PetscErrorCode SetupDiscretization(DM dm, AppCtx *user)
{
DM cdm = dm;
const PetscInt dim = user->dim;
PetscFE fe[2];
PetscQuadrature q;
Parameter *param;
MPI_Comm comm;
PetscErrorCode ierr;
PetscFunctionBeginUser;
/* Create finite element */
ierr = PetscObjectGetComm((PetscObject) dm, &comm);CHKERRQ(ierr);
ierr = PetscFECreateDefault(comm, dim, dim, user->simplex, "vel_", PETSC_DEFAULT, &fe[0]);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) fe[0], "velocity");CHKERRQ(ierr);
ierr = PetscFEGetQuadrature(fe[0], &q);CHKERRQ(ierr);
ierr = PetscFECreateDefault(comm, dim, 1, user->simplex, "pres_", PETSC_DEFAULT, &fe[1]);CHKERRQ(ierr);
ierr = PetscFESetQuadrature(fe[1], q);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) fe[1], "pressure");CHKERRQ(ierr);
/* Set discretization and boundary conditions for each mesh */
ierr = DMSetField(dm, 0, NULL, (PetscObject) fe[0]);CHKERRQ(ierr);
ierr = DMSetField(dm, 1, NULL, (PetscObject) fe[1]);CHKERRQ(ierr);
ierr = DMCreateDS(dm);CHKERRQ(ierr);
ierr = SetupProblem(dm, user);CHKERRQ(ierr);
ierr = PetscBagGetData(user->bag, (void **) ¶m);CHKERRQ(ierr);
while (cdm) {
ierr = DMCopyDisc(dm, cdm);CHKERRQ(ierr);
ierr = DMPlexCreateBasisRotation(cdm, param->alpha, 0.0, 0.0);CHKERRQ(ierr);
ierr = DMGetCoarseDM(cdm, &cdm);CHKERRQ(ierr);
}
ierr = PetscFEDestroy(&fe[0]);CHKERRQ(ierr);
ierr = PetscFEDestroy(&fe[1]);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int DoOutput(DMMG *dmmg, int n_plot)
/*---------------------------------------------------------------------*/
{
AppCtx *user = (AppCtx*)dmmg[0]->user;
Parameter *param;
int ierr;
char filename[FNAME_LENGTH];
PetscViewer viewer;
DA da;
ierr = PetscBagGetData(user->bag,(void**)¶m);
CHKERRQ(ierr);
da = DMMGGetDA(dmmg);
if (param->output_to_file) { /* send output to binary file */
/* generate filename for time t */
sprintf(filename,"%s_%3.3d",param->output_filename,n_plot);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Generating output: time t = %g, ",param->t);
ierr = PetscPrintf(PETSC_COMM_WORLD,"file = \"%s\"\n",filename);
/* make output files */
ierr = PetscViewerBinaryMatlabOpen(PETSC_COMM_WORLD,filename,&viewer);
CHKERRQ(ierr);
ierr = PetscViewerBinaryMatlabOutputBag(viewer,"par",user->bag);
CHKERRQ(ierr);
ierr = DASetFieldNames("u","v","phi",da);
CHKERRQ(ierr);
ierr = PetscViewerBinaryMatlabOutputVecDA(viewer,"field",DMMGGetx(dmmg),da);
CHKERRQ(ierr);
ierr = PetscViewerBinaryMatlabDestroy(viewer);
CHKERRQ(ierr);
}
return 0;
}
PetscErrorCode SetupProblem(DM dm, AppCtx *user)
{
PetscDS prob;
Parameter *ctx;
PetscInt id;
PetscErrorCode ierr;
PetscFunctionBeginUser;
ierr = DMGetDS(dm, &prob);CHKERRQ(ierr);
ierr = PetscDSSetResidual(prob, 0, NULL, f1_u);CHKERRQ(ierr);
ierr = PetscDSSetResidual(prob, 1, f0_p, NULL);CHKERRQ(ierr);
ierr = PetscDSSetBdResidual(prob, 0, f0_bd_u, NULL);CHKERRQ(ierr);
ierr = PetscDSSetJacobian(prob, 0, 0, NULL, NULL, NULL, g3_uu);CHKERRQ(ierr);
ierr = PetscDSSetJacobian(prob, 0, 1, NULL, NULL, g2_up, NULL);CHKERRQ(ierr);
ierr = PetscDSSetJacobian(prob, 1, 0, NULL, g1_pu, NULL, NULL);CHKERRQ(ierr);
/* Setup constants */
{
Parameter *param;
PetscScalar constants[4];
ierr = PetscBagGetData(user->bag, (void **) ¶m);CHKERRQ(ierr);
constants[0] = param->Delta;
constants[1] = param->nu;
constants[2] = param->u_0;
