From 464443e958f806fdc2b64ae77661a67c199b6204 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@fe.uni-lj.si>
Date: Thu, 11 Sep 2014 11:46:13 +0000
Subject: [PATCH] Fix in src makefile.
---
src/bondflip.c | 392 +++++++++++++++++++++++++++++++------------------------
1 files changed, 220 insertions(+), 172 deletions(-)
diff --git a/src/bondflip.c b/src/bondflip.c
index 478027d..4c8b50c 100644
--- a/src/bondflip.c
+++ b/src/bondflip.c
@@ -11,6 +11,8 @@
#include "bondflip.h"
//#include "io.h"
#include<stdio.h>
+#include<string.h>
+#include "constvol.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:
@@ -28,11 +30,15 @@
ts_vertex *it=bond->vtx1;
ts_vertex *k=bond->vtx2;
ts_uint nei,neip,neim;
- ts_uint i; //j;
- ts_double oldenergy, delta_energy;
- // ts_triangle *lm=NULL,*lp=NULL, *lp1=NULL, *lp2=NULL, *lm1=NULL, *lm2=NULL;
+ ts_uint i,j;
+ ts_double oldenergy, delta_energy, dvol=0.0;
+ ts_triangle *lm=NULL,*lp=NULL, *lp1=NULL, *lm2=NULL;
ts_vertex *kp,*km;
+
+ ts_double delta_energy_cv;
+ ts_vertex *constvol_vtx_moved, *constvol_vtx_backup;
+ ts_bool retval;
if(it->neigh_no< 3) return TS_FAIL;
if(k->neigh_no< 3) return TS_FAIL;
@@ -73,112 +79,7 @@
// fprintf(stderr,"Bond will not be too long.. Continue.\n");
/* we make a bond flip. this is different than in original fortran */
-// 0. step. Get memory prior the flip
- oldenergy=0;
- oldenergy+=k->xk* k->energy;
- oldenergy+=kp->xk* kp->energy;
- oldenergy+=km->xk* km->energy;
- oldenergy+=it->xk* it->energy;
-// for(i=0;i<k->neigh_no;i++) oldenergy+=k->neigh[i]->xk*k->neigh[i]->energy;
-// for(i=0;i<kp->neigh_no;i++) oldenergy+=kp->neigh[i]->xk*kp->neigh[i]->energy;
-// for(i=0;i<km->neigh_no;i++) oldenergy+=km->neigh[i]->xk*km->neigh[i]->energy;
-// for(i=0;i<it->neigh_no;i++) oldenergy+=it->neigh[i]->xk*it->neigh[i]->energy;
-/*
-fprintf(stderr,"*** Naslov k=%ld\n",(long)k);
-fprintf(stderr,"*** Naslov it=%ld\n",(long)it);
-fprintf(stderr,"*** Naslov km=%ld\n",(long)km);
-fprintf(stderr,"*** Naslov kp=%ld\n",(long)kp);
-
-for(i=0;i<k->neigh_no;i++)
- fprintf(stderr,"k sosed=%ld\n",(long)k->neigh[i]);
-for(i=0;i<it->neigh_no;i++)
- fprintf(stderr,"it sosed=%ld\n",(long)it->neigh[i]);
-
-for(i=0;i<km->neigh_no;i++)
- fprintf(stderr,"km sosed=%ld\n",(long)km->neigh[i]);
-for(i=0;i<kp->neigh_no;i++)
- fprintf(stderr,"kp sosed=%ld\n",(long)kp->neigh[i]);
-
-
-*/
-// fprintf(stderr,"I WAS HERE! Before bondflip!\n");
- ts_flip_bond(k,it,km,kp, bond);
-// fprintf(stderr,"I WAS HERE! Bondflip successful!\n");
-
-/* Calculating the new energy */
- delta_energy=0;
- for(i=0;i<k->neigh_no;i++) energy_vertex(k->neigh[i]);
- for(i=0;i<kp->neigh_no;i++) energy_vertex(kp->neigh[i]);
