1004 lines
39 KiB
C++
1004 lines
39 KiB
C++
/*
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Copyright 2020 Equinor ASA
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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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Greyscale lattice boltzmann model
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*/
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#include "models/GreyscaleModel.h"
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#include "analysis/distance.h"
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#include "analysis/morphology.h"
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#include <stdlib.h>
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#include <time.h>
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template <class TYPE> void DeleteArray(const TYPE *p) { delete[] p; }
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ScaLBL_GreyscaleModel::ScaLBL_GreyscaleModel(int RANK, int NP,
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const Utilities::MPI &COMM)
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: rank(RANK), nprocs(NP), Restart(0), timestep(0), timestepMax(0), tau(0),
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tau_eff(0), Den(0), Fx(0), Fy(0), Fz(0), flux(0), din(0), dout(0),
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GreyPorosity(0), Nx(0), Ny(0), Nz(0), N(0), Np(0), nprocx(0), nprocy(0),
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nprocz(0), BoundaryCondition(0), Lx(0), Ly(0), Lz(0), comm(COMM) {
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SignDist.resize(Nx, Ny, Nz);
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SignDist.fill(0);
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}
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ScaLBL_GreyscaleModel::~ScaLBL_GreyscaleModel() {}
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void ScaLBL_GreyscaleModel::ReadParams(string filename) {
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// read the input database
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db = std::make_shared<Database>(filename);
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domain_db = db->getDatabase("Domain");
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greyscale_db = db->getDatabase("Greyscale");
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analysis_db = db->getDatabase("Analysis");
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vis_db = db->getDatabase("Visualization");
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// set defaults
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timestepMax = 100000;
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tau = 1.0;
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tau_eff = tau;
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Den = 1.0; //constant density
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tolerance = 0.01;
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Fx = Fy = Fz = 0.0;
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Restart = false;
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din = dout = 1.0;
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flux = 0.0;
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dp = 10.0; //unit of 'dp': voxel
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CollisionType = 1; //1: IMRT; 2: BGK; 3: MRT
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// ---------------------- Greyscale Model parameters -----------------------//
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if (greyscale_db->keyExists("timestepMax")) {
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timestepMax = greyscale_db->getScalar<int>("timestepMax");
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}
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if (greyscale_db->keyExists("tau")) {
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tau = greyscale_db->getScalar<double>("tau");
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}
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tau_eff = greyscale_db->getWithDefault<double>("tau_eff", tau);
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if (greyscale_db->keyExists("Den")) {
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Den = greyscale_db->getScalar<double>("Den");
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}
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if (greyscale_db->keyExists("dp")) {
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dp = greyscale_db->getScalar<double>("dp");
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}
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if (greyscale_db->keyExists("F")) {
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Fx = greyscale_db->getVector<double>("F")[0];
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Fy = greyscale_db->getVector<double>("F")[1];
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Fz = greyscale_db->getVector<double>("F")[2];
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}
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if (greyscale_db->keyExists("Restart")) {
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Restart = greyscale_db->getScalar<bool>("Restart");
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}
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if (greyscale_db->keyExists("din")) {
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din = greyscale_db->getScalar<double>("din");
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}
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if (greyscale_db->keyExists("dout")) {
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dout = greyscale_db->getScalar<double>("dout");
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}
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if (greyscale_db->keyExists("flux")) {
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flux = greyscale_db->getScalar<double>("flux");
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}
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if (greyscale_db->keyExists("tolerance")) {
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tolerance = greyscale_db->getScalar<double>("tolerance");
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}
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auto collision =
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greyscale_db->getWithDefault<std::string>("collision", "IMRT");
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if (collision == "BGK") {
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CollisionType = 2;
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} else if (collision == "MRT") {
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CollisionType = 3;
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}
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// ------------------------------------------------------------------------//
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//------------------------ Other Domain parameters ------------------------//
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BoundaryCondition = 0;
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if (greyscale_db->keyExists("BC")) {
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BoundaryCondition = greyscale_db->getScalar<int>("BC");
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} else if (domain_db->keyExists("BC")) {
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BoundaryCondition = domain_db->getScalar<int>("BC");
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}
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// ------------------------------------------------------------------------//
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}
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void ScaLBL_GreyscaleModel::SetDomain() {
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Dm = std::shared_ptr<Domain>(
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new Domain(domain_db, comm)); // full domain for analysis
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Mask = std::shared_ptr<Domain>(
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new Domain(domain_db, comm)); // mask domain removes immobile phases
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// domain parameters
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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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Lx = Dm->Lx;
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Ly = Dm->Ly;
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Lz = Dm->Lz;
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N = Nx * Ny * Nz;
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SignDist.resize(Nx, Ny, Nz);
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Velocity_x.resize(Nx, Ny, Nz);
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Velocity_y.resize(Nx, Ny, Nz);
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Velocity_z.resize(Nx, Ny, Nz);
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PorosityMap.resize(Nx, Ny, Nz);
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Pressure.resize(Nx, Ny, Nz);
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id = new signed char[N];
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for (int i = 0; i < Nx * Ny * Nz; i++)
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Dm->id[i] = 1; // initialize this way
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comm.barrier();
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Dm->CommInit();
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comm.barrier();
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// Read domain parameters
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rank = Dm->rank();
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nprocx = Dm->nprocx();
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nprocy = Dm->nprocy();
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nprocz = Dm->nprocz();
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}
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void ScaLBL_GreyscaleModel::ReadInput() {
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sprintf(LocalRankString, "%05d", rank);
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sprintf(LocalRankFilename, "%s%s", "ID.", LocalRankString);
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sprintf(LocalRestartFile, "%s%s", "Restart.", LocalRankString);
