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LBPM/models/GreyscaleColorModel.cpp
James McClure 7f4f74779c fix the build
2021-01-05 18:43:44 -05:00

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/*
Two-fluid greyscale color lattice boltzmann model
*/
#include "models/GreyscaleColorModel.h"
#include "analysis/distance.h"
#include "analysis/morphology.h"
#include "common/Communication.h"
#include "common/ReadMicroCT.h"
#include <stdlib.h>
#include <time.h>
template<class TYPE>
void DeleteArray( const TYPE *p )
{
delete [] p;
}
ScaLBL_GreyscaleColorModel::ScaLBL_GreyscaleColorModel(int RANK, int NP, const Utilities::MPI& COMM):
rank(RANK), nprocs(NP), Restart(0),timestep(0),timestepMax(0),tauA(0),tauB(0),tauA_eff(0),tauB_eff(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),GreyPorosity(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_GreyscaleColorModel::~ScaLBL_GreyscaleColorModel(){
}
void ScaLBL_GreyscaleColorModel::ReadParams(string filename){
// read the input database
db = std::make_shared<Database>( filename );
domain_db = db->getDatabase( "Domain" );
greyscaleColor_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 (greyscaleColor_db->keyExists( "timestepMax" )){
timestepMax = greyscaleColor_db->getScalar<int>( "timestepMax" );
}
if (greyscaleColor_db->keyExists( "tauA" )){
tauA = greyscaleColor_db->getScalar<double>( "tauA" );
}
if (greyscaleColor_db->keyExists( "tauB" )){
tauB = greyscaleColor_db->getScalar<double>( "tauB" );
}
tauA_eff = greyscaleColor_db->getWithDefault<double>( "tauA_eff", tauA );
tauB_eff = greyscaleColor_db->getWithDefault<double>( "tauB_eff", tauB );
if (greyscaleColor_db->keyExists( "rhoA" )){
rhoA = greyscaleColor_db->getScalar<double>( "rhoA" );
}
if (greyscaleColor_db->keyExists( "rhoB" )){
rhoB = greyscaleColor_db->getScalar<double>( "rhoB" );
}
if (greyscaleColor_db->keyExists( "F" )){
Fx = greyscaleColor_db->getVector<double>( "F" )[0];
Fy = greyscaleColor_db->getVector<double>( "F" )[1];
Fz = greyscaleColor_db->getVector<double>( "F" )[2];
}
if (greyscaleColor_db->keyExists( "alpha" )){
alpha = greyscaleColor_db->getScalar<double>( "alpha" );
}
if (greyscaleColor_db->keyExists( "beta" )){
beta = greyscaleColor_db->getScalar<double>( "beta" );
}
if (greyscaleColor_db->keyExists( "Restart" )){
Restart = greyscaleColor_db->getScalar<bool>( "Restart" );
}
if (greyscaleColor_db->keyExists( "din" )){
din = greyscaleColor_db->getScalar<double>( "din" );
}
if (greyscaleColor_db->keyExists( "dout" )){
dout = greyscaleColor_db->getScalar<double>( "dout" );
}
if (greyscaleColor_db->keyExists( "flux" )){
flux = greyscaleColor_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 = greyscaleColor_db->getWithDefault<std::string>( "protocol", "none" );
if (protocol == "seed water"){
if (BoundaryCondition != 0 && BoundaryCondition != 5){
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 != 5){
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 != 5){
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_GreyscaleColorModel::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<GreyPhaseAnalysis> ( new GreyPhaseAnalysis(Dm) ); // TwoPhase analysis object
comm.barrier();
Dm->CommInit();
comm.barrier();
// Read domain parameters
rank = Dm->rank();
nprocx = Dm->nprocx();
nprocy = Dm->nprocy();
nprocz = Dm->nprocz();
}
void ScaLBL_GreyscaleColorModel::ReadInput(){
sprintf(LocalRankString,"%05d",rank);
sprintf(LocalRankFilename,"%s%s","ID.",LocalRankString);
sprintf(LocalRestartFile,"%s%s","Restart.",LocalRankString);
if (greyscaleColor_db->keyExists( "image_sequence" )){
auto ImageList = greyscaleColor_db->getVector<std::string>( "image_sequence");
int IMAGE_INDEX = greyscaleColor_db->getWithDefault<int>( "image_index", 0 );
std::string first_image = ImageList[IMAGE_INDEX];
Mask->Decomp(first_image);
IMAGE_INDEX++;
}
else if (domain_db->keyExists( "GridFile" )){
// Read the local domain data
auto input_id = readMicroCT( *domain_db, MPI_COMM_WORLD );
// 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( MPI_COMM_WORLD, 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 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);
// 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++){
// 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;
}
void ScaLBL_GreyscaleColorModel::AssignComponentLabels()
{
// Initialize impermeability solid nodes and grey nodes
// Key input parameters:
// 1. ComponentLabels
// labels for various impermeable minerals and grey nodes
// 2. ComponentAffinity
// for impermeable minerals, this is same as the wettability phase field in the normal color model
// for grey nodes, this is effectively the initial phase field values
// **Convention for ComponentLabels:
// (1) zero and negative integers are for impermeability minerals
// (2) positive integers > 2 are for grey nodes
// (3) label = 1 and 2 are always conserved for open node of non-wetting and wetting phase, respectively.
