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hang fix / workaround

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This commit is contained in:
James E McClure 2022-02-10 13:43:31 -05:00
parent e2f198759d
commit 6b0b8daddd
6 changed files with 658 additions and 407 deletions
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4
common/Utilities.cpp
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@ -69,7 +69,7 @@ void Utilities::startup(int argc, char **argv, bool multiple) {
"thread support, thread support will be disabled"
<< std::endl;
}
StackTrace::globalCallStackInitialize(MPI_COMM_WORLD);
//StackTrace::globalCallStackInitialize(MPI_COMM_WORLD);
} else {
MPI_Init(&argc, &argv);
}
@ -86,7 +86,7 @@ void Utilities::shutdown() {
int rank = 0;
#ifdef USE_MPI
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
StackTrace::globalCallStackFinalize();
//StackTrace::globalCallStackFinalize();
MPI_Barrier(MPI_COMM_WORLD);
MPI_Finalize();
#endif

538
models/BGKModel.cpp Normal file
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@ -0,0 +1,538 @@
/*
Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
Copyright Equnior ASA
This file is part of the Open Porous Media project (OPM).
OPM is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
OPM is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with OPM. If not, see <http://www.gnu.org/licenses/>.
*/
/*
* Multi-relaxation time LBM Model
*/
#include "models/BGKModel.h"
#include "analysis/distance.h"
#include "common/ReadMicroCT.h"
ScaLBL_BGKModel::ScaLBL_BGKModel(int RANK, int NP, const Utilities::MPI &COMM)
: rank(RANK), nprocs(NP), Restart(0), timestep(0), timestepMax(0), tau(0),
Fx(0), Fy(0), Fz(0), flux(0), din(0), dout(0), mu(0), Nx(0), Ny(0), Nz(0),
N(0), Np(0), nprocx(0), nprocy(0), nprocz(0), BoundaryCondition(0), Lx(0),
Ly(0), Lz(0), comm(COMM) {}
ScaLBL_BGKModel::~ScaLBL_BGKModel() {}
void ScaLBL_BGKModel::ReadParams(string filename) {
// read the input database
db = std::make_shared<Database>(filename);
domain_db = db->getDatabase("Domain");
mrt_db = db->getDatabase("BGK");
vis_db = db->getDatabase("Visualization");
tau = 1.0;
timestepMax = 100000;
ANALYSIS_INTERVAL = 1000;
tolerance = 1.0e-8;
Fx = Fy = 0.0;
Fz = 1.0e-5;
dout = 1.0;
din = 1.0;
// Color Model parameters
if (mrt_db->keyExists("timestepMax")) {
timestepMax = mrt_db->getScalar<int>("timestepMax");
}
if (mrt_db->keyExists("analysis_interval")) {
ANALYSIS_INTERVAL = mrt_db->getScalar<int>("analysis_interval");
}
if (mrt_db->keyExists("tolerance")) {
tolerance = mrt_db->getScalar<double>("tolerance");
}
if (mrt_db->keyExists("tau")) {
tau = mrt_db->getScalar<double>("tau");
}
if (mrt_db->keyExists("F")) {
Fx = mrt_db->getVector<double>("F")[0];
Fy = mrt_db->getVector<double>("F")[1];
Fz = mrt_db->getVector<double>("F")[2];
}
if (mrt_db->keyExists("Restart")) {
Restart = mrt_db->getScalar<bool>("Restart");
}
if (mrt_db->keyExists("din")) {
din = mrt_db->getScalar<double>("din");
}
if (mrt_db->keyExists("dout")) {
dout = mrt_db->getScalar<double>("dout");
}
if (mrt_db->keyExists("flux")) {
flux = mrt_db->getScalar<double>("flux");
}
// Read domain parameters
if (mrt_db->keyExists("BoundaryCondition")) {
BoundaryCondition = mrt_db->getScalar<int>("BC");
} else if (domain_db->keyExists("BC")) {
BoundaryCondition = domain_db->getScalar<int>("BC");
}
mu = (tau - 0.5) / 3.0;
}
void ScaLBL_BGKModel::SetDomain() {
Dm = std::shared_ptr<Domain>(
new Domain(domain_db, comm)); // full domain for analysis
Mask = std::shared_ptr<Domain>(
new Domain(domain_db, comm)); // mask domain removes immobile phases
// domain parameters
Nx = Dm->Nx;
Ny = Dm->Ny;
Nz = Dm->Nz;
Lx = Dm->Lx;
Ly = Dm->Ly;
Lz = Dm->Lz;
N = Nx * Ny * Nz;
Distance.resize(Nx, Ny, Nz);
Velocity_x.resize(Nx, Ny, Nz);
Velocity_y.resize(Nx, Ny, Nz);
Velocity_z.resize(Nx, Ny, Nz);
for (int i = 0; i < Nx * Ny * Nz; i++)
