From bd826de2f539f2e48c8c01d2d7f9f34c7e97104a Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Fri, 13 May 2016 07:43:27 +0000
Subject: [PATCH] Fix in trisurf output, inhibiting print of successful reconstruction. Multiple fixes and improvements in python module. Added symlinking of tapes into the running directories and dumping tapes from snapshots into tape files.
---
src/dumpstate.c | 112 ++++++++++++++++++++++++++++++++++++++++++++++++++++---
1 files changed, 105 insertions(+), 7 deletions(-)
diff --git a/src/dumpstate.c b/src/dumpstate.c
index 4d7dde2..4493f71 100644
--- a/src/dumpstate.c
+++ b/src/dumpstate.c
@@ -1,3 +1,4 @@
+/* vim: set ts=4 sts=4 sw=4 noet : */
#include <string.h>
#include "general.h"
#include <stdio.h>
@@ -6,6 +7,8 @@
#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 +49,23 @@
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 +82,91 @@
//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;
+}
+
+
--
Gitblit v1.9.3