static void constr_dum3OUT(rvec xi,rvec xj,rvec xk,rvec x,real a,real b,real c)
{
rvec xij,xik,temp;
rvec_sub(xj,xi,xij);
rvec_sub(xk,xi,xik);
oprod(xij,xik,temp);
/* 15 Flops */
x[XX] = xi[XX] + a*xij[XX] + b*xik[XX] + c*temp[XX];
x[YY] = xi[YY] + a*xij[YY] + b*xik[YY] + c*temp[YY];
x[ZZ] = xi[ZZ] + a*xij[ZZ] + b*xik[ZZ] + c*temp[ZZ];
/* 18 Flops */
/* TOTAL: 33 flops */
}
void calc_h_pos(int nht, rvec xa[], rvec xh[])
{
#define alfaH (DEG2RAD*109.5)
#define distH 0.1
#define alfaCOM (DEG2RAD*117)
#define alfaCO (DEG2RAD*121)
#define alfaCOA (DEG2RAD*115)
#define distO 0.123
#define distOA 0.125
#define distOM 0.136
rvec sa,sb,sij;
real s6,rij,ra,rb,xd;
int d;
s6=0.5*sqrt(3.e0);
/* common work for constructing one, two or three dihedral hydrogens */
switch (nht) {
case 2:
case 3:
case 4:
case 8:
case 9:
rij = 0.e0;
for(d=0; (d<DIM); d++) {
xd = xAJ[d];
sij[d] = xAI[d]-xd;
sb[d] = xd-xAK[d];
rij += sqr(sij[d]);
}
rij = sqrt(rij);
sa[XX] = sij[YY]*sb[ZZ]-sij[ZZ]*sb[YY];
sa[YY] = sij[ZZ]*sb[XX]-sij[XX]*sb[ZZ];
sa[ZZ] = sij[XX]*sb[YY]-sij[YY]*sb[XX];
ra = 0.e0;
for(d=0; (d<DIM); d++) {
sij[d] = sij[d]/rij;
ra += sqr(sa[d]);
}
ra = sqrt(ra);
for(d=0; (d<DIM); d++)
sa[d] = sa[d]/ra;
sb[XX] = sa[YY]*sij[ZZ]-sa[ZZ]*sij[YY];
sb[YY] = sa[ZZ]*sij[XX]-sa[XX]*sij[ZZ];
sb[ZZ] = sa[XX]*sij[YY]-sa[YY]*sij[XX];
break;
}/* end switch */
switch (nht) {
case 1: /* construct one planar hydrogen (peptide,rings) */
rij = 0.e0;
rb = 0.e0;
for(d=0; (d<DIM); d++) {
sij[d] = xAI[d]-xAJ[d];
sb[d] = xAI[d]-xAK[d];
rij += sqr(sij[d]);
rb += sqr(sb[d]);
}
rij = sqrt(rij);
rb = sqrt(rb);
ra = 0.e0;
for(d=0; (d<DIM); d++) {
sa[d] = sij[d]/rij+sb[d]/rb;
ra += sqr(sa[d]);
}
ra = sqrt(ra);
for(d=0; (d<DIM); d++)
xH1[d] = xAI[d]+distH*sa[d]/ra;
break;
case 2: /* one single hydrogen, e.g. hydroxyl */
for(d=0; (d<DIM); d++) {
xH1[d] = xAI[d]+distH*sin(alfaH)*sb[d]-distH*cos(alfaH)*sij[d];
}
break;
case 3: /* two planar hydrogens, e.g. -NH2 */
for(d=0; (d<DIM); d++) {
xH1[d] = xAI[d]-distH*sin(alfaH)*sb[d]-distH*cos(alfaH)*sij[d];
xH2[d] = xAI[d]+distH*sin(alfaH)*sb[d]-distH*cos(alfaH)*sij[d];
}
break;
case 4: /* two or three tetrahedral hydrogens, e.g. -CH3 */
for(d=0; (d<DIM); d++) {
xH1[d] = xAI[d]+distH*sin(alfaH)*sb[d]-distH*cos(alfaH)*sij[d];
xH2[d] = ( xAI[d]
- distH*sin(alfaH)*0.5*sb[d]
+ distH*sin(alfaH)*s6*sa[d]
- distH*cos(alfaH)*sij[d] );
if ( fabs(xH3[XX]-NOTSET)>GMX_REAL_MIN &&
fabs(xH3[YY]-NOTSET)>GMX_REAL_MIN &&
fabs(xH3[ZZ]-NOTSET)>GMX_REAL_MIN )
xH3[d] = ( xAI[d]
- distH*sin(alfaH)*0.5*sb[d]
- distH*sin(alfaH)*s6*sa[d]
- distH*cos(alfaH)*sij[d] );
}
break;
case 5: { /* one tetrahedral hydrogen, e.g. C3CH */
real center;
rvec dxc;
for(d=0; (d<DIM); d++) {
center=(xAJ[d]+xAK[d]+xAL[d])/3.0;
dxc[d]=xAI[d]-center;
}
center=norm(dxc);
for(d=0; (d<DIM); d++)
xH1[d]=xAI[d]+dxc[d]*distH/center;
break;
}
case 6: { /* two tetrahedral hydrogens, e.g. C-CH2-C */
rvec rBB,rCC1,rCC2,rNN;
real bb,nn;
for(d=0; (d<DIM); d++)
rBB[d]=xAI[d]-0.5*(xAJ[d]+xAK[d]);
bb=norm(rBB);
rvec_sub(xAI,xAJ,rCC1);
rvec_sub(xAI,xAK,rCC2);
oprod(rCC1,rCC2,rNN);
nn=norm(rNN);
for(d=0; (d<DIM); d++) {
