diff --git a/Examples/KelvinHelmholtz/SingleFluidIdealRandomMPIHDF5/main.cc b/Examples/KelvinHelmholtz/SingleFluidIdealRandomMPIHDF5/main.cc
index e745dacf..1e3c7c94 100644
--- a/Examples/KelvinHelmholtz/SingleFluidIdealRandomMPIHDF5/main.cc
+++ b/Examples/KelvinHelmholtz/SingleFluidIdealRandomMPIHDF5/main.cc
@@ -38,6 +38,7 @@ int main(int argc, char *argv[]) {
   bool output(false);
   if (argc != 2) throw std::invalid_argument("Expected ./main seed!\n");
   int seed(atoi(argv[1]));
+  int reportItersPeriod(50);
 
   double nxRanks(2);
   double nyRanks(2);
@@ -45,8 +46,19 @@ int main(int argc, char *argv[]) {
 
   ParallelEnv env(&argc, &argv, nxRanks, nyRanks, nzRanks);
 
-  Data data(nx, ny, nz, xmin, xmax, ymin, ymax, zmin, zmax, endTime, &env,
-            cfl, Ng, gamma, sigma, cp, mu1, mu2, frameSkip);
+  const int nOptionalSimArgs = 1;
+  std::vector<double> optionalSimArgs = {seed};
+  std::vector<std::string> optionalSimArgNames = {"seed"}; 
+
+  // Create an arg object that will contain all parameters needed by the simulation, that will be stored on the Data object.  
+  // The DataArgs constructor takes those parameters that are required rather than optional.
+  // The chained setter functions can be used to set any of the optional parameters. They can be used in any order and default
+  // values will be used for any parameters that are not set
+  DataArgs dataArgs = DataArgs(nx, ny, nz, xmin, xmax, ymin, ymax, zmin, zmax, endTime)
+        .sCfl(cfl).sNg(Ng).sGamma(gamma).sCp(cp).sMu1(mu1).sMu2(mu2).sFrameSkip(frameSkip).sSigma(sigma)
+	.sReportItersPeriod(reportItersPeriod).sOptionalSimArgs(optionalSimArgs, optionalSimArgNames, nOptionalSimArgs);
+
+  Data data = Data(dataArgs, &env);
 
   // Choose particulars of simulation
   SRMHD model(&data);
diff --git a/Examples/KelvinHelmholtz/SingleFluidIdealRandomMPIHDF5CheckpointRestart/data_t0.checkpoint.hdf5 b/Examples/KelvinHelmholtz/SingleFluidIdealRandomMPIHDF5CheckpointRestart/data_t0.checkpoint.hdf5
index b0b53345..cd38c7d3 100644
Binary files a/Examples/KelvinHelmholtz/SingleFluidIdealRandomMPIHDF5CheckpointRestart/data_t0.checkpoint.hdf5 and b/Examples/KelvinHelmholtz/SingleFluidIdealRandomMPIHDF5CheckpointRestart/data_t0.checkpoint.hdf5 differ
diff --git a/Examples/KelvinHelmholtz/SingleFluidIdealRandomMPIHDF5CheckpointRestart/main.cc b/Examples/KelvinHelmholtz/SingleFluidIdealRandomMPIHDF5CheckpointRestart/main.cc
index 9b1ac9f2..d6c9db0c 100644
--- a/Examples/KelvinHelmholtz/SingleFluidIdealRandomMPIHDF5CheckpointRestart/main.cc
+++ b/Examples/KelvinHelmholtz/SingleFluidIdealRandomMPIHDF5CheckpointRestart/main.cc
@@ -28,7 +28,8 @@ int main(int argc, char *argv[]) {
   double ymax(1.0);
   double zmin(0.0);
   double zmax(1.0);
-  double endTime(3.0);
+  //double endTime(3.0);
+  double endTime(0.01);
   double cfl(0.6);
   double gamma(4.0/3.0);
   double sigma(10);
@@ -43,16 +44,16 @@ int main(int argc, char *argv[]) {
 
   ParallelEnv env(&argc, &argv, 2, 2, 1);
 
-  //const char* filename = "data_t3.checkpoint.hdf5";
   const char* filename = "data_t0.checkpoint.hdf5";
 
-  //Data data(nx, ny, nz, xmin, xmax, ymin, ymax, zmin, zmax, endTime, &env,
-            //cfl, Ng, gamma, sigma, cp, mu1, mu2, frameSkip, reportItersPeriod);
+  // Create an arg object that will contain all parameters needed by the simulation, that will be stored on the Data object.  
+  // ParallelCheckpointArgs sets those parameters that can be read from the restart file, while the chained setter functions 
+  // that follow can be used to set the additional variables that are not stored in the restart file, as well as override
+  // any other variables (should only need to overwrite endTime when starting from a restart file)
+  ParallelCheckpointArgs checkpointArgs = ParallelCheckpointArgs(filename, &env).sEndTime(endTime)
+        .sMu1(mu1).sMu2(mu2).sFrameSkip(frameSkip).sReportItersPeriod(reportItersPeriod);
 
-  ParallelCheckpointArgs checkpointArgs(filename, &env);
-  checkpointArgs.endTime=endTime;
-  
-  Data data(checkpointArgs, &env, mu1, mu2, frameSkip, reportItersPeriod);
+  Data data = Data(checkpointArgs, &env);
 
   // Choose particulars of simulation
   SRMHD model(&data);
@@ -67,11 +68,11 @@ int main(int argc, char *argv[]) {
 
   printf("Seed: %d\n", seed);
 
-  KHRandomInstabilitySingleFluid init(&data, 1, seed);
-  //ParallelCheckpointRestart init(&data, filename, &env);
-
+  //KHRandomInstabilitySingleFluid init(&data, 1, seed);
+  ParallelCheckpointRestart init(&data, filename, &env);
+  
   RKSplit timeInt(&data, &model, &bcs, &fluxMethod);
-
+ 
   ParallelSaveDataHDF5 save(&data, &env, "data_parallel", ParallelSaveDataHDF5::OUTPUT_ALL);
 
   // Now objects have been created, set up the simulation
diff --git a/Examples/KelvinHelmholtz/SingleFluidIdealRandomSerialHDF5/main.cc b/Examples/KelvinHelmholtz/SingleFluidIdealRandomSerialHDF5/main.cc
index 08bb68d2..4e435129 100644
--- a/Examples/KelvinHelmholtz/SingleFluidIdealRandomSerialHDF5/main.cc
+++ b/Examples/KelvinHelmholtz/SingleFluidIdealRandomSerialHDF5/main.cc
@@ -10,6 +10,8 @@
 #include "serialSaveDataHDF5.h"
 #include "weno.h"
 #include <cstring>
+#include <vector>
+#include <string>
 
 using namespace std;
 
@@ -27,7 +29,7 @@ int main(int argc, char *argv[]) {
   double zmin(0.0);
   double zmax(1.0);
   //double endTime(3.0);
-  double endTime(0.0);
+  double endTime(0.01);
   double cfl(0.6);
   double gamma(4.0/3.0);
   double sigma(10);
@@ -42,8 +44,24 @@ int main(int argc, char *argv[]) {
 
   SerialEnv env(&argc, &argv, 1, 1, 1);
 
-  Data data(nx, ny, nz, xmin, xmax, ymin, ymax, zmin, zmax, endTime, &env,
-            cfl, Ng, gamma, sigma, cp, mu1, mu2, frameSkip, reportItersPeriod);
+  const int nOptionalSimArgs = 1;
+  std::vector<double> optionalSimArgs = {seed};
+  std::vector<std::string> optionalSimArgNames = {"seed"}; 
+
+  // Create an arg object that will contain all parameters needed by the simulation, that will be stored on the Data object.  
+  // The DataArgs constructor takes those parameters that are required rather than optional.
+  // The chained setter functions can be used to set any of the optional parameters. They can be used in any order and default
+  // values will be used for any parameters that are not set
+  DataArgs dataArgs = DataArgs(nx, ny, nz, xmin, xmax, ymin, ymax, zmin, zmax, endTime)
+        .sCfl(cfl).sNg(Ng).sGamma(gamma).sCp(cp).sMu1(mu1).sMu2(mu2).sFrameSkip(frameSkip).sSigma(sigma)
+	.sReportItersPeriod(reportItersPeriod).sOptionalSimArgs(optionalSimArgs, optionalSimArgNames, nOptionalSimArgs);
+
+  Data data = Data(dataArgs, &env);
+
+  // The following is an example of creating the Data object without using named parameters -- in this case vars must be specified
+  // in order and all optional parameters before the last optional parameter of interest must be listed
+  //Data data(nx, ny, nz, xmin, xmax, ymin, ymax, zmin, zmax, endTime, &env,
+            //cfl, Ng, gamma, sigma, cp, mu1, mu2, frameSkip, reportItersPeriod);
 
