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add shell aggregation to FlowAdaptor

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This commit is contained in:
JamesEMcclure 2021-06-15 16:22:13 -04:00
parent d2d12af0f4
commit b856544341
3 changed files with 286 additions and 90 deletions
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190
models/ColorModel.cpp
View File

@ -2284,3 +2284,193 @@ double FlowAdaptor::MoveInterface(ScaLBL_ColorModel &M){
return total_interface_sites;
}
double FlowAdaptor::ShellAggregation(ScaLBL_ColorModel &M, const double target_delta_volume){
const RankInfoStruct rank_info(M.rank,M.nprocx,M.nprocy,M.nprocz);
auto rank = M.rank;
auto Nx = M.Nx; auto Ny = M.Ny; auto Nz = M.Nz;
auto N = Nx*Ny*Nz;
double vF = 0.f;
double vS = 0.f;
double delta_volume;
double WallFactor = 1.0;
bool USE_CONNECTED_NWP = false;
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(M.Dm->Comm,M.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(), M.Phi, N*sizeof(double));
double 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 && M.Averages->SDs(i,j,k) > 0.f) count+=1.f;
}
}
}
double volume_initial = M.Dm->Comm.sumReduce( count);
double PoreVolume = M.Dm->Volume*M.Dm->Porosity();
/*ensure target isn't an absurdly small fraction of pore volume */
if (volume_initial < target_delta_volume*PoreVolume){
volume_initial = target_delta_volume*PoreVolume;
}
// 2. Identify connected components of phase field -> phase_label
double volume_connected = 0.0;
double second_biggest = 0.0;
if (USE_CONNECTED_NWP){
ComputeGlobalBlobIDs(Nx-2,Ny-2,Nz-2,rank_info,phase,M.Averages->SDs,vF,vS,phase_label,M.Dm->Comm);
M.Dm->Comm.barrier();
// only operate on component "0"
count = 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 = M.Dm->Comm.sumReduce( count);
second_biggest = M.Dm->Comm.sumReduce( second_biggest);
}
else {
// use the whole NWP
for (int k=0; k<Nz; k++){
for (int j=0; j<Ny; j++){
for (int i=0; i<Nx; i++){
if (M.Averages->SDs(i,j,k) > 0.f){
if (phase(i,j,k) > 0.f ){
phase_id(i,j,k) = 0;
}
else {
phase_id(i,j,k) = 1;
}
}
else {
phase_id(i,j,k) = 1;
}
}
}
}
}
// 3. Generate a distance map to the largest object -> phase_distance
CalcDist(phase_distance,phase_id,*M.Dm);
double temp,value;
double factor=0.5/M.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 && M.Averages->SDs(i,j,k) > 1.f ){
phase_distance(i,j,k) = temp;
}
// erase the original object
phase(i,j,k) = -1.0;
}
}
}
}
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(M.Averages->SDs,phase_distance,phase_id,M.Averages->Dm, target_delta_volume_incremental, WallFactor);
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,*M.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++){
double d = phase_distance(i,j,k);
if (M.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*M.beta*d))/(1.f+exp(-2.f*M.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 && M.Averages->SDs(i,j,k) > 0.f){
count+=1.f;
}
}
}
}
double volume_final= M.Dm->Comm.sumReduce( count);
delta_volume = (volume_final-volume_initial);
if (rank == 0) printf("Shell Aggregation: change fluid volume fraction by %f \n", delta_volume/volume_initial);
if (rank == 0) printf(" new saturation = %f \n", volume_final/(M.Mask->Porosity()*double((Nx-2)*(Ny-2)*(Nz-2)*M.nprocs)));
// 6. copy back to the device
//if (rank==0) printf("MorphInit: copy data back to device\n");
ScaLBL_CopyToDevice(M.Phi,phase.data(),N*sizeof(double));
// 7. Re-initialize phase field and density
ScaLBL_PhaseField_Init(M.dvcMap, M.Phi, M.Den, M.Aq, M.Bq, 0, M.ScaLBL_Comm->LastExterior(), M.Np);
ScaLBL_PhaseField_Init(M.dvcMap, M.Phi, M.Den, M.Aq, M.Bq, M.ScaLBL_Comm->FirstInterior(), M.ScaLBL_Comm->LastInterior(), M.Np);
auto BoundaryCondition = M.BoundaryCondition;
if (BoundaryCondition == 1 || BoundaryCondition == 2 || BoundaryCondition == 3 || BoundaryCondition == 4){
if (M.Dm->kproc()==0){
ScaLBL_SetSlice_z(M.Phi,1.0,Nx,Ny,Nz,0);
ScaLBL_SetSlice_z(M.Phi,1.0,Nx,Ny,Nz,1);
ScaLBL_SetSlice_z(M.Phi,1.0,Nx,Ny,Nz,2);
}
if (M.Dm->kproc() == M.nprocz-1){
ScaLBL_SetSlice_z(M.Phi,-1.0,Nx,Ny,Nz,Nz-1);
ScaLBL_SetSlice_z(M.Phi,-1.0,Nx,Ny,Nz,Nz-2);
ScaLBL_SetSlice_z(M.Phi,-1.0,Nx,Ny,Nz,Nz-3);
}
}
return delta_volume;
}

