bool new_data(t_xrama *xr)
{
if (!read_next_x(xr->traj,&xr->t,xr->natoms,xr->x,xr->box))
return FALSE;
calc_dihs(xr);
return TRUE;
}
gmx_bool new_data(t_xrama *xr)
{
if (!read_next_x(xr->oenv, xr->traj, &xr->t, xr->x, xr->box))
{
return FALSE;
}
calc_dihs(xr);
return TRUE;
}
void init_rama(char *infile,char *topfile,t_xrama *xr)
{
static t_topology *top;
real t;
top=read_top(topfile);
/*get_dih2(xr,top->idef.functype,&(top->idef.bondeds),&(top->atoms));*/
get_dih(xr,&(top->atoms));
get_dih_props(xr,&(top->idef));
xr->natoms=read_first_x(&xr->traj,infile,&t,&(xr->x),xr->box);
xr->idef=&(top->idef);
min_max(xr);
calc_dihs(xr);
}
t_topology *init_rama(char *infile,char *topfile,t_xrama *xr,int mult)
{
t_topology *top;
int ePBC;
real t;
top=read_top(topfile,&xr->ePBC);
/*get_dih2(xr,top->idef.functype,&(top->idef.bondeds),&(top->atoms));*/
get_dih(xr,&(top->atoms));
get_dih_props(xr,&(top->idef),mult);
xr->natoms=read_first_x(&xr->traj,infile,&t,&(xr->x),xr->box);
xr->idef=&(top->idef);
min_max(xr);
calc_dihs(xr);
return top;
}
void read_ang_dih(const char *trj_fn,
gmx_bool bAngles, gmx_bool bSaveAll, gmx_bool bRb, gmx_bool bPBC,
int maxangstat, int angstat[],
int *nframes, real **time,
int isize, atom_id index[],
real **trans_frac,
real **aver_angle,
real *dih[],
const output_env_t oenv)
{
t_pbc *pbc;
t_trxstatus *status;
int i, angind, natoms, total, teller;
int nangles, n_alloc;
real t, fraction, pifac, aa, angle;
real *angles[2];
matrix box;
rvec *x;
int cur = 0;
#define prev (1-cur)
snew(pbc, 1);
natoms = read_first_x(oenv, &status, trj_fn, &t, &x, box);
if (bAngles)
{
nangles = isize/3;
pifac = M_PI;
}
else
{
nangles = isize/4;
pifac = 2.0*M_PI;
}
snew(angles[cur], nangles);
snew(angles[prev], nangles);
/* Start the loop over frames */
total = 0;
teller = 0;
n_alloc = 0;
*time = NULL;
*trans_frac = NULL;
*aver_angle = NULL;
do
{
if (teller >= n_alloc)
{
n_alloc += 100;
if (bSaveAll)
{
for (i = 0; (i < nangles); i++)
{
srenew(dih[i], n_alloc);
}
}
srenew(*time, n_alloc);
srenew(*trans_frac, n_alloc);
srenew(*aver_angle, n_alloc);
}
(*time)[teller] = t;
if (pbc)
{
set_pbc(pbc, -1, box);
}
if (bAngles)
{
calc_angles(pbc, isize, index, angles[cur], x);
}
else
{
calc_dihs(pbc, isize, index, angles[cur], x);
/* Trans fraction */
fraction = calc_fraction(angles[cur], nangles);
(*trans_frac)[teller] = fraction;
/* Change Ryckaert-Bellemans dihedrals to polymer convention
* Modified 990913 by Erik:
* We actually shouldn't change the convention, since it's
* calculated from polymer above, but we change the intervall
* from [-180,180] to [0,360].
*/
if (bRb)
{
for (i = 0; (i < nangles); i++)
{
if (angles[cur][i] <= 0.0)
{
angles[cur][i] += 2*M_PI;
}
}
}
/* Periodicity in dihedral space... */
if (bPBC)
{
for (i = 0; (i < nangles); i++)
{
real dd = angles[cur][i];
angles[cur][i] = atan2(sin(dd), cos(dd));
}
}
else
{
if (teller > 1)
{
for (i = 0; (i < nangles); i++)
{
while (angles[cur][i] <= angles[prev][i] - M_PI)
{
angles[cur][i] += 2*M_PI;
}
while (angles[cur][i] > angles[prev][i] + M_PI)
{
angles[cur][i] -= 2*M_PI;
}
}
}
}
}
/* Average angles */
aa = 0;
for (i = 0; (i < nangles); i++)
{
aa = aa+angles[cur][i];
/* angle in rad / 2Pi * max determines bin. bins go from 0 to maxangstat,
even though scale goes from -pi to pi (dihedral) or -pi/2 to pi/2
(angle) Basically: translate the x-axis by Pi. Translate it back by
-Pi when plotting.
*/
angle = angles[cur][i];
if (!bAngles)
{
while (angle < -M_PI)
{
angle += 2*M_PI;
}
while (angle >= M_PI)
{
angle -= 2*M_PI;
}
angle += M_PI;
}
/* Update the distribution histogram */
angind = (int) ((angle*maxangstat)/pifac + 0.5);
if (angind == maxangstat)
{
angind = 0;
}
if ( (angind < 0) || (angind >= maxangstat) )
{
/* this will never happen */
gmx_fatal(FARGS, "angle (%f) index out of range (0..%d) : %d\n",
angle, maxangstat, angind);
}
angstat[angind]++;
if (angind == maxangstat)
{
fprintf(stderr, "angle %d fr %d = %g\n", i, cur, angle);
}
total++;
}
/* average over all angles */
(*aver_angle)[teller] = (aa/nangles);
/* this copies all current dih. angles to dih[i], teller is frame */
if (bSaveAll)
{
for (i = 0; i < nangles; i++)
{
dih[i][teller] = angles[cur][i];
}
}
/* Swap buffers */
cur = prev;
/* Increment loop counter */
teller++;
}
while (read_next_x(oenv, status, &t, x, box));
close_trj(status);
sfree(x);
sfree(angles[cur]);
sfree(angles[prev]);
*nframes = teller;
}