double *phase;
phase = new double[N];
size_t NLABELS=0;
signed char VALUE=0;
double AFFINITY=0.f;
auto LabelList = greyscaleColor_db->getVector<int>( "ComponentLabels" );
auto AffinityList = greyscaleColor_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 (size_t 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 (size_t idx=0; idx<NLABELS; idx++)
label_count_global[idx] = Dm->Comm.sumReduce( label_count[idx]);
if (rank==0){
printf("Number of 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);
}
}
ScaLBL_CopyToDevice(Phi, phase, N*sizeof(double));
ScaLBL_Comm->Barrier();
delete [] phase;
}
void ScaLBL_GreyscaleColorModel::AssignGreySolidLabels()//Model-4
{
// ONLY initialize grey nodes
// Key input parameters:
// 1. GreySolidLabels
// labels for grey nodes
// 2. GreySolidAffinity
// affinity ranges [-1,1]
// oil-wet > 0
// water-wet < 0
// neutral = 0
double *SolidPotential_host = new double [Nx*Ny*Nz];
double *GreySolidGrad_host = new double [3*Np];
size_t NLABELS=0;
signed char VALUE=0;
double AFFINITY=0.f;
auto LabelList = greyscaleColor_db->getVector<int>( "GreySolidLabels" );
auto AffinityList = greyscaleColor_db->getVector<double>( "GreySolidAffinity" );
NLABELS=LabelList.size();
if (NLABELS != AffinityList.size()){
ERROR("Error: GreySolidLabels and GreySolidAffinity must be the same length! \n");
}
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];
AFFINITY=0.f;//all nodes except the specified grey nodes have grey-solid affinity = 0.0
// 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];
idx = NLABELS;
//Mask->id[n] = 0; // set mask to zero since this is an immobile component
}
}
SolidPotential_host[n] = AFFINITY;
}
}
}
// Calculate grey-solid color-gradient
double *Dst;
Dst = new double [3*3*3];
for (int kk=0; kk<3; kk++){
for (int jj=0; jj<3; jj++){
for (int ii=0; ii<3; ii++){
int index = kk*9+jj*3+ii;
Dst[index] = sqrt(double(ii-1)*double(ii-1) + double(jj-1)*double(jj-1)+ double(kk-1)*double(kk-1));
}
}
}
double w_face = 1.f;
double w_edge = 0.5;
double w_corner = 0.f;
//local
Dst[13] = 0.f;
//faces
Dst[4] = w_face;
Dst[10] = w_face;
Dst[12] = w_face;
Dst[14] = w_face;
Dst[16] = w_face;
Dst[22] = w_face;
// corners
Dst[0] = w_corner;
Dst[2] = w_corner;
Dst[6] = w_corner;
Dst[8] = w_corner;
Dst[18] = w_corner;
Dst[20] = w_corner;
Dst[24] = w_corner;
Dst[26] = w_corner;
// edges
Dst[1] = w_edge;
Dst[3] = w_edge;
Dst[5] = w_edge;
Dst[7] = w_edge;
Dst[9] = w_edge;
Dst[11] = w_edge;
Dst[15] = w_edge;
Dst[17] = w_edge;
Dst[19] = w_edge;
Dst[21] = w_edge;
Dst[23] = w_edge;
Dst[25] = w_edge;
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)){
double phi_x = 0.f;
double phi_y = 0.f;
double phi_z = 0.f;
for (int kk=0; kk<3; kk++){
for (int jj=0; jj<3; jj++){
for (int ii=0; ii<3; ii++){
int index = kk*9+jj*3+ii;
double weight= Dst[index];
int idi=i+ii-1;
int idj=j+jj-1;
int idk=k+kk-1;
if (idi < 0) idi=0;
if (idj < 0) idj=0;
if (idk < 0) idk=0;
if (!(idi < Nx)) idi=Nx-1;
if (!(idj < Ny)) idj=Ny-1;
if (!(idk < Nz)) idk=Nz-1;
int nn = idk*Nx*Ny + idj*Nx + idi;
double vec_x = double(ii-1);
double vec_y = double(jj-1);
double vec_z = double(kk-1);
double GWNS=SolidPotential_host[nn];
phi_x += GWNS*weight*vec_x;
phi_y += GWNS*weight*vec_y;
phi_z += GWNS*weight*vec_z;
}
}
}
if (Averages->SDs(i,j,k)<2.0){
GreySolidGrad_host[idx+0*Np] = phi_x;
GreySolidGrad_host[idx+1*Np] = phi_y;
GreySolidGrad_host[idx+2*Np] = phi_z;
}
else{
GreySolidGrad_host[idx+0*Np] = 0.0;
GreySolidGrad_host[idx+1*Np] = 0.0;
GreySolidGrad_host[idx+2*Np] = 0.0;
}
}
}
}
}
if (rank==0){
printf("Number of Grey-solid labels: %lu \n",NLABELS);
for (unsigned int idx=0; idx<NLABELS; idx++){
VALUE=LabelList[idx];
AFFINITY=AffinityList[idx];
printf(" grey-solid label=%d, grey-solid affinity=%f\n",VALUE,AFFINITY);
}
}
ScaLBL_CopyToDevice(GreySolidGrad, GreySolidGrad_host, 3*Np*sizeof(double));
ScaLBL_Comm->Barrier();
delete [] SolidPotential_host;
delete [] GreySolidGrad_host;
delete [] Dst;
}
////----------------------------------------------------------------------------------------------------------//
void ScaLBL_GreyscaleColorModel::AssignGreyPoroPermLabels()
{
double *Porosity, *Permeability;
Porosity = new double[Np];
Permeability = new double[Np];
size_t NLABELS=0;
signed char VALUE=0;
double POROSITY=1.f;//default: label 1 or 2, i.e. open nodes and porosity=1.0
double PERMEABILITY=1.f;
auto LabelList = greyscaleColor_db->getVector<int>( "GreySolidLabels" );
auto PorosityList = greyscaleColor_db->getVector<double>( "PorosityList" );
auto PermeabilityList = greyscaleColor_db->getVector<double>( "PermeabilityList" );
NLABELS=LabelList.size();
if (LabelList.size() != PorosityList.size()){
ERROR("Error: GreySolidLabels and PorosityList 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];
POROSITY=1.f;//default: label 1 or 2, i.e. open nodes and porosity=1.0
// 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]){
POROSITY=PorosityList[idx];
label_count[idx] += 1.0;
idx = NLABELS;
//Mask->id[n] = 0; // set mask to zero since this is an immobile component
}
}
int idx = Map(i,j,k);
if (!(idx < 0)){
if (POROSITY<=0.0){
ERROR("Error: Porosity for grey voxels must be 0.0 < Porosity <= 1.0 !\n");
}
else{
Porosity[idx] = POROSITY;
}
}
}
}
}
if (NLABELS != PermeabilityList.size()){
ERROR("Error: GreySolidLabels and PermeabilityList must be the same length! \n");
}
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];
PERMEABILITY=1.f;
// 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]){
PERMEABILITY=PermeabilityList[idx];
idx = NLABELS;
//Mask->id[n] = 0; // set mask to zero since this is an immobile component
}
}
int idx = Map(i,j,k);
if (!(idx < 0)){
if (PERMEABILITY<=0.0){
ERROR("Error: Permeability for grey voxel must be > 0.0 ! \n");
}
else{
Permeability[idx] = PERMEABILITY/Dm->voxel_length/Dm->voxel_length;
}
}
}
}
}
// 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]=Dm->Comm.sumReduce( label_count[idx]);
//Initialize a weighted porosity after considering grey voxels
GreyPorosity=0.0;
for (unsigned int idx=0; idx<NLABELS; idx++){
double volume_fraction = double(label_count_global[idx])/double((Nx-2)*(Ny-2)*(Nz-2)*nprocs);
GreyPorosity+=volume_fraction*PorosityList[idx];
}
if (rank==0){
printf("Image resolution: %.5g [um/voxel]\n",Dm->voxel_length);
printf("Number of Grey-fluid labels: %lu \n",NLABELS);
for (unsigned int idx=0; idx<NLABELS; idx++){
VALUE=LabelList[idx];
POROSITY=PorosityList[idx];
PERMEABILITY=PermeabilityList[idx];
double volume_fraction = double(label_count_global[idx])/double((Nx-2)*(Ny-2)*(Nz-2)*nprocs);
printf(" grey-fluid label=%d, porosity=%.3g, permeability=%.3g [um^2] (=%.3g [voxel^2]), volume fraction=%.3g\n",
VALUE,POROSITY,PERMEABILITY,PERMEABILITY/Dm->voxel_length/Dm->voxel_length,volume_fraction);
printf(" effective porosity=%.3g\n",volume_fraction*POROSITY);
}
printf("The weighted porosity, considering both open and grey voxels, is %.3g\n",GreyPorosity);
}
ScaLBL_CopyToDevice(Porosity_dvc, Porosity, Np*sizeof(double));
ScaLBL_CopyToDevice(Permeability_dvc, Permeability, Np*sizeof(double));
ScaLBL_Comm->Barrier();
delete [] Porosity;
delete [] Permeability;
}
void ScaLBL_GreyscaleColorModel::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.data(),Np);
comm.barrier();
//...........................................................................