constants[3] = param->alpha;
ierr = PetscDSSetConstants(prob, 4, constants);CHKERRQ(ierr);
}
/* Setup Boundary Conditions */
ierr = PetscBagGetData(user->bag, (void **) &ctx);CHKERRQ(ierr);
id = 3;
ierr = PetscDSAddBoundary(prob, DM_BC_ESSENTIAL, "top wall", "marker", 0, 0, NULL, (void (*)(void)) wall_velocity, 1, &id, ctx);CHKERRQ(ierr);
id = 1;
ierr = PetscDSAddBoundary(prob, DM_BC_ESSENTIAL, "bottom wall", "marker", 0, 0, NULL, (void (*)(void)) wall_velocity, 1, &id, ctx);CHKERRQ(ierr);
id = 2;
ierr = PetscDSAddBoundary(prob, DM_BC_NATURAL, "right wall", "marker", 0, 0, NULL, (void (*)(void)) NULL, 1, &id, ctx);CHKERRQ(ierr);
/* Setup exact solution */
user->exactFuncs[0] = quadratic_u;
user->exactFuncs[1] = linear_p;
ierr = PetscDSSetExactSolution(prob, 0, user->exactFuncs[0], ctx);CHKERRQ(ierr);
ierr = PetscDSSetExactSolution(prob, 1, user->exactFuncs[1], ctx);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int main(int argc, char **argv)
{
SNES snes; /* nonlinear solver */
DM dm; /* problem definition */
Vec u, r; /* solution and residual */
AppCtx user; /* user-defined work context */
PetscErrorCode ierr;
ierr = PetscInitialize(&argc, &argv, NULL,help);if (ierr) return ierr;
ierr = ProcessOptions(PETSC_COMM_WORLD, &user);CHKERRQ(ierr);
ierr = PetscBagCreate(PETSC_COMM_WORLD, sizeof(Parameter), &user.bag);CHKERRQ(ierr);
ierr = SetupParameters(&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 = DMSetApplicationContext(dm, &user);CHKERRQ(ierr);
/* Setup problem */
ierr = PetscMalloc(2 * sizeof(void (*)(const PetscReal[], PetscScalar *, void *)), &user.exactFuncs);CHKERRQ(ierr);
ierr = SetupDiscretization(dm, &user);CHKERRQ(ierr);
ierr = DMPlexCreateClosureIndex(dm, NULL);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(dm, &u);CHKERRQ(ierr);
ierr = VecDuplicate(u, &r);CHKERRQ(ierr);
ierr = DMPlexSetSNESLocalFEM(dm,&user,&user,&user);CHKERRQ(ierr);
ierr = SNESSetFromOptions(snes);CHKERRQ(ierr);
{
Parameter *param;
void *ctxs[2];
ierr = PetscBagGetData(user.bag, (void **) ¶m);CHKERRQ(ierr);
ctxs[0] = ctxs[1] = param;
ierr = DMProjectFunction(dm, 0.0, user.exactFuncs, ctxs, INSERT_ALL_VALUES, u);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) u, "Exact Solution");CHKERRQ(ierr);
ierr = VecViewFromOptions(u, NULL, "-exact_vec_view");CHKERRQ(ierr);
}
ierr = DMSNESCheckFromOptions(snes, u, NULL, NULL);CHKERRQ(ierr);
ierr = VecSet(u, 0.0);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) u, "Solution");CHKERRQ(ierr);
ierr = SNESSolve(snes, NULL, u);CHKERRQ(ierr);
ierr = VecViewFromOptions(u, NULL, "-sol_vec_view");CHKERRQ(ierr);
ierr = VecDestroy(&u);CHKERRQ(ierr);
ierr = VecDestroy(&r);CHKERRQ(ierr);
ierr = PetscFree(user.exactFuncs);CHKERRQ(ierr);
ierr = DMDestroy(&dm);CHKERRQ(ierr);
ierr = SNESDestroy(&snes);CHKERRQ(ierr);
ierr = PetscBagDestroy(&user.bag);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
PetscErrorCode CreateMesh(MPI_Comm comm, AppCtx *user, DM *dm)
{
PetscInt dim = user->dim;
PetscErrorCode ierr;
PetscFunctionBeginUser;
ierr = DMPlexCreateBoxMesh(comm, dim, user->simplex, user->cells, NULL, NULL, NULL, PETSC_TRUE, dm);CHKERRQ(ierr);
{
Parameter *param;
Vec coordinates;
PetscScalar *coords;
PetscReal alpha;
PetscInt cdim, N, bs, i;
ierr = DMGetCoordinateDim(*dm, &cdim);CHKERRQ(ierr);
