triangle data removed

Samo Penic

2012-02-23 41a0355002fda513dbf8d878b6793e1f21a20ef1

triangle data removed

 src/energy.c

@@ -89,9 +89,9 @@
        xh+=tot*(j->data->x - data->x);
        yh+=tot*(j->data->y - data->y);
        zh+=tot*(j->data->z - data->z);
        txn+=jt->data->xnorm;
        tyn+=jt->data->ynorm;
        tzn+=jt->data->znorm;
        txn+=jt->xnorm;
        tyn+=jt->ynorm;
        tzn+=jt->znorm;
    }
    
    h=xh*xh+yh*yh+zh*zh;

 src/frame.c

@@ -52,5 +52,7 @@
    }

*/
    if(dcell);
    if(shift);
    return TS_SUCCESS;
}

 src/general.h

@@ -170,22 +170,14 @@
};
typedef struct ts_bond_list ts_bond_list;

/** ts_triangle_data is a structure that describes a triangle */
struct ts_triangle_data {
    ts_uint idx;
struct ts_triangle {
    ts_uint idx;
    ts_vertex *vertex[3];
    ts_uint neigh_no;
    struct ts_triangle **neigh;
    ts_double xnorm;
    ts_double ynorm;
    ts_double znorm;
	
};
typedef struct ts_triangle_data ts_triangle_data;

struct ts_triangle {
    ts_uint idx;
    ts_triangle_data *data;
};
typedef struct ts_triangle ts_triangle;


 src/initial_distribution.c

@@ -28,6 +28,7 @@
    retval = init_normal_vectors(vesicle->tlist);
    retval = mean_curvature_and_energy(vesicle);
 ts_fprintf(stderr,"initial_distribution finished!\n");
    if(retval);
    return vesicle;
} 

@@ -249,7 +250,7 @@
    for(i=0;i<tlist->n;i++){
        k=0;
        for(j=0;j<3;j++){
            if(tlist->tria[i]->data->vertex[j]!=NULL)
            if(tlist->tria[i]->vertex[j]!=NULL)
            k++;
        }
            if(k!=3){
@@ -273,14 +274,14 @@
    ts_triangle **tria=tlist->tria -1;
    nobo=0;
    for(i=1;i<=tlist->n;i++){
        i1=tria[i]->data->vertex[0]; 
        i2=tria[i]->data->vertex[1]; 
        i3=tria[i]->data->vertex[2]; 
        i1=tria[i]->vertex[0]; 
        i2=tria[i]->vertex[1]; 
        i3=tria[i]->vertex[2]; 
        for(j=1;j<=tlist->n;j++){
            if(j==i) continue;
            j1=tria[j]->data->vertex[0]; 
            j2=tria[j]->data->vertex[1]; 
            j3=tria[j]->data->vertex[2]; 
            j1=tria[j]->vertex[0]; 
            j2=tria[j]->vertex[1]; 
            j3=tria[j]->vertex[2]; 
            if((i1==j1 && i3==j2) || (i1==j2 && i3==j3) || (i1==j3 && i3==j1)){
                    triangle_add_neighbour(tria[i],tria[j]);
                    nobo++;
@@ -288,14 +289,14 @@
        }
    }
    for(i=1;i<=tlist->n;i++){
        i1=tria[i]->data->vertex[0]; 
        i2=tria[i]->data->vertex[1]; 
        i3=tria[i]->data->vertex[2]; 
        i1=tria[i]->vertex[0]; 
        i2=tria[i]->vertex[1]; 
        i3=tria[i]->vertex[2]; 
        for(j=1;j<=tlist->n;j++){
            if(j==i) continue;
            j1=tria[j]->data->vertex[0]; 
            j2=tria[j]->data->vertex[1]; 
            j3=tria[j]->data->vertex[2]; 
            j1=tria[j]->vertex[0]; 
            j2=tria[j]->vertex[1]; 
            j3=tria[j]->vertex[2]; 
            if((i1==j1 && i2==j3) || (i1==j3 && i2==j2) || (i1==j2 && i2==j1)){
                triangle_add_neighbour(tria[i],tria[j]);
                nobo++;
@@ -303,14 +304,14 @@
        }
    }
    for(i=1;i<=tlist->n;i++){
        i1=tria[i]->data->vertex[0]; 
        i2=tria[i]->data->vertex[1]; 
        i3=tria[i]->data->vertex[2]; 
        i1=tria[i]->vertex[0]; 
        i2=tria[i]->vertex[1]; 
        i3=tria[i]->vertex[2]; 
        for(j=1;j<=tlist->n;j++){
            if(j==i) continue;
            j1=tria[j]->data->vertex[0]; 
            j2=tria[j]->data->vertex[1]; 
            j3=tria[j]->data->vertex[2]; 
            j1=tria[j]->vertex[0]; 
            j2=tria[j]->vertex[1]; 
            j3=tria[j]->vertex[2]; 
            if((i2==j1 && i3==j3) || (i2==j3 && i3==j2) || (i2==j2 && i3==j1)){
                triangle_add_neighbour(tria[i],tria[j]);
                nobo++;
@@ -339,9 +340,9 @@
            if(j == vtx[i]->data->neigh_no) jp=1;
            k2=vtx[i]->data->neigh[jp-1];
            for(k=1;k<=tlist->n;k++){        // VERY NON-OPTIMAL!!! too many loops (vlist.n * vtx.neigh * tlist.n )!
                k3=tria[k]->data->vertex[0];
                k4=tria[k]->data->vertex[1];
                k5=tria[k]->data->vertex[2];
                k3=tria[k]->vertex[0];
                k4=tria[k]->vertex[1];
                k5=tria[k]->vertex[2];
//                ts_fprintf(stderr,"%u %u: k=(%u %u %u)\n",k1,k2,k3,k4,k5);
                if((vtx[i]==k3 && k1==k4 && k2==k5) ||
                (vtx[i]==k4 && k1==k5 && k2==k3) ||

