Helpers.cc 15.2 KB
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#include "Helpers.h"

using namespace AMDiS;

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namespace Helpers {
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void calcMaxOnXAxis(DOFVector<double> *rho, std::vector<std::pair<WorldVector<double>, double> > &maxima)
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{ FUNCNAME("Helpers::calcMaxOnXAxis()");

  std::vector<WorldVector<double> > x;
  std::vector<double> y;

  double dimX=1.0,dimY=1.0;
  Parameters::get("mesh->dimension[x]",dimX);
  Parameters::get("mesh->dimension[y]",dimY);

  interpolOverLine(*rho,-dimX,0.0,dimX,0.0,1000,x,y);
  if (x.size() != y.size())
    throw(std::runtime_error("x.size /= y.size! Sollte nicht passieren!"));

  if(x.size()>0) {
    for(unsigned i=1; i<x.size()-1; ++i) {
      if(y[i-1]<y[i] && y[i+1]<y[i]) {
	maxima.push_back(std::make_pair(x[i],y[i]));
      }
    }
  }
};

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void calcMaxOnYAxis(DOFVector<double> *rho, std::vector<std::pair<WorldVector<double>, double> > &maxima)
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{ FUNCNAME("Helpers::calcMaxOnYAxis()");

  std::vector<WorldVector<double> > x;
  std::vector<double> y;

  double dimX,dimY;
  Parameters::get("mesh->dimension[x]",dimX);
  Parameters::get("mesh->dimension[y]",dimY);

  interpolOverLine(*rho,0.0,-dimY,0.0,dimY,1000,x,y);

  #ifdef HAVE_PARALLEL_DOMAIN_AMDIS
  if (MPI::COMM_WORLD.Get_rank() == 0)
  #endif
  {
  for(unsigned i=1; i<x.size()-1; ++i) {
    if(y[i-1]<y[i] && y[i+1]<y[i]) {
      maxima.push_back(make_pair(x[i],y[i]));
    }
  }
  }
};


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void transformMesh(Mesh *mesh, WorldVector<double> scale, WorldVector<double> shift, WorldVector<double> rotate)
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{ FUNCNAME("Helpers::scaleMesh()");

  int dow = Global::getGeo(WORLD);
  mtl::dense2D<double> Rx(dow,dow),Ry(dow,dow),Rz(dow,dow),T_(dow,dow),S(dow,dow);
  Rx = 1.0;
  Ry = 1.0;
  Rz = 1.0;
  S = 1.0;
  if (dow == 3) {
    Rx[1][1] = cos(rotate[0]);  Rx[1][2] = -sin(rotate[0]);
    Rx[2][1] = sin(rotate[0]);  Rx[2][2] = cos(rotate[0]);

    Ry[0][0] = cos(rotate[1]);  Ry[0][2] = sin(rotate[1]);
    Ry[2][0] = -sin(rotate[1]); Ry[2][2] = cos(rotate[1]);

    Rz[0][0] = cos(rotate[2]);  Rz[0][1] = -sin(rotate[2]);
    Rz[1][0] = sin(rotate[2]);  Rz[1][1] = cos(rotate[2]);

    S[0][0] = scale[0];  S[1][1] = scale[1];  S[2][2] = scale[2];
  } else if (dow == 2) {
    Rx[0][0] = cos(rotate[0]);  Rx[0][1] = -sin(rotate[0]);
    Rx[1][0] = sin(rotate[0]);  Rx[1][1] = cos(rotate[0]);

    Ry = 1.0;
    Rz = 1.0;

    S[0][0] = scale[0];  S[1][1] = scale[1];
  } else {
    S[0][0] = scale[0];
  }

  T_ = Rz*Ry*Rx*S;

  WorldMatrix<double> T;
  vector_operations::fillMatrix(T,T_);

  FixVec<WorldVector<double>, VERTEX> coords;
  deque<MacroElement*>::iterator macro;

  for(macro = mesh->firstMacroElement(); macro != mesh->endOfMacroElements(); macro++) {
    for (int i = 0; i < mesh->getDim()+1; ++i) {
      WorldVector<double> x = (*macro)->getCoord(i);
      WorldVector<double> x_temp = x;
      x.multMatrixVec(T,x_temp);
      x+= shift;
      (*macro)->setCoord(i, x);
    }
  }
};

