| | |
| | | fwrite(vesicle->clist, sizeof(ts_cell_list),1,fh); |
| | | /* dump poly list */ |
| | | fwrite(vesicle->poly_list, sizeof(ts_poly_list),1,fh); |
| | | /* dump filament list */ |
| | | fwrite(vesicle->filament_list, sizeof(ts_poly_list),1,fh); |
| | | /* level 1 complete */ |
| | | |
| | | /*dump vertices*/ |
| | |
| | | } |
| | | } |
| | | |
| | | |
| | | /*dump filamentes grandes svinjas */ |
| | | for(i=0;i<vesicle->filament_list->n;i++){ |
| | | fwrite(vesicle->filament_list->poly[i],sizeof(ts_poly),1,fh); |
| | | fwrite(vesicle->filament_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh); |
| | | fwrite(vesicle->filament_list->poly[i]->blist,sizeof(ts_bond_list),1,fh); |
| | | } |
| | | |
| | | /* dump filamentes vertex(monomer) list*/ |
| | | for(i=0;i<vesicle->filament_list->n;i++){ |
| | | for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){ |
| | | fwrite(vesicle->filament_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh); |
| | | /* dump offset for neigh and bond */ |
| | | for(k=0;k<vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh_no;k++){ |
| | | // off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->neigh[k]-vesicle->poly_list->poly[i]->vlist->vtx[0]); |
| | | fwrite(&vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh[k]->idx,sizeof(ts_uint),1,fh); |
| | | } |
| | | for(k=0;k<vesicle->filament_list->poly[i]->vlist->vtx[j]->bond_no;k++){ |
| | | //off=(ts_ulong)(vesicle->poly_list->poly[i]->vlist->vtx[j]->bond[k]-vesicle->poly_list->poly[i]->blist->bond[0]); |
| | | fwrite(&vesicle->filament_list->poly[i]->vlist->vtx[j]->bond[k]->idx,sizeof(ts_uint),1,fh); |
| | | } |
| | | } |
| | | } |
| | | /* dump poly bonds between monomers list*/ |
| | | for(i=0;i<vesicle->filament_list->n;i++){ |
| | | for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){ |
| | | fwrite(vesicle->filament_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh); |
| | | /* dump vtx1 and vtx2 offsets */ |
| | | //off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx1-vesicle->poly_list->poly[i]->vlist->vtx[0]); |
| | | fwrite(&vesicle->filament_list->poly[i]->blist->bond[j]->vtx1->idx,sizeof(ts_uint),1,fh); |
| | | // off=(ts_ulong)(vesicle->poly_list->poly[i]->blist->bond[j]->vtx2-vesicle->poly_list->poly[i]->vlist->vtx[0]); |
| | | fwrite(&vesicle->filament_list->poly[i]->blist->bond[j]->vtx2->idx,sizeof(ts_uint),1,fh); |
| | | } |
| | | } |
| | | |
| | | |
| | | |
| | | /* pointer offsets for fixing the restored pointers */ |
| | | /* need pointers for |
| | | vlist->vtx |
| | |
| | | /* restore poly list */ |
| | | vesicle->poly_list=(ts_poly_list *)calloc(1,sizeof(ts_poly_list)); |
| | | retval=fread(vesicle->poly_list, sizeof(ts_poly_list),1,fh); |
| | | /* restore filament list */ |
| | | vesicle->filament_list=(ts_poly_list *)calloc(1,sizeof(ts_poly_list)); |
| | | retval=fread(vesicle->filament_list, sizeof(ts_poly_list),1,fh); |
| | | /* level 1 complete */ |
| | | |
| | | /* prerequisity. Bonds must be malloced before vertexes are recreated */ |
| | |
