#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 "analysis/TwoPhase.h"
#include "common/MPI_Helpers.h"

int main(int argc, char **argv)
{
	//*****************************************
	// ***** MPI STUFF ****************
	//*****************************************
	// Initialize MPI
	Utilities::startup( argc, argv );
        Utilities::MPI comm( MPI_COMM_WORLD );
        int rank = comm.getRank();
        int nprocs = comm.getSize();
	{
	// parallel domain size (# of sub-domains)
	int nprocx,nprocy,nprocz;
	int iproc,jproc,kproc;
	int sendtag,recvtag;
	//*****************************************
	// MPI ranks for all 18 neighbors
	//**********************************
	int rank_x,rank_y,rank_z,rank_X,rank_Y,rank_Z;
	int rank_xy,rank_XY,rank_xY,rank_Xy;
	int rank_xz,rank_XZ,rank_xZ,rank_Xz;
	int rank_yz,rank_YZ,rank_yZ,rank_Yz;
	//**********************************
	MPI_Request req1[18],req2[18];
	MPI_Status stat1[18],stat2[18];

	int ORIENTATION=2; //default: the tube is aligned with Z axis
	                   //ORIENTATION = 0: tube is aligned with X axis
	                   //ORIENTATION = 1: tube is aligned with Y axis
	double TubeWidth =15.0;
	int BC;
	int BubbleTop,BubbleBottom;
	TubeWidth=strtod(argv[1],NULL);
	BC=atoi(argv[2]);
	BubbleBottom = atoi(argv[3]);
	BubbleTop = atoi(argv[4]);
	ORIENTATION = atoi(argv[5]);


	if (rank == 0){
		printf("********************************************************\n");
		printf("Generate 3D capillary tube geometry with side = %f voxels \n",TubeWidth);
		printf("********************************************************\n");
	}

	// Variables that specify the computational domain  
	string FILENAME;
	int Nx,Ny,Nz;		// local sub-domain size
	int nspheres;		// number of spheres in the packing
	double Lx,Ly,Lz;	// Domain length
	int i,j,k,n;

	// pmmc threshold values

	if (rank==0){
		//.......................................................................
		// Reading the domain information file
		//.......................................................................
		ifstream domain("Domain.in");
		domain >> nprocx;
		domain >> nprocy;
		domain >> nprocz;
		domain >> Nx;
		domain >> Ny;
		domain >> Nz;
		domain >> nspheres;
		domain >> Lx;
		domain >> Ly;
		domain >> Lz;
		//.......................................................................
	}
	// **************************************************************
	// Broadcast simulation parameters from rank 0 to all other procs
	MPI_Barrier(comm);
	// Computational domain
	MPI_Bcast(&Nx,1,MPI_INT,0,comm);
	MPI_Bcast(&Ny,1,MPI_INT,0,comm);
	MPI_Bcast(&Nz,1,MPI_INT,0,comm);
	MPI_Bcast(&nprocx,1,MPI_INT,0,comm);
	MPI_Bcast(&nprocy,1,MPI_INT,0,comm);
	MPI_Bcast(&nprocz,1,MPI_INT,0,comm);
	MPI_Bcast(&nspheres,1,MPI_INT,0,comm);
	MPI_Bcast(&Lx,1,MPI_DOUBLE,0,comm);
	MPI_Bcast(&Ly,1,MPI_DOUBLE,0,comm);
	MPI_Bcast(&Lz,1,MPI_DOUBLE,0,comm);
	//.................................................
	MPI_Barrier(comm);
	
	// **************************************************************
	if (nprocs != nprocx*nprocy*nprocz){
		printf("nprocx =  %i \n",nprocx);
		printf("nprocy =  %i \n",nprocy);
		printf("nprocz =  %i \n",nprocz);
		INSIST(nprocs == nprocx*nprocy*nprocz,"Fatal error in processor count!");
	}

	if (rank==0){
		printf("********************************************************\n");
		printf("Sub-domain size = %i x %i x %i\n",Nz,Nz,Nz);
		printf("Parallel domain size = %i x %i x %i\n",nprocx,nprocy,nprocz);
		printf("********************************************************\n");
	}

	// Initialized domain and averaging framework for Two-Phase Flow
	std::shared_ptr<Domain> Dm(new Domain(Nx,Ny,Nz,rank,nprocx,nprocy,nprocz,Lx,Ly,Lz,BC));
	Dm->CommInit();
	std::shared_ptr<TwoPhase> Averages(new TwoPhase(Dm));

	InitializeRanks( rank, nprocx, nprocy, nprocz, iproc, jproc, kproc,
			 	 	 rank_x, rank_y, rank_z, rank_X, rank_Y, rank_Z,
			 	 	 rank_xy, rank_XY, rank_xY, rank_Xy, rank_xz, rank_XZ, rank_xZ, rank_Xz,
			 	 	 rank_yz, rank_YZ, rank_yZ, rank_Yz );
	 
	MPI_Barrier(comm);

