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;
}
/* Get the dimensions of the molecule stored in thee->alist */
VPRIVATE void Vclist_getMolDims(
Vclist *thee,
double lower_corner[VAPBS_DIM], /* Set to lower corner of molecule */
double upper_corner[VAPBS_DIM], /* Set to lower corner of molecule */
double *r_max /* Set to max atom radius */
) {
int i, j;
double pos;
Valist *alist;
Vatom *atom;
alist = thee->alist;
/* Initialize */
for (i=0; i<VAPBS_DIM; i++) {
lower_corner[i] = VLARGE;
upper_corner[i] = -VLARGE;
}
*r_max = -1.0;
/* Check each atom */
for (i=0; i<Valist_getNumberAtoms(alist); i++) {
atom = Valist_getAtom(alist, i);
for (j=0; j<VAPBS_DIM; j++) {
pos = (Vatom_getPosition(atom))[j];
if ( pos < lower_corner[j] ) lower_corner[j] = pos;
if ( pos > upper_corner[j] ) upper_corner[j] = pos;
}
if (Vatom_getRadius(atom) > *r_max) *r_max = Vatom_getRadius(atom);
}
}
/* 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 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;
}
VPUBLIC int Vcsm_update(Vcsm *thee, SS **simps, int num) {
/* Counters */
int isimp, jsimp, iatom, jatom, atomID, simpID;
int nsimps, gotMem;
/* Object info */
Vatom *atom;
SS *simplex;
double *position;
/* Lists */
int *qParent, nqParent;
int **sqmNew, *nsqmNew;
int *affAtoms, nAffAtoms;
int *dnqsm, *nqsmNew, **qsmNew;
VASSERT(thee != VNULL);
VASSERT(thee->initFlag);
/* If we don't have enough memory to accommodate the new entries,
* add more by doubling the existing amount */
isimp = thee->nsimp + num - 1;
gotMem = 0;
while (!gotMem) {
if (isimp > thee->msimp) {
isimp = 2 * isimp;
thee->nsqm = Vmem_realloc(thee->vmem, thee->msimp, sizeof(int),
(void **)&(thee->nsqm), isimp);
VASSERT(thee->nsqm != VNULL);
thee->sqm = Vmem_realloc(thee->vmem, thee->msimp, sizeof(int *),
(void **)&(thee->sqm), isimp);
VASSERT(thee->sqm != VNULL);
thee->msimp = isimp;
} else gotMem = 1;
}
/* Initialize the nsqm entires we just allocated */
for (isimp = thee->nsimp; isimp<thee->nsimp+num-1 ; isimp++) {
thee->nsqm[isimp] = 0;
}
thee->nsimp = thee->nsimp + num - 1;
/* There's a simple case to deal with: if simps[0] didn't have a
* charge in the first place */
isimp = SS_id(simps[0]);
if (thee->nsqm[isimp] == 0) {
for (isimp=1; isimp<num; isimp++) {
thee->nsqm[SS_id(simps[isimp])] = 0;
}
return 1;
}
/* The more complicated case has occured; the parent simplex had one or
* more charges. First, generate the list of affected charges. */
isimp = SS_id(simps[0]);
nqParent = thee->nsqm[isimp];
qParent = thee->sqm[isimp];
sqmNew = Vmem_malloc(thee->vmem, num, sizeof(int *));
VASSERT(sqmNew != VNULL);
nsqmNew = Vmem_malloc(thee->vmem, num, sizeof(int));
VASSERT(nsqmNew != VNULL);
for (isimp=0; isimp<num; isimp++) nsqmNew[isimp] = 0;
/* Loop throught the affected atoms to determine how many atoms each
* simplex will get. */
for (iatom=0; iatom<nqParent; iatom++) {
atomID = qParent[iatom];
atom = Valist_getAtom(thee->alist, atomID);
position = Vatom_getPosition(atom);
nsimps = 0;
jsimp = 0;
for (isimp=0; isimp<num; isimp++) {
simplex = simps[isimp];
if (Gem_pointInSimplex(thee->gm, simplex, position)) {
nsqmNew[isimp]++;
jsimp = 1;
}
}
VASSERT(jsimp != 0);
}
/* Sanity check that we didn't lose any atoms... */
iatom = 0;
for (isimp=0; isimp<num; isimp++) iatom += nsqmNew[isimp];
if (iatom < nqParent) {
Vnm_print(2,"Vcsm_update: Lost %d (of %d) atoms!\n",
nqParent - iatom, nqParent);
VASSERT(0);
}
/* Allocate the storage */
for (isimp=0; isimp<num; isimp++) {
if (nsqmNew[isimp] > 0) {
sqmNew[isimp] = Vmem_malloc(thee->vmem, nsqmNew[isimp],
sizeof(int));
VASSERT(sqmNew[isimp] != VNULL);
}
}
/* Assign charges to simplices */
for (isimp=0; isimp<num; isimp++) {
jsimp = 0;
simplex = simps[isimp];
/* Loop over the atoms associated with the parent simplex */
for (iatom=0; iatom<nqParent; iatom++) {
atomID = qParent[iatom];
atom = Valist_getAtom(thee->alist, atomID);
position = Vatom_getPosition(atom);
if (Gem_pointInSimplex(thee->gm, simplex, position)) {
sqmNew[isimp][jsimp] = atomID;
jsimp++;
}
}
}
/* Update the QSM map using the old and new SQM lists */
/* The affected atoms are those contained in the parent simplex; i.e.
