output_vtu_foreach.h

/*
This function writes one XML VTK file per PID process of type unstructured grid
(*.vtu) which can be read using Paraview. File stores scalar and vector fields
defined at the center points. Results are recorded on binary format. If one
writes one *.vtu file per PID process this function may be combined with
output_pvtu() above to read in parallel. Tested in (quad- and oct-)trees using
MPI. Also works with solids (when not using MPI).
*/

struct OutputFieldsVTU {
  scalar * list;
  vector * vlist;
  char * subname;
};

// For periodic boxes, the last cell is not written due to a difference in the
// vertex points. We define a macro for readability
#define shortcut_periodic()     \
  if (Period.x)                 \
    foreach()                   \
      if (x + Delta > X0 + L0)  \
        per_mask[] = 0.;        \
  if (Period.y)                 \
    foreach()                   \
      if (y + Delta > Y0 + L0)  \
        per_mask[] = 0.;        \
  if (Period.z)                 \
    foreach()                   \
      if (z + Delta > Z0 + L0)  \
        per_mask[] = 0.;        \

void output_vtu_pid (struct OutputFieldsVTU p )
{
  char name[80];
  sprintf(name, "%s.vtu", p.subname);
  FILE * fp = fopen(name, "w");

#if defined(_OPENMP)
  int num_omp = omp_get_max_threads();
  omp_set_num_threads(1);
#endif

  // This a diry way to match the number of points and vertices when using
  // periodic conditions since vertex are not defined in that case.
  scalar per_mask[];
  foreach ()
    per_mask[] = 1.;

  shortcut_periodic();

  // We obtain the number of points, cells and a marker used to recover the
  // connectivity.
  vertex scalar marker[];
  long no_points = 0, no_cells=0 ;
  foreach_vertex(serial, noauto){
#if TREE
    marker[] = _k;
#else
# if dimension == 2
    marker[] = (point.i-2)*((1 << point.level) + 1) + (point.j-2);
# else
    marker[] = (point.i-2)*sq((1 << point.level) + 1) + (point.j-2)*((1 << point.level) + 1) + (point.k-2);
# endif
#endif
    no_points++;
  }

  foreach (serial, noauto)
    if (per_mask[])
      no_cells++;

  // We write the light data of the VTU file. Since data is appended at the end
  // of the file, we must specify the starting position of each datablock using
  // a counter.
  long count = 0;
  fputs("<?xml version=\"1.0\"?>\n", fp);
  fputs("<VTKFile type=\"UnstructuredGrid\" version=\"1.0\" byte_order=\"LittleEndian\" header_type=\"UInt64\">\n", fp);
  fputs("\t <UnstructuredGrid>\n", fp);
  fprintf(fp, "\t\t <Piece NumberOfPoints=\"%ld\" NumberOfCells=\"%ld\">\n", no_points, no_cells);
  fputs("\t\t\t <CellData Scalars=\"scalars\">\n", fp);

  for (scalar s in p.list)
  {
    fprintf(fp, "\t\t\t\t <DataArray type=\"Float64\" Name=\"%s\" format=\"appended\" offset=\"%ld\"/>\n", s.name, count);
    count += (no_cells * sizeof(double)) + sizeof(long);
  }

  for (vector v in p.vlist)
  {
    fprintf(fp, "\t\t\t\t <DataArray type=\"Float64\" Name=\"%s\" NumberOfComponents=\"3\"  format=\"appended\" offset=\"%ld\"/>\n", v.x.name, count);
    count += (3 * no_cells * sizeof(double)) + sizeof(long);
  }
  fputs("\t\t\t </CellData>\n", fp);
  fputs("\t\t\t <Points>\n", fp);
  fprintf(fp, "\t\t\t\t <DataArray type=\"Float64\" NumberOfComponents=\"3\"  format=\"appended\" offset=\"%ld\"/>\n", count);
  fputs("\t\t\t </Points>\n", fp);
  fputs("\t\t\t <Cells>\n", fp);
  count += (3 * no_points * sizeof(double)) + sizeof(long);