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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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Mask->Decomp(Filename);
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} else {
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if (rank == 0)
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printf(
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"Filename of input image is not found, reading ID.0* instead.");
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Mask->ReadIDs();
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}
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for (int i = 0; i < Nx * Ny * Nz; i++)
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id[i] = Mask->id[i]; // save what was read
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// Generate the signed distance map
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// Initialize the domain and communication
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Array<char> id_solid(Nx, Ny, Nz);
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// Solve for the position of the solid phase
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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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int n = k * Nx * Ny + j * Nx + i;
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// Initialize the solid phase
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signed char label = Mask->id[n];
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if (label > 0)
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id_solid(i, j, k) = 1;
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else
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id_solid(i, j, k) = 0;
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}
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}
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}
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// Initialize the signed distance function
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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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// Initialize distance to +/- 1
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SignDist(i, j, k) = 2.0 * double(id_solid(i, j, k)) - 1.0;
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}
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}
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}
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// MeanFilter(SignDist);
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if (rank == 0)
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printf("Initialized solid phase -- Converting to Signed Distance "
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"function \n");
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CalcDist(SignDist, id_solid, *Mask);
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if (rank == 0)
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cout << "Domain set." << endl;
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}
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/********************************************************
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* AssignComponentLabels *
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********************************************************/
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void ScaLBL_GreyscaleModel::AssignComponentLabels(double *Porosity,
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double *Permeability) {
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size_t NLABELS = 0;
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signed char VALUE = 0;
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double POROSITY = 0.f;
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double PERMEABILITY = 0.f;
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auto LabelList = greyscale_db->getVector<int>("ComponentLabels");
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auto PorosityList = greyscale_db->getVector<double>("PorosityList");
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auto PermeabilityList = greyscale_db->getVector<double>("PermeabilityList");
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NLABELS = LabelList.size();
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if (NLABELS != PorosityList.size()) {
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ERROR("Error: ComponentLabels and PorosityList must be the same "
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"length! \n");
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}
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// Assign the labels
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double *label_count;
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double *label_count_global;
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label_count = new double[NLABELS];
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label_count_global = new double[NLABELS];
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for (size_t idx = 0; idx < NLABELS; idx++)
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label_count[idx] = 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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int n = k * Nx * Ny + j * Nx + i;
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VALUE = id[n];
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// Assign the affinity from the paired list
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for (size_t idx = 0; idx < NLABELS; idx++) {
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//printf("idx=%i, value=%i, %i, \n",idx, VALUE,LabelList[idx]);
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if (VALUE == LabelList[idx]) {
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POROSITY = PorosityList[idx];
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label_count[idx] += 1.0;
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idx = NLABELS;
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//Mask->id[n] = 0; // set mask to zero since this is an immobile component
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}
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}
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int idx = Map(i, j, k);
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if (!(idx < 0)) {
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if (POROSITY <= 0.0) {
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ERROR("Error: Porosity for grey voxels must be 0.0 < "
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"Porosity <= 1.0 !\n");
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} else {
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Porosity[idx] = POROSITY;
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}
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}
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}
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}
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}
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if (NLABELS != PermeabilityList.size()) {
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ERROR("Error: ComponentLabels and PermeabilityList must be the same "
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"length! \n");
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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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int n = k * Nx * Ny + j * Nx + i;
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VALUE = id[n];
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// Assign the affinity from the paired list
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for (size_t idx = 0; idx < NLABELS; idx++) {
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//printf("idx=%i, value=%i, %i, \n",idx, VALUE,LabelList[idx]);
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if (VALUE == LabelList[idx]) {
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PERMEABILITY = PermeabilityList[idx];
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idx = NLABELS;
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//Mask->id[n] = 0; // set mask to zero since this is an immobile component
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}
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}
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int idx = Map(i, j, k);
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if (!(idx < 0)) {
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if (PERMEABILITY <= 0.0) {
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ERROR("Error: Permeability for grey voxel must be > "
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"0.0 ! \n");
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} else {
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Permeability[idx] =
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PERMEABILITY / Dm->voxel_length / Dm->voxel_length;
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}
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}
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}
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}
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}
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// Set Dm to match Mask
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for (int i = 0; i < Nx * Ny * Nz; i++)
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Dm->id[i] = Mask->id[i];
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for (size_t idx = 0; idx < NLABELS; idx++)
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label_count_global[idx] = Dm->Comm.sumReduce(label_count[idx]);
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//Initialize a weighted porosity after considering grey voxels
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GreyPorosity = 0.0;
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for (unsigned int idx = 0; idx < NLABELS; idx++) {
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double volume_fraction =
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double(label_count_global[idx]) /
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double((Nx - 2) * (Ny - 2) * (Nz - 2) * nprocs);
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GreyPorosity += volume_fraction * PorosityList[idx];
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}
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if (rank == 0) {