	Nz += 2;
	Nx = Ny = Nz;	// Cubic domain

	int N = Nx*Ny*Nz;
	int dist_mem_size = N*sizeof(double);

	//.......................................................................
	// Filenames used
	char LocalRankString[8];
	char LocalRankFilename[40];
	char LocalRestartFile[40];
	char tmpstr[10];
	sprintf(LocalRankString,"%05d",rank);
	sprintf(LocalRankFilename,"%s%s","ID.",LocalRankString);
	sprintf(LocalRestartFile,"%s%s","Restart.",LocalRankString);
	
//	printf("Local File Name =  %s \n",LocalRankFilename);
	// .......... READ THE INPUT FILE .......................................
//	char value;
	char *id;
	id = new char[N];
	int sum = 0;
	double sum_local;
	double iVol_global = 1.0/(1.0*(Nx-2)*(Ny-2)*(Nz-2)*nprocs);
	//if (pBC) iVol_global = 1.0/(1.0*(Nx-2)*nprocx*(Ny-2)*nprocy*((Nz-2)*nprocz-6));
	double pore_vol;

	sum=0;
        //double wall_width = (Nx - TubeWidth)/2;
	for (k=0;k<Nz;k++){
		for (j=0;j<Ny;j++){
			for (i=0;i<Nx;i++){
				n = k*Nx*Ny + j*Nz + i;

				if (ORIENTATION==0){
					// square capillary tube aligned with the x direction
					Averages->SDs(i,j,k) = TubeWidth/2 - fabs(j-0.5*Ny);
					Averages->SDs(i,j,k) = min(Averages->SDs(i,j,k),TubeWidth/2-fabs(k-0.5*Nz));
					// Initialize phase positions
					if (Averages->SDs(i,j,k) < 0.0){
						id[n] = 0;
					}
					else if (Dm->iproc()*Nx+k<BubbleBottom){
						id[n] = 2;
						sum++;
					}
					else if (Dm->iproc()*Nx+k<BubbleTop){
						id[n] = 1;
						sum++;
					}
					else{
						id[n] = 2;
						sum++;
					}
				}
				else if (ORIENTATION==1){
					// square capillary tube aligned with the y direction
					Averages->SDs(i,j,k) = TubeWidth/2 - fabs(i-0.5*Nx);
					Averages->SDs(i,j,k) = min(Averages->SDs(i,j,k),TubeWidth/2-fabs(k-0.5*Nz));
					// Initialize phase positions
					if (Averages->SDs(i,j,k) < 0.0){
						id[n] = 0;
					}
					else if (Dm->jproc()*Ny+k<BubbleBottom){
						id[n] = 2;
						sum++;
					}
					else if (Dm->jproc()*Ny+k<BubbleTop){
						id[n] = 1;
						sum++;
					}
					else{
						id[n] = 2;
						sum++;
					}
				}
				else { //
					// square capillary tube aligned with the z direction
					Averages->SDs(i,j,k) = TubeWidth/2 - fabs(i-0.5*Nx);
					Averages->SDs(i,j,k) = min(Averages->SDs(i,j,k),TubeWidth/2-fabs(j-0.5*Ny));
					// Initialize phase positions
					if (Averages->SDs(i,j,k) < 0.0){
						id[n] = 0;
					}
					else if (Dm->kproc()*Nz+k<BubbleBottom){
						id[n] = 2;
						sum++;
					}
					else if (Dm->kproc()*Nz+k<BubbleTop){
						id[n] = 1;
						sum++;
					}
					else{
						id[n] = 2;
						sum++;
					}
				}
			}
		}
	}
	// Compute the pore volume
	sum_local = 0.0;
	for ( k=1;k<Nz-1;k++){
		for ( j=1;j<Ny-1;j++){
			for ( i=1;i<Nx-1;i++){
				n = k*Nx*Ny+j*Nx+i;
				if (id[n] > 0){
					sum_local += 1.0;
				}
			}
		}
	}
	MPI_Allreduce(&sum_local,&pore_vol,1,MPI_DOUBLE,MPI_SUM,comm);

	//.........................................................
	// don't perform computations at the eight corners
	id[0] = id[Nx-1] = id[(Ny-1)*Nx] = id[(Ny-1)*Nx + Nx-1] = 0;
	id[(Nz-1)*Nx*Ny] = id[(Nz-1)*Nx*Ny+Nx-1] = id[(Nz-1)*Nx*Ny+(Ny-1)*Nx] = id[(Nz-1)*Nx*Ny+(Ny-1)*Nx + Nx-1] = 0;
	//.........................................................

    sprintf(LocalRankFilename,"SignDist.%05i",rank);
    FILE *DIST = fopen(LocalRankFilename,"wb");
    fwrite(Averages->SDs.data(),8,Averages->SDs.length(),DIST);
    fclose(DIST);

	sprintf(LocalRankFilename,"ID.%05i",rank);
	FILE *ID = fopen(LocalRankFilename,"wb");
	fwrite(id,1,N,ID);
	fclose(ID);

	}
        // ****************************************************
	comm.barrier();
	Utilities::shutdown();
	// ****************************************************
}