static PetscErrorCode CreateMatrix(DM shell,Mat *A) { PetscErrorCode ierr; DM da; ierr = DMShellGetContext(shell,(void**)&da);CHKERRQ(ierr); ierr = DMCreateMatrix(da,A);CHKERRQ(ierr); return 0; }
int main(int argc, char **argv) { SNES snes; /* nonlinear solver */ Mat A,J; /* Jacobian,preconditioner matrix */ Vec u,r; /* solution, residual vectors */ AppCtx user; /* user-defined work context */ PetscReal error = 0.0; /* L_2 error in the solution */ 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);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 = DMSetMatType(user.dm,MATAIJ);CHKERRQ(ierr); ierr = DMCreateMatrix(user.dm, &J);CHKERRQ(ierr); A = J; ierr = DMSNESSetFunctionLocal(user.dm, (PetscErrorCode (*)(DM,Vec,Vec,void*))FormFunctionLocal,&user);CHKERRQ(ierr); ierr = DMSNESSetJacobianLocal(user.dm, (PetscErrorCode (*)(DM,Vec,Mat,Mat,void*))FormJacobianLocal,&user);CHKERRQ(ierr); ierr = SNESSetFromOptions(snes);CHKERRQ(ierr); { PetscReal res; /* Check discretization error */ ierr = PetscPrintf(PETSC_COMM_WORLD, "Initial guess\n");CHKERRQ(ierr); ierr = VecView(u, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); /* ierr = ComputeError(u, &error, &user);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); } 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; }
example is used for testing the subroutine MatLoad_MPI_DA\n\n"; #include <petscdm.h> #include <petscdmda.h> int main(int argc,char **argv) { PetscInt X = 10,Y = 8,Z=8; PetscErrorCode ierr; DM da; PetscViewer viewer; Mat A; ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr; ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"temp.dat",FILE_MODE_WRITE,&viewer);CHKERRQ(ierr); /* Read options */ ierr = PetscOptionsGetInt(NULL,NULL,"-X",&X,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,NULL,"-Y",&Y,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,NULL,"-Z",&Z,NULL);CHKERRQ(ierr); /* Create distributed array and get vectors */ ierr = DMDACreate3d(PETSC_COMM_WORLD,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DMDA_STENCIL_STAR,X,Y,Z,PETSC_DECIDE,PETSC_DECIDE,PETSC_DECIDE,1,1,NULL,NULL,NULL,&da);CHKERRQ(ierr); ierr = DMSetFromOptions(da);CHKERRQ(ierr); ierr = DMSetUp(da);CHKERRQ(ierr); ierr = DMSetMatType(da,MATMPIAIJ);CHKERRQ(ierr); ierr = DMCreateMatrix(da,&A);CHKERRQ(ierr); ierr = MatShift(A,X);CHKERRQ(ierr); ierr = MatView(A,viewer);CHKERRQ(ierr); ierr = MatDestroy(&A);CHKERRQ(ierr); ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"temp.dat",FILE_MODE_READ,&viewer);CHKERRQ(ierr); ierr = DMCreateMatrix(da,&A);CHKERRQ(ierr); ierr = MatLoad(A,viewer);CHKERRQ(ierr); /* Free memory */ ierr = MatDestroy(&A);CHKERRQ(ierr); ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); ierr = DMDestroy(&da);CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; }
PetscErrorCode DMCreateMatrix_Network(DM dm,Mat *J) { PetscErrorCode ierr; DM_Network *network = (DM_Network*) dm->data; PetscFunctionBegin; ierr = DMCreateMatrix(network->plex,J);CHKERRQ(ierr); ierr = MatSetDM(*J,dm);CHKERRQ(ierr); PetscFunctionReturn(0); }
int main(int argc, char **argv) { PetscErrorCode ierr; Vec x; /* Solution vector */ TS ts; /* Time-stepping context */ AppCtx user; /* Application context */ Mat J; PetscViewer viewer; PetscInitialize(&argc,&argv,"petscopt_ex6", help); /* Get physics and time parameters */ ierr = Parameter_settings(&user);CHKERRQ(ierr); /* Create a 2D DA with dof = 1 */ ierr = DMDACreate2d(PETSC_COMM_WORLD,DMDA_BOUNDARY_NONE,DMDA_BOUNDARY_NONE,DMDA_STENCIL_STAR,-4,-4,PETSC_DECIDE,PETSC_DECIDE,1,1,NULL,NULL,&user.da);CHKERRQ(ierr); /* Set x and y coordinates */ ierr = DMDASetUniformCoordinates(user.da,user.xmin,user.xmax,user.ymin,user.ymax,NULL,NULL);CHKERRQ(ierr); /* Get global vector x from DM */ ierr = DMCreateGlobalVector(user.da,&x);CHKERRQ(ierr); ierr = ini_bou(x,&user);CHKERRQ(ierr); ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"ini_x",FILE_MODE_WRITE,&viewer);CHKERRQ(ierr); ierr = VecView(x,viewer);CHKERRQ(ierr); ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); /* Get Jacobian matrix structure from the da */ ierr = DMSetMatType(user.da,MATAIJ);CHKERRQ(ierr); ierr = DMCreateMatrix(user.da,&J);CHKERRQ(ierr); ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr); ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr); ierr = TSSetIFunction(ts,NULL,IFunction,&user);CHKERRQ(ierr); ierr = TSSetIJacobian(ts,J,J,IJacobian,&user);CHKERRQ(ierr); ierr = TSSetApplicationContext(ts,&user);CHKERRQ(ierr); ierr = TSSetDuration(ts,PETSC_DEFAULT,user.tmax);CHKERRQ(ierr); ierr = TSSetInitialTimeStep(ts,user.t0,.005);CHKERRQ(ierr); ierr = TSSetFromOptions(ts);CHKERRQ(ierr); ierr = TSSetPostStep(ts,PostStep);CHKERRQ(ierr); ierr = TSSolve(ts,x);CHKERRQ(ierr); ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"fin_x",FILE_MODE_WRITE,&viewer);CHKERRQ(ierr); ierr = VecView(x,viewer);CHKERRQ(ierr); ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); ierr = VecDestroy(&x);CHKERRQ(ierr); ierr = MatDestroy(&J);CHKERRQ(ierr); ierr = DMDestroy(&user.da);CHKERRQ(ierr); ierr = TSDestroy(&ts);CHKERRQ(ierr); PetscFinalize(); return 0; }
int main(int argc,char **argv) { PetscInt M = 3,N = 4,P = 2,s = 1,w = 2,i, m = PETSC_DECIDE,n = PETSC_DECIDE,p = PETSC_DECIDE; PetscErrorCode ierr; DM da; Mat mat; DMDAStencilType stencil_type = DMDA_STENCIL_BOX; PetscBool flg = PETSC_FALSE; MatStencil idx[2],idy[2]; PetscScalar *values; ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr); /* Read options */ ierr = PetscOptionsGetInt(NULL,"-M",&M,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,"-N",&N,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,"-P",&P,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,"-m",&m,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,"-n",&n,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,"-p",&p,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,"-s",&s,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,"-w",&w,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetBool(NULL,"-star",&flg,NULL);CHKERRQ(ierr); if (flg) stencil_type = DMDA_STENCIL_STAR; /* Create distributed array and get vectors */ ierr = DMDACreate3d(PETSC_COMM_WORLD,DMDA_BOUNDARY_NONE,DMDA_BOUNDARY_NONE,DMDA_BOUNDARY_NONE,stencil_type,M,N,P,m,n,p,w,s, 0,0,0,&da);CHKERRQ(ierr); ierr = DMSetMatType(da,MATMPIBAIJ);CHKERRQ(ierr); ierr = DMCreateMatrix(da,&mat);CHKERRQ(ierr); idx[0].i = 1; idx[0].j = 1; idx[0].k = 0; idx[1].i = 2; idx[1].j = 1; idx[1].k = 0; idy[0].i = 1; idy[0].j = 2; idy[0].k = 0; idy[1].i = 2; idy[1].j = 2; idy[1].k = 0; ierr = PetscMalloc1(2*2*w*w,&values);CHKERRQ(ierr); for (i=0; i<2*2*w*w; i++) values[i] = i; ierr = MatSetValuesBlockedStencil(mat,2,idx,2,idy,values,INSERT_VALUES);CHKERRQ(ierr); ierr = MatAssemblyBegin(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(mat,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); /* Free memory */ ierr = PetscFree(values);CHKERRQ(ierr); ierr = MatDestroy(&mat);CHKERRQ(ierr); ierr = DMDestroy(&da);CHKERRQ(ierr); ierr = PetscFinalize(); return 0; }
PetscErrorCode MyDMComputeFunction(DM dm,Vec x,Vec F) { PetscErrorCode ierr; Mat J; PetscFunctionBegin; ierr = DMGetApplicationContext(dm,&J);CHKERRQ(ierr); if (!J) { ierr = DMCreateMatrix(dm,MATAIJ,&J);CHKERRQ(ierr); ierr = PetscObjectCompose((PetscObject)J,"DM",(PetscObject)PETSC_NULL);CHKERRQ(ierr); ierr = FormMatrix(dm,J);CHKERRQ(ierr); ierr = DMSetApplicationContext(dm,J);CHKERRQ(ierr); ierr = DMSetApplicationContextDestroy(dm,(PetscErrorCode (*)(void**))MatDestroy);CHKERRQ(ierr); } ierr = MatMult(J,x,F);CHKERRQ(ierr); PetscFunctionReturn(0); }
PetscErrorCode MyComputeFunction(SNES snes,Vec x,Vec F,void *ctx) { PetscErrorCode ierr; Mat J; DM dm; PetscFunctionBeginUser; ierr = SNESGetDM(snes,&dm);CHKERRQ(ierr); ierr = DMGetApplicationContext(dm,&J);CHKERRQ(ierr); if (!J) { ierr = DMCreateMatrix(dm,MATAIJ,&J);CHKERRQ(ierr); ierr = MatSetDM(J, PETSC_NULL);CHKERRQ(ierr); ierr = FormMatrix(dm,J);CHKERRQ(ierr); ierr = DMSetApplicationContext(dm,J);CHKERRQ(ierr); ierr = DMSetApplicationContextDestroy(dm,(PetscErrorCode (*)(void**))MatDestroy);CHKERRQ(ierr); } ierr = MatMult(J,x,F);CHKERRQ(ierr); PetscFunctionReturn(0); }
int main(int argc,char **args) { PetscErrorCode ierr; DM da; KSP ksp; Mat A; Vec b,u,uexact; PetscReal errnorm; DMDALocalInfo info; PetscInitialize(&argc,&args,(char*)0,help); ierr = DMDACreate1d(PETSC_COMM_WORLD, DM_BOUNDARY_NONE, 9,1,1,NULL, &da); CHKERRQ(ierr); ierr = DMSetFromOptions(da); CHKERRQ(ierr); ierr = DMSetUp(da); CHKERRQ(ierr); ierr = DMDASetUniformCoordinates(da,0.0,1.0,-1.0,-1.0,-1.0,-1.0); CHKERRQ(ierr); ierr = DMCreateMatrix(da,&A);CHKERRQ(ierr); ierr = MatSetOptionsPrefix(A,"a_"); CHKERRQ(ierr); ierr = MatSetFromOptions(A); CHKERRQ(ierr); ierr = DMCreateGlobalVector(da,&b);CHKERRQ(ierr); ierr = VecDuplicate(b,&u); CHKERRQ(ierr); ierr = VecDuplicate(b,&uexact); CHKERRQ(ierr); ierr = formExactAndRHS(da,uexact,b); CHKERRQ(ierr); ierr = formdirichletlaplacian(da,A); CHKERRQ(ierr); ierr = KSPCreate(PETSC_COMM_WORLD,&ksp); CHKERRQ(ierr); ierr = KSPSetOperators(ksp,A,A); CHKERRQ(ierr); ierr = KSPSetFromOptions(ksp); CHKERRQ(ierr); ierr = KSPSolve(ksp,b,u); CHKERRQ(ierr); ierr = VecAXPY(u,-1.0,uexact); CHKERRQ(ierr); // u <- u + (-1.0) uxact ierr = VecNorm(u,NORM_INFINITY,&errnorm); CHKERRQ(ierr); ierr = DMDAGetLocalInfo(da,&info);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "on %d point grid: error |u-uexact|_inf = %g\n", info.mx,errnorm); CHKERRQ(ierr); VecDestroy(&u); VecDestroy(&uexact); VecDestroy(&b); MatDestroy(&A); KSPDestroy(&ksp); DMDestroy(&da); PetscFinalize(); return 0; }
static PetscErrorCode DMCreateMatrix_Composite_Nest(DM dm,MatType mtype,Mat *J) { const DM_Composite *com = (DM_Composite*)dm->data; const struct DMCompositeLink *rlink,*clink; PetscErrorCode ierr; IS *isg; Mat *submats; PetscInt i,j,n; PetscFunctionBegin; n = com->nDM; /* Total number of entries */ /* Explicit index sets are not required for MatCreateNest, but getting them here allows MatNest to do consistency * checking and allows ISEqual to compare by identity instead of by contents. */ ierr = DMCompositeGetGlobalISs(dm,&isg);CHKERRQ(ierr); /* Get submatrices */ ierr = PetscMalloc(n*n*sizeof(Mat),&submats);CHKERRQ(ierr); for (i=0,rlink=com->next; rlink; i++,rlink=rlink->next) { for (j=0,clink=com->next; clink; j++,clink=clink->next) { Mat sub = NULL; if (i == j) { ierr = DMCreateMatrix(rlink->dm,NULL,&sub);CHKERRQ(ierr); } else if (com->FormCoupleLocations) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"Cannot manage off-diagonal parts yet"); submats[i*n+j] = sub; } } ierr = MatCreateNest(PetscObjectComm((PetscObject)dm),n,isg,n,isg,submats,J);CHKERRQ(ierr); /* Disown references */ for (i=0; i<n; i++) {ierr = ISDestroy(&isg[i]);CHKERRQ(ierr);} ierr = PetscFree(isg);CHKERRQ(ierr); for (i=0; i<n*n; i++) { if (submats[i]) {ierr = MatDestroy(&submats[i]);CHKERRQ(ierr);} } ierr = PetscFree(submats);CHKERRQ(ierr); PetscFunctionReturn(0); }
int main(int argc,char **argv) { PetscErrorCode ierr; KSP ksp; PC pc; Vec x,b; DM da; Mat A; PetscInt dof=1; PetscBool flg; PetscScalar zero=0.0; PetscInitialize(&argc,&argv,(char *)0,help); ierr = PetscOptionsGetInt(PETSC_NULL,"-dof",&dof,PETSC_NULL);CHKERRQ(ierr); ierr = DMDACreate(PETSC_COMM_WORLD,&da);CHKERRQ(ierr); ierr = DMDASetDim(da,3);CHKERRQ(ierr); ierr = DMDASetBoundaryType(da,DMDA_BOUNDARY_NONE,DMDA_BOUNDARY_NONE,DMDA_BOUNDARY_NONE);CHKERRQ(ierr); ierr = DMDASetStencilType(da,DMDA_STENCIL_STAR);CHKERRQ(ierr); ierr = DMDASetSizes(da,3,3,3);CHKERRQ(ierr); ierr = DMDASetNumProcs(da,PETSC_DECIDE,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr); ierr = DMDASetDof(da,dof);CHKERRQ(ierr); ierr = DMDASetStencilWidth(da,1);CHKERRQ(ierr); ierr = DMDASetOwnershipRanges(da,PETSC_NULL,PETSC_NULL,PETSC_NULL);CHKERRQ(ierr); ierr = DMSetFromOptions(da);CHKERRQ(ierr); ierr = DMSetUp(da);CHKERRQ(ierr); ierr = DMCreateGlobalVector(da,&x);CHKERRQ(ierr); ierr = DMCreateGlobalVector(da,&b);CHKERRQ(ierr); ierr = DMCreateMatrix(da,MATAIJ,&A);CHKERRQ(ierr); ierr = VecSet(b,zero);CHKERRQ(ierr); /* Test sbaij matrix */ flg = PETSC_FALSE; ierr = PetscOptionsGetBool(PETSC_NULL,"-test_sbaij",&flg,PETSC_NULL);CHKERRQ(ierr); if (flg) { Mat sA; ierr = MatSetOption(A,MAT_SYMMETRIC,PETSC_TRUE);CHKERRQ(ierr); ierr = MatConvert(A,MATSBAIJ,MAT_INITIAL_MATRIX,&sA);CHKERRQ(ierr); ierr = MatDestroy(&A);CHKERRQ(ierr); A = sA; } ierr = KSPCreate(PETSC_COMM_WORLD,&ksp);CHKERRQ(ierr); ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr); ierr = KSPSetOperators(ksp,A,A,SAME_NONZERO_PATTERN);CHKERRQ(ierr); ierr = KSPGetPC(ksp,&pc);CHKERRQ(ierr); ierr = PCSetDM(pc,(DM)da);CHKERRQ(ierr); ierr = KSPSolve(ksp,b,x);CHKERRQ(ierr); /* check final residual */ flg = PETSC_FALSE; ierr = PetscOptionsGetBool(PETSC_NULL, "-check_final_residual", &flg,PETSC_NULL);CHKERRQ(ierr); if (flg){ Vec b1; PetscReal norm; ierr = KSPGetSolution(ksp,&x);CHKERRQ(ierr); ierr = VecDuplicate(b,&b1);CHKERRQ(ierr); ierr = MatMult(A,x,b1);CHKERRQ(ierr); ierr = VecAXPY(b1,-1.0,b);CHKERRQ(ierr); ierr = VecNorm(b1,NORM_2,&norm);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD,"Final residual %g\n",norm);CHKERRQ(ierr); ierr = VecDestroy(&b1);CHKERRQ(ierr); } ierr = KSPDestroy(&ksp);CHKERRQ(ierr); ierr = VecDestroy(&x);CHKERRQ(ierr); ierr = VecDestroy(&b);CHKERRQ(ierr); ierr = MatDestroy(&A);CHKERRQ(ierr); ierr = DMDestroy(&da);CHKERRQ(ierr); ierr = PetscFinalize(); return 0; }
