Did restore. Segfaults.

Samo Penic

2019-10-19 1eb75bcca71b97196c1ad29da5d082a21b12cf00

 src/restore.c

@@ -7,7 +7,7 @@
#include <general.h>
#include <restore.h>
#include <snapshot.h>
#include <zlib.h>
#include <b64zlib_compression.h>
#include "vesicle.h"
#include "vertex.h"
#include "triangle.h"
@@ -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);
   }
@@ -54,9 +55,14 @@
            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)
                        //fprintf(stderr,"Fils: %ld, Nfono: %ld\n", vesicle->tape->nfil, vesicle->tape->nfono);
                        parseXMLVertexPosition(vesicle, doc, cur2);
                  }
                  if ((!xmlStrcmp(cur2->name, (const xmlChar *)"Cells"))){
@@ -73,17 +79,22 @@
      // 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");
//   ts_fprintf(stdout,"Restoration completed\n");
//   write_vertex_xml_file(vesicle,999);
//   vesicle_free(vesicle);
//   exit(0);
@@ -145,7 +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);
@@ -164,20 +176,55 @@
       if ((!xmlStrcmp(child->name, (const xmlChar *)"tristar"))){
         parseTrisurfTristar(vesicle, doc, child);
      }
       if ((!xmlStrcmp(child->name, (const xmlChar *)"nucleus"))){
         parseTrisurfNucleus(vesicle, doc, child);
      }
        if ((!xmlStrcmp(child->name, (const xmlChar *)"constant_volume"))){
         parseTrisurfConstantVolume(doc, child);
      }
        if ((!xmlStrcmp(child->name, (const xmlChar *)"constant_area"))){
         parseTrisurfConstantArea(doc, child);
      }


   child = child->next;
   }


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

//   set_vesicle_values_from_tape(vesicle);
   return vesicle;
}



/* Low level tags parsers */
ts_bool parseTrisurfConstantVolume(xmlDocPtr doc, xmlNodePtr cur){
   xmlChar *cvol = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1);
   char *n=(char *)cvol;
   V0=atof(n);
   xmlFree(cvol);
   return TS_SUCCESS;
}
ts_bool parseTrisurfConstantArea(xmlDocPtr doc, xmlNodePtr cur){
   xmlChar *carea = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1);
   char *n=(char *)carea;
   A0=atof(n);
   xmlFree(carea);
   return TS_SUCCESS;
}

ts_bool parseTrisurfNucleus(ts_vesicle *vesicle, xmlDocPtr doc, xmlNodePtr cur){
   xmlChar *coords = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1);
   char *n=(char *)coords;
   char *token=strtok(n," ");
   ts_uint i;
   for(i=0;i<3;i++){
      vesicle->nucleus_center[i]=atof(token);
      token=strtok(NULL," ");
   }
   xmlFree(coords);
   return TS_SUCCESS;
}

