void ApplyBCsElement(PetscInt mx,PetscInt my, PetscInt mz, PetscInt i, PetscInt j, PetscInt k,PetscScalar *jacobian)
{
PetscInt ii,jj,kk,ll,ei,ej,ek,el;
for (kk=0;kk<NB;kk++){
for (jj=0;jj<NB;jj++) {
for (ii=0;ii<NB;ii++) {
for(ll = 0;ll<3;ll++) {
PetscInt tridx = ll + 3*(ii + jj*NB + kk*NB*NB);
for (ek=0;ek<NB;ek++){
for (ej=0;ej<NB;ej++) {
for (ei=0;ei<NB;ei++) {
for (el=0;el<3;el++) {
if (OnBoundary(i+ii,j+jj,k+kk,mx,my,mz) || OnBoundary(i+ei,j+ej,k+ek,mx,my,mz)) {
PetscInt teidx = el + 3*(ei + ej*NB + ek*NB*NB);
if (teidx == tridx) {
jacobian[tridx + NPB*teidx] = 1.;
} else {
jacobian[tridx + NPB*teidx] = 0.;
}
}
}
}
}
}
}
}
}
}
}
void GatherElementData(PetscInt mx,PetscInt my,PetscInt mz,Field ***x,CoordField ***c,PetscInt i,PetscInt j,PetscInt k,Field *ex,CoordField *ec,AppCtx *user)
{
PetscInt m;
PetscInt ii,jj,kk;
/* gather the data -- loop over element unknowns */
for (kk=0;kk<NB;kk++){
for (jj=0;jj<NB;jj++) {
for (ii=0;ii<NB;ii++) {
PetscInt idx = ii + jj*NB + kk*NB*NB;
/* decouple the boundary nodes for the displacement variables */
if (OnBoundary(i+ii,j+jj,k+kk,mx,my,mz)) {
BoundaryValue(i+ii,j+jj,k+kk,mx,my,mz,ex[idx],user);
} else {
for (m=0;m<3;m++) {
ex[idx][m] = x[k+kk][j+jj][i+ii][m];
}
}
for (m=0;m<3;m++) {
ec[idx][m] = c[k+kk][j+jj][i+ii][m];
}
}
}
}
}
bool CListContour::CompactStrips()
{
CLineStrip* pStrip;
CLineStrip* pStripBase;
size_t i;
CLineStripList::iterator pos,pos2;
CLineStripList newList;
bool again, changed;
const double weldDist = 10*(m_dDx*m_dDx+m_dDy*m_dDy);
const size_t size = m_vStripLists.size();
assert__( size == GetNPlanes() );
for ( i = 0; i < size; i++ )
{
if ( i == size / 2 )
mProgress( 1 );
again=true;
while(again)
{
// REPEAT COMPACT PROCESS UNTILL LAST PROCESS MAKES NO CHANGE
again=false;
// building compacted list
assert__(newList.empty());
for (pos=m_vStripLists[i].begin(); pos!=m_vStripLists[i].end(); pos++)
{
pStrip=(*pos);
for (pos2=newList.begin(); pos2!=newList.end(); pos2++)
{
pStripBase=(*pos2);
changed=MergeStrips(pStripBase,pStrip);
if (changed)
again=true;
if (pStrip->empty())
break;
}
if (pStrip->empty())
delete pStrip;
else
newList.insert(newList.begin(),pStrip);
}
// deleting old list
m_vStripLists[i].clear();
// Copying all
for (pos2=newList.begin(); pos2 != newList.end(); pos2++)
{
pStrip=(*pos2);
CLineStrip::iterator pos1 = pStrip->begin(),pos3;
while (pos1!=pStrip->end())
{
pos3 = pos1;
pos3++;
if ( pos3 != pStrip->end() && (*pos1) == (*pos3)) //femm, from if ( (*pos1) == (*pos3))
pStrip->erase(pos3);
else
pos1++;
}
//if (!(pStrip->front()==pStrip->back() && pStrip->size()==2))
if (pStrip->size()!=1)
m_vStripLists[i].insert(m_vStripLists[i].begin(),pStrip );
else
delete pStrip;
}
// emptying temp list
newList.clear();
} // OF WHILE(AGAIN) (LAST COMPACT PROCESS MADE NO CHANGES)
if (m_vStripLists[i].empty())
continue;
///////////////////////////////////////////////////////////////////////
// compact more
long_t Nstrip,j,index,count;
Nstrip = m_vStripLists[i].size();
std::vector<bool> closed(Nstrip);
double x,y;
// First let's find the open and closed lists in m_vStripLists
for(pos2 = m_vStripLists[i].begin(), j=0, count=0; pos2 != m_vStripLists[i].end(); pos2++, j++)
{
pStrip = (*pos2);
// is it open ?
