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merged to master -- fixed runAnalysis

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This commit is contained in:
James E McClure
2018-09-07 14:10:57 -04:00
parent b9b07bc4db 40cc07d508
commit a990bd2f75
25 changed files with 865 additions and 374 deletions
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79
models/ColorModel.cpp
View File

@@ -2,6 +2,7 @@
color lattice boltzmann model
*/
#include "models/ColorModel.h"
#include "analysis/distance.h"
ScaLBL_ColorModel::ScaLBL_ColorModel(int RANK, int NP, MPI_Comm COMM):
rank(RANK), nprocs(NP), Restart(0),timestep(0),timestepMax(0),tauA(0),tauB(0),rhoA(0),rhoB(0),alpha(0),beta(0),
@@ -113,24 +114,42 @@ void ScaLBL_ColorModel::SetDomain(){
void ScaLBL_ColorModel::ReadInput(){
size_t readID;
//.......................................................................
if (rank == 0) printf("Read input media... \n");
//.......................................................................
Mask->ReadIDs();
for (int i=0; i<Nx*Ny*Nz; i++) id[i] = Mask->id[i]; // save what was read
sprintf(LocalRankString,"%05d",rank);
sprintf(LocalRankFilename,"%s%s","ID.",LocalRankString);
sprintf(LocalRestartFile,"%s%s","Restart.",LocalRankString);
// .......... READ THE INPUT FILE .......................................
//...........................................................................
if (rank == 0) cout << "Reading in signed distance function..." << endl;
//.......................................................................
sprintf(LocalRankString,"%05d",rank);
sprintf(LocalRankFilename,"%s%s","SignDist.",LocalRankString);
ReadBinaryFile(LocalRankFilename, Averages->SDs.data(), N);
MPI_Barrier(comm);
// Generate the signed distance map
// Initialize the domain and communication
Array<char> id_solid(Nx,Ny,Nz);
int count = 0;
// Solve for the position of the solid phase
for (int k=0;k<Nz;k++){
for (int j=0;j<Ny;j++){
for (int i=0;i<Nx;i++){
int n = k*Nx*Ny+j*Nx+i;
// Initialize the solid phase
if (Mask->id[n] > 0) id_solid(i,j,k) = 1;
else id_solid(i,j,k) = 0;
}
}
}
// Initialize the signed distance function
for (int k=0;k<Nz;k++){
for (int j=0;j<Ny;j++){
for (int i=0;i<Nx;i++){
int n=k*Nx*Ny+j*Nx+i;
// Initialize distance to +/- 1
Averages->SDs(i,j,k) = 2.0*double(id_solid(i,j,k))-1.0;
}
}
}
// MeanFilter(Averages->SDs);
if (rank==0) printf("Initialized solid phase -- Converting to Signed Distance function \n");
CalcDist(Averages->SDs,id_solid,*Mask);
if (rank == 0) cout << "Domain set." << endl;
}
@@ -272,6 +291,9 @@ void ScaLBL_ColorModel::Create(){
********************************************************/
void ScaLBL_ColorModel::Initialize(){
if (rank==0) printf ("Initializing distributions \n");
ScaLBL_D3Q19_Init(fq, Np);
/*
* This function initializes model
*/
@@ -290,13 +312,29 @@ void ScaLBL_ColorModel::Initialize(){
}
MPI_Bcast(&timestep,1,MPI_INT,0,comm);
// Read in the restart file to CPU buffers
double *cPhi = new double[Np];
double *cDist = new double[19*Np];
int *TmpMap;
TmpMap = new int[Np];
double *cPhi, *cDist;
cPhi = new double[N];
cDist = new double[19*Np];
ifstream File(LocalRestartFile,ios::binary);
double value;
int idx;
double value,va,vb;
ScaLBL_CopyToHost(TmpMap, dvcMap, Np*sizeof(int));
ScaLBL_CopyToHost(cPhi, Phi, N*sizeof(double));
for (int n=0; n<Np; n++){
File.read((char*) &va, sizeof(va));
File.read((char*) &vb, sizeof(vb));
value = (va-vb)/(va+vb);
idx = TmpMap[n];
if (!(idx < 0) && idx<N)
cPhi[idx] = value;
}
for (int n=0; n<Np; n++){
File.read((char*) &value, sizeof(value));
cPhi[n] = value;
// Read the distributions
for (int q=0; q<19; q++){
File.read((char*) &value, sizeof(value));
@@ -306,15 +344,12 @@ void ScaLBL_ColorModel::Initialize(){
File.close();
// Copy the restart data to the GPU
ScaLBL_CopyToDevice(fq,cDist,19*Np*sizeof(double));
ScaLBL_CopyToDevice(Phi,cPhi,Np*sizeof(double));
ScaLBL_CopyToDevice(Phi,cPhi,N*sizeof(double));
ScaLBL_DeviceBarrier();
delete [] cPhi;
delete [] cDist;
MPI_Barrier(comm);
}
if (rank==0) printf ("Initializing distributions \n");
ScaLBL_D3Q19_Init(fq, 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);