ierr = DMGetCoordinates(*dm, &coordinates);CHKERRQ(ierr);
ierr = VecGetLocalSize(coordinates, &N);CHKERRQ(ierr);
ierr = VecGetBlockSize(coordinates, &bs);CHKERRQ(ierr);
if (bs != cdim) SETERRQ2(comm, PETSC_ERR_ARG_WRONG, "Invalid coordinate blocksize %D != embedding dimension %D", bs, cdim);
ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr);
ierr = PetscBagGetData(user->bag, (void **) ¶m);CHKERRQ(ierr);
alpha = param->alpha;
for (i = 0; i < N; i += cdim) {
PetscScalar x = coords[i+0];
PetscScalar y = coords[i+1];
coords[i+0] = PetscCosReal(alpha)*x - PetscSinReal(alpha)*y;
coords[i+1] = PetscSinReal(alpha)*x + PetscCosReal(alpha)*y;
}
ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr);
ierr = DMSetCoordinates(*dm, coordinates);CHKERRQ(ierr);
}
{
DM pdm = NULL;
PetscPartitioner part;
ierr = DMPlexGetPartitioner(*dm, &part);CHKERRQ(ierr);
ierr = PetscPartitionerSetFromOptions(part);CHKERRQ(ierr);
ierr = DMPlexDistribute(*dm, 0, NULL, &pdm);CHKERRQ(ierr);
if (pdm) {
ierr = DMDestroy(dm);CHKERRQ(ierr);
*dm = pdm;
}
}
ierr = DMSetFromOptions(*dm);CHKERRQ(ierr);
ierr = DMViewFromOptions(*dm, NULL, "-dm_view");CHKERRQ(ierr);
PetscFunctionReturn(0);
}
static PetscErrorCode SetupParameters(AppCtx *user)
{
PetscBag bag;
Parameter *p;
PetscErrorCode ierr;
PetscFunctionBeginUser;
/* setup PETSc parameter bag */
ierr = PetscBagGetData(user->bag, (void **) &p);CHKERRQ(ierr);
ierr = PetscBagSetName(user->bag, "par", "Poiseuille flow parameters");CHKERRQ(ierr);
bag = user->bag;
ierr = PetscBagRegisterReal(bag, &p->Delta, 1.0, "Delta", "Pressure drop per unit length");CHKERRQ(ierr);
ierr = PetscBagRegisterReal(bag, &p->nu, 1.0, "nu", "Kinematic viscosity");CHKERRQ(ierr);
ierr = PetscBagRegisterReal(bag, &p->u_0, 0.0, "u_0", "Tangential velocity at the wall");CHKERRQ(ierr);
ierr = PetscBagRegisterReal(bag, &p->alpha, 0.0, "alpha", "Angle of pipe wall to x-axis");CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int Initialize(DMMG *dmmg)
/* ------------------------------------------------------------------- */
{
AppCtx *user = (AppCtx*)dmmg[0]->user;
Parameter *param;
DA da;
PetscReal PI = 3.14159265358979323846;
PetscReal sigma,xc,zc;
PetscReal dx=user->grid->dx,dz=user->grid->dz;
int i,j,ierr,is,js,im,jm;
Field **x;
ierr = PetscBagGetData(user->bag,(void**)¶m);
CHKERRQ(ierr);
sigma=param->sigma;
xc=param->xctr;
zc=param->zctr;
/* Get the DA and grid */
da = (DA)(dmmg[0]->dm);
ierr = DAGetCorners(da,&is,&js,PETSC_NULL,&im,&jm,PETSC_NULL);
CHKERRQ(ierr);
ierr = DAVecGetArray(da,user->Xold,(void**)&x);
CHKERRQ(ierr);
for (j=js; j<js+jm; j++) {
for (i=is; i<is+im; i++) {
if (param->flow_type == SHEAR_CELL) {
x[j][i].u = -sin(PI*i*dx)*cos(PI*j*dz)/dx;
x[j][i].w = sin(PI*j*dz)*cos(PI*i*dx)/dz;
} else {
x[j][i].u = 0.0;
x[j][i].w = -1.0/dz;
}
x[j][i].phi = 100*exp(-0.5*((i*dx-xc)*(i*dx-xc)+(j*dz-zc)*(j*dz-zc))/sigma/sigma);
}
}
/* restore the grid to it's vector */
ierr = DAVecRestoreArray(da,user->Xold,(void**)&x);
CHKERRQ(ierr);
ierr = VecCopy(user->Xold, DMMGGetx(dmmg));
CHKERRQ(ierr);
return 0;
}
int DoVerification(DMMG *dmmg, AppCtx *user)
/*---------------------------------------------------------------------*/
{
Parameter *param;
PetscReal t1,t2,t3,norms[3];
int ierr;
ierr = PetscBagGetData(user->bag,(void**)¶m);
CHKERRQ(ierr);
ierr = CalcSolnNorms(dmmg, norms);
