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/vertex.c | 269 ++++++++++++++++++++++++++++++++++++++---------------
1 files changed, 194 insertions(+), 75 deletions(-)
diff --git a/src/vertex.c b/src/vertex.c
index 379d43e..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>
@@ -6,9 +7,16 @@
#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;
- ts_vertex *tlist;
ts_vertex_list *vlist=(ts_vertex_list *)malloc(sizeof(ts_vertex_list));
if(N==0){
@@ -18,27 +26,27 @@
return vlist;
}
- vlist->vtx=(ts_vertex **)malloc(N*sizeof(ts_vertex *));
- tlist=(ts_vertex *)malloc(N*sizeof(ts_vertex));
- if(vlist->vtx==NULL || tlist==NULL)
+ vlist->vtx=(ts_vertex **)calloc(N,sizeof(ts_vertex *));
+ if(vlist->vtx==NULL)
fatal("Fatal error reserving memory space for vertex list! Could number of requsted vertices be too large?", 100);
for(i=0;i<N;i++) {
- vlist->vtx[i]=&tlist[i];
- vlist->vtx[i]->data=init_vertex_data();
+ vlist->vtx[i]=(ts_vertex *)calloc(1,sizeof(ts_vertex));
vlist->vtx[i]->idx=i;
+
+ /* initialize Ylm for spherical hamonics DONE in sh.c */
+/* for(i=0;i<l;i++){
+ vlist->vtx[i]->Ylm[i]=(ts_double **)calloc(2*i+1,sizeof(ts_double *));
+ for(j=0;j<(2*i+1);j++){
+ clist->vtx[i]->Ylm[i][j]=(ts_double *)calloc(sizeof(ts_double));
+ }
+ }
+*/
+
+
}
vlist->n=N;
return vlist;
}
-
-ts_vertex_data *init_vertex_data(){
- ts_vertex_data *data;
- data=(ts_vertex_data *)calloc(1,sizeof(ts_vertex_data));
- if(data==NULL)
- fatal("Fatal error reserving memory space for ts_vertex! Memory full?", 100);
- return data;
-}
-
ts_bool vtx_add_neighbour(ts_vertex *vtx, ts_vertex *nvtx){
ts_uint i;
@@ -46,22 +54,25 @@
if(vtx==NULL || nvtx==NULL) return TS_FAIL;
/*if it is already a neighbour don't add it to the list */
- for(i=0; i<vtx->data->neigh_no;i++){
- if(vtx->data->neigh[i]==nvtx) return TS_FAIL;
+ for(i=0; i<vtx->neigh_no;i++){
+ if(vtx->neigh[i]==nvtx) return TS_FAIL;
}
- ts_uint nn=++vtx->data->neigh_no;
- vtx->data->neigh=(ts_vertex **)realloc(vtx->data->neigh, nn*sizeof(ts_vertex *));
- vtx->data->neigh[nn-1]=nvtx;
-
+ ts_uint nn=++vtx->neigh_no;
+ vtx->neigh=(ts_vertex **)realloc(vtx->neigh, nn*sizeof(ts_vertex *));
+ vtx->neigh[nn-1]=nvtx;
+/* This was a bug in creating DIPYRAMID (the neighbours were not in right
+ * order).