- for(i=0;i<km->neigh_no;i++) energy_vertex(km->neigh[i]);
- for(i=0;i<it->neigh_no;i++) energy_vertex(it->neigh[i]);
- delta_energy+=k->xk* k->energy;
- delta_energy+=kp->xk* kp->energy;
- delta_energy+=km->xk* km->energy;
- delta_energy+=it->xk* it->energy;
-// for(i=0;i<k->neigh_no;i++) delta_energy+=k->neigh[i]->xk*k->neigh[i]->energy;
-// for(i=0;i<kp->neigh_no;i++) delta_energy+=kp->neigh[i]->xk*kp->neigh[i]->energy;
-// for(i=0;i<km->neigh_no;i++) delta_energy+=km->neigh[i]->xk*km->neigh[i]->energy;
-// for(i=0;i<it->neigh_no;i++) delta_energy+=it->neigh[i]->xk*it->neigh[i]->energy;
- delta_energy-=oldenergy;
- // fprintf(stderr,"I WAS HERE! Got energy!\n");
-/* MONTE CARLO */
- if(delta_energy>=0){
-#ifdef TS_DOUBLE_DOUBLE
- if(exp(-delta_energy)< drand48() )
-#endif
-#ifdef TS_DOUBLE_FLOAT
- if(expf(-delta_energy)< (ts_float)drand48())
-#endif
-#ifdef TS_DOUBLE_LONGDOUBLE
- if(expl(-delta_energy)< (ts_ldouble)drand48())
-#endif
- {
- //not accepted, reverting changes
- // fprintf(stderr,"Failed to move, due to MC\n");
-
-// ts_flip_bond(km,kp,it,k, bond);
- ts_flip_bond(kp,km,k,it, bond);
-
-
-/*
-fprintf(stderr,"*** Naslov k=%d\n",k);
-fprintf(stderr,"*** Naslov it=%d\n",it);
-fprintf(stderr,"*** Naslov km=%d\n",km);
-fprintf(stderr,"*** Naslov kp=%d\n",kp);
-for(i=0;i<k->neigh_no;i++)
- fprintf(stderr,"k sosed=%d\n",k->neigh[i]);
-for(i=0;i<it->neigh_no;i++)
- fprintf(stderr,"it sosed=%d\n",it->neigh[i]);
-
-
-for(i=0;i<km->neigh_no;i++)
- fprintf(stderr,"km sosed=%d\n",km->neigh[i]);
-for(i=0;i<kp->neigh_no;i++)
- fprintf(stderr,"kp sosed=%d\n",kp->neigh[i]);
-*/
-
-
-
- // fprintf(stderr,"Reverted condition!\n");
- return TS_FAIL;
- }
- }
- // fprintf(stderr,"Success\n");
-
-
-/* IF BONDFLIP ACCEPTED, THEN RETURN SUCCESS! */
- return TS_SUCCESS;
-}
-
-
-ts_bool ts_flip_bond(ts_vertex *k,ts_vertex *it,ts_vertex *km, ts_vertex *kp,
-ts_bond *bond){
-
- ts_triangle *lm=NULL,*lp=NULL, *lp1=NULL, *lm2=NULL;
- ts_uint i,j; //lmidx, lpidx;
-if(k==NULL || it==NULL || km==NULL || kp==NULL){
- fatal("ts_flip_bond: You called me with invalid pointers to vertices",999);
-}
+// find lm, lp
// 1. step. We find lm and lp from k->tristar !
for(i=0;i<it->tristar_no;i++){
for(j=0;j<k->tristar_no;j++){
@@ -216,57 +117,228 @@
}
}
}
-/*
-// DEBUG TESTING!
-fprintf(stderr,"*** Naslov k=%d\n",k);
-fprintf(stderr,"*** Naslov it=%d\n",it);
-fprintf(stderr,"*** Naslov km=%d\n",km);
-fprintf(stderr,"*** Naslov kp=%d\n",kp);
-for(i=0;i<k->neigh_no;i++)
- fprintf(stderr,"k sosed=%d\n",k->neigh[i]);
-for(i=0;i<it->neigh_no;i++)
- fprintf(stderr,"it sosed=%d\n",it->neigh[i]);
-
-
-// END DEBUG TESTING!
