From 8f6a69d8fddcae6b54d25cf02dd56f0afce6a075 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Thu, 23 Feb 2012 16:35:11 +0000
Subject: [PATCH] vertex data removed and memory leaks fixed
---
src/cell.c | 6
src/main.c | 6
src/io.c | 58 +++---
src/vesicle.c | 6
src/initial_distribution.c | 90 +++++----
src/general.h | 12 -
src/vertexmove.c | 68 ++++---
src/shdiscover.c | 16
src/vertex.c | 139 ++++++---------
src/energy.c | 60 +++---
src/frame.c | 8
src/triangle.c | 12
src/vertex.h | 2
13 files changed, 228 insertions(+), 255 deletions(-)
diff --git a/src/cell.c b/src/cell.c
index 18586ee..47d7fab 100644
--- a/src/cell.c
+++ b/src/cell.c
@@ -49,9 +49,9 @@
ts_uint cellidx;
ts_uint ncx, ncy,ncz;
ts_cell_list *clist=vesicle->clist;
- ncx=(ts_uint)((vtx->data->x-vesicle->cm[0])*clist->dcell+clist->shift);
- ncy=(ts_uint)((vtx->data->y-vesicle->cm[1])*clist->dcell+clist->shift);
- ncz=(ts_uint)((vtx->data->z-vesicle->cm[2])*clist->dcell+clist->shift);
+ ncx=(ts_uint)((vtx->x-vesicle->cm[0])*clist->dcell+clist->shift);
+ ncy=(ts_uint)((vtx->y-vesicle->cm[1])*clist->dcell+clist->shift);
+ ncz=(ts_uint)((vtx->z-vesicle->cm[2])*clist->dcell+clist->shift);
if(ncx == clist->ncmax[0]-1 || ncx == 2){
fatal("Vesicle is positioned outside the cell covered area. Coordinate x is the problem.",1500);
diff --git a/src/energy.c b/src/energy.c
index 7cd96f5..4d93753 100644
--- a/src/energy.c
+++ b/src/energy.c
@@ -23,7 +23,7 @@
inline ts_bool energy_vertex(ts_vertex *vtx){
// ts_vertex *vtx=&vlist->vertex[n]-1; // Caution! 0 Indexed value!
// ts_triangle *tristar=vtx->tristar-1;
- ts_vertex_data *data=vtx->data;
+ //ts_vertex_data *data=vtx->data;
ts_uint jj;
ts_uint jjp,jjm;
ts_vertex *j,*jp, *jm;
@@ -31,21 +31,21 @@
ts_double s=0,xh=0,yh=0,zh=0,txn=0,tyn=0,tzn=0;
ts_double x1,x2,x3,ctp,ctm,tot,xlen;
ts_double h,ht;
- for(jj=1; jj<=data->neigh_no;jj++){
+ for(jj=1; jj<=vtx->neigh_no;jj++){
jjp=jj+1;
- if(jjp>data->neigh_no) jjp=1;
+ if(jjp>vtx->neigh_no) jjp=1;
jjm=jj-1;
- if(jjm<1) jjm=data->neigh_no;
- j=data->neigh[jj-1];
- jp=data->neigh[jjp-1];
- jm=data->neigh[jjm-1];
+ if(jjm<1) jjm=vtx->neigh_no;
+ j=vtx->neigh[jj-1];
+ jp=vtx->neigh[jjp-1];
+ jm=vtx->neigh[jjm-1];
// printf("tristar_no=%u, neigh_no=%u, jj=%u\n",data->tristar_no,data->neigh_no,jj);
- jt=data->tristar[jj-1];
+ jt=vtx->tristar[jj-1];
x1=vtx_distance_sq(vtx,jp); //shouldn't be zero!
x2=vtx_distance_sq(j,jp); // shouldn't be zero!
- x3=(j->data->x-jp->data->x)*(data->x-jp->data->x)+
- (j->data->y-jp->data->y)*(data->y-jp->data->y)+
- (j->data->z-jp->data->z)*(data->z-jp->data->z);
+ x3=(j->x-jp->x)*(vtx->x-jp->x)+
+ (j->y-jp->y)*(vtx->y-jp->y)+
+ (j->z-jp->z)*(vtx->z-jp->z);
#ifdef TS_DOUBLE_DOUBLE
ctp=x3/sqrt(x1*x2-x3*x3);
@@ -58,9 +58,9 @@
#endif
x1=vtx_distance_sq(vtx,jm);
x2=vtx_distance_sq(j,jm);
- x3=(j->data->x-jm->data->x)*(data->x-jm->data->x)+
- (j->data->y-jm->data->y)*(data->y-jm->data->y)+
- (j->data->z-jm->data->z)*(data->z-jm->data->z);
+ x3=(j->x-jm->x)*(vtx->x-jm->x)+
+ (j->y-jm->y)*(vtx->y-jm->y)+
+ (j->z-jm->z)*(vtx->z-jm->z);
#ifdef TS_DOUBLE_DOUBLE
ctm=x3/sqrt(x1*x2-x3*x3);
#endif
@@ -74,21 +74,21 @@
tot=0.5*tot;
xlen=vtx_distance_sq(j,vtx);
#ifdef TS_DOUBLE_DOUBLE
- data->bond[jj-1]->bond_length=sqrt(xlen);
+ vtx->bond[jj-1]->bond_length=sqrt(xlen);
#endif
#ifdef TS_DOUBLE_FLOAT
- data->bond[jj-1]->bond_length=sqrtf(xlen);
+ vtx->bond[jj-1]->bond_length=sqrtf(xlen);
#endif
#ifdef TS_DOUBLE_LONGDOUBLE
- data->bond[jj-1]->bond_length=sqrtl(xlen);
+ vtx->bond[jj-1]->bond_length=sqrtl(xlen);
#endif
- data->bond[jj-1]->bond_length_dual=tot*data->bond[jj-1]->bond_length;
+ vtx->bond[jj-1]->bond_length_dual=tot*vtx->bond[jj-1]->bond_length;
