PetscErrorCode PETScExternalSolverCreate(MPI_Comm comm, TS * ts) { DM da; PetscErrorCode ierr; PetscFunctionBeginUser; /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create distributed array (DMDA) to manage parallel grid and vectors - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = DMDACreate2d(comm, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DMDA_STENCIL_STAR, 11, 11, PETSC_DECIDE, PETSC_DECIDE, 1, 1, NULL, NULL, &da); CHKERRQ(ierr); ierr = DMSetFromOptions(da); CHKERRQ(ierr); ierr = DMSetUp(da); CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create timestepping solver context - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSCreate(comm, ts); CHKERRQ(ierr); ierr = TSSetProblemType(*ts, TS_NONLINEAR); CHKERRQ(ierr); ierr = TSSetType(*ts, TSBEULER); CHKERRQ(ierr); ierr = TSSetDM(*ts, da); CHKERRQ(ierr); ierr = DMDestroy(&da); CHKERRQ(ierr); ierr = TSSetIFunction(*ts, NULL, FormIFunction, nullptr); CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set Jacobian evaluation routine - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSetIJacobian(*ts, NULL, NULL, FormIJacobian, NULL); 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 */ PetscViewer viewer; PetscInitialize(&argc,&argv,"petscopt_ex7", help); /* Get physics and time parameters */ ierr = Parameter_settings(&user);CHKERRQ(ierr); /* Create a 2D DA with dof = 1 */ ierr = DMDACreate2d(PETSC_COMM_WORLD,user.bx,user.by,DMDA_STENCIL_STAR,-4,-4,PETSC_DECIDE,PETSC_DECIDE,1,user.st_width,NULL,NULL,&user.da);CHKERRQ(ierr); /* Set x and y coordinates */ ierr = DMDASetUniformCoordinates(user.da,user.xmin,user.xmax,user.ymin,user.ymax,0,0);CHKERRQ(ierr); ierr = DMDASetCoordinateName(user.da,0,"X - the angle"); ierr = DMDASetCoordinateName(user.da,1,"Y - the speed"); /* 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); ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr); ierr = TSSetDM(ts,user.da);CHKERRQ(ierr); ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr); ierr = TSSetType(ts,TSARKIMEX);CHKERRQ(ierr); ierr = TSSetIFunction(ts,NULL,IFunction,&user);CHKERRQ(ierr); /* ierr = TSSetIJacobian(ts,NULL,NULL,IJacobian,&user);CHKERRQ(ierr); */ ierr = TSSetApplicationContext(ts,&user);CHKERRQ(ierr); ierr = TSSetInitialTimeStep(ts,0.0,.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 = DMDestroy(&user.da);CHKERRQ(ierr); ierr = TSDestroy(&ts);CHKERRQ(ierr); PetscFinalize(); return 0; }
int main(int argc,char **argv) { TS ts; SNES snes; SNESLineSearch linesearch; Vec x; AppCtx ctx; PetscErrorCode ierr; DM da; ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr; ierr = SetFromOptions(&ctx);CHKERRQ(ierr); ierr = TSCreate(PETSC_COMM_WORLD, &ts);CHKERRQ(ierr); ierr = TSSetType(ts,TSCN);CHKERRQ(ierr); ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr); ierr = TSSetIFunction(ts, NULL, FormIFunction, &ctx);CHKERRQ(ierr); ierr = DMDACreate2d(PETSC_COMM_WORLD, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE,DMDA_STENCIL_STAR,-4,-4,PETSC_DECIDE,PETSC_DECIDE,N_SPECIES,1,NULL,NULL,&da);CHKERRQ(ierr); ierr = DMDASetUniformCoordinates(da, 0.0, 1.0, 0.0, 1.0, 0.0, 1.0);CHKERRQ(ierr); ierr = DMDASetFieldName(da,0,"species A");CHKERRQ(ierr); ierr = DMDASetFieldName(da,1,"species B");CHKERRQ(ierr); ierr = DMDASetFieldName(da,2,"species C");CHKERRQ(ierr); ierr = DMSetApplicationContext(da,&ctx);CHKERRQ(ierr); ierr = DMCreateGlobalVector(da,&x);CHKERRQ(ierr); ierr = FormInitialGuess(da, &ctx, x);CHKERRQ(ierr); ierr = TSSetDM(ts, da);CHKERRQ(ierr); ierr = TSSetDuration(ts,10000,1000.0);CHKERRQ(ierr); ierr = TSSetExactFinalTime(ts,TS_EXACTFINALTIME_STEPOVER);CHKERRQ(ierr); ierr = TSSetInitialTimeStep(ts,0.0,1.0);CHKERRQ(ierr); ierr = TSSetSolution(ts,x);CHKERRQ(ierr); ierr = TSSetFromOptions(ts);CHKERRQ(ierr); ierr = TSGetSNES(ts,&snes);CHKERRQ(ierr); ierr = SNESGetLineSearch(snes,&linesearch);CHKERRQ(ierr); ierr = SNESLineSearchSetPostCheck(linesearch, ReactingFlowPostCheck, (void*)&ctx);CHKERRQ(ierr); ierr = SNESSetFromOptions(snes);CHKERRQ(ierr); ierr = TSSolve(ts,x);CHKERRQ(ierr); ierr = VecDestroy(&x);CHKERRQ(ierr); ierr = TSDestroy(&ts);CHKERRQ(ierr); ierr = DMDestroy(&da);CHKERRQ(ierr); ierr = PetscFinalize(); PetscFunctionReturn(0); }
int main(int argc,char **argv) { TS ts; Vec x,c; PetscErrorCode ierr; DM da; PetscInitialize(&argc,&argv,(char *)0,help); ierr = TSCreate(PETSC_COMM_WORLD, &ts);CHKERRQ(ierr); ierr = TSSetType(ts,TSCN);CHKERRQ(ierr); ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr); ierr = DMDACreate2d(PETSC_COMM_WORLD, DMDA_BOUNDARY_NONE, DMDA_BOUNDARY_NONE,DMDA_STENCIL_STAR,-4,-4,PETSC_DECIDE,PETSC_DECIDE,1,1,PETSC_NULL,PETSC_NULL,&da);CHKERRQ(ierr); ierr = DMDASetUniformCoordinates(da, 0.0, 1.0, 0.0, 1.0, 0.0, 1.0);CHKERRQ(ierr); ierr = DMDASetFieldName(da,0,"Heat");CHKERRQ(ierr); ierr = DMCreateGlobalVector(da,&x);CHKERRQ(ierr); ierr = FormInitialGuess(da,PETSC_NULL,x);CHKERRQ(ierr); ierr = DMDATSSetIFunctionLocal(da,INSERT_VALUES,(PetscErrorCode (*)(DMDALocalInfo*,PetscReal,void*,void*,void*,void*))FormIFunctionLocal,PETSC_NULL);CHKERRQ(ierr); /* set up the coefficient */ ierr = DMGetNamedGlobalVector(da,"coefficient",&c);CHKERRQ(ierr); ierr = FormDiffusionCoefficient(da,PETSC_NULL,c);CHKERRQ(ierr); ierr = DMRestoreNamedGlobalVector(da,"coefficient",&c);CHKERRQ(ierr); ierr = DMCoarsenHookAdd(da,PETSC_NULL,CoefficientRestrictHook,ts);CHKERRQ(ierr); ierr = DMSubDomainHookAdd(da,PETSC_NULL,CoefficientSubDomainRestrictHook,ts);CHKERRQ(ierr); ierr = TSSetDM(ts, da);CHKERRQ(ierr); ierr = TSSetDuration(ts,10000,1000.0);CHKERRQ(ierr); ierr = TSSetInitialTimeStep(ts,0.0,0.05);CHKERRQ(ierr); ierr = TSSetSolution(ts,x);CHKERRQ(ierr); ierr = TSSetFromOptions(ts);CHKERRQ(ierr); ierr = TSSolve(ts,x);CHKERRQ(ierr); ierr = VecDestroy(&x);CHKERRQ(ierr); ierr = TSDestroy(&ts);CHKERRQ(ierr); ierr = DMDestroy(&da);CHKERRQ(ierr); ierr = PetscFinalize(); PetscFunctionReturn(0); }
int main(int argc,char **argv) { PetscErrorCode ierr; PatternCtx user; TS ts; Vec x; DMDALocalInfo info; double noiselevel = -1.0; // negative value means no initial noise PetscInitialize(&argc,&argv,(char*)0,help); // parameter values from pages 21-22 in Hundsdorfer & Verwer (2003) user.L = 2.5; user.Du = 8.0e-5; user.Dv = 4.0e-5; user.phi = 0.024; user.kappa = 0.06; ierr = PetscOptionsBegin(PETSC_COMM_WORLD, "ptn_", "options for patterns", ""); CHKERRQ(ierr); ierr = PetscOptionsReal("-noisy_init", "initialize u,v with this much random noise (e.g. 0.2) on top of usual initial values", "pattern.c",noiselevel,&noiselevel,NULL);CHKERRQ(ierr); ierr = PetscOptionsReal("-L","square domain side length; recommend L >= 0.5", "pattern.c",user.L,&user.L,NULL);CHKERRQ(ierr); ierr = PetscOptionsReal("-Du","diffusion coefficient of first equation", "pattern.c",user.Du,&user.Du,NULL);CHKERRQ(ierr); ierr = PetscOptionsReal("-Dv","diffusion coefficient of second equation", "pattern.c",user.Dv,&user.Dv,NULL);CHKERRQ(ierr); ierr = PetscOptionsReal("-phi","dimensionless feed rate (=F in (Pearson, 1993))", "pattern.c",user.phi,&user.phi,NULL);CHKERRQ(ierr); ierr = PetscOptionsReal("-kappa","dimensionless rate constant (=k in (Pearson, 1993))", "pattern.c",user.kappa,&user.kappa,NULL);CHKERRQ(ierr); ierr = PetscOptionsEnd(); CHKERRQ(ierr); //DMDACREATE ierr = DMDACreate2d(PETSC_COMM_WORLD, DM_BOUNDARY_PERIODIC, DM_BOUNDARY_PERIODIC, DMDA_STENCIL_BOX, // for 9-point stencil 4,4,PETSC_DECIDE,PETSC_DECIDE, 2, 1, // degrees of freedom, stencil width NULL,NULL,&user.da); CHKERRQ(ierr); //ENDDMDACREATE ierr = DMSetFromOptions(user.da); CHKERRQ(ierr); ierr = DMSetUp(user.da); CHKERRQ(ierr); ierr = DMDASetFieldName(user.da,0,"u"); CHKERRQ(ierr); ierr = DMDASetFieldName(user.da,1,"v"); CHKERRQ(ierr); ierr = DMDAGetLocalInfo(user.da,&info); CHKERRQ(ierr); if (info.mx != info.my) { SETERRQ(PETSC_COMM_WORLD,1,"pattern.c requires mx == my"); } ierr = DMDASetUniformCoordinates(user.da, 0.0, user.L, 0.0, user.L, -1.0, -1.0); CHKERRQ(ierr); ierr = DMSetApplicationContext(user.da,&user); CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD, "running on %d x %d grid with square cells of side h = %.6f ...\n", info.mx,info.my,user.L/(double)(info.mx)); CHKERRQ(ierr); //TSSETUP ierr = TSCreate(PETSC_COMM_WORLD,&ts); CHKERRQ(ierr); ierr = TSSetProblemType(ts,TS_NONLINEAR); CHKERRQ(ierr); ierr = TSSetDM(ts,user.da); CHKERRQ(ierr); ierr = DMDATSSetRHSFunctionLocal(user.da,INSERT_VALUES, (DMDATSRHSFunctionLocal)FormRHSFunctionLocal,&user); CHKERRQ(ierr); ierr = DMDATSSetIFunctionLocal(user.da,INSERT_VALUES, (DMDATSIFunctionLocal)FormIFunctionLocal,&user); CHKERRQ(ierr); ierr = DMDATSSetIJacobianLocal(user.da, (DMDATSIJacobianLocal)FormIJacobianLocal,&user); CHKERRQ(ierr); ierr = TSSetType(ts,TSARKIMEX); CHKERRQ(ierr); ierr = TSSetExactFinalTime(ts,TS_EXACTFINALTIME_MATCHSTEP); CHKERRQ(ierr); ierr = TSSetInitialTimeStep(ts,0.0,5.0); CHKERRQ(ierr); // t_0 = 0.0, dt = 5.0 ierr = TSSetDuration(ts,1000000,200.0); CHKERRQ(ierr); // t_f = 200 ierr = TSSetFromOptions(ts);CHKERRQ(ierr); //ENDTSSETUP ierr = DMCreateGlobalVector(user.da,&x); CHKERRQ(ierr); ierr = InitialState(x,noiselevel,&user); CHKERRQ(ierr); ierr = TSSolve(ts,x); CHKERRQ(ierr); VecDestroy(&x); TSDestroy(&ts); DMDestroy(&user.da); PetscFinalize(); return 0; }