   // Choose particulars of simulation
   SRMHD model(&data);
diff --git a/Examples/KelvinHelmholtz/SingleFluidIdealRandomSerialHDF5CheckpointRestart/data_t0.checkpoint.hdf5 b/Examples/KelvinHelmholtz/SingleFluidIdealRandomSerialHDF5CheckpointRestart/data_t0.checkpoint.hdf5
index b0b53345..cd38c7d3 100644
Binary files a/Examples/KelvinHelmholtz/SingleFluidIdealRandomSerialHDF5CheckpointRestart/data_t0.checkpoint.hdf5 and b/Examples/KelvinHelmholtz/SingleFluidIdealRandomSerialHDF5CheckpointRestart/data_t0.checkpoint.hdf5 differ
diff --git a/Examples/KelvinHelmholtz/SingleFluidIdealRandomSerialHDF5CheckpointRestart/main.cc b/Examples/KelvinHelmholtz/SingleFluidIdealRandomSerialHDF5CheckpointRestart/main.cc
index eb2b236c..0eee90ee 100644
--- a/Examples/KelvinHelmholtz/SingleFluidIdealRandomSerialHDF5CheckpointRestart/main.cc
+++ b/Examples/KelvinHelmholtz/SingleFluidIdealRandomSerialHDF5CheckpointRestart/main.cc
@@ -11,7 +11,8 @@
 #include "serialEnv.h"
 #include "serialSaveDataHDF5.h"
 #include "weno.h"
-#include <cstring>
+#include <string>
+#include <vector>
 
 using namespace std;
 
@@ -28,7 +29,8 @@ int main(int argc, char *argv[]) {
   double ymax(1.0);
   double zmin(0.0);
   double zmax(1.0);
-  double endTime(3.0);
+  //double endTime(3.0);
+  double endTime(0.01);
   double cfl(0.6);
   double gamma(4.0/3.0);
   double sigma(10);
@@ -43,16 +45,21 @@ int main(int argc, char *argv[]) {
 
   SerialEnv env(&argc, &argv, 1, 1, 1);
 
-  //const char* filename = "data_t3.checkpoint.hdf5";
   const char* filename = "data_t0.checkpoint.hdf5";
 
-  //Data data(nx, ny, nz, xmin, xmax, ymin, ymax, zmin, zmax, endTime, &env,
-  //          cfl, Ng, gamma, sigma, cp, mu1, mu2, frameSkip, reportItersPeriod);
-
-  SerialCheckpointArgs checkpointArgs(filename, &env);
-  checkpointArgs.endTime=endTime;
-  
-  Data data(checkpointArgs, &env, mu1, mu2, frameSkip, reportItersPeriod);
+  const int nOptionalSimArgs = 1;
+  std::vector<double> optionalSimArgs = {seed};
+  std::vector<std::string> optionalSimArgNames = {"seed"};
+
+  // Create an arg object that will contain all parameters needed by the simulation, that will be stored on the Data object.  
+  // SerialCheckpointArgs sets those parameters that can be read from the restart file, while the chained setter functions 
+  // that follow can be used to set the additional variables that are not stored in the restart file, as well as override
+  // any other variables (should only need to overwrite endTime when starting from a restart file)
+  SerialCheckpointArgs checkpointArgs = SerialCheckpointArgs(filename, &env).sEndTime(endTime)
+	.sMu1(mu1).sMu2(mu2).sFrameSkip(frameSkip).sReportItersPeriod(reportItersPeriod);
+        //.sOptionalSimArgs(optionalSimArgs, optionalSimArgNames, nOptionalSimArgs);
+ 
+  Data data = Data(checkpointArgs, &env);
 
   // Choose particulars of simulation
   SRMHD model(&data);
diff --git a/Project/CPU/Include/checkpointArgs.h b/Project/CPU/Include/checkpointArgs.h
deleted file mode 100644
index 68a48018..00000000
--- a/Project/CPU/Include/checkpointArgs.h
+++ /dev/null
@@ -1,63 +0,0 @@
-#ifndef CHECKPOINTARGS_H
-#define CHECKPOINTARGS_H
-
-#include <vector>
-#include <string>
-#include "platformEnv.h"
-
-
-//! <b> Object containing parameters required to populate Data from a restart file</b>
-/*!
-  @par
-      Parameters are read into CheckpointArgs from a checkpoint restart file. These are then used
-      to initialise Data. This is the best way to make sure that simulation parameters are consistent with
-      the restart file being used for initialisation.
-
-*/
-class CheckpointArgs 
-{
-  public:
-
-int
-    //@{
-    nx, ny, nz;            //!< Number of physical cells in specified direction
-    //@}
-    double
-    //@{
-    xmin, xmax,
-    ymin, ymax,            //!< Positional limits of domain in specified direction
-    zmin, zmax,
-    //@}
-    endTime,               //!< End time of simulation
-    cfl;                   //!< Courant factor
-    int Ng;                //!< Number of ghost cells
-    double
-    gamma,                 //!< Adiabatic index
-    sigma;                 //!< Resistivity
-    int
-    //@{
-    Ncons, Nprims, Naux;   //!< Number of specified variables
-    //@}
-    double
-    cp;                    //!< Constant divergence cleaning term
-    double
-    gam;                   //!< Exponent in the functional conductivity
-    double
-    t,                     //!< Current time
-    dt;                    //!< Width of current timestep
-    int
-    //@{
-    Nx, Ny, Nz;      //!< Total number of compute cells in domain in the specified direction
-    //@}
-
-
-    //! Constructor
-    /*!
-      @par 
-	reads parameters from a checkpoint restart file into this object for use in Data constructor
-    */
-    CheckpointArgs() {};
-
-};
-
-#endif
diff --git a/Project/CPU/Include/dataArgs.h b/Project/CPU/Include/dataArgs.h
new file mode 100644
index 00000000..0f75ec5e
--- /dev/null
+++ b/Project/CPU/Include/dataArgs.h
@@ -0,0 +1,165 @@
+#ifndef DATAARGS_H
+#define DATAARGS_H
+
+#include <vector>
+#include <string>
+#include "platformEnv.h"
+
+
+//! <b> Object containing parameters required to populate Data, including from a restart file</b>
+/*!
+  @par
+      Parameters can be read into DataArgs from a checkpoint restart file. These are then used
+      to initialise Data. This is the best way to make sure that simulation parameters are consistent with
+      the restart file being used for initialisation.
+
+      Note that the defaults here should be the same as the defaults set in the Data constructor in simData.h
+      that does not use named parameters. 
+
+*/
+class DataArgsBase
+{
+  public:
+
+    // The following Args are written to a checkpoint restart file and can therefore be initialised from file
+    // if one is provided. They can also be manually set by the user. 
+    // -------------------------------------------------------------------------
+    
+    int
+    //@{
+    nx, ny, nz;            //!< Number of physical cells in specified direction
+    //@}
+    double
+    //@{
+    xmin, xmax,
+    ymin, ymax,            //!< Positional limits of domain in specified direction
+    zmin, zmax,
+    //@}
+    frameSkip=10,          //!< Number of timesteps per file output
+    endTime,               //!< End time of simulation
+    cfl=0.5;               //!< Courant factor
+    int Ng=4;              //!< Number of ghost cells
+    double
+    gamma=5.0/3.0,         //!< Adiabatic index
+    sigma=1e3;             //!< Resistivity
+    int
+    //@{
+    Ncons, Nprims, Naux;   //!< Number of specified variables
+    //@}
+    double
+    cp=0.1;                //!< Constant divergence cleaning term
+    double
+    t=0,                   //!< Current time
+    dt;                    //!< Width of current timestep
+    int
+    //@{
+    Nx, Ny, Nz;            //!< Total number of compute cells in domain in the specified direction
+    //@}
+
+    // The following Args are never written to a restart file and therefore must always be manually set by the user
+    // in all cases. 
+    // -------------------------------------------------------------------------
+    double mu1=-1.0e4, mu2=1.0e4;              //!< Charge mass ratio of specified fluid species, q/m (for two fluid model)
+    int
+    reportItersPeriod=1;     //!< Period with which time step data is reported to screen during program execution
+    bool
+    functionalSigma=false;       //!< Are we using a functional (vs homogeneous) conductivity?
+    double
+    gam=12;                   //!< Exponent in the functional conductivity
+
+    std::vector<double> 
+    optionalSimArgs;	      //!< Array of optional arguments that depend on the simulation being run
+    std::vector<std::string>
+    optionalSimArgNames;     //!< Names of optionalSimArgs array elements
+    int
+    nOptionalSimArgs=0;      //!< Number of elements to include in optionalSimArgs array
+
+    //! Constructor
+    DataArgsBase() {
+    };
+
+};
+
+//! <b> Object containing parameters required to populate Data manually (as opposed to from a restart file)</b>
+/*!
+  @par
+      Required parameters must be set in the constructor. 
+      Setters are created for each optional parameter to allow creation of the object using chained 
+      named parameters, according to the strategy described in (https://isocpp.org/wiki/faq/ctors#named-parameter-idiom). 
+*/
+class DataArgs : public DataArgsBase
+{
+  public:
+
+    //! Constructor
+    /*!
+      @par 
+        Set required parameters to be used by the Data object.
+    */
+    DataArgs(int nx, int ny, int nz,
+         double xmin, double xmax,
+         double ymin, double ymax,
+         double zmin, double zmax,
+         double endTime) {
+      this->nx = nx; this->ny = ny; this->nz = nz;
+      this->xmin = xmin; this->ymin = ymin; this->zmin = zmin;
+      this->xmax = xmax; this->ymax = ymax; this->zmax = zmax;
+      this->endTime = endTime;
+    };
+
+    DataArgs& sCfl(double cfl) {
+      this->cfl = cfl; return *this; 
+    }
+
+    DataArgs& sNg(double Ng) {
+      this->Ng = Ng; return *this; 
+    }
+
+    DataArgs& sGamma(double gamma) {
+      this->gamma = gamma; return *this; 
+    }
+
+    DataArgs& sSigma(double sigma) {
+      this->sigma = sigma; return *this; 
+    }
+
+    DataArgs& sCp(double cp) {
+      this->cp = cp; return *this; 
+    }
+
+    DataArgs& sMu1(double mu1) {
+      this->mu1 = mu1; return *this; 
+    }
+
+    DataArgs& sMu2(double mu2) {
+      this->mu2 = mu2; return *this; 
+    }
+
+    DataArgs& sReportItersPeriod(int reportItersPeriod) {
+      this->reportItersPeriod = reportItersPeriod; return *this; 
+    }
+
+    DataArgs& sfunctionalSigma(bool functionalSigma) {
+      this->functionalSigma = functionalSigma; return *this; 
+    }
+
+    DataArgs& sGam(double gam) {
+      this->gam = gam; return *this; 
+    }
+
+    DataArgs& sFrameSkip(double frameSkip) {
+      this->frameSkip = frameSkip; return *this; 
+    }
+
+    // input arrays are copied to memory on this object. The input arrays are unchanged and their memory remains allocated 
+    // if optionalSimArgs and optionalSimArgNames have already been defined on this object, they are overwritten
+    DataArgs& sOptionalSimArgs(std::vector<double> optionalSimArgs, std::vector<std::string> optionalSimArgNames, int nOptionalSimArgs) {
+      this->nOptionalSimArgs = nOptionalSimArgs;
+      this->optionalSimArgs = optionalSimArgs;
+      this->optionalSimArgNames = optionalSimArgNames;
+      return *this;
+    }
+
+};
+
+#endif
diff --git a/Project/CPU/Include/parallelCheckpointArgs.h b/Project/CPU/Include/parallelCheckpointArgs.h
index 588b1bba..600c4a15 100644
--- a/Project/CPU/Include/parallelCheckpointArgs.h
+++ b/Project/CPU/Include/parallelCheckpointArgs.h
@@ -4,6 +4,7 @@
 #include <vector>
 #include <string>
 #include "parallelEnv.h"
+#include "dataArgs.h"
 