+ */
/* pa se sosedu dodamo vertex */
/*if it is already a neighbour don't add it to the list */
+/*
for(i=0; i<nvtx->data->neigh_no;i++){
if(nvtx->data->neigh[i]==vtx) return TS_FAIL;
}
nn=++nvtx->data->neigh_no;
nvtx->data->neigh=(ts_vertex **)realloc(nvtx->data->neigh, nn*sizeof(ts_vertex *));
nvtx->data->neigh[nn-1]=vtx;
-
+*/
return TS_SUCCESS;
}
@@ -71,32 +82,37 @@
/* find a neighbour */
/* remove it from the list while shifting remaining neighbours up */
ts_uint i,j=0;
- for(i=0;i<vtx->data->neigh_no;i++){
- if(vtx->data->neigh[i]!=nvtx){
- vtx->data->neigh[j]=vtx->data->neigh[i];
+ 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++;
}
}
+// fprintf(stderr,"remove_neighbour: vtx1_addr=%ld, vtx2_addr=%ld\n",(long)vtx,(long)nvtx);
/* resize memory. potentionally time consuming */
- vtx->data->neigh_no--;
- vtx->data->neigh=(ts_vertex **)realloc(vtx->data->neigh,vtx->data->neigh_no*sizeof(ts_vertex *));
- if(vtx->data->neigh == NULL && vtx->data->neigh_no!=0)
- fatal("Reallocation of memory failed during removal of vertex neighbour in vtx_remove_neighbour",100);
-
+ 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("(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 */
- for(i=0;i<nvtx->data->neigh_no;i++){
- if(nvtx->data->neigh[i]!=vtx){
- nvtx->data->neigh[j]=nvtx->data->neigh[i];
+ j=0;
+ for(i=0;i<nvtx->neigh_no;i++){
+ if(nvtx->neigh[i]!=vtx){
+ nvtx->neigh[j]=nvtx->neigh[i];
j++;
}
}
/* resize memory. potentionally time consuming. */
- nvtx->data->neigh_no--;
- nvtx->data->neigh=(ts_vertex **)realloc(nvtx->data->neigh,nvtx->data->neigh_no*sizeof(ts_vertex *));
- if(nvtx->data->neigh == NULL && nvtx->data->neigh_no!=0)
- fatal("Reallocation of memory failed during removal of vertex neighbour in vtx_remove_neighbour",100);
+// fprintf(stderr,"Neigbours=%d\n",nvtx->neigh_no);
+ nvtx->neigh_no--;
+ 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("(2) Reallocation of memory failed during removal of vertex neighbour in vtx_remove_neighbour",100);
return TS_SUCCESS;
}
@@ -107,19 +123,23 @@
ts_bond *bond;
bond=bond_add(blist,vtx1,vtx2);
if(bond==NULL) return TS_FAIL;
- vtx1->data->bond_no++;
- vtx2->data->bond_no++;
+ vtx1->bond_no++;
+ vtx2->bond_no++;
+ // vtx2->data->bond_no++;
- vtx1->data->bond=(ts_bond **)realloc(vtx1->data->bond, vtx1->data->bond_no*sizeof(ts_bond *));
- vtx2->data->bond=(ts_bond **)realloc(vtx2->data->bond, vtx2->data->bond_no*sizeof(ts_bond *));
- vtx1->data->bond[vtx1->data->bond_no-1]=bond;
- vtx2->data->bond[vtx2->data->bond_no-1]=bond;
+ vtx1->bond=(ts_bond **)realloc(vtx1->bond, vtx1->bond_no*sizeof(ts_bond *));
+ vtx2->bond=(ts_bond **)realloc(vtx2->bond, vtx2->bond_no*sizeof(ts_bond *));
+ // vtx2->data->bond=(ts_bond **)realloc(vtx2->data->bond, vtx2->data->bond_no*sizeof(ts_bond *));
+ vtx1->bond[vtx1->bond_no-1]=bond;
+ vtx2->bond[vtx2->bond_no-1]=bond;
+ // vtx2->ata->bond[vtx2->data->bond_no-1]=bond;
return TS_SUCCESS;
}
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;
@@ -136,19 +156,10 @@
}
-
-ts_bool vtx_data_free(ts_vertex_data *data){
- if(data->neigh!=NULL) free(data->neigh);
- if(data->tristar!=NULL) free(data->tristar);
