539 lines
20 KiB
C++
539 lines
20 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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/*
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* Multi-relaxation time LBM Model
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*/
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#include "models/BGKModel.h"
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#include "analysis/distance.h"
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#include "common/ReadMicroCT.h"
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ScaLBL_BGKModel::ScaLBL_BGKModel(int RANK, int NP, const Utilities::MPI &COMM)
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: rank(RANK), nprocs(NP), Restart(0), timestep(0), timestepMax(0), tau(0),
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Fx(0), Fy(0), Fz(0), flux(0), din(0), dout(0), mu(0), Nx(0), Ny(0), Nz(0),
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N(0), Np(0), nprocx(0), nprocy(0), nprocz(0), BoundaryCondition(0), Lx(0),
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Ly(0), Lz(0), comm(COMM) {}
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ScaLBL_BGKModel::~ScaLBL_BGKModel() {}
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void ScaLBL_BGKModel::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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mrt_db = db->getDatabase("BGK");
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vis_db = db->getDatabase("Visualization");
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tau = 1.0;
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timestepMax = 100000;
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ANALYSIS_INTERVAL = 1000;
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tolerance = 1.0e-8;
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Fx = Fy = 0.0;
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Fz = 1.0e-5;
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dout = 1.0;
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din = 1.0;
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// Color Model parameters
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if (mrt_db->keyExists("timestepMax")) {
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timestepMax = mrt_db->getScalar<int>("timestepMax");
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}
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if (mrt_db->keyExists("analysis_interval")) {
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ANALYSIS_INTERVAL = mrt_db->getScalar<int>("analysis_interval");
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}
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if (mrt_db->keyExists("tolerance")) {
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tolerance = mrt_db->getScalar<double>("tolerance");
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}
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if (mrt_db->keyExists("tau")) {
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tau = mrt_db->getScalar<double>("tau");
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}
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if (mrt_db->keyExists("F")) {
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Fx = mrt_db->getVector<double>("F")[0];
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Fy = mrt_db->getVector<double>("F")[1];
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Fz = mrt_db->getVector<double>("F")[2];
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}
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if (mrt_db->keyExists("Restart")) {
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Restart = mrt_db->getScalar<bool>("Restart");
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}
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if (mrt_db->keyExists("din")) {
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din = mrt_db->getScalar<double>("din");
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}
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if (mrt_db->keyExists("dout")) {
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dout = mrt_db->getScalar<double>("dout");
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}
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if (mrt_db->keyExists("flux")) {
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flux = mrt_db->getScalar<double>("flux");
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}
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// Read domain parameters
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if (mrt_db->keyExists("BoundaryCondition")) {
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BoundaryCondition = mrt_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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mu = (tau - 0.5) / 3.0;
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}
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void ScaLBL_BGKModel::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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Distance.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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for (int i = 0; i < Nx * Ny * Nz; i++)
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Dm->id[i] = 1; // initialize this way
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//Averages = std::shared_ptr<TwoPhase> ( new TwoPhase(Dm) ); // TwoPhase analysis object
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comm.barrier();
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Dm->CommInit();
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comm.barrier();
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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_BGKModel::ReadInput() {
