From 304510886da7e3969efd6d506e68652b533c0975 Mon Sep 17 00:00:00 2001
From: Miha <mihaf@hapi.(none)>
Date: Fri, 21 Feb 2014 12:22:07 +0000
Subject: [PATCH] Removed harmonic potential between poly-monomers for now. Added min and max distance between neighboring poly-vertices.
---
src/energy.c | 82 ++++++++++++++++++++++++-----------------
1 files changed, 48 insertions(+), 34 deletions(-)
diff --git a/src/energy.c b/src/energy.c
index 540686b..440f319 100644
--- a/src/energy.c
+++ b/src/energy.c
@@ -13,37 +13,47 @@
for(i=0;i<vlist->n;i++){
energy_vertex(vtx[i]);
+
}
return TS_SUCCESS;
}
+inline ts_bool bond_energy(ts_bond *bond,ts_poly *poly){
+//TODO: This value to be changed and implemented in data structure:
+ ts_double d_relaxed=1.0;
+ bond->energy=poly->k*pow(bond->bond_length-d_relaxed,2);
+ return TS_SUCCESS;
+};
+
+
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;
ts_triangle *jt;
- ts_double s=0,xh=0,yh=0,zh=0,txn=0,tyn=0,tzn=0;
+ ts_double s=0.0,xh=0.0,yh=0.0,zh=0.0,txn=0.0,tyn=0.0,tzn=0.0;
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];
- jt=data->tristar[jj-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=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);
@@ -56,9 +66,9 @@
#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
@@ -70,26 +80,28 @@
#endif
tot=ctp+ctm;
tot=0.5*tot;
+
xlen=vtx_distance_sq(j,vtx);
+/*
#ifdef TS_DOUBLE_DOUBLE
- data->bond[jj-1]->data->bond_length=sqrt(xlen);
+ vtx->bond[jj-1]->bond_length=sqrt(xlen);
#endif
#ifdef TS_DOUBLE_FLOAT
- data->bond[jj-1]->data->bond_length=sqrtf(xlen);
+ vtx->bond[jj-1]->bond_length=sqrtf(xlen);
#endif
#ifdef TS_DOUBLE_LONGDOUBLE
- data->bond[jj-1]->data->bond_length=sqrtl(xlen);
+ vtx->bond[jj-1]->bond_length=sqrtl(xlen);
#endif
- data->bond[jj-1]->data->bond_length_dual=tot*data->bond[jj-1]->data->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);
- txn+=jt->data->xnorm;
- tyn+=jt->data->ynorm;
- tzn+=jt->data->znorm;
+ 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;
}
h=xh*xh+yh*yh+zh*zh;
@@ -97,27 +109,29 @@
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
-//TODO: MAJOR!!!! What is vtx->data->c?????????????? Here it is 0!
- data->energy=0.5*s*(data->curvature/s-data->c)*(data->curvature/s-data->c);
+// What is vtx->c?????????????? Here it is 0!
+// c is forced curvature energy for each vertex. Should be set to zero for
+// normal circumstances.
+ vtx->energy=0.5*s*(vtx->curvature/s-vtx->c)*(vtx->curvature/s-vtx->c);
return TS_SUCCESS;
}
--
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