CHKERRQ(ierr);
t1 = (norms[0]-param->L1)/param->L1*100.0;
t2 = (norms[1]-param->L2)/param->L2*100.0;
t3 = (norms[2]-param->LINF)/param->LINF*100.0;
if ((fabs(t1)>1.0) || (fabs(t2)>1.0) || (fabs(t3)>5.0)) {
param->verify_result = 1;
}
PetscPrintf(PETSC_COMM_WORLD," Step: %d, Soln norms: %g (L1) %g (L2) %g (LINF)\n",param->n,norms[0],norms[1],norms[2]);
PetscPrintf(PETSC_COMM_WORLD," Step: %d, Soln norms %%err: %5.2g (L1) %5.2g (L2) %5.2g (LINF)\n",param->n,t1,t2,t3);
return 0;
}
/* uses analytic velocity fields */
PetscErrorCode InterpVelocity2D(void *f, PetscReal ij_real[], PetscInt numComp,
PetscInt components[], PetscReal velocity[],
void *ctx)
/*---------------------------------------------------------------------*/
{
AppCtx *user = (AppCtx *) ctx;
Parameter *param;
PetscReal dx=user->grid->dx, dz=user->grid->dz;
PetscReal PI = 3.14159265358979323846;
int ierr;
ierr = PetscBagGetData(user->bag,(void**)¶m);
CHKERRQ(ierr);
if (param->flow_type == SHEAR_CELL) {
velocity[0] = -sin(PI*ij_real[0]*dx)*cos(PI*ij_real[1]*dz)/dx;
velocity[1] = sin(PI*ij_real[1]*dz)*cos(PI*ij_real[0]*dx)/dz;
} else {
velocity[0] = 0.;
velocity[1] = -1./dz;
}
return 0;
}
int ReportParams(AppCtx *user)
/*---------------------------------------------------------------------*/
{
Parameter *param;
GridInfo *grid = user->grid;
int ierr, ierr_out=0;
ierr = PetscBagGetData(user->bag,(void**)¶m);
CHKERRQ(ierr);
PetscPrintf(PETSC_COMM_WORLD,"---------------MOC test 1----------------\n");
PetscPrintf(PETSC_COMM_WORLD,"Prescribed wind, method of\n");
PetscPrintf(PETSC_COMM_WORLD,"characteristics advection, explicit time-\n");
PetscPrintf(PETSC_COMM_WORLD,"stepping.\n\n");
if (param->flow_type == 0) {
PetscPrintf(PETSC_COMM_WORLD,"Flow_type: %d (shear cell).\n\n",param->flow_type);
}
if (param->flow_type == 1) {
PetscPrintf(PETSC_COMM_WORLD,"Flow_type: %d (rigid body rotation).\n\n",param->flow_type);
}
if (param->verify) {
PetscPrintf(PETSC_COMM_WORLD," ** VERIFICATION RUN ** \n\n");
}
ierr = PetscPrintf(PETSC_COMM_WORLD," [ni,nj] = %d, %d [dx,dz] = %5.4g, %5.4g\n",grid->ni,grid->nj,grid->dx,grid->dz);
CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD," t_max = %g, cfl = %g, dt = %5.4g,",param->t_max,param->cfl,param->dt);
CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD," t_output = %g\n",param->t_output_interval);
CHKERRQ(ierr);
if (param->output_to_file) {
PetscPrintf(PETSC_COMM_WORLD,"Output File: Binary file \"%s\"\n",param->output_filename);
}
if (!param->output_to_file)
PetscPrintf(PETSC_COMM_WORLD,"Output File: NO OUTPUT!\n");
ierr = PetscPrintf(PETSC_COMM_WORLD,"----------------------------------------\n");
CHKERRQ(ierr);
if (param->param_test) PetscEnd();
return ierr_out;
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
PetscBag bag;
Parameter *params;
PetscViewer viewer;
PetscBool flg;
char filename[PETSC_MAX_PATH_LEN] = "binaryoutput";
/*
Every PETSc routine should begin with the PetscInitialize() routine.
argc, argv - These command line arguments are taken to extract the options
supplied to PETSc and options supplied to MPI.
help - When PETSc executable is invoked with the option -help,
it prints the various options that can be applied at
runtime. The user can use the "help" variable place
additional help messages in this printout.
