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LBPM/models/ColorModel.cpp

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/*
Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
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/>.
*/
/*
color lattice boltzmann model
*/
#include "models/ColorModel.h"
#include "analysis/distance.h"
#include "analysis/morphology.h"
#include <stdlib.h>
#include <time.h>
ScaLBL_ColorModel::ScaLBL_ColorModel(int RANK, int NP, MPI_Comm COMM):
rank(RANK), nprocs(NP), Restart(0),timestep(0),timestepMax(0),tauA(0),tauB(0),rhoA(0),rhoB(0),alpha(0),beta(0),
Fx(0),Fy(0),Fz(0),flux(0),din(0),dout(0),inletA(0),inletB(0),outletA(0),outletB(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)
{
REVERSE_FLOW_DIRECTION = false;
}
ScaLBL_ColorModel::~ScaLBL_ColorModel(){
}
/*void ScaLBL_ColorModel::WriteCheckpoint(const char *FILENAME, const double *cPhi, const double *cfq, int Np)
{
int q,n;
double value;
ofstream File(FILENAME,ios::binary);
for (n=0; n<Np; n++){
// Write the two density values
value = cPhi[n];
File.write((char*) &value, sizeof(value));
// Write the even distributions
for (q=0; q<19; q++){
value = cfq[q*Np+n];
File.write((char*) &value, sizeof(value));
}
}
File.close();
}
void ScaLBL_ColorModel::ReadCheckpoint(char *FILENAME, double *cPhi, double *cfq, int Np)
{
int q=0, n=0;
double value=0;
ifstream File(FILENAME,ios::binary);
for (n=0; n<Np; n++){
File.read((char*) &value, sizeof(value));
cPhi[n] = value;
// Read the distributions
for (q=0; q<19; q++){
File.read((char*) &value, sizeof(value));
cfq[q*Np+n] = value;
}
}
File.close();
}
*/
void ScaLBL_ColorModel::ReadParams(string filename){
// read the input database
db = std::make_shared<Database>( filename );
domain_db = db->getDatabase( "Domain" );
color_db = db->getDatabase( "Color" );
analysis_db = db->getDatabase( "Analysis" );
vis_db = db->getDatabase( "Visualization" );
// set defaults
timestepMax = 100000;
tauA = tauB = 1.0;
rhoA = rhoB = 1.0;
Fx = Fy = Fz = 0.0;
alpha=1e-3;
beta=0.95;
Restart=false;
din=dout=1.0;
flux=0.0;
// Color Model parameters
if (color_db->keyExists( "timestepMax" )){
timestepMax = color_db->getScalar<int>( "timestepMax" );
}
if (color_db->keyExists( "tauA" )){
tauA = color_db->getScalar<double>( "tauA" );
}
if (color_db->keyExists( "tauB" )){
tauB = color_db->getScalar<double>( "tauB" );
}
if (color_db->keyExists( "rhoA" )){
rhoA = color_db->getScalar<double>( "rhoA" );
}
if (color_db->keyExists( "rhoB" )){
rhoB = color_db->getScalar<double>( "rhoB" );
}
if (color_db->keyExists( "F" )){
Fx = color_db->getVector<double>( "F" )[0];
Fy = color_db->getVector<double>( "F" )[1];
Fz = color_db->getVector<double>( "F" )[2];
}
if (color_db->keyExists( "alpha" )){
alpha = color_db->getScalar<double>( "alpha" );
}
if (color_db->keyExists( "beta" )){
beta = color_db->getScalar<double>( "beta" );
}
if (color_db->keyExists( "Restart" )){
Restart = color_db->getScalar<bool>( "Restart" );
}
if (color_db->keyExists( "din" )){
din = color_db->getScalar<double>( "din" );
}
if (color_db->keyExists( "dout" )){
dout = color_db->getScalar<double>( "dout" );
}
if (color_db->keyExists( "flux" )){
flux = color_db->getScalar<double>( "flux" );
}
inletA=1.f;
inletB=0.f;
outletA=0.f;
outletB=1.f;
if (BoundaryCondition==4) flux *= rhoA; // mass flux must adjust for density (see formulation for details)
BoundaryCondition = 0;
if (domain_db->keyExists( "BC" )){
BoundaryCondition = domain_db->getScalar<int>( "BC" );
}
// Override user-specified boundary condition for specific protocols
auto protocol = color_db->getWithDefault<std::string>( "protocol", "none" );
if (protocol == "seed water"){
if (BoundaryCondition != 0 ){
BoundaryCondition = 0;
if (rank==0) printf("WARNING: protocol (seed water) supports only full periodic boundary condition \n");
}
domain_db->putScalar<int>( "BC", BoundaryCondition );
}
else if (protocol == "open connected oil"){
if (BoundaryCondition != 0 ){
BoundaryCondition = 0;
if (rank==0) printf("WARNING: protocol (open connected oil) supports only full periodic boundary condition \n");
}
domain_db->putScalar<int>( "BC", BoundaryCondition );
}
else if (protocol == "shell aggregation"){
if (BoundaryCondition != 0 ){
BoundaryCondition = 0;
if (rank==0) printf("WARNING: protocol (shell aggregation) supports only full periodic boundary condition \n");
}
domain_db->putScalar<int>( "BC", BoundaryCondition );
}
}
void ScaLBL_ColorModel::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;
id = new signed char [N];
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
Averages = std::shared_ptr<SubPhase> ( new SubPhase(Dm) ); // TwoPhase analysis object
MPI_Barrier(comm);
Dm->CommInit();
MPI_Barrier(comm);
// Read domain parameters
rank = Dm->rank();
nprocx = Dm->nprocx();
nprocy = Dm->nprocy();
nprocz = Dm->nprocz();
}
void ScaLBL_ColorModel::ReadInput(){
sprintf(LocalRankString,"%05d",rank);
sprintf(LocalRankFilename,"%s%s","ID.",LocalRankString);
sprintf(LocalRestartFile,"%s%s","Restart.",LocalRankString);
if (color_db->keyExists( "image_sequence" )){
auto ImageList = color_db->getVector<std::string>( "image_sequence");
int IMAGE_INDEX = color_db->getWithDefault<int>( "image_index", 0 );
int IMAGE_COUNT = ImageList.size();
std::string first_image = ImageList[IMAGE_INDEX];
Mask->Decomp(first_image);
IMAGE_INDEX++;
}
else if (domain_db->keyExists( "Filename" )){
auto Filename = domain_db->getScalar<std::string>( "Filename" );
Mask->Decomp(Filename);
}
else{
Mask->ReadIDs();
}
for (int i=0; i<Nx*Ny*Nz; i++) id[i] = Mask->id[i]; // save what was read
// Generate the signed distance map
// Initialize the domain and communication
Array<char> id_solid(Nx,Ny,Nz);
int count = 0;
// 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
signed char label = Mask->id[n];
if (label > 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++){
int n=k*Nx*Ny+j*Nx+i;
// Initialize distance to +/- 1
Averages->SDs(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(Averages->SDs,id_solid,*Mask);
if (rank == 0) cout << "Domain set." << endl;
Averages->SetParams(rhoA,rhoB,tauA,tauB,Fx,Fy,Fz,alpha,beta);
}
void ScaLBL_ColorModel::AssignComponentLabels(double *phase)
{
size_t NLABELS=0;
signed char VALUE=0;
double AFFINITY=0.f;
auto LabelList = color_db->getVector<int>( "ComponentLabels" );
auto AffinityList = color_db->getVector<double>( "ComponentAffinity" );
NLABELS=LabelList.size();
if (NLABELS != AffinityList.size()){
ERROR("Error: ComponentLabels and ComponentAffinity must be the same length! \n");
}
double label_count[NLABELS];
double label_count_global[NLABELS];
// Assign the labels
for (int idx=0; idx<NLABELS; idx++) label_count[idx]=0;
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;
VALUE=id[n];
// Assign the affinity from the paired list
for (unsigned int idx=0; idx < NLABELS; idx++){
//printf("idx=%i, value=%i, %i, \n",idx, VALUE,LabelList[idx]);
if (VALUE == LabelList[idx]){
AFFINITY=AffinityList[idx];
label_count[idx] += 1.0;
idx = NLABELS;
//Mask->id[n] = 0; // set mask to zero since this is an immobile component
}
}
// fluid labels are reserved
if (VALUE == 1) AFFINITY=1.0;
else if (VALUE == 2) AFFINITY=-1.0;
phase[n] = AFFINITY;
}
}
}
// Set Dm to match Mask
for (int i=0; i<Nx*Ny*Nz; i++) Dm->id[i] = Mask->id[i];
for (int idx=0; idx<NLABELS; idx++) label_count_global[idx]=sumReduce( Dm->Comm, label_count[idx]);
if (rank==0){
printf("Component labels: %lu \n",NLABELS);
for (unsigned int idx=0; idx<NLABELS; idx++){
VALUE=LabelList[idx];
AFFINITY=AffinityList[idx];
double volume_fraction = double(label_count_global[idx])/double((Nx-2)*(Ny-2)*(Nz-2)*nprocs);
printf(" label=%d, affinity=%f, volume fraction==%f\n",VALUE,AFFINITY,volume_fraction);
}
}
}
void ScaLBL_ColorModel::Create(){
/*
* This function creates the variables needed to run a LBM
*/
//.........................................................
