From dcd35081a6f08c911169aca6913fd71b88531b97 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Thu, 12 Jul 2012 16:14:11 +0000
Subject: [PATCH] Is it worth it? I've changed dynamically alocated space to statically alocated one and gained some little time
---
src/vertexmove.c | 106 +++++++++++++++++++++++++++++------------------------
1 files changed, 58 insertions(+), 48 deletions(-)
diff --git a/src/vertexmove.c b/src/vertexmove.c
index 243463f..7f3c661 100644
--- a/src/vertexmove.c
+++ b/src/vertexmove.c
@@ -11,60 +11,67 @@
//#include "io.h"
#include<stdio.h>
#include "vertexmove.h"
+#include <string.h>
ts_bool single_verticle_timestep(ts_vesicle *vesicle,ts_vertex *vtx,ts_double
*rn){
ts_uint i;
ts_double dist;
- ts_vertex *tvtx=(ts_vertex *)malloc(sizeof(ts_vertex));
- tvtx->data=init_vertex_data();
ts_bool retval;
ts_uint cellidx;
- ts_double xold,yold,zold;
ts_double delta_energy,oenergy;
- 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);
- //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;
+ //This will hold all the information of vtx and its neighbours
+// ts_vertex **backupvtx=(ts_vertex **)calloc(vtx->neigh_no+1,sizeof(ts_vertex *));
+ ts_vertex backupvtx[20];
+// backupvtx[0]=(ts_vertex *)malloc(sizeof(ts_vertex));
+ memcpy((void *)&backupvtx[0],(void *)vtx,sizeof(ts_vertex));
+ //temporarly moving the vertex
+ vtx->x=vtx->x+vesicle->stepsize*(2.0*rn[0]-1.0);
+ vtx->y=vtx->y+vesicle->stepsize*(2.0*rn[1]-1.0);
+ vtx->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->neigh_no;i++){
+ dist=vtx_distance_sq(vtx,vtx->neigh[i]);
+ if(dist<1.0 || dist>vesicle->dmax) {
+ vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
+// free(backupvtx[0]);
+// free(backupvtx);
+// fprintf(stderr,"Fail 1, dist=%f, vesicle->dmax=%f\n", dist, vesicle->dmax);
+ return TS_FAIL;
+ }
}
-fprintf(stderr,"Was here!\n");
//self avoidance check with distant vertices
- cellidx=vertex_self_avoidance(vesicle, tvtx);
+ cellidx=vertex_self_avoidance(vesicle, vtx);
//check occupation number
- retval=cell_occupation_number_and_internal_proximity(vesicle->clist,cellidx,vtx,tvtx);
+ retval=cell_occupation_number_and_internal_proximity(vesicle->clist,cellidx,&backupvtx[0],vtx);
if(retval==TS_FAIL){
+ vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
+// free(backupvtx[0]);
+// free(backupvtx);
+// fprintf(stderr,"Fail 2\n");
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;
- 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;
+
+
+ //if all the tests are successful, then energy for vtx and neighbours is calculated
+ for(i=0;i<vtx->neigh_no;i++){
+// backupvtx[i+1]=(ts_vertex *)malloc(sizeof(ts_vertex));
+ memcpy((void *)&backupvtx[i+1],(void *)vtx->neigh[i],sizeof(ts_vertex));
+ }
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 - (&backupvtx[0])->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
@@ -78,28 +85,31 @@
#endif
{
//not accepted, reverting changes
- vtx->data->x=xold;
- vtx->data->y=yold;
- vtx->data->z=zold;
+ vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
+// free(backupvtx[0]);
+ for(i=0;i<vtx->neigh_no;i++){
+ vtx->neigh[i]=memcpy((void *)vtx->neigh[i],(void *)&backupvtx[i+1],sizeof(ts_vertex));
+// free(backupvtx[i+1]);
+ }
+// free(backupvtx);
+// fprintf(stderr,"Reverted\n");
+
//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]);
- //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);
- free(ovtx);
+ for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);
+
return TS_FAIL;
}
}
//END MONTE CARLOOOOOOO
//TODO: change cell occupation if necessary!
-
- free(ovtx->data->bond_length);
- free(ovtx->data->bond_length_dual);
- free(ovtx);
+// fprintf(stderr,"Success!!\n");
+// free(backupvtx[0]);
+// for(i=0;i<vtx->neigh_no;i++){
+// free(backupvtx[i+1]);
+// }
+// free(backupvtx);
+// fprintf(stderr,"Accepted\n");
return TS_SUCCESS;
}
--
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