s+=tot*xlen;
- xh+=tot*(j->data->x - data->x);
- yh+=tot*(j->data->y - data->y);
- zh+=tot*(j->data->z - data->z);
+ xh+=tot*(j->x - vtx->x);
+ yh+=tot*(j->y - vtx->y);
+ zh+=tot*(j->z - vtx->z);
txn+=jt->xnorm;
tyn+=jt->ynorm;
tzn+=jt->znorm;
@@ -99,29 +99,29 @@
s=s/4.0;
#ifdef TS_DOUBLE_DOUBLE
if(ht>=0.0) {
- data->curvature=sqrt(h);
+ vtx->curvature=sqrt(h);
} else {
- data->curvature=-sqrt(h);
+ vtx->curvature=-sqrt(h);
}
#endif
#ifdef TS_DOUBLE_FLOAT
if(ht>=0.0) {
- data->curvature=sqrtf(h);
+ vtx->curvature=sqrtf(h);
} else {
- data->curvature=-sqrtf(h);
+ vtx->curvature=-sqrtf(h);
}
#endif
#ifdef TS_DOUBLE_LONGDOUBLE
if(ht>=0.0) {
- data->curvature=sqrtl(h);
+ vtx->curvature=sqrtl(h);
} else {
- data->curvature=-sqrtl(h);
+ vtx->curvature=-sqrtl(h);
}
#endif
-// What is vtx->data->c?????????????? Here it is 0!
+// What is vtx->c?????????????? Here it is 0!
// c is forced curvature energy for each vertex. Should be set to zero for
-// norman circumstances.
- data->energy=0.5*s*(data->curvature/s-data->c)*(data->curvature/s-data->c);
+// normal circumstances.
+ vtx->energy=0.5*s*(vtx->curvature/s-vtx->c)*(vtx->curvature/s-vtx->c);
return TS_SUCCESS;
}
diff --git a/src/frame.c b/src/frame.c
index a4a9d32..63a4f7b 100644
--- a/src/frame.c
+++ b/src/frame.c
@@ -9,9 +9,9 @@
vesicle->cm[1]=0;
vesicle->cm[2]=0;
for(i=0;i<n;i++){
- vesicle->cm[0]+=vtx[i]->data->x;
- vesicle->cm[1]+=vtx[i]->data->y;
- vesicle->cm[2]+=vtx[i]->data->z;
+ vesicle->cm[0]+=vtx[i]->x;
+ vesicle->cm[1]+=vtx[i]->y;
+ vesicle->cm[2]+=vtx[i]->z;
}
vesicle->cm[0]/=(ts_float)n;
vesicle->cm[1]/=(ts_float)n;
@@ -30,7 +30,7 @@
cell_list_cell_occupation_clear(vesicle->clist);
for(i=0;i<n;i++){
cellidx=vertex_self_avoidance(vesicle, vesicle->vlist->vtx[i]);
- vesicle->vlist->vtx[i]->data->cell=vesicle->clist->cell[cellidx];
+ vesicle->vlist->vtx[i]->cell=vesicle->clist->cell[cellidx];
cell_add_vertex(vesicle->clist->cell[cellidx],vesicle->vlist->vtx[i]);
diff --git a/src/general.h b/src/general.h
index 6d2ab06..aff7680 100644
--- a/src/general.h
+++ b/src/general.h
@@ -112,10 +112,10 @@
/** @brief Data structure of all data connected to a vertex
*
- * ts_vertex_data holds the data for one single point (bead, vertex). To understand how to use it
+ * ts_vertex holds the data for one single point (bead, vertex). To understand how to use it
* here is a detailed description of the fields in the data structure. */
-struct ts_vertex_data {
- ts_uint idx; /**< Represents index of the vertex point. Should become obsolete, since it is also present in ts_vertex structure. */
+struct ts_vertex {
+ ts_uint idx;
ts_double x; /**< The x coordinate of vertex. */
ts_double y; /**< The y coordinate of vertex. */
ts_double z; /**< The z coordinate of vertex. */
@@ -134,12 +134,6 @@
ts_double xk;
ts_double c;
ts_uint id;
-};
-typedef struct ts_vertex_data ts_vertex_data;
-
-struct ts_vertex {
- ts_uint idx;
- ts_vertex_data *data;
};
typedef struct ts_vertex ts_vertex;
diff --git a/src/initial_distribution.c b/src/initial_distribution.c
index 0f59aec..a7a8202 100644
--- a/src/initial_distribution.c
+++ b/src/initial_distribution.c
@@ -64,40 +64,40 @@
ts_double dx,dy; // end loop prereq
/* topmost vertex */
- vtx[1]->data->x=0.0;
- vtx[1]->data->y=0.0;
- vtx[1]->data->z=z0*(ts_double)nshell;
+ vtx[1]->x=0.0;
+ vtx[1]->y=0.0;
+ vtx[1]->z=z0*(ts_double)nshell;
/* starting from to in circular order on pentagrams */
for(i=1;i<=nshell;i++){
n0=2+5*i*(i-1)/2; //-1 would be for the reason that C index starts from 0
- vtx[n0]->data->x=0.0;
- vtx[n0]->data->y=(ts_double)i*xl0;
- vtx[n0+i]->data->x=vtx[n0]->data->y*s1;