| | | vesicle->poly_list->poly[i]->blist->bond[j]->vtx1=vesicle->poly_list->poly[i]->vlist->vtx[idx]; |
| | | retval=fread(&idx,sizeof(ts_uint),1,fh); |
| | | vesicle->poly_list->poly[i]->blist->bond[j]->vtx2=vesicle->poly_list->poly[i]->vlist->vtx[idx]; |
| | | } |
| | | } |
| | | |
| | | /*restore filaments */ |
| | | vesicle->filament_list->poly = (ts_poly **)calloc(vesicle->filament_list->n,sizeof(ts_poly *)); |
| | | for(i=0;i<vesicle->filament_list->n;i++){ |
| | | vesicle->filament_list->poly[i]=(ts_poly *)calloc(1,sizeof(ts_poly)); |
| | | retval=fread(vesicle->filament_list->poly[i],sizeof(ts_poly),1,fh); |
| | | vesicle->filament_list->poly[i]->vlist=(ts_vertex_list *)calloc(1,sizeof(ts_vertex_list)); |
| | | retval=fread(vesicle->filament_list->poly[i]->vlist,sizeof(ts_vertex_list),1,fh); |
| | | vesicle->filament_list->poly[i]->blist=(ts_bond_list *)calloc(1,sizeof(ts_bond_list)); |
| | | retval=fread(vesicle->filament_list->poly[i]->blist,sizeof(ts_bond_list),1,fh); |
| | | /* initialize adress space for pointers that will hold specific vertices (monomers) and bonds */ |
| | | vesicle->filament_list->poly[i]->vlist->vtx=(ts_vertex **)calloc(vesicle->filament_list->poly[i]->vlist->n,sizeof(ts_vertex *)); |
| | | vesicle->filament_list->poly[i]->blist->bond=(ts_bond **)calloc(vesicle->filament_list->poly[i]->blist->n,sizeof(ts_bond *)); |
| | | for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){ |
| | | vesicle->filament_list->poly[i]->vlist->vtx[j]=(ts_vertex *)malloc(sizeof(ts_vertex)); |
| | | } |
| | | for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){ |
| | | vesicle->filament_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond)); |
| | | } |
| | | |
| | | } |
| | | |
| | | |
| | | /* restore poly vertex(monomer) list*/ |
| | | for(i=0;i<vesicle->filament_list->n;i++){ |
| | | for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){ |
| | | retval=fread(vesicle->filament_list->poly[i]->vlist->vtx[j],sizeof(ts_vertex),1,fh); |
| | | |
| | | /* restore neigh and bonds */ |
| | | vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh=(ts_vertex **)calloc(vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh_no, sizeof(ts_vertex *)); |
| | | for(k=0;k<vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh_no;k++){ |
| | | retval=fread(&idx,sizeof(ts_uint),1,fh); |
| | | vesicle->filament_list->poly[i]->vlist->vtx[j]->neigh[k]=vesicle->filament_list->poly[i]->vlist->vtx[idx]; |
| | | } |
| | | vesicle->filament_list->poly[i]->vlist->vtx[j]->bond=(ts_bond **)calloc(vesicle->filament_list->poly[i]->vlist->vtx[j]->bond_no, sizeof(ts_bond *)); |
| | | for(k=0;k<vesicle->filament_list->poly[i]->vlist->vtx[j]->bond_no;k++){ |
| | | retval=fread(&idx,sizeof(ts_uint),1,fh); |
| | | vesicle->filament_list->poly[i]->vlist->vtx[j]->bond[k]=vesicle->filament_list->poly[i]->blist->bond[idx]; |
| | | } |
| | | |
| | | } |
| | | } |
| | | |
| | | /* restore poly bonds between monomers list*/ |
| | | for(i=0;i<vesicle->filament_list->n;i++){ |
| | | for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){ |
| | | // vesicle->poly_list->poly[i]->blist->bond[j]=(ts_bond *)malloc(sizeof(ts_bond)); |
