Polymeres are restored

Samo Penic

2016-03-01 86b69b3803b1b31c040cede6b47bf617561b3b81

Polymeres are restored

 src/restore.c

@@ -75,7 +75,7 @@
    
    xmlFreeDoc(doc);

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

    init_normal_vectors(vesicle->tlist);
    mean_curvature_and_energy(vesicle);
@@ -83,7 +83,7 @@
/* TODO: cells, polymeres, filaments, core, tape */

    fprintf(stderr,"Restoration completed\n");
//    write_vertex_xml_file(vesicle,999);
    write_vertex_xml_file(vesicle,999);
    vesicle_free(vesicle);
    exit(0);
    return TS_SUCCESS;
@@ -136,10 +136,10 @@
    free(subtree);
#endif
    /*parse xml subtree */
    xmlChar *nvtx, *npoly, *nfono;
    xmlChar *nvtx, *npoly, *nmono;
    nvtx = xmlGetProp(cur, (xmlChar *)"nvtx");
    npoly=xmlGetProp(cur, (xmlChar *)"npoly");
    nfono=xmlGetProp(cur, (xmlChar *)"nfono");
    nmono=xmlGetProp(cur, (xmlChar *)"nmono");
    ts_tape *tape=parsetapebuffer(tapetxt);
    //fprintf(stderr,"nvtx=%u\n",atoi((char *)nvtx));
    //TODO: check if nvtx is in agreement with nshell from tape
@@ -147,7 +147,7 @@
    //vesicle->poly_list=init_poly_list(atoi((char *)npoly),atoi((char *)nmono), vesicle->vlist, vesicle);
    xmlFree(nvtx);
    xmlFree(npoly);
    xmlFree(nfono);
    xmlFree(nmono);

    child = cur->xmlChildrenNode;
    while (child != NULL) {
@@ -285,7 +285,7 @@
    xmlNodePtr child = cur->xmlChildrenNode;
    xmlChar *points;
    char *pts;
    int i, idx;
    int i, idx, polyidx, monoidx;
    char *token[3];
    while (child != NULL) {
        if ((!xmlStrcmp(child->name, (const xmlChar *)"DataArray"))){
@@ -296,9 +296,17 @@
            token[2]=strtok(NULL,"\n");
            idx=0;
            while(token[0]!=NULL){
                vesicle->vlist->vtx[idx]->x=atof(token[0]);
                vesicle->vlist->vtx[idx]->y=atof(token[1]);
                vesicle->vlist->vtx[idx]->z=atof(token[2]);
                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 {
                    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]);
                }
                for(i=0;i<2;i++)    token[i]=strtok(NULL," ");    
                token[2]=strtok(NULL,"\n");
                idx++;
@@ -315,7 +323,7 @@
    xmlNodePtr child = cur->xmlChildrenNode;
    xmlChar *bonds, *conname;
    char *b;
    int idx;
    int idx, polyidx;
    char *token[2];
    while (child != NULL) {
        conname=xmlGetProp(child, (xmlChar *)"Name");
@@ -326,7 +334,18 @@
            token[1]=strtok(NULL,"\n");
            idx=0;
            while(token[0]!=NULL){
                bond_add(vesicle->blist, vesicle->vlist->vtx[atoi(token[0])], vesicle->vlist->vtx[atoi(token[1])]);
                if(idx<3*(vesicle->vlist->n-2)){
                    bond_add(vesicle->blist, vesicle->vlist->vtx[atoi(token[0])], vesicle->vlist->vtx[atoi(token[1])]);
                }
                else {
                //find grafted vtx
                    if((vesicle->tape->nmono-1)==(idx-3*(vesicle->vlist->n-2))%(vesicle->tape->nmono)){
                        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];
                    }
                }
                token[0]=strtok(NULL," ");    
                token[1]=strtok(NULL,"\n");    
                idx++;

 src/snapshot.c

@@ -69,7 +69,7 @@
        npoly=0;
        nfono=0;
    }
    fprintf(fh, "<trisurf nvtx=\"%u\" npoly=\"%u\" nfono=\"%u\" compressed=\"false\">\n", vesicle->vlist->n, npoly, nfono);
    fprintf(fh, "<trisurf nvtx=\"%u\" npoly=\"%u\" nmono=\"%u\" compressed=\"false\">\n", vesicle->vlist->n, npoly, nfono);
    return TS_SUCCESS;
}


 src/tape

@@ -25,7 +25,7 @@

####### Polymer (brush) definitions ###########
# npoly is a number of polymers attached to npoly distinct vertices on vesicle
npoly=0
npoly=2
# nmono is a number of monomers in each polymer
nmono=10
# Spring constant between monomers of the polymer