PetscErrorCode SNESComputeJacobianDefaultColor(SNES snes,Vec x1,Mat J,Mat B,void *ctx)
{
MatFDColoring color = (MatFDColoring)ctx;
PetscErrorCode ierr;
DM dm;
MatColoring mc;
ISColoring iscoloring;
PetscBool hascolor;
PetscBool solvec,matcolor = PETSC_FALSE;
PetscFunctionBegin;
if (color) PetscValidHeaderSpecific(color,MAT_FDCOLORING_CLASSID,6);
if (!color) {ierr = PetscObjectQuery((PetscObject)B,"SNESMatFDColoring",(PetscObject*)&color);CHKERRQ(ierr);}
if (!color) {
ierr = SNESGetDM(snes,&dm);CHKERRQ(ierr);
ierr = DMHasColoring(dm,&hascolor);CHKERRQ(ierr);
matcolor = PETSC_FALSE;
ierr = PetscOptionsGetBool(((PetscObject)snes)->options,((PetscObject)snes)->prefix,"-snes_fd_color_use_mat",&matcolor,NULL);CHKERRQ(ierr);
if (hascolor && !matcolor) {
ierr = DMCreateColoring(dm,IS_COLORING_GLOBAL,&iscoloring);CHKERRQ(ierr);
ierr = MatFDColoringCreate(B,iscoloring,&color);CHKERRQ(ierr);
ierr = MatFDColoringSetFunction(color,(PetscErrorCode (*)(void))SNESComputeFunctionCtx,NULL);CHKERRQ(ierr);
ierr = MatFDColoringSetFromOptions(color);CHKERRQ(ierr);
ierr = MatFDColoringSetUp(B,iscoloring,color);CHKERRQ(ierr);
ierr = ISColoringDestroy(&iscoloring);CHKERRQ(ierr);
} else {
ierr = MatColoringCreate(B,&mc);CHKERRQ(ierr);
ierr = MatColoringSetDistance(mc,2);CHKERRQ(ierr);
ierr = MatColoringSetType(mc,MATCOLORINGSL);CHKERRQ(ierr);
ierr = MatColoringSetFromOptions(mc);CHKERRQ(ierr);
ierr = MatColoringApply(mc,&iscoloring);CHKERRQ(ierr);
ierr = MatColoringDestroy(&mc);CHKERRQ(ierr);
ierr = MatFDColoringCreate(B,iscoloring,&color);CHKERRQ(ierr);
ierr = MatFDColoringSetFunction(color,(PetscErrorCode (*)(void))SNESComputeFunctionCtx,NULL);CHKERRQ(ierr);
ierr = MatFDColoringSetFromOptions(color);CHKERRQ(ierr);
ierr = MatFDColoringSetUp(B,iscoloring,color);CHKERRQ(ierr);
ierr = ISColoringDestroy(&iscoloring);CHKERRQ(ierr);
}
ierr = PetscObjectCompose((PetscObject)B,"SNESMatFDColoring",(PetscObject)color);CHKERRQ(ierr);
ierr = PetscObjectDereference((PetscObject)color);CHKERRQ(ierr);
}
/* F is only usable if there is no RHS on the SNES and the full solution corresponds to x1 */
ierr = VecEqual(x1,snes->vec_sol,&solvec);CHKERRQ(ierr);
if (!snes->vec_rhs && solvec) {
Vec F;
ierr = SNESGetFunction(snes,&F,NULL,NULL);CHKERRQ(ierr);
ierr = MatFDColoringSetF(color,F);CHKERRQ(ierr);
}
ierr = MatFDColoringApply(B,color,x1,snes);CHKERRQ(ierr);
if (J != B) {
ierr = MatAssemblyBegin(J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