112
models/MRTModel.cpp
View File

@@ -53,6 +53,10 @@ void ScaLBL_MRTModel::SetDomain(){
Nx+=2; Ny+=2; Nz += 2;
N = Nx*Ny*Nz;
Distance.resize(Nx,Ny,Nz);
Velocity_x.resize(Nx,Ny,Nz);
Velocity_y.resize(Nx,Ny,Nz);
Velocity_z.resize(Nx,Ny,Nz);
for (int i=0; i<Nx*Ny*Nz; i++) Dm->id[i] = 1; // initialize this way
//Averages = std::shared_ptr<TwoPhase> ( new TwoPhase(Dm) ); // TwoPhase analysis object
MPI_Barrier(comm);
@@ -138,6 +142,13 @@ void ScaLBL_MRTModel::Initialize(){
void ScaLBL_MRTModel::Run(){
double rlx_setA=1.0/tau;
double rlx_setB = 8.f*(2.f-rlx_setA)/(8.f-rlx_setA);
Minkowski Morphology(Mask);
int SIZE=Np*sizeof(double);
memcpy(Morphology.SDn.data(), Distance.data(), Nx*Ny*Nz*sizeof(double));
if (rank==0) printf("time Fx Fy Fz mu Vs As Js Xs vx vy vz\n");
//.......create and start timer............
double starttime,stoptime,cputime;
ScaLBL_DeviceBarrier(); MPI_Barrier(comm);
@@ -160,6 +171,49 @@ void ScaLBL_MRTModel::Run(){
ScaLBL_D3Q19_AAeven_MRT(fq, 0, ScaLBL_Comm->LastExterior(), Np, rlx_setA, rlx_setB, Fx, Fy, Fz);
ScaLBL_DeviceBarrier(); MPI_Barrier(comm);
//************************************************************************/
if (timestep%1000==0){
ScaLBL_D3Q19_Momentum(fq,Velocity, Np);
ScaLBL_DeviceBarrier(); MPI_Barrier(comm);
ScaLBL_Comm->RegularLayout(Map,&Velocity[0],Velocity_x);
ScaLBL_Comm->RegularLayout(Map,&Velocity[Np],Velocity_y);
ScaLBL_Comm->RegularLayout(Map,&Velocity[2*Np],Velocity_z);
Morphology.Initialize();
Morphology.UpdateMeshValues();
Morphology.ComputeLocal();
Morphology.Reduce();
double count_loc=0;
double count;
double vax,vay,vaz;
double vax_loc,vay_loc,vaz_loc;
vax_loc = vay_loc = vaz_loc = 0.f;
for (int k=1; k<Nz-1; k++){
for (int j=1; j<Ny-1; j++){
for (int i=1; i<Nx-1; i++){
if (Distance(i,j,k) > 0){
vax_loc += Velocity_x(i,j,k);
vay_loc += Velocity_y(i,j,k);
vaz_loc += Velocity_z(i,j,k);
count_loc+=1.0;
}
}
}
}
MPI_Allreduce(&vax_loc,&vax,1,MPI_DOUBLE,MPI_SUM,Mask->Comm);
MPI_Allreduce(&vay_loc,&vay,1,MPI_DOUBLE,MPI_SUM,Mask->Comm);
MPI_Allreduce(&vaz_loc,&vaz,1,MPI_DOUBLE,MPI_SUM,Mask->Comm);
MPI_Allreduce(&count_loc,&count,1,MPI_DOUBLE,MPI_SUM,Mask->Comm);
vax /= count;
vay /= count;
vaz /= count;
double mu = (tau-0.5)/3.f;
if (rank==0) printf("%i %.8g %.8g %.8g %.8g %.8g %.8g %.8g %.8g %.8g %.8g %.8g\n",timestep, Fx, Fy, Fz, mu,
Morphology.V(),Morphology.A(),Morphology.J(),Morphology.X(),vax,vay,vaz);
}
}
//************************************************************************/
stoptime = MPI_Wtime();
@@ -178,9 +232,9 @@ void ScaLBL_MRTModel::Run(){
}
void ScaLBL_MRTModel::VelocityField(double *VELOCITY){
void ScaLBL_MRTModel::VelocityField(){
Minkowski Morphology(Mask);
/* Minkowski Morphology(Mask);
