int
find_gb_anglelength(t_params *plist,int ai,int ak, real *length)
{
int i,j,a1,a2,a3;
real r12,r23,a123;
int found=0;
int status,status1,status2;
r12 = r23 = 0;
for(i=0;i<F_NRE && !found;i++)
{
if(IS_ANGLE(i))
{
for(j=0;j<plist[i].nr; j++)
{
a1=plist[i].param[j].a[0];
a2=plist[i].param[j].a[1];
a3=plist[i].param[j].a[2];
/* We dont care what the middle atom is, but use it below */
if( (a1==ai && a3==ak) || (a1==ak && a3==ai) )
{
/* Equilibrium bond distance */
a123 = plist[i].param[j].c[0];
/* Use middle atom to find reference distances r12 and r23 */
status1 = find_gb_bondlength(plist,a1,a2,&r12);
status2 = find_gb_bondlength(plist,a2,a3,&r23);
if(status1==0 && status2==0)
{
/* cosine theorem to get r13 */
*length=sqrt(r12*r12+r23*r23-(2*r12*r23*cos(a123/RAD2DEG)));
found=1;
}
}
}
}
}
status = !found;
return status;
}
/* A return value of 0 means parameters were assigned successfully,
* returning -1 means this is an all-zero interaction that should not be added.
*/
static int
assign_param(t_functype ftype, t_iparams *newparam,
real old[MAXFORCEPARAM], int comb, double reppow)
{
int i, j;
gmx_bool all_param_zero = TRUE;
/* Set to zero */
for (j = 0; (j < MAXFORCEPARAM); j++)
{
newparam->generic.buf[j] = 0.0;
/* If all parameters are zero we might not add some interaction types (selected below).
* We cannot apply this to ALL interactions, since many have valid reasons for having
* zero parameters (e.g. an index to a Cmap interaction, or LJ parameters), but
* we use it for angles and torsions that are typically generated automatically.
*/
all_param_zero = (all_param_zero == TRUE) && fabs(old[j]) < GMX_REAL_MIN;
}
if (all_param_zero == TRUE)
{
if (IS_ANGLE(ftype) || IS_RESTRAINT_TYPE(ftype) || ftype == F_IDIHS ||
ftype == F_PDIHS || ftype == F_PIDIHS || ftype == F_RBDIHS || ftype == F_FOURDIHS)
{
return -1;
}
}
switch (ftype)
{
case F_G96ANGLES:
/* Post processing of input data: store cosine iso angle itself */
newparam->harmonic.rA = cos(old[0]*DEG2RAD);
newparam->harmonic.krA = old[1];
newparam->harmonic.rB = cos(old[2]*DEG2RAD);
newparam->harmonic.krB = old[3];
break;
case F_G96BONDS:
/* Post processing of input data: store square of length itself */
newparam->harmonic.rA = gmx::square(old[0]);
newparam->harmonic.krA = old[1];
newparam->harmonic.rB = gmx::square(old[2]);
newparam->harmonic.krB = old[3];
break;
case F_FENEBONDS:
newparam->fene.bm = old[0];
newparam->fene.kb = old[1];
break;
case F_RESTRBONDS:
newparam->restraint.lowA = old[0];
newparam->restraint.up1A = old[1];
newparam->restraint.up2A = old[2];
newparam->restraint.kA = old[3];
newparam->restraint.lowB = old[4];
newparam->restraint.up1B = old[5];
newparam->restraint.up2B = old[6];
newparam->restraint.kB = old[7];
break;
case F_TABBONDS:
case F_TABBONDSNC:
case F_TABANGLES:
case F_TABDIHS:
newparam->tab.table = round_check(old[0], 0, ftype, "table index");
newparam->tab.kA = old[1];
newparam->tab.kB = old[3];
break;
case F_CROSS_BOND_BONDS:
newparam->cross_bb.r1e = old[0];
newparam->cross_bb.r2e = old[1];
newparam->cross_bb.krr = old[2];
break;
case F_CROSS_BOND_ANGLES:
newparam->cross_ba.r1e = old[0];
newparam->cross_ba.r2e = old[1];
