added analysis tools for TwoPhase object
This commit is contained in:
James McClure
229
tests/lbpm_TwoPhase_analysis.cpp
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229
tests/lbpm_TwoPhase_analysis.cpp
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/*
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* Compute porous media marching cubes analysis (PMMC) based on input image data
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*/
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#include <stdio.h>
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#include <stdlib.h>
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#include <math.h>
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#include <iostream>
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#include <fstream>
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#include <sstream>
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#include <functional>
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#include "common/Array.h"
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#include "common/Domain.h"
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#include "common/Communication.h"
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#include "common/MPI.h"
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#include "IO/MeshDatabase.h"
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#include "IO/Mesh.h"
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#include "IO/Writer.h"
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#include "IO/netcdf.h"
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#include "analysis/analysis.h"
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#include "analysis/filters.h"
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#include "analysis/distance.h"
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#include "analysis/Minkowski.h"
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#include "analysis/TwoPhase.h"
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#include "ProfilerApp.h"
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int main(int argc, char **argv)
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{
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// Initialize MPI
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Utilities::startup( argc, argv );
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Utilities::MPI comm( MPI_COMM_WORLD );
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int rank = comm.getRank();
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//int nprocs = comm.getSize();
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{
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Utilities::setErrorHandlers();
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PROFILE_START("Main");
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//std::vector<std::string> filenames;
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if ( argc<2 ) {
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if ( rank == 0 ){
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printf("At least one filename must be specified\n");
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}
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return 1;
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}
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std::string filename = std::string(argv[1]);
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if ( rank == 0 ){
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printf("Input data file: %s\n",filename.c_str());
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}
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auto db = std::make_shared<Database>( filename );
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auto domain_db = db->getDatabase( "Domain" );
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auto vis_db = db->getDatabase( "Visualization" );
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// Read domain parameters
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auto Filename = domain_db->getScalar<std::string>( "Filename" );
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auto size = domain_db->getVector<int>( "n" );
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auto SIZE = domain_db->getVector<int>( "N" );
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auto nproc = domain_db->getVector<int>( "nproc" );
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auto ReadValues = domain_db->getVector<char>( "ReadValues" );
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auto WriteValues = domain_db->getVector<char>( "WriteValues" );
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auto nx = size[0];
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auto ny = size[1];
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auto nz = size[2];
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int i,j,k,n;
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std::shared_ptr<Domain> Dm = std::shared_ptr<Domain>(new Domain(domain_db,comm)); // full domain for analysis
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comm.barrier();
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for (k=0;k<nz;k++){
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for (j=0;j<ny;j++){
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for (i=0;i<nx;i++){
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n = k*nx*ny+j*nx+i;
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// Initialize the object
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Dm->id[n] = 1;
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}
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}
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}
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Dm->CommInit();
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/* read the data */
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if (domain_db->keyExists( "Filename" )){
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auto Filename = domain_db->getScalar<std::string>( "Filename" );
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Dm->Decomp(Filename);
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}
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else{
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Dm->ReadIDs();
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}
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fillHalo<double> fillDouble(Dm->Comm, Dm->rank_info, {nx,ny,nz}, {1, 1, 1}, 0, 1);
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// Compute the Minkowski functionals
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comm.barrier();
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std::shared_ptr<TwoPhase> Averages( new TwoPhase(Dm) );
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std::shared_ptr<Minkowski> Geometry(new Minkowski(Dm));
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// Calculate the distance
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// Initialize the domain and communication
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nx+=2; ny+=2; nz+=2;
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Array<char> id(nx,ny,nz);
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DoubleArray Distance(nx,ny,nz);
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/* * * * * * * * * * * * * * * * * * * * * */
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// Solve for the position of the solid phase
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for (k=0;k<nz;k++){
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for (j=0;j<ny;j++){
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for (i=0;i<nx;i++){
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n = k*nx*ny+j*nx+i;
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// Initialize the object
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if (Dm->id[n] == ReadValues[0]) id(i,j,k) = 0;
