311 lines
11 KiB
C++
311 lines
11 KiB
C++
/*
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Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
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Copyright Equnior ASA
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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.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), LOGFILE(NULL), Dm(dm),
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Vi(0), Vi_global(0) {
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Nx = dm->Nx;
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Ny = dm->Ny;
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Nz = dm->Nz;
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Volume = double((Nx - 2) * (Ny - 2) * (Nz - 2)) *
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double(Dm->nprocx() * Dm->nprocy() * Dm->nprocz());
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id.resize(Nx, Ny, Nz);
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id.fill(0);
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label.resize(Nx, Ny, Nz);
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label.fill(0);
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distance.resize(Nx, Ny, Nz);
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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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// 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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if (LOGFILE != NULL) {
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fclose(LOGFILE);
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}
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}
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void Minkowski::ComputeScalar(const DoubleArray &Field, const double isovalue) {
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PROFILE_START("ComputeScalar");
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Xi = Ji = Ai = 0.0;
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DCEL 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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// check if vertices are at corners
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for (int idx = 0; idx < object.VertexCount; idx++) {
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/*auto P1 = object.vertex.coords(idx);
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if ( remainder(P1.x,1.0)==0.0 && remainder(P1.y,1.0)==0.0 && remainder(P1.z,1.0)==0.0 ){
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Xi += 0.125;
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}
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else
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*/
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Xi += 0.25;
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}
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/*double nside_extern = double(npts);
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double nside_intern = double(npts)-3.0;
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EulerChar=0.0;
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if (npts > 0) EulerChar = (0.25*nvert - nside_intern - 0.5*nside_extern + nface); */
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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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Dm->Comm.barrier();
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// Phase averages
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Vi_global = Dm->Comm.sumReduce(Vi);
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Xi_global = Dm->Comm.sumReduce(Xi);
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Ai_global = Dm->Comm.sumReduce(Ai);
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Ji_global = Dm->Comm.sumReduce(Ji);
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Dm->Comm.barrier();
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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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//DoubleArray smooth_distance(Nx,Ny,Nz);
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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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Dm->CommunicateMeshHalo(distance);
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//Mean3D(distance,smooth_distance);
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//Eikonal(distance, id, *Dm, 20, {true, true, true});
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ComputeScalar(distance, 0.0);
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}
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void Minkowski::MeasureObject(double factor, const DoubleArray &Phi) {
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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
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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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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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double value = Phi(i, j, k);
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double dist_value = distance(i, j, k);
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if (dist_value < 2.5 && dist_value > -2.5) {
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double new_distance =
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factor * log((1.0 + value) / (1.0 - value));
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if (dist_value * new_distance < 0.0)
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new_distance = (-1.0) * new_distance;
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distance(i, j, k) = new_distance;
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}
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}
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}
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}
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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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} 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 =
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ComputeGlobalBlobIDs(Nx - 2, Ny - 2, Nz - 2, Dm->rank_info, distance,
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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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Dm->Comm.barrier();
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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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} 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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int Minkowski::MeasureConnectedPathway(double factor, const DoubleArray &Phi) {
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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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} 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 =
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ComputeGlobalBlobIDs(Nx - 2, Ny - 2, Nz - 2, Dm->rank_info, distance,
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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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Dm->Comm.barrier();
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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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} 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(factor, Phi);
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return n_connected_components;
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}
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void Minkowski::PrintAll() {
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if (Dm->rank() == 0) {
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fprintf(LOGFILE, "%.5g %.5g %.5g %.5g\n", Vi_global, Ai_global,
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Ji_global, Xi_global); // minkowski measures
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fflush(LOGFILE);
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}
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}
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