int main(int argc,char **argv) { AppCtx appctx; /* user-defined application context */ TS ts; /* timestepping context */ Vec U; /* approximate solution vector */ PetscErrorCode ierr; PetscReal dt; DM da; PetscInt M; /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Initialize program and set problem parameters - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr); appctx.a = 1.0; appctx.d = 0.0; ierr = PetscOptionsGetScalar(NULL,"-a",&appctx.a,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetScalar(NULL,"-d",&appctx.d,NULL);CHKERRQ(ierr); appctx.upwind = PETSC_TRUE; ierr = PetscOptionsGetBool(NULL,"-upwind",&appctx.upwind,NULL);CHKERRQ(ierr); ierr = DMDACreate1d(PETSC_COMM_WORLD,DMDA_BOUNDARY_PERIODIC, -60, 1, 1,NULL,&da);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create vector data structures - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ /* Create vector data structures for approximate and exact solutions */ ierr = DMCreateGlobalVector(da,&U);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create timestepping solver context - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr); ierr = TSSetDM(ts,da);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 = TSSetRHSFunction(ts,NULL,TSComputeRHSFunctionLinear,&appctx);CHKERRQ(ierr); ierr = TSSetRHSJacobian(ts,NULL,NULL,RHSMatrixHeat,&appctx);CHKERRQ(ierr); ierr = TSSetSolutionFunction(ts,(PetscErrorCode (*)(TS,PetscReal,Vec,void*))Solution,&appctx);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Customize timestepping solver: - Set timestepping duration info Then set runtime options, which can override these defaults. For example, -ts_max_steps <maxsteps> -ts_final_time <maxtime> to override the defaults set by TSSetDuration(). - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = DMDAGetInfo(da,PETSC_IGNORE,&M,0,0,0,0,0,0,0,0,0,0,0);CHKERRQ(ierr); dt = .48/(M*M); ierr = TSSetInitialTimeStep(ts,0.0,dt);CHKERRQ(ierr); ierr = TSSetDuration(ts,1000,100.0);CHKERRQ(ierr); ierr = TSSetType(ts,TSARKIMEX);CHKERRQ(ierr); ierr = TSSetFromOptions(ts);CHKERRQ(ierr); /* Evaluate initial conditions */ ierr = InitialConditions(ts,U,&appctx);CHKERRQ(ierr); /* Run the timestepping solver */ ierr = TSSolve(ts,U);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Free work space. All PETSc objects should be destroyed when they are no longer needed. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSDestroy(&ts);CHKERRQ(ierr); ierr = VecDestroy(&U);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) { PetscErrorCode ierr; Wash wash; Junction junctions,junction; Pipe pipe,pipes; PetscInt numEdges,numVertices,KeyPipe,KeyJunction; int *edgelist = NULL; PetscInt i,e,v,eStart,eEnd,vStart,vEnd,pipeOffset,key,frombType,tobType; PetscInt vfrom,vto,vkey,fromOffset,toOffset,type,varoffset,pipeoffset; PetscInt from_nedge_in,from_nedge_out,to_nedge_in; const PetscInt *cone; DM networkdm; PetscMPIInt size,rank; PetscReal ftime = 2500.0; Vec X; TS ts; PetscInt maxsteps=-1,steps; TSConvergedReason reason; PetscBool viewpipes; PetscInt pipesCase; DMNetworkMonitor monitor; DMNetworkComponentGenericDataType *nwarr; ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr; ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr); ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr); /* Create and setup network */ /*--------------------------*/ ierr = DMNetworkCreate(PETSC_COMM_WORLD,&networkdm);CHKERRQ(ierr); if (size == 1) { ierr = DMNetworkMonitorCreate(networkdm,&monitor);CHKERRQ(ierr); } /* Register the components in the network */ ierr = DMNetworkRegisterComponent(networkdm,"junctionstruct",sizeof(struct _p_Junction),&KeyJunction);CHKERRQ(ierr); ierr = DMNetworkRegisterComponent(networkdm,"pipestruct",sizeof(struct _p_Pipe),&KeyPipe);CHKERRQ(ierr); /* Set global number of pipes, edges, and vertices */ pipesCase = 2; ierr = PetscOptionsGetInt(NULL,NULL, "-case", &pipesCase, NULL);CHKERRQ(ierr); ierr = WashNetworkCreate(PETSC_COMM_WORLD,pipesCase,&wash,&edgelist);CHKERRQ(ierr); numEdges = wash->nedge; numVertices = wash->nvertex; junctions = wash->junction; pipes = wash->pipe; /* Set number of vertices and edges */ ierr = DMNetworkSetSizes(networkdm,numVertices,numEdges,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); /* Add edge connectivity */ ierr = DMNetworkSetEdgeList(networkdm,edgelist);CHKERRQ(ierr); /* Set up the network layout */ ierr = DMNetworkLayoutSetUp(networkdm);CHKERRQ(ierr); /* Add EDGEDATA component to all edges -- currently networkdm is a sequential network */ ierr = DMNetworkGetEdgeRange(networkdm,&eStart,&eEnd);CHKERRQ(ierr); ierr = DMNetworkGetVertexRange(networkdm,&vStart,&vEnd);CHKERRQ(ierr); for (e = eStart; e < eEnd; e++) { /* Add Pipe component to all edges -- create pipe here */ ierr = DMNetworkAddComponent(networkdm,e,KeyPipe,&pipes[e-eStart]);CHKERRQ(ierr); /* Add number of variables to each edge */ ierr = DMNetworkAddNumVariables(networkdm,e,2*pipes[e-eStart].nnodes);CHKERRQ(ierr); if (size == 1) { /* Add monitor -- show Q_{pipes[e-eStart].id}? */ ierr = DMNetworkMonitorAdd(monitor, "Pipe Q", e, pipes[e-eStart].nnodes, 0, 2, -0.8, 0.8, PETSC_TRUE);CHKERRQ(ierr); ierr = DMNetworkMonitorAdd(monitor, "Pipe H", e, pipes[e-eStart].nnodes, 1, 2, -400.0, 800.0, PETSC_TRUE);CHKERRQ(ierr); } } /* Add Junction component to all vertices */ for (v = vStart; v < vEnd; v++) { ierr = DMNetworkAddComponent(networkdm,v,KeyJunction,&junctions[v-vStart]);CHKERRQ(ierr); /* Add number of variables to vertex */ ierr = DMNetworkAddNumVariables(networkdm,v,2);CHKERRQ(ierr); } /* Set up DM for use */ ierr = DMSetUp(networkdm);CHKERRQ(ierr); ierr = WashNetworkCleanUp(wash,edgelist);CHKERRQ(ierr); /* Network partitioning and distribution of data */ if (size > 1) { DM distnetworkdm; ierr = DMNetworkDistribute(networkdm,0,&distnetworkdm);CHKERRQ(ierr); ierr = DMDestroy(&networkdm);CHKERRQ(ierr); networkdm = distnetworkdm; } /* PipeSetUp -- each process only sets its own pipes */ /*---------------------------------------------------*/ ierr = DMNetworkGetComponentDataArray(networkdm,&nwarr);CHKERRQ(ierr); ierr = DMNetworkGetEdgeRange(networkdm,&eStart,&eEnd);CHKERRQ(ierr); for (e=eStart; e<eEnd; e++) { /* each edge has only one component, pipe */ ierr = DMNetworkGetComponentTypeOffset(networkdm,e,0,&type,&pipeoffset);CHKERRQ(ierr); ierr = DMNetworkGetVariableOffset(networkdm,e,&varoffset);CHKERRQ(ierr); pipe = (Pipe)(nwarr + pipeoffset); /* Setup conntected vertices */ ierr = DMNetworkGetConnectedNodes(networkdm,e,&cone);CHKERRQ(ierr); vfrom = cone[0]; /* local ordering */ vto = cone[1]; /* vfrom */ ierr = DMNetworkGetComponentTypeOffset(networkdm,vfrom,0,&vkey,&fromOffset);CHKERRQ(ierr); junction = (Junction)(nwarr+fromOffset); from_nedge_in = junction->nedges_in; from_nedge_out = junction->nedges_out; /* vto */ ierr = DMNetworkGetComponentTypeOffset(networkdm,vto,0,&vkey,&toOffset);CHKERRQ(ierr); junction = (Junction)(nwarr+toOffset); to_nedge_in = junction->nedges_in; pipe->comm = PETSC_COMM_SELF; /* must be set here, otherwise crashes in my mac??? */ wash->nnodes_loc += pipe->nnodes; /* local total num of nodes, will be used by PipesView() */ ierr = PipeSetParameters(pipe, 600.0, /* length */ pipe->nnodes, /* nnodes -- rm from PipeSetParameters */ 0.5, /* diameter */ 1200.0, /* a */ 0.018);CHKERRQ(ierr); /* friction */ /* set boundary conditions for this pipe */ if (from_nedge_in <= 1 && from_nedge_out > 0) { frombType = 0; } else { frombType = 1; } if (to_nedge_in == 1) { tobType = 0; } else { tobType = 1; } if (frombType == 0) { pipe->boundary.Q0 = PIPE_CHARACTERISTIC; /* will be obtained from characteristic */ pipe->boundary.H0 = wash->H0; } else { pipe->boundary.Q0 = wash->Q0; pipe->boundary.H0 = PIPE_CHARACTERISTIC; /* will be obtained from characteristic */ } if (tobType == 0) { pipe->boundary.QL = wash->QL; pipe->boundary.HL = PIPE_CHARACTERISTIC; /* will be obtained from characteristic */ } else { pipe->boundary.QL = PIPE_CHARACTERISTIC; /* will be obtained from characteristic */ pipe->boundary.HL = wash->HL; } ierr = PipeSetUp(pipe);CHKERRQ(ierr); } /* create vectors */ ierr = DMCreateGlobalVector(networkdm,&X);CHKERRQ(ierr); ierr = DMCreateLocalVector(networkdm,&wash->localX);CHKERRQ(ierr); ierr = DMCreateLocalVector(networkdm,&wash->localXdot);CHKERRQ(ierr); /* Setup solver */ /*--------------------------------------------------------*/ ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr); ierr = TSSetDM(ts,(DM)networkdm);CHKERRQ(ierr); ierr = TSSetIFunction(ts,NULL,WASHIFunction,wash);CHKERRQ(ierr); ierr = TSSetDuration(ts,maxsteps,ftime);CHKERRQ(ierr); ierr = TSSetExactFinalTime(ts,TS_EXACTFINALTIME_STEPOVER);CHKERRQ(ierr); ierr = TSSetInitialTimeStep(ts,0.0,0.1);CHKERRQ(ierr); ierr = TSSetType(ts,TSBEULER);CHKERRQ(ierr); if (size == 1) { ierr = TSMonitorSet(ts, TSDMNetworkMonitor, monitor, NULL);CHKERRQ(ierr); } ierr = TSSetFromOptions(ts);CHKERRQ(ierr); ierr = WASHSetInitialSolution(networkdm,X,wash);CHKERRQ(ierr); 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); /* ierr = VecView(X,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); */ /* View solution q