/* vim: set ts=4 sts=4 sw=4 noet : */
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#include"general.h"
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#include"poly.h"
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#include<stdlib.h>
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#include"vertex.h"
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#include"bond.h"
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#include<math.h>
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#include"energy.h"
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#include"cell.h"
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#include"frame.h"
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ts_bool poly_assign_filament_xi(ts_vesicle *vesicle, ts_tape *tape){
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ts_uint i;
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for(i=0;i<vesicle->filament_list->n;i++){
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vesicle->filament_list->poly[i]->k = tape->xi;
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}
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return TS_SUCCESS;
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}
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ts_bool poly_assign_spring_const(ts_vesicle *vesicle){
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ts_uint i;
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for(i=0;i<vesicle->poly_list->n;i++){
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vesicle->poly_list->poly[i]->k = vesicle->spring_constant;
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}
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return TS_SUCCESS;
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}
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ts_poly *init_poly(ts_uint n, ts_vertex *grafted_vtx){
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ts_poly *poly=(ts_poly *)calloc(1,sizeof(ts_poly));
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poly->vlist = init_vertex_list(n);
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poly->blist = init_bond_list();
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if (grafted_vtx!=NULL){
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poly->grafted_vtx = grafted_vtx;
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grafted_vtx->grafted_poly = poly;
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}
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ts_uint i;
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for(i=0;i<n-1;i++){
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vtx_add_cneighbour(poly->blist, poly->vlist->vtx[i], poly->vlist->vtx[i+1]);
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vtx_add_neighbour(poly->vlist->vtx[i+1], poly->vlist->vtx[i]);
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}
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for(i=0;i<poly->blist->n;i++){
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poly->blist->bond[i]->bond_length=sqrt(vtx_distance_sq(poly->blist->bond[i]->vtx1,poly->blist->bond[i]->vtx2));
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bond_energy(poly->blist->bond[i],poly);
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}
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vertex_list_assign_id(poly->vlist,TS_ID_FILAMENT);
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return poly;
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}
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ts_bool poly_initial_distribution(ts_poly_list *poly_list, ts_int i, ts_vesicle *vesicle){
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/* Make straight grafted poylmers normal to membrane (polymer brush). Dist. between poly vertices put to 1*/
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ts_double xnorm,ynorm,znorm,normlength;
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ts_int intpoly=vesicle->tape->internal_poly;
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ts_int cellidx;
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ts_double posX,posY,posZ,prevPosX,prevPosY,prevPosZ, phi,costheta,sintheta;
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ts_bool retval;
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ts_int j,k,l,m;
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xnorm=0.0;
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ynorm=0.0;
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znorm=0.0;
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for (j=0;j<poly_list->poly[i]->grafted_vtx->tristar_no;j++){
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xnorm-=poly_list->poly[i]->grafted_vtx->tristar[j]->xnorm;
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ynorm-=poly_list->poly[i]->grafted_vtx->tristar[j]->ynorm;
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znorm-=poly_list->poly[i]->grafted_vtx->tristar[j]->znorm;
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}
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normlength=sqrt(xnorm*xnorm+ynorm*ynorm+znorm*znorm);
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if(intpoly && i%2){
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normlength=-normlength;
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}
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xnorm=xnorm/normlength;
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ynorm=ynorm/normlength;
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znorm=znorm/normlength;
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//prepare starting position for building the polymeres
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prevPosX=poly_list->poly[i]->grafted_vtx->x;
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prevPosY=poly_list->poly[i]->grafted_vtx->y;
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prevPosZ=poly_list->poly[i]->grafted_vtx->z;
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for (j=0;j<poly_list->poly[i]->vlist->n;j++){
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//if(j==0){
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posX=prevPosX+xnorm*(vesicle->clist->dmin_interspecies);
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posY=prevPosY+ynorm*(vesicle->clist->dmin_interspecies);
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posZ=prevPosZ+znorm*(vesicle->clist->dmin_interspecies);
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//}else{
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// posX=prevPosX+xnorm;
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// posY=prevPosY+ynorm;
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// posZ=prevPosZ+znorm;
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//}
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//trying to go towards normal
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k=0;
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while(1){
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poly_list->poly[i]->vlist->vtx[j]->x = posX;
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poly_list->poly[i]->vlist->vtx[j]->y = posY;
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poly_list->poly[i]->vlist->vtx[j]->z = posZ;
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cellidx=vertex_self_avoidance(vesicle, poly_list->poly[i]->vlist->vtx[j]);
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retval=cell_occupation_number_and_internal_proximity(vesicle->clist,cellidx,poly_list->poly[i]->vlist->vtx[j]);
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if(retval==TS_SUCCESS){
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retval=cell_add_vertex(vesicle->clist->cell[cellidx],poly_list->poly[i]->vlist->vtx[j]);
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break;
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}
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else{
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// printf("%d %d Cannot put the vertex here. Finding another position\n",i,j);
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//randomly change the direction.
