real ca_phi(int gnx, int index[], rvec x[])
/* Assume we have a list of Calpha atoms only! */
{
real phi, phitot;
int i, ai, aj, ak, al, t1, t2, t3;
rvec r_ij, r_kj, r_kl, m, n;
real sign;
if (gnx <= 4)
{
return 0;
}
phitot = 0;
for (i = 0; (i < gnx-4); i++)
{
ai = index[i+0];
aj = index[i+1];
ak = index[i+2];
al = index[i+3];
phi = RAD2DEG*
dih_angle(x[ai], x[aj], x[ak], x[al], NULL,
r_ij, r_kj, r_kl, m, n,
&sign, &t1, &t2, &t3);
phitot += phi;
}
return (phitot/(gnx-4.0));
}
void calc_hxprops(int nres, t_bb bb[], rvec x[])
{
int i, ao, an, t1, t2, t3;
rvec dx, r_ij, r_kj, r_kl, m, n;
real sign;
for (i = 0; (i < nres); i++)
{
ao = bb[i].O;
bb[i].d4 = bb[i].d3 = bb[i].d5 = 0;
if (i < nres-3)
{
an = bb[i+3].N;
rvec_sub(x[ao], x[an], dx);
bb[i].d3 = norm(dx);
}
if (i < nres-4)
{
an = bb[i+4].N;
rvec_sub(x[ao], x[an], dx);
bb[i].d4 = norm(dx);
}
if (i < nres-5)
{
an = bb[i+5].N;
rvec_sub(x[ao], x[an], dx);
bb[i].d5 = norm(dx);
}
bb[i].phi = RAD2DEG*
dih_angle(x[bb[i].Cprev], x[bb[i].N], x[bb[i].CA], x[bb[i].C], NULL,
r_ij, r_kj, r_kl, m, n,
&sign, &t1, &t2, &t3);
bb[i].psi = RAD2DEG*
dih_angle(x[bb[i].N], x[bb[i].CA], x[bb[i].C], x[bb[i].Nnext], NULL,
r_ij, r_kj, r_kl, m, n,
&sign, &t1, &t2, &t3);
bb[i].pprms2 = sqr(bb[i].phi-PHI_AHX)+sqr(bb[i].psi-PSI_AHX);
bb[i].jcaha +=
1.4*std::sin((bb[i].psi+138.0)*DEG2RAD) -
4.1*std::cos(2.0*DEG2RAD*(bb[i].psi+138.0)) +
2.0*std::cos(2.0*DEG2RAD*(bb[i].phi+30.0));
}
}
static void calc_dihs(FILE *log,t_pbc *pbc,
int n4,atom_id index[],real ang[],rvec x_s[])
{
int i,ix,t1,t2,t3;
rvec r_ij,r_kj,r_kl,m,n;
real cos_phi,sign,aaa;
for(i=ix=0; (ix<n4); i++,ix+=4) {
aaa=dih_angle(x_s[index[ix]],x_s[index[ix+1]],x_s[index[ix+2]],
x_s[index[ix+3]],pbc,
r_ij,r_kj,r_kl,m,n,
&cos_phi,&sign,&t1,&t2,&t3);
ang[i]=aaa; /* not taking into account ryckaert bellemans yet */
}
}
void calc_angles_dihs(t_params *ang, t_params *dih, rvec x[], gmx_bool bPBC,
matrix box)
{
int i, ai, aj, ak, al, t1, t2, t3;
rvec r_ij, r_kj, r_kl, m, n;
real sign, th, costh, ph;
t_pbc pbc;
if (bPBC)
{
set_pbc(&pbc, epbcXYZ, box);
}
if (debug)
{
pr_rvecs(debug, 0, "X2TOP", box, DIM);
}
for (i = 0; (i < ang->nr); i++)
{
ai = ang->param[i].AI;
aj = ang->param[i].AJ;
ak = ang->param[i].AK;
th = RAD2DEG*bond_angle(x[ai], x[aj], x[ak], bPBC ? &pbc : NULL,
r_ij, r_kj, &costh, &t1, &t2);
if (debug)
{
fprintf(debug, "X2TOP: ai=%3d aj=%3d ak=%3d r_ij=%8.3f r_kj=%8.3f th=%8.3f\n",
ai, aj, ak, norm(r_ij), norm(r_kj), th);
}
ang->param[i].C0 = th;
}
for (i = 0; (i < dih->nr); i++)
{
ai = dih->param[i].AI;
aj = dih->param[i].AJ;
ak = dih->param[i].AK;
al = dih->param[i].AL;
