step in rewritting

Samo Penic

2013-11-30 20ae8328e6eb4b99c8e9c306ab6e09ac4922f395

step in rewritting

 src/bondflip.c

@@ -34,27 +34,27 @@

    ts_vertex *kp,*km;

    if(it->neigh_no< 3) return TS_FAIL;
    if(k->neigh_no< 3) return TS_FAIL;
    if(it->neigh->n< 3) return TS_FAIL;
    if(k->neigh->n< 3) return TS_FAIL;
    if(k==NULL || it==NULL){
        fatal("In bondflip, number of neighbours of k or it is less than 3!",999);
    }

    nei=0;
    for(i=0;i<it->neigh_no;i++){ // Finds the nn of it, that is k 
        if(it->neigh[i]==k){
    for(i=0;i<it->neigh->n;i++){ // Finds the nn of it, that is k 
        if(it->neigh->vtx[i]==k){
            nei=i;
            break;
        }
    }
    neip=nei+1;  // I don't like it.. Smells like I must have it in correct order
    neim=nei-1;
    if(neip>=it->neigh_no) neip=0;
    if((ts_int)neim<0) neim=it->neigh_no-1; /* casting is essential... If not
    if(neip>=it->neigh->n) neip=0;
    if((ts_int)neim<0) neim=it->neigh->n-1; /* casting is essential... If not
there the neim is never <0 !!! */
  //  fprintf(stderr,"The numbers are: %u %u\n",neip, neim);
    km=it->neigh[neim];  // We located km and kp
    kp=it->neigh[neip];
    km=it->neigh->vtx[neim];  // We located km and kp
    kp=it->neigh->vtx[neip];

    if(km==NULL || kp==NULL){
        fatal("In bondflip, cannot determine km and kp!",999);
@@ -64,8 +64,8 @@

/* test if the membrane is wrapped too much, so that kp is nearest neighbour of
 * km. If it is true, then don't flip! */
    for(i=0;i<km->neigh_no;i++){
        if(km->neigh[i] == kp) return TS_FAIL;
    for(i=0;i<km->neigh->n;i++){
        if(km->neigh->vtx[i] == kp) return TS_FAIL;
    }
 //   fprintf(stderr,"Membrane didn't wrap too much.. Continue.\n");
/* if bond would be too long, return... */
@@ -107,10 +107,10 @@

/* Calculating the new energy */
  delta_energy=0;
  for(i=0;i<k->neigh_no;i++) energy_vertex(k->neigh[i]);
  for(i=0;i<kp->neigh_no;i++) energy_vertex(kp->neigh[i]);
  for(i=0;i<km->neigh_no;i++) energy_vertex(km->neigh[i]);
  for(i=0;i<it->neigh_no;i++) energy_vertex(it->neigh[i]);
  for(i=0;i<k->neigh->n;i++) energy_vertex(k->neigh->vtx[i]);
  for(i=0;i<kp->neigh->n;i++) energy_vertex(kp->neigh->vtx[i]);
  for(i=0;i<km->neigh->n;i++) energy_vertex(km->neigh->vtx[i]);
  for(i=0;i<it->neigh->n;i++) energy_vertex(it->neigh->vtx[i]);
  delta_energy+=k->xk* k->energy;
  delta_energy+=kp->xk* kp->energy;
  delta_energy+=km->xk* km->energy;
@@ -279,15 +279,18 @@
// 3. step. Correct neighbours in vertex_list


            vtx_remove_neighbour(k,it);
            vertex_list_remove_vtx(k->neigh, it);
            vertex_list_remove_vtx(it->neigh, k);
    //vtx_remove_neighbour(k,it);
//            vtx_remove_neighbour(it,k);
//fprintf(stderr,"3. step (PROGRESS): removed k and it neighbours\n");
    
            //Tukaj pa nastopi tezava... Kam dodati soseda?
            vtx_insert_neighbour(km,kp,k);
            vtx_insert_neighbour(kp,km,it);
//            vertex_add_neighbour(km,kp); //pazi na vrstni red.
//            vertex_add_neighbour(kp,km);
		
//            vtx_insert_neighbour(km,kp,k);
//            vtx_insert_neighbour(kp,km,it);
            vtx_add_neighbour(km,kp); //pazi na vrstni red.
            vtx_add_neighbour(kp,km);
//fprintf(stderr,"3. step: vertex neighbours corrected\n");

// 3a. step. If any changes to ts_vertex, do it here!

 src/energy.c

@@ -31,14 +31,14 @@
    ts_double s=0.0,xh=0.0,yh=0.0,zh=0.0,txn=0.0,tyn=0.0,tzn=0.0;
    ts_double x1,x2,x3,ctp,ctm,tot,xlen;
    ts_double h,ht;
    for(jj=1; jj<=vtx->neigh_no;jj++){
    for(jj=1; jj<=vtx->neigh->n;jj++){
        jjp=jj+1;
        if(jjp>vtx->neigh_no) jjp=1;
        if(jjp>vtx->neigh->n) jjp=1;
        jjm=jj-1;
        if(jjm<1) jjm=vtx->neigh_no;
        j=vtx->neigh[jj-1];
        jp=vtx->neigh[jjp-1];
        jm=vtx->neigh[jjm-1];
        if(jjm<1) jjm=vtx->neigh->n;
        j=vtx->neigh->vtx[jj-1];
        jp=vtx->neigh->vtx[jjp-1];
        jm=vtx->neigh->vtx[jjm-1];
//        printf("tristar_no=%u, neigh_no=%u, jj=%u\n",data->tristar_no,data->neigh_no,jj);
        jt=vtx->tristar[jj-1];
        x1=vtx_distance_sq(vtx,jp); //shouldn't be zero!

 src/io.c

@@ -59,9 +59,9 @@
    for(i=0;i<vlist->n;i++){
        fprintf(fh," %.17E\t%.17E\t%.17E\t%u\n",vlist->vtx[i]->x,
            vlist->vtx[i]->y, vlist->vtx[i]->z,
            vlist->vtx[i]->neigh_no);
        for(j=0;j<vlist->vtx[i]->neigh_no;j++){
            fprintf(fh,"\t%u",(ts_uint)(vlist->vtx[i]->neigh[j]->idx));
            vlist->vtx[i]->neigh->n);
        for(j=0;j<vlist->vtx[i]->neigh->n;j++){
            fprintf(fh,"\t%u",(ts_uint)(vlist->vtx[i]->neigh->vtx[j]->idx));
        //-vlist->vtx+1));
        }
        fprintf(fh,"\n");
@@ -107,11 +107,11 @@
        fprintf(fh," %.17E\t%.17E\t%.17E\t%.17E\t%.17E\t%u\n",
        vlist->vtx[i]->xk,vlist->vtx[i]->c,vlist->vtx[i]->energy,
        vlist->vtx[i]->energy_h, vlist->vtx[i]->curvature, 0);
        for(j=0;j<vlist->vtx[i]->neigh_no;j++){
        for(j=0;j<vlist->vtx[i]->neigh->n;j++){
            fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length_dual);
        }
            fprintf(fh,"\n");
        for(j=0;j<vlist->vtx[i]->neigh_no;j++){
        for(j=0;j<vlist->vtx[i]->neigh->n;j++){
            fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length);
        }
            fprintf(fh,"\n");