| | | retval=fread(vesicle->filament_list->poly[i]->blist->bond[j],sizeof(ts_bond),1,fh); |
| | | /* restore vtx1 and vtx2 */ |
| | | retval=fread(&idx,sizeof(ts_uint),1,fh); |
| | | vesicle->filament_list->poly[i]->blist->bond[j]->vtx1=vesicle->filament_list->poly[i]->vlist->vtx[idx]; |
| | | retval=fread(&idx,sizeof(ts_uint),1,fh); |
| | | vesicle->filament_list->poly[i]->blist->bond[j]->vtx2=vesicle->filament_list->poly[i]->vlist->vtx[idx]; |
| | | } |
| | | } |
| | | |
| | |
| | | /* Here comes header of the file */ |
| | | |
| | | //find number of extra vtxs and bonds of polymeres |
| | | ts_uint monono=0, polyno=0, poly_idx=0; |
| | | ts_bool poly=0; |
| | | ts_uint monono=0, polyno=0, poly_idx=0, filno=0, fonono=0; |
| | | ts_bool poly=0, fil=0; |
| | | if(vesicle->poly_list!=NULL){ |
| | | if(vesicle->poly_list->poly[0]!=NULL){ |
| | | polyno=vesicle->poly_list->n; |
| | |
| | | poly=1; |
| | | } |
| | | } |
| | | |
| | | if(vesicle->filament_list!=NULL){ |
| | | if(vesicle->filament_list->poly[0]!=NULL){ |
| | | filno=vesicle->filament_list->n; |
| | | fonono=vesicle->filament_list->poly[0]->vlist->n; |
| | | fil=1; |
| | | } |
| | | } |
| | | |
| | | fprintf(fh, "<?xml version=\"1.0\"?>\n<VTKFile type=\"UnstructuredGrid\" version=\"0.1\" byte_order=\"LittleEndian\" compressor=\"vtkZLibDataCompressor\">\n <UnstructuredGrid>\n"); |
| | | fprintf(fh, "<Piece NumberOfPoints=\"%u\" NumberOfCells=\"%u\">\n",vlist->n+monono*polyno, blist->n+monono*polyno); |
| | | fprintf(fh, "<Piece NumberOfPoints=\"%u\" NumberOfCells=\"%u\">\n",vlist->n+monono*polyno+fonono*filno, blist->n+monono*polyno+filno*(fonono-1)); |
| | | fprintf(fh,"<PointData Scalars=\"scalars\">\n<DataArray type=\"Int64\" Name=\"scalars\" format=\"ascii\">"); |
| | | for(i=0;i<vlist->n;i++){ |
| | | fprintf(fh,"%u ",vtx[i]->idx); |
| | |
| | | poly_idx=vlist->n; |
| | | for(i=0;i<vesicle->poly_list->n;i++){ |
| | | for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++,poly_idx++){ |
| | | fprintf(fh,"%u ", poly_idx); |
| | | } |
| | | } |
| | | } |
| | | //filaments |
| | | if(fil){ |
| | | poly_idx=vlist->n+monono*polyno; |
| | | for(i=0;i<vesicle->filament_list->n;i++){ |
| | | for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++,poly_idx++){ |
| | | // fprintf(stderr,"was here\n"); |
| | | fprintf(fh,"%u ", poly_idx); |
| | | } |
| | | } |
| | |
| | | for(i=0;i<vesicle->poly_list->n;i++){ |
| | | for(j=0;j<vesicle->poly_list->poly[i]->vlist->n;j++){ |
| | | fprintf(fh,"%e %e %e\n", vesicle->poly_list->poly[i]->vlist->vtx[j]->x,vesicle->poly_list->poly[i]->vlist->vtx[j]->y, vesicle->poly_list->poly[i]->vlist->vtx[j]->z ); |
| | | } |
| | | } |
| | | } |
| | | //filaments |
| | | if(fil){ |
| | | for(i=0;i<vesicle->filament_list->n;i++){ |
| | | for(j=0;j<vesicle->filament_list->poly[i]->vlist->n;j++){ |
| | | fprintf(fh,"%e %e %e\n", vesicle->filament_list->poly[i]->vlist->vtx[j]->x,vesicle->filament_list->poly[i]->vlist->vtx[j]->y, vesicle->filament_list->poly[i]->vlist->vtx[j]->z ); |
| | | } |
| | | } |
| | | } |
| | |
| | | |
| | | } |
| | | |