static PetscErrorCode SNESComputeJacobian_DMLocal(SNES snes,Vec X,Mat A,Mat B,void *ctx)
{
PetscErrorCode ierr;
DM dm;
DMSNES_Local *dmlocalsnes = (DMSNES_Local*)ctx;
Vec Xloc;
PetscFunctionBegin;
ierr = SNESGetDM(snes,&dm);CHKERRQ(ierr);
if (dmlocalsnes->jacobianlocal) {
ierr = DMGetLocalVector(dm,&Xloc);CHKERRQ(ierr);
ierr = VecZeroEntries(Xloc);CHKERRQ(ierr);
if (dmlocalsnes->boundarylocal) {ierr = (*dmlocalsnes->boundarylocal)(dm,Xloc,dmlocalsnes->boundarylocalctx);CHKERRQ(ierr);}
ierr = DMGlobalToLocalBegin(dm,X,INSERT_VALUES,Xloc);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(dm,X,INSERT_VALUES,Xloc);CHKERRQ(ierr);
CHKMEMQ;
ierr = (*dmlocalsnes->jacobianlocal)(dm,Xloc,A,B,dmlocalsnes->jacobianlocalctx);CHKERRQ(ierr);
CHKMEMQ;
ierr = DMRestoreLocalVector(dm,&Xloc);CHKERRQ(ierr);
} else {
MatFDColoring fdcoloring;
ierr = PetscObjectQuery((PetscObject)dm,"DMDASNES_FDCOLORING",(PetscObject*)&fdcoloring);CHKERRQ(ierr);
if (!fdcoloring) {
ISColoring coloring;
ierr = DMCreateColoring(dm,dm->coloringtype,&coloring);CHKERRQ(ierr);
ierr = MatFDColoringCreate(B,coloring,&fdcoloring);CHKERRQ(ierr);
ierr = ISColoringDestroy(&coloring);CHKERRQ(ierr);
switch (dm->coloringtype) {
case IS_COLORING_GLOBAL:
ierr = MatFDColoringSetFunction(fdcoloring,(PetscErrorCode (*)(void))SNESComputeFunction_DMLocal,dmlocalsnes);CHKERRQ(ierr);
break;
default: SETERRQ1(PetscObjectComm((PetscObject)snes),PETSC_ERR_SUP,"No support for coloring type '%s'",ISColoringTypes[dm->coloringtype]);
}
ierr = PetscObjectSetOptionsPrefix((PetscObject)fdcoloring,((PetscObject)dm)->prefix);CHKERRQ(ierr);
ierr = MatFDColoringSetFromOptions(fdcoloring);CHKERRQ(ierr);
ierr = MatFDColoringSetUp(B,coloring,fdcoloring);CHKERRQ(ierr);
ierr = PetscObjectCompose((PetscObject)dm,"DMDASNES_FDCOLORING",(PetscObject)fdcoloring);CHKERRQ(ierr);
ierr = PetscObjectDereference((PetscObject)fdcoloring);CHKERRQ(ierr);
/* The following breaks an ugly reference counting loop that deserves a paragraph. MatFDColoringApply() will call
* VecDuplicate() with the state Vec and store inside the MatFDColoring. This Vec will duplicate the Vec, but the
* MatFDColoring is composed with the DM. We dereference the DM here so that the reference count will eventually
* drop to 0. Note the code in DMDestroy() that exits early for a negative reference count. That code path will be
* taken when the PetscObjectList for the Vec inside MatFDColoring is destroyed.
