LBPM/analysis/Minkowski.cpp

#include "analysis/Minkowski.h"
#include "analysis/pmmc.h"
#include "common/Domain.h"
#include "common/Communication.h"
#include "analysis/analysis.h"

#include "shared_ptr.h"
#include "common/Utilities.h"
#include "common/MPI_Helpers.h"
#include "IO/MeshDatabase.h"
#include "IO/Reader.h"
#include "IO/Writer.h"

#define PI 3.14159265359

// Constructor
Minkowski::Minkowski(std::shared_ptr <Domain> dm):
	n_obj_pts(0), n_obj_tris(0), kstart(0), kfinish(0), isovalue(0), Volume(0),
    LOGFILE(NULL), Dm(dm), vol_n(0), vol_n_global(0)
{
	Nx=dm->Nx; Ny=dm->Ny; Nz=dm->Nz;
	Volume=double((Nx-2)*(Ny-2)*(Nz-2))*double(Dm->nprocx()*Dm->nprocy()*Dm->nprocz());

	TempID = new char[Nx*Ny*Nz];

	// Global arrays
	PhaseID.resize(Nx,Ny,Nz);       PhaseID.fill(0);
	SDn.resize(Nx,Ny,Nz);           SDn.fill(0);
	MeanCurvature.resize(Nx,Ny,Nz); MeanCurvature.fill(0);
	GaussCurvature.resize(Nx,Ny,Nz); GaussCurvature.fill(0);
	SDn_x.resize(Nx,Ny,Nz);         SDn_x.fill(0);      // Gradient of the signed distance
	SDn_y.resize(Nx,Ny,Nz);         SDn_y.fill(0);
	SDn_z.resize(Nx,Ny,Nz);         SDn_z.fill(0);
	//.........................................
	// Allocate cube storage space
	CubeValues.resize(2,2,2);
	obj_tris.resize(3,20);
	obj_pts=DTMutableList<Point>(20);
	tmp=DTMutableList<Point>(20);
	//.........................................
	Values.resize(20);
	//DistanceValues.resize(20);
	NormalVector.resize(60);
	
	if (Dm->rank()==0){
		LOGFILE = fopen("minkowski.csv","a+");
		if (fseek(LOGFILE,0,SEEK_SET) == fseek(LOGFILE,0,SEEK_CUR))
		{
			// If LOGFILE is empty, write a short header to list the averages
			//fprintf(LOGFILE,"--------------------------------------------------------------------------------------\n");
			fprintf(LOGFILE,"Vn An Jn Xn\n"); 			//miknowski measures,
		}
	}
}


// Destructor
Minkowski::~Minkowski()
{
    if ( LOGFILE!=NULL ) { fclose(LOGFILE); }
}


void Minkowski::Initialize()
{
	isovalue=0.0;
	vol_n = euler = Jn = An = Kn = 0.0;
}

double Minkowski::V(){
	return vol_n_global;
}

double Minkowski::A(){
	return An_global;
}

double Minkowski::J(){
	return Jn_global;
}

double Minkowski::X(){
	return euler_global;
}


void Minkowski::UpdateMeshValues()
{
	int i,j,k,n;
	//...........................................................................
	Dm->CommunicateMeshHalo(SDn);
	//...........................................................................
	// Compute the gradients of the phase indicator and signed distance fields
	pmmc_MeshGradient(SDn,SDn_x,SDn_y,SDn_z,Nx,Ny,Nz);
	//...........................................................................
	// Gradient of the phase indicator field
	//...........................................................................
	Dm->CommunicateMeshHalo(SDn_x);
	//...........................................................................
	Dm->CommunicateMeshHalo(SDn_y);
	//...........................................................................
	Dm->CommunicateMeshHalo(SDn_z);
	//...........................................................................
	//...........................................................................
	// Compute the mesh curvature of the phase indicator field
	pmmc_MeshCurvature(SDn, MeanCurvature, GaussCurvature, Nx, Ny, Nz);
	//...........................................................................
	//...........................................................................
	Dm->CommunicateMeshHalo(MeanCurvature);
	//...........................................................................
	Dm->CommunicateMeshHalo(GaussCurvature);
	//...........................................................................
	// Initializing the blob ID
	for (k=0; k<Nz; k++){
		for (j=0; j<Ny; j++){
			for (i=0; i<Nx; i++){
				n = k*Nx*Ny+j*Nx+i;
				if (Dm->id[n] == 0){
					// Solid phase
					PhaseID(i,j,k) = 0;
				}
				else {
					// non-wetting phase
					PhaseID(i,j,k) = 1;
				}
			}
		}
	}