// 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;
//.........................................................
// 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));
ScaLBL_Comm_Regular = std::shared_ptr<ScaLBL_Communicator>(new ScaLBL_Communicator(Mask));
int Npad=(Np/16 + 2)*16;
if (rank==0) printf ("Set up memory efficient layout, %i | %i | %i \n", Np, Npad, N);
Map.resize(Nx,Ny,Nz); Map.fill(-2);
auto neighborList= new int[18*Npad];
Np = ScaLBL_Comm->MemoryOptimizedLayoutAA(Map,neighborList,Mask->id,Np);
MPI_Barrier(comm);
//...........................................................................
// MAIN VARIABLES ALLOCATED HERE
//...........................................................................
// LBM variables
if (rank==0) printf ("Allocating distributions \n");
//......................device distributions.................................
dist_mem_size = Np*sizeof(double);
neighborSize=18*(Np*sizeof(int));
//...........................................................................
ScaLBL_AllocateDeviceMemory((void **) &NeighborList, neighborSize);
ScaLBL_AllocateDeviceMemory((void **) &dvcMap, sizeof(int)*Np);
ScaLBL_AllocateDeviceMemory((void **) &fq, 19*dist_mem_size);
ScaLBL_AllocateDeviceMemory((void **) &Aq, 7*dist_mem_size);
ScaLBL_AllocateDeviceMemory((void **) &Bq, 7*dist_mem_size);
ScaLBL_AllocateDeviceMemory((void **) &Den, 2*dist_mem_size);
ScaLBL_AllocateDeviceMemory((void **) &Phi, sizeof(double)*Nx*Ny*Nz);
ScaLBL_AllocateDeviceMemory((void **) &Pressure, sizeof(double)*Np);
ScaLBL_AllocateDeviceMemory((void **) &Velocity, 3*sizeof(double)*Np);
ScaLBL_AllocateDeviceMemory((void **) &ColorGrad, 3*sizeof(double)*Np);
//...........................................................................
// Update GPU data structures
if (rank==0) printf ("Setting up device map and neighbor list \n");
fflush(stdout);
int *TmpMap;
TmpMap=new int[Np];
for (int k=1; k<Nz-1; k++){
for (int j=1; j<Ny-1; j++){
for (int i=1; i<Nx-1; i++){
int idx=Map(i,j,k);
if (!(idx < 0))
TmpMap[idx] = k*Nx*Ny+j*Nx+i;
}
}
}
// check that TmpMap is valid
for (int idx=0; idx<ScaLBL_Comm->LastExterior(); idx++){
int n = TmpMap[idx];
if (n > Nx*Ny*Nz){
printf("Bad value! idx=%i \n");
TmpMap[idx] = Nx*Ny*Nz-1;
}
}
for (int idx=ScaLBL_Comm->FirstInterior(); idx<ScaLBL_Comm->LastInterior(); idx++){
int n = TmpMap[idx];
if (n > Nx*Ny*Nz){
printf("Bad value! idx=%i \n");
TmpMap[idx] = Nx*Ny*Nz-1;
}
}
ScaLBL_CopyToDevice(dvcMap, TmpMap, sizeof(int)*Np);
ScaLBL_DeviceBarrier();
delete [] TmpMap;
// copy the neighbor list
ScaLBL_CopyToDevice(NeighborList, neighborList, neighborSize);
// initialize phi based on PhaseLabel (include solid component labels)
double *PhaseLabel;
PhaseLabel = new double[N];
AssignComponentLabels(PhaseLabel);
ScaLBL_CopyToDevice(Phi, PhaseLabel, N*sizeof(double));
}
/********************************************************
* AssignComponentLabels *
********************************************************/
void ScaLBL_ColorModel::Initialize(){
if (rank==0) printf ("Initializing distributions \n");
ScaLBL_D3Q19_Init(fq, Np);
/*
* This function initializes model
*/
if (Restart == true){
if (rank==0){
printf("Reading restart file! \n");
}
// Read in the restart file to CPU buffers
int *TmpMap;
TmpMap = new int[Np];
double *cPhi, *cDist, *cDen;
cPhi = new double[N];
cDen = new double[2*Np];
cDist = new double[19*Np];
ScaLBL_CopyToHost(TmpMap, dvcMap, Np*sizeof(int));
ScaLBL_CopyToHost(cPhi, Phi, N*sizeof(double));
ifstream File(LocalRestartFile,ios::binary);
int idx;
double value,va,vb;
for (int n=0; n<Np; n++){
File.read((char*) &va, sizeof(va));
File.read((char*) &vb, sizeof(vb));
cDen[n] = va;
cDen[Np+n] = vb;
}
for (int n=0; n<Np; n++){
// Read the distributions
for (int q=0; q<19; q++){
File.read((char*) &value, sizeof(value));
cDist[q*Np+n] = value;
}
}
File.close();
for (int n=0; n<ScaLBL_Comm->LastExterior(); n++){
va = cDen[n];
vb = cDen[Np + n];
value = (va-vb)/(va+vb);
idx = TmpMap[n];
if (!(idx < 0) && idx<N)
cPhi[idx] = value;
}
for (int n=ScaLBL_Comm->FirstInterior(); n<ScaLBL_Comm->LastInterior(); n++){
va = cDen[n];
vb = cDen[Np + n];
value = (va-vb)/(va+vb);
idx = TmpMap[n];
if (!(idx < 0) && idx<N)
cPhi[idx] = value;
}
// Copy the restart data to the GPU
ScaLBL_CopyToDevice(Den,cDen,2*Np*sizeof(double));
ScaLBL_CopyToDevice(fq,cDist,19*Np*sizeof(double));
ScaLBL_CopyToDevice(Phi,cPhi,N*sizeof(double));
ScaLBL_DeviceBarrier();
MPI_Barrier(comm);
}
if (rank==0) printf ("Initializing phase field \n");
ScaLBL_PhaseField_Init(dvcMap, Phi, Den, Aq, Bq, 0, ScaLBL_Comm->LastExterior(), Np);
ScaLBL_PhaseField_Init(dvcMap, Phi, Den, Aq, Bq, ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np);
if (BoundaryCondition >0 ){
if (Dm->kproc()==0){
ScaLBL_SetSlice_z(Phi,1.0,Nx,Ny,Nz,0);
ScaLBL_SetSlice_z(Phi,1.0,Nx,Ny,Nz,1);
ScaLBL_SetSlice_z(Phi,1.0,Nx,Ny,Nz,2);
}
if (Dm->kproc() == nprocz-1){
ScaLBL_SetSlice_z(Phi,-1.0,Nx,Ny,Nz,Nz-1);
ScaLBL_SetSlice_z(Phi,-1.0,Nx,Ny,Nz,Nz-2);
ScaLBL_SetSlice_z(Phi,-1.0,Nx,Ny,Nz,Nz-3);
}
}
ScaLBL_CopyToHost(Averages->Phi.data(),Phi,N*sizeof(double));
}
void ScaLBL_ColorModel::Run(){
int nprocs=nprocx*nprocy*nprocz;
const RankInfoStruct rank_info(rank,nprocx,nprocy,nprocz);
int IMAGE_INDEX = 0;
int IMAGE_COUNT = 0;