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printf("Image resolution: %.5g [um/voxel]\n", Dm->voxel_length);
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printf("Number of component labels: %lu \n", NLABELS);
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for (unsigned int idx = 0; idx < NLABELS; idx++) {
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VALUE = LabelList[idx];
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POROSITY = PorosityList[idx];
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PERMEABILITY = PermeabilityList[idx];
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double volume_fraction =
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double(label_count_global[idx]) /
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double((Nx - 2) * (Ny - 2) * (Nz - 2) * nprocs);
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printf(" label=%d: porosity=%.3g, permeability=%.3g [um^2] "
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"(=%.3g [voxel^2]), volume fraction=%.3g\n",
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VALUE, POROSITY, PERMEABILITY,
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PERMEABILITY / Dm->voxel_length / Dm->voxel_length,
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volume_fraction);
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printf(" effective porosity=%.3g\n",
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volume_fraction * POROSITY);
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}
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printf("The weighted porosity, considering both open and grey voxels, "
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"is %.3g\n",
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GreyPorosity);
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}
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}
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void ScaLBL_GreyscaleModel::AssignComponentLabels(
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double *Porosity, double *Permeability,
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const vector<std::string> &File_poro,
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const vector<std::string> &File_perm) {
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double *Porosity_host, *Permeability_host;
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Porosity_host = new double[N];
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Permeability_host = new double[N];
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double POROSITY = 0.f;
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double PERMEABILITY = 0.f;
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//Initialize a weighted porosity after considering grey voxels
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double GreyPorosity_loc = 0.0;
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GreyPorosity = 0.0;
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//double label_count_loc = 0.0;
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//double label_count_glb = 0.0;
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Mask->ReadFromFile(File_poro[0], File_poro[1], Porosity_host);
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Mask->ReadFromFile(File_perm[0], File_perm[1], Permeability_host);
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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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int idx = Map(i, j, k);
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if (!(idx < 0)) {
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int n = k * Nx * Ny + j * Nx + i;
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POROSITY = Porosity_host[n];
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PERMEABILITY = Permeability_host[n];
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if (POROSITY <= 0.0) {
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ERROR("Error: Porosity for grey voxels must be 0.0 < "
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"Porosity <= 1.0 !\n");
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} else if (PERMEABILITY <= 0.0) {
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ERROR("Error: Permeability for grey voxel must be > "
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"0.0 ! \n");
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} else {
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Porosity[idx] = POROSITY;
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Permeability[idx] = PERMEABILITY;
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GreyPorosity_loc += POROSITY;
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//label_count_loc += 1.0;
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}
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}
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}
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}
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}
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GreyPorosity = Dm->Comm.sumReduce(GreyPorosity_loc);
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GreyPorosity =
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GreyPorosity / double((Nx - 2) * (Ny - 2) * (Nz - 2) * nprocs);
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if (rank == 0) {
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printf("Image resolution: %.5g [um/voxel]\n", Dm->voxel_length);
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printf("The weighted porosity, considering both open and grey voxels, "
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"is %.3g\n",
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GreyPorosity);
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}
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delete[] Porosity_host;
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delete[] Permeability_host;
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}
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void ScaLBL_GreyscaleModel::Create() {
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/*
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* This function creates the variables needed to run a LBM
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*/
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//.........................................................
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// don't perform computations at the eight corners
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//id[0] = id[Nx-1] = id[(Ny-1)*Nx] = id[(Ny-1)*Nx + Nx-1] = 0;
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//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;
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//.........................................................
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// Initialize communication structures in averaging domain
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for (int i = 0; i < Nx * Ny * Nz; i++)
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Dm->id[i] = Mask->id[i];
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Mask->CommInit();
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Np = Mask->PoreCount();
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//...........................................................................
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if (rank == 0)
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printf("Create ScaLBL_Communicator \n");
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// Create a communicator for the device (will use optimized layout)
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// ScaLBL_Communicator ScaLBL_Comm(Mask); // original
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ScaLBL_Comm =
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std::shared_ptr<ScaLBL_Communicator>(new ScaLBL_Communicator(Mask));
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int Npad = (Np / 16 + 2) * 16;
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if (rank == 0)
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printf("Set up memory efficient layout, %i | %i | %i \n", Np, Npad, N);
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Map.resize(Nx, Ny, Nz);
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Map.fill(-2);
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auto neighborList = new int[18 * Npad];
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Np = ScaLBL_Comm->MemoryOptimizedLayoutAA(Map, neighborList,
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Mask->id.data(), Np, 1);
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comm.barrier();
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//...........................................................................
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// MAIN VARIABLES ALLOCATED HERE
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//...........................................................................
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// LBM variables
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if (rank == 0)
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printf("Allocating distributions \n");
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//......................device distributions.................................
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dist_mem_size = Np * sizeof(double);
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neighborSize = 18 * (Np * sizeof(int));
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//...........................................................................
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ScaLBL_AllocateDeviceMemory((void **)&NeighborList, neighborSize);
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ScaLBL_AllocateDeviceMemory((void **)&fq, 19 * dist_mem_size);
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ScaLBL_AllocateDeviceMemory((void **)&Permeability, sizeof(double) * Np);
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ScaLBL_AllocateDeviceMemory((void **)&Porosity, sizeof(double) * Np);
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ScaLBL_AllocateDeviceMemory((void **)&Pressure_dvc, sizeof(double) * Np);
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ScaLBL_AllocateDeviceMemory((void **)&Velocity, 3 * sizeof(double) * Np);
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//...........................................................................
