add cell simulator

tests/CMakeLists.txt

@@ -6,6 +6,7 @@ ADD_LBPM_EXECUTABLE( lbpm_permeability_simulator )
 ADD_LBPM_EXECUTABLE( lbpm_greyscale_simulator )
 ADD_LBPM_EXECUTABLE( lbpm_greyscaleColor_simulator )
 ADD_LBPM_EXECUTABLE( lbpm_electrokinetic_SingleFluid_simulator )
+ADD_LBPM_EXECUTABLE( lbpm_cell_simulator )
 ADD_LBPM_EXECUTABLE( lbpm_freelee_simulator )
 ADD_LBPM_EXECUTABLE( lbpm_freelee_SingleFluidBGK_simulator )
 #ADD_LBPM_EXECUTABLE( lbpm_BGK_simulator )

tests/lbpm_cell_simulator.cpp

@@ -0,0 +1,131 @@
+#include <stdio.h>
+#include <stdlib.h>
+#include <sys/stat.h>
+#include <iostream>
+#include <exception>
+#include <stdexcept>
+#include <fstream>
+#include <math.h>
+
+#include "models/IonModel.h"
+#include "models/StokesModel.h"
+#include "models/PoissonSolver.h"
+#include "models/MultiPhysController.h"
+#include "common/Utilities.h"
+#include "analysis/ElectroChemistry.h"
+
+using namespace std;
+
+//***************************************************************************
+// Test lattice-Boltzmann Ion Model coupled with Poisson equation
+//***************************************************************************
+
+int main(int argc, char **argv)
+{
+    // Initialize MPI and error handlers
+    	Utilities::startup( argc, argv );
+    	Utilities::MPI comm( MPI_COMM_WORLD );
+    	int rank = comm.getRank();
+    	int nprocs = comm.getSize();
+
+    { // Limit scope so variables that contain communicators will free before MPI_Finialize
+
+        if (rank == 0){
+            printf("********************************************************\n");
+            printf("Running LBPM electrokinetic single-fluid solver \n");
+            printf("********************************************************\n");
+        }
+    	// Initialize compute device
+    	int device=ScaLBL_SetDevice(rank);
+        NULL_USE( device );
+    	ScaLBL_DeviceBarrier();
+    	comm.barrier();
+
+        PROFILE_ENABLE(1);
+        //PROFILE_ENABLE_TRACE();
+        //PROFILE_ENABLE_MEMORY();
+        PROFILE_SYNCHRONIZE();
+        PROFILE_START("Main");
+        Utilities::setErrorHandlers();
+
+        auto filename = argv[1];
+        ScaLBL_StokesModel StokesModel(rank,nprocs,comm);
+        ScaLBL_IonModel IonModel(rank,nprocs,comm);
+        ScaLBL_Poisson PoissonSolver(rank,nprocs,comm); 
+        ScaLBL_Multiphys_Controller Study(rank,nprocs,comm);//multiphysics controller coordinating multi-model coupling
+        
+        // Load controller information
+        Study.ReadParams(filename);
+
+        // Load user input database files for Navier-Stokes and Ion solvers
+        StokesModel.ReadParams(filename);
+        IonModel.ReadParams(filename);
+
+        // Setup other model specific structures
+        StokesModel.SetDomain();    
+        StokesModel.ReadInput();    
+        StokesModel.Create();       // creating the model will create data structure to match the pore structure and allocate variables
+
+        IonModel.SetDomain();    
+        IonModel.ReadInput();    
+        IonModel.Create();      
+        
+        // Create analysis object
+        ElectroChemistryAnalyzer Analysis(IonModel.Dm);
+
+        // Get internal iteration number
+        StokesModel.timestepMax = Study.getStokesNumIter_PNP_coupling(StokesModel.time_conv,IonModel.time_conv);
+        StokesModel.Initialize();   // initializing the model will set initial conditions for variables
+
+        IonModel.timestepMax = Study.getIonNumIter_PNP_coupling(StokesModel.time_conv,IonModel.time_conv);
+        IonModel.Initialize();   
+        // Get maximal time converting factor based on Sotkes and Ion solvers
+        Study.getTimeConvMax_PNP_coupling(StokesModel.time_conv,IonModel.time_conv);
+
+        // Initialize LB-Poisson model
+        PoissonSolver.ReadParams(filename);
+        PoissonSolver.SetDomain();    
+        PoissonSolver.ReadInput();    
+        PoissonSolver.Create();       
+        PoissonSolver.Initialize(Study.time_conv_max);   
+
+
+        int timestep=0;
+        while (timestep < Study.timestepMax){
+            
+            timestep++;
+            PoissonSolver.Run(IonModel.ChargeDensity,timestep);//solve Poisson equtaion to get steady-state electrical potental
+            StokesModel.Run_Lite(IonModel.ChargeDensity, PoissonSolver.ElectricField);// Solve the N-S equations to get velocity
+            IonModel.Run(StokesModel.Velocity,PoissonSolver.ElectricField); //solve for ion transport and electric potential
+            
+            timestep++;//AA operations
+
+            if (timestep%Study.analysis_interval==0){
+            	Analysis.Basic(IonModel,PoissonSolver,StokesModel,timestep);
+            }
+            if (timestep%Study.visualization_interval==0){
+            	Analysis.WriteVis(IonModel,PoissonSolver,StokesModel,Study.db,timestep);
+            	/*  PoissonSolver.getElectricPotential(timestep);
+                PoissonSolver.getElectricField(timestep);
+                IonModel.getIonConcentration(timestep);
+                StokesModel.getVelocity(timestep);
+            	 */
+            }
+        }
+
+        if (rank==0) printf("Save simulation raw data at maximum timestep\n");
+    	Analysis.WriteVis(IonModel,PoissonSolver,StokesModel,Study.db,timestep);
+
+        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_SingleFluid_simulator",1);
+        // ****************************************************
+
+    } // Limit scope so variables that contain communicators will free before MPI_Finialize
+
+  Utilities::shutdown();
+}
+
+