and h */ /* --------------------- */ viewpipes = PETSC_FALSE; ierr = PetscOptionsGetBool(NULL,NULL, "-pipe_view", &viewpipes,NULL);CHKERRQ(ierr); if (viewpipes) { ierr = PipesView(X,networkdm,wash);CHKERRQ(ierr); } /* Free spaces */ /* ----------- */ ierr = TSDestroy(&ts);CHKERRQ(ierr); ierr = VecDestroy(&X);CHKERRQ(ierr); ierr = VecDestroy(&wash->localX);CHKERRQ(ierr); ierr = VecDestroy(&wash->localXdot);CHKERRQ(ierr); /* Destroy objects from each pipe that are created in PipeSetUp() */ ierr = DMNetworkGetEdgeRange(networkdm,&eStart, &eEnd);CHKERRQ(ierr); for (i = eStart; i < eEnd; i++) { ierr = DMNetworkGetComponentTypeOffset(networkdm,i,0,&key,&pipeOffset);CHKERRQ(ierr); pipe = (Pipe)(nwarr+pipeOffset); ierr = DMDestroy(&(pipe->da));CHKERRQ(ierr); ierr = VecDestroy(&pipe->x);CHKERRQ(ierr); } if (size == 1) { ierr = DMNetworkMonitorDestroy(&monitor);CHKERRQ(ierr); } ierr = DMDestroy(&networkdm);CHKERRQ(ierr); ierr = PetscFree(wash);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) { AppCtx ctx; DM dm; TS ts; Vec u, r; PetscReal t = 0.0; PetscReal L2error = 0.0; PetscErrorCode ierr; ierr = PetscInitialize(&argc, &argv, NULL, help); CHKERRQ(ierr); ierr = ProcessOptions(PETSC_COMM_WORLD, &ctx); CHKERRQ(ierr); ierr = CreateMesh(PETSC_COMM_WORLD, &dm, &ctx); CHKERRQ(ierr); ierr = DMSetApplicationContext(dm, &ctx); CHKERRQ(ierr); ierr = PetscMalloc1(1, &ctx.exactFuncs); CHKERRQ(ierr); ierr = SetupDiscretization(dm, &ctx); CHKERRQ(ierr); ierr = DMCreateGlobalVector(dm, &u); CHKERRQ(ierr); ierr = PetscObjectSetName((PetscObject) u, "temperature"); CHKERRQ(ierr); ierr = VecDuplicate(u, &r); CHKERRQ(ierr); ierr = TSCreate(PETSC_COMM_WORLD, &ts); CHKERRQ(ierr); ierr = TSSetDM(ts, dm); CHKERRQ(ierr); ierr = DMTSSetBoundaryLocal(dm, DMPlexTSComputeBoundary, &ctx); CHKERRQ(ierr); ierr = DMTSSetIFunctionLocal(dm, DMPlexTSComputeIFunctionFEM, &ctx); CHKERRQ(ierr); ierr = DMTSSetIJacobianLocal(dm, DMPlexTSComputeIJacobianFEM, &ctx); CHKERRQ(ierr); ierr = TSSetExactFinalTime(ts, TS_EXACTFINALTIME_STEPOVER); CHKERRQ(ierr); ierr = TSSetFromOptions(ts); CHKERRQ(ierr); ierr = DMProjectFunction(dm, t, ctx.exactFuncs, NULL, INSERT_ALL_VALUES, u); CHKERRQ(ierr); ierr = TSSolve(ts, u); CHKERRQ(ierr); ierr = TSGetTime(ts, &t); CHKERRQ(ierr); ierr = DMComputeL2Diff(dm, t, ctx.exactFuncs, NULL, u, &L2error); CHKERRQ(ierr); if (L2error < 1.0e-11) { ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: < 1.0e-11\n"); CHKERRQ(ierr); } else { ierr = PetscPrintf(PETSC_COMM_WORLD, "L_2 Error: %g\n", L2error); CHKERRQ(ierr); } ierr = VecViewFromOptions(u, NULL, "-sol_vec_view"); CHKERRQ(ierr); ierr = VecDestroy(&u); CHKERRQ(ierr); ierr = VecDestroy(&r); CHKERRQ(ierr); ierr = TSDestroy(&ts); CHKERRQ(ierr); ierr = DMDestroy(&dm); CHKERRQ(ierr); ierr = PetscFree(ctx.exactFuncs); CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; }
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; }
void PETSC_STDCALL tssetdm_(TS ts,DM dm, int *__ierr ){ *__ierr = TSSetDM( (TS)PetscToPointer((ts) ), (DM)PetscToPointer((dm) )); }
int main(int argc, char **argv) { DM dm; TS ts; Vec X; Mat J; PetscInt steps, maxsteps, mx; PetscReal ftime, hx, dt; TSConvergedReason reason; struct _User user; PetscErrorCode ierr; ierr = PetscInitialize(&argc, &argv, NULL,help);if (ierr) return ierr; ierr = DMDACreate1d(PETSC_COMM_WORLD, DM_BOUNDARY_NONE, -11, 3, 1, NULL, &dm);CHKERRQ(ierr); ierr = DMSetFromOptions(dm);CHKERRQ(ierr); ierr = DMSetUp(dm);CHKERRQ(ierr); ierr = DMDASetUniformCoordinates(dm, 0.0, 20.0, 0.0, 0.0, 0.0, 0.0);CHKERRQ(ierr); ierr = DMCreateGlobalVector(dm, &X);CHKERRQ(ierr); ierr = PetscOptionsBegin(PETSC_COMM_WORLD, NULL, "Dynamic Friction Options", ""); { user.epsilon = 0.1; user.gamma = 0.5; user.gammaTilde = 0.5; user.xi = 0.5; user.c = 0.5; ierr = PetscOptionsReal("-epsilon", "Inverse of seismic ratio", "", user.epsilon, &user.epsilon, NULL);CHKERRQ(ierr); ierr = PetscOptionsReal("-gamma", "Wave frequency for interblock coupling", "", user.gamma, &user.gamma, NULL);CHKERRQ(ierr); ierr = PetscOptionsReal("-gamma_tilde", "Wave frequency for plate coupling", "", user.gammaTilde, &user.gammaTilde, NULL);CHKERRQ(ierr); ierr = PetscOptionsReal("-xi", "Interblock spring constant", "", user.xi, &user.xi, NULL);CHKERRQ(ierr); ierr = PetscOptionsReal("-c", "Wavespeed", "", user.c, &user.c, NULL);CHKERRQ(ierr); } ierr = PetscOptionsEnd();CHKERRQ(ierr); ierr = TSCreate(PETSC_COMM_WORLD, &ts);CHKERRQ(ierr); ierr = TSSetDM(ts, dm);CHKERRQ(ierr); ierr = TSSetRHSFunction(ts, NULL, FormRHSFunction, &user);CHKERRQ(ierr); ierr = TSSetIFunction(ts, NULL, FormIFunction, &user);CHKERRQ(ierr); ierr = DMSetMatType(dm, MATAIJ);CHKERRQ(ierr); ierr = DMCreateMatrix(dm, &J);CHKERRQ(ierr); ierr = TSSetIJacobian(ts, J, J, FormIJacobian, &user);CHKERRQ(ierr); ftime = 800.0; maxsteps = 10000; ierr = TSSetDuration(ts, maxsteps, ftime);CHKERRQ(ierr); ierr = TSSetExactFinalTime(ts,TS_EXACTFINALTIME_STEPOVER);CHKERRQ(ierr); ierr = FormInitialSolution(ts, X, &user);CHKERRQ(ierr); ierr = TSSetSolution(ts, X);CHKERRQ(ierr); ierr = VecGetSize(X, &mx);CHKERRQ(ierr); hx = 20.0/(PetscReal)(mx-1); dt = 0.4 * PetscSqr(hx) / PetscSqr(user.c); /* Diffusive stability limit */ ierr = TSSetInitialTimeStep(ts, 0.0, dt);CHKERRQ(ierr); ierr = TSSetFromOptions(ts);CHKERRQ(ierr); 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); ierr = MatDestroy(&J);CHKERRQ(ierr); ierr = VecDestroy(&X);CHKERRQ(ierr); ierr = TSDestroy(&ts);CHKERRQ(ierr); ierr = DMDestroy(&dm);CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; }
int main(int argc,char **argv) { AppCtx appctx; /* user-defined application context */ TS ts; /* timestepping context */ Vec U; /* approximate solution vector */ PetscErrorCode ierr; PetscReal dt; DM da; PetscInt M; PetscMPIInt rank; PetscBool useLaxWendroff = PETSC_TRUE; /* Initialize program and set problem parameters */ ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr; ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr); appctx.a = -1.0; ierr = PetscOptionsGetReal(NULL,NULL,"-a",&appctx.a,NULL);CHKERRQ(ierr); ierr = DMDACreate1d(PETSC_COMM_WORLD,DM_BOUNDARY_PERIODIC, 60, 1, 1,NULL,&da);CHKERRQ(ierr); ierr = DMSetFromOptions(da);CHKERRQ(ierr); ierr = DMSetUp(da);CHKERRQ(ierr); /* Create vector data structures for approximate and exact solutions */ ierr = DMCreateGlobalVector(da,&U);CHKERRQ(ierr); /* Create timestepping solver context */ ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr); ierr = TSSetDM(ts,da);CHKERRQ(ierr); /* Function evaluation */ ierr = PetscOptionsGetBool(NULL,NULL,"-useLaxWendroff",&useLaxWendroff,NULL);CHKERRQ(ierr); if (useLaxWendroff) { if (!rank) { ierr = PetscPrintf(PETSC_COMM_SELF,"... Use Lax-Wendroff finite volume\n");CHKERRQ(ierr); } ierr = TSSetIFunction(ts,NULL,IFunction_LaxWendroff,&appctx);CHKERRQ(ierr); } else { if (!rank) { ierr = PetscPrintf(PETSC_COMM_SELF,"... Use Lax-LaxFriedrichs finite difference\n");CHKERRQ(ierr); } ierr = TSSetIFunction(ts,NULL,IFunction_LaxFriedrichs,&appctx);CHKERRQ(ierr); } /* Customize timestepping solver */ ierr = DMDAGetInfo(da,PETSC_IGNORE,&M,0,0,0,0,0,0,0,0,0,0,0);CHKERRQ(ierr); dt = 1.0/(PetscAbsReal(appctx.a)*M); ierr = TSSetTimeStep(ts,dt);CHKERRQ(ierr); ierr = TSSetMaxSteps(ts,100);CHKERRQ(ierr); ierr = TSSetMaxTime(ts,100.0);CHKERRQ(ierr); ierr = TSSetExactFinalTime(ts,TS_EXACTFINALTIME_STEPOVER);CHKERRQ(ierr); ierr = TSSetType(ts,TSBEULER);CHKERRQ(ierr); ierr = TSSetFromOptions(ts);CHKERRQ(ierr); /* Evaluate initial conditions */ ierr = InitialConditions(ts,U,&appctx);CHKERRQ(ierr); /* For testing accuracy of TS with already known solution, e.g., '-ts_monitor_lg_error' */ ierr = TSSetSolutionFunction(ts,(PetscErrorCode (*)(TS,PetscReal,Vec,void*))Solution,&appctx);CHKERRQ(ierr); /* Run the timestepping solver */ ierr = TSSolve(ts,U);CHKERRQ(ierr); /* Free work space */ ierr = TSDestroy(&ts);CHKERRQ(ierr); ierr = VecDestroy(&U);CHKERRQ(ierr); ierr = DMDestroy(&da);CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; }