// 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);
//ScaLBL_AllocateDeviceMemory((void **) &GreySolidPhi, sizeof(double)*Nx*Ny*Nz);
ScaLBL_AllocateDeviceMemory((void **) &GreySolidGrad, 3*sizeof(double)*Np);
ScaLBL_AllocateDeviceMemory((void **) &Porosity_dvc, sizeof(double)*Np);
ScaLBL_AllocateDeviceMemory((void **) &Permeability_dvc, 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++){
auto n = TmpMap[idx];
if (n > Nx*Ny*Nz){
printf("Bad value! idx=%i \n", n);
TmpMap[idx] = Nx*Ny*Nz-1;
}
}
for (int idx=ScaLBL_Comm->FirstInterior(); idx<ScaLBL_Comm->LastInterior(); idx++){
auto n = TmpMap[idx];
if ( n > Nx*Ny*Nz ){
printf("Bad value! idx=%i \n",n);
TmpMap[idx] = Nx*Ny*Nz-1;
}
}
ScaLBL_CopyToDevice(dvcMap, TmpMap, sizeof(int)*Np);
ScaLBL_Comm->Barrier();
delete [] TmpMap;
// copy the neighbor list
ScaLBL_CopyToDevice(NeighborList, neighborList, neighborSize);
// initialize phi based on PhaseLabel (include solid component labels)
AssignComponentLabels();//do open/black/grey nodes initialization
AssignGreySolidLabels();
AssignGreyPoroPermLabels();
Averages->SetParams(rhoA,rhoB,tauA,tauB,Fx,Fy,Fz,alpha,beta,GreyPorosity);
ScaLBL_Comm->RegularLayout(Map,Porosity_dvc,Averages->Porosity);//porosity doesn't change over time
}
void ScaLBL_GreyscaleColorModel::Initialize(){
/*
* This function initializes model
*/
if (rank==0) printf ("Initializing distributions \n");
ScaLBL_D3Q19_Init(fq, Np);
//ScaLBL_D3Q19_GreyscaleColor_Init(fq, Porosity_dvc, Np);
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 (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_Comm->Barrier();
comm.barrier();
if (rank==0) printf ("Initializing phase field from Restart\n");
ScaLBL_PhaseField_InitFromRestart(Den, Aq, Bq, 0, ScaLBL_Comm->LastExterior(), Np);
ScaLBL_PhaseField_InitFromRestart(Den, Aq, Bq, ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np);
}
// establish reservoirs for external bC
if (BoundaryCondition == 1 || BoundaryCondition == 2 || BoundaryCondition == 3 || BoundaryCondition == 4 ){
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_GreyscaleColorModel::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 RESCALE_FORCE = 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 RESCALE_FORCE_AFTER_TIMESTEP = 0;
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 = 100000;
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;
//TODO -------- For temporary use - should be included in the analysis framework later -------------
int visualization_interval = 50000;
int restart_interval = 100000;
if (analysis_db->keyExists( "visualization_interval" )){
visualization_interval = analysis_db->getScalar<int>( "visualization_interval" );
}
if (analysis_db->keyExists( "restart_interval" )){
restart_interval = analysis_db->getScalar<int>( "restart_interval" );
}
//-------------------------------------------------------------------------------------------------
/* history for morphological algoirthm */
double KRA_MORPH_FACTOR=0.5;
double volA_prev = 0.0;
double log_krA_prev = 1.0;
double log_krA_target = 1.0;
double log_krA = 1.0;
double slope_krA_volume = 0.0;
if (greyscaleColor_db->keyExists( "vol_A_previous" )){
volA_prev = greyscaleColor_db->getScalar<double>( "vol_A_previous" );
}
if (greyscaleColor_db->keyExists( "log_krA_previous" )){
log_krA_prev = greyscaleColor_db->getScalar<double>( "log_krA_previous" );
}
if (greyscaleColor_db->keyExists( "krA_morph_factor" )){
KRA_MORPH_FACTOR = greyscaleColor_db->getScalar<double>( "krA_morph_factor" );
}
/* defaults for simulation protocols */
auto protocol = greyscaleColor_db->getWithDefault<std::string>( "protocol", "none" );
if (protocol == "image sequence"){
// Get the list of images
USE_DIRECT = true;
ImageList = greyscaleColor_db->getVector<std::string>( "image_sequence");
IMAGE_INDEX = greyscaleColor_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;
}
if (greyscaleColor_db->keyExists( "capillary_number" )){
capillary_number = greyscaleColor_db->getScalar<double>( "capillary_number" );
SET_CAPILLARY_NUMBER=true;
}
if (greyscaleColor_db->keyExists( "rescale_force_after_timestep" )){
RESCALE_FORCE_AFTER_TIMESTEP = greyscaleColor_db->getScalar<int>( "rescale_force_after_timestep" );
RESCALE_FORCE = true;
}
if (greyscaleColor_db->keyExists( "timestep" )){
timestep = greyscaleColor_db->getScalar<int>( "timestep" );
}
if (BoundaryCondition != 0 && BoundaryCondition != 5 && SET_CAPILLARY_NUMBER==true){
if (rank == 0) printf("WARINING: capillary number target only supported for BC = 0 or 5 \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( "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);
}
printf("No. of timesteps: %i \n", timestepMax);
fflush(stdout);
}
//.......create and start timer............
