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 horizontal()
{
gmx_rng_t rng;
gmx_stats_t straight;
int i, ok, n = 1000;
real y, a, b, da, db, aver, sigma, error, chi2, R, *xh, *yh;
FILE *fp;
rng = gmx_rng_init(13);
straight = gmx_stats_init();
for (i = 0; (i < n); i++)
{
y = gmx_rng_uniform_real(rng);
if ((ok = gmx_stats_add_point(straight, i, y, 0, 0)) != estatsOK)
{
fprintf(stderr, "%s\n", gmx_stats_message(ok));
}
}
/* Horizontal test */
if ((ok = gmx_stats_get_ase(straight, &aver, &sigma, &error)) != estatsOK)
{
fprintf(stderr, "%s\n", gmx_stats_message(ok));
}
fp = fopen("straight.xvg", "w");
if ((ok = gmx_stats_dump_xy(straight, fp)) != estatsOK)
{
fprintf(stderr, "%s\n", gmx_stats_message(ok));
}
fclose(fp);
printf("Horizontal line: average %g, sigma %g, error %g\n", aver, sigma, error);
if ((ok = gmx_stats_done(straight)) != estatsOK)
{
fprintf(stderr, "%s\n", gmx_stats_message(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 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);
}
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);
}
}
/* 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;
}
static void histogram()
{
gmx_rng_t rng;
gmx_stats_t camel;
int i, ok, n = 1000, norm;
real y, a, b, da, db, aver, sigma, error, chi2, R, *xh, *yh;
const real a0 = 0.23, b0 = 2.7;
FILE *fp;
char fn[256];
for (norm = 0; (norm < 2); norm++)
{
rng = gmx_rng_init(13);
camel = gmx_stats_init();
for (i = 0; (i < n); i++)
{
y = sqr(gmx_rng_uniform_real(rng));
if ((ok = gmx_stats_add_point(camel, i, y+1, 0, 0)) != estatsOK)
{
fprintf(stderr, "%s\n", gmx_stats_message(ok));
}
y = sqr(gmx_rng_uniform_real(rng));
if ((ok = gmx_stats_add_point(camel, i+0.5, y+2, 0, 0)) != estatsOK)
{
fprintf(stderr, "%s\n", gmx_stats_message(ok));
}
}
/* Histogram test */
if ((ok = gmx_stats_make_histogram(camel, 0, 101, norm, &xh, &yh)) != estatsOK)
{
fprintf(stderr, "%s\n", gmx_stats_message(ok));
}
sprintf(fn, "histo%d-data.xvg", norm);
fp = fopen(fn, "w");
gmx_stats_dump_xy(camel, fp);
fclose(fp);
sprintf(fn, "histo%d.xvg", norm);
fp = fopen(fn, "w");
for (i = 0; (i < 101); i++)
{
fprintf(fp, "%12g %12g\n", xh[i], yh[i]);
}
fclose(fp);
sfree(xh);
sfree(yh);
}
}
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);
if ((ok = gmx_stats_get_a(lsq, elsqWEIGHT_NONE, a, &da, &chi2, &Rfit)) != estatsOK)
{
return ok;
}
/* int i;
double xx,yx;
yx=xx=0.0;
for (i=0; i<n; i++) {
yx+=y[i]*x[i];
xx+=x[i]*x[i];
}
* a=yx/xx;
*/
return estatsOK;
}
/* this is the main loop for the correlation type functions
* fx and nx are file pointers to things like read_first_x and
* read_next_x
*/
int corr_loop(t_corr *curr, const char *fn, t_topology *top, int ePBC,
gmx_bool bMol, int gnx[], atom_id *index[],
t_calc_func *calc1, gmx_bool bTen, int *gnx_com, atom_id *index_com[],
real dt, real t_pdb, rvec **x_pdb, matrix box_pdb,
const output_env_t oenv)
{
rvec *x[2]; /* the coordinates to read */
rvec *xa[2]; /* the coordinates to calculate displacements for */
