static int low_lsq_y_ax_b(int n, real *xr, double *xd, real yr[],
real *a, real *b, real *r, real *chi2)
{
gmx_stats_t lsq = gmx_stats_init();
int ok;
for (int i = 0; (i < n); i++)
{
double pt;
if (xd != NULL)
{
pt = xd[i];
}
else if (xr != NULL)
{
pt = xr[i];
}
else
{
gmx_incons("Either xd or xr has to be non-NULL in low_lsq_y_ax_b()");
}
if ((ok = gmx_stats_add_point(lsq, pt, yr[i], 0, 0)) != estatsOK)
{
gmx_stats_free(lsq);
return ok;
}
}
ok = gmx_stats_get_ab(lsq, elsqWEIGHT_NONE, a, b, NULL, NULL, chi2, r);
gmx_stats_free(lsq);
return ok;
}
static int low_lsq_y_ax_b(int n, real *xr, double *xd, real yr[],
real *a, real *b, real *r, real *chi2)
{
int i, ok;
gmx_stats_t lsq;
lsq = gmx_stats_init();
for (i = 0; (i < n); i++)
{
if ((ok = gmx_stats_add_point(lsq, (NULL != xd) ? xd[i] : xr[i], yr[i], 0, 0))
!= estatsOK)
{
return ok;
}
}
if ((ok = gmx_stats_get_ab(lsq, elsqWEIGHT_NONE, a, b, NULL, NULL, chi2, r)) != estatsOK)
{
return ok;
}
return estatsOK;
/*
double x,y,yx,xx,yy,sx,sy,chi2;
yx=xx=yy=sx=sy=0.0;
for (i=0; i<n; i++) {
if (xd != NULL) {
x = xd[i];
} else {
x = xr[i];
}
y = yr[i];
yx += y*x;
xx += x*x;
yy += y*y;
sx += x;
sy += y;
}
* a = (n*yx-sy*sx)/(n*xx-sx*sx);
* b = (sy-(*a)*sx)/n;
* r = sqrt((xx-sx*sx)/(yy-sy*sy));
chi2 = 0;
if (xd != NULL) {
for(i=0; i<n; i++)
chi2 += dsqr(yr[i] - ((*a)*xd[i] + (*b)));
} else {
for(i=0; i<n; i++)
chi2 += dsqr(yr[i] - ((*a)*xr[i] + (*b)));
}
if (n > 2)
return sqrt(chi2/(n-2));
else
return 0;
*/
}
static void line()
{
gmx_rng_t rng;
gmx_stats_t line;
int i, dy, ok, n = 1000;
real y, a, b, da, db, aver, sigma, error, chi2, R, rfit;
const real a0 = 0.23, b0 = 2.7;
FILE *fp;
for (dy = 0; (dy < 2); dy++)
{
rng = gmx_rng_init(13);
line = gmx_stats_init();
for (i = 0; (i < n); i++)
{
y = a0*i+b0+50*(gmx_rng_uniform_real(rng)-0.5);
if ((ok = gmx_stats_add_point(line, i, y, 0, dy*0.1)) != estatsOK)
{
fprintf(stderr, "%s\n", gmx_stats_message(ok));
}
}
/* Line with slope test */
if ((ok = gmx_stats_get_ab(line, elsqWEIGHT_NONE, &a, &b, &da, &db, &chi2, &rfit)) != estatsOK)
{
fprintf(stderr, "%s\n", gmx_stats_message(ok));
}
if ((ok = gmx_stats_get_corr_coeff(line, &R)) != estatsOK)
{
fprintf(stderr, "%s\n", gmx_stats_message(ok));
}
if (dy == 0)
{
fp = fopen("line0.xvg", "w");
}
else
{
fp = fopen("line1.xvg", "w");
}
if ((ok = gmx_stats_dump_xy(line, fp)) != estatsOK)
{
fprintf(stderr, "%s\n", gmx_stats_message(ok));
}
fclose(fp);
printf("Line with eqn. y = %gx + %g with noise%s\n", a0, b0,
(dy == 0) ? "" : " and uncertainties");
printf("Found: a = %g +/- %g, b = %g +/- %g\n", a, da, b, db);
if ((ok = gmx_stats_done(line)) != estatsOK)
{
fprintf(stderr, "%s\n", gmx_stats_message(ok));
}
gmx_rng_destroy(rng);
}
}
int lsq_y_ax_b_error(int n, real x[], real y[], real dy[],
real *a, real *b, real *da, real *db,
real *r, real *chi2)
{
gmx_stats_t lsq = gmx_stats_init();
int ok;
for (int i = 0; (i < n); i++)
{
ok = gmx_stats_add_point(lsq, x[i], y[i], 0, dy[i]);
if (ok != estatsOK)
{
gmx_stats_free(lsq);
return ok;
}
}
ok = gmx_stats_get_ab(lsq, elsqWEIGHT_Y, a, b, da, db, chi2, r);
gmx_stats_free(lsq);
return ok;
}
void printmol(t_corr *curr, const char *fn,
