From 6487a03362d35589c286d0660eba123a7ab00535 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Mon, 10 May 2021 11:14:04 +0000
Subject: [PATCH] Raj and Yoav session in making multiple protein species
---
src/triangle.c | 202 +++++++++++++++++++++++++------------------------
1 files changed, 103 insertions(+), 99 deletions(-)
diff --git a/src/triangle.c b/src/triangle.c
index 959205a..da9d7a8 100644
--- a/src/triangle.c
+++ b/src/triangle.c
@@ -1,3 +1,4 @@
+/* vim: set ts=4 sts=4 sw=4 noet : */
#include<stdlib.h>
#include<stdio.h>
#include "general.h"
@@ -5,6 +6,7 @@
#include<math.h>
/** @brief Prepares the list for triangles.
+ * @returns pointer to empty data structure for maintaining triangle list.
*
* Create empty list for holding the information on triangles. Triangles are
* added later on with triangle_add().
@@ -27,14 +29,17 @@
}
/** @brief Add the triangle to the triangle list and create necessary data
- * structures.
+ * structures.
+ * @param *tlist is a pointer to triangle list where triangle should be created
+ * @param *vtx1, *vtx2, *vtx3 are the three vertices defining the triangle
+ * @returns pointer to the newly created triangle on success and NULL if
+ * triangle could not be created. It breaks program execution if memory
+ * allocation of triangle list can't be done.
*
- * Add the triangle ts_triangle with ts_triangle_data to the ts_triangle_list.
+ * Add the triangle ts_triangle to the ts_triangle_list.
* The triangle list is resized, the ts_triangle is allocated and
- * ts_triangle_data is allocated and zeroed. The function receives 4 arguments:
- * ts_triangle_list *tlist as list of triangles and 3 ts_vertex *vtx as
- * vertices that are used to form a triangle. Returns a pointer to newly
- * created triangle. This pointer doesn't need assigning, since it is
+ * triangle data is zeroed. Returned pointer to newly
+ * created triangle doesn't need assigning, since it is
* referenced by triangle list.
*
* WARNING: Function can be accelerated a bit by removing the NULL checks.
@@ -57,22 +62,27 @@
tlist->tria[tlist->n-1]=(ts_triangle *)calloc(1,sizeof(ts_triangle));
if(tlist->tria[tlist->n-1]==NULL) fatal("Cannot reallocate memory for additional ts_triangle.",5);
- tlist->tria[tlist->n-1]->data=(ts_triangle_data *)calloc(1,sizeof(ts_triangle_data));
//NOW insert vertices!
tlist->tria[tlist->n - 1]->idx=tlist->n-1;
- tlist->tria[tlist->n - 1]->data->vertex[0]=vtx1;
- tlist->tria[tlist->n - 1]->data->vertex[1]=vtx2;
- tlist->tria[tlist->n - 1]->data->vertex[2]=vtx3;
+ tlist->tria[tlist->n - 1]->vertex[0]=vtx1;
+ tlist->tria[tlist->n - 1]->vertex[1]=vtx2;
+ tlist->tria[tlist->n - 1]->vertex[2]=vtx3;
return tlist->tria[tlist->n-1];
}
/** @brief Add the neigbour to triangles.
+ * @param *tria is a first triangle.
+ * @param *ntria is a second triangle.
+ * @returns TS_SUCCES on sucessful adition to the list, TS_FAIL if triangles
+ * are NULL and breaks execution FATALY if memory allocation error occurs.
*
* Add the neigbour to the list of neighbouring triangles. The
- * neighbouring triangles are those, who share two vertices. Function resizes
+ * neighbouring triangles are those, who share two vertices and corresponding
+ * bond. Function resizes
* the list and adds the pointer to neighbour. It receives two arguments of
- * ts_triangle type. It then adds eachother to eachother's list. Upon
+ * ts_triangle type. It then adds second triangle to the list of first
+ * triangle, but not the opposite. Upon
* success it returns TS_SUCCESS, upon detecting NULL pointers
* returns TS_FAIL and it FATALY ends when the data structure
* cannot be resized.