 src/io.c

@@ -85,17 +85,17 @@
        ts_triangle_list *tlist=vesicle->tlist;
      ts_uint i,j;
    for(i=0;i<tlist->n;i++){
        fprintf(fh,"\t%u",tlist->tria[i]->data->neigh_no);
        for(j=0;j<tlist->tria[i]->data->neigh_no;j++){
            fprintf(fh,"\t%u",(ts_uint)(tlist->tria[i]->data->neigh[j]->idx));//-tlist->tria+1)); 
        fprintf(fh,"\t%u",tlist->tria[i]->neigh_no);
        for(j=0;j<tlist->tria[i]->neigh_no;j++){
            fprintf(fh,"\t%u",(ts_uint)(tlist->tria[i]->neigh[j]->idx));//-tlist->tria+1)); 
        }
        fprintf(fh,"\n");
            for(j=0;j<3;j++){
            fprintf(fh,"\t%u",(ts_uint)(tlist->tria[i]->data->vertex[j]->idx));//-vesicle->vlist->vtx+1)); 
            fprintf(fh,"\t%u",(ts_uint)(tlist->tria[i]->vertex[j]->idx));//-vesicle->vlist->vtx+1)); 
            }
        fprintf(fh,"\n");
        fprintf(fh,"%.17E\t%.17E\t%.17E\n",tlist->tria[i]->data->xnorm,
tlist->tria[i]->data->ynorm,tlist->tria[i]->data->znorm);
        fprintf(fh,"%.17E\t%.17E\t%.17E\n",tlist->tria[i]->xnorm,
tlist->tria[i]->ynorm,tlist->tria[i]->znorm);
        fprintf(fh,"0.00000000000000000\n0.00000000000000000\n");
    }
    return TS_SUCCESS;
@@ -373,6 +373,7 @@
        
    }
    */
    if(retval);
    fclose(fh);    



 src/main.c

@@ -65,12 +65,10 @@
centermass(vesicle);
cell_occupation(vesicle);

for(i=0;i<100;i++)
for(i=0;i<100;i++){
single_timestep(vesicle);



write_vertex_xml_file(vesicle,0);
write_vertex_xml_file(vesicle,i);
}
write_master_xml_file("test.pvd");
write_dout_fcompat_file(vesicle,"dout");
vesicle_free(vesicle);

 src/timestep.c

@@ -26,7 +26,7 @@
//        retval=single_bondflip_timestep(vesicle,&vesicle->blist.bond[i],rnvec);
        
