Moved all global variables to separate file and defined extern keyword wher...

Samo Penic

2022-05-04 06afc729f9061c1cfa14c78728d61d518324c2f0

 src/poly.c

@@ -1,3 +1,4 @@
/* vim: set ts=4 sts=4 sw=4 noet : */
#include"general.h"
#include"poly.h"
#include<stdlib.h>
@@ -5,7 +6,8 @@
#include"bond.h"
#include<math.h>
#include"energy.h"

#include"cell.h"
#include"frame.h"
ts_bool poly_assign_filament_xi(ts_vesicle *vesicle, ts_tape *tape){
   ts_uint i;

@@ -46,8 +48,106 @@
   poly->blist->bond[i]->bond_length=sqrt(vtx_distance_sq(poly->blist->bond[i]->vtx1,poly->blist->bond[i]->vtx2));
   bond_energy(poly->blist->bond[i],poly);
   }

   vertex_list_assign_id(poly->vlist,TS_ID_FILAMENT);
   return poly;
}



ts_bool poly_initial_distribution(ts_poly_list *poly_list, ts_int i, ts_vesicle *vesicle){
   /* Make straight grafted poylmers normal to membrane (polymer brush). Dist. between poly vertices put to 1*/
      ts_double xnorm,ynorm,znorm,normlength;
      ts_int intpoly=vesicle->tape->internal_poly;
      ts_int cellidx;
      ts_double posX,posY,posZ,prevPosX,prevPosY,prevPosZ, phi,costheta,sintheta;
      ts_bool retval;
      ts_int j,k,l,m;
         xnorm=0.0;
         ynorm=0.0;
         znorm=0.0;
         for (j=0;j<poly_list->poly[i]->grafted_vtx->tristar_no;j++){
            xnorm-=poly_list->poly[i]->grafted_vtx->tristar[j]->xnorm;
            ynorm-=poly_list->poly[i]->grafted_vtx->tristar[j]->ynorm;
            znorm-=poly_list->poly[i]->grafted_vtx->tristar[j]->znorm;	
         }
         normlength=sqrt(xnorm*xnorm+ynorm*ynorm+znorm*znorm);
         if(intpoly && i%2){
            normlength=-normlength;
         }
         xnorm=xnorm/normlength;
         ynorm=ynorm/normlength;
         znorm=znorm/normlength;
         //prepare starting position for building the polymeres
         prevPosX=poly_list->poly[i]->grafted_vtx->x;
         prevPosY=poly_list->poly[i]->grafted_vtx->y;
         prevPosZ=poly_list->poly[i]->grafted_vtx->z;
         for (j=0;j<poly_list->poly[i]->vlist->n;j++){
            //if(j==0){
               posX=prevPosX+xnorm*(vesicle->clist->dmin_interspecies);
               posY=prevPosY+ynorm*(vesicle->clist->dmin_interspecies);
               posZ=prevPosZ+znorm*(vesicle->clist->dmin_interspecies);
            //}else{
            //   posX=prevPosX+xnorm;
            //   posY=prevPosY+ynorm;
            //   posZ=prevPosZ+znorm;
            //}
            //trying to go towards normal
            k=0;
            while(1){
               poly_list->poly[i]->vlist->vtx[j]->x = posX;
               poly_list->poly[i]->vlist->vtx[j]->y = posY;
               poly_list->poly[i]->vlist->vtx[j]->z = posZ;
               cellidx=vertex_self_avoidance(vesicle, poly_list->poly[i]->vlist->vtx[j]);
               retval=cell_occupation_number_and_internal_proximity(vesicle->clist,cellidx,poly_list->poly[i]->vlist->vtx[j]);
               if(retval==TS_SUCCESS){
                  retval=cell_add_vertex(vesicle->clist->cell[cellidx],poly_list->poly[i]->vlist->vtx[j]);
                  break;
               }
               else{
               //   printf("%d %d Cannot put the vertex here. Finding another position\n",i,j);
                  //randomly change the direction.
                  m=0;
                  //we must move first vertex into the vesicle if the normal is in or out of the vesicle if the normal is out
                  do{
                     costheta=2.0*drand48()-1.0;
                     sintheta=sqrt(1-pow(costheta,2));
                     phi=drand48()*2.0*M_PI;
                     if(j==0){
                  //for special cases, when we are on the edge of bipyramid  the distance od dmin_interspecies is not enough
                        posX=prevPosX+vesicle->dmax*sintheta*cos(phi);
                        posY=prevPosY+vesicle->dmax*sintheta*sin(phi);
                        posZ=prevPosZ+vesicle->dmax*costheta;

