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 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 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);
}