#if dimension == 2
  char type = 9, noffset = 4;
#elif dimension == 3
  char type = 12, noffset = 8;
#endif
  long offset, connectivity[noffset];

  fprintf(fp, "\t\t\t\t <DataArray type=\"Int64\" Name=\"offsets\" format=\"appended\" offset=\"%ld\"/>\n", count);
  count += (no_cells * sizeof(long)) + sizeof(long);

  fprintf(fp, "\t\t\t\t <DataArray type=\"Int8\" Name=\"types\" format=\"appended\" offset=\"%ld\"/>\n", count);
  count += (no_cells * sizeof(char)) + sizeof(long);

  fprintf(fp, "\t\t\t\t <DataArray type=\"Int64\" Name=\"connectivity\" format=\"appended\" offset=\"%ld\"/>\n", count);
  count += (no_cells * noffset * sizeof(long)) + sizeof(long);

  fputs("\t\t\t </Cells>\n", fp);
  fputs("\t\t </Piece>\n", fp);
  fputs("\t </UnstructuredGrid>\n", fp);
  fputs("\t <AppendedData encoding=\"raw\">\n", fp);
  fputs("_", fp);

  // Finally we write the heavy data, where each block is preceded by the block
  // lenght.
  long block_len=no_cells*sizeof (double);
  for (scalar s in p.list)
  {
    fwrite(&block_len, sizeof(long), 1, fp);
    foreach ()
      if (per_mask[])
        fwrite(&val(s), sizeof(double), 1, fp);
  }

  block_len = no_cells * 3 * sizeof(double);
  for (vector v in p.vlist)
  {
    fwrite(&block_len, sizeof(long), 1, fp);
    foreach (){
      if (per_mask[])
      {
        fwrite(&val(v.x), sizeof(double), 1, fp);
        fwrite(&val(v.y), sizeof(double), 1, fp);
#if dimension == 2
        double vz = 0;
        fwrite(&vz, sizeof(double), 1, fp);
#elif dimension == 3
        fwrite(&val(v.z), sizeof(double), 1, fp);
#endif
      }
    }
  }

  block_len = no_points * 3 * sizeof(double);
  fwrite(&block_len, sizeof(long), 1, fp);
  foreach_vertex() {
    fwrite(&x, sizeof(double), 1, fp);
    fwrite(&y, sizeof(double), 1, fp);
    fwrite(&z, sizeof(double), 1, fp);
  }

  block_len = no_cells * sizeof(long);
  fwrite(&block_len, sizeof(long), 1, fp);
  for (int i = 0; i < no_cells; i++)
  {
    offset = (i + 1) * noffset;
    fwrite(&offset, sizeof(int64_t), 1, fp);
  }

  block_len = no_cells * sizeof(char);
  fwrite(&block_len, sizeof(long), 1, fp);
  for (int i = 0; i < no_cells; i++)
    fwrite(&type, sizeof(char), 1, fp);

  block_len = no_cells * noffset * sizeof(long);
  fwrite(&block_len, sizeof(long), 1, fp);

  foreach (serial, noauto){
    if (per_mask[])
    {
      connectivity[0] = (long)marker[];
      connectivity[1] = (long)marker[1];
      connectivity[2] = (long)marker[1, 1];
      connectivity[3] = (long)marker[0, 1];
#if dimension == 3
      connectivity[4] = (long)marker[0, 0, 1];
      connectivity[5] = (long)marker[1, 0, 1];
      connectivity[6] = (long)marker[1, 1, 1];
      connectivity[7] = (long)marker[0, 1, 1];
#endif
      fwrite(&connectivity, sizeof(long), noffset, fp);
    }
  }
  fputs("\t\n", fp);
  fputs("\t </AppendedData>\n", fp);
  fputs("</VTKFile>\n", fp);
  fflush(fp);
#if defined(_OPENMP)
  omp_set_num_threads(num_omp);
#endif
  fclose (fp);
}

/*
This function writes one XML file which allows to read the *.vtu files generated
by output_vtu() when used in MPI. Tested in (quad- and oct-)trees
using MPI.
*/