std::vector<std::string> ImageList;
bool SET_CAPILLARY_NUMBER = false;
bool MORPH_ADAPT = false;
bool USE_MORPH = false;
bool USE_SEED = false;
bool USE_DIRECT = false;
bool USE_MORPHOPEN_OIL = false;
int MAX_MORPH_TIMESTEPS = 50000; // maximum number of LBM timesteps to spend in morphological adaptation routine
int MIN_STEADY_TIMESTEPS = 100000;
int MAX_STEADY_TIMESTEPS = 200000;
int RAMP_TIMESTEPS = 0;//50000; // number of timesteps to run initially (to get a reasonable velocity field before other pieces kick in)
int CURRENT_MORPH_TIMESTEPS=0; // counter for number of timesteps spent in morphological adaptation routine (reset each time)
int CURRENT_STEADY_TIMESTEPS=0; // counter for number of timesteps spent in morphological adaptation routine (reset each time)
int morph_interval = 1000000;
int analysis_interval = 1000; // number of timesteps in between in situ analysis
int morph_timesteps = 0;
double morph_delta = 0.0;
double seed_water = 0.0;
double capillary_number = 0.0;
double tolerance = 0.01;
double Ca_previous = 0.f;
double initial_volume = 0.0;
double delta_volume = 0.0;
double delta_volume_target = 0.0;
double RESIDUAL_ENDPOINT_THRESHOLD = 0.04;
auto protocol = color_db->getWithDefault<std::string>( "protocol", "none" );
if (protocol == "image sequence"){
// Get the list of images
USE_DIRECT = true;
ImageList = color_db->getVector<std::string>( "image_sequence");
IMAGE_INDEX = color_db->getWithDefault<int>( "image_index", 0 );
IMAGE_COUNT = ImageList.size();
morph_interval = 10000;
USE_MORPH = true;
}
else if (protocol == "seed water"){
morph_delta = 0.05;
seed_water = 0.01;
USE_SEED = true;
USE_MORPH = true;
}
else if (protocol == "open connected oil"){
morph_delta = 0.05;
USE_MORPH = true;
USE_MORPHOPEN_OIL = true;
}
else if (protocol == "shell aggregation"){
morph_delta = 0.05;
USE_MORPH = true;
}
if (color_db->keyExists( "residual_endpoint_threshold" )){
RESIDUAL_ENDPOINT_THRESHOLD = color_db->getScalar<double>( "residual_endpoint_threshold" );
}
if (color_db->keyExists( "capillary_number" )){
capillary_number = color_db->getScalar<double>( "capillary_number" );
SET_CAPILLARY_NUMBER=true;
}
if (color_db->keyExists( "timestep" )){
timestep = color_db->getScalar<int>( "timestep" );
}
if (BoundaryCondition != 0 && SET_CAPILLARY_NUMBER==true){
if (rank == 0) printf("WARINING: capillary number target only supported for BC = 0 \n");
SET_CAPILLARY_NUMBER=false;
}
if (analysis_db->keyExists( "seed_water" )){
seed_water = analysis_db->getScalar<double>( "seed_water" );
if (rank == 0) printf("Seed water in oil %f (seed_water) \n",seed_water);
USE_SEED = true;
}
if (analysis_db->keyExists( "morph_delta" )){
morph_delta = analysis_db->getScalar<double>( "morph_delta" );
if (rank == 0) printf("Target volume change %f (morph_delta) \n",morph_delta);
}
if (analysis_db->keyExists( "morph_interval" )){
morph_interval = analysis_db->getScalar<int>( "morph_interval" );
USE_MORPH = true;
}
if (analysis_db->keyExists( "use_morphopen_oil" )){
USE_MORPHOPEN_OIL = analysis_db->getScalar<bool>( "use_morphopen_oil" );
if (rank == 0 && USE_MORPHOPEN_OIL) printf("Volume change by morphological opening \n");
USE_MORPH = true;
}
if (analysis_db->keyExists( "tolerance" )){
tolerance = analysis_db->getScalar<double>( "tolerance" );
}
if (analysis_db->keyExists( "analysis_interval" )){
analysis_interval = analysis_db->getScalar<int>( "analysis_interval" );
}
if (analysis_db->keyExists( "min_steady_timesteps" )){
MIN_STEADY_TIMESTEPS = analysis_db->getScalar<int>( "min_steady_timesteps" );
}
if (analysis_db->keyExists( "max_steady_timesteps" )){
MAX_STEADY_TIMESTEPS = analysis_db->getScalar<int>( "max_steady_timesteps" );
}
if (analysis_db->keyExists( "max_morph_timesteps" )){
MAX_MORPH_TIMESTEPS = analysis_db->getScalar<int>( "max_morph_timesteps" );
}
if (rank==0){
printf("********************************************************\n");
if (protocol == "image sequence"){
printf(" using protocol = image sequence \n");
printf(" min_steady_timesteps = %i \n",MIN_STEADY_TIMESTEPS);
printf(" max_steady_timesteps = %i \n",MAX_STEADY_TIMESTEPS);
printf(" tolerance = %f \n",tolerance);
std::string first_image = ImageList[IMAGE_INDEX];
printf(" first image in sequence: %s ***\n", first_image.c_str());
}
else if (protocol == "seed water"){
printf(" using protocol = seed water \n");
printf(" min_steady_timesteps = %i \n",MIN_STEADY_TIMESTEPS);
printf(" max_steady_timesteps = %i \n",MAX_STEADY_TIMESTEPS);
printf(" tolerance = %f \n",tolerance);
printf(" morph_delta = %f \n",morph_delta);
printf(" seed_water = %f \n",seed_water);
}
else if (protocol == "open connected oil"){
printf(" using protocol = open connected oil \n");
printf(" min_steady_timesteps = %i \n",MIN_STEADY_TIMESTEPS);
printf(" max_steady_timesteps = %i \n",MAX_STEADY_TIMESTEPS);
printf(" tolerance = %f \n",tolerance);
printf(" morph_delta = %f \n",morph_delta);
}
else if (protocol == "shell aggregation"){
printf(" using protocol = shell aggregation \n");
printf(" min_steady_timesteps = %i \n",MIN_STEADY_TIMESTEPS);
printf(" max_steady_timesteps = %i \n",MAX_STEADY_TIMESTEPS);
printf(" tolerance = %f \n",tolerance);
printf(" morph_delta = %f \n",morph_delta);
}
printf("No. of timesteps: %i \n", timestepMax);
fflush(stdout);
}
//.......create and start timer............
