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: 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 */
}
