From 58230a2591414fb38b9ec8d3a76439b290cb0a6f Mon Sep 17 00:00:00 2001
From: mihaf <miha.fosnaric@gmail.com>
Date: Tue, 18 Mar 2014 13:09:23 +0000
Subject: [PATCH] Adding ending energy to filaments. In progress. Continue in single_filament_vertex_move

---
 src/vertexmove.c |  311 ++++++++++++++++++++++++++++++++++++++++++++++-----
 1 files changed, 278 insertions(+), 33 deletions(-)

diff --git a/src/vertexmove.c b/src/vertexmove.c
index 7f3c661..04325ef 100644
--- a/src/vertexmove.c
+++ b/src/vertexmove.c
@@ -13,64 +13,105 @@
 #include "vertexmove.h"
 #include <string.h>
 
-ts_bool single_verticle_timestep(ts_vesicle *vesicle,ts_vertex *vtx,ts_double
-*rn){
+ts_bool single_verticle_timestep(ts_vesicle *vesicle,ts_vertex *vtx,ts_double *rn){
     ts_uint i;
     ts_double dist;
     ts_bool retval; 
     ts_uint cellidx; 
-    ts_double delta_energy,oenergy;
+    ts_double delta_energy,oenergy,dvol=0.0;
+    ts_double costheta,sintheta,phi,r;
 	//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));
+
+	//Some stupid tests for debugging cell occupation!
+/*     	cellidx=vertex_self_avoidance(vesicle, vtx);
+	if(vesicle->clist->cell[cellidx]==vtx->cell){
+		fprintf(stderr,"Idx match!\n");
+	} else {
+		fprintf(stderr,"***** Idx don't match!\n");
+		fatal("ENding.",1);
+	}
+*/
+
     	//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
+//	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);
+
+	//random move in a sphere with radius stepsize:
+	r=vesicle->stepsize*rn[0];
+	phi=rn[1]*2*M_PI;
+	costheta=2*rn[2]-1;
+	sintheta=sqrt(1-pow(costheta,2));
+	vtx->x=vtx->x+r*sintheta*cos(phi);
+	vtx->y=vtx->y+r*sintheta*sin(phi);
+	vtx->z=vtx->z+r*costheta;
+
+
+    	//distance with neighbours check
     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;
 		}
     }
+
+// Distance with grafted poly-vertex check:	
+	if(vtx->grafted_poly!=NULL){
+		dist=vtx_distance_sq(vtx,vtx->grafted_poly->vlist->vtx[0]);
+        if(dist<1.0 || dist>vesicle->dmax) {
+		vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
+		return TS_FAIL;
+		}
+	}
+
     //self avoidance check with distant vertices
      cellidx=vertex_self_avoidance(vesicle, vtx);
     //check occupation number
-     retval=cell_occupation_number_and_internal_proximity(vesicle->clist,cellidx,&backupvtx[0],vtx);
+     retval=cell_occupation_number_and_internal_proximity(vesicle->clist,cellidx,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 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));
 	}
+
+	if(vesicle->pswitch == 1){
+		for(i=0;i<vtx->tristar_no;i++) dvol-=vtx->tristar[i]->volume;
+	};
 
     delta_energy=0;
     //update the normals of triangles that share bead i.
     for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);
-    //energy and curvature
+	oenergy=vtx->energy;
     energy_vertex(vtx);
-    delta_energy=vtx->xk*(vtx->energy - (&backupvtx[0])->energy);
+    delta_energy=vtx->xk*(vtx->energy - oenergy);
     //the same is done for neighbouring vertices
     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);
     }
+
+	if(vesicle->pswitch == 1){
+		for(i=0;i<vtx->tristar_no;i++) dvol+=vtx->tristar[i]->volume;
+		delta_energy-=vesicle->pressure*dvol;
+	};
+
+/* No poly-bond energy for now!
+	if(vtx->grafted_poly!=NULL){
+		delta_energy+=
+			(pow(sqrt(vtx_distance_sq(vtx, vtx->grafted_poly->vlist->vtx[0])-1),2)-
+			pow(sqrt(vtx_distance_sq(&backupvtx[0], vtx->grafted_poly->vlist->vtx[0])-1),2)) *vtx->grafted_poly->k;
+	}
+*/
 //   fprintf(stderr, "DE=%f\n",delta_energy);
     //MONTE CARLOOOOOOOO
     if(delta_energy>=0){
@@ -86,13 +127,9 @@
     {
     //not accepted, reverting changes
 	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]);
+		vtx->neigh[i]=memcpy((void *)vtx->neigh[i],(void *)&backupvtx[i+1],sizeof(ts_vertex));
 	}
-//	free(backupvtx);
-//	fprintf(stderr,"Reverted\n");
 	
