Merge branch 'Greyscale' of github.com:OPM/LBPM into Greyscale

IO/netcdf.cpp

@@ -204,7 +204,6 @@ std::vector<size_t> getAttDim( int fid, const std::string& att )
 {
     std::vector<size_t> dim(1,0);
     int err = nc_inq_attlen( fid, NC_GLOBAL, att.c_str(), dim.data() );
-    CHECK_NC_ERR( err );
     return dim;
 }
 std::vector<std::string> getVarNames( int fid )

README.md

@@ -23,7 +23,7 @@ Configure, build & install procedure
 
 * edit configure script from sample_scripts directory and configure (e.g.)
 
-   `/path/to/LBPM/sample_scripts/configure_desktop`
+   `/path/to/LBPM-WIA/sample_scripts/configure_desktop`
 
 * compile and install
 

StackTrace/StackTrace.cpp

@@ -7,7 +7,6 @@
 
 #include <algorithm>
 #include <atomic>
-#include <cerrno>
 #include <csignal>
 #include <cstring>
 #include <iostream>
@@ -349,11 +348,8 @@ static inline int exec3( const char *cmd, FUNCTION &fun )
         if ( buffer[0] != 0 )
             fun( buffer );
     }
-    int code = pclose( pipe );
-    if ( errno == ECHILD ) {
-        errno = 0;
-        code  = 0;
-    }
+    auto status = pclose( pipe );
+    int code    = WEXITSTATUS( status );
     std::this_thread::yield(); // Allow any signals to process
     resetSignal( SIGCHLD );    // Clear child exited
     return code;
@@ -1745,7 +1741,7 @@ std::vector<int> StackTrace::defaultSignalsToCatch()
  *  Set the signal handlers                                                  *
  ****************************************************************************/
 static std::function<void( const StackTrace::abort_error &err )> abort_fun;
-StackTrace::abort_error rethrow()
+static StackTrace::abort_error rethrow()
 {
     StackTrace::abort_error error;
 #ifdef USE_LINUX
@@ -1779,14 +1775,14 @@ StackTrace::abort_error rethrow()
     }
     return error;
 }
-void StackTrace::terminateFunctionSignal( int sig )
+static void term_func_abort( int sig )
 {
     StackTrace::abort_error err;
     err.type      = StackTrace::terminateType::signal;
     err.signal    = sig;
     err.bytes     = StackTrace::Utilities::getMemoryUsage();
     err.stack     = StackTrace::backtrace();
-    err.stackType = StackTrace::getDefaultStackType();
+    err.stackType = StackTrace::printStackType::global;
     abort_fun( err );
 }
 static bool signals_set[256] = { false };
@@ -1833,7 +1829,7 @@ void StackTrace::setErrorHandler( std::function<void( const StackTrace::abort_er
 {
     abort_fun = abort;
     std::set_terminate( term_func );
-    setSignals( defaultSignalsToCatch(), &terminateFunctionSignal );
+    setSignals( defaultSignalsToCatch(), &term_func_abort );
     std::set_unexpected( term_func );
 }
 void StackTrace::clearErrorHandler()
@@ -2219,7 +2215,7 @@ void StackTrace::cleanupStackTrace( multi_stack_info &stack )
             // Remove callstack (and all children) for threads that are just contributing
             bool test = function.find( "_callstack_signal_handler" ) != npos ||
                         function.find( "getGlobalCallStacks" ) != npos ||
-                        function.find( "backtrace" ) != npos || function.find( "(" ) == npos;
+                        function.find( "(" ) == npos;
             if ( test ) {
                 it = stack.children.erase( it );
                 continue;
@@ -2519,11 +2515,3 @@ const char *StackTrace::abort_error::what() const noexcept
             d_msg.erase( i, 1 );
     return d_msg.c_str();
 }
-
-
-/****************************************************************************
- * Get/Set default stack type                                                *
- ****************************************************************************/
-static StackTrace::printStackType abort_stackType = StackTrace::printStackType::global;
-void StackTrace::setDefaultStackType( StackTrace::printStackType type ) { abort_stackType = type; }
-StackTrace::printStackType StackTrace::getDefaultStackType() { return abort_stackType; }

StackTrace/StackTrace.h

@@ -261,10 +261,6 @@ void clearSignals();
 void raiseSignal( int signal );
 
 
-//! Default function to abort after catching a signal
-void terminateFunctionSignal( int signal );
-
-
 //! Return a list of all signals that can be caught
 std::vector<int> allSignalsToCatch();
 
@@ -308,13 +304,6 @@ multi_stack_info generateFromString( const std::vector<std::string> &str );
 multi_stack_info generateFromString( const std::string &str );
 
 
-//! Set default stack type
-void setDefaultStackType( StackTrace::printStackType );
-
-//! Get default stack type
-StackTrace::printStackType getDefaultStackType();
-
-
 } // namespace StackTrace
 
 

StackTrace/Utilities.cpp

@@ -8,10 +8,8 @@
 #include <cstring>
 #include <fstream>
 #include <iostream>
-#include <mutex>
 #include <sstream>
 #include <stdexcept>
-#include <typeinfo>
 
 #ifdef USE_MPI
 #include "mpi.h"
@@ -21,10 +19,6 @@
 #include "MemoryApp.h"
 #endif
 
-#ifdef USE_GCOV
-extern "C" void __gcov_flush( void );
-#endif
-
 
 #define perr std::cerr
 
@@ -71,12 +65,6 @@ extern "C" void __gcov_flush( void );
 // clang-format on
 
 
-#ifdef __GNUC__
-#define USE_ABI
-#include <cxxabi.h>
-#endif
-
-
 namespace StackTrace {
 
 
@@ -108,12 +96,13 @@ inline size_t findfirst( const std::vector<TYPE> &X, TYPE Y )
 /****************************************************************************
  *  Function to terminate the program                                        *
  ****************************************************************************/
-static bool abort_throwException = false;
-static int force_exit            = 0;
+static bool abort_throwException      = false;
+static printStackType abort_stackType = printStackType::global;
+static int force_exit                 = 0;
 void Utilities::setAbortBehavior( bool throwException, int stackType )
 {
     abort_throwException = throwException;
-    StackTrace::setDefaultStackType( static_cast<printStackType>( stackType ) );
+    abort_stackType      = static_cast<printStackType>( stackType );
 }
 void Utilities::abort( const std::string &message, const std::string &filename, const int line )
 {
@@ -123,28 +112,16 @@ void Utilities::abort( const std::string &message, const std::string &filename,
     err.type      = terminateType::abort;
     err.line      = line;
     err.bytes     = Utilities::getMemoryUsage();
-    err.stackType = StackTrace::getDefaultStackType();
+    err.stackType = abort_stackType;
     err.stack     = StackTrace::backtrace();
     throw err;
 }
-static std::mutex terminate_mutex;
-static inline void callAbort()
+static void terminate( const StackTrace::abort_error &err )
 {
-#ifdef USE_GCOV
-    __gcov_flush();
-#endif
-    terminate_mutex.unlock();
-    std::abort();
-}
-void Utilities::terminate( const StackTrace::abort_error &err )
-{
-    // Lock mutex to ensure multiple threads do not try to abort simultaneously
-    terminate_mutex.lock();
-    // Clear the error handlers
     clearErrorHandler();
     // Print the message and abort
     if ( force_exit > 1 ) {
-        callAbort();
+        std::abort();
     } else if ( !abort_throwException ) {
         // Use MPI_abort (will terminate all processes)
         force_exit = 2;
@@ -158,11 +135,10 @@ void Utilities::terminate( const StackTrace::abort_error &err )
             MPI_Abort( MPI_COMM_WORLD, -1 );
         }
 #endif
-        callAbort();
+        std::abort();
     } else {
         perr << err.what();
-        perr.flush();
-        callAbort();
+        std::abort();
     }
 }
 
@@ -173,7 +149,7 @@ void Utilities::terminate( const StackTrace::abort_error &err )
 static void setTerminateErrorHandler()
 {
     // Set the terminate routine for runtime errors
-    StackTrace::setErrorHandler( Utilities::terminate );
+    StackTrace::setErrorHandler( terminate );
 }
 void Utilities::setErrorHandlers()
 {
@@ -317,18 +293,4 @@ std::string Utilities::exec( const string_view &cmd, int &exit_code )
 }
 
 
-/****************************************************************************
- *  Get the type name                                                        *
- ****************************************************************************/
-std::string Utilities::getTypeName( const std::type_info &id )
-{
-    std::string name = id.name();
-#if defined( USE_ABI )
-    int status;
-    name = abi::__cxa_demangle( name.c_str(), 0, 0, &status );
-#endif
-    return name;
-}
-
-
 } // namespace StackTrace

StackTrace/Utilities.h

@@ -4,7 +4,6 @@
 #include <stdexcept>
 #include <string>
 #include <thread>
-#include <typeinfo>
 
 #include "StackTrace/StackTrace.h"
 #include "StackTrace/string_view.h"
@@ -29,14 +28,9 @@ void abort( const std::string &message, const std::string &filename, const int l
 void setAbortBehavior( bool throwException, int stackType = 2 );
 
 
-//! Function to terminate the application
-void terminate( const StackTrace::abort_error &err );
-
-
 //! Function to set the error handlers
 void setErrorHandlers();
 
-
 //! Function to clear the error handlers
 void clearErrorHandlers();
 
@@ -98,18 +92,6 @@ void cause_segfault();
 std::string exec( const StackTrace::string_view &cmd, int &exit_code );
 
 
-//! Return the hopefully demangled name of the given type
-std::string getTypeName( const std::type_info &id );
-
-
-//! Return the hopefully demangled name of the given type
-template<class TYPE>
-inline std::string getTypeName()
-{
-    return getTypeName( typeid( TYPE ) );
-}
-
-
 } // namespace Utilities
 } // namespace StackTrace
 

StackTrace/string_view.h

@@ -119,7 +119,7 @@ public:
         int result = 0;
         for ( int i = 0; i < N && result == 0; i++ )
             if ( d_data[i] != other[i] )
-                result = d_data[i] < other[i] ? -( i + 1 ) : ( i + 1 );
+                result = d_data[i] < other[i] ? -i : i;
         if ( result == 0 )
             result = size() == other.size() ? 0 : size() < other.size() ? -1 : 1;
         return result;

analysis/GreyPhase.cpp

@@ -1,259 +0,0 @@
-#include "analysis/GreyPhase.h"
-
-// Constructor
-GreyPhaseAnalysis::GreyPhaseAnalysis(std::shared_ptr <Domain> dm):
-	Dm(dm)
-{
-	Nx=dm->Nx; Ny=dm->Ny; Nz=dm->Nz;
-	Volume=(Nx-2)*(Ny-2)*(Nz-2)*Dm->nprocx()*Dm->nprocy()*Dm->nprocz()*1.0;
-	
-	// Global arrays
-    SDs.resize(Nx,Ny,Nz);           SDs.fill(0);
-	Porosity.resize(Nx,Ny,Nz);      Porosity.fill(0);
-	//PhaseID.resize(Nx,Ny,Nz);       PhaseID.fill(0);
-	Rho_n.resize(Nx,Ny,Nz);       	Rho_n.fill(0);
-	Rho_w.resize(Nx,Ny,Nz);       	Rho_w.fill(0);
-	Pressure.resize(Nx,Ny,Nz);      Pressure.fill(0);
-	//Phi.resize(Nx,Ny,Nz);         	Phi.fill(0);
-	//DelPhi.resize(Nx,Ny,Nz);        DelPhi.fill(0);
-	Vel_x.resize(Nx,Ny,Nz);         Vel_x.fill(0);	    // Gradient of the phase indicator field
-	Vel_y.resize(Nx,Ny,Nz);         Vel_y.fill(0);
-	Vel_z.resize(Nx,Ny,Nz);         Vel_z.fill(0);
-	//.........................................
-	
-	if (Dm->rank()==0){
-		bool WriteHeader=false;
-		TIMELOG = fopen("timelog.csv","r");
-		if (TIMELOG != NULL)
-			fclose(TIMELOG);
-		else
-			WriteHeader=true;
-
-		TIMELOG = fopen("timelog.csv","a+");
-		if (WriteHeader)
-		{
-			// If timelog is empty, write a short header to list the averages
-			//fprintf(TIMELOG,"--------------------------------------------------------------------------------------\n");
-			fprintf(TIMELOG,"sw krw krn vw vn pw pn\n");				
-		}
-	}
-}
-
-
-// Destructor
-GreyPhaseAnalysis::~GreyPhaseAnalysis()
-{
-
-}
-
-void GreyPhaseAnalysis::Write(int timestep)
-{
-
-}
-
-void GreyPhaseAnalysis::SetParams(double rhoA, double rhoB, double tauA, double tauB, double force_x, double force_y, double force_z, double alpha, double B, double GreyPorosity)
-{
-	Fx = force_x;
-	Fy = force_y;
-	Fz = force_z;
-	rho_n = rhoA;
-	rho_w = rhoB;
-	nu_n = (tauA-0.5)/3.f;
-	nu_w = (tauB-0.5)/3.f;
-	gamma_wn = 6.0*alpha;
-	beta = B;
-    grey_porosity = GreyPorosity;
-}
-
-void GreyPhaseAnalysis::Basic(){
-	int i,j,k,n,imin,jmin,kmin,kmax;
-
-	// If external boundary conditions are set, do not average over the inlet
-	kmin=1; kmax=Nz-1;
-	imin=jmin=1;
-	if (Dm->inlet_layers_z > 0 && Dm->kproc() == 0) kmin += Dm->inlet_layers_z; 
-	if (Dm->outlet_layers_z > 0 && Dm->kproc() == Dm->nprocz()-1) kmax -= Dm->outlet_layers_z; 
-
-	Water_local.reset();
-	Oil_local.reset();
-	double count_w = 0.0;
-	double count_n = 0.0;
-	for (k=kmin; k<kmax; k++){
-		for (j=jmin; j<Ny-1; j++){
-			for (i=imin; i<Nx-1; i++){
-				n = k*Nx*Ny + j*Nx + i;
-				// Compute volume averages
-				if ( Dm->id[n] > 0 ){
-					// compute density
-					double nA = Rho_n(n);
-					double nB = Rho_w(n);				
-					double phi = (nA-nB)/(nA+nB);					
-					double porosity = Porosity(n);
-					Water_local.M += rho_w*nB*porosity;
-					Water_local.Px += porosity*rho_w*nB*Vel_x(n);
-					Water_local.Py += porosity*rho_w*nB*Vel_y(n);
-					Water_local.Pz += porosity*rho_w*nB*Vel_z(n);
-					Oil_local.M += rho_n*nA*porosity;
-					Oil_local.Px += porosity*rho_n*nA*Vel_x(n);
-					Oil_local.Py += porosity*rho_n*nA*Vel_y(n);
-					Oil_local.Pz += porosity*rho_n*nA*Vel_z(n);
-
-					if ( phi > 0.99 ){
-						Oil_local.p += Pressure(n);
-					    //Oil_local.p += pressure*(rho_n*nA)/(rho_n*nA+rho_w*nB);
-						count_n += 1.0;
-					}
-					else if ( phi < -0.99 ){
-						Water_local.p += Pressure(n);
-					    //Water_local.p += pressure*(rho_w*nB)/(rho_n*nA+rho_w*nB);
-						count_w += 1.0;
-					}
-				}
-			}
-		}
-	}
-	Oil.M=sumReduce( Dm->Comm, Oil_local.M);
-	Oil.Px=sumReduce( Dm->Comm, Oil_local.Px);
-	Oil.Py=sumReduce( Dm->Comm, Oil_local.Py);
-	Oil.Pz=sumReduce( Dm->Comm, Oil_local.Pz);
-
-	Water.M=sumReduce( Dm->Comm, Water_local.M);
-	Water.Px=sumReduce( Dm->Comm, Water_local.Px);
-	Water.Py=sumReduce( Dm->Comm, Water_local.Py);
-	Water.Pz=sumReduce( Dm->Comm, Water_local.Pz);
-
-
-	//Oil.p /= Oil.M;	
-	//Water.p /= Water.M;
-	count_w=sumReduce( Dm->Comm, count_w);
-	count_n=sumReduce( Dm->Comm, count_n);
-	if (count_w > 0.0)
-		Water.p=sumReduce( Dm->Comm, Water_local.p) / count_w;
-	else 
-		Water.p = 0.0;
-	if (count_n > 0.0)
-		Oil.p=sumReduce( Dm->Comm, Oil_local.p) / count_n;
-	else 
-		Oil.p = 0.0;
-
-	// check for NaN
-	bool err=false;
-	if (Water.M != Water.M) err=true;
-	if (Water.p != Water.p) err=true;
-	if (Water.Px != Water.Px) err=true;
-	if (Water.Py != Water.Py) err=true;
-	if (Water.Pz != Water.Pz) err=true;
-
-	if (Oil.M != Oil.M) err=true;
-	if (Oil.p != Oil.p) err=true;
-	if (Oil.Px != Oil.Px) err=true;
-	if (Oil.Py != Oil.Py) err=true;
-	if (Oil.Pz != Oil.Pz) err=true;
-	
-	if (Dm->rank() == 0){
-		double force_mag = sqrt(Fx*Fx+Fy*Fy+Fz*Fz);
-		double dir_x = 0.0;
-		double dir_y = 0.0;
-		double dir_z = 0.0;
-		if (force_mag > 0.0){
-			dir_x = Fx/force_mag;
-			dir_y = Fy/force_mag;
-			dir_z = Fz/force_mag;
-		}
-		else {
-			// default to z direction
-			dir_x = 0.0;
-			dir_y = 0.0;
-			dir_z = 1.0;
-		}
-		if (Dm->BoundaryCondition == 1 || Dm->BoundaryCondition == 2 || Dm->BoundaryCondition == 3 || Dm->BoundaryCondition == 4 ){
-			// compute the pressure drop
-			double pressure_drop = (Pressure(Nx*Ny + Nx + 1) - 1.0) / 3.0;
-			double length = ((Nz-2)*Dm->nprocz());
-			force_mag -= pressure_drop/length;
-		}
-		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;
-		}
-		saturation=Water.M/(Water.M + Oil.M); // assume constant density
-		water_flow_rate=grey_porosity*saturation*(Water.Px*dir_x + Water.Py*dir_y + Water.Pz*dir_z)/Water.M;
-		oil_flow_rate  =grey_porosity*(1.0-saturation)*(Oil.Px*dir_x + Oil.Py*dir_y + Oil.Pz*dir_z)/Oil.M;
-
-		double h = Dm->voxel_length;		
-        //TODO check if need greyporosity or domain porosity ? - compare to analytical solution
-		double krn = h*h*nu_n*oil_flow_rate / force_mag ;
-		double krw = h*h*nu_w*water_flow_rate / force_mag;
-		//printf("   water saturation = %f, fractional flow =%f \n",saturation,fractional_flow);
-		fprintf(TIMELOG,"%.5g %.5g %.5g %.5g %.5g %.5g %.5g\n",saturation,krw,krn,h*water_flow_rate,h*oil_flow_rate, Water.p, Oil.p); 
-		fflush(TIMELOG); 
-	}
-
-	if (err==true){
-		// exception if simulation produceds NaN
-		printf("GreyPhaseAnalysis.cpp: NaN encountered, may need to check simulation parameters \n");
-	}	
-	ASSERT(err==false);
-}
-/*
-inline void InterfaceTransportMeasures( double beta, double rA, double rB, double nA, double nB, 
-		double nx, double ny, double nz, double ux, double uy, double uz, interface &I){
-	
-	double A1,A2,A3,A4,A5,A6;
-	double B1,B2,B3,B4,B5,B6;
-	double nAB,delta;
-	// Instantiate mass transport distributions
-	// Stationary value - distribution 0
-	nAB = 1.0/(nA+nB);
-	//...............................................
-	// q = 0,2,4
-	// Cq = {1,0,0}, {0,1,0}, {0,0,1}
-	delta = beta*nA*nB*nAB*0.1111111111111111*nx;
-	if (!(nA*nB*nAB>0)) delta=0;
-	A1 = nA*(0.1111111111111111*(1+4.5*ux))+delta;
-	B1 = nB*(0.1111111111111111*(1+4.5*ux))-delta;
-	A2 = nA*(0.1111111111111111*(1-4.5*ux))-delta;
-	B2 = nB*(0.1111111111111111*(1-4.5*ux))+delta;
-
-	//...............................................
-	// Cq = {0,1,0}
-	delta = beta*nA*nB*nAB*0.1111111111111111*ny;
-	if (!(nA*nB*nAB>0)) delta=0;
-	A3 = nA*(0.1111111111111111*(1+4.5*uy))+delta;
-	B3 = nB*(0.1111111111111111*(1+4.5*uy))-delta;
-	A4 = nA*(0.1111111111111111*(1-4.5*uy))-delta;
-	B4 = nB*(0.1111111111111111*(1-4.5*uy))+delta;
-
-	//...............................................
-	// q = 4
-	// Cq = {0,0,1}
-	delta = beta*nA*nB*nAB*0.1111111111111111*nz;
-	if (!(nA*nB*nAB>0)) delta=0;
-	A5 = nA*(0.1111111111111111*(1+4.5*uz))+delta;
-	B5 = nB*(0.1111111111111111*(1+4.5*uz))-delta;
-	A6 = nA*(0.1111111111111111*(1-4.5*uz))-delta;
-	B6 = nB*(0.1111111111111111*(1-4.5*uz))+delta;
-	
-	double unx = (A1-A2);
-	double uny = (A3-A4);
-	double unz = (A5-A6);
-	double uwx = (B1-B2);
-	double uwy = (B3-B4);
-	double uwz = (B5-B6);
-	
-	I.Mn += rA*nA;
-	I.Mw += rB*nB;
-	I.Pnx += rA*nA*unx;
-	I.Pny += rA*nA*uny;
-	I.Pnz += rA*nA*unz;
-	I.Pwx += rB*nB*uwx;
-	I.Pwy += rB*nB*uwy;
-	I.Pwz += rB*nB*uwz;
-	I.Kn += rA*nA*(unx*unx + uny*uny + unz*unz);
-	I.Kw += rB*nB*(uwx*uwx + uwy*uwy + uwz*uwz);
-
-}
-*/

analysis/GreyPhase.h

@@ -1,71 +0,0 @@
-/*
- * Sub-phase averaging tools
- */
-
-#ifndef GreyPhase_INC
-#define GreyPhase_INC
-
-#include <vector>
-#include "common/ScaLBL.h"
-#include "common/Communication.h"
-#include "analysis/analysis.h"
-#include "common/Utilities.h"
-#include "common/MPI_Helpers.h"
-#include "IO/MeshDatabase.h"
-#include "IO/Reader.h"
-#include "IO/Writer.h"
-
-class GreyPhase{
- public:
-  double p;
-  double M,Px,Py,Pz;
-  void reset(){
-    p=M=Px=Py=Pz=0.0;
-  }
-
- private:
-};
-
-class GreyPhaseAnalysis{
-public:
-	std::shared_ptr <Domain> Dm;
-	double Volume;
-	// input variables
-	double rho_n, rho_w;
-	double nu_n, nu_w;
-	double gamma_wn, beta;
-	double Fx, Fy, Fz;
-    double grey_porosity;
-	// outputs
-	double saturation,water_flow_rate, oil_flow_rate;
-
-	//simulation outputs (averaged values)
-	GreyPhase Water, Oil;
-	GreyPhase Water_local, Oil_local;
-	//...........................................................................
-    int Nx,Ny,Nz;
-	//IntArray PhaseID;		// Phase ID array 
-	DoubleArray SDs;		// contains porosity map 
-	DoubleArray Porosity;		// contains porosity map 
-	DoubleArray Rho_n;	// density field 
-	DoubleArray Rho_w;	// density field 
-	//DoubleArray Phi;		// phase indicator field
-	//DoubleArray DelPhi;		// Magnitude of Gradient of the phase indicator field
-	DoubleArray Pressure; 	// pressure field
-	DoubleArray Vel_x;		// velocity field
-	DoubleArray Vel_y;
-	DoubleArray Vel_z;
-
-	GreyPhaseAnalysis(std::shared_ptr <Domain> Dm);
-	~GreyPhaseAnalysis();
-	
-	void SetParams(double rhoA, double rhoB, double tauA, double tauB, double force_x, double force_y, double force_z, double alpha, double beta, double GreyPorosity);
-	void Basic();
-	void Write(int time);
-
-private:
-	FILE *TIMELOG;
-};
-
-#endif
-

analysis/Minkowski.cpp

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify
@@ -107,21 +106,7 @@ void Minkowski::ComputeScalar(const DoubleArray& Field, const double isovalue)
 					Xi -= 0.5;
 				}
 				// Euler characteristic -- each vertex shared by four cubes
-				//Xi += 0.25*double(object.VertexCount);
-				// check if vertices are at corners
-				for (int idx=0; idx<object.VertexCount; idx++){
-				  /*auto P1 = object.vertex.coords(idx);
-					if ( remainder(P1.x,1.0)==0.0 && remainder(P1.y,1.0)==0.0  && remainder(P1.z,1.0)==0.0 ){
-					  Xi += 0.125;
-					}
-					else
-				  */
-					Xi += 0.25;
-				}
-				/*double nside_extern = double(npts);
-				double nside_intern = double(npts)-3.0;
-				EulerChar=0.0;
-				if (npts > 0)	EulerChar = (0.25*nvert - nside_intern - 0.5*nside_extern + nface); */
+				Xi += 0.25*double(object.VertexCount);
 			}
 		}
 	}
@@ -158,7 +143,7 @@ void Minkowski::MeasureObject(){
 	 *    0 - labels the object
 	 *    1 - labels the rest of the 
 	 */
-        //DoubleArray smooth_distance(Nx,Ny,Nz);
+
 	for (int k=0; k<Nz; k++){
 		for (int j=0; j<Ny; j++){
 			for (int i=0; i<Nx; i++){
@@ -167,44 +152,6 @@ void Minkowski::MeasureObject(){
 		}
 	}	
 	CalcDist(distance,id,*Dm);
-	//Mean3D(distance,smooth_distance);
-	//Eikonal(distance, id, *Dm, 20, {true, true, true});
-	ComputeScalar(distance,0.0);
-}
-
-
-void Minkowski::MeasureObject(double factor, const DoubleArray &Phi){
-	/*
-	 *  compute the distance to an object 
-	 * 
-	 * THIS ALGORITHM ASSUMES THAT id() is populated with phase id to distinguish objects
-	 *    0 - labels the object
-	 *    1 - labels the rest of the 
-	 */
-	for (int k=0; k<Nz; k++){
-		for (int j=0; j<Ny; j++){
-			for (int i=0; i<Nx; i++){
-				distance(i,j,k) =2.0*double(id(i,j,k))-1.0;
-			}
-		}
-	}	
-	CalcDist(distance,id,*Dm);
-	
-	for (int k=0; k<Nz; k++){
-		for (int j=0; j<Ny; j++){
-			for (int i=0; i<Nx; i++){
-				double value = Phi(i,j,k);
-				double dist_value = distance(i,j,k);
-				if (dist_value < 2.5 &&  dist_value > -2.5) {
-					double new_distance = factor*log((1.0+value)/(1.0-value));
-					if (dist_value*new_distance < 0.0 )
-						new_distance = (-1.0)*new_distance;
-					distance(i,j,k) = new_distance;					
-				}
-			}
-		}
-	}
-	
 	ComputeScalar(distance,0.0);
 
 }
@@ -254,50 +201,6 @@ int Minkowski::MeasureConnectedPathway(){
 	return n_connected_components; 
 }
 
-int Minkowski::MeasureConnectedPathway(double factor, const DoubleArray &Phi){
-	/*
-	 * compute the connected pathway for object with LABEL in id field
-	 * compute the labels for connected components
-	 * compute the distance to the connected pathway
-	 * 
-	 * THIS ALGORITHM ASSUMES THAT id() is populated with phase id to distinguish objects
-	 */
-	
-	char LABEL = 0;
-	for (int k=0; k<Nz; k++){
-		for (int j=0; j<Ny; j++){
-			for (int i=0; i<Nx; i++){
-				if (id(i,j,k) == LABEL){
-					distance(i,j,k) = 1.0;
-				}
-				else
-					distance(i,j,k) = -1.0;
-			}
-		}
-	}
-	
-	// Extract only the connected part of NWP
-	double vF=0.0; 
-	n_connected_components = ComputeGlobalBlobIDs(Nx-2,Ny-2,Nz-2,Dm->rank_info,distance,distance,vF,vF,label,Dm->Comm);
-//	int n_connected_components = ComputeGlobalPhaseComponent(Nx-2,Ny-2,Nz-2,Dm->rank_info,const IntArray &PhaseID, int &VALUE, BlobIDArray &GlobalBlobID, Dm->Comm )
-	MPI_Barrier(Dm->Comm);
-	
-	for (int k=0; k<Nz; k++){
-		for (int j=0; j<Ny; j++){
-			for (int i=0; i<Nx; i++){
-				if ( label(i,j,k) == 0){
-					id(i,j,k) = 0;
-				}
-				else{
-					id(i,j,k) = 1;
-				}
-			}
-		}
-	}
-	MeasureObject(factor,Phi);
-	return n_connected_components; 
-}
-
 
 void Minkowski::PrintAll()
 {

analysis/Minkowski.h

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify
@@ -26,7 +25,6 @@
 #include "common/Communication.h"
 #include "analysis/analysis.h"
 #include "analysis/distance.h"
-#include "analysis/filters.h"
 
 #include "common/Utilities.h"
 #include "common/MPI_Helpers.h"
@@ -79,9 +77,7 @@ public:
 	Minkowski(std::shared_ptr <Domain> Dm);
 	~Minkowski();
 	void MeasureObject();
-	void MeasureObject(double factor, const DoubleArray &Phi);
 	int MeasureConnectedPathway();
-	int MeasureConnectedPathway(double factor, const DoubleArray &Phi);
 	void ComputeScalar(const DoubleArray& Field, const double isovalue);
 
 	void PrintAll();

analysis/PointList.h

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify

analysis/SubPhase.cpp

@@ -161,14 +161,15 @@ void SubPhase::Basic(){
 	// If external boundary conditions are set, do not average over the inlet
 	kmin=1; kmax=Nz-1;
 	imin=jmin=1;
-	/*// If inlet/outlet 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 && Dm->kproc() == 0) kmin += Dm->inlet_layers_z; 
 	if (Dm->outlet_layers_z > 0 && Dm->kproc() == Dm->nprocz()-1) kmax -= Dm->outlet_layers_z; 
-	*/
+	
 	nb.reset(); wb.reset();
 
+	double nA,nB;
 	double count_w = 0.0;
 	double count_n = 0.0;
 	
@@ -280,7 +281,7 @@ void SubPhase::Basic(){
 			dir_y = 0.0;
 			dir_z = 1.0;
 		}
-		if (Dm->BoundaryCondition == 1 || Dm->BoundaryCondition == 2 || Dm->BoundaryCondition == 3 || Dm->BoundaryCondition == 4 ){
+		if (Dm->BoundaryCondition > 0 ){
 			// compute the pressure drop
 			double pressure_drop = (Pressure(Nx*Ny + Nx + 1) - 1.0) / 3.0;
 			double length = ((Nz-2)*Dm->nprocz());
@@ -296,8 +297,8 @@ void SubPhase::Basic(){
 		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 total_flow_rate = water_flow_rate + not_water_flow_rate;
-		//double fractional_flow = water_flow_rate / total_flow_rate;
+		double total_flow_rate = water_flow_rate + not_water_flow_rate;
+		double fractional_flow= water_flow_rate / total_flow_rate;
 
 		double h = Dm->voxel_length;		
 		double krn = h*h*nu_n*not_water_flow_rate / force_mag ;
@@ -376,17 +377,16 @@ void SubPhase::Full(){
 
 	// If external boundary conditions are set, do not average over the inlet
 	kmin=1; kmax=Nz-1;
-	/*if (Dm->BoundaryCondition > 0 && Dm->BoundaryCondition != 5 && Dm->kproc() == 0) kmin=4;
-	if (Dm->BoundaryCondition > 0 && Dm->BoundaryCondition != 5 && Dm->kproc() == Dm->nprocz()-1) kmax=Nz-4;
-	*/
+	if (Dm->BoundaryCondition > 0 && Dm->kproc() == 0) kmin=4;
+	if (Dm->BoundaryCondition > 0 && Dm->kproc() == Dm->nprocz()-1) kmax=Nz-4;
+
 	imin=jmin=1;
-	/*// If inlet layers exist use these as default
-	 * NOTE -- excluding inlet / outlet will screw up topological averages!!!
+	// If inlet 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 && Dm->kproc() == 0) kmin += Dm->inlet_layers_z; 
 	if (Dm->outlet_layers_z > 0 && Dm->kproc() == Dm->nprocz()-1) kmax -= Dm->outlet_layers_z; 
-	*/
+		
 	nd.reset();	nc.reset(); wd.reset();	wc.reset();	iwn.reset();	iwnc.reset();
 
  	Dm->CommunicateMeshHalo(Phi);
@@ -427,13 +427,13 @@ void SubPhase::Full(){
 		}
 	}
 	// measure the whole object
-	morph_n->MeasureObject();//0.5/beta,Phi);
+	morph_n->MeasureObject();
 	nd.V = morph_n->V(); 
 	nd.A = morph_n->A(); 
 	nd.H = morph_n->H(); 
 	nd.X = morph_n->X(); 
 	// measure only the connected part
-	nd.Nc = morph_n->MeasureConnectedPathway();//0.5/beta,Phi);
+	nd.Nc = morph_n->MeasureConnectedPathway();
 	nc.V = morph_n->V(); 
 	nc.A = morph_n->A(); 
 	nc.H = morph_n->H(); 
@@ -475,13 +475,13 @@ void SubPhase::Full(){
 			}
 		}
 	}	
-	morph_w->MeasureObject();//-0.5/beta,Phi);
+	morph_w->MeasureObject();
 	wd.V = morph_w->V(); 
 	wd.A = morph_w->A(); 
 	wd.H = morph_w->H(); 
 	wd.X = morph_w->X(); 
 	// measure only the connected part
-	wd.Nc = morph_w->MeasureConnectedPathway();//-0.5/beta,Phi);
+	wd.Nc = morph_w->MeasureConnectedPathway();
 	wc.V = morph_w->V(); 
 	wc.A = morph_w->A(); 
 	wc.H = morph_w->H(); 
@@ -697,8 +697,7 @@ void SubPhase::Full(){
 }
 
 
-void SubPhase::AggregateLabels( const std::string& filename )
-{
+void SubPhase::AggregateLabels(char *FILENAME){
 	
 	int nx = Dm->Nx;
 	int ny = Dm->Ny;
@@ -722,7 +721,7 @@ void SubPhase::AggregateLabels( const std::string& filename )
 	}
 	MPI_Barrier(Dm->Comm);
 
-	Dm->AggregateLabels( filename );
+	Dm->AggregateLabels(FILENAME);
 
 }
 

analysis/SubPhase.h

@@ -101,7 +101,7 @@ public:
 	void Basic();
 	void Full();
 	void Write(int time);
-    void AggregateLabels( const std::string& filename );
+    void AggregateLabels(char *FILENAME);
 
 private:
 	FILE *TIMELOG;

analysis/TwoPhase.cpp

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify
@@ -16,7 +15,6 @@
 */
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify
@@ -236,7 +234,6 @@ TwoPhase::~TwoPhase()
 
 void TwoPhase::ColorToSignedDistance(double Beta, DoubleArray &ColorData, DoubleArray &DistData)
 {
-    NULL_USE( Beta );
   /*double factor,temp,value;
 		factor=0.5/Beta;
 	// Initialize to -1,1 (segmentation)
@@ -660,8 +657,8 @@ void TwoPhase::ComputeLocal()
 
 void TwoPhase::AssignComponentLabels()
 {
-	//int LabelNWP=1;
-	//int LabelWP=2;
+	int LabelNWP=1;
+	int LabelWP=2;
 	// NOTE: labeling the wetting phase components is tricky! One sandstone media had over 800,000 components
 	// NumberComponents_WP = ComputeGlobalPhaseComponent(Dm->Nx-2,Dm->Ny-2,Dm->Nz-2,Dm->rank_info,PhaseID,LabelWP,Label_WP);
 	// treat all wetting phase is connected
@@ -1205,8 +1202,6 @@ void TwoPhase::Reduce()
 
 void TwoPhase::NonDimensionalize(double D, double viscosity, double IFT)
 {
-    NULL_USE( viscosity );
-    NULL_USE( IFT );
 	awn_global *= D;
 	ans_global *= D;
 	ans_global *= D;

analysis/TwoPhase.h

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify

analysis/analysis.cpp

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify

analysis/analysis.h

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify

analysis/dcel.cpp

@@ -1,5 +1,7 @@
 #include "analysis/dcel.h"
 
