--- a/examples/pitot/gas-giant-h2he-theory/gas-giant-theory.cfg	Thu Jan 04 18:46:02 2018 +1000
+++ b/examples/pitot/gas-giant-h2he-theory/gas-giant-theory.cfg	Thu Jan 04 19:06:21 2018 +1000
@@ -16,7 +16,7 @@
 # Boolean statement controlling if pitot will clean up temporary files after running
 # Use false unless you really want to clean everything up.
 
-cleanup = False 
+cleanup = True
 
 # Testcase to run. There are three options:
 # 'fulltheory-pressure' = a fully theoretical run where shock speeds are found from set fill pressures
@@ -28,7 +28,13 @@
 # Solver to use. There are three options:
 # 'eq' = equilibrium calculations using CEA code
 # 'pg' = perfect gas solver
-# "pg-eq' = a combination of pg and eq solvers, used for CO2 based gases. Sets state1 as a pg, but everything else (including the shock to state 2, are done as eq)
+# 'pg-eq' = a combination of pg and eq solvers, used for CO2 based gases IN THE PAST. It sets state1 as a perfect gas state
+# but everything else (including the shock to state 2, are done as eq). The problem with the perfect gas eq state is that
+# it means that state 8 (which is eq) has a difference enthalpy reference temperature to state 1 (which is perfect gas),
+# causing issues with the stagnation enthalpy value that are not insignificant. All other results would be correct,
+# but Ht, an important value for expansion tube test flows, would be wrong. For this reason I do not recommend using it anymore.
+# The code now sets the CO2 based starting state by doing a calculation which only includes the fill gases (i.e. just CO2 or just CO2 and N2),
+# a constraint which is then turned off for the other gas states.
 
 solver = 'eq'
 
@@ -43,18 +49,17 @@
 
 mode = 'printout'
 
-# Here you can specify how many steps are used for the various unsteady expansions
-# You should use at least 200 steps for these secondary driver and shock tube expansion
-# to check the accuracy.
+# Here you can specify how many steps are used for the various unsteady expansions,
+# These have been commented out so that the latest default versions will be used
 
-secondary_driver_expansion_steps = 300
+#secondary_driver_expansion_steps = 400
 
-shock_tube_expansion_steps = 300
+#shock_tube_expansion_steps = 400
 
 # need to use 800 - 1000 steps on the acceleration tube unsteady expansion to match the
 # pressure across the contact surface properly, which is important.
 
-acc_tube_expansion_steps = 1000
+#acc_tube_expansion_steps = 1200
 
 # Can specify your own bounds and initial guesses for the secant solver in 
 # the acceleration tube if you so desire

--- a/examples/pitot/high-speed-air-theory-with-area-ratio-check/high-speed-air-theory-with-area-ratio-check.cfg	Thu Jan 04 18:46:02 2018 +1000
+++ b/examples/pitot/high-speed-air-theory-with-area-ratio-check/high-speed-air-theory-with-area-ratio-check.cfg	Thu Jan 04 19:06:21 2018 +1000
@@ -16,7 +16,7 @@
 # Boolean statement controlling if pitot will clean up temporary files after running
 # Use false unless you really want to clean everything up.
 
-cleanup = False 
+cleanup = True
 
 # Testcase to run. There are three options:
 # 'fulltheory-pressure' = a fully theoretical run where shock speeds are found from set fill pressures
@@ -28,7 +28,13 @@
 # Solver to use. There are three options:
 # 'eq' = equilibrium calculations using CEA code
 # 'pg' = perfect gas solver
-# "pg-eq' = a combination of pg and eq solvers, used for CO2 based gases. Sets state1 as a pg, but everything else (including the shock to state 2, are done as eq)
+# 'pg-eq' = a combination of pg and eq solvers, used for CO2 based gases IN THE PAST. It sets state1 as a perfect gas state
+# but everything else (including the shock to state 2, are done as eq). The problem with the perfect gas eq state is that
+# it means that state 8 (which is eq) has a difference enthalpy reference temperature to state 1 (which is perfect gas),
+# causing issues with the stagnation enthalpy value that are not insignificant. All other results would be correct,
+# but Ht, an important value for expansion tube test flows, would be wrong. For this reason I do not recommend using it anymore.
+# The code now sets the CO2 based starting state by doing a calculation which only includes the fill gases (i.e. just CO2 or just CO2 and N2),
+# a constraint which is then turned off for the other gas states.
 
