static void interfaces_txy (real ****Densmap, int xslices, int yslices, int zslices,
int tblocks, real binwidth, int method,
real dens1, real dens2, t_interf ****intf1,
t_interf ****intf2, const gmx_output_env_t *oenv)
{
/*Returns two pointers to 3D arrays of t_interf structs containing (position,thickness) of the interface(s)*/
FILE *xvg;
real *zDensavg; /* zDensavg[z]*/
int i, j, k, n;
int xysize;
int ndx1, ndx2, *zperm;
real densmid;
real splitpoint, startpoint, endpoint;
real *sigma1, *sigma2;
double beginfit1[4];
double beginfit2[4];
double *fit1 = NULL, *fit2 = NULL;
const double *avgfit1;
const double *avgfit2;
const real onehalf = 1.00/2.00;
t_interf ***int1 = NULL, ***int2 = NULL; /*Interface matrices [t][x,y] - last index in row-major order*/
/*Create int1(t,xy) and int2(t,xy) arrays with correct number of interf_t elements*/
xysize = xslices*yslices;
snew(int1, tblocks);
snew(int2, tblocks);
for (i = 0; i < tblocks; i++)
{
snew(int1[i], xysize);
snew(int2[i], xysize);
for (j = 0; j < xysize; j++)
{
snew(int1[i][j], 1);
snew(int2[i][j], 1);
init_interf(int1[i][j]);
init_interf(int2[i][j]);
}
}
if (method == methBISECT)
{
densmid = onehalf*(dens1+dens2);
snew(zperm, zslices);
for (n = 0; n < tblocks; n++)
{
for (i = 0; i < xslices; i++)
{
for (j = 0; j < yslices; j++)
{
rangeArray(zperm, zslices); /*reset permutation array to identity*/
/*Binsearch returns slice-nr where the order param is <= setpoint sgmid*/
ndx1 = start_binsearch(Densmap[n][i][j], zperm, 0, zslices/2-1, densmid, 1);
ndx2 = start_binsearch(Densmap[n][i][j], zperm, zslices/2, zslices-1, densmid, -1);
/* Linear interpolation (for use later if time allows)
* rho_1s= Densmap[n][i][j][zperm[ndx1]]
* rho_1e =Densmap[n][i][j][zperm[ndx1+1]] - in worst case might be far off
* rho_2s =Densmap[n][i][j][zperm[ndx2+1]]
* rho_2e =Densmap[n][i][j][zperm[ndx2]]
* For 1st interface we have:
densl= Densmap[n][i][j][zperm[ndx1]];
densr= Densmap[n][i][j][zperm[ndx1+1]];
alpha=(densmid-densl)/(densr-densl);
deltandx=zperm[ndx1+1]-zperm[ndx1];
if(debug){
printf("Alpha, Deltandx %f %i\n", alpha,deltandx);
}
if(abs(alpha)>1.0 || abs(deltandx)>3){
pos=zperm[ndx1];
spread=-1;
}
else {
pos=zperm[ndx1]+alpha*deltandx;
spread=binwidth*deltandx;
}
* For the 2nd interface can use the same formulation, since alpha should become negative ie:
* alpha=(densmid-Densmap[n][i][j][zperm[ndx2]])/(Densmap[n][i][j][zperm[nxd2+1]]-Densmap[n][i][j][zperm[ndx2]]);
* deltandx=zperm[ndx2+1]-zperm[ndx2];
* pos=zperm[ndx2]+alpha*deltandx; */
/*After filtering we use the direct approach */
int1[n][j+(i*yslices)]->Z = (zperm[ndx1]+onehalf)*binwidth;
int1[n][j+(i*yslices)]->t = binwidth;