double starttime,stoptime,cputime;
ScaLBL_DeviceBarrier();
MPI_Barrier(comm);
starttime = MPI_Wtime();
//.........................................
//************ MAIN ITERATION LOOP ***************************************/
PROFILE_START("Loop");
//std::shared_ptr<Database> analysis_db;
bool Regular = false;
auto current_db = db->cloneDatabase();
runAnalysis analysis( current_db, rank_info, ScaLBL_Comm, Dm, Np, Regular, Map );
//analysis.createThreads( analysis_method, 4 );
while (timestep < timestepMax ) {
//if ( rank==0 ) { printf("Running timestep %i (%i MB)\n",timestep+1,(int)(Utilities::getMemoryUsage()/1048576)); }
PROFILE_START("Update");
// *************ODD TIMESTEP*************
timestep++;
// Compute the Phase indicator field
// Read for Aq, Bq happens in this routine (requires communication)
ScaLBL_Comm->BiSendD3Q7AA(Aq,Bq); //READ FROM NORMAL
ScaLBL_D3Q7_AAodd_PhaseField(NeighborList, dvcMap, Aq, Bq, Den, Phi, ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np);
ScaLBL_Comm->BiRecvD3Q7AA(Aq,Bq); //WRITE INTO OPPOSITE
ScaLBL_DeviceBarrier();
ScaLBL_D3Q7_AAodd_PhaseField(NeighborList, dvcMap, Aq, Bq, Den, Phi, 0, ScaLBL_Comm->LastExterior(), Np);
// Perform the collision operation
ScaLBL_Comm->SendD3Q19AA(fq); //READ FROM NORMAL
if (BoundaryCondition > 0){
ScaLBL_Comm->Color_BC_z(dvcMap, Phi, Den, inletA, inletB);
ScaLBL_Comm->Color_BC_Z(dvcMap, Phi, Den, outletA, outletB);
}
// Halo exchange for phase field
ScaLBL_Comm_Regular->SendHalo(Phi);
ScaLBL_D3Q19_AAodd_Color(NeighborList, dvcMap, fq, Aq, Bq, Den, Phi, Velocity, rhoA, rhoB, tauA, tauB,
alpha, beta, Fx, Fy, Fz, Nx, Nx*Ny, ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np);
ScaLBL_Comm_Regular->RecvHalo(Phi);
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);
}
if (BoundaryCondition == 4){
din = ScaLBL_Comm->D3Q19_Flux_BC_z(NeighborList, fq, flux, timestep);
ScaLBL_Comm->D3Q19_Pressure_BC_Z(NeighborList, fq, dout, timestep);
}
ScaLBL_D3Q19_AAodd_Color(NeighborList, dvcMap, fq, Aq, Bq, Den, Phi, Velocity, rhoA, rhoB, tauA, tauB,
alpha, beta, Fx, Fy, Fz, Nx, Nx*Ny, 0, ScaLBL_Comm->LastExterior(), Np);
ScaLBL_DeviceBarrier(); MPI_Barrier(comm);
// *************EVEN TIMESTEP*************
timestep++;
// Compute the Phase indicator field
ScaLBL_Comm->BiSendD3Q7AA(Aq,Bq); //READ FROM NORMAL
ScaLBL_D3Q7_AAeven_PhaseField(dvcMap, Aq, Bq, Den, Phi, ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np);
ScaLBL_Comm->BiRecvD3Q7AA(Aq,Bq); //WRITE INTO OPPOSITE
ScaLBL_DeviceBarrier();
ScaLBL_D3Q7_AAeven_PhaseField(dvcMap, Aq, Bq, Den, Phi, 0, ScaLBL_Comm->LastExterior(), Np);
// Perform the collision operation
ScaLBL_Comm->SendD3Q19AA(fq); //READ FORM NORMAL
// Halo exchange for phase field
if (BoundaryCondition > 0){
ScaLBL_Comm->Color_BC_z(dvcMap, Phi, Den, inletA, inletB);
ScaLBL_Comm->Color_BC_Z(dvcMap, Phi, Den, outletA, outletB);
}
ScaLBL_Comm_Regular->SendHalo(Phi);
ScaLBL_D3Q19_AAeven_Color(dvcMap, fq, Aq, Bq, Den, Phi, Velocity, rhoA, rhoB, tauA, tauB,
alpha, beta, Fx, Fy, Fz, Nx, Nx*Ny, ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np);
ScaLBL_Comm_Regular->RecvHalo(Phi);
ScaLBL_Comm->RecvD3Q19AA(fq); //WRITE INTO OPPOSITE
ScaLBL_DeviceBarrier();
// 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);
}
ScaLBL_D3Q19_AAeven_Color(dvcMap, fq, Aq, Bq, Den, Phi, Velocity, rhoA, rhoB, tauA, tauB,
alpha, beta, Fx, Fy, Fz, Nx, Nx*Ny, 0, ScaLBL_Comm->LastExterior(), Np);
ScaLBL_DeviceBarrier(); MPI_Barrier(comm);
//************************************************************************
MPI_Barrier(comm);
PROFILE_STOP("Update");
// Run the analysis
//analysis.run( timestep, *Averages, Phi, Pressure, Velocity, fq, Den );
color_db->putScalar<int>("timestep",timestep);
current_db->putDatabase("Color", color_db);
analysis.basic( current_db, *Averages, Phi, Pressure, Velocity, fq, Den );
if (rank==0 && timestep%analysis_interval == 0 && BoundaryCondition > 0){
printf("....inlet pressure=%f \n",din);
}
// allow initial ramp-up to get closer to steady state
if (timestep > RAMP_TIMESTEPS && timestep%analysis_interval == 0 && USE_MORPH){
analysis.finish();
CURRENT_STEADY_TIMESTEPS += analysis_interval;
double volB = Averages->gwb.V;
double volA = Averages->gnb.V;
volA /= Dm->Volume;
volB /= Dm->Volume;;
initial_volume = volA*Dm->Volume;
double vA_x = Averages->gnb.Px/Averages->gnb.M;
double vA_y = Averages->gnb.Py/Averages->gnb.M;
double vA_z = Averages->gnb.Pz/Averages->gnb.M;
double vB_x = Averages->gwb.Px/Averages->gwb.M;
double vB_y = Averages->gwb.Py/Averages->gwb.M;
double vB_z = Averages->gwb.Pz/Averages->gwb.M;
double muA = rhoA*(tauA-0.5)/3.f;
double muB = rhoB*(tauB-0.5)/3.f;
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 current_saturation = volB/(volA+volB);
double flow_rate_A = volA*(vA_x*dir_x + vA_y*dir_y + vA_z*dir_z);
double flow_rate_B = volB*(vB_x*dir_x + vB_y*dir_y + vB_z*dir_z);
double Ca = fabs(muA*flow_rate_A + muB*flow_rate_B)/(5.796*alpha);
if ( morph_timesteps > morph_interval ){
bool isSteady = false;
if ( (fabs((Ca - Ca_previous)/Ca) < tolerance && CURRENT_STEADY_TIMESTEPS > MIN_STEADY_TIMESTEPS))