 //! <b> Object containing parameters required to populate Data from a restart file in parallel</b>
 /*!
@@ -13,7 +14,7 @@
       the restart file being used for initialisation.
 
 */
-class ParallelCheckpointArgs : public CheckpointArgs
+class ParallelCheckpointArgs : public DataArgsBase
 {
   public:
 
@@ -28,6 +29,100 @@ class ParallelCheckpointArgs : public CheckpointArgs
          const char* name,
 	 ParallelEnv *env);
 
+    ParallelCheckpointArgs& sNx(int nx) {
+      this->nx = nx; return *this;
+    }
+
+    ParallelCheckpointArgs& sNy(int ny) {
+      this->ny = ny; return *this;
+    }
+
+    ParallelCheckpointArgs& sNz(int nz) {
+      this->nz = nz; return *this;
+    }
+
+    ParallelCheckpointArgs& sXmin(double xmin) {
+      this->xmin = xmin; return *this;
+    }
+
+    ParallelCheckpointArgs& sYmin(double ymin) {
+      this->ymin = ymin; return *this;
+    }
+
+    ParallelCheckpointArgs& sZmin(double zmin) {
+      this->zmin = zmin; return *this;
+    }
+
+    ParallelCheckpointArgs& sXmax(double xmax) {
+      this->xmax = xmax; return *this;
+    }
+
+    ParallelCheckpointArgs& sYmax(double ymax) {
+      this->ymax = ymax; return *this;
+    }
+
+    ParallelCheckpointArgs& sZmax(double zmax) {
+      this->zmax = zmax; return *this;
+    }
+
+    ParallelCheckpointArgs& sEndTime(double endTime) {
+      this->endTime = endTime; return *this;
+    }
+
+    ParallelCheckpointArgs& sCfl(double cfl) {
+      this->cfl = cfl; return *this;
+    }
+
+    ParallelCheckpointArgs& sNg(double Ng) {
+      this->Ng = Ng; return *this;
+    }
+
+    ParallelCheckpointArgs& sGamma(double gamma) {
+      this->gamma = gamma; return *this;
+    }
+
+    ParallelCheckpointArgs& sSigma(double sigma) {
+      this->sigma = sigma; return *this;
+    }
+
+    ParallelCheckpointArgs& sCp(double cp) {
+      this->cp = cp; return *this;
+    }
+
+    ParallelCheckpointArgs& sMu1(double mu1) {
+      this->mu1 = mu1; return *this;
+    }
+
+    ParallelCheckpointArgs& sMu2(double mu2) {
+      this->mu2 = mu2; return *this;
+    }
+
+    ParallelCheckpointArgs& sReportItersPeriod(int reportItersPeriod) {
+      this->reportItersPeriod = reportItersPeriod; return *this;
+    }
+
+    ParallelCheckpointArgs& sfunctionalSigma(bool functionalSigma) {
+      this->functionalSigma = functionalSigma; return *this;
+    }
+
+    ParallelCheckpointArgs& sGam(double gam) {
+      this->gam = gam; return *this;
+    } 
+ 
+    ParallelCheckpointArgs& sFrameSkip(double frameSkip) {
+      this->frameSkip = frameSkip; return *this;
+    }
+
+    // input arrays are copied to memory on this object. The input arrays are unchanged and their memory remains allocated
+    // if optionalSimArgs and optionalSimArgNames are already set on this object, they are overwritten
+    ParallelCheckpointArgs& sOptionalSimArgs(std::vector<double> optionalSimArgs, std::vector<std::string> optionalSimArgNames, int nOptionalSimArgs) {
+      this->nOptionalSimArgs = nOptionalSimArgs;
+      this->optionalSimArgs = optionalSimArgs;
+      this->optionalSimArgNames = optionalSimArgNames;
+      return *this;
+    }
+
+
 };
 
 #endif
diff --git a/Project/CPU/Include/serialCheckpointArgs.h b/Project/CPU/Include/serialCheckpointArgs.h
index 42d4e06d..07ea818c 100644
--- a/Project/CPU/Include/serialCheckpointArgs.h
+++ b/Project/CPU/Include/serialCheckpointArgs.h
@@ -4,6 +4,7 @@
 #include <vector>
 #include <string>
 #include "platformEnv.h"
+#include "dataArgs.h"
 
 //! <b> Object containing parameters required to populate Data from a restart file in serial</b>
 /*!
@@ -13,7 +14,7 @@
       the restart file being used for initialisation.
 
 */
-class SerialCheckpointArgs : public CheckpointArgs
+class SerialCheckpointArgs : public DataArgsBase
 {
   public:
 
@@ -28,6 +29,100 @@ class SerialCheckpointArgs : public CheckpointArgs
          const char* name,
 	 PlatformEnv *env);
 
+    SerialCheckpointArgs& sNx(int nx) {
+      this->nx = nx; return *this;
+    }
+
+    SerialCheckpointArgs& sNy(int ny) {
+      this->ny = ny; return *this;
+    }
+
+    SerialCheckpointArgs& sNz(int nz) {
+      this->nz = nz; return *this;
+    }
+
+    SerialCheckpointArgs& sXmin(double xmin) {
+      this->xmin = xmin; return *this;
+    }
+
+    SerialCheckpointArgs& sYmin(double ymin) {
+      this->ymin = ymin; return *this;
+    }
+
+    SerialCheckpointArgs& sZmin(double zmin) {
+      this->zmin = zmin; return *this;
+    }
+
+    SerialCheckpointArgs& sXmax(double xmax) {
+      this->xmax = xmax; return *this;
+    }
+
+    SerialCheckpointArgs& sYmax(double ymax) {
+      this->ymax = ymax; return *this;
+    }
+
+    SerialCheckpointArgs& sZmax(double zmax) {
+      this->zmax = zmax; return *this;
+    }
+
+    SerialCheckpointArgs& sEndTime(double endTime) {
+      this->endTime = endTime; return *this;
+    }
+
+    SerialCheckpointArgs& sCfl(double cfl) {
+      this->cfl = cfl; return *this;
+    }
+
+    SerialCheckpointArgs& sNg(double Ng) {
+      this->Ng = Ng; return *this;
+    }
+
+    SerialCheckpointArgs& sGamma(double gamma) {
+      this->gamma = gamma; return *this;
+    }
+
+    SerialCheckpointArgs& sSigma(double sigma) {
+      this->sigma = sigma; return *this;
+    }
+
+    SerialCheckpointArgs& sCp(double cp) {
+      this->cp = cp; return *this;
+    }
+
+    SerialCheckpointArgs& sMu1(double mu1) {
+      this->mu1 = mu1; return *this;
+    }
+
+    SerialCheckpointArgs& sMu2(double mu2) {
+      this->mu2 = mu2; return *this;
+    }
+
+    SerialCheckpointArgs& sReportItersPeriod(int reportItersPeriod) {
+      this->reportItersPeriod = reportItersPeriod; return *this;
+    }
+
+    SerialCheckpointArgs& sfunctionalSigma(bool functionalSigma) {
+      this->functionalSigma = functionalSigma; return *this;
+    }
+
+    SerialCheckpointArgs& sGam(double gam) {
+      this->gam = gam; return *this;
+    }
+
+    SerialCheckpointArgs& sFrameSkip(double frameSkip) {
+      this->frameSkip = frameSkip; return *this;
+    }
+
+    // input arrays are copied to memory on this object. The input arrays are unchanged and their memory remains allocated
+    // if optionalSimArgs and optionalSimArgNames are already set on this object, they are overwritten
+    SerialCheckpointArgs& sOptionalSimArgs(std::vector<double> optionalSimArgs, std::vector<std::string> optionalSimArgNames, int nOptionalSimArgs) {
+      this->nOptionalSimArgs = nOptionalSimArgs;
+      this->optionalSimArgs = optionalSimArgs;
+      this->optionalSimArgNames = optionalSimArgNames;
+      return *this;
+    } 
 };
 