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sprintf(LocalRankString, "%05d", Dm->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 if (domain_db->keyExists("GridFile")) {
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// Read the local domain data
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auto input_id = readMicroCT(*domain_db, comm);
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// Fill the halo (assuming GCW of 1)
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array<int, 3> size0 = {(int)input_id.size(0), (int)input_id.size(1),
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(int)input_id.size(2)};
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ArraySize size1 = {(size_t)Mask->Nx, (size_t)Mask->Ny,
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(size_t)Mask->Nz};
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ASSERT((int)size1[0] == size0[0] + 2 && (int)size1[1] == size0[1] + 2 &&
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(int)size1[2] == size0[2] + 2);
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fillHalo<signed char> fill(comm, Mask->rank_info, size0, {1, 1, 1}, 0,
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1);
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Array<signed char> id_view;
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id_view.viewRaw(size1, Mask->id.data());
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fill.copy(input_id, id_view);
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fill.fill(id_view);
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} else {
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Mask->ReadIDs();
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}
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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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if (Mask->id[n] > 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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Distance(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(Averages->SDs);
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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(Distance, id_solid, *Dm);
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if (rank == 0)
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cout << "Domain set." << endl;
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}
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void ScaLBL_BGKModel::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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int rank = Mask->rank();
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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 \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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size_t dist_mem_size = Np * sizeof(double);
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size_t 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 **)&Pressure, 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 map and neighbor list \n");
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// copy the neighbor list
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ScaLBL_CopyToDevice(NeighborList, neighborList, neighborSize);
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comm.barrier();
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double MLUPS = ScaLBL_Comm->GetPerformance(NeighborList, fq, Np);
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printf(" MLPUS=%f from rank %i\n", MLUPS, rank);
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}
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void ScaLBL_BGKModel::Initialize() {
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/*
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* This function initializes model
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*/
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if (rank == 0)
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printf("Initializing distributions \n");
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ScaLBL_D3Q19_Init(fq, Np);
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}
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void ScaLBL_BGKModel::Run() {
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double rlx = 1.0 / tau;
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Minkowski Morphology(Mask);
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if (rank == 0) {
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bool WriteHeader = false;
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FILE *log_file = fopen("Permeability.csv", "r");
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if (log_file != NULL)
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fclose(log_file);
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else
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WriteHeader = true;
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if (WriteHeader) {
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log_file = fopen("Permeability.csv", "a+");
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fprintf(log_file, "time Fx Fy Fz mu Vs As Js Xs vx vy vz k\n");
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fclose(log_file);
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}
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}
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//.......create and start timer............
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ScaLBL_DeviceBarrier();
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comm.barrier();
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if (rank == 0)
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printf("Beginning AA timesteps, timestepMax = %i \n", timestepMax);