@@ -83,40 +93,40 @@
* debugging stupid NULL pointers.
*
* Example of usage:
- * triangle_remove_neighbour(tlist->tria[3], tlist->tria[4]);
+ * triangle_add_neighbour(tlist->tria[3], tlist->tria[4]);
*
- * Triangles 3 and 4 are not neighbours anymore.
+ * Triangle 4 is a neighbour of triangle 3, but (strangely) not the
+ * oposite. The function should be called again with the changed order of
+ * triangles to make neighbourship mutual.
*
*/
ts_bool triangle_add_neighbour(ts_triangle *tria, ts_triangle *ntria){
if(tria==NULL || ntria==NULL) return TS_FAIL;
-/*TODO: check if the neighbour already exists! Now there is no such check
- * because of the performance issue. */
- tria->data->neigh_no++;
- tria->data->neigh=realloc(tria->data->neigh,tria->data->neigh_no*sizeof(ts_triangle *));
- if(tria->data->neigh == NULL)
+ tria->neigh_no++;
+ tria->neigh=realloc(tria->neigh,tria->neigh_no*sizeof(ts_triangle *));
+ if(tria->neigh == NULL)
fatal("Reallocation of memory failed during insertion of triangle neighbour in triangle_add_neighbour",3);
- tria->data->neigh[tria->data->neigh_no-1]=ntria;
-
-/* we repeat the procedure for the neighbour */
- ntria->data->neigh_no++;
- ntria->data->neigh=realloc(ntria->data->neigh,ntria->data->neigh_no*sizeof(ts_triangle *));
- if(ntria->data->neigh == NULL)
- fatal("Reallocation of memory failed during insertion of triangle neighbour in triangle_add_neighbour",3);
- ntria->data->neigh[ntria->data->neigh_no-1]=tria;
+ tria->neigh[tria->neigh_no-1]=ntria;
return TS_SUCCESS;
}
/** @brief Remove the neigbours from triangle.
+ * @param *tria is a first triangle.
+ * @param *ntria is neighbouring triangle.
+ * @returns TS_SUCCESS on successful removal, TS_FAIL if triangles are not
+ * neighbours and it breaks program execution FATALY if memory allocation
+ * problem occurs.
*
* Removes the neigbour from the list of neighbouring triangles. The
- * neighbouring triangles are those, who share two vertices. Function resizes
+ * neighbouring triangles are those, who share two vertices and corresponding
+ * bond. Function resizes
* the list and deletes the pointer to neighbour. It receives two arguments of
- * ts_triangle type. It then removes eachother form eachother's list. Upon
+ * ts_triangle type. It then mutually removes triangles from eachouther
+ * neighbour list. Upon
* success it returns TS_SUCCESS, upon failure to find the triangle in the
- * neighbour list returns TS_FAIL and it FATALY ends when the datastructure
- * cannot be resized.
+ * neighbour list returns TS_FAIL. It FATALY breaks program execution when the datastructure
+ * cannot be resized due to memory constrain problems.
*
* WARNING: The function doesn't check whether the pointer is NULL or invalid. It is the
* job of programmer to make sure the pointer is valid.
