#include<stdlib.h>
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#include<math.h>
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#include<string.h>
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#include "general.h"
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#include "vertex.h"
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#include "bond.h"
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#include<stdio.h>
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ts_vertex_list *init_vertex_list(ts_uint N){
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ts_int i;
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ts_vertex_list *vlist=(ts_vertex_list *)malloc(sizeof(ts_vertex_list));
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if(N==0){
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err("Initialized vertex list with zero elements. Pointer set to NULL");
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vlist->n=0;
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vlist->vtx=NULL;
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return vlist;
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}
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vlist->vtx=(ts_vertex **)calloc(N,sizeof(ts_vertex *));
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if(vlist->vtx==NULL)
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fatal("Fatal error reserving memory space for vertex list! Could number of requsted vertices be too large?", 100);
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for(i=0;i<N;i++) {
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vlist->vtx[i]=(ts_vertex *)calloc(1,sizeof(ts_vertex));
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vlist->vtx[i]->idx=i;
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/* initialize Ylm for spherical hamonics DONE in sh.c */
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/* for(i=0;i<l;i++){
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vlist->vtx[i]->Ylm[i]=(ts_double **)calloc(2*i+1,sizeof(ts_double *));
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for(j=0;j<(2*i+1);j++){
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clist->vtx[i]->Ylm[i][j]=(ts_double *)calloc(sizeof(ts_double));
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}
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}
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*/
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}
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vlist->n=N;
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return vlist;
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}
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ts_bool vertex_list_add_vtx(ts_vertex_list *vlist, ts_vertex *vtx){
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#ifdef DEBUG
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if(vtx==NULL || vlist==NULL) return TS_FAIL;
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#endif
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if(vlist->list_size < vlist->n+1){
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vlist->vtx=(ts_vertex **)realloc(vlist->vtx, (vlist->list_size+TS_VLIST_CHUNK)*sizeof(ts_vertex*));
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if(vlist->vtx==NULL){
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fatal("Error in vertex_list_add. Could not reallocate memory space.",9999);
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}
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vlist->list_size+=TS_VLIST_CHUNK;
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}
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vlist->vtx[n]=vtx;
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vlist->n++;
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return TS_SUCCESS;
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}
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/* Idea is to delete vertex by removing it from list. The emply place is then filled in by the last
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vertex in the list. List can then be resized by one -- unless resize is required when max list size -
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real list size > predefined value */
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ts_bool vertex_list_remove_vtx(ts_vertex_list *vlist, ts_vertex *vtx){
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#ifdef DEBUG
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if(vtx==NULL || vlist==NULL) return TS_FAIL;
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#endif
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for(i=0; i<vlist->n;i++){
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if(vlist->vtx[i]==vtx){
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vlist->vtx[i]=vlist->vtx[n-1];
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vlist->n--;
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if(vlist->list_size-vlist->n > TS_VLIST_CHUNK){
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vlist->vtx=(ts_vertex **)realloc(vlist->vtx, (vlist->list_size-TS_VLIST_CHUNK)*sizeof(ts_vertex*));
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if(vlist->vtx==NULL){
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fatal("Error in vertex_list_add. Could not reallocate memory space.",9999);
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}
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vlist->list_size-=TS_VLIST_CHUNK;
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}
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return TS_SUCCESS;
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}
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}
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return TS_FAIL;
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}
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ts_bool vtx_add_neighbour(ts_vertex *vtx, ts_vertex *nvtx){
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ts_uint i;
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/* no neighbour can be null! */