int main(int argc,char **argv) { TS ts; /* nonlinear solver */ Vec x,r; /* solution, residual vectors */ Mat J; /* Jacobian matrix */ PetscInt steps,Mx,maxsteps = 10000000; PetscErrorCode ierr; DM da; MatFDColoring matfdcoloring; ISColoring iscoloring; PetscReal dt; PetscReal vbounds[] = {-100000,100000,-1.1,1.1}; PetscBool wait; Vec ul,uh; SNES snes; UserCtx ctx; /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Initialize program - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr; ctx.kappa = 1.0; ierr = PetscOptionsGetReal(NULL,"-kappa",&ctx.kappa,NULL);CHKERRQ(ierr); ctx.cahnhillard = PETSC_FALSE; ierr = PetscOptionsGetBool(NULL,NULL,"-cahn-hillard",&ctx.cahnhillard,NULL);CHKERRQ(ierr); ierr = PetscViewerDrawSetBounds(PETSC_VIEWER_DRAW_(PETSC_COMM_WORLD),2,vbounds);CHKERRQ(ierr); ierr = PetscViewerDrawResize(PETSC_VIEWER_DRAW_(PETSC_COMM_WORLD),600,600);CHKERRQ(ierr); ctx.energy = 1; /* ierr = PetscOptionsGetInt(NULL,NULL,"-energy",&ctx.energy,NULL);CHKERRQ(ierr); */ ierr = PetscOptionsGetInt(NULL,NULL,"-energy",&ctx.energy,NULL);CHKERRQ(ierr); ctx.tol = 1.0e-8; ierr = PetscOptionsGetReal(NULL,"-tol",&ctx.tol,NULL);CHKERRQ(ierr); ctx.theta = .001; ctx.theta_c = 1.0; ierr = PetscOptionsGetReal(NULL,"-theta",&ctx.theta,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetReal(NULL,"-theta_c",&ctx.theta_c,NULL);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create distributed array (DMDA) to manage parallel grid and vectors - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = DMDACreate1d(PETSC_COMM_WORLD, DM_BOUNDARY_PERIODIC, -10,2,2,NULL,&da);CHKERRQ(ierr); ierr = DMSetFromOptions(da);CHKERRQ(ierr); ierr = DMSetUp(da);CHKERRQ(ierr); ierr = DMDASetFieldName(da,0,"Biharmonic heat equation: w = -kappa*u_xx");CHKERRQ(ierr); ierr = DMDASetFieldName(da,1,"Biharmonic heat equation: u");CHKERRQ(ierr); ierr = DMDAGetInfo(da,0,&Mx,0,0,0,0,0,0,0,0,0,0,0);CHKERRQ(ierr); dt = 1.0/(10.*ctx.kappa*Mx*Mx*Mx*Mx); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Extract global 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); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create timestepping solver context - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr); ierr = TSSetDM(ts,da);CHKERRQ(ierr); ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr); ierr = TSSetIFunction(ts,NULL,FormFunction,&ctx);CHKERRQ(ierr); ierr = TSSetDuration(ts,maxsteps,.02);CHKERRQ(ierr); ierr = TSSetExactFinalTime(ts,TS_EXACTFINALTIME_STEPOVER);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create matrix data structure; set Jacobian evaluation routine < Set Jacobian matrix data structure and default Jacobian evaluation routine. User can override with: -snes_mf : matrix-free Newton-Krylov method with no preconditioning (unless user explicitly sets preconditioner) -snes_mf_operator : form preconditioning matrix as set by the user, but use matrix-free approx for Jacobian-vector products within Newton-Krylov method - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSGetSNES(ts,&snes);CHKERRQ(ierr); ierr = DMCreateColoring(da,IS_COLORING_GLOBAL,&iscoloring);CHKERRQ(ierr); ierr = DMSetMatType(da,MATAIJ);CHKERRQ(ierr); ierr = DMCreateMatrix(da,&J);CHKERRQ(ierr); ierr = MatFDColoringCreate(J,iscoloring,&matfdcoloring);CHKERRQ(ierr); ierr = ISColoringDestroy(&iscoloring);CHKERRQ(ierr); ierr = MatFDColoringSetFunction(matfdcoloring,(PetscErrorCode (*)(void))SNESTSFormFunction,ts);CHKERRQ(ierr); ierr = MatFDColoringSetFromOptions(matfdcoloring);CHKERRQ(ierr); ierr = MatFDColoringSetUp(J,iscoloring,matfdcoloring);CHKERRQ(ierr); ierr = SNESSetJacobian(snes,J,J,SNESComputeJacobianDefaultColor,matfdcoloring);CHKERRQ(ierr); { ierr = VecDuplicate(x,&ul);CHKERRQ(ierr); ierr = VecDuplicate(x,&uh);CHKERRQ(ierr); ierr = VecStrideSet(ul,0,PETSC_NINFINITY);CHKERRQ(ierr); ierr = VecStrideSet(ul,1,-1.0);CHKERRQ(ierr); ierr = VecStrideSet(uh,0,PETSC_INFINITY);CHKERRQ(ierr); ierr = VecStrideSet(uh,1,1.0);CHKERRQ(ierr); ierr = TSVISetVariableBounds(ts,ul,uh);CHKERRQ(ierr); } /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Customize nonlinear solver - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSetType(ts,TSBEULER);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set initial conditions - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = FormInitialSolution(da,x,ctx.kappa);CHKERRQ(ierr); ierr = TSSetInitialTimeStep(ts,0.0,dt);CHKERRQ(ierr); ierr = TSSetSolution(ts,x);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set runtime options - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSetFromOptions(ts);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Solve nonlinear system - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSolve(ts,x);CHKERRQ(ierr); wait = PETSC_FALSE; ierr = PetscOptionsGetBool(NULL,NULL,"-wait",&wait,NULL);CHKERRQ(ierr); if (wait) { ierr = PetscSleep(-1);CHKERRQ(ierr); } ierr = TSGetTimeStepNumber(ts,&steps);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Free work space. All PETSc objects should be destroyed when they are no longer needed. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ { ierr = VecDestroy(&ul);CHKERRQ(ierr); ierr = VecDestroy(&uh);CHKERRQ(ierr); } ierr = MatDestroy(&J);CHKERRQ(ierr); ierr = MatFDColoringDestroy(&matfdcoloring);CHKERRQ(ierr); ierr = VecDestroy(&x);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) { TS ts; /* nonlinear solver */ Vec C; /* solution */ PetscErrorCode ierr; DM da; /* manages the grid data */ AppCtx ctx; /* holds problem specific paramters */ PetscInt He,dof = 3*N+N*N,*ofill; /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Initialize program - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ PetscInitialize(&argc,&argv,(char *)0,help); PetscFunctionBeginUser; ctx.noreactions = PETSC_FALSE; ctx.nodissociations = PETSC_FALSE; ierr = PetscOptionsHasName(PETSC_NULL,"-noreactions",&ctx.noreactions);CHKERRQ(ierr); ierr = PetscOptionsHasName(PETSC_NULL,"-nodissociations",&ctx.nodissociations);CHKERRQ(ierr); ctx.HeDiffusion[1] = 1000*2.95e-4; /* From Tibo's notes times 1,000 */ ctx.HeDiffusion[2] = 1000*3.24e-4; ctx.HeDiffusion[3] = 1000*2.26e-4; ctx.HeDiffusion[4] = 1000*1.68e-4; ctx.HeDiffusion[5] = 1000*5.20e-5; ctx.VDiffusion[1] = 1000*2.71e-3; ctx.IDiffusion[1] = 1000*2.13e-4; ctx.forcingScale = 100.; /* made up numbers */ ctx.reactionScale = .001; ctx.dissociationScale = .0001; /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create distributed array (DMDA) to manage parallel grid and vectors - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = DMDACreate1d(PETSC_COMM_WORLD, DMDA_BOUNDARY_MIRROR,-8,dof,1,PETSC_NULL,&da);CHKERRQ(ierr); /* The only spatial coupling in the Jacobian (diffusion) is for the first 5 He, the first V, and the first I. The ofill (thought of as a dof by dof 2d (row-oriented) array represents the nonzero coupling between degrees of freedom at one point with degrees of freedom on the adjacent point to the left or right. A 1 at i,j in the ofill array indicates that the degree of freedom i at a point is coupled to degree of freedom j at the adjacent point. In this case ofill has only a few diagonal entries since the only spatial coupling is regular diffusion. */ ierr = PetscMalloc(dof*dof*sizeof(PetscInt),&ofill);CHKERRQ(ierr); ierr = PetscMemzero(ofill,dof*dof*sizeof(PetscInt));CHKERRQ(ierr); for (He=0; He<PetscMin(N,5); He++) ofill[He*dof + He] = 1; ofill[N*dof + N] = ofill[2*N*dof + 2*N] = 1; ierr = DMDASetBlockFills(da,PETSC_NULL,ofill);CHKERRQ(ierr); ierr = PetscFree(ofill);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Extract global vector from DMDA to hold solution - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = DMCreateGlobalVector(da,&C);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,PETSC_NULL,IFunction,&ctx);CHKERRQ(ierr); ierr = TSSetSolution(ts,C);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set solver options - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSetInitialTimeStep(ts,0.0,.001);CHKERRQ(ierr); ierr = TSSetDuration(ts,100,50.0);CHKERRQ(ierr); ierr = TSSetFromOptions(ts);CHKERRQ(ierr); ierr = MyMonitorSetUp(ts);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set initial conditions - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = InitialConditions(da,C);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Solve the ODE system - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSolve(ts,C);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Free work space. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = VecDestroy(&C);CHKERRQ(ierr); ierr = TSDestroy(&ts);CHKERRQ(ierr); ierr = DMDestroy(&da);CHKERRQ(ierr); ierr = PetscFinalize(); PetscFunctionReturn(0); }
int main(int argc,char **argv) { TS ts; /* nonlinear solver */ Vec u; /* solution, residual vectors */ Mat J; /* Jacobian matrix */ PetscInt steps,maxsteps = 1000; /* iterations for convergence */ PetscErrorCode ierr; DM da; MatFDColoring matfdcoloring = PETSC_NULL; PetscReal ftime,dt; MonitorCtx usermonitor; /* user-defined monitor context */ AppCtx user; /* user-defined work context */ JacobianType jacType; PetscInitialize(&argc,&argv,(char *)0,help); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create distributed array (DMDA) to manage parallel grid and vectors - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = DMDACreate1d(PETSC_COMM_WORLD,DMDA_BOUNDARY_NONE,-11,1,1,PETSC_NULL,&da);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Extract global vectors from DMDA; - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = DMCreateGlobalVector(da,&u);CHKERRQ(ierr); /* Initialize user application context */ user.c = -30.0; user.boundary = 0; /* 0: Dirichlet BC; 1: Neumann BC */ user.viewJacobian = PETSC_FALSE; ierr = PetscOptionsGetInt(PETSC_NULL,"-boundary",&user.boundary,PETSC_NULL);CHKERRQ(ierr); ierr = PetscOptionsHasName(PETSC_NULL,"-viewJacobian",&user.viewJacobian);CHKERRQ(ierr); usermonitor.drawcontours = PETSC_FALSE; ierr = PetscOptionsHasName(PETSC_NULL,"-drawcontours",&usermonitor.drawcontours);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create timestepping solver context - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr); ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr); ierr = TSSetType(ts,TSTHETA);CHKERRQ(ierr); ierr = TSThetaSetTheta(ts,1.0);CHKERRQ(ierr); /* Make the