*/
ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
/* Create an empty bag */
ierr = PetscBagCreate(PETSC_COMM_WORLD,sizeof(Parameter),&bag);CHKERRQ(ierr);
ierr = PetscBagGetData(bag,(void**)¶ms);CHKERRQ(ierr);
/* register variables, defaults, names, help strings */
ierr = PetscBagSetName(bag,"ParameterBag","contains parameters for simulations of top-secret, dangerous physics");CHKERRQ(ierr);
ierr = PetscBagSetOptionsPrefix(bag, "pbag_");CHKERRQ(ierr);
ierr = PetscBagRegisterString(bag,¶ms->filename,PETSC_MAX_PATH_LEN,"myfile","filename","Name of secret file");CHKERRQ(ierr);
ierr = PetscBagRegisterReal (bag,¶ms->rho,3.0,"rho","Density, kg/m^3");CHKERRQ(ierr);
ierr = PetscBagRegisterScalar(bag,¶ms->W, 5.0,"W","Vertical velocity, m/sec");CHKERRQ(ierr);
ierr = PetscBagRegisterInt (bag,¶ms->Ii, 2,"modes_x","Number of modes in x-direction");CHKERRQ(ierr);
params->iarray[0] = 1;
params->iarray[1] = 2;
params->iarray[2] = 3;
ierr = PetscBagRegisterIntArray(bag,¶ms->iarray, 3,"int_array","Int array with 3 locations");CHKERRQ(ierr);
params->rarray[0] = -1.0;
params->rarray[1] = -2.0;
ierr = PetscBagRegisterRealArray(bag,¶ms->rarray, 2,"real_array","Real array with 2 locations");CHKERRQ(ierr);
ierr = PetscBagRegisterBool (bag,¶ms->T, PETSC_FALSE,"do_output","Write output file (yes/no)");CHKERRQ(ierr);
ierr = PetscBagRegisterBoolArray(bag,¶ms->Tarray, 3,"bool_array","Bool array with 3 locations");CHKERRQ(ierr);
ierr = PetscBagRegisterEnum (bag,¶ms->dt, PetscDataTypes,(PetscEnum)PETSC_INT,"dt","meaningless datatype");CHKERRQ(ierr);
ierr = PetscBagRegisterReal (bag,¶ms->pos.x1,1.0,"x1","x position");CHKERRQ(ierr);
ierr = PetscBagRegisterReal (bag,¶ms->pos.x2,1.9,"x2","y position");CHKERRQ(ierr);
ierr = PetscBagRegisterEnum (bag,¶ms->which, EnumeratedChoices, (PetscEnum)THAT, "choose","Express yourself by choosing among enumerated things");CHKERRQ(ierr);
/* This option allows loading user-provided PetscBag */
ierr = PetscOptionsGetString(NULL,NULL,"-f",filename,sizeof(filename),&flg);CHKERRQ(ierr);
if (!flg) {
/* write bag to stdio & binary file */
ierr = PetscBagView(bag,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,filename,FILE_MODE_WRITE,&viewer);CHKERRQ(ierr);
ierr = PetscBagView(bag,viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
}
ierr = PetscMemzero(params,sizeof(Parameter));CHKERRQ(ierr);
/* load bag from file & write to stdio */
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,filename,FILE_MODE_READ,&viewer);CHKERRQ(ierr);
ierr = PetscBagLoad(viewer,bag);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = PetscBagSetFromOptions(bag);CHKERRQ(ierr);
ierr = PetscBagView(bag,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
/* reuse the parameter struct */
ierr = PetscBagGetData(bag,(void**)¶ms);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"The value of rho after loading is: %f\n",(double)params->rho);CHKERRQ(ierr);
/* clean up and exit */
ierr = PetscBagDestroy(&bag);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
PetscBag bag;
Parameter *params;
PetscViewer viewer;
DM da;
Vec global,local;
PetscMPIInt rank;
/*
Every PETSc routine should begin with the PetscInitialize() routine.
argc, argv - These command line arguments are taken to extract the options
supplied to PETSc and options supplied to MPI.
help - When PETSc executable is invoked with the option -help,
it prints the various options that can be applied at
runtime. The user can use the "help" variable place
additional help messages in this printout.
*/
ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
/* Create a DMDA and an associated vector */
ierr = DMDACreate2d(PETSC_COMM_WORLD, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE,DMDA_STENCIL_BOX,10,10,PETSC_DECIDE,PETSC_DECIDE,2,1,NULL,NULL,&da);CHKERRQ(ierr);
ierr = DMSetFromOptions(da);CHKERRQ(ierr);
ierr = DMSetUp(da);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da,&global);CHKERRQ(ierr);
ierr = DMCreateLocalVector(da,&local);CHKERRQ(ierr);
ierr = VecSet(global,-1.0);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(da,global,INSERT_VALUES,local);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(da,global,INSERT_VALUES,local);CHKERRQ(ierr);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
ierr = VecScale(local,rank+1);CHKERRQ(ierr);
ierr = DMLocalToGlobalBegin(da,local,ADD_VALUES,global);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(da,local,ADD_VALUES,global);CHKERRQ(ierr);
/* Create an empty bag */
ierr = PetscBagCreate(PETSC_COMM_WORLD,sizeof(Parameter),&bag);CHKERRQ(ierr);
