Code for incremental adding of inclusions done

Samo Penic

2020-04-26 3006183b769f2e126b1a96e6bf697c2b7f657df7

 src/restore.c

@@ -16,13 +16,14 @@
#include "poly.h"
#include "initial_distribution.h"
#include "io.h"
#include <math.h>

ts_vesicle *parseDump(char *dumpfname) {
   xmlDocPtr doc;
   xmlNodePtr cur, cur1,cur2;
   ts_vesicle *vesicle=NULL;
   doc = xmlParseFile(dumpfname);
	
   int i;
   if (doc == NULL ) {
      fatal("Dump file could not be found or parsed. It is correct file?",1);
   }
@@ -78,15 +79,19 @@
      // END Point Position data & Bonds
   cur = cur->next;
   }
	
   xmlFreeDoc(doc);

//   vesicle->poly_list=init_poly_list(0, 0, vesicle->vlist, vesicle);

   set_vesicle_values_from_tape(vesicle);
   init_normal_vectors(vesicle->tlist);
   mean_curvature_and_energy(vesicle);
   sweep_attraction_bond_energy(vesicle);

   if(vesicle->tape->stretchswitch==1){
      vesicle->tlist->a0=sqrt(3)/4.0*pow((vesicle->tape->dmax+1.0)/2.0,2);  
      for(i=0;i<vesicle->tlist->n;i++){
         stretchenergy(vesicle, vesicle->tlist->tria[i]);
      }
   }
/* TODO: filaments */

//   ts_fprintf(stdout,"Restoration completed\n");
@@ -151,7 +156,8 @@
   //fprintf(stderr,"nvtx=%u\n",atoi((char *)nvtx));
   //TODO: check if nvtx is in agreement with nshell from tape
   ts_vesicle *vesicle=init_vesicle(atoi((char *)nvtx),tape->ncxmax,tape->ncymax,tape->nczmax,tape->stepsize);
   //vesicle->poly_list=init_poly_list(atoi((char *)npoly),atoi((char *)nmono), vesicle->vlist, vesicle);
//   vesicle->poly_list=init_poly_list(atoi((char *)npoly),atoi((char *)nmono), vesicle->vlist, vesicle);
   vesicle->poly_list=init_empty_poly_list(atoi((char *)npoly),atoi((char *)nmono));
   xmlFree(nvtx);
   xmlFree(npoly);
   xmlFree(nmono);
@@ -184,9 +190,8 @@
   child = child->next;
   }


   vesicle->tape=tape;
   set_vesicle_values_from_tape(vesicle);
//   set_vesicle_values_from_tape(vesicle);
   return vesicle;
}

@@ -417,6 +422,7 @@
   char *b;
   int idx, polyidx;
   char *token[2];
   int temp_cnt=0;
   while (child != NULL) {
      conname=xmlGetProp(child, (xmlChar *)"Name");
      if ((!xmlStrcmp(child->name, (const xmlChar *)"DataArray")) && !xmlStrcmp(conname, (const xmlChar *)"connectivity") ){
@@ -428,11 +434,15 @@
         while(token[0]!=NULL){
            if(idx<3*(vesicle->vlist->n-2)){
               bond_add(vesicle->blist, vesicle->vlist->vtx[atoi(token[0])], vesicle->vlist->vtx[atoi(token[1])]);
               //fprintf(stderr,"Bonds in vesicle count idx=%d\n",idx);
            }
            else {
            //find grafted vtx
               if(vesicle->tape->npoly && vesicle->tape->nmono && (vesicle->tape->nmono-1)==(idx-3*(vesicle->vlist->n-2))%(vesicle->tape->nmono)
                  && idx<(3*vesicle->vlist->n-2+vesicle->tape->nmono*vesicle->tape->npoly+vesicle->tape->npoly)){
                  && idx<(3*vesicle->vlist->n-2+vesicle->tape->nmono*vesicle->tape->npoly)){
                  temp_cnt++;
                  //fprintf(stderr,"%d: Bonds in poly count idx=%d, t1=%s t2=%s\n",temp_cnt,idx, token[0], token[1]);
						
                  polyidx=(idx-3*(vesicle->vlist->n-2))/(vesicle->tape->nmono);
                  //fprintf(stderr,"poly=%d, vertex=%d\n",polyidx,atoi(token[0]));
                  vesicle->poly_list->poly[polyidx]->grafted_vtx=vesicle->vlist->vtx[atoi(token[0])];