double starttime,stoptime,cputime;
ScaLBL_Comm->Barrier();
comm.barrier();
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_Comm->Barrier();
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 && BoundaryCondition < 5){
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);
//Model-1&4
ScaLBL_D3Q19_AAodd_GreyscaleColor(NeighborList, dvcMap, fq, Aq, Bq, Den, Phi,GreySolidGrad,Porosity_dvc,Permeability_dvc,Velocity,Pressure,
rhoA, rhoB, tauA, tauB,tauA_eff, tauB_eff,
alpha, beta, Fx, Fy, Fz, Nx, Nx*Ny, ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np);
////Model-2&3
//ScaLBL_D3Q19_AAodd_GreyscaleColor(NeighborList, dvcMap, fq, Aq, Bq, Den, Phi,GreySolidPhi,Porosity_dvc,Permeability_dvc,Velocity,
// rhoA, rhoB, tauA, tauB,tauA_eff, tauB_eff,
// 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_Comm->Barrier();
// 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);
}
else if (BoundaryCondition == 5){
ScaLBL_Comm->D3Q19_Reflection_BC_z(fq);
ScaLBL_Comm->D3Q19_Reflection_BC_Z(fq);
}
//Model-1&4
ScaLBL_D3Q19_AAodd_GreyscaleColor(NeighborList, dvcMap, fq, Aq, Bq, Den, Phi,GreySolidGrad,Porosity_dvc,Permeability_dvc,Velocity,Pressure,
rhoA, rhoB, tauA, tauB,tauA_eff, tauB_eff,
alpha, beta, Fx, Fy, Fz, Nx, Nx*Ny, 0, ScaLBL_Comm->LastExterior(), Np);
////Model-2&3
//ScaLBL_D3Q19_AAodd_GreyscaleColor(NeighborList, dvcMap, fq, Aq, Bq, Den, Phi,GreySolidPhi,Porosity_dvc,Permeability_dvc,Velocity,
// rhoA, rhoB, tauA, tauB,tauA_eff, tauB_eff,
// alpha, beta, Fx, Fy, Fz, Nx, Nx*Ny, 0, ScaLBL_Comm->LastExterior(), Np);
ScaLBL_Comm->Barrier();
// *************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_Comm->Barrier();
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 && BoundaryCondition < 5){
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);
//Model-1&4
ScaLBL_D3Q19_AAeven_GreyscaleColor(dvcMap, fq, Aq, Bq, Den, Phi,GreySolidGrad,Porosity_dvc,Permeability_dvc,Velocity,Pressure,
rhoA, rhoB, tauA, tauB,tauA_eff, tauB_eff,
alpha, beta, Fx, Fy, Fz, Nx, Nx*Ny, ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np);
////Model-2&3
//ScaLBL_D3Q19_AAeven_GreyscaleColor(dvcMap, fq, Aq, Bq, Den, Phi,GreySolidPhi,Porosity_dvc,Permeability_dvc,Velocity,
// rhoA, rhoB, tauA, tauB,tauA_eff, tauB_eff,
// 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_Comm->Barrier();
// 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);
}
//Model-1&4
ScaLBL_D3Q19_AAeven_GreyscaleColor(dvcMap, fq, Aq, Bq, Den, Phi,GreySolidGrad,Porosity_dvc,Permeability_dvc,Velocity,Pressure,
rhoA, rhoB, tauA, tauB,tauA_eff, tauB_eff,
alpha, beta, Fx, Fy, Fz, Nx, Nx*Ny, 0, ScaLBL_Comm->LastExterior(), Np);
////Model-2&3
//ScaLBL_D3Q19_AAeven_GreyscaleColor(dvcMap, fq, Aq, Bq, Den, Phi,GreySolidPhi,Porosity_dvc,Permeability_dvc,Velocity,
// rhoA, rhoB, tauA, tauB,tauA_eff, tauB_eff,
// alpha, beta, Fx, Fy, Fz, Nx, Nx*Ny, 0, ScaLBL_Comm->LastExterior(), Np);
ScaLBL_Comm->Barrier();
//************************************************************************
PROFILE_STOP("Update");
//TODO For temporary use - writing Restart and Vis files should be included in the analysis framework in the future
if (timestep%restart_interval==0){
//Use rank=0 write out Restart.db
if (rank==0) {
greyscaleColor_db->putScalar<int>("timestep",timestep);
greyscaleColor_db->putScalar<bool>( "Restart", true );
current_db->putDatabase("Color", greyscaleColor_db);
std::ofstream OutStream("Restart.db");
current_db->print(OutStream, "");
OutStream.close();
}
//Write out Restart data.
std::shared_ptr<double> cDen;
std::shared_ptr<double> cfq;
cDen = std::shared_ptr<double>(new double[2*Np], DeleteArray<double>);
cfq = std::shared_ptr<double>(new double[19*Np],DeleteArray<double>);
ScaLBL_CopyToHost(cDen.get(),Den,2*Np*sizeof(double));// Copy restart data to the CPU
ScaLBL_CopyToHost(cfq.get(), fq,19*Np*sizeof(double));// Copy restart data to the CPU
ofstream RESTARTFILE(LocalRestartFile,ios::binary);
double value;
for (int n=0; n<Np; n++){
// Write the two density values
value = cDen.get()[n];
RESTARTFILE.write((char*) &value, sizeof(value));
value = cDen.get()[Np+n];
RESTARTFILE.write((char*) &value, sizeof(value));
}
for (int n=0; n<Np; n++){
// Write the distributions
for (int q=0; q<19; q++){
value = cfq.get()[q*Np+n];
RESTARTFILE.write((char*) &value, sizeof(value));
}
}
RESTARTFILE.close();
comm.barrier();
}
if (timestep%visualization_interval==0){
WriteVisFiles();
}
//-----------------------------------------------------------------------------------------------------------------
if (rank==0 && timestep%analysis_interval == 0 && BoundaryCondition == 4){
printf("%i %.5g \n",timestep,din);
}
if (timestep%analysis_interval == 0){
ScaLBL_Comm->RegularLayout(Map,Pressure,Averages->Pressure);
ScaLBL_Comm->RegularLayout(Map,&Den[0],Averages->Rho_n);
ScaLBL_Comm->RegularLayout(Map,&Den[Np],Averages->Rho_w);
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);
Averages->Basic();
}
// 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 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 = Averages->saturation;
double volA = current_saturation*GreyPorosity;
double volB = (1.0-current_saturation)*GreyPorosity;
double flow_rate_A = Averages->oil_flow_rate;
double flow_rate_B = Averages->water_flow_rate;
