VPUBLIC int Vgreen_coulomb_direct(Vgreen *thee, int npos, double *x,
double *y, double *z, double *val) {
Vatom *atom;
double *apos, charge, dist, dx, dy, dz, scale;
double *q, qtemp, fx, fy, fz;
int iatom, ipos;
if (thee == VNULL) {
Vnm_print(2, "Vgreen_coulomb: Got NULL thee!\n");
return 0;
}
for (ipos=0; ipos<npos; ipos++) val[ipos] = 0.0;
for (iatom=0; iatom<Valist_getNumberAtoms(thee->alist); iatom++) {
atom = Valist_getAtom(thee->alist, iatom);
apos = Vatom_getPosition(atom);
charge = Vatom_getCharge(atom);
for (ipos=0; ipos<npos; ipos++) {
dx = apos[0] - x[ipos];
dy = apos[1] - y[ipos];
dz = apos[2] - z[ipos];
dist = VSQRT(VSQR(dx) + VSQR(dy) + VSQR(dz));
if (dist > VSMALL) val[ipos] += (charge/dist);
}
}
scale = Vunit_ec/(4*Vunit_pi*Vunit_eps0*1.0e-10);
for (ipos=0; ipos<npos; ipos++) val[ipos] = val[ipos]*scale;
return 1;
}
VPUBLIC int Vgreen_coulombD_direct(Vgreen *thee, int npos,
double *x, double *y, double *z, double *pot, double *gradx,
double *grady, double *gradz) {
Vatom *atom;
double *apos, charge, dist, dist2, idist3, dy, dz, dx, scale;
double *q, qtemp;
int iatom, ipos;
if (thee == VNULL) {
Vnm_print(2, "Vgreen_coulombD: Got VNULL thee!\n");
return 0;
}
for (ipos=0; ipos<npos; ipos++) {
pot[ipos] = 0.0;
gradx[ipos] = 0.0;
grady[ipos] = 0.0;
gradz[ipos] = 0.0;
}
for (iatom=0; iatom<Valist_getNumberAtoms(thee->alist); iatom++) {
atom = Valist_getAtom(thee->alist, iatom);
apos = Vatom_getPosition(atom);
charge = Vatom_getCharge(atom);
for (ipos=0; ipos<npos; ipos++) {
dx = apos[0] - x[ipos];
dy = apos[1] - y[ipos];
dz = apos[2] - z[ipos];
dist2 = VSQR(dx) + VSQR(dy) + VSQR(dz);
dist = VSQRT(dist2);
if (dist > VSMALL) {
idist3 = 1.0/(dist*dist2);
gradx[ipos] -= (charge*dx*idist3);
grady[ipos] -= (charge*dy*idist3);
gradz[ipos] -= (charge*dz*idist3);
pot[ipos] += (charge/dist);
}
}
}
scale = Vunit_ec/(4*VPI*Vunit_eps0*(1.0e-10));
for (ipos=0; ipos<npos; ipos++) {
gradx[ipos] = gradx[ipos]*scale;
grady[ipos] = grady[ipos]*scale;
gradz[ipos] = gradz[ipos]*scale;
pot[ipos] = pot[ipos]*scale;
}
return 1;
}
/*
* ***************************************************************************
* Routine: markSimplex_default
*
* Purpose: DEFAULT: Simplex marking routine for refinement.
*
* Author: Michael Holst
* ***************************************************************************
*/
VPRIVATE int markSimplex_default(int dim, int dimII,
int simplexType, int faceType[4], int vertexType[4],
int chart[], double vx[][3], void *data)
{
int j, k, less, more;
double radius, d[4];
/* radius = radius of a refinement sphere for testing */
radius = 0.1; /* must be > 0 */
less = 0;
more = 0;
for (j=0; j<dim+1; j++) {
d[j] = 0.0;
for (k=0; k<3; k++)
d[j] += VSQR( vx[j][k] );
d[j] = VSQRT( d[j] );
if (d[j] <= radius+VSMALL) less = 1;
else more = 1;
}
/* return true if simplex touches or stradles surface of sphere */