int2[n][j+(i*yslices)]->Z = (zperm[ndx2]+onehalf)*binwidth;
int2[n][j+(i*yslices)]->t = binwidth;
}
}
}
}
if (method == methFUNCFIT)
{
/*Assume a box divided in 2 along midpoint of z for starters*/
startpoint = 0.0;
endpoint = binwidth*zslices;
splitpoint = (startpoint+endpoint)/2.0;
/*Initial fit proposals*/
beginfit1[0] = dens1;
beginfit1[1] = dens2;
beginfit1[2] = (splitpoint/2);
beginfit1[3] = 0.5;
beginfit2[0] = dens2;
beginfit2[1] = dens1;
beginfit2[2] = (3*splitpoint/2);
beginfit2[3] = 0.5;
snew(zDensavg, zslices);
snew(sigma1, zslices);
snew(sigma2, zslices);
for (k = 0; k < zslices; k++)
{
sigma1[k] = sigma2[k] = 1;
}
/*Calculate average density along z - avoid smoothing by using coarse-grained-mesh*/
for (k = 0; k < zslices; k++)
{
for (n = 0; n < tblocks; n++)
{
for (i = 0; i < xslices; i++)
{
for (j = 0; j < yslices; j++)
{
zDensavg[k] += (Densmap[n][i][j][k]/(xslices*yslices*tblocks));
}
}
}
}
if (debug)
{
xvg = xvgropen("DensprofileonZ.xvg", "Averaged Densityprofile on Z", "z[nm]", "Density[kg/m^3]", oenv);
for (k = 0; k < zslices; k++)
{
fprintf(xvg, "%4f.3 %8f.4\n", k*binwidth, zDensavg[k]);
}
xvgrclose(xvg);
}
/*Fit average density in z over whole trajectory to obtain tentative fit-parameters in fit1 and fit2*/
/*Fit 1st half of box*/
do_lmfit(zslices, zDensavg, sigma1, binwidth, NULL, startpoint, splitpoint, oenv, FALSE, effnERF, beginfit1, 8, NULL);
/*Fit 2nd half of box*/
do_lmfit(zslices, zDensavg, sigma2, binwidth, NULL, splitpoint, endpoint, oenv, FALSE, effnERF, beginfit2, 8, NULL);
/*Initialise the const arrays for storing the average fit parameters*/
avgfit1 = beginfit1;
avgfit2 = beginfit2;
/*Now do fit over each x y and t slice to get Zint(x,y,t) - loop is very large, we potentially should average over time directly*/
for (n = 0; n < tblocks; n++)
{
for (i = 0; i < xslices; i++)
{
for (j = 0; j < yslices; j++)
{
/*Reinitialise fit for each mesh-point*/
srenew(fit1, 4);
srenew(fit2, 4);
for (k = 0; k < 4; k++)
{
fit1[k] = avgfit1[k];
fit2[k] = avgfit2[k];
}
/*Now fit and store in structures in row-major order int[n][i][j]*/
do_lmfit(zslices, Densmap[n][i][j], sigma1, binwidth, NULL, startpoint, splitpoint, oenv, FALSE, effnERF, fit1, 0, NULL);
int1[n][j+(yslices*i)]->Z = fit1[2];
int1[n][j+(yslices*i)]->t = fit1[3];
do_lmfit(zslices, Densmap[n][i][j], sigma2, binwidth, NULL, splitpoint, endpoint, oenv, FALSE, effnERF, fit2, 0, NULL);
int2[n][j+(yslices*i)]->Z = fit2[2];
int2[n][j+(yslices*i)]->t = fit2[3];
}
}
}
}
*intf1 = int1;
*intf2 = int2;
}
static void calc_tetra_order_interface(const char *fnNDX, const char *fnTPS, const char *fnTRX, real binw, int tblock,
int *nframes, int *nslicex, int *nslicey,
real sgang1, real sgang2, real ****intfpos,