*/
ierr = PetscObjectDereference((PetscObject)dm);CHKERRQ(ierr);
}
ierr = MatFDColoringApply(B,fdcoloring,X,snes);CHKERRQ(ierr);
}
/* This will be redundant if the user called both, but it's too common to forget. */
if (A != B) {
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
PetscErrorCode SNESComputeJacobianDefaultColor(SNES snes,Vec x1,Mat *J,Mat *B,MatStructure *flag,void *ctx)
{
MatFDColoring color = (MatFDColoring)ctx;
PetscErrorCode ierr;
DM dm;
PetscErrorCode (*func)(SNES,Vec,Vec,void*);
Vec F;
void *funcctx;
ISColoring iscoloring;
PetscBool hascolor;
PetscBool solvec;
PetscFunctionBegin;
if (color) PetscValidHeaderSpecific(color,MAT_FDCOLORING_CLASSID,6);
else {ierr = PetscObjectQuery((PetscObject)*B,"SNESMatFDColoring",(PetscObject*)&color);CHKERRQ(ierr);}
*flag = SAME_NONZERO_PATTERN;
ierr = SNESGetFunction(snes,&F,&func,&funcctx);CHKERRQ(ierr);
if (!color) {
ierr = SNESGetDM(snes,&dm);CHKERRQ(ierr);
ierr = DMHasColoring(dm,&hascolor);CHKERRQ(ierr);
if (hascolor) {
ierr = DMCreateColoring(dm,IS_COLORING_GLOBAL,&iscoloring);CHKERRQ(ierr);
ierr = MatFDColoringCreate(*B,iscoloring,&color);CHKERRQ(ierr);
ierr = ISColoringDestroy(&iscoloring);CHKERRQ(ierr);
ierr = MatFDColoringSetFunction(color,(PetscErrorCode (*)(void))func,funcctx);CHKERRQ(ierr);
ierr = MatFDColoringSetFromOptions(color);CHKERRQ(ierr);
} else {
ierr = MatGetColoring(*B,MATCOLORINGSL,&iscoloring);CHKERRQ(ierr);
ierr = MatFDColoringCreate(*B,iscoloring,&color);CHKERRQ(ierr);
ierr = ISColoringDestroy(&iscoloring);CHKERRQ(ierr);
ierr = MatFDColoringSetFunction(color,(PetscErrorCode (*)(void))func,(void*)funcctx);CHKERRQ(ierr);
ierr = MatFDColoringSetFromOptions(color);CHKERRQ(ierr);
}
ierr = PetscObjectCompose((PetscObject)*B,"SNESMatFDColoring",(PetscObject)color);CHKERRQ(ierr);
ierr = PetscObjectDereference((PetscObject)color);CHKERRQ(ierr);
}
/* F is only usable if there is no RHS on the SNES and the full solution corresponds to x1 */
ierr = VecEqual(x1,snes->vec_sol,&solvec);CHKERRQ(ierr);
if (!snes->vec_rhs && solvec) {
ierr = MatFDColoringSetF(color,F);CHKERRQ(ierr);
}
ierr = MatFDColoringApply(*B,color,x1,flag,snes);CHKERRQ(ierr);
if (*J != *B) {
ierr = MatAssemblyBegin(*J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(*J,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
PetscErrorCode DMCreateColoring_Composite(DM dm,ISColoringType ctype,MatType mtype,ISColoring *coloring)
{
PetscErrorCode ierr;
PetscInt n,i,cnt;
ISColoringValue *colors;
PetscBool dense = PETSC_FALSE;
ISColoringValue maxcol = 0;
DM_Composite *com = (DM_Composite*)dm->data;
PetscFunctionBegin;
PetscValidHeaderSpecific(dm,DM_CLASSID,1);
if (ctype == IS_COLORING_GHOSTED) SETERRQ(((PetscObject)dm)->comm,PETSC_ERR_SUP,"Only global coloring supported" );
else if (ctype == IS_COLORING_GLOBAL) {
n = com->n;
} else SETERRQ(((PetscObject)dm)->comm,PETSC_ERR_ARG_OUTOFRANGE,"Unknown ISColoringType");
ierr = PetscMalloc(n*sizeof(ISColoringValue),&colors);CHKERRQ(ierr); /* freed in ISColoringDestroy() */
ierr = PetscOptionsGetBool(PETSC_NULL,"-dmcomposite_dense_jacobian",&dense,PETSC_NULL);CHKERRQ(ierr);