isSteady = true;
if (CURRENT_STEADY_TIMESTEPS > MAX_STEADY_TIMESTEPS)
isSteady = true;
if ( isSteady ){
MORPH_ADAPT = true;
CURRENT_MORPH_TIMESTEPS=0;
delta_volume_target = Dm->Volume*volA *morph_delta; // set target volume change
Averages->Full();
Averages->Write(timestep);
analysis.WriteVisData( current_db, *Averages, Phi, Pressure, Velocity, fq, Den );
analysis.finish();
if (rank==0){
printf("** WRITE STEADY POINT *** ");
printf("Ca = %f, (previous = %f) \n",Ca,Ca_previous);
double h = Dm->voxel_length;
// pressures
double pA = Averages->gnb.p;
double pB = Averages->gwb.p;
double pAc = Averages->gnc.p;
double pBc = Averages->gwc.p;
double pAB = (pA-pB)/(h*5.796*alpha);
double pAB_connected = (pAc-pBc)/(h*5.796*alpha);
// connected contribution
double Vol_nc = Averages->gnc.V/Dm->Volume;
double Vol_wc = Averages->gwc.V/Dm->Volume;
double Vol_nd = Averages->gnd.V/Dm->Volume;
double Vol_wd = Averages->gwd.V/Dm->Volume;
double Mass_n = Averages->gnc.M + Averages->gnd.M;
double Mass_w = Averages->gwc.M + Averages->gwd.M;
double vAc_x = Averages->gnc.Px/Mass_n;
double vAc_y = Averages->gnc.Py/Mass_n;
double vAc_z = Averages->gnc.Pz/Mass_n;
double vBc_x = Averages->gwc.Px/Mass_w;
double vBc_y = Averages->gwc.Py/Mass_w;
double vBc_z = Averages->gwc.Pz/Mass_w;
// disconnected contribution
double vAd_x = Averages->gnd.Px/Mass_n;
double vAd_y = Averages->gnd.Py/Mass_n;
double vAd_z = Averages->gnd.Pz/Mass_n;
double vBd_x = Averages->gwd.Px/Mass_w;
double vBd_y = Averages->gwd.Py/Mass_w;
double vBd_z = Averages->gwd.Pz/Mass_w;
double flow_rate_A_connected = Vol_nc*(vAc_x*dir_x + vAc_y*dir_y + vAc_z*dir_z);
double flow_rate_B_connected = Vol_wc*(vBc_x*dir_x + vBc_y*dir_y + vBc_z*dir_z);
double flow_rate_A_disconnected = (Vol_nd)*(vAd_x*dir_x + vAd_y*dir_y + vAd_z*dir_z);
double flow_rate_B_disconnected = (Vol_wd)*(vBd_x*dir_x + vBd_y*dir_y + vBd_z*dir_z);
double kAeff_connected = h*h*muA*flow_rate_A_connected/(force_mag);
double kBeff_connected = h*h*muB*flow_rate_B_connected/(force_mag);
double kAeff_disconnected = h*h*muA*flow_rate_A_disconnected/(rhoA*force_mag);
double kBeff_disconnected = h*h*muB*flow_rate_B_disconnected/(rhoB*force_mag);
double kAeff = h*h*muA*(flow_rate_A)/(rhoA*force_mag);
double kBeff = h*h*muB*(flow_rate_B)/(rhoB*force_mag);
double viscous_pressure_drop = (rhoA*volA + rhoB*volB)*force_mag;
double Mobility = muA/muB;
bool WriteHeader=false;
FILE * kr_log_file = fopen("relperm.csv","r");
if (kr_log_file != NULL)
fclose(kr_log_file);
else
WriteHeader=true;
kr_log_file = fopen("relperm.csv","a");
if (WriteHeader)
fprintf(kr_log_file,"timesteps sat.water eff.perm.oil eff.perm.water eff.perm.oil.connected eff.perm.water.connected eff.perm.oil.disconnected eff.perm.water.disconnected cap.pressure cap.pressure.connected pressure.drop Ca M\n",CURRENT_STEADY_TIMESTEPS,current_saturation,kAeff,kBeff,pAB,viscous_pressure_drop,Ca,Mobility);
fprintf(kr_log_file,"%i %.5g %.5g %.5g %.5g %.5g %.5g %.5g %.5g %.5g %.5g %.5g %.5g\n",CURRENT_STEADY_TIMESTEPS,current_saturation,kAeff,kBeff,kAeff_connected,kBeff_connected,kAeff_disconnected,kBeff_disconnected,pAB,pAB_connected,viscous_pressure_drop,Ca,Mobility);
fclose(kr_log_file);
printf(" Measured capillary number %f \n ",Ca);
}
if (SET_CAPILLARY_NUMBER ){
Fx *= capillary_number / Ca;
Fy *= capillary_number / Ca;
Fz *= capillary_number / Ca;
if (force_mag > 1e-3){
Fx *= 1e-3/force_mag; // impose ceiling for stability
Fy *= 1e-3/force_mag;
Fz *= 1e-3/force_mag;
}
if (force_mag < 1e-7){
Fx *= 1e-7/force_mag; // impose floor
Fy *= 1e-7/force_mag;
Fz *= 1e-7/force_mag;
}
if (rank == 0) printf(" -- adjust force by factor %f \n ",capillary_number / Ca);
Averages->SetParams(rhoA,rhoB,tauA,tauB,Fx,Fy,Fz,alpha,beta);
color_db->putVector<double>("F",{Fx,Fy,Fz});
}
CURRENT_STEADY_TIMESTEPS = 0;
}
else{
if (rank==0){
printf("** Continue to simulate steady *** \n ");
printf("Ca = %f, (previous = %f) \n",Ca,Ca_previous);
}
}
morph_timesteps=0;
Ca_previous = Ca;
}
if (MORPH_ADAPT ){
CURRENT_MORPH_TIMESTEPS += analysis_interval;
if (USE_DIRECT){
// Use image sequence
IMAGE_INDEX++;
MORPH_ADAPT = false;
if (IMAGE_INDEX < IMAGE_COUNT){
std::string next_image = ImageList[IMAGE_INDEX];
if (rank==0) printf("***Loading next image in sequence (%i) ***\n",IMAGE_INDEX);
color_db->putScalar<int>("image_index",IMAGE_INDEX);
ImageInit(next_image);
}
else{
if (rank==0) printf("Finished simulating image sequence \n");
timestep = timestepMax;
}
}
else if (USE_SEED){
delta_volume = volA*Dm->Volume - initial_volume;
CURRENT_MORPH_TIMESTEPS += analysis_interval;
double massChange = SeedPhaseField(seed_water);
if (rank==0) printf("***Seed water in oil %f, volume change %f / %f ***\n", seed_water, delta_volume, delta_volume_target);
}
else if (USE_MORPHOPEN_OIL){
delta_volume = volA*Dm->Volume - initial_volume;
if (rank==0) printf("***Morphological opening of connected oil, target volume change %f ***\n", delta_volume_target);
MorphOpenConnected(delta_volume_target);
}
else {