Dm->id[i] = 1; // initialize this way
//Averages = std::shared_ptr<TwoPhase> ( new TwoPhase(Dm) ); // TwoPhase analysis object
comm.barrier();
Dm->CommInit();
comm.barrier();
rank = Dm->rank();
nprocx = Dm->nprocx();
nprocy = Dm->nprocy();
nprocz = Dm->nprocz();
}
void ScaLBL_BGKModel::ReadInput() {
sprintf(LocalRankString, "%05d", Dm->rank());
sprintf(LocalRankFilename, "%s%s", "ID.", LocalRankString);
sprintf(LocalRestartFile, "%s%s", "Restart.", LocalRankString);
if (domain_db->keyExists("Filename")) {
auto Filename = domain_db->getScalar<std::string>("Filename");
Mask->Decomp(Filename);
} else if (domain_db->keyExists("GridFile")) {
// Read the local domain data
auto input_id = readMicroCT(*domain_db, comm);
// Fill the halo (assuming GCW of 1)
array<int, 3> size0 = {(int)input_id.size(0), (int)input_id.size(1),
(int)input_id.size(2)};
ArraySize size1 = {(size_t)Mask->Nx, (size_t)Mask->Ny,
(size_t)Mask->Nz};
ASSERT((int)size1[0] == size0[0] + 2 && (int)size1[1] == size0[1] + 2 &&
(int)size1[2] == size0[2] + 2);
fillHalo<signed char> fill(comm, Mask->rank_info, size0, {1, 1, 1}, 0,
1);
Array<signed char> id_view;
id_view.viewRaw(size1, Mask->id.data());
fill.copy(input_id, id_view);
fill.fill(id_view);
} else {
Mask->ReadIDs();
}
// Generate the signed distance map
// Initialize the domain and communication
Array<char> id_solid(Nx, Ny, Nz);
// Solve for the position of the solid phase
for (int k = 0; k < Nz; k++) {
for (int j = 0; j < Ny; j++) {
for (int i = 0; i < Nx; i++) {
int n = k * Nx * Ny + j * Nx + i;
// Initialize the solid phase
if (Mask->id[n] > 0)
id_solid(i, j, k) = 1;
else
id_solid(i, j, k) = 0;
}
}
}
// Initialize the signed distance function
for (int k = 0; k < Nz; k++) {
for (int j = 0; j < Ny; j++) {
for (int i = 0; i < Nx; i++) {
// Initialize distance to +/- 1
Distance(i, j, k) = 2.0 * double(id_solid(i, j, k)) - 1.0;
}
}
}
// MeanFilter(Averages->SDs);
if (rank == 0)
printf("Initialized solid phase -- Converting to Signed Distance "
"function \n");
CalcDist(Distance, id_solid, *Dm);
if (rank == 0)
cout << "Domain set." << endl;
}
void ScaLBL_BGKModel::Create() {
/*
* This function creates the variables needed to run a LBM
*/
int rank = Mask->rank();
//.........................................................
// Initialize communication structures in averaging domain
for (int i = 0; i < Nx * Ny * Nz; i++)
Dm->id[i] = Mask->id[i];
Mask->CommInit();
Np = Mask->PoreCount();
//...........................................................................
if (rank == 0)
printf("Create ScaLBL_Communicator \n");
// Create a communicator for the device (will use optimized layout)
// ScaLBL_Communicator ScaLBL_Comm(Mask); // original
ScaLBL_Comm =
std::shared_ptr<ScaLBL_Communicator>(new ScaLBL_Communicator(Mask));
int Npad = (Np / 16 + 2) * 16;
if (rank == 0)
printf("Set up memory efficient layout \n");
Map.resize(Nx, Ny, Nz);
Map.fill(-2);
auto neighborList = new int[18 * Npad];
Np = ScaLBL_Comm->MemoryOptimizedLayoutAA(Map, neighborList,
Mask->id.data(), Np, 1);
comm.barrier();
//...........................................................................
// MAIN VARIABLES ALLOCATED HERE
//...........................................................................
// LBM variables
if (rank == 0)
printf("Allocating distributions \n");
//......................device distributions.................................
int dist_mem_size = Np * sizeof(double);
int neighborSize = 18 * (Np * sizeof(int));
//...........................................................................
ScaLBL_AllocateDeviceMemory((void **)&NeighborList, neighborSize);
ScaLBL_AllocateDeviceMemory((void **)&fq, 19 * dist_mem_size);
ScaLBL_AllocateDeviceMemory((void **)&Pressure, sizeof(double) * Np);
ScaLBL_AllocateDeviceMemory((void **)&Velocity, 3 * sizeof(double) * Np);
//...........................................................................
