mesh {{{

	projection
		lat
		long
		hemisphere

	  x
	  y
	  z
	  elements 
	  dim -> rename dimension
	  numlayers -> rename numberoflayers
	  numberofelements
	  numberofnodes -> rename numberofvertices as well as nodeon...
	  edges

	  uppernodes
	  upperelements
	  lowerelements
	  lowernodes

	  numberofelements2d
	  numberofnodes2d
	  elements2d
	  x2d
	  y2d
	  z2d -> remove

	  extrusionexponent -> remove
	  elementonbed
	  elementonsurface
	  nodeonbed
	  nodeonsurface

	  nodeconnectivity
	  elementconnectivity
	  connectivity ->investigate

	  segments
	  segmentmarkers
	  nodeonboundary

	  extractednodes
	  extractedelements
}}}
geometry {{{
	  surface
	  thickness
	  bed
	  bathymetry

	  bed_slopex ->remove
	  bed_slopey ->remove
	  surface_slopex->remove
	  surface_slopey->remove

	  thickness_coeff -> delete or rename (See with John)?
}}}
mask{{{
	elementoniceshelf -> rename elementonwater
	elementonicesheet -> rename elementonground
	elementonwater -> rename elementelementonground
	nodeoniceshelf
	nodeonicesheet
	nodeonwater

	elementongroundedice 
	elementonfloatingice
	elementonwater

}}}
rifts{{{
	rifts
	numrifts
	riftinfo -> should be removed (constructed by marshall)
	riftproperties
}}}
materials{{{
	rho_ice
	rho_water
	rho_firn -> remove
	heatcapacity
	latentheat
	thermalconductivity
	meltingpoint
	beta
	mixed_layer_capacity
	thermal_exchange_velocity
	rheology_B
	rheology_n
	rheology_law
}}}
friction{{{
	drag_type -> delete
	drag_coefficient
	drag_p
	drag_q
}}}
surfaceforcings{{{
	surface_accumulation_rate -> remove all surface_
	surface_ablation_rate
	surface_mass_balance
}}}
basalforcings{{{
	basal_melting_rate -> remove basal_*
	basal_melting_rate_correction
	basal_melting_rate_correction_apply -> remove (correction 0 has the same effect)
	geothermalflux
}}}
flowequation{{{
	private: 
		ishutter
		ismacayealpattyn
		isstokes

		elements_type -> change to element_equation
		vertices_type -> rename to vertex_equation
		borderstokes -> rename vertex_boundary_equation
		
		elementonhutter ->delete
		elementonmacayeal->delete
		elementonpattyn->delete
		elementonstokes->delete

		nodeonhutter ->delete
		nodeonmacayeal->delete
		nodeonpattyn->delete
		nodeonstokes->delete
		elements_type2d -> delete
		vertices_type2d -> delete
}}}
initialization{{{
	vx
	vy
	vz
	vel
	pressure
	temperature
	watercolumn
	waterfraction
}}}
diagnostic{{{
	spcvx
	spcvy
	spcvz
	stokesreconditioning
	shelf_dampening
	viscosity_overshoot
	pressureload -> rename icefront?
	diagnostic_ref -> rename referential?
	penalties -> rename vertex_pairing

	eps_res -> rename following PETSc: restol
	eps_rel -> rename following PETSc: reltol
	eps_abs-> rename following PETSc:  abstol
	max_nonlinear_iterations -> rename maxiter