int SIZE=Np*sizeof(double);
ScaLBL_D3Q19_Momentum(fq,Velocity, Np);
ScaLBL_DeviceBarrier(); MPI_Barrier(comm);
@@ -223,6 +277,58 @@ void ScaLBL_MRTModel::VelocityField(double *VELOCITY){
if (rank==0) printf("Fx Fy Fz mu Vs As Js Xs vx vy vz\n");
if (rank==0) printf("%.8g %.8g %.8g %.8g %.8g %.8g %.8g %.8g %.8g %.8g %.8g\n",Fx, Fy, Fz, mu,
Morphology.V(),Morphology.A(),Morphology.J(),Morphology.X(),vax,vay,vaz);
*/
std::vector<IO::MeshDataStruct> visData;
fillHalo<double> fillData(Dm->Comm,Dm->rank_info,{Dm->Nx-2,Dm->Ny-2,Dm->Nz-2},{1,1,1},0,1);
auto VxVar = std::make_shared<IO::Variable>();
auto VyVar = std::make_shared<IO::Variable>();
auto VzVar = std::make_shared<IO::Variable>();
auto SignDistVar = std::make_shared<IO::Variable>();
IO::initialize("","silo","false");
// Create the MeshDataStruct
visData.resize(1);
visData[0].meshName = "domain";
visData[0].mesh = std::make_shared<IO::DomainMesh>( Dm->rank_info,Dm->Nx-2,Dm->Ny-2,Dm->Nz-2,Dm->Lx,Dm->Ly,Dm->Lz );
SignDistVar->name = "SignDist";
SignDistVar->type = IO::VariableType::VolumeVariable;
SignDistVar->dim = 1;
SignDistVar->data.resize(Dm->Nx-2,Dm->Ny-2,Dm->Nz-2);
visData[0].vars.push_back(SignDistVar);
VxVar->name = "Velocity_x";
VxVar->type = IO::VariableType::VolumeVariable;
VxVar->dim = 1;
VxVar->data.resize(Dm->Nx-2,Dm->Ny-2,Dm->Nz-2);
visData[0].vars.push_back(VxVar);
VyVar->name = "Velocity_y";
VyVar->type = IO::VariableType::VolumeVariable;
VyVar->dim = 1;
VyVar->data.resize(Dm->Nx-2,Dm->Ny-2,Dm->Nz-2);
visData[0].vars.push_back(VyVar);
VzVar->name = "Velocity_z";
VzVar->type = IO::VariableType::VolumeVariable;
VzVar->dim = 1;
VzVar->data.resize(Dm->Nx-2,Dm->Ny-2,Dm->Nz-2);
visData[0].vars.push_back(VzVar);
Array<double>& SignData = visData[0].vars[0]->data;
Array<double>& VelxData = visData[0].vars[1]->data;
Array<double>& VelyData = visData[0].vars[2]->data;
Array<double>& VelzData = visData[0].vars[3]->data;
ASSERT(visData[0].vars[0]->name=="SignDist");
ASSERT(visData[0].vars[1]->name=="Velocity_x");
ASSERT(visData[0].vars[2]->name=="Velocity_y");
ASSERT(visData[0].vars[3]->name=="Velocity_z");
fillData.copy(Distance,SignData);
fillData.copy(Velocity_x,VelxData);
fillData.copy(Velocity_y,VelyData);
fillData.copy(Velocity_z,VelzData);
IO::writeData( timestep, visData, Dm->Comm );
}

7
models/MRTModel.h
View File

@@ -28,7 +28,7 @@ public:
void Create();
void Initialize();
void Run();
void VelocityField(double *Vz);
void VelocityField();
bool Restart,pBC;
int timestep,timestepMax;
@@ -58,9 +58,12 @@ public:
//Minkowski Morphology;
DoubleArray Velocity_x;
DoubleArray Velocity_y;
DoubleArray Velocity_z;
private:
MPI_Comm comm;
// filenames
char LocalRankString[8];
char LocalRankFilename[40];