// Update GPU data structures
if (rank == 0)
printf("Setting up device map and neighbor list \n");
// copy the neighbor list
ScaLBL_CopyToDevice(NeighborList, neighborList, neighborSize);
comm.barrier();
double MLUPS = ScaLBL_Comm->GetPerformance(NeighborList, fq, Np);
printf(" MLPUS=%f from rank %i\n", MLUPS, rank);
}
void ScaLBL_BGKModel::Initialize() {
/*
* This function initializes model
*/
if (rank == 0)
printf("Initializing distributions \n");
ScaLBL_D3Q19_Init(fq, Np);
}
void ScaLBL_BGKModel::Run() {
double rlx = 1.0 / tau;
Minkowski Morphology(Mask);
if (rank == 0) {
bool WriteHeader = false;
FILE *log_file = fopen("Permeability.csv", "r");
if (log_file != NULL)
fclose(log_file);
else
WriteHeader = true;
if (WriteHeader) {
log_file = fopen("Permeability.csv", "a+");
fprintf(log_file, "time Fx Fy Fz mu Vs As Js Xs vx vy vz k\n");
fclose(log_file);
}
}
//.......create and start timer............
ScaLBL_DeviceBarrier();
comm.barrier();
if (rank == 0)
printf("Beginning AA timesteps, timestepMax = %i \n", timestepMax);
if (rank == 0)
printf("********************************************************\n");
timestep = 0;
double error = 1.0;
double flow_rate_previous = 0.0;
auto t1 = std::chrono::system_clock::now();
while (timestep < timestepMax && error > tolerance) {
//************************************************************************/
/* timestep++;
ScaLBL_Comm.SendD3Q19AA(dist); //READ FROM NORMAL
ScaLBL_D3Q19_AAodd_BGK(NeighborList, dist, ScaLBL_Comm.first_interior, ScaLBL_Comm.last_interior, Np, rlx, Fx, Fy, Fz);
ScaLBL_Comm.RecvD3Q19AA(dist); //WRITE INTO OPPOSITE
ScaLBL_D3Q19_AAodd_BGK(NeighborList, dist, 0, ScaLBL_Comm.next, Np, rlx, Fx, Fy, Fz);
ScaLBL_DeviceBarrier(); MPI_Barrier(comm);
timestep++;
ScaLBL_Comm.SendD3Q19AA(dist); //READ FORM NORMAL
ScaLBL_D3Q19_AAeven_BGK(dist, ScaLBL_Comm.first_interior, ScaLBL_Comm.last_interior, Np, rlx, Fx, Fy, Fz);
ScaLBL_Comm.RecvD3Q19AA(dist); //WRITE INTO OPPOSITE
ScaLBL_D3Q19_AAeven_BGK(dist, 0, ScaLBL_Comm.next, Np, rlx, Fx, Fy, Fz);
ScaLBL_DeviceBarrier(); MPI_Barrie
*/
timestep++;
ScaLBL_Comm->SendD3Q19AA(fq); //READ FROM NORMAL
ScaLBL_D3Q19_AAodd_BGK(NeighborList, fq, ScaLBL_Comm->FirstInterior(),
ScaLBL_Comm->LastInterior(), Np, rlx, Fx, Fy, Fz);
ScaLBL_Comm->RecvD3Q19AA(fq); //WRITE INTO OPPOSITE
// Set boundary conditions
if (BoundaryCondition == 3) {
ScaLBL_Comm->D3Q19_Pressure_BC_z(NeighborList, fq, din, timestep);
ScaLBL_Comm->D3Q19_Pressure_BC_Z(NeighborList, fq, dout, timestep);
} else if (BoundaryCondition == 4) {
din =
ScaLBL_Comm->D3Q19_Flux_BC_z(NeighborList, fq, flux, timestep);
ScaLBL_Comm->D3Q19_Pressure_BC_Z(NeighborList, fq, dout, timestep);
} else if (BoundaryCondition == 5) {
ScaLBL_Comm->D3Q19_Reflection_BC_z(fq);
ScaLBL_Comm->D3Q19_Reflection_BC_Z(fq);
}
ScaLBL_D3Q19_AAodd_BGK(NeighborList, fq, 0, ScaLBL_Comm->LastExterior(),
Np, rlx, Fx, Fy, Fz);
ScaLBL_DeviceBarrier();
comm.barrier();
timestep++;
ScaLBL_Comm->SendD3Q19AA(fq); //READ FORM NORMAL
ScaLBL_D3Q19_AAeven_BGK(fq, ScaLBL_Comm->FirstInterior(),
ScaLBL_Comm->LastInterior(), Np, rlx, Fx, Fy, Fz);
ScaLBL_Comm->RecvD3Q19AA(fq); //WRITE INTO OPPOSITE
// Set boundary conditions
if (BoundaryCondition == 3) {
ScaLBL_Comm->D3Q19_Pressure_BC_z(NeighborList, fq, din, timestep);
ScaLBL_Comm->D3Q19_Pressure_BC_Z(NeighborList, fq, dout, timestep);
} else if (BoundaryCondition == 4) {
din =
ScaLBL_Comm->D3Q19_Flux_BC_z(NeighborList, fq, flux, timestep);
ScaLBL_Comm->D3Q19_Pressure_BC_Z(NeighborList, fq, dout, timestep);
} else if (BoundaryCondition == 5) {
ScaLBL_Comm->D3Q19_Reflection_BC_z(fq);
ScaLBL_Comm->D3Q19_Reflection_BC_Z(fq);
}
ScaLBL_D3Q19_AAeven_BGK(fq, 0, ScaLBL_Comm->LastExterior(), Np,
rlx, Fx, Fy, Fz);
ScaLBL_DeviceBarrier();
comm.barrier();