rvec com = {0};
real t, t_prev = 0;
int natoms, i, j, cur = 0, maxframes = 0;
t_trxstatus *status;
#define prev (1-cur)
matrix box;
gmx_bool bFirst;
gmx_rmpbc_t gpbc = NULL;
natoms = read_first_x(oenv, &status, fn, &curr->t0, &(x[cur]), box);
#ifdef DEBUG
fprintf(stderr, "Read %d atoms for first frame\n", natoms);
#endif
if ((gnx_com != NULL) && natoms < top->atoms.nr)
{
fprintf(stderr, "WARNING: The trajectory only contains part of the system (%d of %d atoms) and therefore the COM motion of only this part of the system will be removed\n", natoms, top->atoms.nr);
}
snew(x[prev], natoms);
if (bMol)
{
curr->ncoords = curr->nmol;
snew(xa[0], curr->ncoords);
snew(xa[1], curr->ncoords);
}
else
{
curr->ncoords = natoms;
xa[0] = x[0];
xa[1] = x[1];
}
bFirst = TRUE;
t = curr->t0;
if (x_pdb)
{
*x_pdb = NULL;
}
if (bMol)
{
gpbc = gmx_rmpbc_init(&top->idef, ePBC, natoms);
}
/* the loop over all frames */
do
{
if (x_pdb && ((bFirst && t_pdb < t) ||
(!bFirst &&
t_pdb > t - 0.5*(t - t_prev) &&
t_pdb < t + 0.5*(t - t_prev))))
{
if (*x_pdb == NULL)
{
snew(*x_pdb, natoms);
}
for (i = 0; i < natoms; i++)
{
copy_rvec(x[cur][i], (*x_pdb)[i]);
}
copy_mat(box, box_pdb);
}
/* check whether we've reached a restart point */
if (bRmod(t, curr->t0, dt))
{
curr->nrestart++;
srenew(curr->x0, curr->nrestart);
snew(curr->x0[curr->nrestart-1], curr->ncoords);
srenew(curr->com, curr->nrestart);
srenew(curr->n_offs, curr->nrestart);
srenew(curr->lsq, curr->nrestart);
snew(curr->lsq[curr->nrestart-1], curr->nmol);
for (i = 0; i < curr->nmol; i++)
{
curr->lsq[curr->nrestart-1][i] = gmx_stats_init();
}
if (debug)
{
fprintf(debug, "Extended data structures because of new restart %d\n",
curr->nrestart);
}
}
/* create or extend the frame-based arrays */
if (curr->nframes >= maxframes-1)
{
if (maxframes == 0)
{
for (i = 0; (i < curr->ngrp); i++)
{
curr->ndata[i] = NULL;
curr->data[i] = NULL;
if (bTen)
{
curr->datam[i] = NULL;
}
}
curr->time = NULL;
}
maxframes += 10;
for (i = 0; (i < curr->ngrp); i++)
{
srenew(curr->ndata[i], maxframes);
srenew(curr->data[i], maxframes);
if (bTen)
{
srenew(curr->datam[i], maxframes);
}
for (j = maxframes-10; j < maxframes; j++)
{
curr->ndata[i][j] = 0;
curr->data[i][j] = 0;
if (bTen)
{
clear_mat(curr->datam[i][j]);
}
}
}
srenew(curr->time, maxframes);
}
/* set the time */
curr->time[curr->nframes] = t - curr->t0;
/* for the first frame, the previous frame is a copy of the first frame */
if (bFirst)
{
std::memcpy(xa[prev], xa[cur], curr->ncoords*sizeof(xa[prev][0]));
bFirst = FALSE;
}
/* make the molecules whole */
if (bMol)
{
gmx_rmpbc(gpbc, natoms, box, x[cur]);
}
/* calculate the molecules' centers of masses and put them into xa */
if (bMol)
{
calc_mol_com(gnx[0], index[0], &top->mols, &top->atoms, x[cur], xa[cur]);
}
/* first remove the periodic boundary condition crossings */
for (i = 0; i < curr->ngrp; i++)
{
prep_data(bMol, gnx[i], index[i], xa[cur], xa[prev], box);
}
/* calculate the center of mass */
if (gnx_com)
{
