/* Calculate the gridpoints an atom spans */
VPRIVATE void Vclist_gridSpan(Vclist *thee,
Vatom *atom, /* Atom */
int imin[VAPBS_DIM], /* Set to min grid indices */
int imax[VAPBS_DIM] /* Set to max grid indices */
) {
int i;
double *coord, dc, idc, rtot;
/* Get the position in the grid's frame of reference */
coord = Vatom_getPosition(atom);
/* Get the range the atom radius + probe radius spans */
rtot = Vatom_getRadius(atom) + thee->max_radius;
/* Calculate the range of grid points the inflated atom spans in the x
* direction. */
for (i=0; i<VAPBS_DIM; i++) {
dc = coord[i] - (thee->lower_corner)[i];
idc = (dc + rtot)/(thee->spacs[i]);
imax[i] = (int)(ceil(idc));
imax[i] = VMIN2(imax[i], thee->npts[i]-1);
idc = (dc - rtot)/(thee->spacs[i]);
imin[i] = (int)(floor(idc));
imin[i] = VMAX2(imin[i], 0);
}
}
VPUBLIC void Vdpbfa(double *abd, int *lda, int *n, int *m, int *info) {
double t, s;
int ik, j, jk, k, mu;
MAT2(abd, *lda, 1);
*info = 0;
for(j = 1; j <= *n; j++) {
s = 0.0;
ik = *m + 1;
jk = VMAX2(j - *m, 1);
mu = VMAX2(*m + 2 - j, 1);
if (*m >= mu ) {
for(k = mu; k <= *m; k++) {
t = VAT2(abd, k, j) - Vddot(k - mu,
RAT2(abd, ik, jk), 1,
RAT2(abd, mu, j), 1);
t /= VAT2(abd, *m + 1, jk);
VAT2(abd, k, j) = t;
s += t * t;
ik--;
jk++;
}
}
s = VAT2(abd, *m + 1, j) - s;
if (s <= 0.0) {
*info = j;
break;
}
VAT2(abd, *m + 1, j) = VSQRT(s);
}
}
/* ///////////////////////////////////////////////////////////////////////////
// Routine: Vpee_markRefine
//
// Author: Nathan Baker (and Michael Holst: the author of AM_markRefine, on
// which this is based)
/////////////////////////////////////////////////////////////////////////// */
VPUBLIC int Vpee_markRefine(Vpee *thee,
AM *am,
int level,
int akey,
int rcol,
double etol,
int bkey
) {
Aprx *aprx;
int marked = 0,
markMe,
i,
smid,
count,
currentQ;
double minError = 0.0,
maxError = 0.0,
errEst = 0.0,
mlevel,
barrier;
SS *sm;
VASSERT(thee != VNULL);
/* Get the Aprx object from AM */
aprx = am->aprx;
/* input check and some i/o */
if ( ! ((-1 <= akey) && (akey <= 4)) ) {
Vnm_print(0,"Vpee_markRefine: bad refine key; simplices marked = %d\n",
marked);
return marked;
}
/* For uniform markings, we have no effect */
if ((-1 <= akey) && (akey <= 0)) {
marked = Gem_markRefine(thee->gm, akey, rcol);
return marked;
}
/* Informative I/O */
if (akey == 2) {
Vnm_print(0,"Vpee_estRefine: using Aprx_estNonlinResid().\n");
} else if (akey == 3) {
Vnm_print(0,"Vpee_estRefine: using Aprx_estLocalProblem().\n");
} else if (akey == 4) {
Vnm_print(0,"Vpee_estRefine: using Aprx_estDualProblem().\n");
} else {
Vnm_print(0,"Vpee_estRefine: bad key given; simplices marked = %d\n",
marked);
return marked;
}
if (thee->killFlag == 0) {
Vnm_print(0, "Vpee_markRefine: No error attenuation -- simplices in all partitions will be marked.\n");
} else if (thee->killFlag == 1) {
Vnm_print(0, "Vpee_markRefine: Maximum error attenuation -- only simplices in local partition will be marked.\n");
} else if (thee->killFlag == 2) {
Vnm_print(0, "Vpee_markRefine: Spherical error attenutation -- simplices within a sphere of %4.3f times the size of the partition will be marked\n",
thee->killParam);
} else if (thee->killFlag == 2) {
Vnm_print(0, "Vpee_markRefine: Neighbor-based error attenuation -- simplices in the local and neighboring partitions will be marked [NOT IMPLEMENTED]!\n");
VASSERT(0);
} else {
Vnm_print(2,"Vpee_markRefine: bogus killFlag given; simplices marked = %d\n",
marked);
return marked;
}
/* set the barrier type */
mlevel = (etol*etol) / Gem_numSS(thee->gm);
if (bkey == 0) {
barrier = (etol*etol);
Vnm_print(0,"Vpee_estRefine: forcing [err per S] < [TOL] = %g\n",
barrier);
} else if (bkey == 1) {
barrier = mlevel;
Vnm_print(0,"Vpee_estRefine: forcing [err per S] < [(TOL^2/numS)^{1/2}] = %g\n",
VSQRT(barrier));
} else {
Vnm_print(0,"Vpee_estRefine: bad bkey given; simplices marked = %d\n",