 solver = 'eq'
 

--- a/examples/pitot/high-speed-air-theory-with-condition-builder/high-speed-air-theory-with-condition-builder.cfg	Thu Jan 04 18:46:02 2018 +1000
+++ b/examples/pitot/high-speed-air-theory-with-condition-builder/high-speed-air-theory-with-condition-builder.cfg	Thu Jan 04 19:06:21 2018 +1000
@@ -16,7 +16,7 @@
 # Boolean statement controlling if pitot will clean up temporary files after running
 # Use false unless you really want to clean everything up.
 
-cleanup = False 
+cleanup = True 
 
 # Testcase to run. There are three options:
 # 'fulltheory-pressure' = a fully theoretical run where shock speeds are found from set fill pressures
@@ -28,7 +28,13 @@
 # Solver to use. There are three options:
 # 'eq' = equilibrium calculations using CEA code
 # 'pg' = perfect gas solver
-# "pg-eq' = a combination of pg and eq solvers, used for CO2 based gases. Sets state1 as a pg, but everything else (including the shock to state 2, are done as eq)
+# 'pg-eq' = a combination of pg and eq solvers, used for CO2 based gases IN THE PAST. It sets state1 as a perfect gas state
+# but everything else (including the shock to state 2, are done as eq). The problem with the perfect gas eq state is that
+# it means that state 8 (which is eq) has a difference enthalpy reference temperature to state 1 (which is perfect gas),
+# causing issues with the stagnation enthalpy value that are not insignificant. All other results would be correct,
+# but Ht, an important value for expansion tube test flows, would be wrong. For this reason I do not recommend using it anymore.
+# The code now sets the CO2 based starting state by doing a calculation which only includes the fill gases (i.e. just CO2 or just CO2 and N2),
+# a constraint which is then turned off for the other gas states.
 
 solver = 'eq'
 
@@ -43,16 +49,17 @@
 
 mode = 'printout'
 
-# Here you can specify how many steps are used for the various unsteady expansions
+# Here you can specify how many steps are used for the various unsteady expansions,
+# These have been commented out so that the latest default versions will be used
 
-#secondary_driver_expansion_steps = 200
+#secondary_driver_expansion_steps = 400
 
-shock_tube_expansion_steps = 200
+#shock_tube_expansion_steps = 400
 
 # need to use 800 - 1000 steps on the acceleration tube unsteady expansion to match the
 # pressure across the contact surface properly, which is important.
 
-acc_tube_expansion_steps = 1000
+#acc_tube_expansion_steps = 1200
 
 # Can specify your own bounds and initial guesses for the secant solver in 
 # the acceleration tube if you so desire

--- a/examples/pitot/high-speed-air-theory-with-custom-piston-and-test-gas/high-speed-air-theory-with-custom-piston-and-test-gas.cfg	Thu Jan 04 18:46:02 2018 +1000
+++ b/examples/pitot/high-speed-air-theory-with-custom-piston-and-test-gas/high-speed-air-theory-with-custom-piston-and-test-gas.cfg	Thu Jan 04 19:06:21 2018 +1000
@@ -17,7 +17,7 @@
 # Boolean statement controlling if pitot will clean up temporary files after running
 # Use false unless you really want to clean everything up.
 