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// Update GPU data structures
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if (rank == 0)
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printf("Setting up device neighbor list \n");
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fflush(stdout);
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// copy the neighbor list
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ScaLBL_CopyToDevice(NeighborList, neighborList, neighborSize);
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// initialize phi based on PhaseLabel (include solid component labels)
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double *Poros, *Perm;
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Poros = new double[Np];
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Perm = new double[Np];
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if (greyscale_db->keyExists("FileVoxelPorosityMap")) {
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//NOTE: FileVoxel**Map is a vector, including "file_name, datatype"
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auto File_poro =
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greyscale_db->getVector<std::string>("FileVoxelPorosityMap");
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auto File_perm =
|
|
greyscale_db->getVector<std::string>("FileVoxelPermeabilityMap");
|
|
AssignComponentLabels(Poros, Perm, File_poro, File_perm);
|
|
} else if (greyscale_db->keyExists("PorosityList")) {
|
|
//initialize voxel porosity and perm from the input list
|
|
AssignComponentLabels(Poros, Perm);
|
|
} else {
|
|
ERROR("Error: PorosityList or FilenameVoxelPorosityMap cannot be "
|
|
"found! \n");
|
|
}
|
|
ScaLBL_CopyToDevice(Porosity, Poros, Np * sizeof(double));
|
|
ScaLBL_CopyToDevice(Permeability, Perm, Np * sizeof(double));
|
|
delete[] Poros;
|
|
delete[] Perm;
|
|
}
|
|
|
|
void ScaLBL_GreyscaleModel::Initialize() {
|
|
if (rank == 0)
|
|
printf("Initializing distributions \n");
|
|
//TODO: for BGK, you need to consider voxel porosity
|
|
// for IMRT, the whole set of feq is different
|
|
// if in the future you have different collison mode, need to write two set of initialization functions
|
|
if (CollisionType == 1) {
|
|
ScaLBL_D3Q19_GreyIMRT_Init(fq, Np, Den);
|
|
if (rank == 0)
|
|
printf("Collision model: Incompressible MRT.\n");
|
|
} else if (CollisionType == 2) {
|
|
ScaLBL_D3Q19_Init(fq, Np);
|
|
if (rank == 0)
|
|
printf("Collision model: BGK.\n");
|
|
} else if (CollisionType == 3) {
|
|
ScaLBL_D3Q19_Init(fq, Np);
|
|
if (rank == 0)
|
|
printf("Collision model: MRT.\n");
|
|
} else {
|
|
if (rank == 0)
|
|
printf("Unknown collison type! IMRT collision is used.\n");
|
|
ScaLBL_D3Q19_GreyIMRT_Init(fq, Np, Den);
|
|
CollisionType = 1;
|
|
greyscale_db->putScalar<std::string>("collision", "IMRT");
|
|
}
|
|
|
|
if (Restart == true) {
|
|
if (rank == 0) {
|
|
printf("Initializing distributions from Restart! \n");
|
|
}
|
|
double value;
|
|
double *cfq;
|
|
cfq = new double[19 * Np];
|
|
ifstream File(LocalRestartFile, ios::binary);
|
|
for (int n = 0; n < Np; n++) {
|
|
// Read the distributions
|
|
for (int q = 0; q < 19; q++) {
|
|
File.read((char *)&value, sizeof(value));
|
|
cfq[q * Np + n] = value;
|
|
}
|
|
}
|
|
File.close();
|
|
|
|
// Copy the restart data to the GPU
|
|
ScaLBL_CopyToDevice(fq, cfq, 19 * Np * sizeof(double));
|
|
ScaLBL_DeviceBarrier();
|
|
|
|
comm.barrier();
|
|
}
|
|
}
|
|
|
|
void ScaLBL_GreyscaleModel::Run() {
|
|
int nprocs = nprocx * nprocy * nprocz;
|
|
const RankInfoStruct rank_info(rank, nprocx, nprocy, nprocz);
|
|
|
|
int analysis_interval =
|
|
1000; // number of timesteps in between in situ analysis
|
|
int visualization_interval = 1000;
|
|
int restart_interval =
|
|
10000; // number of timesteps in between in saving distributions for restart
|
|
if (analysis_db->keyExists("analysis_interval")) {
|
|
analysis_interval = analysis_db->getScalar<int>("analysis_interval");
|
|
}
|
|
if (analysis_db->keyExists("visualization_interval")) {
|
|
visualization_interval =
|
|
analysis_db->getScalar<int>("visualization_interval");
|
|
}
|
|
if (analysis_db->keyExists("restart_interval")) {
|
|
restart_interval = analysis_db->getScalar<int>("restart_interval");
|
|
}
|
|
if (greyscale_db->keyExists("timestep")) {
|
|
timestep = greyscale_db->getScalar<int>("timestep");
|
|
}
|
|
|
|
if (rank == 0) {
|
|
printf("********************************************************\n");
|
|
printf("No. of timesteps: %i \n", timestepMax);
|
|
fflush(stdout);
|
|
}
|
|
|
|
//.......create and start timer............
|
|
ScaLBL_DeviceBarrier();
|
|
comm.barrier();