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void scaleMesh(Mesh *mesh, WorldVector<double> shift, WorldVector<double> scale)
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{ FUNCNAME("Helpers::scaleMesh()");

  deque<MacroElement*>::iterator macro;
  int dim = Global::getGeo(WORLD);

  for(macro = mesh->firstMacroElement(); macro != mesh->endOfMacroElements(); macro++) {
    for (int i = 0; i < mesh->getDim()+1; ++i) {
      WorldVector<double> x = (*macro)->getCoord(i);
      x *= scale;
      x += shift;
      (*macro)->setCoord(i, x);
    }
  }
};

// scale by different values in all directions
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void scaleMesh(Mesh *mesh, WorldVector<double> scale)
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{ FUNCNAME("Helpers::scaleMesh()");

  WorldVector<double> shift; shift.set(0.0);
  scaleMesh(mesh,shift,scale);
}

// scale by different values in all directions
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void scaleMesh(std::vector<Mesh*> meshes, WorldVector<double> scale)
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{ FUNCNAME("Helpers::scaleMesh()");

  WorldVector<double> shift; shift.set(0.0);
  for (size_t i = 0; i < meshes.size(); i++)
    scaleMesh(meshes[i],shift,scale);
}

// scale and shift by the same values in all directions
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void scaleMesh(Mesh *mesh, double shift, double scale)
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{ FUNCNAME("Helpers::scaleMesh()");

  WorldVector<double> wShift, wScale;
  wShift.set(shift);
  wScale.set(scale);
  scaleMesh(mesh,wShift,wScale);
}

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void read_dof_vector(const std::string file, DOFVector<double> *dofvec, long size)
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{ FUNCNAME("Helpers::read_dof_vector()");

  ifstream in;
  string buf;
  long i;

  in.open(file.c_str());
  if (!in)
    throw(std::runtime_error("ERROR! Could not read value file."));

  DOFIterator<double> dofIter(dofvec, USED_DOFS);

  getline(in, buf);
  while(buf.substr(0,14) != "vertex values:") getline(in, buf);
  for (i = 0, dofIter.reset(); !dofIter.end(); ++i, ++dofIter){
    in >> buf;
    (*dofIter) = atof(buf.c_str());
  }
  in.close();

  if (i != size)
    throw(std::runtime_error("#vertices != dofIter.size()"));
}

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WorldVector<double> getMeshDimension(Mesh *mesh)
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{ FUNCNAME("Helpers::getMeshDimension()");

  WorldVector<double> dimension; dimension.set(-1.e10);

  TraverseStack stack;
  ElInfo *elInfo = stack.traverseFirst(mesh, 0, Mesh::CALL_EL_LEVEL | Mesh::FILL_COORDS);
  while (elInfo) {
    for (int i = 0; i <= mesh->getDim(); i++) {
      WorldVector<double> &coords = elInfo->getMacroElement()->getCoord(i);
      for(int j = 0; j < coords.getSize(); ++j) {
	dimension[j] = std::max(dimension[j], coords[j]);
      }
    }
    elInfo = stack.traverseNext(elInfo);
  }
  return dimension;
}

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void getMeshDimension(Mesh *mesh, WorldVector<double> &min_corner, WorldVector<double> &max_corner)
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{ FUNCNAME("Helpers::getMeshDimension()");

  max_corner.set(-1.e10);
  min_corner.set(1.e10);

  TraverseStack stack;
  ElInfo *elInfo = stack.traverseFirst(mesh, 0, Mesh::CALL_EL_LEVEL | Mesh::FILL_COORDS);
  while (elInfo) {
    for (int i = 0; i <= mesh->getDim(); i++) {
      WorldVector<double> &coords = elInfo->getMacroElement()->getCoord(i);
      for(int j = 0; j < coords.getSize(); ++j) {
	max_corner[j] = std::max(max_corner[j], coords[j]);
	min_corner[j] = std::min(min_corner[j], coords[j]);
      }
    }
    elInfo = stack.traverseNext(elInfo);
  }
}

