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); }