|
|
//.........................................
|
|
|
|
Minkowski Morphology(Mask);
|
|
|
|
//************ MAIN ITERATION LOOP ***************************************/
|
|
PROFILE_START("Loop");
|
|
auto current_db = db->cloneDatabase();
|
|
double rlx = 1.0 / tau;
|
|
double rlx_eff = 1.0 / tau_eff;
|
|
double error = 1.0;
|
|
double flow_rate_previous = 0.0;
|
|
auto t1 = std::chrono::system_clock::now();
|
|
while (timestep < timestepMax && error > tolerance) {
|
|
//************************************************************************/
|
|
// *************ODD TIMESTEP*************//
|
|
timestep++;
|
|
ScaLBL_Comm->SendD3Q19AA(fq); //READ FROM NORMAL
|
|
switch (CollisionType) {
|
|
case 1:
|
|
ScaLBL_D3Q19_AAodd_Greyscale_IMRT(
|
|
NeighborList, fq, ScaLBL_Comm->FirstInterior(),
|
|
ScaLBL_Comm->LastInterior(), Np, rlx, rlx_eff, Fx, Fy, Fz,
|
|
Porosity, Permeability, Velocity, Den, Pressure_dvc);
|
|
break;
|
|
case 2:
|
|
ScaLBL_D3Q19_AAodd_Greyscale(
|
|
NeighborList, fq, ScaLBL_Comm->FirstInterior(),
|
|
ScaLBL_Comm->LastInterior(), Np, rlx, rlx_eff, Fx, Fy, Fz,
|
|
Porosity, Permeability, Velocity, Pressure_dvc);
|
|
break;
|
|
case 3:
|
|
ScaLBL_D3Q19_AAodd_Greyscale_MRT(
|
|
NeighborList, fq, ScaLBL_Comm->FirstInterior(),
|
|
ScaLBL_Comm->LastInterior(), Np, rlx, rlx_eff, Fx, Fy, Fz,
|
|
Porosity, Permeability, Velocity, Den, Pressure_dvc);
|
|
break;
|
|
default:
|
|
ScaLBL_D3Q19_AAodd_Greyscale_IMRT(
|
|
NeighborList, fq, ScaLBL_Comm->FirstInterior(),
|
|
ScaLBL_Comm->LastInterior(), Np, rlx, rlx_eff, Fx, Fy, Fz,
|
|
Porosity, Permeability, Velocity, Den, Pressure_dvc);
|
|
break;
|
|
}
|
|
ScaLBL_Comm->RecvD3Q19AA(fq); //WRITE INTO OPPOSITE
|
|
ScaLBL_DeviceBarrier();
|
|
// Set BCs
|
|
if (BoundaryCondition == 3) {
|
|
ScaLBL_Comm->D3Q19_Pressure_BC_z(NeighborList, fq, din, timestep);
|
|
ScaLBL_Comm->D3Q19_Pressure_BC_Z(NeighborList, fq, dout, timestep);
|
|
}
|
|
switch (CollisionType) {
|
|
case 1:
|
|
ScaLBL_D3Q19_AAodd_Greyscale_IMRT(
|
|
NeighborList, fq, 0, ScaLBL_Comm->LastExterior(), Np, rlx,
|
|
rlx_eff, Fx, Fy, Fz, Porosity, Permeability, Velocity, Den,
|
|
Pressure_dvc);
|
|
break;
|
|
case 2:
|
|
ScaLBL_D3Q19_AAodd_Greyscale(NeighborList, fq, 0,
|
|
ScaLBL_Comm->LastExterior(), Np, rlx,
|
|
rlx_eff, Fx, Fy, Fz, Porosity,
|
|
Permeability, Velocity, Pressure_dvc);
|
|
break;
|
|
case 3:
|
|
ScaLBL_D3Q19_AAodd_Greyscale_MRT(
|
|
NeighborList, fq, 0, ScaLBL_Comm->LastExterior(), Np, rlx,
|
|
rlx_eff, Fx, Fy, Fz, Porosity, Permeability, Velocity, Den,
|
|
Pressure_dvc);
|
|
break;
|
|
default:
|
|
ScaLBL_D3Q19_AAodd_Greyscale_IMRT(
|
|
NeighborList, fq, 0, ScaLBL_Comm->LastExterior(), Np, rlx,
|
|
rlx_eff, Fx, Fy, Fz, Porosity, Permeability, Velocity, Den,
|
|
Pressure_dvc);
|
|
break;
|
|
}
|
|
ScaLBL_DeviceBarrier();
|
|
comm.barrier();
|
|
|
|
// *************EVEN TIMESTEP*************//
|
|
timestep++;
|
|
ScaLBL_Comm->SendD3Q19AA(fq); //READ FORM NORMAL
|
|
switch (CollisionType) {
|
|
case 1:
|
|
ScaLBL_D3Q19_AAeven_Greyscale_IMRT(
|
|
fq, ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(),
|
|
Np, rlx, rlx_eff, Fx, Fy, Fz, Porosity, Permeability, Velocity,
|
|
Den, Pressure_dvc);
|
|
break;
|
|
case 2:
|
|
ScaLBL_D3Q19_AAeven_Greyscale(fq, ScaLBL_Comm->FirstInterior(),
|
|
ScaLBL_Comm->LastInterior(), Np, rlx,
|
|
rlx_eff, Fx, Fy, Fz, Porosity,
|
|
Permeability, Velocity, Pressure_dvc);
|
|
break;
|
|
case 3:
|
|
ScaLBL_D3Q19_AAeven_Greyscale_MRT(
|
|
fq, ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(),
|
|
Np, rlx, rlx_eff, Fx, Fy, Fz, Porosity, Permeability, Velocity,
|
|
Den, Pressure_dvc);
|
|
break;
|
|
default:
|
|
ScaLBL_D3Q19_AAeven_Greyscale_IMRT(
|
|
fq, ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(),
|
|
Np, rlx, rlx_eff, Fx, Fy, Fz, Porosity, Permeability, Velocity,
|
|
Den, Pressure_dvc);
|
|
break;
|
|
}
|
|
ScaLBL_Comm->RecvD3Q19AA(fq); //WRITE INTO OPPOSITE
|
|
ScaLBL_DeviceBarrier();
|
|
// Set BCs
|
|
if (BoundaryCondition == 3) {
|
|
ScaLBL_Comm->D3Q19_Pressure_BC_z(NeighborList, fq, din, timestep);
|
|
ScaLBL_Comm->D3Q19_Pressure_BC_Z(NeighborList, fq, dout, timestep);
|
|
}
|
|
switch (CollisionType) {
|
|
case 1:
|
|
ScaLBL_D3Q19_AAeven_Greyscale_IMRT(
|
|
fq, 0, ScaLBL_Comm->LastExterior(), Np, rlx, rlx_eff, Fx, Fy,
|
|
Fz, Porosity, Permeability, Velocity, Den, Pressure_dvc);
|
|
break;
|
|
case 2:
|
|
ScaLBL_D3Q19_AAeven_Greyscale(
|
|
fq, 0, ScaLBL_Comm->LastExterior(), Np, rlx, rlx_eff, Fx, Fy,
|
|
Fz, Porosity, Permeability, Velocity, Pressure_dvc);
|
|
break;
|
|
case 3:
|
|
ScaLBL_D3Q19_AAeven_Greyscale_MRT(
|
|
fq, 0, ScaLBL_Comm->LastExterior(), Np, rlx, rlx_eff, Fx, Fy,
|
|
Fz, Porosity, Permeability, Velocity, Den, Pressure_dvc);