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void getNormalsWeighted(FiniteElemSpace *feSpace, DOFVector<WorldVector<double> > *normals)
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{
  Mesh *mesh = feSpace->getMesh();
  const BasisFunction *basisFcts = feSpace->getBasisFcts();
  int nBasisFcts = basisFcts->getNumber();
  
  std::vector<DegreeOfFreedom> localIndices(nBasisFcts);
  
  DOFVector<double> numNormals(feSpace, "numNormals");
  numNormals.set(0.0);
    
  WorldVector<double> normal; normal.set(0.0);
  normals->set(normal);
  TraverseStack stack;
  ElInfo *elInfo = 
    stack.traverseFirst(mesh, -1, 
                        Mesh::CALL_LEAF_EL | Mesh::FILL_COORDS);
    
  while (elInfo) {
    elInfo->getElementNormal(normal);
    Element *el = elInfo->getElement();
    double det = elInfo->getDet();
    if (det <= DBL_TOL)
      det = elInfo->calcDet();
    
    basisFcts->getLocalIndices(el, feSpace->getAdmin(), localIndices);
    
    for (int i = 0; i < nBasisFcts; i++) {
      (*normals)[localIndices[i]] += normal*(1.0/det);
    }

    elInfo = stack.traverseNext(elInfo);
  }
    
  DOFIterator<WorldVector<double> > normalsIter(normals, USED_DOFS); normalsIter.reset();
  for (; !normalsIter.end(); normalsIter++)
  {
    *normalsIter *= 1.0/norm(*normalsIter);
  }
}

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void getNormals(FiniteElemSpace *feSpace, DOFVector<WorldVector<double> > *normals, DOFVector<WorldMatrix<double> > *gradNormals)
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{
  using namespace mtl;
  using namespace itl;
  
  Mesh *mesh = feSpace->getMesh();
  const BasisFunction *basisFcts = feSpace->getBasisFcts();
  int nBasisFcts = basisFcts->getNumber();

  std::vector<DegreeOfFreedom> localIndices(nBasisFcts);
  DOFVector<std::set<DegreeOfFreedom> > neighbors(feSpace, "neighbors");

  TraverseStack stack;
  ElInfo *elInfo =
    stack.traverseFirst(mesh, -1,
                        Mesh::CALL_LEAF_EL | Mesh::FILL_COORDS);

  while (elInfo) {
    basisFcts->getLocalIndices(elInfo->getElement(), feSpace->getAdmin(), localIndices);

    for (size_t i = 0; i < nBasisFcts; i++) {
      for (size_t j = 0; j < nBasisFcts; j++) {
	neighbors[localIndices[i]].insert(localIndices[j]);
      }
    }
    elInfo = stack.traverseNext(elInfo);
  }

  DOFVector<WorldVector<double> > coordsDOF(feSpace, "coords");
  mesh->getDofIndexCoords(feSpace, coordsDOF);

  Helpers::getNormalsWeighted(feSpace, normals);
  VtkWriter::writeFile(normals, "normals_weighted.vtu");

//   DOFVector<WorldMatrix<double> > *grdDOF = gradNormals;
//   if (grdDOF == NULL)
//     grdDOF = new DOFVector<WorldMatrix<double> >(feSpace, "grd");

  DOFIterator<WorldVector<double> > normalsIter(normals, USED_DOFS); normalsIter.reset();
  DOFIterator<WorldVector<double> > coordsIter(&coordsDOF, USED_DOFS); coordsIter.reset();
/*  DOFIterator<WorldMatrix<double> > grdIter(grdDOF, USED_DOFS); grdIter.reset();*/
  DOFIterator<std::set<DegreeOfFreedom> > neighborsIter(&neighbors, USED_DOFS); neighborsIter.reset();
  for (; !neighborsIter.end(); neighborsIter++, normalsIter++, coordsIter++/*, grdIter++*/)
  {
    int numPoints = 10; // 6 oder 10
    std::set<DegreeOfFreedom> idx = *neighborsIter;
    std::set<DegreeOfFreedom>::iterator it, it2;

