From 86b69b3803b1b31c040cede6b47bf617561b3b81 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@fe.uni-lj.si>
Date: Tue, 01 Mar 2016 08:36:37 +0000
Subject: [PATCH] Polymeres are restored
---
src/dumpstate.c | 111 ++++++++++++++++++++++++++++++++++++++++++++++++++++---
1 files changed, 104 insertions(+), 7 deletions(-)
diff --git a/src/dumpstate.c b/src/dumpstate.c
index 4d7dde2..9d1e2b2 100644
--- a/src/dumpstate.c
+++ b/src/dumpstate.c
@@ -6,6 +6,8 @@
#include "dumpstate.h"
#include <libxml/parser.h>
#include <libxml/tree.h>
+#include "vertex.h"
+#include "energy.h"
ts_vesicle *vtk2vesicle(char *filename, ts_tape *tape){
@@ -46,16 +48,23 @@
cur_node=cur_node->children;
while(cur_node!=NULL){
- fprintf(stderr,"Node name is: %s\n",cur_node->name);
+ //fprintf(stderr,"Node name is: %s\n",cur_node->name);
cur_node=cur_node->next;
if(strcmp((char *)cur_node->name,"PointData")==0) vtk_index2vesicle(cur_node->children->next->children, vesicle);
- if(strcmp((char *)cur_node->name,"Points")==0) break;
- if(strcmp((char *)cur_node->name,"Cells")==0) break;
-
+ if(strcmp((char *)cur_node->name,"Points")==0) vtk_coordinates(cur_node->children->next->children,vesicle);
+ if(strcmp((char *)cur_node->name,"Cells")==0) {
+ vtk_neighbours(cur_node->children->next->children,vesicle);
+ break; //segfaults, because it finds another cells. Why?
+ }
}
-
-
-
+ //we have vertices and neighbour relations all set, but unordered. Let's do bonds, ordering, triangles...
+ vesicle->vlist = vtk_sort_neighbours(vesicle->blist,vesicle->vlist);
+ init_triangles(vesicle);
+ init_triangle_neighbours(vesicle);
+ init_common_vertex_triangle_neighbours(vesicle);
+ init_normal_vectors(vesicle->tlist);
+ mean_curvature_and_energy(vesicle);
+ ts_fprintf(stdout,"restoring from vtk dump finished!\n");
return TS_SUCCESS;
}
@@ -72,3 +81,91 @@
//fprintf(stderr,"idx[11]=%d\n",vesicle->vlist->vtx[11]->idx);
return TS_SUCCESS;
}
+
+ts_bool vtk_coordinates(xmlNode *node, ts_vesicle *vesicle){
+ //fprintf(stderr, "vsebina: %s\n",node->content);
+ ts_uint i;
+ char *token;
+ token = strtok((char *)node->content, " ");
+ for(i=0;i<vesicle->vlist->n;i++){
+ vesicle->vlist->vtx[i]->x=atof(token);
+// fprintf(stderr,"%e, ",atof(token));
+ token=strtok(NULL," ");
+ vesicle->vlist->vtx[i]->y=atof(token);
+ token=strtok(NULL,"\n");
+ vesicle->vlist->vtx[i]->z=atof(token);
+ if(i>0) token=strtok(NULL," ");
+ }
+ return TS_SUCCESS;
+
+}
+
+ts_bool vtk_neighbours(xmlNode *node, ts_vesicle *vesicle){
+ // fprintf(stderr, "vsebina: %s\n",node->content);
+ ts_uint i;
+ ts_uint idx1, idx2;
+ char *token;
+ token = strtok((char *)node->content, " ");
+ for(i=0;i<3*(vesicle->vlist->n-2);i++){
+ idx1=atoi(token);
+ token=strtok(NULL,"\n");
+ idx2=atoi(token);
+ vtx_add_neighbour(vesicle->vlist->vtx[idx1], vesicle->vlist->vtx[idx2]);
+ vtx_add_neighbour(vesicle->vlist->vtx[idx2], vesicle->vlist->vtx[idx1]);
+ fprintf(stderr, "%d. povezujem %d in %d\n",i,idx1,idx2);
+ if(i>0) token=strtok(NULL," ");
+ }
+ return TS_SUCCESS;
+}
+
+/* this is almost exact copy of init_sort_neighbours */
+ts_vertex_list *vtk_sort_neighbours(ts_bond_list *blist,ts_vertex_list *vlist){
+ ts_vertex **vtx=vlist->vtx -1; // take a look at dipyramid function for comment.
+ ts_uint i,l,j,jj,jjj,k=0;
+ ts_double eps=0.001; // Take a look if EPS from math.h can be used
+
+/*lets initialize memory for temporary vertex_list. Should we write a function instead */
+ ts_vertex_list *tvlist=vertex_list_copy(vlist);
+ ts_vertex **tvtx=tvlist->vtx -1; /* again to compensate for 0-indexing */
+
+ ts_double dist2; // Square of distance of neighbours
+ ts_double direct; // Something, dont know what, but could be normal of some kind
+ for(i=1;i<=vlist->n;i++){
+ k++; // WHY i IS NOT GOOD??
+ vtx_add_cneighbour(blist,tvtx[k], tvtx[vtx[i]->neigh[0]->idx+1]); //always add 1st
+ jjj=1;
+ jj=1;
+ for(l=2;l<=vtx[i]->neigh_no;l++){
+ for(j=2;j<=vtx[i]->neigh_no;j++){
+ dist2=vtx_distance_sq(vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
+ direct=vtx_direct(vtx[i],vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
+// TODO: check if fabs can be used with all floating point types!!
+ if( (direct>0.0) && (j!=jjj) ){
+ vtx_add_cneighbour(blist,tvtx[k],tvtx[vtx[i]->neigh[j-1]->idx+1]);
+ jjj=jj;
+ jj=j;
+ // break;
+ }
+ }
+ }
+ if(vtx[i]->neigh_no!=tvtx[i]->neigh_no){
+ fprintf(stderr,"Hej! pri vtx=%d se razikuje stevilo sosedov (prej=%d, potem=%d)\n",i, vtx[i]->neigh_no, tvtx[i]->neigh_no);
+ }
+ }
+ if(eps>dist2);
+/* We use the temporary vertex for our main vertices and we abandon main
+ * vertices, because their neighbours are not correctly ordered */
+ // tvtx=vlist->vtx;
+ // vlist->vtx=tvtx;
+ // tvlist->vtx=vtx;
+ vtx_list_free(vlist);
+/* Let's make a check if the number of bonds is correct */
+ if((blist->n)!=3*(tvlist->n-2)){
+ ts_fprintf(stderr,"Number of bonds is %u should be %u!\n", blist->n, 3*(tvlist->n-2));
+ fatal("Number of bonds is not 3*(no_vertex-2).",4);
+ }
+
+ return tvlist;
+}
+
+
--
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