    } 

    if(retval);
    return TS_SUCCESS;
}


 src/triangle.c

@@ -57,13 +57,13 @@

        tlist->tria[tlist->n-1]=(ts_triangle *)calloc(1,sizeof(ts_triangle));
        if(tlist->tria[tlist->n-1]==NULL) fatal("Cannot reallocate memory for additional ts_triangle.",5);
        tlist->tria[tlist->n-1]->data=(ts_triangle_data *)calloc(1,sizeof(ts_triangle_data));
  //      tlist->tria[tlist->n-1]->data=(ts_triangle_data *)calloc(1,sizeof(ts_triangle_data));

        //NOW insert vertices!
        tlist->tria[tlist->n - 1]->idx=tlist->n-1;
        tlist->tria[tlist->n - 1]->data->vertex[0]=vtx1;
        tlist->tria[tlist->n - 1]->data->vertex[1]=vtx2;
        tlist->tria[tlist->n - 1]->data->vertex[2]=vtx3;
        tlist->tria[tlist->n - 1]->vertex[0]=vtx1;
        tlist->tria[tlist->n - 1]->vertex[1]=vtx2;
        tlist->tria[tlist->n - 1]->vertex[2]=vtx3;
        return tlist->tria[tlist->n-1];
}

@@ -94,11 +94,11 @@
    if(tria==NULL || ntria==NULL) return TS_FAIL;
/*TODO: check if the neighbour already exists! Now there is no such check
 * because of the performance issue. */
    tria->data->neigh_no++;
    tria->data->neigh=realloc(tria->data->neigh,tria->data->neigh_no*sizeof(ts_triangle *));
    if(tria->data->neigh == NULL)
    tria->neigh_no++;
    tria->neigh=realloc(tria->neigh,tria->neigh_no*sizeof(ts_triangle *));
    if(tria->neigh == NULL)
            fatal("Reallocation of memory failed during insertion of triangle neighbour in triangle_add_neighbour",3);
    tria->data->neigh[tria->data->neigh_no-1]=ntria;
    tria->neigh[tria->neigh_no-1]=ntria;
  
 
/* we repeat the procedure for the neighbour */  
@@ -136,9 +136,9 @@
    ts_uint i,j=0; 
    if(tria==NULL || ntria==NULL) return TS_FAIL;

    for(i=0;i<tria->data->neigh_no;i++){
        if(tria->data->neigh[i]!=ntria){
            tria->data->neigh[j]=tria->data->neigh[i];
    for(i=0;i<tria->neigh_no;i++){
        if(tria->neigh[i]!=ntria){
            tria->neigh[j]=tria->neigh[i];
            j++;
        } 
    }
@@ -146,15 +146,15 @@
        return TS_FAIL; 
        //fatal("In triangle_remove_neighbour: Specified neighbour does not exist for given triangle",3);
    }
    tria->data->neigh_no--;
    tria->data->neigh=(ts_triangle **)realloc(tria->data->neigh,tria->data->neigh_no*sizeof(ts_triangle *));
    if(tria->data->neigh == NULL){
    tria->neigh_no--;
    tria->neigh=(ts_triangle **)realloc(tria->neigh,tria->neigh_no*sizeof(ts_triangle *));
    if(tria->neigh == NULL){
        fatal("Reallocation of memory failed during removal of vertex neighbour in triangle_remove_neighbour",100);
    }
/* we repeat the procedure for neighbour */
    for(i=0;i<ntria->data->neigh_no;i++){
        if(ntria->data->neigh[i]!=tria){
            ntria->data->neigh[j]=ntria->data->neigh[i];
    for(i=0;i<ntria->neigh_no;i++){
        if(ntria->neigh[i]!=tria){
            ntria->neigh[j]=ntria->neigh[i];
            j++;
        } 
    }
@@ -162,9 +162,9 @@
        return TS_FAIL; 
        //fatal("In triangle_remove_neighbour: Specified neighbour does not exist for given triangle",3);
    }
    ntria->data->neigh_no--;
    ntria->data->neigh=(ts_triangle **)realloc(ntria->data->neigh,ntria->data->neigh_no*sizeof(ts_triangle *));
    if(ntria->data->neigh == NULL){
    ntria->neigh_no--;
    ntria->neigh=(ts_triangle **)realloc(ntria->neigh,ntria->neigh_no*sizeof(ts_triangle *));
    if(ntria->neigh == NULL){
        fatal("Reallocation of memory failed during removal of vertex neighbour in triangle_remove_neighbour",100);
    }
    return TS_SUCCESS;
@@ -194,19 +194,19 @@
  */
ts_bool triangle_normal_vector(ts_triangle *tria){
    ts_double x21,x31,y21,y31,z21,z31,xden;
    x21=tria->data->vertex[1]->data->x - tria->data->vertex[0]->data->x;
    x31=tria->data->vertex[2]->data->x - tria->data->vertex[0]->data->x;
    y21=tria->data->vertex[1]->data->y - tria->data->vertex[0]->data->y;
    y31=tria->data->vertex[2]->data->y - tria->data->vertex[0]->data->y;
    z21=tria->data->vertex[1]->data->z - tria->data->vertex[0]->data->z;
    z31=tria->data->vertex[2]->data->z - tria->data->vertex[0]->data->z;
    x21=tria->vertex[1]->data->x - tria->vertex[0]->data->x;
    x31=tria->vertex[2]->data->x - tria->vertex[0]->data->x;
    y21=tria->vertex[1]->data->y - tria->vertex[0]->data->y;
    y31=tria->vertex[2]->data->y - tria->vertex[0]->data->y;
    z21=tria->vertex[1]->data->z - tria->vertex[0]->data->z;
    z31=tria->vertex[2]->data->z - tria->vertex[0]->data->z;