-*/
if(lm2==NULL || lp1==NULL) fatal("ts_flip_bond: Cannot find triangles lm2 and lp1!",999);
-/*
-//DEBUG TESTING
-fprintf(stderr,"1. step: lm, lm2, lp1 and lp found!\n");
-fprintf(stderr,"--- Naslov lm=%ld",(long)lm);
+/* 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," vtxs(%ld, %ld, %ld)\n",(long)lm->vertex[0],(long)lm->vertex[1], (long)lm->vertex[2]);
-fprintf(stderr,"--- Naslov lp=%ld",(long)lp);
-fprintf(stderr," vtxs(%ld, %ld, %ld)\n",(long)lp->vertex[0],(long)lp->vertex[1], (long)lp->vertex[2]);
-fprintf(stderr,"--- Naslov lm2=%ld",(long)lm2);
-fprintf(stderr," vtxs(%ld, %ld, %ld)\n",(long)lm2->vertex[0],(long)lm2->vertex[1], (long)lm2->vertex[2]);
-fprintf(stderr,"--- Naslov lp1=%ld",(long)lp1);
-fprintf(stderr," vtxs(%ld, %ld, %ld)\n",(long)lp1->vertex[0],(long)lp1->vertex[1], (long)lp1->vertex[2]);
-
-for(i=0;i<lm->neigh_no;i++)
- fprintf(stderr,"lm sosed=%ld\n",(long)lm->neigh[i]);
-for(i=0;i<lp->neigh_no;i++)
- fprintf(stderr,"lp sosed=%ld\n",(long)lp->neigh[i]);
-// END DEBUG TESTING
+//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");
*/
-/*
-// DEBUG TESTING!
+ 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 */
-for(i=0;i<3;i++){
+ 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 *));
- if(lp1->neigh[i]==lp) fprintf(stderr,"Nasel sem par lp1->lp\n");
- if(lp->neigh[i]==lp1) fprintf(stderr,"Nasel sem par lp->lp1\n");
- if(lm2->neigh[i]==lm) fprintf(stderr,"Nasel sem par lm2->lm\n");
- if(lm->neigh[i]==lm2) fprintf(stderr,"Nasel sem par lm->lm2\n");
+ 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 *));
}
-// END DEBUG TESTING!
+ 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 of k, it, km, kp don't change its energy.
+
+ if(vesicle->pswitch == 1 || vesicle->tape->constvolswitch>0){dvol = -lm->volume - lp->volume;}
+
+/* vesicle_volume(vesicle);
+ fprintf(stderr,"Volume in the beginning=%1.16e\n", vesicle->volume);
*/
+/* fix data structure for flipped bond */
+ ts_flip_bond(k,it,km,kp, bond,lm, lp, lm2, lp1);
+
+/* Calculating the new energy */
+ delta_energy=0;
+ delta_energy+=k->xk* k->energy;
+ delta_energy+=kp->xk* kp->energy;
+ delta_energy+=km->xk* km->energy;
+ delta_energy+=it->xk* it->energy;
+ //Neigbours of k, it, km, kp don't change its energy.
+
+ delta_energy-=oldenergy;
+ if(vesicle->pswitch == 1 || vesicle->tape->constvolswitch>0){
+ dvol = dvol + lm->volume + lp->volume;
+ if(vesicle->pswitch==1) delta_energy-= vesicle->pressure*dvol;
+ }
+
+ if(vesicle->tape->constvolswitch == 2){
+ /*check whether the dvol is gt than epsvol */
+ if(fabs(vesicle->volume+dvol-V0)>epsvol){
+ //restore old state.