/* Notice that this requires the previous momentum solution. The element stiffness matrix for the identity in linear elements is 1 /2 1 1\ - |1 2 1| 12 \1 1 2/ no matter what the shape of the triangle. */ PetscErrorCode TaylorGalerkinStepIIMassEnergy(DM da, UserContext *user) { MPI_Comm comm; Mat mat; Vec rhs_m, rhs_e; PetscScalar identity[9] = {0.16666666667, 0.08333333333, 0.08333333333, 0.08333333333, 0.16666666667, 0.08333333333, 0.08333333333, 0.08333333333, 0.16666666667}; PetscScalar *u_n, *v_n, *p_n, *t_n, *mu_n, *kappa_n; PetscScalar *rho_n, *rho_u_n, *rho_v_n, *rho_e_n; PetscScalar *u_phi, *v_phi; PetscScalar *rho_u_np1, *rho_v_np1; PetscInt idx[3]; PetscScalar psi_x[3], psi_y[3]; PetscScalar values_m[3]; PetscScalar values_e[3]; PetscScalar phi = user->phi; PetscScalar mu, kappa, tau_xx, tau_xy, tau_yy, q_x, q_y; PetscReal hx, hy, area; KSP ksp; const PetscInt *necon; PetscInt j, k, e, ne, nc, mx, my; PetscErrorCode ierr; PetscFunctionBeginUser; ierr = PetscObjectGetComm((PetscObject) da, &comm);CHKERRQ(ierr); ierr = DMSetMatType(da,MATAIJ);CHKERRQ(ierr); ierr = DMCreateMatrix(da, &mat);CHKERRQ(ierr); ierr = MatSetOption(mat,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr); ierr = DMGetGlobalVector(da, &rhs_m);CHKERRQ(ierr); ierr = DMGetGlobalVector(da, &rhs_e);CHKERRQ(ierr); ierr = KSPCreate(comm, &ksp);CHKERRQ(ierr); ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr); ierr = DMDAGetInfo(da, 0, &mx, &my, 0,0,0,0,0,0,0,0,0,0);CHKERRQ(ierr); hx = 1.0 / (PetscReal)(mx-1); hy = 1.0 / (PetscReal)(my-1); area = 0.5*hx*hy; ierr = VecGetArray(user->sol_n.u, &u_n);CHKERRQ(ierr); ierr = VecGetArray(user->sol_n.v, &v_n);CHKERRQ(ierr); ierr = VecGetArray(user->sol_n.p, &p_n);CHKERRQ(ierr); ierr = VecGetArray(user->sol_n.t, &t_n);CHKERRQ(ierr); ierr = VecGetArray(user->mu, &mu_n);CHKERRQ(ierr); ierr = VecGetArray(user->kappa, &kappa_n);CHKERRQ(ierr); ierr = VecGetArray(user->sol_n.rho, &rho_n);CHKERRQ(ierr); ierr = VecGetArray(user->sol_n.rho_u, &rho_u_n);CHKERRQ(ierr); ierr = VecGetArray(user->sol_n.rho_v, &rho_v_n);CHKERRQ(ierr); ierr = VecGetArray(user->sol_n.rho_e, &rho_e_n);CHKERRQ(ierr); ierr = VecGetArray(user->sol_phi.u, &u_phi);CHKERRQ(ierr); ierr = VecGetArray(user->sol_phi.v, &v_phi);CHKERRQ(ierr); ierr = VecGetArray(user->sol_np1.rho_u, &rho_u_np1);CHKERRQ(ierr); ierr = VecGetArray(user->sol_np1.rho_v, &rho_v_np1);CHKERRQ(ierr); ierr = DMDAGetElements(da, &ne, &nc, &necon);CHKERRQ(ierr); for (e = 0; e < ne; e++) { for (j = 0; j < 3; j++) { idx[j] = necon[3*e+j]; values_m[j] = 0.0; values_e[j] = 0.0; } /* Get basis function deriatives (we need the orientation of the element here) */ if (idx[1] > idx[0]) { psi_x[0] = -hy; psi_x[1] = hy; psi_x[2] = 0.0; psi_y[0] = -hx; psi_y[1] = 0.0; psi_y[2] = hx; } else { psi_x[0] = hy; psi_x[1] = -hy; psi_x[2] = 0.0; psi_y[0] = hx; psi_y[1] = 0.0; psi_y[2] = -hx; } /* <\nabla\psi, F^*>: Divergence of the predicted convective fluxes */ for (j = 0; j < 3; j++) { values_m[j] += (psi_x[j]*(phi*rho_u_np1[idx[j]] + rho_u_n[idx[j]]) + psi_y[j]*(rho_v_np1[idx[j]] + rho_v_n[idx[j]]))/3.0; values_e[j] += values_m[j]*((rho_e_n[idx[j]] + p_n[idx[j]]) / rho_n[idx[j]]); } /* -<\nabla\psi, F^n_v>: Divergence of the viscous fluxes */ for (j = 0; j < 3; j++) { /* \tau_{xx} = 2/3 \mu(T) (2 {\partial u\over\partial x} - {\partial v\over\partial y}) */ /* \tau_{xy} = \mu(T) ( {\partial u\over\partial y} + {\partial v\over\partial x}) */ /* \tau_{yy} = 2/3 \mu(T) (2 {\partial v\over\partial y} - {\partial u\over\partial x}) */ /* q_x = -\kappa(T) {\partial T\over\partial x} */ /* q_y = -\kappa(T) {\partial T\over\partial y} */ /* above code commeted out - causing ininitialized variables. */ q_x =0; q_y =0; mu = 0.0; kappa = 0.0; tau_xx = 0.0; tau_xy = 0.0; tau_yy = 0.0; for (k = 0; k < 3; k++) { mu += mu_n[idx[k]]; kappa += kappa_n[idx[k]]; tau_xx += 2.0*psi_x[k]*u_n[idx[k]] - psi_y[k]*v_n[idx[k]]; tau_xy += psi_y[k]*u_n[idx[k]] + psi_x[k]*v_n[idx[k]]; tau_yy += 2.0*psi_y[k]*v_n[idx[k]] - psi_x[k]*u_n[idx[k]]; q_x += psi_x[k]*t_n[idx[k]]; q_y += psi_y[k]*t_n[idx[k]]; } mu /= 3.0; kappa /= 3.0; tau_xx *= (2.0/3.0)*mu; tau_xy *= mu; tau_yy *= (2.0/3.0)*mu; values_e[j] -= area*(psi_x[j]*(u_phi[e]*tau_xx + v_phi[e]*tau_xy + q_x) + psi_y[j]*(u_phi[e]*tau_xy + v_phi[e]*tau_yy + q_y)); } /* Accumulate to global structures */ ierr = VecSetValuesLocal(rhs_m, 3, idx, values_m, ADD_VALUES);CHKERRQ(ierr); ierr = VecSetValuesLocal(rhs_e, 3, idx, values_e, ADD_VALUES);CHKERRQ(ierr); ierr = MatSetValuesLocal(mat, 3, idx, 3, idx, identity, ADD_VALUES);CHKERRQ(ierr); } ierr = DMDARestoreElements(da, &ne, &nc, &necon);CHKERRQ(ierr); ierr = VecRestoreArray(user->sol_n.u, &u_n);CHKERRQ(ierr); ierr = VecRestoreArray(user->sol_n.v, &v_n);CHKERRQ(ierr); ierr = VecRestoreArray(user->sol_n.p, &p_n);CHKERRQ(ierr); ierr = VecRestoreArray(user->sol_n.t, &t_n);CHKERRQ(ierr); ierr = VecRestoreArray(user->mu, &mu_n);CHKERRQ(ierr); ierr = VecRestoreArray(user->kappa, &kappa_n);CHKERRQ(ierr); ierr = VecRestoreArray(user->sol_n.rho, &rho_n);CHKERRQ(ierr); ierr = VecRestoreArray(user->sol_n.rho_u, &rho_u_n);CHKERRQ(ierr); ierr = VecRestoreArray(user->sol_n.rho_v, &rho_v_n);CHKERRQ(ierr); ierr = VecRestoreArray(user->sol_n.rho_e, &rho_e_n);CHKERRQ(ierr); ierr = VecRestoreArray(user->sol_phi.u, &u_phi);CHKERRQ(ierr); ierr = VecRestoreArray(user->sol_phi.v, &v_phi);CHKERRQ(ierr); ierr = VecRestoreArray(user->sol_np1.rho_u, &rho_u_np1);CHKERRQ(ierr); ierr = VecRestoreArray(user->sol_np1.rho_v, &rho_v_np1);CHKERRQ(ierr); ierr = VecAssemblyBegin(rhs_m);CHKERRQ(ierr); ierr = VecAssemblyBegin(rhs_e);CHKERRQ(ierr); ierr = MatAssemblyBegin(mat, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = VecAssemblyEnd(rhs_m);CHKERRQ(ierr); ierr = VecAssemblyEnd(rhs_e);CHKERRQ(ierr); ierr = MatAssemblyEnd(mat, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = VecScale(rhs_m, user->dt);CHKERRQ(ierr); ierr = VecScale(rhs_e, user->dt);CHKERRQ(ierr); ierr = KSPSetOperators(ksp, mat, mat, DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr); ierr = KSPSolve(ksp, rhs_m, user->sol_np1.rho);CHKERRQ(ierr); ierr = KSPSolve(ksp, rhs_e, user->sol_np1.rho_e);CHKERRQ(ierr); ierr = KSPDestroy(&ksp);CHKERRQ(ierr); ierr = MatDestroy(&mat);CHKERRQ(ierr); ierr = DMRestoreGlobalVector(da, &rhs_m);CHKERRQ(ierr); ierr = DMRestoreGlobalVector(da, &rhs_e);CHKERRQ(ierr); PetscFunctionReturn(0); }
/* The element stiffness matrix for the identity in linear elements is 1 /2 1 1\ - |1 2 1| 12 \1 1 2/ no matter what the shape of the triangle. */ PetscErrorCode TaylorGalerkinStepIIMomentum(DM da, UserContext *user) { MPI_Comm comm; KSP ksp; Mat mat; Vec rhs_u, rhs_v; PetscScalar identity[9] = {0.16666666667, 0.08333333333, 0.08333333333, 0.08333333333, 0.16666666667, 0.08333333333, 0.08333333333, 0.08333333333, 0.16666666667}; PetscScalar *u_n, *v_n, *mu_n; PetscScalar *u_phi, *v_phi; PetscScalar *rho_u_phi, *rho_v_phi; PetscInt idx[3]; PetscScalar values_u[3]; PetscScalar values_v[3]; PetscScalar psi_x[3], psi_y[3]; PetscScalar mu, tau_xx, tau_xy, tau_yy; PetscReal hx, hy, area; const PetscInt *necon; PetscInt j, k, e, ne, nc, mx, my; PetscErrorCode ierr; PetscFunctionBeginUser; ierr = PetscObjectGetComm((PetscObject) da, &comm);CHKERRQ(ierr); ierr = DMSetMatType(da,MATAIJ);CHKERRQ(ierr); ierr = DMCreateMatrix(da, &mat);CHKERRQ(ierr); ierr = MatSetOption(mat,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr); ierr = DMGetGlobalVector(da, &rhs_u);CHKERRQ(ierr); ierr = DMGetGlobalVector(da, &rhs_v);CHKERRQ(ierr); ierr = KSPCreate(comm, &ksp);CHKERRQ(ierr); ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr); ierr = DMDAGetInfo(da, 0, &mx, &my, 0,0,0,0,0,0,0,0,0,0);CHKERRQ(ierr); hx = 1.0 / (PetscReal)(mx-1); hy = 1.0 / (PetscReal)(my-1); area = 0.5*hx*hy; ierr = VecGetArray(user->sol_n.u, &u_n);CHKERRQ(ierr); ierr = VecGetArray(user->sol_n.v, &v_n);CHKERRQ(ierr); ierr = VecGetArray(user->mu, &mu_n);CHKERRQ(ierr); ierr = VecGetArray(user->sol_phi.u, &u_phi);CHKERRQ(ierr); ierr = VecGetArray(user->sol_phi.v, &v_phi);CHKERRQ(ierr); ierr = VecGetArray(user->sol_phi.rho_u, &rho_u_phi);CHKERRQ(ierr); ierr = VecGetArray(user->sol_phi.rho_v, &rho_v_phi);CHKERRQ(ierr); ierr = DMDAGetElements(da, &ne, &nc, &necon);CHKERRQ(ierr); for (e = 0; e < ne; e++) { for (j = 0; j < 3; j++) { idx[j] = necon[3*e+j]; values_u[j] = 0.0; values_v[j] = 0.0; } /* Get basis function deriatives (we need the orientation of the element here) */ if (idx[1] > idx[0]) { psi_x[0] = -hy; psi_x[1] = hy; psi_x[2] = 0.0; psi_y[0] = -hx; psi_y[1] = 0.0; psi_y[2] = hx; } else { psi_x[0] = hy; psi_x[1] = -hy; psi_x[2] = 0.0; psi_y[0] = hx; psi_y[1] = 0.0; psi_y[2] = -hx; } /* <\nabla\psi, F^{n+\phi}_e>: Divergence of the element-averaged convective fluxes */ for (j = 0; j < 3; j++) { values_u[j] += psi_x[j]*rho_u_phi[e]*u_phi[e] + psi_y[j]*rho_u_phi[e]*v_phi[e]; values_v[j] += psi_x[j]*rho_v_phi[e]*u_phi[e] + psi_y[j]*rho_v_phi[e]*v_phi[e]; } /* -<\nabla\psi, F^n_v>: Divergence of the viscous fluxes */ for (j = 0; j < 3; j++) { /* \tau_{xx} = 2/3 \mu(T) (2 {\partial u\over\partial x} - {\partial v\over\partial y}) */ /* \tau_{xy} = \mu(T) ( {\partial u\over\partial y} + {\partial v\over\partial x}) */ /* \tau_{yy} = 2/3 \mu(T) (2 {\partial v\over\partial y} - {\partial u\over\partial x}) */ mu = 0.0; tau_xx = 0.0; tau_xy = 0.0; tau_yy = 0.0; for (k = 0; k < 3; k++) { mu += mu_n[idx[k]]; tau_xx += 2.0*psi_x[k]*u_n[idx[k]] - psi_y[k]*v_n[idx[k]]; tau_xy += psi_y[k]*u_n[idx[k]] + psi_x[k]*v_n[idx[k]]; tau_yy += 2.0*psi_y[k]*v_n[idx[k]] - psi_x[k]*u_n[idx[k]]; } mu /= 3.0; tau_xx *= (2.0/3.0)*mu; tau_xy *= mu; tau_yy *= (2.0/3.0)*mu; values_u[j] -= area*(psi_x[j]*tau_xx + psi_y[j]*tau_xy); values_v[j] -= area*(psi_x[j]*tau_xy + psi_y[j]*tau_yy); } /* Accumulate to global structures */ ierr = VecSetValuesLocal(rhs_u, 3, idx, values_u, ADD_VALUES);CHKERRQ(ierr); ierr = VecSetValuesLocal(rhs_v, 3, idx, values_v, ADD_VALUES);CHKERRQ(ierr); ierr = MatSetValuesLocal(mat, 3, idx, 3, idx, identity, ADD_VALUES);CHKERRQ(ierr); } ierr = DMDARestoreElements(da, &ne, &nc, &necon);CHKERRQ(ierr); ierr = VecRestoreArray(user->sol_n.u, &u_n);CHKERRQ(ierr); ierr = VecRestoreArray(user->sol_n.v, &v_n);CHKERRQ(ierr); ierr = VecRestoreArray(user->mu, &mu_n);CHKERRQ(ierr); ierr = VecRestoreArray(user->sol_phi.u, &u_phi);CHKERRQ(ierr); ierr = VecRestoreArray(user->sol_phi.v, &v_phi);CHKERRQ(ierr); ierr = VecRestoreArray(user->sol_phi.rho_u, &rho_u_phi);CHKERRQ(ierr); ierr = VecRestoreArray(user->sol_phi.rho_v, &rho_v_phi);CHKERRQ(ierr); ierr = VecAssemblyBegin(rhs_u);CHKERRQ(ierr); ierr = VecAssemblyBegin(rhs_v);CHKERRQ(ierr); ierr = MatAssemblyBegin(mat, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = VecAssemblyEnd(rhs_u);CHKERRQ(ierr); ierr = VecAssemblyEnd(rhs_v);CHKERRQ(ierr); ierr = MatAssemblyEnd(mat, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = VecScale(rhs_u,user->dt);CHKERRQ(ierr); ierr = VecScale(rhs_v,user->dt);CHKERRQ(ierr); ierr = KSPSetOperators(ksp, mat, mat, DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr); ierr = KSPSolve(ksp, rhs_u, user->sol_np1.rho_u);CHKERRQ(ierr); ierr = KSPSolve(ksp, rhs_v, user->sol_np1.rho_v);CHKERRQ(ierr); ierr = KSPDestroy(&ksp);CHKERRQ(ierr); ierr = MatDestroy(&mat);CHKERRQ(ierr); ierr = DMRestoreGlobalVector(da, &rhs_u);CHKERRQ(ierr); ierr = DMRestoreGlobalVector(da, &rhs_v);CHKERRQ(ierr); PetscFunctionReturn(0); }
int main(int argc,char **args) { Mat Amat; PetscErrorCode ierr; SNES snes; KSP ksp; MPI_Comm comm; PetscMPIInt npe,rank; PetscLogStage stage[7]; PetscBool test_nonzero_cols=PETSC_FALSE,use_nearnullspace=PETSC_TRUE; Vec xx,bb; PetscInt iter,i,N,dim=3,cells[3]={1,1,1},max_conv_its,local_sizes[7],run_type=1; DM dm,distdm,basedm; PetscBool flg; char convType[256]; PetscReal Lx,mdisp[10],err[10]; const char * const options[10] = {"-ex56_dm_refine 0", "-ex56_dm_refine 1", "-ex56_dm_refine 2", "-ex56_dm_refine 3", "-ex56_dm_refine 4", "-ex56_dm_refine 5", "-ex56_dm_refine 6", "-ex56_dm_refine 7", "-ex56_dm_refine 8", "-ex56_dm_refine 9"}; PetscFunctionBeginUser; ierr = PetscInitialize(&argc,&args,(char*)0,help);if (ierr) return ierr; comm = PETSC_COMM_WORLD; ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); ierr = MPI_Comm_size(comm, &npe);CHKERRQ(ierr); /* options */ ierr = PetscOptionsBegin(comm,NULL,"3D bilinear Q1 elasticity options","");CHKERRQ(ierr); { i = 3; ierr = PetscOptionsIntArray("-cells", "Number of (flux tube) processor in each dimension", "ex56.c", cells, &i, NULL);CHKERRQ(ierr); Lx = 1.; /* or ne for rod */ max_conv_its = 3; ierr = PetscOptionsInt("-max_conv_its","Number of iterations in convergence study","",max_conv_its,&max_conv_its,NULL);CHKERRQ(ierr); if (max_conv_its<=0 || max_conv_its>7) SETERRQ1(PETSC_COMM_WORLD, PETSC_ERR_USER, "Bad number of iterations for convergence test (%D)",max_conv_its); ierr = PetscOptionsReal("-lx","Length of domain","",Lx,&Lx,NULL);CHKERRQ(ierr); ierr = PetscOptionsReal("-alpha","material coefficient inside circle","",s_soft_alpha,&s_soft_alpha,NULL);CHKERRQ(ierr); ierr = PetscOptionsBool("-test_nonzero_cols","nonzero test","",test_nonzero_cols,&test_nonzero_cols,NULL);CHKERRQ(ierr); ierr = PetscOptionsBool("-use_mat_nearnullspace","MatNearNullSpace API test","",use_nearnullspace,&use_nearnullspace,NULL);CHKERRQ(ierr); ierr = PetscOptionsInt("-run_type","0: twisting load on cantalever, 1: 3rd order accurate convergence test","",run_type,&run_type,NULL);CHKERRQ(ierr); i = 3; ierr = PetscOptionsInt("-mat_block_size","","",i,&i,&flg);CHKERRQ(ierr); if (!flg || i!=3) SETERRQ2(PETSC_COMM_WORLD, PETSC_ERR_USER, "'-mat_block_size 3' must be set (%D) and = 3 (%D)",flg,flg? i : 3); } ierr = PetscOptionsEnd();CHKERRQ(ierr); ierr = PetscLogStageRegister("Mesh Setup", &stage[6]);CHKERRQ(ierr); ierr = PetscLogStageRegister("1st Setup", &stage[0]);CHKERRQ(ierr); ierr = PetscLogStageRegister("1st Solve", &stage[1]);CHKERRQ(ierr); /* create DM, Plex calls DMSetup */ ierr = PetscLogStagePush(stage[6]);CHKERRQ(ierr); ierr = DMPlexCreateHexBoxMesh(comm, dim, cells, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, &dm);CHKERRQ(ierr); { DMLabel label; IS is; ierr = DMCreateLabel(dm, "boundary");CHKERRQ(ierr); ierr = DMGetLabel(dm, "boundary", &label);CHKERRQ(ierr); ierr = DMPlexMarkBoundaryFaces(dm, label);CHKERRQ(ierr); if (run_type==0) { ierr = DMGetStratumIS(dm, "boundary", 1, &is);CHKERRQ(ierr); ierr = DMCreateLabel(dm,"Faces");CHKERRQ(ierr); if (is) { PetscInt d, f, Nf; const PetscInt *faces; PetscInt csize; PetscSection cs; Vec coordinates ; DM cdm; ierr = ISGetLocalSize(is, &Nf);CHKERRQ(ierr); ierr = ISGetIndices(is, &faces);CHKERRQ(ierr); ierr = DMGetCoordinatesLocal(dm, &coordinates);CHKERRQ(ierr); ierr = DMGetCoordinateDM(dm, &cdm);CHKERRQ(ierr); ierr = DMGetDefaultSection(cdm, &cs);CHKERRQ(ierr); /* Check for each boundary face if any component of its centroid is either 0.0 or 1.0 */ for (f = 0; f < Nf; ++f) { PetscReal faceCoord; PetscInt b,v; PetscScalar *coords = NULL; PetscInt Nv; ierr = DMPlexVecGetClosure(cdm, cs, coordinates, faces[f], &csize, &coords);CHKERRQ(ierr); Nv = csize/dim; /* Calculate mean coordinate vector */ for (d = 0; d < dim; ++d) { faceCoord = 0.0; for (v = 0; v < Nv; ++v) faceCoord += PetscRealPart(coords[v*dim+d]); faceCoord /= Nv; for (b = 0; b < 2; ++b) { if (PetscAbs(faceCoord - b) < PETSC_SMALL) { /* domain have not been set yet, still [0,1]^3 */ ierr = DMSetLabelValue(dm, "Faces", faces[f], d*2+b+1);CHKERRQ(ierr); } } } ierr = DMPlexVecRestoreClosure(cdm, cs, coordinates, faces[f], &csize, &coords);CHKERRQ(ierr); } ierr = ISRestoreIndices(is, &faces);CHKERRQ(ierr); } ierr = ISDestroy(&is);CHKERRQ(ierr); ierr = DMGetLabel(dm, "Faces", &label);CHKERRQ(ierr); ierr = DMPlexLabelComplete(dm, label);CHKERRQ(ierr); } } { PetscInt dimEmbed, i; PetscInt nCoords; PetscScalar *coords,bounds[] = {0,Lx,-.5,.5,-.5,.5,}; /* x_min,x_max,y_min,y_max */ Vec coordinates; if (run_type==1) { for (i = 0; i < 2*dim; i++) bounds[i] = (i%2) ? 