     //update the normals of triangles that share bead i.
    for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);
@@ -100,16 +137,224 @@
     return TS_FAIL; 
     }
 }
+		
+//	oldcellidx=vertex_self_avoidance(vesicle, &backupvtx[0]);
+	if(vtx->cell!=vesicle->clist->cell[cellidx]){
+		retval=cell_add_vertex(vesicle->clist->cell[cellidx],vtx);
+//		if(retval==TS_SUCCESS) cell_remove_vertex(vesicle->clist->cell[oldcellidx],vtx);
+		if(retval==TS_SUCCESS) cell_remove_vertex(backupvtx[0].cell,vtx);
+		
+	}
+//	if(oldcellidx);
     //END MONTE CARLOOOOOOO
-
-    //TODO: change cell occupation if necessary!
-//	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;
 }
 
+
+ts_bool single_poly_vertex_move(ts_vesicle *vesicle,ts_poly *poly,ts_vertex *vtx,ts_double *rn){
+	ts_uint i;
+	ts_bool retval; 
+	ts_uint cellidx; 
+//	ts_double delta_energy;
+	ts_double costheta,sintheta,phi,r;
+	ts_double dist;
+	//This will hold all the information of vtx and its neighbours
+	ts_vertex backupvtx;
+//	ts_bond backupbond[2];
+	memcpy((void *)&backupvtx,(void *)vtx,sizeof(ts_vertex));
+
+	//random move in a sphere with radius stepsize:
+	r=vesicle->stepsize*rn[0];
+	phi=rn[1]*2*M_PI;
+	costheta=2*rn[2]-1;
+	sintheta=sqrt(1-pow(costheta,2));
+	vtx->x=vtx->x+r*sintheta*cos(phi);
+	vtx->y=vtx->y+r*sintheta*sin(phi);
+	vtx->z=vtx->z+r*costheta;
+
+
+	//distance with neighbours check
+	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,sizeof(ts_vertex));
+			return TS_FAIL;
+		}
+	}
+
+// Distance with grafted vesicle-vertex check:	
+	if(vtx==poly->vlist->vtx[0]){
+		dist=vtx_distance_sq(vtx,poly->grafted_vtx);
+        if(dist<1.0 || dist>vesicle->dmax) {
+		vtx=memcpy((void *)vtx,(void *)&backupvtx,sizeof(ts_vertex));
+		return TS_FAIL;
+		}
+	}
+
+
+	//self avoidance check with distant vertices
+	cellidx=vertex_self_avoidance(vesicle, vtx);
+	//check occupation number
+	retval=cell_occupation_number_and_internal_proximity(vesicle->clist,cellidx,vtx);
+	
+	if(retval==TS_FAIL){
+		vtx=memcpy((void *)vtx,(void *)&backupvtx,sizeof(ts_vertex));
+        return TS_FAIL;
+	} 
+
+
+	//if all the tests are successful, then energy for vtx and neighbours is calculated
+/* Energy ignored for now!
+	delta_energy=0;
+	for(i=0;i<vtx->bond_no;i++){
+		memcpy((void *)&backupbond[i],(void *)vtx->bond[i],sizeof(ts_bond));
+
+		vtx->bond[i]->bond_length=sqrt(vtx_distance_sq(vtx->bond[i]->vtx1,vtx->bond[i]->vtx2));
+		bond_energy(vtx->bond[i],poly);
+		delta_energy+= vtx->bond[i]->energy - backupbond[i].energy;
+	}
+
+	if(vtx==poly->vlist->vtx[0]){
+		delta_energy+=
+			(pow(sqrt(vtx_distance_sq(vtx, poly->grafted_vtx)-1),2)-
+			pow(sqrt(vtx_distance_sq(&backupvtx, poly->grafted_vtx)-1),2)) *poly->k;
+		
+	}
+
+
+	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
+	vtx=memcpy((void *)vtx,(void *)&backupvtx,sizeof(ts_vertex));
+	for(i=0;i<vtx->bond_no;i++){
+	vtx->bond[i]=memcpy((void *)vtx->bond[i],(void *)&backupbond[i],sizeof(ts_bond));
+	}
+
+    return TS_FAIL; 
+	}
+	}
+*/
+		
+//	oldcellidx=vertex_self_avoidance(vesicle, &backupvtx[0]);
+	if(vtx->cell!=vesicle->clist->cell[cellidx]){