- vtx[n0+i]->data->y=vtx[n0]->data->y*c1;
- vtx[n0+2*i]->data->x=vtx[n0]->data->y*s2;
- vtx[n0+2*i]->data->y=vtx[n0]->data->y*c2;
- vtx[n0+3*i]->data->x=-vtx[n0+2*i]->data->x;
- vtx[n0+3*i]->data->y=vtx[n0+2*i]->data->y;
- vtx[n0+4*i]->data->x=-vtx[n0+i]->data->x;
- vtx[n0+4*i]->data->y=vtx[n0+i]->data->y;
+ vtx[n0]->x=0.0;
+ vtx[n0]->y=(ts_double)i*xl0;
+ vtx[n0+i]->x=vtx[n0]->y*s1;
+ vtx[n0+i]->y=vtx[n0]->y*c1;
+ vtx[n0+2*i]->x=vtx[n0]->y*s2;
+ vtx[n0+2*i]->y=vtx[n0]->y*c2;
+ vtx[n0+3*i]->x=-vtx[n0+2*i]->x;
+ vtx[n0+3*i]->y=vtx[n0+2*i]->y;
+ vtx[n0+4*i]->x=-vtx[n0+i]->x;
+ vtx[n0+4*i]->y=vtx[n0+i]->y;
}
/* vertexes on the faces of the dipyramid */
for(i=1;i<=nshell;i++){
n0=2+5*i*(i-1)/2; // -1 would be because of C!
for(j=1;j<=i-1;j++){
- dx=(vtx[n0]->data->x-vtx[n0+4*i]->data->x)/(ts_double)i;
- dy=(vtx[n0]->data->y-vtx[n0+4*i]->data->y)/(ts_double)i;
- vtx[n0+4*i+j]->data->x=(ts_double)j*dx+vtx[n0+4*i]->data->x;
- vtx[n0+4*i+j]->data->y=(ts_double)j*dy+vtx[n0+4*i]->data->y;
+ dx=(vtx[n0]->x-vtx[n0+4*i]->x)/(ts_double)i;
+ dy=(vtx[n0]->y-vtx[n0+4*i]->y)/(ts_double)i;
+ vtx[n0+4*i+j]->x=(ts_double)j*dx+vtx[n0+4*i]->x;
+ vtx[n0+4*i+j]->y=(ts_double)j*dy+vtx[n0+4*i]->y;
}
for(k=0;k<=3;k++){ // I would be worried about zero starting of for
- dx=(vtx[n0+(k+1)*i]->data->x - vtx[n0+k*i]->data->x)/(ts_double) i;
- dy=(vtx[n0+(k+1)*i]->data->y - vtx[n0+k*i]->data->y)/(ts_double) i;
+ dx=(vtx[n0+(k+1)*i]->x - vtx[n0+k*i]->x)/(ts_double) i;
+ dy=(vtx[n0+(k+1)*i]->y - vtx[n0+k*i]->y)/(ts_double) i;
for(j=1; j<=i-1;j++){
- vtx[n0+k*i+j]->data->x= (ts_double)j*dx+vtx[n0+k*i]->data->x;
- vtx[n0+k*i+j]->data->y= (ts_double)j*dy+vtx[n0+k*i]->data->y;
+ vtx[n0+k*i+j]->x= (ts_double)j*dx+vtx[n0+k*i]->x;
+ vtx[n0+k*i+j]->y= (ts_double)j*dy+vtx[n0+k*i]->y;
}
}
}
@@ -105,15 +105,15 @@
for(i=1;i<=nshell;i++){
n0= 2+ 5*i*(i-1)/2;
for(j=0;j<=5*i-1;j++){
- vtx[n0+j]->data->z= z0*(ts_double)(nshell-i); // I would be worried about zero starting of for
+ vtx[n0+j]->z= z0*(ts_double)(nshell-i); // I would be worried about zero starting of for
}
}
/* for botom part of dipyramide we calculate the positions of vertices */
for(i=2+5*nshell*(nshell+1)/2;i<=vlist->n;i++){
- vtx[i]->data->x=vtx[vlist->n - i +1]->data->x;
- vtx[i]->data->y=vtx[vlist->n - i +1]->data->y;
- vtx[i]->data->z=-vtx[vlist->n - i +1]->data->z;
+ vtx[i]->x=vtx[vlist->n - i +1]->x;
+ vtx[i]->y=vtx[vlist->n - i +1]->y;
+ vtx[i]->z=-vtx[vlist->n - i +1]->z;
}
for(i=1;i<=vlist->n;i++){
@@ -166,15 +166,16 @@
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]->data->neigh[0]->idx+1]); //always add 1st
+ 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]->data->neigh_no;l++){
- for(j=2;j<=vtx[i]->data->neigh_no;j++){
- dist2=vtx_distance_sq(vtx[i]->data->neigh[j-1],vtx[i]->data->neigh[jj-1]);
- direct=vtx_direct(vtx[i],vtx[i]->data->neigh[j-1],vtx[i]->data->neigh[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( (fabs(dist2-A0*A0)<=eps) && (direct>0.0) && (j!=jjj) ){
- vtx_add_cneighbour(blist,tvtx[k],tvtx[vtx[i]->data->neigh[j-1]->idx+1]);
+ vtx_add_cneighbour(blist,tvtx[k],tvtx[vtx[i]->neigh[j-1]->idx+1]);
jjj=jj;
jj=j;
break;
@@ -206,8 +207,8 @@
ts_uint i,j,k;
for(i=1;i<=vlist->n;i++){
for(j=i+1;j<=vlist->n;j++){
- for(k=0;k<vtx[i]->data->neigh_no;k++){ // has changed 0 to < instead of 1 and <=
- if(vtx[i]->data->neigh[k]==vtx[j]){ //if addresses matches it is the same
+ for(k=0;k<vtx[i]->neigh_no;k++){ // has changed 0 to < instead of 1 and <=
+ if(vtx[i]->neigh[k]==vtx[j]){ //if addresses matches it is the same
bond_add(blist,vtx[i],vtx[j]);
break;
}
@@ -232,14 +233,15 @@
ts_double eps=0.001; // can we use EPS from math.h?
