/* IJacobian - Compute IJacobian = dF/dU + a dF/dUdot */
PetscErrorCode FormIJacobian(TS ts, PetscReal t, Vec U, Vec Udot, PetscReal a, Mat J, Mat Jpre, void *ctx)
{
User user = (User) ctx;
DM dm, cdm;
DMDALocalInfo info;
Vec C;
Field *u, *udot;
PetscScalar *x;
PetscInt i;
PetscErrorCode ierr;
PetscFunctionBeginUser;
ierr = TSGetDM(ts, &dm);CHKERRQ(ierr);
ierr = DMDAGetLocalInfo(dm, &info);CHKERRQ(ierr);
ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr);
ierr = DMGetCoordinatesLocal(dm, &C);CHKERRQ(ierr);
ierr = DMDAVecGetArrayRead(dm, U, &u);CHKERRQ(ierr);
ierr = DMDAVecGetArrayRead(dm, Udot, &udot);CHKERRQ(ierr);
ierr = DMDAVecGetArrayRead(cdm, C, &x);CHKERRQ(ierr);
for (i = info.xs; i < info.xs+info.xm; ++i) {
if (i == 0) {
const PetscScalar hx = x[i+1] - x[i];
const PetscInt row = i, col[] = {i,i+1};
const PetscScalar dxx0 = PetscSqr(user->c)/hx,dxxR = -PetscSqr(user->c)/hx;
const PetscScalar vals[3][2][3] = {{{a*hx, 0,0},{0,0, 0}},
{{0,a*hx+dxx0,0},{0,dxxR,0}},
{{0,0, a*hx},{0,0, 0}}};
ierr = MatSetValuesBlocked(Jpre, 1, &row, 2, col, &vals[0][0][0], INSERT_VALUES);CHKERRQ(ierr);
} else if (i == info.mx-1) {
const PetscScalar hx = x[i+1] - x[i];
const PetscInt row = i, col[] = {i-1,i};
const PetscScalar dxxL = -PetscSqr(user->c)/hx, dxx0 = PetscSqr(user->c)/hx;
const PetscScalar vals[3][2][3] = {{{0,0, 0},{a*hx, 0,0}},
{{0,dxxL,0},{0,a*hx+dxx0,0}},
{{0,0, 0},{0,0, a*hx}}};
ierr = MatSetValuesBlocked(Jpre, 1, &row, 2, col, &vals[0][0][0], INSERT_VALUES);CHKERRQ(ierr);
} else {
const PetscScalar hx = x[i+1] - x[i];
const PetscInt row = i, col[] = {i-1,i,i+1};
const PetscScalar dxxL = -PetscSqr(user->c)/hx, dxx0 = 2.*PetscSqr(user->c)/hx,dxxR = -PetscSqr(user->c)/hx;
const PetscScalar vals[3][3][3] = {{{0,0, 0},{a*hx, 0,0},{0,0, 0}},
{{0,dxxL,0},{0,a*hx+dxx0,0},{0,dxxR,0}},
{{0,0, 0},{0,0, a*hx},{0,0, 0}}};
ierr = MatSetValuesBlocked(Jpre, 1, &row, 3, col, &vals[0][0][0], INSERT_VALUES);CHKERRQ(ierr);
}
}
ierr = DMDAVecRestoreArrayRead(dm, U, &u);CHKERRQ(ierr);
ierr = DMDAVecRestoreArrayRead(dm, Udot, &udot);CHKERRQ(ierr);
ierr = DMDAVecRestoreArrayRead(cdm, C, &x);CHKERRQ(ierr);
ierr = MatAssemblyBegin(Jpre, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(Jpre, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
if (J != Jpre) {
ierr = MatAssemblyBegin(J, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(J, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
void PetscMatrix<T>::add_block_matrix(const DenseMatrix<T>& dm,
const std::vector<numeric_index_type>& brows,
const std::vector<numeric_index_type>& bcols)
{
libmesh_assert (this->initialized());
const numeric_index_type n_rows = dm.m();
const numeric_index_type n_cols = dm.n();
const numeric_index_type n_brows = brows.size();
const numeric_index_type n_bcols = bcols.size();
const numeric_index_type blocksize = n_rows / n_brows;
libmesh_assert_equal_to (n_cols / n_bcols, blocksize);
libmesh_assert_equal_to (blocksize*n_brows, n_rows);
libmesh_assert_equal_to (blocksize*n_bcols, n_cols);
PetscErrorCode ierr=0;
#ifndef NDEBUG
PetscInt petsc_blocksize;
ierr = MatGetBlockSize(_mat, &petsc_blocksize);
LIBMESH_CHKERRABORT(ierr);
libmesh_assert_equal_to (blocksize, static_cast<numeric_index_type>(petsc_blocksize));
#endif
// These casts are required for PETSc <= 2.1.5
ierr = MatSetValuesBlocked(_mat,
n_brows, (PetscInt*) &brows[0],
n_bcols, (PetscInt*) &bcols[0],
(PetscScalar*) &dm.get_values()[0],
ADD_VALUES);
LIBMESH_CHKERRABORT(ierr);
}
PetscErrorCode Assemble(MPI_Comm comm,PetscInt bs,const MatType mtype)
{
const PetscInt rc[] = {0,1,2,3};
