From 2c4278db6ead5c27e30a3000097ed898c968534e Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Sat, 09 Mar 2019 19:45:22 +0000
Subject: [PATCH] Added direct force plugin and fixes in stretching energy

---
 src/vertexmove.c |  419 ++++++++++++++++++++++++++++++++++++++++++++++++++---------
 1 files changed, 351 insertions(+), 68 deletions(-)

diff --git a/src/vertexmove.c b/src/vertexmove.c
index c8ce697..362b895 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"
@@ -8,69 +9,239 @@
 #include "energy.h"
 #include "timestep.h"
 #include "cell.h"
-//#include "io.h"
+#include "io.h"
 #include<stdio.h>
 #include "vertexmove.h"
+#include <string.h>
+#include "constvol.h"
+#include "plugins.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_vertex *tvtx=(ts_vertex *)calloc(1,sizeof(ts_vertex));
-//	tvtx->data=init_vertex_data();
     ts_bool retval; 
     ts_uint cellidx; 
-    ts_double xold,yold,zold;
-    ts_double delta_energy,oenergy;
-    ts_vertex *ovtx;
+    ts_double delta_energy, oenergy;
+    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);
-    //check we if some length to neighbours are too much
-    for(i=0;i<vtx->neigh_no;i++){
-        dist=vtx_distance_sq(tvtx,vtx->neigh[i]);
-        if(dist<1.0 || dist>vesicle->dmax) {
-		vtx_free(tvtx);
-		return TS_FAIL;
+    //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;
+
+
+/* Entry point for plugin vm_hard_constraint() function */
+	vesicle->plist->pointer=vesicle->plist->chain->vm_hard_constraint;
+	while(vesicle->plist->pointer!=NULL){
+		retval = vesicle->plist->pointer->plugin->function->vm_hard_constraint(vesicle,vtx, &backupvtx[0]);
+		if(retval==TS_FAIL){
+			vtx=memcpy((void *)vtx,(void *)&backupvtx[0],sizeof(ts_vertex));
+			return TS_FAIL;
 		}
-    }
-//fprintf(stderr,"Was here!\n");
-    //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);
-    if(retval==TS_FAIL){
-	vtx_free(tvtx);
-        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;
+		vesicle->plist->pointer=vesicle->plist->pointer->next;
+	}
+/* End of vm_hard_constraint() */
 
-    delta_energy=0;
-    //update the normals of triangles that share bead i.
+/* Backuping the neighbours */ 
+	for(i=0;i<vtx->neigh_no;i++){
+	memcpy((void *)&backupvtx[i+1],(void *)vtx->neigh[i],sizeof(ts_vertex));
+	}
+
+/* Entry point for plugin vm_energy_before_prepare() */
+
+	vesicle->plist->pointer=vesicle->plist->chain->vm_energy_before_prepare;
+	while(vesicle->plist->pointer!=NULL){
+		vesicle->plist->pointer->plugin->function->vm_energy_before_prepare(vesicle, vtx);
+		vesicle->plist->pointer=vesicle->plist->pointer->next;
+	}
+/* End of vm_energy_before_prepare() */
+
+//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);
     }
-//    fprintf(stderr, "DE=%f\n",delta_energy);
+
+/* Entry point for plugin vm_energy_after_execute() */
+
+	vesicle->plist->pointer=vesicle->plist->chain->vm_energy_after_execute;
+	while(vesicle->plist->pointer!=NULL){
+		delta_energy+=vesicle->plist->pointer->plugin->function->vm_energy_after_execute(vesicle, vtx, backupvtx);
+		vesicle->plist->pointer=vesicle->plist->pointer->next;
+	}
+/* End of vm_energy_after_execute() */
+
+
+/* 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;
+	}
+*/
+
+
+/* Entry point for plugin vm_before_montecarlo_constraint() function */
+	vesicle->plist->pointer=vesicle->plist->chain->vm_before_montecarlo_constraint;
+	while(vesicle->plist->pointer!=NULL){
+		retval = vesicle->plist->pointer->plugin->function->vm_before_montecarlo_constraint(vesicle,vtx, &backupvtx[0]);
+		if(retval==TS_FAIL){
+			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;
+		}
+		vesicle->plist->pointer=vesicle->plist->pointer->next;
+	}
+/* End of vm_before_montecarlo_constraint() */
+
+
+
+
+
+//   fprintf(stderr, "DE=%f\n",delta_energy);
     //MONTE CARLOOOOOOOO
     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
+    {
+/*************************************************** MC step rejected **************************************************************/
+	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]);
+
+
+/* Entry point for plugin vm_before_montecarlo_constraint() function */
+	vesicle->plist->pointer=vesicle->plist->chain->vm_new_state_rejected;
+	while(vesicle->plist->pointer!=NULL){
+		vesicle->plist->pointer->plugin->function->vm_new_state_rejected(vesicle,vtx, &backupvtx[0]);
+		vesicle->plist->pointer=vesicle->plist->pointer->next;
+	}
+/* End of vm_before_montecarlo_constraint() */
+
+
+    return TS_FAIL; 
+    }
+}
+/*************************************************** MC step accepted **************************************************************/
+	cellidx=vertex_self_avoidance(vesicle, vtx);
+	if(vtx->cell!=vesicle->clist->cell[cellidx]){
+		retval=cell_add_vertex(vesicle->clist->cell[cellidx],vtx);
+		if(retval==TS_SUCCESS) cell_remove_vertex(backupvtx[0].cell,vtx);	
+	}
+
+/* Entry point for plugin vm_before_montecarlo_constraint() function */
+	vesicle->plist->pointer=vesicle->plist->chain->vm_new_state_accepted;
+	while(vesicle->plist->pointer!=NULL){
+		vesicle->plist->pointer->plugin->function->vm_new_state_accepted(vesicle,vtx, &backupvtx[0]);
+		vesicle->plist->pointer=vesicle->plist->pointer->next;
+	}
+/* End of vm_before_montecarlo_constraint() */
+
+    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
@@ -80,32 +251,144 @@
 #ifdef TS_DOUBLE_LONGDOUBLE
         if(expl(-delta_energy)< (ts_ldouble)drand48())
 #endif
-    {
-    //not accepted, reverting changes
-    vtx->x=xold;
-    vtx->y=yold;
-    vtx->z=zold;
-    //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);
+    	{
+	//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
-
-    //TODO: change cell occupation if necessary!
-
-    free(ovtx->bond_length);
-    free(ovtx->bond_length_dual);
-    free(ovtx);
-    vtx_free(tvtx);
     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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