prep_data(bMol, gnx_com[0], index_com[0], xa[cur], xa[prev], box);
calc_com(bMol, gnx_com[0], index_com[0], xa[cur], xa[prev], box,
&top->atoms, com);
}
/* loop over all groups in index file */
for (i = 0; (i < curr->ngrp); i++)
{
/* calculate something useful, like mean square displacements */
calc_corr(curr, i, gnx[i], index[i], xa[cur], (gnx_com != NULL), com,
calc1, bTen);
}
cur = prev;
t_prev = t;
curr->nframes++;
}
while (read_next_x(oenv, status, &t, x[cur], box));
fprintf(stderr, "\nUsed %d restart points spaced %g %s over %g %s\n\n",
curr->nrestart,
output_env_conv_time(oenv, dt), output_env_get_time_unit(oenv),
output_env_conv_time(oenv, curr->time[curr->nframes-1]),
output_env_get_time_unit(oenv) );
if (bMol)
{
gmx_rmpbc_done(gpbc);
}
close_trj(status);
return natoms;
}
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;
*/
}
static void do_bonds(FILE *log, const char *fn, const char *fbond,
const char *fdist, int gnx, atom_id index[],
real blen, real tol, gmx_bool bAver,
t_topology *top, int ePBC, gmx_bool bAverDist,
const output_env_t oenv)
{
#define MAXTAB 1000
FILE *out, *outd = NULL;
int *btab = NULL;
real b0 = 0, b1, db = 0;
real bond, bav;
gmx_stats_t b_one = NULL, *b_all = NULL;
/*real mean, mean2, sqrdev2, sigma2;
int counter;*/
rvec *x;
rvec dx;
t_trxstatus *status;
int natoms;
matrix box;
real t, fac;
int bind, i, nframes, i0, i1;
t_pbc pbc;
int N;
real aver, sigma, error;
if (!bAver)
{
snew(b_all, gnx/2);
for (i = 0; (i < gnx/2); i++)
{
b_all[i] = gmx_stats_init();
}
}
else
{
b_one = gmx_stats_init();
snew(btab, MAXTAB+1);
}
natoms = read_first_x(oenv, &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)", oenv);
if (!bAverDist)
{
make_dist_leg(outd, gnx, index, &(top->atoms), oenv);
}
}
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)
{
gmx_stats_add_point(b_one, t, bond, 0, 0);
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
{
gmx_stats_add_point(b_all[i/2], t, bond, 0, 0);
}
}
if (bAverDist)
{
fprintf(outd, " %.5f", bav*2.0/gnx);
}
if (fdist)
{
fprintf(outd, "\n");
}
}
while (read_next_x(oenv, status, &t, 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");
gmx_stats_get_npoints(b_one, &N);
printf("Total number of samples : %d\n", N);
gmx_stats_get_ase(b_one, &aver, &sigma, &error);
printf("Mean : %g\n", aver);
printf("Standard deviation of the distribution: %g\n", sigma);
printf("Standard deviation of the mean : %g\n", error);
gmx_stats_done(b_one);
sfree(b_one);
out = xvgropen(fbond, "Bond Stretching Distribution",
"Bond Length (nm)", "", oenv);
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);
}
ffclose(out);
}
else
{
fprintf(log, "%5s %5s %8s %8s\n", "i", "j", "b_aver", "sigma");
for (i = 0; (i < gnx/2); i++)
{
gmx_stats_get_ase(b_all[i], &aver, &sigma, NULL);
fprintf(log, "%5u %5u %8.5f %8.5f\n", 1+index[2*i], 1+index[2*i+1],
aver, sigma);
gmx_stats_done(b_all[i]);
sfree(b_all[i]);
}
sfree(b_all);
}
}
static void do_dip(t_topology *top,int ePBC,real volume,
const char *fn,