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if(vtx==NULL || nvtx==NULL) return TS_FAIL;
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/*if it is already a neighbour don't add it to the list */
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for(i=0; i<vtx->neigh->n;i++){
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if(vtx->neigh->vtx[i]==nvtx) return TS_FAIL;
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}
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ts_uint nn=++vtx->neigh->n;
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vtx->neigh=(ts_vertex **)realloc(vtx->neigh, nn*sizeof(ts_vertex *));
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vtx->neigh[nn-1]=nvtx;
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return TS_SUCCESS;
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}
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/* TODO: optimize this. test this. */
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ts_bool vtx_remove_neighbour(ts_vertex *vtx, ts_vertex *nvtx){
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/* find a neighbour */
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/* remove it from the list while shifting remaining neighbours up */
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ts_uint i,j=0;
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for(i=0;i<vtx->neigh_no;i++){
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// fprintf(stderr,"neigh_addr=%ld\n", (long)vtx->neigh[i]);
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if(vtx->neigh[i]!=nvtx){
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vtx->neigh[j]=vtx->neigh[i];
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j++;
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}
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}
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// fprintf(stderr,"remove_neighbour: vtx1_addr=%ld, vtx2_addr=%ld\n",(long)vtx,(long)nvtx);
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/* resize memory. potentionally time consuming */
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vtx->neigh_no--;
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vtx->neigh=(ts_vertex **)realloc(vtx->neigh,vtx->neigh_no*sizeof(ts_vertex *));
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if(vtx->neigh == NULL && vtx->neigh_no!=0)
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fatal("(1) Reallocation of memory failed during removal of vertex neighbour in vtx_remove_neighbour",100);
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//fprintf(stderr,"first alloc");
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/* repeat for the neighbour */
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/* find a neighbour */
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/* remove it from the list while shifting remaining neighbours up */
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j=0;
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for(i=0;i<nvtx->neigh_no;i++){
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if(nvtx->neigh[i]!=vtx){
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nvtx->neigh[j]=nvtx->neigh[i];
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j++;
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}
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}
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/* resize memory. potentionally time consuming. */
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// fprintf(stderr,"Neigbours=%d\n",nvtx->neigh_no);
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nvtx->neigh_no--;
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nvtx->neigh=(ts_vertex **)realloc(nvtx->neigh,nvtx->neigh_no*sizeof(ts_vertex *));
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// fprintf(stderr,"Neigbours=%d\n",nvtx->neigh_no);
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if(nvtx->neigh == NULL && nvtx->neigh_no!=0)
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fatal("(2) Reallocation of memory failed during removal of vertex neighbour in vtx_remove_neighbour",100);
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return TS_SUCCESS;
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}
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ts_bool vtx_add_bond(ts_bond_list *blist,ts_vertex *vtx1,ts_vertex *vtx2){
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ts_bond *bond;
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bond=bond_add(blist,vtx1,vtx2);
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if(bond==NULL) return TS_FAIL;
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vtx1->bond_no++;
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vtx2->bond_no++;
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// vtx2->data->bond_no++;
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vtx1->bond=(ts_bond **)realloc(vtx1->bond, vtx1->bond_no*sizeof(ts_bond *));
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vtx2->bond=(ts_bond **)realloc(vtx2->bond, vtx2->bond_no*sizeof(ts_bond *));
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// vtx2->data->bond=(ts_bond **)realloc(vtx2->data->bond, vtx2->data->bond_no*sizeof(ts_bond *));
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vtx1->bond[vtx1->bond_no-1]=bond;
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vtx2->bond[vtx2->bond_no-1]=bond;
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// vtx2->ata->bond[vtx2->data->bond_no-1]=bond;
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return TS_SUCCESS;
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}
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ts_bool vtx_add_cneighbour(ts_bond_list *blist, ts_vertex *vtx1, ts_vertex *vtx2){
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ts_bool retval;
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retval=vtx_add_neighbour(vtx1,vtx2);
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// retval=vtx_add_neighbour(vtx2,vtx1);
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if(retval==TS_SUCCESS)
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retval=vtx_add_bond(blist,vtx1,vtx2);