+
+
 DECL::DECL(){
 }
 
@@ -13,25 +15,6 @@ int DECL::Face(int index){
 	return FaceData[index];
 }
 
-void DECL::Write(){
-	int e1,e2,e3;
-	FILE *TRIANGLES;
-	TRIANGLES = fopen("triangles.stl","w");
-	fprintf(TRIANGLES,"solid \n");
-	for (int idx=0; idx<TriangleCount; idx++){
-		e1 = Face(idx); 
-		e2 = halfedge.next(e1);
-		e3 = halfedge.next(e2);
-		auto P1 = vertex.coords(halfedge.v1(e1));
-		auto P2 = vertex.coords(halfedge.v1(e2));
-		auto P3 = vertex.coords(halfedge.v1(e3));
-		fprintf(TRIANGLES,"vertex %f %f %f\n",P1.x,P1.y,P1.z);
-		fprintf(TRIANGLES,"vertex %f %f %f\n",P2.x,P2.y,P2.z);
-		fprintf(TRIANGLES,"vertex %f %f %f\n",P3.x,P3.y,P3.z);
-	}
-	fclose(TRIANGLES);
-}
-
 void DECL::LocalIsosurface(const DoubleArray& A, double value, const int i, const int j, const int k){
 	Point P,Q;
 	Point PlaceHolder;
@@ -367,43 +350,241 @@ double DECL::EdgeAngle(int edge)
 	return angle;
 }
 
-void iso_surface(const Array<double>&Field, const double isovalue)
+void Isosurface(DoubleArray &A, const double &v)
 {
-  DECL object;
-  int e1,e2,e3;
-  FILE *TRIANGLES;
-  TRIANGLES = fopen("isosurface.stl","w");
-  fprintf(TRIANGLES,"solid isosurface\n");
-  int Nx = Field.size(0);
-  int Ny = Field.size(1);
-  int Nz = Field.size(2);
-  for (int k=1; k<Nz-1; k++){
-    for (int j=1; j<Ny-1; j++){
-      for (int i=1; i<Nx-1; i++){
-        object.LocalIsosurface(Field,isovalue,i,j,k);
-        for (int idx=0; idx<object.TriangleCount; idx++){
-          e1 = object.Face(idx);
-          e2 = object.halfedge.next(e1);
-          e3 = object.halfedge.next(e2);
-          auto P1 = object.vertex.coords(object.halfedge.v1(e1));
-          auto P2 = object.vertex.coords(object.halfedge.v1(e2));
-          auto P3 = object.vertex.coords(object.halfedge.v1(e3));
-	  auto Normal  = object.TriNormal(e1);
-	  // P1.x += 1.0*i; P1.y += 1.0*j; P1.z +=1.0*k;
-          //P2.x += 1.0*i; P2.y += 1.0*j; P2.z +=1.0*k;
-          //P3.x += 1.0*i; P3.y += 1.0*j; P3.z +=1.0*k;
-          fprintf(TRIANGLES,"facet normal %f %f %f\n",Normal.x,Normal.y,Normal.z);
-	  fprintf(TRIANGLES,"   outer loop\n");
-	  fprintf(TRIANGLES,"      vertex %f %f %f\n",P1.x,P1.y,P1.z);
-          fprintf(TRIANGLES,"      vertex %f %f %f\n",P2.x,P2.y,P2.z);
-          fprintf(TRIANGLES,"      vertex %f %f %f\n",P3.x,P3.y,P3.z);
-	  fprintf(TRIANGLES,"   endloop\n");
-	  fprintf(TRIANGLES,"endfacet\n");
+	Point P,Q;
+	Point PlaceHolder;
+	Point C0,C1,C2,C3,C4,C5,C6,C7;
+
+	int TriangleCount;
+	int VertexCount;
+	int CubeIndex;
+
+	Point VertexList[12];
+	Point NewVertexList[12];
+	int LocalRemap[12];
+
+	Point cellvertices[20];
+    std::array<std::array<int,3>,20> Triangles;
+    Triangles.fill( { 0 } );
+
+	// Values from array 'A' at the cube corners
+	double CubeValues[8];
+
+	int Nx = A.size(0);
+	int Ny = A.size(1);
+	int Nz = A.size(2);
+
+	// Points corresponding to cube corners
+	C0.x = 0.0; C0.y = 0.0; C0.z = 0.0;
+	C1.x = 1.0; C1.y = 0.0; C1.z = 0.0;
+	C2.x = 1.0; C2.y = 1.0; C2.z = 0.0;
+	C3.x = 0.0; C3.y = 1.0; C3.z = 0.0;
+	C4.x = 0.0; C4.y = 0.0; C4.z = 1.0;
+	C5.x = 1.0; C5.y = 0.0; C5.z = 1.0;
+	C6.x = 1.0; C6.y = 1.0; C6.z = 1.0;
+	C7.x = 0.0; C7.y = 1.0; C7.z = 1.0;							
+
+	std::vector<std::array<int,6>> HalfEdge;
+	for (int k=1; k<Nz-1; k++){		
+		for (int j=1; j<Ny-1; j++){
+			for (int i=1; i<Nx-1; i++){
+				// Set the corner values for this cube
+				CubeValues[0] = A(i,j,k);
+				CubeValues[1] = A(i+1,j,k);
+				CubeValues[2] = A(i+1,j+1,k);
+				CubeValues[3] = A(i,j+1,k);
+				CubeValues[4] = A(i,j,k+1);
+				CubeValues[5] = A(i+1,j,k+1);
+				CubeValues[6] = A(i+1,j+1,k+1);
+				CubeValues[7] = A(i,j+1,k+1);
+
+				//Determine the index into the edge table which
+				//tells us which vertices are inside of the surface
+				CubeIndex = 0;
+				if (CubeValues[0] < 0.0f) CubeIndex |= 1;
+				if (CubeValues[1] < 0.0f) CubeIndex |= 2;
+				if (CubeValues[2] < 0.0f) CubeIndex |= 4;
+				if (CubeValues[3] < 0.0f) CubeIndex |= 8;
+				if (CubeValues[4] < 0.0f) CubeIndex |= 16;
+				if (CubeValues[5] < 0.0f) CubeIndex |= 32;
+				if (CubeValues[6] < 0.0f) CubeIndex |= 64;
+				if (CubeValues[7] < 0.0f) CubeIndex |= 128;
+
+				//Find the vertices where the surface intersects the cube
+				if (edgeTable[CubeIndex] & 1){
+					P = VertexInterp(C0,C1,CubeValues[0],CubeValues[1]);
+					VertexList[0] = P;
+					Q = C0;
+				}
+				if (edgeTable[CubeIndex] & 2){
+					P = VertexInterp(C1,C2,CubeValues[1],CubeValues[2]);
+					VertexList[1] = P;
+					Q = C1;
+				}
+				if (edgeTable[CubeIndex] & 4){
+					P = VertexInterp(C2,C3,CubeValues[2],CubeValues[3]);
+					VertexList[2] =	P;
+					Q = C2;
+				}
+				if (edgeTable[CubeIndex] & 8){
+					P = VertexInterp(C3,C0,CubeValues[3],CubeValues[0]);
+					VertexList[3] =	P;
+					Q = C3;
+				}
+				if (edgeTable[CubeIndex] & 16){
+					P = VertexInterp(C4,C5,CubeValues[4],CubeValues[5]);
+					VertexList[4] =	P;
+					Q = C4;
+				}
+				if (edgeTable[CubeIndex] & 32){
+					P = VertexInterp(C5,C6,CubeValues[5],CubeValues[6]);
+					VertexList[5] = P;
+					Q = C5;
+				}
+				if (edgeTable[CubeIndex] & 64){ 
+					P = VertexInterp(C6,C7,CubeValues[6],CubeValues[7]);
+					VertexList[6] = P;
+					Q = C6;
+				}
+				if (edgeTable[CubeIndex] & 128){
+					P = VertexInterp(C7,C4,CubeValues[7],CubeValues[4]);
+					VertexList[7] =	P;
+					Q = C7;
+				}
+				if (edgeTable[CubeIndex] & 256){
+					P = VertexInterp(C0,C4,CubeValues[0],CubeValues[4]);
+					VertexList[8] =	P;
+					Q = C0;
+				}
+				if (edgeTable[CubeIndex] & 512){
+					P = VertexInterp(C1,C5,CubeValues[1],CubeValues[5]);
+					VertexList[9] =	P;
+					Q = C1;
+				}
+				if (edgeTable[CubeIndex] & 1024){
+					P = VertexInterp(C2,C6,CubeValues[2],CubeValues[6]);
+					VertexList[10] = P;
+					Q = C2;
+				}
+				if (edgeTable[CubeIndex] & 2048){
+					P = VertexInterp(C3,C7,CubeValues[3],CubeValues[7]);
+					VertexList[11] = P;
+					Q = C3;
+				}
+
+				VertexCount=0;
+				for (int idx=0;idx<12;idx++)
+					LocalRemap[idx] = -1;
+
+				for (int idx=0;triTable[CubeIndex][idx]!=-1;idx++)
+				{
+					if(LocalRemap[triTable[CubeIndex][idx]] == -1)
+					{
+						NewVertexList[VertexCount] = VertexList[triTable[CubeIndex][idx]];
+						LocalRemap[triTable[CubeIndex][idx]] = VertexCount;
+						VertexCount++;
+					}
+				}
+
+				for (int idx=0;idx<VertexCount;idx++) {
+					P = NewVertexList[idx];
+					//P.x  += i;
+					//P.y  += j;
+					//P.z  += k;
+					cellvertices[idx] = P;
+				}
+
+				TriangleCount = 0;
+				for (int idx=0;triTable[CubeIndex][idx]!=-1;idx+=3) {
+					Triangles[TriangleCount][0] = LocalRemap[triTable[CubeIndex][idx+0]];
+					Triangles[TriangleCount][1] = LocalRemap[triTable[CubeIndex][idx+1]];
+					Triangles[TriangleCount][2] = LocalRemap[triTable[CubeIndex][idx+2]];
+					TriangleCount++;
+				}
+				int nTris = TriangleCount;
+
+				// Now add the local values to the DECL data structure
+				HalfEdge.resize(nTris*3);
+				int idx_edge=0;
+				for (int idx=0; idx<TriangleCount; idx++){
+					int V1 = Triangles[idx][0];
+					int V2 = Triangles[idx][1];
+					int V3 = Triangles[idx][2];
+					// first edge: V1->V2 
+					HalfEdge[idx_edge][0] = V1;  // first vertex
+					HalfEdge[idx_edge][1] = V2;  // second vertex
+					HalfEdge[idx_edge][2] = idx; // triangle
+					HalfEdge[idx_edge][3] = -1;  // twin
+					HalfEdge[idx_edge][4] = idx_edge+2;  // previous edge
+					HalfEdge[idx_edge][5] = idx_edge+1;  // next edge
+					idx_edge++;
+					// second edge: V2->V3
+					HalfEdge[idx_edge][0] = V2;  // first vertex
+					HalfEdge[idx_edge][1] = V3;  // second vertex
+					HalfEdge[idx_edge][2] = idx; // triangle
+					HalfEdge[idx_edge][3] = -1;  // twin
+					HalfEdge[idx_edge][4] = idx_edge-1;  // previous edge
+					HalfEdge[idx_edge][5] = idx_edge+1;  // next edge
+					idx_edge++;
+					// third edge: V3->V1
+					HalfEdge[idx_edge][0] = V3;  // first vertex
+					HalfEdge[idx_edge][1] = V1;  // second vertex
+					HalfEdge[idx_edge][2] = idx; // triangle
+					HalfEdge[idx_edge][3] = -1;  // twin
+					HalfEdge[idx_edge][4] = idx_edge-1;  // previous edge
+					HalfEdge[idx_edge][5] = idx_edge-2;  // next edge
+					idx_edge++;
+				}
+				int EdgeCount=idx_edge;
+				for (int idx=0; idx<EdgeCount; idx++){
+					int V1=HalfEdge[idx][0];
+					int V2=HalfEdge[idx][1];
+					// Find all the twins within the cube
+					for (int jdx=0; idx<EdgeCount; jdx++){
+						if (HalfEdge[jdx][1] == V1 && HalfEdge[jdx][0] == V2){
+							// this is the pair
+							HalfEdge[idx][3] = jdx;
+							HalfEdge[jdx][3] = idx;
+						}
+						if (HalfEdge[jdx][1] == V2 && HalfEdge[jdx][0] == V1 && !(idx==jdx)){
+							std::printf("WARNING: half edges with identical orientation! \n");
+						}
+					}	
+					// Use "ghost" twins if edge is on a cube face
+					P = cellvertices[V1];
+					Q = cellvertices[V2];
+					if (P.x == 0.0 && Q.x == 0.0) HalfEdge[idx_edge][3] = -1;  // ghost twin for x=0 face
+					if (P.x == 1.0 && Q.x == 1.0) HalfEdge[idx_edge][3] = -2;  // ghost twin for x=1 face
+					if (P.y == 0.0 && Q.y == 0.0) HalfEdge[idx_edge][3] = -3;  // ghost twin for y=0 face
+					if (P.y == 1.0 && Q.y == 1.0) HalfEdge[idx_edge][3] = -4;  // ghost twin for y=1 face
+					if (P.z == 0.0 && Q.z == 0.0) HalfEdge[idx_edge][3] = -5;  // ghost twin for z=0 face
+					if (P.z == 1.0 && Q.z == 1.0) HalfEdge[idx_edge][3] = -6;  // ghost twin for z=1 face
+				}
+				// Find all the angles
+				for (int idx=0; idx<EdgeCount; idx++){
+					int V1=HalfEdge[idx][0];
+					int V2=HalfEdge[idx][1];
+					int T1= HalfEdge[idx_edge][2];
+					int twin=HalfEdge[idx_edge][3];
+					if (twin == -1){
+						
+					}
+				}
+
+				// Map vertices to global coordinates
+				for (int idx=0;idx<VertexCount;idx++) {
+					P = cellvertices[idx];
+					P.x  += i;
+					P.y  += j;
+					P.z  += k;
+					cellvertices[idx] = P;
+				}
+			}
+		}
+	}
 
-        }
-      }
-    }
-  }
-  fprintf(TRIANGLES,"endsolid isosurface\n");
-  fclose(TRIANGLES);
 }
+
+
+

analysis/dcel.h

@@ -1,6 +1,3 @@
-#ifndef DCEL_INC
-#define DCEL_INC
-
 #include <vector>
 #include "analysis/pmmc.h"
 
@@ -70,7 +67,6 @@ public:
 	Vertex vertex;
 	Halfedge halfedge;
 	void LocalIsosurface(const DoubleArray& A, double value, int i, int j, int k);
-	void Write();
 	int Face(int index);
 	
 	double origin(int edge);
@@ -82,7 +78,3 @@ public:
 private:
 	std::vector<int> FaceData;
 };
-
-void iso_surface(const Array<double>&Field, const double isovalue);
-
-#endif

analysis/distance.cpp

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify
@@ -198,148 +197,6 @@ void CalcVecDist( Array<Vec> &d, const Array<int> &ID0, const Domain &Dm,
     }
 }
 
-double Eikonal(DoubleArray &Distance, const Array<char> &ID, Domain &Dm, int timesteps, const std::array<bool,3>& periodic){
-
-  /*
-   * This routine converts the data in the Distance array to a signed distance
-   * by solving the equation df/dt = sign(1-|grad f|), where Distance provides
-   * the values of f on the mesh associated with domain Dm
-   * It has been tested with segmented data initialized to values [-1,1]
-   * and will converge toward the signed distance to the surface bounding the associated phases
-   *
-   * Reference:
-   * Min C (2010) On reinitializing level set functions, Journal of Computational Physics229
-   */
-
-  int i,j,k;
-  double dt=0.1;
-  double Dx,Dy,Dz;
-  double Dxp,Dxm,Dyp,Dym,Dzp,Dzm;
-  double Dxxp,Dxxm,Dyyp,Dyym,Dzzp,Dzzm;
-  double sign,norm;
-  double LocalVar,GlobalVar,LocalMax,GlobalMax;
-
-  int xdim,ydim,zdim;
-  xdim=Dm.Nx-2;
-  ydim=Dm.Ny-2;
-  zdim=Dm.Nz-2;
-  //fillHalo<double> fillData(Dm.Comm, Dm.rank_info,xdim,ydim,zdim,1,1,1,0,1);
-  fillHalo<double> fillData(  Dm.Comm, Dm.rank_info, {xdim, ydim, zdim}, {1,1,1}, 50, 1, {true,true,true}, periodic );
-
-  // Arrays to store the second derivatives
-  DoubleArray Dxx(Dm.Nx,Dm.Ny,Dm.Nz);
-  DoubleArray Dyy(Dm.Nx,Dm.Ny,Dm.Nz);
-  DoubleArray Dzz(Dm.Nx,Dm.Ny,Dm.Nz);
-
-  int count = 0;
-  while (count < timesteps){
-
-    // Communicate the halo of values
-    fillData.fill(Distance);
-
-    // Compute second order derivatives
-    for (k=1;k<Dm.Nz-1;k++){
-      for (j=1;j<Dm.Ny-1;j++){
-	for (i=1;i<Dm.Nx-1;i++){
-	  Dxx(i,j,k) = Distance(i+1,j,k) + Distance(i-1,j,k) - 2*Distance(i,j,k);
-	  Dyy(i,j,k) = Distance(i,j+1,k) + Distance(i,j-1,k) - 2*Distance(i,j,k);
-	  Dzz(i,j,k) = Distance(i,j,k+1) + Distance(i,j,k-1) - 2*Distance(i,j,k);
-	}
-      }
-    }
-    fillData.fill(Dxx);
-    fillData.fill(Dyy);
-    fillData.fill(Dzz);
-
-    LocalMax=LocalVar=0.0;
-    // Execute the next timestep
-    for (k=1;k<Dm.Nz-1;k++){
-      for (j=1;j<Dm.Ny-1;j++){
-	for (i=1;i<Dm.Nx-1;i++){
-
-	  int n = k*Dm.Nx*Dm.Ny + j*Dm.Nx + i;
-
-	  sign = -1;
-	  if (ID(i,j,k) == 1) sign = 1;
-
-	  // local second derivative terms
-	  Dxxp = minmod(Dxx(i,j,k),Dxx(i+1,j,k));
-	  Dyyp = minmod(Dyy(i,j,k),Dyy(i,j+1,k));
-	  Dzzp = minmod(Dzz(i,j,k),Dzz(i,j,k+1));
-	  Dxxm = minmod(Dxx(i,j,k),Dxx(i-1,j,k));
-	  Dyym = minmod(Dyy(i,j,k),Dyy(i,j-1,k));
-	  Dzzm = minmod(Dzz(i,j,k),Dzz(i,j,k-1));
-
-	  /* //............Compute upwind derivatives ...................
-                    Dxp = Distance(i+1,j,k) - Distance(i,j,k) + 0.5*Dxxp;
-                    Dyp = Distance(i,j+1,k) - Distance(i,j,k) + 0.5*Dyyp;
-                    Dzp = Distance(i,j,k+1) - Distance(i,j,k) + 0.5*Dzzp;
-                    Dxm = Distance(i,j,k) - Distance(i-1,j,k) + 0.5*Dxxm;
-                    Dym = Distance(i,j,k) - Distance(i,j-1,k) + 0.5*Dyym;
-                    Dzm = Distance(i,j,k) - Distance(i,j,k-1) + 0.5*Dzzm;
-	  */
-	  Dxp = Distance(i+1,j,k)- Distance(i,j,k) - 0.5*Dxxp;
-	  Dyp = Distance(i,j+1,k)- Distance(i,j,k) - 0.5*Dyyp;
-	  Dzp = Distance(i,j,k+1)- Distance(i,j,k) - 0.5*Dzzp;
-
-	  Dxm = Distance(i,j,k) - Distance(i-1,j,k) + 0.5*Dxxm;
-	  Dym = Distance(i,j,k) - Distance(i,j-1,k) + 0.5*Dyym;
-	  Dzm = Distance(i,j,k) - Distance(i,j,k-1) + 0.5*Dzzm;
-
-	  // Compute upwind derivatives for Godunov Hamiltonian
-	  if (sign < 0.0){
-	    if (Dxp + Dxm > 0.f)  Dx = Dxp*Dxp;
-	    else Dx = Dxm*Dxm;
-
-	    if (Dyp + Dym > 0.f)  Dy = Dyp*Dyp;
-	    else Dy = Dym*Dym;
-
-	    if (Dzp + Dzm > 0.f)  Dz = Dzp*Dzp;
-	    else Dz = Dzm*Dzm;
-	  }
-	  else{
-
-	    if (Dxp + Dxm < 0.f)  Dx = Dxp*Dxp;
-	    else Dx = Dxm*Dxm;
-
-	    if (Dyp + Dym < 0.f)  Dy = Dyp*Dyp;
-	    else Dy = Dym*Dym;
-
-	    if (Dzp + Dzm < 0.f)  Dz = Dzp*Dzp;
-	    else Dz = Dzm*Dzm;
-	  }
-
-	  //Dx = max(Dxp*Dxp,Dxm*Dxm);
-	  //Dy = max(Dyp*Dyp,Dym*Dym);
-	  //Dz = max(Dzp*Dzp,Dzm*Dzm);
-
-	  norm=sqrt(Dx + Dy + Dz);
-	  if (norm > 1.0) norm=1.0;
-
-	  Distance(i,j,k) += dt*sign*(1.0 - norm);
-	  LocalVar +=  dt*sign*(1.0 - norm);
-
-	  if (fabs(dt*sign*(1.0 - norm)) > LocalMax)
-	    LocalMax = fabs(dt*sign*(1.0 - norm));
-	}
-      }
-    }
-
-    MPI_Allreduce(&LocalVar,&GlobalVar,1,MPI_DOUBLE,MPI_SUM,Dm.Comm);
-    MPI_Allreduce(&LocalMax,&GlobalMax,1,MPI_DOUBLE,MPI_MAX,Dm.Comm);
-    GlobalVar /= Dm.Volume;
-    count++;
-
-    if (count%50 == 0 && Dm.rank()==0 )
-      printf("Time=%i, Max variation=%f, Global variation=%f \n",count,GlobalMax,GlobalVar);
-
-    if (fabs(GlobalMax) < 1e-5){
-      if (Dm.rank()==0) printf("Exiting with max tolerance of 1e-5 \n");
-      count=timesteps;
-    }
-  }
-  return GlobalVar;
-}
 
 // Explicit instantiations
 template void CalcDist<float>( Array<float>&, const Array<char>&, const Domain&, const std::array<bool,3>&, const std::array<double,3>& );

analysis/distance.h

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify
@@ -32,16 +31,6 @@ struct Vec {
 };
 inline bool operator<(const Vec& l, const Vec& r){ return l.x*l.x+l.y*l.y+l.z*l.z < r.x*r.x+r.y*r.y+r.z*r.z; }
 
-inline double minmod(double &a, double &b){
-
-  double value;
-
-  value = a;
-  if ( a*b < 0.0)    value=0.0;
-  else if (fabs(a) > fabs(b)) value = b;
-
-  return value;
-}
 
 /*!
  * @brief  Calculate the distance using a simple method
@@ -66,16 +55,4 @@ void CalcDist( Array<TYPE> &Distance, const Array<char> &ID, const Domain &Dm,
 void CalcVecDist( Array<Vec> &Distance, const Array<int> &ID, const Domain &Dm,
     const std::array<bool,3>& periodic = {true,true,true}, const std::array<double,3>& dx = {1,1,1} );
 
-
-/*!
- * @brief  Calculate the distance based on solution of Eikonal equation
- * @details  This routine calculates the signed distance to the nearest domain surface.
- * @param[out] Distance     Distance function
- * @param[in] ID            Domain id
- * @param[in] Dm            Domain information
- * @param[in] timesteps      number of timesteps to run for Eikonal solver
- * @param[in] periodic      Directions that are periodic 
- */
-double Eikonal(DoubleArray &Distance,  const Array<char> &ID, Domain &Dm, int timesteps, const std::array<bool,3>& periodic);
-
 #endif

analysis/filters.cpp

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify
@@ -18,33 +17,6 @@
 #include "math.h"
 #include "ProfilerApp.h"
 
-void Mean3D( const Array<double> &Input, Array<double> &Output )
-{
-	PROFILE_START("Mean3D");
-	// Perform a 3D Mean filter on Input array
-	int i,j,k;
-
-	int Nx = int(Input.size(0));
-	int Ny = int(Input.size(1));
-	int Nz = int(Input.size(2));
-
-	for (k=1; k<Nz-1; k++){
-		for (j=1; j<Ny-1; j++){
-			for (i=1; i<Nx-1; i++){
-			  double MeanValue = Input(i,j,k);
-			  // next neighbors
-			  MeanValue += Input(i+1,j,k)+Input(i,j+1,k)+Input(i,j,k+1)+Input(i-1,j,k)+Input(i,j-1,k)+Input(i,j,k-1);
-			  MeanValue += Input(i+1,j+1,k)+Input(i-1,j+1,k)+Input(i+1,j-1,k)+Input(i-1,j-1,k);
-			  MeanValue += Input(i+1,j,k+1)+Input(i-1,j,k+1)+Input(i+1,j,k-1)+Input(i-1,j,k-1);
-			  MeanValue += Input(i,j+1,k+1)+Input(i,j-1,k+1)+Input(i,j+1,k-1)+Input(i,j-1,k-1);
-			  MeanValue += Input(i+1,j+1,k+1)+Input(i-1,j+1,k+1)+Input(i+1,j-1,k+1)+Input(i-1,j-1,k+1);
-			  MeanValue += Input(i+1,j+1,k-1)+Input(i-1,j+1,k-1)+Input(i+1,j-1,k-1)+Input(i-1,j-1,k-1);
-			  Output(i,j,k) = MeanValue/27.0;
-			}
-		}
-	}
-	PROFILE_STOP("Mean3D");
-}
 
 void Med3D( const Array<float> &Input, Array<float> &Output )
 {

analysis/filters.h

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify
@@ -20,13 +19,6 @@
 
 #include "common/Array.h"
 
-/*!
- * @brief  Filter image
- * @details  This routine performs a mean filter
- * @param[in] Input     Input image
- * @param[out] Output   Output image
- */
-void Mean3D( const Array<double> &Input, Array<double> &Output );
 
 /*!
  * @brief  Filter image
@@ -36,6 +28,7 @@ void Mean3D( const Array<double> &Input, Array<double> &Output );
  */
 void Med3D( const Array<float> &Input, Array<float> &Output );
 
+
 /*!
  * @brief  Filter image
  * @details  This routine performs a non-linear local means filter

analysis/histogram.h

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify

analysis/imfilter.h

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify

analysis/imfilter.hpp

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify
@@ -16,7 +15,6 @@
 */
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify

analysis/morphology.cpp

@@ -34,6 +34,9 @@ double MorphOpen(DoubleArray &SignDist, signed char *id, std::shared_ptr<Domain>
 	int nx = Dm->Nx;
 	int ny = Dm->Ny;
 	int nz = Dm->Nz;
+	int iproc = Dm->iproc();
+	int jproc = Dm->jproc();
+	int kproc = Dm->kproc();
 	int nprocx = Dm->nprocx();
 	int nprocy = Dm->nprocy();
 	int nprocz = Dm->nprocz();
@@ -119,6 +122,7 @@ double MorphOpen(DoubleArray &SignDist, signed char *id, std::shared_ptr<Domain>
 	int sendtag,recvtag;
 	sendtag = recvtag = 7;
 
+	int x,y,z;
 	int ii,jj,kk;
 	int Nx = nx;
 	int Ny = ny;
@@ -131,7 +135,7 @@ double MorphOpen(DoubleArray &SignDist, signed char *id, std::shared_ptr<Domain>
 
 	// Increase the critical radius until the target saturation is met
 	double deltaR=0.05; // amount to change the radius in voxel units
-	double Rcrit_old=0.0;
+	double Rcrit_old;
 
 	double GlobalNumber = 1.f;
 	int imin,jmin,kmin,imax,jmax,kmax;
@@ -332,6 +336,9 @@ double MorphDrain(DoubleArray &SignDist, signed char *id, std::shared_ptr<Domain
 	int nx = Dm->Nx;
 	int ny = Dm->Ny;
 	int nz = Dm->Nz;
+	int iproc = Dm->iproc();
+	int jproc = Dm->jproc();
+	int kproc = Dm->kproc();
 	int nprocx = Dm->nprocx();
 	int nprocy = Dm->nprocy();
 	int nprocz = Dm->nprocz();
@@ -420,6 +427,7 @@ double MorphDrain(DoubleArray &SignDist, signed char *id, std::shared_ptr<Domain
 	int sendtag,recvtag;
 	sendtag = recvtag = 7;
 
+	int x,y,z;
 	int ii,jj,kk;
 	int Nx = nx;
 	int Ny = ny;
@@ -685,13 +693,19 @@ double MorphDrain(DoubleArray &SignDist, signed char *id, std::shared_ptr<Domain
 	return final_void_fraction;
 }
 
-double MorphGrow(DoubleArray &BoundaryDist, DoubleArray &Dist, Array<char> &id, std::shared_ptr<Domain> Dm, double TargetGrowth, double WallFactor)
-{
+double MorphGrow(DoubleArray &BoundaryDist, DoubleArray &Dist, Array<char> &id, std::shared_ptr<Domain> Dm, double TargetGrowth){
+	
 	int Nx = Dm->Nx;
 	int Ny = Dm->Ny;
 	int Nz = Dm->Nz;
+	int iproc = Dm->iproc();
+	int jproc = Dm->jproc();
+	int kproc = Dm->kproc();
+	int nprocx = Dm->nprocx();
+	int nprocy = Dm->nprocy();
+	int nprocz = Dm->nprocz();
 	int rank = Dm->rank();
-		
+	
 	double count=0.0;
 	for (int k=1; k<Nz-1; k++){
 		for (int j=1; j<Ny-1; j++){
@@ -722,7 +736,8 @@ double MorphGrow(DoubleArray &BoundaryDist, DoubleArray &Dist, Array<char> &id,
 			for (int j=1; j<Ny-1; j++){
 				for (int i=1; i<Nx-1; i++){
 					double walldist=BoundaryDist(i,j,k);
-					double wallweight = WallFactor/ (1+exp(-5.f*(walldist-1.f))); 
+					double wallweight = 1.0 / (1+exp(-5.f*(walldist-1.f))); 
+					//wallweight = 1.0;
 					if (fabs(wallweight*morph_delta) > MAX_DISPLACEMENT) MAX_DISPLACEMENT= fabs(wallweight*morph_delta);
 					
 					if (Dist(i,j,k) - wallweight*morph_delta < 0.0){
@@ -768,7 +783,7 @@ double MorphGrow(DoubleArray &BoundaryDist, DoubleArray &Dist, Array<char> &id,
 		for (int j=1; j<Ny-1; j++){
 			for (int i=1; i<Nx-1; i++){
 				double walldist=BoundaryDist(i,j,k);
-				double wallweight = WallFactor / (1+exp(-5.f*(walldist-1.f))); 
+				double wallweight = 1.0 / (1+exp(-5.f*(walldist-1.f))); 
 				//wallweight = 1.0;
 				Dist(i,j,k) -= wallweight*morph_delta;
 				if (Dist(i,j,k) < 0.0)	count+=1.0;

analysis/morphology.h

@@ -5,4 +5,4 @@
 
 double MorphOpen(DoubleArray &SignDist, signed char *id, std::shared_ptr<Domain> Dm, double VoidFraction, signed char ErodeLabel, signed char ReplaceLabel);
 double MorphDrain(DoubleArray &SignDist, signed char *id, std::shared_ptr<Domain> Dm, double VoidFraction);
-double MorphGrow(DoubleArray &BoundaryDist, DoubleArray &Dist, Array<char> &id, std::shared_ptr<Domain> Dm, double TargetVol, double WallFactor);
+double MorphGrow(DoubleArray &BoundaryDist, DoubleArray &Dist, Array<char> &id, std::shared_ptr<Domain> Dm, double TargetVol);

analysis/pmmc.h

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify

analysis/runAnalysis.cpp

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify
@@ -783,8 +782,6 @@ void runAnalysis::run(int timestep, std::shared_ptr<Database> input_db, TwoPhase
         double *Pressure, double *Velocity, double *fq, double *Den)
 {
     int N = d_N[0]*d_N[1]*d_N[2];
-    NULL_USE( N );
-    NULL_USE( Phi );
     
 	auto db = input_db->getDatabase( "Analysis" );
     //int timestep = db->getWithDefault<int>( "timestep", 0 );
@@ -923,12 +920,12 @@ void runAnalysis::run(int timestep, std::shared_ptr<Database> input_db, TwoPhase
     // Spawn a thread to write the restart file
     //    if ( matches(type,AnalysisType::CreateRestart) ) {
     if (timestep%d_restart_interval==0){
-    	auto Restart_db = input_db->cloneDatabase();
-	//	Restart_db->putScalar<bool>( "Restart", true );
+
     	if (d_rank==0) {
-	  //	std::ofstream OutStream("Restart.db");
-	  //	Restart_db->print(OutStream, "");
-	  //	OutStream.close();
+    		input_db->putScalar<bool>( "Restart", true );
+    		std::ofstream OutStream("Restart.db");
+    		input_db->print(OutStream, "");
+    		OutStream.close();
     	}
     	// Write the restart file (using a seperate thread)
         auto work = new WriteRestartWorkItem(d_restartFile.c_str(),cDen,cfq,d_Np);
@@ -955,6 +952,8 @@ void runAnalysis::run(int timestep, std::shared_ptr<Database> input_db, TwoPhase
  ******************************************************************/
 void runAnalysis::basic(int timestep, std::shared_ptr<Database> input_db, SubPhase &Averages, const double *Phi, double *Pressure, double *Velocity, double *fq, double *Den)
 {
+    int N = d_N[0]*d_N[1]*d_N[2];
+
     // Check which analysis steps we need to perform
 	auto color_db =  input_db->getDatabase( "Color" );
 	auto vis_db =  input_db->getDatabase( "Visualization" );
@@ -970,7 +969,7 @@ void runAnalysis::basic(int timestep, std::shared_ptr<Database> input_db, SubPha
         finish();
     }
 
-    PROFILE_START("basic");
+    PROFILE_START("run");
 
     // Copy the appropriate variables to the host (so we can spawn new threads)
     ScaLBL_DeviceBarrier();
@@ -999,6 +998,7 @@ void runAnalysis::basic(int timestep, std::shared_ptr<Database> input_db, SubPha
     }
     PROFILE_STOP("Copy data to host");
 
