Index: /issm/trunk/template
===================================================================
--- /issm/trunk/template	(revision 9419)
+++ /issm/trunk/template	(revision 9420)
@@ -151,4 +151,5 @@
 	diagnostic_ref -> rename referential?
 	penalties -> rename vertex_pairing
+	penalty_offset -> rename penalty_factor and change to absolute value
 
 	eps_res -> rename following PETSc: restol
@@ -159,4 +160,5 @@
 	penalty_lock -> rename rift_penalty_lock 
 	min_mechanical_constraints -> rename  rift_penalty_threshold
+	requested_outputs
 }}}
 thermal{{{
@@ -167,4 +169,6 @@
 	max_nonlinear_iterations -> rename maxiter
 	stabilize_constraints -> rename thermal_penalty_lock
+	penalty_offset -> rename penalty_factor and change to absolute value
+	requested_outputs
 }}}
 prognostic{{{
@@ -174,4 +178,6 @@
 	prognostic_DG -> should be merged with stabilization
 	penalties -> rename vertex_pairing
+	penalty_offset -> rename penalty_factor and change to absolute value
+	requested_outputs
 }}}
 balancethickness{{{
@@ -179,8 +185,10 @@
 	dhdt -> rename thickening_rate
 	artificial_diffusivity -> rename stabilization
+	requested_outputs
 }}}
 steadystate{{{
 	eps_rel -> rename following PETSc: reltol
 	max_steadystate_iterations -> rename maxiter
+	requested_outputs
 }}}
 transient{{{
@@ -188,5 +196,6 @@
    isprognostic
    isthermal
-   isgroundingline -> add
+   idsgroundingline -> add
+   requested_outputs
 }}}
 goundingline {{{
@@ -202,5 +211,5 @@
 	hydro_kn
 }}}
-control{{{
+inversion{{{ 
 	private: 
 		num_control_type -> num_control_parameters
@@ -236,11 +245,11 @@
 	qmu_method -> remove all qmu_
 	qmu_params
-	dakotaresults
-	dakotain
-	dakotaout
-	dakotadat
-	qmu_analysis
-	part
-	npart
+	dakotaresults ->results
+	dakotain ->check
+	dakotaout ->check
+	dakotadat ->check
+	qmu_analysis -> isqmu
+	part ->partition
+	npart -> numberofpartitions
 	numberofvariables
 	numberofresponses
@@ -250,9 +259,9 @@
 	qmu_mass_flux_profiles
 	qmu_mass_flux_segments
-	qmu_relax
-	qmu_save_femmodel
+	qmu_relax -> investigate
+	qmu_save_femmodel -> trash
 
 	adjacency
-	vwgt
+	vwgt -> vertex_weight
 }}}
 flaim{{{
@@ -271,16 +280,15 @@
 }}}
 cluster{{{
-	waitonlock -> cluster dependent
+	waitonlock -> cluster dependent to be added to all cluster classes
 	-> already exists
 }}}
 timestepping{{{
-	dt
-	ndt
-	time_adapt -> rename cfl_apply
+	dt ->time_step
+	ndt-> rename final_time
+	time_adapt -> "cfl" "none"
 	adaptative_cfl -> remove
 	cfl_coefficient
 }}}
 results{{{
-	requested_outputs
 	results_on_vertices
 	output_frequency
@@ -289,5 +297,5 @@
 	  + all model results ??? (DiagnosticSolution and others?)
 }}}
-solver{{{ -> or petsc?
+solver{{{
 petscoptions -> could become the class itself
 }}}
@@ -295,14 +303,5 @@
 	gprof
 	mem_debug -> rename valgrind
-	memoryleaks -> never used
-}}}
-private {{{
-	counter
-	runtimename
-	runmefile
-	inputfilename -> is it really needed? it is just runtimename.bon
-	outputfilename -> same
-	solution_type -> rename solution
-	bamg
+	memoryleaks -> delete
 }}}
 constants{{{
@@ -312,15 +311,13 @@
 referencetemperature
 }}}
-computation{{{
+settings{{{
 io_gather
-penalty_offset
 sparsity
 lowmem
 }}}
-
-radarimage{{{
-	sarpwr
-	  sarxm
-	  sarym
+radaroverlay{{{
+	sarpwr %error message if database does not exist
+	sarxm
+	sarym
 }}}
 miscelaneous {{{
@@ -328,4 +325,13 @@
 	name
 	dummy
+}}}
+private {{{
+	counter -> not needed
+	runtimename
+	runmefile -> erase
+	inputfilename -> is it really needed? it is just runtimename.bon
+	outputfilename -> same
+	solution_type -> erase and get this from the outbin
+	bamg
 }}}
 
@@ -348,5 +354,5 @@
 
 forcings -> delete
-minh -> remove or really use in the code!
+minh -> remove and put into prognostic 
 firn_layer -> remove (never used)
 deltaH -> remove (unused)
@@ -371,4 +377,4 @@
 strainrate-> remove (that's a model result)
 
-alloc_cleanup -> remove
+alloc_cleanup -> remove -> and put in cosmos cleanup
 mask -> delete?