- if(data->bond!=NULL) free(data->bond);
- if(data->cell!=NULL) free(data->cell);
- free(data);
- return TS_SUCCESS;
-}
-
-/*not usable. can be deleted */
ts_bool vtx_free(ts_vertex *vtx){
- vtx_data_free(vtx->data);
+ if(vtx->neigh!=NULL) free(vtx->neigh);
+ if(vtx->tristar!=NULL) free(vtx->tristar);
+ if(vtx->bond!=NULL) free(vtx->bond);
free(vtx);
return TS_SUCCESS;
}
@@ -156,9 +167,9 @@
ts_bool vtx_list_free(ts_vertex_list *vlist){
int i;
for(i=0;i<vlist->n;i++){
- vtx_data_free(vlist->vtx[i]->data);
+ if(vlist->vtx[i]!=NULL) vtx_free(vlist->vtx[i]);
}
- free(*(vlist->vtx));
+ //free(*(vlist->vtx));
free(vlist->vtx);
free(vlist);
return TS_SUCCESS;
@@ -166,15 +177,14 @@
inline ts_double vtx_distance_sq(ts_vertex *vtx1, ts_vertex *vtx2){
ts_double dist;
- ts_vertex_data *vd1=vtx1->data, *vd2=vtx2->data;
#ifdef TS_DOUBLE_DOUBLE
- dist=pow(vd1->x-vd2->x,2) + pow(vd1->y-vd2->y,2) + pow(vd1->z-vd2->z,2);
+ dist=pow(vtx1->x-vtx2->x,2) + pow(vtx1->y-vtx2->y,2) + pow(vtx1->z-vtx2->z,2);
#endif
#ifdef TS_DOUBLE_LONGDOUBLE
- dist=powl(vd1->x-vd2->x,2) + powl(vd1->y-vd2->y,2) + powl(vd1->z-vd2->z,2);
+ dist=powl(vtx1->x-vtx2->x,2) + powl(vtx1->y-vtx2->y,2) + powl(vtx1->z-vtx2->z,2);
#endif
#ifdef TS_DOUBLE_FLOAT
- dist=powf(vd1->x-vd2->x,2) + powf(vd1->y-vd2->y,2) + powf(vd1->z-vd2->z,2);
+ dist=powf(vtx1->x-vtx2->x,2) + powf(vtx1->y-vtx2->y,2) + powf(vtx1->z-vtx2->z,2);
#endif
return(dist);
}
@@ -185,32 +195,141 @@
ts_double xk=vesicle->bending_rigidity;
ts_uint i;
for(i=0;i<vesicle->vlist->n;i++){
- vesicle->vlist->vtx[i]->data->xk=xk;
+ vesicle->vlist->vtx[i]->xk=xk;
}
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->data->x-vtx1->data->x;
- ts_double dY2=vtx2->data->y-vtx1->data->y;
- ts_double dZ2=vtx2->data->z-vtx1->data->z;
- ts_double dX3=vtx3->data->x-vtx1->data->x;
- ts_double dY3=vtx3->data->y-vtx1->data->y;
- ts_double dZ3=vtx3->data->z-vtx1->data->z;
- ts_double direct=vtx1->data->x*(dY2*dZ3 -dZ2*dY3)+
- vtx1->data->y*(dZ2*dX3-dX2*dZ3)+
- vtx1->data->z*(dX2*dY3-dY2*dX3);
+ ts_double dX2=vtx2->x-vtx1->x;
+ ts_double dY2=vtx2->y-vtx1->y;
+ ts_double dZ2=vtx2->z-vtx1->z;
+ ts_double dX3=vtx3->x-vtx1->x;
+ ts_double dY3=vtx3->y-vtx1->y;
+ ts_double dZ3=vtx3->z-vtx1->z;
+ ts_double direct=vtx1->x*(dY2*dZ3 -dZ2*dY3)+
+ vtx1->y*(dZ2*dX3-dX2*dZ3)+
+ vtx1->z*(dX2*dY3-dY2*dX3);
return(direct);
}
inline ts_bool vertex_add_tristar(ts_vertex *vtx, ts_triangle *tristarmem){
- vtx->data->tristar_no++;
- vtx->data->tristar=(ts_triangle **)realloc(vtx->data->tristar,vtx->data->tristar_no*sizeof(ts_triangle *));
- if(vtx->data->tristar==NULL){
+ vtx->tristar_no++;
+ vtx->tristar=(ts_triangle **)realloc(vtx->tristar,vtx->tristar_no*sizeof(ts_triangle *));
+ if(vtx->tristar==NULL){
fatal("Reallocation of memory while adding tristar failed.",3);
}
- vtx->data->tristar[vtx->data->tristar_no-1]=tristarmem;
+ vtx->tristar[vtx->tristar_no-1]=tristarmem;
return TS_SUCCESS;
}
+
+/* Insert neighbour is a function that is required in bondflip. It inserts a
+ * neighbour exactly in the right place. */
+inline ts_bool vtx_insert_neighbour(ts_vertex *vtx, ts_vertex *nvtx, ts_vertex *vtxm){
+//nvtx is a vertex that is to be inserted after vtxm!