if (pStrip->front() != pStrip->back())
{
index = pStrip->front();
x = GetXi(index);
y = GetYi(index);
index = pStrip->back();
x -= GetXi(index);
y -= GetYi(index);
// is it "almost closed" ?
if ( x*x+y*y < weldDist)
closed[j] = true;
else
{
closed[j] = false;
// updating not closed counter...
count ++;
}
}
else
closed[j] = true;
}
// is there any open strip ?
if (count > 1)
{
// Merge the open strips into NewList
pos = m_vStripLists[i].begin();
for(j=0; j<Nstrip; j++)
{
if (closed[j] == false )
{
pStrip = (*pos);
newList.insert(newList.begin(),pStrip);
pos = m_vStripLists[i].erase(pos);
}
else
pos ++;
}
// are they open strips to process ?
while(newList.size()>1)
{
pStripBase = newList.front();
// merge the rest to pStripBase
again = true;
while (again)
{
again = false;
pos = newList.begin();
for(pos++; pos!=newList.end();)
{
pStrip = (*pos);
changed = ForceMerge(pStripBase,pStrip);
if (changed)
{
again = true;
delete pStrip;
pos = newList.erase(pos);
}
else
pos ++;
}
} // while(again)
index = pStripBase->front();
x = GetXi(index);
y = GetYi(index);
index = pStripBase->back();
x -= GetXi(index);
y -= GetYi(index);
// if pStripBase is closed or not
if (x*x+y*y < weldDist)
{
m_vStripLists[i].insert(m_vStripLists[i].begin(),pStripBase);
newList.pop_front();
}
else
{
if (OnBoundary(pStripBase))
{
LOG_TRACE("# open strip ends on boundary, continue.\n");
m_vStripLists[i].insert(m_vStripLists[i].begin(),pStripBase);
newList.pop_front();
}
else
{
LOG_TRACE("unpaired open strip at 1!");
//newList.pop_front();//femmfemmfemmefemm
//continue; //femmfemmfemmefemm
return false;
}
}
} // while(newList.size()>1);
if (newList.size() ==1)
{
pStripBase = newList.front();
if (OnBoundary(pStripBase))
{
LOG_TRACE("# open strip ends on boundary, continue.\n");
m_vStripLists[i].insert(m_vStripLists[i].begin(),pStripBase);
newList.pop_front();
}
else
{
LOG_TRACE("unpaired open strip at 2!");
DumpPlane(i);
return false;
}
}
newList.clear();
}
else if (count == 1)
{
pos = m_vStripLists[i].begin();
for(j=0; j<Nstrip; j++)
{
if (closed[j] == false )
{
pStripBase = (*pos);
break;
}
pos ++;
}
if (OnBoundary(pStripBase))
{
LOG_TRACE("# open strip ends on boundary, continue.\n");
}
else
{
LOG_TRACE("unpaired open strip at 3!");
DumpPlane(i);
return false;
}
}
//////////////////////////////////////////////////////////////////////////////////////////////////
}
return true;
}
PetscErrorCode NonlinearGS(SNES snes,Vec X,Vec B,void *ptr)
{
/* values for each basis function at each quadrature point */
AppCtx *user = (AppCtx*)ptr;
PetscInt i,j,k,l,m,n,s;