output_env_t oenv)
{
FILE *fpsg = NULL, *fpsk = NULL;
char *sgslfn = "sg_ang_mesh"; /* Hardcoded filenames for debugging*/
char *skslfn = "sk_dist_mesh";
t_topology top;
int ePBC;
char title[STRLEN], subtitle[STRLEN];
t_trxstatus *status;
int natoms;
real t;
rvec *xtop, *x;
matrix box;
real sg, sk, sgintf, pos;
atom_id **index = NULL;
char **grpname = NULL;
int i, j, k, n, *isize, ng, nslicez, framenr;
real ***sg_grid = NULL, ***sk_grid = NULL, ***sg_fravg = NULL, ***sk_fravg = NULL, ****sk_4d = NULL, ****sg_4d = NULL;
int *perm;
int ndx1, ndx2;
int bins;
const real onehalf = 1.0/2.0;
/* real ***intfpos[2]; pointers to arrays of two interface positions zcoord(framenr,xbin,ybin): intfpos[interface_index][t][nslicey*x+y]
* i.e 1D Row-major order in (t,x,y) */
read_tps_conf(fnTPS, title, &top, &ePBC, &xtop, NULL, box, FALSE);
*nslicex = (int)(box[XX][XX]/binw + onehalf); /*Calculate slicenr from binwidth*/
*nslicey = (int)(box[YY][YY]/binw + onehalf);
nslicez = (int)(box[ZZ][ZZ]/binw + onehalf);
ng = 1;
/* get index groups */
printf("Select the group that contains the atoms you want to use for the tetrahedrality order parameter calculation:\n");
snew(grpname, ng);
snew(index, ng);
snew(isize, ng);
get_index(&top.atoms, fnNDX, ng, isize, index, grpname);
/* Analyze trajectory */
natoms = read_first_x(oenv, &status, fnTRX, &t, &x, box);
if (natoms > top.atoms.nr)
{
gmx_fatal(FARGS, "Topology (%d atoms) does not match trajectory (%d atoms)",
top.atoms.nr, natoms);
}
check_index(NULL, ng, index[0], NULL, natoms);
/*Prepare structures for temporary storage of frame info*/
snew(sg_grid, *nslicex);
snew(sk_grid, *nslicex);
for (i = 0; i < *nslicex; i++)
{
snew(sg_grid[i], *nslicey);
snew(sk_grid[i], *nslicey);
for (j = 0; j < *nslicey; j++)
{
snew(sg_grid[i][j], nslicez);
snew(sk_grid[i][j], nslicez);
}
}
sg_4d = NULL;
sk_4d = NULL;
*nframes = 0;
framenr = 0;
/* Loop over frames*/
do
{
/*Initialize box meshes (temporary storage for each tblock frame -reinitialise every tblock steps */
if (framenr%tblock == 0)
{
srenew(sk_4d, *nframes+1);
srenew(sg_4d, *nframes+1);
snew(sg_fravg, *nslicex);
snew(sk_fravg, *nslicex);
for (i = 0; i < *nslicex; i++)
{
snew(sg_fravg[i], *nslicey);
snew(sk_fravg[i], *nslicey);
for (j = 0; j < *nslicey; j++)
{
snew(sg_fravg[i][j], nslicez);
snew(sk_fravg[i][j], nslicez);
}
}
}
find_tetra_order_grid(top, ePBC, natoms, box, x, isize[0], index[0], t,
&sg, &sk, *nslicex, *nslicey, nslicez, sg_grid, sk_grid);
for (i = 0; i < *nslicex; i++)
{
for (j = 0; j < *nslicey; j++)
{
for (k = 0; k < nslicez; k++)
{
sk_fravg[i][j][k] += sk_grid[i][j][k]/tblock;
sg_fravg[i][j][k] += sg_grid[i][j][k]/tblock;
}
}
}