if (dense) {
for (i=0; i<n; i++) {
colors[i] = (ISColoringValue)(com->rstart + i);
}
maxcol = com->N;
} else {
struct DMCompositeLink *next = com->next;
PetscMPIInt rank;
ierr = MPI_Comm_rank(((PetscObject)dm)->comm,&rank);CHKERRQ(ierr);
cnt = 0;
while (next) {
ISColoring lcoloring;
ierr = DMCreateColoring(next->dm,IS_COLORING_GLOBAL,mtype,&lcoloring);CHKERRQ(ierr);
for (i=0; i<lcoloring->N; i++) {
colors[cnt++] = maxcol + lcoloring->colors[i];
}
maxcol += lcoloring->n;
ierr = ISColoringDestroy(&lcoloring);CHKERRQ(ierr);
next = next->next;
}
}
ierr = ISColoringCreate(((PetscObject)dm)->comm,maxcol,n,colors,coloring);CHKERRQ(ierr);
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;
}
int main(int argc,char **argv)
{
PetscInt i,M = 3,N = 5,P=3,s=1,w=2,m = PETSC_DECIDE,n = PETSC_DECIDE,p = PETSC_DECIDE;
PetscErrorCode ierr;
PetscInt *lx = NULL,*ly = NULL,*lz = NULL;
DM da;
PetscBool flg = PETSC_FALSE,test_order = PETSC_FALSE;
ISColoring coloring;
Mat mat;
DMDAStencilType stencil_type = DMDA_STENCIL_BOX;
Vec lvec,dvec;
MatFDColoring fdcoloring;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr);
/* Read options */
ierr = PetscOptionsGetInt(NULL,"-M",&M,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-N",&N,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-P",&P,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-m",&m,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-n",&n,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-p",&p,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-s",&s,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-w",&w,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,"-star",&flg,NULL);CHKERRQ(ierr);
if (flg) stencil_type = DMDA_STENCIL_STAR;
ierr = PetscOptionsGetBool(NULL,"-test_order",&test_order,NULL);CHKERRQ(ierr);
flg = PETSC_FALSE;
ierr = PetscOptionsGetBool(NULL,"-distribute",&flg,NULL);CHKERRQ(ierr);
if (flg) {
if (m == PETSC_DECIDE) SETERRQ(PETSC_COMM_WORLD,1,"Must set -m option with -distribute option");
ierr = PetscMalloc1(m,&lx);CHKERRQ(ierr);
for (i=0; i<m-1; i++) lx[i] = 4;
lx[m-1] = M - 4*(m-1);
if (n == PETSC_DECIDE) SETERRQ(PETSC_COMM_WORLD,1,"Must set -n option with -distribute option");
ierr = PetscMalloc1(n,&ly);CHKERRQ(ierr);
for (i=0; i<n-1; i++) ly[i] = 2;
ly[n-1] = N - 2*(n-1);
if (p == PETSC_DECIDE) SETERRQ(PETSC_COMM_WORLD,1,"Must set -p option with -distribute option");
ierr = PetscMalloc1(p,&lz);CHKERRQ(ierr);
for (i=0; i<p-1; i++) lz[i] = 2;
lz[p-1] = P - 2*(p-1);
}
/* Create distributed array and get vectors */
ierr = DMDACreate3d(PETSC_COMM_WORLD,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,stencil_type,M,N,P,m,n,p,w,s,lx,ly,lz,&da);CHKERRQ(ierr);
ierr = PetscFree(lx);CHKERRQ(ierr);
ierr = PetscFree(ly);CHKERRQ(ierr);
ierr = PetscFree(lz);CHKERRQ(ierr);
ierr = DMSetMatType(da,MATMPIAIJ);CHKERRQ(ierr);
ierr = DMCreateColoring(da,IS_COLORING_GLOBAL,&coloring);CHKERRQ(ierr);
ierr = DMSetMatType(da,MATMPIAIJ);CHKERRQ(ierr);
ierr = DMCreateMatrix(da,&mat);CHKERRQ(ierr);
ierr = MatFDColoringCreate(mat,coloring,&fdcoloring);CHKERRQ(ierr);