+    PROFILE_START("run",1);
     // Spawn threads to do the analysis work
     //if (timestep%d_restart_interval==0){
     // if ( matches(type,AnalysisType::ComputeAverages) ) {
@@ -1025,21 +1025,21 @@ void runAnalysis::basic(int timestep, std::shared_ptr<Database> input_db, SubPha
     	cfq = std::shared_ptr<double>(new double[19*d_Np],DeleteArray<double>);
     	ScaLBL_CopyToHost(cfq.get(),fq,19*d_Np*sizeof(double));
     	ScaLBL_CopyToHost(cDen.get(),Den,2*d_Np*sizeof(double));
-    	// clone the input database to avoid modifying shared data
-    	auto Restart_db = input_db->cloneDatabase();
-    	auto tmp_color_db =  Restart_db->getDatabase( "Color" );
-    	tmp_color_db->putScalar<int>("timestep",timestep);    		
-    	tmp_color_db->putScalar<bool>( "Restart", true );
-    	Restart_db->putDatabase("Color", tmp_color_db);
+
     	if (d_rank==0) {
+    		color_db->putScalar<int>("timestep",timestep);    		
+    		color_db->putScalar<bool>( "Restart", true );
+    		input_db->putDatabase("Color", color_db);
     		std::ofstream OutStream("Restart.db");
-    		Restart_db->print(OutStream, "");
+    		input_db->print(OutStream, "");
     		OutStream.close();
+  
     	}
     	// Write the restart file (using a seperate thread)
     	auto work1 = new WriteRestartWorkItem(d_restartFile.c_str(),cDen,cfq,d_Np);
     	work1->add_dependency(d_wait_restart);
     	d_wait_restart = d_tpool.add_work(work1);
+
     }
     
     if (timestep%d_visualization_interval==0){
@@ -1051,11 +1051,12 @@ void runAnalysis::basic(int timestep, std::shared_ptr<Database> input_db, SubPha
         d_wait_vis = d_tpool.add_work(work);
     }
 
-    PROFILE_STOP("basic");
+    PROFILE_STOP("run");
 }
 
 void runAnalysis::WriteVisData(int timestep, std::shared_ptr<Database> input_db, SubPhase &Averages, const double *Phi, double *Pressure, double *Velocity, double *fq, double *Den)
 {
+    int N = d_N[0]*d_N[1]*d_N[2];
 	auto color_db =  input_db->getDatabase( "Color" );
 	auto vis_db =  input_db->getDatabase( "Visualization" );
     //int timestep = color_db->getWithDefault<int>( "timestep", 0 );
@@ -1082,6 +1083,7 @@ void runAnalysis::WriteVisData(int timestep, std::shared_ptr<Database> input_db,
     d_wait_vis = d_tpool.add_work(work2);
 
     //Averages.WriteVis = false;
+   // }
     
     PROFILE_STOP("write vis");
 }

analysis/runAnalysis.h

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify

analysis/uCT.cpp

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify
@@ -173,7 +172,6 @@ void solve( const Array<float>& VOL, Array<float>& Mean, Array<char>& ID,
     //	int depth = 5;
     //	float sigsq=0.1;
 	int nlm_count = NLM3D( MultiScaleSmooth, Mean, Dist, NonLocalMean, depth, sigsq);
-    NULL_USE( nlm_count );
 	fillFloat.fill(NonLocalMean);
 }
 
@@ -218,7 +216,6 @@ void refine( const Array<float>& Dist_coarse,
 //	int depth = 3;
 //	float sigsq = 0.1;
 	int nlm_count = NLM3D( MultiScaleSmooth, Mean, Dist, NonLocalMean, depth, sigsq);
-    NULL_USE( nlm_count );
 	fillFloat.fill(NonLocalMean);
     segment( NonLocalMean, ID, 0.001 );
     for (size_t i=0; i<ID.length(); i++) {

analysis/uCT.h

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify

cmake/libraries.cmake

@@ -77,7 +77,7 @@ MACRO( CONFIGURE_MPI )
                 ENDIF ()
             ELSE ()
                 # Search for the MPI executable in the current directory
-                FIND_PROGRAM( MPIEXEC  NAMES mpiexec mpirun lamexec  PATHS ${MPI_DIRECTORY}/bin  NO_DEFAULT_PATH )
+                FIND_PROGRAM ( MPIEXEC  NAMES mpiexec mpirun lamexec  PATHS ${MPI_DIRECTORY}/bin  NO_DEFAULT_PATH )
                 IF ( NOT MPIEXEC )
                     MESSAGE( FATAL_ERROR "Could not locate mpi executable" )
                 ENDIF()
@@ -305,9 +305,4 @@ MACRO ( CONFIGURE_LBPM )
         SET( CMAKE_BUILD_WITH_INSTALL_RPATH TRUE )
         SET( CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_RPATH} "${TIMER_DIRECTORY}" "${LBPM_INSTALL_DIR}/lib" )
     ENDIF()
-    # Suppress some common warnings
-    IF ( USING_GCC )
-        SET( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-reorder -Wno-unused-parameter")
-        SET( CMAKE_CUDA_FLAGS "${CMAKE_CUDA_FLAGS} --compiler-options -Wno-reorder,-Wno-unused-parameter")
-    ENDIF()
 ENDMACRO ()

cmake/macros.cmake

@@ -848,7 +848,7 @@ FUNCTION( ADD_${PROJ}_TEST EXEFILE ${ARGN} )
     ADD_PROJ_PROVISIONAL_TEST( ${EXEFILE} )
     CREATE_TEST_NAME( ${EXEFILE} ${ARGN} )
     IF ( USE_MPI_FOR_SERIAL_TESTS )
-        ADD_TEST( NAME ${TESTNAME} COMMAND ${MPIEXEC} ${MPIFLAGS} "${MPIEXEC_NUMPROC_FLAG}" 1 $<TARGET_FILE:${LAST_TEST}> ${ARGN} )
+        ADD_TEST( NAME ${TESTNAME} COMMAND ${MPIEXEC} "${MPIEXEC_NUMPROC_FLAG}" 1 $<TARGET_FILE:${LAST_TEST}> ${ARGN} )
         SET_PROPERTY( TEST ${TESTNAME} APPEND PROPERTY ENVIRONMENT OMPI_MCA_hwloc_base_binding_policy=none )
     ELSE()
         ADD_TEST( NAME ${TESTNAME} COMMAND $<TARGET_FILE:${LAST_TEST}> ${ARGN} )
@@ -877,7 +877,7 @@ FUNCTION( ADD_${PROJ}_WEEKLY_TEST EXEFILE PROCS ${ARGN} )
     ELSEIF( ${PROCS} STREQUAL "1" )
         CREATE_TEST_NAME( "${EXEFILE}_WEEKLY" ${ARGN} )
         IF ( USE_MPI_FOR_SERIAL_TESTS )
-            ADD_TEST( NAME ${TESTNAME} COMMAND ${MPIEXEC} ${MPIFLAGS} "${MPIEXEC_NUMPROC_FLAG}" 1 $<TARGET_FILE:${LAST_TEST}> ${ARGN} )
+            ADD_TEST( NAME ${TESTNAME} COMMAND ${MPIEXEC} "${MPIEXEC_NUMPROC_FLAG}" 1 $<TARGET_FILE:${LAST_TEST}> ${ARGN} )
             SET_PROPERTY( TEST ${TESTNAME} APPEND PROPERTY ENVIRONMENT OMPI_MCA_hwloc_base_binding_policy=none )
         ELSE()
             ADD_TEST( NAME ${TESTNAME} COMMAND $<TARGET_FILE:${LAST_TEST}> ${ARGN} )
@@ -909,7 +909,7 @@ FUNCTION( ADD_${PROJ}_TEST_PARALLEL EXEFILE PROCS ${ARGN} )
     ELSEIF ( ${PROCS} GREATER ${TEST_MAX_PROCS} )
         MESSAGE("Disabling test ${TESTNAME} (exceeds maximum number of processors ${TEST_MAX_PROCS})")
     ELSE()
-        ADD_TEST( NAME ${TESTNAME} COMMAND ${MPIEXEC} ${MPIFLAGS} "${MPIEXEC_NUMPROC_FLAG}" ${PROCS} $<TARGET_FILE:${LAST_TEST}> ${ARGN} )
+        ADD_TEST( NAME ${TESTNAME} COMMAND ${MPIEXEC} "${MPIEXEC_NUMPROC_FLAG}" ${PROCS} $<TARGET_FILE:${LAST_TEST}> ${ARGN} )
         SET_PROPERTY( TEST ${TESTNAME} APPEND PROPERTY ENVIRONMENT OMPI_MCA_hwloc_base_binding_policy=none )
         SET_TESTS_PROPERTIES( ${TESTNAME} PROPERTIES FAIL_REGULAR_EXPRESSION "${TEST_FAIL_REGULAR_EXPRESSION}" PROCESSORS ${PROCS} )
         ADD_RESOURCE_LOCK( ${TESTNAME} ${EXEFILE} ${ARGN} )
@@ -930,7 +930,7 @@ MACRO( ADD_${PROJ}_TEST_THREAD_MPI EXEFILE PROCS THREADS ${ARGN} )
         SET_TESTS_PROPERTIES ( ${TESTNAME} PROPERTIES FAIL_REGULAR_EXPRESSION "${TEST_FAIL_REGULAR_EXPRESSION}" PROCESSORS ${TOT_PROCS} )
         ADD_RESOURCE_LOCK( ${TESTNAME} ${EXEFILE} ${ARGN} )
     ELSEIF ( USE_MPI OR USE_EXT_MPI )
-        ADD_TEST( NAME ${TESTNAME} COMMAND ${MPIEXEC} ${MPIFLAGS} "${MPIEXEC_NUMPROC_FLAG}" ${PROCS} $<TARGET_FILE:${LAST_TEST}> ${ARGN} )
+        ADD_TEST( NAME ${TESTNAME} COMMAND ${MPIEXEC} "${MPIEXEC_NUMPROC_FLAG}" ${PROCS} $<TARGET_FILE:${LAST_TEST}> ${ARGN} )
         SET_PROPERTY( TEST ${TESTNAME} APPEND PROPERTY ENVIRONMENT OMPI_MCA_hwloc_base_binding_policy=none )
         SET_TESTS_PROPERTIES ( ${TESTNAME} PROPERTIES FAIL_REGULAR_EXPRESSION "${TEST_FAIL_REGULAR_EXPRESSION}" PROCESSORS ${TOT_PROCS} )
         ADD_RESOURCE_LOCK( ${TESTNAME} ${EXEFILE} ${ARGN} )
@@ -966,7 +966,7 @@ FUNCTION( ADD_${PROJ}_EXAMPLE EXEFILE PROCS ${ARGN} )
         ADD_TEST( NAME ${TESTNAME} COMMAND $<TARGET_FILE:${LAST_TEST}> ${ARGN} )
     ELSEIF ( USE_EXT_MPI AND NOT (${PROCS} GREATER ${TEST_MAX_PROCS}) )
         CREATE_TEST_NAME( "example--${EXEFILE}_${PROCS}procs" ${ARGN} )
-        ADD_TEST( NAME ${TESTNAME} COMMAND ${MPIEXEC} ${MPIFLAGS} "${MPIEXEC_NUMPROC_FLAG}" ${PROCS} $<TARGET_FILE:${LAST_TEST}> ${ARGN} )
+        ADD_TEST( NAME ${TESTNAME} COMMAND ${MPIEXEC} "${MPIEXEC_NUMPROC_FLAG}" ${PROCS} $<TARGET_FILE:${LAST_TEST}> ${ARGN} )
         SET_PROPERTY( TEST ${TESTNAME} APPEND PROPERTY ENVIRONMENT OMPI_MCA_hwloc_base_binding_policy=none )
     ENDIF()
     SET_TESTS_PROPERTIES( ${TESTNAME} PROPERTIES FAIL_REGULAR_EXPRESSION "${TEST_FAIL_REGULAR_EXPRESSION}" PROCESSORS ${PROCS} )

common/Array.h

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify

common/Array.hpp

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify
@@ -16,7 +15,6 @@
 */
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify

common/Communication.cpp

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify

common/Communication.h

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify

common/Communication.hpp

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify
@@ -16,7 +15,6 @@
 */
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify
@@ -76,9 +74,9 @@ Array<TYPE> redistribute( const RankInfoStruct& src_rank, const Array<TYPE>& src
     if ( !src_data.empty() ) {
         int i1[3] = { src_size[0] * src_rank.ix, src_size[1] * src_rank.jy, src_size[2] * src_rank.kz };
         int i2[3] = { i1[0] + src_size[0] - 1, i1[1] + src_size[1] - 1, i1[2] + src_size[2] - 1 };
-        for ( int i=0; i<dst_rank.nx; i++ ) {
-            for ( int j=0; j<dst_rank.ny; j++ ) {
-                for ( int k=0; k<dst_rank.nz; k++ ) {
+        for ( size_t i=0; i<dst_rank.nx; i++ ) {
+            for ( size_t j=0; j<dst_rank.ny; j++ ) {
+                for ( size_t k=0; k<dst_rank.nz; k++ ) {
                     int j1[3] = { i * dst_size[0], j * dst_size[1], k * dst_size[2] };
                     int j2[3] = { j1[0] + dst_size[0] - 1, j1[1] + dst_size[1] - 1, j1[2] + dst_size[2] - 1 };
                     auto index = calcOverlap( i1, i2, j1, j2 );
@@ -97,9 +95,9 @@ Array<TYPE> redistribute( const RankInfoStruct& src_rank, const Array<TYPE>& src
     Array<TYPE> dst_data( dst_size[0], dst_size[1], dst_size[2] );
     int i1[3] = { dst_size[0] * dst_rank.ix, dst_size[1] * dst_rank.jy, dst_size[2] * dst_rank.kz };
     int i2[3] = { i1[0] + dst_size[0] - 1, i1[1] + dst_size[1] - 1, i1[2] + dst_size[2] - 1 };
-    for ( int i=0; i<src_rank.nx; i++ ) {
-        for ( int j=0; j<src_rank.ny; j++ ) {
-            for ( int k=0; k<src_rank.nz; k++ ) {
+    for ( size_t i=0; i<src_rank.nx; i++ ) {
+        for ( size_t j=0; j<src_rank.ny; j++ ) {
+            for ( size_t k=0; k<src_rank.nz; k++ ) {
                 int j1[3] = { i * src_size[0], j * src_size[1], k * src_size[2] };
                 int j2[3] = { j1[0] + src_size[0] - 1, j1[1] + src_size[1] - 1, j1[2] + src_size[2] - 1 };
                 auto index = calcOverlap( i1, i2, j1, j2 );

common/Database.cpp

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify

common/Database.h

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify

common/Database.hpp

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify
@@ -16,7 +15,6 @@
 */
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify

common/Domain.cpp

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify
@@ -74,9 +73,6 @@ Domain::Domain( int nx, int ny, int nz, int rnk, int npx, int npy, int npz,
 	recvData_xY(NULL), recvData_yZ(NULL), recvData_Xz(NULL), recvData_XY(NULL), recvData_YZ(NULL), recvData_XZ(NULL),
 	id(NULL)
 {	
-    NULL_USE( rnk );
-    NULL_USE( npy );
-    NULL_USE( npz );
 	// set up the neighbor ranks
     int myrank;
     MPI_Comm_rank( Comm, &myrank );
@@ -181,7 +177,6 @@ Domain::~Domain()
 	delete [] recvData_yZ;  delete [] recvData_Yz;  delete [] recvData_YZ;
 	// Free id
 	delete [] id;
- 
 	// Free the communicator
 	if ( Comm != MPI_COMM_WORLD && Comm != MPI_COMM_NULL ) {
 		MPI_Comm_free(&Comm);
@@ -249,7 +244,7 @@ void Domain::initialize( std::shared_ptr<Database> db )
 	if (rank_info.kz < nproc[2]-1) outlet_layers_z = 0;
     // Fill remaining variables
 	N = Nx*Ny*Nz;
-	Volume = nx*ny*nz*nproc[0]*nproc[1]*nproc[2]*1.0;
+	Volume = nx*ny*nx*nproc[0]*nproc[1]*nproc[2]*1.0;
 
 	if (myrank==0) printf("voxel length = %f micron \n", voxel_length);
 
@@ -261,7 +256,7 @@ void Domain::initialize( std::shared_ptr<Database> db )
 	INSIST(nprocs == nproc[0]*nproc[1]*nproc[2],"Fatal error in processor count!");
 }
 
-void Domain::Decomp( const std::string& Filename )
+void Domain::Decomp(std::string Filename)
 {
 	//.......................................................................
 	// Reading the domain information file
@@ -271,9 +266,9 @@ void Domain::Decomp( const std::string& Filename )
 	int nprocs, nprocx, nprocy, nprocz, nx, ny, nz;
 	int64_t global_Nx,global_Ny,global_Nz;
 	int64_t i,j,k,n;
+	int BC=0;
 	int64_t xStart,yStart,zStart;
 	int checkerSize;
-	bool USE_CHECKER = false;
 	//int inlet_layers_x, inlet_layers_y, inlet_layers_z;
 	//int outlet_layers_x, outlet_layers_y, outlet_layers_z;
 	xStart=yStart=zStart=0;
@@ -283,8 +278,8 @@ void Domain::Decomp( const std::string& Filename )
 	outlet_layers_x = 0;
 	outlet_layers_y = 0;
 	outlet_layers_z = 0;
-	inlet_layers_phase=1;
-	outlet_layers_phase=2;
+    inlet_layers_phase=1;
+    outlet_layers_phase=2;
 	checkerSize = 32;
 
 	// Read domain parameters
@@ -313,7 +308,6 @@ void Domain::Decomp( const std::string& Filename )
 	}
 	if (database->keyExists( "checkerSize" )){
 		checkerSize = database->getScalar<int>( "checkerSize" );
-		USE_CHECKER = true;
 	}
 	else {
 		checkerSize = SIZE[0];
@@ -352,7 +346,7 @@ void Domain::Decomp( const std::string& Filename )
 	if (RANK==0){
 		printf("Input media: %s\n",Filename.c_str());
 		printf("Relabeling %lu values\n",ReadValues.size());
-		for (size_t idx=0; idx<ReadValues.size(); idx++){
+		for (int idx=0; idx<ReadValues.size(); idx++){
 			int oldvalue=ReadValues[idx];
 			int newvalue=WriteValues[idx];
 			printf("oldvalue=%d, newvalue =%d \n",oldvalue,newvalue);
@@ -386,7 +380,7 @@ void Domain::Decomp( const std::string& Filename )
 			}
 		}
 		printf("Read segmented data from %s \n",Filename.c_str());
-
+		
 		// relabel the data
 		std::vector<long int> LabelCount(ReadValues.size(),0);
 		for (int k = 0; k<global_Nz; k++){
@@ -395,7 +389,7 @@ void Domain::Decomp( const std::string& Filename )
 					n = k*global_Nx*global_Ny+j*global_Nx+i;
 					//char locval = loc_id[n];
 					char locval = SegData[n];
-					for (size_t idx=0; idx<ReadValues.size(); idx++){
+					for (int idx=0; idx<ReadValues.size(); idx++){
 						signed char oldvalue=ReadValues[idx];
 						signed char newvalue=WriteValues[idx];
 						if (locval == oldvalue){
@@ -407,154 +401,125 @@ void Domain::Decomp( const std::string& Filename )
 				}
 			}
 		}
-		for (size_t idx=0; idx<ReadValues.size(); idx++){
-			long int label=ReadValues[idx];
-			long int count=LabelCount[idx];
-			printf("Label=%ld, Count=%ld \n",label,count);
+		if (RANK==0){
+			for (int idx=0; idx<ReadValues.size(); idx++){
+				long int label=ReadValues[idx];
+				long int count=LabelCount[idx];
+				printf("Label=%ld, Count=%ld \n",label,count);
+			}
 		}
-		if (USE_CHECKER) {
-			if (inlet_layers_x > 0){
-				// use checkerboard pattern
-				printf("Checkerboard pattern at x inlet for %i layers \n",inlet_layers_x);
-				for (int k = 0; k<global_Nz; k++){
-					for (int j = 0; j<global_Ny; j++){
-						for (int i = xStart; i < xStart+inlet_layers_x; i++){
-							if ( (j/checkerSize + k/checkerSize)%2 == 0){
-								// void checkers
-								SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 2;
-							}
-							else{
-								// solid checkers
-								SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 0;
-							}
+
+		if (inlet_layers_x > 0){
+			// use checkerboard pattern
+			printf("Checkerboard pattern at x inlet for %i layers \n",inlet_layers_x);
+			for (int k = 0; k<global_Nz; k++){
+				for (int j = 0; j<global_Ny; j++){
+					for (int i = xStart; i < xStart+inlet_layers_x; i++){
+						if ( (j/checkerSize + k/checkerSize)%2 == 0){
+							// void checkers
+							SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 2;
 						}
-					}
-				}
-			}
-
-			if (inlet_layers_y > 0){
-				printf("Checkerboard pattern at y inlet for %i layers \n",inlet_layers_y);
-				// use checkerboard pattern
-				for (int k = 0; k<global_Nz; k++){
-					for (int j = yStart; j < yStart+inlet_layers_y; j++){
-						for (int i = 0; i<global_Nx; i++){
-							if ( (i/checkerSize + k/checkerSize)%2 == 0){
-								// void checkers
-								SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 2;
-							}
-							else{
-								// solid checkers
-								SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 0;
-							}
-						}
-					}
-				}
-			}
-
-			if (inlet_layers_z > 0){
-				printf("Checkerboard pattern at z inlet for %i layers, saturated with phase label=%i \n",inlet_layers_z,inlet_layers_phase);
-				// use checkerboard pattern
-				for (int k = zStart; k < zStart+inlet_layers_z; k++){
-					for (int j = 0; j<global_Ny; j++){
-						for (int i = 0; i<global_Nx; i++){
-							if ( (i/checkerSize+j/checkerSize)%2 == 0){
-								// void checkers
-								//SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 2;
-								SegData[k*global_Nx*global_Ny+j*global_Nx+i] = inlet_layers_phase;
-							}
-							else{
-								// solid checkers
-								SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 0;
-							}
-						}
-					}
-				}
-			}
-
-			if (outlet_layers_x > 0){
-				// use checkerboard pattern
-				printf("Checkerboard pattern at x outlet for %i layers \n",outlet_layers_x);
-				for (int k = 0; k<global_Nz; k++){
-					for (int j = 0; j<global_Ny; j++){
-						for (int i = xStart + nx*nprocx - outlet_layers_x; i <  xStart + nx*nprocx; i++){
-							if ( (j/checkerSize + k/checkerSize)%2 == 0){
-								// void checkers
-								SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 2;
-							}
-							else{
-								// solid checkers
-								SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 0;
-							}
-						}
-					}
-				}
-			}
-
-			if (outlet_layers_y > 0){
-				printf("Checkerboard pattern at y outlet for %i layers \n",outlet_layers_y);
-				// use checkerboard pattern
-				for (int k = 0; k<global_Nz; k++){
-					for (int j = yStart + ny*nprocy - outlet_layers_y; j < yStart + ny*nprocy; j++){
-						for (int i = 0; i<global_Nx; i++){
-							if ( (i/checkerSize + k/checkerSize)%2 == 0){
-								// void checkers
-								SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 2;
-							}
-							else{
-								// solid checkers
-								SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 0;
-
-							}
-						}
-					}
-				}
-			}
-
-			if (outlet_layers_z > 0){
-				printf("Checkerboard pattern at z outlet for %i layers, saturated with phase label=%i \n",outlet_layers_z,outlet_layers_phase);
-				// use checkerboard pattern
-				for (int k = zStart + nz*nprocz - outlet_layers_z; k < zStart + nz*nprocz; k++){
-					for (int j = 0; j<global_Ny; j++){
-						for (int i = 0; i<global_Nx; i++){
-							if ( (i/checkerSize+j/checkerSize)%2 == 0){
-								// void checkers
-								//SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 2;
-								SegData[k*global_Nx*global_Ny+j*global_Nx+i] = outlet_layers_phase;
-							}
-							else{
-								// solid checkers
-								SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 0;
-							}
+						else{
+							// solid checkers
+							SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 0;
 						}
 					}
 				}
 			}
 		}
-		else {
-			if (inlet_layers_z > 0){
-				printf("Mixed reflection pattern at z inlet for %i layers, saturated with phase label=%i \n",inlet_layers_z,inlet_layers_phase);
-				for (int k = zStart; k < zStart+inlet_layers_z; k++){
-					for (int j = 0; j<global_Ny; j++){
-						for (int i = 0; i<global_Nx; i++){
-							signed char local_id = SegData[k*global_Nx*global_Ny+j*global_Nx+i];
-							signed char reflection_id = SegData[(zStart + nz*nprocz - 1)*global_Nx*global_Ny+j*global_Nx+i];
-							if ( local_id < 1 && reflection_id > 0){
-								SegData[k*global_Nx*global_Ny+j*global_Nx+i] = reflection_id;
-							}
+
+		if (inlet_layers_y > 0){
+			printf("Checkerboard pattern at y inlet for %i layers \n",inlet_layers_y);
+			// use checkerboard pattern
+			for (int k = 0; k<global_Nz; k++){
+				for (int j = yStart; j < yStart+inlet_layers_y; j++){
+					for (int i = 0; i<global_Nx; i++){
+						if ( (i/checkerSize + k/checkerSize)%2 == 0){
+							// void checkers
+							SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 2;
+						}
+						else{
+							// solid checkers
+							SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 0;
 						}
 					}
 				}
 			}
-			if (outlet_layers_z > 0){
-				printf("Mixed reflection pattern at z outlet for %i layers, saturated with phase label=%i \n",outlet_layers_z,outlet_layers_phase);
-				for (int k = zStart + nz*nprocz - outlet_layers_z; k < zStart + nz*nprocz; k++){
-					for (int j = 0; j<global_Ny; j++){
-						for (int i = 0; i<global_Nx; i++){
-							signed char local_id = SegData[k*global_Nx*global_Ny+j*global_Nx+i];
-							signed char reflection_id = SegData[zStart*global_Nx*global_Ny+j*global_Nx+i];
-							if ( local_id < 1 && reflection_id > 0){
-								SegData[k*global_Nx*global_Ny+j*global_Nx+i] = reflection_id;
-							}
+		}
+
+		if (inlet_layers_z > 0){
+			printf("Checkerboard pattern at z inlet for %i layers, saturated with phase label=%i \n",inlet_layers_z,inlet_layers_phase);
+			// use checkerboard pattern
+			for (int k = zStart; k < zStart+inlet_layers_z; k++){
+				for (int j = 0; j<global_Ny; j++){
+					for (int i = 0; i<global_Nx; i++){
+						if ( (i/checkerSize+j/checkerSize)%2 == 0){
+							// void checkers
+							//SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 2;
+							SegData[k*global_Nx*global_Ny+j*global_Nx+i] = inlet_layers_phase;
+						}
+						else{
+							// solid checkers
+							SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 0;
+						}
+					}
+				}
+			}
+		}
+
+		if (outlet_layers_x > 0){
+			// use checkerboard pattern
+			printf("Checkerboard pattern at x outlet for %i layers \n",outlet_layers_x);
+			for (int k = 0; k<global_Nz; k++){
+				for (int j = 0; j<global_Ny; j++){
+					for (int i = xStart + nx*nprocx - outlet_layers_x; i <  xStart + nx*nprocx; i++){
+						if ( (j/checkerSize + k/checkerSize)%2 == 0){
+							// void checkers
+							SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 2;
+						}
+						else{
+							// solid checkers
+							SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 0;
+						}
+					}
+				}
+			}
+		}
+
+		if (outlet_layers_y > 0){
+			printf("Checkerboard pattern at y outlet for %i layers \n",outlet_layers_y);
+			// use checkerboard pattern
+			for (int k = 0; k<global_Nz; k++){
+				for (int j = yStart + ny*nprocy - outlet_layers_y; i < yStart + ny*nprocy; j++){
+					for (int i = 0; i<global_Nx; i++){
+						if ( (i/checkerSize + k/checkerSize)%2 == 0){
+							// void checkers
+							SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 2;
+						}
+						else{
+							// solid checkers
+							SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 0;
+							
+						}
+					}
+				}
+			}
+		}
+
+		if (outlet_layers_z > 0){
+			printf("Checkerboard pattern at z outlet for %i layers, saturated with phase label=%i \n",outlet_layers_z,outlet_layers_phase);
+			// use checkerboard pattern
+			for (int k = zStart + nz*nprocz - outlet_layers_z; k < zStart + nz*nprocz; k++){
+				for (int j = 0; j<global_Ny; j++){
+					for (int i = 0; i<global_Nx; i++){
+						if ( (i/checkerSize+j/checkerSize)%2 == 0){
+							// void checkers
+							//SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 2;
+							SegData[k*global_Nx*global_Ny+j*global_Nx+i] = outlet_layers_phase;
+						}
+						else{
+							// solid checkers
+							SegData[k*global_Nx*global_Ny+j*global_Nx+i] = 0;
 						}
 					}
 				}
@@ -634,16 +599,16 @@ void Domain::Decomp( const std::string& Filename )
 		//printf("Ready to recieve data %i at process %i \n", N,rank);
 		MPI_Recv(id,N,MPI_CHAR,0,15,Comm,MPI_STATUS_IGNORE);
 	}
-	//Comm.barrier();
 	MPI_Barrier(Comm);
+
 	// Compute the porosity
 	double sum;
 	double sum_local=0.0;
 	double iVol_global = 1.0/(1.0*(Nx-2)*(Ny-2)*(Nz-2)*nprocs);
-	if (BoundaryCondition > 0 && BoundaryCondition !=5) iVol_global = 1.0/(1.0*(Nx-2)*nprocx*(Ny-2)*nprocy*((Nz-2)*nprocz-6));
+	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 && BoundaryCondition !=5 && kproc() == 0){
+	if (BoundaryCondition >  0  && kproc() == 0){
     	if (inlet_layers_z < 4){
             inlet_layers_z=4;
             if(RANK==0){
@@ -659,7 +624,7 @@ void Domain::Decomp( const std::string& Filename )
 			}
  		}
  	}
-    if (BoundaryCondition >  0 && BoundaryCondition !=5 && kproc() == nprocz-1){
+    if (BoundaryCondition >  0  && kproc() == nprocz-1){
     	if (outlet_layers_z < 4){
             outlet_layers_z=4;
             if(RANK==nprocs-1){
@@ -686,14 +651,12 @@ void Domain::Decomp( const std::string& Filename )
         }
     }
     MPI_Allreduce(&sum_local,&sum,1,MPI_DOUBLE,MPI_SUM,Comm);
-    //sum = Comm.sumReduce(sum_local);
     porosity = sum*iVol_global;
     if (rank()==0) printf("Media porosity = %f \n",porosity);
  	//.........................................................
 }
 
-
-void Domain::AggregateLabels( const std::string& filename ){
+void Domain::AggregateLabels(char *FILENAME){
 	
 	int nx = Nx;
 	int ny = Ny;
@@ -713,7 +676,7 @@ void Domain::AggregateLabels( const std::string& filename ){
 	int full_ny = npy*(ny-2);
 	int full_nz = npz*(nz-2);
 	int local_size = (nx-2)*(ny-2)*(nz-2);
-	unsigned long int full_size = long(full_nx)*long(full_ny)*long(full_nz);
+	long int full_size = long(full_nx)*long(full_ny)*long(full_nz);
 	
 	signed char *LocalID;
 	LocalID = new signed char [local_size];
@@ -743,7 +706,7 @@ void Domain::AggregateLabels( const std::string& filename ){
 					int y = j-1;
 					int z = k-1;
 					int n_local = (k-1)*(nx-2)*(ny-2) + (j-1)*(nx-2) + i-1;
-					unsigned long int n_full = z*long(full_nx)*long(full_ny) + y*long(full_nx) + x;
+					int n_full = z*full_nx*full_ny + y*full_nx + x;
 					FullID[n_full] = LocalID[n_local];
 				}
 			}
@@ -763,14 +726,15 @@ void Domain::AggregateLabels( const std::string& filename ){
 						int y = j-1 + ipy*(ny-2);
 						int z = k-1 + ipz*(nz-2);
 						int n_local = (k-1)*(nx-2)*(ny-2) + (j-1)*(nx-2) + i-1;
-						unsigned long int n_full = z*long(full_nx)*long(full_ny) + y*long(full_nx) + x;
+						int n_full = z*full_nx*full_ny + y*full_nx + x;
 						FullID[n_full] = LocalID[n_local];
 					}
 				}
 			}
 		}
 		// write the output
-		FILE *OUTFILE = fopen(filename.c_str(),"wb");
+		FILE *OUTFILE;
+		OUTFILE = fopen(FILENAME,"wb");
 		fwrite(FullID,1,full_size,OUTFILE);
 		fclose(OUTFILE);
 	}
@@ -1110,10 +1074,10 @@ void Domain::ReadIDs(){
 	double sum;
 	double sum_local=0.0;
 	double iVol_global = 1.0/(1.0*(Nx-2)*(Ny-2)*(Nz-2)*nprocs);
-	if (BoundaryCondition > 0 && BoundaryCondition !=5) iVol_global = 1.0/(1.0*(Nx-2)*nprocx()*(Ny-2)*nprocy()*((Nz-2)*nprocz()-6));
+	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 && BoundaryCondition !=5 && kproc() == 0){
+	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++){
@@ -1124,7 +1088,7 @@ void Domain::ReadIDs(){
 			}
  		}
  	}
-    if (BoundaryCondition >  0 && BoundaryCondition !=5 && kproc() == nprocz()-1){
+    if (BoundaryCondition >  0  && kproc() == nprocz()-1){
     	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++){
@@ -1249,19 +1213,20 @@ void Domain::CommunicateMeshHalo(DoubleArray &Mesh)
 	UnpackMeshData(recvList_YZ, recvCount_YZ ,recvData_YZ, MeshData);
 }
 
-// TODO Ideally stuff below here should be moved somewhere else -- doesn't really belong here
-void WriteCheckpoint(const char *FILENAME, const double *cDen, const double *cfq, size_t Np)
+// Ideally stuff below here should be moved somewhere else -- doesn't really belong here
+void WriteCheckpoint(const char *FILENAME, const double *cDen, const double *cfq, int Np)
 {
+    int q,n;
     double value;
     ofstream File(FILENAME,ios::binary);
-    for (size_t n=0; n<Np; n++){
+    for (n=0; n<Np; n++){
         // Write the two density values
         value = cDen[n];
         File.write((char*) &value, sizeof(value));
         value = cDen[Np+n];
         File.write((char*) &value, sizeof(value));
         // Write the even distributions
-        for (size_t q=0; q<19; q++){
+        for (q=0; q<19; q++){
             value = cfq[q*Np+n];
             File.write((char*) &value, sizeof(value));
         }
@@ -1270,15 +1235,16 @@ void WriteCheckpoint(const char *FILENAME, const double *cDen, const double *cfq
 
 }
 
-void ReadCheckpoint(char *FILENAME, double *cPhi, double *cfq, size_t Np)
+void ReadCheckpoint(char *FILENAME, double *cPhi, double *cfq, int Np)
 {
+    int q=0, n=0;
     double value=0;
     ifstream File(FILENAME,ios::binary);
-    for (size_t n=0; n<Np; n++){
+    for (n=0; n<Np; n++){
         File.read((char*) &value, sizeof(value));
         cPhi[n] = value;
         // Read the distributions
-        for (size_t q=0; q<19; q++){
+        for (q=0; q<19; q++){
             File.read((char*) &value, sizeof(value));
             cfq[q*Np+n] = value;
         }
@@ -1286,12 +1252,13 @@ void ReadCheckpoint(char *FILENAME, double *cPhi, double *cfq, size_t Np)
     File.close();
 }
 
-void ReadBinaryFile(char *FILENAME, double *Data, size_t N)
+void ReadBinaryFile(char *FILENAME, double *Data, int N)
 {
+  int n;
   double value;
   ifstream File(FILENAME,ios::binary);
   if (File.good()){
-    for (size_t n=0; n<N; n++){
+    for (n=0; n<N; n++){
       // Write the two density values                                                                                
       File.read((char*) &value, sizeof(value));
       Data[n] = value;
@@ -1299,156 +1266,8 @@ void ReadBinaryFile(char *FILENAME, double *Data, size_t N)
     }
   }
   else {
-    for (size_t n=0; n<N; n++) Data[n] = 1.2e-34;
+    for (n=0; n<N; n++) Data[n] = 1.2e-34;
   }
   File.close();
 }
 