1 : 0; } ierr = DMGetCoordinatesLocal(dm,&coordinates);CHKERRQ(ierr); ierr = DMGetCoordinateDim(dm,&dimEmbed);CHKERRQ(ierr); if (dimEmbed != dim) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"dimEmbed != dim %D",dimEmbed);CHKERRQ(ierr); ierr = VecGetLocalSize(coordinates,&nCoords);CHKERRQ(ierr); if (nCoords % dimEmbed) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Coordinate vector the wrong size");CHKERRQ(ierr); ierr = VecGetArray(coordinates,&coords);CHKERRQ(ierr); for (i = 0; i < nCoords; i += dimEmbed) { PetscInt j; PetscScalar *coord = &coords[i]; for (j = 0; j < dimEmbed; j++) { coord[j] = bounds[2 * j] + coord[j] * (bounds[2 * j + 1] - bounds[2 * j]); } } ierr = VecRestoreArray(coordinates,&coords);CHKERRQ(ierr); ierr = DMSetCoordinatesLocal(dm,coordinates);CHKERRQ(ierr); } /* convert to p4est, and distribute */ ierr = PetscOptionsBegin(comm, "", "Mesh conversion options", "DMPLEX");CHKERRQ(ierr); ierr = PetscOptionsFList("-dm_type","Convert DMPlex to another format (should not be Plex!)","ex56.c",DMList,DMPLEX,convType,256,&flg);CHKERRQ(ierr); ierr = PetscOptionsEnd(); if (flg) { DM newdm; ierr = DMConvert(dm,convType,&newdm);CHKERRQ(ierr); if (newdm) { const char *prefix; PetscBool isForest; ierr = PetscObjectGetOptionsPrefix((PetscObject)dm,&prefix);CHKERRQ(ierr); ierr = PetscObjectSetOptionsPrefix((PetscObject)newdm,prefix);CHKERRQ(ierr); ierr = DMIsForest(newdm,&isForest);CHKERRQ(ierr); if (isForest) { } else SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_USER, "Converted to non Forest?"); ierr = DMDestroy(&dm);CHKERRQ(ierr); dm = newdm; } else SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_USER, "Convert failed?"); } else { /* Plex Distribute mesh over processes */ ierr = DMPlexDistribute(dm, 0, NULL, &distdm);CHKERRQ(ierr); if (distdm) { const char *prefix; ierr = PetscObjectGetOptionsPrefix((PetscObject)dm,&prefix);CHKERRQ(ierr); ierr = PetscObjectSetOptionsPrefix((PetscObject)distdm,prefix);CHKERRQ(ierr); ierr = DMDestroy(&dm);CHKERRQ(ierr); dm = distdm; } } ierr = PetscLogStagePop();CHKERRQ(ierr); basedm = dm; dm = NULL; for (iter=0 ; iter<max_conv_its ; iter++) { ierr = PetscLogStagePush(stage[6]);CHKERRQ(ierr); /* make new DM */ ierr = DMClone(basedm, &dm);CHKERRQ(ierr); ierr = PetscObjectSetOptionsPrefix((PetscObject) dm, "ex56_");CHKERRQ(ierr); ierr = PetscObjectSetName( (PetscObject)dm,"Mesh");CHKERRQ(ierr); ierr = PetscOptionsClearValue(NULL,"-ex56_dm_refine");CHKERRQ(ierr); ierr = PetscOptionsInsertString(NULL,options[iter]);CHKERRQ(ierr); ierr = DMSetFromOptions(dm);CHKERRQ(ierr); /* refinement done here in Plex, p4est */ /* snes */ ierr = SNESCreate(comm, &snes);CHKERRQ(ierr); ierr = SNESSetDM(snes, dm);CHKERRQ(ierr); /* fem */ { const PetscInt Ncomp = dim; const PetscInt components[] = {0,1,2}; const PetscInt Nfid = 1, Npid = 1; const PetscInt fid[] = {1}; /* The fixed faces (x=0) */ const PetscInt pid[] = {2}; /* The faces with loading (x=L_x) */ PetscFE fe; PetscDS prob; DM cdm = dm; ierr = PetscFECreateDefault(dm, dim, dim, PETSC_FALSE, NULL, PETSC_DECIDE, &fe);CHKERRQ(ierr); /* elasticity */ ierr = PetscObjectSetName((PetscObject) fe, "deformation");CHKERRQ(ierr); /* FEM prob */ ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); ierr = PetscDSSetDiscretization(prob, 0, (PetscObject) fe);CHKERRQ(ierr); /* setup problem */ if (run_type==1) { ierr = PetscDSSetJacobian(prob, 0, 0, NULL, NULL, NULL, g3_uu_3d);CHKERRQ(ierr); ierr = PetscDSSetResidual(prob, 0, f0_u_x4, f1_u_3d);CHKERRQ(ierr); } else { ierr = PetscDSSetJacobian(prob, 0, 0, NULL, NULL, NULL, g3_uu_3d_alpha);CHKERRQ(ierr); ierr = PetscDSSetResidual(prob, 0, f0_u, f1_u_3d_alpha);CHKERRQ(ierr); ierr = PetscDSSetBdResidual(prob, 0, f0_bd_u_3d, f1_bd_u);CHKERRQ(ierr); } /* bcs */ if (run_type==1) { PetscInt id = 1; ierr = DMAddBoundary(dm, DM_BC_ESSENTIAL, "wall", "boundary", 0, 0, NULL, (void (*)()) zero, 1, &id, NULL);CHKERRQ(ierr); } else { ierr = PetscDSAddBoundary(prob, DM_BC_ESSENTIAL, "fixed", "Faces", 0, Ncomp, components, (void (*)()) zero, Nfid, fid, NULL);CHKERRQ(ierr); ierr = PetscDSAddBoundary(prob, DM_BC_NATURAL, "traction", "Faces", 0, Ncomp, components, NULL, Npid, pid, NULL);CHKERRQ(ierr); } while (cdm) { ierr = DMSetDS(cdm,prob);CHKERRQ(ierr); ierr = DMGetCoarseDM(cdm, &cdm);CHKERRQ(ierr); } ierr = PetscFEDestroy(&fe);CHKERRQ(ierr); } /* vecs & mat */ ierr = DMCreateGlobalVector(dm,&xx);CHKERRQ(ierr); ierr = VecDuplicate(xx, &bb);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) bb, "b");CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) xx, "u");CHKERRQ(ierr); ierr = DMCreateMatrix(dm, &Amat);CHKERRQ(ierr); ierr = VecGetSize(bb,&N);CHKERRQ(ierr); local_sizes[iter] = N; ierr = PetscPrintf(PETSC_COMM_WORLD,"[%d]%s %d global equations, %d vertices\n",rank,PETSC_FUNCTION_NAME,N,N/dim);CHKERRQ(ierr); if (use_nearnullspace && N/dim > 1) { /* Set up the near null space (a.k.a. rigid body modes) that will be used by the multigrid preconditioner */ DM subdm; MatNullSpace nearNullSpace; PetscInt fields = 0; PetscObject deformation; ierr = DMCreateSubDM(dm, 1, &fields, NULL, &subdm);CHKERRQ(ierr); ierr = DMPlexCreateRigidBody(subdm, &nearNullSpace);CHKERRQ(ierr); ierr = DMGetField(dm, 0, &deformation);CHKERRQ(ierr); ierr = PetscObjectCompose(deformation, "nearnullspace", (PetscObject) nearNullSpace);CHKERRQ(ierr); ierr = DMDestroy(&subdm);CHKERRQ(ierr); ierr = MatNullSpaceDestroy(&nearNullSpace);CHKERRQ(ierr); /* created by DM and destroyed by Mat */ } ierr = DMPlexSetSNESLocalFEM(dm,NULL,NULL,NULL);CHKERRQ(ierr); ierr = SNESSetJacobian(snes, Amat, Amat, NULL, NULL);CHKERRQ(ierr); ierr = SNESSetFromOptions(snes);CHKERRQ(ierr); ierr = DMSetUp(dm);CHKERRQ(ierr); ierr = PetscLogStagePop();CHKERRQ(ierr); ierr = PetscLogStagePush(stage[0]);CHKERRQ(ierr); /* ksp */ ierr = SNESGetKSP(snes, &ksp);CHKERRQ(ierr); ierr = KSPSetComputeSingularValues(ksp,PETSC_TRUE);CHKERRQ(ierr); /* test BCs */ ierr = VecZeroEntries(xx);CHKERRQ(ierr); if (test_nonzero_cols) { if (rank==0) ierr = VecSetValue(xx,0,1.0,INSERT_VALUES);CHKERRQ(ierr); ierr = VecAssemblyBegin(xx);CHKERRQ(ierr); ierr = VecAssemblyEnd(xx);CHKERRQ(ierr); } ierr = VecZeroEntries(bb);CHKERRQ(ierr); ierr = VecGetSize(bb,&i);CHKERRQ(ierr); local_sizes[iter] = i; ierr = PetscPrintf(PETSC_COMM_WORLD,"[%d]%s %d equations in vector, %d vertices\n",rank,PETSC_FUNCTION_NAME,i,i/dim);CHKERRQ(ierr); /* setup solver, dummy solve to really setup */ if (0) { ierr = KSPSetTolerances(ksp,PETSC_DEFAULT,PETSC_DEFAULT,PETSC_DEFAULT,1);CHKERRQ(ierr); ierr = SNESSolve(snes, bb, xx);CHKERRQ(ierr); ierr = KSPSetTolerances(ksp,PETSC_DEFAULT,PETSC_DEFAULT,PETSC_DEFAULT,50);CHKERRQ(ierr); ierr = VecZeroEntries(xx);CHKERRQ(ierr); } ierr = PetscLogStagePop();CHKERRQ(ierr); /* solve */ ierr = PetscLogStagePush(stage[1]);CHKERRQ(ierr); ierr = SNESSolve(snes, bb, xx);CHKERRQ(ierr); ierr = PetscLogStagePop();CHKERRQ(ierr); ierr = VecNorm(xx,NORM_INFINITY,&mdisp[iter]);CHKERRQ(ierr); ierr = DMViewFromOptions(dm, NULL, "-dm_view");CHKERRQ(ierr); { PetscViewer viewer = NULL; PetscViewerFormat fmt; ierr = PetscOptionsGetViewer(comm,"ex56_","-vec_view",&viewer,&fmt,&flg);CHKERRQ(ierr); if (flg) { ierr = PetscViewerPushFormat(viewer,fmt);CHKERRQ(ierr); ierr = VecView(xx,viewer);CHKERRQ(ierr); ierr = VecView(bb,viewer);CHKERRQ(ierr); ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr); } ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); } /* Free work space */ ierr = DMDestroy(&dm);CHKERRQ(ierr); ierr = SNESDestroy(&snes);CHKERRQ(ierr); ierr = VecDestroy(&xx);CHKERRQ(ierr); ierr = VecDestroy(&bb);CHKERRQ(ierr); ierr = MatDestroy(&Amat);CHKERRQ(ierr); } ierr = DMDestroy(&basedm);CHKERRQ(ierr); if (run_type==1) { err[0] = 59.975208 - mdisp[0]; /* error with what I think is the exact solution */ } else { err[0] = 171.038 - mdisp[0]; } for (iter=1 ; iter<max_conv_its ; iter++) { if (run_type==1) { err[iter] = 59.975208 - mdisp[iter]; } else { err[iter] = 171.038 - mdisp[iter]; } PetscPrintf(PETSC_COMM_WORLD,"[%d]%s %D) N=%12D, max displ=%9.7e, disp diff=%9.2e, error=%4.3e, rate=%3.2g\n", rank,PETSC_FUNCTION_NAME,iter,local_sizes[iter],mdisp[iter], mdisp[iter]-mdisp[iter-1],err[iter],log(err[iter-1]/err[iter])/log(2.)); } ierr = PetscFinalize(); return ierr; }
int main(int argc,char **argv) { PetscErrorCode ierr; DM da,*subda; PetscInt i,dim=3; PetscMPIInt size,rank; Vec v; Vec slvec,sgvec; IS *ois,*iis; VecScatter oscata; VecScatter *iscat,*oscat,*gscat; DMDALocalInfo info; ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,NULL,"-dim",&dim,NULL);CHKERRQ(ierr); /* Create distributed array and get vectors */ ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr); ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr); if (dim == 2) { ierr = DMDACreate2d(PETSC_COMM_WORLD,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DMDA_STENCIL_STAR,-4,-4,PETSC_DECIDE,PETSC_DECIDE,3,1,NULL,NULL,&da);CHKERRQ(ierr); } else if (dim == 3) { ierr = DMDACreate3d(PETSC_COMM_WORLD, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DMDA_STENCIL_STAR,-4,-4,-4,PETSC_DECIDE,PETSC_DECIDE,PETSC_DECIDE,3,1,NULL,NULL,NULL,&da);CHKERRQ(ierr); } ierr = DMDAGetLocalInfo(da,&info);CHKERRQ(ierr); ierr = DMCreateDomainDecomposition(da,NULL,NULL,&iis,&ois,&subda);CHKERRQ(ierr); ierr = DMCreateDomainDecompositionScatters(da,1,subda,&iscat,&oscat,&gscat);CHKERRQ(ierr); { DMDALocalInfo subinfo; MatStencil lower,upper; IS patchis,subpatchis; Vec smallvec; Vec largevec; VecScatter patchscat; ierr = DMDAGetLocalInfo(subda[0],&subinfo);CHKERRQ(ierr); lower.i = info.xs; lower.j = info.ys; lower.k = info.zs; upper.i = info.xs+info.xm; upper.j = info.ys+info.ym; upper.k = info.zs+info.zm; /* test the patch IS as a thing to scatter to/from */ ierr = DMDACreatePatchIS(da,&lower,&upper,&patchis);CHKERRQ(ierr); ierr = DMGetGlobalVector(da,&largevec);CHKERRQ(ierr); ierr = VecCreate(PETSC_COMM_SELF,&smallvec);CHKERRQ(ierr); ierr = VecSetSizes(smallvec,info.dof*(upper.i - lower.i)*(upper.j - lower.j)*(upper.k - lower.k),PETSC_DECIDE);CHKERRQ(ierr); ierr = VecSetFromOptions(smallvec);CHKERRQ(ierr); ierr = VecScatterCreate(smallvec,NULL,largevec,patchis,&patchscat);CHKERRQ(ierr); ierr = FillLocalSubdomain(subda[0],smallvec);CHKERRQ(ierr); ierr = VecSet(largevec,0);CHKERRQ(ierr); ierr = VecScatterBegin(patchscat,smallvec,largevec,ADD_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); ierr = VecScatterEnd(patchscat,smallvec,largevec,ADD_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); for (i = 0; i < size; i++) { if (i == rank) { ierr = ISView(patchis,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr); ierr = VecScatterView(patchscat,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr); ierr = VecView(smallvec,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr); } ierr = MPI_Barrier(PETSC_COMM_WORLD);CHKERRQ(ierr); } ierr = MPI_Barrier(PETSC_COMM_WORLD);CHKERRQ(ierr); ierr = VecView(largevec,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = VecDestroy(&smallvec);CHKERRQ(ierr); ierr = DMRestoreGlobalVector(da,&largevec);CHKERRQ(ierr); ierr = ISDestroy(&patchis);CHKERRQ(ierr); ierr = VecScatterDestroy(&patchscat);CHKERRQ(ierr); } /* view the various parts */ { for (i = 0; i < size; i++) { if (i == rank) { ierr = PetscPrintf(PETSC_COMM_SELF,"Processor %d: \n",i);CHKERRQ(ierr); ierr = DMView(subda[0],PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr); } ierr = MPI_Barrier(PETSC_COMM_WORLD);CHKERRQ(ierr); } ierr = DMGetLocalVector(subda[0],&slvec);CHKERRQ(ierr); ierr = DMGetGlobalVector(subda[0],&sgvec);CHKERRQ(ierr); ierr = DMGetGlobalVector(da,&v);CHKERRQ(ierr); /* test filling outer between the big DM and the small ones with the IS scatter*/ ierr = VecScatterCreate(v,ois[0],sgvec,NULL,&oscata);CHKERRQ(ierr); ierr = FillLocalSubdomain(subda[0],sgvec);CHKERRQ(ierr); ierr = VecScatterBegin(oscata,sgvec,v,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); ierr = VecScatterEnd(oscata,sgvec,v,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); /* test the local-to-local scatter */ /* fill up the local subdomain and then add them together */ ierr = FillLocalSubdomain(da,v);CHKERRQ(ierr); ierr = VecScatterBegin(gscat[0],v,slvec,ADD_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); ierr = VecScatterEnd(gscat[0],v,slvec,ADD_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); ierr = VecView(v,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); /* test ghost scattering backwards */ ierr = VecSet(v,0);CHKERRQ(ierr); ierr = VecScatterBegin(gscat[0],slvec,v,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); ierr = VecScatterEnd(gscat[0],slvec,v,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); ierr = VecView(v,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); /* test overlap scattering backwards */ ierr = DMLocalToGlobalBegin(subda[0],slvec,ADD_VALUES,sgvec);CHKERRQ(ierr); ierr = DMLocalToGlobalEnd(subda[0],slvec,ADD_VALUES,sgvec);CHKERRQ(ierr); ierr = VecSet(v,0);CHKERRQ(ierr); ierr = VecScatterBegin(oscat[0],sgvec,v,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); ierr = VecScatterEnd(oscat[0],sgvec,v,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); ierr = VecView(v,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); /* test interior scattering backwards */ ierr = VecSet(v,0);CHKERRQ(ierr); ierr = VecScatterBegin(iscat[0],sgvec,v,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); ierr = VecScatterEnd(iscat[0],sgvec,v,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); ierr = VecView(v,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); /* test matrix allocation */ for (i = 0; i < size; i++) { if (i == rank) { Mat m; ierr = PetscPrintf(PETSC_COMM_SELF,"Processor %d: \n",i);CHKERRQ(ierr); ierr = DMSetMatType(subda[0],MATAIJ);CHKERRQ(ierr); ierr = DMCreateMatrix(subda[0],&m);CHKERRQ(ierr); ierr = MatView(m,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr); ierr = MatDestroy(&m);CHKERRQ(ierr); } ierr = MPI_Barrier(PETSC_COMM_WORLD);CHKERRQ(ierr); } ierr = DMRestoreLocalVector(subda[0],&slvec);CHKERRQ(ierr); ierr = DMRestoreGlobalVector(subda[0],&sgvec);CHKERRQ(ierr); ierr = DMRestoreGlobalVector(da,&v);CHKERRQ(ierr); } ierr = DMDestroy(&subda[0]);CHKERRQ(ierr); ierr = ISDestroy(&ois[0]);CHKERRQ(ierr); ierr = ISDestroy(&iis[0]);CHKERRQ(ierr); ierr = VecScatterDestroy(&iscat[0]);CHKERRQ(ierr); ierr = VecScatterDestroy(&oscat[0]);CHKERRQ(ierr); ierr = VecScatterDestroy(&gscat[0]);CHKERRQ(ierr); ierr = VecScatterDestroy(&oscata);CHKERRQ(ierr); ierr = PetscFree(iscat);CHKERRQ(ierr); ierr = PetscFree(oscat);CHKERRQ(ierr); ierr = PetscFree(gscat);CHKERRQ(ierr); ierr = PetscFree(oscata);CHKERRQ(ierr); ierr = PetscFree(subda);CHKERRQ(ierr); ierr = PetscFree(ois);CHKERRQ(ierr); ierr = PetscFree(iis);CHKERRQ(ierr); ierr = DMDestroy(&da);CHKERRQ(ierr); ierr = PetscFinalize(); return 0; }