if (rank==0) printf("***Shell aggregation, target volume change %f ***\n", delta_volume_target);
//double delta_volume_target = volB - (volA + volB)*TARGET_SATURATION; // change in volume to A
delta_volume += MorphInit(beta,delta_volume_target-delta_volume);
}
if ( (delta_volume - delta_volume_target)/delta_volume_target > 0.0 ){
MORPH_ADAPT = false;
CURRENT_STEADY_TIMESTEPS=0;
initial_volume = volA*Dm->Volume;
delta_volume = 0.0;
if (USE_DIRECT){
//BoundaryCondition = 0;
//ScaLBL_Comm->BoundaryCondition = 0;
//ScaLBL_Comm_Regular->BoundaryCondition = 0;
//Fx = capillary_number*dir_x*force_mag / Ca;
//Fy = capillary_number*dir_y*force_mag / Ca;
//Fz = capillary_number*dir_z*force_mag / Ca;
}
}
else if (!(USE_DIRECT) && CURRENT_MORPH_TIMESTEPS > MAX_MORPH_TIMESTEPS) {
MORPH_ADAPT = false;
CURRENT_STEADY_TIMESTEPS=0;
initial_volume = volA*Dm->Volume;
delta_volume = 0.0;
}
if ( REVERSE_FLOW_DIRECTION ){
//if (rank==0) printf("*****REVERSE FLOW DIRECTION***** \n");
delta_volume = 0.0;
// flow direction will reverse after next steady point
MORPH_ADAPT = false;
CURRENT_STEADY_TIMESTEPS=0;
//morph_delta *= (-1.0);
REVERSE_FLOW_DIRECTION = false;
}
MPI_Barrier(comm);
}
morph_timesteps += analysis_interval;
}
}
analysis.finish();
PROFILE_STOP("Loop");
PROFILE_SAVE("lbpm_color_simulator",1);
//************************************************************************
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");
// ************************************************************************
}
double ScaLBL_ColorModel::ImageInit(std::string Filename){
bool suppress = false;
if (rank==0) printf("Re-initializing fluids from file: %s \n", Filename.c_str());
Mask->Decomp(Filename);
for (int i=0; i<Nx*Ny*Nz; i++) id[i] = Mask->id[i]; // save what was read
for (int i=0; i<Nx*Ny*Nz; i++) Dm->id[i] = Mask->id[i]; // save what was read
double *PhaseLabel;
PhaseLabel = new double[Nx*Ny*Nz];
AssignComponentLabels(PhaseLabel);
double Count = 0.0;
double PoreCount = 0.0;
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 (id[Nx*Ny*k+Nx*j+i] == 2){
PoreCount++;
Count++;
}
else if (id[Nx*Ny*k+Nx*j+i] == 1){
PoreCount++;
}
}
}
}
Count=sumReduce( Dm->Comm, Count);
PoreCount=sumReduce( Dm->Comm, PoreCount);
if (rank==0) printf(" new saturation: %f (%f / %f) \n", Count / PoreCount, Count, PoreCount);
ScaLBL_CopyToDevice(Phi, PhaseLabel, Nx*Ny*Nz*sizeof(double));
MPI_Barrier(comm);
ScaLBL_D3Q19_Init(fq, Np);
ScaLBL_PhaseField_Init(dvcMap, Phi, Den, Aq, Bq, 0, ScaLBL_Comm->LastExterior(), Np);
ScaLBL_PhaseField_Init(dvcMap, Phi, Den, Aq, Bq, ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np);
MPI_Barrier(comm);
ScaLBL_CopyToHost(Averages->Phi.data(),Phi,Nx*Ny*Nz*sizeof(double));
double saturation = Count/PoreCount;
return saturation;
}
double ScaLBL_ColorModel::MorphOpenConnected(double target_volume_change){
int nx = Nx;
int ny = Ny;
int nz = Nz;
int n;
int N = nx*ny*nz;
double volume_change=0.0;
if (target_volume_change < 0.0){
Array<char> id_solid(nx,ny,nz);
Array<int> phase_label(nx,ny,nz);
DoubleArray distance(Nx,Ny,Nz);
DoubleArray phase(nx,ny,nz);
signed char *id_connected;
id_connected = new signed char [nx*ny*nz];
ScaLBL_CopyToHost(phase.data(), Phi, N*sizeof(double));
// Extract only the connected part of NWP
BlobIDstruct new_index;
double vF=0.0; double vS=0.0;
ComputeGlobalBlobIDs(nx-2,ny-2,nz-2,Dm->rank_info,phase,Averages->SDs,vF,vS,phase_label,Dm->Comm);
MPI_Barrier(Dm->Comm);
int count_oil=0;
int count_connected=0;
int count_porespace=0;
int count_water=0;
for (int k=1; k<nz-1; k++){
for (int j=1; j<ny-1; j++){
for (int i=1; i<nx-1; i++){
n=k*nx*ny+j*nx+i;
// only apply opening to connected component
if ( phase_label(i,j,k) == 0){
count_connected++;
}
if (id[n] > 0){
count_porespace++;
}
if (id[n] == 2){
count_water++;
}
}
}
}
count_connected=sumReduce( Dm->Comm, count_connected);
count_porespace=sumReduce( Dm->Comm, count_porespace);
count_water=sumReduce( Dm->Comm, count_water);
for (int k=0; k<nz; k++){
for (int j=0; j<ny; j++){
for (int i=0; i<nx; i++){
n=k*nx*ny+j*nx+i;
// only apply opening to connected component
if ( phase_label(i,j,k) == 0){
id_solid(i,j,k) = 1;
id_connected[n] = 2;
id[n] = 2;
/* delete the connected component */
phase(i,j,k) = -1.0;
}
else{
id_solid(i,j,k) = 0;
id_connected[n] = 0;
}
}
}
}
CalcDist(distance,id_solid,*Dm);
signed char water=2;
signed char notwater=1;
double SW=-(target_volume_change)/count_connected;
MorphOpen(distance, id_connected, Dm, SW, water, notwater);
for (int k=0; k<nz; k++){
for (int j=0; j<ny; j++){
for (int i=0; i<nx; i++){
n=k*nx*ny+j*nx+i;
// only apply opening to connected component
if ( id_connected[n] == 1){
id_solid(i,j,k) = 0;
}
else{
id_solid(i,j,k) = 1;
}
}
}
}
CalcDist(distance,id_solid,*Dm);
// re-initialize
double beta = 0.95;
for (int k=0; k<nz; k++){
for (int j=0; j<ny; j++){
for (int i=0; i<nx; i++){
n=k*nx*ny+j*nx+i;
double d = distance(i,j,k);
if (Averages->SDs(i,j,k) > 0.f){
if (d < 3.f){
phase(i,j,k) = (2.f*(exp(-2.f*beta*d))/(1.f+exp(-2.f*beta*d))-1.f);
}
}
}
}
}
int count_morphopen=0.0;
for (int k=1; k<nz-1; k++){