ph = RAD2DEG*dih_angle(x[ai], x[aj], x[ak], x[al], bPBC ? &pbc : NULL,
r_ij, r_kj, r_kl, m, n, &sign, &t1, &t2, &t3);
if (debug)
{
fprintf(debug, "X2TOP: ai=%3d aj=%3d ak=%3d al=%3d r_ij=%8.3f r_kj=%8.3f r_kl=%8.3f ph=%8.3f\n",
ai, aj, ak, al, norm(r_ij), norm(r_kj), norm(r_kl), ph);
}
dih->param[i].C0 = ph;
}
}
static void calc_dihs(struct t_pbc *pbc,
int n4, const int index[], real ang[], rvec x_s[])
{
int i, ix, t1, t2, t3;
rvec r_ij, r_kj, r_kl, m, n;
real aaa;
for (i = ix = 0; (ix < n4); i++, ix += 4)
{
aaa = dih_angle(x_s[index[ix]], x_s[index[ix+1]], x_s[index[ix+2]],
x_s[index[ix+3]], pbc,
r_ij, r_kj, r_kl, m, n,
&t1, &t2, &t3);
ang[i] = aaa; /* not taking into account ryckaert bellemans yet */
}
}
static void calc_dihs(t_xrama *xr)
{
int i;
rvec r_ij,r_kj,r_kl,m,n;
real cos_phi,sign;
t_dih *dd;
rm_pbc(xr->idef,xr->natoms,xr->box,xr->x,xr->x);
for(i=0; (i<xr->ndih); i++) {
dd=&(xr->dih[i]);
dd->ang=dih_angle(xr->box,
xr->x[dd->ai[0]],xr->x[dd->ai[1]],
xr->x[dd->ai[2]],xr->x[dd->ai[3]],
r_ij,r_kj,r_kl,m,n,&cos_phi,&sign);
}
}
static void calc_dihs(t_xrama *xr)
{
int i, t1, t2, t3;
rvec r_ij, r_kj, r_kl, m, n;
t_dih *dd;
gmx_rmpbc_t gpbc = nullptr;
gpbc = gmx_rmpbc_init(xr->idef, xr->ePBC, xr->natoms);
gmx_rmpbc(gpbc, xr->natoms, xr->box, xr->x);
gmx_rmpbc_done(gpbc);
for (i = 0; (i < xr->ndih); i++)
{
dd = &(xr->dih[i]);
dd->ang = dih_angle(xr->x[dd->ai[0]], xr->x[dd->ai[1]],
xr->x[dd->ai[2]], xr->x[dd->ai[3]],
nullptr,
r_ij, r_kj, r_kl, m, n, &t1, &t2, &t3);
}
}
real ta_dihres(int nfa,const t_iatom forceatoms[],const t_iparams ip[],
const rvec x[],rvec f[],rvec fshift[],
const t_pbc *pbc,const t_graph *g,
real lambda,real *dvdlambda,
const t_mdatoms *md,t_fcdata *fcd,
int *ddgatindex)
{
real vtot = 0;
int ai,aj,ak,al,i,k,type,typep,label,power,t1,t2,t3;
real phi0,phi,ddphi,ddp,dp,dp2,dphi,kfac,cos_phi,sign,d2r,fc;
rvec r_ij,r_kj,r_kl,m,n;
fc = fcd->dihre_fc;
d2r = DEG2RAD;
k = 0;
for(i=0; (i<nfa); ) {
type = forceatoms[i++];
ai = forceatoms[i++];
aj = forceatoms[i++];
ak = forceatoms[i++];
al = forceatoms[i++];
phi0 = ip[type].dihres.phi*d2r;
dphi = ip[type].dihres.dphi*d2r;
kfac = ip[type].dihres.kfac*fc;
power = ip[type].dihres.power;
label = ip[type].dihres.label;
phi = dih_angle(x[ai],x[aj],x[ak],x[al],pbc,r_ij,r_kj,r_kl,m,n,
&cos_phi,&sign,&t1,&t2,&t3);
/* 84 flops */
if (debug)
fprintf(debug,"dihres[%d]: %d %d %d %d : phi=%f, dphi=%f, kfac=%f, power=%d, label=%d\n",
k++,ai,aj,ak,al,phi,dphi,kfac,power,label);
/* phi can jump if phi0 is close to Pi/-Pi, which will cause huge
* force changes if we just apply a normal harmonic.