 #endif
+
+
diff --git a/Project/CPU/Include/simData.h b/Project/CPU/Include/simData.h
index 9b074c56..7add0aa5 100644
--- a/Project/CPU/Include/simData.h
+++ b/Project/CPU/Include/simData.h
@@ -4,7 +4,7 @@
 #include <vector>
 #include <string>
 #include "platformEnv.h"
-#include "checkpointArgs.h"
+#include "dataArgs.h"
 
 // Macro for getting array index
 #define ID(variable, idx, jdx, kdx) ((variable)*(d->Nx)*(d->Ny)*(d->Nz) + (idx)*(d->Ny)*(d->Nz) + (jdx)*(d->Nz) + (kdx))
@@ -120,6 +120,12 @@ class Data
     is, js, ks,
     ie, je, ke;            //!< Cell IDs for interior grid points
     //@}
+    std::vector<double>
+    optionalSimArgs;          //!< Array of optional arguments that depend on the simulation being run
+    std::vector<std::string>
+    optionalSimArgNames;     //!< Names of optionalSimArgs array elements
+    int
+    nOptionalSimArgs=0;      //!< Number of elements to include in optionalSimArgs array
 
 
     //! Element ID function
@@ -166,10 +172,10 @@ class Data
       This is separated from the constructor to avoid duplicated code between the two available
       constructors for Data.
      */
-     void initData(PlatformEnv *env);
+     void initData(PlatformEnv *env, int nOptionalSimArgs=0, std::vector<double> optionalSimArgs=std::vector<double>(), std::vector<std::string> optionalSimArgNames=std::vector<std::string>());
 
 
-    //! Constructor
+    //! Constructor  -- all vars specified by comma separated list
     /*!
       @par
         Allocates the memory required for the state arrays and sets the simulation
@@ -218,14 +224,11 @@ class Data
       constants to the given values. Does not set initial state, thats done by
       the initialFunc object.
       @param args simulation arguments such as cfl, sigma etc, as read from checkpoint restart file
-      @param mu1 charge mass ratio of species 1
-      @param mu2 charge mass ratio of species 2
       @param env environment object containing platform details eg MPI ranks
-      @param frameskip number of timesteps per file output
-      @param reportItersPeriod period with which time step data is reported to screen during program execution
     */
-    Data(CheckpointArgs args, PlatformEnv *env, double mu1=-1.0e4, double mu2=1.0e4,
-         int frameskip=10, int reportItersPeriod=1, int functionalSigma=false, double gam=12);
+    Data(DataArgsBase args, PlatformEnv *env);
+
+    ~Data() {};
 
 };
 
diff --git a/Project/CPU/Src/checkpointArgs.cc b/Project/CPU/Src/dataArgs.cc
similarity index 97%
rename from Project/CPU/Src/checkpointArgs.cc
rename to Project/CPU/Src/dataArgs.cc
index c6d2cffb..8644e544 100644
--- a/Project/CPU/Src/checkpointArgs.cc
+++ b/Project/CPU/Src/dataArgs.cc
@@ -8,7 +8,7 @@
 #include <stdexcept>
 
 
-CheckpointArgs::CheckpointArgs(const char* name, PlatformEnv *env)
+DataArgs::DataArgs(const char* name, PlatformEnv *env)
 {
 	herr_t error=0, tmpError=-1;
 	hid_t file = H5Fopen(name, H5F_ACC_RDONLY, H5P_DEFAULT);
diff --git a/Project/CPU/Src/parallelCheckpointArgs.cc b/Project/CPU/Src/parallelCheckpointArgs.cc
index 20b6d485..b2bcb44a 100644
--- a/Project/CPU/Src/parallelCheckpointArgs.cc
+++ b/Project/CPU/Src/parallelCheckpointArgs.cc
@@ -7,8 +7,7 @@
 #include "hdf5_hl.h"
 #include <stdexcept>
 
-
-ParallelCheckpointArgs::ParallelCheckpointArgs(const char* name, ParallelEnv *env) : CheckpointArgs()
+ParallelCheckpointArgs::ParallelCheckpointArgs(const char* name, ParallelEnv *env) : DataArgsBase()
 {
 	herr_t error=0, tmpError=-1;
 
@@ -30,6 +29,33 @@ ParallelCheckpointArgs::ParallelCheckpointArgs(const char* name, ParallelEnv *en
 	if (tmpError < 0) error = tmpError;
 	if (error<0) throw std::runtime_error("Checkpoint restart file is missing some global attributes");
 
+        // Read optional file attributes
+        hid_t optionalGroup = H5Gopen(file, "Optional", H5P_DEFAULT);
+        if (optionalGroup >= 0){
+          // if the hdf5 file we're using has an optional sim args group. This may not be the case if the
+          // file is in an older style
+          tmpError = H5LTget_attribute_int(optionalGroup, ".", "nOptionalSimArgs",  &(this->nOptionalSimArgs));
+
+          hid_t attr;
+          double optionalArg;
+          char *argName = (char*) malloc(256*sizeof(char));
+          // There should be no way for these arrays to have been written to, but clearing them just in case
+          this->optionalSimArgs.clear();
+          this->optionalSimArgNames.clear();
+          for (int i(0); i<this->nOptionalSimArgs; i++){
+            // read all the optional arguments, skipping the first attribute in this group, which is nOptionalSimArgs 
+            // and has already been read 
+            attr = H5Aopen_by_idx(optionalGroup, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, i+1, H5P_DEFAULT, H5P_DEFAULT);
+            tmpError = H5Aread(attr,  H5T_NATIVE_DOUBLE, &optionalArg);
+            tmpError = H5Aget_name(attr, 256, argName);
+            (this->optionalSimArgs).push_back(optionalArg);
+            (this->optionalSimArgNames).push_back(argName);
+            H5Aclose(attr);
+          }
+          free(argName);
+        }
+        H5Gclose(optionalGroup);
+
 	// Remaining required attributes are stored in the Domain group
 	hid_t group = H5Gopen(file, "Domain", H5P_DEFAULT);
 	tmpError = H5LTget_attribute_int(group, ".", "nx",  &(nx));
diff --git a/Project/CPU/Src/parallelInitFuncFromCheckpoint.cc b/Project/CPU/Src/parallelInitFuncFromCheckpoint.cc
index 263a8100..8769820b 100644
--- a/Project/CPU/Src/parallelInitFuncFromCheckpoint.cc
+++ b/Project/CPU/Src/parallelInitFuncFromCheckpoint.cc
@@ -80,13 +80,17 @@ void ParallelCheckpointRestart::readDataSetDouble(const hid_t *group, const char
       }
     }
   }
+
+  H5Pclose(dataset_access_property_list);
+  H5Sclose(dataspace_total);
+  H5Sclose(dataspace_local);
+  H5Dclose(dataset);
 }
 
 ParallelCheckpointRestart::ParallelCheckpointRestart(Data * data, const char *name, ParallelEnv *env) : InitialFunc(data)
 {
   // Syntax
   Data * d(data);
-
   herr_t error=0;
 
   hid_t file_access_property_list = H5Pcreate(H5P_FILE_ACCESS);
@@ -103,16 +107,17 @@ ParallelCheckpointRestart::ParallelCheckpointRestart(Data * data, const char *na
   error = H5LTget_attribute_int(groupCons, ".", "Ncons",  &(NconsFile));
   if (error<0 || NconsFile < d->Ncons) throw std::runtime_error("Too few conserved vars recorded in checkpoint restart file for this model");
 
-  hid_t groupPrims = H5Gopen(file, "Primitive", H5P_DEFAULT);
-  error = H5LTget_attribute_int(groupPrims, ".", "Nprims",  &(NprimsFile));
-  if (error<0 || NconsFile < d->Nprims) throw std::runtime_error("Too few primitive vars recorded in checkpoint restart file for this model");
-
   // Read all cons vars
   for(int var(0); var < d->Ncons; var++) {
     readDataSetDouble(&groupCons, d->consLabels[var].c_str(), &var, d->cons, env);
   }
   H5Gclose(groupCons);
 