k=0;
for(i=1;i<=vesicle->vlist->n;i++){
- for(j=1;j<=vtx[i]->data->neigh_no;j++){
- for(jj=1;jj<=vtx[i]->data->neigh_no;jj++){
+ for(j=1;j<=vtx[i]->neigh_no;j++){
+ for(jj=1;jj<=vtx[i]->neigh_no;jj++){
// ts_fprintf(stderr,"%u: (%u,%u) neigh_no=%u ",i,j,jj,vtx[i].neigh_no);
// ts_fprintf(stderr,"%e, %e",vtx[i].neigh[j-1]->x,vtx[i].neigh[jj-1]->x);
- dist=vtx_distance_sq(vtx[i]->data->neigh[j-1],vtx[i]->data->neigh[jj-1]);
- direct=vtx_direct(vtx[i],vtx[i]->data->neigh[j-1],vtx[i]->data->neigh[jj-1]);
- if(fabs(dist-A0*A0)<=eps && direct < 0.0 && vtx[i]->data->neigh[j-1]->idx+1 > i && vtx[i]->data->neigh[jj-1]->idx+1 >i){
- triangle_add(tlist,vtx[i],vtx[i]->data->neigh[j-1],vtx[i]->data->neigh[jj-1]);
+ dist=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: same as above
+ if(fabs(dist-A0*A0)<=eps && direct < 0.0 && vtx[i]->neigh[j-1]->idx+1 > i && vtx[i]->neigh[jj-1]->idx+1 >i){
+ triangle_add(tlist,vtx[i],vtx[i]->neigh[j-1],vtx[i]->neigh[jj-1]);
}
}
}
@@ -254,7 +256,7 @@
k++;
}
if(k!=3){
- fatal("Some triangles has less than 3 vertices..",4);
+ fatal("Some triangles have less than 3 vertices..",4);
}
}
if(tlist->n!=2*(vesicle->vlist->n -2)){
@@ -334,11 +336,11 @@
ts_triangle **tria=tlist->tria -1;
for(i=1;i<=vesicle->vlist->n;i++){
- for(j=1;j<=vtx[i]->data->neigh_no;j++){
- k1=vtx[i]->data->neigh[j-1];
+ for(j=1;j<=vtx[i]->neigh_no;j++){
+ k1=vtx[i]->neigh[j-1];
jp=j+1;
- if(j == vtx[i]->data->neigh_no) jp=1;
- k2=vtx[i]->data->neigh[jp-1];
+ if(j == vtx[i]->neigh_no) jp=1;
+ k2=vtx[i]->neigh[jp-1];
for(k=1;k<=tlist->n;k++){ // VERY NON-OPTIMAL!!! too many loops (vlist.n * vtx.neigh * tlist.n )!
k3=tria[k]->vertex[0];
k4=tria[k]->vertex[1];
diff --git a/src/io.c b/src/io.c
index 8688067..7421f0d 100644
--- a/src/io.c
+++ b/src/io.c
@@ -15,7 +15,7 @@
printf("Number of vertices: %u\n",vlist->n);
for(i=0;i<vlist->n;i++){
printf("%u: %f %f %f\n",
-vlist->vtx[i]->idx,vlist->vtx[i]->data->x, vlist->vtx[i]->data->y, vlist->vtx[i]->data->z);
+vlist->vtx[i]->idx,vlist->vtx[i]->x, vlist->vtx[i]->y, vlist->vtx[i]->z);
}
return TS_SUCCESS;
}
@@ -25,10 +25,10 @@
ts_vertex **vtx=vlist->vtx;
printf("Vertex id(neigh no): (neighvertex coord) (neighvertex coord) ...\n");
for(i=0;i<vlist->n;i++){
- printf("%u(%u): ",vtx[i]->idx,vtx[i]->data->neigh_no);
- for(j=0;j<vtx[i]->data->neigh_no;j++){
- printf("(%f,%f,%f)",vtx[i]->data->neigh[j]->data->x,
-vtx[i]->data->neigh[j]->data->y,vtx[i]->data->neigh[j]->data->z);
+ printf("%u(%u): ",vtx[i]->idx,vtx[i]->neigh_no);
+ for(j=0;j<vtx[i]->neigh_no;j++){
+ printf("(%f,%f,%f)",vtx[i]->neigh[j]->x,
+vtx[i]->neigh[j]->y,vtx[i]->neigh[j]->z);
}
printf("\n");
}
@@ -47,7 +47,7 @@
return TS_FAIL;
}
for(i=0;i<vlist->n;i++)
- fprintf(fh," %E\t%E\t%E\n",vtx[i]->data->x,vtx[i]->data->y, vtx[i]->data->z);
+ fprintf(fh," %E\t%E\t%E\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
fclose(fh);
return TS_SUCCESS;
@@ -57,11 +57,11 @@
ts_bool fprint_vertex_list(FILE *fh,ts_vertex_list *vlist){
ts_uint i,j;
for(i=0;i<vlist->n;i++){
- fprintf(fh," %.17E\t%.17E\t%.17E\t%u\n",vlist->vtx[i]->data->x,
- vlist->vtx[i]->data->y, vlist->vtx[i]->data->z,
- vlist->vtx[i]->data->neigh_no);
- for(j=0;j<vlist->vtx[i]->data->neigh_no;j++){
- fprintf(fh,"\t%u",(ts_uint)(vlist->vtx[i]->data->neigh[j]->idx));
+ fprintf(fh," %.17E\t%.17E\t%.17E\t%u\n",vlist->vtx[i]->x,
+ vlist->vtx[i]->y, vlist->vtx[i]->z,
