static void
round_pyramide(GwyDataField *tip, gdouble angle, gint n, gdouble ballradius)
{
gdouble center_x, center_y, center_z;
gdouble height = gwy_data_field_get_max(tip);
gint col, row;
gdouble dcol, drow;
gdouble sphere, radius;
gdouble beta, zd;
radius = sqrt((tip->xres/2)*(tip->xres/2) + (tip->yres/2)*(tip->yres/2));
beta = atan(gwy_data_field_itor(tip, radius)/height);
center_x = tip->xreal/2;
center_y = tip->yreal/2;
beta = atan(tan(angle)/cos(G_PI/n));
center_z = height - ballradius/sin(beta);
gwy_debug("z:%g, height=%g, ballradius=%g, cosbeta=%g, beta=%g "
"(%g deg of %g deg)\n",
center_z, height, ballradius, cos(beta), beta,
beta*180/G_PI, angle*180/G_PI);
for (row = 0; row < tip->yres; row++) {
gdouble *datarow = tip->data + tip->xres*row;
for (col = 0; col < tip->xres; col++) {
if (datarow[col] > (center_z + ballradius*sin(beta))) {
dcol = gwy_data_field_itor(tip, col) - center_x;
drow = gwy_data_field_jtor(tip, row) - center_y;
sphere = (ballradius*ballradius - dcol*dcol - drow*drow);
zd = G_LIKELY(sphere >= 0) ? sqrt(sphere) : 0.0;
datarow[col] = MIN(datarow[col], center_z + zd);
}
}
}
gwy_data_field_invalidate(tip);
}
static void
preview(DepositControls *controls,
DepositArgs *args)
{
GwyDataField *dfield, *lfield, *zlfield, *zdfield;
gint xres, yres, oxres, oyres;
gint add, i, ii, m, k;
gdouble size, width;
gint xdata[10000];
gint ydata[10000];
gdouble disizes[10000];
gdouble rdisizes[10000];
gdouble rx[10000];
gdouble ry[10000];
gdouble rz[10000];
gdouble ax[10000];
gdouble ay[10000];
gdouble az[10000];
gdouble vx[10000];
gdouble vy[10000];
gdouble vz[10000];
gdouble fx[10000];
gdouble fy[10000];
gdouble fz[10000];
gint xpos, ypos, ndata, too_close;
gdouble disize, mdisize;
gdouble xreal, yreal, oxreal, oyreal;
gdouble diff;
gdouble mass = 1;
gint presetval;
gint nloc, maxloc = 1;
gint max = 5000000;
gdouble rxv, ryv, rzv, timestep = 3e-7; //5e-7
deposit_dialog_update_values(controls, args);
dfield = GWY_DATA_FIELD(gwy_container_get_object_by_name(controls->mydata,
"/0/data"));
gwy_container_set_object_by_name(controls->mydata, "/0/data", gwy_data_field_duplicate(controls->old_dfield));
dfield = GWY_DATA_FIELD(gwy_container_get_object_by_name(controls->mydata,
"/0/data"));
if (controls->in_init)
{
gwy_data_field_data_changed(dfield);
while (gtk_events_pending())
gtk_main_iteration();
return;
}
oxres = gwy_data_field_get_xres(dfield);
oyres = gwy_data_field_get_yres(dfield);
oxreal = gwy_data_field_get_xreal(dfield);
oyreal = gwy_data_field_get_yreal(dfield);
diff = oxreal/oxres/10;
size = args->size*5e-9;
// width = args->width*5e-9 + 2*size; //increased manually to fill boundaries
width = 2*size;
add = gwy_data_field_rtoi(dfield, size + width);
mdisize = gwy_data_field_rtoi(dfield, size);
xres = oxres + 2*add;
yres = oyres + 2*add;
xreal = oxreal + 2*(size+width);
yreal = oyreal + 2*(size+width);
