Raj and Yoav session in making multiple protein species

Samo Penic

2021-05-10 6487a03362d35589c286d0660eba123a7ab00535

 src/bondflip.c

@@ -1,3 +1,4 @@
/* vim: set ts=4 sts=4 sw=4 noet : */
#include<stdlib.h>
#include<math.h>
#include "general.h"
@@ -11,6 +12,8 @@
#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 +31,15 @@
    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=0.0, delta_energy=0.0, 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;
@@ -73,112 +80,7 @@
 //   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 +118,274 @@
            } 
        }
    }
/*
// 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=0.0;
  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=0.0;
  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.
   if(vesicle->tape->stretchswitch==1){
      oldenergy+=lm->energy+lp->energy;
      stretchenergy(vesicle,lm);
      stretchenergy(vesicle,lp);
      delta_energy+=lm->energy+lp->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);
   if(vesicle->tape->stretchswitch==1){
      stretchenergy(vesicle,lm);
      stretchenergy(vesicle,lp);
   }

      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;
@@ -323,34 +442,11 @@
            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);


  attraction_bond_energy(bond, w_energy);
// END modifications to data structure!


    return TS_SUCCESS;
}