-cleanup = False 
+cleanup = True
 
 # Testcase to run. There are three options:
 # 'fulltheory-pressure' = a fully theoretical run where shock speeds are found from set fill pressures
@@ -29,7 +29,13 @@
 # Solver to use. There are three options:
 # 'eq' = equilibrium calculations using CEA code
 # 'pg' = perfect gas solver
-# "pg-eq' = a combination of pg and eq solvers, used for CO2 based gases. Sets state1 as a pg, but everything else (including the shock to state 2, are done as eq)
+# 'pg-eq' = a combination of pg and eq solvers, used for CO2 based gases IN THE PAST. It sets state1 as a perfect gas state
+# but everything else (including the shock to state 2, are done as eq). The problem with the perfect gas eq state is that
+# it means that state 8 (which is eq) has a difference enthalpy reference temperature to state 1 (which is perfect gas),
+# causing issues with the stagnation enthalpy value that are not insignificant. All other results would be correct,
+# but Ht, an important value for expansion tube test flows, would be wrong. For this reason I do not recommend using it anymore.
+# The code now sets the CO2 based starting state by doing a calculation which only includes the fill gases (i.e. just CO2 or just CO2 and N2),
+# a constraint which is then turned off for the other gas states.
 
 solver = 'eq'
 
@@ -44,11 +50,17 @@
 
 mode = 'printout'
 
-# Here you can specify how many steps are used for the various unsteady expansions
+# Here you can specify how many steps are used for the various unsteady expansions,
+# These have been commented out so that the latest default versions will be used
+
+#secondary_driver_expansion_steps = 400
 
-#secondary_driver_expansion_steps = 200
+#shock_tube_expansion_steps = 400
 
-shock_tube_expansion_steps = 200
+# need to use 800 - 1000 steps on the acceleration tube unsteady expansion to match the
+# pressure across the contact surface properly, which is important.
+
+#acc_tube_expansion_steps = 1200
 
 # need to use 800 - 1000 steps on the acceleration tube unsteady expansion to match the
 # pressure across the contact surface properly, which is important.
@@ -112,7 +124,7 @@
 
 driver_composition = {'He':1.0} #driver composition. Must be a valid Python dictionary.
 driver_inputUnits = 'moles' #input units for custom driver. either 'moles' or 'massf'
-test_gas_with_ions= True #whether to use ions with the test gas.
+driver_gas_with_ions= True #whether to use ions with the test gas.
 
 p4 = 27.9e6 #primary driver burst pressure, Pa 
 # another variable 'compression_ratio' can also be used here to instead specify a compression ratio

--- a/examples/pitot/high-speed-air-theory/high-speed-air-theory.cfg	Thu Jan 04 18:46:02 2018 +1000
+++ b/examples/pitot/high-speed-air-theory/high-speed-air-theory.cfg	Thu Jan 04 19:06:21 2018 +1000
@@ -14,7 +14,7 @@
 # Boolean statement controlling if pitot will clean up temporary files after running
 # Use false unless you really want to clean everything up.
 
-cleanup = False 
+cleanup = True
 
 # Testcase to run. There are three options:
 # 'fulltheory-pressure' = a fully theoretical run where shock speeds are found from set fill pressures
@@ -26,7 +26,13 @@
 # Solver to use. There are three options:
 # 'eq' = equilibrium calculations using CEA code
 # 'pg' = perfect gas solver
-# "pg-eq' = a combination of pg and eq solvers, used for CO2 based gases. Sets state1 as a pg, but everything else (including the shock to state 2, are done as eq)
+# 'pg-eq' = a combination of pg and eq solvers, used for CO2 based gases IN THE PAST. It sets state1 as a perfect gas state
+# but everything else (including the shock to state 2, are done as eq). The problem with the perfect gas eq state is that
+# it means that state 8 (which is eq) has a difference enthalpy reference temperature to state 1 (which is perfect gas),
+# causing issues with the stagnation enthalpy value that are not insignificant. All other results would be correct,
+# but Ht, an important value for expansion tube test flows, would be wrong. For this reason I do not recommend using it anymore.
+# The code now sets the CO2 based starting state by doing a calculation which only includes the fill gases (i.e. just CO2 or just CO2 and N2),
+# a constraint which is then turned off for the other gas states.
 
 solver = 'eq'
 
@@ -41,16 +47,17 @@
 
 mode = 'printout'
 
-# Here you can specify how many steps are used for the various unsteady expansions
+# Here you can specify how many steps are used for the various unsteady expansions,
+# These have been commented out so that the latest default versions will be used
 
-#secondary_driver_expansion_steps = 200
+#secondary_driver_expansion_steps = 400
 
-shock_tube_expansion_steps = 200
+#shock_tube_expansion_steps = 400
 
 # need to use 800 - 1000 steps on the acceleration tube unsteady expansion to match the
 # pressure across the contact surface properly, which is important.
 