ts_bool parseTrisurfVtxn(ts_vertex_list *vlist, xmlDocPtr doc, xmlNodePtr cur){

@@ -280,42 +327,95 @@
   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;
            unsigned long data_len=0;
            ts_double *curv_values=(double *)ts_decompress((unsigned char *)values,strlen((char *)values), &data_len);
//            token=strtok(vals," ");
            for(idx=0;idx<data_len;idx++){
//            while(token!=NULL){
               if(idx<vesicle->vlist->n){
                  vesicle->vlist->vtx[idx]->c=curv_values[idx]; //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=curv_values[idx];//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=curv_values[idx];//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;
   xmlChar *points;
   char *pts;
   int i, idx, polyidx, monoidx;
   char *token[3];
//   char *pts;
   int idx, polyidx, monoidx, filidx, fonoidx;
//   char *token[3];
   while (child != NULL) {
      if ((!xmlStrcmp(child->name, (const xmlChar *)"DataArray"))){
         points = xmlNodeListGetString(doc, child->xmlChildrenNode, 1);
         pts=(char *)points;
         token[0]=strtok(pts," ");
         token[1]=strtok(NULL," ");
         token[2]=strtok(NULL,"\n");
         idx=0;
         while(token[0]!=NULL){
         unsigned long data_len=0;
         ts_double *coords=(double *)ts_decompress((unsigned char *)points,strlen((char *)points), &data_len);
         //pts=(char *)points;
         //token[0]=strtok(pts," ");
         //token[1]=strtok(NULL," ");
         //token[2]=strtok(NULL,"\n");
         for(idx=0;idx<data_len;idx+=3){
//         while(token[0]!=NULL){
            if(idx<vesicle->vlist->n){
               vesicle->vlist->vtx[idx]->x=atof(token[0]);
               vesicle->vlist->vtx[idx]->y=atof(token[1]);
               vesicle->vlist->vtx[idx]->z=atof(token[2]);
            } else {
               vesicle->vlist->vtx[idx]->x=coords[idx];//atof(token[0]);
               vesicle->vlist->vtx[idx]->y=coords[idx+1];//atof(token[1]);
               vesicle->vlist->vtx[idx]->z=coords[idx+2];//atof(token[2]);
            } 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]->x=atof(token[0]);
               vesicle->poly_list->poly[polyidx]->vlist->vtx[monoidx]->y=atof(token[1]);
               vesicle->poly_list->poly[polyidx]->vlist->vtx[monoidx]->z=atof(token[2]);
               vesicle->poly_list->poly[polyidx]->vlist->vtx[monoidx]->x=coords[idx];//atof(token[0]);
               vesicle->poly_list->poly[polyidx]->vlist->vtx[monoidx]->y=coords[idx+1];//atof(token[1]);
               vesicle->poly_list->poly[polyidx]->vlist->vtx[monoidx]->z=coords[idx+2];//atof(token[2]);
            } 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]->x=coords[idx];//atof(token[0]);
               vesicle->filament_list->poly[filidx]->vlist->vtx[fonoidx]->y=coords[idx+1];//atof(token[1]);
               vesicle->filament_list->poly[filidx]->vlist->vtx[fonoidx]->z=coords[idx+2];//atof(token[2]);
            }
            for(i=0;i<2;i++)   token[i]=strtok(NULL," ");	
            token[2]=strtok(NULL,"\n");
            idx++;
            //for(i=0;i<2;i++)   token[i]=strtok(NULL," ");	
            //token[2]=strtok(NULL,"\n");
            //idx++;
         }
         xmlFree(points);
      }
      child=child->next;
   }
   //fprintf(stderr,"Came here\n");
   //fprintf(stderr,"Vertices position j=%d\n",idx);   

   return TS_SUCCESS;
@@ -323,33 +423,37 @@
ts_bool parseXMLBonds(ts_vesicle *vesicle,xmlDocPtr doc, xmlNodePtr cur){
   xmlNodePtr child = cur->xmlChildrenNode;
   xmlChar *bonds, *conname;
   char *b;
//   char *b;
   int idx, polyidx;
   char *token[2];
//   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") ){
         bonds = xmlNodeListGetString(doc, child->xmlChildrenNode, 1);
         b=(char *)bonds;
         token[0]=strtok(b," ");
         token[1]=strtok(NULL,"\n");
         idx=0;
         while(token[0]!=NULL){
         unsigned long data_len=0;
         unsigned long *conn=(unsigned long *)ts_decompress((unsigned char *)bonds,strlen((char *)bonds), &data_len);
         //token[0]=strtok(b," ");
         //token[1]=strtok(NULL,"\n");
         for(idx=0;idx<data_len;idx+=2){
//         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])]);
               bond_add(vesicle->blist, vesicle->vlist->vtx[conn[idx]], vesicle->vlist->vtx[conn[idx+1]]);
               //fprintf(stderr,"Bonds in vesicle count idx=%d\n",idx);
            }
            else {
            //find grafted vtx
               if((vesicle->tape->nmono-1)==(idx-3*(vesicle->vlist->n-2))%(vesicle->tape->nmono)){
               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)){
//                  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])];
                  vesicle->vlist->vtx[atoi(token[0])]->grafted_poly=vesicle->poly_list->poly[polyidx];
                  vesicle->poly_list->poly[polyidx]->grafted_vtx=vesicle->vlist->vtx[conn[idx]];
                  vesicle->vlist->vtx[conn[idx]]->grafted_poly=vesicle->poly_list->poly[polyidx];
               }
            }
            token[0]=strtok(NULL," ");	
            token[1]=strtok(NULL,"\n");	
            idx++;
         }
         xmlFree(bonds);
      }