//************************************************************************/
if (timestep % ANALYSIS_INTERVAL == 0) {
ScaLBL_D3Q19_Momentum(fq, Velocity, Np);
ScaLBL_DeviceBarrier();
comm.barrier();
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);
double count_loc = 0;
double count;
double vax, vay, vaz;
double vax_loc, vay_loc, vaz_loc;
vax_loc = vay_loc = vaz_loc = 0.f;
for (int k = 1; k < Nz - 1; k++) {
for (int j = 1; j < Ny - 1; j++) {
for (int i = 1; i < Nx - 1; i++) {
if (Distance(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 = (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(Distance, 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;
if (rank == 0) {
printf(" %f\n", absperm);
FILE *log_file = fopen("Permeability.csv", "a");
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 (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_BGKModel::VelocityField() {
auto format = vis_db->getWithDefault<string>("format", "silo");
/* memcpy(Morphology.SDn.data(), Distance.data(), Nx*Ny*Nz*sizeof(double));
Morphology.Initialize();
Morphology.UpdateMeshValues();
Morphology.ComputeLocal();
Morphology.Reduce();
double count_loc=0;
double count;
double vax,vay,vaz;
double vax_loc,vay_loc,vaz_loc;
vax_loc = vay_loc = vaz_loc = 0.f;
for (int n=0; n<ScaLBL_Comm->LastExterior(); n++){
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);
}
}

94
models/BGKModel.h Normal file
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@ -0,0 +1,94 @@
/*
Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
Copyright Equnior ASA
This file is part of the Open Porous Media project (OPM).
OPM is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
OPM is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with OPM. If not, see <http://www.gnu.org/licenses/>.
*/
/*
* Multi-relaxation time LBM Model
*/
#include <stdio.h>
#include <stdlib.h>
#include <sys/stat.h>
#include <iostream>
#include <exception>
#include <stdexcept>
#include <fstream>
#include "common/ScaLBL.h"
#include "common/Communication.h"
#include "common/MPI.h"
#include "analysis/Minkowski.h"
#include "ProfilerApp.h"
class ScaLBL_BGKModel {
public:
ScaLBL_BGKModel(int RANK, int NP, const Utilities::MPI &COMM);
~ScaLBL_BGKModel();
// functions in they should be run
void ReadParams(string filename);
void ReadParams(std::shared_ptr<Database> db0);
void SetDomain();
void ReadInput();
void Create();
void Initialize();
void Run();
void VelocityField();
bool Restart, pBC;
int timestep, timestepMax;
int ANALYSIS_INTERVAL;
int BoundaryCondition;
double tau, mu;
double Fx, Fy, Fz, flux;
double din, dout;
double tolerance;
int Nx, Ny, Nz, N, Np;
int rank, nprocx, nprocy, nprocz, nprocs;
double Lx, Ly, Lz;
std::shared_ptr<Domain> Dm; // this domain is for analysis
std::shared_ptr<Domain> Mask; // this domain is for lbm
std::shared_ptr<ScaLBL_Communicator> ScaLBL_Comm;
// input database
std::shared_ptr<Database> db;
std::shared_ptr<Database> domain_db;
std::shared_ptr<Database> mrt_db;
std::shared_ptr<Database> vis_db;
IntArray Map;
DoubleArray Distance;
int *NeighborList;
double *fq;
double *Velocity;
double *Pressure;
//Minkowski Morphology;
DoubleArray Velocity_x;
DoubleArray Velocity_y;
DoubleArray Velocity_z;
private:
Utilities::MPI comm;
// filenames
char LocalRankString[8];
char LocalRankFilename[40];
char LocalRestartFile[40];
//int rank,nprocs;
void LoadParams(std::shared_ptr<Database> db0);
};

2
tests/CMakeLists.txt
View File

@ -8,7 +8,7 @@ ADD_LBPM_EXECUTABLE( lbpm_greyscaleColor_simulator )
ADD_LBPM_EXECUTABLE( lbpm_electrokinetic_SingleFluid_simulator )
ADD_LBPM_EXECUTABLE( lbpm_freelee_simulator )
ADD_LBPM_EXECUTABLE( lbpm_freelee_SingleFluidBGK_simulator )
#ADD_LBPM_EXECUTABLE( lbpm_BGK_simulator )
ADD_LBPM_EXECUTABLE( lbpm_BGK_simulator )
#ADD_LBPM_EXECUTABLE( lbpm_color_macro_simulator )