double Ca = fabs(muA*flow_rate_A + muB*flow_rate_B)/(6.0*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 (RESCALE_FORCE == true && SET_CAPILLARY_NUMBER == true && CURRENT_STEADY_TIMESTEPS > RESCALE_FORCE_AFTER_TIMESTEP){
RESCALE_FORCE = false;
double RESCALE_FORCE_FACTOR = capillary_number / Ca;
if (RESCALE_FORCE_FACTOR > 2.0) RESCALE_FORCE_FACTOR = 2.0;
if (RESCALE_FORCE_FACTOR < 0.5) RESCALE_FORCE_FACTOR = 0.5;
Fx *= RESCALE_FORCE_FACTOR;
Fy *= RESCALE_FORCE_FACTOR;
Fz *= RESCALE_FORCE_FACTOR;
force_mag = sqrt(Fx*Fx+Fy*Fy+Fz*Fz);
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 (rank == 0) printf(" -- adjust force by factor %.5g \n ",capillary_number / Ca);
Averages->SetParams(rhoA,rhoB,tauA,tauB,Fx,Fy,Fz,alpha,beta,GreyPorosity);
greyscaleColor_db->putVector<double>("F",{Fx,Fy,Fz});
}
if ( isSteady ){
MORPH_ADAPT = true;
CURRENT_MORPH_TIMESTEPS=0;
delta_volume_target = Dm->Volume*volA *morph_delta; // set target volume change
//****** ENDPOINT ADAPTATION ********/
double krA_TMP= fabs(muA*flow_rate_A / force_mag);
double krB_TMP= fabs(muB*flow_rate_B / force_mag);
log_krA = log(krA_TMP);
if (krA_TMP < 0.0){
// cannot do endpoint adaptation if kr is negative
log_krA = log_krA_prev;
}
else if (krA_TMP < krB_TMP && morph_delta > 0.0){
/** morphological target based on relative permeability for A **/
log_krA_target = log(KRA_MORPH_FACTOR*(krA_TMP));
slope_krA_volume = (log_krA - log_krA_prev)/(Dm->Volume*(volA - volA_prev));
delta_volume_target=min(delta_volume_target,Dm->Volume*(volA+(log_krA_target - log_krA)/slope_krA_volume));
if (rank==0){
printf(" Enabling endpoint adaptation: krA = %.5g, krB = %.5g \n",krA_TMP,krB_TMP);
printf(" log(kr)=%.5g, volume=%.5g, TARGET log(kr)=%.5g, volume change=%.5g \n",log_krA, volA, log_krA_target, delta_volume_target/(volA*Dm->Volume));
}
}
log_krA_prev = log_krA;
volA_prev = volA;
//******************************** **/
/** compute averages & write data **/
/*Averages->Full();
Averages->Write(timestep);
analysis.WriteVisData(timestep, current_db, *Averages, Phi, Pressure, Velocity, fq, Den );
analysis.finish();
*/
if (rank==0){
printf("** WRITE STEADY POINT *** ");
printf("Ca = %.5g, (previous = %.5g) \n",Ca,Ca_previous);
double h = Dm->voxel_length;
// pressures
double pA = Averages->Oil.p;
double pB = Averages->Water.p;
double pAB = (pA-pB)/(h*6.0*alpha);
// -------- The following quantities may not make sense for greyscale simulation -----------//
// double pAc = Averages->gnc.p;
// double pBc = Averages->gwc.p;
// double pAB_connected = (pAc-pBc)/(h*6.0*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/(force_mag);
// double kBeff_disconnected = h*h*muB*flow_rate_B_disconnected/(force_mag);
// //---------------------------------------------------------------------------------------//
double kAeff = h*h*muA*(flow_rate_A)/(force_mag);
double kBeff = h*h*muB*(flow_rate_B)/(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 cap.pressure.norm pressure.drop Ca M\n");
fprintf(kr_log_file,"%i %.5g %.5g %.5g %.5g %.5g %.5g %.5g\n",
CURRENT_STEADY_TIMESTEPS,current_saturation,kAeff,kBeff,pAB,viscous_pressure_drop,Ca,Mobility);
fclose(kr_log_file);
printf(" Measured capillary number %.5g \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 (rank == 0) printf(" -- adjust force by factor %.5g \n ",capillary_number / Ca);
Averages->SetParams(rhoA,rhoB,tauA,tauB,Fx,Fy,Fz,alpha,beta,GreyPorosity);
greyscaleColor_db->putVector<double>("F",{Fx,Fy,Fz});
}
CURRENT_STEADY_TIMESTEPS = 0;
}
else{
if (rank==0){
printf("** Continue to simulate steady *** \n ");
printf("Ca = %.5g, (previous = %.5g) \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);
greyscaleColor_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 %.5g, volume change %.5g / %.5g ***\n", massChange, delta_volume, delta_volume_target);
}
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 (RESCALE_FORCE_AFTER_TIMESTEP > 0)
RESCALE_FORCE = true;
}
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;
RESCALE_FORCE = true;
if (RESCALE_FORCE_AFTER_TIMESTEP > 0)
RESCALE_FORCE = true;
}
}
morph_timesteps += analysis_interval;
}
ScaLBL_Comm->Barrier();
}
//analysis.finish();
PROFILE_STOP("Loop");
PROFILE_SAVE("lbpm_color_simulator",1);
//************************************************************************
ScaLBL_Comm->Barrier();
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");
// ************************************************************************
}
void ScaLBL_GreyscaleColorModel::ImageInit(std::string Filename){
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
AssignComponentLabels();
AssignGreySolidLabels();
AssignGreyPoroPermLabels();
Averages->SetParams(rhoA,rhoB,tauA,tauB,Fx,Fy,Fz,alpha,beta,GreyPorosity);
ScaLBL_Comm->RegularLayout(Map,Porosity_dvc,Averages->Porosity);
//NOTE in greyscale simulations, water may have multiple labels (e.g. 2, 21, 22, etc)
//so the saturaiton calculation is not that straightforward
// 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=Dm->Comm.sumReduce( Count);
// PoreCount=Dm->Comm.sumReduce( PoreCount);
// if (rank==0) printf(" new saturation: %f (%f / %f) \n", Count / PoreCount, Count, PoreCount);
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);
ScaLBL_Comm->Barrier();
//ScaLBL_CopyToHost(Averages->Phi.data(),Phi,Nx*Ny*Nz*sizeof(double));
//double saturation = Count/PoreCount;
//return saturation;
}