| | | //filaments |
| | | if(fil){ |
| | | poly_idx=vlist->n+monono*polyno; |
| | | for(i=0;i<vesicle->filament_list->n;i++){ |
| | | for(j=0;j<vesicle->filament_list->poly[i]->blist->n;j++){ |
| | | fprintf(fh,"%u %u\n", vesicle->filament_list->poly[i]->blist->bond[j]->vtx1->idx+vlist->n+monono*polyno+i*fonono,vesicle->filament_list->poly[i]->blist->bond[j]->vtx2->idx+vlist->n+monono*polyno+i*fonono); |
| | | // fprintf(stderr,"was here\n"); |
| | | |
| | | } |
| | | } |
| | | |
| | | } |
| | | |
| | | fprintf(fh,"</DataArray>\n<DataArray type=\"Int64\" Name=\"offsets\" format=\"ascii\">"); |
| | | for (i=2;i<(blist->n+monono*polyno)*2+1;i+=2){ |
| | | for (i=2;i<(blist->n+monono*polyno+(fonono-1)*filno)*2+1;i+=2){ |
| | | fprintf(fh,"%u ",i); |
| | | } |
| | | fprintf(fh,"\n"); |
| | | fprintf(fh,"</DataArray>\n<DataArray type=\"UInt8\" Name=\"types\" format=\"ascii\">\n"); |
| | | for (i=0;i<blist->n+monono*polyno;i++){ |
| | | for (i=0;i<blist->n+monono*polyno+fonono*filno;i++){ |
| | | fprintf(fh,"3 "); |
| | | } |
| | | |
| | |
| | | |
| | | |
| | | |
| | | ts_bool write_pov_file(ts_vesicle *vesicle, char *filename){ |
| | | FILE *fh; |
| | | ts_uint i; |
| | | |
| | | fh=fopen(filename, "w"); |
| | | if(fh==NULL){ |
| | | err("Cannot open file %s for writing"); |
| | | return TS_FAIL; |
| | | } |
| | | |
| | | for(i=0;i<vesicle->tlist->n;i++){ |
| | | |
| | | fprintf(fh,"\ttriangle {"); |
| | | fprintf(fh,"\t<%e,%e,%e> <%e,%e,%e> <%e,%e,%e> }\n", |
| | | vesicle->tlist->tria[i]->vertex[0]->x, |
| | | vesicle->tlist->tria[i]->vertex[0]->y, |
| | | vesicle->tlist->tria[i]->vertex[0]->z, |
| | | |
| | | vesicle->tlist->tria[i]->vertex[1]->x, |
| | | vesicle->tlist->tria[i]->vertex[1]->y, |
| | | vesicle->tlist->tria[i]->vertex[1]->z, |
| | | |
| | | vesicle->tlist->tria[i]->vertex[2]->x, |
| | | vesicle->tlist->tria[i]->vertex[2]->y, |
| | | vesicle->tlist->tria[i]->vertex[2]->z |
| | | ); |
| | | } |
| | | |
| | | fclose(fh); |
| | | return TS_SUCCESS; |
| | | } |
| | | |
| | | |
| | | ts_tape *parsetape(char *filename){ |
| | | // long int nshell=17,ncxmax=60, ncymax=60, nczmax=60, npoly=10, nmono=20, pswitch=0; // THIS IS DUE TO CONFUSE BUG! |
| | | ts_tape *tape=(ts_tape *)calloc(1,sizeof(ts_tape)); |
| | |
| | | CFG_SIMPLE_INT("nshell", &tape->nshell), |
| | | CFG_SIMPLE_INT("npoly", &tape->npoly), |
| | | CFG_SIMPLE_INT("nmono", &tape->nmono), |
| | | CFG_SIMPLE_FLOAT("dmax", &tape->dmax), |
| | | CFG_SIMPLE_INT("nfil",&tape->nfil), |
| | | CFG_SIMPLE_INT("nfono",&tape->nfono), |
| | | CFG_SIMPLE_INT("R_nucleus",&tape->R_nucleus), |
| | | CFG_SIMPLE_FLOAT("dmax", &tape->dmax), |
| | | CFG_SIMPLE_FLOAT("dmin_interspecies", &tape->dmin_interspecies), |
| | | CFG_SIMPLE_FLOAT("xk0",&tape->xk0), |
| | | CFG_SIMPLE_INT("pswitch",&tape->pswitch), |
| | | CFG_SIMPLE_FLOAT("pressure",&tape->pressure), |
| | | CFG_SIMPLE_FLOAT("k_spring",&tape->kspring), |
| | | CFG_SIMPLE_FLOAT("xi",&tape->xi), |
| | | CFG_SIMPLE_FLOAT("stepsize",&tape->stepsize), |
| | | CFG_SIMPLE_INT("nxmax", &tape->ncxmax), |
| | | CFG_SIMPLE_INT("nymax", &tape->ncymax), |