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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 E McClure 2019-03-26 16:03:42 -04:00
commit 4a2ffcb700
5 changed files with 107 additions and 45 deletions
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12
analysis/SubPhase.cpp
View File

@ -28,8 +28,15 @@ SubPhase::SubPhase(std::shared_ptr <Domain> dm):
//.........................................
if (Dm->rank()==0){
bool WriteHeader=false;
SUBPHASE = fopen("subphase.csv","r");
if (SUBPHASE != NULL)
fclose(SUBPHASE);
else
WriteHeader=true;
SUBPHASE = fopen("subphase.csv","a+");
if (ftell(SUBPHASE) == 0)
if (WriteHeader)
{
// If timelog is empty, write a short header to list the averages
//fprintf(SUBPHASE,"--------------------------------------------------------------------------------------\n");
@ -141,10 +148,11 @@ void SubPhase::Basic(){
if (Dm->BoundaryCondition > 0 && Dm->kproc() == Dm->nprocz()-1) kmax=Nz-4;
imin=jmin=1;
// If inlet layers exist use these as default
// If inlet/outlet layers exist use these as default
if (Dm->inlet_layers_x > 0) imin = Dm->inlet_layers_x;
if (Dm->inlet_layers_y > 0) jmin = Dm->inlet_layers_y;
if (Dm->inlet_layers_z > 0) kmin = Dm->inlet_layers_z;
if (Dm->outlet_layers_z > 0) kmax = Dm->outlet_layers_z;
nb.reset(); wb.reset();
/*

43
analysis/runAnalysis.cpp
View File

@ -389,9 +389,9 @@ public:
// Averages.ColorToSignedDistance(beta,Averages.Phase,Averages.Phase_tplus);
}
if ( matches(type,AnalysisType::ComputeAverages) ) {
PROFILE_START("Compute subphase",1);
PROFILE_START("Compute basic averages",1);
Averages.Basic();
PROFILE_STOP("Compute subphase",1);
PROFILE_STOP("Compute basic averages",1);
}
}
private:
@ -402,6 +402,29 @@ private:
double beta;
};
class SubphaseWorkItem: public ThreadPool::WorkItemRet<void>
{
public:
SubphaseWorkItem( AnalysisType type_, int timestep_, SubPhase& Averages_ ):
type(type_), timestep(timestep_), Averages(Averages_){ }
~SubphaseWorkItem() { }
virtual void run() {
if ( matches(type,AnalysisType::ComputeAverages) ) {
PROFILE_START("Compute subphase",1);
Averages.Full();
PROFILE_STOP("Compute subphase",1);
}
}
private:
SubphaseWorkItem();
AnalysisType type;
int timestep;
SubPhase& Averages;
double beta;
};
/******************************************************************
* MPI comm wrapper for use with analysis *
@ -468,6 +491,7 @@ runAnalysis::runAnalysis( std::shared_ptr<Database> db,
ThreadPool::thread_id_t d_wait_analysis;
ThreadPool::thread_id_t d_wait_vis;
ThreadPool::thread_id_t d_wait_restart;
ThreadPool::thread_id_t d_wait_subphase;
char rankString[20];
sprintf(rankString,"%05d",Dm->rank());
@ -479,6 +503,12 @@ runAnalysis::runAnalysis( std::shared_ptr<Database> db,
d_blobid_interval = db->getScalar<int>( "blobid_interval" );
d_visualization_interval = db->getScalar<int>( "visualization_interval" );
auto restart_file = db->getScalar<std::string>( "restart_file" );
if (db->keyExists( "subphase_analysis_interval" )){
d_subphase_analysis_interval = db->getScalar<int>( "subphase_analysis_interval" );
}
else{
d_subphase_analysis_interval = INT_MAX;
}
d_restartFile = restart_file + "." + rankString;
d_rank = MPI_WORLD_RANK();
writeIDMap(ID_map_struct(),0,id_map_filename);
@ -892,10 +922,17 @@ void runAnalysis::basic( int timestep, SubPhase &Averages, const double *Phi, do
// if ( matches(type,AnalysisType::ComputeAverages) ) {
if ( timestep%d_analysis_interval == 0 ) {
auto work = new BasicWorkItem(type,timestep,Averages);
work->add_dependency(d_wait_analysis); // Make sure we are done using analysis before modifying
work->add_dependency(d_wait_subphase); // Make sure we are done using analysis before modifying
work->add_dependency(d_wait_analysis);
d_wait_analysis = d_tpool.add_work(work);
}
if ( timestep%d_subphase_analysis_interval == 0 ) {
auto work = new BasicWorkItem(type,timestep,Averages);
work->add_dependency(d_wait_subphase); // Make sure we are done using analysis before modifying
d_wait_subphase = d_tpool.add_work(work);
}
if (timestep%d_restart_interval==0){
std::shared_ptr<double> cfq,cDen;
// Copy restart data to the CPU