@if _MPI
void output_pvtu(struct OutputFieldsVTU p){
  char name[112];
  FILE *fp;
  if (pid() == 0)
  {
    sprintf(name, "%s.pvtu", p.subname);
    fp = fopen(name, "w");
    fputs("<?xml version=\"1.0\"?>\n", fp);
    fputs("<VTKFile type=\"PUnstructuredGrid\" version=\"1.0\" byte_order=\"LittleEndian\" header_type=\"UInt64\">\n", fp);
    fputs("\t <PUnstructuredGrid GhostLevel=\"0\">\n", fp);
    fputs("\t\t\t <PCellData Scalars=\"scalars\">\n", fp);
    for (scalar s in p.list)
    {
      fprintf(fp, "\t\t\t\t <PDataArray type=\"Float64\" Name=\"%s\" format=\"appended\">\n", s.name);
      fputs("\t\t\t\t </PDataArray>\n", fp);
    }
    for (vector v in p.vlist)
    {
      fprintf(fp, "\t\t\t\t <PDataArray type=\"Float64\" NumberOfComponents=\"3\" Name=\"%s\" format=\"appended\">\n", v.x.name);
      fputs("\t\t\t\t </PDataArray>\n", fp);
    }
    fputs("\t\t\t </PCellData>\n", fp);
    fputs("\t\t\t <PPoints>\n", fp);
    fputs("\t\t\t\t <PDataArray type=\"Float64\" NumberOfComponents=\"3\" format=\"appended\">\n", fp);
    fputs("\t\t\t\t </PDataArray>\n", fp);
    fputs("\t\t\t </PPoints>\n", fp);
    for (int i = 0; i < npe(); i++)
      fprintf(fp, "\t\t <Piece Source=\"%s_n%3.3d.vtu\"/> \n", p.subname, i);
    fputs("\t </PUnstructuredGrid>\n", fp);
    fputs("</VTKFile>\n", fp);
    fflush(fp);
    fclose(fp);
  }
  MPI_Barrier(MPI_COMM_WORLD);
  sprintf(name, "%s_n%3.3d", p.subname, pid());
  output_vtu_pid(p.list, p.vlist, name);
}
@endif

trace
void output_vtu (struct OutputFieldsVTU p)
{
  @if _MPI
  output_pvtu (p);
  @else
  output_vtu_pid (p);
  @endif
}

This function writes a slice defined by n={n_x, n_y, n_z} and \alpha using a similar approach to view.h into one XML VTK file per PID process of type unstructured grid (*.vtu) in binary format which can be read using Paraview. Only works for x, y, and/or z planes. Here, _alpha is assumed to intersect a cell face and must be a multiple of L0/1<<MINLEVEL. This also means that scalar and vector fields are written at the corresponding face values.

struct OutputSlicesVTU {
  scalar * list;
  vector * vlist;
  char * subname;
  coord n;
  double _alpha;
};

// We define a macro for readability
#define shortcut_slice(n,_alpha)				                \
  double alpha = (_alpha - n.x*x - n.y*y - n.z*z)/Delta;\
  if (fabs(alpha) > 0.87)                               \
    continue;                                           \

#if dimension > 2
void output_vtu_plane_pid (struct OutputSlicesVTU p){

#if defined(_OPENMP)
  int num_omp = omp_get_max_threads();
  omp_set_num_threads(1);
#endif

  char name[80];
  sprintf(name, "%s.vtu", p.subname);
  FILE * fp = fopen(name, "w");

  // Find the cells in the plane (minus edges if periodic)
  coord n = p.n;
  double _alpha = p._alpha;

  scalar per_mask[];
  foreach(){
    per_mask[] = 0.;
    shortcut_slice(n,_alpha);
    if (alpha > 0.)
      per_mask[] = 1.;
  }
  shortcut_periodic()

  // Count number of points and cells (per domain) and a marker for connectivity
  vertex scalar marker[];
  long no_points = 0, no_cells=0 ;
  foreach_vertex(serial, noauto){
    marker[] = 0.;
    shortcut_slice(n,_alpha);
    marker[] = no_points;
    no_points += 1;
  }
  foreach(serial, noauto)
    if (per_mask[])
      no_cells += 1;

  // Write the light data. Every time we write someting we increase the counter
  // to track where the data array starts. Cells are defined as VTK_QUAD(=9)
  // defined by 4 points.
  long count = 0;
  char type=9, noffset=4;
  fputs ("<?xml version=\"1.0\"?>\n"
  "<VTKFile type=\"UnstructuredGrid\" version=\"1.0\" byte_order=\"LittleEndian\" header_type=\"UInt64\">\n", fp);
  fputs ("\t <UnstructuredGrid>\n", fp);
  fprintf (fp,"\t\t <Piece NumberOfPoints=\"%ld\" NumberOfCells=\"%ld\">\n", no_points, no_cells);
  fputs ("\t\t\t <CellData Scalars=\"scalars\">\n", fp);