const char *out_mtot,const char *out_eps,
const char *out_aver, const char *dipdist,
const char *cosaver, const char *fndip3d,
const char *fnadip, gmx_bool bPairs,
const char *corrtype,const char *corf,
gmx_bool bGkr, const char *gkrfn,
gmx_bool bPhi, int *nlevels, int ndegrees,
int ncos,
const char *cmap, real rcmax,
gmx_bool bQuad, const char *quadfn,
gmx_bool bMU, const char *mufn,
int *gnx, int *molindex[],
real mu_max, real mu_aver,
real epsilonRF,real temp,
int *gkatom, int skip,
gmx_bool bSlab, int nslices,
const char *axtitle, const char *slabfn,
const output_env_t oenv)
{
const char *leg_mtot[] = {
"M\\sx \\N",
"M\\sy \\N",
"M\\sz \\N",
"|M\\stot \\N|"
};
#define NLEGMTOT asize(leg_mtot)
const char *leg_eps[] = {
"epsilon",
"G\\sk",
"g\\sk"
};
#define NLEGEPS asize(leg_eps)
const char *leg_aver[] = {
"< |M|\\S2\\N >",
"< |M| >\\S2\\N",
"< |M|\\S2\\N > - < |M| >\\S2\\N",
"< |M| >\\S2\\N / < |M|\\S2\\N >"
};
#define NLEGAVER asize(leg_aver)
const char *leg_cosaver[] = {
"\\f{4}<|cos\\f{12}q\\f{4}\\sij\\N|>",
"RMSD cos",
"\\f{4}<|cos\\f{12}q\\f{4}\\siX\\N|>",
"\\f{4}<|cos\\f{12}q\\f{4}\\siY\\N|>",
"\\f{4}<|cos\\f{12}q\\f{4}\\siZ\\N|>"
};
#define NLEGCOSAVER asize(leg_cosaver)
const char *leg_adip[] = {
"<mu>",
"Std. Dev.",
"Error"
};
#define NLEGADIP asize(leg_adip)
FILE *outdd,*outmtot,*outaver,*outeps,*caver=NULL;
FILE *dip3d=NULL,*adip=NULL;
rvec *x,*dipole=NULL,mu_t,quad,*dipsp=NULL;
t_gkrbin *gkrbin = NULL;
gmx_enxnm_t *enm=NULL;
t_enxframe *fr;
int nframes=1000,nre,timecheck=0,ncolour=0;
ener_file_t fmu=NULL;
int i,j,k,n,m,natom=0,nmol,gnx_tot,teller,tel3;
t_trxstatus *status;
int *dipole_bin,ndipbin,ibin,iVol,step,idim=-1;
unsigned long mode;
char buf[STRLEN];
real rcut=0,t,t0,t1,dt,lambda,dd,rms_cos;
rvec dipaxis;
matrix box;
gmx_bool bCorr,bTotal,bCont;
double M_diff=0,epsilon,invtel,vol_aver;
double mu_ave,mu_mol,M2_ave=0,M_ave2=0,M_av[DIM],M_av2[DIM];
double M[3],M2[3],M4[3],Gk=0,g_k=0;
gmx_stats_t Mx,My,Mz,Msq,Vol,*Qlsq,mulsq,muframelsq=NULL;
ivec iMu;
real **muall=NULL;
rvec *slab_dipoles=NULL;
t_atom *atom=NULL;
t_block *mols=NULL;
gmx_rmpbc_t gpbc=NULL;
gnx_tot = gnx[0];
if (ncos > 1) {
gnx_tot += gnx[1];
}
vol_aver = 0.0;
iVol=-1;
if (bMU)
{
fmu = open_enx(mufn,"r");
do_enxnms(fmu,&nre,&enm);
/* Determine the indexes of the energy grps we need */
for (i=0; (i<nre); i++) {
if (strstr(enm[i].name,"Volume"))
iVol=i;
else if (strstr(enm[i].name,"Mu-X"))
iMu[XX]=i;
else if (strstr(enm[i].name,"Mu-Y"))
iMu[YY]=i;
else if (strstr(enm[i].name,"Mu-Z"))
iMu[ZZ]=i;
}
}
else
{
atom = top->atoms.atom;
mols = &(top->mols);
}
if ((iVol == -1) && bMU)
printf("Using Volume from topology: %g nm^3\n",volume);
/* Correlation stuff */
bCorr = (corrtype[0] != 'n');
bTotal = (corrtype[0] == 't');
if (bCorr)
{
if (bTotal)
{
snew(muall,1);
snew(muall[0],nframes*DIM);
}
else
{
snew(muall,gnx[0]);
for(i=0; (i<gnx[0]); i++)
snew(muall[i],nframes*DIM);
}
}
/* Allocate array which contains for every molecule in a frame the
* dipole moment.