4
analysis/runAnalysis.h
View File

@ -7,7 +7,7 @@
#include "common/Communication.h"
#include "common/ScaLBL.h"
#include "threadpool/thread_pool.h"
#include <limits.h>
typedef std::shared_ptr<std::pair<int,IntArray>> BlobIDstruct;
typedef std::shared_ptr<std::vector<BlobIDType>> BlobIDList;
@ -88,6 +88,7 @@ private:
int d_Np;
int d_rank;
int d_restart_interval, d_analysis_interval, d_blobid_interval, d_visualization_interval;
int d_subphase_analysis_interval;
double d_beta;
bool d_regular;
ThreadPool d_tpool;
@ -107,6 +108,7 @@ private:
// Ids of work items to use for dependencies
ThreadPool::thread_id_t d_wait_blobID;
ThreadPool::thread_id_t d_wait_analysis;
ThreadPool::thread_id_t d_wait_subphase;
ThreadPool::thread_id_t d_wait_vis;
ThreadPool::thread_id_t d_wait_restart;

90
common/Domain.cpp
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@ -77,6 +77,7 @@ Domain::Domain( std::shared_ptr<Database> db, MPI_Comm Communicator):
Lx(0), Ly(0), Lz(0), Volume(0), BoundaryCondition(0),
Comm(MPI_COMM_NULL),
inlet_layers_x(0), inlet_layers_y(0), inlet_layers_z(0),
outlet_layers_x(0), outlet_layers_y(0), outlet_layers_z(0),
sendCount_x(0), sendCount_y(0), sendCount_z(0), sendCount_X(0), sendCount_Y(0), sendCount_Z(0),
sendCount_xy(0), sendCount_yz(0), sendCount_xz(0), sendCount_Xy(0), sendCount_Yz(0), sendCount_xZ(0),
sendCount_xY(0), sendCount_yZ(0), sendCount_Xz(0), sendCount_XY(0), sendCount_YZ(0), sendCount_XZ(0),
@ -126,6 +127,12 @@ void Domain::initialize( std::shared_ptr<Database> db )
inlet_layers_y = InletCount[1];
inlet_layers_z = InletCount[2];
}
if (d_db->keyExists( "OutletLayers" )){
auto OutletCount = d_db->getVector<int>( "OutletLayers" );
outlet_layers_x = OutletCount[0];
outlet_layers_y = OutletCount[1];
outlet_layers_z = OutletCount[2];
}
ASSERT( n.size() == 3u );
ASSERT( L.size() == 3u );
@ -144,9 +151,13 @@ void Domain::initialize( std::shared_ptr<Database> db )
MPI_Comm_rank( Comm, &myrank );
rank_info = RankInfoStruct(myrank,nproc[0],nproc[1],nproc[2]);
// inlet layers only apply to lower part of domain
if (nproc[0] > 0) inlet_layers_x = 0;
if (nproc[1] > 0) inlet_layers_y = 0;
if (nproc[2] > 0) inlet_layers_z = 0;
if (rank_info.ix > 0) inlet_layers_x = 0;
if (rank_info.jy > 0) inlet_layers_y = 0;
if (rank_info.kz > 0) inlet_layers_z = 0;
// outlet layers only apply to top part of domain
if (rank_info.ix < nproc[0]-1 ) outlet_layers_x = 0;
if (rank_info.jy < nproc[1]-1) outlet_layers_y = 0;
if (rank_info.kz < nproc[2]-1) outlet_layers_z = 0;
// Fill remaining variables
N = Nx*Ny*Nz;
Volume = nx*ny*nx*nproc[0]*nproc[1]*nproc[2]*1.0;
@ -514,43 +525,46 @@ void Domain::CommInit()
void Domain::ReadIDs(){
// Read the IDs from input file
int nprocs=nprocx()*nprocy()*nprocz();
size_t readID;
char LocalRankString[8];
char LocalRankFilename[40];
//.......................................................................
if (rank() == 0) printf("Read input media... \n");
//.......................................................................
sprintf(LocalRankString,"%05d",rank());
sprintf(LocalRankFilename,"%s%s","ID.",LocalRankString);
