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Merge branch 'morphLBM' of github.com:JamesEMcClure/LBPM-WIA into morphLBM

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This commit is contained in:
James McClure 2019-05-08 23:16:56 +02:00
commit 9136b9fc20
16 changed files with 226 additions and 93 deletions
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4
analysis/SubPhase.cpp
View File

@ -245,8 +245,8 @@ void SubPhase::Basic(){
force_mag = 1.0;
}
double saturation=gwb.V/(gwb.V + gnb.V);
double water_flow_rate=gwb.V*(gwb.Px*dir_x + gwb.Py*dir_y + gwb.Pz*dir_z)/gwb.M / Dm->Volume;
double not_water_flow_rate=gnb.V*(gnb.Px*dir_x + gnb.Py*dir_y + gnb.Pz*dir_z)/gnb.M/ Dm->Volume;
double water_flow_rate=gwb.V*sqrt(gwb.Px*gwb.Px + gwb.Py*gwb.Py + gwb.Pz*gwb.Pz)/gwb.M / Dm->Volume;
double not_water_flow_rate=gnb.V*sqrt(gnb.Px*gnb.Px + gnb.Py*gnb.Py + gnb.Pz*gnb.Pz)/gnb.M/ Dm->Volume;
double total_flow_rate = water_flow_rate + not_water_flow_rate;
double fractional_flow= water_flow_rate / total_flow_rate;

4
analysis/morphology.cpp
View File

@ -279,10 +279,10 @@ double MorphOpen(DoubleArray &SignDist, signed char *id, std::shared_ptr<Domain>
MPI_Allreduce(&count,&countGlobal,1,MPI_DOUBLE,MPI_SUM,Dm->Comm);
void_fraction_new = countGlobal/totalGlobal;
void_fraction_diff_new = abs(void_fraction_new-VoidFraction);
if (rank==0){
/* if (rank==0){
printf(" %f ",void_fraction_new);
printf(" %f\n",Rcrit_new);
}
} */
}
if (void_fraction_diff_new<void_fraction_diff_old){

12
common/Domain.cpp
View File

@ -119,11 +119,6 @@ void Domain::initialize( std::shared_ptr<Database> db )
auto nproc = d_db->getVector<int>("nproc");
auto n = d_db->getVector<int>("n");
voxel_length = 1.0;
if (d_db->keyExists( "voxel_length" )){
auto voxel_length = d_db->getScalar<double>("voxel_length");
}
if (d_db->keyExists( "InletLayers" )){
auto InletCount = d_db->getVector<int>( "InletLayers" );
inlet_layers_x = InletCount[0];
@ -136,6 +131,10 @@ void Domain::initialize( std::shared_ptr<Database> db )
outlet_layers_y = OutletCount[1];
outlet_layers_z = OutletCount[2];
}
voxel_length = 1.0;
if (d_db->keyExists( "voxel_length" )){
voxel_length = d_db->getScalar<double>("voxel_length");
}
ASSERT( n.size() == 3u );
ASSERT( nproc.size() == 3u );
@ -163,6 +162,9 @@ void Domain::initialize( std::shared_ptr<Database> db )
// Fill remaining variables
N = Nx*Ny*Nz;
Volume = nx*ny*nx*nproc[0]*nproc[1]*nproc[2]*1.0;
if (myrank==0) printf("voxel length = %f micron \n", voxel_length);
id = new signed char[N];
memset(id,0,N);
BoundaryCondition = d_db->getScalar<int>("BC");

8
example/Bubble/input.db
View File

@ -7,15 +7,7 @@ Color {
beta = 0.95;
F = 0, 0, 0
Restart = false
pBC = 0
din = 1.0
dout = 1.0
flux = 1.0e-3
timestepMax = 200
interval = 1000
tol = 1e-5;
das = 0.1
dbs = 0.9
ComponentLabels = 0, 1, 2
ComponentAffinity = -1.0, 1.0, -1.0
}

