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Commit ac593360 authored by Naumann, Andreas's avatar Naumann, Andreas
Browse files

codestyle and implicit meshes

parent a34f5d82
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Showing with 315 additions and 151 deletions
AMDiS/CMakeLists.txt
View file @ ac593360
project("AMDiS")
project(AMDiS)
cmake_minimum_required(VERSION 2.6)
......@@ -49,7 +49,8 @@ SET(AMDIS_SRC ${SOURCE_DIR}/DOFIndexed.cc
${SOURCE_DIR}/AdaptBase.cc
${SOURCE_DIR}/StandardProblemIteration.cc
${SOURCE_DIR}/ProblemScal.cc
${SOURCE_DIR}/ProblemVec.cc
${SOURCE_DIR}/ProblemVec.cc
${SOURCE_DIR}/ProblemImplicit.cc
${SOURCE_DIR}/ProblemVecDbg.cc
${SOURCE_DIR}/DualTraverse.cc
${SOURCE_DIR}/ElementData.cc
......
AMDiS/src/MathFunctions.h
View file @ ac593360
......@@ -5,26 +5,26 @@
namespace AMDiS {
//converts signed distance to phasefield
inline double Phi1(double r, double eps) { return 0.5*(1-tanh(3*r/eps)); }
inline double Phi2(double r, double eps) { return 0.5*(1+tanh(3*r/eps)); }
inline double Phi1(double r, double eps) { return 0.5 * (1 - tanh(3 * r / eps)); }
inline double Phi2(double r, double eps) { return 0.5 * (1 + tanh(3 * r / eps)); }
//levelset: positive (1) in the set, negative (-1) outside, zero on the boundary
inline double LevelSet(double r)
{
if(r<0)
if (r < 0)
return 1;
if(r>0)
if (r > 0)
return -1;
return 0;
}
//convert Phi1 to r
inline double Phi1ToR(double p1, double eps) {
return eps/3.0 * atanh( max(-1+1.e-14, min(1-1.e-14, 1-2*p1)) );
return eps / 3.0 * atanh( max(-1 + 1.0e-14, min(1 - 1.0e-14, 1 - 2 * p1)) );
}
//convert Phi2 to r
inline double Phi2ToR(double p2, double eps) {
return eps/3.0 * atanh( max(-1+1.e-14, min(1-1.e-14, 1+2*p2)) );
return eps / 3.0 * atanh( max(-1 + 1.0e-14, min(1 - 1.0e-14, 1 + 2 * p2)) );
}
}
#endif
AMDiS/src/ProblemImplicit.cc 0 → 100644
View file @ ac593360
#include "ProblemImplicit.h"
namespace AMDiS {
namespace calcspace {
void readDofvec(std::istream& in, DOFVector< double >* vec, Mesh* mesh)
{
long size = mesh->getNumberOfVertices();
std::string buf;
getline(in, buf);
while(buf != "vertex values: solution") getline(in, buf);
for(long i = 0; i < size; i++)
{
in >> buf;
(*vec)[i] = atof(buf.c_str());
}
}
void readR(std::istream& inStream, double eps,
DOFVector< double >* r, DOFVector< double >* phi1,
DOFVector< double >* phi2, DOFVector< double >* levelSet,
Mesh* mesh)
{
readDofvec(inStream, r, mesh);
std::vector< double >& vecR = r->getVector();
std::vector< double >& vecPhi1 = phi1->getVector();
std::vector< double >& vecPhi2 = phi2->getVector();
std::vector< double >& vecLevelSet = levelSet->getVector();
TEST_EXIT(vecR.size() != vecPhi1.size() && vecPhi2.size() != vecR.size())("something went wrong\n");
for (int i = vecR.size()-1; i >= 0; --i)
{
vecPhi1[i] = Phi1(vecR[i], eps);
vecPhi2[i] = Phi2(vecR[i], eps);
vecLevelSet[i] = LevelSet(vecR[i]);
}
}
void readPhi1(istream& inStream, double eps,