const PetscScalar vals[] = {1, 2, 3, 4, 5, 6, 7, 8,
9,10,11,12,13,14,15,16,
17,18,19,20,21,22,23,24,
25,26,27,28,29,30,31,32,
33,34,35,36,37,38,39,40,
41,42,43,44,45,46,47,48,
49,50,51,52,53,54,55,56,
57,58,49,60,61,62,63,64};
Mat A;
PetscViewer viewer;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = MatCreate(comm,&A);CHKERRQ(ierr);
ierr = MatSetSizes(A,PETSC_DECIDE,PETSC_DECIDE,4*bs,4*bs);CHKERRQ(ierr);
ierr = MatSetType(A,mtype);CHKERRQ(ierr);
ierr = MatMPIBAIJSetPreallocation(A,bs,2,NULL,2,NULL);CHKERRQ(ierr);
ierr = MatMPISBAIJSetPreallocation(A,bs,2,NULL,2,NULL);CHKERRQ(ierr);
ierr = MatSetOption(A,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr);
/* All processes contribute a global matrix */
ierr = MatSetValuesBlocked(A,4,rc,4,rc,vals,ADD_VALUES);CHKERRQ(ierr);
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = PetscPrintf(comm,"Matrix %s(%D)\n",mtype,bs);CHKERRQ(ierr);
ierr = PetscViewerASCIIGetStdout(comm,&viewer);CHKERRQ(ierr);
ierr = PetscViewerPushFormat(viewer,PETSC_VIEWER_ASCII_INFO_DETAIL);CHKERRQ(ierr);
ierr = MatView(A,viewer);CHKERRQ(ierr);
ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr);
ierr = MatView(A,viewer);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode FormIJacobian(TS ts,PetscReal t,Vec X,Vec Xdot,PetscReal a,Mat *J,Mat *Jpre,MatStructure *str,void *ptr)
{
User user = (User)ptr;
PetscErrorCode ierr;
DMDALocalInfo info;
PetscInt i;
PetscReal hx;
DM da;
Field *x,*xdot;
PetscFunctionBeginUser;
ierr = TSGetDM(ts,&da);CHKERRQ(ierr);
ierr = DMDAGetLocalInfo(da,&info);CHKERRQ(ierr);
hx = 1.0/(PetscReal)(info.mx-1);
/* Get pointers to vector data */
ierr = DMDAVecGetArray(da,X,&x);CHKERRQ(ierr);
ierr = DMDAVecGetArray(da,Xdot,&xdot);CHKERRQ(ierr);
/* Compute function over the locally owned part of the grid */
for (i=info.xs; i<info.xs+info.xm; i++) {
if (i == 0 || i == info.mx-1) {
const PetscInt row = i,col = i;
const PetscScalar vals[2][2] = {{hx,0},{0,hx}};
ierr = MatSetValuesBlocked(*Jpre,1,&row,1,&col,&vals[0][0],INSERT_VALUES);CHKERRQ(ierr);
} else {
const PetscInt row = i,col[] = {i-1,i,i+1};
const PetscScalar dxxL = -user->alpha/hx,dxx0 = 2.*user->alpha/hx,dxxR = -user->alpha/hx;
const PetscScalar vals[2][3][2] = {{{dxxL,0},{a *hx+dxx0,0},{dxxR,0}},
{{0,dxxL},{0,a*hx+dxx0},{0,dxxR}}};
ierr = MatSetValuesBlocked(*Jpre,1,&row,3,col,&vals[0][0][0],INSERT_VALUES);CHKERRQ(ierr);
}
}
/* Restore vectors */
ierr = DMDAVecRestoreArray(da,X,&x);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(da,Xdot,&xdot);CHKERRQ(ierr);
ierr = MatAssemblyBegin(*Jpre,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(*Jpre,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
if (*J != *Jpre) {
ierr = MatAssemblyBegin(*J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(*J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
PetscErrorCode MatSetValuesBlockedLocal_IS(Mat A,PetscInt m,const PetscInt *rows, PetscInt n,const PetscInt *cols,const PetscScalar *values,InsertMode addv)
{
PetscErrorCode ierr;
Mat_IS *is = (Mat_IS*)A->data;
PetscFunctionBegin;
ierr = MatSetValuesBlocked(is->A,m,rows,n,cols,values,addv);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int main(int argc,char **args)
{
Mat A;
PetscInt i,j;
PetscErrorCode ierr;
PetscMPIInt size;
PetscViewer fd;
PetscScalar values[16],one = 1.0;
Vec x;
PetscInitialize(&argc,&args,(char *)0,help);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
if (size > 1) SETERRQ(PETSC_COMM_WORLD,1,"Can only run on one processor");
/*
Open binary file. Note that we use FILE_MODE_WRITE to indicate
writing to this file.