    for (int i = 1; i<3 && idx.size() < numPoints; i++) {
    for (it = idx.begin(); it != idx.end() && idx.size() < numPoints; it++) {
      for (it2 = (neighbors[*it]).begin(); it2 != (neighbors[*it]).end() && idx.size() < numPoints; it2++) {
	idx.insert(*it2);
      }
    }
    }
    TEST_EXIT(idx.size()>=numPoints)("Nicht genügend Stützstellen gefunden!\n");
    size_t i = 0;
    mtl::dense2D<double> A(numPoints,6), B(6,6);
    mtl::dense_vector<double> b(numPoints, 1.0), c(6), y(6, 1.0);

    for (it = idx.begin(); it != idx.end() && i < numPoints; it++, i++) {
      WorldVector<double> x = coordsDOF[*it];
      A[i][0] = sqr(x[0]); A[i][1] = sqr(x[1]); A[i][2] = sqr(x[2]);
      A[i][3] = x[0]*x[1]; A[i][4] = x[0]*x[2]; A[i][5] = x[1]*x[2];
//       if(numPoints>6)
// 	A[i][6] = x[0]; A[i][7] = x[1]; A[i][8] = x[2]; A[i][9] = 1.0;
    }
    c = trans(A)*b;
    B = trans(A)*A;
//     pc::ilu_0<mtl::dense2D<double> > P(B);
//     basic_iteration<double>          iter(c, 100, 1.e-6);

//     Solve Ax == b with left preconditioner P
//     bicgstab(B, y, c, P, iter);

    y = mtl::matrix::lu_solve(B,c);

    WorldVector<double> oldNormal = (*normalsIter);

    (*normalsIter)[0] = 2.0*y[0]*(*coordsIter)[0] + y[3]*(*coordsIter)[1] + y[4]*(*coordsIter)[2]/* + (numPoints==10?y[6]:0.0)*/;
    (*normalsIter)[1] = 2.0*y[1]*(*coordsIter)[1] + y[3]*(*coordsIter)[0] + y[5]*(*coordsIter)[2]/* + (numPoints==10?y[7]:0.0)*/;
    (*normalsIter)[2] = 2.0*y[2]*(*coordsIter)[2] + y[4]*(*coordsIter)[0] + y[5]*(*coordsIter)[1]/* + (numPoints==10?y[8]:0.0)*/;

    double nrm = norm(*normalsIter);
    double diff = norm(oldNormal - *normalsIter);
    double signFactor = 1.0;
    if (diff > nrm)
      signFactor = -1.0;
    *normalsIter *= signFactor/nrm;

//     if(gradNormals != NULL) {
//       WorldMatrix<double> grad;
//       grad[0][0] = 2.0*y[0]; grad[0][1] = y[3]; grad[0][2] = y[4];
//       grad[1][0] = y[3]; grad[1][1] = 2.0*y[1]; grad[1][2] = y[5];
//       grad[2][0] = y[4]; grad[2][1] = y[5]; grad[2][2] = 2.0*y[2];
//       grad *= signFactor;
//       
//       double trace_ = 0.0;
//       for (int i=0;i<3;i++)
// 	trace_ += (grad[i][i]/nrm-sqr((*normalsIter)[i]));
//       std::cout<<"nrm(n)="<<nrm<<std::endl;
//       std::cout<<"trace(grad(n))="<<vector_operations::trace(grad)/nrm<<"="<<trace_<<std::endl;
//       
//       WorldMatrix<double> NN;
//       NN.vecProduct(*normalsIter, *normalsIter);
// 
//       grad -= NN;
//       grad *= 1.0/nrm;
//       
//       *grdIter = grad;
// 
//     }
  }

//   if(gradNormals == NULL)
//     delete grdDOF;
}

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void getCurvature(DOFVector<WorldVector<double> >* normals,DOFVector<double>* curvature)
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{
  int dim = normals->getFeSpace()->getMesh()->getDim();
  int dow = Global::getGeo(WORLD);
  
  WorldVector<DOFVector<double>*> normalsVec;
  WorldVector<DOFVector<WorldVector<double> >*> gradNormals;
  for (int i = 0; i < dow; i++) {
    normalsVec[i] = new DOFVector<double>(normals->getFeSpace(), "n_i");
    gradNormals[i] = new DOFVector<WorldVector<double> >(normals->getFeSpace(), "grad_i");
  }
  transform(normals, &normalsVec);
  for (int i = 0; i < dow; i++)
    normalsVec[i]->getRecoveryGradient(gradNormals[i]);