|
|
break;
|
|
default:
|
|
ScaLBL_D3Q19_AAeven_Greyscale_IMRT(
|
|
fq, 0, ScaLBL_Comm->LastExterior(), Np, rlx, rlx_eff, Fx, Fy,
|
|
Fz, Porosity, Permeability, Velocity, Den, Pressure_dvc);
|
|
break;
|
|
}
|
|
ScaLBL_DeviceBarrier();
|
|
comm.barrier();
|
|
//************************************************************************/
|
|
|
|
if (timestep % analysis_interval == 0) {
|
|
ScaLBL_Comm->RegularLayout(Map, &Velocity[0], Velocity_x);
|
|
ScaLBL_Comm->RegularLayout(Map, &Velocity[Np], Velocity_y);
|
|
ScaLBL_Comm->RegularLayout(Map, &Velocity[2 * Np], Velocity_z);
|
|
//ScaLBL_Comm->RegularLayout(Map,Porosity,PorosityMap);
|
|
//ScaLBL_Comm->RegularLayout(Map,Pressure_dvc,Pressure);
|
|
|
|
double count_loc = 0;
|
|
double count;
|
|
double vax, vay, vaz;
|
|
double vax_loc, vay_loc, vaz_loc;
|
|
//double px_loc,py_loc,pz_loc;
|
|
//double px,py,pz;
|
|
//double mass_loc,mass_glb;
|
|
|
|
//parameters for domain average
|
|
int64_t imin, jmin, kmin, kmax;
|
|
// If external boundary conditions are set, do not average over the inlet and outlet
|
|
kmin = 1;
|
|
kmax = Nz - 1;
|
|
//In case user forgets to specify the inlet/outlet buffer layers for BC>0
|
|
if (BoundaryCondition > 0 && Dm->kproc() == 0)
|
|
kmin = 4;
|
|
if (BoundaryCondition > 0 && Dm->kproc() == Dm->nprocz() - 1)
|
|
kmax = Nz - 4;
|
|
|
|
imin = jmin = 1;
|
|
// If inlet/outlet layers exist use these as default
|
|
//if (Dm->inlet_layers_x > 0) imin = Dm->inlet_layers_x;
|
|
//if (Dm->inlet_layers_y > 0) jmin = Dm->inlet_layers_y;
|
|
if (BoundaryCondition > 0 && Dm->inlet_layers_z > 0 &&
|
|
Dm->kproc() == 0)
|
|
kmin = 1 + Dm->inlet_layers_z; //"1" indicates the halo layer
|
|
if (BoundaryCondition > 0 && Dm->outlet_layers_z > 0 &&
|
|
Dm->kproc() == Dm->nprocz() - 1)
|
|
kmax = Nz - 1 - Dm->outlet_layers_z;
|
|
|
|
vax_loc = vay_loc = vaz_loc = 0.f;
|
|
for (int k = kmin; k < kmax; k++) {
|
|
for (int j = jmin; j < Ny - 1; j++) {
|
|
for (int i = imin; i < Nx - 1; i++) {
|
|
if (SignDist(i, j, k) > 0) {
|
|
vax_loc += Velocity_x(i, j, k);
|
|
vay_loc += Velocity_y(i, j, k);
|
|
vaz_loc += Velocity_z(i, j, k);
|
|
count_loc += 1.0;
|
|
}
|
|
}
|
|
}
|
|
}
|
|
vax = Dm->Comm.sumReduce(vax_loc);
|
|
vay = Dm->Comm.sumReduce(vay_loc);
|
|
vaz = Dm->Comm.sumReduce(vaz_loc);
|
|
count = Dm->Comm.sumReduce(count_loc);
|
|
|
|
vax /= count;
|
|
vay /= count;
|
|
vaz /= count;
|
|
|
|
double force_mag = sqrt(Fx * Fx + Fy * Fy + Fz * Fz);
|
|
double dir_x = Fx / force_mag;
|
|
double dir_y = Fy / force_mag;
|
|
double dir_z = Fz / force_mag;
|
|
if (force_mag == 0.0) {
|
|
// default to z direction
|
|
dir_x = 0.0;
|
|
dir_y = 0.0;
|
|
dir_z = 1.0;
|
|
force_mag = 1.0;
|
|
}
|
|
//double flow_rate = (px*dir_x + py*dir_y + pz*dir_z)/mass_glb;
|
|
double flow_rate = (vax * dir_x + vay * dir_y + vaz * dir_z);
|
|
|
|
error = fabs(flow_rate - flow_rate_previous) / fabs(flow_rate);
|
|
flow_rate_previous = flow_rate;
|
|
|
|
//if (rank==0) printf("Computing Minkowski functionals \n");
|
|
Morphology.ComputeScalar(SignDist, 0.f);
|
|
//Morphology.PrintAll();
|
|
double mu = (tau - 0.5) / 3.f;
|
|
double Vs = Morphology.V();
|
|
double As = Morphology.A();
|
|
double Hs = Morphology.H();
|
|
double Xs = Morphology.X();
|
|
Vs = Dm->Comm.sumReduce(Vs);
|
|
As = Dm->Comm.sumReduce(As);
|
|
Hs = Dm->Comm.sumReduce(Hs);
|
|
Xs = Dm->Comm.sumReduce(Xs);
|
|
|
|
double h = Dm->voxel_length;
|
|
//double absperm = h*h*mu*Mask->Porosity()*flow_rate / force_mag;
|
|
double absperm = h * h * mu * GreyPorosity * flow_rate / force_mag;
|
|
|
|
if (rank == 0) {
|
|
printf(" AbsPerm = %.5g [micron^2]\n", absperm);
|
|
bool WriteHeader = false;
|
|
FILE *log_file = fopen("Permeability.csv", "r");
|
|
if (log_file != NULL)
|
|
fclose(log_file);
|
|
else
|
|
WriteHeader = true;
|
|
log_file = fopen("Permeability.csv", "a");
|
|
if (WriteHeader)
|
|
fprintf(log_file, "timestep Fx Fy Fz mu Vs As Hs Xs vax "
|
|
"vay vaz AbsPerm \n");
|
|
|
|
fprintf(log_file,
|
|
"%i %.8g %.8g %.8g %.8g %.8g %.8g %.8g %.8g %.8g %.8g "
|
|
"%.8g %.8g\n",
|
|
timestep, Fx, Fy, Fz, mu, h * h * h * Vs, h * h * As,
|
|
h * Hs, Xs, vax, vay, vaz, absperm);
|
|
fclose(log_file);
|
|
}
|
|
}
|
|
|
|
if (timestep % visualization_interval == 0) {
|
|
VelocityField();
|
|
}
|
|
|
|
if (timestep % restart_interval == 0) {
|
|
//Use rank=0 write out Restart.db
|
|
if (rank == 0) {
|
|
greyscale_db->putScalar<int>("timestep", timestep);
|
|
greyscale_db->putScalar<bool>("Restart", true);
|
|
current_db->putDatabase("Greyscale", greyscale_db);
|
|
std::ofstream OutStream("Restart.db");
|
|
current_db->print(OutStream, "");
|
|
OutStream.close();
|
|
}
|
|
//Write out Restart data.
