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 void clust_stat(FILE *fp, int start, int end, t_pdbfile *pdbf[])
{
int i;
gmx_stats_t ed, ef;
real aver, sigma;
ed = gmx_stats_init();
ef = gmx_stats_init();
for (i = start; (i < end); i++)
{
gmx_stats_add_point(ed, i-start, pdbf[i]->edocked, 0, 0);
gmx_stats_add_point(ef, i-start, pdbf[i]->efree, 0, 0);
}
gmx_stats_get_ase(ed, &aver, &sigma, NULL);
fprintf(fp, " <%12s> = %8.3f (+/- %6.3f)\n", etitles[FALSE], aver, sigma);
gmx_stats_get_ase(ef, &aver, &sigma, NULL);
fprintf(fp, " <%12s> = %8.3f (+/- %6.3f)\n", etitles[TRUE], aver, sigma);
gmx_stats_free(ed);
gmx_stats_free(ef);
}
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;
}
/* Old convenience functions, should be merged with the core
statistics above. */
int lsq_y_ax(int n, real x[], real y[], real *a)
{
gmx_stats_t lsq = gmx_stats_init();
int ok;
real da, chi2, Rfit;
gmx_stats_add_points(lsq, n, x, y, 0, 0);
ok = gmx_stats_get_a(lsq, elsqWEIGHT_NONE, a, &da, &chi2, &Rfit);
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 gmx_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_free(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);
}
}
