions< MeshType, ConstantFunction, Dimensions, Real, Index > BoundaryConditions;
+            typedef tnlMeanCurvatureFlowProblem< MeshType, BoundaryConditions, RightHandSide, ApproximateOperator > Solver;
+            SolverStarter solverStarter;
+            return solverStarter.template run< Solver >( parameters );
+         }
+         typedef tnlNeumannBoundaryConditions< MeshType, ConstantFunction, Real, Index > BoundaryConditions;
+         typedef tnlMeanCurvatureFlowProblem< MeshType, BoundaryConditions, RightHandSide, ApproximateOperator > Solver;
+         SolverStarter solverStarter;
+         return solverStarter.template run< Solver >( parameters );
+      }
+      //typedef tnlVector< Real, Device, Index > VectorType;
+      typedef tnlMeshFunction< MeshType > MeshFunction;
+      if( boundaryConditionsType == "dirichlet" )
+      {
+         typedef tnlDirichletBoundaryConditions< MeshType, MeshFunction, Dimensions, Real, Index > BoundaryConditions;
+         typedef tnlMeanCurvatureFlowProblem< MeshType, BoundaryConditions, RightHandSide, ApproximateOperator > Solver;
+         SolverStarter solverStarter;
+         return solverStarter.template run< Solver >( parameters );
+      }
+      typedef tnlNeumannBoundaryConditions< MeshType, MeshFunction, Real, Index > BoundaryConditions;
+      typedef tnlMeanCurvatureFlowProblem< MeshType, BoundaryConditions, RightHandSide, ApproximateOperator > Solver;
+      SolverStarter solverStarter;
+      return solverStarter.template run< Solver >( parameters );
+   };
+};
+
+int main( int argc, char* argv[] )
+{
+   tnlSolver< meanCurvatureFlowSetter, meanCurvatureFlowConfig, BuildConfig > solver;
+   if( ! solver. run( argc, argv ) )
+      return EXIT_FAILURE;
+   return EXIT_SUCCESS;
+}
+
+#endif /* TNL_MEAN_CURVATIVE_FLOW_H_ */

examples/mean-curvature-flow/tnl-run-mean-curvature-flow

+#!/bin/bash
+
+dofSize=64
+dimension=2;
+proportions=1
+
+analyticFunction="exp-bump"
+timeFunction="cosinus"
+
+amplitude=1.0
+waveLength=1.0
+waveLengthX=1.0
+waveLengthY=1.0
+waveLengthZ=1.0
+wavesNumber=0.0
+wavesNumberX=0.0
+wavesNumberY=0.0
+wavesNumberZ=0.0
+phase=0.0
+phaseX=0.0
+phaseY=0.0
+phaseZ=0.0
+sigma=1.0
+
+tnl-grid-setup --dimensions ${dimension} \
+               --proportions-x ${proportions} \
+               --proportions-y ${proportions} \
+               --proportions-z ${proportions} \
+               --origin-x 0 \
+               --origin-y 0 \
+               --origin-z 0 \
+               --size-x ${dofSize} \
+               --size-y ${dofSize} \
+               --size-z ${dofSize} \
+               
+tnl-init --mesh mesh.tnl \
+         --test-function ${analyticFunction} \
+         --output-file initial.tnl \
+         --amplitude ${amplitude} \
+         --wave-length ${waveLength} \
+         --wave-length-x ${waveLengthX} \
+         --wave-length-y ${waveLengthY} \
+         --wave-length-z ${waveLengthZ} \
+             --waves-number ${wavesNumber} \
+             --waves-number-x ${wavesNumberX} \
+             --waves-number-y ${wavesNumberY} \
+             --waves-number-z ${wavesNumberZ} \
+             --phase ${phase} \
+             --phase-x ${phaseX} \
+             --phase-y ${phaseY} \
+             --phase-z ${phaseZ} \
+             --sigma ${sigma} \
+
+tnl-mean-curvature-flow --time-discretisation explicit \
+                  --boundary-conditions-type dirichlet \
+                  --boundary-conditions-constant 0.5 \
+                  --discrete-solver merson \
+                  --snapshot-period 0.0005 \
+                  --final-time 0.1 \
+              
+tnl-view --mesh mesh.tnl \
+         --input-files *.tnl \ 
+
+seznam=`ls u-*.gplt`
+
+for fname in $seznam ; do
+   echo "Drawing $fname"
+gnuplot << EOF
+    set terminal unknown
+    #set view 33,33 #3D
+    #unset xtics 
+    #unset ytics
+    #unset ztics
+    unset border
+    set output '$fname.png'
+    set yrange [-1.2:1.2]
+    set zrange [0.4:1.1]    
+    set terminal png
+    set title "Numerical solution" 
+    splot '$fname' with line 
+EOF
+done
+
+
+mencoder "mf://u-*.png" -mf fps=22 -o diffusion.avi -ovc lavc -lavcopts vcodec=mpeg4
+
+#rm *.png
+#rm *.tnl         
+#rm *.gplt      
+              

