xref: /petsc/src/dm/tutorials/ex10.c (revision 609caa7c8c030312b00807b4f015fd827bb80932)

/*
   Demonstrates using the HDF5 viewer with a DMDA Vec
 - create a global vector containing a gauss profile (exp(-x^2-y^2))
 - write the global vector in a hdf5 file

   The resulting file gauss.h5 can be viewed with Visit (an open-source visualization package)
   Or with some versions of MATLAB with data=hdfread('gauss.h5','pressure'); mesh(data);

   The file storage of the vector is independent of the number of processes used.
 */

#include <petscdm.h>
#include <petscdmda.h>
#include <petscsys.h>
#include <petscviewerhdf5.h>

static char help[] = "Test to write HDF5 file from PETSc DMDA Vec.\n\n";

int main(int argc, char **argv)
{
  DM            da2D;
  PetscInt      i, j, ixs, ixm, iys, iym;
  PetscViewer   H5viewer;
  PetscScalar   xm = -1.0, xp = 1.0;
  PetscScalar   ym = -1.0, yp = 1.0;
  PetscScalar   value = 1.0, dx, dy;
  PetscInt      Nx = 40, Ny = 40;
  Vec           gauss, input;
  PetscScalar **gauss_ptr;
  PetscReal     norm;
  const char   *vecname;

  dx = (xp - xm) / (Nx - 1);
  dy = (yp - ym) / (Ny - 1);

  /* Initialize the PETSc context */
  PetscFunctionBeginUser;
  PetscCall(PetscInitialize(&argc, &argv, NULL, help));
  PetscCall(DMDACreate2d(PETSC_COMM_WORLD, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DMDA_STENCIL_STAR, Nx, Ny, PETSC_DECIDE, PETSC_DECIDE, 1, 1, NULL, NULL, &da2D));
  PetscCall(DMSetFromOptions(da2D));
  PetscCall(DMSetUp(da2D));

  /* Set the coordinates */
  PetscCall(DMDASetUniformCoordinates(da2D, 0.0, 1.0, 0.0, 1.0, 0.0, 0.0));

  /* Declare gauss as a DMDA component */
  PetscCall(DMCreateGlobalVector(da2D, &gauss));
  PetscCall(PetscObjectSetName((PetscObject)gauss, "pressure"));

  /* Initialize vector gauss with a constant value (=1) */
  PetscCall(VecSet(gauss, value));

  /* Get the coordinates of the corners for each process */
  PetscCall(DMDAGetCorners(da2D, &ixs, &iys, 0, &ixm, &iym, 0));

  /* Build the gaussian profile (exp(-x^2-y^2)) */
  PetscCall(DMDAVecGetArray(da2D, gauss, &gauss_ptr));
  for (j = iys; j < iys + iym; j++) {
    for (i = ixs; i < ixs + ixm; i++) gauss_ptr[j][i] = PetscExpScalar(-(xm + i * dx) * (xm + i * dx) - (ym + j * dy) * (ym + j * dy));
  }
  PetscCall(DMDAVecRestoreArray(da2D, gauss, &gauss_ptr));

  /* Create the HDF5 viewer */
  PetscCall(PetscViewerHDF5Open(PETSC_COMM_WORLD, "gauss.h5", FILE_MODE_WRITE, &H5viewer));
  PetscCall(PetscViewerSetFromOptions(H5viewer));

  /* Write the H5 file */
  PetscCall(VecView(gauss, H5viewer));

  /* Close the viewer */
  PetscCall(PetscViewerDestroy(&H5viewer));

  PetscCall(VecDuplicate(gauss, &input));
  PetscCall(PetscObjectGetName((PetscObject)gauss, &vecname));
  PetscCall(PetscObjectSetName((PetscObject)input, vecname));

  /* Create the HDF5 viewer for reading */
  PetscCall(PetscViewerHDF5Open(PETSC_COMM_WORLD, "gauss.h5", FILE_MODE_READ, &H5viewer));
  PetscCall(PetscViewerSetFromOptions(H5viewer));
  PetscCall(VecLoad(input, H5viewer));
  PetscCall(PetscViewerDestroy(&H5viewer));

  PetscCall(VecAXPY(input, -1.0, gauss));
  PetscCall(VecNorm(input, NORM_2, &norm));
  PetscCheck(norm <= 1.e-6, PETSC_COMM_WORLD, PETSC_ERR_PLIB, "Vec read in does not match vector written out");

  PetscCall(VecDestroy(&input));
  PetscCall(VecDestroy(&gauss));
  PetscCall(DMDestroy(&da2D));
  PetscCall(PetscFinalize());
  return 0;
}

/*TEST

      build:
         requires: hdf5 !defined(PETSC_USE_CXXCOMPLEX)

      test:
         nsize: 4
         output_file: output/empty.out

      test:
         nsize: 4
         suffix: 2
         args: -viewer_hdf5_base_dimension2
         output_file: output/empty.out

      test:
         nsize: 4
         suffix: 3
         args: -viewer_hdf5_sp_output
         output_file: output/empty.out

TEST*/