From 59ffd7bfd66cbfa609386a069bd45aa34ba943bf Mon Sep 17 00:00:00 2001
From: Rex Zhe Li <zhe.rex.li@gmail.com>
Date: Thu, 20 Aug 2020 22:47:10 -0400
Subject: [PATCH] fix several miscellaneous bugs

---
 models/IonModel.cpp                         | 20 +++++++++++---------
 models/PoissonSolver.cpp                    |  2 +-
 models/StokesModel.cpp                      | 17 +++++++++--------
 tests/lbpm_electrokinetic_dfh_simulator.cpp |  3 +++
 4 files changed, 24 insertions(+), 18 deletions(-)

diff --git a/models/IonModel.cpp b/models/IonModel.cpp
index d6265abe..55c848b9 100644
--- a/models/IonModel.cpp
+++ b/models/IonModel.cpp
@@ -48,6 +48,15 @@ void ScaLBL_IonModel::ReadParams(string filename,int num_iter,int num_iter_Stoke
     tau.push_back(0.5+k2_inv*time_conv/(h*1.0e-6)/(h*1.0e-6)*IonDiffusivity[0]);
     //--------------------------------------------------------------------------//
 
+	// Read domain parameters
+	if (domain_db->keyExists( "voxel_length" )){//default unit: um/lu
+		h = domain_db->getScalar<double>( "voxel_length" );
+	}
+    BoundaryCondition = 0;
+	if (domain_db->keyExists( "BC" )){
+		BoundaryCondition = domain_db->getScalar<int>( "BC" );
+	}
+
 	// LB-Ion Model parameters		
 	//if (ion_db->keyExists( "timestepMax" )){
 	//	timestepMax = ion_db->getScalar<int>( "timestepMax" );
@@ -112,14 +121,6 @@ void ScaLBL_IonModel::ReadParams(string filename,int num_iter,int num_iter_Stoke
 		BoundaryConditionSolid = ion_db->getScalar<int>( "BC_Solid" );
 	}
 
-	// Read domain parameters
-	if (domain_db->keyExists( "voxel_length" )){//default unit: um/lu
-		h = domain_db->getScalar<double>( "voxel_length" );
-	}
-    BoundaryCondition = 0;
-	if (domain_db->keyExists( "BC" )){
-		BoundaryCondition = domain_db->getScalar<int>( "BC" );
-	}
 
 	if (rank==0) printf("*****************************************************\n");
 	if (rank==0) printf("LB Ion Transport Solver: \n");
@@ -275,7 +276,7 @@ void ScaLBL_IonModel::AssignSolidBoundary(double *ion_solid)
 		label_count_global[idx]=sumReduce( Dm->Comm, label_count[idx]);
 
 	if (rank==0){
-		printf("LB Ion Solver: Ion Solid labels: %lu \n",NLABELS);
+		printf("LB Ion Solver: number of ion solid labels: %lu \n",NLABELS);
 		for (unsigned int idx=0; idx<NLABELS; idx++){
 			VALUE=LabelList[idx];
 			AFFINITY=AffinityList[idx];
@@ -464,6 +465,7 @@ void ScaLBL_IonModel::Run(double *Velocity, double *ElectricField){
 void ScaLBL_IonModel::getIonConcentration(){
 	for (int ic=0; ic<number_ion_species; ic++){
         ScaLBL_IonConcentration_Phys(Ci, h, ic, ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np);
+        ScaLBL_IonConcentration_Phys(Ci, h, ic, 0, ScaLBL_Comm->LastExterior(), Np);
     }
 
     DoubleArray PhaseField(Nx,Ny,Nz);
diff --git a/models/PoissonSolver.cpp b/models/PoissonSolver.cpp
index 3cf8a6d2..701c009c 100644
--- a/models/PoissonSolver.cpp
+++ b/models/PoissonSolver.cpp
@@ -224,7 +224,7 @@ void ScaLBL_Poisson::AssignSolidBoundary(double *poisson_solid)
 		label_count_global[idx]=sumReduce( Dm->Comm, label_count[idx]);
 
 	if (rank==0){
-		printf("LB-Poisson Solver: Poisson Solid labels: %lu \n",NLABELS);
+		printf("LB-Poisson Solver: number of Poisson solid labels: %lu \n",NLABELS);
 		for (unsigned int idx=0; idx<NLABELS; idx++){
 			VALUE=LabelList[idx];
 			AFFINITY=AffinityList[idx];
diff --git a/models/StokesModel.cpp b/models/StokesModel.cpp
index 1b733745..41520253 100644
--- a/models/StokesModel.cpp
+++ b/models/StokesModel.cpp
@@ -40,6 +40,15 @@ void ScaLBL_StokesModel::ReadParams(string filename,int num_iter){
     Ez = 1.0e-3;
     //--------------------------------------------------------------------------//
 
+	// Read domain parameters
+    BoundaryCondition = 0;
+	if (domain_db->keyExists( "BC" )){
+		BoundaryCondition = domain_db->getScalar<int>( "BC" );
+	}
+	if (domain_db->keyExists( "voxel_length" )){//default unit: um/lu
+		h = domain_db->getScalar<double>( "voxel_length" );
+	}
+
 	// Single-fluid Navier-Stokes Model parameters
 	//if (stokes_db->keyExists( "timestepMax" )){
 	//	timestepMax = stokes_db->getScalar<int>( "timestepMax" );
@@ -75,14 +84,6 @@ void ScaLBL_StokesModel::ReadParams(string filename,int num_iter){
 	if (stokes_db->keyExists( "flux" )){
 		flux = stokes_db->getScalar<double>( "flux" );
 	}	
-	
-	// Read domain parameters
-	if (domain_db->keyExists( "BC" )){
-		BoundaryCondition = domain_db->getScalar<int>( "BC" );
-	}
-	if (domain_db->keyExists( "voxel_length" )){//default unit: um/lu
-		h = domain_db->getScalar<double>( "voxel_length" );
-	}
 
     // Re-calculate model parameters due to parameter read
 	mu=(tau-0.5)/3.0;
diff --git a/tests/lbpm_electrokinetic_dfh_simulator.cpp b/tests/lbpm_electrokinetic_dfh_simulator.cpp
index 7cf835da..156fbc18 100644
--- a/tests/lbpm_electrokinetic_dfh_simulator.cpp
+++ b/tests/lbpm_electrokinetic_dfh_simulator.cpp
@@ -98,6 +98,9 @@ int main(int argc, char **argv)
         PoissonSolver.getElectricalPotential();
         IonModel.getIonConcentration();
 
+        if (rank==0) printf("Maximum timestep is reached and the simulation is completed\n");
+        if (rank==0) printf("*************************************************************\n");
+
         PROFILE_STOP("Main");
         PROFILE_SAVE("lbpm_electrokinetic_simulator",1);
         // ****************************************************