examples/mean-curvature-flow/tnl-run-mean-curvature-flow-contour-video

+#!/bin/bash
+
+device="host"
+sizes="16"
+initFunctions="sin-bumps"
+snapshotPeriod=0.001
+finalTime=0.15
+solverName="mean-curvature-flow"
+boundaryCondition="neumann"
+boundaryValue=0
+minZ=-1
+maxZ=1
+contourHeight=0.3
+
+spaceStep=$(expr 1/($sizes-2) | bc | sed 's/^\./0./')
+
+setupInitFunction()
+{
+   initFunction=$1
+      origin=0
+      proportions=1
+      amplitude=1.0
+      waveLength=1.0
+      waveLengthX=1.0
+      waveLengthY=1.0
+      waveLengthZ=1.0
+      wavesNumber=0.0
+      wavesNumberX=0.0
+      wavesNumberY=0.0
+      wavesNumberZ=0.0
+      phase=0.0
+      phaseX=0.0
+      phaseY=0.0
+      phaseZ=0.0
+      sigma=1
+}
+
+setupGrid()
+{
+   gridSize=$1
+   tnl-grid-setup --dimensions 2 \
+                  --origin-x ${origin} \
+                  --origin-y ${origin} \
+                  --origin-z ${origin} \
+                  --proportions-x ${proportions} \
+                  --proportions-y ${proportions} \
+                  --proportions-z ${proportions} \
+                  --size-x ${gridSize} \
+                  --size-y ${gridSize} \
+                  --size-z ${gridSize} 
+}
+
+setInitialCondition()
+{
+   initFunction=$1
+   tnl-init --test-function ${initFunction} \
+	    --output-file initial.tnl \
+            --amplitude ${amplitude} \
+            --wave-length ${waveLength} \
+            --wave-length-x ${waveLengthX} \
+            --wave-length-y ${waveLengthY} \
+            --wave-length-z ${waveLengthZ} \
+            --waves-number ${wavesNumber} \
+            --waves-number-x ${wavesNumberX} \
+            --waves-number-y ${wavesNumberY} \
+            --waves-number-z ${wavesNumberZ} \
+            --phase ${phase} \
+            --phase-x ${phaseX} \
+            --phase-y ${phaseY} \
+            --phase-z ${phaseZ} \
+            --sigma ${sigma} \
+            --time-dependence none
+}
+
+solve()
+{
+   timeDiscretisation=$1
+   discreteSolver=$2
+   ${solverName} --device ${device} \
+                 --mesh mesh.tnl \
+                 --initial-condition initial.tnl \
+		--snapshot-period ${snapshotPeriod} \
+                 --time-discretisation ${timeDiscretisation} \
+                 --time-step 1 \
+                 --time-step-order 2 \
+                 --discrete-solver ${discreteSolver} \
+                 --merson-adaptivity 1.0e-7 \
+                 --sor-omega 1.95 \
+                 --gmres-restarting 20 \
+                 --min-iterations 20 \
+                 --convergence-residue 1.0e-12 \
+		 --boundary-conditions-type ${boundaryCondition} \
+		 --boundary-conditions-constant ${boundaryValue} \
+		 --final-time ${finalTime}
+}
+
+view()
+{
+   tnl-view --input-files u-*.tnl
+   tnl-view --input-files initial.tnl
+}
+
+generate3DVid()
+{
+seznam=`ls u-*.gplt`
+step=0
+for fname in $seznam ; do
+step=$((${step}+1))
+time=$(expr $step*$snapshotPeriod | bc | sed 's/^\./0./')
+echo "Drawing contour $fname"
+gnuplot << EOF
+set output '${fname}.png'
+set xrange [${1}:${proportions}]
+set yrange [${1}:${proportions}]
+set zrange [${minZ}:${maxZ}]    
+unset surface
+set terminal png size 1200,600
+set view map
+set title 'Numerical solution - contour in height ${contourHeight} - T: ${time}'
+set pm3d interpolate 100,100
+set size square
+set contour base
+unset colorbox
+set cntrparam levels discrete ${contourHeight}
+splot '$fname' with pm3d notitle
+EOF
+done
+
+mencoder "mf://u-*.png" -mf fps=4 -o mean_curvature_contour_${contourHeight}_$size.avi -ovc lavc -lavcopts vcodec=mpeg4
+
+rm *.png
+rm *.tnl         
+rm *.gplt 
+rm mesh.asy
+rm computation-done
+     
+}
+
+runTest()
+{
+   for initFunction in ${initFunctions};
+   do
+      cd ${initFunction}-videos
+      setupInitFunction ${initFunction}
+         
+      for size in $sizes;
+      do
+          cd $size
+          echo ""
+          echo ""
+          echo ""
+          if test ! -f computation-done;
+          then
+             touch computation-in-progress
+             echo "========================================================================="
+             echo "===                   SETTING UP THE GRID                             ==="
+             echo "========================================================================="
+             setupGrid $size 
+             echo "========================================================================="
+             echo "===                WRITING THE EXACT SOLUTION                         ==="
+             echo "========================================================================="
+             setInitialCondition $initFunction
+             echo "========================================================================="
+             echo "===                   STARTING THE SOLVER                             ==="
+             echo "========================================================================="
+             solve explicit merson
+             #solve semi-implicit gmres
+             mv computation-in-progress computation-done
+             echo "========================================================================="
+             echo "===                     COMPUTATION DONE                              ==="            
+             echo "========================================================================="
+	     view
+	     generate3DVid $origin $proportions
+             cd ..
+             lastSize=$size
+          fi
+         cd ..
+      done
+      cd ..
+   done
+}
+
+runTest
+ 