|
|
std::shared_ptr<double> cfq;
|
|
cfq = std::shared_ptr<double>(new double[19 * Np],
|
|
DeleteArray<double>);
|
|
ScaLBL_CopyToHost(
|
|
cfq.get(), fq,
|
|
19 * Np * sizeof(double)); // Copy restart data to the CPU
|
|
|
|
FILE *RESTARTFILE;
|
|
RESTARTFILE = fopen(LocalRestartFile, "wb");
|
|
fwrite(cfq.get(), sizeof(double), 19 * Np, RESTARTFILE);
|
|
fclose(RESTARTFILE);
|
|
comm.barrier();
|
|
}
|
|
}
|
|
|
|
PROFILE_STOP("Loop");
|
|
PROFILE_SAVE("lbpm_greyscale_simulator", 1);
|
|
//************************************************************************
|
|
ScaLBL_DeviceBarrier();
|
|
comm.barrier();
|
|
if (rank == 0)
|
|
printf("---------------------------------------------------------------"
|
|
"----\n");
|
|
// Compute the walltime per timestep
|
|
auto t2 = std::chrono::system_clock::now();
|
|
double cputime = std::chrono::duration<double>(t2 - t1).count() / timestep;
|
|
// Performance obtained from each node
|
|
double MLUPS = double(Np) / cputime / 1000000;
|
|
|
|
if (rank == 0)
|
|
printf("********************************************************\n");
|
|
if (rank == 0)
|
|
printf("CPU time = %f \n", cputime);
|
|
if (rank == 0)
|
|
printf("Lattice update rate (per core)= %f MLUPS \n", MLUPS);
|
|
MLUPS *= nprocs;
|
|
if (rank == 0)
|
|
printf("Lattice update rate (total)= %f MLUPS \n", MLUPS);
|
|
if (rank == 0)
|
|
printf("********************************************************\n");
|
|
|
|
// ************************************************************************
|
|
}
|
|
|
|
void ScaLBL_GreyscaleModel::VelocityField() {
|
|
|
|
std::vector<IO::MeshDataStruct> visData;
|
|
fillHalo<double> fillData(Dm->Comm, Dm->rank_info,
|
|
{Dm->Nx - 2, Dm->Ny - 2, Dm->Nz - 2}, {1, 1, 1},
|
|
0, 1);
|
|
|
|
auto VxVar = std::make_shared<IO::Variable>();
|
|
auto VyVar = std::make_shared<IO::Variable>();
|
|
auto VzVar = std::make_shared<IO::Variable>();
|
|
auto SignDistVar = std::make_shared<IO::Variable>();
|
|
auto PressureVar = std::make_shared<IO::Variable>();
|
|
|
|
IO::initialize("", "silo", "false");
|
|
// 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 =
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std::make_shared<IO::DomainMesh>(Dm->rank_info, Dm->Nx - 2, Dm->Ny - 2,
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Dm->Nz - 2, Dm->Lx, Dm->Ly, 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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|
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VxVar->name = "Velocity_x";
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VxVar->type = IO::VariableType::VolumeVariable;
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VxVar->dim = 1;
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VxVar->data.resize(Dm->Nx - 2, Dm->Ny - 2, Dm->Nz - 2);
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visData[0].vars.push_back(VxVar);
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VyVar->name = "Velocity_y";
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VyVar->type = IO::VariableType::VolumeVariable;
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VyVar->dim = 1;
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VyVar->data.resize(Dm->Nx - 2, Dm->Ny - 2, Dm->Nz - 2);
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visData[0].vars.push_back(VyVar);
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VzVar->name = "Velocity_z";
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|
VzVar->type = IO::VariableType::VolumeVariable;
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VzVar->dim = 1;
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VzVar->data.resize(Dm->Nx - 2, Dm->Ny - 2, Dm->Nz - 2);
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visData[0].vars.push_back(VzVar);
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|
|
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PressureVar->name = "Pressure";
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PressureVar->type = IO::VariableType::VolumeVariable;
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PressureVar->dim = 1;