+ vlist->vtx[i]->neigh_no);
+ for(j=0;j<vlist->vtx[i]->neigh_no;j++){
+ fprintf(fh,"\t%u",(ts_uint)(vlist->vtx[i]->neigh[j]->idx));
//-vlist->vtx+1));
}
fprintf(fh,"\n");
@@ -72,9 +72,9 @@
ts_bool fprint_tristar(FILE *fh, ts_vesicle *vesicle){
ts_uint i,j;
for(i=0;i<vesicle->vlist->n;i++){
- fprintf(fh,"\t%u",vesicle->vlist->vtx[i]->data->tristar_no);
- for(j=0;j<vesicle->vlist->vtx[i]->data->tristar_no;j++){
- fprintf(fh,"\t%u",(ts_uint)(vesicle->vlist->vtx[i]->data->tristar[j]->idx));//-vesicle->tlist->tria+1));
+ fprintf(fh,"\t%u",vesicle->vlist->vtx[i]->tristar_no);
+ for(j=0;j<vesicle->vlist->vtx[i]->tristar_no;j++){
+ fprintf(fh,"\t%u",(ts_uint)(vesicle->vlist->vtx[i]->tristar[j]->idx));//-vesicle->tlist->tria+1));
}
fprintf(fh,"\n");
}
@@ -105,14 +105,14 @@
ts_uint i,j;
for(i=0;i<vlist->n;i++){
fprintf(fh," %.17E\t%.17E\t%.17E\t%.17E\t%.17E\t%u\n",
- vlist->vtx[i]->data->xk,vlist->vtx[i]->data->c,vlist->vtx[i]->data->energy,
- vlist->vtx[i]->data->energy_h, vlist->vtx[i]->data->curvature, 0);
- for(j=0;j<vlist->vtx[i]->data->neigh_no;j++){
- fprintf(fh," %.17E", vlist->vtx[i]->data->bond[j]->bond_length_dual);
+ vlist->vtx[i]->xk,vlist->vtx[i]->c,vlist->vtx[i]->energy,
+ vlist->vtx[i]->energy_h, vlist->vtx[i]->curvature, 0);
+ for(j=0;j<vlist->vtx[i]->neigh_no;j++){
+ fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length_dual);
}
fprintf(fh,"\n");
- for(j=0;j<vlist->vtx[i]->data->neigh_no;j++){
- fprintf(fh," %.17E", vlist->vtx[i]->data->bond[j]->bond_length);
+ for(j=0;j<vlist->vtx[i]->neigh_no;j++){
+ fprintf(fh," %.17E", vlist->vtx[i]->bond[j]->bond_length);
}
fprintf(fh,"\n");
}
@@ -226,7 +226,7 @@
fprintf(fh,"</DataArray>\n</PointData>\n<CellData>\n</CellData>\n<Points>\n<DataArray type=\"Float64\" Name=\"Koordinate tock\" NumberOfComponents=\"3\" format=\"ascii\">\n");
for(i=0;i<vlist->n;i++){
- fprintf(fh,"%e %e %e\n",vtx[i]->data->x,vtx[i]->data->y, vtx[i]->data->z);
+ fprintf(fh,"%e %e %e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
}
fprintf(fh,"</DataArray>\n</Points>\n<Cells>\n<DataArray type=\"Int64\" Name=\"connectivity\" format=\"ascii\">");
@@ -270,7 +270,7 @@
fprintf(fh,"DATASET UNSTRUCTURED_GRID\n");
fprintf(fh,"POINTS %u double\n", vlist->n);
for(i=0;i<vlist->n;i++){
- fprintf(fh,"%e %e %e\n",vtx[i]->data->x,vtx[i]->data->y, vtx[i]->data->z);
+ fprintf(fh,"%e %e %e\n",vtx[i]->x,vtx[i]->y, vtx[i]->z);
}
fprintf(fh,"CELLS %u %u\n",blist->n,3*blist->n);
@@ -286,7 +286,7 @@
fprintf(fh,"LOOKUP_TABLE default\n");
for(i=0;i<vlist->n;i++)
- fprintf(fh,"%u\n",vtx[i]->data->idx);
+ fprintf(fh,"%u\n",vtx[i]->idx);
fclose(fh);
return TS_SUCCESS;
@@ -351,11 +351,11 @@
vesicle->vlist=init_vertex_list(nvtx);
vlist=vesicle->vlist;
for(i=0;i<nvtx;i++){
- // fscanf(fh,"%F %F %F",&vlist->vtx[i]->data->x,&vlist->vtx[i]->data->y,&vlist->vtx[i]->data->z);
+ // fscanf(fh,"%F %F %F",&vlist->vtx[i]->x,&vlist->vtx[i]->y,&vlist->vtx[i]->z);
retval=fscanf(fh,"%F %F %F",&x,&y,&z);
- vlist->vtx[i]->data->x=x;
- vlist->vtx[i]->data->y=y;
- vlist->vtx[i]->data->z=z;
+ vlist->vtx[i]->x=x;
+ vlist->vtx[i]->y=y;
+ vlist->vtx[i]->z=z;
}
for(i=0;i<nedges;i++){
retval=fscanf(fh,"%u %u",&vtxi1,&vtxi2);
@@ -368,8 +368,8 @@
/*
for(i=0;i<ntria;i++){
retval=fscanf(fh,"%u %u %u", &bi1, &bi2, &bi3);
- vtxi1=vesicle->blist->data->vertex1->idx;
- vtxi2=vesicle->blist->data->vertex1->idx;
