/*@C
DMPlexCreateGmshFromFile - Create a DMPlex mesh from a Gmsh file
+ comm - The MPI communicator
. filename - Name of the Gmsh file
- interpolate - Create faces and edges in the mesh
Output Parameter:
. dm - The DM object representing the mesh
Level: beginner
.seealso: DMPlexCreateFromFile(), DMPlexCreateGmsh(), DMPlexCreate()
@*/
PetscErrorCode DMPlexCreateGmshFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm)
{
PetscViewer viewer, vheader;
PetscMPIInt rank;
PetscViewerType vtype;
char line[PETSC_MAX_PATH_LEN];
int snum;
PetscBool match;
int fT;
PetscInt fileType;
float version;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = MPI_Comm_rank(comm, &rank);
CHKERRQ(ierr);
/* Determine Gmsh file type (ASCII or binary) from file header */
ierr = PetscViewerCreate(comm, &vheader);
CHKERRQ(ierr);
ierr = PetscViewerSetType(vheader, PETSCVIEWERASCII);
CHKERRQ(ierr);
ierr = PetscViewerFileSetMode(vheader, FILE_MODE_READ);
CHKERRQ(ierr);
ierr = PetscViewerFileSetName(vheader, filename);
CHKERRQ(ierr);
if (!rank) {
/* Read only the first two lines of the Gmsh file */
ierr = PetscViewerRead(vheader, line, 1, NULL, PETSC_STRING);
CHKERRQ(ierr);
ierr = PetscStrncmp(line, "$MeshFormat", PETSC_MAX_PATH_LEN, &match);
CHKERRQ(ierr);
if (!match) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "File is not a valid Gmsh file");
ierr = PetscViewerRead(vheader, line, 2, NULL, PETSC_STRING);
CHKERRQ(ierr);
snum = sscanf(line, "%f %d", &version, &fT);
fileType = (PetscInt) fT;
if (snum != 2) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Unable to parse Gmsh file header: %s", line);
if (version < 2.0) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Gmsh file must be at least version 2.0");
}
ierr = MPI_Bcast(&fileType, 1, MPIU_INT, 0, comm);
CHKERRQ(ierr);
/* Create appropriate viewer and build plex */
if (fileType == 0) vtype = PETSCVIEWERASCII;
else vtype = PETSCVIEWERBINARY;
ierr = PetscViewerCreate(comm, &viewer);
CHKERRQ(ierr);
ierr = PetscViewerSetType(viewer, vtype);
CHKERRQ(ierr);
ierr = PetscViewerFileSetMode(viewer, FILE_MODE_READ);
CHKERRQ(ierr);
ierr = PetscViewerFileSetName(viewer, filename);
CHKERRQ(ierr);
ierr = DMPlexCreateGmsh(comm, viewer, interpolate, dm);
CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);
CHKERRQ(ierr);
ierr = PetscViewerDestroy(&vheader);
CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/**
* output_singular
* ------
* Output the left and right singular vectors.
*/
PetscErrorCode output_singular(char *output_name, const Vec u, const Vec v)
{
PetscFunctionBegin;
PetscErrorCode ierr;
char output_name_prefixed[PETSC_MAX_PATH_LEN];
//const char *prefix = "/out/";
const char *u_extension = ".U";
const char *v_extension = ".V";
//ierr = PetscStrcpy(output_name_prefixed, getenv("FD3D_ROOT")); CHKERRQ(ierr);
//ierr = PetscStrcat(output_name_prefixed, prefix); CHKERRQ(ierr);
//ierr = PetscStrcat(output_name_prefixed, output_name); CHKERRQ(ierr);
ierr = PetscStrcpy(output_name_prefixed, output_name); CHKERRQ(ierr);
char u_file[PETSC_MAX_PATH_LEN];
char v_file[PETSC_MAX_PATH_LEN];
ierr = PetscStrcpy(u_file, output_name_prefixed); CHKERRQ(ierr);
ierr = PetscStrcat(u_file, u_extension); CHKERRQ(ierr);
ierr = PetscStrcpy(v_file, output_name_prefixed); CHKERRQ(ierr);
ierr = PetscStrcat(v_file, v_extension); CHKERRQ(ierr);
PetscViewer viewer;
//viewer = PETSC_VIEWER_STDOUT_WORLD;
//ierr = PetscViewerHDF5Open(PETSC_COMM_WORLD, h_file, FILE_MODE_WRITE, &viewer); CHKERRQ(ierr);
/** Write the left singular vector u. */
ierr = PetscViewerCreate(PETSC_COMM_WORLD, &viewer); CHKERRQ(ierr);
ierr = PetscViewerSetType(viewer, PETSCVIEWERBINARY); CHKERRQ(ierr);
ierr = PetscViewerFileSetMode(viewer, FILE_MODE_WRITE); CHKERRQ(ierr);
ierr = PetscViewerBinarySkipInfo(viewer); CHKERRQ(ierr);
ierr = PetscViewerFileSetName(viewer, u_file); CHKERRQ(ierr);
/*
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD, e_file, FILE_MODE_WRITE, &viewer); CHKERRQ(ierr);
*/
ierr = VecView(u, viewer); CHKERRQ(ierr);
/** Write the right singular vector v. */
ierr = PetscViewerDestroy(&viewer); CHKERRQ(ierr);
ierr = PetscViewerCreate(PETSC_COMM_WORLD, &viewer); CHKERRQ(ierr);
ierr = PetscViewerSetType(viewer, PETSCVIEWERBINARY); CHKERRQ(ierr);
ierr = PetscViewerFileSetMode(viewer, FILE_MODE_WRITE); CHKERRQ(ierr);
ierr = PetscViewerBinarySkipInfo(viewer); CHKERRQ(ierr);
ierr = PetscViewerFileSetName(viewer, v_file); CHKERRQ(ierr);
/*
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD, h_file, FILE_MODE_WRITE, &viewer); CHKERRQ(ierr);
*/
ierr = VecView(v, viewer); CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer); CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode DMSetFromOptions_Mesh(DM dm)
{
PetscBool flg;
PetscErrorCode ierr;
PetscFunctionBegin;
PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
ierr = PetscOptionsHead("DMMesh Options");CHKERRQ(ierr);
/* Handle DMMesh refinement */
/* Handle associated vectors */
/* Handle viewing */
ierr = PetscOptionsBool("-dm_mesh_view_vtk", "Output mesh in VTK format", "DMView", PETSC_FALSE, &flg, PETSC_NULL);CHKERRQ(ierr);
if (flg) {
PetscViewer viewer;
ierr = PetscViewerCreate(((PetscObject) dm)->comm, &viewer);CHKERRQ(ierr);
ierr = PetscViewerSetType(viewer, PETSCVIEWERASCII);CHKERRQ(ierr);
ierr = PetscViewerSetFormat(viewer, PETSC_VIEWER_ASCII_VTK);CHKERRQ(ierr);
ierr = PetscViewerFileSetName(viewer, "mesh.vtk");CHKERRQ(ierr);
ierr = DMView(dm, viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
ierr = PetscOptionsBool("-dm_mesh_view", "Exhaustive mesh description", "DMView", PETSC_FALSE, &flg, PETSC_NULL);CHKERRQ(ierr);
if (flg) {
PetscViewer viewer;
ierr = PetscViewerCreate(((PetscObject) dm)->comm, &viewer);CHKERRQ(ierr);
ierr = PetscViewerSetType(viewer, PETSCVIEWERASCII);CHKERRQ(ierr);
ierr = PetscViewerSetFormat(viewer, PETSC_VIEWER_ASCII_INFO_DETAIL);CHKERRQ(ierr);
ierr = DMView(dm, viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
ierr = PetscOptionsTail();CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int main(int argc, char **argv)
{
PetscErrorCode ierr;
DM dm, rdm;
PetscViewer vwr;
PetscBool flg;
char datafile[PETSC_MAX_PATH_LEN];
MPI_Comm comm;
ierr = PetscInitialize(&argc, &argv, NULL, help);
if (ierr) return ierr;
comm = PETSC_COMM_WORLD;
ierr = PetscViewerCreate(comm, &vwr);CHKERRQ(ierr);
ierr = PetscViewerSetType(vwr, PETSCVIEWERHDF5);CHKERRQ(ierr);
ierr = PetscViewerFileSetMode(vwr, FILE_MODE_READ);CHKERRQ(ierr);
ierr = PetscOptionsGetString(NULL, NULL, "-f", datafile, PETSC_MAX_PATH_LEN, &flg);CHKERRQ(ierr);
if (!flg) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Must provide meshfile");
ierr = PetscViewerFileSetName(vwr, datafile);CHKERRQ(ierr);
ierr = DMCreate(comm, &dm);CHKERRQ(ierr);
ierr = DMSetType(dm, DMPLEX);CHKERRQ(ierr);
ierr = DMLoad(dm, vwr);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&vwr);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)dm, "BaryDM");CHKERRQ(ierr);
ierr = DMViewFromOptions(dm, NULL, "-dm_view");CHKERRQ(ierr);
ierr = DMPlexSetRefinementUniform(dm, PETSC_TRUE);CHKERRQ(ierr);
ierr = DMRefine(dm, comm, &rdm);CHKERRQ(ierr);
ierr = DMDestroy(&dm);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)rdm, "RefinedDM");CHKERRQ(ierr);
ierr = DMViewFromOptions(rdm, NULL, "-refined_dm_view");CHKERRQ(ierr);
ierr = DMDestroy(&rdm);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
PetscErrorCode MyVecLoad(const char fname[],PetscBool skippheader,PetscBool usempiio,Vec x)
{
MPI_Comm comm;
PetscViewer viewer;
PetscBool ismpiio,isskip;
PetscErrorCode ierr;
PetscFunctionBeginUser;
ierr = PetscObjectGetComm((PetscObject)x,&comm);CHKERRQ(ierr);
ierr = PetscViewerCreate(comm,&viewer);CHKERRQ(ierr);
ierr = PetscViewerSetType(viewer,PETSCVIEWERBINARY);CHKERRQ(ierr);
if (skippheader) { ierr = PetscViewerBinarySetSkipHeader(viewer,PETSC_TRUE);CHKERRQ(ierr); }
ierr = PetscViewerFileSetMode(viewer,FILE_MODE_READ);CHKERRQ(ierr);
if (usempiio) { ierr = PetscViewerBinarySetUseMPIIO(viewer,PETSC_TRUE);CHKERRQ(ierr); }
ierr = PetscViewerFileSetName(viewer,fname);CHKERRQ(ierr);
ierr = VecLoad(x,viewer);CHKERRQ(ierr);
ierr = PetscViewerBinaryGetSkipHeader(viewer,&isskip);CHKERRQ(ierr);
if (isskip) { ierr = PetscPrintf(comm,"*** PetscViewer[load] skipping header ***\n");CHKERRQ(ierr); }
ierr = PetscViewerBinaryGetUseMPIIO(viewer,&ismpiio);CHKERRQ(ierr);
if (ismpiio) { ierr = PetscPrintf(comm,"*** PetscViewer[load] using MPI-IO ***\n");CHKERRQ(ierr); }
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode private_PetscViewerCreate_XDMF(MPI_Comm comm,const char filename[],PetscViewer *v)
{
long int *bytes;
PetscContainer container;
PetscViewer viewer;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscViewerCreate(comm,&viewer);CHKERRQ(ierr);
ierr = PetscViewerSetType(viewer,PETSCVIEWERASCII);CHKERRQ(ierr);
ierr = PetscViewerFileSetMode(viewer,FILE_MODE_WRITE);CHKERRQ(ierr);
ierr = PetscViewerFileSetName(viewer,filename);CHKERRQ(ierr);
ierr = PetscMalloc1(1,&bytes);CHKERRQ(ierr);
bytes[0] = 0;
ierr = PetscContainerCreate(comm,&container);CHKERRQ(ierr);
ierr = PetscContainerSetPointer(container,(void*)bytes);CHKERRQ(ierr);
ierr = PetscObjectCompose((PetscObject)viewer,"XDMFViewerContext",(PetscObject)container);CHKERRQ(ierr);
/* write xdmf header */
ierr = PetscViewerASCIIPrintf(viewer,"<?xml version=\"1.0\" encoding=\"utf-8\"?>\n");CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"<Xdmf xmlns:xi=\"http://www.w3.org/2001/XInclude\" Version=\"2.99\">\n");CHKERRQ(ierr);
/* write xdmf domain */
ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"<Domain>\n");CHKERRQ(ierr);
*v = viewer;
PetscFunctionReturn(0);
}
// Write the sub mesh into a HDF5 file.