newparam->cross_ba.r3e = old[2];
newparam->cross_ba.krt = old[3];
break;
case F_UREY_BRADLEY:
newparam->u_b.thetaA = old[0];
newparam->u_b.kthetaA = old[1];
newparam->u_b.r13A = old[2];
newparam->u_b.kUBA = old[3];
newparam->u_b.thetaB = old[4];
newparam->u_b.kthetaB = old[5];
newparam->u_b.r13B = old[6];
newparam->u_b.kUBB = old[7];
break;
case F_QUARTIC_ANGLES:
newparam->qangle.theta = old[0];
for (i = 0; i < 5; i++)
{
newparam->qangle.c[i] = old[i+1];
}
break;
case F_LINEAR_ANGLES:
newparam->linangle.aA = old[0];
newparam->linangle.klinA = old[1];
newparam->linangle.aB = old[2];
newparam->linangle.klinB = old[3];
break;
case F_BONDS:
case F_ANGLES:
case F_HARMONIC:
case F_IDIHS:
newparam->harmonic.rA = old[0];
newparam->harmonic.krA = old[1];
newparam->harmonic.rB = old[2];
newparam->harmonic.krB = old[3];
break;
case F_RESTRANGLES:
newparam->harmonic.rA = old[0];
newparam->harmonic.krA = old[1];
break;
case F_MORSE:
newparam->morse.b0A = old[0];
newparam->morse.cbA = old[1];
newparam->morse.betaA = old[2];
newparam->morse.b0B = old[3];
newparam->morse.cbB = old[4];
newparam->morse.betaB = old[5];
break;
case F_CUBICBONDS:
newparam->cubic.b0 = old[0];
newparam->cubic.kb = old[1];
newparam->cubic.kcub = old[2];
break;
case F_CONNBONDS:
break;
case F_POLARIZATION:
newparam->polarize.alpha = old[0];
break;
case F_ANHARM_POL:
newparam->anharm_polarize.alpha = old[0];
newparam->anharm_polarize.drcut = old[1];
newparam->anharm_polarize.khyp = old[2];
break;
case F_WATER_POL:
newparam->wpol.al_x = old[0];
newparam->wpol.al_y = old[1];
newparam->wpol.al_z = old[2];
newparam->wpol.rOH = old[3];
newparam->wpol.rHH = old[4];
newparam->wpol.rOD = old[5];
break;
case F_THOLE_POL:
newparam->thole.a = old[0];
newparam->thole.alpha1 = old[1];
newparam->thole.alpha2 = old[2];
if ((old[1] > 0) && (old[2] > 0))
{
newparam->thole.rfac = old[0]*gmx::invsixthroot(old[1]*old[2]);
}
else
{
newparam->thole.rfac = 1;
}
break;
case F_BHAM:
newparam->bham.a = old[0];
newparam->bham.b = old[1];
newparam->bham.c = old[2];
break;
case F_LJ14:
set_ljparams(comb, reppow, old[0], old[1], &newparam->lj14.c6A, &newparam->lj14.c12A);
set_ljparams(comb, reppow, old[2], old[3], &newparam->lj14.c6B, &newparam->lj14.c12B);
break;
case F_LJC14_Q:
newparam->ljc14.fqq = old[0];
newparam->ljc14.qi = old[1];
newparam->ljc14.qj = old[2];
set_ljparams(comb, reppow, old[3], old[4], &newparam->ljc14.c6, &newparam->ljc14.c12);
break;
case F_LJC_PAIRS_NB:
newparam->ljcnb.qi = old[0];
newparam->ljcnb.qj = old[1];
set_ljparams(comb, reppow, old[2], old[3], &newparam->ljcnb.c6, &newparam->ljcnb.c12);
break;
case F_LJ:
set_ljparams(comb, reppow, old[0], old[1], &newparam->lj.c6, &newparam->lj.c12);
break;
case F_PDIHS:
case F_PIDIHS:
case F_ANGRES:
case F_ANGRESZ:
newparam->pdihs.phiA = old[0];
newparam->pdihs.cpA = old[1];
/* Change 20100720: Amber occasionally uses negative multiplicities (mathematically OK),
* so I have changed the lower limit to -99 /EL
*/
newparam->pdihs.phiB = old[3];
newparam->pdihs.cpB = old[4];
/* If both force constants are zero there is no interaction. Return -1 to signal
* this entry should NOT be added.