-acc_tube_expansion_steps = 1000
+#acc_tube_expansion_steps = 1200
 
 # Can specify your own bounds and initial guesses for the secant solver in 
 # the acceleration tube if you so desire

--- a/examples/pitot/mars-theory/mars-theory.cfg	Thu Jan 04 18:46:02 2018 +1000
+++ b/examples/pitot/mars-theory/mars-theory.cfg	Thu Jan 04 19:06:21 2018 +1000
@@ -1,8 +1,10 @@
-# Example input file for pitot.
-# Chris James (c.james4@uq.edu.au) 14/01/14
-# This is a basic mars example I made.
+# Example mars entry input file for pitot.
+# This is a new version where I changed the solver from pg-eq to eq, as eq is better, as is discussed below
+# Chris James (c.james4@uq.edu.au) - 04/01/18
 # I've tried to annotate this config file as much as I can so it will
 # be useful to other people using the program.
+# All of the potential inputs in the program are not included in this config file,
+# but the ones required for a basic simulation are.
 
 #--------------------------- Start-up --------------------------------------
 # This is where the setup of the program is specified.
@@ -13,7 +15,7 @@
 # Boolean statement controlling if pitot will clean up temporary files after running
 # Use false unless you really want to clean everything up.
 
-cleanup = False 
+cleanup = True 
 
 # Testcase to run. There are three options:
 # 'fulltheory-pressure' = a fully theoretical run where shock speeds are found from set fill pressures
@@ -25,9 +27,15 @@
 # Solver to use. There are three options:
 # 'eq' = equilibrium calculations using CEA code
 # 'pg' = perfect gas solver
-# "pg-eq' = a combination of pg and eq solvers, used for CO2 based gases. Sets state1 as a pg, but everything else (including the shock to state 2, are done as eq)
+# 'pg-eq' = a combination of pg and eq solvers, used for CO2 based gases IN THE PAST. It sets state1 as a perfect gas state
+# but everything else (including the shock to state 2, are done as eq). The problem with the perfect gas eq state is that
+# it means that state 8 (which is eq) has a difference enthalpy reference temperature to state 1 (which is perfect gas),
+# causing issues with the stagnation enthalpy value that are not insignificant. All other results would be correct,
+# but Ht, an important value for expansion tube test flows, would be wrong. For this reason I do not recommend using it anymore.
+# The code now sets the CO2 based starting state by doing a calculation which only includes the fill gases (i.e. just CO2 or just CO2 and N2),
+# a constraint which is then turned off for the other gas states.
 
-solver = 'pg-eq'
+solver = 'eq'
 
 # Mode that the program is run in. There are five options:
 # 'printout' = normal run, prints out a summary to the screen, a txt file and a csv file at the end of the program, then quits
@@ -40,16 +48,17 @@
 
 mode = 'printout'
 
-# Here you can specify how many steps are used for the various unsteady expansions
+# Here you can specify how many steps are used for the various unsteady expansions,
+# These have been commented out so that the latest default versions will be used
 
-#secondary_driver_expansion_steps = 200
+#secondary_driver_expansion_steps = 400
 
-shock_tube_expansion_steps = 200.4
+#shock_tube_expansion_steps = 400
 
 # need to use 800 - 1000 steps on the acceleration tube unsteady expansion to match the
 # pressure across the contact surface properly, which is important.
 
-acc_tube_expansion_steps = 800
+#acc_tube_expansion_steps = 1200
 
 # Can specify your own bounds and initial guesses for the secant solver in 
 # the acceleration tube if you so desire
@@ -175,7 +184,7 @@
 
 # Turns on the code that calculates the conditions over a normal shock over a test model in the test section.
 
-shock_over_model = False
+shock_over_model = True