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m=0;
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//we must move first vertex into the vesicle if the normal is in or out of the vesicle if the normal is out
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do{
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costheta=2.0*drand48()-1.0;
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sintheta=sqrt(1-pow(costheta,2));
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phi=drand48()*2.0*M_PI;
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if(j==0){
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//for special cases, when we are on the edge of bipyramid the distance od dmin_interspecies is not enough
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posX=prevPosX+vesicle->dmax*sintheta*cos(phi);
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posY=prevPosY+vesicle->dmax*sintheta*sin(phi);
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posZ=prevPosZ+vesicle->dmax*costheta;
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} else {
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posX=prevPosX+vesicle->clist->dmin_interspecies*sintheta*cos(phi);
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posY=prevPosY+vesicle->clist->dmin_interspecies*sintheta*sin(phi);
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posZ=prevPosZ+vesicle->clist->dmin_interspecies*costheta;
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}
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m++;
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if(m>1000) {
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k=9999; //break also ot of the outer loop
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break;
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}
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}
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while((xnorm*(poly_list->poly[i]->grafted_vtx->x-posX)+ynorm*(poly_list->poly[i]->grafted_vtx->y-posY)+znorm*(poly_list->poly[i]->grafted_vtx->z-posZ))>0.0 && j==0);
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}
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k++;
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if(k>1000){
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//undo changes to the cell
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for(l=0;l<j;l++){
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cellidx=vertex_self_avoidance(vesicle, poly_list->poly[i]->vlist->vtx[l]);
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cell_remove_vertex(vesicle->clist->cell[cellidx],poly_list->poly[i]->vlist->vtx[l]);
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}
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return TS_FAIL;
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}
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}
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prevPosX=posX;
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prevPosY=posY;
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prevPosZ=posZ;
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}
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printf("did it\n");
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return TS_SUCCESS;
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}
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ts_poly_list *init_poly_list(ts_uint n_poly, ts_uint n_mono, ts_vertex_list *vlist, ts_vesicle *vesicle){
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ts_poly_list *poly_list=(ts_poly_list *)calloc(1,sizeof(ts_poly_list));
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poly_list->poly = (ts_poly **)calloc(n_poly,sizeof(ts_poly *));
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ts_uint i=0,j=0; //idx;
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ts_uint gvtxi;
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ts_bool retval;
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ts_double dphi,dh;
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cell_occupation(vesicle); //needed for evading the membrane
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// Grafting polymers:
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int tries=0;
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if (vlist!=NULL){
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if (n_poly > vlist->n){fatal("Number of polymers larger than numbero f vertices on a vesicle.",310);}
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while(i<n_poly){
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gvtxi = rand() % vlist->n;
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if (vlist->vtx[gvtxi]->grafted_poly == NULL){
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poly_list->poly[i] = init_poly(n_mono, vlist->vtx[gvtxi]);
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retval=poly_initial_distribution(poly_list, i, vesicle);
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if(retval==TS_FAIL){
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ts_fprintf(stdout,"Found new potential grafting vertex %d for poly %d\n",gvtxi,i);
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poly_free(poly_list->poly[i]);
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tries++;
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}
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else {
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tries=0;
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i++;
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}
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if(tries>5000){
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fatal("Cannot find space for inner polymeres",1001);
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}
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}
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}
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}
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else
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{
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for(i=0;i<n_poly;i++){
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poly_list->poly[i] = init_poly(n_mono, NULL);
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}
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}
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poly_list->n = n_poly;
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if (vlist!=NULL){
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}
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else
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{
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/* Make filaments inside the vesicle. Helix with radius... Dist. between poly vertices put to 1*/
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ts_double a,R,H,tantheta,h,r,phi,A0=1.2;
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a = A0*(ts_double)vesicle->nshell;
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R = A0*((ts_double)vesicle->nshell)/(2.0*sin(M_PI/5.0));
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H = sqrt(a*a - R*R);
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tantheta = sqrt(R*R - a*a/4.0)/H;
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h = -H + sqrt(vesicle->clist->dmin_interspecies)*1.5;