  for (scalar s in p.list) {
    fprintf (fp,"\t\t\t\t <DataArray type=\"Float64\" Name=\"%s\" format=\"appended\" offset=\"%ld\"/>\n", s.name, count);
    count += (no_cells * sizeof (double)) + sizeof (long);
  }

  for (vector v in p.vlist) {
    fprintf (fp,"\t\t\t\t <DataArray type=\"Float64\" Name=\"%s\" NumberOfComponents=\"3\"  format=\"appended\" offset=\"%ld\"/>\n", v.x.name, count);
    count += (3 * no_cells * sizeof (double)) + sizeof (long);
  }

  fputs ("\t\t\t </CellData>\n", fp);
  fputs ("\t\t\t <Points>\n", fp);
  fprintf (fp,"\t\t\t\t <DataArray type=\"Float64\" NumberOfComponents=\"3\"  format=\"appended\" offset=\"%ld\"/>\n", count);
  fputs ("\t\t\t </Points>\n", fp);
  fputs ("\t\t\t <Cells>\n", fp);
  count += (3 * no_points * sizeof (double)) + sizeof (long);

  long offset ;
  fprintf (fp,"\t\t\t\t <DataArray type=\"Int64\" Name=\"offsets\" format=\"appended\" offset=\"%ld\"/>\n", count);
  count +=  (no_cells * sizeof (long)) + sizeof (long);

  fprintf (fp,"\t\t\t\t <DataArray type=\"Int8\" Name=\"types\" format=\"appended\" offset=\"%ld\"/>\n", count);
  count +=  (no_cells * sizeof (char)) + sizeof (long);

  fprintf (fp,"\t\t\t\t <DataArray type=\"Int64\" Name=\"connectivity\" format=\"appended\" offset=\"%ld\"/>\n", count);
  count +=  (no_cells * noffset * sizeof (long)) + sizeof (long);

  fputs ("\t\t\t </Cells>\n", fp);
  fputs ("\t\t </Piece>\n", fp);
  fputs ("\t </UnstructuredGrid>\n", fp);
  fputs ("\t <AppendedData encoding=\"raw\">\n", fp);
  fputs ("_", fp);

  // Write the heavy data in the same order. We write the lenght of each block
  // before writing the actual data.
  long block_len=no_cells*sizeof (double);
  for (scalar s in p.list) {
    fwrite (&block_len, sizeof (long), 1, fp);
    foreach(){
      if (per_mask[]){
        double sval;
        if (n.x == 1)
          sval = 0.5*(val(s) + val(s,1,0,0));
        else if (n.y == 1)
          sval = 0.5*(val(s) + val(s,0,1,0));
        else
          sval = 0.5*(val(s) + val(s,0,0,1));
        fwrite (&sval, sizeof (double), 1, fp);
      }
    }
  }
  block_len=no_cells*3*sizeof (double);
  for (vector v in p.vlist) {
    fwrite (&block_len, sizeof (long), 1, fp);
    foreach(){
      if (per_mask[]){
        double xval, yval, zval;
        if (n.x == 1) {
          xval = 0.5*(val(v.x) + val(v.x,1,0,0));
          yval = 0.5*(val(v.y) + val(v.y,1,0,0));
          zval = 0.5*(val(v.z) + val(v.z,1,0,0));
        }
        else if (n.y == 1) {
          xval = 0.5*(val(v.x) + val(v.x,0,1,0));
          yval = 0.5*(val(v.y) + val(v.y,0,1,0));
          zval = 0.5*(val(v.z) + val(v.z,0,1,0));
        }
        else {
          xval = 0.5*(val(v.x) + val(v.x,0,0,1));
          yval = 0.5*(val(v.y) + val(v.y,0,0,1));
          zval = 0.5*(val(v.z) + val(v.z,0,0,1));
        }
        fwrite (&xval, sizeof (double), 1, fp);
        fwrite (&yval, sizeof (double), 1, fp);
        fwrite (&zval, sizeof (double), 1, fp);
      }
    }
  }
  block_len=no_points*3*sizeof (double);
  fwrite (&block_len, sizeof (long), 1, fp);
  foreach_vertex(){
    shortcut_slice(n,_alpha);
    fwrite (&x, sizeof (double), 1, fp);
    fwrite (&y, sizeof (double), 1, fp);
    fwrite (&z, sizeof (double), 1, fp);
  }