* Instead, we first calculate phi-phi0 and take it modulo (-Pi,Pi).
* This means we will never have the periodicity problem, unless
* the dihedral is Pi away from phiO, which is very unlikely due to
* the potential.
*/
dp = phi-phi0;
if (fabs(dp) > dphi) {
/* dp cannot be outside (-2*pi,2*pi) */
if (dp >= M_PI)
dp -= 2*M_PI;
else if(dp < -M_PI)
dp += 2*M_PI;
if (dp > dphi)
ddp = dp-dphi;
else if (dp < -dphi)
ddp = dp+dphi;
else
ddp = 0;
if (ddp != 0.0) {
vtot += 0.5*kfac*ddp*ddp;
ddphi = kfac*ddp;
do_dih_fup(ai,aj,ak,al,ddphi,r_ij,r_kj,r_kl,m,n,
f,fshift,pbc,g,x,t1,t2,t3); /* 112 */
}
}
}
return vtot;
}
void do_gkr(t_gkrbin *gb,int ncos,int *ngrp,int *molindex[],
int mindex[],rvec x[],rvec mu[],
int ePBC,matrix box,t_atom *atom,int *nAtom)
{
static rvec *xcm[2] = { NULL, NULL};
int gi,gj,j0,j1,i,j,k,n,index,grp0,grp1;
real qtot,q,r2,cosa,rr,phi;
rvec dx;
t_pbc pbc;
for(n=0; (n<ncos); n++) {
if (!xcm[n])
snew(xcm[n],ngrp[n]);
for(i=0; (i<ngrp[n]); i++) {
/* Calculate center of mass of molecule */
gi = molindex[n][i];
j0 = mindex[gi];
if (nAtom[n] > 0)
copy_rvec(x[j0+nAtom[n]-1],xcm[n][i]);
else {
j1 = mindex[gi+1];
clear_rvec(xcm[n][i]);
qtot = 0;
for(j=j0; j<j1; j++) {
q = fabs(atom[j].q);
qtot += q;
for(k=0; k<DIM; k++)
xcm[n][i][k] += q*x[j][k];
}
svmul(1/qtot,xcm[n][i],xcm[n][i]);
}
}
}
set_pbc(&pbc,ePBC,box);
grp0 = 0;
grp1 = ncos-1;
for(i=0; i<ngrp[grp0]; i++) {
gi = molindex[grp0][i];
j0 = (ncos == 2) ? 0 : i+1;
for(j=j0; j<ngrp[grp1]; j++) {
gj = molindex[grp1][j];
if ((iprod(mu[gi],mu[gi]) > 0) && (iprod(mu[gj],mu[gj]) > 0)) {
/* Compute distance between molecules including PBC */
pbc_dx(&pbc,xcm[grp0][i],xcm[grp1][j],dx);
rr = norm(dx);
if (gb->bPhi) {
rvec xi,xj,xk,xl;
rvec r_ij,r_kj,r_kl,mm,nn;
real sign;
int t1,t2,t3;
copy_rvec(xcm[grp0][i],xj);
copy_rvec(xcm[grp1][j],xk);
rvec_add(xj,mu[gi],xi);
rvec_add(xk,mu[gj],xl);
phi = dih_angle(xi,xj,xk,xl,&pbc,
r_ij,r_kj,r_kl,mm,nn, /* out */
&sign,&t1,&t2,&t3);
cosa = cos(phi);
}
else {
cosa = cos_angle(mu[gi],mu[gj]);
phi = 0;
}
if (debug || (cosa != cosa)) {
fprintf(debug ? debug : stderr,
"mu[%d] = %5.2f %5.2f %5.2f |mi| = %5.2f, mu[%d] = %5.2f %5.2f %5.2f |mj| = %5.2f rr = %5.2f cosa = %5.2f\n",
gi,mu[gi][XX],mu[gi][YY],mu[gi][ZZ],norm(mu[gi]),
gj,mu[gj][XX],mu[gj][YY],mu[gj][ZZ],norm(mu[gj]),
rr,cosa);
}
add2gkr(gb,rr,cosa,phi);
}
}
}
}