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if (rank == 0)
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printf("********************************************************\n");
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timestep = 0;
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double error = 1.0;
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double flow_rate_previous = 0.0;
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auto t1 = std::chrono::system_clock::now();
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while (timestep < timestepMax && error > tolerance) {
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//************************************************************************/
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/* timestep++;
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ScaLBL_Comm.SendD3Q19AA(dist); //READ FROM NORMAL
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ScaLBL_D3Q19_AAodd_BGK(NeighborList, dist, ScaLBL_Comm.first_interior, ScaLBL_Comm.last_interior, Np, rlx, Fx, Fy, Fz);
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ScaLBL_Comm.RecvD3Q19AA(dist); //WRITE INTO OPPOSITE
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ScaLBL_D3Q19_AAodd_BGK(NeighborList, dist, 0, ScaLBL_Comm.next, Np, rlx, Fx, Fy, Fz);
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ScaLBL_DeviceBarrier(); MPI_Barrier(comm);
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timestep++;
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ScaLBL_Comm.SendD3Q19AA(dist); //READ FORM NORMAL
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ScaLBL_D3Q19_AAeven_BGK(dist, ScaLBL_Comm.first_interior, ScaLBL_Comm.last_interior, Np, rlx, Fx, Fy, Fz);
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ScaLBL_Comm.RecvD3Q19AA(dist); //WRITE INTO OPPOSITE
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ScaLBL_D3Q19_AAeven_BGK(dist, 0, ScaLBL_Comm.next, Np, rlx, Fx, Fy, Fz);
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ScaLBL_DeviceBarrier(); MPI_Barrie
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*/
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timestep++;
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ScaLBL_Comm->SendD3Q19AA(fq); //READ FROM NORMAL
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ScaLBL_D3Q19_AAodd_BGK(NeighborList, fq, ScaLBL_Comm->FirstInterior(),
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ScaLBL_Comm->LastInterior(), Np, rlx, Fx, Fy, Fz);
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ScaLBL_Comm->RecvD3Q19AA(fq); //WRITE INTO OPPOSITE
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// Set boundary conditions
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if (BoundaryCondition == 3) {
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ScaLBL_Comm->D3Q19_Pressure_BC_z(NeighborList, fq, din, timestep);
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ScaLBL_Comm->D3Q19_Pressure_BC_Z(NeighborList, fq, dout, timestep);
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} else if (BoundaryCondition == 4) {
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din =
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ScaLBL_Comm->D3Q19_Flux_BC_z(NeighborList, fq, flux, timestep);
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ScaLBL_Comm->D3Q19_Pressure_BC_Z(NeighborList, fq, dout, timestep);
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} else if (BoundaryCondition == 5) {
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ScaLBL_Comm->D3Q19_Reflection_BC_z(fq);
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ScaLBL_Comm->D3Q19_Reflection_BC_Z(fq);
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}
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ScaLBL_D3Q19_AAodd_BGK(NeighborList, fq, 0, ScaLBL_Comm->LastExterior(),
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Np, rlx, Fx, Fy, Fz);
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ScaLBL_DeviceBarrier();
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comm.barrier();
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timestep++;
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ScaLBL_Comm->SendD3Q19AA(fq); //READ FORM NORMAL
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ScaLBL_D3Q19_AAeven_BGK(fq, ScaLBL_Comm->FirstInterior(),
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ScaLBL_Comm->LastInterior(), Np, rlx, Fx, Fy, Fz);
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ScaLBL_Comm->RecvD3Q19AA(fq); //WRITE INTO OPPOSITE
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// Set boundary conditions
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if (BoundaryCondition == 3) {
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ScaLBL_Comm->D3Q19_Pressure_BC_z(NeighborList, fq, din, timestep);
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ScaLBL_Comm->D3Q19_Pressure_BC_Z(NeighborList, fq, dout, timestep);
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} else if (BoundaryCondition == 4) {
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din =
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ScaLBL_Comm->D3Q19_Flux_BC_z(NeighborList, fq, flux, timestep);
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ScaLBL_Comm->D3Q19_Pressure_BC_Z(NeighborList, fq, dout, timestep);
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} else if (BoundaryCondition == 5) {
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ScaLBL_Comm->D3Q19_Reflection_BC_z(fq);
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ScaLBL_Comm->D3Q19_Reflection_BC_Z(fq);
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}
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ScaLBL_D3Q19_AAeven_BGK(fq, 0, ScaLBL_Comm->LastExterior(), Np,
