From b2fa8c6b55c420c079f285224f8d56ed03939767 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@fe.uni-lj.si>
Date: Tue, 29 Apr 2014 18:13:26 +0000
Subject: [PATCH] Bondflip doesnt segfaults anymore. Bondflip is disabled, debugging vertexmove

---
 src/vertexmove.c |  397 +++++++++++++++++++++++++++++++++++++++++++++++++-------
 1 files changed, 343 insertions(+), 54 deletions(-)

diff --git a/src/vertexmove.c b/src/vertexmove.c
index 7edbf04..9f263c8 100644
--- a/src/vertexmove.c
+++ b/src/vertexmove.c
@@ -9,74 +9,134 @@
 #include "timestep.h"
 #include "cell.h"
 //#include "io.h"
+#include "io.h"
 #include<stdio.h>
 #include "vertexmove.h"
+#include <string.h>
+#include "constvol.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 xold,yold,zold;
-    ts_double delta_energy,oenergy;
-    ts_vertex *ovtx;
-    ts_vertex *tvtx=(ts_vertex *)calloc(1,sizeof(ts_vertex));
+    ts_double delta_energy, delta_energy_cv,oenergy,dvol=0.0;
     ts_double costheta,sintheta,phi,r;
+	//This will hold all the information of vtx and its neighbours
+	ts_vertex backupvtx[20], *constvol_vtx_moved=NULL, *constvol_vtx_backup=NULL;
+	memcpy((void *)&backupvtx[0],(void *)vtx,sizeof(ts_vertex));
 
-    //randomly we move the temporary vertex
-//    tvtx->x=vtx->x+vesicle->stepsize*(2.0*rn[0]-1.0);
-//    tvtx->y=vtx->y+vesicle->stepsize*(2.0*rn[1]-1.0);
-//    tvtx->z=vtx->z+vesicle->stepsize*(2.0*rn[2]-1.0);
+	//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);
+
 	//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));
-	tvtx->x=vtx->x+r*sintheta*cos(phi);
-	tvtx->y=vtx->y+r*sintheta*sin(phi);
-	tvtx->z=vtx->z+r*costheta;
-    //check we if some length to neighbours are too much
+	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(tvtx,vtx->neigh[i]);
+        dist=vtx_distance_sq(vtx,vtx->neigh[i]);
         if(dist<1.0 || dist>vesicle->dmax) {
-		vtx_free(tvtx);
-//	fprintf(stderr,"Fail 1, dist=%f, vesicle->dmax=%f\n", 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, tvtx);
-    //check occupation number
-     retval=cell_occupation_number_and_internal_proximity(vesicle->clist,cellidx,vtx,tvtx);
+
+// 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;
+		}
+	}
+
+// TODO: Maybe faster if checks only nucleus-neighboring cells
+// Nucleus penetration check:
+	if (vtx->x*vtx->x + vtx->y*vtx->y + vtx->z*vtx->z < vesicle->R_nucleus){
+		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,vtx);
+
     if(retval==TS_FAIL){
-	vtx_free(tvtx);
-//	fprintf(stderr,"Fail 2\n");
+		vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
         return TS_FAIL;
     } 
-    
-    //if all the tests are successful, then we update the vertex position
-    xold=vtx->x;
-    yold=vtx->y;
-    zold=vtx->z;
-    ovtx=malloc(sizeof(ts_vertex));
-    vtx_copy(ovtx,vtx);
-    vtx->x=tvtx->x;
-    vtx->y=tvtx->y;
-    vtx->z=tvtx->z;
+   
+ 
+    //if all the tests are successful, then energy for vtx and neighbours is calculated
+	for(i=0;i<vtx->neigh_no;i++){
+	memcpy((void *)&backupvtx[i+1],(void *)vtx->neigh[i],sizeof(ts_vertex));
+	}
+
+	if(vesicle->pswitch == 1 || vesicle->tape->constvolswitch==1){
+		for(i=0;i<vtx->tristar_no;i++) dvol-=vtx->tristar[i]->volume;
+	};
 
