bond data removed

Samo Penic

2012-02-23 e016c401c98b6a33392b551b2c40fccded21efe3

bond data removed

 src/bond.c

@@ -15,8 +15,8 @@
    if(vtx1==NULL || vtx2==NULL) return NULL;
    /* Verify if the bond already exists... Don't do multiple bonds */
    for(i=0;i<blist->n;i++){
       if((blist->bond[i]->data->vtx1==vtx1 || blist->bond[i]->data->vtx1==vtx2)
        &&(blist->bond[i]->data->vtx2==vtx1 || blist->bond[i]->data->vtx2==vtx2))
       if((blist->bond[i]->vtx1==vtx1 || blist->bond[i]->vtx1==vtx2)
        &&(blist->bond[i]->vtx2==vtx1 || blist->bond[i]->vtx2==vtx2))
        return blist->bond[i];
    }
    blist->n++;
@@ -24,11 +24,10 @@
    if(blist->bond==NULL) fatal("Cannot reallocate memory for additional **ts_bond.",100);
    blist->bond[blist->n-1]=(ts_bond *)malloc(sizeof(ts_bond));
    if(blist->bond[blist->n-1]==NULL) fatal("Cannot allocate memory for additional *ts_bond.",100);
    blist->bond[blist->n-1]->data=(ts_bond_data *)malloc(sizeof(ts_bond_data));
    
    //NOW insert vertices into data!    
    blist->bond[blist->n - 1]->data->vtx1=vtx1;	
    blist->bond[blist->n - 1]->data->vtx2=vtx2;
    blist->bond[blist->n - 1]->vtx1=vtx1;	
    blist->bond[blist->n - 1]->vtx2=vtx2;

    //Should we calculate bond length NOW?
    
@@ -38,7 +37,6 @@
ts_bool bond_list_free(ts_bond_list *blist){
    ts_uint i;
    for(i=0;i<blist->n;i++){
    free(blist->bond[i]->data);
    free(blist->bond[i]);
    }
    free(blist->bond);

 src/energy.c

@@ -74,16 +74,16 @@
        tot=0.5*tot;
        xlen=vtx_distance_sq(j,vtx);
#ifdef  TS_DOUBLE_DOUBLE 
        data->bond[jj-1]->data->bond_length=sqrt(xlen); 
        data->bond[jj-1]->bond_length=sqrt(xlen); 
#endif
#ifdef  TS_DOUBLE_FLOAT
        data->bond[jj-1]->data->bond_length=sqrtf(xlen); 
        data->bond[jj-1]->bond_length=sqrtf(xlen); 
#endif
#ifdef  TS_DOUBLE_LONGDOUBLE 
        data->bond[jj-1]->data->bond_length=sqrtl(xlen); 
        data->bond[jj-1]->bond_length=sqrtl(xlen); 
#endif

        data->bond[jj-1]->data->bond_length_dual=tot*data->bond[jj-1]->data->bond_length;
        data->bond[jj-1]->bond_length_dual=tot*data->bond[jj-1]->bond_length;

        s+=tot*xlen;
        xh+=tot*(j->data->x - data->x);

 src/general.h

@@ -149,18 +149,12 @@

} ts_vertex_list;


/** ts_bond_data is a structure that describes a bond */
typedef struct {
struct ts_bond {
    ts_uint idx;
    ts_vertex *vtx1;
    ts_vertex *vtx2;
    ts_double bond_length;
    ts_double bond_length_dual;
} ts_bond_data;

struct ts_bond {
    ts_uint idx;
    ts_bond_data *data;
};
typedef struct ts_bond ts_bond;


 src/io.c

@@ -108,11 +108,11 @@
        vlist->vtx[i]->data->xk,vlist->vtx[i]->data->c,vlist->vtx[i]->data->energy,
        vlist->vtx[i]->data->energy_h, vlist->vtx[i]->data->curvature, 0);
        for(j=0;j<vlist->vtx[i]->data->neigh_no;j++){
            fprintf(fh," %.17E", vlist->vtx[i]->data->bond[j]->data->bond_length_dual);
            fprintf(fh," %.17E", vlist->vtx[i]->data->bond[j]->bond_length_dual);
        }
            fprintf(fh,"\n");
        for(j=0;j<vlist->vtx[i]->data->neigh_no;j++){
            fprintf(fh," %.17E", vlist->vtx[i]->data->bond[j]->data->bond_length);
            fprintf(fh," %.17E", vlist->vtx[i]->data->bond[j]->bond_length);
        }
            fprintf(fh,"\n");
    }
@@ -122,9 +122,9 @@
ts_bool fprint_bonds(FILE *fh,ts_vesicle *vesicle){
    ts_uint i;
    for(i=0;i<vesicle->blist->n;i++){
        fprintf(fh,"\t%u\t%u\n",(ts_uint)(vesicle->blist->bond[i]->data->vtx1->idx),
        fprintf(fh,"\t%u\t%u\n",(ts_uint)(vesicle->blist->bond[i]->vtx1->idx),
//-vesicle->vlist->vtx+1),
        (ts_uint)(vesicle->blist->bond[i]->data->vtx2->idx));
        (ts_uint)(vesicle->blist->bond[i]->vtx2->idx));
    //-vesicle->vlist.vtx+1));
    }
    return TS_SUCCESS;
@@ -231,7 +231,7 @@

    fprintf(fh,"</DataArray>\n</Points>\n<Cells>\n<DataArray type=\"Int64\" Name=\"connectivity\" format=\"ascii\">");
    for(i=0;i<blist->n;i++){
            fprintf(fh,"%u %u\n",blist->bond[i]->data->vtx1->idx,blist->bond[i]->data->vtx2->idx);
            fprintf(fh,"%u %u\n",blist->bond[i]->vtx1->idx,blist->bond[i]->vtx2->idx);
    }
    fprintf(fh,"</DataArray>\n<DataArray type=\"Int64\" Name=\"offsets\" format=\"ascii\">");
    for (i=2;i<blist->n*2+1;i+=2){
@@ -275,7 +275,7 @@
    
    fprintf(fh,"CELLS %u %u\n",blist->n,3*blist->n);
    for(i=0;i<blist->n;i++){
            fprintf(fh,"2 %u %u\n",blist->bond[i]->data->vtx1->idx,blist->bond[i]->data->vtx2->idx);
            fprintf(fh,"2 %u %u\n",blist->bond[i]->vtx1->idx,blist->bond[i]->vtx2->idx);
    }
    fprintf(fh,"CELL_TYPES %u\n",blist->n);
    for(i=0;i<blist->n;i++)