double ScaLBL_GreyscaleColorModel::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 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= Dm->Comm.sumReduce( count);
mass_loss= Dm->Comm.sumReduce( mass_loss);
if (rank == 0) printf("Remove mass %.5g from %.5g 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);
}
//TODO for temporary use - writing visualization files should be included in the analysis framework in the future
void ScaLBL_GreyscaleColorModel::WriteVisFiles(){
//NOTE: write_silo is always true
std::vector<IO::MeshDataStruct> visData;
fillHalo<double> fillData(Dm->Comm,Dm->rank_info,{Dm->Nx-2,Dm->Ny-2,Dm->Nz-2},{1,1,1},0,1);
auto VxVar = std::make_shared<IO::Variable>();
auto VyVar = std::make_shared<IO::Variable>();
auto VzVar = std::make_shared<IO::Variable>();
auto SignDistVar = std::make_shared<IO::Variable>();
auto PressureVar = std::make_shared<IO::Variable>();
auto PhaseVar = std::make_shared<IO::Variable>();
// Create the MeshDataStruct
IO::initialize("","silo","false");
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 );
// create a temp data for copy from device
DoubleArray DataTemp(Nx,Ny,Nz);
if (vis_db->getWithDefault<bool>( "save_phase_field", true )){
PhaseVar->name = "Phase";
PhaseVar->type = IO::VariableType::VolumeVariable;
PhaseVar->dim = 1;
PhaseVar->data.resize(Dm->Nx-2,Dm->Ny-2,Dm->Nz-2);
visData[0].vars.push_back(PhaseVar);
ASSERT(visData[0].vars[0]->name=="Phase");
Array<double>& PhaseData = visData[0].vars[0]->data;
ScaLBL_CopyToHost(DataTemp.data(), Phi, sizeof(double)*Nx*Ny*Nz);
fillData.copy(DataTemp,PhaseData);
}
if (vis_db->getWithDefault<bool>( "save_pressure", false )){
PressureVar->name = "Pressure";
PressureVar->type = IO::VariableType::VolumeVariable;
PressureVar->dim = 1;
PressureVar->data.resize(Dm->Nx-2,Dm->Ny-2,Dm->Nz-2);
visData[0].vars.push_back(PressureVar);
ASSERT(visData[0].vars[1]->name=="Pressure");
Array<double>& PressData = visData[0].vars[1]->data;
ScaLBL_Comm->RegularLayout(Map,Pressure,DataTemp);
fillData.copy(DataTemp,PressData);
}
if (vis_db->getWithDefault<bool>( "save_velocity", false )){
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);
ASSERT(visData[0].vars[2]->name=="Velocity_x");
ASSERT(visData[0].vars[3]->name=="Velocity_y");
ASSERT(visData[0].vars[4]->name=="Velocity_z");
Array<double>& VelxData = visData[0].vars[2]->data;
Array<double>& VelyData = visData[0].vars[3]->data;
Array<double>& VelzData = visData[0].vars[4]->data;
ScaLBL_Comm->RegularLayout(Map,&Velocity[0],DataTemp);
fillData.copy(DataTemp,VelxData);
ScaLBL_Comm->RegularLayout(Map,&Velocity[Np],DataTemp);
fillData.copy(DataTemp,VelyData);
ScaLBL_Comm->RegularLayout(Map,&Velocity[2*Np],DataTemp);
fillData.copy(DataTemp,VelzData);
}
if (vis_db->getWithDefault<bool>( "save_distance", false )){
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);
ASSERT(visData[0].vars[5]->name=="SignDist");
Array<double>& SignData = visData[0].vars[5]->data;
fillData.copy(Averages->SDs,SignData);
}
if (vis_db->getWithDefault<bool>( "write_silo", true )){
IO::writeData( timestep, visData, Dm->Comm );
}
if (vis_db->getWithDefault<bool>( "save_8bit_raw", true )){
//TODO
//char CurrentIDFilename[40];
//sprintf(CurrentIDFilename,"id_t%d.raw",timestep);
//Averages.AggregateLabels(CurrentIDFilename);
}
}
void ScaLBL_GreyscaleColorModel::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);
ScaLBL_Comm->RegularLayout(Map,&Den[0],PhaseField);
FILE *AFILE;
sprintf(LocalRankFilename,"A.%05i.raw",rank);
AFILE = fopen(LocalRankFilename,"wb");
fwrite(PhaseField.data(),8,N,AFILE);
fclose(AFILE);
ScaLBL_Comm->RegularLayout(Map,&Den[Np],PhaseField);
FILE *BFILE;
sprintf(LocalRankFilename,"B.%05i.raw",rank);
BFILE = fopen(LocalRankFilename,"wb");
fwrite(PhaseField.data(),8,N,BFILE);
fclose(BFILE);
ScaLBL_Comm->RegularLayout(Map,Pressure,PhaseField);
FILE *PFILE;
sprintf(LocalRankFilename,"Pressure.%05i.raw",rank);
PFILE = fopen(LocalRankFilename,"wb");
fwrite(PhaseField.data(),8,N,PFILE);
fclose(PFILE);
ScaLBL_Comm->RegularLayout(Map,&Velocity[0],PhaseField);
FILE *VELX_FILE;
sprintf(LocalRankFilename,"Velocity_X.%05i.raw",rank);
VELX_FILE = fopen(LocalRankFilename,"wb");
fwrite(PhaseField.data(),8,N,VELX_FILE);
fclose(VELX_FILE);
ScaLBL_Comm->RegularLayout(Map,&Velocity[Np],PhaseField);
FILE *VELY_FILE;
sprintf(LocalRankFilename,"Velocity_Y.%05i.raw",rank);
VELY_FILE = fopen(LocalRankFilename,"wb");
fwrite(PhaseField.data(),8,N,VELY_FILE);
fclose(VELY_FILE);
ScaLBL_Comm->RegularLayout(Map,&Velocity[2*Np],PhaseField);
FILE *VELZ_FILE;
sprintf(LocalRankFilename,"Velocity_Z.%05i.raw",rank);
VELZ_FILE = fopen(LocalRankFilename,"wb");
fwrite(PhaseField.data(),8,N,VELZ_FILE);
fclose(VELZ_FILE);
ScaLBL_Comm->RegularLayout(Map,&Porosity_dvc[0],PhaseField);
FILE *POROS_FILE;
sprintf(LocalRankFilename,"Porosity.%05i.raw",rank);
POROS_FILE = fopen(LocalRankFilename,"wb");
fwrite(PhaseField.data(),8,N,POROS_FILE);
fclose(POROS_FILE);
ScaLBL_Comm->RegularLayout(Map,&Permeability_dvc[0],PhaseField);
FILE *PERM_FILE;
sprintf(LocalRankFilename,"Permeability.%05i.raw",rank);
PERM_FILE = fopen(LocalRankFilename,"wb");
fwrite(PhaseField.data(),8,N,PERM_FILE);
fclose(PERM_FILE);
ScaLBL_Comm->RegularLayout(Map,&GreySolidGrad[0],PhaseField);
FILE *GreySG_X_FILE;
sprintf(LocalRankFilename,"GreySolidGrad_X.%05i.raw",rank);
GreySG_X_FILE = fopen(LocalRankFilename,"wb");
fwrite(PhaseField.data(),8,N,GreySG_X_FILE);
fclose(GreySG_X_FILE);