// .......... READ THE INPUT FILE .......................................
if (rank()==0) printf("Initialize from segmented data: solid=0, NWP=1, WP=2 \n");
sprintf(LocalRankFilename,"ID.%05i",rank());
FILE *IDFILE = fopen(LocalRankFilename,"rb");
if (IDFILE==NULL) ERROR("Domain::ReadIDs -- Error opening file: ID.xxxxx");
readID=fread(id,1,N,IDFILE);
if (readID != size_t(N)) printf("Domain::ReadIDs -- Error reading ID (rank=%i) \n",rank());
fclose(IDFILE);
// Compute the porosity
double sum;
double porosity;
double sum_local=0.0;
double iVol_global = 1.0/(1.0*(Nx-2)*(Ny-2)*(Nz-2)*nprocs);
if (BoundaryCondition > 0) iVol_global = 1.0/(1.0*(Nx-2)*nprocx()*(Ny-2)*nprocy()*((Nz-2)*nprocz()-6));
//.........................................................
// If external boundary conditions are applied remove solid
if (BoundaryCondition > 0 && kproc() == 0){
for (int k=0; k<3; k++){
for (int j=0;j<Ny;j++){
for (int i=0;i<Nx;i++){
int n = k*Nx*Ny+j*Nx+i;
id[n] = 1;
}
}
int nprocs=nprocx()*nprocy()*nprocz();
size_t readID;
char LocalRankString[8];
char LocalRankFilename[40];
//.......................................................................
if (rank() == 0) printf("Read input media... \n");
//.......................................................................
sprintf(LocalRankString,"%05d",rank());
sprintf(LocalRankFilename,"%s%s","ID.",LocalRankString);
// .......... READ THE INPUT FILE .......................................
if (rank()==0) printf("Initialize from segmented data: solid=0, NWP=1, WP=2 \n");
sprintf(LocalRankFilename,"ID.%05i",rank());
FILE *IDFILE = fopen(LocalRankFilename,"rb");
if (IDFILE==NULL) ERROR("Domain::ReadIDs -- Error opening file: ID.xxxxx");
readID=fread(id,1,N,IDFILE);
if (readID != size_t(N)) printf("Domain::ReadIDs -- Error reading ID (rank=%i) \n",rank());
fclose(IDFILE);
// Compute the porosity
double sum;
double porosity;
double sum_local=0.0;
double iVol_global = 1.0/(1.0*(Nx-2)*(Ny-2)*(Nz-2)*nprocs);
if (BoundaryCondition > 0) iVol_global = 1.0/(1.0*(Nx-2)*nprocx()*(Ny-2)*nprocy()*((Nz-2)*nprocz()-6));
//.........................................................
// If external boundary conditions are applied remove solid
if (BoundaryCondition > 0 && kproc() == 0){
if (inlet_layers_z < 4) inlet_layers_z=4;
for (int k=0; k<inlet_layers_z; k++){
for (int j=0;j<Ny;j++){
for (int i=0;i<Nx;i++){
int n = k*Nx*Ny+j*Nx+i;
id[n] = 1;
}
}
}
}
if (BoundaryCondition > 0 && kproc() == nprocz()-1){
for (int k=Nz-3; k<Nz; k++){
if (outlet_layers_z < 4) outlet_layers_z=4;
for (int k=Nz-outlet_layers_z; 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;
@ -559,7 +573,7 @@ void Domain::ReadIDs(){
}
}
}
for (int k=1;k<Nz-1;k++){
for (int k=inlet_layers_z+1; k<Nz-outlet_layers_z-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;

1
common/Domain.h
View File

@ -110,6 +110,7 @@ public: // Public variables (need to create accessors instead)
double Lx,Ly,Lz,Volume;
int Nx,Ny,Nz,N;
int inlet_layers_x, inlet_layers_y, inlet_layers_z;
int outlet_layers_x, outlet_layers_y, outlet_layers_z;
RankInfoStruct rank_info;
MPI_Comm Comm; // MPI Communicator for this domain