Theta method behave like backward Euler */ ierr = TSSetIFunction(ts,PETSC_NULL,FormIFunction,&user);CHKERRQ(ierr); ierr = DMCreateMatrix(da,MATAIJ,&J);CHKERRQ(ierr); jacType = JACOBIAN_ANALYTIC; /* use user-provide Jacobian */ ierr = TSSetIJacobian(ts,J,J,FormIJacobian,&user);CHKERRQ(ierr); ierr = TSSetDM(ts,da);CHKERRQ(ierr); /* Use TSGetDM() to access. Setting here allows easy use of geometric multigrid. */ ftime = 1.0; ierr = TSSetDuration(ts,maxsteps,ftime);CHKERRQ(ierr); ierr = TSMonitorSet(ts,MyTSMonitor,&usermonitor,PETSC_NULL);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set initial conditions - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = FormInitialSolution(ts,u,&user);CHKERRQ(ierr); ierr = TSSetSolution(ts,u);CHKERRQ(ierr); dt = .01; ierr = TSSetInitialTimeStep(ts,0.0,dt);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set runtime options - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSetFromOptions(ts);CHKERRQ(ierr); /* Use slow fd Jacobian or fast fd Jacobian with colorings. Note: this requirs snes which is not created until TSSetUp()/TSSetFromOptions() is called */ ierr = PetscOptionsBegin(((PetscObject)da)->comm,PETSC_NULL,"Options for Jacobian evaluation",PETSC_NULL);CHKERRQ(ierr); ierr = PetscOptionsEnum("-jac_type","Type of Jacobian","",JacobianTypes,(PetscEnum)jacType,(PetscEnum*)&jacType,0);CHKERRQ(ierr); ierr = PetscOptionsEnd();CHKERRQ(ierr); if (jacType == JACOBIAN_FD_COLORING) { SNES snes; ISColoring iscoloring; ierr = DMCreateColoring(da,IS_COLORING_GLOBAL,MATAIJ,&iscoloring);CHKERRQ(ierr); ierr = MatFDColoringCreate(J,iscoloring,&matfdcoloring);CHKERRQ(ierr); ierr = MatFDColoringSetFromOptions(matfdcoloring);CHKERRQ(ierr); ierr = ISColoringDestroy(&iscoloring);CHKERRQ(ierr); ierr = MatFDColoringSetFunction(matfdcoloring,(PetscErrorCode(*)(void))SNESTSFormFunction,ts);CHKERRQ(ierr); ierr = TSGetSNES(ts,&snes);CHKERRQ(ierr); ierr = SNESSetJacobian(snes,J,J,SNESDefaultComputeJacobianColor,matfdcoloring);CHKERRQ(ierr); } else if (jacType == JACOBIAN_FD_FULL){ SNES snes; ierr = TSGetSNES(ts,&snes);CHKERRQ(ierr); ierr = SNESSetJacobian(snes,J,J,SNESDefaultComputeJacobian,&user);CHKERRQ(ierr); } /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Solve nonlinear system - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSolve(ts,u,&ftime);CHKERRQ(ierr); ierr = TSGetTimeStepNumber(ts,&steps);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Free work space. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = MatDestroy(&J);CHKERRQ(ierr); if (matfdcoloring) {ierr = MatFDColoringDestroy(&matfdcoloring);CHKERRQ(ierr);} ierr = VecDestroy(&u);CHKERRQ(ierr); ierr = TSDestroy(&ts);CHKERRQ(ierr); ierr = DMDestroy(&da);CHKERRQ(ierr); ierr = PetscFinalize(); PetscFunctionReturn(0); }
int main(int argc, char **argv) { TS ts; //Time stepper Vec soln; //Holds the solution vector, including all the primitive //variables. DM dmda; //Manages the computational grid and parallelization. int X1Start, X2Start; int X1Size, X2Size; PetscInitialize(&argc, &argv, PETSC_NULL, help); // Create the computational domain. DMDACreate2d(PETSC_COMM_WORLD, DM_BOUNDARY_GHOSTED, DM_BOUNDARY_GHOSTED, DMDA_STENCIL_STAR, N1, N2, PETSC_DECIDE, PETSC_DECIDE, DOF, NG, PETSC_NULL, PETSC_NULL, &dmda); // When running in parallel, each process computes from // [X1Start, X1Start+X1Size] x [X2Start, X2Start+X2Size] DMDAGetCorners(dmda, &X1Start, &X2Start, NULL, &X1Size, &X2Size, NULL); // Create the solution vector. DMCreateGlobalVector(dmda, &soln); // Create the time stepper and link it to the computational grid and the // residual evaluation function. TSCreate(PETSC_COMM_WORLD, &ts); TSSetDM(ts, dmda); TSSetIFunction(ts, PETSC_NULL, ComputeResidual, NULL); // OpenCL boilerplate code. clErr = cl::Platform::get(&platforms); CheckCLErrors(clErr, "cl::Platform::get"); // Select computation device here. clErr = platforms.at(1).getDevices(CL_DEVICE_TYPE_CPU, &devices); CheckCLErrors(clErr, "cl::Platform::getDevices"); context = cl::Context(devices, NULL, NULL, NULL, &clErr); CheckCLErrors(clErr, "cl::Context::Context"); queue = cl::CommandQueue(context, devices.at(0), 0, &clErr); CheckCLErrors(clErr, "cl::CommandQueue::CommandQueue"); std::ifstream sourceFile("computeresidual.cl"); std::string sourceCode((std::istreambuf_iterator<char>(sourceFile)), std::istreambuf_iterator<char>()); cl::Program::Sources source(1, std::make_pair(sourceCode.c_str(), sourceCode.length()+1)); program = cl::Program(context, source, &clErr); CheckCLErrors(clErr, "cl::Program::Program"); // Pass in constants to the OpenCL kernel as compiler switches. This is an // efficient way to handle constants such as domain sizes in OpenCL. std::string BuildOptions("\ -D X1_SIZE=" + std::to_string(X1Size) + " -D X2_SIZE=" + std::to_string(X2Size) + " -D TOTAL_X1_SIZE=" + std::to_string(X1Size+2*NG) + " -D TOTAL_X2_SIZE=" + std::to_string(X2Size+2*NG)); // Compile the OpenCL program and extract the kernel. PetscScalar start = std::clock(); clErr = program.build(devices, BuildOptions.c_str(), NULL, NULL); const char *buildlog = program.getBuildInfo<CL_PROGRAM_BUILD_LOG>( devices.at(0), &clErr).c_str(); PetscPrintf(PETSC_COMM_WORLD, "%s\n", buildlog); CheckCLErrors(clErr, "cl::Program::build"); PetscScalar end = std::clock(); PetscScalar time = (end - start)/(PetscScalar)CLOCKS_PER_SEC; PetscPrintf(PETSC_COMM_WORLD, "Time taken for kernel compilation = %f\n", time); kernel = cl::Kernel(program, "ComputeResidual", &clErr); CheckCLErrors(clErr, "cl::Kernel::Kernel"); // How much memory is the kernel using? cl_ulong localMemSize = kernel.getWorkGroupInfo<CL_KERNEL_LOCAL_MEM_SIZE>( devices.at(0), &clErr); cl_ulong privateMemSize = kernel.getWorkGroupInfo<CL_KERNEL_PRIVATE_MEM_SIZE>( devices.at(0), &clErr); printf("Local memory used = %llu\n", (unsigned long long)localMemSize); printf("Private memory used = %llu\n", (unsigned long long)privateMemSize); // Set initial conditions. InitialCondition(ts, soln); TSSetSolution(ts, soln); TSSetType(ts, TSTHETA); TSSetFromOptions(ts); // Finally solve! All time stepping options can be controlled from the // command line. TSSolve(ts, soln); // Delete the data structures in the following order. DMDestroy(&dmda); VecDestroy(&soln); TSDestroy(&ts); PetscFinalize(); return(0); }
int main(int argc,char **argv) { TS ts; /* ODE integrator */ Vec x; /* solution */ PetscErrorCode ierr; DM da; AppCtx appctx; Vec lambda[1]; PetscScalar *x_ptr; /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Initialize program - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr; PetscFunctionBeginUser; appctx.D1 = 8.0e-5; appctx.D2 = 4.0e-5; appctx.gamma = .024; appctx.kappa = .06; /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create distributed array (DMDA) to manage parallel grid and vectors - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = DMDACreate2d(PETSC_COMM_WORLD,DM_BOUNDARY_PERIODIC,DM_BOUNDARY_PERIODIC,DMDA_STENCIL_STAR,65,65,PETSC_DECIDE,PETSC_DECIDE,2,1,NULL,NULL,&da);CHKERRQ(ierr); ierr = DMSetFromOptions(da);CHKERRQ(ierr); ierr = DMSetUp(da);CHKERRQ(ierr); ierr = DMDASetFieldName(da,0,"u");CHKERRQ(ierr); ierr = DMDASetFieldName(da,1,"v");CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Extract global vectors from DMDA; then duplicate for remaining vectors that are the same types - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = DMCreateGlobalVector(da,&x);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create timestepping solver context - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr); ierr = TSSetType(ts,TSCN);CHKERRQ(ierr); ierr = TSSetDM(ts,da);CHKERRQ(ierr); ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr); ierr = TSSetRHSFunction(ts,NULL,RHSFunction,&appctx);CHKERRQ(ierr); ierr = TSSetRHSJacobian(ts,NULL,NULL,RHSJacobian,&appctx);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set initial conditions - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = InitialConditions(da,x);CHKERRQ(ierr); ierr = TSSetSolution(ts,x);CHKERRQ(ierr); /* Have the TS save its trajectory so that TSAdjointSolve() may be used */ ierr = TSSetSaveTrajectory(ts);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set solver options - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSetDuration(ts,PETSC_DEFAULT,2000.0);CHKERRQ(ierr); ierr = TSSetInitialTimeStep(ts,0.0,.0001);CHKERRQ(ierr); ierr = TSSetExactFinalTime(ts,TS_EXACTFINALTIME_STEPOVER);CHKERRQ(ierr); ierr = TSSetFromOptions(ts);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Solve ODE system - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSolve(ts,x);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Start the Adjoint model - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = VecDuplicate(x,&lambda[0]);CHKERRQ(ierr); /* Reset initial conditions for the adjoint integration */ ierr = VecGetArray(lambda[0],&x_ptr);CHKERRQ(ierr); ierr = InitializeLambda(da,lambda[0],0.5,0.5);CHKERRQ(ierr); ierr = TSSetCostGradients(ts,1,lambda,NULL);CHKERRQ(ierr); ierr = TSAdjointSolve(ts);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Free work space. All PETSc objects should be destroyed when they are no longer needed. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = VecDestroy(&lambda[0]);CHKERRQ(ierr); ierr = VecDestroy(&x);CHKERRQ(ierr); ierr = TSDestroy(&ts);CHKERRQ(ierr); ierr = DMDestroy(&da);CHKERRQ(ierr); 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); }