+ ts_uint i,j,midx;
+ vtx->neigh_no++;
+ if(vtxm==NULL || nvtx==NULL || vtx==NULL)
+ fatal("vertex_insert_neighbour: one of pointers has been zero.. Cannot proceed.",3);
+ //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
+ vtx->neigh=realloc(vtx->neigh,vtx->neigh_no*sizeof(ts_vertex *));
+ if(vtx->neigh == NULL){
+ fatal("Reallocation of memory failed during insertion of vertex neighbour in vertex_insert_neighbour",3);
+ }
+ midx=0;
+ for(i=0;i<vtx->neigh_no-1;i++) if(vtx->neigh[i]==vtxm) {midx=i; break;}
+ // fprintf(stderr,"midx=%d, vseh=%d\n",midx,vtx->neigh_no-2);
+ if(midx==vtx->neigh_no-2) {
+ vtx->neigh[vtx->neigh_no-1]=nvtx;
+ } else {
+ for(j=vtx->neigh_no-2;j>midx;j--) {
+ vtx->neigh[j+1]=vtx->neigh[j];
+// vtx->bond_length[j+1]=vtx->bond_length[j];
+// vtx->bond_length_dual[j+1]=vtx->bond_length_dual[j];
+ }
+ vtx->neigh[midx+1]=nvtx;
+ }
+ return TS_SUCCESS;
+}
+
+
+/* vtx remove tristar is required in bondflip. */
+/* TODO: Check whether it is important to keep the numbering of tristar
+ * elements in some order or not! */
+inline ts_bool vtx_remove_tristar(ts_vertex *vtx, ts_triangle *tristar){
+ ts_uint i,j=0;
+ for(i=0;i<vtx->tristar_no;i++){
+ if(vtx->tristar[i]!=tristar){
+ vtx->tristar[j]=vtx->tristar[i];
+ j++;
+ }
+ }
+ vtx->tristar_no--;
+ vtx->tristar=realloc(vtx->tristar,vtx->tristar_no*sizeof(ts_triangle *));
+ if(vtx->neigh == NULL){
+ fatal("Reallocation of memory failed during insertion of vertex neighbour in vertex_add_neighbour",3);
+ }
+ return TS_SUCCESS;
+}
+
+
+
+/* ****************************************************************** */
+/* ***** New vertex copy operations. Inherently they are slow. ***** */
+/* ****************************************************************** */
+
+ts_bool vtx_copy(ts_vertex *cvtx, ts_vertex *ovtx){
+ memcpy((void *)cvtx,(void *)ovtx,sizeof(ts_vertex));
+ cvtx->neigh=NULL;
+ cvtx->neigh_no=0;
+ cvtx->tristar_no=0;
+ cvtx->bond_no=0;
+ cvtx->tristar=NULL;
+ cvtx->bond=NULL;
+ cvtx->cell=NULL;
+ return TS_SUCCESS;
+}
+
+ts_bool vtx_duplicate(ts_vertex *cvtx, ts_vertex *ovtx){
+ memcpy((void *)cvtx,(void *)ovtx,sizeof(ts_vertex));
+ return TS_SUCCESS;
+}
+
+//TODO: needs to be done
+ts_vertex **vtx_neigh_copy(ts_vertex_list *vlist,ts_vertex *ovtx){
+ return NULL;
+}
+
+
+
+ts_vertex_list *vertex_list_copy(ts_vertex_list *ovlist){
+ ts_uint i;
+ ts_vertex_list *vlist=(ts_vertex_list *)malloc(sizeof(ts_vertex_list));
+ vlist=memcpy((void *)vlist, (void *)ovlist, sizeof(ts_vertex_list));
+ ts_vertex **vtx=(ts_vertex **)malloc(vlist->n*sizeof(ts_vertex *));
+ vlist->vtx=vtx;
+ if(vlist->vtx==NULL)
+ fatal("Fatal error reserving memory space for vertex list! Could number of requsted vertices be too large?", 100);
+ for(i=0;i<vlist->n;i++) {
+ vlist->vtx[i]=(ts_vertex *)calloc(1,sizeof(ts_vertex));
+ vlist->vtx[i]->idx=i;
+ vtx_copy(vlist->vtx[i],ovlist->vtx[i]);
+ }
+
+ return vlist;
+}
--
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