/* vim: set ts=4 sts=4 sw=4 noet : */
|
#include<stdlib.h>
|
#include<math.h>
|
#include "general.h"
|
#include "vertex.h"
|
#include "bond.h"
|
#include "triangle.h"
|
#include "vesicle.h"
|
#include "energy.h"
|
#include "timestep.h"
|
#include "cell.h"
|
#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:
|
c +----- k-------+ +----- k ------+
|
c |lm1 / | \ lp1 | |lm1 / \ lp1 |
|
c | / | \ | | / \ |
|
c |/ | \ | FLIP |/ lm \ |
|
c km lm | lp kp ---> km ---------- kp
|
c |\ | / | |\ lp / |
|
c | \ | / | | \ / |
|
c |lm2 \ | / lp2 | |lm2 \ / lp2 |
|
c +------it------+ +----- it -----+
|
c
|
*/
|
ts_vertex *it=bond->vtx1;
|
ts_vertex *k=bond->vtx2;
|
ts_uint nei,neip,neim;
|
ts_uint i,j;
|
ts_double oldenergy, delta_energy, dvol=0.0, darea=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;
|
if(k==NULL || it==NULL){
|
fatal("In bondflip, number of neighbours of k or it is less than 3!",999);
|
}
|
|
nei=0;
|
for(i=0;i<it->neigh_no;i++){ // Finds the nn of it, that is k
|
if(it->neigh[i]==k){
|
nei=i;
|
break;
|
}
|
}
|
neip=nei+1; // I don't like it.. Smells like I must have it in correct order
|
neim=nei-1;
|
if(neip>=it->neigh_no) neip=0;
|
if((ts_int)neim<0) neim=it->neigh_no-1; /* casting is essential... If not
|
there the neim is never <0 !!! */
|
// fprintf(stderr,"The numbers are: %u %u\n",neip, neim);
|
km=it->neigh[neim]; // We located km and kp
|
kp=it->neigh[neip];
|
|
if(km==NULL || kp==NULL){
|
fatal("In bondflip, cannot determine km and kp!",999);
|
}
|
|
// fprintf(stderr,"I WAS HERE! after the 4 vertices are known!\n");
|
|
/* test if the membrane is wrapped too much, so that kp is nearest neighbour of
|
* km. If it is true, then don't flip! */
|
for(i=0;i<km->neigh_no;i++){
|
if(km->neigh[i] == kp) return TS_FAIL;
|
}
|
// fprintf(stderr,"Membrane didn't wrap too much.. Continue.\n");
|
/* if bond would be too long, return... */
|
if(vtx_distance_sq(km,kp) > vesicle->dmax ) return TS_FAIL;
|
// fprintf(stderr,"Bond will not be too long.. Continue.\n");
|
|
/* we make a bond flip. this is different than in original fortran */
|
// 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++){
|
if((it->tristar[i] == k->tristar[j])){ //ce gre za skupen trikotnik
|
if((it->tristar[i]->vertex[0] == km || it->tristar[i]->vertex[1]
|
== km || it->tristar[i]->vertex[2]== km )){
|
lm=it->tristar[i];
|
// lmidx=i;
|
}
|
else
|
{
|
lp=it->tristar[i];
|
// lpidx=i;
|
}
|
|
}
|
}
|
}
|
if(lm==NULL || lp==NULL) fatal("ts_flip_bond: Cannot find triangles lm and lp!",999);
|
|
//we look for important triangles lp1 and lm2.
|
|
for(i=0;i<k->tristar_no;i++){
|
for(j=0;j<kp->tristar_no;j++){
|
if((k->tristar[i] == kp->tristar[j]) && k->tristar[i]!=lp){ //ce gre za skupen trikotnik
|
lp1=k->tristar[i];
|
}
|
}
|
}
|
|
for(i=0;i<it->tristar_no;i++){
|
for(j=0;j<km->tristar_no;j++){
|
if((it->tristar[i] == km->tristar[j]) && it->tristar[i]!=lm){ //ce gre za skupen trikotnik
|
lm2=it->tristar[i];
|
}
|
}
|
}
|
|
if(lm2==NULL || lp1==NULL) fatal("ts_flip_bond: Cannot find triangles lm2 and lp1!",999);
|
|
|
/* 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;
|
oldenergy+=bond->energy; /* attraction with neighboring vertices, that have spontaneous curvature */
|
//Neigbours of k, it, km, kp don't change its energy.