DOFVector< double >* r, DOFVector< double >* phi1,
DOFVector< double >* phi2, DOFVector< double >* levelSet,
Mesh* mesh)
{
readDofvec(inStream, phi1, mesh);
std::vector< double >& vecR = r->getVector();
std::vector< double >& vecPhi1 = phi1->getVector();
std::vector< double >& vecPhi2 = phi2->getVector();
std::vector< double >& vecLevelSet = levelSet->getVector();
TEST_EXIT(vecR.size() != vecPhi1.size() && vecPhi2.size() != vecR.size())("something went wrong\n");
for (int i = vecR.size()-1; i>= 0; --i)
{
vecR[i] = Phi1ToR(vecPhi1[i], eps);
//vecPhi2[i] = Phi2(vecR[i], eps);
vecPhi2[i] = 1 - vecPhi1[i];
vecLevelSet[i] = LevelSet(vecR[i]);
}
}
void readPhi2(istream& inStream, double eps,
DOFVector< double >* r, DOFVector< double >* phi1,
DOFVector< double >* phi2, DOFVector< double >* levelSet,
Mesh* mesh)
{
readDofvec(inStream, phi2, mesh);
std::vector< double >& vecR = r->getVector();
std::vector< double >& vecPhi1 = phi1->getVector();
std::vector< double >& vecPhi2 = phi2->getVector();
std::vector< double >& vecLevelSet = levelSet->getVector();
TEST_EXIT(vecR.size() != vecPhi1.size() && vecPhi2.size() != vecR.size())("something went wrong\n");
for (int i = vecR.size()-1; i >= 0; --i)
{
vecR[i] = Phi2ToR(vecPhi2[i], eps);
//vecPhi1[i] = Phi1(vecR[i], eps);
vecPhi1[i] = 1 - vecPhi2[i];
vecLevelSet[i] = LevelSet(vecR[i]);
}
}
}
bool ProblemImplicitScal::createImplicitMesh()
{
std::string meshFilename("");
GET_PARAMETER(0, name + "->implicit mesh->mesh file", &meshFilename);
//if no file name is given, there's no implicit mesh
if (meshFilename.length() == 0)
return false;
std::string dofFilename("");
GET_PARAMETER(0, name + "->implicit mesh->dof file", &dofFilename);
if (dofFilename.length() == 0)
return false;
double eps(-1);
GET_PARAMETER(0, name + "->implicit mesh->eps", "%d", &eps);
if (eps<0)
return false;
int serType(-1);
GET_PARAMETER(0, name + "->implicit mesh->type", "%d", &serType);
if (serType<0)
return false;
TEST_EXIT(mesh != NULL)("the mesh was not created\n");
std::ifstream inStream(meshFilename.c_str());
mesh->deserialize(inStream);
inStream.close();
//create the fespace with the correct admin
createFESpace();
r = new DOFVector< double >(getFESpace(), "r");
phi1 = new DOFVector<double>(getFESpace(), "phi1");
phi2 = new DOFVector<double>(getFESpace(), "phi2");
levelSet = new DOFVector< double >(getFESpace(), "levelSet");
inStream.open(dofFilename.c_str());
switch (serType) {
case 0:
calcspace::readR(inStream, eps, r, phi1, phi2, levelSet, mesh);
break;
case 1:
calcspace::readPhi1(inStream, eps, r, phi1, phi2, levelSet, mesh);
break;
case 2:
calcspace::readPhi2(inStream, eps, r, phi1, phi2, levelSet, mesh);
break;
default:
WARNING("unknown implicit mesh type\n");
}
inStream.close();
return true;
}
void ProblemImplicitScal::initialize(Flag initFlag, ProblemScal* adaptProblem, Flag adoptFlag)
{
FUNCNAME("ImplicitScal::initialize()");