1
models/ColorModel.h
View File

@ -99,6 +99,7 @@ public:
~FlowAdaptor();
double MoveInterface(ScaLBL_ColorModel &M);
double ImageInit(ScaLBL_ColorModel &M, std::string Filename);
double ShellAggregation(ScaLBL_ColorModel &M, const double delta_volume);
double UpdateFractionalFlow(ScaLBL_ColorModel &M);
void Flatten(ScaLBL_ColorModel &M);
DoubleArray phi;

9
tests/lbpm_color_simulator.cpp
View File

@ -86,7 +86,7 @@ int main( int argc, char **argv )
if (ColorModel.db->keyExists( "FlowAdaptor" )){
auto flow_db = ColorModel.db->getDatabase( "FlowAdaptor" );
MAX_STEADY_TIME = flow_db->getWithDefault<int>( "max_steady_timesteps", 1000000 );
SKIP_TIMESTEPS = flow_db->getWithDefault<int>( "skip_timesteps", 100000 );
SKIP_TIMESTEPS = flow_db->getWithDefault<int>( "skip_timesteps", 50000 );
FRACTIONAL_FLOW_INCREMENT = flow_db->getWithDefault<double>( "fractional_flow_increment", 0.05);
ENDPOINT_THRESHOLD = flow_db->getWithDefault<double>( "endpoint_threshold", 0.1);
}
@ -109,6 +109,7 @@ int main( int argc, char **argv )
/* update the fluid configuration with the flow adapter */
int skip_time = 0;
timestep = ColorModel.timestep;
/* get the averaged flow measures computed internally for the last simulation point*/
double SaturationChange = 0.0;
double volB = ColorModel.Averages->gwb.V;
double volA = ColorModel.Averages->gnb.V;
@ -121,6 +122,7 @@ int main( int argc, char **argv )
double vB_z = ColorModel.Averages->gwb.Pz/ColorModel.Averages->gwb.M;
double speedA = sqrt(vA_x*vA_x + vA_y*vA_y + vA_z*vA_z);
double speedB = sqrt(vB_x*vB_x + vB_y*vB_y + vB_z*vB_z);
/* stop simulation if previous point was sufficiently close to the endpoint*/
if (volA*speedA < ENDPOINT_THRESHOLD*volB*speedB) ContinueSimulation = false;
if (ContinueSimulation){
while (skip_time < SKIP_TIMESTEPS && fabs(SaturationChange) < fabs(FRACTIONAL_FLOW_INCREMENT) ){
@ -128,8 +130,11 @@ int main( int argc, char **argv )
if (PROTOCOL == "fractional flow") {
Adapt.UpdateFractionalFlow(ColorModel);
}
else if (PROTOCOL == "shell aggregation"){
double target_volume_change = FRACTIONAL_FLOW_INCREMENT*initialSaturation - SaturationChange;
Adapt.ShellAggregation(ColorModel,target_volume_change);
}
else if (PROTOCOL == "image sequence"){
// Use image sequence
IMAGE_INDEX++;
if (IMAGE_INDEX < IMAGE_COUNT){
std::string next_image = ImageList[IMAGE_INDEX];