examples/mean-curvature-flow/tnl-run-mean-curvature-flow-eoc-test

+#!/bin/bash
+
+device="host"
+dimensions="3D"
+sizes3D="16 32 64"
+testFunctions="exp-bump sin-wave sin-bumps"
+snapshotPeriod=0.001
+finalTime=0.01
+timeDependence="cosine"
+solverName="mean-curvature-flow-eoc"
+#solverName="gdb --args tnl-heat-equation-eoc-test-dbg"
+
+setupTestFunction()
+{
+   testFunction=$1
+#   if test x${testFunction} = "xexp-bump";
+#   then
+      origin=2
+      proportions=2
+      amplitude=1.0
+      waveLength=1.0
+      waveLengthX=1.0
+      waveLengthY=1.0
+      waveLengthZ=1.0
+      wavesNumber=0.0
+      wavesNumberX=0.0
+      wavesNumberY=0.0
+      wavesNumberZ=0.0
+      phase=0.0
+      phaseX=0.0
+      phaseY=0.0
+      phaseZ=0.0
+      sigma=1
+#   fi
+}
+
+setupGrid()
+{
+   dimensions=$1
+   gridSize=$2
+   tnl-grid-setup --dimensions ${dimensions} \
+                  --origin-x ${origin} \
+                  --origin-y ${origin} \
+                  --origin-z ${origin} \
+                  --proportions-x ${proportions} \
+                  --proportions-y ${proportions} \
+                  --proportions-z ${proportions} \
+                  --size-x ${gridSize} \
+                  --size-y ${gridSize} \
+                  --size-z ${gridSize} 
+}
+
+setInitialCondition()
+{
+   testFunction=$1
+   tnl-init --test-function ${testFunction} \
+            --output-file exact-u.tnl \
+            --amplitude ${amplitude} \
+            --wave-length ${waveLength} \
+            --wave-length-x ${waveLengthX} \
+            --wave-length-y ${waveLengthY} \
+            --wave-length-z ${waveLengthZ} \
+            --waves-number ${wavesNumber} \
+            --waves-number-x ${wavesNumberX} \
+            --waves-number-y ${wavesNumberY} \
+            --waves-number-z ${wavesNumberZ} \
+            --phase ${phase} \
+            --phase-x ${phaseX} \
+            --phase-y ${phaseY} \
+            --phase-z ${phaseZ} \
+            --sigma ${sigma} \
+            --time-dependence ${timeDependence} \
+            --snapshot-period ${snapshotPeriod} \
+            --final-time ${finalTime}
+}
+
+solve()
+{
+   timeDiscretisation=$1
+   discreteSolver=$2
+   ${solverName} --device ${device} \
+                 --mesh mesh.tnl \
+                 --initial-condition exact-u-00000.tnl \
+                 --time-discretisation ${timeDiscretisation} \
+                 --time-step 1 \
+                 --time-step-order 2 \
+                 --discrete-solver ${discreteSolver} \
+                 --merson-adaptivity 1.0e-10 \
+                 --sor-omega 1.95 \
+                 --gmres-restarting 20  \
+                 --min-iterations 50 \
+                 --convergence-residue 1.0e-14 \
+                 --test-function ${testFunction}\
+                 --amplitude ${amplitude} \
+                 --wave-length ${waveLength} \
+                 --wave-length-x ${waveLengthX} \
+                 --wave-length-y ${waveLengthY} \
+                 --wave-length-z ${waveLengthZ} \
+                 --waves-number ${wavesNumber} \
+                 --waves-number-x ${wavesNumberX} \
+                 --waves-number-y ${wavesNumberY} \
+                 --waves-number-z ${wavesNumberZ} \
+                 --phase ${phase} \
+                 --phase-x ${phaseX} \
+                 --phase-y ${phaseY} \
+                 --phase-z ${phaseZ} \
+                 --sigma ${sigma} \
+                 --time-dependence ${timeDependence} \
