From 514ebcb0e1b01fa41d022e3a92fe08a390a421dd Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Sun, 09 Dec 2018 21:35:42 +0000
Subject: [PATCH] Load settings from tape

---
 src/vertex.c |   41 +++++++++++++++++++++++++++++++++--------
 1 files changed, 33 insertions(+), 8 deletions(-)

diff --git a/src/vertex.c b/src/vertex.c
index 694ee84..59a6419 100644
--- a/src/vertex.c
+++ b/src/vertex.c
@@ -1,3 +1,4 @@
+/* vim: set ts=4 sts=4 sw=4 noet : */
 #include<stdlib.h>
 #include<math.h>
 #include<string.h>
@@ -5,6 +6,14 @@
 #include "vertex.h"
 #include "bond.h"
 #include<stdio.h>
+
+ts_bool vertex_list_assign_id(ts_vertex_list *vlist, ts_uint id){
+	ts_uint i;	
+	for(i=0;i<vlist->n;i++){
+		vlist->vtx[i]->id = id;
+	}
+	return TS_SUCCESS;
+}
 
 ts_vertex_list *init_vertex_list(ts_uint N){	
 	ts_int i;
@@ -72,25 +81,25 @@
 ts_bool vtx_remove_neighbour(ts_vertex *vtx, ts_vertex *nvtx){
 /* find a neighbour */
 /* remove it from the list while shifting remaining neighbours up */
-    ts_int i,j=-1;
+    ts_uint i,j=0;
     for(i=0;i<vtx->neigh_no;i++){
+//		fprintf(stderr,"neigh_addr=%ld\n", (long)vtx->neigh[i]);
         if(vtx->neigh[i]!=nvtx){
             vtx->neigh[j]=vtx->neigh[i];
             j++;
         }
     }
-    if(j==0) { 
-        fatal("vtx_remove_neighbour: Error, vertices are not neighbours", 100);
-    }
+//	fprintf(stderr,"remove_neighbour: vtx1_addr=%ld, vtx2_addr=%ld\n",(long)vtx,(long)nvtx);
 /* resize memory. potentionally time consuming */
     vtx->neigh_no--;
     vtx->neigh=(ts_vertex **)realloc(vtx->neigh,vtx->neigh_no*sizeof(ts_vertex *));
     if(vtx->neigh == NULL && vtx->neigh_no!=0)
-        fatal("Reallocation of memory failed during removal of vertex neighbour in vtx_remove_neighbour",100);
-fprintf(stderr,"first alloc");
+        fatal("(1) Reallocation of memory failed during removal of vertex neighbour in vtx_remove_neighbour",100);
+//fprintf(stderr,"first alloc");
 /* repeat for the neighbour */
 /* find a neighbour */
 /* remove it from the list while shifting remaining neighbours up */
+	j=0;
     for(i=0;i<nvtx->neigh_no;i++){
         if(nvtx->neigh[i]!=vtx){
             nvtx->neigh[j]=nvtx->neigh[i];
@@ -98,10 +107,12 @@
         }
     }
 /* resize memory. potentionally time consuming. */
+//	fprintf(stderr,"Neigbours=%d\n",nvtx->neigh_no);
     nvtx->neigh_no--;
-    nvtx->neigh=(ts_vertex **)realloc(nvtx->neigh,nvtx->neigh_no*sizeof(ts_vertex *));
+    		nvtx->neigh=(ts_vertex **)realloc(nvtx->neigh,nvtx->neigh_no*sizeof(ts_vertex *));
+//	fprintf(stderr,"Neigbours=%d\n",nvtx->neigh_no);
     if(nvtx->neigh == NULL && nvtx->neigh_no!=0)
-        fatal("Reallocation of memory failed during removal of vertex neighbour in vtx_remove_neighbour",100);
+        fatal("(2) Reallocation of memory failed during removal of vertex neighbour in vtx_remove_neighbour",100);
 
     return TS_SUCCESS;
 }
@@ -128,6 +139,7 @@
 ts_bool vtx_add_cneighbour(ts_bond_list *blist, ts_vertex *vtx1, ts_vertex *vtx2){
     ts_bool retval;
     retval=vtx_add_neighbour(vtx1,vtx2);
+  //  retval=vtx_add_neighbour(vtx2,vtx1);
     if(retval==TS_SUCCESS)
     retval=vtx_add_bond(blist,vtx1,vtx2); 
     return retval;
@@ -188,6 +200,19 @@
     return TS_SUCCESS;
 }
 
+/** Calculates the triple product of vectors defined by vertices vtx1, vtx2 and vtx3, ($\mathrm{vtx}_1\cdot(\mathrm{vtx}_2\cross\mathrm{vtx}_3$):
+ *  \begin{vmatrix}
+ *  x_1 & y_1 & z_1 \\
+ *  x_2-x_1 & y_2-y_1 & z_2-z_1\\
+ *  x_3-x_1 & y_3-y_1 & z_3-z_1\\
+ *  \end{vmatrix}
+ *  where the vertices coordinates are denoted by corresponding vertex index number. Function is used to determine the orientation of area formed by triangle formed by the three given vertices.
+ *
+ *      @param vtx1 is first vertex, according to which the orientation is calculated
+ *      @param vtx2 is the second vertex
+ *      @param vtx3 is the third vertex
+ *      @returns directionality of the area of the triangle formed by vertices vtx1, vtx2 and vtx3. It is positive if vtx1, vtx2 and vtx3 are oriented counter-clockwise.
+*/
 inline ts_double vtx_direct(ts_vertex *vtx1, ts_vertex *vtx2, ts_vertex *vtx3){
     ts_double dX2=vtx2->x-vtx1->x;
     ts_double dY2=vtx2->y-vtx1->y;

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