*/
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"4by4",FILE_MODE_WRITE,&fd);CHKERRQ(ierr);
ierr = MatCreateSeqBAIJ(PETSC_COMM_WORLD,4,12,12,0,0,&A);CHKERRQ(ierr);
for (i=0; i<16; i++) values[i] = i; for (i=0; i<4; i++) values[4*i+i] += 5;
i = 0; j = 0;
ierr = MatSetValuesBlocked(A,1,&i,1,&j,values,INSERT_VALUES);CHKERRQ(ierr);
for (i=0; i<16; i++) values[i] = i;
i = 0; j = 2;
ierr = MatSetValuesBlocked(A,1,&i,1,&j,values,INSERT_VALUES);CHKERRQ(ierr);
for (i=0; i<16; i++) values[i] = i;
i = 1; j = 0;
ierr = MatSetValuesBlocked(A,1,&i,1,&j,values,INSERT_VALUES);CHKERRQ(ierr);
for (i=0; i<16; i++) values[i] = i;for (i=0; i<4; i++) values[4*i+i] += 6;
i = 1; j = 1;
ierr = MatSetValuesBlocked(A,1,&i,1,&j,values,INSERT_VALUES);CHKERRQ(ierr);
for (i=0; i<16; i++) values[i] = i;
i = 2; j = 0;
ierr = MatSetValuesBlocked(A,1,&i,1,&j,values,INSERT_VALUES);CHKERRQ(ierr);
for (i=0; i<16; i++) values[i] = i;for (i=0; i<4; i++) values[4*i+i] += 7;
i = 2; j = 2;
ierr = MatSetValuesBlocked(A,1,&i,1,&j,values,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatView(A,fd);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = VecCreateSeq(PETSC_COMM_WORLD,12,&x);CHKERRQ(ierr);
ierr = VecSet(x,one);CHKERRQ(ierr);
ierr = VecView(x,fd);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
PetscErrorCode FormIJacobian(TS ts,PetscReal t,Vec X,Vec Xdot,PetscReal a,Mat *J,Mat *Jpre,MatStructure *str,void *ptr)
{
User user = (User)ptr;
PetscErrorCode ierr;
DMDALocalInfo info;
PetscInt i;
DM da;
Field *x,*xdot;
PetscFunctionBeginUser;
ierr = TSGetDM(ts,&da);CHKERRQ(ierr);
ierr = DMDAGetLocalInfo(da,&info);CHKERRQ(ierr);
/* Get pointers to vector data */
ierr = DMDAVecGetArray(da,X,&x);CHKERRQ(ierr);
ierr = DMDAVecGetArray(da,Xdot,&xdot);CHKERRQ(ierr);
/* Compute function over the locally owned part of the grid */
for (i=info.xs; i<info.xs+info.xm; i++) {
const PetscReal *k = user->k;
PetscScalar v[2][2];
v[0][0] = a + k[0]; v[0][1] = -k[1];
v[1][0] = -k[0]; v[1][1] = a+k[1];
ierr = MatSetValuesBlocked(*Jpre,1,&i,1,&i,&v[0][0],INSERT_VALUES);CHKERRQ(ierr);
}
/* Restore vectors */
ierr = DMDAVecRestoreArray(da,X,&x);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(da,Xdot,&xdot);CHKERRQ(ierr);
ierr = MatAssemblyBegin(*Jpre,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(*Jpre,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
if (*J != *Jpre) {
ierr = MatAssemblyBegin(*J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(*J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
void linearSystemPETSc<fullMatrix<double> >::addToMatrix(int row, int col,
const fullMatrix<double> &val)
{
if (!_entriesPreAllocated)
preAllocateEntries();
#ifdef PETSC_USE_COMPLEX
fullMatrix<std::complex<double> > modval(val.size1(), val.size2());
for (int ii = 0; ii < val.size1(); ii++) {
for (int jj = 0; jj < val.size1(); jj++) {
modval(ii, jj) = val (jj, ii);
modval(jj, ii) = val (ii, jj);
}
}
#else
fullMatrix<double> &modval = *const_cast<fullMatrix<double> *>(&val);
for (int ii = 0; ii < val.size1(); ii++) {
for (int jj = 0; jj < ii; jj++) {
PetscScalar buff = modval(ii, jj);
modval(ii, jj) = modval (jj, ii);
modval(jj, ii) = buff;
}
}
#endif
PetscInt i = row, j = col;
MatSetValuesBlocked(_a, 1, &i, 1, &j, &modval(0,0), ADD_VALUES);
//transpose back so that the original matrix is not modified
#ifndef PETSC_USE_COMPLEX
for (int ii = 0; ii < val.size1(); ii++)
for (int jj = 0; jj < ii; jj++) {
PetscScalar buff = modval(ii,jj);
modval(ii, jj) = modval (jj,ii);
modval(jj, ii) = buff;
}
#endif
_valuesNotAssembled = true;
}
