From 664da10edda672739516e1def7583310e357836e Mon Sep 17 00:00:00 2001
From: James McClure <jemcclur@gmail.com>
Date: Wed, 1 Sep 2021 12:19:47 -0400
Subject: [PATCH 1/3] extra protocol checks

---
 tests/lbpm_color_simulator.cpp | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/tests/lbpm_color_simulator.cpp b/tests/lbpm_color_simulator.cpp
index a0b2859c..c2bdb801 100644
--- a/tests/lbpm_color_simulator.cpp
+++ b/tests/lbpm_color_simulator.cpp
@@ -92,6 +92,8 @@ int main( int argc, char **argv )
 				SKIP_TIMESTEPS = flow_db->getWithDefault<int>( "skip_timesteps", 50000 );
 				ENDPOINT_THRESHOLD = flow_db->getWithDefault<double>( "endpoint_threshold", 0.1);
 				/* protocol specific key values */
+				if (PROTOCOL == "image sequence" || PROTOCOL == "core flooding")
+					SKIP_TIMESTEPS = 0;
 				if (PROTOCOL == "fractional flow")
 					FRACTIONAL_FLOW_INCREMENT = flow_db->getWithDefault<double>( "fractional_flow_increment", 0.05);
 				if (PROTOCOL == "seed water")
@@ -107,10 +109,14 @@ int main( int argc, char **argv )
 			runAnalysis analysis(ColorModel);
 			while (ContinueSimulation){
 				/* this will run steady points */
-				timestep += MAX_STEADY_TIME;
+				if (PROTOCOL == "fractional flow" || PROTOCOL == "seed water" || PROTOCOL == "shell aggregation" || PROTOCOL == "image sequence" )
+					timestep += MAX_STEADY_TIME;
+				else 
+					timestep += ColorModel.timestepMax;
+				/* Run the simulation timesteps*/
 				MLUPS = ColorModel.Run(timestep);
 				if (rank==0) printf("Lattice update rate (per MPI process)= %f MLUPS \n", MLUPS);
-				if (ColorModel.timestep > ColorModel.timestepMax){
+				if (ColorModel.timestep >= ColorModel.timestepMax){
 					ContinueSimulation = false;
 				}
 				

From b3457348bde9efc75a28860c17f0174be9ed1c29 Mon Sep 17 00:00:00 2001
From: James McClure <jemcclur@gmail.com>
Date: Wed, 1 Sep 2021 14:29:31 -0400
Subject: [PATCH 2/3] fix inlet / outlet porosity

---
 common/Domain.cpp | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/common/Domain.cpp b/common/Domain.cpp
index 6a4c61fb..81f74e22 100644
--- a/common/Domain.cpp
+++ b/common/Domain.cpp
@@ -629,7 +629,8 @@ void Domain::ComputePorosity(){
 	double sum;
 	double sum_local=0.0;
 	double iVol_global = 1.0/(1.0*(Nx-2)*(Ny-2)*(Nz-2)*nprocx()*nprocy()*nprocz());
-	if (BoundaryCondition > 0 && BoundaryCondition !=5) iVol_global = 1.0/(1.0*(Nx-2)*nprocx()*(Ny-2)*nprocy()*((Nz-2)*nprocz()-6));
+	if (BoundaryCondition > 0 && BoundaryCondition !=5) 
+		iVol_global = 1.0/(1.0*(Nx-2)*nprocx()*(Ny-2)*nprocy()*((Nz-2)*nprocz()-inlet_layers_z - outlet_layers_z));
 	//.........................................................
     for (int k=inlet_layers_z+1; k<Nz-outlet_layers_z-1;k++){
         for (int j=1;j<Ny-1;j++){

From 47050feb49d6db276d139460e9cfc740c8807c3d Mon Sep 17 00:00:00 2001
From: James McClure <mcclurej@vt.edu>
Date: Thu, 2 Sep 2021 08:19:54 -0400
Subject: [PATCH 3/3] remove random array functionality

---
 common/Array.h           | 2 +-
 common/Array.hpp         | 3 ++-
 common/FunctionTable.cpp | 4 ++--
 common/FunctionTable.hpp | 7 +++----
 4 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/common/Array.h b/common/Array.h
index ccbcbdc8..0e163718 100644
--- a/common/Array.h
+++ b/common/Array.h
@@ -642,7 +642,7 @@ public: // Math operations
     void cat( const Array &x, int dim = 0 );
 
     //! Initialize the array with random values (defined from the function table)
-    void rand();
+    //void rand();
 
     //! Return true if NaNs are present
     bool NaNs() const;
diff --git a/common/Array.hpp b/common/Array.hpp
index 1faaba71..1deaa463 100644
--- a/common/Array.hpp
+++ b/common/Array.hpp
@@ -1292,11 +1292,12 @@ TYPE Array<TYPE, FUN, Allocator>::interp( const double *x ) const
 /********************************************************
  *  Math operations (should call the Math class)         *
  ********************************************************/
-template<class TYPE, class FUN, class Allocator>
+/*template<class TYPE, class FUN, class Allocator>
 void Array<TYPE, FUN, Allocator>::rand()
 {
     FUN::rand( *this );
 }
+*/
 template<class TYPE, class FUN, class Allocator>
 Array<TYPE, FUN, Allocator> &
 Array<TYPE, FUN, Allocator>::operator+=( const Array<TYPE, FUN, Allocator> &rhs )
diff --git a/common/FunctionTable.cpp b/common/FunctionTable.cpp
index 10577c0f..54dc5848 100644
--- a/common/FunctionTable.cpp
+++ b/common/FunctionTable.cpp
@@ -4,7 +4,7 @@
 /********************************************************
  *  Random number generation                             *
  ********************************************************/
-template<> char genRand<char>()
+/*template<> char genRand<char>()
 {
     static std::random_device rd;
     static std::mt19937 gen( rd() );
@@ -88,7 +88,7 @@ template<> long double genRand<long double>()
     static std::uniform_real_distribution<double> dis;
     return dis( gen );
 }
-
+*/
 
 /********************************************************
  *  axpy                                                 *
diff --git a/common/FunctionTable.hpp b/common/FunctionTable.hpp
index 6a611f00..57e6b237 100644
--- a/common/FunctionTable.hpp
+++ b/common/FunctionTable.hpp
@@ -7,21 +7,20 @@
 #include <algorithm>
 #include <cstring>
 #include <limits>
-#include <random>
-
+//#include <random>
 
 
 /********************************************************
  *  Random number initialization                         *
  ********************************************************/
-template<class TYPE> TYPE genRand();
+/*template<class TYPE> TYPE genRand();
 template<class TYPE, class FUN>
 inline void FunctionTable::rand( Array<TYPE, FUN> &x )
 {
     for ( size_t i = 0; i < x.length(); i++ )
         x( i ) = genRand<TYPE>();
 }
-
+*/
 
 /********************************************************
  *  Reduction                                            *