@@ -133,77 +143,86 @@
ts_uint i,j=0;
if(tria==NULL || ntria==NULL) return TS_FAIL;
- for(i=0;i<tria->data->neigh_no;i++){
- if(tria->data->neigh[i]!=ntria){
- tria->data->neigh[j]=tria->data->neigh[i];
+ for(i=0;i<tria->neigh_no;i++){
+ if(tria->neigh[i]!=ntria){
+ tria->neigh[j]=tria->neigh[i];
j++;
}
}
if(j==i) {
return TS_FAIL;
- //fatal("In triangle_remove_neighbour: Specified neighbour does not exist for given triangle",3);
}
- tria->data->neigh_no--;
- tria->data->neigh=(ts_triangle **)realloc(tria->data->neigh,tria->data->neigh_no*sizeof(ts_triangle *));
- if(tria->data->neigh == NULL){
+ tria->neigh_no--;
+ tria->neigh=(ts_triangle **)realloc(tria->neigh,tria->neigh_no*sizeof(ts_triangle *));
+ if(tria->neigh == NULL){
+ fprintf(stderr,"Ooops: tria->neigh_no=%d\n",tria->neigh_no);
fatal("Reallocation of memory failed during removal of vertex neighbour in triangle_remove_neighbour",100);
}
/* we repeat the procedure for neighbour */
- for(i=0;i<ntria->data->neigh_no;i++){
- if(ntria->data->neigh[i]!=tria){
- ntria->data->neigh[j]=ntria->data->neigh[i];
+ j=0;
+ for(i=0;i<ntria->neigh_no;i++){
+ if(ntria->neigh[i]!=tria){
+ ntria->neigh[j]=ntria->neigh[i];
j++;
}
}
if(j==i) {
return TS_FAIL;
- //fatal("In triangle_remove_neighbour: Specified neighbour does not exist for given triangle",3);
}
- ntria->data->neigh_no--;
- ntria->data->neigh=(ts_triangle **)realloc(ntria->data->neigh,ntria->data->neigh_no*sizeof(ts_triangle *));
- if(ntria->data->neigh == NULL){
+ ntria->neigh_no--;
+ ntria->neigh=(ts_triangle **)realloc(ntria->neigh,ntria->neigh_no*sizeof(ts_triangle *));
+ if(ntria->neigh == NULL){
+ fprintf(stderr,"Ooops: ntria->neigh_no=%d\n",ntria->neigh_no);
fatal("Reallocation of memory failed during removal of vertex neighbour in triangle_remove_neighbour",100);
}
return TS_SUCCESS;
}
-/** @brief Calculates normal vector of the triangle.
-
+/** @brief Calculates normal vector of the triangle, its corresponding area and volume.
+ * @param *tria is a triangle pointer for which normal, area and volume is
+ * to be calculated.
+ * @returns TS_SUCCESS on success. (always)
*
* Calculate normal vector of the triangle (xnorm, ynorm and znorm) and stores
- * information in underlying ts_triangle_data data_structure.
+ * information. At the same time
+ * triangle area is determined, since we already have the normal and volume of
+ * triangular pyramid with given triangle as a base and vesicle centroid as a
+ * tip.
*
* Function receives one argument of type ts_triangle. It should be corectly
- * initialized with underlying data structure of type ts_triangle_data. the
- * result is stored in triangle->data->xnorm, triangle->data->ynorm,
- * triangle->data->znorm. Returns TS_SUCCESS on completion.
+ * initialized. The
+ * result is stored in triangle->xnorm, triangle->ynorm, triangle->znorm.
+ * Area and volume are stored into triangle->area and triangle->volume.
+ * Returns TS_SUCCESS on completion.
*
- * NOTE: Function uses math.h library. pow function implementation is selected
- * accordind to the setting in genreal.h
+ * NOTE: Function uses math.h library. Function pow implementation is selected
+ * accordind to the used TS_DOUBLE_* definition set in general.h, so it should
+ * be compatible with any type of floating point precision.
*
* Example of usage:
* triangle_normal_vector(tlist->tria[3]);
*
* Computes normals and stores information into tlist->tria[3]->xnorm,
- * tlist->tria[3]->ynorm, tlist->tria[3]->znorm.
+ * tlist->tria[3]->ynorm, tlist->tria[3]->znorm tlist->tria[3]->area and
+ * tlist->tria[3]->volume.