}
void Minkowski::ComputeLocal()
{
	int i,j,k,n,kmin,kmax;
	int cube[8][3] = {{0,0,0},{1,0,0},{0,1,0},{1,1,0},{0,0,1},{1,0,1},{0,1,1},{1,1,1}};

	// If external boundary conditions are set, do not average over the inlet
	kmin=1; kmax=Nz-1;
	if (Dm->BoundaryCondition > 0 && Dm->kproc() == 0) kmin=4;
	if (Dm->BoundaryCondition > 0 && Dm->kproc() == Dm->nprocz()-1) kmax=Nz-4;

	vol_n = euler = Jn = An = Kn = 0.0;
	for (k=kmin; k<kmax; k++){
		for (j=1; j<Ny-1; j++){
			for (i=1; i<Nx-1; i++){
				//...........................................................................
				n_obj_pts=0;
				n_obj_tris=0;
				//...........................................................................
				// Compute volume averages
				for (int p=0;p<8;p++){
					n = i+cube[p][0] + (j+cube[p][1])*Nx + (k+cube[p][2])*Nx*Ny;
					// 1-D index for this cube corner
					if ( SDn(i+cube[p][0],j+cube[p][1],k+cube[p][2]) < 0 ){
						vol_n += 0.125;
					}
				}

				n_obj_pts=n_obj_tris=0;
				// Compute the non-wetting phase surface and associated area
				An += geomavg_MarchingCubes(SDn,isovalue,i,j,k,obj_pts,n_obj_pts,obj_tris,n_obj_tris);

				Jn += pmmc_CubeSurfaceInterpValue(CubeValues,MeanCurvature,obj_pts,obj_tris,Values,
										i,j,k,n_obj_pts,n_obj_tris);
				// Compute Euler characteristic from integral of gaussian curvature
				Kn += pmmc_CubeSurfaceInterpValue(CubeValues,GaussCurvature,obj_pts,obj_tris,Values,
						i,j,k,n_obj_pts,n_obj_tris);

				euler += geomavg_EulerCharacteristic(obj_pts,obj_tris,n_obj_pts,n_obj_tris,i,j,k);

			}
		}
	}
	
}

void Minkowski::ComputeScalar(const DoubleArray Field, const double isovalue)
{
	Xi = Ji = Ai = 0.0;
	DECL object;
	Point P1,P2,P3;
	unsigned long int e1,e2,e3;
	double s,s1,s2,s3;
	double Vx,Vy,Vz,Wx,Wy,Wz,nx,ny,nz,norm;
	for (int k=1; k<Nz-1; k++){
		for (int j=1; j<Ny-1; j++){
			for (int i=1; i<Nx-1; i++){
				object.LocalIsosurface(Field,isovalue,i,j,k);
				for (unsigned long int idx=0; idx<object.TriangleCount; idx++){
					e1 = object.Face(idx); 
					e2 = object.halfedge.next(e1);
					e3 = object.halfedge.next(e2);
					P1 = object.vertex.coords(object.halfedge.v1(e1));
					P2 = object.vertex.coords(object.halfedge.v1(e2));
					P3 = object.vertex.coords(object.halfedge.v1(e3));
					// compute the area
					s1 = sqrt((P1.x-P2.x)*(P1.x-P2.x)+(P1.y-P2.y)*(P1.y-P2.y)+(P1.z-P2.z)*(P1.z-P2.z));
					s2 = sqrt((P1.x-P3.x)*(P1.x-P3.x)+(P1.y-P3.y)*(P1.y-P3.y)+(P1.z-P3.z)*(P1.z-P3.z));
					s3 = sqrt((P2.x-P3.x)*(P2.x-P3.x)+(P2.y-P3.y)*(P2.y-P3.y)+(P2.z-P3.z)*(P2.z-P3.z));
					s = 0.5*(s1+s2+s3);
					Ai += sqrt(s*(s-s1)*(s-s2)*(s-s3));
					// compute the normal vector
					Vx=P2.x-P1.x;
					Vy=P2.y-P1.y;
					Vz=P2.z-P1.z;
					Wx=P3.x-P2.x;
					Wy=P3.y-P2.y;
					Wz=P3.z-P2.z;
					nx = Vy*Wz-Vz*Wy;
					ny = Vz*Wx-Vx*Wz;
					nz = Vx*Wy-Vy*Wx;
					norm = 1.f/sqrt(nx*nx+ny*ny+nz*nz);
					nx *= norm;
					ny *= norm;
					nz *= norm;
					// Euler characteristic (half edge rule: one face - 0.5*(three edges))
					Xi -= 0.5;
				}
				// Euler characteristic -- each vertex shared by four cubes
				Xi += 0.25*double(object.VertexCount);
			}
		}
	}
	// Voxel counting for volume fraction
	Vi = 0.f;
	for (k=1; k<Nz-1; k++){
		for (j=1; j<Ny-1; j++){
			for (i=1; i<Nx-1; i++){
				if (Field(i,j,k) < isovalue){
					Vi += 1.0;
				}
			}
		}
	}
}