+  hid_t groupPrims = H5Gopen(file, "Primitive", H5P_DEFAULT);
+  error = H5LTget_attribute_int(groupPrims, ".", "Nprims",  &(NprimsFile));
+  if (error<0 || NconsFile < d->Nprims) throw std::runtime_error("Too few primitive vars recorded in checkpoint restart file for this model");
+
+
   // Read all prims vars
   for(int var(0); var < d->Nprims; var++) {
     readDataSetDouble(&groupPrims, d->primsLabels[var].c_str(), &var, d->prims, env);
@@ -120,4 +125,5 @@ ParallelCheckpointRestart::ParallelCheckpointRestart(Data * data, const char *na
   H5Gclose(groupPrims);
 
   H5Fclose(file);
+  H5Pclose(file_access_property_list);
 }
diff --git a/Project/CPU/Src/parallelSaveDataHDF5.cc b/Project/CPU/Src/parallelSaveDataHDF5.cc
index 712465d4..845db7bd 100644
--- a/Project/CPU/Src/parallelSaveDataHDF5.cc
+++ b/Project/CPU/Src/parallelSaveDataHDF5.cc
@@ -289,6 +289,16 @@ void ParallelSaveDataHDF5::saveConsts()
   H5LTset_attribute_double(this->file, ".", "sigma", &d->sigma, 1);
   H5LTset_attribute_double(this->file, ".", "cp", &d->cp, 1);
   H5LTset_attribute_double(this->file, ".", "t", &d->t, 1);
+
+  // For each one of the optional simulation arguments, write it to disk
+  hid_t group = H5Gcreate(this->file, "Optional", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+  H5LTset_attribute_int(group, ".", "nOptionalSimArgs", &d->nOptionalSimArgs, 1);
+  for(int i(0); i < d->nOptionalSimArgs; i++) {
+    string name = d->optionalSimArgNames[i];
+    double arg = d->optionalSimArgs[i];
+    H5LTset_attribute_double(group, ".", name.c_str(), &arg, 1);
+  }
+  H5Gclose(group);
 }
 
 
diff --git a/Project/CPU/Src/serialCheckpointArgs.cc b/Project/CPU/Src/serialCheckpointArgs.cc
index 6a222f32..9e66848f 100644
--- a/Project/CPU/Src/serialCheckpointArgs.cc
+++ b/Project/CPU/Src/serialCheckpointArgs.cc
@@ -7,8 +7,7 @@
 #include "hdf5_hl.h"
 #include <stdexcept>
 
-
-SerialCheckpointArgs::SerialCheckpointArgs(const char* name, PlatformEnv *env) : CheckpointArgs()
+SerialCheckpointArgs::SerialCheckpointArgs(const char* name, PlatformEnv *env) : DataArgsBase()
 {
 	herr_t error=0, tmpError=-1;
 	hid_t file = H5Fopen(name, H5F_ACC_RDONLY, H5P_DEFAULT);
@@ -28,6 +27,32 @@ SerialCheckpointArgs::SerialCheckpointArgs(const char* name, PlatformEnv *env) :
 	if (tmpError < 0) error = tmpError;
 	if (error<0) throw std::runtime_error("Checkpoint restart file is missing some global attributes");
 
+        // Read optional file attributes
+	hid_t optionalGroup = H5Gopen(file, "Optional", H5P_DEFAULT);
+        if (optionalGroup >= 0){
+          // if the hdf5 file we're using has an optional sim args group. This may not be the case if the
+          // file is in an older style
+  	  tmpError = H5LTget_attribute_int(optionalGroup, ".", "nOptionalSimArgs",  &(this->nOptionalSimArgs));
+  
+          hid_t attr;
+          double optionalArg;
+          char *argName = (char*) malloc(256*sizeof(char));
+          // There should be no way for these arrays to have been written to, but clearing them just in case
+          this->optionalSimArgs.clear();
+          this->optionalSimArgNames.clear();
+          for (int i(0); i<nOptionalSimArgs; i++){
+            // read all the optional arguments, skipping the first attribute in this group, which is nOptionalSimArgs
+            // and has already been read
+            attr = H5Aopen_by_idx(optionalGroup, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, i+1, H5P_DEFAULT, H5P_DEFAULT);
+  	    tmpError = H5Aread(attr,  H5T_NATIVE_DOUBLE, &optionalArg);
+  	    tmpError = H5Aget_name(attr, 256, argName);
+            (this->optionalSimArgs).push_back(optionalArg);
+            (this->optionalSimArgNames).push_back(argName);
+          }
+          free(argName);
+          H5Gclose(optionalGroup);
+        }
+
 	// Remaining required attributes are stored in the Domain group
 	hid_t group = H5Gopen(file, "Domain", H5P_DEFAULT);
 	tmpError = H5LTget_attribute_int(group, ".", "nx",  &(nx));
@@ -65,3 +90,4 @@ SerialCheckpointArgs::SerialCheckpointArgs(const char* name, PlatformEnv *env) :
 }
 
 
+
diff --git a/Project/CPU/Src/serialSaveDataHDF5.cc b/Project/CPU/Src/serialSaveDataHDF5.cc
index 7b5463d4..d358d6d1 100644
--- a/Project/CPU/Src/serialSaveDataHDF5.cc
+++ b/Project/CPU/Src/serialSaveDataHDF5.cc
@@ -247,6 +247,16 @@ void SerialSaveDataHDF5::saveConsts()
   H5LTset_attribute_double(this->file, ".", "sigma", &d->sigma, 1);
   H5LTset_attribute_double(this->file, ".", "cp", &d->cp, 1);
   H5LTset_attribute_double(this->file, ".", "t", &d->t, 1);
+
+  // For each one of the optional simulation arguments, write it to disk
+  hid_t group = H5Gcreate(this->file, "Optional", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+  H5LTset_attribute_int(group, ".", "nOptionalSimArgs", &d->nOptionalSimArgs, 1);
+  for(int i(0); i < d->nOptionalSimArgs; i++) {
+    string name = d->optionalSimArgNames[i];
+    double arg = d->optionalSimArgs[i];
+    H5LTset_attribute_double(group, ".", name.c_str(), &arg, 1);
+  }
+  H5Gclose(group);
 }
 
 
diff --git a/Project/CPU/Src/simData.cc b/Project/CPU/Src/simData.cc
index 44a97db3..f2c90fd4 100644
--- a/Project/CPU/Src/simData.cc
+++ b/Project/CPU/Src/simData.cc
@@ -2,9 +2,12 @@
 #include "platformEnv.h"
 #include <stdexcept>
 #include <cmath>
+#include <string>
 
 #define IDn(variable, idx, jdx, kdx) ((variable)*(this->Nx)*(this->Ny)*(this->Nz) + (idx)*(this->Ny)*(this->Nz) + (jdx)*(this->Nz) + (kdx))
 
+using namespace std;
+
 Data::Data(int nx, int ny, int nz,
            double xmin, double xmax,
            double ymin, double ymax,
@@ -35,8 +38,7 @@ Data::Data(int nx, int ny, int nz,
 	initData(env);
 }
 
-Data::Data(CheckpointArgs args, PlatformEnv *env, double mu1, double mu2,
-         int frameSkip, int reportItersPeriod, int functionalSigma, double gam)
+Data::Data(DataArgsBase args, PlatformEnv *env)
            :
            nx(args.nx), ny(args.ny), nz(args.nz),
            xmin(args.xmin), xmax(args.xmax),
@@ -47,16 +49,16 @@ Data::Data(CheckpointArgs args, PlatformEnv *env, double mu1, double mu2,
            memSet(0), bcsSet(0),
            Ncons(0), Nprims(0), Naux(0),
            cp(args.cp),
-           mu1(mu1), mu2(mu2),
-           frameSkip(frameSkip),
-           reportItersPeriod(reportItersPeriod),
-           functionalSigma(functionalSigma), gam(gam),
-           t(args.t)
+           mu1(args.mu1), mu2(args.mu2),
+           frameSkip(args.frameSkip),
+           reportItersPeriod(args.reportItersPeriod),
+           functionalSigma(args.functionalSigma), gam(args.gam),
+           t(args.t) 
 {
-	initData(env);
+	initData(env, args.nOptionalSimArgs, args.optionalSimArgs, args.optionalSimArgNames);
 }
 
-void Data::initData(PlatformEnv *env){
+void Data::initData(PlatformEnv *env, int nOptionalSimArgs, std::vector<double> optionalSimArgs, std::vector<std::string> optionalSimArgNames){
   // TODO -- handle nx not dividing perfectly into nxRanks
 
   // Set Nx to be nx per MPI process + ghost cells
@@ -102,6 +104,11 @@ void Data::initData(PlatformEnv *env){
   if (this->mu1 > 0.0 or this->mu2 < 0.0) {
     throw std::invalid_argument("Species 1 must have negative charge, mu1 < 0, and species 2 must have positive charge, mu2 > 0.\n");
   }
+
+  // Allocate and initialise optional simulation parameters if we have been passed any
+  this->nOptionalSimArgs = nOptionalSimArgs;
+  this->optionalSimArgs = optionalSimArgs;
+  this->optionalSimArgNames = optionalSimArgNames;
 }
 
 double Data::sigmaFunc(double * cons, double * prims, double * aux, int i, int j, int k)
@@ -118,3 +125,4 @@ double Data::sigmaFunc(double * cons, double * prims, double * aux, int i, int j
       return sigma * pow(cons[IDn(0, i, j, k)], gam);
   }
 }
+
diff --git a/Project/GPU/Include/parallelCheckpointArgs.h b/Project/GPU/Include/parallelCheckpointArgs.h
index d2a2f09e..d99399e4 100644
--- a/Project/GPU/Include/parallelCheckpointArgs.h
+++ b/Project/GPU/Include/parallelCheckpointArgs.h
@@ -4,6 +4,7 @@
 #include <vector>
 #include <string>
 #include "parallelEnv.h"
+#include "dataArgs.h"
 
