1c4762a1bSJed Brown /* 2c4762a1bSJed Brown Demonstrates using the HDF5 viewer with a DMDA Vec 3c4762a1bSJed Brown - create a global vector containing a gauss profile (exp(-x^2-y^2)) 4c4762a1bSJed Brown - write the global vector in a hdf5 file 5c4762a1bSJed Brown 6c4762a1bSJed Brown The resulting file gauss.h5 can be viewed with Visit (an open source visualization package) 7c4762a1bSJed Brown Or with some versions of MATLAB with data=hdfread('gauss.h5','pressure'); mesh(data); 8c4762a1bSJed Brown 9c4762a1bSJed Brown The file storage of the vector is independent of the number of processes used. 10c4762a1bSJed Brown */ 11c4762a1bSJed Brown 12c4762a1bSJed Brown #include <petscdm.h> 13c4762a1bSJed Brown #include <petscdmda.h> 14c4762a1bSJed Brown #include <petscsys.h> 15c4762a1bSJed Brown #include <petscviewerhdf5.h> 16c4762a1bSJed Brown 17c4762a1bSJed Brown static char help[] = "Test to write HDF5 file from PETSc DMDA Vec.\n\n"; 18c4762a1bSJed Brown 19c4762a1bSJed Brown int main(int argc,char **argv) 20c4762a1bSJed Brown { 21c4762a1bSJed Brown DM da2D; 22c4762a1bSJed Brown PetscInt i,j,ixs, ixm, iys, iym; 23c4762a1bSJed Brown PetscViewer H5viewer; 24c4762a1bSJed Brown PetscScalar xm = -1.0, xp=1.0; 25c4762a1bSJed Brown PetscScalar ym = -1.0, yp=1.0; 26c4762a1bSJed Brown PetscScalar value = 1.0,dx,dy; 27c4762a1bSJed Brown PetscInt Nx = 40, Ny=40; 28c4762a1bSJed Brown Vec gauss,input; 29c4762a1bSJed Brown PetscScalar **gauss_ptr; 30c4762a1bSJed Brown PetscReal norm; 31c4762a1bSJed Brown const char *vecname; 32c4762a1bSJed Brown 33c4762a1bSJed Brown dx=(xp-xm)/(Nx-1); 34c4762a1bSJed Brown dy=(yp-ym)/(Ny-1); 35c4762a1bSJed Brown 36c4762a1bSJed Brown /* Initialize the Petsc context */ 379566063dSJacob Faibussowitsch PetscCall(PetscInitialize(&argc,&argv,(char*)0,help)); 389566063dSJacob Faibussowitsch 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)); 399566063dSJacob Faibussowitsch PetscCall(DMSetFromOptions(da2D)); 409566063dSJacob Faibussowitsch PetscCall(DMSetUp(da2D)); 41c4762a1bSJed Brown 42c4762a1bSJed Brown /* Set the coordinates */ 439566063dSJacob Faibussowitsch PetscCall(DMDASetUniformCoordinates(da2D, 0.0, 1.0, 0.0, 1.0, 0.0, 0.0)); 44c4762a1bSJed Brown 45c4762a1bSJed Brown /* Declare gauss as a DMDA component */ 469566063dSJacob Faibussowitsch PetscCall(DMCreateGlobalVector(da2D,&gauss)); 479566063dSJacob Faibussowitsch PetscCall(PetscObjectSetName((PetscObject) gauss, "pressure")); 48c4762a1bSJed Brown 49c4762a1bSJed Brown /* Initialize vector gauss with a constant value (=1) */ 509566063dSJacob Faibussowitsch PetscCall(VecSet(gauss,value)); 51c4762a1bSJed Brown 52c4762a1bSJed Brown /* Get the coordinates of the corners for each process */ 539566063dSJacob Faibussowitsch PetscCall(DMDAGetCorners(da2D, &ixs, &iys, 0, &ixm, &iym, 0)); 54c4762a1bSJed Brown 55c4762a1bSJed Brown /* Build the gaussian profile (exp(-x^2-y^2)) */ 569566063dSJacob Faibussowitsch PetscCall(DMDAVecGetArray(da2D,gauss,&gauss_ptr)); 