*
*/
ts_bool triangle_normal_vector(ts_triangle *tria){
ts_double x21,x31,y21,y31,z21,z31,xden;
- x21=tria->data->vertex[1]->data->x - tria->data->vertex[0]->data->x;
- x31=tria->data->vertex[2]->data->x - tria->data->vertex[0]->data->x;
- y21=tria->data->vertex[1]->data->y - tria->data->vertex[0]->data->y;
- y31=tria->data->vertex[2]->data->y - tria->data->vertex[0]->data->y;
- z21=tria->data->vertex[1]->data->z - tria->data->vertex[0]->data->z;
- z31=tria->data->vertex[2]->data->z - tria->data->vertex[0]->data->z;
+ x21=tria->vertex[1]->x - tria->vertex[0]->x;
+ x31=tria->vertex[2]->x - tria->vertex[0]->x;
+ y21=tria->vertex[1]->y - tria->vertex[0]->y;
+ y31=tria->vertex[2]->y - tria->vertex[0]->y;
+ z21=tria->vertex[1]->z - tria->vertex[0]->z;
+ z31=tria->vertex[2]->z - tria->vertex[0]->z;
- tria->data->xnorm=y21*z31 - z21*y31;
- tria->data->ynorm=z21*x31 - x21*z31;
- tria->data->znorm=x21*y31 - y21*x31;
- xden=tria->data->xnorm*tria->data->xnorm +
- tria->data->ynorm*tria->data->ynorm +
- tria->data->znorm*tria->data->znorm;
+ tria->xnorm=y21*z31 - z21*y31;
+ tria->ynorm=z21*x31 - x21*z31;
+ tria->znorm=x21*y31 - y21*x31;
+ xden=tria->xnorm*tria->xnorm +
+ tria->ynorm*tria->ynorm +
+ tria->znorm*tria->znorm;
#ifdef TS_DOUBLE_DOUBLE
xden=sqrt(xden);
#endif
@@ -213,42 +232,27 @@
#ifdef TS_DOUBLE_LONGDOUBLE
xden=sqrtl(xden);
#endif
- tria->data->xnorm=tria->data->xnorm/xden;
- tria->data->ynorm=tria->data->ynorm/xden;
- tria->data->znorm=tria->data->znorm/xden;
+ tria->xnorm=tria->xnorm/xden;
+ tria->ynorm=tria->ynorm/xden;
+ tria->znorm=tria->znorm/xden;
+
+/* Here it is an excellent point to recalculate volume of the triangle and
+ * store it into datastructure. Volume is required at least by constant volume
+ * calculation of vertex move and bondflip and spherical harmonics. */
+ tria->volume=(tria->vertex[0]->x+ tria->vertex[1]->x + tria->vertex[2]->x) * tria->xnorm +
+ (tria->vertex[0]->y+ tria->vertex[1]->y + tria->vertex[2]->y) * tria->ynorm +
+ (tria->vertex[0]->z+ tria->vertex[1]->z + tria->vertex[2]->z) * tria->znorm;
+ tria->volume=-xden*tria->volume/18.0;
+/* Also, area can be calculated in each triangle */
+ tria->area=xden/2;
+
+
return TS_SUCCESS;
}
-
-
-
-
-/** @brief Frees the memory allocated for data structure of triangle data
- * (ts_triangle_data)
- *
- * Function frees the memory of ts_triangle_data previously allocated. It
- * accepts one argument, the address of data structure. It destroys all
- * pointers the structure might have (currently only neigh -- the pointer to
- * list of neighbouring triangles) and data structure itself. The return value
- * is always TS_SUCCESS.
- *
- * WARNING: The function doesn't check whether the pointer is NULL or invalid. It is the
- * job of programmer to make sure the pointer is valid.
- *
- * Example of usage:
- * triangle_data_free(tlist->tria[3]->data);
- *
- * Clears the data structure with all pointers.
- *
- */
-ts_bool triangle_data_free(ts_triangle_data *data){
- if(data->neigh!=NULL) free(data->neigh);
- free(data);
- return TS_SUCCESS;
-}
-
/** @brief Frees the memory allocated for data structure of triangle list
- * (ts_triangle_list)
+ * @param *tlist is a pointer to datastructure triangle list to be freed.
+ * @returns TS_SUCCESS on success (always).
*
* Function frees the memory of ts_triangle_list previously allocated. It
* accepts one argument, the address of data structure. It destroys all
@@ -274,7 +278,7 @@
ts_bool triangle_list_free(ts_triangle_list *tlist){
ts_uint i;
for(i=0;i<tlist->n;i++){
- triangle_data_free(tlist->tria[i]->data);
+ if(tlist->tria[i]->neigh!=NULL) free(tlist->tria[i]->neigh);
free(tlist->tria[i]);
}
free(tlist->tria);
--
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