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rlx, Fx, Fy, Fz);
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ScaLBL_DeviceBarrier();
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comm.barrier();
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//************************************************************************/
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if (timestep % ANALYSIS_INTERVAL == 0) {
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ScaLBL_D3Q19_Momentum(fq, Velocity, Np);
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ScaLBL_DeviceBarrier();
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comm.barrier();
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ScaLBL_Comm->RegularLayout(Map, &Velocity[0], Velocity_x);
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ScaLBL_Comm->RegularLayout(Map, &Velocity[Np], Velocity_y);
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ScaLBL_Comm->RegularLayout(Map, &Velocity[2 * Np], Velocity_z);
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double count_loc = 0;
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double count;
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double vax, vay, vaz;
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double vax_loc, vay_loc, vaz_loc;
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vax_loc = vay_loc = vaz_loc = 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 (Distance(i, j, k) > 0) {
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vax_loc += Velocity_x(i, j, k);
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vay_loc += Velocity_y(i, j, k);
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vaz_loc += Velocity_z(i, j, k);
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count_loc += 1.0;
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}
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}
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}
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}
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vax = Dm->Comm.sumReduce(vax_loc);
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vay = Dm->Comm.sumReduce(vay_loc);
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vaz = Dm->Comm.sumReduce(vaz_loc);
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count = Dm->Comm.sumReduce(count_loc);
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vax /= count;
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vay /= count;
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vaz /= count;
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double force_mag = sqrt(Fx * Fx + Fy * Fy + Fz * Fz);
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double dir_x = Fx / force_mag;
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double dir_y = Fy / force_mag;
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double dir_z = Fz / force_mag;
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if (force_mag == 0.0) {
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// default to z direction
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dir_x = 0.0;
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dir_y = 0.0;
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dir_z = 1.0;
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force_mag = 1.0;
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}
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double flow_rate = (vax * dir_x + vay * dir_y + vaz * dir_z);
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error = fabs(flow_rate - flow_rate_previous) / fabs(flow_rate);
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flow_rate_previous = flow_rate;
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//if (rank==0) printf("Computing Minkowski functionals \n");
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Morphology.ComputeScalar(Distance, 0.f);
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//Morphology.PrintAll();
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double mu = (tau - 0.5) / 3.f;
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double Vs = Morphology.V();
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double As = Morphology.A();
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double Hs = Morphology.H();
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double Xs = Morphology.X();
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Vs = Dm->Comm.sumReduce(Vs);
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As = Dm->Comm.sumReduce(As);
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Hs = Dm->Comm.sumReduce(Hs);
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Xs = Dm->Comm.sumReduce(Xs);
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double h = Dm->voxel_length;
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double absperm =
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h * h * mu * Mask->Porosity() * flow_rate / force_mag;
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if (rank == 0) {
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printf(" %f\n", absperm);
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FILE *log_file = fopen("Permeability.csv", "a");
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fprintf(log_file,
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"%i %.8g %.8g %.8g %.8g %.8g %.8g %.8g %.8g %.8g %.8g "
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"%.8g %.8g\n",
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timestep, Fx, Fy, Fz, mu, h * h * h * Vs, h * h * As,
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h * Hs, Xs, vax, vay, vaz, absperm);
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fclose(log_file);
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}
