From aab4ad46109f8361d0235a07ba1edbf188ad442f Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@fe.uni-lj.si>
Date: Tue, 11 Mar 2014 10:52:57 +0000
Subject: [PATCH] Fixed counting of iterations when invoked with --reset-iteration-count
---
src/bondflip.c | 114 ++++++++++++++++++++++++++++++++++++++++++++++++++-------
1 files changed, 100 insertions(+), 14 deletions(-)
diff --git a/src/bondflip.c b/src/bondflip.c
index da2c664..23afbc9 100644
--- a/src/bondflip.c
+++ b/src/bondflip.c
@@ -11,6 +11,7 @@
#include "bondflip.h"
//#include "io.h"
#include<stdio.h>
+#include<string.h>
ts_bool single_bondflip_timestep(ts_vesicle *vesicle, ts_bond *bond, ts_double *rn){
/*c Vertex and triangle (lm and lp) indexing for bond flip:
@@ -29,7 +30,7 @@
ts_vertex *k=bond->vtx2;
ts_uint nei,neip,neim;
ts_uint i,j;
- ts_double oldenergy, delta_energy;
+ ts_double oldenergy, delta_energy, dvol=0.0;
ts_triangle *lm=NULL,*lp=NULL, *lp1=NULL, *lm2=NULL;
ts_vertex *kp,*km;
@@ -113,19 +114,60 @@
}
if(lm2==NULL || lp1==NULL) fatal("ts_flip_bond: Cannot find triangles lm2 and lp1!",999);
- // fprintf(stderr,"I WAS HERE! Before bondflip!\n");
- // fprintf(stderr,"%e, %e, %e\n", lm->xnorm, lm->ynorm, lm->znorm);
-
- ts_flip_bond(k,it,km,kp, bond,lm, lp, lm2, lp1);
-// fprintf(stderr,"I WAS HERE! Bondflip successful!\n");
+
+/* backup old structure */
+/* need to backup:
+ * vertices k, kp, km, it
+ * triangles lm, lp, lm2, lp1
+ * bond
+ */
+ts_vertex *bck_vtx[4];
+ts_triangle *bck_tria[4];
+ts_bond *bck_bond;
+ts_vertex *orig_vtx[]={k,it,kp,km};
+ts_triangle *orig_tria[]={lm,lp,lm2,lp1};
+
+//fprintf(stderr,"Backuping!!!\n");
+ bck_bond=(ts_bond *)malloc(sizeof(ts_bond));
+for(i=0;i<4;i++){
+/* fprintf(stderr,"vtx neigh[%d]=",i);
+ for(j=0;j<orig_vtx[i]->neigh_no;j++) fprintf(stderr," %d", orig_vtx[i]->neigh[j]->idx);
+ fprintf(stderr,"\n");
+*/
+ bck_vtx[i]=(ts_vertex *)malloc(sizeof(ts_vertex));
+ bck_tria[i]=(ts_triangle *)malloc(sizeof(ts_triangle));
+ memcpy((void *)bck_vtx[i],(void *)orig_vtx[i],sizeof(ts_vertex));
+ memcpy((void *)bck_tria[i],(void *)orig_tria[i],sizeof(ts_triangle));
+ /* level 2 pointers */
+
+ bck_vtx[i]->neigh=(ts_vertex **)malloc(orig_vtx[i]->neigh_no*sizeof(ts_vertex *));
+ bck_vtx[i]->tristar=(ts_triangle **)malloc(orig_vtx[i]->tristar_no*sizeof(ts_triangle *));
+ bck_vtx[i]->bond=(ts_bond **)malloc(orig_vtx[i]->bond_no*sizeof(ts_bond *));
+ bck_tria[i]->neigh=(ts_triangle **)malloc(orig_tria[i]->neigh_no*sizeof(ts_triangle *));
+
+ memcpy((void *)bck_vtx[i]->neigh,(void *)orig_vtx[i]->neigh,orig_vtx[i]->neigh_no*sizeof(ts_vertex *));
+ memcpy((void *)bck_vtx[i]->tristar,(void *)orig_vtx[i]->tristar,orig_vtx[i]->tristar_no*sizeof(ts_triangle *));
+ memcpy((void *)bck_vtx[i]->bond,(void *)orig_vtx[i]->bond,orig_vtx[i]->bond_no*sizeof(ts_bond *));
+
+ memcpy((void *)bck_tria[i]->neigh,(void *)orig_tria[i]->neigh,orig_tria[i]->neigh_no*sizeof(ts_triangle *));
+}
+ memcpy(bck_bond,bond,sizeof(ts_bond));
+//fprintf(stderr,"Backup complete!!!\n");
+/* end backup vertex */
+
+/* Save old energy */
oldenergy=0;
oldenergy+=k->xk* k->energy;
oldenergy+=kp->xk* kp->energy;
oldenergy+=km->xk* km->energy;
oldenergy+=it->xk* it->energy;
- //Neigbours don't change its energy.