* thee->sqm[SS_id(simps[0])] */
affAtoms = thee->sqm[SS_id(simps[0])];
nAffAtoms = thee->nsqm[SS_id(simps[0])];
/* Each of these atoms will go somewhere else; i.e., the entries in
* thee->qsm are never destroyed and thee->nqsm never decreases.
* However, it is possible that a subdivision could cause an atom to be
* shared by two child simplices. Here we record the change, if any,
* in the number of simplices associated with each atom. */
dnqsm = Vmem_malloc(thee->vmem, nAffAtoms, sizeof(int));
VASSERT(dnqsm != VNULL);
nqsmNew = Vmem_malloc(thee->vmem, nAffAtoms, sizeof(int));
VASSERT(nqsmNew != VNULL);
qsmNew = Vmem_malloc(thee->vmem, nAffAtoms, sizeof(int*));
VASSERT(qsmNew != VNULL);
for (iatom=0; iatom<nAffAtoms; iatom++) {
dnqsm[iatom] = -1;
atomID = affAtoms[iatom];
for (isimp=0; isimp<num; isimp++) {
for (jatom=0; jatom<nsqmNew[isimp]; jatom++) {
if (sqmNew[isimp][jatom] == atomID) dnqsm[iatom]++;
}
}
VASSERT(dnqsm[iatom] > -1);
}
/* Setup the new entries in the array */
for (iatom=0;iatom<nAffAtoms; iatom++) {
atomID = affAtoms[iatom];
qsmNew[iatom] = Vmem_malloc(thee->vmem,
(dnqsm[iatom] + thee->nqsm[atomID]),
sizeof(int));
nqsmNew[iatom] = 0;
VASSERT(qsmNew[iatom] != VNULL);
}
/* Fill the new entries in the array */
/* First, do the modified entries */
for (isimp=0; isimp<num; isimp++) {
simpID = SS_id(simps[isimp]);
for (iatom=0; iatom<nsqmNew[isimp]; iatom++) {
atomID = sqmNew[isimp][iatom];
for (jatom=0; jatom<nAffAtoms; jatom++) {
if (atomID == affAtoms[jatom]) break;
}
if (jatom < nAffAtoms) {
qsmNew[jatom][nqsmNew[jatom]] = simpID;
nqsmNew[jatom]++;
}
}
}
/* Now do the unmodified entries */
for (iatom=0; iatom<nAffAtoms; iatom++) {
atomID = affAtoms[iatom];
for (isimp=0; isimp<thee->nqsm[atomID]; isimp++) {
for (jsimp=0; jsimp<num; jsimp++) {
simpID = SS_id(simps[jsimp]);
if (thee->qsm[atomID][isimp] == simpID) break;
}
if (jsimp == num) {
qsmNew[iatom][nqsmNew[iatom]] = thee->qsm[atomID][isimp];
nqsmNew[iatom]++;
}
}
}
/* Replace the existing entries in the table. Do the QSM entires
* first, since they require affAtoms = thee->sqm[simps[0]] */
for (iatom=0; iatom<nAffAtoms; iatom++) {
atomID = affAtoms[iatom];
Vmem_free(thee->vmem, thee->nqsm[atomID], sizeof(int),
(void **)&(thee->qsm[atomID]));
thee->qsm[atomID] = qsmNew[iatom];
thee->nqsm[atomID] = nqsmNew[iatom];
}
for (isimp=0; isimp<num; isimp++) {
simpID = SS_id(simps[isimp]);
if (thee->nsqm[simpID] > 0) Vmem_free(thee->vmem, thee->nsqm[simpID],
sizeof(int), (void **)&(thee->sqm[simpID]));
thee->sqm[simpID] = sqmNew[isimp];
thee->nsqm[simpID] = nsqmNew[isimp];
}
Vmem_free(thee->vmem, num, sizeof(int *), (void **)&sqmNew);
Vmem_free(thee->vmem, num, sizeof(int), (void **)&nsqmNew);
Vmem_free(thee->vmem, nAffAtoms, sizeof(int *), (void **)&qsmNew);
Vmem_free(thee->vmem, nAffAtoms, sizeof(int), (void **)&nqsmNew);
Vmem_free(thee->vmem, nAffAtoms, sizeof(int), (void **)&dnqsm);