ierr = MatFDColoringSetUp(mat,coloring,fdcoloring);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da,&dvec);CHKERRQ(ierr);
ierr = DMCreateLocalVector(da,&lvec);CHKERRQ(ierr);
/* Free memory */
ierr = MatFDColoringDestroy(&fdcoloring);CHKERRQ(ierr);
ierr = VecDestroy(&dvec);CHKERRQ(ierr);
ierr = VecDestroy(&lvec);CHKERRQ(ierr);
ierr = MatDestroy(&mat);CHKERRQ(ierr);
ierr = ISColoringDestroy(&coloring);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
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 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);
}
static PetscErrorCode SNESComputeJacobian_DMDA(SNES snes,Vec X,Mat *A,Mat *B,MatStructure *mstr,void *ctx)
{
PetscErrorCode ierr;
DM dm;
DMSNES_DA *dmdasnes = (DMSNES_DA*)ctx;
DMDALocalInfo info;
Vec Xloc;
void *x;
PetscFunctionBegin;
if (!dmdasnes->residuallocal) SETERRQ(PetscObjectComm((PetscObject)snes),PETSC_ERR_PLIB,"Corrupt context");
ierr = SNESGetDM(snes,&dm);CHKERRQ(ierr);
if (dmdasnes->jacobianlocal) {
ierr = DMGetLocalVector(dm,&Xloc);CHKERRQ(ierr);
ierr = DMGlobalToLocalBegin(dm,X,INSERT_VALUES,Xloc);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(dm,X,INSERT_VALUES,Xloc);CHKERRQ(ierr);
ierr = DMDAGetLocalInfo(dm,&info);CHKERRQ(ierr);
ierr = DMDAVecGetArray(dm,Xloc,&x);CHKERRQ(ierr);
CHKMEMQ;
ierr = (*dmdasnes->jacobianlocal)(&info,x,*A,*B,mstr,dmdasnes->jacobianlocalctx);CHKERRQ(ierr);
CHKMEMQ;
ierr = DMDAVecRestoreArray(dm,Xloc,&x);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(dm,&Xloc);CHKERRQ(ierr);
} else {
MatFDColoring fdcoloring;
ierr = PetscObjectQuery((PetscObject)dm,"DMDASNES_FDCOLORING",(PetscObject*)&fdcoloring);CHKERRQ(ierr);
if (!fdcoloring) {
ISColoring coloring;
ierr = DMCreateColoring(dm,dm->coloringtype,&coloring);CHKERRQ(ierr);
ierr = MatFDColoringCreate(*B,coloring,&fdcoloring);CHKERRQ(ierr);
ierr = ISColoringDestroy(&coloring);CHKERRQ(ierr);
switch (dm->coloringtype) {
case IS_COLORING_GLOBAL:
ierr = MatFDColoringSetFunction(fdcoloring,(PetscErrorCode (*)(void))SNESComputeFunction_DMDA,dmdasnes);CHKERRQ(ierr);
break;
default: SETERRQ1(PetscObjectComm((PetscObject)snes),PETSC_ERR_SUP,"No support for coloring type '%s'",ISColoringTypes[dm->coloringtype]);
}
ierr = PetscObjectSetOptionsPrefix((PetscObject)fdcoloring,((PetscObject)dm)->prefix);CHKERRQ(ierr);
ierr = MatFDColoringSetFromOptions(fdcoloring);CHKERRQ(ierr);
ierr = PetscObjectCompose((PetscObject)dm,"DMDASNES_FDCOLORING",(PetscObject)fdcoloring);CHKERRQ(ierr);
ierr = PetscObjectDereference((PetscObject)fdcoloring);CHKERRQ(ierr);
/* The following breaks an ugly reference counting loop that deserves a paragraph. MatFDColoringApply() will call
* VecDuplicate() with the state Vec and store inside the MatFDColoring. This Vec will duplicate the Vec, but the
* MatFDColoring is composed with the DM. We dereference the DM here so that the reference count will eventually
* drop to 0. Note the code in DMDestroy() that exits early for a negative reference count. That code path will be
* taken when the PetscObjectList for the Vec inside MatFDColoring is destroyed.