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PressureVar->data.resize(Dm->Nx - 2, Dm->Ny - 2, Dm->Nz - 2);
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visData[0].vars.push_back(PressureVar);
|
|
|
|
Array<double> &SignData = visData[0].vars[0]->data;
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|
Array<double> &VelxData = visData[0].vars[1]->data;
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Array<double> &VelyData = visData[0].vars[2]->data;
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Array<double> &VelzData = visData[0].vars[3]->data;
|
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Array<double> &PressureData = visData[0].vars[4]->data;
|
|
|
|
ASSERT(visData[0].vars[0]->name == "SignDist");
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|
ASSERT(visData[0].vars[1]->name == "Velocity_x");
|
|
ASSERT(visData[0].vars[2]->name == "Velocity_y");
|
|
ASSERT(visData[0].vars[3]->name == "Velocity_z");
|
|
ASSERT(visData[0].vars[4]->name == "Pressure");
|
|
|
|
ScaLBL_Comm->RegularLayout(Map, &Velocity[0], Velocity_x);
|
|
ScaLBL_Comm->RegularLayout(Map, &Velocity[Np], Velocity_y);
|
|
ScaLBL_Comm->RegularLayout(Map, &Velocity[2 * Np], Velocity_z);
|
|
ScaLBL_Comm->RegularLayout(Map, Pressure_dvc, Pressure);
|
|
|
|
fillData.copy(SignDist, SignData);
|
|
fillData.copy(Velocity_x, VelxData);
|
|
fillData.copy(Velocity_y, VelyData);
|
|
fillData.copy(Velocity_z, VelzData);
|
|
fillData.copy(Pressure, PressureData);
|
|
|
|
IO::writeData(timestep, visData, Dm->Comm);
|
|
}
|
|
|
|
void ScaLBL_GreyscaleModel::WriteDebug() {
|
|
// Copy back final phase indicator field and convert to regular layout
|
|
DoubleArray PhaseField(Nx, Ny, Nz);
|
|
|
|
//ScaLBL_CopyToHost(Porosity.data(), Poros, sizeof(double)*N);
|
|
|
|
// FILE *OUTFILE;
|
|
// sprintf(LocalRankFilename,"Phase.%05i.raw",rank);
|
|
// OUTFILE = fopen(LocalRankFilename,"wb");
|
|
// fwrite(PhaseField.data(),8,N,OUTFILE);
|
|
// fclose(OUTFILE);
|
|
//
|
|
// ScaLBL_Comm->RegularLayout(Map,&Den[0],PhaseField);
|
|
// FILE *AFILE;
|
|
// sprintf(LocalRankFilename,"A.%05i.raw",rank);
|
|
// AFILE = fopen(LocalRankFilename,"wb");
|
|
// fwrite(PhaseField.data(),8,N,AFILE);
|
|
// fclose(AFILE);
|
|
//
|
|
// ScaLBL_Comm->RegularLayout(Map,&Den[Np],PhaseField);
|
|
// FILE *BFILE;
|
|
// sprintf(LocalRankFilename,"B.%05i.raw",rank);
|
|
// BFILE = fopen(LocalRankFilename,"wb");
|
|
// fwrite(PhaseField.data(),8,N,BFILE);
|
|
// fclose(BFILE);
|
|
//
|
|
// ScaLBL_Comm->RegularLayout(Map,Pressure,PhaseField);
|
|
// FILE *PFILE;
|
|
// sprintf(LocalRankFilename,"Pressure.%05i.raw",rank);
|
|
// PFILE = fopen(LocalRankFilename,"wb");
|
|
// fwrite(PhaseField.data(),8,N,PFILE);
|
|
// fclose(PFILE);
|
|
|
|
ScaLBL_Comm->RegularLayout(Map, &Velocity[0], PhaseField);
|
|
FILE *VELX_FILE;
|
|
sprintf(LocalRankFilename, "Velocity_X.%05i.raw", rank);
|
|
VELX_FILE = fopen(LocalRankFilename, "wb");
|
|
fwrite(PhaseField.data(), 8, N, VELX_FILE);
|
|
fclose(VELX_FILE);
|
|
|
|
ScaLBL_Comm->RegularLayout(Map, &Velocity[Np], PhaseField);
|
|
FILE *VELY_FILE;
|
|
sprintf(LocalRankFilename, "Velocity_Y.%05i.raw", rank);
|
|
VELY_FILE = fopen(LocalRankFilename, "wb");
|
|
fwrite(PhaseField.data(), 8, N, VELY_FILE);
|
|
fclose(VELY_FILE);
|
|
|
|
ScaLBL_Comm->RegularLayout(Map, &Velocity[2 * Np], PhaseField);
|
|
FILE *VELZ_FILE;
|
|
sprintf(LocalRankFilename, "Velocity_Z.%05i.raw", rank);
|
|
VELZ_FILE = fopen(LocalRankFilename, "wb");
|
|
fwrite(PhaseField.data(), 8, N, VELZ_FILE);
|
|
fclose(VELZ_FILE);
|
|
|
|
ScaLBL_Comm->RegularLayout(Map, &Porosity[0], PhaseField);
|
|
FILE *POROS_FILE;
|
|
sprintf(LocalRankFilename, "Porosity.%05i.raw", rank);
|
|
POROS_FILE = fopen(LocalRankFilename, "wb");
|
|
fwrite(PhaseField.data(), 8, N, POROS_FILE);
|
|
fclose(POROS_FILE);
|
|
|
|
ScaLBL_Comm->RegularLayout(Map, &Permeability[0], PhaseField);
|
|
FILE *PERM_FILE;
|
|
sprintf(LocalRankFilename, "Permeability.%05i.raw", rank);
|
|
PERM_FILE = fopen(LocalRankFilename, "wb");
|
|
fwrite(PhaseField.data(), 8, N, PERM_FILE);
|
|
fclose(PERM_FILE);
|
|
}
|