From fc6f3ef0a9822f3d5f06d38e556dbb5f2e985f4a Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Wed, 13 Jul 2016 17:33:28 +0000
Subject: [PATCH] First attempt in solving an issue of dense packed internal pegs. They are recreated as many times as needed.

---
 src/vertexmove.c |  304 ++++++++++++++++++++++++++++++++++++++++++++++----
 1 files changed, 279 insertions(+), 25 deletions(-)

diff --git a/src/vertexmove.c b/src/vertexmove.c
index f78fd61..fb74a06 100644
--- a/src/vertexmove.c
+++ b/src/vertexmove.c
@@ -1,3 +1,4 @@
+/* vim: set ts=4 sts=4 sw=4 noet : */
 #include<stdlib.h>
 #include<math.h>
 #include "general.h"
@@ -9,19 +10,21 @@
 #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_uint i;
     ts_double dist;
     ts_bool retval; 
     ts_uint cellidx; 
-    ts_double delta_energy,oenergy;
+    ts_double delta_energy, delta_energy_cv,oenergy,dvol=0.0, darea=0.0;
     ts_double costheta,sintheta,phi,r;
 	//This will hold all the information of vtx and its neighbours
-	ts_vertex backupvtx[20];
+	ts_vertex backupvtx[20], *constvol_vtx_moved=NULL, *constvol_vtx_backup=NULL;
 	memcpy((void *)&backupvtx[0],(void *)vtx,sizeof(ts_vertex));
 
 	//Some stupid tests for debugging cell occupation!
@@ -39,7 +42,7 @@
 //    	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:
+//random move in a sphere with radius stepsize:
 	r=vesicle->stepsize*rn[0];
 	phi=rn[1]*2*M_PI;
 	costheta=2*rn[2]-1;
@@ -49,33 +52,73 @@
 	vtx->z=vtx->z+r*costheta;
 
 
-    	//distance with neighbours check
+//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));
+    		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,vtx);
-	
+	}
+
+// TODO: Maybe faster if checks only nucleus-neighboring cells
+// Nucleus penetration check:
+//#define SQ(x) x*x
+if(vesicle->R_nucleus>0.0){
+	if ((vtx->x-vesicle->nucleus_center[0])*(vtx->x-vesicle->nucleus_center[0])+ (vtx->y-vesicle->nucleus_center[1])*(vtx->y-vesicle->nucleus_center[1]) + (vtx->z-vesicle->nucleus_center[2])*(vtx->z-vesicle->nucleus_center[2]) < vesicle->R_nucleus){
+		vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
+		return TS_FAIL;
+	}
+} else if(vesicle->R_nucleusX>0.0){
+//	fprintf(stderr,"DEBUG, (Rx, Ry,Rz)^2=(%f,%f,%f)\n",vesicle->R_nucleusX, vesicle->R_nucleusY, vesicle->R_nucleusZ);
+//	if (SQ(vtx->x-vesicle->nucleus_center[0])/vesicle->R_nucleusX + SQ(vtx->y-vesicle->nucleus_center[1])/vesicle->R_nucleusY + SQ(vtx->z-vesicle->nucleus_center[2])/vesicle->R_nucleusZ < 1.0){
+	if ((vtx->x-vesicle->nucleus_center[0])*(vtx->x-vesicle->nucleus_center[0])/vesicle->R_nucleusX + (vtx->y-vesicle->nucleus_center[1])*(vtx->y-vesicle->nucleus_center[1])/vesicle->R_nucleusY + (vtx->z-vesicle->nucleus_center[2])*(vtx->z-vesicle->nucleus_center[2])/vesicle->R_nucleusZ < 1.0){
+//	if (SQ(vtx->x)/vesicle->R_nucleusX + SQ(vtx->y)/vesicle->R_nucleusY + SQ(vtx->z)/vesicle->R_nucleusZ < 1.0){
+		vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
+		return TS_FAIL;
+	}
+
+}
+//#undef SQ
+//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[0],sizeof(ts_vertex));
         return TS_FAIL;
     } 
    
  
-    //if all the tests are successful, then energy for vtx and neighbours is calculated
+//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>0){
+		for(i=0;i<vtx->tristar_no;i++) dvol-=vtx->tristar[i]->volume;
+	}
 
+    if(vesicle->tape->constareaswitch==2){
+		for(i=0;i<vtx->tristar_no;i++) darea-=vtx->tristar[i]->area;
+    
+    }
 
     delta_energy=0;
+    
+//    vesicle_volume(vesicle);
+//    fprintf(stderr,"Volume in the beginning=%1.16e\n", vesicle->volume);
+
     //update the normals of triangles that share bead i.
     for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);
 	oenergy=vtx->energy;
@@ -88,19 +131,76 @@
         delta_energy+=vtx->neigh[i]->xk*(vtx->neigh[i]->energy-oenergy);
     }
 