6
example/Piston/Color.in
View File

@ -1,6 +0,0 @@
1.0 1.0
1.0 1.0
1.0e-3 0.95
0.0 0.0 0.0
0 4 10.0 1.0
10000 2000 1e-5

3
example/Piston/ComponentLabels.csv
View File

@ -1,3 +0,0 @@
0 -0.5
1 1.0
2 -1.0
1 0 -0.5
2 1 1.0
3 2 -1.0

4
example/Piston/Domain.in
View File

@ -1,4 +0,0 @@
1 1 10
40 40 40
229
1.0 1.0 1.0

8
example/Piston/input.db
View File

@ -7,14 +7,7 @@ Color {
beta = 0.95;
F = 0, 0, 0
Restart = false
pBC = 0
din = 1.0
dout = 1.0
timestepMax = 3000
interval = 1000
tol = 1e-5;
das = 0.1
dbs = 0.9
flux = 2.0
ComponentLabels = 0
ComponentAffinity = -1.0;
@ -25,7 +18,6 @@ Domain {
nproc = 1, 1, 4 // Number of processors (Npx,Npy,Npz)
n = 24, 24, 24 // Size of local domain (Nx,Ny,Nz)
N = 24, 24, 96 // size of the input image
n_spheres = 1 // Number of spheres
L = 1, 1, 1 // Length of domain (x,y,z)
BC = 4 // Boundary condition type
ReadType = "8bit"

8
example/Plates/input.db
View File

@ -7,14 +7,7 @@ Color {
beta = 0.95;
F = 0, 0, 0
Restart = false
pBC = 0
din = 1.0
dout = 1.0
timestepMax = 3000
interval = 1000
tol = 1e-5;
das = 0.1
dbs = 0.9
flux = 0.0
ComponentLabels = -2, -1
ComponentAffinity = -1.0, -0.5;
@ -25,7 +18,6 @@ Domain {
nproc = 1, 1, 4 // Number of processors (Npx,Npy,Npz)
n = 24, 24, 24 // Size of local domain (Nx,Ny,Nz)
N = 24, 24, 96 // size of the input image
n_spheres = 1 // Number of spheres
L = 1, 1, 1 // Length of domain (x,y,z)
BC = 0 // Boundary condition type
ReadType = "8bit"

