From e2db4a0e170272935ccc8532bc245938aadc36fc Mon Sep 17 00:00:00 2001 From: Samo Penic <samo.penic@gmail.com> Date: Wed, 13 Jul 2016 21:29:09 +0000 Subject: [PATCH] Improved the code, still breaks --- src/poly.c | 166 ++++++++++++++++++++++++------------------------------- 1 files changed, 73 insertions(+), 93 deletions(-) diff --git a/src/poly.c b/src/poly.c index 9f66c0f..39d0723 100644 --- a/src/poly.c +++ b/src/poly.c @@ -53,44 +53,15 @@ } -ts_poly_list *init_poly_list(ts_uint n_poly, ts_uint n_mono, ts_vertex_list *vlist, ts_vesicle *vesicle){ - 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=0,j=0,k; //idx; - ts_uint gvtxi; - ts_double xnorm,ynorm,znorm,normlength; - ts_double dphi,dh; - cell_occupation(vesicle); //needed for evading the membrane - // Grafting polymers: - if (vlist!=NULL){ - 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++; - } - } - } - else - { - for(i=0;i<n_poly;i++){ - poly_list->poly[i] = init_poly(n_mono, NULL); - } - } - poly_list->n = n_poly; - - if (vlist!=NULL){ +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 l; - for (i=0;i<poly_list->n;i++){ - + ts_int j,k,l,m; xnorm=0.0; ynorm=0.0; znorm=0.0; @@ -106,7 +77,6 @@ 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; @@ -123,94 +93,104 @@ //} //trying to go towards normal k=0; - l=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]); + 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. - 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 bipytamid 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; - } - // if(j>0) break; - // if((xnorm*sintheta*cos(phi)+ynorm*sintheta*sin(phi)+znorm*costheta)<0.0 && j==0) break; - } - // while(j==0); + 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 + printf("was here\n"); + 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){ - //lets choose another grafting vertex; - while(1){ - gvtxi = rand() % vesicle->vlist->n; - if (vesicle->vlist->vtx[gvtxi]->grafted_poly == NULL){ - ts_fprintf(stdout,"Found new potential grafting vertex %d for poly %d\n",gvtxi,i); - poly_list->poly[i]->grafted_vtx->grafted_poly=NULL; - poly_list->poly[i]->grafted_vtx = vesicle->vlist->vtx[gvtxi]; - vesicle->vlist->vtx[gvtxi]->grafted_poly = poly_list->poly[i]; - l++; - k=0; - xnorm=0.0; - ynorm=0.0; - znorm=0.0; - int o; - for (o=0;o<poly_list->poly[i]->grafted_vtx->tristar_no;o++){ - xnorm-=poly_list->poly[i]->grafted_vtx->tristar[o]->xnorm; - ynorm-=poly_list->poly[i]->grafted_vtx->tristar[o]->ynorm; - znorm-=poly_list->poly[i]->grafted_vtx->tristar[o]->znorm; - } - normlength=sqrt(xnorm*xnorm+ynorm*ynorm+znorm*znorm); - if(intpoly && i%2){ - normlength=-normlength; - } - xnorm=xnorm/normlength; - ynorm=ynorm/normlength; - znorm=znorm/normlength; - prevPosX=poly_list->poly[i]->grafted_vtx->x; - prevPosY=poly_list->poly[i]->grafted_vtx->y; - prevPosZ=poly_list->poly[i]->grafted_vtx->z; - //prepare starting position for building the polymeres - posX=prevPosX+xnorm*(vesicle->clist->dmin_interspecies); - posY=prevPosY+ynorm*(vesicle->clist->dmin_interspecies); - posZ=prevPosZ+znorm*(vesicle->clist->dmin_interspecies); - break; - } + //undo changes to the cell + for(l=0;l<j-1;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]); } - if(l>1000) - fatal("Cannot make internal polymeres. No space inside the vesicle?",1001); + return TS_FAIL; } } prevPosX=posX; prevPosY=posY; prevPosZ=posZ; } + printf("did it\n"); + return TS_SUCCESS; + +} + + +ts_poly_list *init_poly_list(ts_uint n_poly, ts_uint n_mono, ts_vertex_list *vlist, ts_vesicle *vesicle){ + 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=0,j=0; //idx; + ts_uint gvtxi; + ts_bool retval; + ts_double dphi,dh; + cell_occupation(vesicle); //needed for evading the membrane + // Grafting polymers: + if (vlist!=NULL){ + 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]); + 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); + } + else { + i++; + } + } } } else { + for(i=0;i<n_poly;i++){ + poly_list->poly[i] = init_poly(n_mono, NULL); + } + } + + poly_list->n = n_poly; + + if (vlist!=NULL){ + } + else + { /* Make filaments inside the vesicle. Helix with radius... Dist. between poly vertices put to 1*/ ts_double a,R,H,tantheta,h,r,phi,A0=1.2; -- Gitblit v1.9.3