213 lines
6.3 KiB
C++
213 lines
6.3 KiB
C++
/*
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Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
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This file is part of the Open Porous Media project (OPM).
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OPM is free software: you can redistribute it and/or modify
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it under the terms of the GNU General Public License as published by
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the Free Software Foundation, either version 3 of the License, or
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(at your option) any later version.
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OPM is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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GNU General Public License for more details.
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You should have received a copy of the GNU General Public License
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along with OPM. If not, see <http://www.gnu.org/licenses/>.
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*/
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#include "analysis/Minkowski.h"
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#include "analysis/pmmc.h"
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#include "analysis/analysis.h"
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#include "common/Domain.h"
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#include "common/Communication.h"
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#include "common/Utilities.h"
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#include "common/MPI_Helpers.h"
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#include "IO/MeshDatabase.h"
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#include "IO/Reader.h"
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#include "IO/Writer.h"
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#include "ProfilerApp.h"
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#include <memory>
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#define PI 3.14159265359
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// Constructor
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Minkowski::Minkowski(std::shared_ptr <Domain> dm):
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kstart(0), kfinish(0), isovalue(0), Volume(0),
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LOGFILE(NULL), Dm(dm), Vi(0), Vi_global(0)
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{
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Nx=dm->Nx; Ny=dm->Ny; Nz=dm->Nz;
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Volume=double((Nx-2)*(Ny-2)*(Nz-2))*double(Dm->nprocx()*Dm->nprocy()*Dm->nprocz());
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id.resize(Nx,Ny,Nz); id.fill(0);
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label.resize(Nx,Ny,Nz); label.fill(0);
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distance.resize(Nx,Ny,Nz); distance.fill(0);
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if (Dm->rank()==0){
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LOGFILE = fopen("minkowski.csv","a+");
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if (fseek(LOGFILE,0,SEEK_SET) == fseek(LOGFILE,0,SEEK_CUR))
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{
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// If LOGFILE is empty, write a short header to list the averages
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//fprintf(LOGFILE,"--------------------------------------------------------------------------------------\n");
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fprintf(LOGFILE,"Vn An Jn Xn\n"); //miknowski measures,
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}
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}
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}
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// Destructor
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Minkowski::~Minkowski()
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{
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if ( LOGFILE!=NULL ) { fclose(LOGFILE); }
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}
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void Minkowski::ComputeScalar(const DoubleArray& Field, const double isovalue)
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{
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PROFILE_START("ComputeScalar");
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Xi = Ji = Ai = 0.0;
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DECL object;
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int e1,e2,e3;
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double s,s1,s2,s3;
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double a1,a2,a3;
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//double Vx,Vy,Vz,Wx,Wy,Wz,nx,ny,nz,norm;
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//int Nx = Field.size(0);
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//int Ny = Field.size(1);
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//int Nz = Field.size(2);
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for (int k=1; k<Nz-1; k++){
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for (int j=1; j<Ny-1; j++){
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for (int i=1; i<Nx-1; i++){
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object.LocalIsosurface(Field,isovalue,i,j,k);
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for (int idx=0; idx<object.TriangleCount; idx++){
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e1 = object.Face(idx);
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e2 = object.halfedge.next(e1);
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e3 = object.halfedge.next(e2);
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auto P1 = object.vertex.coords(object.halfedge.v1(e1));
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auto P2 = object.vertex.coords(object.halfedge.v1(e2));
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auto P3 = object.vertex.coords(object.halfedge.v1(e3));
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// Surface area
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s1 = Distance( P1, P2 );
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s2 = Distance( P2, P3 );
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s3 = Distance( P1, P3 );
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s = 0.5*(s1+s2+s3);
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Ai += sqrt(s*(s-s1)*(s-s2)*(s-s3));
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// Mean curvature based on half edge angle
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a1 = object.EdgeAngle(e1);
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a2 = object.EdgeAngle(e2);
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a3 = object.EdgeAngle(e3);
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Ji += (a1*s1+a2*s2+a3*s3);
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//if (0.08333333333333*(a1*s1+a2*s2+a3*s3) < 0.f){
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//double intcurv=0.08333333333333*(a1*s1+a2*s2+a3*s3);
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//double surfarea=sqrt(s*(s-s1)*(s-s2)*(s-s3));
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//printf(" (%i,%i,%i) PQ(%i,%i)={%f,%f,%f} {%f,%f,%f} a=%f l=%f \n",i,j,k,e1,object.halfedge.twin(e1),P1.x,P1.y,P1.z,P2.x,P2.y,P2.z,a1,s1);