PetscErrorCode ProbeVolume::writeSubMeshHDF5(const std::string &filePath)
{
PetscErrorCode ierr;
PetscFunctionBeginUser;
// only the first process in the communicator write the sub-mesh into a file
if (commRank == 0)
{
// because only one process is involved in writing the sub-mesh,
// we need to create a temporary viewer
PetscViewer viewer2;
ierr = PetscViewerCreate(PETSC_COMM_SELF, &viewer2); CHKERRQ(ierr);
ierr = PetscViewerSetType(viewer2, PETSCVIEWERHDF5); CHKERRQ(ierr);
ierr = PetscViewerFileSetMode(viewer2, FILE_MODE_WRITE); CHKERRQ(ierr);
ierr = PetscViewerFileSetName(
viewer2, filePath.c_str()); CHKERRQ(ierr);
ierr = PetscViewerHDF5PushGroup(viewer2, "mesh"); CHKERRQ(ierr);
std::vector<std::string> dirs{"x", "y", "z"};
for (unsigned int d = 0; d < coord.size(); ++d)
{
Vec tmp;
ierr = VecCreateSeqWithArray(PETSC_COMM_SELF, 1, nPtsDir[d],
&coord[d][0], &tmp); CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) tmp,
dirs[d].c_str()); CHKERRQ(ierr);
ierr = VecView(tmp, viewer2); CHKERRQ(ierr);
ierr = VecDestroy(&tmp); CHKERRQ(ierr);
}
ierr = PetscViewerDestroy(&viewer2); CHKERRQ(ierr);
}
PetscFunctionReturn(0);
} // ProbeVolume::writeSubMeshHDF5
// Initialize the probe.
PetscErrorCode ProbeVolume::init(const MPI_Comm &comm,
const YAML::Node &node,
const type::Mesh &mesh)
{
PetscErrorCode ierr;
PetscFunctionBeginUser;
ierr = ProbeBase::init(comm, node, mesh); CHKERRQ(ierr);
// store information about the type of PETSc Viewer object to use
std::string vtype_str = node["viewer"].as<std::string>("ascii");
if (vtype_str == "ascii")
viewerType = PETSCVIEWERASCII;
else if (vtype_str == "hdf5")
viewerType = PETSCVIEWERHDF5;
// tolerance to define if a point belong to the sub-volume
atol = node["atol"].as<PetscReal>(1e-6);
// number of the time-steps over which we accumulate the data
// data are added together and we write the time averaged data
n_sum = node["n_sum"].as<PetscInt>(0);
is = PETSC_NULL;
dvec = PETSC_NULL;
// store information about the sub-volume to monitor
box = type::RealVec2D(3, type::RealVec1D(2, 0.0));
for (auto item : node["box"])
{
type::Dir dir = type::str2dir[item.first.as<std::string>()];
box[dir][0] = item.second[0].as<PetscReal>();
box[dir][1] = item.second[1].as<PetscReal>();
}
nPtsDir.resize(3, 1);
startIdxDir.resize(3, 0);
// get information about the location of the sub-mesh
ierr = getSubMeshInfo(mesh, box); CHKERRQ(ierr);
// create gridline coordinates for the sub-mesh
ierr = createSubMesh(mesh); CHKERRQ(ierr);
// write the sub-mesh to file
ierr = writeSubMesh(path); CHKERRQ(ierr);
// create a PETSc Index Set object to easily grab a sub-vector
ierr = createIS(mesh); CHKERRQ(ierr);
// create a PETSc Viewer to output the data
ierr = PetscViewerCreate(comm, &viewer); CHKERRQ(ierr);
ierr = PetscViewerSetType(viewer, viewerType); CHKERRQ(ierr);
// Note: we set the "append" mode as the output file already exists
// (it was created when the sub-mesh was written into it)
ierr = PetscViewerFileSetMode(viewer, FILE_MODE_APPEND); CHKERRQ(ierr);
ierr = PetscViewerFileSetName(viewer, path.c_str()); CHKERRQ(ierr);
PetscFunctionReturn(0);
} // ProbeVolume::init
PetscErrorCode OutputVTK(DM dm, const char *filename, PetscViewer *viewer)
{
PetscErrorCode ierr;
PetscFunctionBeginUser;
ierr = PetscViewerCreate(PetscObjectComm((PetscObject)dm), viewer);CHKERRQ(ierr);
ierr = PetscViewerSetType(*viewer, PETSCVIEWERVTK);CHKERRQ(ierr);
ierr = PetscViewerFileSetName(*viewer, filename);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@C
PetscViewerVTKOpen - Opens a file for VTK output.
Collective on MPI_Comm
Input Parameters:
+ comm - MPI communicator
. name - name of file
- type - type of file
$ FILE_MODE_WRITE - create new file for binary output
$ FILE_MODE_READ - open existing file for binary input (not currently supported)
$ FILE_MODE_APPEND - open existing file for binary output (not currently supported)
Output Parameter:
. vtk - PetscViewer for VTK input/output to use with the specified file
Level: beginner
Note:
This PetscViewer should be destroyed with PetscViewerDestroy().
Concepts: VTK files
Concepts: PetscViewer^creating
.seealso: PetscViewerASCIIOpen(), PetscViewerSetFormat(), PetscViewerDestroy(),
VecView(), MatView(), VecLoad(), MatLoad(),
PetscFileMode, PetscViewer
@*/
PetscErrorCode PetscViewerVTKOpen(MPI_Comm comm,const char name[],PetscFileMode type,PetscViewer *vtk)
{
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscViewerCreate(comm,vtk);CHKERRQ(ierr);
ierr = PetscViewerSetType(*vtk,PETSCVIEWERVTK);CHKERRQ(ierr);
ierr = PetscViewerFileSetMode(*vtk,type);CHKERRQ(ierr);
ierr = PetscViewerFileSetName(*vtk,name);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode OutputBIN(const char *filename, PetscViewer *viewer)
{
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscViewerCreate(PETSC_COMM_WORLD, viewer);CHKERRQ(ierr);
ierr = PetscViewerSetType(*viewer, PETSCVIEWERBINARY);CHKERRQ(ierr);
ierr = PetscViewerFileSetMode(*viewer,FILE_MODE_WRITE);CHKERRQ(ierr);
ierr = PetscViewerFileSetName(*viewer, filename);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@C
PetscViewerHDF5Open - Opens a file for HDF5 input/output.
Collective on MPI_Comm
Input Parameters:
+ comm - MPI communicator
. name - name of file
- type - type of file
$ FILE_MODE_WRITE - create new file for binary output
$ FILE_MODE_READ - open existing file for binary input
$ FILE_MODE_APPEND - open existing file for binary output
Output Parameter:
. hdf5v - PetscViewer for HDF5 input/output to use with the specified file
Level: beginner
Note:
This PetscViewer should be destroyed with PetscViewerDestroy().
Concepts: HDF5 files
Concepts: PetscViewerHDF5^creating
.seealso: PetscViewerASCIIOpen(), PetscViewerSetFormat(), PetscViewerDestroy(),
VecView(), MatView(), VecLoad(), MatLoad(),
PetscFileMode, PetscViewer
@*/
PetscErrorCode PetscViewerHDF5Open(MPI_Comm comm, const char name[], PetscFileMode type, PetscViewer *hdf5v)
{
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscViewerCreate(comm, hdf5v);CHKERRQ(ierr);
ierr = PetscViewerSetType(*hdf5v, PETSCVIEWERHDF5);CHKERRQ(ierr);
ierr = PetscViewerFileSetMode(*hdf5v, type);CHKERRQ(ierr);
ierr = PetscViewerFileSetName(*hdf5v, name);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@C
PetscViewerBinaryOpen - Opens a file for binary input/output.
Collective on MPI_Comm
Input Parameters:
+ comm - MPI communicator
. name - name of file
- type - type of file
$ FILE_MODE_WRITE - create new file for binary output
$ FILE_MODE_READ - open existing file for binary input
$ FILE_MODE_APPEND - open existing file for binary output
Output Parameter:
. binv - PetscViewer for binary input/output to use with the specified file
Options Database Keys:
+ -viewer_binary_skip_info
. -viewer_binary_skip_options
- -viewer_binary_skip_header
Level: beginner
Note:
This PetscViewer should be destroyed with PetscViewerDestroy().
For reading files, the filename may begin with ftp:// or http:// and/or
end with .gz; in this case file is brought over and uncompressed.
For creating files, if the file name ends with .gz it is automatically
compressed when closed.
For writing files it only opens the file on processor 0 in the communicator.
For readable files it opens the file on all nodes that have the file. If
node 0 does not have the file it generates an error even if other nodes
do have the file.
Concepts: binary files
Concepts: PetscViewerBinary^creating
Concepts: gzip
Concepts: accessing remote file
Concepts: remote file
.seealso: PetscViewerASCIIOpen(), PetscViewerSetFormat(), PetscViewerDestroy(),
VecView(), MatView(), VecLoad(), MatLoad(), PetscViewerBinaryGetDescriptor(),
PetscViewerBinaryGetInfoPointer(), PetscFileMode, PetscViewer, PetscViewerBinaryRead()
@*/
PetscErrorCode PetscViewerBinaryOpen(MPI_Comm comm,const char name[],PetscFileMode type,PetscViewer *binv)
{
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscViewerCreate(comm,binv);CHKERRQ(ierr);
ierr = PetscViewerSetType(*binv,PETSCVIEWERBINARY);CHKERRQ(ierr);
ierr = PetscViewerFileSetMode(*binv,type);CHKERRQ(ierr);
ierr = PetscViewerFileSetName(*binv,name);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@C
DMPlexCreateFluentFromFile - Create a DMPlex mesh from a Fluent mesh file
+ comm - The MPI communicator
. filename - Name of the Fluent mesh file
- interpolate - Create faces and edges in the mesh
Output Parameter:
. dm - The DM object representing the mesh
Level: beginner
.seealso: DMPlexCreateFromFile(), DMPlexCreateFluent(), DMPlexCreate()
@*/
PetscErrorCode DMPlexCreateFluentFromFile(MPI_Comm comm, const char filename[], PetscBool interpolate, DM *dm)
{
PetscViewer viewer;
PetscErrorCode ierr;
PetscFunctionBegin;
/* Create file viewer and build plex */
ierr = PetscViewerCreate(comm, &viewer);CHKERRQ(ierr);
ierr = PetscViewerSetType(viewer, PETSCVIEWERASCII);CHKERRQ(ierr);
ierr = PetscViewerFileSetMode(viewer, FILE_MODE_READ);CHKERRQ(ierr);
ierr = PetscViewerFileSetName(viewer, filename);CHKERRQ(ierr);
ierr = DMPlexCreateFluent(comm, viewer, interpolate, dm);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int main(int argc,char **args)
{
PetscViewer viewer;
PetscInt i;
PetscErrorCode ierr;
ierr = PetscInitialize(&argc,&args,(char*)0,help);if (ierr) return ierr;
ierr = PetscViewerCreate(PETSC_COMM_WORLD, &viewer);CHKERRQ(ierr);
ierr = PetscViewerSetType(viewer, PETSCVIEWERASCII);CHKERRQ(ierr);
ierr = PetscViewerFileSetMode(viewer, FILE_MODE_APPEND);CHKERRQ(ierr);
ierr = PetscViewerFileSetName(viewer, "test.txt");CHKERRQ(ierr);
for (i = 0; i < 10; ++i) {
ierr = PetscViewerASCIIPrintf(viewer, "test line %d\n", i);CHKERRQ(ierr);
}
ierr = PetscFinalize();
return ierr;
}
PetscErrorCode TSTrajectorySet_Singlefile(TSTrajectory jac,TS ts,PetscInt stepnum,PetscReal time,Vec X)
{
TSTrajectory_Singlefile *sf = (TSTrajectory_Singlefile*)jac->data;
PetscErrorCode ierr;
const char *filename;
PetscFunctionBeginUser;
if (stepnum == 0) {
ierr = PetscViewerCreate(PETSC_COMM_WORLD, &sf->viewer);CHKERRQ(ierr);
ierr = PetscViewerSetType(sf->viewer, PETSCVIEWERBINARY);CHKERRQ(ierr);
ierr = PetscViewerFileSetMode(sf->viewer,FILE_MODE_WRITE);CHKERRQ(ierr);
ierr = PetscObjectGetName((PetscObject)jac,&filename);CHKERRQ(ierr);
ierr = PetscViewerFileSetName(sf->viewer, filename);CHKERRQ(ierr);
}
ierr = VecView(X,sf->viewer);CHKERRQ(ierr);
ierr = PetscViewerBinaryWrite(sf->viewer,&time,1,PETSC_REAL,PETSC_FALSE);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
EXTERN_C_END
#undef __FUNCT__
#define __FUNCT__ "PetscViewerHDF5Open"
/*@C
PetscViewerHDF5Open - Opens a file for HDF5 input/output.
