static void clust_stat(FILE *fp,int start,int end,t_pdbfile *pdbf[])
{
int i;
t_lsq ed,ef;
init_lsq(&ed);
init_lsq(&ef);
for(i=start; (i<end); i++) {
add_lsq(&ed,i-start,pdbf[i]->edocked);
add_lsq(&ef,i-start,pdbf[i]->efree);
}
fprintf(fp," <%12s> = %8.3f (+/- %6.3f)\n",etitles[FALSE],
aver_lsq(&ed),sigma_lsq(&ed));
fprintf(fp," <%12s> = %8.3f (+/- %6.3f)\n",etitles[TRUE],
aver_lsq(&ef),sigma_lsq(&ef));
done_lsq(&ed);
done_lsq(&ef);
}
real error_lsq(t_lsq *lsq)
{
return sigma_lsq(lsq)/sqrt(lsq->np);
}
static void do_bonds(FILE *log,char *fn,char *fbond,char *fdist,
int gnx,atom_id index[],
real blen,real tol,bool bAver,
t_topology *top,int ePBC,bool bAverDist)
{
#define MAXTAB 1000
FILE *out,*outd=NULL;
int *btab=NULL;
real b0=0,b1,db=0;
real bond,bav;
t_lsq b_one,*b_all=NULL;
/*real mean, mean2, sqrdev2, sigma2;
int counter;*/
rvec *x;
rvec dx;
int status,natoms;
matrix box;
real t,fac;
int bind,i,nframes,i0,i1;
t_pbc pbc;
if (!bAver) {
snew(b_all,gnx/2);
for(i=0; (i<gnx/2); i++)
init_lsq(&(b_all[i]));
}
else {
init_lsq(&b_one);
snew(btab,MAXTAB+1);
}
natoms=read_first_x(&status,fn,&t,&x,box);
if (natoms == 0)
gmx_fatal(FARGS,"No atoms in trajectory!");
if (fdist) {
outd = xvgropen(fdist,bAverDist ? "Average distance" : "Distances",
"Time (ps)","Distance (nm)");
if (!bAverDist)
make_dist_leg(outd,gnx,index,&(top->atoms));
}
nframes=0;
do {
set_pbc(&pbc,ePBC,box);
if (fdist)
fprintf(outd," %8.4f",t);
nframes++; /* count frames */
bav = 0.0;
for(i=0; (i<gnx); i+=2) {
pbc_dx(&pbc,x[index[i]],x[index[i+1]],dx);
bond = norm(dx);
if (bAverDist)
bav += bond;
else if (fdist)
fprintf(outd," %.3f",bond);
if (bAver) {
add_lsq(&b_one,t,bond);
if (db == 0) {
if (blen == -1) {
b0 = 0;
b1 = 0.2;
db = (b1-b0)/MAXTAB;
}
else {
b0 = (1.0-tol)*blen;
b1 = (1.0+tol)*blen;
db = (2.0*(b1-b0))/MAXTAB;
}
}
bind = (int)((bond-b0)/db+0.5);
if ((bind >= 0) && (bind <= MAXTAB))
btab[bind]++;
else {
/*
printf("bond: %4d-%4d bond=%10.5e, dx=(%10.5e,%10.5e,%10.5e)\n",
index[i],index[i+1],bond,dx[XX],dx[YY],dx[ZZ]);
*/
}
}
else {
add_lsq(&(b_all[i/2]),t,bond);
}
}
if (bAverDist)
fprintf(outd," %.5f",bav*2.0/gnx);
if (fdist)
fprintf(outd,"\n");
} while (read_next_x(status,&t,natoms,x,box));
close_trj(status);
if (fdist)
ffclose(outd);
/*
mean = mean / counter;
mean2 = mean2 / counter;
sqrdev2 = (mean2 - mean*mean);
sigma2 = sqrdev2*counter / (counter - 1);
*/
/* For definitions see "Weet wat je meet" */
if (bAver) {
printf("\n");
printf("Total number of samples : %d\n",
npoints_lsq(&b_one));
printf("Mean : %g\n",
aver_lsq(&b_one));
printf("Standard deviation of the distribution: %g\n",
sigma_lsq(&b_one));
printf("Standard deviation of the mean : %g\n",
error_lsq(&b_one));
out=xvgropen(fbond,"Bond Stretching Distribution",
"Bond Length (nm)","");
for(i0=0; ((i0 < MAXTAB) && (btab[i0]==0)); i0++)
;
i0=max(0,i0-1);
for(i1=MAXTAB; ((i1 > 0) && (btab[i1]==0)); i1--)
;
i1=min(MAXTAB,i1+1);
if (i0 >= i1)
gmx_fatal(FARGS,"No distribution... (i0 = %d, i1 = %d)? ? ! ! ? !",i0,i1);
fac=2.0/(nframes*gnx*db);
for(i=i0; (i<=i1); i++)
fprintf(out,"%8.5f %8.5f\n",b0+i*db,btab[i]*fac);
fclose(out);
}
else {
fprintf(log,"%5s %5s %8s %8s\n","i","j","b_aver","sigma");
for(i=0; (i<gnx/2); i++) {
fprintf(log,"%5u %5u %8.5f %8.5f\n",1+index[2*i],1+index[2*i+1],
aver_lsq(&b_all[i]),sigma_lsq(&b_all[i]));
}
}
}