return 1;
}
VPUBLIC void Vcsm_init(Vcsm *thee) {
/* Counters */
int iatom, jatom, isimp, jsimp, gotSimp;
/* Atomic information */
Vatom *atom;
double *position;
/* Simplex/Vertex information */
SS *simplex;
/* Basis function values */
if (thee == VNULL) {
Vnm_print(2, "Vcsm_init: Error! Got NULL thee!\n");
VASSERT(0);
}
if (thee->gm == VNULL) {
VASSERT(thee->gm != VNULL);
Vnm_print(2, "Vcsm_init: Error! Got NULL thee->gm!\n");
VASSERT(0);
}
thee->nsimp = Gem_numSS(thee->gm);
if (thee->nsimp <= 0) {
Vnm_print(2, "Vcsm_init: Error! Got %d simplices!\n", thee->nsimp);
VASSERT(0);
}
thee->natom = Valist_getNumberAtoms(thee->alist);
/* Allocate and initialize space for the first dimensions of the
* simplex-charge map, the simplex array, and the counters */
thee->sqm = Vmem_malloc(thee->vmem, thee->nsimp, sizeof(int *));
VASSERT(thee->sqm != VNULL);
thee->nsqm = Vmem_malloc(thee->vmem, thee->nsimp, sizeof(int));
VASSERT(thee->nsqm != VNULL);
for (isimp=0; isimp<thee->nsimp; isimp++) (thee->nsqm)[isimp] = 0;
/* Count the number of charges per simplex. */
for (iatom=0; iatom<thee->natom; iatom++) {
atom = Valist_getAtom(thee->alist, iatom);
position = Vatom_getPosition(atom);
gotSimp = 0;
for (isimp=0; isimp<thee->nsimp; isimp++) {
simplex = Gem_SS(thee->gm, isimp);
if (Gem_pointInSimplex(thee->gm, simplex, position)) {
(thee->nsqm)[isimp]++;
gotSimp = 1;
}
}
}
/* Allocate the space for the simplex-charge map */
for (isimp=0; isimp<thee->nsimp; isimp++) {
if ((thee->nsqm)[isimp] > 0) {
thee->sqm[isimp] = Vmem_malloc(thee->vmem, (thee->nsqm)[isimp],
sizeof(int));
VASSERT(thee->sqm[isimp] != VNULL);
}
}
/* Finally, set up the map */
for (isimp=0; isimp<thee->nsimp; isimp++) {
jsimp = 0;
simplex = Gem_SS(thee->gm, isimp);
for (iatom=0; iatom<thee->natom; iatom++) {
atom = Valist_getAtom(thee->alist, iatom);
position = Vatom_getPosition(atom);
/* Check to see if the atom's in this simplex */
if (Gem_pointInSimplex(thee->gm, simplex, position)) {
/* Assign the entries in the next vacant spot */
(thee->sqm)[isimp][jsimp] = iatom;
jsimp++;
}
}
}
thee->msimp = thee->nsimp;
/* Allocate space for the charge-simplex map */
thee->qsm = Vmem_malloc(thee->vmem, thee->natom, sizeof(int *));
VASSERT(thee->qsm != VNULL);
thee->nqsm = Vmem_malloc(thee->vmem, thee->natom, sizeof(int));
VASSERT(thee->nqsm != VNULL);
for (iatom=0; iatom<thee->natom; iatom++) (thee->nqsm)[iatom] = 0;
/* Loop through the list of simplices and count the number of times
* each atom appears */
for (isimp=0; isimp<thee->nsimp; isimp++) {
for (iatom=0; iatom<thee->nsqm[isimp]; iatom++) {
jatom = thee->sqm[isimp][iatom];
thee->nqsm[jatom]++;
}
}
/* Do a TIME-CONSUMING SANITY CHECK to make sure that each atom was
* placed in at simplex */
for (iatom=0; iatom<thee->natom; iatom++) {
if (thee->nqsm[iatom] == 0) {
Vnm_print(2, "Vcsm_init: Atom %d not placed in simplex!\n", iatom);