                     } else {
                        posX=prevPosX+vesicle->clist->dmin_interspecies*sintheta*cos(phi);
                        posY=prevPosY+vesicle->clist->dmin_interspecies*sintheta*sin(phi);
                        posZ=prevPosZ+vesicle->clist->dmin_interspecies*costheta;
                     }
                     m++;
                     if(m>1000) {
                        k=9999; //break also ot of the outer loop
                        break;
                     }
                  }
                  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);
               }
               k++;
               if(k>1000){
                  //undo changes to the cell
                  for(l=0;l<j;l++){
                     cellidx=vertex_self_avoidance(vesicle, poly_list->poly[i]->vlist->vtx[l]);
                     cell_remove_vertex(vesicle->clist->cell[cellidx],poly_list->poly[i]->vlist->vtx[l]);
                  }
                  return TS_FAIL;
               }
            }
            prevPosX=posX;
            prevPosY=posY;
            prevPosZ=posZ;
         }
   printf("did it\n");
   return TS_SUCCESS;

}


@@ -56,19 +156,31 @@
   poly_list->poly   = (ts_poly **)calloc(n_poly,sizeof(ts_poly *));
   ts_uint i=0,j=0; //idx;
   ts_uint gvtxi;
   ts_double xnorm,ynorm,znorm,normlength;
   ts_bool retval;
   ts_double dphi,dh;
   ts_uint ji;

   cell_occupation(vesicle); //needed for evading the membrane
   // Grafting polymers:
   int tries=0;
   if (vlist!=NULL){
      if (n_poly > vlist->n){fatal("Number of polymers larger then numbero f vertices on a vesicle.",310);}
	
      if (n_poly > vlist->n){fatal("Number of polymers larger than numbero f vertices on a vesicle.",310);}
      while(i<n_poly){
         gvtxi = rand() % vlist->n;
         if (vlist->vtx[gvtxi]->grafted_poly == NULL){
         poly_list->poly[i] = init_poly(n_mono, vlist->vtx[gvtxi]);
         i++;
            poly_list->poly[i] = init_poly(n_mono, vlist->vtx[gvtxi]);
            retval=poly_initial_distribution(poly_list, i, vesicle);
            if(retval==TS_FAIL){
               ts_fprintf(stdout,"Found new potential grafting vertex %d for poly %d\n",gvtxi,i);
               poly_free(poly_list->poly[i]);
               tries++;
            }
            else {
               tries=0;
               i++;
            }
            if(tries>5000){
               fatal("Cannot find space for inner polymeres",1001);
            }
         }
      }
   }
@@ -82,40 +194,33 @@
   poly_list->n = n_poly;

   if (vlist!=NULL){
   /* Make straight grafted poylmers normal to membrane (polymer brush). Dist. between poly vertices put to 1*/
      for (i=0;i<poly_list->n;i++){
	
         xnorm=0.0;
         ynorm=0.0;
         znorm=0.0;
         for (j=0;j<poly_list->poly[i]->grafted_vtx->tristar_no;j++){
            xnorm-=poly_list->poly[i]->grafted_vtx->tristar[j]->xnorm;
            ynorm-=poly_list->poly[i]->grafted_vtx->tristar[j]->ynorm;
            znorm-=poly_list->poly[i]->grafted_vtx->tristar[j]->znorm;	
         }
         normlength=sqrt(xnorm*xnorm+ynorm*ynorm+znorm*znorm);
         xnorm=xnorm/normlength;
         ynorm=ynorm/normlength;
         znorm=znorm/normlength;

         for (j=0;j<poly_list->poly[i]->vlist->n;j++){
            poly_list->poly[i]->vlist->vtx[j]->x = poly_list->poly[i]->grafted_vtx->x + xnorm*(ts_double)(j+1);
            poly_list->poly[i]->vlist->vtx[j]->y = poly_list->poly[i]->grafted_vtx->y + ynorm*(ts_double)(j+1);
            poly_list->poly[i]->vlist->vtx[j]->z = poly_list->poly[i]->grafted_vtx->z + znorm*(ts_double)(j+1);
         }
      }
   }
   else
   {
   /* Make filaments inside the vesicle. Helix with radius... Dist. between poly vertices put to 1*/
      dphi = 2.0*asin(1.0/2.0/vesicle->R_nucleus)*1.01;
      dh = dphi/2.0/M_PI*1.01;
   ts_double a,R,H,tantheta,h,r,phi,A0=1.2;

      a = A0*(ts_double)vesicle->nshell;
      R = A0*((ts_double)vesicle->nshell)/(2.0*sin(M_PI/5.0));
      H = sqrt(a*a - R*R);
      tantheta = sqrt(R*R - a*a/4.0)/H;
		