*/
ierr = PetscObjectDereference((PetscObject)dm);CHKERRQ(ierr);
}
*mstr = SAME_NONZERO_PATTERN;
ierr = MatFDColoringApply(*B,fdcoloring,X,mstr,snes);CHKERRQ(ierr);
}
/* This will be redundant if the user called both, but it's too common to forget. */
if (*A != *B) {
ierr = MatAssemblyBegin(*A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(*A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
PETSC_EXTERN PetscErrorCode SNESComputeNGSDefaultSecant(SNES snes,Vec X,Vec B,void *ctx)
{
PetscErrorCode ierr;
SNES_NGS *gs = (SNES_NGS*)snes->data;
PetscInt i,j,k,ncolors;
DM dm;
PetscBool flg;
ISColoring coloring = gs->coloring;
MatColoring mc;
Vec W,G,F;
PetscScalar h=gs->h;
IS *coloris;
PetscScalar f,g,x,w,d;
PetscReal dxt,xt,ft,ft1=0;
const PetscInt *idx;
PetscInt size,s;
PetscReal atol,rtol,stol;
PetscInt its;
PetscErrorCode (*func)(SNES,Vec,Vec,void*);
void *fctx;
PetscBool mat = gs->secant_mat,equal,isdone,alldone;
PetscScalar *xa,*fa,*wa,*ga;
PetscFunctionBegin;
if (snes->nwork < 3) {
ierr = SNESSetWorkVecs(snes,3);CHKERRQ(ierr);
}
W = snes->work[0];
G = snes->work[1];
F = snes->work[2];
ierr = VecGetOwnershipRange(X,&s,NULL);CHKERRQ(ierr);
ierr = SNESNGSGetTolerances(snes,&atol,&rtol,&stol,&its);CHKERRQ(ierr);
ierr = SNESGetDM(snes,&dm);CHKERRQ(ierr);
ierr = SNESGetFunction(snes,NULL,&func,&fctx);CHKERRQ(ierr);
if (!coloring) {
/* create the coloring */
ierr = DMHasColoring(dm,&flg);CHKERRQ(ierr);
if (flg && !mat) {
ierr = DMCreateColoring(dm,IS_COLORING_GLOBAL,&coloring);CHKERRQ(ierr);
} else {
if (!snes->jacobian) {ierr = SNESSetUpMatrices(snes);CHKERRQ(ierr);}
ierr = MatColoringCreate(snes->jacobian,&mc);CHKERRQ(ierr);
ierr = MatColoringSetDistance(mc,1);CHKERRQ(ierr);
ierr = MatColoringSetFromOptions(mc);CHKERRQ(ierr);
ierr = MatColoringApply(mc,&coloring);CHKERRQ(ierr);
ierr = MatColoringDestroy(&mc);CHKERRQ(ierr);
}
gs->coloring = coloring;
}
ierr = ISColoringGetIS(coloring,&ncolors,&coloris);CHKERRQ(ierr);
ierr = VecEqual(X,snes->vec_sol,&equal);CHKERRQ(ierr);
if (equal && snes->normschedule == SNES_NORM_ALWAYS) {
/* assume that the function is already computed */
ierr = VecCopy(snes->vec_func,F);CHKERRQ(ierr);
} else {
ierr = PetscLogEventBegin(SNES_NGSFuncEval,snes,X,B,0);CHKERRQ(ierr);
