Index: /issm/trunk/template
===================================================================
--- /issm/trunk/template	(revision 9413)
+++ /issm/trunk/template	(revision 9413)
@@ -0,0 +1,323 @@
+Mesh {{{
+bamg
+dim
+numberofelements
+numberofnodes
+elements -> rename ?
+x
+y
+z
+edges
+numberofelements2d
+numberofnodes2d
+elements2d
+x2d
+y2d
+z2d
+uppernodes
+upperelements
+lowerelements
+lowernodes
+numlayers
+extrusionexponent
+elementonbed
+elementonsurface
+nodeonbed
+nodeonsurface
+nodeconnectivity
+elementconnectivity
+nodeonboundary
+extractednodes
+extractedelements
+}}}
+Projection{{{
+lat
+long
+hemisphere
+}}}
+Geometry {{{
+bed_slopex
+bed_slopey
+surface_slopex
+surface_slopey
+surface
+thickness
+thickness_coeff -> delete or rename ?
+bed
+bathymetry
+}}}
+Miscelaneous {{{
+notes
+name
+}}}
+Private {{{
+runtimename
+counter
+runmefile
+}}}
+flowapproximation{{{
+elements_type
+vertices_type
+ishutter
+ismacayealpattyn
+isstokes
+elementonhutter
+elementonmacayeal
+elementonpattyn
+elementonstokes
+nodeonhutter
+nodeonmacayeal
+nodeonpattyn
+nodeonstokes
+borderstokes
+elements_type2d -> remove
+vertices_type2d -> remove
+}}}
+Materials{{{
+rho_ice
+rho_water
+rho_firn -> remove
+heatcapacity
+latentheat
+thermalconductivity
+meltingpoint
+referencetemperature
+beta
+mixed_layer_capacity
+thermal_exchange_velocity
+rheology_B
+rheology_n
+rheology_law
+}}}
+diagnostic{{{
+spcvx
+spcvy
+spcvz
+}}}
+friction{{{
+drag_type
+drag_coefficient
+drag_p
+drag_q
+}}}
+control{{{
+cm_responses
+tolx
+optscal
+eps_cm
+cm_min
+cm_max
+cm_jump
+cm_gradient
+epsvel
+meanvel
+num_control_type
+num_cm_responses
+}}}
+qmu{{{
+variables
+responses
+qmu_method
+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
+}}}
+flaim{{{
+fm_tracks
+fm_flightreqs
+fm_criterion
+fm_gridsatequator
+fm_usevalueordering
+fm_split_antimeridian
+fm_solution
+fm_quality
+}}}
+
+
+domainoutline -> remove
+riftoutline -> remove
+iceshelfoutline ->remove
+icesheetoutline -> remove
+wateroutline -> remove
+parameterfile -> remove
+
+io_gather
+
+stokesreconditioning
+shelf_dampening
+penalties
+penalty_offset
+penalty_melting
+penalty_lock
+segments
+segmentmarkers
+rifts
+riftinfo
+riftproperties
+numrifts
+minh -> remove
+firn_layer -> remove
+
+min_thermal_constraints
+min_mechanical_constraints
+stabilize_constraints
+
+g
+yts
+
+elementoniceshelf
+elementonicesheet
+elementonwater
+nodeoniceshelf
+nodeonicesheet
+nodeonwater
+
+mask -> delete?
+
+pressureload
+
+spctemperature
+spcthickness
+spcwatercolumn
+diagnostic_ref
+
+%Observations
+vx_obs
+vy_obs
+vel_obs
+vx_obs_raw
+vy_obs_raw
+vx_bal
+vy_bal
+vel_bal
+vel_obs_raw
+surface_accumulation_rate
+surface_ablation_rate
+surface_mass_balance
+dhdt
+geothermalflux
+observed_temperature
+thickness_obs
+
+forcings -> delete?
+
+eps_res
+eps_rel
+eps_abs
+max_nonlinear_iterations
+max_steadystate_iterations
+sparsity
+connectivity
+lowmem
+viscosity_overshoot
+
+dt
+ndt
+time_adapt
+cfl_coefficient
+adaptative_cfl
+artificial_diffusivity
+prognostic_DG
+deltaH
+DeltaH
+deltaT
+DeltaT
+timeacc
+timedec
+hydrostatic_adjustment
+isprognostic
+isdiagnostic
+isthermal
+%Control
+control_analysis
+control_type
+weights
+nsteps
+maxiter
+
+requested_outputs
+viscousheating
+pressure_elem
+stress
+stress_surface
+stress_bed
+deviatoricstress
+strainrate
+
+verbose
+element_debug
+element_debugid
+mem_debug
+gprof
+memoryleaks
+
+output_frequency
+results_on_vertices
+inputfilename
+outputfilename
+results
+vx
+vy
+vz
+vel
+temperature
+waterfraction
+groundingline_melting_rate
+basal_melting_rate
+basal_melting_rate_correction
+basal_melting_rate_correction_apply
+pressure
+
+watercolumn
+
+
+hydro_n
+hydro_CR
+hydro_p
+hydro_q
+hydro_kn
+
+
+cluster
+outlog
+errlog
+alloc_cleanup
+waitonlock
+
+
+dummy
+
+mesh_domainoutline
+mesh_riftoutline
+mesh_resolution
+
+petscoptions
+
+solution_type
+
+repository
+
+sarpwr
+sarxm
+sarym
+
+groundingline_migration
+
+loadresults
+
+adjacency
+vwgt