Cleanup of stretching energy plugin

Samo Penic

2019-03-09 60c2b879f26c5f008af0df7d7f159d33077225ac

 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);
   }
@@ -54,6 +55,10 @@
            if ((!xmlStrcmp(cur1->name, (const xmlChar *)"Piece"))){
               cur2=cur1->xmlChildrenNode;
               while(cur2!=NULL){
                  if ((!xmlStrcmp(cur2->name, (const xmlChar *)"PointData"))){
                     if(vesicle!=NULL)
                        parseXMLPointData(vesicle,doc,cur2);
                  }
                  if ((!xmlStrcmp(cur2->name, (const xmlChar *)"Points"))){
                     //fprintf(stderr,"Found point data\n");
                     if(vesicle!=NULL)
@@ -81,7 +86,13 @@

   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");
@@ -182,7 +193,6 @@

   vesicle->tape=tape;
   set_vesicle_values_from_tape(vesicle);

   return vesicle;
}

@@ -318,7 +328,48 @@
   return TS_SUCCESS;
}


/* this parses the data for vertices (like spontaneous curvature, etc.) */
ts_bool parseXMLPointData(ts_vesicle *vesicle,xmlDocPtr doc, xmlNodePtr cur){
   xmlNodePtr child = cur->xmlChildrenNode;
   xmlChar *property_name;
   xmlChar *values;
   char *vals;
   char *token;
   int idx, polyidx, monoidx, filidx, fonoidx;
   while (child != NULL) {
      if ((!xmlStrcmp(child->name, (const xmlChar *)"DataArray"))){
         property_name=xmlGetProp(child, (xmlChar *)"Name");
      //   fprintf(stderr,"Name: %s\n", property_name);
         if(!xmlStrcmp(property_name,(const xmlChar *)"spontaneous_curvature")){
            values=xmlNodeListGetString(doc,child->xmlChildrenNode,1);
            vals=(char *)values;
            token=strtok(vals," ");
            idx=0;
            while(token!=NULL){
               if(idx<vesicle->vlist->n){
                  vesicle->vlist->vtx[idx]->c=atof(token);
               } else if(vesicle->tape->nmono && vesicle->tape->npoly && idx<vesicle->vlist->n+vesicle->tape->nmono*vesicle->tape->npoly) {
                  polyidx=(idx-vesicle->vlist->n)/vesicle->tape->nmono;
                  monoidx=(idx-vesicle->vlist->n)%vesicle->tape->nmono;
                  vesicle->poly_list->poly[polyidx]->vlist->vtx[monoidx]->c=atof(token);
               } else {
                  filidx=(idx-vesicle->vlist->n-vesicle->tape->nmono*vesicle->tape->npoly)/vesicle->tape->nfono;
                  fonoidx=(idx-vesicle->vlist->n-vesicle->tape->nmono*vesicle->tape->npoly)%vesicle->tape->nfono;
                  //fprintf(stderr,"filidx=%d, fonoidx=%d, coord=%s,%s,%s\n",filidx,fonoidx,token[0],token[1],token[2]);
                  vesicle->filament_list->poly[filidx]->vlist->vtx[fonoidx]->c=atof(token);
               }
               idx++;
               token=strtok(NULL," ");
            }
            xmlFree(values);		
         }
         xmlFree(property_name);
      }
		
      child=child->next;
   }
   return TS_SUCCESS;
}
/* this is a parser of vertex positions and bonds from main xml data */
ts_bool parseXMLVertexPosition(ts_vesicle *vesicle,xmlDocPtr doc, xmlNodePtr cur){
   xmlNodePtr child = cur->xmlChildrenNode;