From d43116b7d609fa9cabae4068d037c1af3a20dae8 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Thu, 08 Aug 2019 17:42:46 +0000
Subject: [PATCH] An attempt to fix polymer error while recreating vesicle from vtu.

---
 src/initial_distribution.c |   35 ++++++++++++++++++++++++++++++++---
 1 files changed, 32 insertions(+), 3 deletions(-)

diff --git a/src/initial_distribution.c b/src/initial_distribution.c
index 45a4124..87cfb68 100644
--- a/src/initial_distribution.c
+++ b/src/initial_distribution.c
@@ -43,7 +43,10 @@
 
 	vesicle=initial_distribution_dipyramid(tape->nshell,tape->ncxmax,tape->ncymax,tape->nczmax,tape->stepsize);
     	vesicle->tape=tape;
+	vesicle->clist->dmin_interspecies = tape->dmin_interspecies*tape->dmin_interspecies;
+	vesicle->poly_list=init_poly_list(tape->npoly,tape->nmono, vesicle->vlist, vesicle);
 	set_vesicle_values_from_tape(vesicle);
+		initial_population_with_c0(vesicle,tape);
 	return vesicle;
 }
 
@@ -58,7 +61,7 @@
 	vesicle->clist->dmin_interspecies = tape->dmin_interspecies*tape->dmin_interspecies;
 
 	//Initialize grafted polymers (brush):
-	vesicle->poly_list=init_poly_list(tape->npoly,tape->nmono, vesicle->vlist, vesicle);
+	//vesicle->poly_list=init_poly_list(tape->npoly,tape->nmono, vesicle->vlist, vesicle);
 	vesicle->spring_constant=tape->kspring;
 	poly_assign_spring_const(vesicle);
 
@@ -100,7 +103,7 @@
 	vesicle->clist->ncmax[0]=tape->ncxmax;
 	vesicle->clist->ncmax[1]=tape->ncymax;
 	vesicle->clist->ncmax[2]=tape->nczmax;
-	vesicle->clist->max_occupancy=8; /* hard coded max occupancy? */
+	vesicle->clist->max_occupancy=16; /* hard coded max occupancy? */
 
 	vesicle->pressure= tape->pressure;
 	vesicle->pswitch=tape->pswitch;
@@ -110,12 +113,38 @@
     else {
         vesicle->sphHarmonics=NULL;
     }
+
+	vesicle->tlist->a0=sqrt(3)/4*pow((vesicle->tape->dmax+1.0)/2.0,2);  
     return TS_SUCCESS;
 
 }
 
 
-
+ts_bool initial_population_with_c0(ts_vesicle *vesicle, ts_tape *tape){
+	int rndvtx,i,j;
+	if(tape->number_of_vertices_with_c0>0){
+//		ts_fprintf(stderr,"Setting values for spontaneous curvature as defined in tape\n");
+		j=0;
+		for(i=0;i<tape->number_of_vertices_with_c0;i++){
+			rndvtx=rand() % vesicle->vlist->n;
+			if(fabs(vesicle->vlist->vtx[rndvtx]->c-tape->c0)<1e-15){
+				j++;
+				i--;
+				if(j>10*vesicle->vlist->n){
+					fatal("cannot populate vesicle with vertices with spontaneous curvature. Too many spontaneous curvature vertices?",100);
+				}
+				continue;
+			}
+			vesicle->vlist->vtx[rndvtx]->c=tape->c0;
+		}
+		mean_curvature_and_energy(vesicle);
+		if(fabs(tape->w)>1e-16){ //if nonzero energy
+//			ts_fprintf(stderr,"Setting attraction between vertices with spontaneous curvature\n");
+			sweep_attraction_bond_energy(vesicle);
+		}
+	}
+	return TS_SUCCESS;
+}
 
 
 ts_bool pentagonal_dipyramid_vertex_distribution(ts_vertex_list *vlist){

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