ierr = PetscBagGetData(bag,(void**)¶ms);CHKERRQ(ierr);
/* fill bag: register variables, defaults, names, help strings */
ierr = PetscBagSetName(bag,"ParameterBag","contains problem parameters");CHKERRQ(ierr);
ierr = PetscBagRegisterString(bag,¶ms->filename,PETSC_MAX_PATH_LEN,"output_file","filename","Name of secret file");CHKERRQ(ierr);
ierr = PetscBagRegisterReal (bag,¶ms->ra,1.0,"param_1","The first parameter");CHKERRQ(ierr);
ierr = PetscBagRegisterInt (bag,¶ms->ia,5,"param_2","The second parameter");CHKERRQ(ierr);
ierr = PetscBagRegisterBool (bag,¶ms->ta,PETSC_TRUE,"do_output","Write output file (true/false)");CHKERRQ(ierr);
/*
Write output file with PETSC_VIEWER_BINARY_MATLAB format
NOTE: the output generated with this viewer can be loaded into
MATLAB using $PETSC_DIR/share/petsc/matlab/PetscReadBinaryMatlab.m
*/
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,params->filename,FILE_MODE_WRITE,&viewer);CHKERRQ(ierr);
ierr = PetscViewerPushFormat(viewer,PETSC_VIEWER_BINARY_MATLAB);CHKERRQ(ierr);
ierr = PetscBagView(bag,viewer);CHKERRQ(ierr);
ierr = DMDASetFieldName(da,0,"field1");CHKERRQ(ierr);
ierr = DMDASetFieldName(da,1,"field2");CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)global,"da1");CHKERRQ(ierr);
ierr = VecView(global,viewer);CHKERRQ(ierr);
ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
/* clean up and exit */
ierr = PetscBagDestroy(&bag);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = VecDestroy(&local);CHKERRQ(ierr);
ierr = VecDestroy(&global);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
int main(int argc,char **argv)
/*-----------------------------------------------------------------------*/
{
DMMG *dmmg; /* multilevel grid structure */
AppCtx *user; /* user-defined work context */
Parameter *param;
GridInfo grid;
int ierr,result;
MPI_Comm comm;
DA da;
PetscInitialize(&argc,&argv,(char *)0,help);
comm = PETSC_COMM_WORLD;
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Set up the problem parameters.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = PetscMalloc(sizeof(AppCtx),&user);
CHKERRQ(ierr);
ierr = PetscBagCreate(comm,sizeof(Parameter),&(user->bag));
CHKERRQ(ierr);
user->grid = &grid;
ierr = SetParams(user);
CHKERRQ(ierr);
ierr = ReportParams(user);
CHKERRQ(ierr);
ierr = PetscBagGetData(user->bag,(void**)¶m);
CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create distributed array multigrid object (DMMG) to manage parallel grid and vectors
for principal unknowns (x) and governing residuals (f)
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = DMMGCreate(comm,grid.mglevels,user,&dmmg);
CHKERRQ(ierr);
ierr = DACreate2d(comm,grid.periodic,grid.stencil,grid.ni,grid.nj,PETSC_DECIDE,PETSC_DECIDE,grid.dof,grid.stencil_width,0,0,&da);
CHKERRQ(ierr);
ierr = DMMGSetDM(dmmg,(DM)da);
CHKERRQ(ierr);
ierr = DADestroy(da);
CHKERRQ(ierr);
ierr = DAGetInfo(da,PETSC_NULL,PETSC_NULL,PETSC_NULL,PETSC_NULL,&(param->pi),&(param->pj),PETSC_NULL,PETSC_NULL,PETSC_NULL,PETSC_NULL,PETSC_NULL);
CHKERRQ(ierr);
REG_INTG(user->bag,¶m->pi,param->pi ,"procs_x","<DO NOT SET> Processors in the x-direction");
REG_INTG(user->bag,¶m->pj,param->pj ,"procs_y","<DO NOT SET> Processors in the y-direction");
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create user context, set problem data, create vector data structures.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = DAGetGlobalVector(da, &(user->Xold));
CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Initialize and solve the nonlinear system
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = Initialize(dmmg);
CHKERRQ(ierr);
ierr = DoSolve(dmmg);
CHKERRQ(ierr);
if (param->verify) result = param->verify_result;
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Free work space.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = DARestoreGlobalVector(da, &(user->Xold));
CHKERRQ(ierr);
ierr = PetscBagDestroy(user->bag);
CHKERRQ(ierr);
ierr = PetscFree(user);
CHKERRQ(ierr);
ierr = DMMGDestroy(dmmg);
CHKERRQ(ierr);
ierr = PetscFinalize();
CHKERRQ(ierr);
return result;
}
int DoSolve(DMMG *dmmg)
/* ------------------------------------------------------------------- */
{
AppCtx *user = (AppCtx*)dmmg[0]->user;
Parameter *param;
PetscReal t_output = 0.0;
int ierr, n_plot = 0, Ncomponents, components[3];
DA da = DMMGGetDA(dmmg);
Vec Xstar;
Characteristic c;
ierr = PetscBagGetData(user->bag,(void**)¶m);
CHKERRQ(ierr);
ierr = DAGetGlobalVector(da, &Xstar);
CHKERRQ(ierr);
/*------------ BEGIN CHARACTERISTIC SETUP ---------------*/