3
example/Poiseuille/Domain.in
View File

@ -1,3 +0,0 @@
1 1 1
100 100 100
1.0 1.0 1.0

4
example/Poiseuille/Permeability.in
View File

@ -1,4 +0,0 @@
1.0
0.0 0.0 1.0e-5
0 0 1.0 1.0
1000 1000 1.0e-5

3
example/Sph125/Domain.in
View File

@ -1,3 +0,0 @@
2 2 2
100 100 100
1.0 1.0 1.0

49
example/Workflow/HelperFunctions.R
View File

@ -1,7 +1,6 @@
require("ggplot2")
IngestRelperm<-function(PATH){
ReadSubphase<-function(PATH){
FILE=paste0(PATH,"/subphase.csv")
S<-read.csv(FILE,head=TRUE,sep=" ")
S$Vw<-S$Vwc+S$Vwd
@ -15,14 +14,28 @@ IngestRelperm<-function(PATH){
return(S)
}
ReadTimelog<-function(PATH){
FILE=paste0(PATH,"/timelog.csv")
D<-read.csv(file=FILE,head=TRUE,sep=" ")
D$time<-seq(0,nrow(D))
return(D)
}
ReadRelperm<-function(PATH){
FILE=paste0(PATH,"/relperm.csv")
D<-read.csv(file=FILE,head=FALSE,sep=" ")
colnames(D)<-c("time","nun","nuw","ift","Fx","Fy","Fz","Vn","Vw","unx","uny","unz","uwx","uwy","uwz")
D$Sw<-D$Vw/(D$Vn+D$Vw)
D$Krn<-D$Vn*D$nun*D$unx/D$Fx
D$Krw<-D$Vw*D$nuw*D$uwx/D$Fx
subset(D,D$time>100000)
D<-read.csv(file=FILE,head=TRUE,sep=" ")
D$Case<-PATH
p<-ggplot(D)+
geom_line(aes(sat.water,eff.perm.oil,color="oil"))+
geom_line(aes(sat.water,eff.perm.water,color="water"))+
xlab("Water saturation")+ylab("Effective permeability")+
theme(panel.grid.major = element_blank(),panel.grid.minor = element_blank())+
theme_bw()
FILE=paste0(PATH,"-relperm.png")
ggsave(FILE,p,height=4.0,width=6.0)
return(D)
}
@ -39,18 +52,18 @@ ReadCase<-function(PATTERN){
}
D<-ReadCase("benth_w")
require("ggplot2")
ReadMorphDrain<-function(PATH){
FILE=paste0(PATH,"/morphdrain.csv")
B<-read.csv(FILE,head=TRUE,sep=" ")
B$Media<-PATH
B<-read.csv("bentheimer/drain.csv",head=TRUE,sep=" ")
B$Media<-"Bentheimer"
M1<-read.csv("mineral_model_1/drain.csv",head=TRUE,sep=" ")
M1$Media<-"Mineral Sandstone #1"
p<-ggplot()+
p<-ggplot()+
geom_line(data=B,aes(Sw,2/R,colour=Media))+
geom_line(data=M1,aes(Sw,2/R,colour=Media))+
theme(panel.grid.major = element_blank(),panel.grid.minor = element_blank())+
theme_bw()
ggsave("morph-drain.png",p,height=4.0,width=6.0)
FILE=paste0(PATH,"-morphdrain.png")
ggsave(FILE,p,height=4.0,width=6.0)
return(B)
}

180
models/ColorModel.cpp
View File

@ -451,6 +451,7 @@ void ScaLBL_ColorModel::Run(){
bool MORPH_ADAPT = false;
bool USE_MORPH = false;
bool USE_SEED = false;
bool USE_MORPHOPEN_OIL = false;
int analysis_interval = 1000; // number of timesteps in between in situ analysis
int MAX_MORPH_TIMESTEPS = 50000; // maximum number of LBM timesteps to spend in morphological adaptation routine
int MIN_STEADY_TIMESTEPS = 100000;
@ -483,15 +484,22 @@ void ScaLBL_ColorModel::Run(){
}
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" );
}
@ -641,8 +649,8 @@ void ScaLBL_ColorModel::Run(){
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 flow_rate_A = volA*sqrt(vA_x*vA_x + vA_y*vA_y + vA_z*vA_z);
double flow_rate_B = volB*sqrt(vB_x*vB_x + vB_y*vB_y + vB_z*vB_z);
double Ca = fabs(muA*flow_rate_A + muB*flow_rate_B)/(5.796*alpha);
if ( morph_timesteps > morph_interval ){
@ -656,7 +664,7 @@ void ScaLBL_ColorModel::Run(){
if ( isSteady ){
MORPH_ADAPT = true;
CURRENT_MORPH_TIMESTEPS=0;
delta_volume_target = (volA )*morph_delta; // set target volume change
delta_volume_target = Dm->Volume*volA *morph_delta; // set target volume change
Averages->Full();
Averages->Write(timestep);
analysis.WriteVisData( timestep, *Averages, Phi, Pressure, Velocity, fq, Den );
@ -690,7 +698,6 @@ void ScaLBL_ColorModel::Run(){
printf(" Measured capillary number %f \n ",Ca);
}
if (SET_CAPILLARY_NUMBER ){
Fx *= capillary_number / Ca;
Fy *= capillary_number / Ca;
@ -709,6 +716,7 @@ void ScaLBL_ColorModel::Run(){
if (rank == 0) printf(" -- adjust force by factor %f \n ",capillary_number / Ca);
Averages->SetParams(rhoA,rhoB,tauA,tauB,Fx,Fy,Fz,alpha,beta);
}
CURRENT_STEADY_TIMESTEPS = 0;
}
else{
if (rank==0){
@ -723,10 +731,15 @@ void ScaLBL_ColorModel::Run(){
if (MORPH_ADAPT ){
CURRENT_MORPH_TIMESTEPS += analysis_interval;
if (USE_SEED){
delta_volume = volA - initial_volume;
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, mass change %f ***\n", seed_water, massChange);
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, with target volume change %f ***\n", delta_volume_target);
MorphOpenConnected(delta_volume_target);
}
else{
if (rank==0) printf("***Morphological step with target volume change %f ***\n", delta_volume_target);
@ -735,13 +748,13 @@ void ScaLBL_ColorModel::Run(){
}
if ( (delta_volume - delta_volume_target)/delta_volume_target > 0.0 ){
MORPH_ADAPT = false;
initial_volume = volA;
initial_volume = volA*Dm->Volume;
delta_volume = 0.0;
CURRENT_STEADY_TIMESTEPS=0;
}
else if (CURRENT_MORPH_TIMESTEPS > MAX_MORPH_TIMESTEPS) {
delta_volume = 0.0;
initial_volume = volA;
initial_volume = volA*Dm->Volume;
MORPH_ADAPT = false;
CURRENT_STEADY_TIMESTEPS=0;
}
@ -781,6 +794,151 @@ void ScaLBL_ColorModel::Run(){
// ************************************************************************
}
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;
@ -812,12 +970,6 @@ double ScaLBL_ColorModel::SeedPhaseField(const double seed_water_in_oil){
if (rank == 0) printf("Remove mass %f from %f voxels \n",mass_loss,count);
ScaLBL_CopyToDevice(Phi,phase.data(),N*sizeof(double));
FILE *OUTFILE;
sprintf(LocalRankFilename,"Phase.%05i.raw",rank);
OUTFILE = fopen(LocalRankFilename,"wb");
fwrite(phase.data(),8,N,OUTFILE);
fclose(OUTFILE);
// 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);