+ vtxi1=vesicle->blist->vertex1->idx;
+ vtxi2=vesicle->blist->vertex1->idx;
}
*/
diff --git a/src/main.c b/src/main.c
index 94e64ec..b846658 100644
--- a/src/main.c
+++ b/src/main.c
@@ -36,8 +36,8 @@
retval=vtx_remove_neighbour(vlist->vtx[0],vlist->vtx[1]);
vtx_add_neighbour(vlist->vtx[0],vlist->vtx[1]);
-vlist->vtx[0]->data->x=1.0;
-vlist->vtx[0]->data->x=1.1;
+vlist->vtx[0]->x=1.0;
+vlist->vtx[0]->x=1.1;
vlist1=vertex_list_copy(vlist);
bond_add(blist, vlist->vtx[1],vlist->vtx[0]);
triangle_add(tlist,vlist->vtx[1],vlist->vtx[2],vlist->vtx[3]);
@@ -47,7 +47,7 @@
printf("Cell idx=1 has vertices=%u\n",clist->cell[0]->nvertex);
cell_add_vertex(clist->cell[0], vlist->vtx[0]);
printf("Cell idx=1 has vertices=%u\n",clist->cell[0]->nvertex);
-printf("Cell idx=1 has vertex[0] has x coordinate=%e\n",clist->cell[0]->vertex[0]->data->x);
+printf("Cell idx=1 has vertex[0] has x coordinate=%e\n",clist->cell[0]->vertex[0]->x);
cell_list_cell_occupation_clear(clist);
printf("Cell idx=1 has vertices=%u\n",clist->cell[0]->nvertex);
cell_add_vertex(clist->cell[0], vlist->vtx[0]);
diff --git a/src/shdiscover.c b/src/shdiscover.c
index f16239f..008d522 100644
--- a/src/shdiscover.c
+++ b/src/shdiscover.c
@@ -42,17 +42,17 @@
/*we calculate new position of each vertex of vesicle */
for(i=0;i<n;i++){
- fi=atan2(vlist->vtx[i]->data->y, vlist->vtx[i]->data->x);
+ fi=atan2(vlist->vtx[i]->y, vlist->vtx[i]->x);
/* theta=atan2(
sqrt(vlist->vtx[i]->data->x*vlist->vtx[i]->data->x +
vlist->vtx[i]->data->y*vlist->vtx[i]->data->y),
vlist->vtx[i]->data->z
); */
theta=acos(
- vlist->vtx[i]->data->z /
- sqrt(vlist->vtx[i]->data->x*vlist->vtx[i]->data->x +
- vlist->vtx[i]->data->y*vlist->vtx[i]->data->y+
- vlist->vtx[i]->data->z*vlist->vtx[i]->data->z)
+ vlist->vtx[i]->z /
+ sqrt(vlist->vtx[i]->x*vlist->vtx[i]->x +
+ vlist->vtx[i]->y*vlist->vtx[i]->y+
+ vlist->vtx[i]->z*vlist->vtx[i]->z)
);
@@ -67,9 +67,9 @@
/*ts_fprintf(stdout,"l=%d, m=%d, u=%s\n",l,m,argv[j]);*/
}
- vlist->vtx[i]->data->z=fabs(r)*cos(theta);
- vlist->vtx[i]->data->x=fabs(r)*sin(theta)*cos(fi);
- vlist->vtx[i]->data->y=fabs(r)*sin(theta)*sin(fi);
+ vlist->vtx[i]->z=fabs(r)*cos(theta);
+ vlist->vtx[i]->x=fabs(r)*sin(theta)*cos(fi);
+ vlist->vtx[i]->y=fabs(r)*sin(theta)*sin(fi);
}
write_vertex_xml_file(vesicle,0);
diff --git a/src/triangle.c b/src/triangle.c
index f842130..bcd074b 100644
--- a/src/triangle.c
+++ b/src/triangle.c
@@ -194,12 +194,12 @@
*/
ts_bool triangle_normal_vector(ts_triangle *tria){
ts_double x21,x31,y21,y31,z21,z31,xden;
- x21=tria->vertex[1]->data->x - tria->vertex[0]->data->x;
- x31=tria->vertex[2]->data->x - tria->vertex[0]->data->x;
- y21=tria->vertex[1]->data->y - tria->vertex[0]->data->y;
- y31=tria->vertex[2]->data->y - tria->vertex[0]->data->y;
- z21=tria->vertex[1]->data->z - tria->vertex[0]->data->z;
- z31=tria->vertex[2]->data->z - tria->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->xnorm=y21*z31 - z21*y31;
tria->ynorm=z21*x31 - x21*z31;
diff --git a/src/vertex.c b/src/vertex.c
index b5f8519..4a6aeb9 100644
--- a/src/vertex.c
+++ b/src/vertex.c
@@ -8,7 +8,6 @@
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 +17,16 @@
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;
}
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;
@@ -46,12 +34,12 @@
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).