PETSC_EXTERN void PETSC_STDCALL matsetvaluesblocked_(Mat *mat,PetscInt *m, PetscInt idxm[],PetscInt *n, PetscInt idxn[], PetscScalar v[],InsertMode *addv, int *ierr ){
*ierr = MatSetValuesBlocked(*mat,*m,idxm,*n,idxn,v,*addv);
}
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 **args)
{
Mat A;
PetscInt bs=3,m=4,n=6,i,j,val = 10,row[2],col[3],eval,rstart;
PetscErrorCode ierr;
PetscMPIInt size,rank;
PetscScalar x[6][9],y[3][3],one=1.0;
PetscBool flg,testsbaij=PETSC_FALSE;
PetscInitialize(&argc,&args,(char*)0,help);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
ierr = PetscOptionsHasName(NULL,"-test_mat_sbaij",&testsbaij);CHKERRQ(ierr);
if (testsbaij) {
ierr = MatCreateSBAIJ(PETSC_COMM_WORLD,bs,m*bs,n*bs,PETSC_DECIDE,PETSC_DECIDE,1,NULL,1,NULL,&A);CHKERRQ(ierr);
} else {
ierr = MatCreateBAIJ(PETSC_COMM_WORLD,bs,m*bs,n*bs,PETSC_DECIDE,PETSC_DECIDE,1,NULL,1,NULL,&A);CHKERRQ(ierr);
}
ierr = MatSetOption(A,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr);
eval = 9;
ierr = PetscOptionsHasName(NULL,"-ass_extern",&flg);CHKERRQ(ierr);
if (flg && (size != 1)) rstart = m*((rank+1)%size);
else rstart = m*(rank);
row[0] =rstart+0; row[1] =rstart+2;
col[0] =rstart+0; col[1] =rstart+1; col[2] =rstart+3;
for (i=0; i<6; i++) {
for (j =0; j< 9; j++) x[i][j] = (PetscScalar)val++;
}
ierr = MatSetValuesBlocked(A,2,row,3,col,&x[0][0],INSERT_VALUES);CHKERRQ(ierr);
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
/*
This option does not work for rectangular matrices
ierr = MatSetOption(A,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr);
*/
ierr = MatSetValuesBlocked(A,2,row,3,col,&x[0][0],INSERT_VALUES);CHKERRQ(ierr);
/* Do another MatSetValues to test the case when only one local block is specified */
for (i=0; i<3; i++) {
for (j =0; j<3; j++) y[i][j] = (PetscScalar)(10 + i*eval + j);
}
ierr = MatSetValuesBlocked(A,1,row,1,col,&y[0][0],INSERT_VALUES);CHKERRQ(ierr);
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = PetscOptionsHasName(NULL,"-zero_rows",&flg);CHKERRQ(ierr);
if (flg) {
col[0] = rstart*bs+0;
col[1] = rstart*bs+1;
col[2] = rstart*bs+2;
ierr = MatZeroRows(A,3,col,one,0,0);CHKERRQ(ierr);
}
ierr = MatView(A,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc,char **argv)
{
Mat M,Mo,C,K,Ko,A[3]; /* problem matrices */
PEP pep; /* polynomial eigenproblem solver context */
IS isf,isbc,is;
PetscInt n=200,nele,Istart,Iend,i,j,mloc,nloc,bc[2];
PetscReal width=0.05,height=0.005,glength=1.0,dlen,EI,area,rho;
PetscScalar K1[4],K2[4],K2t[4],K3[4],M1[4],M2[4],M2t[4],M3[4],damp=5.0;
PetscBool terse;
PetscErrorCode ierr;
PetscLogDouble time1,time2;
SlepcInitialize(&argc,&argv,(char*)0,help);
ierr = PetscOptionsGetInt(NULL,"-n",&n,NULL);CHKERRQ(ierr);
nele = n/2;
n = 2*nele;
ierr = PetscPrintf(PETSC_COMM_WORLD,"\nSimply supported beam damped in the middle, n=%D (nele=%D)\n\n",n,nele);CHKERRQ(ierr);
dlen = glength/nele;
EI = 7e10*width*height*height*height/12.0;
area = width*height;
rho = 0.674/(area*glength);
K1[0] = 12; K1[1] = 6*dlen; K1[2] = 6*dlen; K1[3] = 4*dlen*dlen;
K2[0] = -12; K2[1] = 6*dlen; K2[2] = -6*dlen; K2[3] = 2*dlen*dlen;
K2t[0] = -12; K2t[1] = -6*dlen; K2t[2] = 6*dlen; K2t[3] = 2*dlen*dlen;
K3[0] = 12; K3[1] = -6*dlen; K3[2] = -6*dlen; K3[3] = 4*dlen*dlen;
M1[0] = 156; M1[1] = 22*dlen; M1[2] = 22*dlen; M1[3] = 4*dlen*dlen;
M2[0] = 54; M2[1] = -13*dlen; M2[2] = 13*dlen; M2[3] = -3*dlen*dlen;
M2t[0] = 54; M2t[1] = 13*dlen; M2t[2] = -13*dlen; M2t[3] = -3*dlen*dlen;
M3[0] = 156; M3[1] = -22*dlen; M3[2] = -22*dlen; M3[3] = 4*dlen*dlen;
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Compute the matrices that define the eigensystem, (k^2*M+k*C+K)x=0
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/* K is block-tridiagonal */