+	if(vesicle->pswitch == 1 || vesicle->tape->constvolswitch >0){
+		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->constareaswitch==2){
+        /* check whether the darea is gt epsarea */
+		for(i=0;i<vtx->tristar_no;i++) darea+=vtx->tristar[i]->area;
+        if(fabs(vesicle->area+darea-A0)>epsarea){
+	        //restore old state.
+ 			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]); 
+            		//fprintf(stderr,"fajlam!\n");
+            		return TS_FAIL;
+		}
+
+
+    }
+
+	if(vesicle->tape->constvolswitch==2){
+		/*check whether the dvol is gt than epsvol */
+			//fprintf(stderr,"DVOL=%1.16e\n",dvol);
+		if(fabs(vesicle->volume+dvol-V0)>epsvol){
+			//restore old state.
+ 			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]); 
+            		//fprintf(stderr,"fajlam!\n");
+            		return TS_FAIL;
+		}
+
+	} else
+//    vesicle_volume(vesicle);
+//    fprintf(stderr,"Volume before=%1.16e\n", vesicle->volume);
+   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]); 
+ //           fprintf(stderr,"fajlam!\n");
+            return TS_FAIL;
+        }
+//    vesicle_volume(vesicle);
+//    fprintf(stderr,"Volume after=%1.16e\n", vesicle->volume);
+//    fprintf(stderr,"Volume after-dvol=%1.16e\n", vesicle->volume-dvol);
+//    fprintf(stderr,"Denergy before=%e\n",delta_energy);
+    
+    delta_energy+=delta_energy_cv;
+//    fprintf(stderr,"Denergy after=%e\n",delta_energy);
+    }
+/* 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){
 #ifdef TS_DOUBLE_DOUBLE
-        if(exp(-delta_energy)< drand48() )
+        if(exp(-delta_energy)< drand48())
 #endif
 #ifdef TS_DOUBLE_FLOAT
         if(expf(-delta_energy)< (ts_float)drand48())
@@ -110,6 +210,7 @@
 #endif
     {
     //not accepted, reverting changes
+  //  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));
@@ -118,10 +219,18 @@
     //update the normals of triangles that share bead i.
    for(i=0;i<vtx->tristar_no;i++) triangle_normal_vector(vtx->tristar[i]);
 
+//    fprintf(stderr, "before vtx(x,y,z)=%e,%e,%e\n",constvol_vtx_moved->x, constvol_vtx_moved->y, constvol_vtx_moved->z);
+    if(vesicle->tape->constvolswitch == 1){
+        constvolumerestore(constvol_vtx_moved,constvol_vtx_backup);
+    }
+//    fprintf(stderr, "after vtx(x,y,z)=%e,%e,%e\n",constvol_vtx_moved->x, constvol_vtx_moved->y, constvol_vtx_moved->z);
+//    vesicle_volume(vesicle);
+//    fprintf(stderr,"Volume after fail=%1.16e\n", vesicle->volume);
     return TS_FAIL; 
     }
 }
-		
+	//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);
@@ -129,8 +238,21 @@
 		if(retval==TS_SUCCESS) cell_remove_vertex(backupvtx[0].cell,vtx);
 		
 	}
+
+    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;
+    }
 //	if(oldcellidx);
     //END MONTE CARLOOOOOOO
+//    vesicle_volume(vesicle);
+//    fprintf(stderr,"Volume after success=%1.16e\n", vesicle->volume);
     return TS_SUCCESS;
 }
 
@@ -139,11 +261,12 @@
 	ts_uint i;
 	ts_bool retval; 
 	ts_uint cellidx; 
-	ts_double delta_energy;
+//	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];
+//	ts_bond backupbond[2];
 	memcpy((void *)&backupvtx,(void *)vtx,sizeof(ts_vertex));
 
 	//random move in a sphere with radius stepsize:
@@ -157,13 +280,23 @@
 
 
 	//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));
-//	return TS_FAIL;
-//		}
-//	}
+	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);
@@ -177,6 +310,7 @@
 
 
 	//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));
@@ -214,6 +348,7 @@
     return TS_FAIL; 
 	}
 	}
+*/
 		
 //	oldcellidx=vertex_self_avoidance(vesicle, &backupvtx[0]);
 	if(vtx->cell!=vesicle->clist->cell[cellidx]){
@@ -225,3 +360,122 @@
     //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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