*/
@@ -74,31 +62,31 @@
/* 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++){
+ if(vtx->neigh[i]!=nvtx){
+ vtx->neigh[j]=vtx->neigh[i];
j++;
}
}
/* 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)
+ 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);
/* 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];
+ 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)
+ nvtx->neigh_no--;
+ nvtx->neigh=(ts_vertex **)realloc(nvtx->neigh,nvtx->neigh_no*sizeof(ts_vertex *));
+ if(nvtx->neigh == NULL && nvtx->neigh_no!=0)
fatal("Reallocation of memory failed during removal of vertex neighbour in vtx_remove_neighbour",100);
return TS_SUCCESS;
@@ -110,13 +98,13 @@
ts_bond *bond;
bond=bond_add(blist,vtx1,vtx2);
if(bond==NULL) return TS_FAIL;
- vtx1->data->bond_no++;
+ vtx1->bond_no++;
// vtx2->data->bond_no++;
- vtx1->data->bond=(ts_bond **)realloc(vtx1->data->bond, vtx1->data->bond_no*sizeof(ts_bond *));
+ vtx1->bond=(ts_bond **)realloc(vtx1->bond, vtx1->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[vtx1->bond_no-1]=bond;
+ // vtx2->ata->bond[vtx2->data->bond_no-1]=bond;
return TS_SUCCESS;
}
@@ -139,20 +127,11 @@
}
-
-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);
-//Cells are freed separately.
- // 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;
}
@@ -160,9 +139,9 @@
ts_bool vtx_list_free(ts_vertex_list *vlist){
int i;
for(i=0;i<vlist->n;i++){
- if(vlist->vtx[i]->data!=NULL) 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;
@@ -170,15 +149,14 @@
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);
}
@@ -189,32 +167,32 @@
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;
}
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;
}
@@ -225,22 +203,18 @@
ts_bool vtx_copy(ts_vertex *cvtx, ts_vertex *ovtx){
memcpy((void *)cvtx,(void *)ovtx,sizeof(ts_vertex));
- cvtx->data=(ts_vertex_data *)malloc(sizeof(ts_vertex_data));
- memcpy((void *)cvtx->data,(void *)ovtx->data,sizeof(ts_vertex_data));
- cvtx->data->neigh=NULL;
- cvtx->data->neigh_no=0;
- cvtx->data->tristar_no=0;
- cvtx->data->bond_no=0;
- cvtx->data->tristar=NULL;
- cvtx->data->bond=NULL;
- cvtx->data->cell=NULL;
+ 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));
- cvtx->data=(ts_vertex_data *)malloc(sizeof(ts_vertex_data));
- memcpy((void *)cvtx->data,(void *)ovtx->data,sizeof(ts_vertex_data));
return TS_SUCCESS;
}
@@ -256,12 +230,11 @@
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 *));
- ts_vertex *tlist=(ts_vertex *)calloc(vlist->n,sizeof(ts_vertex));
vlist->vtx=vtx;
- if(vlist->vtx==NULL || tlist==NULL)
+ 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]=&tlist[i];
+ vlist->vtx[i]=(ts_vertex *)calloc(1,sizeof(ts_vertex));
vlist->vtx[i]->idx=i;
vtx_copy(vlist->vtx[i],ovlist->vtx[i]);
}
diff --git a/src/vertex.h b/src/vertex.h
index 0d0c27c..98efff5 100644
--- a/src/vertex.h
+++ b/src/vertex.h
@@ -14,12 +14,10 @@
* @returns ts_bool value 1 on success, 0 otherwise
*/
ts_vertex_list *init_vertex_list(ts_uint N);
-ts_vertex_data *init_vertex_data(void);
ts_bool vtx_add_neighbour(ts_vertex *vtx, ts_vertex *nvtx);
ts_bool vtx_add_cneighbour(ts_bond_list *blist,ts_vertex *vtx1,ts_vertex *vtx2);
ts_bool vtx_add_bond(ts_bond_list *blist,ts_vertex *vtx1,ts_vertex *vtx2);
ts_bool vtx_remove_neighbour(ts_vertex *vtx, ts_vertex *nvtx);
-ts_bool vtx_data_free(ts_vertex_data *data);
ts_bool vtx_free(ts_vertex *vtx);
ts_bool vtx_list_free(ts_vertex_list *vlist);
inline ts_double vtx_distance_sq(ts_vertex *vtx1, ts_vertex *vtx2);
diff --git a/src/vertexmove.c b/src/vertexmove.c
index 243463f..c8ce697 100644
--- a/src/vertexmove.c
+++ b/src/vertexmove.c
@@ -16,8 +16,8 @@
*rn){
ts_uint i;
ts_double dist;
- ts_vertex *tvtx=(ts_vertex *)malloc(sizeof(ts_vertex));
- tvtx->data=init_vertex_data();
+ ts_vertex *tvtx=(ts_vertex *)calloc(1,sizeof(ts_vertex));
+// tvtx->data=init_vertex_data();
ts_bool retval;
ts_uint cellidx;