*/
if (!bMU)
snew(dipole,gnx_tot);
/* Statistics */
snew(Qlsq,DIM);
for(i=0; (i<DIM); i++)
Qlsq[i] = gmx_stats_init();
mulsq = gmx_stats_init();
/* Open all the files */
outmtot = xvgropen(out_mtot,
"Total dipole moment of the simulation box vs. time",
"Time (ps)","Total Dipole Moment (Debye)",oenv);
outeps = xvgropen(out_eps,"Epsilon and Kirkwood factors",
"Time (ps)","",oenv);
outaver = xvgropen(out_aver,"Total dipole moment",
"Time (ps)","D",oenv);
if (bSlab)
{
idim = axtitle[0] - 'X';
if ((idim < 0) || (idim >= DIM))
idim = axtitle[0] - 'x';
if ((idim < 0) || (idim >= DIM))
bSlab = FALSE;
if (nslices < 2)
bSlab = FALSE;
fprintf(stderr,"axtitle = %s, nslices = %d, idim = %d\n",
axtitle,nslices,idim);
if (bSlab)
{
snew(slab_dipoles,nslices);
fprintf(stderr,"Doing slab analysis\n");
}
}
if (fnadip)
{
adip = xvgropen(fnadip, "Average molecular dipole","Dipole (D)","",oenv);
xvgr_legend(adip,NLEGADIP,leg_adip, oenv);
}
if (cosaver)
{
caver = xvgropen(cosaver,bPairs ? "Average pair orientation" :
"Average absolute dipole orientation","Time (ps)","",oenv);
xvgr_legend(caver,NLEGCOSAVER,bPairs ? leg_cosaver : &(leg_cosaver[1]),
oenv);
}
if (fndip3d)
{
snew(dipsp,gnx_tot);
/* we need a dummy file for gnuplot */
dip3d = (FILE *)ffopen("dummy.dat","w");
fprintf(dip3d,"%f %f %f", 0.0,0.0,0.0);
ffclose(dip3d);
dip3d = (FILE *)ffopen(fndip3d,"w");
fprintf(dip3d,"# This file was created by %s\n",Program());
fprintf(dip3d,"# which is part of G R O M A C S:\n");
fprintf(dip3d,"#\n");
}
/* Write legends to all the files */
xvgr_legend(outmtot,NLEGMTOT,leg_mtot,oenv);
xvgr_legend(outaver,NLEGAVER,leg_aver,oenv);
if (bMU && (mu_aver == -1))
xvgr_legend(outeps,NLEGEPS-2,leg_eps,oenv);
else
xvgr_legend(outeps,NLEGEPS,leg_eps,oenv);
snew(fr,1);
clear_rvec(mu_t);
teller = 0;
/* Read the first frame from energy or traj file */
if (bMU)
do
{
bCont = read_mu_from_enx(fmu,iVol,iMu,mu_t,&volume,&t,nre,fr);
if (bCont)
{
timecheck=check_times(t);
if (timecheck < 0)
teller++;
if ((teller % 10) == 0)
fprintf(stderr,"\r Skipping Frame %6d, time: %8.3f", teller, t);
}
else
{
printf("End of %s reached\n",mufn);
break;
}
} while (bCont && (timecheck < 0));
else
natom = read_first_x(oenv,&status,fn,&t,&x,box);
/* Calculate spacing for dipole bin (simple histogram) */
ndipbin = 1+(mu_max/0.01);
snew(dipole_bin, ndipbin);
epsilon = 0.0;
mu_ave = 0.0;
for(m=0; (m<DIM); m++)
{
M[m] = M2[m] = M4[m] = 0.0;
}
if (bGkr)
{
/* Use 0.7 iso 0.5 to account for pressure scaling */
/* rcut = 0.7*sqrt(max_cutoff2(box)); */
rcut = 0.7*sqrt(sqr(box[XX][XX])+sqr(box[YY][YY])+sqr(box[ZZ][ZZ]));
gkrbin = mk_gkrbin(rcut,rcmax,bPhi,ndegrees);
}
gpbc = gmx_rmpbc_init(&top->idef,ePBC,natom,box);
/* Start while loop over frames */
t1 = t0 = t;
teller = 0;
do
{
if (bCorr && (teller >= nframes))
{
nframes += 1000;
if (bTotal)
{
srenew(muall[0],nframes*DIM);
}
else
{
for(i=0; (i<gnx_tot); i++)
srenew(muall[i],nframes*DIM);
}
}
t1 = t;
muframelsq = gmx_stats_init();
/* Initialise */
for(m=0; (m<DIM); m++)
M_av2[m] = 0;
if (bMU)
{
/* Copy rvec into double precision local variable */
for(m=0; (m<DIM); m++)