ProblemScal::initialize(CREATE_MESH);
createImplicitMesh();
initFlag = initFlag & ~CREATE_MESH;
ProblemScal::initialize(initFlag);
}
bool ProblemImplicitVec::createImplicitMesh()
{
//check each mesh if it's an implicit one
r.resize(meshes.size());
phi1.resize(meshes.size());
phi2.resize(meshes.size());
levelSet.resize(meshes.size());
for(int i=0;i<meshes.size();++i) {
createImplicitMesh(i);
}
}
bool ProblemImplicitVec::createImplicitMesh(int p)
{
std::string path=name + "->implicit mesh[" + boost::lexical_cast< std::string >(p) + "]->";
std::string meshFilename("");
GET_PARAMETER(0, path + "mesh file", &meshFilename);
//if no file name is given, there's no implicit mesh
if (meshFilename.length() == 0)
return false;
std::string dofFilename("");
GET_PARAMETER(0,path + "dof file", &dofFilename);
if (dofFilename.length() == 0)
return false;
double eps(-1);
GET_PARAMETER(0, path + "eps", "%d", &eps);
if(eps < 0)
return false;
int serType(-1);
GET_PARAMETER(0, path + "type", "%d", &serType);
if (serType < 0)
return false;
TEST_EXIT(meshes[p] != NULL)("the mesh was not created\n");
std::ifstream inStream(meshFilename.c_str());
meshes[p]->deserialize(inStream);
inStream.close();
//create the fespace with the correct admin
createFESpace(NULL);
r[p] = new DOFVector< double >(getFESpace(p), "r");
phi1[p] = new DOFVector<double>(getFESpace(p), "phi1");
phi2[p] = new DOFVector<double>(getFESpace(p), "phi2");
levelSet[p] = new DOFVector< double >(getFESpace(p), "levelSet");
inStream.open(dofFilename.c_str());
switch (serType)
{
case 0:
calcspace::readR(inStream, eps,r[p], phi1[p], phi2[p], levelSet[p], meshes[p]);
break;
case 1:
calcspace::readPhi1(inStream, eps, r[p], phi1[p], phi2[p], levelSet[p], meshes[p]);
break;
case 2:
calcspace::readPhi2(inStream,eps, r[p], phi1[p], phi2[p], levelSet[p], meshes[p]);
break;
default:
WARNING("unknown implicit mesh type\n");
}
inStream.close();
return true;
}
void ProblemImplicitVec::initialize(Flag initFlag, ProblemScal* adaptProblem, Flag adoptFlag)
{
FUNCNAME("ImplicitScal::initialize()");
ProblemVec::initialize(CREATE_MESH);
createImplicitMesh();
initFlag = initFlag & ~CREATE_MESH;
ProblemVec::initialize(initFlag);
}
}
AMDiS/src/ProblemImplicit.h 0 → 100644
View file @ ac593360
#ifndef AMDIS_PROBLEMIMPLICIT_H
#define AMDIS_PROBLEMIMPLICIT_H
#include "AMDiS.h"
#include "ProblemScal.h"
#include "ProblemVec.h"
namespace AMDiS {
class ProblemImplicitScal : public ProblemScal
{
public:
ProblemImplicitScal(std::string name, ProblemIterationInterface* pis = NULL)
: ProblemScal(name, pis),
r(NULL),
phi1(NULL),
phi2(NULL),
levelSet(NULL)
{}
/// @return: true if implicit mesh type is ok (see below) and false in all other cases
/// initfile entries:
/// name+"->implicit mesh->mesh file": name of serialized mesh
/// name+"->implicit mesh->dof file": name of serialized dofvector
/// name+"->implicit mesh->type": type of serialized dofvector.