// printf("For field of size %g and particle nominak %g, real %g (%g), the final size will change from %d to %d\n",
// gwy_data_field_get_xreal(dfield), args->size, size, disize, oxres, xres);
/*make copy of datafield, with mirrored boundaries*/
lfield = gwy_data_field_new(xres, yres,
gwy_data_field_itor(dfield, xres),
gwy_data_field_jtor(dfield, yres),
TRUE);
gwy_data_field_area_copy(dfield, lfield, 0, 0, oxres, oyres, add, add);
gwy_data_field_invert(dfield, 1, 0, 0);
gwy_data_field_area_copy(dfield, lfield, 0, oyres-add-1, oxres, add, add, 0);
gwy_data_field_area_copy(dfield, lfield, 0, 0, oxres, add, add, yres-add-1);
gwy_data_field_invert(dfield, 1, 0, 0);
gwy_data_field_invert(dfield, 0, 1, 0);
gwy_data_field_area_copy(dfield, lfield, oxres-add-1, 0, add, oyres, 0, add);
gwy_data_field_area_copy(dfield, lfield, 0, 0, add, oyres, xres-add-1, add);
gwy_data_field_invert(dfield, 0, 1, 0);
gwy_data_field_invert(dfield, 1, 1, 0);
gwy_data_field_area_copy(dfield, lfield, oxres-add-1, oyres-add-1, add, add, 0, 0);
gwy_data_field_area_copy(dfield, lfield, 0, 0, add, add, xres-add-1, yres-add-1);
gwy_data_field_area_copy(dfield, lfield, oxres-add-1, 0, add, add, 0, yres-add-1);
gwy_data_field_area_copy(dfield, lfield, 0, oyres-add-1, add, add, xres-add-1, 0);
gwy_data_field_invert(dfield, 1, 1, 0);
zlfield = gwy_data_field_duplicate(lfield);
zdfield = gwy_data_field_duplicate(dfield);
/*determine number of spheres necessary for given coverage*/
for (i=0; i<10000; i++)
{
ax[i] = ay[i] = az[i] = vx[i] = vy[i] = vz[i] = 0;
}
srand ( time(NULL) );
ndata = 0;
/* for test only */
/*
disize = mdisize;
xpos = oxres/2 - 2*disize;
ypos = oyres/2;
xdata[ndata] = xpos;
ydata[ndata] = ypos;
disizes[ndata] = disize;
rdisizes[ndata] = size;
rx[ndata] = (gdouble)xpos*oxreal/(gdouble)oxres;
ry[ndata] = (gdouble)ypos*oyreal/(gdouble)oyres;
rz[ndata] = 2.0*gwy_data_field_get_val(lfield, xpos, ypos) + rdisizes[ndata];
ndata++;
xpos = oxres/2 + 2*disize;
ypos = oyres/2;
xdata[ndata] = xpos;
ydata[ndata] = ypos;
disizes[ndata] = disize;
rdisizes[ndata] = size;
rx[ndata] = (gdouble)xpos*oxreal/(gdouble)oxres;
ry[ndata] = (gdouble)ypos*oyreal/(gdouble)oyres;
rz[ndata] = 2.0*gwy_data_field_get_val(lfield, xpos, ypos) + rdisizes[ndata];
ndata++;
*/
/*end of test*/
i = 0;
presetval = args->coverage*10;
while (ndata < presetval && i<max)
{
//disize = mdisize*(0.8+(double)(rand()%20)/40.0);
disize = mdisize;
xpos = disize+(rand()%(xres-2*(gint)(disize+1))) + 1;
ypos = disize+(rand()%(yres-2*(gint)(disize+1))) + 1;
i++;
{
too_close = 0;
/*sync real to integer positions*/
for (k=0; k<ndata; k++)
{
if (((xpos-xdata[k])*(xpos-xdata[k]) + (ypos-ydata[k])*(ypos-ydata[k]))<(4*disize*disize))
{
too_close = 1;
break;
}
}
if (too_close) continue;
if (ndata>=10000) {
break;
}
xdata[ndata] = xpos;
ydata[ndata] = ypos;
disizes[ndata] = disize;
rdisizes[ndata] = size;