int main(int argc,char **argv) { SNES snes; /* SNES context */ Mat J; /* Jacobian matrix */ DM da; Vec x,r; /* vectors */ PetscErrorCode ierr; PetscInt N = 5; MatNullSpace constants; ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr; ierr = PetscOptionsGetInt(NULL,NULL,"-n",&N,NULL);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create nonlinear solver context - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = SNESCreate(PETSC_COMM_WORLD,&snes);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create vector data structures; set function evaluation routine - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ /* Create distributed array (DMDA) to manage parallel grid and vectors */ ierr = DMDACreate1d(PETSC_COMM_WORLD,DM_BOUNDARY_PERIODIC,N,1,1,NULL,&da);CHKERRQ(ierr); ierr = DMSetFromOptions(da);CHKERRQ(ierr); ierr = DMSetUp(da);CHKERRQ(ierr); /* Extract global and local vectors from DMDA; then duplicate for remaining vectors that are the same types */ ierr = DMCreateGlobalVector(da,&x);CHKERRQ(ierr); ierr = VecDuplicate(x,&r);CHKERRQ(ierr); /* Set function evaluation routine and vector. Whenever the nonlinear solver needs to compute the nonlinear function, it will call this routine. - Note that the final routine argument is the user-defined context that provides application-specific data for the function evaluation routine. */ ierr = SNESSetFunction(snes,r,FormFunction,da);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create matrix data structure; set Jacobian evaluation routine - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = DMCreateMatrix(da,&J);CHKERRQ(ierr); ierr = MatNullSpaceCreate(PETSC_COMM_WORLD,PETSC_TRUE,0,NULL,&constants);CHKERRQ(ierr); ierr = MatSetNullSpace(J,constants);CHKERRQ(ierr); ierr = SNESSetJacobian(snes,J,J,FormJacobian,da);CHKERRQ(ierr); ierr = SNESSetFromOptions(snes);CHKERRQ(ierr); ierr = SNESSolve(snes,NULL,x);CHKERRQ(ierr); ierr = VecDestroy(&x);CHKERRQ(ierr); ierr = VecDestroy(&r);CHKERRQ(ierr); ierr = MatDestroy(&J);CHKERRQ(ierr); ierr = MatNullSpaceDestroy(&constants);CHKERRQ(ierr); ierr = SNESDestroy(&snes);CHKERRQ(ierr); ierr = DMDestroy(&da);CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; }
int main(int argc,char **argv) { AppCtx appctx; /* user-defined application context */ PetscErrorCode ierr; PetscInt i, xs, xm, ind, j, lenglob; PetscReal x, *wrk_ptr1, *wrk_ptr2; MatNullSpace nsp; PetscMPIInt size; /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Initialize program and set problem parameters - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ PetscFunctionBegin; ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr; /*initialize parameters */ appctx.param.N = 10; /* order of the spectral element */ appctx.param.E = 10; /* number of elements */ appctx.param.L = 4.0; /* length of the domain */ appctx.param.mu = 0.01; /* diffusion coefficient */ appctx.initial_dt = 5e-3; appctx.param.steps = PETSC_MAX_INT; appctx.param.Tend = 4; ierr = PetscOptionsGetInt(NULL,NULL,"-N",&appctx.param.N,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,NULL,"-E",&appctx.param.E,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetReal(NULL,NULL,"-Tend",&appctx.param.Tend,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetReal(NULL,NULL,"-mu",&appctx.param.mu,NULL);CHKERRQ(ierr); appctx.param.Le = appctx.param.L/appctx.param.E; ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr); if (appctx.param.E % size) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_ARG_WRONG,"Number of elements must be divisible by number of processes"); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create GLL data structures - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = PetscGLLCreate(appctx.param.N,PETSCGLL_VIA_LINEARALGEBRA,&appctx.SEMop.gll);CHKERRQ(ierr); lenglob = appctx.param.E*(appctx.param.N-1); /* Create distributed array (DMDA) to manage parallel grid and vectors and to set up the ghost point communication pattern. There are E*(Nl-1)+1 total grid values spread equally among all the processors, except first and last */ ierr = DMDACreate1d(PETSC_COMM_WORLD,DM_BOUNDARY_PERIODIC,lenglob,1,1,NULL,&appctx.da);CHKERRQ(ierr); ierr = DMSetFromOptions(appctx.da);CHKERRQ(ierr); ierr = DMSetUp(appctx.da);CHKERRQ(ierr); /* Extract global and local vectors from DMDA; we use these to store the approximate solution. Then duplicate these for remaining vectors that have the same types. */ ierr = DMCreateGlobalVector(appctx.da,&appctx.dat.curr_sol);CHKERRQ(ierr); ierr = VecDuplicate(appctx.dat.curr_sol,&appctx.SEMop.grid);CHKERRQ(ierr); ierr = VecDuplicate(appctx.dat.curr_sol,&appctx.SEMop.mass);CHKERRQ(ierr); ierr = DMDAGetCorners(appctx.da,&xs,NULL,NULL,&xm,NULL,NULL);CHKERRQ(ierr); ierr = DMDAVecGetArray(appctx.da,appctx.SEMop.grid,&wrk_ptr1);CHKERRQ(ierr); ierr = DMDAVecGetArray(appctx.da,appctx.SEMop.mass,&wrk_ptr2);CHKERRQ(ierr); /* Compute function over the locally owned part of the grid */ xs=xs/(appctx.param.N-1); xm=xm/(appctx.param.N-1); /* Build total grid and mass over entire mesh (multi-elemental) */ for (i=xs; i<xs+xm; i++) { for (j=0; j<appctx.param.N-1; j++) { x = (appctx.param.Le/2.0)*(appctx.SEMop.gll.nodes[j]+1.0)+appctx.param.Le*i; ind=i*(appctx.param.N-1)+j; wrk_ptr1[ind]=x; wrk_ptr2[ind]=.5*appctx.param.Le*appctx.SEMop.gll.weights[j]; if (j==0) wrk_ptr2[ind]+=.5*appctx.param.Le*appctx.SEMop.gll.weights[j]; } } ierr = DMDAVecRestoreArray(appctx.da,appctx.SEMop.grid,&wrk_ptr1);CHKERRQ(ierr); ierr = DMDAVecRestoreArray(appctx.da,appctx.SEMop.mass,&wrk_ptr2);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create matrix data structure; set matrix evaluation routine. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = DMSetMatrixPreallocateOnly(appctx.da, PETSC_TRUE);CHKERRQ(ierr); ierr = DMCreateMatrix(appctx.da,&appctx.SEMop.stiff);CHKERRQ(ierr); ierr = DMCreateMatrix(appctx.da,&appctx.SEMop.grad);CHKERRQ(ierr); /* For linear problems with a time-dependent f(u,t) in the equation u_t = f(u,t), the user provides the discretized right-hand-side as a time-dependent matrix. */ ierr = RHSMatrixLaplaciangllDM(appctx.ts,0.0,appctx.dat.curr_sol,appctx.SEMop.stiff,appctx.SEMop.stiff,&appctx);CHKERRQ(ierr); ierr = RHSMatrixAdvectiongllDM(appctx.ts,0.0,appctx.dat.curr_sol,appctx.SEMop.grad,appctx.SEMop.grad,&appctx);CHKERRQ(ierr); /* For linear problems with a time-dependent f(u,t) in the equation u_t = f(u,t), the user provides the discretized right-hand-side as a time-dependent matrix. */ ierr = MatDuplicate(appctx.SEMop.stiff,MAT_COPY_VALUES,&appctx.SEMop.keptstiff);CHKERRQ(ierr); /* attach the null space to the matrix, this probably is not needed but does no harm */ ierr = MatNullSpaceCreate(PETSC_COMM_WORLD,PETSC_TRUE,0,NULL,&nsp);CHKERRQ(ierr); ierr = MatSetNullSpace(appctx.SEMop.stiff,nsp);CHKERRQ(ierr); ierr = MatSetNullSpace(appctx.SEMop.keptstiff,nsp);CHKERRQ(ierr); ierr = MatNullSpaceTest(nsp,appctx.SEMop.stiff,NULL);CHKERRQ(ierr); ierr = MatNullSpaceDestroy(&nsp);CHKERRQ(ierr); /* attach the null space to the matrix, this probably is not needed but does no harm */ ierr = MatNullSpaceCreate(PETSC_COMM_WORLD,PETSC_TRUE,0,NULL,&nsp);CHKERRQ(ierr); ierr = MatSetNullSpace(appctx.SEMop.grad,nsp);CHKERRQ(ierr); ierr = MatNullSpaceTest(nsp,appctx.SEMop.grad,NULL);CHKERRQ(ierr); ierr = MatNullSpaceDestroy(&nsp);CHKERRQ(ierr); /* Create the TS solver that solves the ODE and its adjoint; set its options */ ierr = TSCreate(PETSC_COMM_WORLD,&appctx.ts);CHKERRQ(ierr); ierr = TSSetProblemType(appctx.ts,TS_NONLINEAR);CHKERRQ(ierr); ierr = TSSetType(appctx.ts,TSRK);CHKERRQ(ierr); ierr = TSSetDM(appctx.ts,appctx.da);CHKERRQ(ierr); ierr = TSSetTime(appctx.ts,0.0);CHKERRQ(ierr); ierr = TSSetTimeStep(appctx.ts,appctx.initial_dt);CHKERRQ(ierr); ierr = TSSetMaxSteps(appctx.ts,appctx.param.steps);CHKERRQ(ierr); ierr = TSSetMaxTime(appctx.ts,appctx.param.Tend);CHKERRQ(ierr); ierr = TSSetExactFinalTime(appctx.ts,TS_EXACTFINALTIME_MATCHSTEP);CHKERRQ(ierr); ierr = TSSetTolerances(appctx.ts,1e-7,NULL,1e-7,NULL);CHKERRQ(ierr); ierr = TSSetSaveTrajectory(appctx.ts);CHKERRQ(ierr); ierr = TSSetFromOptions(appctx.ts);CHKERRQ(ierr); ierr = TSSetRHSFunction(appctx.ts,NULL,RHSFunction,&appctx);CHKERRQ(ierr); ierr = TSSetRHSJacobian(appctx.ts,appctx.SEMop.stiff,appctx.SEMop.stiff,RHSJacobian,&appctx);CHKERRQ(ierr); /* Set Initial conditions for the problem */ ierr = TrueSolution(appctx.ts,0,appctx.dat.curr_sol,&appctx);CHKERRQ(ierr); ierr = TSSetSolutionFunction(appctx.ts,(PetscErrorCode (*)(TS,PetscReal,Vec,void *))TrueSolution,&appctx);CHKERRQ(ierr); ierr = TSSetTime(appctx.ts,0.0);CHKERRQ(ierr); ierr = TSSetStepNumber(appctx.ts,0);CHKERRQ(ierr); ierr = TSSolve(appctx.ts,appctx.dat.curr_sol);CHKERRQ(ierr); ierr = MatDestroy(&appctx.SEMop.stiff);CHKERRQ(ierr); ierr = MatDestroy(&appctx.SEMop.keptstiff);CHKERRQ(ierr); ierr = MatDestroy(&appctx.SEMop.grad);CHKERRQ(ierr); ierr = VecDestroy(&appctx.SEMop.grid);CHKERRQ(ierr); ierr = VecDestroy(&appctx.SEMop.mass);CHKERRQ(ierr); ierr = VecDestroy(&appctx.dat.curr_sol);CHKERRQ(ierr); ierr = PetscGLLDestroy(&appctx.SEMop.gll);CHKERRQ(ierr); ierr = DMDestroy(&appctx.da);CHKERRQ(ierr); ierr = TSDestroy(&appctx.ts);CHKERRQ(ierr); /* Always call PetscFinalize() before exiting a program. This routine - finalizes the PETSc libraries as well as MPI - provides summary and diagnostic information if certain runtime options are chosen (e.g., -log_summary). */ ierr = PetscFinalize(); return ierr; }
int main(int argc,char **argv) { TS ts; /* nonlinear solver */ Vec u,r; /* solution, residual vectors */ Mat J,Jmf = PETSC_NULL; /* Jacobian matrices */ PetscInt maxsteps = 1000; /* iterations for convergence */ PetscErrorCode ierr; DM da; PetscReal dt; AppCtx user; /* user-defined work context */ SNES snes; PetscInt Jtype; /* Jacobian type 0: user provide Jacobian; 1: slow finite difference; 2: fd with coloring; */ PetscInitialize(&argc,&argv,(char *)0,help); /* Initialize user application context */ user.da = PETSC_NULL; user.nstencilpts = 5; user.c = -30.0; user.boundary = 0; /* 0: Drichlet BC; 1: Neumann BC */ user.viewJacobian = PETSC_FALSE; ierr = PetscOptionsGetInt(PETSC_NULL,"-nstencilpts",&user.nstencilpts,PETSC_NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(PETSC_NULL,"-boundary",&user.boundary,PETSC_NULL);CHKERRQ(ierr); ierr = PetscOptionsHasName(PETSC_NULL,"-viewJacobian",&user.viewJacobian);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create distributed array (DMDA) to manage parallel grid and vectors - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ if (user.nstencilpts == 5){ ierr = DMDACreate2d(PETSC_COMM_WORLD, DMDA_BOUNDARY_NONE, DMDA_BOUNDARY_NONE,DMDA_STENCIL_STAR,-11,-11,PETSC_DECIDE,PETSC_DECIDE,1,1,PETSC_NULL,PETSC_NULL,&da);CHKERRQ(ierr); } else if (user.nstencilpts == 9){ ierr = DMDACreate2d(PETSC_COMM_WORLD, DMDA_BOUNDARY_NONE, DMDA_BOUNDARY_NONE,DMDA_STENCIL_BOX,-11,-11,PETSC_DECIDE,PETSC_DECIDE,1,1,PETSC_NULL,PETSC_NULL,&da);CHKERRQ(ierr); } else { SETERRQ1(PETSC_COMM_WORLD,PETSC_ERR_SUP,"nstencilpts %d is not supported",user.nstencilpts); } user.da = da; /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Extract global vectors from DMDA; - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = DMCreateGlobalVector(da,&u);CHKERRQ(ierr); ierr = VecDuplicate(u,&r);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create timestepping solver context - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr); ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr); ierr = TSSetType(ts,TSBEULER);CHKERRQ(ierr); ierr = TSSetDM(ts,da);CHKERRQ(ierr); ierr = TSSetIFunction(ts,r,FormIFunction,&user);CHKERRQ(ierr); ierr = TSSetDuration(ts,maxsteps,1.0);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set initial conditions - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = FormInitialSolution(u,&user);CHKERRQ(ierr); ierr = TSSetSolution(ts,u);CHKERRQ(ierr); dt = .01; ierr = TSSetInitialTimeStep(ts,0.0,dt);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set Jacobian evaluation routine - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = DMCreateMatrix(da,MATAIJ,&J);CHKERRQ(ierr); Jtype = 0; ierr = PetscOptionsGetInt(PETSC_NULL, "-Jtype",&Jtype,PETSC_NULL);CHKERRQ(ierr); if (Jtype == 0){ /* use user provided Jacobian evaluation routine */ if (user.nstencilpts != 5) SETERRQ1(PETSC_COMM_WORLD,PETSC_ERR_SUP,"user Jacobian routine FormIJacobian() does not support nstencilpts=%D",user.nstencilpts); ierr = TSSetIJacobian(ts,J,J,FormIJacobian,&user);CHKERRQ(ierr); } else { /* use finite difference Jacobian J as preconditioner and '-snes_mf_operator' for Mat*vec */ ierr = TSGetSNES(ts,&snes);CHKERRQ(ierr); ierr = MatCreateSNESMF(snes,&Jmf);CHKERRQ(ierr); if (Jtype == 1){ /* slow finite difference J; */ ierr = SNESSetJacobian(snes,Jmf,J,SNESDefaultComputeJacobian,PETSC_NULL);CHKERRQ(ierr); } else if (Jtype == 2){ /* Use coloring to compute finite difference J efficiently */ ierr = SNESSetJacobian(snes,Jmf,J,SNESDefaultComputeJacobianColor,0);CHKERRQ(ierr); } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Jtype is not supported"); } /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Sets various TS parameters from user options - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSetFromOptions(ts);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Solve nonlinear system - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSolve(ts,u);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Free work space. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = MatDestroy(&J);CHKERRQ(ierr); ierr = MatDestroy(&Jmf);CHKERRQ(ierr); ierr = VecDestroy(&u);CHKERRQ(ierr); ierr = VecDestroy(&r);CHKERRQ(ierr); ierr = TSDestroy(&ts);CHKERRQ(ierr); ierr = DMDestroy(&da);CHKERRQ(ierr); ierr = PetscFinalize(); PetscFunctionReturn(0); }