2
models/ColorModel.h
View File

@ -81,6 +81,6 @@ private:
void AssignComponentLabels(double *phase);
double MorphInit(const double beta, const double morph_delta);
double SeedPhaseField(const double seed_water_in_oil);
double MorphOpenConnected(double target_volume_change);
};

15
models/MRTModel.cpp
View File

@ -246,6 +246,19 @@ void ScaLBL_MRTModel::Run(){
vay /= count;
vaz /= count;
double force_mag = sqrt(Fx*Fx+Fy*Fy+Fz*Fz);
double dir_x = Fx/force_mag;
double dir_y = Fy/force_mag;
double dir_z = Fz/force_mag;
if (force_mag == 0.0){
// default to z direction
dir_x = 0.0;
dir_y = 0.0;
dir_z = 1.0;
force_mag = 1.0;
}
double flow_rate = (vax*dir_x + vay*dir_y + vaz*dir_z);
//if (rank==0) printf("Computing Minkowski functionals \n");
Morphology.ComputeScalar(Distance,0.f);
//Morphology.PrintAll();
@ -260,7 +273,7 @@ void ScaLBL_MRTModel::Run(){
Xs=sumReduce( Dm->Comm, Xs);
if (rank==0) {
double h = Dm->voxel_length;
double absperm = h*h*mu*Mask->Porosity()*sqrt(vax*vax+vay*vay+vaz*vaz)/sqrt(Fx*Fx+Fy*Fy+Fz*Fz);
double absperm = h*h*mu*Mask->Porosity()*flow_rate / force_mag;
printf(" %f\n",absperm);
FILE * log_file = fopen("Permeability.csv","a");
fprintf(log_file,"%i %.8g %.8g %.8g %.8g %.8g %.8g %.8g %.8g %.8g %.8g %.8g %.8g\n",timestep, Fx, Fy, Fz, mu,