PetscInt pi,pj,pk;
Field ef[1];
Field ex[8];
PetscScalar ej[9];
CoordField ec[8];
PetscScalar pjac[9],pjinv[9];
PetscScalar pf[3],py[3];
PetscErrorCode ierr;
PetscInt xs,ys,zs;
PetscInt xm,ym,zm;
PetscInt mx,my,mz;
DM cda;
CoordField ***c;
Vec C;
DM da;
Vec Xl,Bl;
Field ***x,***b;
PetscInt sweeps,its;
PetscReal atol,rtol,stol;
PetscReal fnorm0 = 0.0,fnorm,ynorm,xnorm = 0.0;
PetscFunctionBegin;
ierr = SNESNGSGetSweeps(snes,&sweeps);CHKERRQ(ierr);
ierr = SNESNGSGetTolerances(snes,&atol,&rtol,&stol,&its);CHKERRQ(ierr);
ierr = SNESGetDM(snes,&da);CHKERRQ(ierr);
ierr = DMGetLocalVector(da,&Xl);CHKERRQ(ierr);
if (B) {
ierr = DMGetLocalVector(da,&Bl);CHKERRQ(ierr);
}
ierr = DMGlobalToLocalBegin(da,X,INSERT_VALUES,Xl);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(da,X,INSERT_VALUES,Xl);CHKERRQ(ierr);
if (B) {
ierr = DMGlobalToLocalBegin(da,B,INSERT_VALUES,Bl);CHKERRQ(ierr);
ierr = DMGlobalToLocalEnd(da,B,INSERT_VALUES,Bl);CHKERRQ(ierr);
}
ierr = DMDAVecGetArray(da,Xl,&x);CHKERRQ(ierr);
if (B) ierr = DMDAVecGetArray(da,Bl,&b);CHKERRQ(ierr);
ierr = DMGetCoordinateDM(da,&cda);CHKERRQ(ierr);
ierr = DMGetCoordinatesLocal(da,&C);CHKERRQ(ierr);
ierr = DMDAVecGetArray(cda,C,&c);CHKERRQ(ierr);
ierr = DMDAGetInfo(da,0,&mx,&my,&mz,0,0,0,0,0,0,0,0,0);CHKERRQ(ierr);
ierr = DMDAGetCorners(da,&xs,&ys,&zs,&xm,&ym,&zm);CHKERRQ(ierr);
for (s=0;s<sweeps;s++) {
for (k=zs; k<zs+zm; k++) {
for (j=ys; j<ys+ym; j++) {
for (i=xs; i<xs+xm; i++) {
if (OnBoundary(i,j,k,mx,my,mz)) {
BoundaryValue(i,j,k,mx,my,mz,x[k][j][i],user);
} else {
for (n=0;n<its;n++) {
for (m=0;m<9;m++) pjac[m] = 0.;
for (m=0;m<3;m++) pf[m] = 0.;
/* gather the elements for this point */
for (pk=-1; pk<1; pk++) {
for (pj=-1; pj<1; pj++) {
for (pi=-1; pi<1; pi++) {
/* check that this element exists */
if (i+pi >= 0 && i+pi < mx-1 && j+pj >= 0 && j+pj < my-1 && k+pk >= 0 && k+pk < mz-1) {
/* create the element function and jacobian */
GatherElementData(mx,my,mz,x,c,i+pi,j+pj,k+pk,ex,ec,user);
FormPBJacobian(-pi,-pj,-pk,ex,ec,ef,ej,user);
/* extract the point named by i,j,k from the whole element jacobian and function */
for (l=0;l<3;l++) {
pf[l] += ef[0][l];
for (m=0;m<3;m++) {
pjac[3*m+l] += ej[3*m+l];
}
}
}
}
}
}
/* invert */
InvertTensor(pjac,pjinv,NULL);
/* apply */
if (B) for (m=0;m<3;m++) {
pf[m] -= b[k][j][i][m];
}
TensorVector(pjinv,pf,py);
xnorm=0.;
for (m=0;m<3;m++) {
x[k][j][i][m] -= py[m];
xnorm += PetscRealPart(x[k][j][i][m]*x[k][j][i][m]);
}
fnorm = PetscRealPart(pf[0]*pf[0]+pf[1]*pf[1]+pf[2]*pf[2]);
if (n==0) fnorm0 = fnorm;