PetscErrorCode SetUpMatrices(AppCtx *user) { PetscErrorCode ierr; PetscInt nele,nen,i,j; const PetscInt *ele; PetscScalar dt=user->dt; PetscScalar y[3]; PetscInt idx[3]; PetscScalar eM_0[3][3],eM_2_odd[3][3],eM_2_even[3][3]; Mat M =user->M; PetscScalar epsilon=user->epsilon; PetscScalar hx; PetscInt n,Mda,Nda; DM da; PetscFunctionBeginUser; /* Create the mass matrix M_0 */ ierr = MatGetLocalSize(M,&n,NULL);CHKERRQ(ierr); /* ierr = MatCreate(PETSC_COMM_WORLD,&user->M_0);CHKERRQ(ierr);*/ ierr = DMDAGetInfo(user->da,NULL,&Mda,&Nda,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL); hx = 1.0/(Mda-1); ierr = DMDACreate2d(PETSC_COMM_WORLD,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DMDA_STENCIL_BOX,Mda,Nda,PETSC_DECIDE,PETSC_DECIDE,1,1,NULL,NULL,&da);CHKERRQ(ierr); ierr = DMSetMatType(da,MATAIJ);CHKERRQ(ierr); ierr = DMCreateMatrix(da,&user->M_0);CHKERRQ(ierr); ierr = DMDestroy(&da);CHKERRQ(ierr); eM_0[0][0]=eM_0[1][1]=eM_0[2][2]=hx*hx/12.0; eM_0[0][1]=eM_0[0][2]=eM_0[1][0]=eM_0[1][2]=eM_0[2][0]=eM_0[2][1]=hx*hx/24.0; eM_2_odd[0][0] = eM_2_odd[0][1] = eM_2_odd[0][2] = 0.0; eM_2_odd[1][0] = eM_2_odd[1][1] = eM_2_odd[1][2] = 0.0; eM_2_odd[2][0] = eM_2_odd[2][1] = eM_2_odd[2][2] = 0.0; eM_2_odd[0][0]=1.0; eM_2_odd[1][1]=eM_2_odd[2][2]=0.5; eM_2_odd[0][1]=eM_2_odd[0][2]=eM_2_odd[1][0]=eM_2_odd[2][0]=-0.5; eM_2_even[0][0] = eM_2_even[0][1] = eM_2_even[0][2] = 0.0; eM_2_even[0][0] = eM_2_even[0][1] = eM_2_even[0][2] = 0.0; eM_2_even[0][0] = eM_2_even[0][1] = eM_2_even[0][2] = 0.0; eM_2_even[1][1]=1; eM_2_even[0][0]=eM_2_even[2][2]=0.5; eM_2_even[0][1]=eM_2_even[1][0]=eM_2_even[1][2]=eM_2_even[2][1]=-0.5; /* Get local element info */ ierr = DMDAGetElements(user->da,&nele,&nen,&ele);CHKERRQ(ierr); for (i=0; i < nele; i++) { idx[0] = ele[3*i]; idx[1] = ele[3*i+1]; idx[2] = ele[3*i+2]; PetscInt row,cols[3],r,row_M_0; PetscScalar vals[3],vals_M_0[3]; for (r=0; r<3; r++) { row_M_0 = idx[r]; vals_M_0[0]=eM_0[r][0]; vals_M_0[1]=eM_0[r][1]; vals_M_0[2]=eM_0[r][2]; ierr = MatSetValues(user->M_0,1,&row_M_0,3,idx,vals_M_0,ADD_VALUES);CHKERRQ(ierr); if (y[1]==y[0]) { row = 4*idx[r]; cols[0] = 4*idx[0]; vals[0] = eM_0[r][0]+dt*epsilon*epsilon*eM_2_odd[r][0]; cols[1] = 4*idx[1]; vals[1] = eM_0[r][1]+dt*epsilon*epsilon*eM_2_odd[r][1]; cols[2] = 4*idx[2]; vals[2] = eM_0[r][2]+dt*epsilon*epsilon*eM_2_odd[r][2]; /* Insert values in matrix M for 1st dof */ ierr = MatSetValuesLocal(M,1,&row,3,cols,vals,ADD_VALUES);CHKERRQ(ierr); row = 4*idx[r]+1; cols[0] = 4*idx[0]+1; vals[0] = eM_0[r][0]+dt*epsilon*epsilon*eM_2_odd[r][0]; cols[1] = 4*idx[1]+1; vals[1] = eM_0[r][1]+dt*epsilon*epsilon*eM_2_odd[r][1]; cols[2] = 4*idx[2]+1; vals[2] = eM_0[r][2]+dt*epsilon*epsilon*eM_2_odd[r][2]; /* Insert values in matrix M for 2nd dof */ ierr = MatSetValuesLocal(M,1,&row,3,cols,vals,ADD_VALUES);CHKERRQ(ierr); row = 4*idx[r]+2; cols[0] = 4*idx[0]+2; vals[0] = eM_0[r][0]+dt*epsilon*epsilon*eM_2_odd[r][0]; cols[1] = 4*idx[1]+2; vals[1] = eM_0[r][1]+dt*epsilon*epsilon*eM_2_odd[r][1]; cols[2] = 4*idx[2]+2; vals[2] = eM_0[r][2]+dt*epsilon*epsilon*eM_2_odd[r][2]; /* Insert values in matrix M for 3nd dof */ ierr = MatSetValuesLocal(M,1,&row,3,cols,vals,ADD_VALUES);CHKERRQ(ierr); } else { row = 4*idx[r]; cols[0] = 4*idx[0]; vals[0] = eM_0[r][0]+dt*epsilon*epsilon*eM_2_even[r][0]; cols[1] = 4*idx[1]; vals[1] = eM_0[r][1]+dt*epsilon*epsilon*eM_2_even[r][1]; cols[2] = 4*idx[2]; vals[2] = eM_0[r][2]+dt*epsilon*epsilon*eM_2_even[r][2]; /* Insert values in matrix M for 1st dof */ ierr = MatSetValuesLocal(M,1,&row,3,cols,vals,ADD_VALUES);CHKERRQ(ierr); row = 4*idx[r]+1; cols[0] = 4*idx[0]+1; vals[0] = eM_0[r][0]+dt*epsilon*epsilon*eM_2_even[r][0]; cols[1] = 4*idx[1]+1; vals[1] = eM_0[r][1]+dt*epsilon*epsilon*eM_2_even[r][1]; cols[2] = 4*idx[2]+1; vals[2] = eM_0[r][2]+dt*epsilon*epsilon*eM_2_even[r][2]; /* Insert values in matrix M for 2nd dof */ ierr = MatSetValuesLocal(M,1,&row,3,cols,vals,ADD_VALUES);CHKERRQ(ierr); row = 4*idx[r]+2; cols[0] = 4*idx[0]+2; vals[0] = eM_0[r][0]+dt*epsilon*epsilon*eM_2_even[r][0]; cols[1] = 4*idx[1]+2; vals[1] = eM_0[r][1]+dt*epsilon*epsilon*eM_2_even[r][1]; cols[2] = 4*idx[2]+2; vals[2] = eM_0[r][2]+dt*epsilon*epsilon*eM_2_even[r][2]; /* Insert values in matrix M for 3nd dof */ ierr = MatSetValuesLocal(M,1,&row,3,cols,vals,ADD_VALUES);CHKERRQ(ierr); } } } ierr = MatAssemblyBegin(user->M_0,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(user->M_0,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyBegin(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); PetscScalar vals[9]; vals[0] = -1.0; vals[1] = 0.0; vals[2] = 0.0; vals[3] = 0.0; vals[4] = -1.0; vals[5] = 0.0; vals[6] = 0.0; vals[7] = 0.0; vals[8] = -1.0; for (j=0; j < nele; j++) { idx[0] = ele[3*j]; idx[1] = ele[3*j+1]; idx[2] = ele[3*j+2]; PetscInt r,rows[3],cols[3]; for (r=0; r<3; r++) { rows[0] = 4*idx[0]+r; cols[0] = 4*idx[0]+3; rows[1] = 4*idx[1]+r; cols[1] = 4*idx[1]+3; rows[2] = 4*idx[2]+r; cols[2] = 4*idx[2]+3; ierr = MatSetValuesLocal(M,3,rows,3,cols,vals,INSERT_VALUES);CHKERRQ(ierr); ierr = MatSetValuesLocal(M,3,cols,3,rows,vals,INSERT_VALUES);CHKERRQ(ierr); } } ierr = DMDARestoreElements(user->da,&nele,&nen,&ele);CHKERRQ(ierr); ierr = MatAssemblyBegin(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(M,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = VecCreate(PETSC_COMM_WORLD,&user->u1);CHKERRQ(ierr); ierr = VecSetSizes(user->u1,n/4,PETSC_DECIDE);CHKERRQ(ierr); ierr = VecSetFromOptions(user->u1);CHKERRQ(ierr); ierr = VecDuplicate(user->u1,&user->u2);CHKERRQ(ierr); ierr = VecDuplicate(user->u1,&user->u3);CHKERRQ(ierr); ierr = VecDuplicate(user->u1,&user->work1);CHKERRQ(ierr); ierr = VecDuplicate(user->u1,&user->work2);CHKERRQ(ierr); ierr = VecDuplicate(user->u1,&user->work3);CHKERRQ(ierr); ierr = VecDuplicate(user->u1,&user->work4);CHKERRQ(ierr); PetscFunctionReturn(0); }
int main(int argc,char **argv) { TS ts; /* nonlinear solver */ Vec u,r; /* solution, residual vector */ Mat J; /* Jacobian matrix */ PetscInt steps,maxsteps = 1000; /* iterations for convergence */ PetscErrorCode ierr; DM da; PetscReal ftime,dt; AppCtx user; /* user-defined work context */ PetscInitialize(&argc,&argv,(char*)0,help); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create distributed array (DMDA) to manage parallel grid and vectors - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = DMDACreate2d(PETSC_COMM_WORLD, DMDA_BOUNDARY_NONE, DMDA_BOUNDARY_NONE,DMDA_STENCIL_STAR,-8,-8,PETSC_DECIDE,PETSC_DECIDE, 1,1,NULL,NULL,&da);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Extract global vectors from DMDA; - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = DMCreateGlobalVector(da,&u);CHKERRQ(ierr); ierr = VecDuplicate(u,&r);CHKERRQ(ierr); /* Initialize user application context */ user.c = -30.0; /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create timestepping solver context - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr); ierr = TSSetDM(ts,da);CHKERRQ(ierr); ierr = TSSetType(ts,TSBEULER);CHKERRQ(ierr); ierr = TSSetRHSFunction(ts,r,RHSFunction,&user);CHKERRQ(ierr); /* Set Jacobian */ ierr = DMCreateMatrix(da,MATAIJ,&J);CHKERRQ(ierr); ierr = TSSetRHSJacobian(ts,J,J,RHSJacobian,NULL);CHKERRQ(ierr); ftime = 1.0; ierr = TSSetDuration(ts,maxsteps,ftime);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set initial conditions - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = FormInitialSolution(da,u,&user);CHKERRQ(ierr); dt = .01; ierr = TSSetInitialTimeStep(ts,0.0,dt);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set runtime options - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSetFromOptions(ts);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Solve nonlinear system - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSolve(ts,u);CHKERRQ(ierr); ierr = TSGetSolveTime(ts,&ftime);CHKERRQ(ierr); ierr = TSGetTimeStepNumber(ts,&steps);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Free work space. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = MatDestroy(&J);CHKERRQ(ierr); ierr = VecDestroy(&u);CHKERRQ(ierr); ierr = VecDestroy(&r);CHKERRQ(ierr); ierr = TSDestroy(&ts);CHKERRQ(ierr); ierr = DMDestroy(&da);CHKERRQ(ierr); ierr = PetscFinalize(); PetscFunctionReturn(0); }
int main(int argc,char ** argv) { PetscErrorCode ierr; char pfdata_file[PETSC_MAX_PATH_LEN]="datafiles/case9.m"; PFDATA *pfdata; PetscInt numEdges=0,numVertices=0; int *edges = NULL; PetscInt i; DM networkdm; PetscInt componentkey[4]; UserCtx User; PetscLogStage stage1,stage2; PetscMPIInt size,rank; PetscInt eStart, eEnd, vStart, vEnd,j; PetscInt genj,loadj; Vec X,F; Mat J; SNES snes; ierr = PetscInitialize(&argc,&argv,"pfoptions",help);CHKERRQ(ierr); ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr); { /* introduce the const crank so the clang static analyzer realizes that if it enters any of the if (crank) then it must have entered the first */ /* this is an experiment to see how the analyzer reacts */ const PetscMPIInt crank = rank; /* Create an empty network object */ ierr = DMNetworkCreate(PETSC_COMM_WORLD,&networkdm);CHKERRQ(ierr); /* Register the components in the network */ ierr = DMNetworkRegisterComponent(networkdm,"branchstruct",sizeof(struct _p_EDGEDATA),&componentkey[0]);CHKERRQ(ierr); ierr = DMNetworkRegisterComponent(networkdm,"busstruct",sizeof(struct _p_VERTEXDATA),&componentkey[1]);CHKERRQ(ierr); ierr = DMNetworkRegisterComponent(networkdm,"genstruct",sizeof(struct _p_GEN),&componentkey[2]);CHKERRQ(ierr); ierr = DMNetworkRegisterComponent(networkdm,"loadstruct",sizeof(struct _p_LOAD),&componentkey[3]);CHKERRQ(ierr); ierr = PetscLogStageRegister("Read Data",&stage1);CHKERRQ(ierr); PetscLogStagePush(stage1); /* READ THE DATA */ if (!crank) { /* READ DATA */ /* Only rank 0 reads the data */ ierr = PetscOptionsGetString(NULL,NULL,"-pfdata",pfdata_file,PETSC_MAX_PATH_LEN-1,NULL);CHKERRQ(ierr); ierr = PetscNew(&pfdata);CHKERRQ(ierr); ierr = PFReadMatPowerData(pfdata,pfdata_file);CHKERRQ(ierr); User.Sbase = pfdata->sbase; numEdges = pfdata->nbranch; numVertices = pfdata->nbus; ierr = PetscMalloc(2*numEdges*sizeof(int),&edges);CHKERRQ(ierr); ierr = GetListofEdges(pfdata->nbranch,pfdata->branch,edges);CHKERRQ(ierr); } PetscLogStagePop(); ierr = MPI_Barrier(PETSC_COMM_WORLD);CHKERRQ(ierr); ierr = PetscLogStageRegister("Create network",&stage2);CHKERRQ(ierr); PetscLogStagePush(stage2); /* Set number of nodes/edges */ ierr = DMNetworkSetSizes(networkdm,numVertices,numEdges,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); /* Add edge connectivity */ ierr = DMNetworkSetEdgeList(networkdm,edges);CHKERRQ(ierr); /* Set up the network layout */ ierr = DMNetworkLayoutSetUp(networkdm);CHKERRQ(ierr); if (!crank) { ierr = PetscFree(edges);CHKERRQ(ierr); } /* Add network components only process 0 has any data to add*/ if (!crank) { genj=0; loadj=0; ierr = DMNetworkGetEdgeRange(networkdm,&eStart,&eEnd);CHKERRQ(ierr); for (i = eStart; i < eEnd; i++) { ierr = DMNetworkAddComponent(networkdm,i,componentkey[0],&pfdata->branch[i-eStart]);CHKERRQ(ierr); } ierr = DMNetworkGetVertexRange(networkdm,&vStart,&vEnd);CHKERRQ(ierr); for (i = vStart; i < vEnd; i++) { ierr = DMNetworkAddComponent(networkdm,i,componentkey[1],&pfdata->bus[i-vStart]);CHKERRQ(ierr); if (pfdata->bus[i-vStart].ngen) { for (j = 0; j < pfdata->bus[i-vStart].ngen; j++) { ierr = DMNetworkAddComponent(networkdm,i,componentkey[2],&pfdata->gen[genj++]);CHKERRQ(ierr); } } if (pfdata->bus[i-vStart].nload) { for (j=0; j < pfdata->bus[i-vStart].nload; j++) { ierr = DMNetworkAddComponent(networkdm,i,componentkey[3],&pfdata->load[loadj++]);CHKERRQ(ierr); } } /* Add number of variables */ ierr = DMNetworkAddNumVariables(networkdm,i,2);CHKERRQ(ierr); } } /* Set up DM for use */ ierr = DMSetUp(networkdm);CHKERRQ(ierr); if (!crank) { ierr = PetscFree(pfdata->bus);CHKERRQ(ierr); ierr = PetscFree(pfdata->gen);CHKERRQ(ierr); ierr = PetscFree(pfdata->branch);CHKERRQ(ierr); ierr = PetscFree(pfdata->load);CHKERRQ(ierr); ierr = PetscFree(pfdata);CHKERRQ(ierr); } ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr); if (size > 1) { DM distnetworkdm; /* Network partitioning and distribution of data */ ierr = DMNetworkDistribute(networkdm,0,&distnetworkdm);CHKERRQ(ierr); ierr = DMDestroy(&networkdm);CHKERRQ(ierr); networkdm = distnetworkdm; } PetscLogStagePop(); ierr = DMNetworkGetEdgeRange(networkdm,&eStart,&eEnd);CHKERRQ(ierr); ierr = DMNetworkGetVertexRange(networkdm,&vStart,&vEnd);CHKERRQ(ierr); #if 0 PetscInt numComponents; EDGEDATA edge; PetscInt offset,key,kk; DMNetworkComponentGenericDataType *arr; VERTEXDATA bus; GEN gen; LOAD load; for (i = eStart; i < eEnd; i++) { ierr = DMNetworkGetComponentDataArray(networkdm,&arr);CHKERRQ(ierr); ierr = DMNetworkGetComponentTypeOffset(networkdm,i,0,&key,&offset);CHKERRQ(ierr); edge = (EDGEDATA)(arr+offset); ierr = DMNetworkGetNumComponents(networkdm,i,&numComponents);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_SELF,"Rank %d ncomps = %d Line %d ---- %d\n",crank,numComponents,edge->internal_i,edge->internal_j);CHKERRQ(ierr); } for (i = vStart; i < vEnd; i++) { ierr = DMNetworkGetComponentDataArray(networkdm,&arr);CHKERRQ(ierr); ierr = DMNetworkGetNumComponents(networkdm,i,&numComponents);CHKERRQ(ierr); for (kk=0; kk < numComponents; kk++) { ierr = DMNetworkGetComponentTypeOffset(networkdm,i,kk,&key,&offset);CHKERRQ(ierr); if (key == 1) { bus = (VERTEXDATA)(arr+offset); ierr = PetscPrintf(PETSC_COMM_SELF,"Rank %d ncomps = %d Bus %d\n",crank,numComponents,bus->internal_i);CHKERRQ(ierr); } else if (key == 2) { gen = (GEN)(arr+offset); ierr = PetscPrintf(PETSC_COMM_SELF,"Rank %d Gen pg = %f qg = %f\n",crank,gen->pg,gen->qg);CHKERRQ(ierr); } else if (key == 3) { load = (LOAD)(arr+offset); ierr = PetscPrintf(PETSC_COMM_SELF,"Rank %d Load pl = %f ql = %f\n",crank,load->pl,load->ql);CHKERRQ(ierr); } } } #endif /* Broadcast Sbase to all processors */ ierr = MPI_Bcast(&User.Sbase,1,MPIU_SCALAR,0,PETSC_COMM_WORLD);CHKERRQ(ierr); ierr = DMCreateGlobalVector(networkdm,&X);CHKERRQ(ierr); ierr = VecDuplicate(X,&F);CHKERRQ(ierr); ierr = DMCreateMatrix(networkdm,&J);CHKERRQ(ierr); ierr = MatSetOption(J,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr); ierr = SetInitialValues(networkdm,X,&User);CHKERRQ(ierr); /* HOOK UP SOLVER */ ierr = SNESCreate(PETSC_COMM_WORLD,&snes);CHKERRQ(ierr); ierr = SNESSetDM(snes,networkdm);CHKERRQ(ierr); ierr = SNESSetFunction(snes,F,FormFunction,&User);CHKERRQ(ierr); ierr = SNESSetJacobian(snes,J,J,FormJacobian,&User);CHKERRQ(ierr); ierr = SNESSetFromOptions(snes);CHKERRQ(ierr); ierr = SNESSolve(snes,NULL,X);CHKERRQ(ierr); ierr = VecDestroy(&X);CHKERRQ(ierr); ierr = VecDestroy(&F);CHKERRQ(ierr); ierr = MatDestroy(&J);CHKERRQ(ierr); ierr = SNESDestroy(&snes);CHKERRQ(ierr); ierr = DMDestroy(&networkdm);CHKERRQ(ierr); } ierr = PetscFinalize(); return ierr; }