     delta_energy=0;
+
+ 
+//    fprintf(stderr,"Success for now.\n");
+
     //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 - ovtx->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 || vesicle->tape->constvolswitch == 1){
+		for(i=0;i<vtx->tristar_no;i++) dvol+=vtx->tristar[i]->volume;
+        if(vesicle->pswitch==1) delta_energy-=vesicle->pressure*dvol;
+	};
+
+   if(vesicle->tape->constvolswitch == 1){
+        retval=constvolume(vesicle, vtx, dvol, &delta_energy_cv, &constvol_vtx_moved,&constvol_vtx_backup);
+        if(retval==TS_FAIL){ // if we couldn't move the vertex to assure constant volume
+            vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
+	        for(i=0;i<vtx->neigh_no;i++){
+		        vtx->neigh[i]=memcpy((void *)vtx->neigh[i],(void *)&backupvtx[i+1],sizeof(ts_vertex));
+	        }
+            for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]); 
+            return TS_FAIL;
+        }
+    delta_energy+=delta_energy_cv;
+    }
+/* 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){
@@ -91,30 +151,259 @@
 #endif
     {
     //not accepted, reverting changes
-    vtx->x=xold;
-    vtx->y=yold;
-    vtx->z=zold;
+  //  fprintf(stderr,"MC failed\n");
+	vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
+	for(i=0;i<vtx->neigh_no;i++){
+		vtx->neigh[i]=memcpy((void *)vtx->neigh[i],(void *)&backupvtx[i+1],sizeof(ts_vertex));
+	}
+	
     //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
-    energy_vertex(vtx);
-    //the same is done for neighbouring vertices
-	for(i=0;i<vtx->neigh_no;i++) energy_vertex(vtx->neigh[i]);
-	free(ovtx->bond_length);
-    free(ovtx->bond_length_dual);
-    free(ovtx);
-    vtx_free(tvtx);
+   for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);
+
+    if(vesicle->tape->constvolswitch == 1){
+        constvolumerestore(constvol_vtx_moved,constvol_vtx_backup);
+    }
     return TS_FAIL; 
     }
 }
-    //END MONTE CARLOOOOOOO
+	//accepted	
+ //   fprintf(stderr,"MC accepted\n");
+//	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);
+		
+	}
 
-    //TODO: change cell occupation if necessary!
-//	fprintf(stderr,"Success!!\n");
-    free(ovtx->bond_length);
-    free(ovtx->bond_length_dual);
-    free(ovtx);
-    vtx_free(tvtx);
+    if(vesicle->tape->constvolswitch == 1){
+        constvolumeaccept(vesicle,constvol_vtx_moved,constvol_vtx_backup);
+    }
+//	if(oldcellidx);
+    //END MONTE CARLOOOOOOO
     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,backupneigh[2];
+	ts_bond backupbond[2];
+
+	//backup vertex:		
+	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;
+		}
+	}
+
+// TODO: Maybe faster if checks only nucleus-neighboring cells
+// Nucleus penetration check:
+	if (vtx->x*vtx->x + vtx->y*vtx->y + vtx->z*vtx->z < vesicle->R_nucleus){
+		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]);
+	}
+
+	//backup neighboring vertices:
+	for(i=0;i<vtx->neigh_no;i++){
+		memcpy(&backupneigh[i],vtx->neigh[i], sizeof(ts_vertex));
+	}
+	
+	//if all the tests are successful, then energy for vtx and neighbours is calculated
+	delta_energy=0;
+	
+	if(vtx->bond_no == 2){
+		vtx->energy = -(vtx->bond[0]->x*vtx->bond[1]->x + vtx->bond[0]->y*vtx->bond[1]->y + vtx->bond[0]->z*vtx->bond[1]->z)/vtx->bond[0]->bond_length/vtx->bond[1]->bond_length;
+		delta_energy += vtx->energy - backupvtx.energy;
+	}
+
+	for(i=0;i<vtx->neigh_no;i++){
+		if(vtx->neigh[i]->bond_no == 2){
+			vtx->neigh[i]->energy = -(vtx->neigh[i]->bond[0]->x*vtx->neigh[i]->bond[1]->x + vtx->neigh[i]->bond[0]->y*vtx->neigh[i]->bond[1]->y + vtx->neigh[i]->bond[0]->z*vtx->neigh[i]->bond[1]->z)/vtx->neigh[i]->bond[0]->bond_length/vtx->neigh[i]->bond[1]->bond_length;
+			delta_energy += vtx->neigh[i]->energy - backupneigh[i].energy;
+		}
+	}
+
+	// poly->k is filament persistence length (in units l_min)
+	delta_energy *= 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->neigh_no;i++){
+		memcpy(vtx->neigh[i],&backupneigh[i],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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