ierr = MatCreate(PETSC_COMM_WORLD,&Ko);CHKERRQ(ierr);
ierr = MatSetSizes(Ko,PETSC_DECIDE,PETSC_DECIDE,n+2,n+2);CHKERRQ(ierr);
ierr = MatSetBlockSize(Ko,2);CHKERRQ(ierr);
ierr = MatSetFromOptions(Ko);CHKERRQ(ierr);
ierr = MatSetUp(Ko);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(Ko,&Istart,&Iend);CHKERRQ(ierr);
for (i=Istart/2;i<Iend/2;i++) {
if (i>0) {
j = i-1;
ierr = MatSetValuesBlocked(Ko,1,&i,1,&j,K2t,ADD_VALUES);CHKERRQ(ierr);
ierr = MatSetValuesBlocked(Ko,1,&i,1,&i,K3,ADD_VALUES);CHKERRQ(ierr);
}
if (i<nele) {
j = i+1;
ierr = MatSetValuesBlocked(Ko,1,&i,1,&j,K2,ADD_VALUES);CHKERRQ(ierr);
ierr = MatSetValuesBlocked(Ko,1,&i,1,&i,K1,ADD_VALUES);CHKERRQ(ierr);
}
}
ierr = MatAssemblyBegin(Ko,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(Ko,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatScale(Ko,EI/(dlen*dlen*dlen));CHKERRQ(ierr);
/* M is block-tridiagonal */
ierr = MatCreate(PETSC_COMM_WORLD,&Mo);CHKERRQ(ierr);
ierr = MatSetSizes(Mo,PETSC_DECIDE,PETSC_DECIDE,n+2,n+2);CHKERRQ(ierr);
ierr = MatSetBlockSize(Mo,2);CHKERRQ(ierr);
ierr = MatSetFromOptions(Mo);CHKERRQ(ierr);
ierr = MatSetUp(Mo);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(Mo,&Istart,&Iend);CHKERRQ(ierr);
for (i=Istart/2;i<Iend/2;i++) {
if (i>0) {
j = i-1;
ierr = MatSetValuesBlocked(Mo,1,&i,1,&j,M2t,ADD_VALUES);CHKERRQ(ierr);
ierr = MatSetValuesBlocked(Mo,1,&i,1,&i,M3,ADD_VALUES);CHKERRQ(ierr);
}
if (i<nele) {
j = i+1;
ierr = MatSetValuesBlocked(Mo,1,&i,1,&j,M2,ADD_VALUES);CHKERRQ(ierr);
ierr = MatSetValuesBlocked(Mo,1,&i,1,&i,M1,ADD_VALUES);CHKERRQ(ierr);
}
}
ierr = MatAssemblyBegin(Mo,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(Mo,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatScale(Mo,rho*area*dlen/420);CHKERRQ(ierr);
/* remove rows/columns from K and M corresponding to boundary conditions */
ierr = ISCreateStride(PETSC_COMM_WORLD,Iend-Istart,Istart,1,&isf);CHKERRQ(ierr);
bc[0] = 0; bc[1] = n;
ierr = ISCreateGeneral(PETSC_COMM_SELF,2,bc,PETSC_USE_POINTER,&isbc);CHKERRQ(ierr);
ierr = ISDifference(isf,isbc,&is);CHKERRQ(ierr);
ierr = MatGetSubMatrix(Ko,is,is,MAT_INITIAL_MATRIX,&K);CHKERRQ(ierr);
ierr = MatGetSubMatrix(Mo,is,is,MAT_INITIAL_MATRIX,&M);CHKERRQ(ierr);
ierr = MatGetLocalSize(M,&mloc,&nloc);CHKERRQ(ierr);
/* C is zero except for the (nele,nele)-entry */
ierr = MatCreate(PETSC_COMM_WORLD,&C);CHKERRQ(ierr);
ierr = MatSetSizes(C,mloc,nloc,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr);
ierr = MatSetFromOptions(C);CHKERRQ(ierr);
ierr = MatSetUp(C);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(C,&Istart,&Iend);CHKERRQ(ierr);
if (nele-1>=Istart && nele-1<Iend) {
ierr = MatSetValue(C,nele-1,nele-1,damp,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create the eigensolver and solve the problem
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = PEPCreate(PETSC_COMM_WORLD,&pep);CHKERRQ(ierr);
A[0] = K; A[1] = C; A[2] = M;
ierr = PEPSetOperators(pep,3,A);CHKERRQ(ierr);
ierr = PEPSetFromOptions(pep);CHKERRQ(ierr);
ierr = PetscTime(&time1); CHKERRQ(ierr);
ierr = PEPSolve(pep);CHKERRQ(ierr);
ierr = PetscTime(&time2); CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Display solution and clean up
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/* show detailed info unless -terse option is given by user */
ierr = PetscOptionsHasName(NULL,"-terse",&terse);CHKERRQ(ierr);
if (terse) {
ierr = PEPErrorView(pep,PEP_ERROR_BACKWARD,NULL);CHKERRQ(ierr);
} else {
ierr = PetscViewerPushFormat(PETSC_VIEWER_STDOUT_WORLD,PETSC_VIEWER_ASCII_INFO_DETAIL);CHKERRQ(ierr);