rx[ndata] = (gdouble)xpos*oxreal/(gdouble)oxres;
ry[ndata] = (gdouble)ypos*oyreal/(gdouble)oyres;
//printf("surface at %g, particle size %g\n", gwy_data_field_get_val(lfield, xpos, ypos), rdisizes[ndata]);
rz[ndata] = 1.0*gwy_data_field_get_val(lfield, xpos, ypos) + rdisizes[ndata]; //2
ndata++;
}
};
// if (i==max) printf("Maximum reached, only %d particles depositd instead of %d\n", ndata, presetval);
// else printf("%d particles depositd\n", ndata);
/*refresh shown data and integer positions (necessary in md calculation)*/
gwy_data_field_copy(zlfield, lfield, 0);
showit(lfield, zdfield, rdisizes, rx, ry, rz, xdata, ydata, ndata,
oxres, oxreal, oyres, oyreal, add, xres, yres);
gwy_data_field_area_copy(lfield, dfield, add, add, oxres, oyres, 0, 0);
gwy_data_field_data_changed(dfield);
for (i=0; i<(20*args->revise); i++)
{
// printf("###### step %d of %d ##########\n", i, (gint)(20*args->revise));
/*try to add some particles if necessary, do this only for first half of molecular dynamics*/
if (ndata<presetval && i<(10*args->revise)) {
ii = 0;
nloc = 0;
while (ndata < presetval && ii<(max/1000) && nloc<maxloc)
{
disize = mdisize;
xpos = disize+(rand()%(xres-2*(gint)(disize+1))) + 1;
ypos = disize+(rand()%(yres-2*(gint)(disize+1))) + 1;
ii++;
{
too_close = 0;
rxv = ((gdouble)xpos*oxreal/(gdouble)oxres);
ryv = ((gdouble)ypos*oyreal/(gdouble)oyres);
rzv = gwy_data_field_get_val(zlfield, xpos, ypos) + 5*size;
for (k=0; k<ndata; k++)
{
if (((rxv-rx[k])*(rxv-rx[k])
+ (ryv-ry[k])*(ryv-ry[k])
+ (rzv-rz[k])*(rzv-rz[k]))<(4.0*size*size))
{
too_close = 1;
break;
}
}
if (too_close) continue;
if (ndata>=10000) {
// printf("Maximum reached!\n");
break;
}
xdata[ndata] = xpos;
ydata[ndata] = ypos;
disizes[ndata] = disize;
rdisizes[ndata] = size;
rx[ndata] = rxv;
ry[ndata] = ryv;
rz[ndata] = rzv;
vz[ndata] = -0.01;
ndata++;
nloc++;
}
};
// if (ii==(max/100)) printf("Maximum reached, only %d particles now present instead of %d\n", ndata, presetval);
// else printf("%d particles now at surface\n", ndata);
}
/*test succesive LJ steps on substrate (no relaxation)*/
for (k=0; k<ndata; k++)
{
fx[k] = fy[k] = fz[k] = 0;
/*calculate forces for all particles on substrate*/
if (gwy_data_field_rtoi(lfield, rx[k])<0
|| gwy_data_field_rtoj(lfield, ry[k])<0
|| gwy_data_field_rtoi(lfield, rx[k])>=xres
|| gwy_data_field_rtoj(lfield, ry[k])>=yres)
continue;
for (m=0; m<ndata; m++)
{
if (m==k) continue;
// printf("(%g %g %g) on (%g %g %g)\n", rx[m], ry[m], rz[m], rx[k], ry[k], rz[k]);
fx[k] -= (get_lj_potential_spheres(rx[m], ry[m], rz[m], rx[k]+diff, ry[k], rz[k], gwy_data_field_itor(dfield, disizes[k]))
-get_lj_potential_spheres(rx[m], ry[m], rz[m], rx[k]-diff, ry[k], rz[k], gwy_data_field_itor(dfield, disizes[k])))/2/diff;
fy[k] -= (get_lj_potential_spheres(rx[m], ry[m], rz[m], rx[k], ry[k]+diff, rz[k], gwy_data_field_itor(dfield, disizes[k]))