ierr = (*func)(snes,X,F,fctx);CHKERRQ(ierr);
ierr = PetscLogEventEnd(SNES_NGSFuncEval,snes,X,B,0);CHKERRQ(ierr);
if (B) {ierr = VecAXPY(F,-1.0,B);CHKERRQ(ierr);}
}
ierr = VecGetArray(X,&xa);CHKERRQ(ierr);
ierr = VecGetArray(F,&fa);CHKERRQ(ierr);
ierr = VecGetArray(G,&ga);CHKERRQ(ierr);
ierr = VecGetArray(W,&wa);CHKERRQ(ierr);
for (i=0;i<ncolors;i++) {
ierr = ISGetIndices(coloris[i],&idx);CHKERRQ(ierr);
ierr = ISGetLocalSize(coloris[i],&size);CHKERRQ(ierr);
ierr = VecCopy(X,W);CHKERRQ(ierr);
for (j=0;j<size;j++) {
wa[idx[j]-s] += h;
}
ierr = PetscLogEventBegin(SNES_NGSFuncEval,snes,X,B,0);CHKERRQ(ierr);
ierr = (*func)(snes,W,G,fctx);CHKERRQ(ierr);
ierr = PetscLogEventEnd(SNES_NGSFuncEval,snes,X,B,0);CHKERRQ(ierr);
if (B) {ierr = VecAXPY(G,-1.0,B);CHKERRQ(ierr);}
for (k=0;k<its;k++) {
dxt = 0.;
xt = 0.;
ft = 0.;
for (j=0;j<size;j++) {
f = fa[idx[j]-s];
x = xa[idx[j]-s];
g = ga[idx[j]-s];
w = wa[idx[j]-s];
if (PetscAbsScalar(g-f) > atol) {
/* This is equivalent to d = x - (h*f) / PetscRealPart(g-f) */
d = (x*g-w*f) / PetscRealPart(g-f);
} else {
d = x;
}
dxt += PetscRealPart(PetscSqr(d-x));
xt += PetscRealPart(PetscSqr(x));
ft += PetscRealPart(PetscSqr(f));
xa[idx[j]-s] = d;
}
if (k == 0) ft1 = PetscSqrtReal(ft);
if (k<its-1) {
isdone = PETSC_FALSE;
if (stol*PetscSqrtReal(xt) > PetscSqrtReal(dxt)) isdone = PETSC_TRUE;
if (PetscSqrtReal(ft) < atol) isdone = PETSC_TRUE;
if (rtol*ft1 > PetscSqrtReal(ft)) isdone = PETSC_TRUE;
ierr = MPIU_Allreduce(&isdone,&alldone,1,MPIU_BOOL,MPI_BAND,PetscObjectComm((PetscObject)snes));CHKERRQ(ierr);
if (alldone) break;
}
if (i < ncolors-1 || k < its-1) {
ierr = PetscLogEventBegin(SNES_NGSFuncEval,snes,X,B,0);CHKERRQ(ierr);
ierr = (*func)(snes,X,F,fctx);CHKERRQ(ierr);
ierr = PetscLogEventEnd(SNES_NGSFuncEval,snes,X,B,0);CHKERRQ(ierr);
if (B) {ierr = VecAXPY(F,-1.0,B);CHKERRQ(ierr);}
}
if (k<its-1) {
ierr = VecSwap(X,W);CHKERRQ(ierr);
ierr = VecSwap(F,G);CHKERRQ(ierr);
}
}
}
ierr = VecRestoreArray(X,&xa);CHKERRQ(ierr);
ierr = VecRestoreArray(F,&fa);CHKERRQ(ierr);
ierr = VecRestoreArray(G,&ga);CHKERRQ(ierr);
ierr = VecRestoreArray(W,&wa);CHKERRQ(ierr);
ierr = ISColoringRestoreIS(coloring,&coloris);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