57c4762a1bSJed Brown for (j=iys; j<iys+iym; j++) { 58c4762a1bSJed Brown for (i=ixs; i<ixs+ixm; i++) { 59c4762a1bSJed Brown gauss_ptr[j][i]=PetscExpScalar(-(xm+i*dx)*(xm+i*dx)-(ym+j*dy)*(ym+j*dy)); 60c4762a1bSJed Brown } 61c4762a1bSJed Brown } 629566063dSJacob Faibussowitsch PetscCall(DMDAVecRestoreArray(da2D,gauss,&gauss_ptr)); 63c4762a1bSJed Brown 64c4762a1bSJed Brown /* Create the HDF5 viewer */ 659566063dSJacob Faibussowitsch PetscCall(PetscViewerHDF5Open(PETSC_COMM_WORLD,"gauss.h5",FILE_MODE_WRITE,&H5viewer)); 669566063dSJacob Faibussowitsch PetscCall(PetscViewerSetFromOptions(H5viewer)); 67c4762a1bSJed Brown 68c4762a1bSJed Brown /* Write the H5 file */ 699566063dSJacob Faibussowitsch PetscCall(VecView(gauss,H5viewer)); 70c4762a1bSJed Brown 71c4762a1bSJed Brown /* Close the viewer */ 729566063dSJacob Faibussowitsch PetscCall(PetscViewerDestroy(&H5viewer)); 73c4762a1bSJed Brown 749566063dSJacob Faibussowitsch PetscCall(VecDuplicate(gauss,&input)); 759566063dSJacob Faibussowitsch PetscCall(PetscObjectGetName((PetscObject)gauss,&vecname)); 769566063dSJacob Faibussowitsch PetscCall(PetscObjectSetName((PetscObject)input,vecname)); 77c4762a1bSJed Brown 78c4762a1bSJed Brown /* Create the HDF5 viewer for reading */ 799566063dSJacob Faibussowitsch PetscCall(PetscViewerHDF5Open(PETSC_COMM_WORLD,"gauss.h5",FILE_MODE_READ,&H5viewer)); 809566063dSJacob Faibussowitsch PetscCall(PetscViewerSetFromOptions(H5viewer)); 819566063dSJacob Faibussowitsch PetscCall(VecLoad(input,H5viewer)); 829566063dSJacob Faibussowitsch PetscCall(PetscViewerDestroy(&H5viewer)); 83c4762a1bSJed Brown 849566063dSJacob Faibussowitsch PetscCall(VecAXPY(input,-1.0,gauss)); 859566063dSJacob Faibussowitsch PetscCall(VecNorm(input,NORM_2,&norm)); 86*08401ef6SPierre Jolivet PetscCheck(norm <= 1.e-6,PETSC_COMM_WORLD,PETSC_ERR_PLIB,"Vec read in does not match vector written out"); 87c4762a1bSJed Brown 889566063dSJacob Faibussowitsch PetscCall(VecDestroy(&input)); 899566063dSJacob Faibussowitsch PetscCall(VecDestroy(&gauss)); 909566063dSJacob Faibussowitsch PetscCall(DMDestroy(&da2D)); 919566063dSJacob Faibussowitsch PetscCall(PetscFinalize()); 92b122ec5aSJacob Faibussowitsch return 0; 93c4762a1bSJed Brown } 94c4762a1bSJed Brown 95c4762a1bSJed Brown /*TEST 96c4762a1bSJed Brown 97c4762a1bSJed Brown build: 98dfd57a17SPierre Jolivet requires: hdf5 !defined(PETSC_USE_CXXCOMPLEX) 99c4762a1bSJed Brown 100c4762a1bSJed Brown test: 101c4762a1bSJed Brown nsize: 4 102c4762a1bSJed Brown 103c4762a1bSJed Brown test: 104c4762a1bSJed Brown nsize: 4 105c4762a1bSJed Brown suffix: 2 106c4762a1bSJed Brown args: -viewer_hdf5_base_dimension2 107c4762a1bSJed Brown output_file: output/ex10_1.out 108c4762a1bSJed Brown 109c4762a1bSJed Brown test: 110c4762a1bSJed Brown nsize: 4 111c4762a1bSJed Brown suffix: 3 112c4762a1bSJed Brown args: -viewer_hdf5_sp_output 113c4762a1bSJed Brown output_file: output/ex10_1.out 114c4762a1bSJed Brown 115c4762a1bSJed Brown TEST*/ 116