+                 --snapshot-period ${snapshotPeriod} \
+                 --final-time ${finalTime}
+}
+               
+computeError()
+{
+   tnl-diff --mesh mesh.tnl \
+            --input-files exact-u-*.tnl u-*.tnl \
+            --mode halves \
+            --snapshot-period ${snapshotPeriod} \
+            --output-file errors.txt \
+            --write-difference yes
+}
+
+runTest()
+{
+   for testFunction in ${testFunctions};
+   do
+      mkdir -p ${testFunction}
+      cd ${testFunction}
+      setupTestFunction ${testFunction}
+      
+      for dim in ${dimensions};
+      do
+         mkdir -p $dim
+         cd ${dim}
+         if test $dim = 1D;
+         then 
+            sizes=$sizes1D
+         fi
+         if test $dim = 2D;
+         then 
+            sizes=$sizes2D
+         fi
+         if test $dim = 3D;
+         then 
+            sizes=$sizes3D
+         fi
+         
+         lastSize=""
+         for size in $sizes;
+         do
+            mkdir -p $size
+            cd $size
+            echo ""
+            echo ""
+            echo ""
+            if test ! -f computation-done;
+            then
+               touch computation-in-progress
+               echo "========================================================================="
+               echo "===                   SETTING UP THE GRID                             ==="
+               echo "========================================================================="
+               setupGrid $dim $size 
+               echo "========================================================================="
+               echo "===                WRITING THE EXACT SOLUTION                         ==="
+               echo "========================================================================="
+               setInitialCondition $testFunction
+               echo "========================================================================="
+               echo "===                   STARTING THE SOLVER                             ==="
+               echo "========================================================================="
+               #solve explicit merson
+               solve semi-implicit gmres
+               mv computation-in-progress computation-done
+            fi            
+            echo "========================================================================="
+            echo "===                   COMPUTING THE ERROR                             ==="
+            echo "========================================================================="
+            computeError
+            echo "========================================================================="
+            echo "===                     COMPUTING THE EOC                             ==="            
+            echo "========================================================================="
+            if test ! x$lastSize = x;
+            then
+               tnl-err2eoc ../$lastSize/errors.txt errors.txt
+            fi
+            echo "========================================================================="
+            echo "===                     COMPUTATION DONE                              ==="            
+            echo "========================================================================="
+            cd ..
+            lastSize=$size
+         done
+
+         cd ..
+      done
+      cd ..
+   done
+}
+
+runTest