|
|
if(vesicle->pswitch == 1 || vesicle->tape->constvolswitch>0){dvol = -lm->volume - lp->volume;}
|
if(vesicle->tape->constareaswitch==2){darea=-lm->area-lp->area;}
|
/* 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, vesicle->tape->w);
|
|
|
/* 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;
|
delta_energy+=bond->energy; /* attraction with neighboring vertices, that have spontaneous curvature */
|
//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->constareaswitch==2){
|
darea=darea+lm->area+lp->area;
|
/*check whether the dvol is gt than epsvol */
|
if(fabs(vesicle->area+darea-A0)>epsarea){
|
//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;
|
|
}
|
}
|
|
|
|
|
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);
|
}
|
if(vesicle->tape->constareaswitch==2){
|
vesicle->area+=darea;
|
}
|
// 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_double w_energy){
|
|
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;
|
//fprintf(stderr,"2. step: actual bondflip made\n");
|
// 2a. step. If any changes in triangle calculations must be done, do it here!
|
// * normals are recalculated here
|
triangle_normal_vector(lp);
|
triangle_normal_vector(lm);
|
//fprintf(stderr,"2a. step: triangle normals recalculated\n");
|
// 3. step. Correct neighbours in vertex_list
|
|
|
vtx_remove_neighbour(k,it);
|
// vtx_remove_neighbour(it,k);
|
//fprintf(stderr,"3. step (PROGRESS): removed k and it neighbours\n");
|
|
//Tukaj pa nastopi tezava... Kam dodati soseda?
|
vtx_insert_neighbour(km,kp,k);
|
vtx_insert_neighbour(kp,km,it);
|
// vertex_add_neighbour(km,kp); //pazi na vrstni red.
|
// vertex_add_neighbour(kp,km);
|
//fprintf(stderr,"3. step: vertex neighbours corrected\n");
|
|
// 3a. step. If any changes to ts_vertex, do it here!
|
// bond_length calculatons not required for it is done in energy.c
|
|
// 4. step. Correct bond_list (don't know why I still have it!)
|
bond->vtx1=km;
|
bond->vtx2=kp;
|
//fprintf(stderr,"4. step: bondlist corrected\n");
|
|
|
// 5. step. Correct neighbouring triangles
|
|
triangle_remove_neighbour(lp,lp1);
|
// fprintf(stderr,".\n");
|
triangle_remove_neighbour(lp1,lp);
|
// fprintf(stderr,".\n");
|
triangle_remove_neighbour(lm,lm2);
|
// fprintf(stderr,".\n");
|
triangle_remove_neighbour(lm2,lm);
|
|
triangle_add_neighbour(lm,lp1);
|
triangle_add_neighbour(lp1,lm);
|
triangle_add_neighbour(lp,lm2); //Vrstni red?!
|
triangle_add_neighbour(lm2,lp);
|
|
//fprintf(stderr,"5. step: triangle neigbours corrected\n");
|
|
|
// 6. step. Correct tristar for vertices km, kp, k and it
|
vertex_add_tristar(km,lp); // Preveri vrstni red!
|
vertex_add_tristar(kp,lm);
|
vtx_remove_tristar(it,lm);
|
vtx_remove_tristar(k,lp);
|
//fprintf(stderr,"6. step: tristar corrected\n");
|
energy_vertex(k);
|
energy_vertex(kp);
|
energy_vertex(km);
|
energy_vertex(it);
|
attraction_bond_energy(bond, w_energy);
|
// END modifications to data structure!
|
return TS_SUCCESS;
|
}
|
