LBPM/tests/lbpm_nernst_planck_cell_simulator.cpp

#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::startup( argc, argv, true );

	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 Nernst-Planck Membrane 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

		bool SlipBC = false;

		// Load controller information
		Study.ReadParams(filename);

		// Load user input database files for Navier-Stokes and Ion solvers
		//StokesModel.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
		//comm.barrier();
		//if (rank == 0) printf("Stokes model setup complete\n");

		IonModel.ReadParams(filename);
		IonModel.SetDomain();    
		IonModel.ReadInput();    
		IonModel.Create();      
		IonModel.SetMembrane();
		comm.barrier();
		if (rank == 0) printf("Ion model setup complete\n");
		fflush(stdout);

		// Create analysis object
		ElectroChemistryAnalyzer Analysis(IonModel);

		// 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
		//comm.barrier();
		//if (rank == 0) printf("Stokes model initialized \n");
		//fflush(stdout);

		//IonModel.timestepMax = Study.getIonNumIter_PNP_coupling(StokesModel.time_conv,IonModel.time_conv);
		IonModel.timestepMax = Study.getIonNumIter_NernstPlanck_coupling(IonModel.time_conv);
		IonModel.Initialize();   
		IonModel.DummyFluidVelocity();
		comm.barrier();
		if (rank == 0) printf("Ion model initialized \n");
		// Get maximal time converting factor based on Sotkes and Ion solvers
		//Study.getTimeConvMax_PNP_coupling(StokesModel.time_conv,IonModel.time_conv);
		Study.time_conv_MainLoop = IonModel.timestepMax[0]*IonModel.time_conv[0];

		//----------------------------------- print out for debugging ------------------------------------------//
		if (rank==0){
			for (size_t i=0;i<IonModel.timestepMax.size();i++){
				printf("Main loop time_conv computed from ion %lu: %.5g[s/lt]\n",i+1,IonModel.timestepMax[i]*IonModel.time_conv[i]);
			}
		}
		//----------------------------------- print out for debugging ------------------------------------------//

		// Initialize LB-Poisson model
		PoissonSolver.ReadParams(filename);
		PoissonSolver.SetDomain();    
		PoissonSolver.ReadInput();    
		PoissonSolver.Create();       
		comm.barrier();
		if (rank == 0) printf("Poisson solver created \n");
		fflush(stdout);
		PoissonSolver.Initialize(Study.time_conv_MainLoop);   
		comm.barrier();
		if (rank == 0) printf("Poisson solver initialized \n");
		fflush(stdout);

		int timestep=0;
		while (timestep < Study.timestepMax){

			timestep++;
			PoissonSolver.Run(IonModel.ChargeDensity,IonModel.MembraneDistance,SlipBC,timestep);//solve Poisson equtaion to get steady-state electrical potental
			//comm.barrier();
			//if (rank == 0) printf("    Poisson step %i \n",timestep);
			//StokesModel.Run_Lite(IonModel.ChargeDensity, PoissonSolver.ElectricField);// Solve the N-S equations to get velocity
			//fflush(stdout);

			IonModel.RunMembrane(IonModel.FluidVelocityDummy,PoissonSolver.ElectricField,PoissonSolver.Psi); //solve for ion transport with membrane
			//comm.barrier();
			//if (rank == 0) printf("    Membrane step %i \n",timestep);
			fflush(stdout);


			if (timestep%Study.analysis_interval==0){
				Analysis.Membrane(IonModel,PoissonSolver,timestep);
			}
			if (timestep%Study.visualization_interval==0){

				Analysis.WriteVis(IonModel,PoissonSolver,Study.db,timestep);
				//StokesModel.getVelocity(timestep);
				//PoissonSolver.getElectricPotential_debug(timestep);
				// PoissonSolver.getElectricField_debug(timestep);
				//IonModel.getIonConcentration_debug(timestep);

			}
			
			if (timestep%Study.restart_interval==0){
				IonModel.Checkpoint();
				PoissonSolver.Checkpoint();
			}
		}

		if (rank==0) printf("Save simulation raw data at maximum timestep\n");
		Analysis.WriteVis(IonModel,PoissonSolver,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_nernst_planck_membrane_simulator",1);
		// ****************************************************

	} // Limit scope so variables that contain communicators will free before MPI_Finialize

	Utilities::shutdown();
}