examples/mean-curvature-flow/tnl-run-mean-curvature-flow-videos

+#!/bin/bash
+
+device="host"
+sizes="64"
+initFunctions="pseudoSquare"
+snapshotPeriod=0.001
+finalTime=0.1
+solverName="mean-curvature-flow"
+boundaryCondition="neumann"
+boundaryValue=0
+minZ=-3
+maxZ=6
+contourHeight=0
+numberOfContours=8
+numberOfInterpolations=10
+eps=0.00001
+
+setupInitFunction()
+{
+   initFunction=$1
+      origin=-2
+      proportions=4
+      amplitude=1.0
+      waveLength=1.0
+      waveLengthX=1.0
+      waveLengthY=1.0
+      waveLengthZ=1.0
+      wavesNumber=0.0
+      wavesNumberX=0.0
+      wavesNumberY=0.0
+      wavesNumberZ=0.0
+      phase=0.0
+      phaseX=0.0
+      phaseY=0.0
+      phaseZ=0.0
+      sigma=1.0
+      diameter=0.6
+      height=1.2
+}
+
+setupGrid()
+{
+   gridSize=$1
+   tnl-grid-setup --dimensions 2 \
+                  --origin-x ${origin} \
+                  --origin-y ${origin} \
+                  --origin-z ${origin} \
+                  --proportions-x ${proportions} \
+                  --proportions-y ${proportions} \
+                  --proportions-z ${proportions} \
+                  --size-x ${gridSize} \
+                  --size-y ${gridSize} \
+                  --size-z ${gridSize} 
+}
+
+setInitialCondition()
+{
+   initFunction=$1
+   tnl-init --test-function ${initFunction} \
+	    --output-file initial.tnl \
+            --amplitude ${amplitude} \
+            --wave-length ${waveLength} \
+            --wave-length-x ${waveLengthX} \
+            --wave-length-y ${waveLengthY} \
+            --wave-length-z ${waveLengthZ} \
+            --waves-number ${wavesNumber} \
+            --waves-number-x ${wavesNumberX} \
+            --waves-number-y ${wavesNumberY} \
+            --waves-number-z ${wavesNumberZ} \
+            --phase ${phase} \
+            --phase-x ${phaseX} \
+            --phase-y ${phaseY} \
+            --phase-z ${phaseZ} \
+            --sigma ${sigma} \
+	    --diameter ${diameter} \
+	    --height ${height} \
+            --time-dependence none
+}
+
+solve()
+{
+   timeDiscretisation=$1
+   discreteSolver=$2
+   ${solverName} --device ${device} \
+                 --mesh mesh.tnl \
+                 --initial-condition initial.tnl \
+		--snapshot-period ${snapshotPeriod} \
+                 --time-discretisation ${timeDiscretisation} \
+                 --time-step 1 \
+                 --time-step-order 2 \
+                 --discrete-solver ${discreteSolver} \
+                 --merson-adaptivity 1.0e-7 \
+                 --sor-omega 1.95 \
+                 --gmres-restarting 20 \
+                 --min-iterations 20 \
+                 --convergence-residue 1.0e-12 \
+		 --boundary-conditions-type ${boundaryCondition} \
+		 --boundary-conditions-constant ${boundaryValue} \
+		 --eps ${eps} \
+		 --final-time ${finalTime}
+}
+
+view()
+{
+   tnl-view --input-files u-*.tnl
+   tnl-view --input-files initial.tnl
+}
+
+generate3DVid()
+{
+domainEnd=$( expr ${origin}+${proportions} | bc | sed 's/^\./0./' | sed 's/^-\./-0./' )
+
+seznam=`ls u-*.gplt`
+step=0
+for fname in $seznam ; do
+time=$(expr $step*$snapshotPeriod | bc | sed 's/^\./0./')
+echo "Drawing $fname"
+gnuplot << EOF
+set output '$fname.png'
+set xrange [${1}:${domainEnd}]
+set yrange [${1}:${domainEnd}]
+set zrange [${minZ}:${maxZ}]    
+set pm3d
+unset surface
+set terminal png size 1200,600
+set cbrange [-1:1]
+set view 22,33,0.8,3
+set title 'Numerical solution - T: ${time}'
+set pm3d interpolate ${numberOfInterpolations},${numberOfInterpolations}
+splot '$fname' with pm3d notitle
+EOF
+step=$((${step}+1))
+done
+
+mencoder "mf://u-*.png" -mf fps=4 -o mean_curvature_$size.avi -ovc lavc -lavcopts vcodec=mpeg4
+rm *.png
+
+seznam=`ls u-*.gplt`
+step=0
+for fname in $seznam ; do
+time=$(expr $step*$snapshotPeriod | bc | sed 's/^\./0./')
+echo "Drawing map $fname"
+gnuplot << EOF
+set output '${fname}.png'
+set xrange [${1}:${domainEnd}]
+set yrange [${1}:${domainEnd}]
+set zrange [${minZ}:${maxZ}]    
+set pm3d
+unset surface
+set terminal png size 1200,600