for (int j=1; j<ny-1; j++){
for (int i=1; i<nx-1; i++){
n=k*nx*ny+j*nx+i;
// only apply opening to connected component
if ( id_connected[n] == 1){
count_morphopen++;
}
}
}
}
count_morphopen=sumReduce( Dm->Comm, count_morphopen);
volume_change = double(count_morphopen - count_connected);
if (rank==0) printf(" opening of connected oil %f \n",volume_change/count_connected);
ScaLBL_CopyToDevice(Phi,phase.data(),N*sizeof(double));
ScaLBL_PhaseField_Init(dvcMap, Phi, Den, Aq, Bq, 0, ScaLBL_Comm->LastExterior(), Np);
ScaLBL_PhaseField_Init(dvcMap, Phi, Den, Aq, Bq, ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np);
if (BoundaryCondition >0 ){
if (Dm->kproc()==0){
ScaLBL_SetSlice_z(Phi,1.0,Nx,Ny,Nz,0);
ScaLBL_SetSlice_z(Phi,1.0,Nx,Ny,Nz,1);
ScaLBL_SetSlice_z(Phi,1.0,Nx,Ny,Nz,2);
}
if (Dm->kproc() == nprocz-1){
ScaLBL_SetSlice_z(Phi,-1.0,Nx,Ny,Nz,Nz-1);
ScaLBL_SetSlice_z(Phi,-1.0,Nx,Ny,Nz,Nz-2);
ScaLBL_SetSlice_z(Phi,-1.0,Nx,Ny,Nz,Nz-3);
}
}
}
return(volume_change);
}
double ScaLBL_ColorModel::SeedPhaseField(const double seed_water_in_oil){
srand(time(NULL));
double mass_loss =0.f;
double count =0.f;
double *Aq_tmp, *Bq_tmp;
Aq_tmp = new double [7*Np];
Bq_tmp = new double [7*Np];
ScaLBL_CopyToHost(Aq_tmp, Aq, 7*Np*sizeof(double));
ScaLBL_CopyToHost(Bq_tmp, Bq, 7*Np*sizeof(double));
/* for (int k=1; k<Nz-1; k++){
for (int j=1; j<Ny-1; j++){
for (int i=1; i<Nx-1; i++){
double random_value = double(rand())/ RAND_MAX;
if (Averages->SDs(i,j,k) < 0.f){
// skip
}
else if (phase(i,j,k) > 0.f ){
phase(i,j,k) -= random_value*seed_water_in_oil;
mass_loss += random_value*seed_water_in_oil;
count++;
}
else {
}
}
}
}
*/
for (int n=0; n < ScaLBL_Comm->LastExterior(); n++){
double random_value = seed_water_in_oil*double(rand())/ RAND_MAX;
double dA = Aq_tmp[n] + Aq_tmp[n+Np] + Aq_tmp[n+2*Np] + Aq_tmp[n+3*Np] + Aq_tmp[n+4*Np] + Aq_tmp[n+5*Np] + Aq_tmp[n+6*Np];
double dB = Bq_tmp[n] + Bq_tmp[n+Np] + Bq_tmp[n+2*Np] + Bq_tmp[n+3*Np] + Bq_tmp[n+4*Np] + Bq_tmp[n+5*Np] + Bq_tmp[n+6*Np];
double phase_id = (dA - dB) / (dA + dB);
if (phase_id > 0.0){
Aq_tmp[n] -= 0.3333333333333333*random_value;
Aq_tmp[n+Np] -= 0.1111111111111111*random_value;
Aq_tmp[n+2*Np] -= 0.1111111111111111*random_value;
Aq_tmp[n+3*Np] -= 0.1111111111111111*random_value;
Aq_tmp[n+4*Np] -= 0.1111111111111111*random_value;
Aq_tmp[n+5*Np] -= 0.1111111111111111*random_value;
Aq_tmp[n+6*Np] -= 0.1111111111111111*random_value;
Bq_tmp[n] += 0.3333333333333333*random_value;
Bq_tmp[n+Np] += 0.1111111111111111*random_value;
Bq_tmp[n+2*Np] += 0.1111111111111111*random_value;
Bq_tmp[n+3*Np] += 0.1111111111111111*random_value;
Bq_tmp[n+4*Np] += 0.1111111111111111*random_value;
Bq_tmp[n+5*Np] += 0.1111111111111111*random_value;
Bq_tmp[n+6*Np] += 0.1111111111111111*random_value;
}
mass_loss += random_value*seed_water_in_oil;
}
for (int n=ScaLBL_Comm->FirstInterior(); n < ScaLBL_Comm->LastInterior(); n++){
double random_value = seed_water_in_oil*double(rand())/ RAND_MAX;
double dA = Aq_tmp[n] + Aq_tmp[n+Np] + Aq_tmp[n+2*Np] + Aq_tmp[n+3*Np] + Aq_tmp[n+4*Np] + Aq_tmp[n+5*Np] + Aq_tmp[n+6*Np];
double dB = Bq_tmp[n] + Bq_tmp[n+Np] + Bq_tmp[n+2*Np] + Bq_tmp[n+3*Np] + Bq_tmp[n+4*Np] + Bq_tmp[n+5*Np] + Bq_tmp[n+6*Np];
double phase_id = (dA - dB) / (dA + dB);
if (phase_id > 0.0){
Aq_tmp[n] -= 0.3333333333333333*random_value;
Aq_tmp[n+Np] -= 0.1111111111111111*random_value;
Aq_tmp[n+2*Np] -= 0.1111111111111111*random_value;
Aq_tmp[n+3*Np] -= 0.1111111111111111*random_value;
Aq_tmp[n+4*Np] -= 0.1111111111111111*random_value;
Aq_tmp[n+5*Np] -= 0.1111111111111111*random_value;
Aq_tmp[n+6*Np] -= 0.1111111111111111*random_value;
Bq_tmp[n] += 0.3333333333333333*random_value;
Bq_tmp[n+Np] += 0.1111111111111111*random_value;
Bq_tmp[n+2*Np] += 0.1111111111111111*random_value;
Bq_tmp[n+3*Np] += 0.1111111111111111*random_value;
Bq_tmp[n+4*Np] += 0.1111111111111111*random_value;
Bq_tmp[n+5*Np] += 0.1111111111111111*random_value;
Bq_tmp[n+6*Np] += 0.1111111111111111*random_value;
}
mass_loss += random_value*seed_water_in_oil;
}
count= sumReduce( Dm->Comm, count);
mass_loss= sumReduce( Dm->Comm, mass_loss);
if (rank == 0) printf("Remove mass %f from %f voxels \n",mass_loss,count);
// Need to initialize Aq, Bq, Den, Phi directly
//ScaLBL_CopyToDevice(Phi,phase.data(),7*Np*sizeof(double));
ScaLBL_CopyToDevice(Aq, Aq_tmp, 7*Np*sizeof(double));
ScaLBL_CopyToDevice(Bq, Bq_tmp, 7*Np*sizeof(double));
return(mass_loss);
}
double ScaLBL_ColorModel::MorphInit(const double beta, const double target_delta_volume){
const RankInfoStruct rank_info(rank,nprocx,nprocy,nprocz);
double vF = 0.f;
double vS = 0.f;
double delta_volume;
DoubleArray phase(Nx,Ny,Nz);
IntArray phase_label(Nx,Ny,Nz);;
DoubleArray phase_distance(Nx,Ny,Nz);
Array<char> phase_id(Nx,Ny,Nz);
fillHalo<double> fillDouble(Dm->Comm,Dm->rank_info,{Nx-2,Ny-2,Nz-2},{1,1,1},0,1);
// Basic algorithm to
// 1. Copy phase field to CPU
ScaLBL_CopyToHost(phase.data(), Phi, N*sizeof(double));
double count,count_global,volume_initial,volume_final,volume_connected;