int main(int argc, char *argv[]) { PetscErrorCode ierr; PetscMPIInt rank; AppCtx user; PetscInt p=2,N=64,C=1; PetscInt ng = p+2; /* integration in each direction */ PetscInt Nx,Ny; Vec U; /* solution vector */ Mat J; TS ts; PetscInt steps; PetscReal ftime; /* This code solve the dimensionless form of the isothermal Navier-Stokes-Korteweg equations as presented in: Gomez, Hughes, Nogueira, Calo Isogeometric analysis of the isothermal Navier-Stokes-Korteweg equations CMAME, 2010 Equation/section numbers reflect this publication. */ // Petsc Initialization rite of passage ierr = PetscInitialize(&argc,&argv,0,help);CHKERRQ(ierr); ierr = MPI_Comm_rank(PETSC_COMM_WORLD, &rank);CHKERRQ(ierr); // Define simulation specific parameters user.L0 = 1.0; // length scale user.C1x = 0.75; user.C1y = 0.50; // bubble centers user.C2x = 0.25; user.C2y = 0.50; user.C3x = 0.40; user.C3y = 0.75; user.R1 = 0.10; user.R2 = 0.15; user.R3 = 0.08; // bubble radii user.alpha = 2.0; // (Eq. 41) user.theta = 0.85; // temperature parameter (just before section 5.1) // Set discretization options ierr = PetscOptionsBegin(PETSC_COMM_WORLD, "", "NavierStokesKorteweg Options", "IGA");CHKERRQ(ierr); ierr = PetscOptionsInt("-p", "polynomial order", __FILE__, p, &p, PETSC_NULL);CHKERRQ(ierr); ierr = PetscOptionsInt("-C", "global continuity order", __FILE__, C, &C, PETSC_NULL);CHKERRQ(ierr); ierr = PetscOptionsInt("-N", "number of elements (along one dimension)", __FILE__, N, &N, PETSC_NULL);CHKERRQ(ierr); ierr = PetscOptionsEnd();CHKERRQ(ierr); // Compute simulation parameters user.h = user.L0/N; // characteristic length scale of mesh (Eq. 43, simplified for uniform elements) user.Ca = user.h/user.L0; // capillarity number (Eq. 38) user.Re = user.alpha/user.Ca; // Reynolds number (Eq. 39) // Test C < p if(p <= C){ SETERRQ(PETSC_COMM_WORLD, PETSC_ERR_ARG_OUTOFRANGE, "Discretization inconsistent: polynomial order must be greater than degree of continuity"); } Nx=Ny=N; // Initialize B-spline space ierr = DMCreate(PETSC_COMM_WORLD,&user.iga);CHKERRQ(ierr); ierr = DMSetType(user.iga, DMIGA);CHKERRQ(ierr); ierr = DMIGAInitializeUniform2d(user.iga,PETSC_FALSE,2,3, p,Nx,C,0.0,1.0,PETSC_TRUE,ng, p,Ny,C,0.0,1.0,PETSC_TRUE,ng);CHKERRQ(ierr); ierr = DMCreateGlobalVector(user.iga,&U);CHKERRQ(ierr); ierr = FormInitialCondition(&user,U);CHKERRQ(ierr); ierr = DMIGASetFieldName(user.iga, 0, "density");CHKERRQ(ierr); ierr = DMIGASetFieldName(user.iga, 1, "velocity-u");CHKERRQ(ierr); ierr = DMIGASetFieldName(user.iga, 2, "velocity-v");CHKERRQ(ierr); ierr = DMCreateMatrix(user.iga, MATAIJ, &J);CHKERRQ(ierr); ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr); ierr = TSSetType(ts,TSALPHA);CHKERRQ(ierr); ierr = TSAlphaSetRadius(ts,0.5);CHKERRQ(ierr); ierr = TSSetDM(ts,user.iga);CHKERRQ(ierr); ierr = TSSetSolution(ts,U);CHKERRQ(ierr); ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr); ierr = TSSetIFunction(ts,PETSC_NULL,FormResidual,&user);CHKERRQ(ierr); ierr = TSSetIJacobian(ts,J,J,FormTangent,&user);CHKERRQ(ierr); ierr = TSSetDuration(ts,1000000,1000.0);CHKERRQ(ierr); ierr = TSSetInitialTimeStep(ts,0.0,0.001);CHKERRQ(ierr); ierr = TSAlphaSetAdapt(ts,TSAlphaAdaptDefault,PETSC_NULL);CHKERRQ(ierr); ierr = TSMonitorSet(ts,OutputMonitor,PETSC_NULL,PETSC_NULL);CHKERRQ(ierr); ierr = TSSetFromOptions(ts);CHKERRQ(ierr); ierr = TSSolve(ts,U,&ftime);CHKERRQ(ierr); ierr = TSGetTimeStepNumber(ts,&steps);CHKERRQ(ierr); // Cleanup ierr = TSDestroy(&ts);CHKERRQ(ierr); ierr = DMDestroy(&user.iga);CHKERRQ(ierr); 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); }
int main(int argc,char **argv) { TS ts; /* time integrator */ Vec x,r; /* solution, residual vectors */ PetscInt steps,Mx; PetscErrorCode ierr; DM da; PetscReal dt; UserCtx ctx; PetscBool mymonitor; PetscViewer viewer; PetscBool flg; /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Initialize program - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr; ctx.kappa = 1.0; ierr = PetscOptionsGetReal(NULL,NULL,"-kappa",&ctx.kappa,NULL);CHKERRQ(ierr); ctx.allencahn = PETSC_FALSE; ierr = PetscOptionsHasName(NULL,NULL,"-allen-cahn",&ctx.allencahn);CHKERRQ(ierr); ierr = PetscOptionsHasName(NULL,NULL,"-mymonitor",&mymonitor);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create distributed array (DMDA) to manage parallel grid and vectors - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = DMDACreate1d(PETSC_COMM_WORLD, DM_BOUNDARY_PERIODIC, 10,1,2,NULL,&da);CHKERRQ(ierr); ierr = DMSetFromOptions(da);CHKERRQ(ierr); ierr = DMSetUp(da);CHKERRQ(ierr); ierr = DMDASetFieldName(da,0,"Heat equation: u");CHKERRQ(ierr); ierr = DMDAGetInfo(da,0,&Mx,0,0,0,0,0,0,0,0,0,0,0);CHKERRQ(ierr); dt = 1.0/(ctx.kappa*Mx*Mx); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Extract global 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); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create timestepping solver context - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr); ierr = TSSetDM(ts,da);CHKERRQ(ierr); ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr); ierr = TSSetRHSFunction(ts,NULL,FormFunction,&ctx);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Customize nonlinear solver - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSetType(ts,TSCN);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set initial conditions - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = FormInitialSolution(da,x);CHKERRQ(ierr); ierr = TSSetTimeStep(ts,dt);CHKERRQ(ierr); ierr = TSSetMaxTime(ts,.02);CHKERRQ(ierr); ierr = TSSetExactFinalTime(ts,TS_EXACTFINALTIME_INTERPOLATE);CHKERRQ(ierr); ierr = TSSetSolution(ts,x);CHKERRQ(ierr); if (mymonitor) { ctx.ports = NULL; ierr = TSMonitorSet(ts,MyMonitor,&ctx,MyDestroy);CHKERRQ(ierr); } /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set runtime options - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSetFromOptions(ts);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Solve nonlinear system - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSolve(ts,x);CHKERRQ(ierr); ierr = TSGetStepNumber(ts,&steps);CHKERRQ(ierr); ierr = PetscOptionsHasName(NULL,NULL,"-square_initial",&flg);CHKERRQ(ierr); if (flg) { ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"InitialSolution.heat",FILE_MODE_WRITE,&viewer);CHKERRQ(ierr); ierr = VecView(x,viewer);CHKERRQ(ierr); ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); } /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Free work space. All PETSc objects should be destroyed when they are no longer needed. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = VecDestroy(&x);CHKERRQ(ierr); ierr = VecDestroy(&r);CHKERRQ(ierr); ierr = TSDestroy(&ts);CHKERRQ(ierr); ierr = DMDestroy(&da);CHKERRQ(ierr); ierr = PetscFinalize(); return ierr; }
int main(int argc,char **argv) { TS ts; /* nonlinear solver */ Vec U; /* solution, residual vectors */ PetscErrorCode ierr; DM da; AppCtx appctx; /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Initialize program - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ PetscInitialize(&argc,&argv,(char*)0,help); appctx.epsilon = 1.0e-3; appctx.delta = 1.0; appctx.alpha = 10.0; appctx.beta = 4.0; appctx.gamma = 1.0; appctx.kappa = .75; appctx.lambda = 1.0; appctx.mu = 100.; appctx.cstar = .2; appctx.upwind = PETSC_TRUE; ierr = PetscOptionsGetScalar(NULL,"-delta",&appctx.delta,NULL);CHKERRQ(ierr); ierr = PetscOptionsGetBool(NULL,"-upwind",&appctx.upwind,NULL);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create distributed array (DMDA) to manage parallel grid and vectors - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = DMDACreate1d(PETSC_COMM_WORLD, DM_BOUNDARY_NONE,-8,2,1,NULL,&da);CHKERRQ(ierr); ierr = DMDASetFieldName(da,0,"rho");CHKERRQ(ierr); ierr = DMDASetFieldName(da,1,"c");CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Extract global vectors from DMDA; then duplicate for remaining vectors that are the same types - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = DMCreateGlobalVector(da,&U);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create timestepping solver context - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr); ierr = TSSetType(ts,TSROSW);CHKERRQ(ierr); ierr = TSSetDM(ts,da);CHKERRQ(ierr); ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr); ierr = TSSetIFunction(ts,NULL,IFunction,&appctx);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,.0001);CHKERRQ(ierr); ierr = TSSetDuration(ts,PETSC_DEFAULT,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 = TSDestroy(&ts);CHKERRQ(ierr); ierr = DMDestroy(&da);CHKERRQ(ierr); ierr = PetscFinalize(); PetscFunctionReturn(0); }