*/
if (fabs(newparam->pdihs.cpA) < GMX_REAL_MIN && fabs(newparam->pdihs.cpB) < GMX_REAL_MIN)
{
return -1;
}
newparam->pdihs.mult = round_check(old[2], -99, ftype, "multiplicity");
break;
case F_RESTRDIHS:
newparam->pdihs.phiA = old[0];
newparam->pdihs.cpA = old[1];
break;
case F_POSRES:
newparam->posres.fcA[XX] = old[0];
newparam->posres.fcA[YY] = old[1];
newparam->posres.fcA[ZZ] = old[2];
newparam->posres.fcB[XX] = old[3];
newparam->posres.fcB[YY] = old[4];
newparam->posres.fcB[ZZ] = old[5];
newparam->posres.pos0A[XX] = old[6];
newparam->posres.pos0A[YY] = old[7];
newparam->posres.pos0A[ZZ] = old[8];
newparam->posres.pos0B[XX] = old[9];
newparam->posres.pos0B[YY] = old[10];
newparam->posres.pos0B[ZZ] = old[11];
break;
case F_FBPOSRES:
newparam->fbposres.geom = round_check(old[0], 0, ftype, "geometry");
if (!(newparam->fbposres.geom > efbposresZERO && newparam->fbposres.geom < efbposresNR))
{
gmx_fatal(FARGS, "Invalid geometry for flat-bottomed position restraint.\n"
"Expected number between 1 and %d. Found %d\n", efbposresNR-1,
newparam->fbposres.geom);
}
newparam->fbposres.r = old[1];
newparam->fbposres.k = old[2];
newparam->fbposres.pos0[XX] = old[3];
newparam->fbposres.pos0[YY] = old[4];
newparam->fbposres.pos0[ZZ] = old[5];
break;
case F_DISRES:
newparam->disres.label = round_check(old[0], 0, ftype, "label");
newparam->disres.type = round_check(old[1], 1, ftype, "type'");
newparam->disres.low = old[2];
newparam->disres.up1 = old[3];
newparam->disres.up2 = old[4];
newparam->disres.kfac = old[5];
break;
case F_ORIRES:
newparam->orires.ex = round_check(old[0], 1, ftype, "experiment") - 1;
newparam->orires.label = round_check(old[1], 1, ftype, "label");
newparam->orires.power = round_check(old[2], 0, ftype, "power");
newparam->orires.c = old[3];
newparam->orires.obs = old[4];
newparam->orires.kfac = old[5];
break;
case F_DIHRES:
newparam->dihres.phiA = old[0];
newparam->dihres.dphiA = old[1];
newparam->dihres.kfacA = old[2];
newparam->dihres.phiB = old[3];
newparam->dihres.dphiB = old[4];
newparam->dihres.kfacB = old[5];
break;
case F_RBDIHS:
for (i = 0; (i < NR_RBDIHS); i++)
{
newparam->rbdihs.rbcA[i] = old[i];
newparam->rbdihs.rbcB[i] = old[NR_RBDIHS+i];
}
break;
case F_CBTDIHS:
for (i = 0; (i < NR_CBTDIHS); i++)
{
newparam->cbtdihs.cbtcA[i] = old[i];
}
break;
case F_FOURDIHS:
/* Read the dihedral parameters to temporary arrays,
* and convert them to the computationally faster
* Ryckaert-Bellemans form.
*/
/* Use conversion formula for OPLS to Ryckaert-Bellemans: */
newparam->rbdihs.rbcA[0] = old[1]+0.5*(old[0]+old[2]);
newparam->rbdihs.rbcA[1] = 0.5*(3.0*old[2]-old[0]);
newparam->rbdihs.rbcA[2] = 4.0*old[3]-old[1];
newparam->rbdihs.rbcA[3] = -2.0*old[2];
newparam->rbdihs.rbcA[4] = -4.0*old[3];
newparam->rbdihs.rbcA[5] = 0.0;
newparam->rbdihs.rbcB[0] = old[NR_FOURDIHS+1]+0.5*(old[NR_FOURDIHS+0]+old[NR_FOURDIHS+2]);
newparam->rbdihs.rbcB[1] = 0.5*(3.0*old[NR_FOURDIHS+2]-old[NR_FOURDIHS+0]);
newparam->rbdihs.rbcB[2] = 4.0*old[NR_FOURDIHS+3]-old[NR_FOURDIHS+1];
newparam->rbdihs.rbcB[3] = -2.0*old[NR_FOURDIHS+2];
newparam->rbdihs.rbcB[4] = -4.0*old[NR_FOURDIHS+3];
newparam->rbdihs.rbcB[5] = 0.0;
break;
case F_CONSTR:
case F_CONSTRNC:
newparam->constr.dA = old[0];
newparam->constr.dB = old[1];
break;
case F_SETTLE:
newparam->settle.doh = old[0];
newparam->settle.dhh = old[1];
break;
case F_VSITE2:
case F_VSITE3:
case F_VSITE3FD:
case F_VSITE3OUT:
case F_VSITE4FD:
case F_VSITE4FDN:
newparam->vsite.a = old[0];
newparam->vsite.b = old[1];
newparam->vsite.c = old[2];
newparam->vsite.d = old[3];
newparam->vsite.e = old[4];
newparam->vsite.f = old[5];
break;
case F_VSITE3FAD:
newparam->vsite.a = old[1] * cos(DEG2RAD * old[0]);
newparam->vsite.b = old[1] * sin(DEG2RAD * old[0]);
newparam->vsite.c = old[2];
newparam->vsite.d = old[3];
newparam->vsite.e = old[4];
newparam->vsite.f = old[5];
break;
case F_VSITEN:
newparam->vsiten.n = round_check(old[0], 1, ftype, "number of atoms");
newparam->vsiten.a = old[1];
break;
case F_CMAP:
newparam->cmap.cmapA = static_cast<int>(old[0]);
newparam->cmap.cmapB = static_cast<int>(old[1]);
break;
case F_GB12:
case F_GB13:
case F_GB14:
newparam->gb.sar = old[0];
newparam->gb.st = old[1];
newparam->gb.pi = old[2];
newparam->gb.gbr = old[3];
newparam->gb.bmlt = old[4];
break;
default:
gmx_fatal(FARGS, "unknown function type %d in %s line %d",
ftype, __FILE__, __LINE__);
}
return 0;
}