xH1[d]=xAI[d]+distH*(cos(alfaH/2.0)*rBB[d]/bb+
sin(alfaH/2.0)*rNN[d]/nn);
xH2[d]=xAI[d]+distH*(cos(alfaH/2.0)*rBB[d]/bb-
sin(alfaH/2.0)*rNN[d]/nn);
}
break;
}
case 7: /* two water hydrogens */
gen_waterhydrogen(xa, xh);
break;
case 8: /* two carboxyl oxygens, -COO- */
for(d=0; (d<DIM); d++) {
xH1[d] = xAI[d]-distOM*sin(alfaCOM)*sb[d]-distOM*cos(alfaCOM)*sij[d];
xH2[d] = xAI[d]+distOM*sin(alfaCOM)*sb[d]-distOM*cos(alfaCOM)*sij[d];
}
break;
case 9: { /* carboxyl oxygens and hydrogen, -COOH */
rvec xa2[4]; /* i,j,k,l */
/* first add two oxygens */
for(d=0; (d<DIM); d++) {
xH1[d] = xAI[d]-distO *sin(alfaCO )*sb[d]-distO *cos(alfaCO )*sij[d];
xH2[d] = xAI[d]+distOA*sin(alfaCOA)*sb[d]-distOA*cos(alfaCOA)*sij[d];
}
/* now use rule 2 to add hydrogen to 2nd oxygen */
copy_rvec(xH2, xa2[0]); /* new i = n' */
copy_rvec(xAI, xa2[1]); /* new j = i */
copy_rvec(xAJ, xa2[2]); /* new k = j */
copy_rvec(xAK, xa2[3]); /* new l = k, not used */
calc_h_pos(2, xa2, (xh+2));
break;
}
default:
fatal_error(0,"Invalid argument (%d) for nht in routine genh\n",nht);
} /* end switch */
}
void PREFIX angle_restraint(int i_c, struct mtd_data_s *mtd_data)
{
int i, j, iat, k, ix;
real myp[3][3], totmasse[3], d[3][3];
rvec rij, sij, tij;
real mod_rij, mod_sij;
real eps, sign0;
real caa, cbb, cab, ccc, sab;
real ac, Vac, bc, dVac, cos_psi, sin_psi;
totmasse[0] = totmasse[1] = totmasse[2] = 0.;
myp[0][0] = myp[0][1] = myp[0][2] = 0.;
myp[1][0] = myp[1][1] = myp[1][2] = 0.;
myp[2][0] = myp[2][1] = myp[2][2] = 0.;
k = 0;
for(j=0;j<3;j++) {
for(i=0;i<colvar.list[i_c][j];i++){
iat = colvar.cvatoms[i_c][k];
myp[j][0] += mtd_data->mass[iat]*mtd_data->pos[iat][0];
myp[j][1] += mtd_data->mass[iat]*mtd_data->pos[iat][1];
myp[j][2] += mtd_data->mass[iat]*mtd_data->pos[iat][2];
totmasse[j] += mtd_data->mass[iat];
k++;
}
myp[j][0] /= totmasse[j];
myp[j][1] /= totmasse[j];
myp[j][2] /= totmasse[j];
}
minimal_image(myp[1], myp[0], &mod_rij, rij);
minimal_image(myp[1], myp[2], &mod_sij, sij);
caa = norm2(rij);
cab = iprod(rij,sij);
cbb = norm2(sij);
oprod(rij,sij,tij);
sab = norm(tij);
ccc = 1.0/sqrt(caa*cbb);
ac = cab*ccc; // cosine of teta
Vac = acos(ac);
dVac = -ccc/sqrt(1.-ac*ac);
for(ix=0;ix<3;ix++) {
d[0][ix] = -dVac*(-cab/caa*rij[ix]+sij[ix]);
d[1][ix] = dVac*(-cab/caa*rij[ix]-cab/cbb*sij[ix]+rij[ix]+sij[ix]);
d[2][ix] = dVac*(cab/cbb*sij[ix]-rij[ix]);
}
// Now we do appropriate multiplication of the derivatives to get what we are interested in
if( colvar.doTrig[i_c]==0 ){ colvar.ss0[i_c] = Vac; }
else if( colvar.doTrig[i_c]==1 ){
cos_psi=cos( Vac );
for(i=0;i<3;++i){d[0][i]*= cos_psi; d[1][i]*= cos_psi; d[2][i]*= cos_psi;}
colvar.ss0[i_c] = sin( Vac );
}
else if( colvar.doTrig[i_c]==2 ){
sin_psi=-sin( Vac );
for(i=0;i<3;++i){d[0][i]*= sin_psi; d[1][i]*= sin_psi; d[2][i]*= sin_psi;}
colvar.ss0[i_c] = cos( Vac );
}
else{ plumed_error("No trigonometric mode defined in torsion restraint"); }
k=0;
for(j=0;j<3;j++) {
for(i=0;i<colvar.list[i_c][j];i++){
iat = colvar.cvatoms[i_c][k];
for(ix=0;ix<3;ix++) colvar.myder[i_c][k][ix] = d[j][ix]*mtd_data->mass[iat]/totmasse[j];
k++;
}
}
//colvar.ss0[i_c] = Vac;
}