static PetscErrorCode DMCreateMatrix_Composite_AIJ(DM dm,MatType mtype,Mat *J) { PetscErrorCode ierr; DM_Composite *com = (DM_Composite*)dm->data; struct DMCompositeLink *next; PetscInt m,*dnz,*onz,i,j,mA; Mat Atmp; PetscMPIInt rank; PetscBool dense = PETSC_FALSE; PetscFunctionBegin; /* use global vector to determine layout needed for matrix */ m = com->n; ierr = MatCreate(PetscObjectComm((PetscObject)dm),J);CHKERRQ(ierr); ierr = MatSetSizes(*J,m,m,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); ierr = MatSetType(*J,mtype);CHKERRQ(ierr); /* Extremely inefficient but will compute entire Jacobian for testing */ ierr = PetscOptionsGetBool(((PetscObject)dm)->prefix,"-dmcomposite_dense_jacobian",&dense,NULL);CHKERRQ(ierr); if (dense) { PetscInt rstart,rend,*indices; PetscScalar *values; mA = com->N; ierr = MatMPIAIJSetPreallocation(*J,mA,NULL,mA-m,NULL);CHKERRQ(ierr); ierr = MatSeqAIJSetPreallocation(*J,mA,NULL);CHKERRQ(ierr); ierr = MatGetOwnershipRange(*J,&rstart,&rend);CHKERRQ(ierr); ierr = PetscMalloc2(mA,PetscScalar,&values,mA,PetscInt,&indices);CHKERRQ(ierr); ierr = PetscMemzero(values,mA*sizeof(PetscScalar));CHKERRQ(ierr); for (i=0; i<mA; i++) indices[i] = i; for (i=rstart; i<rend; i++) { ierr = MatSetValues(*J,1,&i,mA,indices,values,INSERT_VALUES);CHKERRQ(ierr); } ierr = PetscFree2(values,indices);CHKERRQ(ierr); ierr = MatAssemblyBegin(*J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(*J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); PetscFunctionReturn(0); } ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm),&rank);CHKERRQ(ierr); ierr = MatPreallocateInitialize(PetscObjectComm((PetscObject)dm),m,m,dnz,onz);CHKERRQ(ierr); /* loop over packed objects, handling one at at time */ next = com->next; while (next) { PetscInt nc,rstart,*ccols,maxnc; const PetscInt *cols,*rstarts; PetscMPIInt proc; ierr = DMCreateMatrix(next->dm,mtype,&Atmp);CHKERRQ(ierr); ierr = MatGetOwnershipRange(Atmp,&rstart,NULL);CHKERRQ(ierr); ierr = MatGetOwnershipRanges(Atmp,&rstarts);CHKERRQ(ierr); ierr = MatGetLocalSize(Atmp,&mA,NULL);CHKERRQ(ierr); maxnc = 0; for (i=0; i<mA; i++) { ierr = MatGetRow(Atmp,rstart+i,&nc,NULL,NULL);CHKERRQ(ierr); ierr = MatRestoreRow(Atmp,rstart+i,&nc,NULL,NULL);CHKERRQ(ierr); maxnc = PetscMax(nc,maxnc); } ierr = PetscMalloc(maxnc*sizeof(PetscInt),&ccols);CHKERRQ(ierr); for (i=0; i<mA; i++) { ierr = MatGetRow(Atmp,rstart+i,&nc,&cols,NULL);CHKERRQ(ierr); /* remap the columns taking into how much they are shifted on each process */ for (j=0; j<nc; j++) { proc = 0; while (cols[j] >= rstarts[proc+1]) proc++; ccols[j] = cols[j] + next->grstarts[proc] - rstarts[proc]; } ierr = MatPreallocateSet(com->rstart+next->rstart+i,nc,ccols,dnz,onz);CHKERRQ(ierr); ierr = MatRestoreRow(Atmp,rstart+i,&nc,&cols,NULL);CHKERRQ(ierr); } ierr = PetscFree(ccols);CHKERRQ(ierr); ierr = MatDestroy(&Atmp);CHKERRQ(ierr); next = next->next; } if (com->FormCoupleLocations) { ierr = (*com->FormCoupleLocations)(dm,NULL,dnz,onz,__rstart,__nrows,__start,__end);CHKERRQ(ierr); } ierr = MatMPIAIJSetPreallocation(*J,0,dnz,0,onz);CHKERRQ(ierr); ierr = MatSeqAIJSetPreallocation(*J,0,dnz);CHKERRQ(ierr); ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); if (dm->prealloc_only) PetscFunctionReturn(0); next = com->next; while (next) { PetscInt nc,rstart,row,maxnc,*ccols; const PetscInt *cols,*rstarts; const PetscScalar *values; PetscMPIInt proc; ierr = DMCreateMatrix(next->dm,mtype,&Atmp);CHKERRQ(ierr); ierr = MatGetOwnershipRange(Atmp,&rstart,NULL);CHKERRQ(ierr); ierr = MatGetOwnershipRanges(Atmp,&rstarts);CHKERRQ(ierr); ierr = MatGetLocalSize(Atmp,&mA,NULL);CHKERRQ(ierr); maxnc = 0; for (i=0; i<mA; i++) { ierr = MatGetRow(Atmp,rstart+i,&nc,NULL,NULL);CHKERRQ(ierr); ierr = MatRestoreRow(Atmp,rstart+i,&nc,NULL,NULL);CHKERRQ(ierr); maxnc = PetscMax(nc,maxnc); } ierr = PetscMalloc(maxnc*sizeof(PetscInt),&ccols);CHKERRQ(ierr); for (i=0; i<mA; i++) { ierr = MatGetRow(Atmp,rstart+i,&nc,(const PetscInt**)&cols,&values);CHKERRQ(ierr); for (j=0; j<nc; j++) { proc = 0; while (cols[j] >= rstarts[proc+1]) proc++; ccols[j] = cols[j] + next->grstarts[proc] - rstarts[proc]; } row = com->rstart+next->rstart+i; ierr = MatSetValues(*J,1,&row,nc,ccols,values,INSERT_VALUES);CHKERRQ(ierr); ierr = MatRestoreRow(Atmp,rstart+i,&nc,(const PetscInt**)&cols,&values);CHKERRQ(ierr); } ierr = PetscFree(ccols);CHKERRQ(ierr); ierr = MatDestroy(&Atmp);CHKERRQ(ierr); next = next->next; } if (com->FormCoupleLocations) { PetscInt __rstart; ierr = MatGetOwnershipRange(*J,&__rstart,NULL);CHKERRQ(ierr); ierr = (*com->FormCoupleLocations)(dm,*J,NULL,NULL,__rstart,0,0,0);CHKERRQ(ierr); } ierr = MatAssemblyBegin(*J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(*J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); PetscFunctionReturn(0); }
int main(int argc, char **argv) { MPI_Comm comm; PetscMPIInt rank; PetscErrorCode ierr; User user; PetscLogDouble v1, v2; PetscInt nplot = 0; char filename1[2048], fileName[2048]; PetscBool set = PETSC_FALSE; PetscInt steps_output; ierr = PetscInitialize(&argc, &argv, (char*) 0, help);CHKERRQ(ierr); comm = PETSC_COMM_WORLD; ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); ierr = PetscNew(&user);CHKERRQ(ierr); ierr = PetscNew(&user->algebra);CHKERRQ(ierr); ierr = PetscNew(&user->model);CHKERRQ(ierr); ierr = PetscNew(&user->model->physics);CHKERRQ(ierr); Algebra algebra = user->algebra; ierr = LoadOptions(comm, user);CHKERRQ(ierr); ierr = PetscTime(&v1);CHKERRQ(ierr); ierr = CreateMesh(comm, user);CHKERRQ(ierr); ierr = PetscTime(&v2);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "Read and Distribute mesh takes %f sec \n", v2 - v1);CHKERRQ(ierr); ierr = SetUpLocalSpace(user);CHKERRQ(ierr); //Set up the dofs of each element ierr = ConstructGeometryFVM(&user->facegeom, &user->cellgeom, user);CHKERRQ(ierr); ierr = LimiterSetup(user);CHKERRQ(ierr); if(user->output_solution){ // the output file options ierr = PetscOptionsBegin(PETSC_COMM_WORLD,0,"Options for output solution",0);CHKERRQ(ierr); ierr = PetscOptionsString("-solutionfile", "solution file", "AeroSim.c", filename1,filename1, 2048, &set);CHKERRQ(ierr); if(!set){SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_NULL,"please use option -solutionfile to specify solution file name \n");} ierr = PetscOptionsInt("-steps_output", "the number of time steps between two outputs", "", steps_output, &steps_output, &set);CHKERRQ(ierr); if(!set){ steps_output = 1;} ierr = PetscOptionsEnd();CHKERRQ(ierr); } if (user->TimeIntegralMethod == EXPLICITMETHOD) { if(user->myownexplicitmethod){ ierr = PetscPrintf(PETSC_COMM_WORLD,"Using the fully explicit method based on my own routing\n");CHKERRQ(ierr); user->current_time = user->initial_time; user->current_step = 1; ierr = DMCreateGlobalVector(user->dm, &algebra->solution);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) algebra->solution, "solution");CHKERRQ(ierr); ierr = SetInitialCondition(user->dm, algebra->solution, user);CHKERRQ(ierr); ierr = VecDuplicate(algebra->solution, &algebra->fn);CHKERRQ(ierr); ierr = VecDuplicate(algebra->solution, &algebra->oldsolution);CHKERRQ(ierr); if(user->Explicit_RK2){ ierr = PetscPrintf(PETSC_COMM_WORLD,"Use the second order Runge Kutta method \n");CHKERRQ(ierr); }else{ ierr = PetscPrintf(PETSC_COMM_WORLD,"Use the first order forward Euler method \n");CHKERRQ(ierr); } nplot = 0; //the plot step while(user->current_time < (user->final_time - 0.05 * user->dt)){ user->current_time = user->current_time + user->dt; ierr = FormTimeStepFunction(user, algebra, algebra->solution, algebra->fn);CHKERRQ(ierr); PetscReal fnnorm; ierr = VecNorm(algebra->fn,NORM_INFINITY,&fnnorm);CHKERRQ(ierr); if(0){ PetscViewer viewer; ierr = OutputVTK(user->dm, "function.vtk", &viewer);CHKERRQ(ierr); ierr = VecView(algebra->fn, viewer);CHKERRQ(ierr); ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD,"Step %D at time %g with founction norm = %g \n", user->current_step, user->current_time, fnnorm);CHKERRQ(ierr); //break; } if(user->Explicit_RK2){ ierr = VecCopy(algebra->solution, algebra->oldsolution);CHKERRQ(ierr);//U^n ierr = VecAXPY(algebra->solution, user->dt, algebra->fn);CHKERRQ(ierr);//U^{(1)} ierr = FormTimeStepFunction(user, algebra, algebra->solution, algebra->fn);CHKERRQ(ierr);//f(U^{(1)}) ierr = VecAXPY(algebra->solution, 1.0, algebra->oldsolution);CHKERRQ(ierr);//U^n + U^{(1)} ierr = VecAXPY(algebra->solution, user->dt, algebra->fn);CHKERRQ(ierr);// + dt*f(U^{(1)}) ierr = VecScale(algebra->solution, 0.5);CHKERRQ(ierr); }else{ ierr = VecCopy(algebra->solution, algebra->oldsolution);CHKERRQ(ierr); ierr = VecAXPY(algebra->solution, user->dt, algebra->fn);CHKERRQ(ierr); } {// Monitor the solution and function norms PetscReal norm; PetscLogDouble space =0; PetscInt size; ierr = VecNorm(algebra->solution,NORM_INFINITY,&norm);CHKERRQ(ierr); ierr = VecGetSize(algebra->solution, &size);CHKERRQ(ierr); norm = norm/size; if (norm>1.e5) { SETERRQ2(PETSC_COMM_WORLD, PETSC_ERR_LIB, "The norm of the solution is: %f (current time: %f). The explicit method is going to DIVERGE!!!", norm, user->current_time); } if (user->current_step%10==0) { ierr = PetscPrintf(PETSC_COMM_WORLD,"Step %D at time %g with solution norm = %g and founction norm = %g \n", user->current_step, user->current_time, norm, fnnorm);CHKERRQ(ierr); } ierr = PetscMallocGetCurrentUsage(&space);CHKERRQ(ierr); // if (user->current_step%10==0) { // ierr = PetscPrintf(PETSC_COMM_WORLD,"Current space PetscMalloc()ed %g M\n", // space/(1024*1024));CHKERRQ(ierr); // } } { // Monitor the difference of two steps' solution PetscReal norm; ierr = VecAXPY(algebra->oldsolution, -1, algebra->solution);CHKERRQ(ierr); ierr = VecNorm(algebra->oldsolution,NORM_INFINITY,&norm);CHKERRQ(ierr); if (user->current_step%10==0) { ierr = PetscPrintf(PETSC_COMM_WORLD,"Step %D at time %g with ||u_k-u_{k-1}|| = %g \n", user->current_step, user->current_time, norm);CHKERRQ(ierr); } if((norm<1.e-6)||(user->current_step > user->max_time_its)) break; } // output the solution if (user->output_solution && (user->current_step%steps_output==0)){ PetscViewer viewer; // update file name for the current time step ierr = PetscSNPrintf(fileName, sizeof(fileName),"%s_%d.vtk",filename1, nplot);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD,"Outputing solution %s (current time %f)\n", fileName, user->current_time);CHKERRQ(ierr); ierr = OutputVTK(user->dm, fileName, &viewer);CHKERRQ(ierr); ierr = VecView(algebra->solution, viewer);CHKERRQ(ierr); ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); nplot++; } user->current_step++; } ierr = VecDestroy(&algebra->fn);CHKERRQ(ierr); }else{ PetscReal ftime; TS ts; TSConvergedReason reason; PetscInt nsteps; ierr = PetscPrintf(PETSC_COMM_WORLD,"Using the fully explicit method based on the PETSC TS routing\n");CHKERRQ(ierr); ierr = DMCreateGlobalVector(user->dm, &algebra->solution);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) algebra->solution, "solution");CHKERRQ(ierr); ierr = SetInitialCondition(user->dm, algebra->solution, user);CHKERRQ(ierr); ierr = TSCreate(comm, &ts);CHKERRQ(ierr); ierr = TSSetType(ts, TSEULER);CHKERRQ(ierr); ierr = TSSetDM(ts, user->dm);CHKERRQ(ierr); ierr = TSMonitorSet(ts,TSMonitorFunctionError,&user,NULL);CHKERRQ(ierr); ierr = TSSetRHSFunction(ts, NULL, MyRHSFunction, user);CHKERRQ(ierr); ierr = TSSetDuration(ts, 1000, user->final_time);CHKERRQ(ierr); ierr = TSSetInitialTimeStep(ts, user->initial_time, user->dt);CHKERRQ(ierr); ierr = TSSetFromOptions(ts);CHKERRQ(ierr); ierr = TSSolve(ts, algebra->solution);CHKERRQ(ierr); ierr = TSGetSolveTime(ts, &ftime);CHKERRQ(ierr); ierr = TSGetTimeStepNumber(ts, &nsteps);CHKERRQ(ierr); ierr = TSGetConvergedReason(ts, &reason);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD,"%s at time %g after %D steps\n",TSConvergedReasons[reason],ftime,nsteps);CHKERRQ(ierr); ierr = TSDestroy(&ts);CHKERRQ(ierr); } if(user->benchmark_couette) { ierr = DMCreateGlobalVector(user->dm, &algebra->exactsolution);CHKERRQ(ierr); ierr = ComputeExactSolution(user->dm, user->final_time, algebra->exactsolution, user);CHKERRQ(ierr); } if (user->output_solution){ PetscViewer viewer; ierr = OutputVTK(user->dm, "solution.vtk", &viewer);CHKERRQ(ierr); ierr = VecView(algebra->solution, viewer);CHKERRQ(ierr); ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); } if(user->benchmark_couette) { PetscViewer viewer; PetscReal norm; ierr = OutputVTK(user->dm, "exact_solution.vtk", &viewer);CHKERRQ(ierr); ierr = VecView(algebra->exactsolution, viewer);CHKERRQ(ierr); ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); ierr = VecAXPY(algebra->exactsolution, -1, algebra->solution);CHKERRQ(ierr); ierr = VecNorm(algebra->exactsolution,NORM_INFINITY,&norm);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD,"Final time at %f, Error: ||u_k-u|| = %g \n", user->final_time, norm);CHKERRQ(ierr); ierr = OutputVTK(user->dm, "Error.vtk", &viewer);CHKERRQ(ierr); ierr = VecView(algebra->exactsolution, viewer);CHKERRQ(ierr); ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); } ierr = VecDestroy(&algebra->solution);CHKERRQ(ierr); ierr = VecDestroy(&algebra->oldsolution);CHKERRQ(ierr); ierr = DMDestroy(&user->dm);CHKERRQ(ierr); } else if (user->TimeIntegralMethod == IMPLICITMETHOD) { ierr = PetscPrintf(PETSC_COMM_WORLD,"Using the fully implicit method\n");CHKERRQ(ierr); ierr = SNESCreate(comm,&user->snes);CHKERRQ(ierr); ierr = SNESSetDM(user->snes,user->dm);CHKERRQ(ierr); ierr = DMCreateGlobalVector(user->dm, &algebra->solution);CHKERRQ(ierr); ierr = VecDuplicate(algebra->solution, &algebra->oldsolution);CHKERRQ(ierr); ierr = VecDuplicate(algebra->solution, &algebra->f);CHKERRQ(ierr); ierr = VecDuplicate(algebra->solution, &algebra->fn);CHKERRQ(ierr); ierr = VecDuplicate(algebra->solution, &algebra->oldfn);CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) algebra->solution, "solution");CHKERRQ(ierr); ierr = SetInitialCondition(user->dm, algebra->solution, user);CHKERRQ(ierr); ierr = DMSetMatType(user->dm, MATAIJ);CHKERRQ(ierr); // ierr = DMCreateMatrix(user->dm, &algebra->A);CHKERRQ(ierr); ierr = DMCreateMatrix(user->dm, &algebra->J);CHKERRQ(ierr); if (user->JdiffP) { /*Set up the preconditioner matrix*/ ierr = DMCreateMatrix(user->dm, &algebra->P);CHKERRQ(ierr); }else{ algebra->P = algebra->J; } ierr = MatSetOption(algebra->J, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE);CHKERRQ(ierr); /*set nonlinear function */ ierr = SNESSetFunction(user->snes, algebra->f, FormFunction, (void*)user);CHKERRQ(ierr); /* compute Jacobian */ ierr = SNESSetJacobian(user->snes, algebra->J, algebra->P, FormJacobian, (void*)user);CHKERRQ(ierr); ierr = SNESSetFromOptions(user->snes);CHKERRQ(ierr); /* do the solve */ if (user->timestep == TIMESTEP_STEADY_STATE) { ierr = SolveSteadyState(user);CHKERRQ(ierr); } else { ierr = SolveTimeDependent(user);CHKERRQ(ierr); } if (user->output_solution){ PetscViewer viewer; ierr = OutputVTK(user->dm, "solution.vtk", &viewer);CHKERRQ(ierr); ierr = VecView(algebra->solution, viewer);CHKERRQ(ierr); ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); } if(user->benchmark_couette) { PetscViewer viewer; PetscReal norm; ierr = OutputVTK(user->dm, "exact_solution.vtk", &viewer);CHKERRQ(ierr); ierr = VecView(algebra->exactsolution, viewer);CHKERRQ(ierr); ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); ierr = VecAXPY(algebra->exactsolution, -1, algebra->solution);CHKERRQ(ierr); ierr = VecNorm(algebra->exactsolution,NORM_INFINITY,&norm);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD,"Error: ||u_k-u|| = %g \n", norm);CHKERRQ(ierr); ierr = OutputVTK(user->dm, "Error.vtk", &viewer);CHKERRQ(ierr); ierr = VecView(algebra->exactsolution, viewer);CHKERRQ(ierr); ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); } ierr = VecDestroy(&algebra->solution);CHKERRQ(ierr); ierr = VecDestroy(&algebra->f);CHKERRQ(ierr); ierr = VecDestroy(&algebra->oldsolution);CHKERRQ(ierr); ierr = VecDestroy(&algebra->fn);CHKERRQ(ierr); ierr = VecDestroy(&algebra->oldfn);CHKERRQ(ierr); ierr = SNESDestroy(&user->snes);CHKERRQ(ierr); ierr = DMDestroy(&user->dm);CHKERRQ(ierr); } else { SETERRQ(PETSC_COMM_SELF,PETSC_ERR_USER,"WRONG option for the time integral method. Using the option '-time_integral_method 0 or 1'"); } ierr = VecDestroy(&user->cellgeom);CHKERRQ(ierr); ierr = VecDestroy(&user->facegeom);CHKERRQ(ierr); ierr = DMDestroy(&user->dmGrad);CHKERRQ(ierr); ierr = PetscFunctionListDestroy(&LimitList);CHKERRQ(ierr); ierr = PetscFree(user->model->physics);CHKERRQ(ierr); ierr = PetscFree(user->algebra);CHKERRQ(ierr); ierr = PetscFree(user->model);CHKERRQ(ierr); ierr = PetscFree(user);CHKERRQ(ierr); { PetscLogDouble space =0; ierr = PetscMallocGetCurrentUsage(&space);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD,"Unfreed space at the End %g M\n", space/(1024*1024));CHKERRQ(ierr); } ierr = PetscFinalize(); return(0); }
int main(int argc,char **argv) { PetscErrorCode ierr; KSP ksp; PC pc; Vec x,b; DM da; Mat A,Atrans; PetscInt dof=1,M=8; PetscBool flg,trans=PETSC_FALSE; ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr; ierr = PetscOptionsGetInt(NULL,NULL,"-dof",&dof,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetInt(NULL,NULL,"-M",&M,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetBool(NULL,NULL,"-trans",&trans,NULL);CHKERRQ(ierr); ierr = DMDACreate(PETSC_COMM_WORLD,&da);CHKERRQ(ierr); ierr = DMSetDimension(da,3);CHKERRQ(ierr); ierr = DMDASetBoundaryType(da,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE);CHKERRQ(ierr); ierr = DMDASetStencilType(da,DMDA_STENCIL_STAR);CHKERRQ(ierr); ierr = DMDASetSizes(da,M,M,M);CHKERRQ(ierr); ierr = DMDASetNumProcs(da,PETSC_DECIDE,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr); ierr = DMDASetDof(da,dof);CHKERRQ(ierr); ierr = DMDASetStencilWidth(da,1);CHKERRQ(ierr); ierr = DMDASetOwnershipRanges(da,NULL,NULL,NULL);CHKERRQ(ierr); ierr = DMSetFromOptions(da);CHKERRQ(ierr); ierr = DMSetUp(da);CHKERRQ(ierr); ierr = DMCreateGlobalVector(da,&x);CHKERRQ(ierr); ierr = DMCreateGlobalVector(da,&b);CHKERRQ(ierr); ierr = ComputeRHS(da,b);CHKERRQ(ierr); ierr = DMSetMatType(da,MATBAIJ);CHKERRQ(ierr); ierr = DMSetFromOptions(da);CHKERRQ(ierr); ierr = DMCreateMatrix(da,&A);CHKERRQ(ierr); ierr = ComputeMatrix(da,A);CHKERRQ(ierr); /* A is non-symmetric. Make A = 0.5*(A + Atrans) symmetric for testing icc and cholesky */ ierr = MatTranspose(A,MAT_INITIAL_MATRIX,&Atrans);CHKERRQ(ierr); ierr = MatAXPY(A,1.0,Atrans,DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr); ierr = MatScale(A,0.5);CHKERRQ(ierr); ierr = MatDestroy(&Atrans);CHKERRQ(ierr); /* Test sbaij matrix */ flg = PETSC_FALSE; ierr = PetscOptionsGetBool(NULL,NULL, "-test_sbaij1", &flg,NULL);CHKERRQ(ierr); if (flg) { Mat sA; PetscBool issymm; ierr = MatIsTranspose(A,A,0.0,&issymm);CHKERRQ(ierr); if (issymm) { ierr = MatSetOption(A,MAT_SYMMETRIC,PETSC_TRUE);CHKERRQ(ierr); } else {ierr = PetscPrintf(PETSC_COMM_WORLD,"Warning: A is non-symmetric\n");CHKERRQ(ierr);} ierr = MatConvert(A,MATSBAIJ,MAT_INITIAL_MATRIX,&sA);CHKERRQ(ierr); ierr = MatDestroy(&A);CHKERRQ(ierr); A = sA; } ierr = KSPCreate(PETSC_COMM_WORLD,&ksp);CHKERRQ(ierr); ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr); ierr = KSPSetOperators(ksp,A,A);CHKERRQ(ierr); ierr = KSPGetPC(ksp,&pc);CHKERRQ(ierr); ierr = PCSetDM(pc,(DM)da);CHKERRQ(ierr); if (trans) { ierr = KSPSolveTranspose(ksp,b,x);CHKERRQ(ierr); } else { ierr = KSPSolve(ksp,b,x);CHKERRQ(ierr); } /* check final residual */ flg = PETSC_FALSE; ierr = PetscOptionsGetBool(NULL,NULL, "-check_final_residual", &flg,NULL);CHKERRQ(ierr); if (flg) { Vec b1; PetscReal norm; ierr = KSPGetSolution(ksp,&x);CHKERRQ(ierr); ierr = VecDuplicate(b,&b1);CHKERRQ(ierr); ierr = MatMult(A,x,b1);CHKERRQ(ierr); ierr = VecAXPY(b1,-1.0,b);CHKERRQ(ierr); ierr = VecNorm(b1,NORM_2,&norm);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD,"Final residual %g\n",norm);CHKERRQ(ierr); ierr = VecDestroy(&b1);CHKERRQ(ierr); } ierr = KSPDestroy(&ksp);CHKERRQ(ierr); ierr = VecDestroy(&x);CHKERRQ(ierr); ierr = VecDestroy(&b);CHKERRQ(ierr); ierr = MatDestroy(&A);CHKERRQ(ierr); ierr = DMDestroy(&da);CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; }
int main(int argc,char **argv) { TS ts; /* time integrator */ SNES snes; /* nonlinear solver */ SNESLineSearch linesearch; /* line search */ Vec X; /* solution, residual vectors */ Mat J; /* Jacobian matrix */ PetscInt steps,maxsteps,mx; PetscErrorCode ierr; DM da; PetscReal ftime,dt; struct _User user; /* user-defined work context */ TSConvergedReason reason; PetscInitialize(&argc,&argv,(char*)0,help); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create distributed array (DMDA) to manage parallel grid and vectors - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = DMDACreate1d(PETSC_COMM_WORLD,DMDA_BOUNDARY_NONE,-11,2,2,NULL,&da);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Extract global vectors from DMDA; - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = DMCreateGlobalVector(da,&X);CHKERRQ(ierr); /* Initialize user application context */ ierr = PetscOptionsBegin(PETSC_COMM_WORLD,NULL,"Advection-reaction options",""); { user.a[0] = 1; ierr = PetscOptionsReal("-a0","Advection rate 0","",user.a[0],&user.a[0],NULL);CHKERRQ(ierr); user.a[1] = 0; ierr = PetscOptionsReal("-a1","Advection rate 1","",user.a[1],&user.a[1],NULL);CHKERRQ(ierr); user.k[0] = 1e6; ierr = PetscOptionsReal("-k0","Reaction rate 0","",user.k[0],&user.k[0],NULL);CHKERRQ(ierr); user.k[1] = 2*user.k[0]; ierr = PetscOptionsReal("-k1","Reaction rate 1","",user.k[1],&user.k[1],NULL);CHKERRQ(ierr); user.s[0] = 0; ierr = PetscOptionsReal("-s0","Source 0","",user.s[0],&user.s[0],NULL);CHKERRQ(ierr); user.s[1] = 1; ierr = PetscOptionsReal("-s1","Source 1","",user.s[1],&user.s[1],NULL);CHKERRQ(ierr); } ierr = PetscOptionsEnd();CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create timestepping solver context - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr); ierr = TSSetDM(ts,da);CHKERRQ(ierr); ierr = TSSetType(ts,TSARKIMEX);CHKERRQ(ierr); ierr = TSSetRHSFunction(ts,NULL,FormRHSFunction,&user);CHKERRQ(ierr); ierr = TSSetIFunction(ts,NULL,FormIFunction,&user);CHKERRQ(ierr); ierr = DMCreateMatrix(da,MATAIJ,&J);CHKERRQ(ierr); ierr = TSSetIJacobian(ts,J,J,FormIJacobian,&user);CHKERRQ(ierr); /* A line search in the nonlinear solve can fail due to ill-conditioning unless an absolute tolerance is set. Since * this problem is linear, we deactivate the line search. For a linear problem, it is usually recommended to also use * SNESSetType(snes,SNESKSPONLY). */ ierr = TSGetSNES(ts,&snes);CHKERRQ(ierr); ierr = SNESGetLineSearch(snes,&linesearch);CHKERRQ(ierr); ierr = SNESLineSearchSetType(linesearch,SNESLINESEARCHBASIC);CHKERRQ(ierr); ftime = 1.0; maxsteps = 10000; ierr = TSSetDuration(ts,maxsteps,ftime);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set initial conditions - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = FormInitialSolution(ts,X,&user);CHKERRQ(ierr); ierr = TSSetSolution(ts,X);CHKERRQ(ierr); ierr = VecGetSize(X,&mx);CHKERRQ(ierr); dt = .1 * PetscMax(user.a[0],user.a[1]) / mx; /* Advective CFL, I don't know why it needs so much safety factor. */ ierr = TSSetInitialTimeStep(ts,0.0,dt);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set runtime options - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSetFromOptions(ts);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Solve nonlinear system - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSolve(ts,X);CHKERRQ(ierr); ierr = TSGetSolveTime(ts,&ftime);CHKERRQ(ierr); ierr = TSGetTimeStepNumber(ts,&steps);CHKERRQ(ierr); ierr = TSGetConvergedReason(ts,&reason);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD,"%s at time %G after %D steps\n",TSConvergedReasons[reason],ftime,steps);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Free work space. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = MatDestroy(&J);CHKERRQ(ierr); ierr = VecDestroy(&X);CHKERRQ(ierr); ierr = TSDestroy(&ts);CHKERRQ(ierr); ierr = DMDestroy(&da);CHKERRQ(ierr); ierr = PetscFinalize(); return 0; }
int main(int argc,char **argv) { TS ts; /* time integrator */ TSAdapt adapt; Vec X; /* solution vector */ Mat J; /* Jacobian matrix */ PetscInt steps,maxsteps,ncells,xs,xm,i; PetscErrorCode ierr; PetscReal ftime,dt; char chemfile[PETSC_MAX_PATH_LEN] = "chem.inp",thermofile[PETSC_MAX_PATH_LEN] = "therm.dat"; struct _User user; TSConvergedReason reason; PetscBool showsolutions = PETSC_FALSE; char **snames,*names; Vec lambda; /* used with TSAdjoint for sensitivities */ ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr; ierr = PetscOptionsBegin(PETSC_COMM_WORLD,NULL,"Chemistry solver options","");CHKERRQ(ierr); ierr = PetscOptionsString("-chem","CHEMKIN input file","",chemfile,chemfile,sizeof(chemfile),NULL);CHKERRQ(ierr); ierr = PetscOptionsString("-thermo","NASA thermo input file","",thermofile,thermofile,sizeof(thermofile),NULL);CHKERRQ(ierr); user.pressure = 1.01325e5; /* Pascal */ ierr = PetscOptionsReal("-pressure","Pressure of reaction [Pa]","",user.pressure,&user.pressure,NULL);CHKERRQ(ierr); user.Tini = 1550; ierr = PetscOptionsReal("-Tini","Initial temperature [K]","",user.Tini,&user.Tini,NULL);CHKERRQ(ierr); user.diffus = 100; ierr = PetscOptionsReal("-diffus","Diffusion constant","",user.diffus,&user.diffus,NULL);CHKERRQ(ierr); ierr = PetscOptionsBool("-draw_solution","Plot the solution for each cell","",showsolutions,&showsolutions,NULL);CHKERRQ(ierr); user.diffusion = PETSC_TRUE; ierr = PetscOptionsBool("-diffusion","Have diffusion","",user.diffusion,&user.diffusion,NULL);CHKERRQ(ierr); user.reactions = PETSC_TRUE; ierr = PetscOptionsBool("-reactions","Have reactions","",user.reactions,&user.reactions,NULL);CHKERRQ(ierr); ierr = PetscOptionsEnd();CHKERRQ(ierr); ierr = TC_initChem(chemfile, thermofile, 0, 1.0);TCCHKERRQ(ierr); user.Nspec = TC_getNspec(); user.Nreac = TC_getNreac(); ierr = DMDACreate1d(PETSC_COMM_WORLD,DM_BOUNDARY_PERIODIC,-1,user.Nspec+1,1,NULL,&user.dm);CHKERRQ(ierr); ierr = DMDAGetInfo(user.dm,NULL,&ncells,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL);CHKERRQ(ierr); user.dx = 1.0/ncells; /* Set the coordinates of the cell centers; note final ghost cell is at x coordinate 1.0 */ ierr = DMDASetUniformCoordinates(user.dm,0.0,1.0,0.0,1.0,0.0,1.0);CHKERRQ(ierr); /* set the names of each field in the DMDA based on the species name */ ierr = PetscMalloc1((user.Nspec+1)*LENGTHOFSPECNAME,&names);CHKERRQ(ierr); ierr = PetscStrcpy(names,"Temp");CHKERRQ(ierr); TC_getSnames(user.Nspec,names+LENGTHOFSPECNAME);CHKERRQ(ierr); ierr = PetscMalloc1((user.Nspec+2),&snames);CHKERRQ(ierr); for (i=0; i<user.Nspec+1; i++) snames[i] = names+i*LENGTHOFSPECNAME; snames[user.Nspec+1] = NULL; ierr = DMDASetFieldNames(user.dm,(const char * const *)snames);CHKERRQ(ierr); ierr = PetscFree(snames);CHKERRQ(ierr); ierr = PetscFree(names);CHKERRQ(ierr); ierr = DMCreateMatrix(user.dm,&J);CHKERRQ(ierr); ierr = DMCreateGlobalVector(user.dm,&X);CHKERRQ(ierr); ierr = PetscMalloc3(user.Nspec+1,&user.tchemwork,PetscSqr(user.Nspec+1),&user.Jdense,user.Nspec+1,&user.rows);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create timestepping solver context - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr); ierr = TSSetDM(ts,user.dm);CHKERRQ(ierr); ierr = TSSetType(ts,TSARKIMEX);CHKERRQ(ierr); ierr = TSARKIMEXSetFullyImplicit(ts,PETSC_TRUE);CHKERRQ(ierr); ierr = TSARKIMEXSetType(ts,TSARKIMEX4);CHKERRQ(ierr); ierr = TSSetRHSFunction(ts,NULL,FormRHSFunction,&user);CHKERRQ(ierr); ierr = TSSetRHSJacobian(ts,J,J,FormRHSJacobian,&user);CHKERRQ(ierr); ftime = 1.0; maxsteps = 10000; ierr = TSSetDuration(ts,maxsteps,ftime);CHKERRQ(ierr); ierr = TSSetExactFinalTime(ts,TS_EXACTFINALTIME_STEPOVER);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set initial conditions - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = FormInitialSolution(ts,X,&user);CHKERRQ(ierr); ierr = TSSetSolution(ts,X);CHKERRQ(ierr); dt = 1e-10; /* Initial time step */ ierr = TSSetInitialTimeStep(ts,0.0,dt);CHKERRQ(ierr); ierr = TSGetAdapt(ts,&adapt);CHKERRQ(ierr); ierr = TSAdaptSetStepLimits(adapt,1e-12,1e-4);CHKERRQ(ierr); /* Also available with -ts_adapt_dt_min/-ts_adapt_dt_max */ ierr = TSSetMaxSNESFailures(ts,-1);CHKERRQ(ierr); /* Retry step an unlimited number of times */ /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Pass information to graphical monitoring routine - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ if (showsolutions) { ierr = DMDAGetCorners(user.dm,&xs,NULL,NULL,&xm,NULL,NULL);CHKERRQ(ierr); for (i=xs;i<xs+xm;i++) { ierr = MonitorCell(ts,&user,i);CHKERRQ(ierr); } } /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set runtime options - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSetFromOptions(ts);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set final conditions for sensitivities - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = DMCreateGlobalVector(user.dm,&lambda);CHKERRQ(ierr); ierr = TSSetCostGradients(ts,1,&lambda,NULL);CHKERRQ(ierr); ierr = VecSetValue(lambda,0,1.0,INSERT_VALUES);CHKERRQ(ierr); ierr = VecAssemblyBegin(lambda);CHKERRQ(ierr); ierr = VecAssemblyEnd(lambda);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Solve ODE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSolve(ts,X);CHKERRQ(ierr); ierr = TSGetSolveTime(ts,&ftime);CHKERRQ(ierr); ierr = TSGetTimeStepNumber(ts,&steps);CHKERRQ(ierr); ierr = TSGetConvergedReason(ts,&reason);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD,"%s at time %g after %D steps\n",TSConvergedReasons[reason],(double)ftime,steps);CHKERRQ(ierr); { Vec max; const char * const *names; PetscInt i; const PetscReal *bmax; ierr = TSMonitorEnvelopeGetBounds(ts,&max,NULL);CHKERRQ(ierr); if (max) { ierr = TSMonitorLGGetVariableNames(ts,&names);CHKERRQ(ierr); if (names) { ierr = VecGetArrayRead(max,&bmax);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_SELF,"Species - maximum mass fraction\n");CHKERRQ(ierr); for (i=1; i<user.Nspec; i++) { if (bmax[i] > .01) {ierr = PetscPrintf(PETSC_COMM_SELF,"%s %g\n",names[i],bmax[i]);CHKERRQ(ierr);} } ierr = VecRestoreArrayRead(max,&bmax);CHKERRQ(ierr); } } } /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Free work space. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ TC_reset(); ierr = DMDestroy(&user.dm);CHKERRQ(ierr); ierr = MatDestroy(&J);CHKERRQ(ierr); ierr = VecDestroy(&X);CHKERRQ(ierr); ierr = VecDestroy(&lambda);CHKERRQ(ierr); ierr = TSDestroy(&ts);CHKERRQ(ierr); ierr = PetscFree3(user.tchemwork,user.Jdense,user.rows);CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; }
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; }
PetscErrorCode DMSetUp_AKKT(DM dm) { DM_AKKT *kkt = (DM_AKKT*)(dm->data); PetscErrorCode ierr; PetscFunctionBegin; if(dm->setupcalled) PetscFunctionReturn(0); if(!kkt->Aff){ if(kkt->dm) { ierr = DMCreateMatrix(kkt->dm, MATAIJ, &kkt->Aff); CHKERRQ(ierr); } else SETERRQ(((PetscObject)dm)->comm, PETSC_ERR_ARG_WRONGSTATE, "Neither matrix nor DM set"); } if(!kkt->isf[0] && !kkt->isf[0]) { if(kkt->detect_saddle_point) { ierr = MatFindZeroDiagonals(kkt->Aff,&kkt->isf[1]);CHKERRQ(ierr); } else if(kkt->dm && kkt->dname) { DM ddm; PetscInt n; char **names; IS *iss; DM *dms; PetscInt i; ierr = DMCreateFieldDecompositionDM(kkt->dm, kkt->dname, &ddm); CHKERRQ(ierr); ierr = DMCreateFieldDecomposition(ddm, &n, &names, &iss, &dms); CHKERRQ(ierr); if(n < 1 || n > 2) SETERRQ2(((PetscObject)dm)->comm, PETSC_ERR_ARG_WRONG, "Number of parts in decomposition %s must be between 1 and 2. Got %D instead",kkt->dname, n); for(i = 0; i < n; ++i) { if(!iss[i] && dms[i]) { const char* label; if(i == 0) label = "primal"; else label = "dual"; SETERRQ1(((PetscObject)dm)->comm, PETSC_ERR_ARG_WRONG, "Decomposition defines %s subDM, but no embedding IS is given", label); } } ierr = DMAKKTSetFieldDecomposition(dm, n, (const char**)names, iss, dms); CHKERRQ(ierr); for(i = 0; i < n; ++i) { ierr = PetscFree(names[i]); CHKERRQ(ierr); ierr = ISDestroy(&(iss[i])); CHKERRQ(ierr); ierr = DMDestroy(&(dms[i])); CHKERRQ(ierr); } } } if(!kkt->isf[0] && !kkt->isf[1]) SETERRQ(((PetscObject)dm)->comm, PETSC_ERR_ARG_WRONGSTATE, "Decomposition ISs not set and could not be derived. "); if(!kkt->isf[0] || !kkt->isf[1]) { PetscInt lstart, lend; ierr = MatGetOwnershipRange(kkt->Aff, &lstart, &lend); CHKERRQ(ierr); if(!kkt->isf[0]) { ierr = ISComplement(kkt->isf[0], lstart, lend, kkt->isf+1); CHKERRQ(ierr); } else { ierr = ISComplement(kkt->isf[1], lstart, lend, kkt->isf+0); CHKERRQ(ierr); } } /* FIX: Should we allow a combination of empty kkt->dmf[0] and non-empty kkt->dmf[1]? */ if(!kkt->dmf[0]) { /* Construct a GAMG proxy to coarsen the primal block. */ Mat A0f0f; IS is00; PetscInt lstart, lend; const char* primal = {"all"}; ierr = DMCreate(((PetscObject)dm)->comm, kkt->dmf+0); CHKERRQ(ierr); ierr = DMSetType(kkt->dmf[0],DMAKKT); CHKERRQ(ierr); ierr = MatGetSubMatrix(kkt->Aff, kkt->isf[0], kkt->isf[0], MAT_INITIAL_MATRIX, &A0f0f); CHKERRQ(ierr); ierr = DMAKKTSetMatrix(kkt->dmf[0], A0f0f); CHKERRQ(ierr); ierr = MatGetOwnershipRange(A0f0f, &lstart, &lend); CHKERRQ(ierr); ierr = ISCreateStride(((PetscObject)A0f0f)->comm, lend-lstart, lstart, 1, &is00); CHKERRQ(ierr); ierr = DMAKKTSetFieldDecomposition(kkt->dmf[0], 1, &primal, &is00, PETSC_NULL); CHKERRQ(ierr); } dm->setupcalled = PETSC_TRUE; PetscFunctionReturn(0); }
int main(int argc,char **argv) { DM da; /* distributed array */ Vec x,b,u; /* approx solution, RHS, exact solution */ Mat A; /* linear system matrix */ KSP ksp; /* linear solver context */ PetscRandom rctx; /* random number generator context */ PetscReal norm; /* norm of solution error */ PetscInt i,j,its; PetscErrorCode ierr; PetscBool flg = PETSC_FALSE; PetscLogStage stage; DMDALocalInfo info; ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr); /* Create distributed array to handle parallel distribution. The problem size will default to 8 by 7, but this can be changed using -da_grid_x M -da_grid_y N */ ierr = DMDACreate2d(PETSC_COMM_WORLD, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE,DMDA_STENCIL_STAR,-8,-7,PETSC_DECIDE,PETSC_DECIDE,1,1,NULL,NULL,&da);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Compute the matrix and right-hand-side vector that define the linear system, Ax = b. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ /* Create parallel matrix preallocated according to the DMDA, format AIJ by default. To use symmetric storage, run with -dm_mat_type sbaij -mat_ignore_lower_triangular */ ierr = DMSetMatType(da,MATAIJ);CHKERRQ(ierr); ierr = DMCreateMatrix(da,&A);CHKERRQ(ierr); /* Set matrix elements for the 2-D, five-point stencil in parallel. - Each processor needs to insert only elements that it owns locally (but any non-local elements will be sent to the appropriate processor during matrix assembly). - Rows and columns are specified by the stencil - Entries are normalized for a domain [0,1]x[0,1] */ ierr = PetscLogStageRegister("Assembly", &stage);CHKERRQ(ierr); ierr = PetscLogStagePush(stage);CHKERRQ(ierr); ierr = DMDAGetLocalInfo(da,&info);CHKERRQ(ierr); for (j=info.ys; j<info.ys+info.ym; j++) { for (i=info.xs; i<info.xs+info.xm; i++) { PetscReal hx = 1./info.mx,hy = 1./info.my; MatStencil row = {0},col[5] = {{0}}; PetscScalar v[5]; PetscInt ncols = 0; row.j = j; row.i = i; col[ncols].j = j; col[ncols].i = i; v[ncols++] = 2*(hx/hy + hy/hx); /* boundaries */ if (i>0) {col[ncols].j = j; col[ncols].i = i-1; v[ncols++] = -hy/hx;} if (i<info.mx-1) {col[ncols].j = j; col[ncols].i = i+1; v[ncols++] = -hy/hx;} if (j>0) {col[ncols].j = j-1; col[ncols].i = i; v[ncols++] = -hx/hy;} if (j<info.my-1) {col[ncols].j = j+1; col[ncols].i = i; v[ncols++] = -hx/hy;} ierr = MatSetValuesStencil(A,1,&row,ncols,col,v,INSERT_VALUES);CHKERRQ(ierr); } } /* Assemble matrix, using the 2-step process: MatAssemblyBegin(), MatAssemblyEnd() Computations can be done while messages are in transition by placing code between these two statements. */ ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); ierr = PetscLogStagePop();CHKERRQ(ierr); /* Create parallel vectors compatible with the DMDA. */ ierr = DMCreateGlobalVector(da,&u);CHKERRQ(ierr); ierr = VecDuplicate(u,&b);CHKERRQ(ierr); ierr = VecDuplicate(u,&x);CHKERRQ(ierr); /* Set exact solution; then compute right-hand-side vector. By default we use an exact solution of a vector with all elements of 1.0; Alternatively, using the runtime option -random_sol forms a solution vector with random components. */ ierr = PetscOptionsGetBool(NULL,"-random_exact_sol",&flg,NULL);CHKERRQ(ierr); if (flg) { ierr = PetscRandomCreate(PETSC_COMM_WORLD,&rctx);CHKERRQ(ierr); ierr = PetscRandomSetFromOptions(rctx);CHKERRQ(ierr); ierr = VecSetRandom(u,rctx);CHKERRQ(ierr); ierr = PetscRandomDestroy(&rctx);CHKERRQ(ierr); } else { ierr = VecSet(u,1.);CHKERRQ(ierr); } ierr = MatMult(A,u,b);CHKERRQ(ierr); /* View the exact solution vector if desired */ flg = PETSC_FALSE; ierr = PetscOptionsGetBool(NULL,"-view_exact_sol",&flg,NULL);CHKERRQ(ierr); if (flg) {ierr = VecView(u,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);} /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create the linear solver and set various options - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ /* Create linear solver context */ ierr = KSPCreate(PETSC_COMM_WORLD,&ksp);CHKERRQ(ierr); /* Set operators. Here the matrix that defines the linear system also serves as the preconditioning matrix. */ ierr = KSPSetOperators(ksp,A,A);CHKERRQ(ierr); /* Set runtime options, e.g., -ksp_type <type> -pc_type <type> -ksp_monitor -ksp_rtol <rtol> These options will override those specified above as long as KSPSetFromOptions() is called _after_ any other customization routines. */ ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Solve the linear system - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = KSPSolve(ksp,b,x);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Check solution and clean up - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ /* Check the error */ ierr = VecAXPY(x,-1.,u);CHKERRQ(ierr); ierr = VecNorm(x,NORM_2,&norm);CHKERRQ(ierr); ierr = KSPGetIterationNumber(ksp,&its);CHKERRQ(ierr); /* Print convergence information. PetscPrintf() produces a single print statement from all processes that share a communicator. An alternative is PetscFPrintf(), which prints to a file. */ ierr = PetscPrintf(PETSC_COMM_WORLD,"Norm of error %g iterations %D\n",(double)norm,its);CHKERRQ(ierr); /* Free work space. All PETSc objects should be destroyed when they are no longer needed. */ ierr = KSPDestroy(&ksp);CHKERRQ(ierr); ierr = VecDestroy(&u);CHKERRQ(ierr); ierr = VecDestroy(&x);CHKERRQ(ierr); ierr = VecDestroy(&b);CHKERRQ(ierr); ierr = MatDestroy(&A);CHKERRQ(ierr); ierr = DMDestroy(&da);CHKERRQ(ierr); /* Always call PetscFinalize() before exiting a program. This routine - finalizes the PETSc libraries as well as MPI - provides summary and diagnostic information if certain runtime options are chosen (e.g., -log_summary). */ ierr = PetscFinalize(); return 0; }
int main(int argc,char **argv) { TS ts; /* nonlinear solver */ Vec U; /* solution, residual vectors */ Mat J; /* Jacobian matrix */ PetscInt maxsteps = 1000; PetscErrorCode ierr; DM da; AppCtx user; PetscInt i; char Name[16]; /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Initialize program - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ PetscInitialize(&argc,&argv,(char*)0,help); user.N = 1; ierr = PetscOptionsGetInt(NULL,"-N",&user.N,NULL);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create distributed array (DMDA) to manage parallel grid and vectors - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = DMDACreate1d(PETSC_COMM_WORLD, DMDA_BOUNDARY_MIRROR,-8,user.N,1,NULL,&da);CHKERRQ(ierr); for (i=0; i<user.N; i++) { ierr = PetscSNPrintf(Name,16,"Void size %d",(int)(i+1)); ierr = DMDASetFieldName(da,i,Name);CHKERRQ(ierr); } /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Extract global vectors from DMDA; then duplicate for remaining vectors that are the same types - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = DMCreateGlobalVector(da,&U);CHKERRQ(ierr); ierr = DMCreateMatrix(da,MATAIJ,&J);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create timestepping solver context - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr); ierr = TSSetType(ts,TSARKIMEX);CHKERRQ(ierr); ierr = TSSetDM(ts,da);CHKERRQ(ierr); ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr); ierr = TSSetIFunction(ts,NULL,IFunction,&user);CHKERRQ(ierr); ierr = TSSetIJacobian(ts,J,J,IJacobian,&user);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set initial conditions - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = InitialConditions(da,U);CHKERRQ(ierr); ierr = TSSetSolution(ts,U);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set solver options - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSetInitialTimeStep(ts,0.0,.001);CHKERRQ(ierr); ierr = TSSetDuration(ts,maxsteps,1.0);CHKERRQ(ierr); ierr = TSSetFromOptions(ts);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Solve nonlinear system - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSolve(ts,U);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Free work space. All PETSc objects should be destroyed when they are no longer needed. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = VecDestroy(&U);CHKERRQ(ierr); ierr = MatDestroy(&J);CHKERRQ(ierr); ierr = TSDestroy(&ts);CHKERRQ(ierr); ierr = DMDestroy(&da);CHKERRQ(ierr); ierr = PetscFinalize(); PetscFunctionReturn(0); }