ScaLBL_Comm->RegularLayout(Map,&GreySolidGrad[Np],PhaseField);
FILE *GreySG_Y_FILE;
sprintf(LocalRankFilename,"GreySolidGrad_Y.%05i.raw",rank);
GreySG_Y_FILE = fopen(LocalRankFilename,"wb");
fwrite(PhaseField.data(),8,N,GreySG_Y_FILE);
fclose(GreySG_Y_FILE);
ScaLBL_Comm->RegularLayout(Map,&GreySolidGrad[2*Np],PhaseField);
FILE *GreySG_Z_FILE;
sprintf(LocalRankFilename,"GreySolidGrad_Z.%05i.raw",rank);
GreySG_Z_FILE = fopen(LocalRankFilename,"wb");
fwrite(PhaseField.data(),8,N,GreySG_Z_FILE);
fclose(GreySG_Z_FILE);
/* ScaLBL_Comm->RegularLayout(Map,&ColorGrad[0],PhaseField);
FILE *CGX_FILE;
sprintf(LocalRankFilename,"Gradient_X.%05i.raw",rank);
CGX_FILE = fopen(LocalRankFilename,"wb");
fwrite(PhaseField.data(),8,N,CGX_FILE);
fclose(CGX_FILE);
ScaLBL_Comm->RegularLayout(Map,&ColorGrad[Np],PhaseField);
FILE *CGY_FILE;
sprintf(LocalRankFilename,"Gradient_Y.%05i.raw",rank);
CGY_FILE = fopen(LocalRankFilename,"wb");
fwrite(PhaseField.data(),8,N,CGY_FILE);
fclose(CGY_FILE);
ScaLBL_Comm->RegularLayout(Map,&ColorGrad[2*Np],PhaseField);
FILE *CGZ_FILE;
sprintf(LocalRankFilename,"Gradient_Z.%05i.raw",rank);
CGZ_FILE = fopen(LocalRankFilename,"wb");
fwrite(PhaseField.data(),8,N,CGZ_FILE);
fclose(CGZ_FILE);
*/
}
//void ScaLBL_GreyscaleColorModel::AssignGreySolidLabels()//Model-1
//{
// // ONLY initialize grey nodes
// // Key input parameters:
// // 1. GreySolidLabels
// // labels for grey nodes
// // 2. GreySolidAffinity
// // affinity ranges [-1,1]
// // oil-wet > 0
// // water-wet < 0
// // neutral = 0
// double *SolidPotential_host = new double [Nx*Ny*Nz];
// double *GreySolidGrad_host = new double [3*Np];
//
// size_t NLABELS=0;
// signed char VALUE=0;
// double AFFINITY=0.f;
//
// auto LabelList = greyscaleColor_db->getVector<int>( "GreySolidLabels" );
// auto AffinityList = greyscaleColor_db->getVector<double>( "GreySolidAffinity" );
//
// NLABELS=LabelList.size();
// if (NLABELS != AffinityList.size()){
// ERROR("Error: GreySolidLabels and GreySolidAffinity must be the same length! \n");
// }
//
// 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];
// AFFINITY=0.f;//all nodes except the specified grey nodes have grey-solid affinity = 0.0
// // 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];
// idx = NLABELS;
// //Mask->id[n] = 0; // set mask to zero since this is an immobile component
// }
// }
// SolidPotential_host[n] = AFFINITY;
// }
// }
// }
//
// // Calculate grey-solid color-gradient
// double *Dst;
// Dst = new double [3*3*3];
// for (int kk=0; kk<3; kk++){
// for (int jj=0; jj<3; jj++){
// for (int ii=0; ii<3; ii++){
// int index = kk*9+jj*3+ii;
// Dst[index] = sqrt(double(ii-1)*double(ii-1) + double(jj-1)*double(jj-1)+ double(kk-1)*double(kk-1));
// }
// }
// }
// double w_face = 1.f;
// double w_edge = 0.5;
// double w_corner = 0.f;
// //local
// Dst[13] = 0.f;
// //faces
// Dst[4] = w_face;
// Dst[10] = w_face;
// Dst[12] = w_face;
// Dst[14] = w_face;
// Dst[16] = w_face;
// Dst[22] = w_face;
// // corners
// Dst[0] = w_corner;
// Dst[2] = w_corner;
// Dst[6] = w_corner;
// Dst[8] = w_corner;
// Dst[18] = w_corner;
// Dst[20] = w_corner;
// Dst[24] = w_corner;
// Dst[26] = w_corner;
// // edges
// Dst[1] = w_edge;
// Dst[3] = w_edge;
// Dst[5] = w_edge;
// Dst[7] = w_edge;
// Dst[9] = w_edge;
// Dst[11] = w_edge;
// Dst[15] = w_edge;
// Dst[17] = w_edge;
// Dst[19] = w_edge;
// Dst[21] = w_edge;
// Dst[23] = w_edge;
// Dst[25] = w_edge;
//
// 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)){
// double phi_x = 0.f;
// double phi_y = 0.f;
// double phi_z = 0.f;
// for (int kk=0; kk<3; kk++){
// for (int jj=0; jj<3; jj++){
// for (int ii=0; ii<3; ii++){
//
// int index = kk*9+jj*3+ii;
// double weight= Dst[index];
//
// int idi=i+ii-1;
// int idj=j+jj-1;
// int idk=k+kk-1;
//
// if (idi < 0) idi=0;
// if (idj < 0) idj=0;
// if (idk < 0) idk=0;
// if (!(idi < Nx)) idi=Nx-1;
// if (!(idj < Ny)) idj=Ny-1;
// if (!(idk < Nz)) idk=Nz-1;
//
// int nn = idk*Nx*Ny + idj*Nx + idi;
// double vec_x = double(ii-1);
// double vec_y = double(jj-1);
// double vec_z = double(kk-1);
// double GWNS=SolidPotential_host[nn];
// phi_x += GWNS*weight*vec_x;
// phi_y += GWNS*weight*vec_y;
// phi_z += GWNS*weight*vec_z;
// }
// }
// }
// GreySolidGrad_host[idx+0*Np] = phi_x;
// GreySolidGrad_host[idx+1*Np] = phi_y;
// GreySolidGrad_host[idx+2*Np] = phi_z;
// }
// }
// }
// }
//
// if (rank==0){
// printf("Number of Grey-solid labels: %lu \n",NLABELS);
// for (unsigned int idx=0; idx<NLABELS; idx++){
// VALUE=LabelList[idx];
// AFFINITY=AffinityList[idx];
// printf(" grey-solid label=%d, grey-solid affinity=%f\n",VALUE,AFFINITY);
// }
// }
//
//
// ScaLBL_CopyToDevice(GreySolidGrad, GreySolidGrad_host, 3*Np*sizeof(double));
// ScaLBL_Comm->Barrier();
// delete [] SolidPotential_host;
// delete [] GreySolidGrad_host;
// delete [] Dst;
//}
////----------------------------------------------------------------------------------------------------------//
//void ScaLBL_GreyscaleColorModel::AssignGreySolidLabels()//Model-2 & Model-3
//{
// // ONLY initialize grey nodes
// // Key input parameters:
// // 1. GreySolidLabels
// // labels for grey nodes
// // 2. GreySolidAffinity
// // affinity ranges [-1,1]
// // oil-wet > 0
// // water-wet < 0
// // neutral = 0
//
// double *GreySolidPhi_host = new double [Nx*Ny*Nz];
// //initialize grey solid phase field