ADD_LBPM_EXECUTABLE( lbpm_dfh_simulator )
#ADD_LBPM_EXECUTABLE( lbpm_sphere_pp )

425
tests/lbpm_BGK_simulator.cpp
View File

@ -9,8 +9,8 @@
#include "common/ScaLBL.h"
#include "common/Communication.h"
#include "analysis/TwoPhase.h"
#include "common/MPI_Helpers.h"
#include "common/MPI.h"
#include "models/BGKModel.h"
//#define WRITE_SURFACES
/*
@ -23,414 +23,33 @@ using namespace std;
int main(int argc, char **argv)
{
//*****************************************
// ***** MPI STUFF ****************
//*****************************************
// Initialize MPI
int rank,nprocs;
Utilities::startup( argc, argv );
Utilities::MPI comm( MPI_COMM_WORLD );
int rank = comm.getRank();
int nprocs = comm.getSize();
Utilities::startup( argc, argv );
Utilities::MPI comm( MPI_COMM_WORLD );
int rank = comm.getRank();
int nprocs = comm.getSize();
{
// parallel domain size (# of sub-domains)
int nprocx,nprocy,nprocz;
if (rank == 0){
printf("********************************************************\n");
printf("Running Single Phase Permeability Calculation \n");
printf("********************************************************\n");
}
// Variables that specify the computational domain
string FILENAME;
int Nx,Ny,Nz; // local sub-domain size
int nspheres; // number of spheres in the packing
double Lx,Ly,Lz; // Domain length
double D = 1.0; // reference length for non-dimensionalization
// Color Model parameters
int timestepMax, interval;
double tau,Fx,Fy,Fz,tol,err;
double din,dout;
bool pBC,Restart;
int i,j,k,n;
int RESTART_INTERVAL=20000;
if (rank==0){
//.............................................................
// READ SIMULATION PARMAETERS FROM INPUT FILE
//.............................................................
ifstream input("Permeability.in");
// Line 1: model parameters (tau, alpha, beta, das, dbs)
input >> tau; // Viscosity parameter
// Line 2: External force components (Fx,Fy, Fz)
input >> Fx;
input >> Fy;
input >> Fz;
// Line 3: Pressure Boundary conditions
input >> Restart;
input >> pBC;
input >> din;
input >> dout;
// Line 4: time-stepping criteria
input >> timestepMax; // max no. of timesteps
input >> interval; // restart interval
input >> tol; // error tolerance
//.............................................................
//.......................................................................
// Reading the domain information file
//.......................................................................
ifstream domain("Domain.in");
domain >> nprocx;
domain >> nprocy;
domain >> nprocz;
domain >> Nx;
domain >> Ny;
domain >> Nz;
//domain >> nspheres;
domain >> Lx;
domain >> Ly;
domain >> Lz;
//.......................................................................
}
// **************************************************************
// Broadcast simulation parameters from rank 0 to all other procs
MPI_Barrier(comm);
//.................................................
MPI_Bcast(&tau,1,MPI_DOUBLE,0,comm);
//MPI_Bcast(&pBC,1,MPI_LOGICAL,0,comm);
// MPI_Bcast(&Restart,1,MPI_LOGICAL,0,comm);
MPI_Bcast(&din,1,MPI_DOUBLE,0,comm);
MPI_Bcast(&dout,1,MPI_DOUBLE,0,comm);
MPI_Bcast(&Fx,1,MPI_DOUBLE,0,comm);
MPI_Bcast(&Fy,1,MPI_DOUBLE,0,comm);
MPI_Bcast(&Fz,1,MPI_DOUBLE,0,comm);
MPI_Bcast(&timestepMax,1,MPI_INT,0,comm);
MPI_Bcast(&interval,1,MPI_INT,0,comm);
MPI_Bcast(&tol,1,MPI_DOUBLE,0,comm);
// Computational domain
MPI_Bcast(&Nx,1,MPI_INT,0,comm);
MPI_Bcast(&Ny,1,MPI_INT,0,comm);
MPI_Bcast(&Nz,1,MPI_INT,0,comm);
MPI_Bcast(&nprocx,1,MPI_INT,0,comm);
MPI_Bcast(&nprocy,1,MPI_INT,0,comm);
MPI_Bcast(&nprocz,1,MPI_INT,0,comm);
//MPI_Bcast(&nspheres,1,MPI_INT,0,comm);
MPI_Bcast(&Lx,1,MPI_DOUBLE,0,comm);
MPI_Bcast(&Ly,1,MPI_DOUBLE,0,comm);
MPI_Bcast(&Lz,1,MPI_DOUBLE,0,comm);
//.................................................