 
 //! <b> Wrapper around Data object for populating Data from a checkpoint restart file</b>
@@ -15,7 +16,7 @@
   known to lower objects---good practice. <br>
 
 */
-class ParallelCheckpointArgs : public CheckpointArgs
+class ParallelCheckpointArgs : public DataArgsBase
 {
   public:
 
@@ -32,6 +33,101 @@ class ParallelCheckpointArgs : public CheckpointArgs
          const char* name,
 	 ParallelEnv *env);
 
+
+    ParallelCheckpointArgs& sNx(int nx) {
+      this->nx = nx; return *this;
+    }
+
+    ParallelCheckpointArgs& sNy(int ny) {
+      this->ny = ny; return *this;
+    }
+
+    ParallelCheckpointArgs& sNz(int nz) {
+      this->nz = nz; return *this;
+    }
+
+    ParallelCheckpointArgs& sXmin(double xmin) {
+      this->xmin = xmin; return *this;
+    }
+
+    ParallelCheckpointArgs& sYmin(double ymin) {
+      this->ymin = ymin; return *this;
+    }
+
+    ParallelCheckpointArgs& sZmin(double zmin) {
+      this->zmin = zmin; return *this;
+    }
+
+    ParallelCheckpointArgs& sXmax(double xmax) {
+      this->xmax = xmax; return *this;
+    }
+
+    ParallelCheckpointArgs& sYmax(double ymax) {
+      this->ymax = ymax; return *this;
+    }
+
+    ParallelCheckpointArgs& sZmax(double zmax) {
+      this->zmax = zmax; return *this;
+    }
+
+    ParallelCheckpointArgs& sEndTime(double endTime) {
+      this->endTime = endTime; return *this;
+    }
+
+    ParallelCheckpointArgs& sCfl(double cfl) {
+      this->cfl = cfl; return *this;
+    }
+
+    ParallelCheckpointArgs& sNg(double Ng) {
+      this->Ng = Ng; return *this;
+    }
+
+    ParallelCheckpointArgs& sGamma(double gamma) {
+      this->gamma = gamma; return *this;
+    }
+
+    ParallelCheckpointArgs& sSigma(double sigma) {
+      this->sigma = sigma; return *this;
+    }
+
+    ParallelCheckpointArgs& sCp(double cp) {
+      this->cp = cp; return *this;
+    }
+
+    ParallelCheckpointArgs& sMu1(double mu1) {
+      this->mu1 = mu1; return *this;
+    }
+
+    ParallelCheckpointArgs& sMu2(double mu2) {
+      this->mu2 = mu2; return *this;
+    }
+
+    ParallelCheckpointArgs& sReportItersPeriod(int reportItersPeriod) {
+      this->reportItersPeriod = reportItersPeriod; return *this;
+    }
+
+    ParallelCheckpointArgs& sfunctionalSigma(bool functionalSigma) {
+      this->functionalSigma = functionalSigma; return *this;
+    }
+
+    ParallelCheckpointArgs& sGam(double gam) {
+      this->gam = gam; return *this;
+    } 
+
+    ParallelCheckpointArgs& sFrameSkip(double frameSkip) {
+      this->frameSkip = frameSkip; return *this;
+    }
+
+    // input arrays are copied to memory on this object. The input arrays are unchanged and their memory remains allocated
+    // if optionalSimArgs and optionalSimArgNames are already set on this object, they are overwritten
+    ParallelCheckpointArgs& sOptionalSimArgs(std::vector<double> optionalSimArgs, std::vector<std::string> optionalSimArgNames, int nOptionalSimArgs) {
+      this->nOptionalSimArgs = nOptionalSimArgs;
+      this->optionalSimArgs = optionalSimArgs;
+      this->optionalSimArgNames = optionalSimArgNames;
+      return *this;
+    }
+
+
 };
 
 #endif
diff --git a/Project/GPU/Include/serialCheckpointArgs.h b/Project/GPU/Include/serialCheckpointArgs.h
index 8b072fbd..bc3bf35b 100644
--- a/Project/GPU/Include/serialCheckpointArgs.h
+++ b/Project/GPU/Include/serialCheckpointArgs.h
@@ -4,6 +4,7 @@
 #include <vector>
 #include <string>
 #include "platformEnv.h"
+#include "dataArgs.h"
 
 
 //! <b> Wrapper around Data object for populating Data from a checkpoint restart file</b>
@@ -15,7 +16,7 @@
   known to lower objects---good practice. <br>
 
 */
-class SerialCheckpointArgs : public CheckpointArgs
+class SerialCheckpointArgs : public DataArgsBase
 {
   public:
 
@@ -32,6 +33,98 @@ class SerialCheckpointArgs : public CheckpointArgs
          const char* name,
 	 PlatformEnv *env);
 
+    SerialCheckpointArgs& sNx(int nx) {
+      this->nx = nx; return *this;
+    }
+
+    SerialCheckpointArgs& sNy(int ny) {
+      this->ny = ny; return *this;
+    }
+
+    SerialCheckpointArgs& sNz(int nz) {
+      this->nz = nz; return *this;
+    }
+
+    SerialCheckpointArgs& sXmin(double xmin) {
+      this->xmin = xmin; return *this;
+    }
+
+    SerialCheckpointArgs& sYmin(double ymin) {
+      this->ymin = ymin; return *this;
+    }
+
+    SerialCheckpointArgs& sZmin(double zmin) {
+      this->zmin = zmin; return *this;
+    }
+
+    SerialCheckpointArgs& sXmax(double xmax) {
+      this->xmax = xmax; return *this;
+    }
+
+    SerialCheckpointArgs& sYmax(double ymax) {
+      this->ymax = ymax; return *this;
+    }
+
+    SerialCheckpointArgs& sZmax(double zmax) {
+      this->zmax = zmax; return *this;
+    }
+
+    SerialCheckpointArgs& sEndTime(double endTime) {
+      this->endTime = endTime; return *this;
+    }
+
+    SerialCheckpointArgs& sCfl(double cfl) {
+      this->cfl = cfl; return *this;
+    }
+
+    SerialCheckpointArgs& sNg(double Ng) {
+      this->Ng = Ng; return *this;
+    }
+
+    SerialCheckpointArgs& sGamma(double gamma) {
+      this->gamma = gamma; return *this;
+    }
+
+    SerialCheckpointArgs& sSigma(double sigma) {
+      this->sigma = sigma; return *this;
+    }
+
+    SerialCheckpointArgs& sCp(double cp) {
+      this->cp = cp; return *this;
+    }
+
+    SerialCheckpointArgs& sMu1(double mu1) {
+      this->mu1 = mu1; return *this;
+    }
+
+    SerialCheckpointArgs& sMu2(double mu2) {
+      this->mu2 = mu2; return *this;
+    }
+
+    SerialCheckpointArgs& sReportItersPeriod(int reportItersPeriod) {
+      this->reportItersPeriod = reportItersPeriod; return *this;
+    }
+
+    SerialCheckpointArgs& sfunctionalSigma(bool functionalSigma) {
+      this->functionalSigma = functionalSigma; return *this;
+    }
+
+    SerialCheckpointArgs& sGam(double gam) {
+      this->gam = gam; return *this;
+    }
+
+    SerialCheckpointArgs& sFrameSkip(double frameSkip) {
+      this->frameSkip = frameSkip; return *this;
+    }
+
+    // input arrays are copied to memory on this object. The input arrays are unchanged and their memory remains allocated
+    // if optionalSimArgs and optionalSimArgNames are already set on this object, they are overwritten
+    SerialCheckpointArgs& sOptionalSimArgs(std::vector<double> optionalSimArgs, std::vector<std::string> optionalSimArgNames, int nOptionalSimArgs) {
+      this->nOptionalSimArgs = nOptionalSimArgs;
+      this->optionalSimArgs = optionalSimArgs;
+      this->optionalSimArgNames = optionalSimArgNames;
+      return *this;
+    } 
 };
 
 #endif
diff --git a/Project/GPU/Include/simData.h b/Project/GPU/Include/simData.h
index 24665c62..d60ed404 100644
--- a/Project/GPU/Include/simData.h
+++ b/Project/GPU/Include/simData.h
@@ -4,7 +4,7 @@
 #include <vector>
 #include <string>
 #include "platformEnv.h"
-#include "checkpointArgs.h"
+#include "dataArgs.h"
 
 
 /*!
@@ -125,8 +125,15 @@ class Data
     dims,                  //!< Number of dimensions of simulation
     //@{
     is, js, ks,
-    ie, je, ke,            //!< Cell IDs for interior grid points
+    ie, je, ke;            //!< Cell IDs for interior grid points
     //@}
+    std::vector<double>
+    optionalSimArgs;          //!< Array of optional arguments that depend on the simulation being run
+    std::vector<std::string>
+    optionalSimArgNames;     //!< Names of optionalSimArgs array elements
+    int
+    nOptionalSimArgs=0;      //!< Number of elements to include in optionalSimArgs array
+    int
     GPUcount;              //!< Number of NVIDIA devices detected
     cudaDeviceProp
     prop;                  //!< Properties of NVIDIA device (assuming all are same)
@@ -158,10 +165,10 @@ class Data
       This is separated from the constructor to avoid duplicated code between the two available
       constructors for Data.
      */
-     void initData(PlatformEnv *env);
+     void initData(PlatformEnv *env, int nOptionalSimArgs=0, std::vector<double> optionalSimArgs=std::vector<double>(), std::vector<std::string> optionalSimArgNames=std::vector<std::string>());
 