Collective on MPI_Comm
Input Parameters:
+ comm - MPI communicator
. name - name of file
- type - type of file
$ FILE_MODE_WRITE - create new file for binary output
$ FILE_MODE_READ - open existing file for binary input
$ FILE_MODE_APPEND - open existing file for binary output
Output Parameter:
. hdf5v - PetscViewer for HDF5 input/output to use with the specified file
Level: beginner
Note:
This PetscViewer should be destroyed with PetscViewerDestroy().
Concepts: HDF5 files
Concepts: PetscViewerHDF5^creating
.seealso: PetscViewerASCIIOpen(), PetscViewerSetFormat(), PetscViewerDestroy(),
VecView(), MatView(), VecLoad(), MatLoad(),
PetscFileMode, PetscViewer
@*/
PetscErrorCode PETSC_DLLEXPORT PetscViewerHDF5Open(MPI_Comm comm, const char name[], PetscFileMode type, PetscViewer *hdf5v)
{
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscViewerCreate(comm, hdf5v);CHKERRQ(ierr);
ierr = PetscViewerSetType(*hdf5v, PETSC_VIEWER_HDF5);CHKERRQ(ierr);
ierr = PetscViewerFileSetMode(*hdf5v, type);CHKERRQ(ierr);
ierr = PetscViewerFileSetName(*hdf5v, name);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
EXTERN_C_END
#undef __FUNCT__
#define __FUNCT__ "PetscViewerVTKOpen"
/*@C
PetscViewerVTKOpen - Opens a file for VTK output.
Collective on MPI_Comm
Input Parameters:
+ comm - MPI communicator
. name - name of file
- type - type of file
$ FILE_MODE_WRITE - create new file for binary output
$ FILE_MODE_READ - open existing file for binary input (not currently supported)
$ FILE_MODE_APPEND - open existing file for binary output (not currently supported)
Output Parameter:
. vtk - PetscViewer for VTK input/output to use with the specified file
Level: beginner
Note:
This PetscViewer should be destroyed with PetscViewerDestroy().
Concepts: VTK files
Concepts: PetscViewer^creating
.seealso: PetscViewerASCIIOpen(), PetscViewerSetFormat(), PetscViewerDestroy(),
VecView(), MatView(), VecLoad(), MatLoad(),
PetscFileMode, PetscViewer
@*/
PetscErrorCode PetscViewerVTKOpen(MPI_Comm comm,const char name[],PetscFileMode type,PetscViewer *vtk)
{
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscViewerCreate(comm,vtk);CHKERRQ(ierr);
ierr = PetscViewerSetType(*vtk,PETSCVIEWERVTK);CHKERRQ(ierr);
ierr = PetscViewerFileSetMode(*vtk,type);CHKERRQ(ierr);
ierr = PetscViewerFileSetName(*vtk,name);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
// Initialize the probe.
PetscErrorCode ProbePoint::init(const MPI_Comm &comm,
const YAML::Node &node,
const type::Mesh &mesh)
{
PetscErrorCode ierr;
PetscFunctionBeginUser;
ierr = ProbeBase::init(comm, node, mesh); CHKERRQ(ierr);
// only ASCII output format is supported
viewerType = PETSCVIEWERASCII;
// get location of the point to interpolate
loc = type::RealVec1D(3, 0.0);
for (PetscInt d = 0; d < mesh->dim; ++d)
loc[d] = node["loc"][d].as<PetscReal>();
// is the target point in on the current process sub-domain?
pointOnLocalProc = mesh->isPointOnLocalProc(loc, field);
// create a PETSc Viewer to output the data
// Note: as the target point belongs to only one sub-domain,
// we create a Viewer that involves only one process
ierr = PetscViewerCreate(PETSC_COMM_SELF, &viewer); CHKERRQ(ierr);
ierr = PetscViewerSetType(viewer, viewerType); CHKERRQ(ierr);
ierr = PetscViewerFileSetMode(viewer, FILE_MODE_WRITE); CHKERRQ(ierr);
ierr = PetscViewerFileSetName(viewer, path.c_str()); CHKERRQ(ierr);
if (pointOnLocalProc)
{
// create the interpolation object (2D: bi-linear, 3D: tri-linear)
ierr = createLinInterp(PETSC_COMM_SELF,
loc, mesh, field, interp); CHKERRQ(ierr);
}
// create a local vector that will have ghost-point values
ierr = DMCreateLocalVector(mesh->da[field], &svec); CHKERRQ(ierr);
PetscFunctionReturn(0);
} // ProbePoint::init
// write coordinates of the Lagrangian points into ASCII file
PetscErrorCode SingleBodyPoints::writeBody(const std::string &filepath)
{
PetscErrorCode ierr;
PetscFunctionBeginUser;
PetscViewer viewer;
ierr = PetscViewerCreate(comm, &viewer); CHKERRQ(ierr);
ierr = PetscViewerSetType(viewer, PETSCVIEWERASCII); CHKERRQ(ierr);
ierr = PetscViewerFileSetMode(viewer, FILE_MODE_WRITE); CHKERRQ(ierr);
ierr = PetscViewerFileSetName(viewer, filepath.c_str()); CHKERRQ(ierr);
if (dim == 3)
{
for (PetscInt k = 0; k < nPts; ++k)
{
ierr = PetscViewerASCIIPrintf(
viewer, "%10.8e\t%10.8e\t%10.8e\n",
coords[k][0], coords[k][1], coords[k][2]); CHKERRQ(ierr);
}
}
else if (dim == 2)
{
for (PetscInt k = 0; k < nPts; ++k)
{
ierr = PetscViewerASCIIPrintf(
viewer, "%10.8e\t%10.8e\n",
coords[k][0], coords[k][1]); CHKERRQ(ierr);
}
}
else
SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_FILE_WRITE,
"Function only supports 2D and 3D bodies.\n");
ierr = PetscViewerDestroy(&viewer); CHKERRQ(ierr);
PetscFunctionReturn(0);
} // writeBody
/*@C
PetscViewerASCIIOpen - Opens an ASCII file as a PetscViewer.
Collective on MPI_Comm
Input Parameters:
+ comm - the communicator
- name - the file name
Output Parameter:
. lab - the PetscViewer to use with the specified file
Level: beginner
Notes:
This PetscViewer can be destroyed with PetscViewerDestroy().
The MPI communicator used here must match that used by the object one is viewing. For example if the
Mat was created with a PETSC_COMM_WORLD, then the Viewer must be created with PETSC_COMM_WORLD
As shown below, PetscViewerASCIIOpen() is useful in conjunction with
MatView() and VecView()
.vb
PetscViewerASCIIOpen(PETSC_COMM_WORLD,"mat.output",&viewer);
MatView(matrix,viewer);
.ve
Concepts: PetscViewerASCII^creating
Concepts: printf
Concepts: printing
Concepts: accessing remote file
Concepts: remote file
.seealso: MatView(), VecView(), PetscViewerDestroy(), PetscViewerBinaryOpen(),
PetscViewerASCIIGetPointer(), PetscViewerPushFormat(), PETSC_VIEWER_STDOUT_, PETSC_VIEWER_STDERR_,
PETSC_VIEWER_STDOUT_WORLD, PETSC_VIEWER_STDOUT_SELF,
@*/
PetscErrorCode PetscViewerASCIIOpen(MPI_Comm comm,const char name[],PetscViewer *lab)
{
PetscErrorCode ierr;
PetscViewerLink *vlink,*nv;
PetscBool flg,eq;
size_t len;
PetscFunctionBegin;
ierr = PetscStrlen(name,&len);CHKERRQ(ierr);
if (!len) {
ierr = PetscViewerASCIIGetStdout(comm,lab);CHKERRQ(ierr);
ierr = PetscObjectReference((PetscObject)*lab);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
ierr = PetscSpinlockLock(&PetscViewerASCIISpinLockOpen);CHKERRQ(ierr);
if (Petsc_Viewer_keyval == MPI_KEYVAL_INVALID) {
ierr = MPI_Keyval_create(MPI_NULL_COPY_FN,Petsc_DelViewer,&Petsc_Viewer_keyval,(void*)0);CHKERRQ(ierr);
}
/*
It would be better to move this code to PetscFileSetName() but since it must return a preexiting communicator
we cannot do that, since PetscFileSetName() takes a communicator that already exists.