-
-void Domain::ReadFromFile(const std::string& Filename,const std::string& Datatype, double *UserData)
-{
-	//........................................................................................
-	// Reading the user-defined input file
-    // NOTE: so far it only supports BC=0 (periodic) and BC=5 (mixed reflection)
-    //       because if checkerboard or inlet/outlet buffer layers are added, the
-    //       value of the void space is undefined. 
-    // NOTE: if BC=5 is used, where the inlet and outlet layers of the domain are modified, 
-    //       user needs to modify the input file accordingly before LBPM simulator read
-    //       the input file.
-	//........................................................................................
-	int rank_offset = 0;
-	int RANK = rank();
-	int nprocs, nprocx, nprocy, nprocz, nx, ny, nz;
-	int64_t global_Nx,global_Ny,global_Nz;
-	int64_t i,j,k,n;
-    //TODO These offset we may still need them
-	int64_t xStart,yStart,zStart;
-	xStart=yStart=zStart=0;
-
-	// Read domain parameters
-    // TODO currently the size of the data is still read from Domain{}; 
-    //      but user may have a user-specified size
-	auto size = database->getVector<int>( "n" );
-	auto SIZE = database->getVector<int>( "N" );
-	auto nproc = database->getVector<int>( "nproc" );
-    //TODO currently the funcationality "offset" is disabled as the user-defined input data may have a different size from that of the input domain 
-	if (database->keyExists( "offset" )){
-		auto offset = database->getVector<int>( "offset" );
-		xStart = offset[0];
-		yStart = offset[1];
-		zStart = offset[2];
-	}
-	
-	nx = size[0];
-	ny = size[1];
-	nz = size[2];
-	nprocx = nproc[0];
-	nprocy = nproc[1];
-	nprocz = nproc[2];
-	global_Nx = SIZE[0];
-	global_Ny = SIZE[1];
-	global_Nz = SIZE[2];
-	nprocs=nprocx*nprocy*nprocz;
-
-	double *SegData = NULL;
-	if (RANK==0){
-		printf("User-defined input file: %s (data type: %s)\n",Filename.c_str(),Datatype.c_str());
-        printf("NOTE: currently only BC=0 or 5 supports user-defined input file!\n");
-		// Rank=0 reads the entire segmented data and distributes to worker processes
-		printf("Dimensions of the user-defined input file: %ld x %ld x %ld \n",global_Nx,global_Ny,global_Nz);
-		int64_t SIZE = global_Nx*global_Ny*global_Nz;
-
-		if (Datatype == "double"){
-			printf("Reading input data as double precision floating number\n");
-		    SegData = new double[SIZE];
-			FILE *SEGDAT = fopen(Filename.c_str(),"rb");
-			if (SEGDAT==NULL) ERROR("Domain.cpp: Error reading user-defined file!\n");
-			size_t ReadSeg;
-			ReadSeg=fread(SegData,8,SIZE,SEGDAT);
-			if (ReadSeg != size_t(SIZE)) printf("Domain.cpp: Error reading file: %s\n",Filename.c_str());
-			fclose(SEGDAT);
-		}
-        else{
-            ERROR("Error: User-defined input file only supports double-precision floating number!\n"); 
-        }
-		printf("Read file successfully from %s \n",Filename.c_str());
-	}
-	
-	// Get the rank info
-	int64_t N = (nx+2)*(ny+2)*(nz+2);
-
-	// number of sites to use for periodic boundary condition transition zone
-	//int64_t z_transition_size = (nprocz*nz - (global_Nz - zStart))/2;
-	//if (z_transition_size < 0) z_transition_size=0;
-	int64_t z_transition_size = 0;
-
-	//char LocalRankFilename[1000];//just for debug
-	double *loc_id;
-	loc_id = new double [(nx+2)*(ny+2)*(nz+2)];
-
-	// Set up the sub-domains
-	if (RANK==0){
-        printf("Decomposing user-defined input file\n");
-		printf("Distributing subdomains across %i processors \n",nprocs);
-		printf("Process grid: %i x %i x %i \n",nprocx,nprocy,nprocz);
-		printf("Subdomain size: %i x %i x %i \n",nx,ny,nz);
-		printf("Size of transition region: %ld \n", z_transition_size);
-
-		for (int kp=0; kp<nprocz; kp++){
-			for (int jp=0; jp<nprocy; jp++){
-				for (int ip=0; ip<nprocx; ip++){
-					// rank of the process that gets this subdomain
-					int rnk = kp*nprocx*nprocy + jp*nprocx + ip;
-					// Pack and send the subdomain for rnk
-					for (k=0;k<nz+2;k++){
-						for (j=0;j<ny+2;j++){
-							for (i=0;i<nx+2;i++){
-								int64_t x = xStart + ip*nx + i-1;
-								int64_t y = yStart + jp*ny + j-1;
-								// int64_t z = zStart + kp*nz + k-1;
-								int64_t z = zStart + kp*nz + k-1 - z_transition_size;
-								if (x<xStart) 	x=xStart;
-								if (!(x<global_Nx))	x=global_Nx-1;
-								if (y<yStart) 	y=yStart;
-								if (!(y<global_Ny))	y=global_Ny-1;
-								if (z<zStart) 	z=zStart;
-								if (!(z<global_Nz))	z=global_Nz-1;
-								int64_t nlocal = k*(nx+2)*(ny+2) + j*(nx+2) + i;
-								int64_t nglobal = z*global_Nx*global_Ny+y*global_Nx+x;
-								loc_id[nlocal] = SegData[nglobal];
-							}
-						}
-					}
-					if (rnk==0){
-						for (k=0;k<nz+2;k++){
-							for (j=0;j<ny+2;j++){
-								for (i=0;i<nx+2;i++){
-									int nlocal = k*(nx+2)*(ny+2) + j*(nx+2) + i;
-									UserData[nlocal] = loc_id[nlocal];
-								}
-							}
-						}
-					}
-					else{
-						//printf("Sending data to process %i \n", rnk);
-						MPI_Send(loc_id,N,MPI_DOUBLE,rnk,15,Comm);
-					}
-					// Write the data for this rank data 
-                    // NOTE just for debug
-					//sprintf(LocalRankFilename,"%s.%05i",Filename.c_str(),rnk+rank_offset);
-					//FILE *ID = fopen(LocalRankFilename,"wb");
-					//fwrite(loc_id,8,(nx+2)*(ny+2)*(nz+2),ID);
-					//fclose(ID);
-				}
-			}
-		}
-
-	}
-	else{
-		// Recieve the subdomain from rank = 0
-		//printf("Ready to recieve data %i at process %i \n", N,rank);
-		MPI_Recv(UserData,N,MPI_DOUBLE,0,15,Comm,MPI_STATUS_IGNORE);
-	}
-	//Comm.barrier();
-	MPI_Barrier(Comm);
-}

common/Domain.h

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify
@@ -193,12 +192,11 @@ public: // Public variables (need to create accessors instead)
     signed char *id;
 
     void ReadIDs();
-    void Decomp( const std::string& filename );
-    void ReadFromFile(const std::string& Filename,const std::string& Datatype, double *UserData);
+    void Decomp(std::string Filename);
     void CommunicateMeshHalo(DoubleArray &Mesh);
     void CommInit(); 
     int PoreCount();
-    void AggregateLabels( const std::string& filename );
+    void AggregateLabels(char *FILENAME);
 
 private:
 
@@ -261,13 +259,10 @@ private:
 
 };
 
-//void ReadFromFile(const std::string& Filename,const std::string& Datatype, double *UserData);
-//void ReadFromFile(const std::string& Filename, DoubleArray &Mesh);
+void WriteCheckpoint(const char *FILENAME, const double *cDen, const double *cfq, int Np);
 
-void WriteCheckpoint(const char *FILENAME, const double *cDen, const double *cfq, size_t Np);
+void ReadCheckpoint(char *FILENAME, double *cDen, double *cfq, int Np);
 
-void ReadCheckpoint(char *FILENAME, double *cDen, double *cfq, size_t Np);
-
-void ReadBinaryFile(char *FILENAME, double *Data, size_t N);
+void ReadBinaryFile(char *FILENAME, double *Data, int N);
 
 #endif

common/FunctionTable.h

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify

common/FunctionTable.hpp

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify
@@ -16,7 +15,6 @@
 */
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify

common/MPI_Helpers.cpp

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify

common/MPI_Helpers.h

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify
@@ -204,12 +203,6 @@ inline int sumReduce( MPI_Comm comm, int x )
 	MPI_Allreduce(&x,&y,1,MPI_INT,MPI_SUM,comm);
     return y;
 }
-inline long long sumReduce( MPI_Comm comm, long long x )
-{
-    long long y = 0;
-	MPI_Allreduce(&x,&y,1,MPI_LONG_LONG,MPI_SUM,comm);
-    return y;
-}
 inline bool sumReduce( MPI_Comm comm, bool x )
 {
     int y = sumReduce( comm, x?1:0 );

common/MPI_Helpers.hpp

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify
@@ -16,7 +15,6 @@
 */
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify

common/ReadMicroCT.cpp

@@ -70,6 +70,8 @@ Array<uint8_t> readMicroCT( const Database& domain, MPI_Comm comm )
     auto n = domain.getVector<int>( "n" );
     int rank = comm_rank(MPI_COMM_WORLD);
     auto nproc = domain.getVector<int>( "nproc" );
+	auto ReadValues = domain.getVector<int>( "ReadValues" );
+	auto WriteValues = domain.getVector<int>( "WriteValues" );
     RankInfoStruct rankInfo( rank, nproc[0], nproc[1], nproc[2] );
     
     // Determine the largest file number to get
@@ -93,26 +95,29 @@ Array<uint8_t> readMicroCT( const Database& domain, MPI_Comm comm )
     		ERROR( "Invalid name for first file" );
     	}
     	data = readMicroCT( filename );
+
+    	// Relabel the data
+    	for (int k = 0; k<1024; k++){
+    		for (int j = 0; j<1024; j++){
+    			for (int i = 0; i<1024; i++){
+    				//n = k*Nfx*Nfy + j*Nfx + i;
+    				//char locval = loc_id[n];
+    				char locval = data(i,j,k);
+    				for (int idx=0; idx<ReadValues.size(); idx++){
+    					signed char oldvalue=ReadValues[idx];
+    					signed char newvalue=WriteValues[idx];
+    					if (locval == oldvalue){
+    						data(i,j,k) = newvalue;
+    						idx = ReadValues.size();
+    					}
+    				}
+    			}
+    		}
+    	}
     }
 
     // Redistribute the data
     data = redistribute( srcRankInfo, data, rankInfo, { n[0], n[1], n[2] }, comm );
 
-	// Relabel the data
-    auto ReadValues = domain.getVector<int>( "ReadValues" );
-    auto WriteValues = domain.getVector<int>( "WriteValues" );
-    ASSERT( ReadValues.size() == WriteValues.size() );
-    int readMaxValue = 0;
-    for ( auto v : ReadValues )
-        readMaxValue = std::max( data.max()+1, v );
-    std::vector<int> map( readMaxValue + 1, -1 );
-    for ( size_t i=0; i<ReadValues.size(); i++ )
-        map[ReadValues[i]] = WriteValues[i];
-    for ( size_t i=0; i<data.length(); i++ ) {
-        int t = data(i);
-        ASSERT( t >= 0 && t <= readMaxValue );
-        data(i) = map[t];
-    }
-
     return data;
 }

common/ScaLBL.cpp

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify
@@ -96,43 +95,43 @@ ScaLBL_Communicator::ScaLBL_Communicator(std::shared_ptr <Domain> Dm){
 	BoundaryCondition = Dm->BoundaryCondition;
 	//......................................................................................
 
-	ScaLBL_AllocateZeroCopy((void **) &sendbuf_x, 2*5*sendCount_x*sizeof(double));	// Allocate device memory
-	ScaLBL_AllocateZeroCopy((void **) &sendbuf_X, 2*5*sendCount_X*sizeof(double));	// Allocate device memory
-	ScaLBL_AllocateZeroCopy((void **) &sendbuf_y, 2*5*sendCount_y*sizeof(double));	// Allocate device memory
-	ScaLBL_AllocateZeroCopy((void **) &sendbuf_Y, 2*5*sendCount_Y*sizeof(double));	// Allocate device memory
-	ScaLBL_AllocateZeroCopy((void **) &sendbuf_z, 2*5*sendCount_z*sizeof(double));	// Allocate device memory
-	ScaLBL_AllocateZeroCopy((void **) &sendbuf_Z, 2*5*sendCount_Z*sizeof(double));	// Allocate device memory
-	ScaLBL_AllocateZeroCopy((void **) &sendbuf_xy, 2*sendCount_xy*sizeof(double));	// Allocate device memory
-	ScaLBL_AllocateZeroCopy((void **) &sendbuf_xY, 2*sendCount_xY*sizeof(double));	// Allocate device memory
-	ScaLBL_AllocateZeroCopy((void **) &sendbuf_Xy, 2*sendCount_Xy*sizeof(double));	// Allocate device memory
-	ScaLBL_AllocateZeroCopy((void **) &sendbuf_XY, 2*sendCount_XY*sizeof(double));	// Allocate device memory
-	ScaLBL_AllocateZeroCopy((void **) &sendbuf_xz, 2*sendCount_xz*sizeof(double));	// Allocate device memory
-	ScaLBL_AllocateZeroCopy((void **) &sendbuf_xZ, 2*sendCount_xZ*sizeof(double));	// Allocate device memory
-	ScaLBL_AllocateZeroCopy((void **) &sendbuf_Xz, 2*sendCount_Xz*sizeof(double));	// Allocate device memory
-	ScaLBL_AllocateZeroCopy((void **) &sendbuf_XZ, 2*sendCount_XZ*sizeof(double));	// Allocate device memory
-	ScaLBL_AllocateZeroCopy((void **) &sendbuf_yz, 2*sendCount_yz*sizeof(double));	// Allocate device memory
-	ScaLBL_AllocateZeroCopy((void **) &sendbuf_yZ, 2*sendCount_yZ*sizeof(double));	// Allocate device memory
-	ScaLBL_AllocateZeroCopy((void **) &sendbuf_Yz, 2*sendCount_Yz*sizeof(double));	// Allocate device memory
-	ScaLBL_AllocateZeroCopy((void **) &sendbuf_YZ, 2*sendCount_YZ*sizeof(double));	// Allocate device memory
+	ScaLBL_AllocateZeroCopy((void **) &sendbuf_x, 5*sendCount_x*sizeof(double));	// Allocate device memory
+	ScaLBL_AllocateZeroCopy((void **) &sendbuf_X, 5*sendCount_X*sizeof(double));	// Allocate device memory
+	ScaLBL_AllocateZeroCopy((void **) &sendbuf_y, 5*sendCount_y*sizeof(double));	// Allocate device memory
+	ScaLBL_AllocateZeroCopy((void **) &sendbuf_Y, 5*sendCount_Y*sizeof(double));	// Allocate device memory
+	ScaLBL_AllocateZeroCopy((void **) &sendbuf_z, 5*sendCount_z*sizeof(double));	// Allocate device memory
+	ScaLBL_AllocateZeroCopy((void **) &sendbuf_Z, 5*sendCount_Z*sizeof(double));	// Allocate device memory
+	ScaLBL_AllocateZeroCopy((void **) &sendbuf_xy, sendCount_xy*sizeof(double));	// Allocate device memory
+	ScaLBL_AllocateZeroCopy((void **) &sendbuf_xY, sendCount_xY*sizeof(double));	// Allocate device memory
+	ScaLBL_AllocateZeroCopy((void **) &sendbuf_Xy, sendCount_Xy*sizeof(double));	// Allocate device memory
+	ScaLBL_AllocateZeroCopy((void **) &sendbuf_XY, sendCount_XY*sizeof(double));	// Allocate device memory
+	ScaLBL_AllocateZeroCopy((void **) &sendbuf_xz, sendCount_xz*sizeof(double));	// Allocate device memory
+	ScaLBL_AllocateZeroCopy((void **) &sendbuf_xZ, sendCount_xZ*sizeof(double));	// Allocate device memory
+	ScaLBL_AllocateZeroCopy((void **) &sendbuf_Xz, sendCount_Xz*sizeof(double));	// Allocate device memory
+	ScaLBL_AllocateZeroCopy((void **) &sendbuf_XZ, sendCount_XZ*sizeof(double));	// Allocate device memory
+	ScaLBL_AllocateZeroCopy((void **) &sendbuf_yz, sendCount_yz*sizeof(double));	// Allocate device memory
+	ScaLBL_AllocateZeroCopy((void **) &sendbuf_yZ, sendCount_yZ*sizeof(double));	// Allocate device memory
+	ScaLBL_AllocateZeroCopy((void **) &sendbuf_Yz, sendCount_Yz*sizeof(double));	// Allocate device memory
+	ScaLBL_AllocateZeroCopy((void **) &sendbuf_YZ, sendCount_YZ*sizeof(double));	// Allocate device memory
 	//......................................................................................
-	ScaLBL_AllocateZeroCopy((void **) &recvbuf_x, 2*5*recvCount_x*sizeof(double));	// Allocate device memory
-	ScaLBL_AllocateZeroCopy((void **) &recvbuf_X, 2*5*recvCount_X*sizeof(double));	// Allocate device memory
-	ScaLBL_AllocateZeroCopy((void **) &recvbuf_y, 2*5*recvCount_y*sizeof(double));	// Allocate device memory
-	ScaLBL_AllocateZeroCopy((void **) &recvbuf_Y, 2*5*recvCount_Y*sizeof(double));	// Allocate device memory
-	ScaLBL_AllocateZeroCopy((void **) &recvbuf_z, 2*5*recvCount_z*sizeof(double));	// Allocate device memory
-	ScaLBL_AllocateZeroCopy((void **) &recvbuf_Z, 2*5*recvCount_Z*sizeof(double));	// Allocate device memory
-	ScaLBL_AllocateZeroCopy((void **) &recvbuf_xy, 2*recvCount_xy*sizeof(double));	// Allocate device memory
-	ScaLBL_AllocateZeroCopy((void **) &recvbuf_xY, 2*recvCount_xY*sizeof(double));	// Allocate device memory
-	ScaLBL_AllocateZeroCopy((void **) &recvbuf_Xy, 2*recvCount_Xy*sizeof(double));	// Allocate device memory
-	ScaLBL_AllocateZeroCopy((void **) &recvbuf_XY, 2*recvCount_XY*sizeof(double));	// Allocate device memory
-	ScaLBL_AllocateZeroCopy((void **) &recvbuf_xz, 2*recvCount_xz*sizeof(double));	// Allocate device memory
-	ScaLBL_AllocateZeroCopy((void **) &recvbuf_xZ, 2*recvCount_xZ*sizeof(double));	// Allocate device memory
-	ScaLBL_AllocateZeroCopy((void **) &recvbuf_Xz, 2*recvCount_Xz*sizeof(double));	// Allocate device memory
-	ScaLBL_AllocateZeroCopy((void **) &recvbuf_XZ, 2*recvCount_XZ*sizeof(double));	// Allocate device memory
-	ScaLBL_AllocateZeroCopy((void **) &recvbuf_yz, 2*recvCount_yz*sizeof(double));	// Allocate device memory
-	ScaLBL_AllocateZeroCopy((void **) &recvbuf_yZ, 2*recvCount_yZ*sizeof(double));	// Allocate device memory
-	ScaLBL_AllocateZeroCopy((void **) &recvbuf_Yz, 2*recvCount_Yz*sizeof(double));	// Allocate device memory
-	ScaLBL_AllocateZeroCopy((void **) &recvbuf_YZ, 2*recvCount_YZ*sizeof(double));	// Allocate device memory
+	ScaLBL_AllocateZeroCopy((void **) &recvbuf_x, 5*recvCount_x*sizeof(double));	// Allocate device memory
+	ScaLBL_AllocateZeroCopy((void **) &recvbuf_X, 5*recvCount_X*sizeof(double));	// Allocate device memory
+	ScaLBL_AllocateZeroCopy((void **) &recvbuf_y, 5*recvCount_y*sizeof(double));	// Allocate device memory
+	ScaLBL_AllocateZeroCopy((void **) &recvbuf_Y, 5*recvCount_Y*sizeof(double));	// Allocate device memory
+	ScaLBL_AllocateZeroCopy((void **) &recvbuf_z, 5*recvCount_z*sizeof(double));	// Allocate device memory
+	ScaLBL_AllocateZeroCopy((void **) &recvbuf_Z, 5*recvCount_Z*sizeof(double));	// Allocate device memory
+	ScaLBL_AllocateZeroCopy((void **) &recvbuf_xy, recvCount_xy*sizeof(double));	// Allocate device memory
+	ScaLBL_AllocateZeroCopy((void **) &recvbuf_xY, recvCount_xY*sizeof(double));	// Allocate device memory
+	ScaLBL_AllocateZeroCopy((void **) &recvbuf_Xy, recvCount_Xy*sizeof(double));	// Allocate device memory
+	ScaLBL_AllocateZeroCopy((void **) &recvbuf_XY, recvCount_XY*sizeof(double));	// Allocate device memory
+	ScaLBL_AllocateZeroCopy((void **) &recvbuf_xz, recvCount_xz*sizeof(double));	// Allocate device memory
+	ScaLBL_AllocateZeroCopy((void **) &recvbuf_xZ, recvCount_xZ*sizeof(double));	// Allocate device memory
+	ScaLBL_AllocateZeroCopy((void **) &recvbuf_Xz, recvCount_Xz*sizeof(double));	// Allocate device memory
+	ScaLBL_AllocateZeroCopy((void **) &recvbuf_XZ, recvCount_XZ*sizeof(double));	// Allocate device memory
+	ScaLBL_AllocateZeroCopy((void **) &recvbuf_yz, recvCount_yz*sizeof(double));	// Allocate device memory
+	ScaLBL_AllocateZeroCopy((void **) &recvbuf_yZ, recvCount_yZ*sizeof(double));	// Allocate device memory
+	ScaLBL_AllocateZeroCopy((void **) &recvbuf_Yz, recvCount_Yz*sizeof(double));	// Allocate device memory
+	ScaLBL_AllocateZeroCopy((void **) &recvbuf_YZ, recvCount_YZ*sizeof(double));	// Allocate device memory
 	//......................................................................................
 	ScaLBL_AllocateZeroCopy((void **) &dvcSendList_x, sendCount_x*sizeof(int));	// Allocate device memory
 	ScaLBL_AllocateZeroCopy((void **) &dvcSendList_X, sendCount_X*sizeof(int));	// Allocate device memory
@@ -1027,6 +1026,19 @@ void ScaLBL_Communicator::RecvD3Q19AA(double *dist){
 	ScaLBL_D3Q19_Unpack(15,dvcRecvDist_Y,3*recvCount_Y,recvCount_Y,recvbuf_Y,dist,N);
 	ScaLBL_D3Q19_Unpack(17,dvcRecvDist_Y,4*recvCount_Y,recvCount_Y,recvbuf_Y,dist,N);
 	//...................................................................................
+	//...Packing for z face(6,12,13,16,17)................................
+	ScaLBL_D3Q19_Unpack(6,dvcRecvDist_z,0,recvCount_z,recvbuf_z,dist,N);
+	ScaLBL_D3Q19_Unpack(12,dvcRecvDist_z,recvCount_z,recvCount_z,recvbuf_z,dist,N);
+	ScaLBL_D3Q19_Unpack(13,dvcRecvDist_z,2*recvCount_z,recvCount_z,recvbuf_z,dist,N);
+	ScaLBL_D3Q19_Unpack(16,dvcRecvDist_z,3*recvCount_z,recvCount_z,recvbuf_z,dist,N);
+	ScaLBL_D3Q19_Unpack(17,dvcRecvDist_z,4*recvCount_z,recvCount_z,recvbuf_z,dist,N);
+	//...Packing for Z face(5,11,14,15,18)................................
+	ScaLBL_D3Q19_Unpack(5,dvcRecvDist_Z,0,recvCount_Z,recvbuf_Z,dist,N);
+	ScaLBL_D3Q19_Unpack(11,dvcRecvDist_Z,recvCount_Z,recvCount_Z,recvbuf_Z,dist,N);
+	ScaLBL_D3Q19_Unpack(14,dvcRecvDist_Z,2*recvCount_Z,recvCount_Z,recvbuf_Z,dist,N);
+	ScaLBL_D3Q19_Unpack(15,dvcRecvDist_Z,3*recvCount_Z,recvCount_Z,recvbuf_Z,dist,N);
+	ScaLBL_D3Q19_Unpack(18,dvcRecvDist_Z,4*recvCount_Z,recvCount_Z,recvbuf_Z,dist,N);
+	//..................................................................................
 	//...Pack the xy edge (8)................................
 	ScaLBL_D3Q19_Unpack(8,dvcRecvDist_xy,0,recvCount_xy,recvbuf_xy,dist,N);
 	//...Pack the Xy edge (9)................................
@@ -1035,75 +1047,22 @@ void ScaLBL_Communicator::RecvD3Q19AA(double *dist){
 	ScaLBL_D3Q19_Unpack(10,dvcRecvDist_xY,0,recvCount_xY,recvbuf_xY,dist,N);
 	//...Pack the XY edge (7)................................
 	ScaLBL_D3Q19_Unpack(7,dvcRecvDist_XY,0,recvCount_XY,recvbuf_XY,dist,N);
-
-	if (BoundaryCondition > 0){
-		if (kproc != 0){
-			//...Packing for z face(6,12,13,16,17)................................
-			ScaLBL_D3Q19_Unpack(6,dvcRecvDist_z,0,recvCount_z,recvbuf_z,dist,N);
-			ScaLBL_D3Q19_Unpack(12,dvcRecvDist_z,recvCount_z,recvCount_z,recvbuf_z,dist,N);
-			ScaLBL_D3Q19_Unpack(13,dvcRecvDist_z,2*recvCount_z,recvCount_z,recvbuf_z,dist,N);
-			ScaLBL_D3Q19_Unpack(16,dvcRecvDist_z,3*recvCount_z,recvCount_z,recvbuf_z,dist,N);
-			ScaLBL_D3Q19_Unpack(17,dvcRecvDist_z,4*recvCount_z,recvCount_z,recvbuf_z,dist,N);
-			//...Pack the xz edge (12)................................
-			ScaLBL_D3Q19_Unpack(12,dvcRecvDist_xz,0,recvCount_xz,recvbuf_xz,dist,N);
-			//...Pack the Xz edge (13)................................
-			ScaLBL_D3Q19_Unpack(13,dvcRecvDist_Xz,0,recvCount_Xz,recvbuf_Xz,dist,N);
-			//...Pack the yz edge (16)................................
-			ScaLBL_D3Q19_Unpack(16,dvcRecvDist_yz,0,recvCount_yz,recvbuf_yz,dist,N);
-			//...Pack the Yz edge (17)................................
-			ScaLBL_D3Q19_Unpack(17,dvcRecvDist_Yz,0,recvCount_Yz,recvbuf_Yz,dist,N);
-			//..................................................................................
-		}
-		if (kproc != nprocz-1){
-			//...Packing for Z face(5,11,14,15,18)................................
-			ScaLBL_D3Q19_Unpack(5,dvcRecvDist_Z,0,recvCount_Z,recvbuf_Z,dist,N);
-			ScaLBL_D3Q19_Unpack(11,dvcRecvDist_Z,recvCount_Z,recvCount_Z,recvbuf_Z,dist,N);
-			ScaLBL_D3Q19_Unpack(14,dvcRecvDist_Z,2*recvCount_Z,recvCount_Z,recvbuf_Z,dist,N);
-			ScaLBL_D3Q19_Unpack(15,dvcRecvDist_Z,3*recvCount_Z,recvCount_Z,recvbuf_Z,dist,N);
-			ScaLBL_D3Q19_Unpack(18,dvcRecvDist_Z,4*recvCount_Z,recvCount_Z,recvbuf_Z,dist,N);
-			//...Pack the xZ edge (14)................................
-			ScaLBL_D3Q19_Unpack(14,dvcRecvDist_xZ,0,recvCount_xZ,recvbuf_xZ,dist,N);
-			//...Pack the XZ edge (11)................................
-			ScaLBL_D3Q19_Unpack(11,dvcRecvDist_XZ,0,recvCount_XZ,recvbuf_XZ,dist,N);
-			//...Pack the yZ edge (18)................................
-			ScaLBL_D3Q19_Unpack(18,dvcRecvDist_yZ,0,recvCount_yZ,recvbuf_yZ,dist,N);
-			//...Pack the YZ edge (15)................................
-			ScaLBL_D3Q19_Unpack(15,dvcRecvDist_YZ,0,recvCount_YZ,recvbuf_YZ,dist,N);
-			//..................................................................................
-		}
-	}
-	else {
-		//...Packing for z face(6,12,13,16,17)................................
-		ScaLBL_D3Q19_Unpack(6,dvcRecvDist_z,0,recvCount_z,recvbuf_z,dist,N);
-		ScaLBL_D3Q19_Unpack(12,dvcRecvDist_z,recvCount_z,recvCount_z,recvbuf_z,dist,N);
-		ScaLBL_D3Q19_Unpack(13,dvcRecvDist_z,2*recvCount_z,recvCount_z,recvbuf_z,dist,N);
-		ScaLBL_D3Q19_Unpack(16,dvcRecvDist_z,3*recvCount_z,recvCount_z,recvbuf_z,dist,N);
-		ScaLBL_D3Q19_Unpack(17,dvcRecvDist_z,4*recvCount_z,recvCount_z,recvbuf_z,dist,N);
-		//...Packing for Z face(5,11,14,15,18)................................
-		ScaLBL_D3Q19_Unpack(5,dvcRecvDist_Z,0,recvCount_Z,recvbuf_Z,dist,N);
-		ScaLBL_D3Q19_Unpack(11,dvcRecvDist_Z,recvCount_Z,recvCount_Z,recvbuf_Z,dist,N);
-		ScaLBL_D3Q19_Unpack(14,dvcRecvDist_Z,2*recvCount_Z,recvCount_Z,recvbuf_Z,dist,N);
-		ScaLBL_D3Q19_Unpack(15,dvcRecvDist_Z,3*recvCount_Z,recvCount_Z,recvbuf_Z,dist,N);
-		ScaLBL_D3Q19_Unpack(18,dvcRecvDist_Z,4*recvCount_Z,recvCount_Z,recvbuf_Z,dist,N);
-		//..................................................................................
-		//...Pack the xz edge (12)................................
-		ScaLBL_D3Q19_Unpack(12,dvcRecvDist_xz,0,recvCount_xz,recvbuf_xz,dist,N);
-		//...Pack the xZ edge (14)................................
-		ScaLBL_D3Q19_Unpack(14,dvcRecvDist_xZ,0,recvCount_xZ,recvbuf_xZ,dist,N);
-		//...Pack the Xz edge (13)................................
-		ScaLBL_D3Q19_Unpack(13,dvcRecvDist_Xz,0,recvCount_Xz,recvbuf_Xz,dist,N);
-		//...Pack the XZ edge (11)................................
-		ScaLBL_D3Q19_Unpack(11,dvcRecvDist_XZ,0,recvCount_XZ,recvbuf_XZ,dist,N);
-		//...Pack the yz edge (16)................................
-		ScaLBL_D3Q19_Unpack(16,dvcRecvDist_yz,0,recvCount_yz,recvbuf_yz,dist,N);
-		//...Pack the yZ edge (18)................................
-		ScaLBL_D3Q19_Unpack(18,dvcRecvDist_yZ,0,recvCount_yZ,recvbuf_yZ,dist,N);
-		//...Pack the Yz edge (17)................................
-		ScaLBL_D3Q19_Unpack(17,dvcRecvDist_Yz,0,recvCount_Yz,recvbuf_Yz,dist,N);
-		//...Pack the YZ edge (15)................................
-		ScaLBL_D3Q19_Unpack(15,dvcRecvDist_YZ,0,recvCount_YZ,recvbuf_YZ,dist,N);
-	}
-
+	//...Pack the xz edge (12)................................
+	ScaLBL_D3Q19_Unpack(12,dvcRecvDist_xz,0,recvCount_xz,recvbuf_xz,dist,N);
+	//...Pack the xZ edge (14)................................
+	ScaLBL_D3Q19_Unpack(14,dvcRecvDist_xZ,0,recvCount_xZ,recvbuf_xZ,dist,N);
+	//...Pack the Xz edge (13)................................
+	ScaLBL_D3Q19_Unpack(13,dvcRecvDist_Xz,0,recvCount_Xz,recvbuf_Xz,dist,N);
+	//...Pack the XZ edge (11)................................
+	ScaLBL_D3Q19_Unpack(11,dvcRecvDist_XZ,0,recvCount_XZ,recvbuf_XZ,dist,N);
+	//...Pack the yz edge (16)................................
+	ScaLBL_D3Q19_Unpack(16,dvcRecvDist_yz,0,recvCount_yz,recvbuf_yz,dist,N);
+	//...Pack the yZ edge (18)................................
+	ScaLBL_D3Q19_Unpack(18,dvcRecvDist_yZ,0,recvCount_yZ,recvbuf_yZ,dist,N);
+	//...Pack the Yz edge (17)................................
+	ScaLBL_D3Q19_Unpack(17,dvcRecvDist_Yz,0,recvCount_Yz,recvbuf_Yz,dist,N);
+	//...Pack the YZ edge (15)................................
+	ScaLBL_D3Q19_Unpack(15,dvcRecvDist_YZ,0,recvCount_YZ,recvbuf_YZ,dist,N);
 	//...................................................................................
 	Lock=false; // unlock the communicator after communications complete
 	//...................................................................................
@@ -1126,7 +1085,6 @@ void ScaLBL_Communicator::RecvGrad(double *phi, double *grad){
 	ScaLBL_Gradient_Unpack(1.0,-1,0,0,dvcRecvDist_x,0,recvCount_x,recvbuf_x,phi,grad,N);
 	ScaLBL_Gradient_Unpack(0.5,-1,-1,0,dvcRecvDist_x,recvCount_x,recvCount_x,recvbuf_x,phi,grad,N);
 	ScaLBL_Gradient_Unpack(0.5,-1,1,0,dvcRecvDist_x,2*recvCount_x,recvCount_x,recvbuf_x,phi,grad,N);
-	ScaLBL_Gradient_Unpack(0.5,-1,0,-1,dvcRecvDist_x,3*recvCount_x,recvCount_x,recvbuf_x,phi,grad,N);
 	ScaLBL_Gradient_Unpack(0.5,-1,0,1,dvcRecvDist_x,4*recvCount_x,recvCount_x,recvbuf_x,phi,grad,N);
 	//...................................................................................
 	//...Packing for X face(1,7,9,11,13)................................
@@ -1282,18 +1240,18 @@ void ScaLBL_Communicator::BiRecvD3Q7AA(double *Aq, double *Bq){
 	ScaLBL_D3Q7_Unpack(3,dvcRecvDist_Y,0,recvCount_Y,recvbuf_Y,Aq,N);
 	ScaLBL_D3Q7_Unpack(3,dvcRecvDist_Y,recvCount_Y,recvCount_Y,recvbuf_Y,Bq,N);
 	//...................................................................................
-
-	if (BoundaryCondition > 0){
-		if (kproc != 0){
-			//...Packing for z face(6,12,13,16,17)................................
-			ScaLBL_D3Q7_Unpack(6,dvcRecvDist_z,0,recvCount_z,recvbuf_z,Aq,N);
-			ScaLBL_D3Q7_Unpack(6,dvcRecvDist_z,recvCount_z,recvCount_z,recvbuf_z,Bq,N);
-		}
-		if (kproc != nprocz-1){
-			//...Packing for Z face(5,11,14,15,18)................................
-			ScaLBL_D3Q7_Unpack(5,dvcRecvDist_Z,0,recvCount_Z,recvbuf_Z,Aq,N);
-			ScaLBL_D3Q7_Unpack(5,dvcRecvDist_Z,recvCount_Z,recvCount_Z,recvbuf_Z,Bq,N);
-		}
+	
+	if (BoundaryCondition > 0 && kproc == 0){
+		// don't unpack little z
+		//...Packing for Z face(5,11,14,15,18)................................
+		ScaLBL_D3Q7_Unpack(5,dvcRecvDist_Z,0,recvCount_Z,recvbuf_Z,Aq,N);
+		ScaLBL_D3Q7_Unpack(5,dvcRecvDist_Z,recvCount_Z,recvCount_Z,recvbuf_Z,Bq,N);
+	}
+	else if (BoundaryCondition > 0 && kproc == nprocz-1){
+		// don't unpack big z
+		//...Packing for z face(6,12,13,16,17)................................
+		ScaLBL_D3Q7_Unpack(6,dvcRecvDist_z,0,recvCount_z,recvbuf_z,Aq,N);
+		ScaLBL_D3Q7_Unpack(6,dvcRecvDist_z,recvCount_z,recvCount_z,recvbuf_z,Bq,N);
 	}
 	else {
 		//...Packing for z face(6,12,13,16,17)................................
@@ -1303,17 +1261,7 @@ void ScaLBL_Communicator::BiRecvD3Q7AA(double *Aq, double *Bq){
 		ScaLBL_D3Q7_Unpack(5,dvcRecvDist_Z,0,recvCount_Z,recvbuf_Z,Aq,N);
 		ScaLBL_D3Q7_Unpack(5,dvcRecvDist_Z,recvCount_Z,recvCount_Z,recvbuf_Z,Bq,N);
 	}
-/*	if (BoundaryCondition == 5){
-		if (kproc == 0){
-			ScaLBL_D3Q7_Reflection_BC_z(dvcSendList_z, Aq, sendCount_z, N);
-			ScaLBL_D3Q7_Reflection_BC_z(dvcSendList_z, Bq, sendCount_z, N);
-		}
-		if (kproc == nprocz-1){
-			ScaLBL_D3Q7_Reflection_BC_Z(dvcSendList_Z, Aq, sendCount_Z, N);
-			ScaLBL_D3Q7_Reflection_BC_Z(dvcSendList_Z, Bq, sendCount_Z, N);
-		}
-	}
-	*/
+	
 	//...................................................................................
 	Lock=false; // unlock the communicator after communications complete
 	//...................................................................................
@@ -1410,19 +1358,19 @@ void ScaLBL_Communicator::TriRecvD3Q7AA(double *Aq, double *Bq, double *Cq){
 	ScaLBL_D3Q7_Unpack(3,dvcRecvDist_Y,2*recvCount_Y,recvCount_Y,recvbuf_Y,Cq,N);
 	//...................................................................................
 	