ynorm = PetscRealPart(py[0]*py[0]+py[1]*py[1]+py[2]*py[2]);
if (fnorm < atol*atol || fnorm < rtol*rtol*fnorm0 || ynorm < stol*stol*xnorm) break;
}
}
}
}
}
}
ierr = DMDAVecRestoreArray(da,Xl,&x);CHKERRQ(ierr);
ierr = DMLocalToGlobalBegin(da,Xl,INSERT_VALUES,X);CHKERRQ(ierr);
ierr = DMLocalToGlobalEnd(da,Xl,INSERT_VALUES,X);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(da,&Xl);CHKERRQ(ierr);
if (B) {
ierr = DMDAVecRestoreArray(da,Bl,&b);CHKERRQ(ierr);
ierr = DMRestoreLocalVector(da,&Bl);CHKERRQ(ierr);
}
ierr = DMDAVecRestoreArray(cda,C,&c);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode FormFunctionLocal(DMDALocalInfo *info,Field ***x,Field ***f,void *ptr)
{
/* values for each basis function at each quadrature point */
AppCtx *user = (AppCtx*)ptr;
PetscInt i,j,k,l;
PetscInt ii,jj,kk;
Field ef[NEB];
Field ex[NEB];
CoordField ec[NEB];
PetscErrorCode ierr;
PetscInt xs=info->xs,ys=info->ys,zs=info->zs;
PetscInt xm=info->xm,ym=info->ym,zm=info->zm;
PetscInt xes,yes,zes,xee,yee,zee;
PetscInt mx=info->mx,my=info->my,mz=info->mz;
DM cda;
CoordField ***c;
Vec C;
PetscFunctionBegin;
ierr = DMGetCoordinateDM(info->da,&cda);CHKERRQ(ierr);
ierr = DMGetCoordinatesLocal(info->da,&C);CHKERRQ(ierr);
ierr = DMDAVecGetArray(cda,C,&c);CHKERRQ(ierr);
ierr = DMDAGetInfo(info->da,0,&mx,&my,&mz,0,0,0,0,0,0,0,0,0);CHKERRQ(ierr);
ierr = DMDAGetCorners(info->da,&xs,&ys,&zs,&xm,&ym,&zm);CHKERRQ(ierr);
/* loop over elements */
for (k=zs; k<zs+zm; k++) {
for (j=ys; j<ys+ym; j++) {
for (i=xs; i<xs+xm; i++) {
for (l=0;l<3;l++) {
f[k][j][i][l] = 0.;
}
}
}
}
/* element starts and ends */
xes = xs;
yes = ys;
zes = zs;
xee = xs+xm;
yee = ys+ym;
zee = zs+zm;
if (xs > 0) xes = xs - 1;
if (ys > 0) yes = ys - 1;
if (zs > 0) zes = zs - 1;
if (xs+xm == mx) xee = xs+xm-1;
if (ys+ym == my) yee = ys+ym-1;
if (zs+zm == mz) zee = zs+zm-1;
for (k=zes; k<zee; k++) {
for (j=yes; j<yee; j++) {
for (i=xes; i<xee; i++) {
GatherElementData(mx,my,mz,x,c,i,j,k,ex,ec,user);
FormElementJacobian(ex,ec,ef,NULL,user);
/* put this element's additions into the residuals */
for (kk=0;kk<NB;kk++){
for (jj=0;jj<NB;jj++) {
for (ii=0;ii<NB;ii++) {
PetscInt idx = ii + jj*NB + kk*NB*NB;
if (k+kk >= zs && j+jj >= ys && i+ii >= xs && k+kk < zs+zm && j+jj < ys+ym && i+ii < xs+xm) {
if (OnBoundary(i+ii,j+jj,k+kk,mx,my,mz)) {
for (l=0;l<3;l++)
f[k+kk][j+jj][i+ii][l] = x[k+kk][j+jj][i+ii][l] - ex[idx][l];
} else {
for (l=0;l<3;l++)
f[k+kk][j+jj][i+ii][l] += ef[idx][l];
}
}
}
}
}
}
}
}
ierr = DMDAVecRestoreArray(cda,C,&c);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode FormJacobianLocal(DMDALocalInfo *info,Field ***x,Mat jacpre,Mat jac,void *ptr)