// 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;
// GreySolidPhi_host[n]=0.f;
// }
// }
// }
//
// auto LabelList = greyscaleColor_db->getVector<int>( "GreySolidLabels" );
// auto AffinityList = greyscaleColor_db->getVector<double>( "GreySolidAffinity" );
//
// size_t NLABELS=0;
// NLABELS=LabelList.size();
// if (NLABELS != AffinityList.size()){
// ERROR("Error: GreySolidLabels and GreySolidAffinity must be the same length! \n");
// }
//
// double *Dst;
// Dst = new double [3*3*3];
// for (int kk=0; kk<3; kk++){
// for (int jj=0; jj<3; jj++){
// for (int ii=0; ii<3; ii++){
// int index = kk*9+jj*3+ii;
// Dst[index] = sqrt(double(ii-1)*double(ii-1) + double(jj-1)*double(jj-1)+ double(kk-1)*double(kk-1));
// }
// }
// }
// double w_face = 1.f;
// double w_edge = 1.f;
// double w_corner = 0.f;
// //local
// Dst[13] = 0.f;
// //faces
// Dst[4] = w_face;
// Dst[10] = w_face;
// Dst[12] = w_face;
// Dst[14] = w_face;
// Dst[16] = w_face;
// Dst[22] = w_face;
// // corners
// Dst[0] = w_corner;
// Dst[2] = w_corner;
// Dst[6] = w_corner;
// Dst[8] = w_corner;
// Dst[18] = w_corner;
// Dst[20] = w_corner;
// Dst[24] = w_corner;
// Dst[26] = w_corner;
// // edges
// Dst[1] = w_edge;
// Dst[3] = w_edge;
// Dst[5] = w_edge;
// Dst[7] = w_edge;
// Dst[9] = w_edge;
// Dst[11] = w_edge;
// Dst[15] = w_edge;
// Dst[17] = w_edge;
// Dst[19] = w_edge;
// Dst[21] = w_edge;
// Dst[23] = w_edge;
// Dst[25] = w_edge;
//
// 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 n = k*Nx*Ny+j*Nx+i;
// signed char VALUE=Mask->id[n];
// double AFFINITY=0.f;
// // 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];
// idx = NLABELS;
// //Mask->id[n] = 0; // set mask to zero since this is an immobile component
// }
// }
//
// if (VALUE>2){//i.e. a grey node
// double neighbor_counter = 0;
// for (int kk=0; kk<3; kk++){
// for (int jj=0; jj<3; jj++){
// for (int ii=0; ii<3; ii++){
//
// int index = kk*9+jj*3+ii;
// double weight= Dst[index];
//
// int idi=i+ii-1;
// int idj=j+jj-1;
// int idk=k+kk-1;
//
// if (idi < 0) idi=0;
// if (idj < 0) idj=0;
// if (idk < 0) idk=0;
// if (!(idi < Nx)) idi=Nx-1;
// if (!(idj < Ny)) idj=Ny-1;
// if (!(idk < Nz)) idk=Nz-1;
//
// int nn = idk*Nx*Ny + idj*Nx + idi;
// //if (Mask->id[nn] != VALUE){//Model-2:i.e. open nodes, impermeable solid nodes or any other type of greynodes
// if (Mask->id[nn] <=0){//Model-3:i.e. only impermeable solid nodes or any other type of greynodes
// neighbor_counter +=weight;
// }
// }
// }
// }
// if (neighbor_counter>0){
// GreySolidPhi_host[n] = AFFINITY;
// }
// }
// }
// }
// }
//
// if (rank==0){
// printf("Number of grey-solid labels: %lu \n",NLABELS);
// for (unsigned int idx=0; idx<NLABELS; idx++){
// signed char VALUE=LabelList[idx];
// double AFFINITY=AffinityList[idx];
// printf(" grey-solid label=%d, grey-solid affinity=%f\n",VALUE,AFFINITY);
// }
// }
//
// ScaLBL_CopyToDevice(GreySolidPhi, GreySolidPhi_host, Nx*Ny*Nz*sizeof(double));
// ScaLBL_Comm->Barrier();
//
// //debug
// //FILE *OUTFILE;
// //sprintf(LocalRankFilename,"GreySolidInit.%05i.raw",rank);
// //OUTFILE = fopen(LocalRankFilename,"wb");
// //fwrite(GreySolidPhi_host,8,N,OUTFILE);
// //fclose(OUTFILE);
//
// delete [] GreySolidPhi_host;
// delete [] Dst;
//}
//--------- This is another old version of calculating greyscale-solid color-gradient modification-------//
// **not working effectively, to be deprecated
//void ScaLBL_GreyscaleColorModel::AssignGreySolidLabels()
//{
// // ONLY initialize grey nodes
// // Key input parameters:
// // 1. GreySolidLabels
// // labels for grey nodes
// // 2. GreySolidAffinity
// // affinity ranges [-1,1]
// // oil-wet > 0
// // water-wet < 0
// // neutral = 0
//
// //double *SolidPotential_host = new double [Nx*Ny*Nz];
// double *GreySolidPhi_host = new double [Nx*Ny*Nz];
// signed char VALUE=0;
// double AFFINITY=0.f;
//
// auto LabelList = greyscaleColor_db->getVector<int>( "GreySolidLabels" );
// auto AffinityList = greyscaleColor_db->getVector<double>( "GreySolidAffinity" );
//
// size_t NLABELS=0;
// NLABELS=LabelList.size();
// if (NLABELS != AffinityList.size()){
// ERROR("Error: GreySolidLabels and GreySolidAffinity must be the same length! \n");
// }
//
// 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];
// AFFINITY=0.f;//all nodes except the specified grey nodes have grey-solid affinity = 0.0
// // 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];
// idx = NLABELS;
// //Mask->id[n] = 0; // set mask to zero since this is an immobile component
// }
// }
// GreySolidPhi_host[n] = AFFINITY;
// }
// }
// }
//
// if (rank==0){
// printf("Number of grey-solid labels: %lu \n",NLABELS);
// for (unsigned int idx=0; idx<NLABELS; idx++){
// VALUE=LabelList[idx];
// AFFINITY=AffinityList[idx];
// printf(" grey-solid label=%d, solid-affinity=%f\n",VALUE,AFFINITY);
// }
// }
//
// ScaLBL_CopyToDevice(GreySolidPhi, GreySolidPhi_host, Nx*Ny*Nz*sizeof(double));
// ScaLBL_Comm->Barrier();
//
// //debug
// FILE *OUTFILE;
// sprintf(LocalRankFilename,"GreySolidInit.%05i.raw",rank);
// OUTFILE = fopen(LocalRankFilename,"wb");
// fwrite(GreySolidPhi_host,8,N,OUTFILE);
// fclose(OUTFILE);
//
// //delete [] SolidPotential_host;
// delete [] GreySolidPhi_host;
//}
//----------------------------------------------------------------------------------------------------------//
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