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r = (H-fabs(h))*tantheta - sqrt(vesicle->clist->dmin_interspecies)*1.5;
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dphi = 2.0*asin(1.0/2.0/r)*1.001;
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dh = dphi/2.0/M_PI*1.001;
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phi=0.0;
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for(i=0;i<poly_list->n;i++){
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for (j=0;j<poly_list->poly[i]->vlist->n;j++){
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h = h + dh;
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r = (H-fabs(h))*tantheta - sqrt(vesicle->clist->dmin_interspecies)*1.5;
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dphi = 2.0*asin(1.0/2.0/r)*1.001;
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dh = dphi/2.0/M_PI*1.001;
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phi+=dphi;
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//ji = j + i*poly_list->poly[i]->vlist->n;
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poly_list->poly[i]->vlist->vtx[j]->x = r*cos(phi);
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poly_list->poly[i]->vlist->vtx[j]->y = r*sin(phi);
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poly_list->poly[i]->vlist->vtx[j]->z = h;// ji*dh - (dh*poly_list->n*poly_list->poly[i]->vlist->n/2.0);
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}
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}
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}
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//index correction for polymeres. Important, since each vtx has to have unique id
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/* idx=vlist->n;
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for(i=0;i<n_poly;i++){
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for(j=0;j<n_mono;j++,idx++){
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poly_list->poly[i]->vlist->vtx[j]->idx=idx;
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}
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}
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*/
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return poly_list;
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}
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ts_bool poly_free(ts_poly *poly){
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// if (poly->grafted_vtx!=NULL){
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// poly->grafted_vtx->grafted_poly=NULL;
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// }
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vtx_list_free(poly->vlist);
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bond_list_free(poly->blist);
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free(poly);
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return TS_SUCCESS;
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}
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ts_bool poly_list_free(ts_poly_list *poly_list){
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ts_uint i;
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//fprintf(stderr,"no. of polys=%d\n", poly_list->n);
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for(i=0;i<poly_list->n;i++){
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// fprintf(stderr,"%d poly address in mem=%ld\n",i+1,(long)&(poly_list->poly[i]));
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poly_free(poly_list->poly[i]);
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}
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free(poly_list->poly);
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free(poly_list);
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return TS_SUCCESS;
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}
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ts_poly *remove_poly_with_index(ts_poly_list *poly_list, ts_uint idx){
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ts_uint i;
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ts_poly *removed_poly=poly_list->poly[idx];
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poly_list->n--; //decrease the total number of polymeres
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for(i=idx;i<poly_list->n;i++){ //move the rest of the polymeres up.
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poly_list->poly[i]=poly_list->poly[i+1];
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// poly_list->poly[idx]->idx=idx;
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}
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return removed_poly;
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}
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ts_bool remove_random_polymeres(ts_poly_list *poly_list, ts_uint number){
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ts_uint i, idx;
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ts_poly *poly;
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ts_poly **new_poly_array;
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if(number>poly_list->n) fatal("The number of polymeres to be removed from the list is greater than the number of total polymeres in the list",999);
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for(i=number;i>0;i--){
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idx=rand() % poly_list->n;
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poly=remove_poly_with_index(poly_list, idx);
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poly_free(poly);
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}
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printf("Addr before %ld\n", (long)poly_list->poly);
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new_poly_array=(ts_poly **)calloc(poly_list->n,sizeof(ts_poly *));
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for(i=0;i<poly_list->n;i++){
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new_poly_array[i]=poly_list->poly[i];
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}
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free(poly_list->poly);
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poly_list->poly=new_poly_array;
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printf("Addr after %ld\n", (long)poly_list->poly);
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return TS_SUCCESS;
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}
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ts_poly_list *init_empty_poly_list(ts_uint n_poly, ts_uint n_mono){
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ts_poly_list *poly_list=(ts_poly_list *)calloc(1,sizeof(ts_poly_list));
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poly_list->poly=(ts_poly **)calloc(n_poly,sizeof(ts_poly *));
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ts_uint i;
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for (i=0; i<n_poly;i++){
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poly_list->poly[i]=init_poly(n_mono, NULL);
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}
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poly_list->n = n_poly;
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return poly_list;
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}
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