ierr = PEPReasonView(pep,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = PEPErrorView(pep,PEP_ERROR_BACKWARD,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = PetscViewerPopFormat(PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
ierr = PetscPrintf(PETSC_COMM_WORLD,"Time: %g\n\n\n",time2-time1);CHKERRQ(ierr);
ierr = PEPDestroy(&pep);CHKERRQ(ierr);
ierr = ISDestroy(&isf);CHKERRQ(ierr);
ierr = ISDestroy(&isbc);CHKERRQ(ierr);
ierr = ISDestroy(&is);CHKERRQ(ierr);
ierr = MatDestroy(&M);CHKERRQ(ierr);
ierr = MatDestroy(&C);CHKERRQ(ierr);
ierr = MatDestroy(&K);CHKERRQ(ierr);
ierr = MatDestroy(&Ko);CHKERRQ(ierr);
ierr = MatDestroy(&Mo);CHKERRQ(ierr);
ierr = SlepcFinalize();CHKERRQ(ierr);
return 0;
}
int main(int argc,char **args)
{
Mat A;
PetscInt m=2,bs=1,M,row,col,start,end,i,j,k;
PetscErrorCode ierr;
PetscMPIInt rank,size;
PetscScalar data=100;
PetscBool flg;
ierr = PetscInitialize(&argc,&args,(char*)0,help);if (ierr) return ierr;
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
/* Test MatSetValues() and MatGetValues() */
ierr = PetscOptionsGetInt(NULL,NULL,"-mat_block_size",&bs,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-mat_size",&m,NULL);CHKERRQ(ierr);
M = m*bs*size;
ierr = MatCreateBAIJ(PETSC_COMM_WORLD,bs,PETSC_DECIDE,PETSC_DECIDE,M,M,PETSC_DECIDE,NULL,PETSC_DECIDE,NULL,&A);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(A,&start,&end);CHKERRQ(ierr);
ierr = PetscOptionsHasName(NULL,NULL,"-column_oriented",&flg);CHKERRQ(ierr);
if (flg) {
ierr = MatSetOption(A,MAT_ROW_ORIENTED,PETSC_FALSE);CHKERRQ(ierr);
}
/* inproc assembly */
for (row=start; row<end; row++) {
for (col=start; col<end; col++,data+=1) {
ierr = MatSetValues(A,1,&row,1,&col,&data,INSERT_VALUES);CHKERRQ(ierr);
}
}
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
/* offproc assembly */
data = 5.0;
row = (M+start-1)%M;
for (col=0; col<M; col++) {
ierr = MatSetValues(A,1,&row,1,&col,&data,ADD_VALUES);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
/* Test MatSetValuesBlocked() */
ierr = PetscOptionsHasName(NULL,NULL,"-test_setvaluesblocked",&flg);CHKERRQ(ierr);
if (flg) {
PetscScalar *bval;
row /= bs;
col = start/bs;
ierr = PetscMalloc1(bs*bs,&bval);CHKERRQ(ierr);
k = 1;
/* row oriented - defalt */
for (i=0; i<bs; i++) {
for (j=0; j<bs; j++) {
bval[i*bs+j] = (PetscScalar)k; k++;
}
}
ierr = MatSetValuesBlocked(A,1,&row,1,&col,bval,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = PetscFree(bval);CHKERRQ(ierr);
}
ierr = MatView(A,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
void
MAST::ComplexAssemblyBase::
residual_and_jacobian_blocked (const libMesh::NumericVector<Real>& X,
libMesh::NumericVector<Real>& R,
libMesh::SparseMatrix<Real>& J,
MAST::Parameter* p) {
libmesh_assert(_system);
libmesh_assert(_discipline);
libmesh_assert(_elem_ops);
START_LOG("residual_and_jacobian()", "ComplexSolve");
MAST::NonlinearSystem& nonlin_sys = _system->system();
R.zero();
J.zero();
// iterate over each element, initialize it and get the relevant
// analysis quantities
RealVectorX
sol;
ComplexVectorX
delta_sol,
vec;
ComplexMatrixX
mat,
dummy;
// get the petsc vector and matrix objects
Mat
jac_bmat = dynamic_cast<libMesh::PetscMatrix<Real>&>(J).mat();
PetscInt ierr;
std::vector<libMesh::dof_id_type> dof_indices;
const libMesh::DofMap& dof_map = nonlin_sys.get_dof_map();
const std::vector<libMesh::dof_id_type>&
send_list = nonlin_sys.get_dof_map().get_send_list();
std::unique_ptr<libMesh::NumericVector<Real> >
localized_base_solution,
localized_complex_sol(libMesh::NumericVector<Real>::build(nonlin_sys.comm()).release());
// prepare a send list for localization of the complex solution