return ( less && more );
}
/* ///////////////////////////////////////////////////////////////////////////
// Routine: Vopot_gradient
//
// Authors: Nathan Baker
/////////////////////////////////////////////////////////////////////////// */
VPUBLIC int Vopot_gradient(Vopot *thee, double pt[3], double grad[3]) {
Vatom *atom;
int iatom;
double T, charge, eps_w, xkappa, size, val, *position;
double dx, dy, dz, dist;
Valist *alist;
VASSERT(thee != VNULL);
eps_w = Vpbe_getSolventDiel(thee->pbe);
xkappa = (1.0e10)*Vpbe_getXkappa(thee->pbe);
T = Vpbe_getTemperature(thee->pbe);
alist = Vpbe_getValist(thee->pbe);
if (!Vmgrid_gradient(thee->mgrid, pt, grad)) {
switch (thee->bcfl) {
case BCFL_ZERO:
grad[0] = 0.0;
grad[1] = 0.0;
grad[2] = 0.0;
break;
case BCFL_SDH:
grad[0] = 0.0;
grad[1] = 0.0;
grad[2] = 0.0;
size = (1.0e-10)*Vpbe_getSoluteRadius(thee->pbe);
position = Vpbe_getSoluteCenter(thee->pbe);
charge = Vunit_ec*Vpbe_getSoluteCharge(thee->pbe);
dx = position[0] - pt[0];
dy = position[1] - pt[1];
dz = position[2] - pt[2];
dist = VSQR(dx) + VSQR(dy) + VSQR(dz);
dist = (1.0e-10)*VSQRT(dist);
val = (charge)/(4*VPI*Vunit_eps0*eps_w);
if (xkappa != 0.0)
val = val*(exp(-xkappa*(dist-size))/(1+xkappa*size));
val = val*Vunit_ec/(Vunit_kb*T);
grad[0] = val*dx/dist*(-1.0/dist/dist + xkappa/dist);
grad[1] = val*dy/dist*(-1.0/dist/dist + xkappa/dist);
grad[2] = val*dz/dist*(-1.0/dist/dist + xkappa/dist);
break;
case BCFL_MDH:
grad[0] = 0.0;
grad[1] = 0.0;
grad[2] = 0.0;
for (iatom=0; iatom<Valist_getNumberAtoms(alist); iatom++) {
atom = Valist_getAtom(alist, iatom);
position = Vatom_getPosition(atom);
charge = Vunit_ec*Vatom_getCharge(atom);
size = (1e-10)*Vatom_getRadius(atom);
dx = position[0] - pt[0];
dy = position[1] - pt[1];
dz = position[2] - pt[2];
dist = VSQR(dx) + VSQR(dy) + VSQR(dz);
dist = (1.0e-10)*VSQRT(dist);
val = (charge)/(4*VPI*Vunit_eps0*eps_w);
if (xkappa != 0.0)
val = val*(exp(-xkappa*(dist-size))/(1+xkappa*size));
val = val*Vunit_ec/(Vunit_kb*T);
grad[0] += (val*dx/dist*(-1.0/dist/dist + xkappa/dist));
grad[1] += (val*dy/dist*(-1.0/dist/dist + xkappa/dist));
grad[2] += (val*dz/dist*(-1.0/dist/dist + xkappa/dist));
}
break;
case BCFL_UNUSED:
Vnm_print(2, "Vopot: Invalid bcfl (%d)!\n", thee->bcfl);
return 0;
case BCFL_FOCUS:
Vnm_print(2, "Vopot: Invalid bcfl (%d)!\n", thee->bcfl);
return 0;
default:
Vnm_print(2, "Vopot_pot: Bogus thee->bcfl flag (%d)!\n",
thee->bcfl);
return 0;
break;
}
return 1;
}
return 1;
}
/* ///////////////////////////////////////////////////////////////////////////
// Routine: Vopot_curvature
//
// Notes: cflag=0 ==> Reduced Maximal Curvature
// cflag=1 ==> Mean Curvature (Laplace)
// cflag=2 ==> Gauss Curvature
// cflag=3 ==> True Maximal Curvature
// If we are off the grid, we can still evaluate the Laplacian; assuming, we
// are away from the molecular surface, it is simply equal to the DH factor.