MPI_Barrier(comm);
RESTART_INTERVAL=interval;
// **************************************************************
// **************************************************************
double rlx = 1.f/tau;
if (nprocs != nprocx*nprocy*nprocz){
printf("nprocx = %i \n",nprocx);
printf("nprocy = %i \n",nprocy);
printf("nprocz = %i \n",nprocz);
INSIST(nprocs == nprocx*nprocy*nprocz,"Fatal error in processor count!");
}
if (rank==0){
printf("********************************************************\n");
printf("tau = %f \n", tau);
printf("Force(x) = %.5g \n", Fx);
printf("Force(y) = %.5g \n", Fy);
printf("Force(z) = %.5g \n", Fz);
printf("Sub-domain size = %i x %i x %i\n",Nx,Ny,Nz);
printf("Process grid = %i x %i x %i\n",nprocx,nprocy,nprocz);
printf("********************************************************\n");
}
double viscosity=(tau-0.5)/3.0;
// Initialized domain and averaging framework for Two-Phase Flow
int BC=pBC;
Domain Dm(Nx,Ny,Nz,rank,nprocx,nprocy,nprocz,Lx,Ly,Lz,BC);
for (i=0; i<Dm.Nx*Dm.Ny*Dm.Nz; i++) Dm.id[i] = 1;
Dm.CommInit();
TwoPhase Averages(Dm);
// Mask that excludes the solid phase
Domain Mask(Nx,Ny,Nz,rank,nprocx,nprocy,nprocz,Lx,Ly,Lz,BC);
MPI_Barrier(comm);
Nx += 2; Ny += 2; Nz += 2;
int N = Nx*Ny*Nz;
//.......................................................................
if (rank == 0) printf("Read input media... \n");
//.......................................................................
//.......................................................................
// Filenames used
char LocalRankString[8];
char LocalRankFilename[40];
char LocalRestartFile[40];
char tmpstr[10];
sprintf(LocalRankString,"%05d",rank);
sprintf(LocalRankFilename,"%s%s","ID.",LocalRankString);
sprintf(LocalRestartFile,"%s%s","Restart.",LocalRankString);
// printf("Local File Name = %s \n",LocalRankFilename);
// .......... READ THE INPUT FILE .......................................
// char value;
char *id;
id = new char[N];
double sum, sum_local;
double iVol_global = 1.0/(1.0*(Nx-2)*(Ny-2)*(Nz-2)*nprocs);
//if (BoundaryCondition > 0) iVol_global = 1.0/(1.0*(Nx-2)*nprocx*(Ny-2)*nprocy*((Nz-2)*nprocz-6));
double porosity, pore_vol;
//...........................................................................
if (rank == 0) cout << "Reading in domain from signed distance function..." << endl;
//.......................................................................
// Read the signed distance
sprintf(LocalRankString,"%05d",rank);
sprintf(LocalRankFilename,"%s%s","SignDist.",LocalRankString);
ReadBinaryFile(LocalRankFilename, Averages.SDs.data(), N);
MPI_Barrier(comm);
if (rank == 0) cout << "Domain set." << endl;
//.......................................................................
// Assign the phase ID field based on the signed distance
//.......................................................................
for (k=0;k<Nz;k++){
for (j=0;j<Ny;j++){
for (i=0;i<Nx;i++){
int n = k*Nx*Ny+j*Nx+i;
id[n] = 0;
}
}
}
sum=0.f;
pore_vol = 0.0;
for ( k=0;k<Nz;k++){
for ( j=0;j<Ny;j++){
for ( i=0;i<Nx;i++){
int n = k*Nx*Ny+j*Nx+i;
if (Averages.SDs(n) > 0.0){
id[n] = 2;
}
// compute the porosity (actual interface location used)
if (Averages.SDs(n) > 0.0){
sum++;
}
}
}
}
if (rank==0) printf("Initialize from segmented data: solid=0, NWP=1, WP=2 \n");
sprintf(LocalRankFilename,"ID.%05i",rank);
size_t readID;
FILE *IDFILE = fopen(LocalRankFilename,"rb");
if (IDFILE==NULL) ERROR("lbpm_permeability_simulator: Error opening file: ID.xxxxx");
readID=fread(id,1,N,IDFILE);
if (readID != size_t(N)) printf("lbpm_permeability_simulator: Error reading ID (rank=%i) \n",rank);
fclose(IDFILE);
//.......................................................................