 
-    //! Constructor
+    //! Constructor   -- all vars specified by comma separated list
     /*!
       @par
         Allocates the memory required for the state arrays and sets the simulation
@@ -206,8 +213,9 @@ class Data
       @param mu1 charge mass ratio of species 1
       @param mu2 charge mass ratio of species 2
     */
-    Data(CheckpointArgs args, PlatformEnv *env, double mu1=-1.0e4, double mu2=1.0e4,
-         int frameskip=10);
+    Data(DataArgsBase args, PlatformEnv *env);
+
+    ~Data() {};
 
    
 };
diff --git a/Project/GPU/Src/checkpointArgs.cu b/Project/GPU/Src/dataArgs.cu
similarity index 97%
rename from Project/GPU/Src/checkpointArgs.cu
rename to Project/GPU/Src/dataArgs.cu
index c6d2cffb..8644e544 100644
--- a/Project/GPU/Src/checkpointArgs.cu
+++ b/Project/GPU/Src/dataArgs.cu
@@ -8,7 +8,7 @@
 #include <stdexcept>
 
 
-CheckpointArgs::CheckpointArgs(const char* name, PlatformEnv *env)
+DataArgs::DataArgs(const char* name, PlatformEnv *env)
 {
 	herr_t error=0, tmpError=-1;
 	hid_t file = H5Fopen(name, H5F_ACC_RDONLY, H5P_DEFAULT);
diff --git a/Project/GPU/Src/main.cu b/Project/GPU/Src/main.cu
index 60e4f941..f3ecf9c8 100644
--- a/Project/GPU/Src/main.cu
+++ b/Project/GPU/Src/main.cu
@@ -3,7 +3,7 @@
 #include "parallelCheckpointArgs.h"
 #include "simulation.h"
 #include "initFunc.h"
-#include "initFuncFromCheckpoint.h"
+#include "parallelInitFuncFromCheckpoint.h"
 #include "srmhd.h"
 #include "srrmhd.h"
 #include "boundaryConds.h"
@@ -62,13 +62,38 @@ int main(int argc, char *argv[]) {
 
   const char* filename = "data_t0.checkpoint.hdf5";
 
-  ParallelCheckpointArgs checkpointArgs(filename, &env);
-  checkpointArgs.endTime=endTime;
-
-  Data data(checkpointArgs, &env);
-
-  //Data data(nx, ny, nz, xmin, xmax, ymin, ymax, zmin, zmax, endTime, &env,
-            //cfl, Ng, gamma, sigma);
+  //ParallelCheckpointArgs checkpointArgs(filename, &env);
+  //checkpointArgs.endTime=endTime;
+
+  // Create an arg object that will contain all parameters needed by the simulation, that will be stored on the Data object.  
+  // ParallelCheckpointArgs sets those parameters that can be read from the restart file, while the chained setter functions 
+  // that follow can be used to set the additional variables that are not stored in the restart file, as well as override
+  // any other variables (should only need to overwrite endTime when starting from a restart file)
+/*
+  ParallelCheckpointArgs checkpointArgs = ParallelCheckpointArgs(filename, &env).sEndTime(endTime);
+
+  Data data = Data(checkpointArgs, &env);
+*/
+
+  const int nOptionalSimArgs = 1;
+  std::vector<double> optionalSimArgs = {100};
+  std::vector<std::string> optionalSimArgNames = {"seed"};
+
+  // Create an arg object that will contain all parameters needed by the simulation, that will be stored on the Data object.  
+  // The DataArgs constructor takes those parameters that are required rather than optional.
+  // The chained setter functions can be used to set any of the optional parameters. They can be used in any order and default
+  // values will be used for any parameters that are not set
+  DataArgs dataArgs = DataArgs(nx, ny, nz, xmin, xmax, ymin, ymax, zmin, zmax, endTime)
+        .sCfl(cfl).sNg(Ng).sGamma(gamma).sSigma(sigma)
+        .sOptionalSimArgs(optionalSimArgs, optionalSimArgNames, nOptionalSimArgs);
+  
+  Data data = Data(dataArgs, &env);
+
+  // Create a data object using the old interface
+  /*
+  Data data(nx, ny, nz, xmin, xmax, ymin, ymax, zmin, zmax, endTime, &env,
+            cfl, Ng, gamma, sigma);
+  */
 
   // Choose particulars of simulation
   SRMHD model(&data);
@@ -79,7 +104,8 @@ int main(int argc, char *argv[]) {
 
   Simulation sim(&data, &env);
 
-  KHInstabilitySingleFluid init(&data, 1);
+  //KHInstabilitySingleFluid init(&data, 1);
+  ParallelCheckpointRestart init(&data, filename, &env);
 
   RK2 timeInt(&data, &model, &bcs, &fluxMethod);
 
diff --git a/Project/GPU/Src/parallelCheckpointArgs.cu b/Project/GPU/Src/parallelCheckpointArgs.cu
index 20b6d485..7a1902bd 100644
--- a/Project/GPU/Src/parallelCheckpointArgs.cu
+++ b/Project/GPU/Src/parallelCheckpointArgs.cu
@@ -8,7 +8,7 @@
 #include <stdexcept>
 
 
-ParallelCheckpointArgs::ParallelCheckpointArgs(const char* name, ParallelEnv *env) : CheckpointArgs()
+ParallelCheckpointArgs::ParallelCheckpointArgs(const char* name, ParallelEnv *env) : DataArgsBase()
 {
 	herr_t error=0, tmpError=-1;
 
@@ -30,6 +30,33 @@ ParallelCheckpointArgs::ParallelCheckpointArgs(const char* name, ParallelEnv *en
 	if (tmpError < 0) error = tmpError;
 	if (error<0) throw std::runtime_error("Checkpoint restart file is missing some global attributes");
 
+        // Read optional file attributes
+        hid_t optionalGroup = H5Gopen(file, "Optional", H5P_DEFAULT);
+        if (optionalGroup >= 0){
+          // if the hdf5 file we're using has an optional sim args group. This may not be the case if the
+          // file is in an older style
+          tmpError = H5LTget_attribute_int(optionalGroup, ".", "nOptionalSimArgs",  &(this->nOptionalSimArgs));
+
+          hid_t attr;
+          double optionalArg;
+          char *argName = (char*) malloc(256*sizeof(char));
+          // There should be no way for these arrays to have been written to, but clearing them just in case
+          this->optionalSimArgs.clear();
+          this->optionalSimArgNames.clear();
+          for (int i(0); i<this->nOptionalSimArgs; i++){
+            // read all the optional arguments, skipping the first attribute in this group, which is nOptionalSimArgs 
+            // and has already been read 
+            attr = H5Aopen_by_idx(optionalGroup, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, i+1, H5P_DEFAULT, H5P_DEFAULT);
+            tmpError = H5Aread(attr,  H5T_NATIVE_DOUBLE, &optionalArg);
+            tmpError = H5Aget_name(attr, 256, argName);
+            (this->optionalSimArgs).push_back(optionalArg);
+            (this->optionalSimArgNames).push_back(argName);
+            H5Aclose(attr);
+          }
+          free(argName);
+        }
+        H5Gclose(optionalGroup);
+
 	// Remaining required attributes are stored in the Domain group
 	hid_t group = H5Gopen(file, "Domain", H5P_DEFAULT);
 	tmpError = H5LTget_attribute_int(group, ".", "nx",  &(nx));
diff --git a/Project/GPU/Src/parallelInitFuncFromCheckpoint.cu b/Project/GPU/Src/parallelInitFuncFromCheckpoint.cu
index f9533624..15a3d4aa 100644
--- a/Project/GPU/Src/parallelInitFuncFromCheckpoint.cu
+++ b/Project/GPU/Src/parallelInitFuncFromCheckpoint.cu
@@ -93,6 +93,11 @@ void ParallelCheckpointRestart::readDataSetDouble(const hid_t *group, const char
       }
     }
   }
+
+  H5Pclose(dataset_access_property_list);
+  H5Sclose(dataspace_total);
+  H5Sclose(dataspace_local);
+  H5Dclose(dataset);
 }
 
 ParallelCheckpointRestart::ParallelCheckpointRestart(Data * data, const char *name, ParallelEnv *env) : InitialFunc(data)
@@ -116,16 +121,17 @@ ParallelCheckpointRestart::ParallelCheckpointRestart(Data * data, const char *na
   error = H5LTget_attribute_int(groupCons, ".", "Ncons",  &(NconsFile));
   if (error<0 || NconsFile < d->Ncons) throw std::runtime_error("Too few conserved vars recorded in checkpoint restart file for this model");
 