+		retval=cell_add_vertex(vesicle->clist->cell[cellidx],vtx);
+//		if(retval==TS_SUCCESS) cell_remove_vertex(vesicle->clist->cell[oldcellidx],vtx);
+		if(retval==TS_SUCCESS) cell_remove_vertex(backupvtx.cell,vtx);	
+	}
+//	if(oldcellidx);
+    //END MONTE CARLOOOOOOO
+    return TS_SUCCESS;
+}
+
+
+
+
+ts_bool single_filament_vertex_move(ts_vesicle *vesicle,ts_poly *poly,ts_vertex *vtx,ts_double *rn){
+	ts_uint i;
+	ts_bool retval; 
+	ts_uint cellidx; 
+//	ts_double delta_energy;
+	ts_double costheta,sintheta,phi,r;
+	ts_double dist[2];
+	//This will hold all the information of vtx and its neighbours
+	ts_vertex backupvtx;
+	ts_bond backupbond[2];
+	memcpy((void *)&backupvtx,(void *)vtx,sizeof(ts_vertex));
+
+	//random move in a sphere with radius stepsize:
+	r=vesicle->stepsize*rn[0];
+	phi=rn[1]*2*M_PI;
+	costheta=2*rn[2]-1;
+	sintheta=sqrt(1-pow(costheta,2));
+	vtx->x=vtx->x+r*sintheta*cos(phi);
+	vtx->y=vtx->y+r*sintheta*sin(phi);
+	vtx->z=vtx->z+r*costheta;
+
+
+	//distance with neighbours check
+	for(i=0;i<vtx->bond_no;i++){
+		dist[i]=vtx_distance_sq(vtx->bond[i]->vtx1,vtx->bond[i]->vtx2);
+		if(dist[i]<1.0 || dist[i]>vesicle->dmax) {
+			vtx=memcpy((void *)vtx,(void *)&backupvtx,sizeof(ts_vertex));
+			return TS_FAIL;
+		}
+	}
+
+
+	//self avoidance check with distant vertices
+	cellidx=vertex_self_avoidance(vesicle, vtx);
+	//check occupation number
+	retval=cell_occupation_number_and_internal_proximity(vesicle->clist,cellidx,vtx);
+	
+	if(retval==TS_FAIL){
+		vtx=memcpy((void *)vtx,(void *)&backupvtx,sizeof(ts_vertex));
+        return TS_FAIL;
+	} 
+
+	//backup bonds
+	for(i=0;i<vtx->bond_no;i++){
+		memcpy(&backupbond[i],vtx->bond[i], sizeof(ts_bond));
+		vtx->bond[i]->bond_length=sqrt(dist[i]);
+		bond_vector(vtx->bond[i]);
+		
+	}
+	
+	//if all the tests are successful, then energy for vtx and neighbours is calculated
+//	delta_energy=0;
+/*	for(i=0;i<vtx->neigh_no;i++){
+//		memcpy((void *)&backupbond[i],(void *)vtx->bond[i],sizeof(ts_bond));
+		xp = vtx->neigh[i]
+		vtx->bond[i]->bond_length=sqrt(vtx_distance_sq(vtx->bond[i]->vtx1,vtx->bond[i]->vtx2));
+		bond_energy(vtx->bond[i],poly);
+		delta_energy+= vtx->bond[i]->energy - backupbond[i].energy;
+	}
+
+	if(vtx==poly->vlist->vtx[0]){
+		delta_energy+=
+			(pow(sqrt(vtx_distance_sq(vtx, poly->grafted_vtx)-1),2)-
+			pow(sqrt(vtx_distance_sq(&backupvtx, poly->grafted_vtx)-1),2)) *poly->k;
+		
+	}
+
+
+	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
+	vtx=memcpy((void *)vtx,(void *)&backupvtx,sizeof(ts_vertex));
+	for(i=0;i<vtx->bond_no;i++){
+	vtx->bond[i]=memcpy((void *)vtx->bond[i],(void *)&backupbond[i],sizeof(ts_bond));
+	}
+
+    return TS_FAIL; 
+	}
+	}
+	
+*/	
+//	oldcellidx=vertex_self_avoidance(vesicle, &backupvtx[0]);
+	if(vtx->cell!=vesicle->clist->cell[cellidx]){
+		retval=cell_add_vertex(vesicle->clist->cell[cellidx],vtx);
+//		if(retval==TS_SUCCESS) cell_remove_vertex(vesicle->clist->cell[oldcellidx],vtx);
+		if(retval==TS_SUCCESS) cell_remove_vertex(backupvtx.cell,vtx);	
+	}
+//	if(oldcellidx);
+    //END MONTE CARLOOOOOOO
+    return TS_SUCCESS;
+}

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