Plus if the original communicator that created the file has since been close this will not detect the old
communictor and hence will overwrite the old data. It may be better to simply remove all this code
*/
/* make sure communicator is a PETSc communicator */
ierr = PetscCommDuplicate(comm,&comm,NULL);CHKERRQ(ierr);
/* has file already been opened into a viewer */
ierr = MPI_Attr_get(comm,Petsc_Viewer_keyval,(void**)&vlink,(PetscMPIInt*)&flg);CHKERRQ(ierr);
if (flg) {
while (vlink) {
ierr = PetscStrcmp(name,((PetscViewer_ASCII*)(vlink->viewer->data))->filename,&eq);CHKERRQ(ierr);
if (eq) {
ierr = PetscObjectReference((PetscObject)vlink->viewer);CHKERRQ(ierr);
*lab = vlink->viewer;
ierr = PetscCommDestroy(&comm);CHKERRQ(ierr);
ierr = PetscSpinlockUnlock(&PetscViewerASCIISpinLockOpen);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
vlink = vlink->next;
}
}
ierr = PetscViewerCreate(comm,lab);CHKERRQ(ierr);
ierr = PetscViewerSetType(*lab,PETSCVIEWERASCII);CHKERRQ(ierr);
if (name) {
ierr = PetscViewerFileSetName(*lab,name);CHKERRQ(ierr);
}
/* save viewer into communicator if needed later */
ierr = PetscNew(&nv);CHKERRQ(ierr);
nv->viewer = *lab;
if (!flg) {
ierr = MPI_Attr_put(comm,Petsc_Viewer_keyval,nv);CHKERRQ(ierr);
} else {
ierr = MPI_Attr_get(comm,Petsc_Viewer_keyval,(void**)&vlink,(PetscMPIInt*)&flg);CHKERRQ(ierr);
if (vlink) {
while (vlink->next) vlink = vlink->next;
vlink->next = nv;
} else {
ierr = MPI_Attr_put(comm,Petsc_Viewer_keyval,nv);CHKERRQ(ierr);
}
}
ierr = PetscCommDestroy(&comm);CHKERRQ(ierr);
ierr = PetscSpinlockUnlock(&PetscViewerASCIISpinLockOpen);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@C
PetscOptionsGetViewer - Gets a viewer appropriate for the type indicated by the user
Collective on MPI_Comm
Input Parameters:
+ comm - the communicator to own the viewer
. pre - the string to prepend to the name or NULL
- name - the option one is seeking
Output Parameter:
+ viewer - the viewer, pass NULL if not needed
. format - the PetscViewerFormat requested by the user, pass NULL if not needed
- set - PETSC_TRUE if found, else PETSC_FALSE
Level: intermediate
Notes: If no value is provided ascii:stdout is used
$ ascii[:[filename][:[format][:append]]] defaults to stdout - format can be one of ascii_info, ascii_info_detail, or ascii_matlab,
for example ascii::ascii_info prints just the information about the object not all details
unless :append is given filename opens in write mode, overwriting what was already there
$ binary[:[filename][:[format][:append]]] defaults to the file binaryoutput
$ draw[:drawtype] for example, draw:tikz or draw:x
$ socket[:port] defaults to the standard output port
$ saws[:communicatorname] publishes object to the Scientific Application Webserver (SAWs)
Use PetscViewerDestroy() after using the viewer, otherwise a memory leak will occur
.seealso: PetscOptionsGetReal(), PetscOptionsHasName(), PetscOptionsGetString(),
PetscOptionsGetIntArray(), PetscOptionsGetRealArray(), PetscOptionsBool()
PetscOptionsInt(), PetscOptionsString(), PetscOptionsReal(), PetscOptionsBool(),
PetscOptionsName(), PetscOptionsBegin(), PetscOptionsEnd(), PetscOptionsHead(),
PetscOptionsStringArray(),PetscOptionsRealArray(), PetscOptionsScalar(),
PetscOptionsBoolGroupBegin(), PetscOptionsBoolGroup(), PetscOptionsBoolGroupEnd(),
PetscOptionsFList(), PetscOptionsEList()
@*/
PetscErrorCode PetscOptionsGetViewer(MPI_Comm comm,const char pre[],const char name[],PetscViewer *viewer,PetscViewerFormat *format,PetscBool *set)
{
char *value;
PetscErrorCode ierr;
PetscBool flag,hashelp;
PetscFunctionBegin;
PetscValidCharPointer(name,3);
ierr = PetscOptionsHasName(NULL,"-help",&hashelp);CHKERRQ(ierr);
if (hashelp) {
ierr = (*PetscHelpPrintf)(comm," -%s%s ascii[:[filename][:[format][:append]]]: %s (%s)\n",pre ? pre : "",name+1,"Triggers display of a PETSc object to screen or ASCII file","PetscOptionsGetViewer");CHKERRQ(ierr);
ierr = (*PetscHelpPrintf)(comm," -%s%s binary[:[filename][:[format][:append]]]: %s (%s)\n",pre ? pre : "",name+1,"Triggers saving of a PETSc object to a binary file","PetscOptionsGetViewer");CHKERRQ(ierr);
ierr = (*PetscHelpPrintf)(comm," -%s%s draw[:drawtype]: %s (%s)\n",pre ? pre : "",name+1,"Triggers drawing of a PETSc object","PetscOptionsGetViewer");CHKERRQ(ierr);
ierr = (*PetscHelpPrintf)(comm," -%s%s socket[:port]: %s (%s)\n",pre ? pre : "",name+1,"Triggers push of a PETSc object to a Unix socket","PetscOptionsGetViewer");CHKERRQ(ierr);
ierr = (*PetscHelpPrintf)(comm," -%s%s saws[:communicatorname]: %s (%s)\n",pre ? pre : "",name+1,"Triggers publishing of a PETSc object to SAWs","PetscOptionsGetViewer");CHKERRQ(ierr);
}
if (format) *format = PETSC_VIEWER_DEFAULT;
if (set) *set = PETSC_FALSE;
ierr = PetscOptionsFindPair_Private(pre,name,&value,&flag);CHKERRQ(ierr);
if (flag) {
if (set) *set = PETSC_TRUE;
if (!value) {
if (viewer) {
ierr = PetscViewerASCIIGetStdout(comm,viewer);CHKERRQ(ierr);
ierr = PetscObjectReference((PetscObject)*viewer);CHKERRQ(ierr);
}
} else {
char *loc0_vtype,*loc1_fname,*loc2_fmt = NULL,*loc3_fmode = NULL;
PetscInt cnt;
const char *viewers[] = {PETSCVIEWERASCII,PETSCVIEWERBINARY,PETSCVIEWERDRAW,PETSCVIEWERSOCKET,PETSCVIEWERMATLAB,PETSCVIEWERSAWS,PETSCVIEWERVTK,PETSCVIEWERHDF5,0};
ierr = PetscStrallocpy(value,&loc0_vtype);CHKERRQ(ierr);
ierr = PetscStrchr(loc0_vtype,':',&loc1_fname);CHKERRQ(ierr);
if (loc1_fname) {
*loc1_fname++ = 0;
ierr = PetscStrchr(loc1_fname,':',&loc2_fmt);CHKERRQ(ierr);
}
if (loc2_fmt) {
*loc2_fmt++ = 0;
ierr = PetscStrchr(loc2_fmt,':',&loc3_fmode);CHKERRQ(ierr);
}
if (loc3_fmode) *loc3_fmode++ = 0;
ierr = PetscStrendswithwhich(*loc0_vtype ? loc0_vtype : "ascii",viewers,&cnt);CHKERRQ(ierr);
if (cnt > (PetscInt) sizeof(viewers)-1) SETERRQ1(comm,PETSC_ERR_ARG_OUTOFRANGE,"Unknown viewer type: %s",loc0_vtype);
if (viewer) {
if (!loc1_fname) {
switch (cnt) {
case 0:
ierr = PetscViewerASCIIGetStdout(comm,viewer);CHKERRQ(ierr);
break;
case 1:
if (!(*viewer = PETSC_VIEWER_BINARY_(comm))) CHKERRQ(PETSC_ERR_PLIB);
break;
case 2:
if (!(*viewer = PETSC_VIEWER_DRAW_(comm))) CHKERRQ(PETSC_ERR_PLIB);
break;
#if defined(PETSC_USE_SOCKET_VIEWER)
case 3:
if (!(*viewer = PETSC_VIEWER_SOCKET_(comm))) CHKERRQ(PETSC_ERR_PLIB);
break;
#endif
#if defined(PETSC_HAVE_MATLAB_ENGINE)
case 4:
if (!(*viewer = PETSC_VIEWER_MATLAB_(comm))) CHKERRQ(PETSC_ERR_PLIB);
break;
#endif
#if defined(PETSC_HAVE_SAWS)
case 5:
if (!(*viewer = PETSC_VIEWER_SAWS_(comm))) CHKERRQ(PETSC_ERR_PLIB);
break;
#endif
#if defined(PETSC_HAVE_HDF5)
case 7:
if (!(*viewer = PETSC_VIEWER_HDF5_(comm))) CHKERRQ(PETSC_ERR_PLIB);
break;
#endif
default: SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Unsupported viewer %s",loc0_vtype);
}
ierr = PetscObjectReference((PetscObject)*viewer);CHKERRQ(ierr);
} else {
if (loc2_fmt && !*loc1_fname && (cnt == 0)) { /* ASCII format without file name */
ierr = PetscViewerASCIIGetStdout(comm,viewer);CHKERRQ(ierr);
ierr = PetscObjectReference((PetscObject)*viewer);CHKERRQ(ierr);
} else {
PetscFileMode fmode;
ierr = PetscViewerCreate(comm,viewer);CHKERRQ(ierr);
ierr = PetscViewerSetType(*viewer,*loc0_vtype ? loc0_vtype : "ascii");CHKERRQ(ierr);
fmode = FILE_MODE_WRITE;
if (loc3_fmode && *loc3_fmode) { /* Has non-empty file mode ("write" or "append") */
ierr = PetscEnumFind(PetscFileModes,loc3_fmode,(PetscEnum*)&fmode,&flag);CHKERRQ(ierr);
if (!flag) SETERRQ1(comm,PETSC_ERR_ARG_UNKNOWN_TYPE,"Unknown file mode: %s",loc3_fmode);
}
ierr = PetscViewerFileSetMode(*viewer,flag?fmode:FILE_MODE_WRITE);CHKERRQ(ierr);
ierr = PetscViewerFileSetName(*viewer,loc1_fname);CHKERRQ(ierr);
ierr = PetscViewerDrawSetDrawType(*viewer,loc1_fname);CHKERRQ(ierr);
}
}
}
if (viewer) {
ierr = PetscViewerSetUp(*viewer);CHKERRQ(ierr);
}
if (loc2_fmt && *loc2_fmt) {
ierr = PetscEnumFind(PetscViewerFormats,loc2_fmt,(PetscEnum*)format,&flag);CHKERRQ(ierr);
if (!flag) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Unknown viewer format %s",loc2_fmt);CHKERRQ(ierr);
}
ierr = PetscFree(loc0_vtype);CHKERRQ(ierr);
}
}
PetscFunctionReturn(0);
}
PetscErrorCode private_DMSwarmView_XDMF(DM dm,PetscViewer viewer)
{
PetscBool isswarm = PETSC_FALSE;
const char *viewername;
char datafile[PETSC_MAX_PATH_LEN];
PetscViewer fviewer;
PetscInt k,ng,dim;
Vec dvec;
long int *bytes = NULL;
PetscContainer container = NULL;
const char *dmname;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscObjectQuery((PetscObject)viewer,"XDMFViewerContext",(PetscObject*)&container);CHKERRQ(ierr);
if (container) {
ierr = PetscContainerGetPointer(container,(void**)&bytes);CHKERRQ(ierr);
} else SETERRQ(PetscObjectComm((PetscObject)viewer),PETSC_ERR_SUP,"Valid to find attached data XDMFViewerContext");
ierr = PetscObjectTypeCompare((PetscObject)dm,DMSWARM,&isswarm);CHKERRQ(ierr);
if (!isswarm) SETERRQ(PetscObjectComm((PetscObject)viewer),PETSC_ERR_SUP,"Only valid for DMSwarm");
ierr = PetscObjectCompose((PetscObject)viewer,"DMSwarm",(PetscObject)dm);CHKERRQ(ierr);
ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr);
ierr = PetscObjectGetName((PetscObject)dm,&dmname);CHKERRQ(ierr);
if (!dmname) {
ierr = DMGetOptionsPrefix(dm,&dmname);CHKERRQ(ierr);
}
if (!dmname) {