	penalty_lock -> rename rift_penalty_lock 
	min_mechanical_constraints -> rename  rift_penalty_threshold
}}}
thermal{{{
	spctemperature
	penalty_melting -> delete
	min_thermal_constraints -> rename thermal_penalty_threshold
	artificial_diffusivity -> rename stabilization
	max_nonlinear_iterations -> rename maxiter
	stabilize_constraints -> rename thermal_penalty_lock
}}}
prognostic{{{
	spcthickness
	hydrostatic_adjustment
	artificial_diffusivity -> rename stabilization
	prognostic_DG -> should be merged with stabilization
	penalties -> rename vertex_pairing
}}}
balancethickness{{{
	spcthickness
	dhdt -> rename thickening_rate
	artificial_diffusivity -> rename stabilization
}}}
steadystate{{{
	eps_rel -> rename following PETSc: reltol
	max_steadystate_iterations -> rename maxiter
}}}
transient{{{
   isdiagnostic
   isprognostic
   isthermal
   isgroundingline -> add
}}}
goundingline {{{
	groundingline_migration -> rename migration_type
	groundingline_melting_rate -> rename melting_rate
}}}
hydrology{{{
	spwatercolumn
	hydro_n -> remove all hydro_
	hydro_CR
	hydro_p
	hydro_q
	hydro_kn
}}}
control{{{
	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 -> rename cost_functions_coefficients

	cm_min -> min_parameters
	cm_max -> max_parameters

	nsteps
	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
	vy_obs
	vel_obs
	thickness_obs
}}}
qmu{{{
	variables
	responses
	qmu_method -> remove all qmu_
	qmu_params
	dakotaresults
	dakotain
	dakotaout
	dakotadat
	qmu_analysis
	part
	npart
	numberofvariables
	numberofresponses
	variabledescriptors
	responsedescriptors
	qmu_mass_flux_profile_directory
	qmu_mass_flux_profiles
	qmu_mass_flux_segments
	qmu_relax
	qmu_save_femmodel

	adjacency
	vwgt
}}}
flaim{{{
	fm_tracks -> remove all fm_
	  fm_flightreqs
	  fm_criterion
	  fm_gridsatequator
	  fm_usevalueordering
	  fm_split_antimeridian
	  fm_solution
	  fm_quality
}}}

verbose {{{
	-> already exists
}}}
cluster{{{
	waitonlock -> cluster dependent
	-> already exists
}}}
timestepping{{{
	dt
	ndt
	time_adapt -> rename cfl_apply
	adaptative_cfl -> remove
	cfl_coefficient
}}}
results{{{
	requested_outputs
	results_on_vertices
	output_frequency
	outlog
	errlog
	  + all model results ??? (DiagnosticSolution and others?)
}}}
solver{{{ -> or petsc?
petscoptions -> could become the class itself
}}}
debug{{{
	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
}}}
constants{{{
	%not material dependent
g
yts
referencetemperature
}}}
computation{{{
io_gather
penalty_offset
sparsity
lowmem
}}}

radarimage{{{
	sarpwr
	  sarxm
	  sarym
}}}
miscelaneous {{{
	notes
	name
	dummy
}}}

mesh_domainoutline -> remove
mesh_riftoutline -> remove
mesh_resolution -> remove
domainoutline -> remove
riftoutline -> remove
iceshelfoutline ->remove
icesheetoutline -> remove
wateroutline -> remove
parameterfile -> remove

vx_obs_raw -> remove (should be in dummy)
vy_obs_raw -> remove (should be in dummy)
vel_obs_raw -> remove (should be in dummy)
vx_bal -> remove (should be in dummy)
vy_bal -> remove (should be in dummy)
vel_bal -> remove (should be in dummy)

forcings -> delete
minh -> remove or really use in the code!
firn_layer -> remove (never used)
deltaH -> remove (unused)
DeltaH -> remove (unused)
deltaT -> remove (unused)
DeltaT -> remove (unused)
timeacc -> remove (unused)
timedec -> remove (unused)
observed_temperature -> remove
repository -> remove (out of core never used)
loadresults -> remove (should be an option of solve: md=solve(md,DiagnosticSolutionEnum,'loadonly',1))

element_debug -> remove
element_debugid -> remove

viscousheating -> remove (that's a model result)
pressure_elem -> remove (that's a model result)
stress-> remove (that's a model result)
stress_surface-> remove (that's a model result)
stress_bed-> remove (that's a model result)
deviatoricstress-> remove (that's a model result)
strainrate-> remove (that's a model result)

alloc_cleanup -> remove
mask -> delete?