  DOFIterator<WorldVector<double> > grd0Iter(gradNormals[0], USED_DOFS); grd0Iter.reset();
  DOFIterator<WorldVector<double> > grd1Iter(gradNormals[1], USED_DOFS); grd1Iter.reset();
  DOFIterator<WorldVector<double> > grd2Iter(gradNormals[2], USED_DOFS); grd2Iter.reset();
  DOFIterator<double> hIter(curvature, USED_DOFS); hIter.reset();
  
  for (; !grd0Iter.end(); grd0Iter++,grd1Iter++,grd2Iter++,hIter++)
  {
    *hIter = ((*grd0Iter)[0] + (*grd1Iter)[1] + (*grd2Iter)[2])/static_cast<double>(dim);
  }

  for (int i = 0; i < dow; i++) {
    delete normalsVec[i];
    delete gradNormals[i];
  }
}

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void process_mem_usage(double& vm_usage, double& resident_set)
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{
  using std::ios_base;
  using std::ifstream;
  using std::string;
  
  vm_usage     = 0.0;
  resident_set = 0.0;
  
  // 'file' stat seems to give the most reliable results
  //
  ifstream stat_stream("/proc/self/stat",ios_base::in);
  
  // dummy vars for leading entries in stat that we don't care about
  //
  string pid, comm, state, ppid, pgrp, session, tty_nr;
  string tpgid, flags, minflt, cminflt, majflt, cmajflt;
  string utime, stime, cutime, cstime, priority, nice;
  string O, itrealvalue, starttime;
  
  // the two fields we want
  //
  unsigned long vsize;
  long rss;
  
  stat_stream >> pid >> comm >> state >> ppid >> pgrp >> session >> tty_nr
	      >> tpgid >> flags >> minflt >> cminflt >> majflt >> cmajflt
	      >> utime >> stime >> cutime >> cstime >> priority >> nice
	      >> O >> itrealvalue >> starttime >> vsize >> rss; // don't care about the rest
  
  long page_size_kb = sysconf(_SC_PAGE_SIZE) / 1024; // in case x86-64 is configured to use 2MB pages
  vm_usage     = vsize / 1024.0;
  resident_set = rss * page_size_kb;
}

// plots a vector with ascii-code
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void plot(std::vector<double> &values, int numRows, int numCols, std::string symbol)
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{
  unsigned num=values.size();
  unsigned cols=std::min(numCols,(int)num), rows=std::min(numRows,(int)num);
  unsigned step=(unsigned)floor(num/(double)cols);
  cols=(unsigned)ceil(num/(double)step);

  double maxVal=*max_element(values.begin(),values.end());
  double minVal=*min_element(values.begin(),values.end());
  std::stringstream ssMax; ssMax.setf(std::ios::fixed,std::ios::floatfield); ssMax.precision(2); ssMax<<maxVal;
  std::stringstream ssMin; ssMin.setf(std::ios::fixed,std::ios::floatfield); ssMin.precision(2); ssMin<<minVal;
  unsigned cols0 = std::max(ssMax.str().length(),ssMin.str().length());
  std::stringstream ssNum; ssNum<<num;

  std::string emptyLine(cols+cols0,' ');emptyLine.replace(cols0-1,1,"|");
  std::vector<std::string> lines(rows+1,emptyLine);

  double range=maxVal-minVal;
  
  for(unsigned i=0;i<cols; i+=1) {
    int v=(int)round((rows-1)*(values[i*step]-minVal)/range,0);
    int r=rows-v-1, c=i+cols0;
    
    lines[r].replace(c,1,symbol);
    lines[rows].replace(c,1,"-");
  }

  lines[0].replace(cols0-ssMax.str().length(),ssMax.str().length(),ssMax.str());
  lines[rows-1].replace(cols0-ssMin.str().length(),ssMin.str().length(),ssMin.str());
  lines[rows].replace(cols0-1,2," 0");
  lines[rows].erase(cols+cols0-1,1);
  lines[rows].append(ssNum.str());

  for(unsigned i=0;i<lines.size(); ++i)
    std::cout<<lines[i]<<std::endl;
}
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} // end namespace Helpers