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return retval;
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}
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/*TODO: write and optimize this urgently before use! */
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ts_bool vtx_remove_cneighbour(ts_bond_list *blist, ts_vertex *vtx1, ts_vertex
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*vtx2){
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// ts_bool retval;
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/* remove the bond */
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//retval=vtx_remove_bond(blist,vtx1,vtx2);
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/* remove the vertices */
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return TS_SUCCESS;
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}
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ts_bool vtx_free(ts_vertex *vtx){
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if(vtx->neigh!=NULL) free(vtx->neigh);
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if(vtx->tristar!=NULL) free(vtx->tristar);
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if(vtx->bond!=NULL) free(vtx->bond);
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free(vtx);
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return TS_SUCCESS;
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}
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ts_bool vtx_list_free(ts_vertex_list *vlist){
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int i;
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for(i=0;i<vlist->n;i++){
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if(vlist->vtx[i]!=NULL) vtx_free(vlist->vtx[i]);
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}
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//free(*(vlist->vtx));
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free(vlist->vtx);
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free(vlist);
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return TS_SUCCESS;
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}
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inline ts_double vtx_distance_sq(ts_vertex *vtx1, ts_vertex *vtx2){
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ts_double dist;
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#ifdef TS_DOUBLE_DOUBLE
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dist=pow(vtx1->x-vtx2->x,2) + pow(vtx1->y-vtx2->y,2) + pow(vtx1->z-vtx2->z,2);
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#endif
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#ifdef TS_DOUBLE_LONGDOUBLE
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dist=powl(vtx1->x-vtx2->x,2) + powl(vtx1->y-vtx2->y,2) + powl(vtx1->z-vtx2->z,2);
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#endif
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#ifdef TS_DOUBLE_FLOAT
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dist=powf(vtx1->x-vtx2->x,2) + powf(vtx1->y-vtx2->y,2) + powf(vtx1->z-vtx2->z,2);
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#endif
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return(dist);
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}
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ts_bool vtx_set_global_values(ts_vesicle *vesicle){
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ts_double xk=vesicle->bending_rigidity;
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ts_uint i;
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for(i=0;i<vesicle->vlist->n;i++){
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vesicle->vlist->vtx[i]->xk=xk;
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}
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return TS_SUCCESS;
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}
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inline ts_double vtx_direct(ts_vertex *vtx1, ts_vertex *vtx2, ts_vertex *vtx3){
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ts_double dX2=vtx2->x-vtx1->x;
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ts_double dY2=vtx2->y-vtx1->y;
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ts_double dZ2=vtx2->z-vtx1->z;
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ts_double dX3=vtx3->x-vtx1->x;
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ts_double dY3=vtx3->y-vtx1->y;
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ts_double dZ3=vtx3->z-vtx1->z;
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ts_double direct=vtx1->x*(dY2*dZ3 -dZ2*dY3)+
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vtx1->y*(dZ2*dX3-dX2*dZ3)+
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vtx1->z*(dX2*dY3-dY2*dX3);
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return(direct);
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}
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inline ts_bool vertex_add_tristar(ts_vertex *vtx, ts_triangle *tristarmem){
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vtx->tristar_no++;
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vtx->tristar=(ts_triangle **)realloc(vtx->tristar,vtx->tristar_no*sizeof(ts_triangle *));
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if(vtx->tristar==NULL){
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fatal("Reallocation of memory while adding tristar failed.",3);
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}
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vtx->tristar[vtx->tristar_no-1]=tristarmem;
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return TS_SUCCESS;
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}
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/* Insert neighbour is a function that is required in bondflip. It inserts a
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* neighbour exactly in the right place. */
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inline ts_bool vtx_insert_neighbour(ts_vertex *vtx, ts_vertex *nvtx, ts_vertex *vtxm){
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//nvtx is a vertex that is to be inserted after vtxm!