+set cbrange [-1:1]
+set view map
+set title 'Numerical solution - map - T: ${time}'
+set pm3d interpolate 100,100
+set size square
+set contour base
+set cntrparam levels ${numberOfContours}
+splot '$fname' with pm3d notitle
+EOF
+step=$((${step}+1))
+done
+
+mencoder "mf://u-*.png" -mf fps=4 -o mean_curvature_map_$size.avi -ovc lavc -lavcopts vcodec=mpeg4
+rm *.png
+
+seznam=`ls u-*.gplt`
+step=0
+for fname in $seznam ; do
+time=$(expr $step*$snapshotPeriod | bc | sed 's/^\./0./')
+echo "Drawing contour $fname"
+gnuplot << EOF
+set output '${fname}.png'
+set xrange [${1}:${domainEnd}]
+set yrange [${1}:${domainEnd}]
+set zrange [${minZ}:${maxZ}]    
+unset surface
+set terminal png size 1200,600
+set view map
+set title 'Numerical solution - contour in height ${contourHeight} - T: ${time}'
+set pm3d interpolate 100,100
+set size square
+set contour base
+unset colorbox
+set cntrparam levels discrete ${contourHeight}
+splot '$fname' with pm3d notitle
+EOF
+step=$((${step}+1))
+done
+
+mencoder "mf://u-*.png" -mf fps=4 -o mean_curvature_contour_${contourHeight}_$size.avi -ovc lavc -lavcopts vcodec=mpeg4
+
+rm *.png
+rm *.tnl         
+rm *.gplt 
+rm mesh.asy
+rm computation-done
+     
+}
+
+runTest()
+{
+   for initFunction in ${initFunctions};
+   do
+      mkdir -p ${initFunction}-videos
+      cd ${initFunction}-videos
+      setupInitFunction ${initFunction}
+         
+      for size in $sizes;
+      do
+          mkdir -p $size
+          cd $size
+          echo ""
+          echo ""
+          echo ""
+          if test ! -f computation-done;
+          then
+             touch computation-in-progress
+             echo "========================================================================="
+             echo "===                   SETTING UP THE GRID                             ==="
+             echo "========================================================================="
+             setupGrid $size 
+             echo "========================================================================="
+             echo "===                WRITING THE EXACT SOLUTION                         ==="
+             echo "========================================================================="
+             setInitialCondition $initFunction
+             echo "========================================================================="
+             echo "===                   STARTING THE SOLVER                             ==="
+             echo "========================================================================="
+             solve explicit merson
+             #solve semi-implicit gmres
+             mv computation-in-progress computation-done
+             echo "========================================================================="
+             echo "===                     COMPUTATION DONE                              ==="            
+             echo "========================================================================="
+	     view
+	     generate3DVid $origin $proportions
+             cd ..
+             lastSize=$size
+          fi
+         cd ..
+      done
+      cd ..
+   done
+}
+
+runTest
+ 

install

@@ -35,12 +35,12 @@ then
        mkdir Debug
     fi
     cd Debug
-    ../build --root-dir=.. --build=Debug ${OPTIONS}
-    if test $? != 0;
+    if ../build --root-dir=.. --build=Debug ${OPTIONS};
     then
+        make install
+    else    
        exit 1
     fi
-    make install
     cd ..
 fi
 
@@ -51,12 +51,12 @@ then
        mkdir Release
     fi
     cd Release
-    ../build --root-dir=.. --build=Release ${OPTIONS}
-    if test $? != 0;
+    if ../build --root-dir=.. --build=Release ${OPTIONS};
     then
+        make install
+    else
         exit 1
     fi
-    make install
     cd ..
 fi
 

src/config/tnlParameterContainer.cpp

@@ -18,7 +18,9 @@
 #include <ctype.h>
 #include <cstring>
 #include <stdio.h>
+
 #include "tnlParameterContainer.h"
+#include <core/tnlObject.h>
 
 bool matob( const char* value, bool& ret_val )
 {