std::vector<libMesh::dof_id_type>
complex_send_list(2*send_list.size());
for (unsigned int i=0; i<send_list.size(); i++) {
complex_send_list[2*i ] = 2*send_list[i];
complex_send_list[2*i+1] = 2*send_list[i]+1;
}
localized_complex_sol->init(2*nonlin_sys.n_dofs(),
2*nonlin_sys.n_local_dofs(),
complex_send_list,
false,
libMesh::GHOSTED);
X.localize(*localized_complex_sol, complex_send_list);
// localize the base solution, if it was provided
if (_base_sol)
localized_base_solution.reset(build_localized_vector(nonlin_sys,
*_base_sol).release());
// if a solution function is attached, initialize it
//if (_sol_function)
// _sol_function->init( X);
libMesh::MeshBase::const_element_iterator el =
nonlin_sys.get_mesh().active_local_elements_begin();
const libMesh::MeshBase::const_element_iterator end_el =
nonlin_sys.get_mesh().active_local_elements_end();
MAST::ComplexAssemblyElemOperations&
ops = dynamic_cast<MAST::ComplexAssemblyElemOperations&>(*_elem_ops);
for ( ; el != end_el; ++el) {
const libMesh::Elem* elem = *el;
dof_map.dof_indices (elem, dof_indices);
ops.init(*elem);
// get the solution
unsigned int ndofs = (unsigned int)dof_indices.size();
sol.setZero(ndofs);
delta_sol.setZero(ndofs);
vec.setZero(ndofs);
mat.setZero(ndofs, ndofs);
// first set the velocity to be zero
ops.set_elem_velocity(sol);
// next, set the base solution, if provided
if (_base_sol)
for (unsigned int i=0; i<dof_indices.size(); i++)
sol(i) = (*localized_base_solution)(dof_indices[i]);
ops.set_elem_solution(sol);
// set the value of the small-disturbance solution
for (unsigned int i=0; i<dof_indices.size(); i++) {
// get the complex block for this dof
delta_sol(i) = Complex((*localized_complex_sol)(2*dof_indices[i]),
(*localized_complex_sol)(2*dof_indices[i]+1));
}
ops.set_elem_complex_solution(delta_sol);
// if (_sol_function)
// physics_elem->attach_active_solution_function(*_sol_function);
// perform the element level calculations
ops.elem_calculations(true, vec, mat);
// if sensitivity was requested, then ask the element for sensitivity
// of the residual
if (p) {
// set the sensitivity of complex sol to zero
delta_sol.setZero();
ops.set_elem_complex_solution_sensitivity(delta_sol);
vec.setZero();
ops.elem_sensitivity_calculations(*p, vec);
}
ops.clear_elem();
//physics_elem->detach_active_solution_function();
// extract the real or the imaginary part of the matrix/vector
// The complex system of equations
// (J_R + i J_I) (x_R + i x_I) + (r_R + i r_I) = 0
// is rewritten as
// [ J_R -J_I] {x_R} + {r_R} = {0}
// [ J_I J_R] {x_I} + {r_I} = {0}
//
DenseRealVector v_R, v_I;
DenseRealMatrix m_R, m_I1, m_I2;
std::vector<Real> vals(4);
// copy the real part of the residual and Jacobian
MAST::copy( m_R, mat.real());
MAST::copy(m_I1, mat.imag()); m_I1 *= -1.; // this is the -J_I component
MAST::copy(m_I2, mat.imag()); // this is the J_I component
MAST::copy( v_R, vec.real());
MAST::copy( v_I, vec.imag());
dof_map.constrain_element_matrix(m_R, dof_indices);
dof_map.constrain_element_matrix(m_I1, dof_indices);
dof_map.constrain_element_matrix(m_I2, dof_indices);
dof_map.constrain_element_vector(v_R, dof_indices);
dof_map.constrain_element_vector(v_I, dof_indices);
for (unsigned int i=0; i<dof_indices.size(); i++) {
R.add(2*dof_indices[i], v_R(i));
R.add(2*dof_indices[i]+1, v_I(i));
for (unsigned int j=0; j<dof_indices.size(); j++) {
vals[0] = m_R (i,j);
vals[1] = m_I1(i,j);
vals[2] = m_I2(i,j);
vals[3] = m_R (i,j);
ierr = MatSetValuesBlocked(jac_bmat,
1, (PetscInt*)&dof_indices[i],
1, (PetscInt*)&dof_indices[j],
&vals[0],
ADD_VALUES);
}
}
}
// if a solution function is attached, clear it
//if (_sol_function)