-get_lj_potential_spheres(rx[m], ry[m], rz[m], rx[k], ry[k]-diff, rz[k], gwy_data_field_itor(dfield, disizes[k])))/2/diff;
fz[k] -= (get_lj_potential_spheres(rx[m], ry[m], rz[m], rx[k], ry[k], rz[k]+diff, gwy_data_field_itor(dfield, disizes[k]))
-get_lj_potential_spheres(rx[m], ry[m], rz[m], rx[k], ry[k], rz[k]-diff, gwy_data_field_itor(dfield, disizes[k])))/2/diff;
}
fx[k] -= (integrate_lj_substrate(zlfield, rx[k]+diff, ry[k], rz[k], rdisizes[k])
- integrate_lj_substrate(zlfield, rx[k]-diff, ry[k], rz[k], rdisizes[k]))/2/diff;
fy[k] -= (integrate_lj_substrate(zlfield, rx[k], ry[k]-diff, rz[k], rdisizes[k])
- integrate_lj_substrate(zlfield, rx[k], ry[k]+diff, rz[k], rdisizes[k]))/2/diff;
fz[k] -= (integrate_lj_substrate(zlfield, rx[k], ry[k], rz[k]+diff, rdisizes[k])
- integrate_lj_substrate(zlfield, rx[k], ry[k], rz[k]-diff, rdisizes[k]))/2/diff;
}
for (k=0; k<ndata; k++)
{
if (gwy_data_field_rtoi(lfield, rx[k])<0
|| gwy_data_field_rtoj(lfield, ry[k])<0
|| gwy_data_field_rtoi(lfield, rx[k])>=xres
|| gwy_data_field_rtoj(lfield, ry[k])>=yres)
continue;
/*move all particles*/
rx[k] += vx[k]*timestep + 0.5*ax[k]*timestep*timestep;
vx[k] += 0.5*ax[k]*timestep;
ax[k] = fx[k]/mass;
vx[k] += 0.5*ax[k]*timestep;
vx[k] *= 0.9;
if (fabs(vx[k])>0.01) vx[k] = 0; //0.2
ry[k] += vy[k]*timestep + 0.5*ay[k]*timestep*timestep;
vy[k] += 0.5*ay[k]*timestep;
ay[k] = fy[k]/mass;
vy[k] += 0.5*ay[k]*timestep;
vy[k] *= 0.9;
if (fabs(vy[k])>0.01) vy[k] = 0; //0.2
rz[k] += vz[k]*timestep + 0.5*az[k]*timestep*timestep;
vz[k] += 0.5*az[k]*timestep;
az[k] = fz[k]/mass;
vz[k] += 0.5*az[k]*timestep;
vz[k] *= 0.9;
if (fabs(vz[k])>0.01) vz[k] = 0;
if (rx[k]<=gwy_data_field_itor(dfield, disizes[k])) rx[k] = gwy_data_field_itor(dfield, disizes[k]);
if (ry[k]<=gwy_data_field_itor(dfield, disizes[k])) ry[k] = gwy_data_field_itor(dfield, disizes[k]);
if (rx[k]>=(xreal-gwy_data_field_itor(dfield, disizes[k]))) rx[k] = xreal-gwy_data_field_itor(dfield, disizes[k]);
if (ry[k]>=(yreal-gwy_data_field_itor(dfield, disizes[k]))) ry[k] = yreal-gwy_data_field_itor(dfield, disizes[k]);
}
gwy_data_field_copy(zlfield, lfield, 0);
showit(lfield, zdfield, rdisizes, rx, ry, rz, xdata, ydata, ndata,
oxres, oxreal, oyres, oyreal, add, xres, yres);
gwy_data_field_area_copy(lfield, dfield, add, add, oxres, oyres, 0, 0);
gwy_data_field_data_changed(dfield);
while (gtk_events_pending())
gtk_main_iteration();
}
gwy_data_field_area_copy(lfield, dfield, add, add, oxres, oyres, 0, 0);
gwy_data_field_data_changed(dfield);
args->computed = TRUE;
gwy_object_unref(lfield);
gwy_object_unref(zlfield);
gwy_object_unref(zdfield);
}
static void
immerse_search(ImmerseControls *controls,
gint search_type)
{
GwyDataField *dfield, *dfieldsub, *ifield, *iarea;
gdouble wr, hr, xpos, ypos, deltax, deltay;
gint w, h, xfrom, xto, yfrom, yto, ixres, iyres, col, row;
GwyContainer *data;
GQuark quark;