M_av[m] = mu_t[m];
}
else
{
/* Initialise */
for(m=0; (m<DIM); m++)
M_av[m] = 0;
gmx_rmpbc(gpbc,natom,box,x);
/* Begin loop of all molecules in frame */
for(n=0; (n<ncos); n++)
{
for(i=0; (i<gnx[n]); i++)
{
int gi,ind0,ind1;
ind0 = mols->index[molindex[n][i]];
ind1 = mols->index[molindex[n][i]+1];
mol_dip(ind0,ind1,x,atom,dipole[i]);
gmx_stats_add_point(mulsq,0,norm(dipole[i]),0,0);
gmx_stats_add_point(muframelsq,0,norm(dipole[i]),0,0);
if (bSlab)
update_slab_dipoles(ind0,ind1,x,
dipole[i],idim,nslices,slab_dipoles,box);
if (bQuad)
{
mol_quad(ind0,ind1,x,atom,quad);
for(m=0; (m<DIM); m++)
gmx_stats_add_point(Qlsq[m],0,quad[m],0,0);
}
if (bCorr && !bTotal)
{
tel3=DIM*teller;
muall[i][tel3+XX] = dipole[i][XX];
muall[i][tel3+YY] = dipole[i][YY];
muall[i][tel3+ZZ] = dipole[i][ZZ];
}
mu_mol = 0.0;
for(m=0; (m<DIM); m++)
{
M_av[m] += dipole[i][m]; /* M per frame */
mu_mol += dipole[i][m]*dipole[i][m]; /* calc. mu for distribution */
}
mu_mol = sqrt(mu_mol);
mu_ave += mu_mol; /* calc. the average mu */
/* Update the dipole distribution */
ibin = (int)(ndipbin*mu_mol/mu_max + 0.5);
if (ibin < ndipbin)
dipole_bin[ibin]++;
if (fndip3d)
{
rvec2sprvec(dipole[i],dipsp[i]);
if (dipsp[i][YY] > -M_PI && dipsp[i][YY] < -0.5*M_PI) {
if (dipsp[i][ZZ] < 0.5 * M_PI)
{
ncolour = 1;
}
else
{
ncolour = 2;
}
}
else if (dipsp[i][YY] > -0.5*M_PI && dipsp[i][YY] < 0.0*M_PI)
{
if (dipsp[i][ZZ] < 0.5 * M_PI)
{
ncolour = 3;
}
else
{
ncolour = 4;
}
}else if (dipsp[i][YY] > 0.0 && dipsp[i][YY] < 0.5*M_PI) {
if (dipsp[i][ZZ] < 0.5 * M_PI) {
ncolour = 5;
} else {
ncolour = 6;
}
}
else if (dipsp[i][YY] > 0.5*M_PI && dipsp[i][YY] < M_PI)
{
if (dipsp[i][ZZ] < 0.5 * M_PI)
{
ncolour = 7;
}
else
{
ncolour = 8;
}
}
if (dip3d)
fprintf(dip3d,"set arrow %d from %f, %f, %f to %f, %f, %f lt %d # %d %d\n",
i+1,
x[ind0][XX],
x[ind0][YY],
x[ind0][ZZ],
x[ind0][XX]+dipole[i][XX]/25,
x[ind0][YY]+dipole[i][YY]/25,
x[ind0][ZZ]+dipole[i][ZZ]/25,
ncolour, ind0, i);
}
} /* End loop of all molecules in frame */
if (dip3d)
{
fprintf(dip3d,"set title \"t = %4.3f\"\n",t);
fprintf(dip3d,"set xrange [0.0:%4.2f]\n",box[XX][XX]);
fprintf(dip3d,"set yrange [0.0:%4.2f]\n",box[YY][YY]);
fprintf(dip3d,"set zrange [0.0:%4.2f]\n\n",box[ZZ][ZZ]);
fprintf(dip3d,"splot 'dummy.dat' using 1:2:3 w vec\n");
fprintf(dip3d,"pause -1 'Hit return to continue'\n");
}
}
}
/* Compute square of total dipole */
for(m=0; (m<DIM); m++)
M_av2[m] = M_av[m]*M_av[m];
if (cosaver)
{
compute_avercos(gnx_tot,dipole,&dd,dipaxis,bPairs);
rms_cos = sqrt(sqr(dipaxis[XX]-0.5)+
sqr(dipaxis[YY]-0.5)+
sqr(dipaxis[ZZ]-0.5));
if (bPairs)
fprintf(caver,"%10.3e %10.3e %10.3e %10.3e %10.3e %10.3e\n",
t,dd,rms_cos,dipaxis[XX],dipaxis[YY],dipaxis[ZZ]);
else
fprintf(caver,"%10.3e %10.3e %10.3e %10.3e %10.3e\n",
t,rms_cos,dipaxis[XX],dipaxis[YY],dipaxis[ZZ]);
}
if (bGkr)
{
do_gkr(gkrbin,ncos,gnx,molindex,mols->index,x,dipole,ePBC,box,
atom,gkatom);
}
if (bTotal)
{
tel3 = DIM*teller;
muall[0][tel3+XX] = M_av[XX];
muall[0][tel3+YY] = M_av[YY];
muall[0][tel3+ZZ] = M_av[ZZ];
}
/* Write to file the total dipole moment of the box, and its components
* for this frame.
