Index: /issm/trunk/template
===================================================================
--- /issm/trunk/template	(revision 9418)
+++ /issm/trunk/template	(revision 9419)
@@ -131,10 +131,15 @@
 		vertices_type2d -> delete
 }}}
-diagnostic{{{
-	isdiagnostic
+initialization{{{
 	vx
 	vy
 	vz
 	vel
+	pressure
+	temperature
+	watercolumn
+	waterfraction
+}}}
+diagnostic{{{
 	spcvx
 	spcvy
@@ -145,6 +150,5 @@
 	pressureload -> rename icefront?
 	diagnostic_ref -> rename referential?
-	penalties
-	pressure
+	penalties -> rename vertex_pairing
 
 	eps_res -> rename following PETSc: restol
@@ -153,29 +157,25 @@
 	max_nonlinear_iterations -> rename maxiter
 
-	penalty_lock -> rename riftpenaltylock or equiv?
-	min_mechanical_constraints -> rename (not clear)
+	penalty_lock -> rename rift_penalty_lock 
+	min_mechanical_constraints -> rename  rift_penalty_threshold
 }}}
 thermal{{{
-	isthermal
-	temperature
 	spctemperature
-	penalty_melting
-	min_thermal_constraints -> rename (see min_mechanical_constraints)
-	waterfraction
+	penalty_melting -> delete
+	min_thermal_constraints -> rename thermal_penalty_threshold
 	artificial_diffusivity -> rename stabilization
 	max_nonlinear_iterations -> rename maxiter
-	stabilize_constraints -> rename (not clear)
+	stabilize_constraints -> rename thermal_penalty_lock
 }}}
 prognostic{{{
-	isprognostic
 	spcthickness
 	hydrostatic_adjustment
 	artificial_diffusivity -> rename stabilization
 	prognostic_DG -> should be merged with stabilization
-	penalties
+	penalties -> rename vertex_pairing
 }}}
 balancethickness{{{
 	spcthickness
-	dhdt
+	dhdt -> rename thickening_rate
 	artificial_diffusivity -> rename stabilization
 }}}
@@ -184,12 +184,17 @@
 	max_steadystate_iterations -> rename maxiter
 }}}
+transient{{{
+   isdiagnostic
+   isprognostic
+   isthermal
+   isgroundingline -> add
+}}}
 goundingline {{{
-	groundingline_migration
-	groundingline_melting_rate
+	groundingline_migration -> rename migration_type
+	groundingline_melting_rate -> rename melting_rate
 }}}
 hydrology{{{
-	watercolumn
 	spwatercolumn
-	hydro_n
+	hydro_n -> remove all hydro_
 	hydro_CR
 	hydro_p
@@ -198,11 +203,13 @@
 }}}
 control{{{
-	control_analysis
-	num_control_type -> num_controls
-	control_type -> rename control_paramters?
-	num_cm_responses
-	cm_responses -> rename objective_functions
+	private: 
+		num_control_type -> num_control_parameters
+		num_cm_responses -> rename num_cost_functions
+
+	control_analysis ->rename iscontrol
+	control_type -> rename control_parameters?
+	cm_responses -> rename cost_functions
 	cm_gradient -> rename gradient_only
-	weights
+	weights -> rename cost_functions_coefficients
 
 	cm_min -> min_parameters
@@ -210,11 +217,12 @@
 
 	nsteps
-	maxiter
-	tolx
-	optscal
-	cm_jump -> jump
-	eps_cm  -> remove (never used)
-	epsvel  -> hardcoded?
-	meanvel -> hardcoded?
+	maxiter -> rename maxiter_per_step
+	tolx    -> hardcoded,delete
+	optscal -> gradient_scaling
+	cm_jump -> step_threshold
+	eps_cm  -> misfit_threshold
+
+	epsvel  -> hardcoded, delete
+	meanvel -> hardcoded, delete
 
 	vx_obs