ts_double xold,yold,zold;
@@ -25,46 +25,50 @@
ts_vertex *ovtx;
//randomly we move the temporary vertex
- tvtx->data->x=vtx->data->x+vesicle->stepsize*(2.0*rn[0]-1.0);
- tvtx->data->y=vtx->data->y+vesicle->stepsize*(2.0*rn[1]-1.0);
- tvtx->data->z=vtx->data->z+vesicle->stepsize*(2.0*rn[2]-1.0);
+ tvtx->x=vtx->x+vesicle->stepsize*(2.0*rn[0]-1.0);
+ tvtx->y=vtx->y+vesicle->stepsize*(2.0*rn[1]-1.0);
+ tvtx->z=vtx->z+vesicle->stepsize*(2.0*rn[2]-1.0);
//check we if some length to neighbours are too much
- for(i=0;i<vtx->data->neigh_no;i++){
- dist=vtx_distance_sq(tvtx,vtx->data->neigh[i]);
- if(dist<1.0 || dist>vesicle->dmax) return TS_FAIL;
+ for(i=0;i<vtx->neigh_no;i++){
+ dist=vtx_distance_sq(tvtx,vtx->neigh[i]);
+ if(dist<1.0 || dist>vesicle->dmax) {
+ vtx_free(tvtx);
+ return TS_FAIL;
+ }
}
-fprintf(stderr,"Was here!\n");
+//fprintf(stderr,"Was here!\n");
//self avoidance check with distant vertices
cellidx=vertex_self_avoidance(vesicle, tvtx);
//check occupation number
retval=cell_occupation_number_and_internal_proximity(vesicle->clist,cellidx,vtx,tvtx);
if(retval==TS_FAIL){
+ vtx_free(tvtx);
return TS_FAIL;
}
//if all the tests are successful, then we update the vertex position
- xold=vtx->data->x;
- yold=vtx->data->y;
- zold=vtx->data->z;
+ xold=vtx->x;
+ yold=vtx->y;
+ zold=vtx->z;
ovtx=malloc(sizeof(ts_vertex));
vtx_copy(ovtx,vtx);
- vtx->data->x=tvtx->data->x;
- vtx->data->y=tvtx->data->y;
- vtx->data->z=tvtx->data->z;
+ vtx->x=tvtx->x;
+ vtx->y=tvtx->y;
+ vtx->z=tvtx->z;
delta_energy=0;
//update the normals of triangles that share bead i.
- for(i=0;i<vtx->data->tristar_no;i++) triangle_normal_vector(vtx->data->tristar[i]);
+ for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);
//energy and curvature
energy_vertex(vtx);
- delta_energy=vtx->data->xk*(vtx->data->energy - ovtx->data->energy);
+ delta_energy=vtx->xk*(vtx->energy - ovtx->energy);
//the same is done for neighbouring vertices
- for(i=0;i<vtx->data->neigh_no;i++){
- oenergy=vtx->data->neigh[i]->data->energy;
- energy_vertex(vtx->data->neigh[i]);
- delta_energy+=vtx->data->neigh[i]->data->xk*(vtx->data->neigh[i]->data->energy-oenergy);
+ for(i=0;i<vtx->neigh_no;i++){
+ oenergy=vtx->neigh[i]->energy;
+ energy_vertex(vtx->neigh[i]);
+ delta_energy+=vtx->neigh[i]->xk*(vtx->neigh[i]->energy-oenergy);
}
- fprintf(stderr, "DE=%f\n",delta_energy);
+// fprintf(stderr, "DE=%f\n",delta_energy);
//MONTE CARLOOOOOOOO
if(delta_energy>=0){
#ifdef TS_DOUBLE_DOUBLE
@@ -78,18 +82,19 @@
#endif
{
//not accepted, reverting changes
- vtx->data->x=xold;
- vtx->data->y=yold;
- vtx->data->z=zold;
+ vtx->x=xold;
+ vtx->y=yold;
+ vtx->z=zold;
//update the normals of triangles that share bead i.
- for(i=0;i<vtx->data->tristar_no;i++) triangle_normal_vector(vtx->data->tristar[i]);
+ for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);
//energy and curvature
energy_vertex(vtx);
//the same is done for neighbouring vertices
- for(i=0;i<vtx->data->neigh_no;i++) energy_vertex(vtx->data->neigh[i]);
- free(ovtx->data->bond_length);
- free(ovtx->data->bond_length_dual);
+ for(i=0;i<vtx->neigh_no;i++) energy_vertex(vtx->neigh[i]);
+ free(ovtx->bond_length);
+ free(ovtx->bond_length_dual);
free(ovtx);
+ vtx_free(tvtx);
return TS_FAIL;
}
}
@@ -97,9 +102,10 @@
//TODO: change cell occupation if necessary!
- free(ovtx->data->bond_length);
- free(ovtx->data->bond_length_dual);
+ free(ovtx->bond_length);
+ free(ovtx->bond_length_dual);
free(ovtx);
+ vtx_free(tvtx);
return TS_SUCCESS;
}
diff --git a/src/vesicle.c b/src/vesicle.c
index de7f9a1..d6c29e1 100644
--- a/src/vesicle.c
+++ b/src/vesicle.c
@@ -21,9 +21,9 @@
ts_vertex **vtx=vesicle->vlist->vtx;
ts_uint nn=vesicle->vlist->n;
for(i=0;i<nn;i++){
- vtx[i]->data->x+=x;
- vtx[i]->data->y+=y;
- vtx[i]->data->z+=z;
+ vtx[i]->x+=x;
+ vtx[i]->y+=y;
+ vtx[i]->z+=z;
}
return TS_SUCCESS;
}
--
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