== 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 penalty_offset -> rename penalty_factor and change to absolute value 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 requested_outputs == 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 penalty_offset -> rename penalty_factor and change to absolute value requested_outputs == prognostic == spcthickness hydrostatic_adjustment artificial_diffusivity -> rename stabilization prognostic_DG -> should be merged with stabilization penalties -> rename vertex_pairing penalty_offset -> rename penalty_factor and change to absolute value requested_outputs == balancethickness == spcthickness 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 == isdiagnostic isprognostic isthermal idsgroundingline -> add requested_outputs == 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 == inversion == 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 ->results dakotain ->check dakotaout ->check dakotadat ->check qmu_analysis -> isqmu part ->partition npart -> numberofpartitions numberofvariables numberofresponses variabledescriptors responsedescriptors qmu_mass_flux_profile_directory qmu_mass_flux_profiles qmu_mass_flux_segments qmu_relax -> investigate qmu_save_femmodel -> trash adjacency vwgt -> vertex_weight == 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 to be added to all cluster classes -> already exists == timestepping == dt ->time_step ndt-> rename final_time time_adapt -> "cfl" "none" adaptative_cfl -> remove cfl_coefficient == results == results_on_vertices output_frequency outlog errlog + all model results ??? (DiagnosticSolution and others?) == solver == petscoptions -> could become the class itself == debug == gprof mem_debug -> rename valgrind memoryleaks -> delete == constants == %not material dependent g yts referencetemperature == settings == io_gather sparsity lowmem == radaroverlay == sarpwr %error message if database does not exist sarxm sarym == miscelaneous == notes 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 == DELETED FIELDS == 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 and put into prognostic 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 -> and put in cosmos cleanup mask -> delete?