/*
void Minkowski::AssignComponentLabels()
{
	
	int LabelNWP=1;
	int LabelWP=2;
	// NOTE: labeling the wetting phase components is tricky! One sandstone media had over 800,000 components
	// NumberComponents_WP = ComputeGlobalPhaseComponent(Dm->Nx-2,Dm->Ny-2,Dm->Nz-2,Dm->rank_info,PhaseID,LabelWP,Label_WP);
	// treat all wetting phase is connected
	NumberComponents_WP=1;
	for (int k=0; k<Nz; k++){
		for (int j=0; j<Ny; j++){
			for (int i=0; i<Nx; i++){
				Label_WP(i,j,k) = 0;
				//if (SDs(i,j,k) > 0.0) PhaseID(i,j,k) = 0;
				//else if (Phase(i,j,k) > 0.0) PhaseID(i,j,k) = LabelNWP;
				//else PhaseID(i,j,k) = LabelWP;
			}
		}
	}

	// Fewer non-wetting phase features are present
	//NumberComponents_NWP = ComputeGlobalPhaseComponent(Dm->Nx-2,Dm->Ny-2,Dm->Nz-2,Dm->rank_info,PhaseID,LabelNWP,Label_NWP);
	NumberComponents_NWP = ComputeGlobalBlobIDs(Dm->Nx-2,Dm->Ny-2,Dm->Nz-2,Dm->rank_info,SDs,SDn,solid_isovalue,isovalue,Label_NWP,Dm->Comm);
	
}
*/
void Minkowski::Reduce()
{
	int i;
	double iVol_global=1.0/Volume;
	//...........................................................................
	MPI_Barrier(Dm->Comm);
	// Phase averages
	MPI_Allreduce(&vol_n,&vol_n_global,1,MPI_DOUBLE,MPI_SUM,Dm->Comm);
	MPI_Allreduce(&euler,&euler_global,1,MPI_DOUBLE,MPI_SUM,Dm->Comm);
	MPI_Allreduce(&An,&An_global,1,MPI_DOUBLE,MPI_SUM,Dm->Comm);
	MPI_Allreduce(&Jn,&Jn_global,1,MPI_DOUBLE,MPI_SUM,Dm->Comm);
	MPI_Barrier(Dm->Comm);

	// normalize to per unit volume basis
	vol_n_global /=Volume;
	An_global /=Volume;
	Jn_global /=Volume;
	euler_global /=Volume;
	euler_global /= (2*PI);

}

void Minkowski::NonDimensionalize(double D)
{
	An_global *= D;
	Jn_global *= D*D;
	euler_global *= D*D*D;
}

void Minkowski::PrintAll()
{
	if (Dm->rank()==0){
		fprintf(LOGFILE,"%.5g %.5g %.5g %.5g\n",vol_n_global, An_global, Jn_global, euler_global);			// minkowski measures
		fflush(LOGFILE);
	}
}