*/
if ((skip == 0) || ((teller % skip) == 0))
fprintf(outmtot,"%10g %12.8e %12.8e %12.8e %12.8e\n",
t,M_av[XX],M_av[YY],M_av[ZZ],
sqrt(M_av2[XX]+M_av2[YY]+M_av2[ZZ]));
for(m=0; (m<DIM); m++)
{
M[m] += M_av[m];
M2[m] += M_av2[m];
M4[m] += sqr(M_av2[m]);
}
/* Increment loop counter */
teller++;
/* Calculate for output the running averages */
invtel = 1.0/teller;
M2_ave = (M2[XX]+M2[YY]+M2[ZZ])*invtel;
M_ave2 = invtel*(invtel*(M[XX]*M[XX] + M[YY]*M[YY] + M[ZZ]*M[ZZ]));
M_diff = M2_ave - M_ave2;
/* Compute volume from box in traj, else we use the one from above */
if (!bMU)
volume = det(box);
vol_aver += volume;
epsilon = calc_eps(M_diff,(vol_aver/teller),epsilonRF,temp);
/* Calculate running average for dipole */
if (mu_ave != 0)
mu_aver = (mu_ave/gnx_tot)*invtel;
if ((skip == 0) || ((teller % skip) == 0))
{
/* Write to file < |M|^2 >, |< M >|^2. And the difference between
* the two. Here M is sum mu_i. Further write the finite system
* Kirkwood G factor and epsilon.
*/
fprintf(outaver,"%10g %10.3e %10.3e %10.3e %10.3e\n",
t,M2_ave,M_ave2,M_diff,M_ave2/M2_ave);
if (fnadip)
{
real aver;
gmx_stats_get_average(muframelsq,&aver);
fprintf(adip, "%10g %f \n", t,aver);
}
/*if (dipole)
printf("%f %f\n", norm(dipole[0]), norm(dipole[1]));
*/
if (!bMU || (mu_aver != -1))
{
/* Finite system Kirkwood G-factor */
Gk = M_diff/(gnx_tot*mu_aver*mu_aver);
/* Infinite system Kirkwood G-factor */
if (epsilonRF == 0.0)
g_k = ((2*epsilon+1)*Gk/(3*epsilon));
else
g_k = ((2*epsilonRF+epsilon)*(2*epsilon+1)*
Gk/(3*epsilon*(2*epsilonRF+1)));
fprintf(outeps,"%10g %10.3e %10.3e %10.3e\n",t,epsilon,Gk,g_k);
}
else
fprintf(outeps,"%10g %12.8e\n",t,epsilon);
}
gmx_stats_done(muframelsq);
if (bMU)
bCont = read_mu_from_enx(fmu,iVol,iMu,mu_t,&volume,&t,nre,fr);
else
bCont = read_next_x(oenv,status,&t,natom,x,box);
timecheck=check_times(t);
} while (bCont && (timecheck == 0) );
gmx_rmpbc_done(gpbc);
if (!bMU)
close_trj(status);
ffclose(outmtot);
ffclose(outaver);
ffclose(outeps);
if (fnadip)
ffclose(adip);
if (cosaver)
ffclose(caver);
if (dip3d) {
fprintf(dip3d,"set xrange [0.0:%4.2f]\n",box[XX][XX]);
fprintf(dip3d,"set yrange [0.0:%4.2f]\n",box[YY][YY]);
fprintf(dip3d,"set zrange [0.0:%4.2f]\n\n",box[ZZ][ZZ]);
fprintf(dip3d,"splot 'dummy.dat' using 1:2:3 w vec\n");
fprintf(dip3d,"pause -1 'Hit return to continue'\n");
ffclose(dip3d);
}
if (bSlab) {
dump_slab_dipoles(slabfn,idim,nslices,slab_dipoles,box,teller,oenv);