//
// Authors: Nathan Baker
/////////////////////////////////////////////////////////////////////////// */
VPUBLIC int Vopot_curvature(Vopot *thee, double pt[3], int cflag,
double *value) {
Vatom *atom;
int i, iatom;
double u, T, charge, eps_w, xkappa, dist, size, val, *position, zkappa2;
Valist *alist;
VASSERT(thee != VNULL);
eps_w = Vpbe_getSolventDiel(thee->pbe);
xkappa = (1.0e10)*Vpbe_getXkappa(thee->pbe);
zkappa2 = Vpbe_getZkappa2(thee->pbe);
T = Vpbe_getTemperature(thee->pbe);
alist = Vpbe_getValist(thee->pbe);
u = 0;
if (Vmgrid_curvature(thee->mgrid, pt, cflag, value)) return 1;
else if (cflag != 1) {
Vnm_print(2, "Vopot_curvature: Off mesh!\n");
return 1;
} else {
switch (thee->bcfl) {
case BCFL_ZERO:
u = 0;
break;
case BCFL_SDH:
size = (1.0e-10)*Vpbe_getSoluteRadius(thee->pbe);
position = Vpbe_getSoluteCenter(thee->pbe);
charge = Vunit_ec*Vpbe_getSoluteCharge(thee->pbe);
dist = 0;
for (i=0; i<3; i++)
dist += VSQR(position[i] - pt[i]);
dist = (1.0e-10)*VSQRT(dist);
if (xkappa != 0.0)
u = zkappa2*(exp(-xkappa*(dist-size))/(1+xkappa*size));
break;
case BCFL_MDH:
u = 0;
for (iatom=0; iatom<Valist_getNumberAtoms(alist); iatom++) {
atom = Valist_getAtom(alist, iatom);
position = Vatom_getPosition(atom);
charge = Vunit_ec*Vatom_getCharge(atom);
size = (1e-10)*Vatom_getRadius(atom);
dist = 0;
for (i=0; i<3; i++)
dist += VSQR(position[i] - pt[i]);
dist = (1.0e-10)*VSQRT(dist);
if (xkappa != 0.0)
val = zkappa2*(exp(-xkappa*(dist-size))/(1+xkappa*size));
u = u + val;
}
break;
case BCFL_UNUSED:
Vnm_print(2, "Vopot_pot: Invlid bcfl (%d)!\n", thee->bcfl);
return 0;
case BCFL_FOCUS:
Vnm_print(2, "Vopot_pot: Invlid bcfl (%d)!\n", thee->bcfl);
return 0;
default:
Vnm_print(2, "Vopot_pot: Bogus thee->bcfl flag (%d)!\n",
thee->bcfl);
return 0;
break;
}
*value = u;
}
return 1;
}
VPUBLIC int Vopot_pot(Vopot *thee, double pt[3], double *value) {
Vatom *atom;
int i, iatom;
double u, T, charge, eps_w, xkappa, dist, size, val, *position;
Valist *alist;
VASSERT(thee != VNULL);
eps_w = Vpbe_getSolventDiel(thee->pbe);
xkappa = (1.0e10)*Vpbe_getXkappa(thee->pbe);
T = Vpbe_getTemperature(thee->pbe);
alist = Vpbe_getValist(thee->pbe);
u = 0;
/* See if we're on the mesh */
if (Vmgrid_value(thee->mgrid, pt, &u)) {
*value = u;
} else {
switch (thee->bcfl) {
case BCFL_ZERO:
u = 0;
break;
case BCFL_SDH:
size = (1.0e-10)*Vpbe_getSoluteRadius(thee->pbe);
position = Vpbe_getSoluteCenter(thee->pbe);
charge = Vunit_ec*Vpbe_getSoluteCharge(thee->pbe);
dist = 0;
for (i=0; i<3; i++)
dist += VSQR(position[i] - pt[i]);
dist = (1.0e-10)*VSQRT(dist);
val = (charge)/(4*VPI*Vunit_eps0*eps_w*dist);
if (xkappa != 0.0)
val = val*(exp(-xkappa*(dist-size))/(1+xkappa*size));
val = val*Vunit_ec/(Vunit_kb*T);
u = val;
break;
case BCFL_MDH:
u = 0;
for (iatom=0; iatom<Valist_getNumberAtoms(alist); iatom++) {
atom = Valist_getAtom(alist, iatom);
position = Vatom_getPosition(atom);
charge = Vunit_ec*Vatom_getCharge(atom);
size = (1e-10)*Vatom_getRadius(atom);
dist = 0;
for (i=0; i<3; i++)
dist += VSQR(position[i] - pt[i]);
dist = (1.0e-10)*VSQRT(dist);
val = (charge)/(4*VPI*Vunit_eps0*eps_w*dist);
if (xkappa != 0.0)
val = val*(exp(-xkappa*(dist-size))/(1+xkappa*size));
val = val*Vunit_ec/(Vunit_kb*T);
u = u + val;
}
break;
case BCFL_UNUSED:
Vnm_print(2, "Vopot_pot: Invalid bcfl flag (%d)!\n",
thee->bcfl);
return 0;
case BCFL_FOCUS:
Vnm_print(2, "Vopot_pot: Invalid bcfl flag (%d)!\n",
thee->bcfl);
return 0;
default:
Vnm_print(2, "Vopot_pot: Bogus thee->bcfl flag (%d)!\n",
thee->bcfl);
return 0;
break;
}
*value = u;
}
return 1;
}
/*
* ***************************************************************************
* Routine: Gem_formFix
*
* Purpose: Make some specified hacked fix to a given mesh.
*
* Notes: key==0 --> ?