ierr = CharacteristicCreate(PETSC_COMM_WORLD, &c);
CHKERRQ(ierr);
/* set up the velocity interpolation system */
Ncomponents = 2;
components[0] = 0;
components[1] = 1;
ierr = CharacteristicSetVelocityInterpolationLocal(c, da, DMMGGetx(dmmg), user->Xold, Ncomponents, components, InterpVelocity2D, user);
CHKERRQ(ierr);
/* set up the fields interpolation system */
Ncomponents = 1;
components[0] = 2;
ierr = CharacteristicSetFieldInterpolationLocal(c, da, user->Xold, Ncomponents, components, InterpFields2D, user);
CHKERRQ(ierr);
/*------------ END CHARACTERISTIC SETUP ----------------*/
/* output initial data */
PetscPrintf(PETSC_COMM_WORLD," Initialization, Time: %5.4g\n", param->t);
if (param->verify) {
ierr = DoVerification(dmmg,user);
CHKERRQ(ierr);
}
ierr = DoOutput(dmmg,n_plot);
CHKERRQ(ierr);
t_output += param->t_output_interval;
n_plot++;
/* timestep loop */
for (param->t=param->dt; param->t<=param->t_max; param->t+=param->dt) {
if (param->n > param->N_steps) {
PetscPrintf(PETSC_COMM_WORLD,"EXCEEDED MAX NUMBER OF TIMESTEPS! EXITING SOLVE!\n");
return 0;
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Solve at time t & copy solution into solution vector.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/* Copy in the velocities to Xstar */
ierr = VecCopy(DMMGGetx(dmmg), Xstar);
CHKERRQ(ierr);
/* Put \phi_* into Xstar */
ierr = CharacteristicSolve(c, param->dt, Xstar);
CHKERRQ(ierr);
/* Copy the advected field into the solution \phi_t = \phi_* */
ierr = VecCopy(Xstar, DMMGGetx(dmmg));
CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Copy new solution to old solution in prep for the next timestep.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = VecCopy(DMMGGetx(dmmg), user->Xold);
CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Timestep complete, report and update counter.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
PetscPrintf(PETSC_COMM_WORLD," Step: %d, Time: %5.4g\n", param->n, param->t);
param->n++;
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Verify and make output.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
if (param->verify) {
ierr = DoVerification(dmmg,user);
CHKERRQ(ierr);
}
if (param->t >= t_output) {
ierr = DoOutput(dmmg,n_plot);
CHKERRQ(ierr);
t_output += param->t_output_interval;
n_plot++;
}
}
ierr = DARestoreGlobalVector(da, &Xstar);
CHKERRQ(ierr);
ierr = CharacteristicDestroy(c);
CHKERRQ(ierr);
return 0;
}
int SetParams(AppCtx *user)
/*---------------------------------------------------------------------*/
{
PetscBag bag = user->bag;
Parameter *p;
GridInfo *grid = user->grid;
int ierr, ierr_out=0;
ierr = PetscBagGetData(bag,(void**)&p);
CHKERRQ(ierr);
/* give the bag a name */
ierr = PetscBagSetName(bag,"ex1_params","Parameter bag for ex1.c");
CHKERRQ(ierr);
/* verification */
REG_TRUE(bag,&p->verify,PETSC_FALSE ,"verify","Do verification run (T/F)");
/* domain geometry & grid size */
REG_INTG(bag,&p->ni,40 ,"ni","Grid points in x-dir");
REG_INTG(bag,&p->nj,40 ,"nj","Grid points in y-dir");
grid->dx = 1.0/((double)(p->ni - 1));
grid->dz = 1.0/((double)(p->nj - 1));
/* initial conditions */
REG_INTG(bag,&p->flow_type,SHEAR_CELL ,"flow_type","Flow field mode: 0=shear cell, 1=translation");
REG_REAL(bag,&p->sigma,0.07 ,"sigma","Standard deviation of the gaussian IC");
REG_REAL(bag,&p->xctr,0.5 ,"xctr","x-position of the center of the gaussian IC");
REG_REAL(bag,&p->zctr,0.75 ,"zctr","z-position of the center of the gaussian IC");
/* time stepping */
REG_REAL(bag,&p->t_max,1 ,"t_max","Maximum dimensionless time");
REG_REAL(bag,&p->cfl,5 ,"cfl","Courant number");
REG_REAL(bag,&p->t_output_interval,0.1 ,"t_output","Dimensionless time interval for output");
REG_INTG(bag,&p->N_steps,1000 ,"nsteps","Maximum time-steps");
REG_INTG(bag,&p->n,1 ,"nsteps","<DO NOT SET> current time-step");
REG_REAL(bag,&p->t,0.0 ,"time","<DO NOT SET> initial time");
REG_REAL(bag,&p->dt,p->cfl*PetscMin(grid->dx,grid->dz),"dt","<DO NOT SET> time-step size");
/* output options */
REG_TRUE(bag,&p->param_test ,PETSC_FALSE ,"test","Run parameter test only (T/F)");
REG_STRG(bag,&p->output_filename,FNAME_LENGTH ,"null","output_file","Name base for output files, set with: -output_file <filename>");
REG_TRUE(bag,&p->output_to_file,PETSC_FALSE ,"do_output","<DO NOT SET> flag will be true if you specify an output file name");
p->output_to_file = OptionsHasName("-output_file");
if (p->verify) {
REG_INTG(bag,&p->verify_result,0 ,"ver_result","<DO NOT SET> Result of verification test");