ierr = PetscViewerASCIIPrintf(viewer,"<Grid Name=\"DMSwarm\" GridType=\"Uniform\">\n");CHKERRQ(ierr);
} else {
ierr = PetscViewerASCIIPrintf(viewer,"<Grid Name=\"DMSwarm[%s]\" GridType=\"Uniform\">\n",dmname);CHKERRQ(ierr);
}
/* create a sub-viewer for topology, geometry and all data fields */
/* name is viewer.name + "_swarm_fields.pbin" */
ierr = PetscViewerCreate(PetscObjectComm((PetscObject)viewer),&fviewer);CHKERRQ(ierr);
ierr = PetscViewerSetType(fviewer,PETSCVIEWERBINARY);CHKERRQ(ierr);
ierr = PetscViewerBinarySetSkipHeader(fviewer,PETSC_TRUE);CHKERRQ(ierr);
ierr = PetscViewerBinarySetSkipInfo(fviewer,PETSC_TRUE);CHKERRQ(ierr);
ierr = PetscViewerFileSetMode(fviewer,FILE_MODE_WRITE);CHKERRQ(ierr);
ierr = PetscViewerFileGetName(viewer,&viewername);CHKERRQ(ierr);
ierr = private_CreateDataFileNameXDMF(viewername,datafile);CHKERRQ(ierr);
ierr = PetscViewerFileSetName(fviewer,datafile);CHKERRQ(ierr);
ierr = DMSwarmGetSize(dm,&ng);CHKERRQ(ierr);
/* write topology header */
ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"<Topology Dimensions=\"%D\" TopologyType=\"Mixed\">\n",ng);CHKERRQ(ierr);
ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"<DataItem Format=\"Binary\" Endian=\"Big\" DataType=\"Int\" Dimensions=\"%D\" Seek=\"%D\">\n",ng*3,bytes[0]);CHKERRQ(ierr);
ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"%s\n",datafile);CHKERRQ(ierr);
ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"</DataItem>\n");CHKERRQ(ierr);
ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"</Topology>\n");CHKERRQ(ierr);
ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr);
/* write topology data */
for (k=0; k<ng; k++) {
PetscInt pvertex[3];
pvertex[0] = 1;
pvertex[1] = 1;
pvertex[2] = k;
ierr = PetscViewerBinaryWrite(fviewer,pvertex,3,PETSC_INT,PETSC_FALSE);CHKERRQ(ierr);
}
bytes[0] += sizeof(PetscInt) * ng * 3;
/* write geometry header */
ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr);
ierr = DMGetDimension(dm,&dim);CHKERRQ(ierr);
switch (dim) {
case 1:
SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"No support for 1D");
break;
case 2:
ierr = PetscViewerASCIIPrintf(viewer,"<Geometry Type=\"XY\">\n");CHKERRQ(ierr);
break;
case 3:
ierr = PetscViewerASCIIPrintf(viewer,"<Geometry Type=\"XYZ\">\n");CHKERRQ(ierr);
break;
}
ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"<DataItem Format=\"Binary\" Endian=\"Big\" DataType=\"Float\" Precision=\"8\" Dimensions=\"%D %D\" Seek=\"%D\">\n",ng,dim,bytes[0]);CHKERRQ(ierr);
ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"%s\n",datafile);CHKERRQ(ierr);
ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"</DataItem>\n");CHKERRQ(ierr);
ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"</Geometry>\n");CHKERRQ(ierr);
ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr);
/* write geometry data */
ierr = DMSwarmCreateGlobalVectorFromField(dm,DMSwarmPICField_coor,&dvec);CHKERRQ(ierr);
ierr = VecView(dvec,fviewer);CHKERRQ(ierr);
ierr = DMSwarmDestroyGlobalVectorFromField(dm,DMSwarmPICField_coor,&dvec);CHKERRQ(ierr);
bytes[0] += sizeof(PetscReal) * ng * dim;
ierr = PetscViewerDestroy(&fviewer);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode private_ISView_Swarm_XDMF(IS is,PetscViewer viewer)
{
long int *bytes = NULL;
PetscContainer container = NULL;
const char *viewername;
char datafile[PETSC_MAX_PATH_LEN];
PetscViewer fviewer;
PetscInt N,bs;
const char *vecname;
char fieldname[PETSC_MAX_PATH_LEN];
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscObjectQuery((PetscObject)viewer,"XDMFViewerContext",(PetscObject*)&container);CHKERRQ(ierr);
if (container) {
ierr = PetscContainerGetPointer(container,(void**)&bytes);CHKERRQ(ierr);
} else SETERRQ(PetscObjectComm((PetscObject)viewer),PETSC_ERR_SUP,"Valid to find attached data XDMFViewerContext");
ierr = PetscViewerFileGetName(viewer,&viewername);CHKERRQ(ierr);
ierr = private_CreateDataFileNameXDMF(viewername,datafile);CHKERRQ(ierr);
/* re-open a sub-viewer for all data fields */
/* name is viewer.name + "_swarm_fields.pbin" */
ierr = PetscViewerCreate(PetscObjectComm((PetscObject)viewer),&fviewer);CHKERRQ(ierr);
ierr = PetscViewerSetType(fviewer,PETSCVIEWERBINARY);CHKERRQ(ierr);
ierr = PetscViewerBinarySetSkipHeader(fviewer,PETSC_TRUE);CHKERRQ(ierr);
ierr = PetscViewerBinarySetSkipInfo(fviewer,PETSC_TRUE);CHKERRQ(ierr);
ierr = PetscViewerFileSetMode(fviewer,FILE_MODE_APPEND);CHKERRQ(ierr);
ierr = PetscViewerFileSetName(fviewer,datafile);CHKERRQ(ierr);
ierr = ISGetSize(is,&N);CHKERRQ(ierr);
ierr = ISGetBlockSize(is,&bs);CHKERRQ(ierr);
N = N/bs;
ierr = PetscObjectGetName((PetscObject)is,&vecname);CHKERRQ(ierr);
if (!vecname) {
ierr = PetscSNPrintf(fieldname,PETSC_MAX_PATH_LEN-1,"swarmfield_%D",((PetscObject)is)->tag);CHKERRQ(ierr);
} else {
ierr = PetscSNPrintf(fieldname,PETSC_MAX_PATH_LEN-1,"%s",vecname);CHKERRQ(ierr);
}
/* write data header */
ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"<Attribute Center=\"Node\" Name=\"%s\" Type=\"None\">\n",fieldname);CHKERRQ(ierr);
ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr);
if (bs == 1) {
ierr = PetscViewerASCIIPrintf(viewer,"<DataItem Format=\"Binary\" Endian=\"Big\" DataType=\"Int\" Precision=\"4\" Dimensions=\"%D\" Seek=\"%D\">\n",N,bytes[0]);CHKERRQ(ierr);
} else {
ierr = PetscViewerASCIIPrintf(viewer,"<DataItem Format=\"Binary\" Endian=\"Big\" DataType=\"Int\" Precision=\"4\" Dimensions=\"%D %D\" Seek=\"%D\">\n",N,bs,bytes[0]);CHKERRQ(ierr);
}
ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"%s\n",datafile);CHKERRQ(ierr);
ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"</DataItem>\n");CHKERRQ(ierr);
ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr);
ierr = PetscViewerASCIIPrintf(viewer,"</Attribute>\n");CHKERRQ(ierr);
ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr);
/* write data */
ierr = ISView(is,fviewer);CHKERRQ(ierr);
bytes[0] += sizeof(PetscInt) * N * bs;
ierr = PetscViewerDestroy(&fviewer);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int main(int argc, char **argv)
{
DM dm, dmDist = NULL;
Vec u;
PetscSection section;
PetscViewer viewer;
PetscInt dim = 2, numFields, numBC, i;
PetscInt numComp[3];
PetscInt numDof[12];
PetscInt bcField[1];
IS bcPointIS[1];
PetscBool interpolate = PETSC_TRUE;
PetscErrorCode ierr;
ierr = PetscInitialize(&argc, &argv, NULL,help);if (ierr) return ierr;
ierr = PetscOptionsGetInt(NULL,NULL, "-dim", &dim, NULL);CHKERRQ(ierr);
/* Create a mesh */
ierr = DMPlexCreateBoxMesh(PETSC_COMM_WORLD, dim, PETSC_TRUE, NULL, NULL, NULL, NULL, interpolate, &dm);CHKERRQ(ierr);
/* Distribute mesh over processes */
ierr = DMPlexDistribute(dm, 0, NULL, &dmDist);CHKERRQ(ierr);
if (dmDist) {ierr = DMDestroy(&dm);CHKERRQ(ierr); dm = dmDist;}
/* Create a scalar field u, a vector field v, and a surface vector field w */
numFields = 3;
numComp[0] = 1;
numComp[1] = dim;
numComp[2] = dim-1;
for (i = 0; i < numFields*(dim+1); ++i) numDof[i] = 0;
/* Let u be defined on vertices */
numDof[0*(dim+1)+0] = 1;
/* Let v be defined on cells */
numDof[1*(dim+1)+dim] = dim;
/* Let v be defined on faces */
numDof[2*(dim+1)+dim-1] = dim-1;
/* Setup boundary conditions */
numBC = 1;
/* Prescribe a Dirichlet condition on u on the boundary
Label "marker" is made by the mesh creation routine */
bcField[0] = 0;
ierr = DMGetStratumIS(dm, "marker", 1, &bcPointIS[0]);CHKERRQ(ierr);
/* Create a PetscSection with this data layout */
ierr = DMSetNumFields(dm, numFields);CHKERRQ(ierr);
ierr = DMPlexCreateSection(dm, NULL, numComp, numDof, numBC, bcField, NULL, bcPointIS, NULL, §ion);CHKERRQ(ierr);
ierr = ISDestroy(&bcPointIS[0]);CHKERRQ(ierr);
/* Name the Field variables */
ierr = PetscSectionSetFieldName(section, 0, "u");CHKERRQ(ierr);
ierr = PetscSectionSetFieldName(section, 1, "v");CHKERRQ(ierr);
ierr = PetscSectionSetFieldName(section, 2, "w");CHKERRQ(ierr);
ierr = PetscSectionView(section, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
/* Tell the DM to use this data layout */
ierr = DMSetSection(dm, section);CHKERRQ(ierr);
/* Create a Vec with this layout and view it */
ierr = DMGetGlobalVector(dm, &u);CHKERRQ(ierr);
ierr = PetscViewerCreate(PETSC_COMM_WORLD, &viewer);CHKERRQ(ierr);
ierr = PetscViewerSetType(viewer, PETSCVIEWERVTK);CHKERRQ(ierr);
ierr = PetscViewerPushFormat(viewer, PETSC_VIEWER_ASCII_VTK);CHKERRQ(ierr);
ierr = PetscViewerFileSetName(viewer, "sol.vtk");CHKERRQ(ierr);
ierr = VecView(u, viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = DMRestoreGlobalVector(dm, &u);CHKERRQ(ierr);
/* Cleanup */
ierr = PetscSectionDestroy(§ion);CHKERRQ(ierr);
ierr = DMDestroy(&dm);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
#define petscviewerasciisynchronizedprintf_ PETSCVIEWERASCIISYNCHRONIZEDPRINTF
#define petscviewerasciisynchronizedallow_ PETSCVIEWERASCIISYNCHRONIZEALLOW
#elif !defined(PETSC_HAVE_FORTRAN_UNDERSCORE)
#define petscviewerfilesetname_ petscviewerfilesetname
#define petscviewerasciiprintf_ petscviewerasciiprintf
#define petscviewerasciisynchronizedprintf_ petscviewerasciisynchronizedprintf
#define petscviewerasciisynchronizedallow_ petscviewerasciisynchronizedallow
#endif
PETSC_EXTERN void PETSC_STDCALL petscviewerfilesetname_(PetscViewer *viewer,CHAR name PETSC_MIXED_LEN(len),PetscErrorCode *ierr PETSC_END_LEN(len))