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// printf(" (%i,%i,%i) QR(%i,%i)={%f,%f,%f} {%f,%f,%f} a=%f l=%f \n",i,j,k,e2,object.halfedge.twin(e2),P2.x,P2.y,P2.z,P3.x,P3.y,P3.z,a2,s2);
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// printf(" (%i,%i,%i) RP(%i,%i)={%f,%f,%f} {%f,%f,%f} a=%f l=%f \n",i,j,k,e3,object.halfedge.twin(e3),P3.x,P3.y,P3.z,P1.x,P1.y,P1.z,a3,s3);
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//}
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// Euler characteristic (half edge rule: one face - 0.5*(three edges))
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Xi -= 0.5;
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}
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// Euler characteristic -- each vertex shared by four cubes
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Xi += 0.25*double(object.VertexCount);
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}
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}
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}
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// Voxel counting for volume fraction
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Vi = 0.f;
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for (int k=1; k<Nz-1; k++){
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for (int j=1; j<Ny-1; j++){
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for (int i=1; i<Nx-1; i++){
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if (Field(i,j,k) < isovalue){
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Vi += 1.0;
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}
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}
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}
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}
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// convert X for 2D manifold to 3D object
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Xi *= 0.5;
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MPI_Barrier(Dm->Comm);
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// Phase averages
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MPI_Allreduce(&Vi,&Vi_global,1,MPI_DOUBLE,MPI_SUM,Dm->Comm);
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MPI_Allreduce(&Xi,&Xi_global,1,MPI_DOUBLE,MPI_SUM,Dm->Comm);
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MPI_Allreduce(&Ai,&Ai_global,1,MPI_DOUBLE,MPI_SUM,Dm->Comm);
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MPI_Allreduce(&Ji,&Ji_global,1,MPI_DOUBLE,MPI_SUM,Dm->Comm);
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MPI_Barrier(Dm->Comm);
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PROFILE_STOP("ComputeScalar");
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}
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void Minkowski::MeasureObject(){
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/*
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* compute the distance to an object
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*
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* THIS ALGORITHM ASSUMES THAT id() is populated with phase id to distinguish objects
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* 0 - labels the object
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* 1 - labels the rest of the
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*/
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for (int k=0; k<Nz; k++){
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for (int j=0; j<Ny; j++){
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for (int i=0; i<Nx; i++){
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distance(i,j,k) =2.0*double(id(i,j,k))-1.0;
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}
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}
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}
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CalcDist(distance,id,*Dm);
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ComputeScalar(distance,0.0);
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}
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int Minkowski::MeasureConnectedPathway(){
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/*
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* compute the connected pathway for object with LABEL in id field
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* compute the labels for connected components
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* compute the distance to the connected pathway
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*
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* THIS ALGORITHM ASSUMES THAT id() is populated with phase id to distinguish objects
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*/
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char LABEL = 0;
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for (int k=0; k<Nz; k++){
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for (int j=0; j<Ny; j++){
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for (int i=0; i<Nx; i++){
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if (id(i,j,k) == LABEL){
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distance(i,j,k) = 1.0;
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}
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else
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distance(i,j,k) = -1.0;
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}
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}
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}
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// Extract only the connected part of NWP
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double vF=0.0;
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n_connected_components = ComputeGlobalBlobIDs(Nx-2,Ny-2,Nz-2,Dm->rank_info,distance,distance,vF,vF,label,Dm->Comm);
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// int n_connected_components = ComputeGlobalPhaseComponent(Nx-2,Ny-2,Nz-2,Dm->rank_info,const IntArray &PhaseID, int &VALUE, BlobIDArray &GlobalBlobID, Dm->Comm )
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MPI_Barrier(Dm->Comm);
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for (int k=0; k<Nz; k++){
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for (int j=0; j<Ny; j++){
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for (int i=0; i<Nx; i++){
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if ( label(i,j,k) == 0){
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id(i,j,k) = 0;
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}
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else{
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id(i,j,k) = 1;
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}
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}
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}
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}
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MeasureObject();
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return n_connected_components;
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}
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void Minkowski::PrintAll()
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{
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if (Dm->rank()==0){
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fprintf(LOGFILE,"%.5g %.5g %.5g %.5g\n",Vi_global, Ai_global, Ji_global, Xi_global); // minkowski measures
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fflush(LOGFILE);
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}
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}
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