+ //Neigbours of k, it, km, kp don't change its energy.
+ if(vesicle->pswitch == 1){dvol = -lm->volume - lp->volume;}
+
+/* fix data structure for flipped bond */
+ ts_flip_bond(k,it,km,kp, bond,lm, lp, lm2, lp1);
/* Calculating the new energy */
@@ -134,9 +176,14 @@
delta_energy+=kp->xk* kp->energy;
delta_energy+=km->xk* km->energy;
delta_energy+=it->xk* it->energy;
- //Neigbours don't change its energy.
+ //Neigbours of k, it, km, kp don't change its energy.
+
delta_energy-=oldenergy;
- // fprintf(stderr,"I WAS HERE! Got energy!\n");
+ if(vesicle->pswitch == 1){
+ dvol = dvol + lm->volume + lp->volume;
+ delta_energy-= vesicle->pressure*dvol;
+ }
+
/* MONTE CARLO */
if(delta_energy>=0){
#ifdef TS_DOUBLE_DOUBLE
@@ -150,15 +197,54 @@
#endif
{
//not accepted, reverting changes
-// fprintf(stderr,"Failed to move, due to MC\n");
+ //restore all backups
+// fprintf(stderr,"Restoring!!!\n");
- ts_flip_bond(kp,km,k,it, bond, lm,lp,lm2,lp1);
-// fprintf(stderr,"%e, %e, %e\n", lp->xnorm, lp->ynorm, lp->znorm);
- return TS_FAIL;
+ for(i=0;i<4;i++){
+// fprintf(stderr,"Restoring vtx neigh[%d] with neighbours %d\n",i, orig_vtx[i]->neigh_no );
+ free(orig_vtx[i]->neigh);
+ free(orig_vtx[i]->tristar);
+ free(orig_vtx[i]->bond);
+ free(orig_tria[i]->neigh);
+ memcpy((void *)orig_vtx[i],(void *)bck_vtx[i],sizeof(ts_vertex));
+ memcpy((void *)orig_tria[i],(void *)bck_tria[i],sizeof(ts_triangle));
+// fprintf(stderr,"Restored vtx neigh[%d] with neighbours %d\n",i, orig_vtx[i]->neigh_no );
+ /* level 2 pointers are redirected*/
+ }
+ memcpy(bond,bck_bond,sizeof(ts_bond));
+
+ for(i=0;i<4;i++){
+ free(bck_vtx[i]);
+ free(bck_tria[i]);
+/* fprintf(stderr,"Restoring vtx neigh[%d] with neighbours %d =",i, orig_vtx[i]->neigh_no );
+ for(j=0;j<orig_vtx[i]->neigh_no;j++) fprintf(stderr," %d", orig_vtx[i]->neigh[j]->idx);
+ fprintf(stderr,"\n"); */
+ }
+
+ free(bck_bond);
+// fprintf(stderr,"Restoration complete!!!\n");
+
+ return TS_FAIL;
}
}
/* IF BONDFLIP ACCEPTED, THEN RETURN SUCCESS! */
-// fprintf(stderr,"SUCCESS!!!\n");
+ // fprintf(stderr,"SUCCESS!!!\n");
+
+ // delete all backups
+ for(i=0;i<4;i++){
+ free(bck_vtx[i]->neigh);
+ free(bck_vtx[i]->bond);
+ free(bck_vtx[i]->tristar);
+ free(bck_vtx[i]);
+ free(bck_tria[i]->neigh);
+ free(bck_tria[i]);
+/* fprintf(stderr,"Afret backup deletion vtx neigh[%d]=",i);
+ for(j=0;j<orig_vtx[i]->neigh_no;j++) fprintf(stderr," %d", orig_vtx[i]->neigh[j]->idx);
+ fprintf(stderr,"\n");
+*/
+ }
+ free(bck_bond);
+
return TS_SUCCESS;
}
--
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