{
char *c1;
PetscViewer v;
PetscPatchDefaultViewers_Fortran(viewer,v);
FIXCHAR(name,len,c1);
*ierr = PetscViewerFileSetName(v,c1);
FREECHAR(name,c1);
}
#undef __FUNCT__
#define __FUNCT__ "PetscFixSlashN"
static PetscErrorCode PetscFixSlashN(const char *in, char **out)
{
PetscErrorCode ierr;
PetscInt i;
size_t len;
PetscFunctionBegin;
ierr = PetscStrallocpy(in,out);CHKERRQ(ierr);
ierr = PetscStrlen(*out,&len);CHKERRQ(ierr);
for (i=0; i<(int)len-1; i++) {
int main(int argc, char **argv)
{
SNES snes; /* nonlinear solver */
DM dm; /* problem definition */
Vec u,r; /* solution, residual vectors */
Mat A,J; /* Jacobian matrix */
MatNullSpace nullSpace; /* May be necessary for pressure */
AppCtx user; /* user-defined work context */
JacActionCtx userJ; /* context for Jacobian MF action */
PetscInt its; /* iterations for convergence */
PetscReal error = 0.0; /* L_2 error in the solution */
PetscInt numComponents = 0, f;
PetscErrorCode ierr;
ierr = PetscInitialize(&argc, &argv, NULL, help);CHKERRQ(ierr);
ierr = ProcessOptions(PETSC_COMM_WORLD, &user);CHKERRQ(ierr);
ierr = SNESCreate(PETSC_COMM_WORLD, &snes);CHKERRQ(ierr);
ierr = CreateMesh(PETSC_COMM_WORLD, &user, &dm);CHKERRQ(ierr);
ierr = SNESSetDM(snes, dm);CHKERRQ(ierr);
ierr = SetupElement(dm, &user);CHKERRQ(ierr);
for (f = 0; f < NUM_FIELDS; ++f) {
PetscInt numComp;
ierr = PetscFEGetNumComponents(user.fe[f], &numComp);CHKERRQ(ierr);
numComponents += numComp;
}
ierr = PetscMalloc(NUM_FIELDS * sizeof(void (*)(const PetscReal[], PetscScalar *)), &user.exactFuncs);CHKERRQ(ierr);
user.fem.bcFuncs = (void (**)(const PetscReal[], PetscScalar *)) user.exactFuncs;
ierr = SetupExactSolution(dm, &user);CHKERRQ(ierr);
ierr = SetupSection(dm, &user);CHKERRQ(ierr);
ierr = DMPlexCreateClosureIndex(dm, NULL);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(dm, &u);CHKERRQ(ierr);
ierr = VecDuplicate(u, &r);CHKERRQ(ierr);
ierr = DMSetMatType(dm,MATAIJ);CHKERRQ(ierr);
ierr = DMCreateMatrix(dm, &J);CHKERRQ(ierr);
if (user.jacobianMF) {
PetscInt M, m, N, n;
ierr = MatGetSize(J, &M, &N);CHKERRQ(ierr);
ierr = MatGetLocalSize(J, &m, &n);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD, &A);CHKERRQ(ierr);
ierr = MatSetSizes(A, m, n, M, N);CHKERRQ(ierr);
ierr = MatSetType(A, MATSHELL);CHKERRQ(ierr);
ierr = MatSetUp(A);CHKERRQ(ierr);
ierr = MatShellSetOperation(A, MATOP_MULT, (void (*)(void))FormJacobianAction);CHKERRQ(ierr);
userJ.dm = dm;
userJ.J = J;
userJ.user = &user;
ierr = DMCreateLocalVector(dm, &userJ.u);CHKERRQ(ierr);
ierr = DMPlexProjectFunctionLocal(dm, user.fe, user.exactFuncs, INSERT_BC_VALUES, userJ.u);CHKERRQ(ierr);
ierr = MatShellSetContext(A, &userJ);CHKERRQ(ierr);
} else {
A = J;
}
ierr = CreatePressureNullSpace(dm, &user, &nullSpace);CHKERRQ(ierr);
ierr = MatSetNullSpace(J, nullSpace);CHKERRQ(ierr);
if (A != J) {
ierr = MatSetNullSpace(A, nullSpace);CHKERRQ(ierr);
}
ierr = DMSNESSetFunctionLocal(dm, (PetscErrorCode (*)(DM,Vec,Vec,void*))DMPlexComputeResidualFEM,&user);CHKERRQ(ierr);
ierr = DMSNESSetJacobianLocal(dm, (PetscErrorCode (*)(DM,Vec,Mat,Mat,MatStructure*,void*))DMPlexComputeJacobianFEM,&user);CHKERRQ(ierr);
ierr = SNESSetJacobian(snes, A, J, NULL, NULL);CHKERRQ(ierr);
ierr = SNESSetFromOptions(snes);CHKERRQ(ierr);
ierr = DMPlexProjectFunction(dm, user.fe, user.exactFuncs, INSERT_ALL_VALUES, u);CHKERRQ(ierr);
if (user.showInitial) {ierr = DMVecViewLocal(dm, u, PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);}
if (user.runType == RUN_FULL) {
ierr = DMPlexProjectFunction(dm, user.fe, user.initialGuess, INSERT_VALUES, u);CHKERRQ(ierr);
if (user.showInitial) {ierr = DMVecViewLocal(dm, u, PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);}
if (user.debug) {
ierr = PetscPrintf(PETSC_COMM_WORLD, "Initial guess\n");CHKERRQ(ierr);
ierr = VecView(u, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
ierr = SNESSolve(snes, NULL, u);CHKERRQ(ierr);
ierr = SNESGetIterationNumber(snes, &its);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "Number of SNES iterations = %D\n", its);CHKERRQ(ierr);
ierr = DMPlexComputeL2Diff(dm, user.fe, user.exactFuncs, u, &error);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: %.3g\n", error);CHKERRQ(ierr);
if (user.showSolution) {
ierr = PetscPrintf(PETSC_COMM_WORLD, "Solution\n");CHKERRQ(ierr);
ierr = VecChop(u, 3.0e-9);CHKERRQ(ierr);
ierr = VecView(u, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
} else {
PetscReal res = 0.0;
/* Check discretization error */
ierr = PetscPrintf(PETSC_COMM_WORLD, "Initial guess\n");CHKERRQ(ierr);
ierr = VecView(u, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = DMPlexComputeL2Diff(dm, user.fe, user.exactFuncs, u, &error);CHKERRQ(ierr);
if (error >= 1.0e-11) {
ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: %g\n", error);CHKERRQ(ierr);
} else {
ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: < 1.0e-11\n", error);CHKERRQ(ierr);
}
/* Check residual */
ierr = SNESComputeFunction(snes, u, r);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "Initial Residual\n");CHKERRQ(ierr);
ierr = VecChop(r, 1.0e-10);CHKERRQ(ierr);
ierr = VecView(r, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = VecNorm(r, NORM_2, &res);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Residual: %g\n", res);CHKERRQ(ierr);
/* Check Jacobian */
{
Vec b;
MatStructure flag;
PetscBool isNull;
ierr = SNESComputeJacobian(snes, u, &A, &A, &flag);CHKERRQ(ierr);
ierr = MatNullSpaceTest(nullSpace, J, &isNull);CHKERRQ(ierr);
if (!isNull) SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_PLIB, "The null space calculated for the system operator is invalid.");
ierr = VecDuplicate(u, &b);CHKERRQ(ierr);
ierr = VecSet(r, 0.0);CHKERRQ(ierr);
ierr = SNESComputeFunction(snes, r, b);CHKERRQ(ierr);
ierr = MatMult(A, u, r);CHKERRQ(ierr);
ierr = VecAXPY(r, 1.0, b);CHKERRQ(ierr);
ierr = VecDestroy(&b);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "Au - b = Au + F(0)\n");CHKERRQ(ierr);
ierr = VecChop(r, 1.0e-10);CHKERRQ(ierr);
ierr = VecView(r, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = VecNorm(r, NORM_2, &res);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "Linear L_2 Residual: %g\n", res);CHKERRQ(ierr);
}
}
if (user.runType == RUN_FULL) {
PetscViewer viewer;
Vec uLocal;
const char *name;
ierr = PetscViewerCreate(PETSC_COMM_WORLD, &viewer);CHKERRQ(ierr);
ierr = PetscViewerSetType(viewer, PETSCVIEWERVTK);CHKERRQ(ierr);
ierr = PetscViewerSetFormat(viewer, PETSC_VIEWER_ASCII_VTK);CHKERRQ(ierr);
ierr = PetscViewerFileSetName(viewer, "ex62_sol.vtk");CHKERRQ(ierr);
ierr = DMGetLocalVector(dm, &uLocal);CHKERRQ(ierr);
ierr = PetscObjectGetName((PetscObject) u, &name);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) uLocal, name);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(dm, u, INSERT_VALUES, uLocal);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(dm, u, INSERT_VALUES, uLocal);CHKERRQ(ierr);
ierr = VecView(uLocal, viewer);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm, &uLocal);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
ierr = PetscFree(user.exactFuncs);CHKERRQ(ierr);
ierr = DestroyElement(&user);CHKERRQ(ierr);
ierr = MatNullSpaceDestroy(&nullSpace);CHKERRQ(ierr);
if (user.jacobianMF) {
ierr = VecDestroy(&userJ.u);CHKERRQ(ierr);
}
if (A != J) {
ierr = MatDestroy(&A);CHKERRQ(ierr);
}
ierr = MatDestroy(&J);CHKERRQ(ierr);
ierr = VecDestroy(&u);CHKERRQ(ierr);
ierr = VecDestroy(&r);CHKERRQ(ierr);
ierr = SNESDestroy(&snes);CHKERRQ(ierr);
ierr = DMDestroy(&dm);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc, char *args[])
{
PFLOTRANMesh data;
Mat Adj; /* The adjacency matrix of the mesh */
PetscInt bs = 3;
PetscScalar values[9],*cc;
PetscMPIInt size;
PetscInt i;
PetscErrorCode ierr;
PetscViewer binaryviewer;
Vec cellCenters;
PetscViewer hdf5viewer;
hid_t file_id, dataset_id, dataspace_id;
herr_t status;
PetscFunctionBegin;
ierr = PetscInitialize(&argc, &args, (char *) 0, help);
ierr = MPI_Comm_size(PETSC_COMM_WORLD, &size);CHKERRQ(ierr);
if (size > 1) SETERRQ(PETSC_ERR_SUP,"This preprocessor runs only on one process");
/* Open Glenn's file */
ierr = PetscViewerCreate(PETSC_COMM_SELF, &hdf5viewer);CHKERRQ(ierr);
ierr = PetscViewerSetType(hdf5viewer, PETSC_VIEWER_HDF5);CHKERRQ(ierr);
ierr = PetscViewerFileSetMode(hdf5viewer, FILE_MODE_READ);CHKERRQ(ierr);
ierr = PetscViewerFileSetName(hdf5viewer, "mesh.h5");CHKERRQ(ierr);
ierr = PetscViewerHDF5GetFileId(hdf5viewer, &file_id);CHKERRQ(ierr);
/* get number of cells and then number of edges */
dataset_id = H5Dopen(file_id, "/Cells/Natural IDs");
dataspace_id = H5Dget_space(dataset_id);
status = H5Sget_simple_extent_dims(dataspace_id, &data.numCells, NULL);if (status < 0) SETERRQ(PETSC_ERR_LIB,"Bad dimension");
status = H5Sclose(dataspace_id);CHKERRQ(status);
status = H5Dclose(dataset_id);CHKERRQ(status);
dataset_id = H5Dopen(file_id, "/Connections/Areas");
dataspace_id = H5Dget_space(dataset_id);
status = H5Sget_simple_extent_dims(dataspace_id, &data.numFaces, NULL);if (status < 0) SETERRQ(PETSC_ERR_LIB,"Bad dimension");
status = H5Sclose(dataspace_id);CHKERRQ(status);
status = H5Dclose(dataset_id);CHKERRQ(status);