-	if (BoundaryCondition > 0){
-		if (kproc != 0){
-			//...Packing for z face(6,12,13,16,17)................................
-			ScaLBL_D3Q7_Unpack(6,dvcRecvDist_z,0,recvCount_z,recvbuf_z,Aq,N);
-			ScaLBL_D3Q7_Unpack(6,dvcRecvDist_z,recvCount_z,recvCount_z,recvbuf_z,Bq,N);
-			ScaLBL_D3Q7_Unpack(6,dvcRecvDist_z,2*recvCount_z,recvCount_z,recvbuf_z,Cq,N);
-		}
-		if (kproc != nprocz-1){
-			//...Packing for Z face(5,11,14,15,18)................................
-			ScaLBL_D3Q7_Unpack(5,dvcRecvDist_Z,0,recvCount_Z,recvbuf_Z,Aq,N);
-			ScaLBL_D3Q7_Unpack(5,dvcRecvDist_Z,recvCount_Z,recvCount_Z,recvbuf_Z,Bq,N);
-			ScaLBL_D3Q7_Unpack(5,dvcRecvDist_Z,2*recvCount_Z,recvCount_Z,recvbuf_Z,Cq,N);
-		}
+	if (BoundaryCondition > 0 && kproc == 0){
+		// don't unpack little z
+		//...Packing for Z face(5,11,14,15,18)................................
+		ScaLBL_D3Q7_Unpack(5,dvcRecvDist_Z,0,recvCount_Z,recvbuf_Z,Aq,N);
+		ScaLBL_D3Q7_Unpack(5,dvcRecvDist_Z,recvCount_Z,recvCount_Z,recvbuf_Z,Bq,N);
+		ScaLBL_D3Q7_Unpack(5,dvcRecvDist_Z,2*recvCount_Z,recvCount_Z,recvbuf_Z,Cq,N);
+	}
+	else if (BoundaryCondition > 0 && kproc == nprocz-1){
+		// don't unpack big z
+		//...Packing for z face(6,12,13,16,17)................................
+		ScaLBL_D3Q7_Unpack(6,dvcRecvDist_z,0,recvCount_z,recvbuf_z,Aq,N);
+		ScaLBL_D3Q7_Unpack(6,dvcRecvDist_z,recvCount_z,recvCount_z,recvbuf_z,Bq,N);
+		ScaLBL_D3Q7_Unpack(6,dvcRecvDist_z,2*recvCount_z,recvCount_z,recvbuf_z,Cq,N);
 	}
 	else {
 		//...Packing for z face(6,12,13,16,17)................................
@@ -1524,57 +1472,30 @@ void ScaLBL_Communicator::RecvHalo(double *data){
 	//...................................................................................
 	ScaLBL_Scalar_Unpack(dvcRecvList_x, recvCount_x,recvbuf_x, data, N);
 	ScaLBL_Scalar_Unpack(dvcRecvList_y, recvCount_y,recvbuf_y, data, N);
+	ScaLBL_Scalar_Unpack(dvcRecvList_z, recvCount_z,recvbuf_z, data, N);
 	ScaLBL_Scalar_Unpack(dvcRecvList_X, recvCount_X,recvbuf_X, data, N);
 	ScaLBL_Scalar_Unpack(dvcRecvList_Y, recvCount_Y,recvbuf_Y, data, N);
+	ScaLBL_Scalar_Unpack(dvcRecvList_Z, recvCount_Z,recvbuf_Z, data, N);
 	ScaLBL_Scalar_Unpack(dvcRecvList_xy, recvCount_xy,recvbuf_xy, data, N);
 	ScaLBL_Scalar_Unpack(dvcRecvList_xY, recvCount_xY,recvbuf_xY, data, N);
 	ScaLBL_Scalar_Unpack(dvcRecvList_Xy, recvCount_Xy,recvbuf_Xy, data, N);
 	ScaLBL_Scalar_Unpack(dvcRecvList_XY, recvCount_XY,recvbuf_XY, data, N);
-	
-	if (BoundaryCondition > 0){
-		if (kproc != 0){
-			//...Packing for z face(6,12,13,16,17)................................
-			ScaLBL_Scalar_Unpack(dvcRecvList_z, recvCount_z,recvbuf_z, data, N);
-			ScaLBL_Scalar_Unpack(dvcRecvList_xz, recvCount_xz,recvbuf_xz, data, N);
-			ScaLBL_Scalar_Unpack(dvcRecvList_Xz, recvCount_Xz,recvbuf_Xz, data, N);
-			ScaLBL_Scalar_Unpack(dvcRecvList_yz, recvCount_yz,recvbuf_yz, data, N);
-			ScaLBL_Scalar_Unpack(dvcRecvList_Yz, recvCount_Yz,recvbuf_Yz, data, N);
-		}
-		if (kproc != nprocz-1){
-			//...Packing for Z face(5,11,14,15,18)................................
-			ScaLBL_Scalar_Unpack(dvcRecvList_Z, recvCount_Z,recvbuf_Z, data, N);
-			ScaLBL_Scalar_Unpack(dvcRecvList_xZ, recvCount_xZ,recvbuf_xZ, data, N);
-			ScaLBL_Scalar_Unpack(dvcRecvList_XZ, recvCount_XZ,recvbuf_XZ, data, N);
-			ScaLBL_Scalar_Unpack(dvcRecvList_yZ, recvCount_yZ,recvbuf_yZ, data, N);
-			ScaLBL_Scalar_Unpack(dvcRecvList_YZ, recvCount_YZ,recvbuf_YZ, data, N);
-		}
-	}
-	else {
-		ScaLBL_Scalar_Unpack(dvcRecvList_z, recvCount_z,recvbuf_z, data, N);
-		ScaLBL_Scalar_Unpack(dvcRecvList_xz, recvCount_xz,recvbuf_xz, data, N);
-		ScaLBL_Scalar_Unpack(dvcRecvList_Xz, recvCount_Xz,recvbuf_Xz, data, N);
-		ScaLBL_Scalar_Unpack(dvcRecvList_yz, recvCount_yz,recvbuf_yz, data, N);
-		ScaLBL_Scalar_Unpack(dvcRecvList_Yz, recvCount_Yz,recvbuf_Yz, data, N);
-		ScaLBL_Scalar_Unpack(dvcRecvList_Z, recvCount_Z,recvbuf_Z, data, N);
-		ScaLBL_Scalar_Unpack(dvcRecvList_xZ, recvCount_xZ,recvbuf_xZ, data, N);
-		ScaLBL_Scalar_Unpack(dvcRecvList_XZ, recvCount_XZ,recvbuf_XZ, data, N);
-		ScaLBL_Scalar_Unpack(dvcRecvList_yZ, recvCount_yZ,recvbuf_yZ, data, N);
-		ScaLBL_Scalar_Unpack(dvcRecvList_YZ, recvCount_YZ,recvbuf_YZ, data, N);
-	}
+	ScaLBL_Scalar_Unpack(dvcRecvList_xz, recvCount_xz,recvbuf_xz, data, N);
+	ScaLBL_Scalar_Unpack(dvcRecvList_xZ, recvCount_xZ,recvbuf_xZ, data, N);
+	ScaLBL_Scalar_Unpack(dvcRecvList_Xz, recvCount_Xz,recvbuf_Xz, data, N);
+	ScaLBL_Scalar_Unpack(dvcRecvList_XZ, recvCount_XZ,recvbuf_XZ, data, N);
+	ScaLBL_Scalar_Unpack(dvcRecvList_yz, recvCount_yz,recvbuf_yz, data, N);
+	ScaLBL_Scalar_Unpack(dvcRecvList_yZ, recvCount_yZ,recvbuf_yZ, data, N);
+	ScaLBL_Scalar_Unpack(dvcRecvList_Yz, recvCount_Yz,recvbuf_Yz, data, N);
+	ScaLBL_Scalar_Unpack(dvcRecvList_YZ, recvCount_YZ,recvbuf_YZ, data, N);
 	//...................................................................................
 	Lock=false; // unlock the communicator after communications complete
 	//...................................................................................
-	if (BoundaryCondition == 5 && kproc == 0){
-		ScaLBL_CopySlice_z(data,Nx,Ny,Nz,1,0);
-	}
-	if (BoundaryCondition == 5 && kproc == nprocz-1){
-		ScaLBL_CopySlice_z(data,Nx,Ny,Nz,Nz-2,Nz-1);
-	}	
 }
 
 void ScaLBL_Communicator::RegularLayout(IntArray map, const double *data, DoubleArray &regdata){
 	// Gets data from the device and stores in regular layout
-	int i,j,k,idx;
+	int i,j,k,n,idx;
 	int Nx = map.size(0);
 	int Ny = map.size(1);
 	int Nz = map.size(2);
@@ -1603,30 +1524,23 @@ void ScaLBL_Communicator::RegularLayout(IntArray map, const double *data, Double
 	delete [] TmpDat;
 }
 
+
 void ScaLBL_Communicator::Color_BC_z(int *Map, double *Phi, double *Den, double vA, double vB){
+	double Value=(vA-vB)/(vA+vB);
 	if (kproc == 0) {
-		if (BoundaryCondition == 5){
-			//ScaLBL_CopySlice_z(Phi,Nx,Ny,Nz,1,0);
-		}
-		else {
-			// Set the phase indicator field and density on the z inlet
-			ScaLBL_Color_BC_z(dvcSendList_z, Map, Phi, Den, vA, vB, sendCount_z, N);
-		}
+		// Set the phase indicator field and density on the z inlet
+		ScaLBL_Color_BC_z(dvcSendList_z, Map, Phi, Den, vA, vB, sendCount_z, N);
 		//ScaLBL_SetSlice_z(Phi,Value,Nx,Ny,Nz,0);
 	}
 }
 
 void ScaLBL_Communicator::Color_BC_Z(int *Map, double *Phi, double *Den, double vA, double vB){
+	double Value=(vA-vB)/(vA+vB);
 	if (kproc == nprocz-1){
-		if (BoundaryCondition == 5){
-			//ScaLBL_CopySlice_z(Phi,Nx,Ny,Nz,Nz-2,Nz-1);
-		}
-		else {
 		// Set the phase indicator field and density on the Z outlet
-			ScaLBL_Color_BC_Z(dvcSendList_Z, Map, Phi, Den, vA, vB, sendCount_Z, N);
-		}
+		ScaLBL_Color_BC_Z(dvcSendList_Z, Map, Phi, Den, vA, vB, sendCount_Z, N);
+		//ScaLBL_SetSlice_z(Phi,Value,Nx,Ny,Nz,Nz-1);
 	}
-
 }
 
 void ScaLBL_Communicator::D3Q19_Pressure_BC_z(int *neighborList, double *fq, double din, int time){
@@ -1694,17 +1608,6 @@ double ScaLBL_Communicator::D3Q19_Flux_BC_z(int *neighborList, double *fq, doubl
 	return din;
 }
 
-void ScaLBL_Communicator::D3Q19_Reflection_BC_z(double *fq){
-	if (kproc == 0)
-		ScaLBL_D3Q19_Reflection_BC_z(dvcSendList_z, fq, sendCount_z, N);
-	
-}
-
-void ScaLBL_Communicator::D3Q19_Reflection_BC_Z(double *fq){
-	if (kproc == nprocz-1)
-		ScaLBL_D3Q19_Reflection_BC_Z(dvcSendList_Z, fq, sendCount_Z, N);
-}
-
 void ScaLBL_Communicator::PrintD3Q19(){
 	printf("Printing D3Q19 communication buffer contents \n");
 

common/ScaLBL.h

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify
@@ -72,7 +71,7 @@ extern "C" void ScaLBL_D3Q19_AAeven_BGK(double *dist, int start, int finish, int
 
 extern "C" void ScaLBL_D3Q19_AAodd_BGK(int *neighborList, double *dist, int start, int finish, int Np, double rlx, double Fx, double Fy, double Fz);
 
-// GREYSCALE MODEL (Single-component)
+// GREYSCALE MODEL
 
 extern "C" void ScaLBL_D3Q19_GreyIMRT_Init(double *Dist, int Np, double Den);
 
@@ -88,119 +87,6 @@ extern "C" void ScaLBL_D3Q19_AAeven_Greyscale_IMRT(double *dist, int start, int
 extern "C" void ScaLBL_D3Q19_AAodd_Greyscale_IMRT(int *neighborList, double *dist, int start, int finish, int Np, double rlx, double rlx_eff, double Fx, double Fy, double Fz, 
                                              double *Poros,double *Perm, double *Velocity,double Den,double *Pressure);
 
-extern "C" void ScaLBL_D3Q19_AAeven_Greyscale_MRT(double *dist, int start, int finish, int Np, double rlx, double rlx_eff, double Fx, double Fy, double Fz,
-                                              double *Poros,double *Perm, double *Velocity,double Den,double *Pressure);
-
-extern "C" void ScaLBL_D3Q19_AAodd_Greyscale_MRT(int *neighborList, double *dist, int start, int finish, int Np, double rlx, double rlx_eff, double Fx, double Fy, double Fz, 
-                                             double *Poros,double *Perm, double *Velocity,double Den,double *Pressure);
-// GREYSCALE FREE-ENERGY MODEL (Two-component)
-
-//extern "C" void ScaLBL_D3Q19_AAeven_GreyscaleFE(double *dist, double *Aq, double *Bq, double *Den,
-//                double *DenGradA, double *DenGradB, double *SolidForce, int start, int finish, int Np,
-//                double tauA,double tauB,double tauA_eff,double tauB_eff,double rhoA,double rhoB,double Gsc, double Gx, double Gy, double Gz,
-//                double *Poros,double *Perm, double *Velocity,double *Pressure);
-//
-//extern "C" void ScaLBL_D3Q19_AAodd_GreyscaleFE(int *neighborList, double *dist, double *Aq, double *Bq, double *Den,
-//                double *DenGradA, double *DenGradB, double *SolidForce, int start, int finish, int Np,
-//                double tauA,double tauB,double tauA_eff,double tauB_eff,double rhoA,double rhoB,double Gsc, double Gx, double Gy, double Gz,
-//                double *Poros,double *Perm, double *Velocity,double *Pressure);
-//
-//extern "C" void ScaLBL_D3Q19_AAeven_GreyscaleFEChem(double *dist, double *Cq, double *Phi, double *SolidForce, int start, int finish, int Np,
-//                double tauA,double tauB,double tauA_eff,double tauB_eff,double rhoA,double rhoB,double gamma,double kappaA,double kappaB,double lambdaA,double lambdaB,
-//                double Gx, double Gy, double Gz,
-//                double *Poros,double *Perm, double *Velocity,double *Pressure,double *PressureGrad,double *PressTensorGrad,double *PhiLap);
-//
-//extern "C" void ScaLBL_D3Q19_AAodd_GreyscaleFEChem(int *neighborList, double *dist, double *Cq, double *Phi, double *SolidForce, int start, int finish, int Np,
-//                double tauA,double tauB,double tauA_eff,double tauB_eff,double rhoA,double rhoB,double gamma,double kappaA,double kappaB,double lambdaA,double lambdaB,
-//                double Gx, double Gy, double Gz,
-//                double *Poros,double *Perm, double *Velocity,double *Pressure,double *PressureGrad,double *PressTensorGrad,double *PhiLap);
-//
-//extern "C" void ScaLBL_D3Q7_GreyscaleFE_Init(double *Den, double *Cq, double *PhiLap, double gamma, double kappaA, double kappaB, double lambdaA, double lambdaB, int start, int finish, int Np);
-//
-//extern "C" void ScaLBL_D3Q19_GreyscaleFE_IMRT_Init(double *dist, double *Den, double rhoA, double rhoB, int Np);
-//
-//extern "C" void ScaLBL_D3Q7_AAodd_GreyscaleFEDensity(int *NeighborList, double *Aq, double *Bq, double *Den, double *Phi, int start, int finish, int Np);
-//
-//extern "C" void ScaLBL_D3Q7_AAeven_GreyscaleFEDensity(double *Aq, double *Bq, double *Den, double *Phi, int start, int finish, int Np);
-//
-//extern "C" void ScaLBL_D3Q7_AAodd_GreyscaleFEPhi(int *NeighborList, double *Cq, double *Phi, int start, int finish, int Np);
-//
-//extern "C" void ScaLBL_D3Q7_AAeven_GreyscaleFEPhi(double *Cq, double *Phi, int start, int finish, int Np);
-//
-//extern "C" void ScaLBL_D3Q19_GreyscaleFE_Gradient(int *neighborList, double *Den, double *DenGrad, int start, int finish, int Np);
-//
-//extern "C" void ScaLBL_D3Q19_GreyscaleFE_Laplacian(int *neighborList, double *Den, double *DenLap, int start, int finish, int Np);
-//
-//extern "C" void ScaLBL_D3Q19_GreyscaleFE_Pressure(double *dist, double *Den, double *Porosity,double *Velocity,
-//                double *Pressure, double rhoA,double rhoB, int Np);
-//
-//extern "C" void ScaLBL_D3Q19_GreyscaleFE_PressureTensor(int *neighborList, double *Phi,double *Pressure, double *PressTensor, double *PhiLap,
-//      		     double kappaA,double kappaB,double lambdaA,double lambdaB, int start, int finish, int Np);
-
-// GREYSCALE SHAN-CHEN MODEL (Two-component)
-
-//extern "C" void ScaLBL_D3Q19_GreyscaleSC_Init(int *Map, double *distA, double *distB, double *DenA, double *DenB, int Np);
-//
-//extern "C" void ScaLBL_D3Q19_AAodd_GreyscaleSC_Density(int *NeighborList, int *Map, double *distA, double *distB, double *DenA, double *DenB, int start, int finish, int Np);
-//
-//extern "C" void ScaLBL_D3Q19_AAeven_GreyscaleSC_Density(int *Map, double *distA, double *distB, double *DenA, double *DenB, int start, int finish, int Np);
-//
-//extern "C" void ScaLBL_D3Q19_AAodd_GreyscaleSC_MRT(int *neighborList, int *Mpa, double *distA, double *distB, double *DenA,double *DenB, double *DenGradA, double *DenGradB, 
-//                double *SolidForceA, double *SolidForceB, double *Poros,double *Perm, double *Velocity,double *Pressure, 
-//                double tauA,double tauB,double tauA_eff,double tauB_eff, double Gsc, double Gx, double Gy, double Gz,                                                 
-//                int start, int finish, int Np);
-//
-//extern "C" void ScaLBL_D3Q19_AAeven_GreyscaleSC_MRT(int *Map,double *distA, double *distB, double *DenA,double *DenB, double *DenGradA, double *DenGradB, 
-//                double *SolidForceA, double *SolidForceB, double *Poros,double *Perm, double *Velocity,double *Pressure, 
-//                double tauA,double tauB,double tauA_eff,double tauB_eff, double Gsc, double Gx, double Gy, double Gz,                                                 
-//                int start, int finish, int Np);
-//
-//extern "C" void ScaLBL_D3Q19_AAodd_GreyscaleSC_BGK(int *neighborList, int *Map, double *distA, double *distB, double *DenA, double *DenB, double *DenGradA, double *DenGradB, 
-//                double *SolidForceA, double *SolidForceB, double *Poros,double *Perm, double *Velocity,double *Pressure, 
-//                double tauA,double tauB,double tauA_eff,double tauB_eff, double Gsc, double Gx, double Gy, double Gz,                                                 
-//                int start, int finish, int Np);
-//
-//extern "C" void ScaLBL_D3Q19_AAeven_GreyscaleSC_BGK(int *Map, double *distA, double *distB, double *DenA, double *DenB, double *DenGradA, double *DenGradB, 
-//                double *SolidForceA, double *SolidForceB, double *Poros,double *Perm, double *Velocity,double *Pressure, 
-//                double tauA,double tauB,double tauA_eff,double tauB_eff, double Gsc, double Gx, double Gy, double Gz,                                                 
-//                int start, int finish, int Np);
-//
-//extern "C" void ScaLBL_D3Q19_GreyscaleSC_Gradient(int *neighborList, int *Map, double *Den, double *DenGrad, int strideY, int strideZ,int start, int finish, int Np);
-//
-//extern "C" void ScaLBL_GreyscaleSC_BC_z(int *list, int *Map, double *DenA, double *DenB, double vA, double vB, int count);
-//
-//extern "C" void ScaLBL_GreyscaleSC_BC_Z(int *list, int *Map, double *DenA, double *DenB, double vA, double vB, int count);
-//
-//extern "C" void ScaLBL_GreyscaleSC_AAeven_Pressure_BC_z(int *list, double *distA, double *distB, double dinA, double dinB, int count, int N);
-//
-//extern "C" void ScaLBL_GreyscaleSC_AAeven_Pressure_BC_Z(int *list, double *distA, double *distB, double doutA, double doutB, int count, int N);
-//
-//extern "C" void ScaLBL_GreyscaleSC_AAodd_Pressure_BC_z(int *neighborList, int *list, double *distA, double *distB, double dinA, double dinB, int count, int N);
-//
-//extern "C" void ScaLBL_GreyscaleSC_AAodd_Pressure_BC_Z(int *neighborList, int *list, double *distA, double *distB, double doutA, double doutB, int count, int N);
-
-// GREYSCALE COLOR MODEL (Two-component)
-//extern "C" void ScaLBL_D3Q19_GreyscaleColor_Init(double *dist, double *Porosity, int Np);
-
-//extern "C" void ScaLBL_D3Q19_AAeven_GreyscaleColor(int *Map, double *dist, double *Aq, double *Bq, double *Den, 
-//        double *ColorGrad,double *Phi,double *GreySolidGrad, double *Poros,double *Perm,double *Vel, 
-//        double rhoA, double rhoB, double tauA, double tauB,double tauA_eff,double tauB_eff, double alpha, double beta,
-//		double Fx, double Fy, double Fz, int strideY, int strideZ, int start, int finish, int Np);
-//
-//extern "C" void ScaLBL_D3Q19_AAodd_GreyscaleColor(int *d_neighborList, int *Map, double *dist, double *Aq, double *Bq, double *Den, 
-//		double *ColorGrad,double *Phi, double *GreySolidGrad, double *Poros,double *Perm,double *Vel, 
-//        double rhoA, double rhoB, double tauA, double tauB, double tauA_eff,double tauB_eff, double alpha, double beta,
-//		double Fx, double Fy, double Fz, int strideY, int strideZ, int start, int finish, int Np);
-
-extern "C" void ScaLBL_D3Q19_AAeven_GreyscaleColor(int *Map, double *dist, double *Aq, double *Bq, double *Den, 
-        double *Phi,double *GreySolidGrad, double *Poros,double *Perm,double *Vel,double *Pressure,
-        double rhoA, double rhoB, double tauA, double tauB,double tauA_eff,double tauB_eff, double alpha, double beta,
-		double Fx, double Fy, double Fz, int strideY, int strideZ, int start, int finish, int Np);
-
-extern "C" void ScaLBL_D3Q19_AAodd_GreyscaleColor(int *d_neighborList, int *Map, double *dist, double *Aq, double *Bq, double *Den, 
-		double *Phi, double *GreySolidGrad, double *Poros,double *Perm,double *Vel,double *Pressure, 
-        double rhoA, double rhoB, double tauA, double tauB, double tauA_eff,double tauB_eff, double alpha, double beta,
-		double Fx, double Fy, double Fz, int strideY, int strideZ, int start, int finish, int Np);
 
 // MRT MODEL
 extern "C" void ScaLBL_D3Q19_AAeven_MRT(double *dist, int start, int finish, int Np, double rlx_setA, double rlx_setB, double Fx,
@@ -248,6 +134,11 @@ extern "C" void ScaLBL_D3Q19_Gradient_DFH(int *NeighborList, double *Phi, double
 
 // BOUNDARY CONDITION ROUTINES
 
+//extern "C" void ScaLBL_D3Q19_Pressure_BC_z(double *disteven, double *distodd, double din,
+//		int Nx, int Ny, int Nz);
+//extern "C" void ScaLBL_D3Q19_Pressure_BC_Z(double *disteven, double *distodd, double dout,
+//		int Nx, int Ny, int Nz, int outlet);
+
 extern "C" void ScaLBL_D3Q19_AAodd_Pressure_BC_z(int *neighborList, int *list, double *dist, double din, int count, int Np);
 
 extern "C" void ScaLBL_D3Q19_AAodd_Pressure_BC_Z(int *neighborList, int *list, double *dist, double dout, int count, int Np);
@@ -266,18 +157,8 @@ extern "C" void ScaLBL_Color_BC_z(int *list, int *Map, double *Phi, double *Den,
 
 extern "C" void ScaLBL_Color_BC_Z(int *list, int *Map, double *Phi, double *Den, double vA, double vB, int count, int Np);
 
-extern "C" void ScaLBL_D3Q19_Reflection_BC_z(int *list, double *dist, int count, int Np);
-
-extern "C" void ScaLBL_D3Q19_Reflection_BC_Z(int *list, double *dist, int count, int Np);
-
-extern "C" void ScaLBL_D3Q7_Reflection_BC_z(int *list, double *dist, int count, int Np);
-
-extern "C" void ScaLBL_D3Q7_Reflection_BC_Z(int *list, double *dist, int count, int Np);
-
 extern "C" void ScaLBL_SetSlice_z(double *Phi, double value, int Nx, int Ny, int Nz, int Slice);
 
-extern "C" void ScaLBL_CopySlice_z(double *Phi, int Nx, int Ny, int Nz, int Source, int Destination);
-
 class ScaLBL_Communicator{
 public:
 	//......................................................................................
@@ -286,7 +167,6 @@ public:
 	//ScaLBL_Communicator(Domain &Dm, IntArray &Map);
 	~ScaLBL_Communicator();
 	//......................................................................................
-	MPI_Comm MPI_COMM_SCALBL;		// MPI Communicator
 	unsigned long int CommunicationCount,SendCount,RecvCount;
 	int Nx,Ny,Nz,N;
 	int BoundaryCondition;
@@ -312,6 +192,14 @@ public:
 	int LastInterior();
 	
 	int MemoryOptimizedLayoutAA(IntArray &Map, int *neighborList, signed char *id, int Np);
+//	void MemoryOptimizedLayout(IntArray &Map, int *neighborList, char *id, int Np);
+//	void MemoryOptimizedLayoutFull(IntArray &Map, int *neighborList, char *id, int Np);
+//	void MemoryDenseLayout(IntArray &Map, int *neighborList, char *id, int Np);
+//	void MemoryDenseLayoutFull(IntArray &Map, int *neighborList, char *id, int Np);
+//	void SendD3Q19(double *f_even, double *f_odd);
+//	void RecvD3Q19(double *f_even, double *f_odd);
+//	void SendD3Q19AA(double *f_even, double *f_odd);
+//	void RecvD3Q19AA(double *f_even, double *f_odd);
 	void SendD3Q19AA(double *dist);
 	void RecvD3Q19AA(double *dist);
 //	void BiSendD3Q7(double *A_even, double *A_odd, double *B_even, double *B_odd);
@@ -330,13 +218,8 @@ public:
 	void Color_BC_Z(int *Map, double *Phi, double *Den, double vA, double vB);
 	void D3Q19_Pressure_BC_z(int *neighborList, double *fq, double din, int time);
 	void D3Q19_Pressure_BC_Z(int *neighborList, double *fq, double dout, int time);
-	void D3Q19_Reflection_BC_z(double *fq);
-	void D3Q19_Reflection_BC_Z(double *fq);
 	double D3Q19_Flux_BC_z(int *neighborList, double *fq, double flux, int time);
-	void GreyscaleSC_BC_z(int *Map, double *DenA, double *DenB, double vA, double vB);
-	void GreyscaleSC_BC_Z(int *Map, double *DenA, double *DenB, double vA, double vB);
-    void GreyscaleSC_Pressure_BC_z(int *neighborList, double *fqA, double *fqB, double dinA, double dinB, int time);
-    void GreyscaleSC_Pressure_BC_Z(int *neighborList, double *fqA, double *fqB, double doutA, double doutB, int time);
+
 //	void TestSendD3Q19(double *f_even, double *f_odd);
 //	void TestRecvD3Q19(double *f_even, double *f_odd);
 
@@ -357,6 +240,7 @@ private:
 	// Give the object it's own MPI communicator
 	RankInfoStruct rank_info;
 	MPI_Group Group;	// Group of processors associated with this domain
+	MPI_Comm MPI_COMM_SCALBL;		// MPI Communicator for this domain
 	MPI_Request req1[18],req2[18];
 	MPI_Status stat1[18],stat2[18];
 	//......................................................................................

common/SpherePack.cpp

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify
@@ -16,7 +15,6 @@
 */
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify

common/SpherePack.h

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify

common/UnitTest.cpp

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify

common/UnitTest.h

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify

common/Units.cpp

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify

common/Units.h

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify

common/Utilities.cpp

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify
@@ -15,132 +14,12 @@
   along with OPM.  If not, see <http://www.gnu.org/licenses/>.
 */
 #include "common/Utilities.h"
-#include "StackTrace/StackTrace.h"
-#include "StackTrace/ErrorHandlers.h"
 
-#ifdef USE_TIMER
-#include "MemoryApp.h"
-#include "ProfilerApp.h"
-#endif
-
-#ifdef USE_MPI
-#include "mpi.h"
-#endif
-
-#include <algorithm>
 #include <math.h>
-#include <mutex>
+#include <algorithm>
 
 
-// OS specific includes / definitions
-// clang-format off
-#if defined( WIN32 ) || defined( _WIN32 ) || defined( WIN64 ) || defined( _WIN64 )
-    #define USE_WINDOWS
-#elif defined( __APPLE__ )
-    #define USE_MAC
-#elif defined( __linux ) || defined( __linux__ ) || defined( __unix ) || defined( __posix )
-    #define USE_LINUX
-#else
-    #error Unknown OS
-#endif
-// clang-format on
-
-
-// Mutex for Utility functions
-static std::mutex Utilities_mutex;
-
-
-/****************************************************************************
- *  Function to perform the default startup/shutdown sequences               *
- ****************************************************************************/
-void Utilities::startup( int argc, char **argv )
-{
-    NULL_USE( argc );
-    NULL_USE( argv );
-    // Disable OpenMP
-    Utilities::setenv( "OMP_NUM_THREADS", "1" );
-    Utilities::setenv( "MKL_NUM_THREADS", "1" );
-    // Start MPI
-#ifdef USE_MPI
-    int provided;
-    MPI_Init_thread( &argc, &argv, MPI_THREAD_MULTIPLE, &provided );
-    if ( provided < MPI_THREAD_MULTIPLE ) {
-        int rank;
-        MPI_Comm_rank( MPI_COMM_WORLD, &rank );
-        if ( rank == 0 )
-            std::cerr << "Warning: Failed to start MPI with necessary thread support, thread support will be disabled" << std::endl;
-    }
-    StackTrace::globalCallStackInitialize( MPI_COMM_WORLD );
-#endif
-    // Set the error handlers
-    Utilities::setAbortBehavior( true, 3 );
-    Utilities::setErrorHandlers();
-}
-void Utilities::shutdown()
-{
-    // Clear the error handlers
-    Utilities::clearErrorHandlers();
-    StackTrace::clearSignals();
-    StackTrace::clearSymbols();
-    int rank = 0;
-#ifdef USE_MPI
-    MPI_Comm_rank( MPI_COMM_WORLD, &rank );
-    StackTrace::globalCallStackFinalize();
-    MPI_Barrier( MPI_COMM_WORLD );
-    MPI_Finalize();
-#endif
-#ifdef USE_TIMER
-    PROFILE_DISABLE();
-    auto memory = MemoryApp::getMemoryStats();
-    if ( rank == 0 && memory.N_new > memory.N_delete )
-        MemoryApp::print( std::cout );
-#endif
-}
-
-
-/****************************************************************************
- *  Function to set an environemental variable                               *
- ****************************************************************************/
-void Utilities::setenv( const std::string &name, const std::string &value )
-{
-    Utilities_mutex.lock();
-#if defined( USE_LINUX ) || defined( USE_MAC )
-    bool pass = false;
-    if ( !value.empty() )
-        pass = ::setenv( name.data(), value.data(), 1 ) == 0;
-    else
-        pass = ::unsetenv( name.data() ) == 0;
-#elif defined( USE_WINDOWS )
-    bool pass = SetEnvironmentVariable( name.data(), value.data() ) != 0;
-#else
-#error Unknown OS
-#endif
-    Utilities_mutex.unlock();
-    if ( !pass ) {
-        char msg[1024];
-        if ( !value.empty() )
-            sprintf(
-                msg, "Error setting enviornmental variable: %s=%s\n", name.data(), value.data() );
-        else
-            sprintf( msg, "Error clearing enviornmental variable: %s\n", name.data() );
-        ERROR( msg );
-    }
-}
-std::string Utilities::getenv( const std::string &name )
-{
-    std::string var;
-    Utilities_mutex.lock();
-    auto tmp = std::getenv( name.data() );
-    if ( tmp )
-        var = std::string( tmp );
-    Utilities_mutex.unlock();
-    return var;
-}
-
-
-/****************************************************************************
- *  Factor a number into it's prime factors                                  *
- ****************************************************************************/
+// Factor a number into it's prime factors
 std::vector<int> Utilities::factor(size_t number)
 {
     if ( number<=3 ) 
@@ -190,13 +69,9 @@ std::vector<int> Utilities::factor(size_t number)
 }
 
 
-/****************************************************************************
- *  Dummy function to prevent compiler from optimizing away variable         *
- ****************************************************************************/
+// Dummy function to prevent compiler from optimizing away variable
 void Utilities::nullUse( void* data )
 {
     NULL_USE(data);
 }
 
-
-

common/Utilities.h

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify
@@ -41,37 +40,6 @@ using StackTrace::Utilities::sleep_ms;
 using StackTrace::Utilities::sleep_s;
 