framenr++;
if (framenr%tblock == 0)
{
sk_4d[*nframes] = sk_fravg;
sg_4d[*nframes] = sg_fravg;
(*nframes)++;
}
}
while (read_next_x(oenv, status, &t, natoms, x, box));
close_trj(status);
sfree(grpname);
sfree(index);
sfree(isize);
/*Debugging for printing out the entire order parameter meshes.*/
if (debug)
{
fpsg = xvgropen(sgslfn, "S\\sg\\N Angle Order Parameter / Meshpoint", "(nm)", "S\\sg\\N", oenv);
fpsk = xvgropen(skslfn, "S\\sk\\N Distance Order Parameter / Meshpoint", "(nm)", "S\\sk\\N", oenv);
for (n = 0; n < (*nframes); n++)
{
fprintf(fpsg, "%i\n", n);
fprintf(fpsk, "%i\n", n);
for (i = 0; (i < *nslicex); i++)
{
for (j = 0; j < *nslicey; j++)
{
for (k = 0; k < nslicez; k++)
{
fprintf(fpsg, "%4f %4f %4f %8f\n", (i+0.5)*box[XX][XX]/(*nslicex), (j+0.5)*box[YY][YY]/(*nslicey), (k+0.5)*box[ZZ][ZZ]/nslicez, sg_4d[n][i][j][k]);
fprintf(fpsk, "%4f %4f %4f %8f\n", (i+0.5)*box[XX][XX]/(*nslicex), (j+0.5)*box[YY][YY]/(*nslicey), (k+0.5)*box[ZZ][ZZ]/nslicez, sk_4d[n][i][j][k]);
}
}
}
}
xvgrclose(fpsg);
xvgrclose(fpsk);
}
/* Find positions of interface z by scanning orderparam for each frame and for each xy-mesh cylinder along z*/
/*Simple trial: assume interface is in the middle of -sgang1 and sgang2*/
sgintf = 0.5*(sgang1+sgang2);
/*Allocate memory for interface arrays; */
snew((*intfpos), 2);
snew((*intfpos)[0], *nframes);
snew((*intfpos)[1], *nframes);
bins = (*nslicex)*(*nslicey);
snew(perm, nslicez); /*permutation array for sorting along normal coordinate*/
for (n = 0; n < *nframes; n++)
{
snew((*intfpos)[0][n], bins);
snew((*intfpos)[1][n], bins);
for (i = 0; i < *nslicex; i++)
{
for (j = 0; j < *nslicey; j++)
{
rangeArray(perm, nslicez); /*reset permutation array to identity*/
/*Binsearch returns 2 bin-numbers where the order param is <= setpoint sgintf*/
ndx1 = start_binsearch(sg_4d[n][i][j], perm, 0, nslicez/2-1, sgintf, 1);
ndx2 = start_binsearch(sg_4d[n][i][j], perm, nslicez/2, nslicez-1, sgintf, -1);
/*Use linear interpolation to smooth out the interface position*/
/*left interface (0)*/
/*if((sg_4d[n][i][j][perm[ndx1+1]]-sg_4d[n][i][j][perm[ndx1]])/sg_4d[n][i][j][perm[ndx1]] > 0.01){
pos=( (sgintf-sg_4d[n][i][j][perm[ndx1]])*perm[ndx1+1]+(sg_4d[n][i][j][perm[ndx1+1]]-sgintf)*perm[ndx1 ])*/
(*intfpos)[0][n][j+*nslicey*i] = (perm[ndx1]+onehalf)*binw;
/*right interface (1)*/
/*alpha=(sgintf-sg_4d[n][i][j][perm[ndx2]])/(sg_4d[n][i][j][perm[ndx2]+1]-sg_4d[n][i][j][perm[ndx2]]);*/
/*(*intfpos)[1][n][j+*nslicey*i]=((1-alpha)*perm[ndx2]+alpha*(perm[ndx2]+1)+onehalf)*box[ZZ][ZZ]/nslicez;*/
(*intfpos)[1][n][j+*nslicey*i] = (perm[ndx2]+onehalf)*binw;
}
}
}
/*sfree(perm);*/
sfree(sk_4d);
sfree(sg_4d);
/*sfree(sg_grid);*/
/*sfree(sk_grid);*/
}