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ts_uint i,j,midx;
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vtx->neigh_no++;
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if(vtxm==NULL || nvtx==NULL || vtx==NULL)
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fatal("vertex_insert_neighbour: one of pointers has been zero.. Cannot proceed.",3);
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//We need to reallocate space! The pointer *neight must be zero if not having neighbours jey (if neigh_no was 0 at thime of calling
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vtx->neigh=realloc(vtx->neigh,vtx->neigh_no*sizeof(ts_vertex *));
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if(vtx->neigh == NULL){
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fatal("Reallocation of memory failed during insertion of vertex neighbour in vertex_insert_neighbour",3);
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}
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midx=0;
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for(i=0;i<vtx->neigh_no-1;i++) if(vtx->neigh[i]==vtxm) {midx=i; break;}
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// fprintf(stderr,"midx=%d, vseh=%d\n",midx,vtx->neigh_no-2);
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if(midx==vtx->neigh_no-2) {
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vtx->neigh[vtx->neigh_no-1]=nvtx;
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} else {
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for(j=vtx->neigh_no-2;j>midx;j--) {
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vtx->neigh[j+1]=vtx->neigh[j];
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// vtx->bond_length[j+1]=vtx->bond_length[j];
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// vtx->bond_length_dual[j+1]=vtx->bond_length_dual[j];
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}
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vtx->neigh[midx+1]=nvtx;
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}
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return TS_SUCCESS;
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}
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/* vtx remove tristar is required in bondflip. */
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/* TODO: Check whether it is important to keep the numbering of tristar
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* elements in some order or not! */
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inline ts_bool vtx_remove_tristar(ts_vertex *vtx, ts_triangle *tristar){
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ts_uint i,j=0;
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for(i=0;i<vtx->tristar_no;i++){
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if(vtx->tristar[i]!=tristar){
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vtx->tristar[j]=vtx->tristar[i];
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j++;
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}
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}
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vtx->tristar_no--;
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vtx->tristar=realloc(vtx->tristar,vtx->tristar_no*sizeof(ts_triangle *));
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if(vtx->neigh == NULL){
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fatal("Reallocation of memory failed during insertion of vertex neighbour in vertex_add_neighbour",3);
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}
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return TS_SUCCESS;
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}
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/* ****************************************************************** */
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/* ***** New vertex copy operations. Inherently they are slow. ***** */
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/* ****************************************************************** */
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ts_bool vtx_copy(ts_vertex *cvtx, ts_vertex *ovtx){
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memcpy((void *)cvtx,(void *)ovtx,sizeof(ts_vertex));
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cvtx->neigh=NULL;
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cvtx->neigh_no=0;
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cvtx->tristar_no=0;
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cvtx->bond_no=0;
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cvtx->tristar=NULL;
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cvtx->bond=NULL;
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cvtx->cell=NULL;
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return TS_SUCCESS;
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}
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ts_bool vtx_duplicate(ts_vertex *cvtx, ts_vertex *ovtx){
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memcpy((void *)cvtx,(void *)ovtx,sizeof(ts_vertex));
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return TS_SUCCESS;
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}
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//TODO: needs to be done
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ts_vertex **vtx_neigh_copy(ts_vertex_list *vlist,ts_vertex *ovtx){
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return NULL;
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}
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ts_vertex_list *vertex_list_copy(ts_vertex_list *ovlist){
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ts_uint i;
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ts_vertex_list *vlist=(ts_vertex_list *)malloc(sizeof(ts_vertex_list));
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vlist=memcpy((void *)vlist, (void *)ovlist, sizeof(ts_vertex_list));
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ts_vertex **vtx=(ts_vertex **)malloc(vlist->n*sizeof(ts_vertex *));
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vlist->vtx=vtx;
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if(vlist->vtx==NULL)
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fatal("Fatal error reserving memory space for vertex list! Could number of requsted vertices be too large?", 100);
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for(i=0;i<vlist->n;i++) {
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vlist->vtx[i]=(ts_vertex *)calloc(1,sizeof(ts_vertex));
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vlist->vtx[i]->idx=i;
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vtx_copy(vlist->vtx[i],ovlist->vtx[i]);
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}
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return vlist;
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}
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