VASSERT(0);
}
}
/* Allocate the appropriate amount of space for each entry in the
* charge-simplex map and clear the counter for re-use in assignment */
for (iatom=0; iatom<thee->natom; iatom++) {
thee->qsm[iatom] = Vmem_malloc(thee->vmem, (thee->nqsm)[iatom],
sizeof(int));
VASSERT(thee->qsm[iatom] != VNULL);
thee->nqsm[iatom] = 0;
}
/* Assign the simplices to atoms */
for (isimp=0; isimp<thee->nsimp; isimp++) {
for (iatom=0; iatom<thee->nsqm[isimp]; iatom++) {
jatom = thee->sqm[isimp][iatom];
thee->qsm[jatom][thee->nqsm[jatom]] = isimp;
thee->nqsm[jatom]++;
}
}
thee->initFlag = 1;
}
/* ///////////////////////////////////////////////////////////////////////////
// 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;
}
VPRIVATE int treesetup(Vgreen *thee) {
#ifdef HAVE_TREE
double dist_tol = FMM_DIST_TOL;
int iflag = FMM_IFLAG;
double order = FMM_ORDER;
int theta = FMM_THETA;
int shrink = FMM_SHRINK;
int maxparnode = FMM_MAXPARNODE;
int minlevel = FMM_MINLEVEL;
int maxlevel = FMM_MAXLEVEL;
int level = 0;
int one = 1;
Vatom *atom;
double xyzminmax[6], *pos;
int i;
/* Set up particle arrays with atomic coordinates and charges */
Vnm_print(0, "treesetup: Initializing FMM particle arrays...\n");
thee->np = Valist_getNumberAtoms(thee->alist);
thee->xp = VNULL;
thee->xp = (double *)Vmem_malloc(thee->vmem, thee->np, sizeof(double));
if (thee->xp == VNULL) {
Vnm_print(2, "Vgreen_ctor2: Failed to allocate %d*sizeof(double)!\n",
thee->np);
return 0;
}
thee->yp = VNULL;
thee->yp = (double *)Vmem_malloc(thee->vmem, thee->np, sizeof(double));
if (thee->yp == VNULL) {
Vnm_print(2, "Vgreen_ctor2: Failed to allocate %d*sizeof(double)!\n",
thee->np);
return 0;
}
thee->zp = VNULL;
thee->zp = (double *)Vmem_malloc(thee->vmem, thee->np, sizeof(double));
if (thee->zp == VNULL) {
Vnm_print(2, "Vgreen_ctor2: Failed to allocate %d*sizeof(double)!\n",
thee->np);
return 0;
}
thee->qp = VNULL;
thee->qp = (double *)Vmem_malloc(thee->vmem, thee->np, sizeof(double));
if (thee->qp == VNULL) {
Vnm_print(2, "Vgreen_ctor2: Failed to allocate %d*sizeof(double)!\n",
thee->np);
return 0;
}
for (i=0; i<thee->np; i++) {
atom = Valist_getAtom(thee->alist, i);
pos = Vatom_getPosition(atom);
thee->xp[i] = pos[0];
thee->yp[i] = pos[1];
thee->zp[i] = pos[2];
thee->qp[i] = Vatom_getCharge(atom);
}
Vnm_print(0, "treesetup: Setting things up...\n");
F77SETUP(thee->xp, thee->yp, thee->zp, &(thee->np), &order, &theta, &iflag,
&dist_tol, xyzminmax, &(thee->np));
Vnm_print(0, "treesetup: Initializing levels...\n");
F77INITLEVELS(&minlevel, &maxlevel);
Vnm_print(0, "treesetup: Creating tree...\n");
F77CREATE_TREE(&one, &(thee->np), thee->xp, thee->yp, thee->zp, thee->qp,
&shrink, &maxparnode, xyzminmax, &level, &(thee->np));
return 1;
#else /* ifdef HAVE_TREE */
Vnm_print(2, "treesetup: Error! APBS not linked with treecode!\n");
return 0;
#endif /* ifdef HAVE_TREE */
}