 
-/*!
- * \brief Start MPI, error handlers
- * \details This routine will peform the default startup sequence
- * \param argc              argc from main
- * \param argv              argv from main
- */
-void startup( int argc, char **argv );
-
-/*!
- * \brief Stop MPI, error handlers
- * \details This routine will peform the default shutdown sequence to match startup
- */
-void shutdown();
-
-
-/*!
- * Get an environmental variable
- * @param name              The name of the environmental variable
- * @return                  The value of the enviornmental variable
- */
-std::string getenv( const std::string &name );
-
-
-/*!
- * Set an environmental variable
- * @param name              The name of the environmental variable
- * @param value             The value to set
- */
-void setenv( const std::string &name, const std::string &value );
-
-
 //! std::string version of sprintf
 inline std::string stringf( const char *format, ... );
 

common/UtilityMacros.h

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify

cpu/BGK.cpp

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify

cpu/Color.cpp

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify
@@ -1885,7 +1884,7 @@ extern "C" void ScaLBL_D3Q19_AAodd_Color(int *neighborList, int *Map, double *di
 	const double mrt_V12=0.04166666666666666;
 
 	for (int n=start; n<finish; n++){
-	
+		
 		// read the component number densities
 		nA = Den[n];
 		nB = Den[Np + n];
@@ -2826,11 +2825,3 @@ extern "C" void ScaLBL_PhaseField_Init(int *Map, double *Phi, double *Den, doubl
 	}
 }
 
-extern "C" void ScaLBL_CopySlice_z(double *Phi, int Nx, int Ny, int Nz, int Source, int Dest){
-	int n; double value;
-	for (n=0; n<Nx*Ny; n++){
-		value = Phi[Source*Nx*Ny+n];
-		Phi[Dest*Nx*Ny+n] = value;
-	}
-}
-

cpu/D3Q7.cpp

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify
@@ -88,23 +87,6 @@ extern  "C" void ScaLBL_UnpackDenD3Q7(int *list, int count, double *recvbuf, int
 	}
 }
 
-extern "C" void ScaLBL_D3Q7_Reflection_BC_z(int *list, double *dist, int count, int Np){
-  int n;
-	for (int idx=0; idx<count; idx++){
-		n = list[idx];
-		double f5 = 0.222222222222222222222222 - dist[6*Np+n];
-		dist[6*Np+n] = f5;
-	}
-}
-
-extern "C" void ScaLBL_D3Q7_Reflection_BC_Z(int *list, double *dist, int count, int Np){
-  int n;
-  for (int idx=0; idx<count; idx++){
-		n = list[idx];
-		double f6 = 0.222222222222222222222222 - dist[5*Np+n];
-		dist[5*Np+n] = f6;
-	}
-}
 extern "C" void ScaLBL_D3Q7_Init(char *ID, double *f_even, double *f_odd, double *Den, int Nx, int Ny, int Nz)
 {
 	int n,N;

cpu/dfh.cpp

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify
@@ -16,7 +15,6 @@
 */
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify
@@ -55,10 +53,11 @@ extern "C" void ScaLBL_Gradient_Unpack(double weight, double Cqx, double Cqy, do
 	}
 }
 
-extern "C" void ScaLBL_DFH_Init(double *Phi, double *Den, double *Aq, double *Bq, int start, int finish, int Np)
-{
-	for (int idx=start; idx<finish; idx++){
-	    double phi,nA,nB;
+extern "C" void ScaLBL_DFH_Init(double *Phi, double *Den, double *Aq, double *Bq, int start, int finish, int Np){
+	int idx,n;
+	double phi,nA,nB;
+
+	for (idx=start; idx<finish; idx++){
 		phi = Phi[idx];
 		if (phi > 0.f){
 			nA = 1.0; nB = 0.f;
@@ -91,13 +90,15 @@ extern "C" void ScaLBL_DFH_Init(double *Phi, double *Den, double *Aq, double *Bq
 // LBM based on density functional hydrodynamics
 extern "C" void ScaLBL_D3Q19_AAeven_DFH(int *neighborList, double *dist, double *Aq, double *Bq, double *Den, double *Phi,
 		double *Gradient, double *SolidForce, double rhoA, double rhoB, double tauA, double tauB, double alpha, double beta,
-		double Fx, double Fy, double Fz, int start, int finish, int Np)
-{
+		double Fx, double Fy, double Fz, int start, int finish, int Np){
+
+	int ijk,nn,n;
 	double fq;
 	// conserved momemnts
 	double rho,jx,jy,jz;
 	// non-conserved moments
 	double m1,m2,m4,m6,m8,m9,m10,m11,m12,m13,m14,m15,m16,m17,m18;
+	double m3,m5,m7;
 	double nA,nB; // number density
 	double a1,b1,a2,b2,nAB,delta;
 	double C,nx,ny,nz; //color gradient magnitude and direction
@@ -615,7 +616,7 @@ extern "C" void ScaLBL_D3Q19_AAodd_DFH(int *neighborList, double *dist, double *
 		double *Phi, double *Gradient, double *SolidForce, double rhoA, double rhoB, double tauA, double tauB, double alpha, double beta,
 		double Fx, double Fy, double Fz, int start, int finish, int Np){
 	
-	int nread;
+	int n,nn,ijk,nread;
 	int nr1,nr2,nr3,nr4,nr5,nr6;
 	int nr7,nr8,nr9,nr10;
 	int nr11,nr12,nr13,nr14;
@@ -625,6 +626,7 @@ extern "C" void ScaLBL_D3Q19_AAodd_DFH(int *neighborList, double *dist, double *
 	double rho,jx,jy,jz;
 	// non-conserved moments
 	double m1,m2,m4,m6,m8,m9,m10,m11,m12,m13,m14,m15,m16,m17,m18;
+	double m3,m5,m7;
 	double nA,nB; // number density
 	double a1,b1,a2,b2,nAB,delta;
 	double C,nx,ny,nz; //color gradient magnitude and direction
@@ -1210,12 +1212,12 @@ extern "C" void ScaLBL_D3Q19_AAodd_DFH(int *neighborList, double *dist, double *
 }
 
 extern "C" void ScaLBL_D3Q7_AAodd_DFH(int *neighborList, double *Aq, double *Bq, 
-			double *Den, double *Phi, int start, int finish, int Np)
-{
+			double *Den, double *Phi, int start, int finish, int Np){
+
+	int idx,n,nread;
+	double fq,nA,nB;
 
 	for (int n=start; n<finish; n++){
-		int nread;
-		double fq,nA,nB;
 		
 		//..........Compute the number density for component A............
 		// q=0
@@ -1298,10 +1300,11 @@ extern "C" void ScaLBL_D3Q7_AAodd_DFH(int *neighborList, double *Aq, double *Bq,
 }
 
 extern "C" void ScaLBL_D3Q7_AAeven_DFH(double *Aq, double *Bq, double *Den, double *Phi, 
-			int start, int finish, int Np)
-{
+			int start, int finish, int Np){
+	int idx,n,nread;
+	double fq,nA,nB;
 	for (int n=start; n<finish; n++){
-		double fq,nA,nB;
+		
 		// compute number density for component A
 		// q=0
 		fq = Aq[n];

example/Workflow/ComputeSaturation.py

@@ -1,37 +0,0 @@
-import sys
-import numpy as np
-import matplotlib.pylab as plt
-
-FILENAME=sys.argv[1]
-Nx=int(sys.argv[2])
-Ny=int(sys.argv[3])
-Nz=int(sys.argv[4])
-
-# read the input image
-Output = np.fromfile(FILENAME,dtype = np.uint8)
-Output.shape = (Nz,Ny,Nx)
-
-Oil=np.count_nonzero(Output==1)
-Water=np.count_nonzero(Output==2)
-Sw=Water/(Oil+Water)
-
-Porosity=1.0-(Oil+Water)/(Nx*Ny*Nz)
-
-print(FILENAME,"Porosity=", Porosity)
-
-SaturationProfile=np.zeros(Nz)
-PorosityProfile=np.zeros(Nz)
-# Compute saturation slice by slice 
-for idx in range(0, Nz):
-   Slice = Output[idx,:,:]
-   Oil=np.count_nonzero(Slice==1)
-   Water=np.count_nonzero(Slice==2)
-   SaturationProfile[idx]=Water/(Oil+Water)
-   PorosityProfile[idx]=(Oil+Water)/(Nx*Ny)
-   
-
-plt.figure()
-plt.plot(SaturationProfile)
-plt.xlabel('Position (z)')
-plt.ylabel('Water Saturation')
-plt.show()

example/Workflow/HelperFunctions.R

@@ -2,32 +2,6 @@ require("ggplot2")
 
 GG_THEME=theme_bw()+theme(panel.grid.major = element_blank(),panel.grid.minor = element_blank())
 
-ReadDatabase<-function(FILE){
-
-    INPUT<-gsub(';','',readLines(FILE))
-
-    S<-gsub('tauA = ','',gsub("\\s+"," ",(grep("tauA",INPUT,value=TRUE))))
-    TAU_A = as.numeric(gsub("/.*","",S))
-    S<-gsub('tauB = ','',gsub("\\s+"," ",(grep("tauB",INPUT,value=TRUE))))
-    TAU_B = as.numeric(gsub("/.*","",S))
-    S<-gsub('rhoA = ','',gsub("\\s+"," ",(grep("rhoA",INPUT,value=TRUE))))
-    RHO_A = as.numeric(gsub("/.*","",S))
-    S<-gsub('rhoB = ','',gsub("\\s+"," ",(grep("rhoB",INPUT,value=TRUE))))
-    RHO_B = as.numeric(gsub("/.*","",S))
-
-    S<-gsub('alpha = ','',gsub("\\s+"," ",(grep("alpha",INPUT,value=TRUE))))
-    ALPHA = as.numeric(gsub("/.*","",S))
-
-    # Read the affinity
-    S<-gsub('ComponentAffinity = ','',gsub("\\s+"," ",(grep("ComponentAffinity",INPUT,value=TRUE))))
-    S<-gsub("/.*","",S)
-    AFFINITY<-as.numeric(unlist(strsplit(S,", ")))
-
-    PARAMETERS<-c(TAU_A,TAU_B,RHO_A,RHO_B,ALPHA,AFFINITY)
-    
-    return(PARAMETERS)
-}
-
 ReadSubphase<-function(PATH){
   FILE=paste0(PATH,"/subphase.csv")
   S<-read.csv(FILE,head=TRUE,sep=" ")

gpu/BGK.cu

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify

gpu/Color.cu

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify
@@ -144,7 +143,7 @@ __global__  void dvc_ScaLBL_Color_InitDistance(char *ID, double *Den, double *Ph
 
 __global__  void dvc_ScaLBL_Color_BC(int *list, int *Map, double *Phi, double *Den, double vA, double vB, int count, int Np)
 {
-	int idx,n;
+	int idx,n,nm;
 	// Fill the outlet with component b
 	idx = blockIdx.x*blockDim.x + threadIdx.x;
 	if (idx < count){
@@ -1256,15 +1255,6 @@ __global__  void dvc_ScaLBL_SetSlice_z(double *Phi, double value, int Nx, int Ny
 }
 
 
-__global__  void dvc_ScaLBL_CopySlice_z(double *Phi, int Nx, int Ny, int Nz, int Source, int Dest){
-	double value;
-	int n =  blockIdx.x*blockDim.x + threadIdx.x;
-	if (n < Nx*Ny){
-		value = Phi[Source*Nx*Ny+n];
-		Phi[Dest*Nx*Ny+n] = value;
-	}
-}
-
 
 __global__  void dvc_ScaLBL_D3Q19_AAeven_Color(int *Map, double *dist, double *Aq, double *Bq, double *Den, double *Phi,
 		double *Velocity, double rhoA, double rhoB, double tauA, double tauB, double alpha, double beta,
@@ -3496,11 +3486,13 @@ __global__ void dvc_ScaLBL_D3Q19_AAeven_ColorMass(double *Aq, double *Bq, double
 		double *Velocity, double *ColorGrad, double beta, int start, int finish, int Np){
 
 	int n;
+	double fq;
 	// non-conserved moments
 	double nA,nB; // number density
 	double a1,b1,a2,b2,nAB,delta;
 	double C,nx,ny,nz; //color gradient magnitude and direction
 	double ux,uy,uz;
+	double phi,tau,rho0,rlx_setA,rlx_setB;
 
 	int S = Np/NBLOCKS/NTHREADS + 1;
 	for (int s=0; s<S; s++){
@@ -3588,11 +3580,13 @@ __global__ void dvc_ScaLBL_D3Q19_AAodd_ColorMass(int *neighborList, double *Aq,
 		double *Velocity, double *ColorGrad, double beta, int start, int finish, int Np){
 
 	int n,nread;
+	double fq;
 	// non-conserved moments
 	double nA,nB; // number density
 	double a1,b1,a2,b2,nAB,delta;
 	double C,nx,ny,nz; //color gradient magnitude and direction
 	double ux,uy,uz;
+	double phi,tau,rho0,rlx_setA,rlx_setB;
 
 	int S = Np/NBLOCKS/NTHREADS + 1;
 	for (int s=0; s<S; s++){
@@ -4159,9 +4153,5 @@ extern "C" void ScaLBL_Color_BC_Z(int *list, int *Map, double *Phi, double *Den,
 	}
 }
 
-extern "C" void ScaLBL_CopySlice_z(double *Phi, int Nx, int Ny, int Nz, int Source, int Dest){
-	int GRID = Nx*Ny / 512 + 1;
-	dvc_ScaLBL_CopySlice_z<<<GRID,512>>>(Phi,Nx,Ny,Nz,Source,Dest);
-}
 
 

gpu/CudaExtras.cu

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify

gpu/D3Q19.cu

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify
@@ -283,6 +282,37 @@ __global__ void dvc_ScaLBL_D3Q19_Init(double *dist, int Np)
 	}
 }
 
+__global__ void dvc_ScaLBL_D3Q19_GreyIMRT_Init(double *dist, int Np, double Den)
+{
+	int n;
+	int S = Np/NBLOCKS/NTHREADS + 1;
+	for (int s=0; s<S; s++){
+		//........Get 1-D index for this thread....................
+		n = S*blockIdx.x*blockDim.x + s*blockDim.x + threadIdx.x;
+		if (n<Np ){
+			dist[n] = Den - 0.6666666666666667;
+			dist[Np+n] = 0.055555555555555555;		//double(100*n)+1.f;
+			dist[2*Np+n] = 0.055555555555555555;	//double(100*n)+2.f;
+			dist[3*Np+n] = 0.055555555555555555;	//double(100*n)+3.f;
+			dist[4*Np+n] = 0.055555555555555555;	//double(100*n)+4.f;
+			dist[5*Np+n] = 0.055555555555555555;	//double(100*n)+5.f;
+			dist[6*Np+n] = 0.055555555555555555;	//double(100*n)+6.f;
+			dist[7*Np+n] = 0.0277777777777778;   //double(100*n)+7.f;
+			dist[8*Np+n] = 0.0277777777777778;   //double(100*n)+8.f;
+			dist[9*Np+n] = 0.0277777777777778;   //double(100*n)+9.f;
+			dist[10*Np+n] = 0.0277777777777778;  //double(100*n)+10.f;
+			dist[11*Np+n] = 0.0277777777777778;  //double(100*n)+11.f;
+			dist[12*Np+n] = 0.0277777777777778;  //double(100*n)+12.f;
+			dist[13*Np+n] = 0.0277777777777778;  //double(100*n)+13.f;
+			dist[14*Np+n] = 0.0277777777777778;  //double(100*n)+14.f;
+			dist[15*Np+n] = 0.0277777777777778;  //double(100*n)+15.f;
+			dist[16*Np+n] = 0.0277777777777778;  //double(100*n)+16.f;
+			dist[17*Np+n] = 0.0277777777777778;  //double(100*n)+17.f;
+			dist[18*Np+n] = 0.0277777777777778;  //double(100*n)+18.f;
+		}
+	}
+}
+
 //*************************************************************************
 __global__  void dvc_ScaLBL_D3Q19_Swap_Compact(int *neighborList, double *disteven, double *distodd, int Np, int q){
 	int n,nn;
@@ -1553,6 +1583,7 @@ __global__  void dvc_ScaLBL_D3Q19_Momentum(double *dist, double *vel, int N)
 	double f1,f2,f3,f4,f5,f6,f7,f8,f9;
 	double f10,f11,f12,f13,f14,f15,f16,f17,f18;
 	double vx,vy,vz;
+	char id;
 
 	int S = N/NBLOCKS/NTHREADS + 1;
 	for (int s=0; s<S; s++){
@@ -1743,43 +1774,6 @@ __global__  void dvc_ScaLBL_D3Q19_AAeven_Pressure_BC_Z(int *list, double *dist,
 		//...................................................
 	}
 }
-__global__  void dvc_ScaLBL_D3Q19_Reflection_BC_z(int *list, double *dist, int count, int Np){
-	int idx, n;
-	idx = blockIdx.x*blockDim.x + threadIdx.x;
-	if (idx < count){
-		n = list[idx];
-		double f5 = 0.111111111111111111111111 - dist[6*Np+n];
-		double f11 = 0.05555555555555555555556 - dist[12*Np+n];
-		double f14 = 0.05555555555555555555556 - dist[13*Np+n];
-		double f15 = 0.05555555555555555555556 - dist[16*Np+n];
-		double f18 = 0.05555555555555555555556 - dist[17*Np+n];
-		
-		dist[6*Np+n] = f5;
-		dist[12*Np+n] = f11;
-		dist[13*Np+n] = f14;
-		dist[16*Np+n] = f15;
-		dist[17*Np+n] = f18;
-	}
-}
-
-__global__  void dvc_ScaLBL_D3Q19_Reflection_BC_Z(int *list, double *dist, int count, int Np){
-	int idx, n;
-	idx = blockIdx.x*blockDim.x + threadIdx.x;
-	if (idx < count){
-		n = list[idx];
-		double f6 = 0.111111111111111111111111 - dist[5*Np+n];
-		double f12 = 0.05555555555555555555556 - dist[11*Np+n];
-		double f13 = 0.05555555555555555555556 - dist[14*Np+n] ;
-		double f16 = 0.05555555555555555555556 - dist[15*Np+n];
-		double f17 = 0.05555555555555555555556 - dist[18*Np+n];
-		
-		dist[5*Np+n] = f6;
-		dist[11*Np+n] = f12;
-		dist[14*Np+n] = f13;
-		dist[15*Np+n] = f16;
-		dist[18*Np+n] = f17;
-	}
-}
 
 __global__  void dvc_ScaLBL_D3Q19_AAodd_Pressure_BC_z(int *d_neighborList, int *list, double *dist, double din, int count, int Np)
 {
@@ -2380,6 +2374,13 @@ extern "C" void ScaLBL_D3Q19_Init(double *dist, int Np){
 	}
 }
 
+extern "C" void ScaLBL_D3Q19_GreyIMRT_Init(double *dist, int Np, double Den){
+	dvc_ScaLBL_D3Q19_GreyIMRT_Init<<<NBLOCKS,NTHREADS >>>(dist, Np, Den);
+	cudaError_t err = cudaGetLastError();
+	if (cudaSuccess != err){
+		printf("CUDA error in ScaLBL_D3Q19_GreyIMRT_Init: %s \n",cudaGetErrorString(err));
+	}
+}
 
 extern "C" void ScaLBL_D3Q19_Swap(char *ID, double *disteven, double *distodd, int Nx, int Ny, int Nz){
 	dvc_ScaLBL_D3Q19_Swap<<<NBLOCKS,NTHREADS >>>(ID, disteven, distodd, Nx, Ny, Nz);
@@ -2667,23 +2668,11 @@ extern "C" double deviceReduce(double *in, double* out, int N) {
 	return sum;
 }
 
-extern "C" void ScaLBL_D3Q19_Reflection_BC_z(int *list, double *dist, int count, int Np){
-	int GRID = count / 512 + 1;
-	dvc_ScaLBL_D3Q19_Reflection_BC_z<<<GRID,512>>>(list, dist, count, Np);
-	cudaError_t err = cudaGetLastError();
-	if (cudaSuccess != err){
-		printf("CUDA error in ScaLBL_D3Q19_Reflection_BC_z (kernel): %s \n",cudaGetErrorString(err));
-	}
-}
-
-extern "C" void ScaLBL_D3Q19_Reflection_BC_Z(int *list, double *dist, int count, int Np){
-	int GRID = count / 512 + 1;
-	dvc_ScaLBL_D3Q19_Reflection_BC_Z<<<GRID,512>>>(list, dist, count, Np);
-	cudaError_t err = cudaGetLastError();
-	if (cudaSuccess != err){
-		printf("CUDA error in ScaLBL_D3Q19_Reflection_BC_Z (kernel): %s \n",cudaGetErrorString(err));
-	}
-}
+//
+//extern "C" void ScaLBL_D3Q19_Pressure_BC_Z(int *list, double *dist, double dout, int count, int Np){
+//	int GRID = count / 512 + 1;
+//	dvc_ScaLBL_D3Q19_Pressure_BC_Z<<<GRID,512>>>(disteven, distodd, dout, Nx, Ny, Nz, outlet);
+//}
 
 extern "C" void ScaLBL_D3Q19_AAeven_MRT(double *dist, int start, int finish, int Np, double rlx_setA, double rlx_setB, double Fx,
        double Fy, double Fz){

gpu/D3Q7.cu

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify
@@ -15,7 +14,6 @@
   along with OPM.  If not, see <http://www.gnu.org/licenses/>.
 */
 // GPU Functions for D3Q7 Lattice Boltzmann Methods
-#include <stdio.h>
 
 #define NBLOCKS 560
 #define NTHREADS 128
@@ -96,25 +94,6 @@ __global__ void dvc_ScaLBL_D3Q7_Unpack(int q,  int *list,  int start, int count,
 	}
 }
 
-__global__  void dvc_ScaLBL_D3Q7_Reflection_BC_z(int *list, double *dist, int count, int Np){
-	int idx, n;
-	idx = blockIdx.x*blockDim.x + threadIdx.x;
-	if (idx < count){
-		n = list[idx];
-		double f5 = 0.222222222222222222222222 - dist[6*Np+n];
-		dist[6*Np+n] = f5;
-	}
-}
-
-__global__  void dvc_ScaLBL_D3Q7_Reflection_BC_Z(int *list, double *dist, int count, int Np){
-	int idx, n;
-	idx = blockIdx.x*blockDim.x + threadIdx.x;
-	if (idx < count){
-		n = list[idx];
-		double f6 = 0.222222222222222222222222 - dist[5*Np+n];
-		dist[5*Np+n] = f6;
-	}
-}
 __global__ void dvc_ScaLBL_D3Q7_Init(char *ID, double *f_even, double *f_odd, double *Den, int Nx, int Ny, int Nz)
 {
 	int n,N;
@@ -243,24 +222,6 @@ __global__  void dvc_ScaLBL_D3Q7_Density(char *ID, double *disteven, double *dis
 	}
 }
 
-extern "C" void ScaLBL_D3Q7_Reflection_BC_z(int *list, double *dist, int count, int Np){
-	int GRID = count / 512 + 1;
-	dvc_ScaLBL_D3Q7_Reflection_BC_z<<<GRID,512>>>(list, dist, count, Np);
-	cudaError_t err = cudaGetLastError();
-	if (cudaSuccess != err){
-		printf("CUDA error in ScaLBL_D3Q7_Reflection_BC_z (kernel): %s \n",cudaGetErrorString(err));
-	}
-}
-
-extern "C" void ScaLBL_D3Q7_Reflection_BC_Z(int *list, double *dist, int count, int Np){
-	int GRID = count / 512 + 1;
-	dvc_ScaLBL_D3Q7_Reflection_BC_Z<<<GRID,512>>>(list, dist, count, Np);
-	cudaError_t err = cudaGetLastError();
-	if (cudaSuccess != err){
-		printf("CUDA error in ScaLBL_D3Q7_Reflection_BC_Z (kernel): %s \n",cudaGetErrorString(err));
-	}
-}
-
 extern "C" void ScaLBL_D3Q7_Unpack(int q, int *list,  int start, int count, double *recvbuf, double *dist, int N){
 	int GRID = count / 512 + 1;
 	dvc_ScaLBL_D3Q7_Unpack <<<GRID,512 >>>(q, list, start, count, recvbuf, dist, N);

gpu/dfh.cu

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify
@@ -16,7 +15,6 @@
 */
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify

models/ColorModel.cpp

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify
@@ -20,7 +19,6 @@ color lattice boltzmann model
 #include "models/ColorModel.h"
 #include "analysis/distance.h"
 #include "analysis/morphology.h"
-#include "common/Communication.h"
 #include "common/ReadMicroCT.h"
 #include <stdlib.h>
 #include <time.h>
@@ -72,6 +70,8 @@ void ScaLBL_ColorModel::ReadCheckpoint(char *FILENAME, double *cPhi, double *cfq
     File.close();
 }
  */
+
+
 void ScaLBL_ColorModel::ReadParams(string filename){
 	// read the input database 
 	db = std::make_shared<Database>( filename );
@@ -144,21 +144,21 @@ void ScaLBL_ColorModel::ReadParams(string filename){
 	// Override user-specified boundary condition for specific protocols
 	auto protocol = color_db->getWithDefault<std::string>( "protocol", "none" );
 	if (protocol == "seed water"){
-		if (BoundaryCondition != 0 && BoundaryCondition != 5){
+		if (BoundaryCondition != 0 ){
 			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){
+		if (BoundaryCondition != 0 ){
 			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){
+		if (BoundaryCondition != 0 ){
 			BoundaryCondition = 0;
 			if (rank==0) printf("WARNING: protocol (shell aggregation) supports only full periodic boundary condition \n");
 		}
@@ -200,22 +200,14 @@ void ScaLBL_ColorModel::ReadInput(){
 	if (color_db->keyExists( "image_sequence" )){
 		auto ImageList = color_db->getVector<std::string>( "image_sequence");
 		int IMAGE_INDEX = color_db->getWithDefault<int>( "image_index", 0 );
+		int IMAGE_COUNT = ImageList.size();
 		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 );
-        fill.copy( input_id, id_view );
-        fill.fill( id_view );
+	    for (int i=0; i<Nx*Ny*Nz; i++) Mask->id[i] = input_id(i);
 	}
 	else if (domain_db->keyExists( "Filename" )){
 		auto Filename = domain_db->getScalar<std::string>( "Filename" );
@@ -229,6 +221,7 @@ void ScaLBL_ColorModel::ReadInput(){
 	// 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++){
@@ -245,6 +238,7 @@ void ScaLBL_ColorModel::ReadInput(){
 	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;
 			}
@@ -277,7 +271,7 @@ void ScaLBL_ColorModel::AssignComponentLabels(double *phase)
 	double label_count_global[NLABELS];
 	// Assign the labels
 
-	for (size_t idx=0; idx<NLABELS; idx++) label_count[idx]=0;
+	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++){
@@ -305,8 +299,7 @@ void ScaLBL_ColorModel::AssignComponentLabels(double *phase)
 	// 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]=sumReduce( Dm->Comm, label_count[idx]);
+	for (int idx=0; idx<NLABELS; idx++)		label_count_global[idx]=sumReduce( Dm->Comm, label_count[idx]);
 
 	if (rank==0){
 		printf("Component labels: %lu \n",NLABELS);
@@ -385,16 +378,16 @@ void ScaLBL_ColorModel::Create(){
 	}
 	// check that TmpMap is valid
 	for (int idx=0; idx<ScaLBL_Comm->LastExterior(); idx++){
-		auto n = TmpMap[idx];
+		int n = TmpMap[idx];
 		if (n > Nx*Ny*Nz){
-			printf("Bad value! idx=%i \n", n);
+			printf("Bad value! idx=%i \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);
+		int n = TmpMap[idx];
+		if (n > Nx*Ny*Nz){
+			printf("Bad value! idx=%i \n");
 			TmpMap[idx] = Nx*Ny*Nz-1;
 		}
 	}
@@ -486,8 +479,7 @@ void ScaLBL_ColorModel::Initialize(){
 	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);
 
-	// establish reservoirs for external bC
-	if (BoundaryCondition == 1 || BoundaryCondition == 2 ||  BoundaryCondition == 3 || BoundaryCondition == 4 ){
+	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);
@@ -510,7 +502,6 @@ void ScaLBL_ColorModel::Run(){
 	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;
@@ -519,7 +510,6 @@ void ScaLBL_ColorModel::Run(){
 	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)
@@ -534,25 +524,13 @@ void ScaLBL_ColorModel::Run(){
 	double initial_volume = 0.0;
 	double delta_volume = 0.0;
 	double delta_volume_target = 0.0;
+	double RESIDUAL_ENDPOINT_THRESHOLD = 0.04;
+	double NOISE_THRESHOLD = 0.0;
+	double BUMP_RATE = 2.0;
+	bool USE_BUMP_RATE = false;
+	int RESCALE_FORCE_COUNT = 0;
+	int RESCALE_FORCE_MAX = 0;
 	
-	/* 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 (color_db->keyExists( "vol_A_previous" )){
-		volA_prev  = color_db->getScalar<double>( "vol_A_previous" );
-	}
-	if (color_db->keyExists( "log_krA_previous" )){
-		log_krA_prev  = color_db->getScalar<double>( "log_krA_previous" );
-	}
-	if (color_db->keyExists( "krA_morph_factor" )){
-		KRA_MORPH_FACTOR  = color_db->getScalar<double>( "krA_morph_factor" );
-	}
-	
-	/* defaults for simulation protocols */
 	auto protocol = color_db->getWithDefault<std::string>( "protocol", "none" );
 	if (protocol == "image sequence"){
 		// Get the list of images
@@ -564,33 +542,45 @@ void ScaLBL_ColorModel::Run(){
 		USE_MORPH = true;
 	}
 	else if (protocol == "seed water"){
-		morph_delta = -0.05;
+		morph_delta = 0.05;
 		seed_water = 0.01;
 		USE_SEED = true;
 		USE_MORPH = true;
 	}
 	else if (protocol == "open connected oil"){
-		morph_delta = -0.05;
+		morph_delta = 0.05;
 		USE_MORPH = true;
 		USE_MORPHOPEN_OIL = true;
 	}
 	else if (protocol == "shell aggregation"){
-		morph_delta = -0.05;
+		morph_delta = 0.05;
 		USE_MORPH = true;
 	}  
+	
+	if (color_db->keyExists( "residual_endpoint_threshold" )){
+		RESIDUAL_ENDPOINT_THRESHOLD  = color_db->getScalar<double>( "residual_endpoint_threshold" );
+	}
+	if (color_db->keyExists( "noise_threshold" )){
+		NOISE_THRESHOLD  = color_db->getScalar<double>( "noise_threshold" );
+		USE_BUMP_RATE = true;
+	}
+	if (color_db->keyExists( "bump_rate" )){
+		BUMP_RATE  = color_db->getScalar<double>( "bump_rate" );
+		USE_BUMP_RATE = true;
+	}
 	if (color_db->keyExists( "capillary_number" )){
 		capillary_number = color_db->getScalar<double>( "capillary_number" );
 		SET_CAPILLARY_NUMBER=true;
+		//RESCALE_FORCE_MAX = 1;
 	}
-	if (color_db->keyExists( "rescale_force_after_timestep" )){
-		RESCALE_FORCE_AFTER_TIMESTEP = color_db->getScalar<int>( "rescale_force_after_timestep" );
-		RESCALE_FORCE = true;
+	if (analysis_db->keyExists( "rescale_force_count" )){
+		RESCALE_FORCE_MAX = analysis_db->getScalar<int>( "rescale_force_count" );
 	}
 	if (color_db->keyExists( "timestep" )){
 		timestep = color_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");
+	if (BoundaryCondition != 0 && SET_CAPILLARY_NUMBER==true){
+		if (rank == 0) printf("WARINING: capillary number target only supported for BC = 0 \n");
 		SET_CAPILLARY_NUMBER=false;
 	}
 	if (analysis_db->keyExists( "seed_water" )){
@@ -693,7 +683,7 @@ void ScaLBL_ColorModel::Run(){
 
 		// Perform the collision operation
 		ScaLBL_Comm->SendD3Q19AA(fq); //READ FROM NORMAL
-		if (BoundaryCondition > 0 && BoundaryCondition < 5){
+		if (BoundaryCondition > 0){
 			ScaLBL_Comm->Color_BC_z(dvcMap, Phi, Den, inletA, inletB);
 			ScaLBL_Comm->Color_BC_Z(dvcMap, Phi, Den, outletA, outletB);
 		}
@@ -714,14 +704,9 @@ void ScaLBL_ColorModel::Run(){
 			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);
-		}
 		ScaLBL_D3Q19_AAodd_Color(NeighborList, dvcMap, fq, Aq, Bq, Den, Phi, Velocity, rhoA, rhoB, tauA, tauB,
 				alpha, beta, Fx, Fy, Fz, Nx, Nx*Ny, 0, ScaLBL_Comm->LastExterior(), Np);
-		ScaLBL_DeviceBarrier(); 
-		MPI_Barrier(ScaLBL_Comm->MPI_COMM_SCALBL);
+		ScaLBL_DeviceBarrier(); MPI_Barrier(comm);
 
 		// *************EVEN TIMESTEP*************
 		timestep++;
@@ -735,7 +720,7 @@ void ScaLBL_ColorModel::Run(){
 		// Perform the collision operation
 		ScaLBL_Comm->SendD3Q19AA(fq); //READ FORM NORMAL
 		// Halo exchange for phase field
-		if (BoundaryCondition > 0 && BoundaryCondition < 5){
+		if (BoundaryCondition > 0){
 			ScaLBL_Comm->Color_BC_z(dvcMap, Phi, Den, inletA, inletB);
 			ScaLBL_Comm->Color_BC_Z(dvcMap, Phi, Den, outletA, outletB);
 		}
@@ -754,23 +739,21 @@ void ScaLBL_ColorModel::Run(){
 			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);
-		}
 		ScaLBL_D3Q19_AAeven_Color(dvcMap, fq, Aq, Bq, Den, Phi, Velocity, rhoA, rhoB, tauA, tauB,
 				alpha, beta, Fx, Fy, Fz, Nx, Nx*Ny, 0, ScaLBL_Comm->LastExterior(), Np);
-		ScaLBL_DeviceBarrier(); 
-		MPI_Barrier(ScaLBL_Comm->MPI_COMM_SCALBL);
+		ScaLBL_DeviceBarrier(); MPI_Barrier(comm);
 		//************************************************************************
+		
+		MPI_Barrier(comm);
 		PROFILE_STOP("Update");
 
-		if (rank==0 && timestep%analysis_interval == 0 && BoundaryCondition == 4){
+		if (rank==0 && timestep%analysis_interval == 0 && BoundaryCondition > 0){
 			printf("%i %f \n",timestep,din);
 		}
 		// Run the analysis
 		analysis.basic(timestep, current_db, *Averages, Phi, Pressure, Velocity, fq, Den );
 