marked);
return marked;
}
/* timer */
Vnm_tstart(30, "error estimation");
/* count = num generations to produce from marked simplices (minimally) */
count = 1; /* must be >= 1 */
/* check the refinement Q for emptyness */
currentQ = 0;
if (Gem_numSQ(thee->gm,currentQ) > 0) {
Vnm_print(0,"Vpee_markRefine: non-empty refinement Q%d....clearing..",
currentQ);
Gem_resetSQ(thee->gm,currentQ);
Vnm_print(0,"..done.\n");
}
if (Gem_numSQ(thee->gm,!currentQ) > 0) {
Vnm_print(0,"Vpee_markRefine: non-empty refinement Q%d....clearing..",
!currentQ);
Gem_resetSQ(thee->gm,!currentQ);
Vnm_print(0,"..done.\n");
}
VASSERT( Gem_numSQ(thee->gm,currentQ) == 0 );
VASSERT( Gem_numSQ(thee->gm,!currentQ) == 0 );
/* clear everyone's refinement flags */
Vnm_print(0,"Vpee_markRefine: clearing all simplex refinement flags..");
for (i=0; i<Gem_numSS(thee->gm); i++) {
if ( (i>0) && (i % VPRTKEY) == 0 ) Vnm_print(0,"[MS:%d]",i);
sm = Gem_SS(thee->gm,i);
SS_setRefineKey(sm,currentQ,0);
SS_setRefineKey(sm,!currentQ,0);
SS_setRefinementCount(sm,0);
}
Vnm_print(0,"..done.\n");
/* NON-ERROR-BASED METHODS */
/* Simplex flag clearing */
if (akey == -1) return marked;
/* Uniform & user-defined refinement*/
if ((akey == 0) || (akey == 1)) {
smid = 0;
while ( smid < Gem_numSS(thee->gm)) {
/* Get the simplex and find out if it's markable */
sm = Gem_SS(thee->gm,smid);
markMe = Vpee_ourSimp(thee, sm, rcol);
if (markMe) {
if (akey == 0) {
marked++;
Gem_appendSQ(thee->gm,currentQ, sm);
SS_setRefineKey(sm,currentQ,1);
SS_setRefinementCount(sm,count);
} else if (Vpee_userDefined(thee, sm)) {
marked++;
Gem_appendSQ(thee->gm,currentQ, sm);
SS_setRefineKey(sm,currentQ,1);
SS_setRefinementCount(sm,count);
}
}
smid++;
}
}
/* ERROR-BASED METHODS */
/* gerror = global error accumulation */
aprx->gerror = 0.;
/* traverse the simplices and process the error estimates */
Vnm_print(0,"Vpee_markRefine: estimating error..");
smid = 0;
while ( smid < Gem_numSS(thee->gm)) {
/* Get the simplex and find out if it's markable */
sm = Gem_SS(thee->gm,smid);
markMe = Vpee_ourSimp(thee, sm, rcol);
if ( (smid>0) && (smid % VPRTKEY) == 0 ) Vnm_print(0,"[MS:%d]",smid);
/* Produce an error estimate for this element if it is in the set */
if (markMe) {
if (akey == 2) {
errEst = Aprx_estNonlinResid(aprx, sm, am->u,am->ud,am->f);
} else if (akey == 3) {
errEst = Aprx_estLocalProblem(aprx, sm, am->u,am->ud,am->f);
} else if (akey == 4) {
errEst = Aprx_estDualProblem(aprx, sm, am->u,am->ud,am->f);
}
VASSERT( errEst >= 0. );
/* if error estimate above tol, mark element for refinement */
if ( errEst > barrier ) {
marked++;
Gem_appendSQ(thee->gm,currentQ, sm); /*add to refinement Q*/
SS_setRefineKey(sm,currentQ,1); /* note now on refine Q */
SS_setRefinementCount(sm,count); /* refine X many times? */
}
/* keep track of min/max errors over the mesh */
minError = VMIN2( VSQRT(VABS(errEst)), minError );
maxError = VMAX2( VSQRT(VABS(errEst)), maxError );
/* store the estimate */
Bvec_set( aprx->wev, smid, errEst );
/* accumlate into global error (errEst is SQUAREd already) */
aprx->gerror += errEst;
/* otherwise store a zero for the estimate */
} else {
Bvec_set( aprx->wev, smid, 0. );
}
smid++;
}
/* do some i/o */
Vnm_print(0,"..done. [marked=<%d/%d>]\n",marked,Gem_numSS(thee->gm));
Vnm_print(0,"Vpee_estRefine: TOL=<%g> Global_Error=<%g>\n",
etol, aprx->gerror);
Vnm_print(0,"Vpee_estRefine: (TOL^2/numS)^{1/2}=<%g> Max_Ele_Error=<%g>\n",
VSQRT(mlevel),maxError);
Vnm_tstop(30, "error estimation");
/* check for making the error tolerance */
if ((bkey == 1) && (aprx->gerror <= etol)) {
Vnm_print(0,
"Vpee_estRefine: *********************************************\n");
Vnm_print(0,
"Vpee_estRefine: Global Error criterion met; setting marked=0.\n");
Vnm_print(0,
"Vpee_estRefine: *********************************************\n");
marked = 0;
}
/* return */
return marked;
}