/// type can be:
/// 0: dofvector is a signed distance r
/// 1: dofvector is a phasefield phi=0.5*(1-tanh(3*r/eps))
/// 2: dofvector is a phasefield phi=0.5*(1+tanh(3*r/eps))
/// assumes:
/// a) already created, but not yet initialized mesh
/// b) already created feSpace
virtual bool createImplicitMesh();
virtual void initialize(Flag initFlag, ProblemScal *adoptProblem = NULL,
Flag adoptFlag = INIT_NOTHING);
protected:
/// DOFVector for a signed distance
DOFVector< double > *r;
/// DOFVector for the phasefield function 0.5*(1-tanh(3*r/eps))
DOFVector< double > *phi1;
/// DOFVector for the phasefield function 0.5*(1+tanh(3*r/eps))
DOFVector< double > *phi2;
/// DOFVector for the levelset function (levelSet(x): x \in \Omega: 1, x \not \in Omega: -1, x \in \Gamma: 0)
DOFVector< double > *levelSet;
};
class ProblemImplicitVec : public ProblemVec
{
public:
ProblemImplicitVec(std::string name, ProblemIterationInterface* problem = NULL)
: ProblemVec(name, problem),
r(0),
phi1(0),
phi2(0),
levelSet(0)
{}
virtual bool createImplicitMesh();
virtual void initialize(Flag initFlag, ProblemScal *adoptProblem=NULL,
Flag adoptFlag = INIT_NOTHING);
protected:
bool createImplicitMesh(int p);
/// DOFVector for a signed distance
std::vector< DOFVector< double >* > r;
/// DOFVector for the phasefield function 0.5*(1-tanh(3*r/eps))
std::vector< DOFVector< double >* > phi1;
/// DOFVector for the phasefield function 0.5*(1+tanh(3*r/eps))
std::vector< DOFVector< double >* > phi2;
/// DOFVector for the levelset function (levelSet(x): x \in \Omega: 1, x \not \in Omega: -1, x \in \Gamma: 0)
std::vector< DOFVector< double >* > levelSet;
};
}
#endif
AMDiS/src/ProblemScal.cc
View file @ ac593360
......@@ -151,110 +151,6 @@ namespace AMDiS {
rhs->getBoundaryManager()->addBoundaryCondition(periodic);
}
void ProblemScal::readR(std::istream& inStream,double eps) {
readDofvec(inStream,r);
std::vector< double >& vecR=r->getVector();
std::vector< double >& vecPhi1=phi1->getVector();
std::vector< double >& vecPhi2=phi2->getVector();
std::vector< double >& vecLevelSet=levelSet->getVector();
TEST_EXIT(vecR.size()!=vecPhi1.size() && vecPhi2.size()!=vecR.size())("something went wrong\n");
for(int i=vecR.size()-1;i>=0;--i) {
vecPhi1[i]=Phi1(vecR[i],eps);
vecPhi2[i]=Phi2(vecR[i],eps);
vecLevelSet[i]=LevelSet(vecR[i]);
}
}
void ProblemScal::readPhi1(istream& inStream,double eps) {
readDofvec(inStream,phi1);
std::vector< double >& vecR=r->getVector();
std::vector< double >& vecPhi1=phi1->getVector();
std::vector< double >& vecPhi2=phi2->getVector();
std::vector< double >& vecLevelSet=levelSet->getVector();
TEST_EXIT(vecR.size()!=vecPhi1.size() && vecPhi2.size()!=vecR.size())("something went wrong\n");
for(int i=vecR.size()-1;i>=0;--i) {
vecR[i]=Phi1ToR(vecPhi1[i],eps);
vecPhi2[i]=Phi2(vecR[i],eps);
vecLevelSet[i]=LevelSet(vecR[i]);
}
}
void ProblemScal::readPhi2(istream& inStream,double eps) {
readDofvec(inStream,phi2);
std::vector< double >& vecR=r->getVector();
std::vector< double >& vecPhi1=phi1->getVector();
std::vector< double >& vecPhi2=phi2->getVector();
std::vector< double >& vecLevelSet=levelSet->getVector();
TEST_EXIT(vecR.size()!=vecPhi1.size() && vecPhi2.size()!=vecR.size())("something went wrong\n");
for(int i=vecR.size()-1;i>=0;--i) {
vecR[i]=Phi2ToR(vecPhi1[i],eps);
vecPhi1[i]=Phi1(vecR[i],eps);
vecLevelSet[i]=LevelSet(vecR[i]);
}
}
void ProblemScal::readDofvec(std::istream& in, DOFVector< double >* vec)
{
long size = mesh->getNumberOfVertices();
std::string buf;
getline(in, buf);
while(buf != "vertex values: solution") getline(in, buf);
for(long i=0; i<size; i++){
in >> buf;
(*vec)[i] = atof(buf.c_str());
}
}
bool ProblemScal::createImplicitMesh()