*
* Author: Michael Holst
* ***************************************************************************
*/
VPUBLIC void Gem_formFix(Gem *thee, int key)
{
int i, j, k, l, m, nabors, btype;
double radk, radl, radm, myTol;
VV *v[4];
SS *sm, *sm0, *sm1, *sm2;
/* input check and some i/o */
btype = key;
VASSERT( (0 <= btype) && (btype <= 2) );
/* go through all simplices and zero all boundary faces */
Vnm_print(0,"Gem_makeBnd: zeroing boundary faces/vertices..");
Gem_setNumBF(thee, 0);
Gem_setNumBV(thee, 0);
for (i=0; i<Gem_numSS(thee); i++) {
sm = Gem_SS(thee,i);
if ( (i>0) && (i % VPRTKEY) == 0 ) Vnm_print(0,"[BS:%d]",i);
/* get local vertices */
for (j=0; j<Gem_dimVV(thee); j++)
v[j] = SS_vertex(sm,j);
/* reset all vertices and faces to interior type */
for (j=0; j<Gem_dimVV(thee); j++) {
/* the other three local vertex/face numbers besides "j" */
k=(j+1) % Gem_dimVV(thee);
l=(k+1) % Gem_dimVV(thee);
m=(l+1) % Gem_dimVV(thee);
SS_setFaceType(sm, j, 0);
VV_setType(v[k], 0);
VV_setType(v[l], 0);
if (Gem_dim(thee) == 3) VV_setType(v[m], 0);
}
}
Vnm_print(0,"..done.\n");
/* are we done */
/* if (btype == 0) return; */
/* okay now make a boundary */
Vnm_print(0,"Gem_makeBnd: rebuilding boundary faces/vertices..");
for (i=0; i<Gem_numSS(thee); i++) {
sm = Gem_SS(thee,i);
if ( (i>0) && (i % VPRTKEY) == 0 ) Vnm_print(0,"[BS:%d]",i);
/* get local vertices */
for (j=0; j<Gem_dimVV(thee); j++)
v[j] = SS_vertex(sm,j);
/* rebuild everything */
for (j=0; j<Gem_dimVV(thee); j++) {
/* the other three local vertex/face numbers besides "j" */
k=(j+1) % Gem_dimVV(thee);
l=(k+1) % Gem_dimVV(thee);
m=(l+1) % Gem_dimVV(thee);
/* look for a face nabor sharing face "j" (opposite vertex "j") */
nabors = 0;
for (sm0=VV_firstSS(v[k]); sm0!=VNULL;sm0=SS_link(sm0,v[k])) {
for (sm1=VV_firstSS(v[l]); sm1!=VNULL; sm1=SS_link(sm1,v[l])) {
if (Gem_dim(thee) == 2) {
if ((sm0!=sm) && (sm0==sm1)) nabors++;
} else {
for (sm2=VV_firstSS(v[m]); sm2!=VNULL;
sm2=SS_link(sm2,v[m])) {
if ((sm0!=sm) && (sm0==sm1) && (sm0==sm2)) {
nabors++;
}
}
}
}
}
/* if no one there, then face "j" is actually a boundary face */
if (nabors == 0) {
myTol = 1.0e-2;
if ( ( VABS(VV_coord(v[k],2) - 0.0) < myTol)
&& ( VABS(VV_coord(v[l],2) - 0.0) < myTol)
&& ( VABS(VV_coord(v[m],2) - 0.0) < myTol) ) {
btype = 1;
} else if ( ( VABS(VV_coord(v[k],2) - 68.03512) < myTol)
&& ( VABS(VV_coord(v[l],2) - 68.03512) < myTol)
&& ( VABS(VV_coord(v[m],2) - 68.03512) < myTol) ) {
btype = 3;
} else {
radk = VSQRT( VSQR( VV_coord(v[k],0) )
+ VSQR( VV_coord(v[k],1) ) );
radl = VSQRT( VSQR( VV_coord(v[l],0) )
+ VSQR( VV_coord(v[l],1) ) );
radm = VSQRT( VSQR( VV_coord(v[m],0) )
+ VSQR( VV_coord(v[m],1) ) );
if ( ( VABS(radk - 1.5) < myTol)
&& ( VABS(radl - 1.5) < myTol)
&& ( VABS(radm - 1.5) < myTol) ) {
btype = 2;
} else if ( ( VABS(radk - 2.0) < myTol)
&& ( VABS(radl - 2.0) < myTol)
&& ( VABS(radm - 2.0) < myTol) ){
btype = 4;
} else {
btype = 0;
}
}
SS_setFaceType(sm, j, btype);
Gem_numBFpp(thee);
if (VINTERIOR( VV_type(v[k])) ) {
VV_setType(v[k], btype);
Gem_numBVpp(thee);
}
if (VINTERIOR( VV_type(v[l])) ) {
VV_setType(v[l], btype);
Gem_numBVpp(thee);
}
if (Gem_dim(thee) == 3) {
if (VINTERIOR( VV_type(v[m])) ) {
VV_setType(v[m], btype);
Gem_numBVpp(thee);
}
}
}
}
}
Vnm_print(0,"..done.\n");
}