    tria->data->xnorm=y21*z31 - z21*y31;
    tria->data->ynorm=z21*x31 - x21*z31;
    tria->data->znorm=x21*y31 - y21*x31;
    xden=tria->data->xnorm*tria->data->xnorm +
         tria->data->ynorm*tria->data->ynorm + 
         tria->data->znorm*tria->data->znorm;
    tria->xnorm=y21*z31 - z21*y31;
    tria->ynorm=z21*x31 - x21*z31;
    tria->znorm=x21*y31 - y21*x31;
    xden=tria->xnorm*tria->xnorm +
         tria->ynorm*tria->ynorm + 
         tria->znorm*tria->znorm;
#ifdef TS_DOUBLE_DOUBLE
    xden=sqrt(xden);
#endif
@@ -216,9 +216,9 @@
#ifdef TS_DOUBLE_LONGDOUBLE
    xden=sqrtl(xden);
#endif
    tria->data->xnorm=tria->data->xnorm/xden;
    tria->data->ynorm=tria->data->ynorm/xden;
    tria->data->znorm=tria->data->znorm/xden;	
    tria->xnorm=tria->xnorm/xden;
    tria->ynorm=tria->ynorm/xden;
    tria->znorm=tria->znorm/xden;	
    return TS_SUCCESS;
}

@@ -226,29 +226,6 @@



/** @brief Frees the memory allocated for data structure of triangle data
 * (ts_triangle_data)
  *
  * Function frees the memory of ts_triangle_data previously allocated. It
  * accepts one argument, the address of data structure. It destroys all
  * pointers the structure might have (currently only neigh -- the pointer to
  * list of neighbouring triangles) and data structure itself. The return value
  * is always TS_SUCCESS.
  *
  * WARNING: The function doesn't check whether the pointer is NULL or invalid. It is the
  * job of programmer to make sure the pointer is valid.
  *
  * Example of usage:
  *        triangle_data_free(tlist->tria[3]->data);
  *
  *        Clears the data structure with all pointers.
  *		
  */
ts_bool triangle_data_free(ts_triangle_data *data){
    if(data->neigh!=NULL) free(data->neigh);
    free(data);
    return TS_SUCCESS;
}

/** @brief Frees the memory allocated for data structure of triangle list
 * (ts_triangle_list)
@@ -277,7 +254,7 @@
ts_bool triangle_list_free(ts_triangle_list *tlist){
    ts_uint i;
    for(i=0;i<tlist->n;i++){
        triangle_data_free(tlist->tria[i]->data);
        if(tlist->tria[i]->neigh!=NULL) free(tlist->tria[i]->neigh);
        free(tlist->tria[i]);
    }
    free(tlist->tria);

 src/triangle.h

@@ -5,7 +5,6 @@
ts_triangle *triangle_add(ts_triangle_list *tlist, ts_vertex *vtx1, ts_vertex *vtx2, ts_vertex *vtx3);
ts_bool triangle_add_neighbour(ts_triangle *tria, ts_triangle *ntria);
ts_bool triangle_normal_vector(ts_triangle *tria);
ts_bool triangle_data_free(ts_triangle_data *triang);
ts_bool triangle_list_free(ts_triangle_list *tlist);

#endif