// Compute the media porosity, assign phase labels and solid composition
//.......................................................................
sum_local=0.0;
int Np=0; // number of local pore nodes
//.......................................................................
for (k=1;k<Nz-1;k++){
for (j=1;j<Ny-1;j++){
for (i=1;i<Nx-1;i++){
n = k*Nx*Ny+j*Nx+i;
if (id[n] > 0){
sum_local+=1.0;
Np++;
}
}
}
}
MPI_Allreduce(&sum_local,&sum,1,MPI_DOUBLE,MPI_SUM,comm);
porosity = sum*iVol_global;
if (rank==0) printf("Media porosity = %f \n",porosity);
//.........................................................
// don't perform computations at the eight corners
id[0] = id[Nx-1] = id[(Ny-1)*Nx] = id[(Ny-1)*Nx + Nx-1] = 0;
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;
//.........................................................
MPI_Barrier(comm);
// Initialize communication structures in averaging domain
for (i=0; i<Mask.Nx*Mask.Ny*Mask.Nz; i++) Mask.id[i] = id[i];
Mask.CommInit(comm);
//...........................................................................
if (rank==0) printf ("Create ScaLBL_Communicator \n");
// Create a communicator for the device
int Npad=(Np/16 + 2)*16;
ScaLBL_Communicator ScaLBL_Comm(Mask);
int *neighborList;
IntArray Map(Nx,Ny,Nz);
neighborList= new int[18*Npad];
Np = ScaLBL_Comm.MemoryOptimizedLayoutAA(Map,neighborList,Mask.id,Np);
MPI_Barrier(comm);
// LBM variables
if (rank==0) printf ("Allocating distributions \n");
//......................device distributions.................................
int dist_mem_size = Np*sizeof(double);
int neighborSize=18*(Np*sizeof(int));
int *NeighborList;
// double *f_even,*f_odd;
double * dist;
double * Velocity;
double * Pressure;
//...........................................................................
ScaLBL_AllocateDeviceMemory((void **) &dist, 19*dist_mem_size);
ScaLBL_AllocateDeviceMemory((void **) &NeighborList, neighborSize);
ScaLBL_AllocateDeviceMemory((void **) &Velocity, 3*sizeof(double)*Np);
ScaLBL_AllocateDeviceMemory((void **) &Pressure, 3*sizeof(double)*Np);
ScaLBL_CopyToDevice(NeighborList, neighborList, neighborSize);
//...........................................................................
//...........................................................................
if (rank==0) printf("Setting the distributions, size = %i\n", N);
//...........................................................................
// Finalize setup for averaging domain
//Averages.SetupCubes(Dm);
Averages.UpdateSolid();
// Initialize two phase flow variables (all wetting phase)
for (k=0;k<Nz;k++){
for (j=0;j<Ny;j++){
for (i=0;i<Nx;i++){
n=k*Nx*Ny+j*Nx+i;
Averages.Phase(i,j,k) = -1.0;
Averages.SDn(i,j,k) = Averages.Phase(i,j,k);
Averages.Phase_tplus(i,j,k) = Averages.SDn(i,j,k);
Averages.Phase_tminus(i,j,k) = Averages.SDn(i,j,k);
Averages.DelPhi(i,j,k) = 0.0;
Averages.Press(i,j,k) = 0.0;
Averages.Vel_x(i,j,k) = 0.0;
Averages.Vel_y(i,j,k) = 0.0;
Averages.Vel_z(i,j,k) = 0.0;
}
}
}
//.......................................................................
ScaLBL_D3Q19_Init(dist, Np);
int timestep = 0;
if (rank==0) printf("********************************************************\n");
if (rank==0) printf("No. of timesteps: %i \n", timestepMax);
//.......create and start timer............
double starttime,stoptime,cputime;
MPI_Barrier(comm);
starttime = MPI_Wtime();
//.........................................
double D32,Fo,Re,velocity,err1D,mag_force,vel_prev;
err = vel_prev = 1.0;
if (rank==0) printf("Begin timesteps: error tolerance is %f \n", tol);
//************ MAIN ITERATION LOOP ***************************************/
while (timestep < timestepMax && err > tol ){
timestep++;
ScaLBL_Comm.SendD3Q19AA(dist); //READ FROM NORMAL
ScaLBL_D3Q19_AAodd_BGK(NeighborList, dist, ScaLBL_Comm.first_interior, ScaLBL_Comm.last_interior, Np, rlx, Fx, Fy, Fz);
ScaLBL_Comm.RecvD3Q19AA(dist); //WRITE INTO OPPOSITE
ScaLBL_D3Q19_AAodd_BGK(NeighborList, dist, 0, ScaLBL_Comm.next, Np, rlx, Fx, Fy, Fz);
ScaLBL_DeviceBarrier(); MPI_Barrier(comm);
timestep++;
ScaLBL_Comm.SendD3Q19AA(dist); //READ FORM NORMAL
ScaLBL_D3Q19_AAeven_BGK(dist, ScaLBL_Comm.first_interior, ScaLBL_Comm.last_interior, Np, rlx, Fx, Fy, Fz);
ScaLBL_Comm.RecvD3Q19AA(dist); //WRITE INTO OPPOSITE
ScaLBL_D3Q19_AAeven_BGK(dist, 0, ScaLBL_Comm.next, Np, rlx, Fx, Fy, Fz);
ScaLBL_DeviceBarrier(); MPI_Barrier(comm);
//************************************************************************/
if (timestep%500 == 0){
//...........................................................................