sfree(slab_dipoles);
}
vol_aver /= teller;
printf("Average volume over run is %g\n",vol_aver);
if (bGkr) {
print_gkrbin(gkrfn,gkrbin,gnx[0],teller,vol_aver,oenv);
print_cmap(cmap,gkrbin,nlevels);
}
/* Autocorrelation function */
if (bCorr) {
if (teller < 2) {
printf("Not enough frames for autocorrelation\n");
}
else {
dt=(t1 - t0)/(teller-1);
printf("t0 %g, t %g, teller %d\n", t0,t,teller);
mode = eacVector;
if (bTotal)
do_autocorr(corf,oenv,"Autocorrelation Function of Total Dipole",
teller,1,muall,dt,mode,TRUE);
else
do_autocorr(corf,oenv,"Dipole Autocorrelation Function",
teller,gnx_tot,muall,dt,
mode,strcmp(corrtype,"molsep"));
}
}
if (!bMU) {
real aver,sigma,error,lsq;
gmx_stats_get_ase(mulsq,&aver,&sigma,&error);
printf("\nDipole moment (Debye)\n");
printf("---------------------\n");
printf("Average = %8.4f Std. Dev. = %8.4f Error = %8.4f\n",
aver,sigma,error);
if (bQuad) {
rvec a,s,e;
int mm;
for(m=0; (m<DIM); m++)
gmx_stats_get_ase(mulsq,&(a[m]),&(s[m]),&(e[m]));
printf("\nQuadrupole moment (Debye-Ang)\n");
printf("-----------------------------\n");
printf("Averages = %8.4f %8.4f %8.4f\n",a[XX],a[YY],a[ZZ]);
printf("Std. Dev. = %8.4f %8.4f %8.4f\n",s[XX],s[YY],s[ZZ]);
printf("Error = %8.4f %8.4f %8.4f\n",e[XX],e[YY],e[ZZ]);
}
printf("\n");
}
printf("The following averages for the complete trajectory have been calculated:\n\n");
printf(" Total < M_x > = %g Debye\n", M[XX]/teller);
printf(" Total < M_y > = %g Debye\n", M[YY]/teller);
printf(" Total < M_z > = %g Debye\n\n", M[ZZ]/teller);
printf(" Total < M_x^2 > = %g Debye^2\n", M2[XX]/teller);
printf(" Total < M_y^2 > = %g Debye^2\n", M2[YY]/teller);
printf(" Total < M_z^2 > = %g Debye^2\n\n", M2[ZZ]/teller);
printf(" Total < |M|^2 > = %g Debye^2\n", M2_ave);
printf(" Total |< M >|^2 = %g Debye^2\n\n", M_ave2);
printf(" < |M|^2 > - |< M >|^2 = %g Debye^2\n\n", M_diff);
if (!bMU || (mu_aver != -1)) {
printf("Finite system Kirkwood g factor G_k = %g\n", Gk);
printf("Infinite system Kirkwood g factor g_k = %g\n\n", g_k);
}
printf("Epsilon = %g\n", epsilon);
if (!bMU) {
/* Write to file the dipole moment distibution during the simulation.
*/
outdd=xvgropen(dipdist,"Dipole Moment Distribution","mu (Debye)","",oenv);
for(i=0; (i<ndipbin); i++)
fprintf(outdd,"%10g %10f\n",
(i*mu_max)/ndipbin,dipole_bin[i]/(double)teller);
ffclose(outdd);
sfree(dipole_bin);
}
if (bGkr)
done_gkrbin(&gkrbin);
}