+ /* restoration procedure copied from few lines below */
+ 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);
+ return TS_FAIL;
+
+ }
+
+ } else
+ if(vesicle->tape->constvolswitch == 1){
+ retval=constvolume(vesicle, it, -dvol, &delta_energy_cv, &constvol_vtx_moved,&constvol_vtx_backup);
+ if(retval==TS_FAIL){
+/* restoration procedure copied from few lines below */
+ 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);
+ return TS_FAIL;
+ }
+ delta_energy+=delta_energy_cv;
+ }
+
+
+/* MONTE CARLO */
+ if(delta_energy>=0){
+#ifdef TS_DOUBLE_DOUBLE
+ if(exp(-delta_energy)< drand48())
+#endif
+#ifdef TS_DOUBLE_FLOAT
+ if(expf(-delta_energy)< (ts_float)drand48())
+#endif
+#ifdef TS_DOUBLE_LONGDOUBLE
+ if(expl(-delta_energy)< (ts_ldouble)drand48())
+#endif
+ {
+ //not accepted, reverting changes
+ //restore all backups
+// fprintf(stderr,"Restoring!!!\n");
+ if(vesicle->tape->constvolswitch == 1){
+ constvolumerestore(constvol_vtx_moved,constvol_vtx_backup);
+ }
+
+ 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");
+// vesicle_volume(vesicle);
+// fprintf(stderr,"Volume after fail=%1.16e\n", vesicle->volume);
+
+ return TS_FAIL;
+ }
+ }
+ /* IF BONDFLIP ACCEPTED, THEN RETURN SUCCESS! */
+// fprintf(stderr,"SUCCESS!!!\n");
+
+ if(vesicle->tape->constvolswitch == 2){
+ vesicle->volume+=dvol;
+ } else
+ if(vesicle->tape->constvolswitch == 1){
+ constvolumeaccept(vesicle,constvol_vtx_moved,constvol_vtx_backup);
+ }
+ // 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);
+
+// vesicle_volume(vesicle);
+// fprintf(stderr,"Volume after success=%1.16e\n", vesicle->volume);
+ return TS_SUCCESS;
+}
+
+
+ts_bool ts_flip_bond(ts_vertex *k,ts_vertex *it,ts_vertex *km, ts_vertex *kp,
+ts_bond *bond, ts_triangle *lm, ts_triangle *lp, ts_triangle *lm2, ts_triangle *lp1){
+
+ ts_uint i; //lmidx, lpidx;
+if(k==NULL || it==NULL || km==NULL || kp==NULL){
+ fatal("ts_flip_bond: You called me with invalid pointers to vertices",999);
+}
// 2. step. We change the triangle vertices... (actual bond flip)
for(i=0;i<3;i++) if(lm->vertex[i]== it) lm->vertex[i]= kp;
for(i=0;i<3;i++) if(lp->vertex[i]== k) lp->vertex[i]= km;
@@ -323,34 +395,10 @@
vtx_remove_tristar(it,lm);
vtx_remove_tristar(k,lp);
//fprintf(stderr,"6. step: tristar corrected\n");
-
-/*
-//DEBUG TESTING
-fprintf(stderr,"--- Naslov lm=%d",lm);
-
-
-fprintf(stderr," vtxs(%d, %d, %d)\n",lm->vertex[0],lm->vertex[1], lm->vertex[2]);
-fprintf(stderr,"--- Naslov lp=%d",lp);
-fprintf(stderr," vtxs(%d, %d, %d)\n",lp->vertex[0],lp->vertex[1], lp->vertex[2]);
-fprintf(stderr,"--- Naslov lm2=%d",lm2);
-fprintf(stderr," vtxs(%d, %d, %d)\n",lm2->vertex[0],lm2->vertex[1], lm2->vertex[2]);
-fprintf(stderr,"--- Naslov lp1=%d",lp1);
-fprintf(stderr," vtxs(%d, %d, %d)\n",lp1->vertex[0],lp1->vertex[1], lp1->vertex[2]);
-
-for(i=0;i<lm->neigh_no;i++)
- fprintf(stderr,"lm sosed=%d\n",lm->neigh[i]);
-for(i=0;i<lp->neigh_no;i++)
- fprintf(stderr,"lp sosed=%d\n",lp->neigh[i]);
-// END DEBUG TESTING
-*/
energy_vertex(k);
energy_vertex(kp);
energy_vertex(km);
energy_vertex(it);
-
-
// END modifications to data structure!
-
-
return TS_SUCCESS;
}
--
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