      h = -H + sqrt(vesicle->clist->dmin_interspecies)*1.5;
      r = (H-fabs(h))*tantheta - sqrt(vesicle->clist->dmin_interspecies)*1.5;
      dphi = 2.0*asin(1.0/2.0/r)*1.001;
      dh = dphi/2.0/M_PI*1.001;
      phi=0.0;
      for(i=0;i<poly_list->n;i++){
         for (j=0;j<poly_list->poly[i]->vlist->n;j++){
            ji = j + i*poly_list->poly[i]->vlist->n;
            poly_list->poly[i]->vlist->vtx[j]->x = vesicle->R_nucleus*cos(ji*dphi);
            poly_list->poly[i]->vlist->vtx[j]->y = vesicle->R_nucleus*sin(ji*dphi);
            poly_list->poly[i]->vlist->vtx[j]->z = ji*dh - (dh*poly_list->n*poly_list->poly[i]->vlist->n/2.0);
            h = h + dh;
            r = (H-fabs(h))*tantheta - sqrt(vesicle->clist->dmin_interspecies)*1.5;
            dphi = 2.0*asin(1.0/2.0/r)*1.001;
            dh = dphi/2.0/M_PI*1.001;
            phi+=dphi;
            //ji = j + i*poly_list->poly[i]->vlist->n;
            poly_list->poly[i]->vlist->vtx[j]->x = r*cos(phi);
            poly_list->poly[i]->vlist->vtx[j]->y = r*sin(phi);
            poly_list->poly[i]->vlist->vtx[j]->z = h;// ji*dh - (dh*poly_list->n*poly_list->poly[i]->vlist->n/2.0);
         }
      }
   }
@@ -130,16 +235,16 @@
      }
   }
*/

	
   return poly_list;
}


ts_bool poly_free(ts_poly *poly){

   if (poly->grafted_vtx!=NULL){
      poly->grafted_vtx->grafted_poly=NULL;
   }
//   if (poly->grafted_vtx!=NULL){
//      poly->grafted_vtx->grafted_poly=NULL;
//   }
   vtx_list_free(poly->vlist);
   bond_list_free(poly->blist);
   free(poly);
@@ -149,8 +254,9 @@

ts_bool poly_list_free(ts_poly_list *poly_list){
   ts_uint i;

   //fprintf(stderr,"no. of polys=%d\n", poly_list->n);
   for(i=0;i<poly_list->n;i++){
   //   fprintf(stderr,"%d poly address in mem=%ld\n",i+1,(long)&(poly_list->poly[i]));
      poly_free(poly_list->poly[i]);
   }
   free(poly_list->poly);
@@ -158,3 +264,54 @@
   
   return TS_SUCCESS;
}


ts_poly *remove_poly_with_index(ts_poly_list *poly_list, ts_uint idx){
   ts_uint i;
   ts_poly *removed_poly=poly_list->poly[idx];

   poly_list->n--; //decrease the total number of polymeres
   for(i=idx;i<poly_list->n;i++){ //move the rest of the polymeres up.
      poly_list->poly[i]=poly_list->poly[i+1];
//      poly_list->poly[idx]->idx=idx;
   }
	
   return removed_poly;
}


ts_bool remove_random_polymeres(ts_poly_list *poly_list, ts_uint number){

   ts_uint i, idx;
   ts_poly *poly;

   ts_poly **new_poly_array;
   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);
   for(i=number;i>0;i--){
      idx=rand() % poly_list->n;
      poly=remove_poly_with_index(poly_list, idx);
      poly_free(poly);
   }
   printf("Addr before %ld\n", (long)poly_list->poly);
   new_poly_array=(ts_poly **)calloc(poly_list->n,sizeof(ts_poly *));
   for(i=0;i<poly_list->n;i++){
      new_poly_array[i]=poly_list->poly[i];
   }
   free(poly_list->poly);
   poly_list->poly=new_poly_array;
   printf("Addr after %ld\n", (long)poly_list->poly);
   return TS_SUCCESS;
}



ts_poly_list *init_empty_poly_list(ts_uint n_poly, ts_uint n_mono){
   ts_poly_list *poly_list=(ts_poly_list *)calloc(1,sizeof(ts_poly_list));
   poly_list->poly=(ts_poly **)calloc(n_poly,sizeof(ts_poly *));
   ts_uint i;
   for (i=0; i<n_poly;i++){
      poly_list->poly[i]=init_poly(n_mono, NULL);
   }
   poly_list->n = n_poly;
   return poly_list;
}