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}
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}
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//************************************************************************/
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if (rank == 0)
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printf("---------------------------------------------------------------"
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"----\n");
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// Compute the walltime per timestep
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auto t2 = std::chrono::system_clock::now();
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double cputime = std::chrono::duration<double>(t2 - t1).count() / timestep;
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// Performance obtained from each node
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double MLUPS = double(Np) / cputime / 1000000;
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|
|
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if (rank == 0)
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|
printf("********************************************************\n");
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if (rank == 0)
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printf("CPU time = %f \n", cputime);
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|
if (rank == 0)
|
|
printf("Lattice update rate (per core)= %f MLUPS \n", MLUPS);
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MLUPS *= nprocs;
|
|
if (rank == 0)
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printf("Lattice update rate (total)= %f MLUPS \n", MLUPS);
|
|
if (rank == 0)
|
|
printf("********************************************************\n");
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|
}
|
|
|
|
void ScaLBL_BGKModel::VelocityField() {
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|
|
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auto format = vis_db->getWithDefault<string>("format", "silo");
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|
|
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/* memcpy(Morphology.SDn.data(), Distance.data(), Nx*Ny*Nz*sizeof(double));
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Morphology.Initialize();
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|
Morphology.UpdateMeshValues();
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|
Morphology.ComputeLocal();
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|
Morphology.Reduce();
|
|
|
|
double count_loc=0;
|
|
double count;
|
|
double vax,vay,vaz;
|
|
double vax_loc,vay_loc,vaz_loc;
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|
vax_loc = vay_loc = vaz_loc = 0.f;
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for (int n=0; n<ScaLBL_Comm->LastExterior(); n++){
|
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vax_loc += VELOCITY[n];
|
|
vay_loc += VELOCITY[Np+n];
|
|
vaz_loc += VELOCITY[2*Np+n];
|
|
count_loc+=1.0;
|
|
}
|
|
|
|
for (int n=ScaLBL_Comm->FirstInterior(); n<ScaLBL_Comm->LastInterior(); n++){
|
|
vax_loc += VELOCITY[n];
|
|
vay_loc += VELOCITY[Np+n];
|
|
vaz_loc += VELOCITY[2*Np+n];
|
|
count_loc+=1.0;
|
|
}
|
|
MPI_Allreduce(&vax_loc,&vax,1,MPI_DOUBLE,MPI_SUM,Mask->Comm);
|
|
MPI_Allreduce(&vay_loc,&vay,1,MPI_DOUBLE,MPI_SUM,Mask->Comm);
|
|
MPI_Allreduce(&vaz_loc,&vaz,1,MPI_DOUBLE,MPI_SUM,Mask->Comm);
|
|
MPI_Allreduce(&count_loc,&count,1,MPI_DOUBLE,MPI_SUM,Mask->Comm);
|
|
|
|
vax /= count;
|
|
vay /= count;
|
|
vaz /= count;
|
|
|
|
double mu = (tau-0.5)/3.f;
|
|
if (rank==0) printf("Fx Fy Fz mu Vs As Js Xs vx vy vz\n");
|
|
if (rank==0) printf("%.8g %.8g %.8g %.8g %.8g %.8g %.8g %.8g %.8g %.8g %.8g\n",Fx, Fy, Fz, mu,
|
|
Morphology.V(),Morphology.A(),Morphology.J(),Morphology.X(),vax,vay,vaz);
|
|
*/
|
|
vis_db = db->getDatabase("Visualization");
|
|
if (vis_db->getWithDefault<bool>("write_silo", false)) {
|
|
|
|
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>();
|
|
|
|
IO::initialize("", format, "false");
|
|
// Create the MeshDataStruct
|
|
visData.resize(1);
|
|
visData[0].meshName = "domain";
|
|
visData[0].mesh = std::make_shared<IO::DomainMesh>(
|
|
Dm->rank_info, Dm->Nx - 2, Dm->Ny - 2, Dm->Nz - 2, Dm->Lx, Dm->Ly,
|
|
Dm->Lz);
|
|
SignDistVar->name = "SignDist";
|
|
SignDistVar->type = IO::VariableType::VolumeVariable;
|
|
SignDistVar->dim = 1;
|
|
SignDistVar->data.resize(Dm->Nx - 2, Dm->Ny - 2, Dm->Nz - 2);
|
|
visData[0].vars.push_back(SignDistVar);
|
|
|
|
VxVar->name = "Velocity_x";
|
|
VxVar->type = IO::VariableType::VolumeVariable;
|
|
VxVar->dim = 1;
|
|
VxVar->data.resize(Dm->Nx - 2, Dm->Ny - 2, Dm->Nz - 2);
|
|
visData[0].vars.push_back(VxVar);
|
|
VyVar->name = "Velocity_y";
|
|
VyVar->type = IO::VariableType::VolumeVariable;
|
|
VyVar->dim = 1;
|
|
VyVar->data.resize(Dm->Nx - 2, Dm->Ny - 2, Dm->Nz - 2);
|
|
visData[0].vars.push_back(VyVar);
|
|
VzVar->name = "Velocity_z";
|
|
VzVar->type = IO::VariableType::VolumeVariable;
|
|
VzVar->dim = 1;
|
|
VzVar->data.resize(Dm->Nx - 2, Dm->Ny - 2, Dm->Nz - 2);
|
|
visData[0].vars.push_back(VzVar);
|
|
|
|
Array<double> &SignData = visData[0].vars[0]->data;
|
|
Array<double> &VelxData = visData[0].vars[1]->data;
|
|
Array<double> &VelyData = visData[0].vars[2]->data;
|
|
Array<double> &VelzData = visData[0].vars[3]->data;
|
|
|
|
ASSERT(visData[0].vars[0]->name == "SignDist");
|
|
ASSERT(visData[0].vars[1]->name == "Velocity_x");
|
|
ASSERT(visData[0].vars[2]->name == "Velocity_y");
|
|
ASSERT(visData[0].vars[3]->name == "Velocity_z");
|
|
|
|
fillData.copy(Distance, SignData);
|
|
fillData.copy(Velocity_x, VelxData);
|
|
fillData.copy(Velocity_y, VelyData);
|
|
fillData.copy(Velocity_z, VelzData);
|
|
|
|
IO::writeData(timestep, visData, Dm->Comm);
|
|
}
|
|
}
|