From 6ff2f6ce1d60b7538f7935f0a2f2a98a2c9de3b7 Mon Sep 17 00:00:00 2001
From: James E McClure <jemcclur@gmail.com>
Date: Fri, 3 May 2019 21:54:50 -0400
Subject: [PATCH] use distance for re-init

---
 models/ColorModel.cpp | 24 ++++++++++++++++++++++--
 1 file changed, 22 insertions(+), 2 deletions(-)

diff --git a/models/ColorModel.cpp b/models/ColorModel.cpp
index fd7bc935..d73cbee8 100644
--- a/models/ColorModel.cpp
+++ b/models/ColorModel.cpp
@@ -877,12 +877,32 @@ double ScaLBL_ColorModel::MorphOpenConnected(double target_volume_change){
 					n=k*nx*ny+j*nx+i;
 					// only apply opening to connected component 
 					if ( id_connected[n] == 1){
-						phase(i,j,k) = 1.0;
+						id_solid(i,j,k) = 0;
+					}
+					else{
+						id_solid(i,j,k) = 1;
 					}
 				}
 			}
 		}
-
+		CalcDist(distance,id_solid,*Dm);
+		
+		// re-initialize
+		double beta = 0.95;
+		for (int k=0; k<nz; k++){
+			for (int j=0; j<ny; j++){
+				for (int i=0; i<nx; i++){
+					n=k*nx*ny+j*nx+i;
+					double d = distance(i,j,k);
+					if (Averages->SDs(i,j,k) > 0.f){
+						if (d < 3.f){
+							phase(i,j,k) = (2.f*(exp(-2.f*beta*d))/(1.f+exp(-2.f*beta*d))-1.f);	
+						}
+					}
+				} 
+			}
+		}
+		
 		int count_morphopen=0.0;
 		for (int k=1; k<nz-1; k++){
 			for (int j=1; j<ny-1; j++){