// _sol_function->clear();
R.close();
J.close();
libMesh::out << "R: " << R.l2_norm() << std::endl;
STOP_LOG("residual_and_jacobian()", "ComplexSolve");
}
PetscErrorCode AssembleSystem(Mat A, Vec b, PetscScalar soft_alpha, PetscScalar x_r, PetscScalar y_r, PetscScalar z_r, PetscScalar r,
PetscInt ne, PetscMPIInt npe, PetscMPIInt rank, PetscInt nn, PetscInt m)
{
PetscErrorCode ierr;
PetscReal h = 1.0 / ne;
PetscScalar DD[24][24], DD2[24][24];
PetscScalar DD1[24][24];
const PetscInt NP = (PetscInt)(PetscPowReal((PetscReal)npe, 1.0 / 3.0) + 0.5);
const PetscInt ipx = rank % NP, ipy = (rank % (NP * NP)) / NP, ipz = rank / (NP * NP);
const PetscInt Ni0 = ipx * (nn / NP), Nj0 = ipy * (nn / NP), Nk0 = ipz * (nn / NP);
const PetscInt Ni1 = Ni0 + (m > 0 ? (nn / NP) : 0), Nj1 = Nj0 + (nn / NP), Nk1 = Nk0 + (nn / NP);
const PetscInt NN = nn / NP, id0 = ipz * nn * nn * NN + ipy * nn * NN * NN + ipx * NN * NN * NN;
PetscScalar vv[24], v2[24];
PetscInt i, j, k;
{
ierr = elem_3d_elast_v_25((PetscScalar*)DD1);
CHKERRQ(ierr);
for (i = 0; i < 24; i++) {
for (j = 0; j < 24; j++) {
if (i < 12 || j < 12) {
if (i == j)
DD2[i][j] = 0.1 * DD1[i][j];
else
DD2[i][j] = 0.0;
}
else
DD2[i][j] = DD1[i][j];
}
}
for (i = 0; i < 24; i++) {
if (i % 3 == 0)
vv[i] = h * h;
else if (i % 3 == 1)
vv[i] = 2.0 * h * h;
else
vv[i] = 0.0;
}
for (i = 0; i < 24; i++) {
if (i % 3 == 0 && i >= 12)
v2[i] = h * h;
else if (i % 3 == 1 && i >= 12)
v2[i] = 2.0 * h * h;
else
v2[i] = 0.0;
}
}
ierr = MatZeroEntries(A);
CHKERRQ(ierr);
ierr = VecZeroEntries(b);
CHKERRQ(ierr);
PetscInt ii, jj, kk;
for (i = Ni0, ii = 0; i < Ni1; i++, ii++) {
for (j = Nj0, jj = 0; j < Nj1; j++, jj++) {
for (k = Nk0, kk = 0; k < Nk1; k++, kk++) {
PetscReal x = h * (PetscReal)i;
PetscReal y = h * (PetscReal)j;
PetscReal z = h * (PetscReal)k;
PetscInt id = id0 + ii + NN * jj + NN * NN * kk;
if (i < ne && j < ne && k < ne) {
PetscReal radius = PetscSqrtReal((x - 0.5 + h / 2) * (x - 0.5 + h / 2) + (y - 0.5 + h / 2) * (y - 0.5 + h / 2) +
(z - 0.5 + h / 2) * (z - 0.5 + h / 2));
PetscReal alpha = 1.0;
PetscInt jx, ix, idx[8];
idx[0] = id;
idx[1] = id + 1;
idx[2] = id + NN + 1;
idx[3] = id + NN;
idx[4] = id + NN * NN;
idx[5] = id + 1 + NN * NN;
idx[6] = id + NN + 1 + NN * NN;
idx[7] = id + NN + NN * NN;
if (i == Ni1 - 1 && Ni1 != nn) {
idx[1] += NN * (NN * NN - 1);
idx[2] += NN * (NN * NN - 1);
idx[5] += NN * (NN * NN - 1);
idx[6] += NN * (NN * NN - 1);
}
if (j == Nj1 - 1 && Nj1 != nn) {
idx[2] += NN * NN * (nn - 1);
idx[3] += NN * NN * (nn - 1);
idx[6] += NN * NN * (nn - 1);
idx[7] += NN * NN * (nn - 1);
}
if (k == Nk1 - 1 && Nk1 != nn) {
idx[4] += NN * (nn * nn - NN * NN);
idx[5] += NN * (nn * nn - NN * NN);
idx[6] += NN * (nn * nn - NN * NN);
idx[7] += NN * (nn * nn - NN * NN);
}
if (radius < r) alpha = soft_alpha;
for (ix = 0; ix < 24; ix++) {
for (jx = 0; jx < 24; jx++) DD[ix][jx] = alpha * DD1[ix][jx];
}
if (k > 0) {
ierr = MatSetValuesBlocked(A, 8, idx, 8, idx, (const PetscScalar*)DD, ADD_VALUES);
CHKERRQ(ierr);
ierr = VecSetValuesBlocked(b, 8, idx, (const PetscScalar*)vv, ADD_VALUES);
CHKERRQ(ierr);
}
else {
for (ix = 0; ix < 24; ix++) {
for (jx = 0; jx < 24; jx++) DD[ix][jx] = alpha * DD2[ix][jx];
}
ierr = MatSetValuesBlocked(A, 8, idx, 8, idx, (const PetscScalar*)DD, ADD_VALUES);
CHKERRQ(ierr);
ierr = VecSetValuesBlocked(b, 8, idx, (const PetscScalar*)v2, ADD_VALUES);
CHKERRQ(ierr);
}
}
}
}
}
ierr = MatAssemblyBegin(A, MAT_FINAL_ASSEMBLY);
CHKERRQ(ierr);
ierr = MatAssemblyEnd(A, MAT_FINAL_ASSEMBLY);
CHKERRQ(ierr);
ierr = VecAssemblyBegin(b);
CHKERRQ(ierr);
ierr = VecAssemblyEnd(b);
CHKERRQ(ierr);
PetscFunctionReturn(0);
}