ierr = PetscPrintf(PETSC_COMM_SELF, "Number of cells %D Number of faces %D \n",(PetscInt)data.numCells,(PetscInt)data.numFaces);CHKERRQ(ierr);
/* read face data */
ierr = PetscMalloc5(data.numFaces,double,&data.faceAreas,data.numFaces,int,&data.downCells,data.numFaces,double,&data.downX,data.numFaces,double,&data.downY,data.numFaces,double,&data.downZ);CHKERRQ(ierr);
dataset_id = H5Dopen(file_id, "/Connections/Areas");
status = H5Dread(dataset_id, H5T_IEEE_F64LE, H5S_ALL, H5S_ALL, H5P_DEFAULT, data.faceAreas);CHKERRQ(status);
status = H5Dclose(dataset_id);CHKERRQ(status);
dataset_id = H5Dopen(file_id, "/Connections/Downwind Cell IDs");
status = H5Dread(dataset_id, H5T_STD_I32LE, H5S_ALL, H5S_ALL, H5P_DEFAULT, data.downCells);CHKERRQ(status);
status = H5Dclose(dataset_id);CHKERRQ(status);
dataset_id = H5Dopen(file_id, "/Connections/Downwind Distance X");
status = H5Dread(dataset_id, H5T_IEEE_F64LE, H5S_ALL, H5S_ALL, H5P_DEFAULT, data.downX);CHKERRQ(status);
status = H5Dclose(dataset_id);CHKERRQ(status);
dataset_id = H5Dopen(file_id, "/Connections/Downwind Distance Y");
status = H5Dread(dataset_id, H5T_IEEE_F64LE, H5S_ALL, H5S_ALL, H5P_DEFAULT, data.downY);CHKERRQ(status);
status = H5Dclose(dataset_id);CHKERRQ(status);
dataset_id = H5Dopen(file_id, "/Connections/Downwind Distance Z");
status = H5Dread(dataset_id, H5T_IEEE_F64LE, H5S_ALL, H5S_ALL, H5P_DEFAULT, data.downZ);CHKERRQ(status);
status = H5Dclose(dataset_id);CHKERRQ(status);
ierr = PetscMalloc4(data.numFaces,int,&data.upCells,data.numFaces,double,&data.upX,data.numFaces,double,&data.upY,data.numFaces,double,&data.upZ);CHKERRQ(ierr);
dataset_id = H5Dopen(file_id, "/Connections/Upwind Cell IDs");
status = H5Dread(dataset_id, H5T_STD_I32LE, H5S_ALL, H5S_ALL, H5P_DEFAULT, data.upCells);CHKERRQ(status);
status = H5Dclose(dataset_id);CHKERRQ(status);
dataset_id = H5Dopen(file_id, "/Connections/Upwind Distance X");
status = H5Dread(dataset_id, H5T_IEEE_F64LE, H5S_ALL, H5S_ALL, H5P_DEFAULT, data.upX);CHKERRQ(status);
status = H5Dclose(dataset_id);CHKERRQ(status);
dataset_id = H5Dopen(file_id, "/Connections/Upwind Distance Y");
status = H5Dread(dataset_id, H5T_IEEE_F64LE, H5S_ALL, H5S_ALL, H5P_DEFAULT, data.upY);CHKERRQ(status);
status = H5Dclose(dataset_id);CHKERRQ(status);
dataset_id = H5Dopen(file_id, "/Connections/Upwind Distance Z");
status = H5Dread(dataset_id, H5T_IEEE_F64LE, H5S_ALL, H5S_ALL, H5P_DEFAULT, data.upZ);CHKERRQ(status);
status = H5Dclose(dataset_id);CHKERRQ(status);
// Put face data into matrix
ierr = MatCreate(PETSC_COMM_WORLD, &Adj);CHKERRQ(ierr);
ierr = MatSetSizes(Adj, data.numCells*bs, data.numCells*bs, PETSC_DECIDE, PETSC_DECIDE);CHKERRQ(ierr);
ierr = MatSetFromOptions(Adj);CHKERRQ(ierr);
ierr = MatSetType(Adj,MATSEQBAIJ);CHKERRQ(ierr);
ierr = MatSeqBAIJSetPreallocation(Adj, bs, 6,PETSC_NULL);CHKERRQ(ierr);
//ierr = MatSetType(Adj,MATSEQAIJ);CHKERRQ(ierr);
//ierr = MatSeqAIJSetPreallocation(Adj, 6,PETSC_NULL);CHKERRQ(ierr);
for(i = 0; i < data.numFaces; ++i) {
values[0] = data.faceAreas[i];
values[1] = data.downCells[i];
values[2] = data.downX[i];
values[3] = data.downY[i];
values[4] = data.downZ[i];
values[5] = data.upCells[i];
values[6] = data.upX[i];
values[7] = data.upY[i];
values[8] = data.upZ[i];
ierr = MatSetValuesBlocked(Adj, 1, &data.downCells[i], 1, &data.upCells[i], values, INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValuesBlocked(Adj, 1, &data.upCells[i], 1, &data.downCells[i], values, INSERT_VALUES);CHKERRQ(ierr);
//ierr = MatSetValues(Adj, 1, &data.downCells[i], 1, &data.upCells[i], values, INSERT_VALUES);CHKERRQ(ierr);
//ierr = MatSetValues(Adj, 1, &data.upCells[i], 1, &data.downCells[i], values, INSERT_VALUES);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(Adj, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(Adj, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = PetscFree5(data.faceAreas, data.downCells, data.downX, data.downY, data.downZ);CHKERRQ(ierr);
ierr = PetscFree4(data.upCells, data.upX, data.upY, data.upZ);CHKERRQ(ierr);
ierr = PetscViewerBinaryOpen(PETSC_COMM_SELF,"mesh.petsc", FILE_MODE_WRITE,&binaryviewer);CHKERRQ(ierr);
ierr = MatView(Adj, binaryviewer);CHKERRQ(ierr);
ierr = MatDestroy(Adj);CHKERRQ(ierr);
/* read cell information */
ierr = PetscMalloc5(data.numCells,int,&data.cellIds,data.numCells,double,&data.cellVols,data.numCells,double,&data.cellX,data.numCells,double,&data.cellY,data.numCells,double,&data.cellZ);CHKERRQ(ierr);
dataset_id = H5Dopen(file_id, "/Cells/Natural IDs");
status = H5Dread(dataset_id, H5T_STD_I32LE, H5S_ALL, H5S_ALL, H5P_DEFAULT, data.cellIds);CHKERRQ(status);
status = H5Dclose(dataset_id);CHKERRQ(status);
dataset_id = H5Dopen(file_id, "/Cells/Volumes");
status = H5Dread(dataset_id, H5T_IEEE_F64LE, H5S_ALL, H5S_ALL, H5P_DEFAULT, data.cellVols);CHKERRQ(status);
status = H5Dclose(dataset_id);CHKERRQ(status);
dataset_id = H5Dopen(file_id, "/Cells/X-Coordinates");
status = H5Dread(dataset_id, H5T_IEEE_F64LE, H5S_ALL, H5S_ALL, H5P_DEFAULT, data.cellX);CHKERRQ(status);
status = H5Dclose(dataset_id);CHKERRQ(status);
dataset_id = H5Dopen(file_id, "/Cells/Y-Coordinates");
status = H5Dread(dataset_id, H5T_IEEE_F64LE, H5S_ALL, H5S_ALL, H5P_DEFAULT, data.cellY);CHKERRQ(status);
status = H5Dclose(dataset_id);CHKERRQ(status);
dataset_id = H5Dopen(file_id, "/Cells/Z-Coordinates");
status = H5Dread(dataset_id, H5T_IEEE_F64LE, H5S_ALL, H5S_ALL, H5P_DEFAULT, data.cellZ);CHKERRQ(status);
status = H5Dclose(dataset_id);CHKERRQ(status);
ierr = PetscViewerDestroy(hdf5viewer);CHKERRQ(ierr);
/* put cell information into vectors */
ierr = VecCreateSeq(PETSC_COMM_SELF,3*data.numCells,&cellCenters);CHKERRQ(ierr);
ierr = VecSetBlockSize(cellCenters,3);CHKERRQ(ierr);
ierr = VecGetArray(cellCenters,&cc);CHKERRQ(ierr);
for (i=0; i<data.numCells; i++) {
cc[3*i] = data.cellX[i];
cc[3*i+1] = data.cellY[i];
cc[3*i+2] = data.cellZ[i];
}
ierr = VecRestoreArray(cellCenters,&cc);CHKERRQ(ierr);
ierr = VecView(cellCenters,binaryviewer);CHKERRQ(ierr);
ierr = VecGetArray(cellCenters,&cc);CHKERRQ(ierr);
for (i=0; i<data.numCells; i++) {
cc[3*i] = data.cellIds[i];
cc[3*i+1] = data.cellVols[i];
cc[3*i+2] = 0.0;
}
ierr = VecRestoreArray(cellCenters,&cc);CHKERRQ(ierr);
ierr = VecView(cellCenters,binaryviewer);CHKERRQ(ierr);
ierr = PetscFree5(data.cellIds, data.cellVols, data.cellX, data.cellY, data.cellZ);CHKERRQ(ierr);
ierr = VecDestroy(cellCenters);
ierr = PetscViewerDestroy(binaryviewer);CHKERRQ(ierr);
ierr = PetscFinalize();CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int main(int argc, char **argv)
{
SNES snes; /* nonlinear solver */
Vec u,r; /* solution, residual vectors */
Mat A,J; /* Jacobian matrix */
MatNullSpace nullSpace; /* May be necessary for pressure */
AppCtx user; /* user-defined work context */
JacActionCtx userJ; /* context for Jacobian MF action */
PetscInt its; /* iterations for convergence */
PetscReal error = 0.0; /* L_2 error in the solution */
const PetscInt numComponents = NUM_BASIS_COMPONENTS_TOTAL;
PetscErrorCode ierr;
ierr = PetscInitialize(&argc, &argv, NULL, help);CHKERRQ(ierr);
ierr = ProcessOptions(PETSC_COMM_WORLD, &user);CHKERRQ(ierr);
ierr = SNESCreate(PETSC_COMM_WORLD, &snes);CHKERRQ(ierr);
ierr = CreateMesh(PETSC_COMM_WORLD, &user, &user.dm);CHKERRQ(ierr);
ierr = SNESSetDM(snes, user.dm);CHKERRQ(ierr);
ierr = SetupExactSolution(user.dm, &user);CHKERRQ(ierr);
ierr = SetupQuadrature(&user);CHKERRQ(ierr);
ierr = SetupSection(user.dm, &user);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(user.dm, &u);CHKERRQ(ierr);
ierr = VecDuplicate(u, &r);CHKERRQ(ierr);
ierr = DMCreateMatrix(user.dm, MATAIJ, &J);CHKERRQ(ierr);
if (user.jacobianMF) {
PetscInt M, m, N, n;
ierr = MatGetSize(J, &M, &N);CHKERRQ(ierr);
ierr = MatGetLocalSize(J, &m, &n);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD, &A);CHKERRQ(ierr);
ierr = MatSetSizes(A, m, n, M, N);CHKERRQ(ierr);
ierr = MatSetType(A, MATSHELL);CHKERRQ(ierr);
ierr = MatSetUp(A);CHKERRQ(ierr);
ierr = MatShellSetOperation(A, MATOP_MULT, (void (*)(void))FormJacobianAction);CHKERRQ(ierr);
userJ.dm = user.dm;
userJ.J = J;
userJ.user = &user;
ierr = DMCreateLocalVector(user.dm, &userJ.u);CHKERRQ(ierr);
ierr = DMPlexProjectFunctionLocal(user.dm, numComponents, user.exactFuncs, INSERT_BC_VALUES, userJ.u);CHKERRQ(ierr);
ierr = MatShellSetContext(A, &userJ);CHKERRQ(ierr);
} else {
A = J;
}
ierr = CreatePressureNullSpace(user.dm, &user, &nullSpace);CHKERRQ(ierr);
ierr = MatSetNullSpace(J, nullSpace);CHKERRQ(ierr);
if (A != J) {
ierr = MatSetNullSpace(A, nullSpace);CHKERRQ(ierr);
}
ierr = DMSNESSetFunctionLocal(user.dm, (PetscErrorCode (*)(DM,Vec,Vec,void*))DMPlexComputeResidualFEM,&user);CHKERRQ(ierr);
ierr = DMSNESSetJacobianLocal(user.dm, (PetscErrorCode (*)(DM,Vec,Mat,Mat,MatStructure*,void*))DMPlexComputeJacobianFEM,&user);CHKERRQ(ierr);
ierr = SNESSetJacobian(snes, A, J, NULL, NULL);CHKERRQ(ierr);
ierr = SNESSetFromOptions(snes);CHKERRQ(ierr);
ierr = DMPlexProjectFunction(user.dm, numComponents, user.exactFuncs, INSERT_ALL_VALUES, u);CHKERRQ(ierr);
if (user.showInitial) {ierr = DMVecViewLocal(user.dm, u, PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);}