{
std::string meshFilename("");
GET_PARAMETER(0,name+"->implicit mesh->mesh file",&meshFilename);
//if no file name is given, there's no implicit mesh
if(meshFilename.length()==0)
return false;
std::string dofFilename("");
GET_PARAMETER(0,name+"->implicit mesh->dof file",&dofFilename);
if(dofFilename.length()==0)
return false;
double eps(-1);
GET_PARAMETER(0,name+"->implicit mesh->eps","%d",&eps);
if(eps<0)
return false;
int serType(-1);
GET_PARAMETER(0,name+"->implicit mesh->type","%d",&serType);
if(serType<0)
return false;
TEST_EXIT(mesh!=NULL)("the mesh was not created\n");
std::ifstream inStream(meshFilename.c_str());
mesh->deserialize(inStream);
inStream.close();
//create the fespace with the correct admin
createFESpace();
r=new DOFVector< double >(getFESpace(),"r");
phi1=new DOFVector<double>(getFESpace(),"phi1");
phi2=new DOFVector<double>(getFESpace(),"phi2");
levelSet=new DOFVector< double >(getFESpace(),"levelSet");
inStream.open(dofFilename.c_str());
switch(serType) {
case 0:
readR(inStream,eps);
break;
case 1:
readPhi1(inStream,eps);
break;
case 2:
readPhi2(inStream,eps);
break;
default:
WARNING("unknown implicit mesh type\n");
}
inStream.close();
return true;
}
void ProblemScal::createMesh()
{
......@@ -364,7 +260,6 @@ namespace AMDiS {
Flag adoptFlag)
{
FUNCNAME("Problem::initialize()");
// === create mesh ===
if (mesh) {
WARNING("mesh already created\n");
......@@ -389,7 +284,9 @@ namespace AMDiS {
if (!mesh)
WARNING("no mesh created\n");
createImplicitMesh();
if (refinementManager == NULL)
WARNING("refinement manager not set\n");
// === create fespace ===
if (feSpace) {
WARNING("feSpace already created\n");
......@@ -529,6 +426,7 @@ namespace AMDiS {
}
}
}
}
void ProblemScal::createFESpace()
......
AMDiS/src/ProblemScal.h
View file @ ac593360
......@@ -52,12 +52,7 @@ namespace AMDiS {
useGetBound(true),
refinementManager(NULL),
coarseningManager(NULL),
info(10),
r(NULL),
phi1(NULL),
phi2(NULL),
levelSet(NULL)
{}
info(10) {}
/// Destructor
virtual ~ProblemScal();
......@@ -70,22 +65,6 @@ namespace AMDiS {
/// Used in \ref initialize().
virtual void createMesh();
/// Used in \ref createMesh().
/// @return: true if implicit mesh type is ok (see below) and false in all other cases
/// initfile entries:
/// name+"->implicit mesh->mesh file": name of serialized mesh
/// name+"->implicit mesh->dof file": name of serialized dofvector
/// name+"->implicit mesh->type": type of serialized dofvector.
/// type can be:
/// 0: dofvector is a signed distance r
/// 1: dofvector is a phasefield phi=0.5*(1-tanh(3*r/eps))
/// 2: dofvector is a phasefield phi=0.5*(1+tanh(3*r/eps))
/// assumes:
/// a) already created, but not yet initialized mesh
/// b) already created feSpace
virtual bool createImplicitMesh();
void readDofvec(std::istream&, DOFVector< double >*);
/// Used in \ref initialize().
virtual void createFESpace();
......@@ -384,18 +363,6 @@ namespace AMDiS {
/// DOFVector for the right hand side
DOFVector<double> *rhs;
/// DOFVector for a signed distance
DOFVector< double > *r;
/// DOFVector for the phasefield function 0.5*(1-tanh(3*r/eps))
DOFVector< double > *phi1;
/// DOFVector for the phasefield function 0.5*(1+tanh(3*r/eps))
DOFVector< double > *phi2;
/// DOFVector for the levelset function (levelSet(x): x \in \Omega: 1, x \not \in Omega: -1, x \in \Gamma: 0)
DOFVector< double > *levelSet;
/// System matrix
DOFMatrix *systemMatrix;
......@@ -422,9 +389,7 @@ namespace AMDiS {
/// Info level.
int info;
void readR(std::istream&, double);
void readPhi1(std::istream&,double);
void readPhi2(std::istream&,double);
};
}
......
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