-  hid_t groupPrims = H5Gopen(file, "Primitive", H5P_DEFAULT);
-  error = H5LTget_attribute_int(groupPrims, ".", "Nprims",  &(NprimsFile));
-  if (error<0 || NconsFile < d->Nprims) throw std::runtime_error("Too few primitive vars recorded in checkpoint restart file for this model");
-
   // Read all cons vars
   for(int var(0); var < d->Ncons; var++) {
     readDataSetDouble(&groupCons, d->consLabels[var].c_str(), &var, d->cons, env);
   }
   H5Gclose(groupCons);
 
+  hid_t groupPrims = H5Gopen(file, "Primitive", H5P_DEFAULT);
+  error = H5LTget_attribute_int(groupPrims, ".", "Nprims",  &(NprimsFile));
+  if (error<0 || NconsFile < d->Nprims) throw std::runtime_error("Too few primitive vars recorded in checkpoint restart file for this model");
+
+
   // Read all prims vars
   for(int var(0); var < d->Nprims; var++) {
     readDataSetDouble(&groupPrims, d->primsLabels[var].c_str(), &var, d->prims, env);
@@ -133,4 +139,5 @@ ParallelCheckpointRestart::ParallelCheckpointRestart(Data * data, const char *na
   H5Gclose(groupPrims);
 
   H5Fclose(file);
+  H5Pclose(file_access_property_list);
 }
diff --git a/Project/GPU/Src/parallelSaveDataHDF5.cu b/Project/GPU/Src/parallelSaveDataHDF5.cu
index c045e432..ffd7dbda 100644
--- a/Project/GPU/Src/parallelSaveDataHDF5.cu
+++ b/Project/GPU/Src/parallelSaveDataHDF5.cu
@@ -290,6 +290,16 @@ void ParallelSaveDataHDF5::saveConsts()
   H5LTset_attribute_double(this->file, ".", "sigma", &d->sigma, 1);
   H5LTset_attribute_double(this->file, ".", "cp", &d->cp, 1);
   H5LTset_attribute_double(this->file, ".", "t", &d->t, 1);
+
+  // For each one of the optional simulation arguments, write it to disk
+  hid_t group = H5Gcreate(this->file, "Optional", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+  H5LTset_attribute_int(group, ".", "nOptionalSimArgs", &d->nOptionalSimArgs, 1);
+  for(int i(0); i < d->nOptionalSimArgs; i++) {
+    string name = d->optionalSimArgNames[i];
+    double arg = d->optionalSimArgs[i];
+    H5LTset_attribute_double(group, ".", name.c_str(), &arg, 1);
+  }
+  H5Gclose(group);
 }
 
 
diff --git a/Project/GPU/Src/serialCheckpointArgs.cu b/Project/GPU/Src/serialCheckpointArgs.cu
index c69ffd93..9c18b288 100644
--- a/Project/GPU/Src/serialCheckpointArgs.cu
+++ b/Project/GPU/Src/serialCheckpointArgs.cu
@@ -8,7 +8,7 @@
 #include <stdexcept>
 
 
-SerialCheckpointArgs::SerialCheckpointArgs(const char* name, PlatformEnv *env) : CheckpointArgs
+SerialCheckpointArgs::SerialCheckpointArgs(const char* name, PlatformEnv *env) : DataArgsBase()
 {
 	herr_t error=0, tmpError=-1;
 	hid_t file = H5Fopen(name, H5F_ACC_RDONLY, H5P_DEFAULT);
@@ -28,6 +28,32 @@ SerialCheckpointArgs::SerialCheckpointArgs(const char* name, PlatformEnv *env) :
 	if (tmpError < 0) error = tmpError;
 	if (error<0) throw std::runtime_error("Checkpoint restart file is missing some global attributes");
 
+        // Read optional file attributes
+	hid_t optionalGroup = H5Gopen(file, "Optional", H5P_DEFAULT);
+        if (optionalGroup >= 0){
+          // if the hdf5 file we're using has an optional sim args group. This may not be the case if the
+          // file is in an older style
+  	  tmpError = H5LTget_attribute_int(optionalGroup, ".", "nOptionalSimArgs",  &(this->nOptionalSimArgs));
+
+          hid_t attr;
+          double optionalArg;
+          char *argName = (char*) malloc(256*sizeof(char));
+          // There should be no way for these arrays to have been written to, but clearing them just in case
+          this->optionalSimArgs.clear();
+          this->optionalSimArgNames.clear();
+          for (int i(0); i<nOptionalSimArgs; i++){
+            // read all the optional arguments, skipping the first attribute in this group, which is nOptionalSimArgs
+            // and has already been read
+            attr = H5Aopen_by_idx(optionalGroup, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, i+1, H5P_DEFAULT, H5P_DEFAULT);
+  	    tmpError = H5Aread(attr,  H5T_NATIVE_DOUBLE, &optionalArg);
+  	    tmpError = H5Aget_name(attr, 256, argName);
+            (this->optionalSimArgs).push_back(optionalArg);
+            (this->optionalSimArgNames).push_back(argName);
+          }
+          free(argName);
+          H5Gclose(optionalGroup);
+        }
+
 	// Remaining required attributes are stored in the Domain group
 	hid_t group = H5Gopen(file, "Domain", H5P_DEFAULT);
 	tmpError = H5LTget_attribute_int(group, ".", "nx",  &(nx));
diff --git a/Project/GPU/Src/serialSaveDataHDF5.cu b/Project/GPU/Src/serialSaveDataHDF5.cu
index 45853d50..4c0b4051 100644
--- a/Project/GPU/Src/serialSaveDataHDF5.cu
+++ b/Project/GPU/Src/serialSaveDataHDF5.cu
@@ -248,6 +248,16 @@ void SerialSaveDataHDF5::saveConsts()
   H5LTset_attribute_double(this->file, ".", "sigma", &d->sigma, 1);
   H5LTset_attribute_double(this->file, ".", "cp", &d->cp, 1);
   H5LTset_attribute_double(this->file, ".", "t", &d->t, 1);
+
+  // For each one of the optional simulation arguments, write it to disk
+  hid_t group = H5Gcreate(this->file, "Optional", H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+  H5LTset_attribute_int(group, ".", "nOptionalSimArgs", &d->nOptionalSimArgs, 1);
+  for(int i(0); i < d->nOptionalSimArgs; i++) {
+    string name = d->optionalSimArgNames[i];
+    double arg = d->optionalSimArgs[i];
+    H5LTset_attribute_double(group, ".", name.c_str(), &arg, 1);
+  }
+  H5Gclose(group);
 }
 
 
diff --git a/Project/GPU/Src/simData.cu b/Project/GPU/Src/simData.cu
index 58bfc73f..9e9109e0 100644
--- a/Project/GPU/Src/simData.cu
+++ b/Project/GPU/Src/simData.cu
@@ -3,6 +3,9 @@
 #include "cudaErrorCheck.h"
 #include <stdexcept>
 #include <cstdio>
+#include <string>
+
+using namespace std;
 
 Data::Data(int nx, int ny, int nz,
            double xmin, double xmax,
@@ -30,8 +33,7 @@ Data::Data(int nx, int ny, int nz,
 	initData(env);
 }
 
-Data::Data(CheckpointArgs args, PlatformEnv *env, double mu1, double mu2,
-         int frameSkip)
+Data::Data(DataArgsBase args, PlatformEnv *env)
            :
            nx(args.nx), ny(args.ny), nz(args.nz),
            xmin(args.xmin), xmax(args.xmax),
@@ -42,14 +44,14 @@ Data::Data(CheckpointArgs args, PlatformEnv *env, double mu1, double mu2,
            memSet(0), bcsSet(0),
            Ncons(0), Nprims(0), Naux(0),
            cp(args.cp),
-           mu1(mu1), mu2(mu2),
-           frameSkip(frameSkip),
+           mu1(args.mu1), mu2(args.mu2),
+           frameSkip(args.frameSkip),
            t(args.t)
 {
-	initData(env);
+	initData(env, args.nOptionalSimArgs, args.optionalSimArgs, args.optionalSimArgNames);
 }
 
-void Data::initData(PlatformEnv *env){
+void Data::initData(PlatformEnv *env, int nOptionalSimArgs, std::vector<double> optionalSimArgs, std::vector<std::string> optionalSimArgNames){
   // TODO -- handle nx not dividing perfectly into nxRanks
 
   // Set Nx to be nx per MPI process + ghost cells
@@ -102,6 +104,11 @@ void Data::initData(PlatformEnv *env){
     throw std::invalid_argument("Species 1 must have negative charge, mu1 < 0, and species 2 must have positive charge, mu2 > 0.\n");
   }
 
+  // Allocate and initialise optional simulation parameters if we have been passed any
+  this->nOptionalSimArgs = nOptionalSimArgs;
+  this->optionalSimArgs = optionalSimArgs;
+  this->optionalSimArgNames = optionalSimArgNames;
+
   // Determine the specs of the GPU(s) and thus set details in simData
   cudaGetDeviceCount(&GPUcount);
   cudaGetDeviceProperties(&prop, 0);
diff --git a/Project/GPU/data_t0.checkpoint.hdf5 b/Project/GPU/data_t0.checkpoint.hdf5
index c3c39aeb..cd38c7d3 100644
Binary files a/Project/GPU/data_t0.checkpoint.hdf5 and b/Project/GPU/data_t0.checkpoint.hdf5 differ