if (user.runType == RUN_FULL) {
PetscScalar (*initialGuess[numComponents])(const PetscReal x[]);
PetscInt c;
for (c = 0; c < numComponents; ++c) initialGuess[c] = zero;
ierr = DMPlexProjectFunction(user.dm, numComponents, initialGuess, INSERT_VALUES, u);CHKERRQ(ierr);
if (user.showInitial) {ierr = DMVecViewLocal(user.dm, u, PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);}
if (user.debug) {
ierr = PetscPrintf(PETSC_COMM_WORLD, "Initial guess\n");CHKERRQ(ierr);
ierr = VecView(u, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
ierr = SNESSolve(snes, NULL, u);CHKERRQ(ierr);
ierr = SNESGetIterationNumber(snes, &its);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "Number of SNES iterations = %D\n", its);CHKERRQ(ierr);
ierr = DMPlexComputeL2Diff(user.dm, user.fem.quad, user.exactFuncs, u, &error);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: %.3g\n", error);CHKERRQ(ierr);
if (user.showSolution) {
ierr = PetscPrintf(PETSC_COMM_WORLD, "Solution\n");CHKERRQ(ierr);
ierr = VecChop(u, 3.0e-9);CHKERRQ(ierr);
ierr = VecView(u, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
} else {
PetscReal res = 0.0;
/* Check discretization error */
ierr = PetscPrintf(PETSC_COMM_WORLD, "Initial guess\n");CHKERRQ(ierr);
ierr = VecView(u, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = DMPlexComputeL2Diff(user.dm, user.fem.quad, user.exactFuncs, u, &error);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: %g\n", error);CHKERRQ(ierr);
/* Check residual */
ierr = SNESComputeFunction(snes, u, r);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "Initial Residual\n");CHKERRQ(ierr);
ierr = VecChop(r, 1.0e-10);CHKERRQ(ierr);
ierr = VecView(r, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = VecNorm(r, NORM_2, &res);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Residual: %g\n", res);CHKERRQ(ierr);
/* Check Jacobian */
{
Vec b;
MatStructure flag;
PetscBool isNull;
ierr = SNESComputeJacobian(snes, u, &A, &A, &flag);CHKERRQ(ierr);
ierr = MatNullSpaceTest(nullSpace, J, &isNull);CHKERRQ(ierr);
if (!isNull) SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_PLIB, "The null space calculated for the system operator is invalid.");
ierr = VecDuplicate(u, &b);CHKERRQ(ierr);
ierr = VecSet(r, 0.0);CHKERRQ(ierr);
ierr = SNESComputeFunction(snes, r, b);CHKERRQ(ierr);
ierr = MatMult(A, u, r);CHKERRQ(ierr);
ierr = VecAXPY(r, 1.0, b);CHKERRQ(ierr);
ierr = VecDestroy(&b);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "Au - b = Au + F(0)\n");CHKERRQ(ierr);
ierr = VecChop(r, 1.0e-10);CHKERRQ(ierr);
ierr = VecView(r, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = VecNorm(r, NORM_2, &res);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "Linear L_2 Residual: %g\n", res);CHKERRQ(ierr);
}
}
if (user.runType == RUN_FULL) {
PetscViewer viewer;
Vec uLocal;
ierr = PetscViewerCreate(PETSC_COMM_WORLD, &viewer);CHKERRQ(ierr);
ierr = PetscViewerSetType(viewer, PETSCVIEWERVTK);CHKERRQ(ierr);
ierr = PetscViewerSetFormat(viewer, PETSC_VIEWER_ASCII_VTK);CHKERRQ(ierr);
ierr = PetscViewerFileSetName(viewer, "ex62_sol.vtk");CHKERRQ(ierr);
ierr = DMGetLocalVector(user.dm, &uLocal);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(user.dm, u, INSERT_VALUES, uLocal);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(user.dm, u, INSERT_VALUES, uLocal);CHKERRQ(ierr);
ierr = PetscObjectReference((PetscObject) user.dm);CHKERRQ(ierr); /* Needed because viewer destroys the DM */
ierr = PetscObjectReference((PetscObject) uLocal);CHKERRQ(ierr); /* Needed because viewer destroys the Vec */
ierr = PetscViewerVTKAddField(viewer, (PetscObject) user.dm, DMPlexVTKWriteAll, PETSC_VTK_POINT_FIELD, (PetscObject) uLocal);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(user.dm, &uLocal);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
ierr = DestroyQuadrature(&user);CHKERRQ(ierr);
ierr = MatNullSpaceDestroy(&nullSpace);CHKERRQ(ierr);
if (user.jacobianMF) {
ierr = VecDestroy(&userJ.u);CHKERRQ(ierr);
}
if (A != J) {
ierr = MatDestroy(&A);CHKERRQ(ierr);
}
ierr = MatDestroy(&J);CHKERRQ(ierr);
ierr = VecDestroy(&u);CHKERRQ(ierr);
ierr = VecDestroy(&r);CHKERRQ(ierr);
ierr = SNESDestroy(&snes);CHKERRQ(ierr);
ierr = DMDestroy(&user.dm);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
/**
* output_mat_and_vec
* ------
* Output the matrices and vectors that can be used in MATLAB to solve various problems.
*/
PetscErrorCode output_mat_and_vec(const Mat A, const Vec b, const Vec right_precond, const Mat CF, const GridInfo gi)
{
PetscFunctionBegin;
PetscErrorCode ierr;
char output_name_prefixed[PETSC_MAX_PATH_LEN];
//const char *prefix = "/out/";
const char *ind_extension = "_ind";
const char *A_extension = "_A";
const char *b_extension = "_b";
const char *precond_extension = "_pR";
const char *CF_extension = "_CF";
//ierr = PetscStrcpy(output_name_prefixed, getenv("FD3D_ROOT")); CHKERRQ(ierr);
//ierr = PetscStrcat(output_name_prefixed, prefix); CHKERRQ(ierr);
//ierr = PetscStrcat(output_name_prefixed, gi.output_name); CHKERRQ(ierr);
ierr = PetscStrcpy(output_name_prefixed, gi.output_name); CHKERRQ(ierr);
char ind_file[PETSC_MAX_PATH_LEN];
char A_file[PETSC_MAX_PATH_LEN];
char b_file[PETSC_MAX_PATH_LEN];
char precond_file[PETSC_MAX_PATH_LEN];
char CF_file[PETSC_MAX_PATH_LEN];
ierr = PetscStrcpy(ind_file, output_name_prefixed); CHKERRQ(ierr);
ierr = PetscStrcat(ind_file, ind_extension); CHKERRQ(ierr);
ierr = PetscStrcpy(A_file, output_name_prefixed); CHKERRQ(ierr);
ierr = PetscStrcat(A_file, A_extension); CHKERRQ(ierr);
ierr = PetscStrcpy(b_file, output_name_prefixed); CHKERRQ(ierr);
ierr = PetscStrcat(b_file, b_extension); CHKERRQ(ierr);
ierr = PetscStrcpy(precond_file, output_name_prefixed); CHKERRQ(ierr);
ierr = PetscStrcat(precond_file, precond_extension); CHKERRQ(ierr);
ierr = PetscStrcpy(CF_file, output_name_prefixed); CHKERRQ(ierr);
ierr = PetscStrcat(CF_file, CF_extension); CHKERRQ(ierr);
PetscViewer viewer;
/** It turns out that VecView() shows the DA vector in natural order. Therefore, even though
indApp is constructed in application order, it is shown in natural order by VecView().
On the other hand, indNat reorder indApp in natural order and then distribute the vector to
processors. However, because VecView() reorder a vector before it prints out the content of
the vector, indNat is shown messy by VecView().
Inconsistently, MatView() does not reorder the matrix elements into natural order before it
shows the matrix. Therefore, when the binaries of matrices and vectors are imported in MATLAB,
I need to reorder the matrices but not the vectors. */
Vec indApp;
//ierr = create_index(&indApp, gi); CHKERRQ(ierr);
ierr = createFieldArray(&indApp, set_index_at, gi); CHKERRQ(ierr);
//ierr = VecView(indApp, PETSC_VIEWER_STDOUT_WORLD); CHKERRQ(ierr);
Vec indNat;
ierr = DMDACreateNaturalVector(gi.da, &indNat); CHKERRQ(ierr);
ierr = VecCopy(indApp, indNat); CHKERRQ(ierr);
ierr = VecDestroy(&indApp); CHKERRQ(ierr);
//ierr = VecView(indNat, PETSC_VIEWER_STDOUT_WORLD); CHKERRQ(ierr);
/** Write the index vector ind_app. */
ierr = PetscViewerCreate(PETSC_COMM_WORLD, &viewer); CHKERRQ(ierr);
ierr = PetscViewerSetType(viewer, PETSCVIEWERBINARY); CHKERRQ(ierr);
ierr = PetscViewerFileSetMode(viewer, FILE_MODE_WRITE); CHKERRQ(ierr);
ierr = PetscViewerFileSetName(viewer, ind_file); CHKERRQ(ierr);
ierr = VecView(indNat, viewer); CHKERRQ(ierr);
ierr = VecDestroy(&indNat); CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer); CHKERRQ(ierr);
/** Write the coefficient matrix A. */
ierr = PetscViewerCreate(PETSC_COMM_WORLD, &viewer); CHKERRQ(ierr);
ierr = PetscViewerSetType(viewer, PETSCVIEWERBINARY); CHKERRQ(ierr);
ierr = PetscViewerFileSetMode(viewer, FILE_MODE_WRITE); CHKERRQ(ierr);
ierr = PetscViewerFileSetName(viewer, A_file); CHKERRQ(ierr);
ierr = MatView(A, viewer); CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer); CHKERRQ(ierr);
/** Write the RHS vector b. */
ierr = PetscViewerCreate(PETSC_COMM_WORLD, &viewer); CHKERRQ(ierr);
ierr = PetscViewerSetType(viewer, PETSCVIEWERBINARY); CHKERRQ(ierr);
ierr = PetscViewerFileSetMode(viewer, FILE_MODE_WRITE); CHKERRQ(ierr);
ierr = PetscViewerFileSetName(viewer, b_file); CHKERRQ(ierr);
ierr = VecView(b, viewer); CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer); CHKERRQ(ierr);
/** Write the right preconditioner vector pR. */
ierr = PetscViewerCreate(PETSC_COMM_WORLD, &viewer); CHKERRQ(ierr);
ierr = PetscViewerSetType(viewer, PETSCVIEWERBINARY); CHKERRQ(ierr);
ierr = PetscViewerFileSetMode(viewer, FILE_MODE_WRITE); CHKERRQ(ierr);
ierr = PetscViewerFileSetName(viewer, precond_file); CHKERRQ(ierr);
ierr = VecView(right_precond, viewer); CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer); CHKERRQ(ierr);
/** Write the E-to-H converter matrix CF. */
ierr = PetscViewerCreate(PETSC_COMM_WORLD, &viewer); CHKERRQ(ierr);
ierr = PetscViewerSetType(viewer, PETSCVIEWERBINARY); CHKERRQ(ierr);
ierr = PetscViewerFileSetMode(viewer, FILE_MODE_WRITE); CHKERRQ(ierr);
ierr = PetscViewerFileSetName(viewer, CF_file); CHKERRQ(ierr);
ierr = MatView(CF, viewer); CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer); CHKERRQ(ierr);
PetscFunctionReturn(0);
}