REG_REAL(bag,&p->L1 ,4924.42 ,"L1","<DO NOT SET> L1");
REG_REAL(bag,&p->L2 ,496.287 ,"L2","<DO NOT SET> L2");
REG_REAL(bag,&p->LINF,100 ,"L3","<DO NOT SET> L3");
p->verify_result = 0;
p->L1 = 4924.42;
p->L2 = 496.287;
p->LINF = 100;
grid->ni = grid->nj = 40;
grid->dx = 1.0/((double)(grid->ni));
grid->dz = 1.0/((double)(grid->nj));
p->flow_type = SHEAR_CELL;
p->sigma = 0.07;
p->xctr = 0.5;
p->zctr = 0.75;
p->t_max = 0.5;
p->cfl = 5;
p->t_output_interval = 0.1;
p->dt = p->cfl*PetscMin(grid->dx,grid->dz);
}
grid->ni = p->ni;
grid->nj = p->nj;
grid->periodic = DA_XYPERIODIC;
grid->stencil = DA_STENCIL_BOX;
grid->dof = 3;
grid->stencil_width = 2;
grid->mglevels = 1;
return ierr_out;
}
int main(int argc,char **argv)
{
DM da;
SNES snes; /* nonlinear solver */
AppCtx *user; /* user-defined work context */
PetscBag bag;
PetscInt its; /* iterations for convergence */
PetscMPIInt size;
SNESConvergedReason reason;
PetscErrorCode ierr;
PetscReal lambda_max = 6.81, lambda_min = 0.0, error;
Vec x;
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Initialize program
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
PetscInitialize(&argc,&argv,(char*)0,help);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
if (size != 1) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP,"Example only works for one process.");
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Initialize problem parameters
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = PetscBagCreate(PETSC_COMM_WORLD, sizeof(AppCtx), &bag);CHKERRQ(ierr);
ierr = PetscBagGetData(bag, (void**) &user);CHKERRQ(ierr);
ierr = PetscBagSetName(bag, "params", "Parameters for SNES example 4");CHKERRQ(ierr);
ierr = PetscBagRegisterReal(bag, &user->alpha, 1.0, "alpha", "Linear coefficient");CHKERRQ(ierr);
ierr = PetscBagRegisterReal(bag, &user->lambda, 6.0, "lambda", "Nonlinear coefficient");CHKERRQ(ierr);
ierr = PetscBagSetFromOptions(bag);CHKERRQ(ierr);
ierr = PetscOptionsGetReal(NULL,"-alpha",&user->alpha,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetReal(NULL,"-lambda",&user->lambda,NULL);CHKERRQ(ierr);
if (user->lambda > lambda_max || user->lambda < lambda_min) SETERRQ3(PETSC_COMM_SELF,1,"Lambda %g is out of range [%g, %g]", (double)user->lambda, (double)lambda_min, (double)lambda_max);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create multilevel DM data structure (SNES) to manage hierarchical solvers
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = SNESCreate(PETSC_COMM_WORLD,&snes);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create distributed array (DMDA) to manage parallel grid and vectors
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = DMDACreate2d(PETSC_COMM_WORLD, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE,DMDA_STENCIL_BOX,-3,-3,PETSC_DECIDE,PETSC_DECIDE,3,1,NULL,NULL,&da);CHKERRQ(ierr);
ierr = DMDASetFieldName(da, 0, "ooblek");CHKERRQ(ierr);
ierr = DMSetApplicationContext(da,user);CHKERRQ(ierr);
ierr = SNESSetDM(snes, (DM) da);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Set the discretization functions
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = DMDASNESSetFunctionLocal(da,INSERT_VALUES,(PetscErrorCode (*)(DMDALocalInfo*,void*,void*,void*))FormFunctionLocal,user);CHKERRQ(ierr);
ierr = DMDASNESSetJacobianLocal(da,(PetscErrorCode (*)(DMDALocalInfo*,void*,Mat,Mat,void*))FormJacobianLocal,user);CHKERRQ(ierr);
ierr = SNESSetFromOptions(snes);CHKERRQ(ierr);
ierr = SNESSetComputeInitialGuess(snes, FormInitialGuess,NULL);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Solve nonlinear system
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = SNESSolve(snes,NULL,NULL);CHKERRQ(ierr);
ierr = SNESGetIterationNumber(snes,&its);CHKERRQ(ierr);
ierr = SNESGetConvergedReason(snes, &reason);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = PetscPrintf(PETSC_COMM_WORLD,"Number of SNES iterations = %D, %s\n",its,SNESConvergedReasons[reason]);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = SNESGetDM(snes,&da);CHKERRQ(ierr);
ierr = SNESGetSolution(snes,&x);CHKERRQ(ierr);
ierr = L_2Error(da, x, &error, user);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"L_2 error in the solution: %g\n", (double)error);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Free work space. All PETSc objects should be destroyed when they
are no longer needed.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = SNESDestroy(&snes);CHKERRQ(ierr);
ierr = PetscBagDestroy(&bag);CHKERRQ(ierr);
ierr = PetscFinalize();
PetscFunctionReturn(0);
}