  block_len=no_cells*sizeof(long);
  fwrite (&block_len, sizeof (long), 1, fp);
  for (int i = 0; i < no_cells; i++){
    offset = (i+1)*noffset;
    fwrite (&offset, sizeof (int64_t), 1, fp);
  }

  block_len=no_cells*sizeof(char);
  fwrite (&block_len, sizeof (long), 1, fp);
  for (int i = 0; i < no_cells; i++)
    fwrite (&type, sizeof (int8_t), 1, fp);

  block_len=no_cells*noffset*sizeof(long);
  fwrite (&block_len, sizeof (long), 1, fp);
  foreach(){
    long connectivity[noffset];
    if (per_mask[]){
      if (n.x == 1) {
        connectivity[0] = (long)marker[1,0,0];
        connectivity[1] = (long)marker[1,1,0];
        connectivity[2] = (long)marker[1,1,1];
        connectivity[3] = (long)marker[1,0,1];
      }
      else if (n.y == 1) {
        connectivity[0] = (long)marker[0,1,0];
        connectivity[1] = (long)marker[1,1,0];
        connectivity[2] = (long)marker[1,1,1];
        connectivity[3] = (long)marker[0,1,1];
      }
      else {
        connectivity[0] = (long)marker[0,0,1];
        connectivity[1] = (long)marker[1,0,1];
        connectivity[2] = (long)marker[1,1,1];
        connectivity[3] = (long)marker[0,1,1];
      }
      fwrite (&connectivity, sizeof (long), noffset, fp);
    }
  }
  fputs ("\t\n", fp);
  fputs ("\t </AppendedData>\n", fp);
  fputs ("</VTKFile>\n", fp);
  fflush (fp);
#if defined(_OPENMP)
  omp_set_num_threads(num_omp);
#endif
}

@if _MPI
void output_pvtu_plane (struct OutputSlicesVTU p) {
  scalar * list  = p.list;
	vector * vlist = p.vlist;

  char name[99];
  FILE * fp;
  if (pid() == 0) {
    sprintf(name, "%s.pvtu", p.subname);
    fp = fopen(name, "w");

    fputs ("<?xml version=\"1.0\"?>\n"
    "<VTKFile type=\"PUnstructuredGrid\" version=\"1.0\" byte_order=\"LittleEndian\" header_type=\"UInt64\">\n", fp);
    fputs ("\t <PUnstructuredGrid GhostLevel=\"0\">\n", fp);
    fputs ("\t\t\t <PCellData Scalars=\"scalars\">\n", fp);
    for (scalar s in list) {
      fprintf (fp,"\t\t\t\t <PDataArray type=\"Float64\" Name=\"%s\" format=\"appended\">\n", s.name);
      fputs ("\t\t\t\t </PDataArray>\n", fp);
    }
    for (vector v in vlist) {
      fprintf (fp,"\t\t\t\t <PDataArray type=\"Float64\" NumberOfComponents=\"3\" Name=\"%s\" format=\"appended\">\n", v.x.name);
      fputs ("\t\t\t\t </PDataArray>\n", fp);
    }
    fputs ("\t\t\t </PCellData>\n", fp);
    fputs ("\t\t\t <PPoints>\n", fp);
    fputs ("\t\t\t\t <PDataArray type=\"Float64\" NumberOfComponents=\"3\" format=\"appended\">\n", fp);
    fputs ("\t\t\t\t </PDataArray>\n", fp);
    fputs ("\t\t\t </PPoints>\n", fp);

    for (int i = 0; i < npe(); i++)
      fprintf (fp, "<Piece Source=\"%s_n%3.3d.vtu\"/> \n", p.subname, i);

    fputs ("\t </PUnstructuredGrid>\n", fp);
    fputs ("</VTKFile>\n", fp);
    fflush (fp);
    fclose (fp);
  }
  MPI_Barrier(MPI_COMM_WORLD);

  sprintf(name, "%s_n%3.3d", p.subname, pid());
  output_vtu_plane_pid (p.list, p.vlist, name, p.n, p._alpha);
}
@endif

trace
void output_slice_vtu (struct OutputSlicesVTU p)
{
@if _MPI
  output_pvtu_plane (p);
@else
  output_vtu_plane_pid (p);
@endif
}
#endif
#undef shortcut_slice
#undef shortcut_periodic