+		
 		// allow initial ramp-up to get closer to steady state
 		if (timestep > RAMP_TIMESTEPS && timestep%analysis_interval == 0 && USE_MORPH){
 			analysis.finish();
@@ -780,7 +763,7 @@ void ScaLBL_ColorModel::Run(){
 			double volA = Averages->gnb.V; 
 			volA /= Dm->Volume;
 			volB /= Dm->Volume;;
-			//initial_volume = volA*Dm->Volume;
+			initial_volume = volA*Dm->Volume;
 			double vA_x = Averages->gnb.Px/Averages->gnb.M; 
 			double vA_y = Averages->gnb.Py/Averages->gnb.M; 
 			double vA_z = Averages->gnb.Pz/Averages->gnb.M; 
@@ -812,50 +795,28 @@ void ScaLBL_ColorModel::Run(){
 					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 %f \n ",capillary_number / Ca);
-				  Averages->SetParams(rhoA,rhoB,tauA,tauB,Fx,Fy,Fz,alpha,beta);
-				  color_db->putVector<double>("F",{Fx,Fy,Fz});
+				
+				if (SET_CAPILLARY_NUMBER  && RESCALE_FORCE_COUNT < RESCALE_FORCE_MAX){
+					RESCALE_FORCE_COUNT++;
+					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 %f \n ",capillary_number / Ca);
+					Averages->SetParams(rhoA,rhoB,tauA,tauB,Fx,Fy,Fz,alpha,beta);
+					color_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 = %f, krB = %f \n",krA_TMP,krB_TMP);	
-							printf("    log(kr)=%f, volume=%f, TARGET log(kr)=%f, volume change=%f \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 );
@@ -870,8 +831,8 @@ void ScaLBL_ColorModel::Run(){
 						double pB = Averages->gwb.p;
 						double pAc = Averages->gnc.p;
 						double pBc = Averages->gwc.p;
-						double pAB = (pA-pB)/(h*6.0*alpha);
-						double pAB_connected = (pAc-pBc)/(h*6.0*alpha);
+						double pAB = (pA-pB)/(h*5.796*alpha);
+						double pAB_connected = (pAc-pBc)/(h*5.796*alpha);
 						// connected contribution
 						double Vol_nc = Averages->gnc.V/Dm->Volume;
 						double Vol_wc = Averages->gwc.V/Dm->Volume;
@@ -918,7 +879,7 @@ void ScaLBL_ColorModel::Run(){
 							WriteHeader=true;
 						kr_log_file = fopen("relperm.csv","a");
 						if (WriteHeader)
-							fprintf(kr_log_file,"timesteps sat.water eff.perm.oil eff.perm.water eff.perm.oil.connected eff.perm.water.connected eff.perm.oil.disconnected eff.perm.water.disconnected cap.pressure cap.pressure.connected pressure.drop Ca M\n");
+							fprintf(kr_log_file,"timesteps sat.water eff.perm.oil eff.perm.water eff.perm.oil.connected eff.perm.water.connected eff.perm.oil.disconnected eff.perm.water.disconnected cap.pressure cap.pressure.connected pressure.drop Ca M\n",CURRENT_STEADY_TIMESTEPS,current_saturation,kAeff,kBeff,pAB,viscous_pressure_drop,Ca,Mobility);
 
 						fprintf(kr_log_file,"%i %.5g %.5g %.5g %.5g %.5g %.5g %.5g %.5g %.5g %.5g %.5g %.5g\n",CURRENT_STEADY_TIMESTEPS,current_saturation,kAeff,kBeff,kAeff_connected,kBeff_connected,kAeff_disconnected,kBeff_disconnected,pAB,pAB_connected,viscous_pressure_drop,Ca,Mobility);
 						fclose(kr_log_file);
@@ -929,16 +890,26 @@ void ScaLBL_ColorModel::Run(){
 						Fx *= capillary_number / Ca;
 						Fy *= capillary_number / Ca;
 						Fz *= capillary_number / Ca;
+						RESCALE_FORCE_COUNT = 1;
 						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 (flow_rate_A < NOISE_THRESHOLD && USE_BUMP_RATE){
+							if (rank==0) printf("Hit noise threshold (%f): bumping capillary number by %f X \n",NOISE_THRESHOLD,BUMP_RATE);
+							Fx *= BUMP_RATE;   // impose bump condition
+							Fy *= BUMP_RATE;   
+							Fz *= BUMP_RATE;   
+							capillary_number *= BUMP_RATE;
+							color_db->putScalar<int>("capillary_number",capillary_number);
+							current_db->putDatabase("Color", color_db);
+							MORPH_ADAPT = false; // re-run current point if below noise threshold
+						}
 						if (rank == 0) printf("    -- adjust force by factor %f \n ",capillary_number / Ca);
 						Averages->SetParams(rhoA,rhoB,tauA,tauB,Fx,Fy,Fz,alpha,beta);
 						color_db->putVector<double>("F",{Fx,Fy,Fz});
 					}
-					
 					CURRENT_STEADY_TIMESTEPS = 0;
 				}
 				else{
@@ -972,7 +943,7 @@ void ScaLBL_ColorModel::Run(){
 					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, volume change %f / %f ***\n", massChange, delta_volume, delta_volume_target);
+					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;
@@ -990,29 +961,41 @@ void ScaLBL_ColorModel::Run(){
 					CURRENT_STEADY_TIMESTEPS=0;
 					initial_volume = volA*Dm->Volume;
 					delta_volume = 0.0;
-					if (RESCALE_FORCE_AFTER_TIMESTEP > 0)
-						RESCALE_FORCE = true;
+					if (USE_DIRECT){
+						//BoundaryCondition = 0;
+						//ScaLBL_Comm->BoundaryCondition = 0;
+						//ScaLBL_Comm_Regular->BoundaryCondition = 0;
+						//Fx = capillary_number*dir_x*force_mag / Ca;
+						//Fy = capillary_number*dir_y*force_mag / Ca;
+						//Fz = capillary_number*dir_z*force_mag / Ca;
+					}
 				}
 				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;
 				}
+				if ( REVERSE_FLOW_DIRECTION ){
+					//if (rank==0) printf("*****REVERSE FLOW DIRECTION***** \n");
+					delta_volume = 0.0;
+					// flow direction will reverse after next steady point
+					MORPH_ADAPT = false;
+					CURRENT_STEADY_TIMESTEPS=0;
+					//morph_delta *= (-1.0);
+					REVERSE_FLOW_DIRECTION = false;
+				}
+				MPI_Barrier(comm);
 			}
 			morph_timesteps += analysis_interval;
 		}
-		MPI_Barrier(ScaLBL_Comm->MPI_COMM_SCALBL);
 	}
 	analysis.finish();
 	PROFILE_STOP("Loop");
 	PROFILE_SAVE("lbpm_color_simulator",1);
 	//************************************************************************
 	ScaLBL_DeviceBarrier();
-	MPI_Barrier(ScaLBL_Comm->MPI_COMM_SCALBL);
+	MPI_Barrier(comm);
 	stoptime = MPI_Wtime();
 	if (rank==0) printf("-------------------------------------------------------------------\n");
 	// Compute the walltime per timestep
@@ -1032,6 +1015,7 @@ void ScaLBL_ColorModel::Run(){
 
 double ScaLBL_ColorModel::ImageInit(std::string Filename){
 	
+	bool suppress = false;
 	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
@@ -1062,12 +1046,12 @@ double ScaLBL_ColorModel::ImageInit(std::string Filename){
 	
 	if (rank==0) printf("   new saturation: %f (%f / %f) \n", Count / PoreCount, Count, PoreCount);
 	ScaLBL_CopyToDevice(Phi, PhaseLabel, Nx*Ny*Nz*sizeof(double));
-	MPI_Barrier(ScaLBL_Comm->MPI_COMM_SCALBL);
+	MPI_Barrier(comm);
 	
 	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);
-	MPI_Barrier(ScaLBL_Comm->MPI_COMM_SCALBL);
+	MPI_Barrier(comm);
 	
 	ScaLBL_CopyToHost(Averages->Phi.data(),Phi,Nx*Ny*Nz*sizeof(double));
 
@@ -1101,9 +1085,10 @@ double ScaLBL_ColorModel::MorphOpenConnected(double target_volume_change){
 		ComputeGlobalBlobIDs(nx-2,ny-2,nz-2,Dm->rank_info,phase,Averages->SDs,vF,vS,phase_label,Dm->Comm);
 		MPI_Barrier(Dm->Comm);
 
-		long long count_connected=0;
-		long long count_porespace=0;
-		long long count_water=0;
+		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++){
@@ -1203,7 +1188,7 @@ double ScaLBL_ColorModel::MorphOpenConnected(double target_volume_change){
 		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 == 1 || BoundaryCondition == 2 || BoundaryCondition == 3 || BoundaryCondition == 4){
+		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);
@@ -1218,79 +1203,99 @@ double ScaLBL_ColorModel::MorphOpenConnected(double target_volume_change){
 	}
 	return(volume_change);
 }
+
 double ScaLBL_ColorModel::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];
+	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;
-  }
+	ScaLBL_CopyToHost(Aq_tmp, Aq, 7*Np*sizeof(double));
+	ScaLBL_CopyToHost(Bq_tmp, Bq, 7*Np*sizeof(double));
+	
+/*	for (int k=1; k<Nz-1; k++){
+		for (int j=1; j<Ny-1; j++){
+			for (int i=1; i<Nx-1; i++){
+				double random_value = double(rand())/ RAND_MAX;
 
-  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;
-  }
+				if (Averages->SDs(i,j,k) < 0.f){
+					// skip
+				}
+				else if (phase(i,j,k) > 0.f ){
+					phase(i,j,k) -= random_value*seed_water_in_oil;
+					mass_loss += random_value*seed_water_in_oil;
+					count++;
+				}
+				else {
 
-  count= sumReduce( Dm->Comm, count);
-  mass_loss= sumReduce( Dm->Comm, mass_loss);
-  if (rank == 0) printf("Remove mass %f from %f voxels \n",mass_loss,count);
+				}
+			}
+		}
+	}
+	*/
+	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;
+	}
 
-  // 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));
+	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;
+	}
 
-  return(mass_loss);
+	count= sumReduce( Dm->Comm, count);
+	mass_loss= sumReduce( Dm->Comm, mass_loss);
+	if (rank == 0) printf("Remove mass %f from %f 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);
 }
 
 double ScaLBL_ColorModel::MorphInit(const double beta, const double target_delta_volume){
@@ -1299,8 +1304,6 @@ double ScaLBL_ColorModel::MorphInit(const double beta, const double target_delta
 	double vF = 0.f;
 	double vS = 0.f;
 	double delta_volume;
-	double WallFactor = 0.0;
-	bool USE_CONNECTED_NWP = false;
 
 	DoubleArray phase(Nx,Ny,Nz);
 	IntArray phase_label(Nx,Ny,Nz);;
@@ -1313,7 +1316,8 @@ double ScaLBL_ColorModel::MorphInit(const double beta, const double target_delta
 	// 1. Copy phase field to CPU
 	ScaLBL_CopyToHost(phase.data(), Phi, N*sizeof(double));
 
-	double count = 0.f;
+	double count,count_global,volume_initial,volume_final,volume_connected;
+	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++){
@@ -1321,7 +1325,7 @@ double ScaLBL_ColorModel::MorphInit(const double beta, const double target_delta
 			}
 		}
 	}
-	double volume_initial = sumReduce( Dm->Comm, count);
+	volume_initial = sumReduce( Dm->Comm, count);
 	/*
 	sprintf(LocalRankFilename,"phi_initial.%05i.raw",rank);
 	FILE *INPUT = fopen(LocalRankFilename,"wb");
@@ -1329,64 +1333,40 @@ double ScaLBL_ColorModel::MorphInit(const double beta, const double target_delta
 	fclose(INPUT);
 	*/
 	// 2. Identify connected components of phase field -> phase_label
+	BlobIDstruct new_index;
+	ComputeGlobalBlobIDs(Nx-2,Ny-2,Nz-2,rank_info,phase,Averages->SDs,vF,vS,phase_label,comm);
+	MPI_Barrier(comm);
 	
-	double volume_connected = 0.0;
-       	double second_biggest = 0.0;
-	if (USE_CONNECTED_NWP){
-		BlobIDstruct new_index;
-		ComputeGlobalBlobIDs(Nx-2,Ny-2,Nz-2,rank_info,phase,Averages->SDs,vF,vS,phase_label,comm);
-		MPI_Barrier(Dm->Comm);
+	// only operate on component "0"
+	count = 0.0;
+	double second_biggest = 0.0;
 
-		// 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;
-					}
+	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;
 				}
-			}
-		}	
-		volume_connected = sumReduce( Dm->Comm, count);
-		second_biggest = sumReduce( Dm->Comm, 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 (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;
-					}
+				else 		
+					phase_id(i,j,k) = 1;
+				if (label == 1 ){
+					second_biggest += 1.0;
 				}
 			}
 		}
-	}
+	}	
+	volume_connected = sumReduce( Dm->Comm, count);
+	second_biggest = sumReduce( Dm->Comm, second_biggest);
 
-	/*int reach_x, reach_y, reach_z;
+	int reach_x, reach_y, reach_z;
 	for (int k=0; k<Nz; k++){
 		for (int j=0; j<Ny; j++){
 			for (int i=0; i<Nx; i++){
 			}
 		}
-	}*/
+	}
 
 	// 3. Generate a distance map to the largest object -> phase_distance
 	CalcDist(phase_distance,phase_id,*Dm);
@@ -1413,21 +1393,18 @@ double ScaLBL_ColorModel::MorphInit(const double beta, const double target_delta
 		}
 	}
 
-	if (USE_CONNECTED_NWP){
 	if (volume_connected - second_biggest < 2.0*fabs(target_delta_volume) && target_delta_volume < 0.0){
 		// if connected volume is less than 2% just delete the whole thing
 		if (rank==0) printf("Connected region has shrunk! \n");
 		REVERSE_FLOW_DIRECTION = true;
 	}
-	
 /*	else{*/
 		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(Averages->SDs,phase_distance,phase_id,Averages->Dm, target_delta_volume_incremental, WallFactor);
+		delta_volume = MorphGrow(Averages->SDs,phase_distance,phase_id,Averages->Dm, target_delta_volume_incremental);
 
 		for (int k=0; k<Nz; k++){
 			for (int j=0; j<Ny; j++){
@@ -1445,6 +1422,7 @@ double ScaLBL_ColorModel::MorphInit(const double beta, const double target_delta
 		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;
 					double d = phase_distance(i,j,k);
 					if (Averages->SDs(i,j,k) > 0.f){
 						if (d < 3.f){
@@ -1468,7 +1446,7 @@ double ScaLBL_ColorModel::MorphInit(const double beta, const double target_delta
 			}
 		}
 	}
-	double volume_final= sumReduce( Dm->Comm, count);
+	volume_final= sumReduce( Dm->Comm, count);
 
 	delta_volume = (volume_final-volume_initial);
 	if (rank == 0)  printf("MorphInit: change fluid volume fraction by %f \n", delta_volume/volume_initial);
@@ -1491,7 +1469,7 @@ double ScaLBL_ColorModel::MorphInit(const double beta, const double target_delta
 	// 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);
-	if (BoundaryCondition == 1 || BoundaryCondition == 2 || BoundaryCondition == 3 || BoundaryCondition == 4){
+	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);
@@ -1560,25 +1538,25 @@ void ScaLBL_ColorModel::WriteDebug(){
 	fwrite(PhaseField.data(),8,N,VELZ_FILE);
 	fclose(VELZ_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[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);
 
-	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);
-*/
 }

models/ColorModel.h

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify

models/DFHModel.cpp

@@ -114,6 +114,7 @@ void ScaLBL_DFHModel::SetDomain(){
 }
 
 void ScaLBL_DFHModel::ReadInput(){
+	size_t readID;
 	//.......................................................................
 	if (rank == 0)    printf("Read input media... \n");
 	//.......................................................................

models/GreyscaleColorModel.h

@@ -1,94 +0,0 @@
-/*
-Implementation of two-fluid greyscale color lattice boltzmann model
- */
-#include <stdio.h>
-#include <stdlib.h>
-#include <sys/stat.h>
-#include <iostream>
-#include <exception>
-#include <stdexcept>
-#include <fstream>
-
-#include "common/Communication.h"
-#include "analysis/GreyPhase.h"
-#include "common/MPI_Helpers.h"
-#include "ProfilerApp.h"
-#include "threadpool/thread_pool.h"
-
-class ScaLBL_GreyscaleColorModel{
-public:
-	ScaLBL_GreyscaleColorModel(int RANK, int NP, MPI_Comm COMM);
-	~ScaLBL_GreyscaleColorModel();	
-	
-	// functions in they should be run
-	void ReadParams(string filename);
-	void ReadParams(std::shared_ptr<Database> db0);
-	void SetDomain();
-	void ReadInput();
-	void Create();
-	void Initialize();
-	void Run();
-	void WriteDebug();
-	
-	bool Restart,pBC;
-	bool REVERSE_FLOW_DIRECTION;
-	int timestep,timestepMax;
-	int BoundaryCondition;
-	double tauA,tauB,rhoA,rhoB,alpha,beta;
-    double tauA_eff,tauB_eff;
-	double Fx,Fy,Fz,flux;
-	double din,dout,inletA,inletB,outletA,outletB;
-    double GreyPorosity;
-	
-	int Nx,Ny,Nz,N,Np;
-	int rank,nprocx,nprocy,nprocz,nprocs;
-	double Lx,Ly,Lz;
-
-	std::shared_ptr<Domain> Dm;   // this domain is for analysis
-	std::shared_ptr<Domain> Mask; // this domain is for lbm
-	std::shared_ptr<ScaLBL_Communicator> ScaLBL_Comm;
-	std::shared_ptr<ScaLBL_Communicator> ScaLBL_Comm_Regular;
-        std::shared_ptr<GreyPhaseAnalysis> Averages;
-    
-    // input database
-    std::shared_ptr<Database> db;
-    std::shared_ptr<Database> domain_db;
-    std::shared_ptr<Database> greyscaleColor_db;
-    std::shared_ptr<Database> analysis_db;
-    std::shared_ptr<Database> vis_db;
-
-    IntArray Map;
-    signed char *id;    
-	int *NeighborList;
-	int *dvcMap;
-	double *fq, *Aq, *Bq;
-	double *Den, *Phi;
-    //double *GreySolidPhi; //Model 2 & 3
-    double *GreySolidGrad;//Model 1 & 4
-	//double *ColorGrad;
-	double *Velocity;
-	double *Pressure;
-    double *Porosity_dvc;
-    double *Permeability_dvc;
-		
-private:
-	MPI_Comm comm;
-    
-	int dist_mem_size;
-	int neighborSize;
-	// filenames
-    char LocalRankString[8];
-    char LocalRankFilename[40];
-    char LocalRestartFile[40];
-   
-    //int rank,nprocs;
-    void LoadParams(std::shared_ptr<Database> db0);
-    void AssignComponentLabels();
-    void AssignGreySolidLabels();
-    void AssignGreyPoroPermLabels();
-    void ImageInit(std::string filename);
-    double MorphInit(const double beta, const double morph_delta);
-    double SeedPhaseField(const double seed_water_in_oil);
-    double MorphOpenConnected(double target_volume_change);
-};
-

models/GreyscaleModel.cpp

@@ -1,20 +1,5 @@
 /*
-  Copyright 2020 Equinor ASA
-  Copyright Equnior ASA
-
-  This file is part of the Open Porous Media project (OPM).
-  OPM is free software: you can redistribute it and/or modify
-  it under the terms of the GNU General Public License as published by
-  the Free Software Foundation, either version 3 of the License, or
-  (at your option) any later version.
-  OPM is distributed in the hope that it will be useful,
-  but WITHOUT ANY WARRANTY; without even the implied warranty of
-  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-  GNU General Public License for more details.
-  You should have received a copy of the GNU General Public License
-  along with OPM.  If not, see <http://www.gnu.org/licenses/>.
-
-  Greyscale lattice boltzmann model
+Greyscale lattice boltzmann model
  */
 #include "models/GreyscaleModel.h"
 #include "analysis/distance.h"
@@ -59,7 +44,7 @@ void ScaLBL_GreyscaleModel::ReadParams(string filename){
 	din=dout=1.0;
 	flux=0.0;
     dp = 10.0; //unit of 'dp': voxel
-    CollisionType = 1; //1: IMRT; 2: BGK; 3: MRT
+    CollisionType = 1; //1: IMRT; 2: BGK
 	
 	// ---------------------- Greyscale Model parameters -----------------------//
 	if (greyscale_db->keyExists( "timestepMax" )){
@@ -99,9 +84,6 @@ void ScaLBL_GreyscaleModel::ReadParams(string filename){
 	if (collision == "BGK"){
         CollisionType=2;
 	}
-    else if (collision == "MRT"){
-        CollisionType=3;
-    }
 	// ------------------------------------------------------------------------//
     
     //------------------------ Other Domain parameters ------------------------//
@@ -217,9 +199,9 @@ void ScaLBL_GreyscaleModel::AssignComponentLabels(double *Porosity, double *Perm
 
 	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++){
+	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;
 				VALUE=id[n];
 				// Assign the affinity from the paired list
@@ -248,9 +230,9 @@ void ScaLBL_GreyscaleModel::AssignComponentLabels(double *Porosity, double *Perm
 	if (NLABELS != PermeabilityList.size()){
 		ERROR("Error: ComponentLabels 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++){
+	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;
 				VALUE=id[n];
 				// Assign the affinity from the paired list
@@ -280,6 +262,7 @@ void ScaLBL_GreyscaleModel::AssignComponentLabels(double *Porosity, double *Perm
 	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]=sumReduce( Dm->Comm, label_count[idx]);
+
     //Initialize a weighted porosity after considering grey voxels
     GreyPorosity=0.0;
 	for (unsigned int idx=0; idx<NLABELS; idx++){
@@ -289,7 +272,7 @@ void ScaLBL_GreyscaleModel::AssignComponentLabels(double *Porosity, double *Perm
 
 	if (rank==0){
         printf("Image resolution: %.5g [um/voxel]\n",Dm->voxel_length);
-		printf("Number of component labels: %lu \n",NLABELS);
+		printf("Component labels: %lu \n",NLABELS);
 		for (unsigned int idx=0; idx<NLABELS; idx++){
 			VALUE=LabelList[idx];
 			POROSITY=PorosityList[idx];
@@ -303,56 +286,6 @@ void ScaLBL_GreyscaleModel::AssignComponentLabels(double *Porosity, double *Perm
 	}
 }
 
-void ScaLBL_GreyscaleModel::AssignComponentLabels(double *Porosity,double *Permeability,const vector<std::string> &File_poro,const vector<std::string> &File_perm)
-{
-    double *Porosity_host, *Permeability_host;
-    Porosity_host = new double[N];
-    Permeability_host = new double[N];
-	double POROSITY=0.f;
-	double PERMEABILITY=0.f;
-    //Initialize a weighted porosity after considering grey voxels
-    double GreyPorosity_loc=0.0;
-    GreyPorosity=0.0;
-    //double label_count_loc = 0.0;
-    //double label_count_glb = 0.0;
-
-    Mask->ReadFromFile(File_poro[0],File_poro[1],Porosity_host);
-    Mask->ReadFromFile(File_perm[0],File_perm[1],Permeability_host);
-
-	for (int k=0;k<Nz;k++){
-		for (int j=0;j<Ny;j++){
-			for (int i=0;i<Nx;i++){
-				int idx = Map(i,j,k);
-				if (!(idx < 0)){
-				    int n = k*Nx*Ny+j*Nx+i;
-                    POROSITY = Porosity_host[n];
-                    PERMEABILITY = Permeability_host[n];
-                    if (POROSITY<=0.0){
-                        ERROR("Error: Porosity for grey voxels must be 0.0 < Porosity <= 1.0 !\n");
-                    }
-                    else if (PERMEABILITY<=0.0){
-                        ERROR("Error: Permeability for grey voxel must be > 0.0 ! \n");
-                    }
-                    else{
-                        Porosity[idx] = POROSITY;
-                        Permeability[idx] = PERMEABILITY;
-                        GreyPorosity_loc += POROSITY;
-                        //label_count_loc += 1.0;
-                    }
-                }
-			}
-		}
-	}
-    GreyPorosity = sumReduce( Dm->Comm, GreyPorosity_loc);
-    GreyPorosity = GreyPorosity/double((Nx-2)*(Ny-2)*(Nz-2)*nprocs);
-
-	if (rank==0){
-        printf("Image resolution: %.5g [um/voxel]\n",Dm->voxel_length);
-        printf("The weighted porosity, considering both open and grey voxels, is %.3g\n",GreyPorosity);
-	}
-    delete [] Porosity_host;
-    delete [] Permeability_host;
-}
 
 void ScaLBL_GreyscaleModel::Create(){
 	/*
@@ -391,6 +324,7 @@ void ScaLBL_GreyscaleModel::Create(){
 	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 **) &Permeability, sizeof(double)*Np);		
 	ScaLBL_AllocateDeviceMemory((void **) &Porosity, sizeof(double)*Np);		
@@ -398,31 +332,47 @@ void ScaLBL_GreyscaleModel::Create(){
 	ScaLBL_AllocateDeviceMemory((void **) &Velocity, 3*sizeof(double)*Np);
 	//...........................................................................
 	// Update GPU data structures
-	if (rank==0)	printf ("Setting up device neighbor list \n");
+	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++){
+		int n = TmpMap[idx];
+		if (n > Nx*Ny*Nz){
+			printf("Bad value! idx=%i \n");
+			TmpMap[idx] = Nx*Ny*Nz-1;
+		}
+	}
+	for (int idx=ScaLBL_Comm->FirstInterior(); idx<ScaLBL_Comm->LastInterior(); idx++){
+		int n = TmpMap[idx];
+		if (n > Nx*Ny*Nz){
+			printf("Bad value! idx=%i \n");
+			TmpMap[idx] = Nx*Ny*Nz-1;
+		}
+	}
+	ScaLBL_CopyToDevice(dvcMap, TmpMap, sizeof(int)*Np);
+	ScaLBL_DeviceBarrier();
+	delete [] TmpMap;
+	
 	// copy the neighbor list 
 	ScaLBL_CopyToDevice(NeighborList, neighborList, neighborSize);
 	// initialize phi based on PhaseLabel (include solid component labels)
 	double *Poros, *Perm;
 	Poros = new double[Np];
-	Perm  = new double[Np];
-    if (greyscale_db->keyExists("FileVoxelPorosityMap")){
-        //NOTE: FileVoxel**Map is a vector, including "file_name, datatype"
-		auto File_poro = greyscale_db->getVector<std::string>( "FileVoxelPorosityMap" );
-		auto File_perm = greyscale_db->getVector<std::string>( "FileVoxelPermeabilityMap" );
-	    AssignComponentLabels(Poros,Perm,File_poro,File_perm);
-    }
-    else if (greyscale_db->keyExists("PorosityList")){
-        //initialize voxel porosity and perm from the input list
-	    AssignComponentLabels(Poros,Perm);
-    }
-    else {
-		ERROR("Error: PorosityList or FilenameVoxelPorosityMap cannot be found! \n");
-    }
+	Perm = new double[Np];
+	AssignComponentLabels(Poros,Perm);
 	ScaLBL_CopyToDevice(Porosity, Poros, Np*sizeof(double));
 	ScaLBL_CopyToDevice(Permeability, Perm, Np*sizeof(double));
-    delete [] Poros;
-    delete [] Perm;
 }        
 
 
@@ -439,10 +389,6 @@ void ScaLBL_GreyscaleModel::Initialize(){
 	    ScaLBL_D3Q19_Init(fq, Np);
         if (rank==0) printf("Collision model: BGK.\n");
     }
-    else if (CollisionType==3){
-	    ScaLBL_D3Q19_Init(fq, Np);
-        if (rank==0) printf("Collision model: MRT.\n");
-    }
     else{
         if (rank==0) printf("Unknown collison type! IMRT collision is used.\n"); 
 	    ScaLBL_D3Q19_GreyIMRT_Init(fq, Np, Den);
@@ -524,9 +470,6 @@ void ScaLBL_GreyscaleModel::Run(){
             case 2: 
                     ScaLBL_D3Q19_AAodd_Greyscale(NeighborList, fq,  ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np, rlx, rlx_eff, Fx, Fy, Fz,Porosity,Permeability,Velocity,Pressure_dvc);
                     break;
-            case 3: 
-                    ScaLBL_D3Q19_AAodd_Greyscale_MRT(NeighborList, fq,  ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np, rlx, rlx_eff, Fx, Fy, Fz,Porosity,Permeability,Velocity,Den,Pressure_dvc);
-                    break;
             default: 
                     ScaLBL_D3Q19_AAodd_Greyscale_IMRT(NeighborList, fq,  ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np, rlx, rlx_eff, Fx, Fy, Fz,Porosity,Permeability,Velocity,Den,Pressure_dvc);
                     break;
@@ -545,9 +488,6 @@ void ScaLBL_GreyscaleModel::Run(){
             case 2: 
 		            ScaLBL_D3Q19_AAodd_Greyscale(NeighborList, fq, 0, ScaLBL_Comm->LastExterior(), Np, rlx, rlx_eff, Fx, Fy, Fz,Porosity,Permeability,Velocity,Pressure_dvc);
                     break;
-            case 3: 
-		            ScaLBL_D3Q19_AAodd_Greyscale_MRT(NeighborList, fq, 0, ScaLBL_Comm->LastExterior(), Np, rlx, rlx_eff, Fx, Fy, Fz,Porosity,Permeability,Velocity,Den,Pressure_dvc);
-                    break;
             default: 
 		            ScaLBL_D3Q19_AAodd_Greyscale_IMRT(NeighborList, fq, 0, ScaLBL_Comm->LastExterior(), Np, rlx, rlx_eff, Fx, Fy, Fz,Porosity,Permeability,Velocity,Den,Pressure_dvc);
                     break;
@@ -564,9 +504,6 @@ void ScaLBL_GreyscaleModel::Run(){
             case 2: 
 		            ScaLBL_D3Q19_AAeven_Greyscale(fq, ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np, rlx, rlx_eff, Fx, Fy, Fz,Porosity,Permeability,Velocity,Pressure_dvc);
                     break;
-            case 3: 
-		            ScaLBL_D3Q19_AAeven_Greyscale_MRT(fq, ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np, rlx, rlx_eff, Fx, Fy, Fz,Porosity,Permeability,Velocity,Den,Pressure_dvc);
-                    break;
             default: 
 		            ScaLBL_D3Q19_AAeven_Greyscale_IMRT(fq, ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np, rlx, rlx_eff, Fx, Fy, Fz,Porosity,Permeability,Velocity,Den,Pressure_dvc);
                     break;
@@ -585,9 +522,6 @@ void ScaLBL_GreyscaleModel::Run(){
             case 2: 
 		            ScaLBL_D3Q19_AAeven_Greyscale(fq, 0, ScaLBL_Comm->LastExterior(), Np, rlx, rlx_eff, Fx, Fy, Fz,Porosity,Permeability,Velocity,Pressure_dvc);
                     break;
-            case 3: 
-		            ScaLBL_D3Q19_AAeven_Greyscale_MRT(fq, 0, ScaLBL_Comm->LastExterior(), Np, rlx, rlx_eff, Fx, Fy, Fz,Porosity,Permeability,Velocity,Den,Pressure_dvc);
-                    break;
             default: 
 		            ScaLBL_D3Q19_AAeven_Greyscale_IMRT(fq, 0, ScaLBL_Comm->LastExterior(), Np, rlx, rlx_eff, Fx, Fy, Fz,Porosity,Permeability,Velocity,Den,Pressure_dvc);
                     break;
@@ -661,11 +595,11 @@ void ScaLBL_GreyscaleModel::Run(){
 					}
 				}
 			}
-            vax = sumReduce( Mask->Comm, vax_loc);
-            vay = sumReduce( Mask->Comm, vay_loc);
-            vaz = sumReduce( Mask->Comm, vaz_loc);
-            count = sumReduce( Mask->Comm, count_loc);
-
+			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;
@@ -695,11 +629,10 @@ void ScaLBL_GreyscaleModel::Run(){
 			double As = Morphology.A();
 			double Hs = Morphology.H();
 			double Xs = Morphology.X();
-			Vs = sumReduce( Dm->Comm, Vs);
-			As = sumReduce( Dm->Comm, As);
-			Hs = sumReduce( Dm->Comm, Hs);
-			Xs = sumReduce( Dm->Comm, Xs);
-
+			Vs=sumReduce( Dm->Comm, Vs);
+			As=sumReduce( Dm->Comm, As);
+			Hs=sumReduce( Dm->Comm, Hs);
+			Xs=sumReduce( Dm->Comm, Xs);
 			double h = Dm->voxel_length;
 			//double absperm = h*h*mu*Mask->Porosity()*flow_rate / force_mag;
 			double absperm = h*h*mu*GreyPorosity*flow_rate / force_mag;

models/GreyscaleModel.h

@@ -1,20 +1,5 @@
 /*
-  Copyright 2020 Equinor ASA                                                          
-  Copyright Equnior ASA
-                                                                                      
-  This file is part of the Open Porous Media project (OPM).                           
-  OPM is free software: you can redistribute it and/or modify                         
-  it under the terms of the GNU General Public License as published by                
-  the Free Software Foundation, either version 3 of the License, or                   
-  (at your option) any later version.                                                 
-  OPM is distributed in the hope that it will be useful,                              
-  but WITHOUT ANY WARRANTY; without even the implied warranty of                      
-  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the                       
-  GNU General Public License for more details.                                        
-  You should have received a copy of the GNU General Public License                   
-  along with OPM.  If not, see <http://www.gnu.org/licenses/>.       
-
- greyscale lattice boltzmann model
+Implementation of color lattice boltzmann model
  */
 #include <stdio.h>
 #include <stdlib.h>
@@ -77,6 +62,7 @@ public:
 
     signed char *id;    
 	int *NeighborList;
+	int *dvcMap;
 	double *fq;
 	double *Permeability;//grey voxel permeability
 	double *Porosity;
@@ -101,6 +87,6 @@ private:
     char LocalRestartFile[40];
    
     void AssignComponentLabels(double *Porosity, double *Permeablity);
-    void AssignComponentLabels(double *Porosity,double *Permeability,const vector<std::string> &File_poro,const vector<std::string> &File_perm);
+    
 };
 

models/MRTModel.cpp

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify
@@ -19,7 +18,6 @@
  */
 #include "models/MRTModel.h"
 #include "analysis/distance.h"
-#include "common/ReadMicroCT.h"
 
 ScaLBL_MRTModel::ScaLBL_MRTModel(int RANK, int NP, MPI_Comm COMM):
 rank(RANK), nprocs(NP), Restart(0),timestep(0),timestepMax(0),tau(0),
@@ -110,36 +108,20 @@ void ScaLBL_MRTModel::SetDomain(){
 }
 
 void ScaLBL_MRTModel::ReadInput(){
+    int rank=Dm->rank();
+    size_t readID;
+    //.......................................................................
+    //.......................................................................
+    Mask->ReadIDs();
     
     sprintf(LocalRankString,"%05d",Dm->rank());
     sprintf(LocalRankFilename,"%s%s","ID.",LocalRankString);
     sprintf(LocalRestartFile,"%s%s","Restart.",LocalRankString);
 
-    
-    if (domain_db->keyExists( "Filename" )){
-    	auto Filename = domain_db->getScalar<std::string>( "Filename" );
-    	Mask->Decomp(Filename);
-    }
-    else if (domain_db->keyExists( "GridFile" )){
-    	// Read the local domain data
-    	auto input_id = readMicroCT( *domain_db, comm );
-    	// 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( comm, Mask->rank_info, size0, { 1, 1, 1 }, 0, 1 );
-    	Array<signed char> id_view;
-    	id_view.viewRaw( size1, Mask->id );
-    	fill.copy( input_id, id_view );
-    	fill.fill( id_view );
-    }
-    else{
-    	Mask->ReadIDs();
-    }
-
-    // Generate the signed distance map
+	// 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++){
@@ -155,6 +137,7 @@ void ScaLBL_MRTModel::ReadInput(){
 	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
 				Distance(i,j,k) = 2.0*double(id_solid(i,j,k))-1.0;
 			}
@@ -223,6 +206,7 @@ void ScaLBL_MRTModel::Run(){
 	double rlx_setB = 8.f*(2.f-rlx_setA)/(8.f-rlx_setA);
 	
 	Minkowski Morphology(Mask);
+	int SIZE=Np*sizeof(double);
 
 	if (rank==0){
 		bool WriteHeader=false;
@@ -254,38 +238,12 @@ void ScaLBL_MRTModel::Run(){
 		ScaLBL_Comm->SendD3Q19AA(fq); //READ FROM NORMAL
 		ScaLBL_D3Q19_AAodd_MRT(NeighborList, fq,  ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np, rlx_setA, rlx_setB, Fx, Fy, Fz);
 		ScaLBL_Comm->RecvD3Q19AA(fq); //WRITE INTO OPPOSITE
-		// 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);
-		}
 		ScaLBL_D3Q19_AAodd_MRT(NeighborList, fq, 0, ScaLBL_Comm->LastExterior(), Np, rlx_setA, rlx_setB, Fx, Fy, Fz);
 		ScaLBL_DeviceBarrier(); MPI_Barrier(comm);
 		timestep++;
 		ScaLBL_Comm->SendD3Q19AA(fq); //READ FORM NORMAL
 		ScaLBL_D3Q19_AAeven_MRT(fq, ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->LastInterior(), Np, rlx_setA, rlx_setB, Fx, Fy, Fz);
 		ScaLBL_Comm->RecvD3Q19AA(fq); //WRITE INTO OPPOSITE
-		// 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);
-		}
 		ScaLBL_D3Q19_AAeven_MRT(fq, 0, ScaLBL_Comm->LastExterior(), Np, rlx_setA, rlx_setB, Fx, Fy, Fz);
 		ScaLBL_DeviceBarrier(); MPI_Barrier(comm);
 		//************************************************************************/
@@ -425,9 +383,7 @@ void ScaLBL_MRTModel::VelocityField(){
 	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);
 						*/
-        vis_db = db->getDatabase( "Visualization" );
-	if (vis_db->getWithDefault<bool>( "write_silo", false )){
-  
+	
 	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);
 