const char *fn_pdb, int *molindex, t_topology *top,
rvec *x, int ePBC, matrix box, const output_env_t oenv)
{
#define NDIST 100
FILE *out;
gmx_stats_t lsq1;
int i, j;
real a, b, D, Dav, D2av, VarD, sqrtD, sqrtD_max, scale;
t_pdbinfo *pdbinfo = NULL;
int *mol2a = NULL;
out = xvgropen(fn, "Diffusion Coefficients / Molecule", "Molecule", "D", oenv);
if (fn_pdb)
{
if (top->atoms.pdbinfo == NULL)
{
snew(top->atoms.pdbinfo, top->atoms.nr);
}
pdbinfo = top->atoms.pdbinfo;
mol2a = top->mols.index;
}
Dav = D2av = 0;
sqrtD_max = 0;
for (i = 0; (i < curr->nmol); i++)
{
lsq1 = gmx_stats_init();
for (j = 0; (j < curr->nrestart); j++)
{
real xx, yy, dx, dy;
while (gmx_stats_get_point(curr->lsq[j][i], &xx, &yy, &dx, &dy, 0) == estatsOK)
{
gmx_stats_add_point(lsq1, xx, yy, dx, dy);
}
}
gmx_stats_get_ab(lsq1, elsqWEIGHT_NONE, &a, &b, NULL, NULL, NULL, NULL);
gmx_stats_done(lsq1);
sfree(lsq1);
D = a*FACTOR/curr->dim_factor;
if (D < 0)
{
D = 0;
}
Dav += D;
D2av += sqr(D);
fprintf(out, "%10d %10g\n", i, D);
if (pdbinfo)
{
sqrtD = std::sqrt(D);
if (sqrtD > sqrtD_max)
{
sqrtD_max = sqrtD;
}
for (j = mol2a[molindex[i]]; j < mol2a[molindex[i]+1]; j++)
{
pdbinfo[j].bfac = sqrtD;
}
}
}
xvgrclose(out);
do_view(oenv, fn, "-graphtype bar");
/* Compute variance, stddev and error */
Dav /= curr->nmol;
D2av /= curr->nmol;
VarD = D2av - sqr(Dav);
printf("<D> = %.4f Std. Dev. = %.4f Error = %.4f\n",
Dav, std::sqrt(VarD), std::sqrt(VarD/curr->nmol));
if (fn_pdb && x)
{
scale = 1;
while (scale*sqrtD_max > 10)
{
scale *= 0.1;
}
while (scale*sqrtD_max < 0.1)
{
scale *= 10;
}
GMX_RELEASE_ASSERT(pdbinfo != NULL, "Internal error - pdbinfo not set for PDB input");
for (i = 0; i < top->atoms.nr; i++)
{
pdbinfo[i].bfac *= scale;
}
write_sto_conf(fn_pdb, "molecular MSD", &top->atoms, x, NULL, ePBC, box);
}
}
int lsq_y_ax_b_error(int n, real x[], real y[], real dy[],
real *a, real *b, real *da, real *db,
real *r, real *chi2)
{
gmx_stats_t lsq;
int i, ok;
lsq = gmx_stats_init();
for (i = 0; (i < n); i++)
{
if ((ok = gmx_stats_add_point(lsq, x[i], y[i], 0, dy[i])) != estatsOK)
{
return ok;
}
}
if ((ok = gmx_stats_get_ab(lsq, elsqWEIGHT_Y, a, b, da, db, chi2, r)) != estatsOK)
{
return ok;
}
if ((ok = gmx_stats_done(lsq)) != estatsOK)
{
return ok;
}
sfree(lsq);
return estatsOK;
/*
double sxy,sxx,syy,sx,sy,w,s_2,dx2,dy2,mins;
sxy=sxx=syy=sx=sy=w=0.0;
mins = dy[0];
for(i=1; (i<n); i++)
mins = min(mins,dy[i]);
if (mins <= 0)
gmx_fatal(FARGS,"Zero or negative weigths in linear regression analysis");
for (i=0; i<n; i++) {
s_2 = dsqr(1.0/dy[i]);
sxx += s_2*dsqr(x[i]);
sxy += s_2*y[i]*x[i];
syy += s_2*dsqr(y[i]);
sx += s_2*x[i];
sy += s_2*y[i];
w += s_2;
}
sxx = sxx/w;
sxy = sxy/w;
syy = syy/w;
sx = sx/w;
sy = sy/w;
dx2 = (sxx-sx*sx);
dy2 = (syy-sy*sy);
* a=(sxy-sy*sx)/dx2;
* b=(sy-(*a)*sx);
* chi2=0;
for(i=0; i<n; i++)
* chi2+=dsqr((y[i]-((*a)*x[i]+(*b)))/dy[i]);
* chi2 = *chi2/w;
* da = sqrt(*chi2/((n-2)*dx2));
* db = *da*sqrt(sxx);
* r = *a*sqrt(dx2/dy2);
if (debug)
fprintf(debug,"sx = %g, sy = %g, sxy = %g, sxx = %g, w = %g\n"
"chi2 = %g, dx2 = %g\n",
sx,sy,sxy,sxx,w,*chi2,dx2);
if (n > 2)
* chi2 = sqrt(*chi2/(n-2));
else
* chi2 = 0;
*/
}