// Copy the data for for the analysis timestep
//...........................................................................
// Copy the phase from the GPU -> CPU
//...........................................................................
ScaLBL_DeviceBarrier();
ScaLBL_D3Q19_Pressure(dist,Pressure,Np);
ScaLBL_D3Q19_Momentum(dist,Velocity,Np);
ScaLBL_Comm.RegularLayout(Map,Pressure,Averages.Press);
ScaLBL_Comm.RegularLayout(Map,&Velocity[0],Averages.Vel_x);
ScaLBL_Comm.RegularLayout(Map,&Velocity[Np],Averages.Vel_y);
ScaLBL_Comm.RegularLayout(Map,&Velocity[2*Np],Averages.Vel_z);
// Way more work than necessary -- this is just to get the solid interfacial area!!
Averages.Initialize();
Averages.UpdateMeshValues();
Averages.ComputeLocal();
Averages.Reduce();
double vawx = Averages.vaw_global(0);
double vawy = Averages.vaw_global(1);
double vawz = Averages.vaw_global(2);
if (rank==0){
// ************* DIMENSIONLESS FORCHEIMER EQUATION *************************
// Dye, A.L., McClure, J.E., Gray, W.G. and C.T. Miller
// Description of Non-Darcy Flows in Porous Medium Systems
// Physical Review E 87 (3), 033012
// Fo := density*D32^3*(density*force) / (viscosity^2)
// Re := density*D32*velocity / viscosity
// Fo = a*Re + b*Re^2
// *************************************************************************
//viscosity = (tau-0.5)*0.333333333333333333;
D32 = 6.0*(Dm.Volume-Averages.vol_w_global)/Averages.As_global;
printf("Sauter Mean Diameter = %f \n",D32);
mag_force = sqrt(Fx*Fx+Fy*Fy+Fz*Fz);
Fo = D32*D32*D32*mag_force/viscosity/viscosity;
// .... 1-D flow should be aligned with force ...
velocity = vawx*Fx/mag_force + vawy*Fy/mag_force + vawz*Fz/mag_force;
err1D = fabs(velocity-sqrt(vawx*vawx+vawy*vawy+vawz*vawz))/velocity;
//.......... Computation of the Reynolds number Re ..............
Re = D32*velocity/viscosity;
printf("Force: %.5g,%.5g,%.5g \n",Fx,Fy,Fz);
printf("Velocity: %.5g,%.5g,%.5g \n",vawx,vawy,vawz);
printf("Relative error for 1D representation: %.5g \n",err1D);
printf("Dimensionless force: %5g \n", Fo);
printf("Reynolds number: %.5g \n", Re);
printf("Dimensionless Permeability (k/D^2): %.5g \n", Re/Fo);
}
}
}
//************************************************************************/
// Initialize compute device
int device=ScaLBL_SetDevice(rank);
NULL_USE( device );
ScaLBL_DeviceBarrier();
MPI_Barrier(comm);
stoptime = MPI_Wtime();
if (rank==0) printf("-------------------------------------------------------------------\n");
// Compute the walltime per timestep
cputime = (stoptime - starttime)/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");
NULL_USE(RESTART_INTERVAL);
comm.barrier();
ScaLBL_BGKModel BGK(rank,nprocs,comm);
auto filename = argv[1];
BGK.ReadParams(filename);
BGK.SetDomain(); // this reads in the domain
BGK.ReadInput();
BGK.Create(); // creating the model will create data structure to match the pore structure and allocate variables
BGK.Initialize(); // initializing the model will set initial conditions for variables
BGK.Run();
BGK.VelocityField();
cout << flush;
}
// ****************************************************
comm.barrier();
Utilities::shutdown();
// ****************************************************
Utilities::shutdown();
}

2
tests/lbpm_color_simulator.cpp
View File

@ -23,7 +23,7 @@ int main( int argc, char **argv )
{
// Initialize
Utilities::startup( argc, argv, false );
Utilities::startup( argc, argv, true );
{ // Limit scope so variables that contain communicators will free before MPI_Finialize