@@ -479,5 +435,5 @@ void ScaLBL_MRTModel::VelocityField(){
     fillData.copy(Velocity_z,VelzData);
 	
     IO::writeData( timestep, visData, Dm->Comm );
-    }
+
 }

models/MRTModel.h

@@ -1,6 +1,5 @@
 /*
   Copyright 2013--2018 James E. McClure, Virginia Polytechnic & State University
-  Copyright Equnior ASA
 
   This file is part of the Open Porous Media project (OPM).
   OPM is free software: you can redistribute it and/or modify
@@ -65,7 +64,6 @@ public:
     std::shared_ptr<Database> db;
     std::shared_ptr<Database> domain_db;
     std::shared_ptr<Database> mrt_db;
-    std::shared_ptr<Database> vis_db;
 
     IntArray Map;
     DoubleArray Distance;

sample_scripts/configure_summit

@@ -7,7 +7,6 @@ module load cuda
 
 export HDF5_DIR=/ccs/proj/csc380/mcclurej/install/hdf5/1.8.12/
 export SILO_DIR=/ccs/proj/csc380/mcclurej/install/silo/4.10.2/
-export NETCDF_DIR=/ccs/proj/geo136/install/netcdf/4.6.1
 
 # configure
 rm -rf CMake*
@@ -29,8 +28,6 @@ cmake                                       \
      -D USE_SILO=1                        \
         -D SILO_LIB="$SILO_DIR/lib/libsiloh5.a"    \
    	-D SILO_DIRECTORY="$SILO_DIR"		     \
-    -D USE_NETCDF=1				     \
-        -D NETCDF_DIRECTORY="$NETCDF_DIR"	     \
     -D USE_DOXYGEN:BOOL=false		        \
     -D USE_TIMER=0			                \
     ~/LBPM-WIA

tests/CMakeLists.txt

@@ -4,7 +4,6 @@
 ADD_LBPM_EXECUTABLE( lbpm_color_simulator )
 ADD_LBPM_EXECUTABLE( lbpm_permeability_simulator )
 ADD_LBPM_EXECUTABLE( lbpm_greyscale_simulator )
-ADD_LBPM_EXECUTABLE( lbpm_greyscaleColor_simulator )
 #ADD_LBPM_EXECUTABLE( lbpm_BGK_simulator )
 #ADD_LBPM_EXECUTABLE( lbpm_color_macro_simulator )
 ADD_LBPM_EXECUTABLE( lbpm_dfh_simulator )
@@ -37,7 +36,6 @@ ADD_LBPM_EXECUTABLE( GenerateSphereTest )
 #ADD_LBPM_EXECUTABLE( BlobAnalyzeParallel )
 ADD_LBPM_EXECUTABLE( lbpm_minkowski_scalar )
 
-
 CONFIGURE_FILE( ${CMAKE_CURRENT_SOURCE_DIR}/cylindertest ${CMAKE_CURRENT_BINARY_DIR}/cylindertest COPYONLY )
 
 # Add the tests
@@ -72,7 +70,6 @@ ADD_LBPM_TEST_PARALLEL( TestCommD3Q19 8 )
 ADD_LBPM_TEST_1_2_4( testCommunication )
 ADD_LBPM_TEST( TestWriter )
 ADD_LBPM_TEST( TestDatabase )
-ADD_LBPM_TEST( TestSetDevice )
 ADD_LBPM_PROVISIONAL_TEST( TestMicroCTReader )
 IF ( USE_NETCDF )
     ADD_LBPM_TEST_PARALLEL( TestNetcdf 8 )

tests/GenerateSphereTest.cpp

@@ -145,8 +145,8 @@ inline void MorphOpen(DoubleArray SignDist, char *id, Domain &Dm, int nx, int ny
 
 	// Increase the critical radius until the target saturation is met
 	double deltaR=0.05; // amount to change the radius in voxel units
-	double Rcrit_old=0.0;
-	double Rcrit_new=0.0;
+	double Rcrit_old;
+	double Rcrit_new;
 
 	double GlobalNumber = 1.f;
 	int imin,jmin,kmin,imax,jmax,kmax;
@@ -363,7 +363,7 @@ int main(int argc, char **argv)
 	        nspheres = domain_db->getScalar<int>( "nspheres");
 
 		//printf("Set domain \n");
-		//int BoundaryCondition=1;
+		int BoundaryCondition=1;
 		//Nz += 2;
 		//Nx = Ny = Nz;	// Cubic domain
 		int N = Nx*Ny*Nz;
@@ -396,7 +396,7 @@ int main(int argc, char **argv)
 		int sum = 0;
 		double sum_local;
 		double iVol_global = 1.0/(1.0*(Nx-2)*(Ny-2)*(Nz-2)*nprocs);
-		double porosity;
+		double porosity, pore_vol;
 		//...........................................................................
 		DoubleArray SignDist(Nx,Ny,Nz);
 		//.......................................................................
@@ -450,6 +450,7 @@ int main(int argc, char **argv)
 			}
 		}
 		sum=0;
+		pore_vol = 0.0;
 		for ( k=1;k<Nz-1;k++){
 			for ( j=1;j<Ny-1;j++){
 				for ( i=1;i<Nx-1;i++){

tests/TestBubbleDFH.cpp

@@ -74,6 +74,11 @@ int main(int argc, char **argv)
         ScaLBL_DeviceBarrier();
         MPI_Barrier(comm);
 
+        PROFILE_ENABLE(1);
+        //PROFILE_ENABLE_TRACE();
+        //PROFILE_ENABLE_MEMORY();
+        PROFILE_SYNCHRONIZE();
+        PROFILE_START("Main");
         Utilities::setErrorHandlers();
 
         // Variables that specify the computational domain  
@@ -159,14 +164,14 @@ int main(int argc, char **argv)
             pBC=false;
 
         // Full domain used for averaging (do not use mask for analysis)
-        auto Dm = std::make_shared<Domain>(domain_db,comm);
+        std::shared_ptr<Domain> Dm(new Domain(domain_db,comm));
         for (int i=0; i<Dm->Nx*Dm->Ny*Dm->Nz; i++) Dm->id[i] = 1;
-        auto Averages = std::make_shared<TwoPhase>(Dm);
+        std::shared_ptr<TwoPhase> Averages( new TwoPhase(Dm) );
         //   TwoPhase Averages(Dm);
         Dm->CommInit();
 
         // Mask that excludes the solid phase
-        auto Mask = std::make_shared<Domain>(domain_db,comm);
+        std::shared_ptr<Domain> Mask(new Domain(domain_db,comm));
         MPI_Barrier(comm);
 
         Nx+=2; Ny+=2; Nz += 2;
@@ -186,8 +191,9 @@ int main(int argc, char **argv)
 		//	printf("Local File Name =  %s \n",LocalRankFilename);
 		// .......... READ THE INPUT FILE .......................................
 		//	char value;
-		auto id = new char[N];
-		double sum;
+		char *id;
+		id = new char[N];
+		double sum, sum_local;
 		//...........................................................................
 		if (rank == 0) cout << "Setting up bubble..." << endl;
 	    double BubbleRadius = 15.5; // Radius of the capillary tube
@@ -238,17 +244,19 @@ int main(int argc, char **argv)
 		// Initialize communication structures in averaging domain
 		for (i=0; i<Mask->Nx*Mask->Ny*Mask->Nz; i++) Mask->id[i] = id[i];
 		Mask->CommInit();
-		auto PhaseLabel = new double[N];
+		double *PhaseLabel;
+		PhaseLabel = new double[N];
 		
 		//...........................................................................
 		if (rank==0)	printf ("Create ScaLBL_Communicator \n");
 		// Create a communicator for the device (will use optimized layout)
-		auto ScaLBL_Comm = std::make_shared<ScaLBL_Communicator>(Mask);
+		std::shared_ptr<ScaLBL_Communicator> ScaLBL_Comm(new ScaLBL_Communicator(Mask));
 		
 		int Npad=(Np/16 + 2)*16;
 		if (rank==0)	printf ("Set up memory efficient layout Npad=%i \n",Npad);
+		int *neighborList;
 		IntArray Map(Nx,Ny,Nz);
-		auto neighborList= new int[18*Npad];
+		neighborList= new int[18*Npad];
 		Np = ScaLBL_Comm->MemoryOptimizedLayoutAA(Map,neighborList,Mask->id,Np);
 		MPI_Barrier(comm);
 
@@ -507,8 +515,9 @@ int main(int argc, char **argv)
 		// Copy back final phase indicator field and convert to regular layout
 		DoubleArray PhaseField(Nx,Ny,Nz);
         ScaLBL_Comm->RegularLayout(Map,Phi,PhaseField);
-		sprintf(LocalRankFilename,"Phase.raw");
-		auto OUTFILE = fopen(LocalRankFilename,"wb");
+    	FILE *OUTFILE;
+		sprintf(LocalRankFilename,"Phase.raw",rank);
+		OUTFILE = fopen(LocalRankFilename,"wb");
     	fwrite(PhaseField.data(),8,N,OUTFILE);
     	fclose(OUTFILE);
     	
@@ -526,8 +535,9 @@ int main(int argc, char **argv)
 				}
 			}
 		}
+    	FILE *GFILE;
 		sprintf(LocalRankFilename,"Gradient.raw");
-		auto GFILE = fopen(LocalRankFilename,"wb");
+		GFILE = fopen(LocalRankFilename,"wb");
     	fwrite(GradNorm.data(),8,N,GFILE);
     	fclose(GFILE);
     	
@@ -535,12 +545,14 @@ int main(int argc, char **argv)
 		DoubleArray Rho2(Nx,Ny,Nz);
         ScaLBL_Comm->RegularLayout(Map,&Den[0],Rho1);
         ScaLBL_Comm->RegularLayout(Map,&Den[Np],Rho2);
+    	FILE *RFILE1;
 		sprintf(LocalRankFilename,"Rho1.raw");
-		auto RFILE1 = fopen(LocalRankFilename,"wb");
+		RFILE1 = fopen(LocalRankFilename,"wb");
     	fwrite(Rho1.data(),8,N,RFILE1);
     	fclose(RFILE1);
+    	FILE *RFILE2;
 		sprintf(LocalRankFilename,"Rho2.raw");
-		auto RFILE2 = fopen(LocalRankFilename,"wb");
+		RFILE2 = fopen(LocalRankFilename,"wb");
     	fwrite(Rho2.data(),8,N,RFILE2);
     	fclose(RFILE2);
     	

tests/TestColorGradDFH.cpp

@@ -53,6 +53,9 @@ int main(int argc, char **argv)
 	    int Nx = db->getVector<int>( "n" )[0];
 	    int Ny = db->getVector<int>( "n" )[1];
 	    int Nz = db->getVector<int>( "n" )[2];
+	    int nprocx = db->getVector<int>( "nproc" )[0];
+	    int nprocy = db->getVector<int>( "nproc" )[1];
+	    int nprocz = db->getVector<int>( "nproc" )[2];
 
 	    if (rank==0){
 	    	printf("********************************************************\n");
@@ -61,7 +64,7 @@ int main(int argc, char **argv)
 	    }
 
 	    // Get the rank info
-		auto Dm = std::make_shared<Domain>(db,comm);
+	    std::shared_ptr<Domain> Dm(new Domain(db,comm));
 		Nx += 2;
 		Ny += 2;
 		Nz += 2;
@@ -108,6 +111,7 @@ int main(int argc, char **argv)
 		MPI_Barrier(comm);
 
 		//......................device distributions.................................
+		int dist_mem_size = Np*sizeof(double);
 		int neighborSize=18*Np*sizeof(int);
 		if (rank==0)	printf ("Allocating distributions \n");
 		int *NeighborList;

tests/TestCommD3Q19.cpp

@@ -49,7 +49,7 @@ extern void GlobalFlipScaLBL_D3Q19_Init(double *dist, IntArray Map, int Np, int
 	{1,1,0},{-1,-1,0},{1,-1,0},{-1,1,0},{1,0,1},{-1,0,-1},{1,0,-1},{-1,0,1},
 	{0,1,1},{0,-1,-1},{0,1,-1},{0,-1,1}};
 	
-	int q,i,j,k;
+	int q,i,j,k,n,N;
 	int Cqx,Cqy,Cqz; // Discrete velocity
 	int x,y,z;		// Global indices
 	int xn,yn,zn; 	// Global indices of neighbor 
@@ -59,6 +59,8 @@ extern void GlobalFlipScaLBL_D3Q19_Init(double *dist, IntArray Map, int Np, int
 	Y = Ny*nprocy;
 	Z = Nz*nprocz;
     NULL_USE(Z);
+	N = (Nx+2)*(Ny+2)*(Nz+2);	// size of the array including halo
+
 
 	for (k=0; k<Nz; k++){ 
 		for (j=0; j<Ny; j++){
@@ -102,13 +104,16 @@ extern int GlobalCheckDebugDist(double *dist, IntArray Map, int Np, int Nx, int
 {
 
 	int returnValue = 0;
-	int q,i,j,k,idx;
+	int q,i,j,k,n,N,idx;
+	int Cqx,Cqy,Cqz; // Discrete velocity
 	int x,y,z;		// Global indices
+	int xn,yn,zn; 	// Global indices of neighbor 
 	int X,Y,Z;		// Global size
 	X = Nx*nprocx;
 	Y = Ny*nprocy;
 	Z = Nz*nprocz;
 	NULL_USE(Z);
+	N = (Nx+2)*(Ny+2)*(Nz+2);	// size of the array including halo
 	for (k=0; k<Nz; k++){ 
 		for (j=0; j<Ny; j++){
 			for (i=0; i<Nx; i++){
@@ -163,6 +168,9 @@ inline void UnpackID(int *list, int count, char *recvbuf, char *ID){
 //***************************************************************************************
 int main(int argc, char **argv)
 {
+	//*****************************************
+	// ***** MPI STUFF ****************
+	//*****************************************
 	// Initialize MPI
 	int rank,nprocs;
 	MPI_Init(&argc,&argv);
@@ -170,7 +178,10 @@ int main(int argc, char **argv)
 	MPI_Comm_rank(comm,&rank);
 	MPI_Comm_size(comm,&nprocs);
 	int check;
+
 	{
+		MPI_Request req1[18],req2[18];
+		MPI_Status stat1[18],stat2[18];
 
 		if (rank == 0){
 			printf("********************************************************\n");
@@ -180,8 +191,11 @@ int main(int argc, char **argv)
 
 		// BGK Model parameters
 		string FILENAME;
+		unsigned int nBlocks, nthreads;
+		int timestepMax, interval;
+		double tau,Fx,Fy,Fz,tol;
 		// Domain variables
-		int i,j,k;
+		int i,j,k,n;
 
         // Load inputs
         auto db = loadInputs( nprocs );
@@ -209,7 +223,8 @@ int main(int argc, char **argv)
 		char LocalRankFilename[40];
 		sprintf(LocalRankFilename,"ID.%05i",rank);
 
-		auto id = new char[Nx*Ny*Nz];
+		char *id;
+		id = new char[Nx*Ny*Nz];
 
 		/*		if (rank==0) printf("Assigning phase ID from file \n");
 		if (rank==0) printf("Initialize from segmented data: solid=0, NWP=1, WP=2 \n");
@@ -222,7 +237,7 @@ int main(int argc, char **argv)
 		for (k=0;k<Nz;k++){
 			for (j=0;j<Ny;j++){
 				for (i=0;i<Nx;i++){
-					int n = k*Nx*Ny+j*Nx+i;
+					n = k*Nx*Ny+j*Nx+i;
 					id[n] = 1;
 					Dm->id[n] = id[n];
 				}
@@ -255,7 +270,7 @@ int main(int argc, char **argv)
 		for (k=1;k<Nz-1;k++){
 			for (j=1;j<Ny-1;j++){
 				for (i=1;i<Nx-1;i++){
-					int n = k*Nx*Ny+j*Nx+i;
+					n = k*Nx*Ny+j*Nx+i;
 					if (id[n] == component){
 						sum_local+=1.0;
 					}

tests/TestFluxBC.cpp

@@ -32,14 +32,21 @@ int main (int argc, char **argv)
 	}
 	{
 	  int i,j,k,n,Np;
+		bool pBC=true;
+		double Lx,Ly,Lz;
+		Lx = Ly = Lz = 1.f;
 		double din,dout;
+		int BC=1;
 
 	    // Load inputs
 	    auto db = loadInputs( nprocs );
 	    int Nx = db->getVector<int>( "n" )[0];
 	    int Ny = db->getVector<int>( "n" )[1];
 	    int Nz = db->getVector<int>( "n" )[2];
-		auto Dm = std::make_shared<Domain>(db,comm);
+	    int nprocx = db->getVector<int>( "nproc" )[0];
+	    int nprocy = db->getVector<int>( "nproc" )[1];
+	    int nprocz = db->getVector<int>( "nproc" )[2];
+		std::shared_ptr<Domain> Dm(new Domain(db,comm));
 		
 		Nx += 2;   Ny+=2;	Nz += 2;
 		Nx = Ny = Nz;	// Cubic domain
@@ -48,7 +55,8 @@ int main (int argc, char **argv)
 		//.......................................................................
 		// Assign the phase ID
 		//.......................................................................
-		auto id = new char[N];
+		char *id;
+		id = new char[N];
 		for (k=0;k<Nz;k++){
 			for (j=0;j<Ny;j++){
 				for (i=0;i<Nx;i++){
@@ -152,7 +160,9 @@ int main (int argc, char **argv)
     	ScaLBL_DeviceBarrier(); MPI_Barrier(comm);
     	ScaLBL_CopyToHost(&VEL[0],&dvc_vel[0],SIZE);
 
-    	double Q = 0.f;    	
+		double err,value,Q;
+
+    	Q = 0.f;    	
     	k=1;
     	for (j=1;j<Ny-1;j++){
     		for (i=1;i<Nx-1;i++){
@@ -166,7 +176,7 @@ int main (int argc, char **argv)
 
     	// respect backwards read / write!!!
 		printf("Inlet Flux: input=%f, output=%f \n",flux,Q);
-		double err = fabs(flux + Q);
+		err = fabs(flux + Q);
 		if (err > 1e-12){
 			error = 1;
 			printf("  Inlet error %f \n",err);
@@ -175,7 +185,7 @@ int main (int argc, char **argv)
 		// Consider a larger number of timesteps and simulate flow
 		double Fx, Fy, Fz;
 		double tau = 1.0;
-		//double mu=(tau-0.5)/3.0;
+		double mu=(tau-0.5)/3.0;
 		double rlx_setA=1.0/tau;
 		double rlx_setB = 8.f*(2.f-rlx_setA)/(8.f-rlx_setA);
 		dout=1.f;

tests/TestForceD3Q19.cpp

@@ -457,16 +457,24 @@ int main (int argc, char **argv)
 		double *x = new double[1];
 		ASSERT(x!=NULL);
 	}
+
+    // set the error code
+    // Note: the error code should be consistent across all processors
+    int error = 0;
     
     int Np = 1;
-    //int Q = 9;
+    int Q = 9;
 
     double Fx = 1.0;
     double Fy = 1.0;
     double Fz = 1.0;
     
-    auto dist = new double [19*Np];
-    //auto Velocity  = new double [3*Np
+    double *dist;    
+    double * Velocity;
+    
+    dist = new double [19*Np];
+    Velocity = new double [3*Np];
+
 
     for (int n=0; n<Np; n++){
     	dist[n] = 0.3333333333333333;

tests/TestInterfaceSpeed.cpp

@@ -24,7 +24,7 @@ int main (int argc, char *argv[])
 	MPI_Comm_rank(comm,&rank);
 	MPI_Comm_size(comm,&nprocs);
 
-	int i,j,k;
+	int i,j,k,n;
 
     // Load inputs
 	string FILENAME = argv[1];
@@ -36,7 +36,7 @@ int main (int argc, char *argv[])
     int Ny = domain_db->getVector<int>( "n" )[1];
     int Nz = domain_db->getVector<int>( "n" )[2];
 
-    auto Dm = std::make_shared<Domain>(domain_db,comm);
+    std::shared_ptr<Domain> Dm(new Domain(domain_db,comm));
 
     Nx+=2; Ny+=2; Nz+=2;
 
@@ -44,7 +44,7 @@ int main (int argc, char *argv[])
 
 	Dm->CommInit();
 
-	auto Averages = std::make_shared<TwoPhase>(Dm);
+	std::shared_ptr<TwoPhase> Averages(new TwoPhase(Dm));
 	int timestep=0;
 
 	double Cx,Cy,Cz;

tests/TestMap.cpp

@@ -56,7 +56,11 @@ int main(int argc, char **argv)
 	    int Nx = db->getVector<int>( "n" )[0];
 	    int Ny = db->getVector<int>( "n" )[1];
 	    int Nz = db->getVector<int>( "n" )[2];
-		auto Dm = std::make_shared<Domain>(db,comm);
+	    int nprocx = db->getVector<int>( "nproc" )[0];
+	    int nprocy = db->getVector<int>( "nproc" )[1];
+	    int nprocz = db->getVector<int>( "nproc" )[2];
+
+		std::shared_ptr<Domain> Dm(new Domain(db,comm));
 
 		Nx += 2;
 		Ny += 2;

tests/TestMassConservationD3Q7.cpp

@@ -41,7 +41,7 @@ inline void InitializeBubble(ScaLBL_ColorModel &ColorModel, double BubbleRadius)
 				int jglobal= j+(Ny-2)*ColorModel.Mask->jproc();
 				int kglobal= k+(Nz-2)*ColorModel.Mask->kproc();
 				// Initialize phase position field for parallel bubble test
-				if (kglobal < 40){
+				if (jglobal < 40){
 					ColorModel.Mask->id[n] = 0;
 				}
 				else if ((iglobal-0.5*(Nx-2)*nprocx)*(iglobal-0.5*(Nx-2)*nprocx)
@@ -66,14 +66,29 @@ inline void InitializeBubble(ScaLBL_ColorModel &ColorModel, double BubbleRadius)
 
 int main(int argc, char **argv)
 {
+	//*****************************************
+	// ***** MPI STUFF ****************
+	//*****************************************
 	// Initialize MPI
 	int rank,nprocs;
 	MPI_Init(&argc,&argv);
-	MPI_Comm comm = MPI_COMM_WORLD;
+    MPI_Comm comm = MPI_COMM_WORLD;
 	MPI_Comm_rank(comm,&rank);
 	MPI_Comm_size(comm,&nprocs);
 	// parallel domain size (# of sub-domains)
-	int CleanCheck = 0;
+	int nprocx,nprocy,nprocz;
+	int iproc,jproc,kproc;
+	int sendtag,recvtag;
+	//*****************************************
+	// MPI ranks for all 18 neighbors
+	//**********************************
+	int rank_x,rank_y,rank_z,rank_X,rank_Y,rank_Z;
+	int rank_xy,rank_XY,rank_xY,rank_Xy;
+	int rank_xz,rank_XZ,rank_xZ,rank_Xz;
+	int rank_yz,rank_YZ,rank_yZ,rank_Yz;
+	//**********************************
+	MPI_Request req1[18],req2[18];
+	MPI_Status stat1[18],stat2[18];
 
 	if (rank == 0){
 		printf("********************************************************\n");
@@ -85,68 +100,71 @@ int main(int argc, char **argv)
 		}
 	}
 	{		
-		auto filename = argv[1];
-		ScaLBL_ColorModel CM(rank,nprocs,comm);
-		CM.ReadParams(filename);
-		CM.SetDomain();    	
-		int i,j,k,n;
-		int Nx,Ny,Nz,N,Np;
-		Nx = CM.Nx;
-		Ny = CM.Ny;
-		Nz = CM.Nz;
-		N = Nx*Ny*Nz;
+	auto filename = argv[1];
+	ScaLBL_ColorModel CM(rank,nprocs,comm);
+	CM.ReadParams(filename);
+	CM.SetDomain();    	
+	int i,j,k,n;
+	int Nx,Ny,Nz,N,Np;
+	Nx = CM.Nx;
+	Ny = CM.Ny;
+	Nz = CM.Nz;
+	N = Nx*Ny*Nz;
+	int dist_mem_size = N*sizeof(double);
 
-		//CM.ReadInput(); 
-		double radius=0.4*double(Nx);
-		InitializeBubble(CM,radius);
-		CM.Create();       // creating the model will create data structure to match the pore structure and allocate variables
-		CM.Initialize();   // initializing the model will set initial conditions for variables
-		//CM.Run();	       
-		//CM.WriteDebug();
+	//CM.ReadInput(); 
+	double radius=0.4*double(Nx);
+	InitializeBubble(CM,radius);
+ 	CM.Create();       // creating the model will create data structure to match the pore structure and allocate variables
+	CM.Initialize();   // initializing the model will set initial conditions for variables
+	//CM.Run();	       
+	//CM.WriteDebug();
 
-		CM.timestepMax = 10;
-		CM.Run();
+	CM.timestepMax = 10;
+	CM.Run();
 
-		Np = CM.Np;
-		double *DenOriginal, *DenFinal;
-		DenOriginal = new double [2*Np];
-		DenFinal = new double [2*Np];
+	Np = CM.Np;
+	double *DenOriginal, *DenFinal;
+	DenOriginal = new double [2*Np];
+	DenFinal = new double [2*Np];
 
-		// Run the odd timestep 
-		ScaLBL_CopyToHost(DenOriginal,CM.Den,2*Np*sizeof(double));
-		/*
+	// Run the odd timestep 
+ 	ScaLBL_CopyToHost(DenOriginal,CM.Den,2*Np*sizeof(double));
+	/*
 	CM.ScaLBL_Comm->BiSendD3Q7AA(CM.Aq,CM.Bq); //READ FROM NORMAL
 	ScaLBL_D3Q7_AAodd_PhaseField(CM.NeighborList, CM.dvcMap, CM.Aq, CM.Bq, CM.Den, CM.Phi, CM.ScaLBL_Comm->FirstInterior(), CM.ScaLBL_Comm->LastInterior(), CM.Np);
 	CM.ScaLBL_Comm->BiRecvD3Q7AA(CM.Aq,CM.Bq); //WRITE INTO OPPOSITE
 	ScaLBL_DeviceBarrier();
 	ScaLBL_D3Q7_AAodd_PhaseField(CM.NeighborList, CM.dvcMap, CM.Aq, CM.Bq, CM.Den, CM.Phi, 0, CM.ScaLBL_Comm->LastExterior(), CM.Np);
-		 */
+	*/
 
-		CM.timestepMax = 2;
-		CM.timestep = 0;
-		CM.Run();
-		int D3Q7[7][3]={{0,0,0},{1,0,0},{-1,0,0},{0,1,0},{0,-1,0},{0,0,1},{0,0,-1}};
-		// Compare and make sure mass is conserved at every lattice site
-		auto Error = new double[N];
-		auto A_q = new double[7*Np];
-		//auto B_q = new double[7*Np];
-		double original,final, sum_q;
-		double total_mass_A_0 = 0.0;
-		double total_mass_B_0= 0.0;
-		double total_mass_A_1 = 0.0;
-		double total_mass_B_1= 0.0;
-		int count_negative_A = 0;
-		int count_negative_B = 0;
-		ScaLBL_CopyToHost(DenFinal,CM.Den,2*Np*sizeof(double));
-		ScaLBL_CopyToHost(A_q,CM.Aq,7*Np*sizeof(double));
-		for (i=0; i<N; i++) Error[i]=0.0;
-		for (k=1;k<Nz-1;k++){
-			for (j=1;j<Ny-1;j++){
-				for (i=1;i<Nx-1;i++){
-					n = k*Nx*Ny+j*Nx+i;
-					int idx = CM.Map(i,j,k);
-					if (idx < Np && idx>-1){
-						//printf("idx=%i\n",idx);
+	CM.timestepMax = 2;
+	CM.Run();
+	int D3Q7[7][3]={{0,0,0},{1,0,0},{-1,0,0},{0,1,0},{0,-1,0},{0,0,1},{0,0,-1}};
+	// Compare and make sure mass is conserved at every lattice site
+	double *Error;
+	Error = new double [N];
+	double *A_q, *B_q;
+	A_q = new double [7*Np];
+	B_q = new double [7*Np];
+	bool CleanCheck = true;
+	double original,final, sum_q;
+	double total_mass_A_0 = 0.0;
+	double total_mass_B_0= 0.0;
+	double total_mass_A_1 = 0.0;
+	double total_mass_B_1= 0.0;
+	int count_negative_A = 0;
+	int count_negative_B = 0;
+	ScaLBL_CopyToHost(DenFinal,CM.Den,2*Np*sizeof(double));
+	ScaLBL_CopyToHost(A_q,CM.Aq,7*Np*sizeof(double));
+	for (i=0; i<N; i++) Error[i]=0.0;
+	for (k=1;k<Nz-1;k++){
+		for (j=1;j<Ny-1;j++){
+			for (i=1;i<Nx-1;i++){
+				n = k*Nx*Ny+j*Nx+i;
+				int idx = CM.Map(i,j,k);
+				if (idx < Np && idx>-1){
+				  //printf("idx=%i\n",idx);
 						final = DenFinal[idx];
 						if (final < 0.0) count_negative_A++;
 						original = DenOriginal[idx];
@@ -154,61 +172,60 @@ int main(int argc, char **argv)
 						total_mass_A_1 += final;
 						sum_q = A_q[idx];
 						for (int q=1; q<7; q++){
-							int Cqx = D3Q7[q][0]; 
-							int Cqy = D3Q7[q][1]; 
-							int Cqz = D3Q7[q][2];
-							int iq = CM.Map(i-Cqx,j-Cqy,k-Cqz);
-							if (iq < Np && iq > -1){
-								sum_q += A_q[q*Np+iq]; 
-							}
-							else if (q%2==0){
-								sum_q += A_q[(q-1)*Np+idx]; 
-							}
-							else{
-								sum_q += A_q[(q+1)*Np+idx]; 
-							}
+						  int Cqx = D3Q7[q][0]; 
+						  int Cqy = D3Q7[q][1]; 
+						  int Cqz = D3Q7[q][2];
+						  int iq = CM.Map(i-Cqx,j-Cqy,k-Cqz);
+						  if (iq < Np && iq > -1){
+						    sum_q += A_q[q*Np+iq]; 
+						  }
+						  else if (q%2==0){
+						    sum_q += A_q[(q-1)*Np+idx]; 
+						  }
+						  else{
+						    sum_q += A_q[(q+1)*Np+idx]; 
+						  }
 						}
 						Error[n] = sum_q - original;
-
-						if (fabs(DenFinal[idx] - DenOriginal[idx]) > 1e-15){		      
-							//if (CM.Dm->id[n] == 0) printf("Solid phase! \n");
-							//if (CM.Dm->id[n] == 1) printf("Wetting phase! \n");
-							//if (CM.Dm->id[n] == 2) printf("Non-wetting phase! \n");							
-							//printf("Mass not conserved: WP density, site=%i,%i,%i, original = %f, final = %f \n",i,j,k,original,final);
-							CleanCheck=false;
-							Error[n] += final-original;
-						}
+						
+					       /*if (fabs(DenFinal[idx] - DenOriginal[idx]) > 1e-15){		      
+						//if (CM.Dm->id[n] == 0) printf("Solid phase! \n");
+						//if (CM.Dm->id[n] == 1) printf("Wetting phase! \n");
+						//if (CM.Dm->id[n] == 2) printf("Non-wetting phase! \n");							
+						printf("Mass not conserved: WP density, site=%i,%i,%i, original = %f, final = %f \n",i,j,k,original,final);
+						CleanCheck=false;
+						Error[n] += final-original;
+						}*/
 						final = DenFinal[Np+idx];
 						if (final < 0.0) count_negative_B++;
 						original = DenOriginal[Np+idx];
 						total_mass_B_0 += original;
 						total_mass_B_1 += final;
 						/*if (fabs(DenFinal[Np+idx] - DenOriginal[Np+idx]) > 1e-15){
-							//if (CM.Dm->id[n] == 0) printf("Solid phase! \n");
-							//if (CM.Dm->id[n] == 1) printf("Wetting phase! \n");
-							//if (CM.Dm->id[n] == 2) printf("Non-wetting phase! \n");
-							//printf("Mass not conserved: NWP density, site=%i,%i,%i, original = %f, final = %f \n",i,j,k,original,final);
-							CleanCheck=false;
-							Error[n] += final-original;
-						} 
-						*/
-					}
+						//if (CM.Dm->id[n] == 0) printf("Solid phase! \n");
+						//if (CM.Dm->id[n] == 1) printf("Wetting phase! \n");
+						//if (CM.Dm->id[n] == 2) printf("Non-wetting phase! \n");
+						printf("Mass not conserved: NWP density, site=%i,%i,%i, original = %f, final = %f \n",i,j,k,original,final);
+						CleanCheck=false;
+						Error[n] += final-original;
+						}*/
 				}
 			}
 		}
-		printf("Negative density values for A = %i \n",count_negative_A);
-		printf("Negative density values for B = %i \n",count_negative_B);
-		printf("Global mass difference A = %.5g\n",total_mass_A_1-total_mass_A_0);
-		printf("Global mass difference B = %.5g\n",total_mass_B_1-total_mass_B_0);
+	}
+	printf("Negative density values for A = %i \n",count_negative_A);
+	printf("Negative density values for B = %i \n",count_negative_B);
+	printf("Global mass difference A = %.5g\n",total_mass_A_1-total_mass_A_0);
+	printf("Global mass difference B = %.5g\n",total_mass_B_1-total_mass_B_0);
 
-		if (count_negative_A > 0 ||count_negative_B > 0) CleanCheck=1;
-		if (fabs(total_mass_A_1-total_mass_A_0) > 1.0e-8 || fabs(total_mass_B_1-total_mass_B_0) > 1.0e-8) CleanCheck=2;
+	if (count_negative_A > 0 ||count_negative_B > 0) CleanCheck=1;
+	if (fabs(total_mass_A_1-total_mass_A_0) > 1.0e-15||fabs(total_mass_B_1-total_mass_B_0) > 1.0e-15 ) CleanCheck=2;
 
-		FILE *OUTFILE;
-		OUTFILE = fopen("error.raw","wb");
-		fwrite(Error,8,N,OUTFILE);
-		fclose(OUTFILE);	
-		/*	
+	/*	
+	 	FILE *OUTFILE;
+	OUTFILE = fopen("error.raw","wb");
+	fwrite(Error,8,N,OUTFILE);
+	fclose(OUTFILE);	
 
 	if (rank==0) printf("Checking that the correct velocity is retained \n");
 	// Swap convention is observed -- velocity is negative
@@ -258,15 +275,15 @@ int main(int argc, char **argv)
 			}
 		}
 	}
-		 */
-		if (CleanCheck == 0){
-			if (rank==0) printf("Test passed: mass conservation for D3Q7 \n");
-		}
-		else {
-			if (rank==0) printf("Test failed!: mass conservation for D3Q7 \n");
-
-		}
+*/
+	if (CleanCheck){
+		if (rank==0) printf("Test passed: mass conservation for D3Q7 \n");
 	}
+	else {
+		if (rank==0) printf("Test failed!: mass conservation for D3Q7 \n");
+
+	}
+}
 	// ****************************************************
 	MPI_Barrier(comm);
 	MPI_Finalize();