data = gwy_app_data_browser_get(controls->args->detail.datano);
quark = gwy_app_get_data_key_for_id(controls->args->detail.id);
dfield = gwy_container_get_object(data, quark);
data = gwy_app_data_browser_get(controls->args->image.datano);
quark = gwy_app_get_data_key_for_id(controls->args->image.id);
ifield = gwy_container_get_object(data, quark);
ixres = gwy_data_field_get_xres(ifield);
iyres = gwy_data_field_get_yres(ifield);
wr = gwy_data_field_get_xreal(dfield)/gwy_data_field_get_xmeasure(ifield);
hr = gwy_data_field_get_yreal(dfield)/gwy_data_field_get_ymeasure(ifield);
if (wr*hr < 6.0) {
g_warning("Detail image is too small for correlation");
return;
}
w = GWY_ROUND(MAX(wr, 1.0));
h = GWY_ROUND(MAX(hr, 1.0));
gwy_debug("w: %d, h: %d", w, h);
g_assert(w <= ixres && h <= iyres);
if (search_type == RESPONSE_REFINE) {
xfrom = gwy_data_field_rtoj(ifield, controls->args->xpos);
yfrom = gwy_data_field_rtoi(ifield, controls->args->ypos);
/* Calculate the area we will search the detail in */
deltax = improve_search_window(w, ixres);
deltay = improve_search_window(h, iyres);
gwy_debug("deltax: %g, deltay: %g", deltax, deltay);
xto = MIN(xfrom + w + deltax, ixres);
yto = MIN(yfrom + h + deltay, iyres);
xfrom = MAX(xfrom - deltax, 0);
yfrom = MAX(yfrom - deltay, 0);
}
else {
xfrom = yfrom = 0;
xto = ixres;
yto = iyres;
}
gwy_debug("x: %d..%d, y: %d..%d", xfrom, xto, yfrom, yto);
/* Cut out only the interesting part from the image data field */
if (xfrom == 0 && yfrom == 0 && xto == ixres && yto == iyres)
iarea = g_object_ref(ifield);
else
iarea = gwy_data_field_area_extract(ifield,
xfrom, yfrom,
xto - xfrom, yto - yfrom);
dfieldsub = gwy_data_field_new_resampled(dfield, w, h,
GWY_INTERPOLATION_LINEAR);
immerse_correlate(iarea, dfieldsub, &col, &row);
gwy_debug("[c] col: %d, row: %d", col, row);
col += xfrom;
row += yfrom;
xpos = gwy_data_field_jtor(dfieldsub, col + 0.5);
ypos = gwy_data_field_itor(dfieldsub, row + 0.5);
g_object_unref(iarea);
g_object_unref(dfieldsub);
gwy_debug("[C] col: %d, row: %d", col, row);
/* Upsample and refine */
xfrom = MAX(col - 1, 0);
yfrom = MAX(row - 1, 0);
xto = MIN(col + w + 1, ixres);
yto = MIN(row + h + 1, iyres);
gwy_debug("x: %d..%d, y: %d..%d", xfrom, xto, yfrom, yto);
iarea = gwy_data_field_area_extract(ifield,
xfrom, yfrom,
xto - xfrom, yto - yfrom);
wr = gwy_data_field_get_xreal(iarea)/gwy_data_field_get_xmeasure(dfield);
hr = gwy_data_field_get_yreal(iarea)/gwy_data_field_get_ymeasure(dfield);
gwy_data_field_resample(iarea, GWY_ROUND(wr), GWY_ROUND(hr),
GWY_INTERPOLATION_LINEAR);
immerse_correlate(iarea, dfield, &col, &row);
gwy_debug("[U] col: %d, row: %d", col, row);
xpos = gwy_data_field_jtor(dfield, col + 0.5)
+ gwy_data_field_jtor(ifield, xfrom);
ypos = gwy_data_field_itor(dfield, row + 0.5)
+ gwy_data_field_itor(ifield, yfrom);
g_object_unref(iarea);
immerse_clamp_detail_offset(controls, xpos, ypos);
}
