restoring vertices with spontaneous curvatures seems to work, however, the ...

Samo Penic

2016-07-03 def8b5262e183297ccee42ebbf9ebdb89c10f44c

restoring vertices with spontaneous curvatures seems to work, however, the dumped energy differs on last few decimal places

 src/initial_distribution.c

@@ -44,6 +44,7 @@
    vesicle=initial_distribution_dipyramid(tape->nshell,tape->ncxmax,tape->ncymax,tape->nczmax,tape->stepsize);
        vesicle->tape=tape;
    set_vesicle_values_from_tape(vesicle);
        initial_population_with_c0(vesicle,tape);
    return vesicle;
}

@@ -111,7 +112,14 @@
        vesicle->sphHarmonics=NULL;
    }

    int rndvtx;
    
    return TS_SUCCESS;

}


ts_bool initial_population_with_c0(ts_vesicle *vesicle, ts_tape *tape){
    int rndvtx,i,j;
    if(tape->number_of_vertices_with_c0>0){
        ts_fprintf(stderr,"Setting values for spontaneous curvature as defined in tape\n");
        j=0;
@@ -133,13 +141,8 @@
            sweep_attraction_bond_energy(vesicle);
        }
    }
    
    return TS_SUCCESS;

}





ts_bool pentagonal_dipyramid_vertex_distribution(ts_vertex_list *vlist){

 src/initial_distribution.h

@@ -15,6 +15,8 @@

ts_vesicle *create_vesicle_from_tape(ts_tape *tape);
ts_bool set_vesicle_values_from_tape(ts_vesicle *vesicle);

ts_bool initial_population_with_c0(ts_vesicle *vesicle, ts_tape *tape);
/** Sets the initial position of the vertexes to dipyramid
 *
 *      @param *vlist is a pointer to list of vertices

 src/main.c

@@ -58,6 +58,7 @@
                }
            fclose(fd);
            start_iteration++;
            write_vertex_xml_file(vesicle,1000);
        }
        else
            ts_fprintf(stdout,"No .status file. The iteration count will start from 0");

 src/restore.c

@@ -54,6 +54,10 @@
                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)
@@ -318,7 +322,48 @@
    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;

 src/restore.h

@@ -9,6 +9,7 @@
ts_bool parseTrisurfTria(ts_vesicle *vesicle, xmlDocPtr doc, xmlNodePtr cur);
ts_bool parseTrisurfTriaNeigh(ts_vesicle *vesicle, xmlDocPtr doc, xmlNodePtr cur);
ts_bool parseTrisurfTristar(ts_vesicle *vesicle, xmlDocPtr doc, xmlNodePtr cur);
ts_bool parseXMLPointData(ts_vesicle *vesicle,xmlDocPtr doc, xmlNodePtr cur);
ts_bool parseXMLVertexPosition(ts_vesicle *vesicle,xmlDocPtr doc, xmlNodePtr cur);
ts_bool parseXMLBonds(ts_vesicle *vesicle,xmlDocPtr doc, xmlNodePtr cur);
ts_bool parseTrisurfNucleus(ts_vesicle *vesicle, xmlDocPtr doc, xmlNodePtr cur);