count = 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 (phase(i,j,k) > 0.f && Averages->SDs(i,j,k) > 0.f) count+=1.f;
}
}
}
volume_initial = sumReduce( Dm->Comm, count);
/*
sprintf(LocalRankFilename,"phi_initial.%05i.raw",rank);
FILE *INPUT = fopen(LocalRankFilename,"wb");
fwrite(phase.data(),8,N,INPUT);
fclose(INPUT);
*/
// 2. Identify connected components of phase field -> phase_label
BlobIDstruct new_index;
ComputeGlobalBlobIDs(Nx-2,Ny-2,Nz-2,rank_info,phase,Averages->SDs,vF,vS,phase_label,comm);
MPI_Barrier(comm);
// only operate on component "0"
count = 0.0;
double second_biggest = 0.0;
for (int k=0; k<Nz; k++){
for (int j=0; j<Ny; j++){
for (int i=0; i<Nx; i++){
int label = phase_label(i,j,k);
if (label == 0 ){
phase_id(i,j,k) = 0;
count += 1.0;
}
else
phase_id(i,j,k) = 1;
if (label == 1 ){
second_biggest += 1.0;
}
}
}
}
volume_connected = sumReduce( Dm->Comm, count);
second_biggest = sumReduce( Dm->Comm, second_biggest);
int reach_x, reach_y, reach_z;
for (int k=0; k<Nz; k++){
for (int j=0; j<Ny; j++){
for (int i=0; i<Nx; i++){
}
}
}
// 3. Generate a distance map to the largest object -> phase_distance
CalcDist(phase_distance,phase_id,*Dm);
double temp,value;
double factor=0.5/beta;
for (int k=0; k<Nz; k++){
for (int j=0; j<Ny; j++){
for (int i=0; i<Nx; i++){
if (phase_distance(i,j,k) < 3.f ){
value = phase(i,j,k);
if (value > 1.f) value=1.f;
if (value < -1.f) value=-1.f;
// temp -- distance based on analytical form McClure, Prins et al, Comp. Phys. Comm.
temp = -factor*log((1.0+value)/(1.0-value));
/// use this approximation close to the object
if (fabs(value) < 0.8 && Averages->SDs(i,j,k) > 1.f ){
phase_distance(i,j,k) = temp;
}
// erase the original object
phase(i,j,k) = -1.0;
}
}
}
}
if (volume_connected - second_biggest < 2.0*fabs(target_delta_volume) && target_delta_volume < 0.0){
// if connected volume is less than 2% just delete the whole thing
if (rank==0) printf("Connected region has shrunk! \n");
REVERSE_FLOW_DIRECTION = true;
}
/* else{*/
if (rank==0) printf("Pathway volume / next largest ganglion %f \n",volume_connected/second_biggest );
if (rank==0) printf("MorphGrow with target volume fraction change %f \n", target_delta_volume/volume_initial);
double target_delta_volume_incremental = target_delta_volume;
if (fabs(target_delta_volume) > 0.01*volume_initial)
target_delta_volume_incremental = 0.01*volume_initial*target_delta_volume/fabs(target_delta_volume);
delta_volume = MorphGrow(Averages->SDs,phase_distance,phase_id,Averages->Dm, target_delta_volume_incremental);
for (int k=0; k<Nz; k++){
for (int j=0; j<Ny; j++){
for (int i=0; i<Nx; i++){
if (phase_distance(i,j,k) < 0.0 ) phase_id(i,j,k) = 0;
else phase_id(i,j,k) = 1;
//if (phase_distance(i,j,k) < 0.0 ) phase(i,j,k) = 1.0;
}
}
}
CalcDist(phase_distance,phase_id,*Dm); // re-calculate distance
// 5. Update phase indicator field based on new distnace
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;
double d = phase_distance(i,j,k);
if (Averages->SDs(i,j,k) > 0.f){
if (d < 3.f){
//phase(i,j,k) = -1.0;
phase(i,j,k) = (2.f*(exp(-2.f*beta*d))/(1.f+exp(-2.f*beta*d))-1.f);
}
}
}
}
}
fillDouble.fill(phase);
//}
count = 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 (phase(i,j,k) > 0.f && Averages->SDs(i,j,k) > 0.f){
count+=1.f;
}
}
}
}
volume_final= sumReduce( Dm->Comm, count);
delta_volume = (volume_final-volume_initial);
if (rank == 0) printf("MorphInit: change fluid volume fraction by %f \n", delta_volume/volume_initial);
if (rank == 0) printf(" new saturation = %f \n", volume_final/(0.238323*double((Nx-2)*(Ny-2)*(Nz-2)*nprocs)));
// 6. copy back to the device
//if (rank==0) printf("MorphInit: copy data back to device\n");
ScaLBL_CopyToDevice(Phi,phase.data(),N*sizeof(double));
/*
sprintf(LocalRankFilename,"dist_final.%05i.raw",rank);
FILE *DIST = fopen(LocalRankFilename,"wb");
fwrite(phase_distance.data(),8,N,DIST);
fclose(DIST);
sprintf(LocalRankFilename,"phi_final.%05i.raw",rank);
FILE *PHI = fopen(LocalRankFilename,"wb");
fwrite(phase.data(),8,N,PHI);
fclose(PHI);
*/
// 7. Re-initialize phase field and density
ScaLBL_PhaseField_Init(dvcMap, Phi, Den, Aq, Bq, 0, ScaLBL_Comm->LastExterior(), Np);
ScaLBL_PhaseField_Init(dvcMap, Phi, Den, Aq, Bq, ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np);
if (BoundaryCondition >0 ){
if (Dm->kproc()==0){
ScaLBL_SetSlice_z(Phi,1.0,Nx,Ny,Nz,0);
ScaLBL_SetSlice_z(Phi,1.0,Nx,Ny,Nz,1);
ScaLBL_SetSlice_z(Phi,1.0,Nx,Ny,Nz,2);
}
if (Dm->kproc() == nprocz-1){
ScaLBL_SetSlice_z(Phi,-1.0,Nx,Ny,Nz,Nz-1);
ScaLBL_SetSlice_z(Phi,-1.0,Nx,Ny,Nz,Nz-2);
ScaLBL_SetSlice_z(Phi,-1.0,Nx,Ny,Nz,Nz-3);
}
}
return delta_volume;
}
void ScaLBL_ColorModel::WriteDebug(){
// Copy back final phase indicator field and convert to regular layout
DoubleArray PhaseField(Nx,Ny,Nz);
//ScaLBL_Comm->RegularLayout(Map,Phi,PhaseField);
ScaLBL_CopyToHost(PhaseField.data(), Phi, sizeof(double)*N);
FILE *OUTFILE;
sprintf(LocalRankFilename,"Phase.%05i.raw",rank);
OUTFILE = fopen(LocalRankFilename,"wb");
fwrite(PhaseField.data(),8,N,OUTFILE);
fclose(OUTFILE);
}
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