Adding skeleton for electrokinetic LBM

models/IonModel.h

@@ -0,0 +1,72 @@
+/*
+ * Multi-relaxation time LBM Model
+ */
+#include <stdio.h>
+#include <stdlib.h>
+#include <sys/stat.h>
+#include <iostream>
+#include <exception>
+#include <stdexcept>
+#include <fstream>
+
+#include "common/ScaLBL.h"
+#include "common/Communication.h"
+#include "common/MPI_Helpers.h"
+#include "analysis/Minkowski.h"
+#include "ProfilerApp.h"
+
+class ScaLBL_IonModel{
+public:
+	ScaLBL_IonModel(int RANK, int NP, MPI_Comm COMM);
+	~ScaLBL_IonModel();	
+	
+	// functions in they should be run
+	void ReadParams(string filename);
+	void ReadParams(std::shared_ptr<Database> db0);
+	void SetDomain();
+	void ReadInput();
+	void Create();
+	void Initialize();
+	void Run(double *Velocity);
+	void VelocityField();
+	
+	bool Restart,pBC;
+	int timestep,timestepMax;
+	int BoundaryCondition;
+	double tau,mu;
+	double Fx,Fy,Fz,flux;
+	double din,dout;
+	double tolerance;
+	
+	int number_ion_species;
+	
+	int Nx,Ny,Nz,N,Np;
+	int rank,nprocx,nprocy,nprocz,nprocs;
+	double Lx,Ly,Lz;
+
+	std::shared_ptr<Domain> Dm;   // this domain is for analysis
+	std::shared_ptr<Domain> Mask; // this domain is for lbm
+	std::shared_ptr<ScaLBL_Communicator> ScaLBL_Comm;
+    // input database
+    std::shared_ptr<Database> db;
+    std::shared_ptr<Database> domain_db;
+    std::shared_ptr<Database> ion_db;
+
+    IntArray Map;
+    DoubleArray Distance;
+    int *NeighborList;
+    double *fq;
+    double *Ci; 
+    double *ChargeDensity; 
+
+private:
+	MPI_Comm comm;
+	
+	// filenames
+    char LocalRankString[8];
+    char LocalRankFilename[40];
+    char LocalRestartFile[40];
+   
+    //int rank,nprocs;
+    void LoadParams(std::shared_ptr<Database> db0);    	
+};