{
/* values for each basis function at each quadrature point */
AppCtx *user = (AppCtx*)ptr;
PetscInt i,j,k,m,l;
PetscInt ii,jj,kk;
PetscScalar ej[NPB*NPB];
PetscScalar vals[NPB*NPB];
Field ex[NEB];
CoordField ec[NEB];
PetscErrorCode ierr;
PetscInt xs=info->xs,ys=info->ys,zs=info->zs;
PetscInt xm=info->xm,ym=info->ym,zm=info->zm;
PetscInt xes,yes,zes,xee,yee,zee;
PetscInt mx=info->mx,my=info->my,mz=info->mz;
DM cda;
CoordField ***c;
Vec C;
PetscInt nrows;
MatStencil col[NPB],row[NPB];
PetscScalar v[9];
PetscFunctionBegin;
ierr = DMGetCoordinateDM(info->da,&cda);CHKERRQ(ierr);
ierr = DMGetCoordinatesLocal(info->da,&C);CHKERRQ(ierr);
ierr = DMDAVecGetArray(cda,C,&c);CHKERRQ(ierr);
ierr = MatScale(jac,0.0);CHKERRQ(ierr);
xes = xs;
yes = ys;
zes = zs;
xee = xs+xm;
yee = ys+ym;
zee = zs+zm;
if (xs > 0) xes = xs-1;
if (ys > 0) yes = ys-1;
if (zs > 0) zes = zs-1;
if (xs+xm == mx) xee = xs+xm-1;
if (ys+ym == my) yee = ys+ym-1;
if (zs+zm == mz) zee = zs+zm-1;
for (k=zes; k<zee; k++) {
for (j=yes; j<yee; j++) {
for (i=xes; i<xee; i++) {
GatherElementData(mx,my,mz,x,c,i,j,k,ex,ec,user);
FormElementJacobian(ex,ec,NULL,ej,user);
ApplyBCsElement(mx,my,mz,i,j,k,ej);
nrows = 0.;
for (kk=0;kk<NB;kk++){
for (jj=0;jj<NB;jj++) {
for (ii=0;ii<NB;ii++) {
PetscInt idx = ii + jj*2 + kk*4;
for (m=0;m<3;m++) {
col[3*idx+m].i = i+ii;
col[3*idx+m].j = j+jj;
col[3*idx+m].k = k+kk;
col[3*idx+m].c = m;
if (i+ii >= xs && i+ii < xm+xs && j+jj >= ys && j+jj < ys+ym && k+kk >= zs && k+kk < zs+zm) {
row[nrows].i = i+ii;
row[nrows].j = j+jj;
row[nrows].k = k+kk;
row[nrows].c = m;
for (l=0;l<NPB;l++) vals[NPB*nrows + l] = ej[NPB*(3*idx+m) + l];
nrows++;
}
}
}
}
}
ierr = MatSetValuesStencil(jac,nrows,row,NPB,col,vals,ADD_VALUES);CHKERRQ(ierr);
}
}
}
ierr = MatAssemblyBegin(jac,MAT_FLUSH_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(jac,MAT_FLUSH_ASSEMBLY);CHKERRQ(ierr);
/* set the diagonal */
v[0] = 1.;v[1] = 0.;v[2] = 0.;v[3] = 0.;v[4] = 1.;v[5] = 0.;v[6] = 0.;v[7] = 0.;v[8] = 1.;
for (k=zs; k<zs+zm; k++) {
for (j=ys; j<ys+ym; j++) {
for (i=xs; i<xs+xm; i++) {
if (OnBoundary(i,j,k,mx,my,mz)) {
for (m=0; m<3;m++) {
col[m].i = i;
col[m].j = j;
col[m].k = k;
col[m].c = m;
}
ierr = MatSetValuesStencil(jac,3,col,3,col,v,INSERT_VALUES);CHKERRQ(ierr);
}
}
}
}
ierr = MatAssemblyBegin(jac,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(jac,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = DMDAVecRestoreArray(cda,C,&c);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