int main(int argc,char **argv) { TS ts; /* nonlinear solver */ Vec x,r; /* solution, residual vectors */ PetscInt steps,maxsteps = 100; /* iterations for convergence */ PetscErrorCode ierr; DM da; PetscReal ftime; SNES ts_snes; /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Initialize program - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ PetscInitialize(&argc,&argv,(char*)0,help); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create distributed array (DMDA) to manage parallel grid and vectors - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = DMDACreate2d(PETSC_COMM_WORLD, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE,DMDA_STENCIL_STAR,-8,-8,PETSC_DECIDE,PETSC_DECIDE, 2,1,NULL,NULL,&da);CHKERRQ(ierr); ierr = DMDASetFieldName(da,0,"u");CHKERRQ(ierr); ierr = DMDASetFieldName(da,1,"v");CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Extract global 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); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Create timestepping solver context - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr); ierr = TSSetDM(ts,da);CHKERRQ(ierr); ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr); ierr = TSSetRHSFunction(ts,NULL,FormFunction,da);CHKERRQ(ierr); ierr = TSSetDuration(ts,maxsteps,1.0);CHKERRQ(ierr); ierr = TSMonitorSet(ts,MyTSMonitor,0,0);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Customize nonlinear solver - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSetType(ts,TSBEULER);CHKERRQ(ierr); ierr = TSGetSNES(ts,&ts_snes); ierr = SNESMonitorSet(ts_snes,MySNESMonitor,NULL,NULL); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set initial conditions - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = FormInitialSolution(da,x);CHKERRQ(ierr); ierr = TSSetInitialTimeStep(ts,0.0,.0001);CHKERRQ(ierr); ierr = TSSetExactFinalTime(ts,TS_EXACTFINALTIME_STEPOVER);CHKERRQ(ierr); ierr = TSSetSolution(ts,x);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); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Free work space. All PETSc objects should be destroyed when they are no longer needed. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = VecDestroy(&x);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) { 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) { TS ts; /* nonlinear solver */ Vec X; /* solution, residual vectors */ Mat J; /* Jacobian matrix */ PetscInt steps,maxsteps,mx; PetscErrorCode ierr; DM da; PetscReal ftime,hx,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 = 1; user.B = 3; user.alpha = 0.02; user.uleft = 1; user.uright = 1; user.vleft = 3; user.vright = 3; ierr = PetscOptionsReal("-A","Reaction rate","",user.A,&user.A,NULL);CHKERRQ(ierr); ierr = PetscOptionsReal("-B","Reaction rate","",user.B,&user.B,NULL);CHKERRQ(ierr); ierr = PetscOptionsReal("-alpha","Diffusion coefficient","",user.alpha,&user.alpha,NULL);CHKERRQ(ierr); ierr = PetscOptionsReal("-uleft","Dirichlet boundary condition","",user.uleft,&user.uleft,NULL);CHKERRQ(ierr); ierr = PetscOptionsReal("-uright","Dirichlet boundary condition","",user.uright,&user.uright,NULL);CHKERRQ(ierr); ierr = PetscOptionsReal("-vleft","Dirichlet boundary condition","",user.vleft,&user.vleft,NULL);CHKERRQ(ierr); ierr = PetscOptionsReal("-vright","Dirichlet boundary condition","",user.vright,&user.vright,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); ftime = 10.0; 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); hx = 1.0/(PetscReal)(mx/2-1); dt = 0.4 * PetscSqr(hx) / user.alpha; /* Diffusive stability limit */ 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 */ 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) { MPI_Comm comm; PetscMPIInt rank; PetscErrorCode ierr; User user; PetscLogDouble v1, v2; PetscInt nplot = 0; char fileName[2048]; 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->TimeIntegralMethod == EXPLICITMETHOD) { // explicit method if(user->myownexplicitmethod){// Using the fully explicit method based on my own routing 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 = VecSet(algebra->solution, 0);CHKERRQ(ierr); ierr = SetInitialCondition(user->dm, algebra->solution, user);CHKERRQ(ierr); if(1){ PetscViewer viewer; ierr = OutputVTK(user->dm, "intialcondition.vtk", &viewer);CHKERRQ(ierr); ierr = VecView(algebra->solution, viewer);CHKERRQ(ierr); ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); ierr = PetscPrintf(PETSC_COMM_WORLD,"Outputing the initial condition intialcondition.vtk!!! \n");CHKERRQ(ierr); } ierr = VecDuplicate(algebra->solution, &algebra->fn);CHKERRQ(ierr); ierr = VecDuplicate(algebra->solution, &algebra->oldsolution);CHKERRQ(ierr); if(user->Explicit_RK2||user->Explicit_RK4){ 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); 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); } if(user->Explicit_RK2){ /* U^n_1 = U^n + 0.5*dt*f(U^n) U^{n+1} = U^n + dt*f(U^n_1) */ ierr = VecCopy(algebra->solution, algebra->oldsolution);CHKERRQ(ierr); //note that algebra->oldsolution and algebra->solution are both U^n ierr = VecAXPY(algebra->solution, 0.5*user->dt, algebra->fn);CHKERRQ(ierr); //U^n_1 = U^n + 0.5*dt*f(U^n), now algebra->solution is U^n_1, and algebra->fn is f(U^n) ierr = FormTimeStepFunction(user, algebra, algebra->solution, algebra->fn);CHKERRQ(ierr); //algebra->fn is f(U^n_1) // reset the algebra->solution to U^n ierr = VecCopy(algebra->oldsolution, algebra->solution);CHKERRQ(ierr); ierr = VecAXPY(algebra->solution, user->dt, algebra->fn);CHKERRQ(ierr); // now algebra->solution is U^{n+1} = U^n + dt*f(U^n_1) }else if(user->Explicit_RK4){ /* refer to https://en.wikipedia.org/wiki/Runge%E2%80%93Kutta_methods k_1 = f(U^n) U^n_1 = U^n + 0.5*dt*k_1 k_2 = f(U^n_1) U^n_2 = U^n + 0.5*dt*k_2 k_3 = f(U^n_2) U^n_3 = U^n + 0.5*dt*k_3 k_4 = f(U^n_3) U^{n+1} = U^n + dt/6*(k_1 + 2*k_2 + 2*k_3 + k_4) */ Vec VecTemp; // store the U^n_1 Vec k1, k2, k3, k4; ierr = VecDuplicate(algebra->solution, &k1);CHKERRQ(ierr); ierr = VecDuplicate(algebra->solution, &k2);CHKERRQ(ierr); ierr = VecDuplicate(algebra->solution, &k3);CHKERRQ(ierr); ierr = VecDuplicate(algebra->solution, &k4);CHKERRQ(ierr); ierr = VecCopy(algebra->solution, algebra->oldsolution);CHKERRQ(ierr); ierr = VecCopy(algebra->fn, k1);CHKERRQ(ierr); //note that algebra->oldsolution and algebra->solution are both U^n ierr = VecAXPY(algebra->solution, 0.5*user->dt, k1);CHKERRQ(ierr); //U^n_1 = U^n + 0.5*dt*k1, now algebra->solution is U^n_1, and algebra->fn is f(U^n) ierr = FormTimeStepFunction(user, algebra, algebra->solution, algebra->fn);CHKERRQ(ierr); //algebra->fn is f(U^n_1) ierr = VecCopy(algebra->fn, k2);CHKERRQ(ierr); // reset the algebra->solution to U^n ierr = VecCopy(algebra->oldsolution, algebra->solution);CHKERRQ(ierr); ierr = VecAXPY(algebra->solution, 0.5*user->dt, k2);CHKERRQ(ierr); //U^n_2 = U^n + 0.5*dt*k2, now algebra->solution is U^n_2, and algebra->fn is f(U^n_1) ierr = FormTimeStepFunction(user, algebra, algebra->solution, algebra->fn);CHKERRQ(ierr); //algebra->fn is f(U^n_2) ierr = VecCopy(algebra->fn, k3);CHKERRQ(ierr); // reset the algebra->solution to U^n ierr = VecCopy(algebra->oldsolution, algebra->solution);CHKERRQ(ierr); ierr = VecAXPY(algebra->solution, 0.5*user->dt, k3);CHKERRQ(ierr); //U^n_3 = U^n + 0.5*dt*k3, now algebra->solution is U^n_3, and algebra->fn is f(U^n_2) ierr = FormTimeStepFunction(user, algebra, algebra->solution, algebra->fn);CHKERRQ(ierr); //algebra->fn is f(U^n_3) ierr = VecCopy(algebra->fn, k4);CHKERRQ(ierr); //U^{n+1} = U^n + dt/6*(k_1 + 2*k_2 + 2*k_3 + k_4) PetscReal temp; temp = user->dt/6; // reset the algebra->solution to U^n ierr = VecCopy(algebra->oldsolution, algebra->solution);CHKERRQ(ierr); ierr = VecAXPY(algebra->solution, temp, k1);CHKERRQ(ierr); // now algebra->solution is U^n + dt/6*k_1 ierr = VecAXPY(algebra->solution, 2*temp, k2);CHKERRQ(ierr); // now algebra->solution is U^n + dt/6*k_1 + 2*dt/6*k_2 ierr = VecAXPY(algebra->solution, 2*temp, k3);CHKERRQ(ierr); // now algebra->solution is U^n + dt/6*k_1 + 2*dt/6*k_2 + 2*dt/6*k_3 ierr = VecAXPY(algebra->solution, temp, k4);CHKERRQ(ierr); // now algebra->solution is U^n + dt/6*k_1 + 2*dt/6*k_2 + 2*dt/6*k_3 + dt/6*k_4 ierr = VecDestroy(&k1);CHKERRQ(ierr); ierr = VecDestroy(&k2);CHKERRQ(ierr); ierr = VecDestroy(&k3);CHKERRQ(ierr); ierr = VecDestroy(&k4);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; PetscReal fnnorm; ierr = VecNorm(algebra->fn,NORM_2,&fnnorm);CHKERRQ(ierr); //ierr = VecView(algebra->fn, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); ierr = VecNorm(algebra->solution,NORM_2,&norm);CHKERRQ(ierr); ierr = VecGetSize(algebra->solution, &size);CHKERRQ(ierr); norm = norm/size; fnnorm = fnnorm/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_2,&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)){ if(norm<1.e-6) ierr = PetscPrintf(PETSC_COMM_WORLD,"\n Convergence with ||u_k-u_{k-1}|| = %g < 1.e-6\n\n", norm);CHKERRQ(ierr); if(user->current_step > user->max_time_its) ierr = PetscPrintf(PETSC_COMM_WORLD,"\n Convergence with reaching the max time its\n\n");CHKERRQ(ierr); break; } } // output the solution if (user->output_solution && (user->current_step%user->steps_output==0)){ PetscViewer viewer; Vec solution_unscaled; // Note the the algebra->solution is scaled by the density, so this is for the unscaled solution nplot = user->current_step/user->steps_output; // update file name for the current time step ierr = VecDuplicate(algebra->solution, &solution_unscaled);CHKERRQ(ierr); ierr = ReformatSolution(algebra->solution, solution_unscaled, user);CHKERRQ(ierr); ierr = PetscSNPrintf(fileName, sizeof(fileName),"%s_%d.vtk",user->solutionfile, 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(solution_unscaled, viewer);CHKERRQ(ierr); ierr = VecDestroy(&solution_unscaled);CHKERRQ(ierr); ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr); } user->current_step++; } ierr = VecDestroy(&algebra->fn);CHKERRQ(ierr); }else{ // Using the fully explicit method based on the PETSC TS routing PetscReal ftime; TS ts; TSConvergedReason reason; PetscInt nsteps; //PetscReal minRadius; //ierr = DMPlexTSGetGeometry(user->dm, NULL, NULL, &minRadius);CHKERRQ(ierr); //user->dt = 0.9*4 * minRadius / 1.0; 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 = VecSet(algebra->solution, 0.0);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,(void*)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->current_time, algebra->exactsolution, user);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->current_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); if(user->myownexplicitmethod){ierr = VecDestroy(&algebra->oldsolution);CHKERRQ(ierr);} ierr = VecDestroy(&algebra->exactsolution);CHKERRQ(ierr); ierr = DMDestroy(&user->dm);CHKERRQ(ierr); } else if (user->TimeIntegralMethod == IMPLICITMETHOD) { // Using the fully implicit method 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; Vec solution_unscaled; // Note the the algebra->solution is scaled by the density, so this is for the unscaled solution ierr = VecDuplicate(algebra->solution, &solution_unscaled);CHKERRQ(ierr); ierr = ReformatSolution(algebra->solution, solution_unscaled, user);CHKERRQ(ierr); ierr = OutputVTK(user->dm, "solution.vtk", &viewer);CHKERRQ(ierr); ierr = VecView(solution_unscaled, viewer);CHKERRQ(ierr); ierr = VecDestroy(&solution_unscaled);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) { 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; int time; /* amount of loops */ struct in put; PetscScalar rh; /* relative humidity */ PetscScalar x; /* memory varialbe for relative humidity calculation */ PetscScalar deep_grnd_temp; /* temperature of ground under top soil surface layer */ PetscScalar emma; /* absorption-emission constant for air */ PetscScalar pressure1 = 101300; /* surface pressure */ PetscScalar mixratio; /* mixing ratio */ PetscScalar airtemp; /* temperature of air near boundary layer inversion */ PetscScalar dewtemp; /* dew point temperature */ PetscScalar sfctemp; /* temperature at surface */ PetscScalar pwat; /* total column precipitable water */ PetscScalar cloudTemp; /* temperature at base of cloud */ AppCtx user; /* user-defined work context */ MonitorCtx usermonitor; /* user-defined monitor context */ PetscMPIInt rank,size; TS ts; SNES snes; DM da; Vec T,rhs; /* solution vector */ Mat J; /* Jacobian matrix */ PetscReal ftime,dt; PetscInt steps,dof = 5; PetscBool use_coloring = PETSC_TRUE; MatFDColoring matfdcoloring = 0; PetscBool monitor_off = PETSC_FALSE; PetscInitialize(&argc,&argv,(char*)0,help); ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr); ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr); /* Inputs */ readinput(&put); sfctemp = put.Ts; dewtemp = put.Td; cloudTemp = put.Tc; airtemp = put.Ta; pwat = put.pwt; if (!rank) PetscPrintf(PETSC_COMM_SELF,"Initial Temperature = %g\n",sfctemp); /* input surface temperature */ deep_grnd_temp = sfctemp - 10; /* set underlying ground layer temperature */ emma = emission(pwat); /* accounts for radiative effects of water vapor */ /* Converts from Fahrenheit to Celsuis */ sfctemp = fahr_to_cel(sfctemp); airtemp = fahr_to_cel(airtemp); dewtemp = fahr_to_cel(dewtemp); cloudTemp = fahr_to_cel(cloudTemp); deep_grnd_temp = fahr_to_cel(deep_grnd_temp); /* Converts from Celsius to Kelvin */ sfctemp += 273; airtemp += 273; dewtemp += 273; cloudTemp += 273; deep_grnd_temp += 273; /* Calculates initial relative humidity */ x = calcmixingr(dewtemp,pressure1); mixratio = calcmixingr(sfctemp,pressure1); rh = (x/mixratio)*100; if (!rank) printf("Initial RH = %.1f percent\n\n",rh); /* prints initial relative humidity */ time = 3600*put.time; /* sets amount of timesteps to run model */ /* Configure PETSc TS solver */ /*------------------------------------------*/ /* Create grid */ ierr = DMDACreate2d(PETSC_COMM_WORLD,DMDA_BOUNDARY_PERIODIC,DMDA_BOUNDARY_PERIODIC,DMDA_STENCIL_STAR,-20,-20, PETSC_DECIDE,PETSC_DECIDE,dof,1,NULL,NULL,&da);CHKERRQ(ierr); ierr = DMDASetUniformCoordinates(da, 0.0, 1.0, 0.0, 1.0, 0.0, 1.0);CHKERRQ(ierr); /* Define output window for each variable of interest */ ierr = DMDASetFieldName(da,0,"Ts");CHKERRQ(ierr); ierr = DMDASetFieldName(da,1,"Ta");CHKERRQ(ierr); ierr = DMDASetFieldName(da,2,"u");CHKERRQ(ierr); ierr = DMDASetFieldName(da,3,"v");CHKERRQ(ierr); ierr = DMDASetFieldName(da,4,"p");CHKERRQ(ierr); /* set values for appctx */ user.da = da; user.Ts = sfctemp; user.fract = put.fr; /* fraction of sky covered by clouds */ user.dewtemp = dewtemp; /* dew point temperature (mositure in air) */ user.csoil = 2000000; /* heat constant for layer */ user.dzlay = 0.08; /* thickness of top soil layer */ user.emma = emma; /* emission parameter */ user.wind = put.wnd; /* wind spped */ user.pressure1 = pressure1; /* sea level pressure */ user.airtemp = airtemp; /* temperature of air near boundar layer inversion */ user.Tc = cloudTemp; /* temperature at base of lowest cloud layer */ user.init = put.init; /* user chosen initiation scenario */ user.lat = 70*0.0174532; /* converts latitude degrees to latitude in radians */ user.deep_grnd_temp = deep_grnd_temp; /* temp in lowest ground layer */ /* set values for MonitorCtx */ usermonitor.drawcontours = PETSC_FALSE; ierr = PetscOptionsHasName(NULL,"-drawcontours",&usermonitor.drawcontours);CHKERRQ(ierr); if (usermonitor.drawcontours) { PetscReal bounds[] = {1000.0,-1000., -1000.,-1000., 1000.,-1000., 1000.,-1000., 1000,-1000, 100700,100800}; ierr = PetscViewerDrawOpen(PETSC_COMM_WORLD,0,0,0,0,300,300,&usermonitor.drawviewer);CHKERRQ(ierr); ierr = PetscViewerDrawSetBounds(usermonitor.drawviewer,dof,bounds);CHKERRQ(ierr); } usermonitor.interval = 1; ierr = PetscOptionsGetInt(NULL,"-monitor_interval",&usermonitor.interval,NULL);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Extract global vectors from DA; - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = DMCreateGlobalVector(da,&T);CHKERRQ(ierr); ierr = VecDuplicate(T,&rhs);CHKERRQ(ierr); /* r: vector to put the computed right hand side */ ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr); ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr); ierr = TSSetType(ts,TSBEULER);CHKERRQ(ierr); ierr = TSSetRHSFunction(ts,rhs,RhsFunc,&user);CHKERRQ(ierr); /* Set Jacobian evaluation routine - use coloring to compute finite difference Jacobian efficiently */ ierr = DMSetMatType(da,MATAIJ);CHKERRQ(ierr); ierr = DMCreateMatrix(da,&J);CHKERRQ(ierr); ierr = TSGetSNES(ts,&snes);CHKERRQ(ierr); if (use_coloring) { ISColoring iscoloring; ierr = DMCreateColoring(da,IS_COLORING_GLOBAL,&iscoloring);CHKERRQ(ierr); ierr = MatFDColoringCreate(J,iscoloring,&matfdcoloring);CHKERRQ(ierr); ierr = MatFDColoringSetFromOptions(matfdcoloring);CHKERRQ(ierr); ierr = MatFDColoringSetUp(J,iscoloring,matfdcoloring);CHKERRQ(ierr); ierr = ISColoringDestroy(&iscoloring);CHKERRQ(ierr); ierr = MatFDColoringSetFunction(matfdcoloring,(PetscErrorCode (*)(void))SNESTSFormFunction,ts);CHKERRQ(ierr); ierr = SNESSetJacobian(snes,J,J,SNESComputeJacobianDefaultColor,matfdcoloring);CHKERRQ(ierr); } else { ierr = SNESSetJacobian(snes,J,J,SNESComputeJacobianDefault,NULL);CHKERRQ(ierr); } /* Define what to print for ts_monitor option */ ierr = PetscOptionsHasName(NULL,"-monitor_off",&monitor_off);CHKERRQ(ierr); if (!monitor_off) { ierr = TSMonitorSet(ts,Monitor,&usermonitor,NULL);CHKERRQ(ierr); } ierr = FormInitialSolution(da,T,&user);CHKERRQ(ierr); dt = TIMESTEP; /* initial time step */ ftime = TIMESTEP*time; if (!rank) printf("time %d, ftime %g hour, TIMESTEP %g\n",time,ftime/3600,dt); ierr = TSSetInitialTimeStep(ts,0.0,dt);CHKERRQ(ierr); ierr = TSSetDuration(ts,time,ftime);CHKERRQ(ierr); ierr = TSSetSolution(ts,T);CHKERRQ(ierr); ierr = TSSetDM(ts,da);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Set runtime options - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSetFromOptions(ts);CHKERRQ(ierr); /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Solve nonlinear system - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */ ierr = TSSolve(ts,T);CHKERRQ(ierr); ierr = TSGetSolveTime(ts,&ftime);CHKERRQ(ierr); ierr = TSGetTimeStepNumber(ts,&steps);CHKERRQ(ierr); if (!rank) PetscPrintf(PETSC_COMM_WORLD,"Solution T after %g hours %d steps\n",ftime/3600,steps); if (matfdcoloring) {ierr = MatFDColoringDestroy(&matfdcoloring);CHKERRQ(ierr);} if (usermonitor.drawcontours) { ierr = PetscViewerDestroy(&usermonitor.drawviewer);CHKERRQ(ierr); } ierr = MatDestroy(&J);CHKERRQ(ierr); ierr = VecDestroy(&T);CHKERRQ(ierr); ierr = VecDestroy(&rhs);CHKERRQ(ierr); ierr = TSDestroy(&ts);CHKERRQ(ierr); ierr = DMDestroy(&da);CHKERRQ(ierr); PetscFinalize(); return 0; }