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else id(i,j,k) = 1;
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}
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}
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}
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for (k=0;k<nz;k++){
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for (j=0;j<ny;j++){
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for (i=0;i<nx;i++){
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n=k*nx*ny+j*nx+i;
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// Initialize distance to +/- 1
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Averages->SDs(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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fillDouble.fill(Averages->SDs);
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if (rank==0) printf("Initialized solid phase -- Converting to Signed Distance function \n");
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CalcDist(Averages->SDs,id,*Dm);
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/* * * * * * * * * * * * * * * * * * * * * */
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// Solve for the position of the fluid phase
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for (k=0;k<nz;k++){
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for (j=0;j<ny;j++){
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for (i=0;i<nx;i++){
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n = k*nx*ny+j*nx+i;
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// Initialize the object
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if (Dm->id[n] == ReadValues[1]){
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id(i,j,k) = 1;
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Averages->Phase(i,j,k) = 1.0;
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}
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else {
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id(i,j,k) = 0;
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Averages->Phase(i,j,k) = -1.0;
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}
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}
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}
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}
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for (k=0;k<nz;k++){
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for (j=0;j<ny;j++){
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for (i=0;i<nx;i++){
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n=k*nx*ny+j*nx+i;
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// Initialize distance to +/- 1
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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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fillDouble.fill(Averages->Phase);
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fillDouble.fill(Distance);
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if (rank==0) printf("Initialized fluid phase -- Converting to Signed Distance function \n");
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CalcDist(Distance,id,*Dm);
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Mean3D(Distance,Averages->SDn);
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/* * * * * * * * * * * * * * * * * * * * * */
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if (rank==0) printf("Computing Minkowski functionals \n");
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Geometry->ComputeScalar(Distance,0.f);
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Geometry->PrintAll();
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Averages->Initialize();
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Averages->UpdateMeshValues();
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Averages->ComputeStatic();
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Averages->Reduce();
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Averages->PrintStatic();
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/*
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Averages.Initialize();
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Averages.ComponentAverages();
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Averages.SortBlobs();
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Averages.PrintComponents(timestep);
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*/
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auto format = vis_db->getWithDefault<string>("format", "hdf5");
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vis_db = db->getDatabase("Visualization");
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std::vector<IO::MeshDataStruct> visData;
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fillHalo<double> fillData(Dm->Comm, Dm->rank_info,
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{Dm->Nx - 2, Dm->Ny - 2, Dm->Nz - 2},
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{1, 1, 1}, 0, 1);
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auto PhaseVar = std::make_shared<IO::Variable>();
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auto SignDistVar = std::make_shared<IO::Variable>();
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IO::initialize("", format, "false");
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// Create the MeshDataStruct
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visData.resize(1);
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visData[0].meshName = "domain";
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visData[0].mesh = std::make_shared<IO::DomainMesh>(
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Dm->rank_info, Dm->Nx - 2, Dm->Ny - 2, Dm->Nz - 2, Dm->Lx, Dm->Ly,
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Dm->Lz);
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SignDistVar->name = "SignDist";
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SignDistVar->type = IO::VariableType::VolumeVariable;
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SignDistVar->dim = 1;
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SignDistVar->data.resize(Dm->Nx - 2, Dm->Ny - 2, Dm->Nz - 2);
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visData[0].vars.push_back(SignDistVar);
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PhaseVar->name = "Phase";
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PhaseVar->type = IO::VariableType::VolumeVariable;
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PhaseVar->dim = 1;
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PhaseVar->data.resize(Dm->Nx - 2, Dm->Ny - 2, Dm->Nz - 2);
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visData[0].vars.push_back(PhaseVar);
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Array<double> &SignData = visData[0].vars[0]->data;
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Array<double> &PhaseData = visData[0].vars[1]->data;
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ASSERT(visData[0].vars[0]->name == "SignDist");
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ASSERT(visData[0].vars[1]->name == "Phase");
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fillData.copy(Averages->SDs, SignData);
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fillData.copy(Averages->SDn, PhaseData);
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int timestep = 0;
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IO::writeData(timestep, visData, Dm->Comm);
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}
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PROFILE_STOP("Main");
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PROFILE_SAVE("TwoPhase",true);
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Utilities::shutdown();
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return 0;
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}
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