= Matlab function changes =

 * setelementstype -> setflowequation
 * geography -> setmask
 * mesh -> setmesh

= Table of correspondence  old vs new model fields =

|| ''' Old field''' || '''New field''' || '''Remarks''' ||
|| adaptative_cfl || ||DELETED ||
|| adjacency || qmu.adjacency || ||
|| alloc_cleanup || || DELETED ||
|| artificial_diffusivity || prognostic.stabilization || One stabilization per type of solution ||
|| artificial_diffusivity || thermal.stabilization || One stabilization per type of solution ||
|| artificial_diffusivity || balancethickness.stabilization || One stabilization per type of solution ||
|| bamg || private.bamg || ||
|| basal_melting_rate || basalforcings.melting_rate || ||
|| basal_melting_rate_correction || basalforcings.melting_rate_correction || ||
|| basal_melting_rate_correction_apply || ||DELETED (set field as 0 instead) ||
|| bathymetry ||  geometry.bathymetry || ||
|| bed || geometry.bed || ||
|| bed_slopex || || DELETED (moved to results) ||
|| bed_slopey || ||  DELETED (moved to results) ||
|| beta || materials.beta || ||
|| borderstokes || || DELETED ||
|| cfl_coefficient || timestepping.cfl_coefficient || ||
|| cluster || cluster || ||
|| cm_gradient || inversion.gradient_only || ||
|| cm_jump || inversion.step_threshold || ||
|| cm_max || inversion.max_parameters || ||
|| cm_min || inversion.min_parameters || ||
|| cm_responses || inversion.cost_functions || ||
|| connectivity || mesh.average_vertex_connectivity || ||
|| control_analysis || inversion.iscontrol || ||
|| control_type || inversion.control_parameters ||cell of string: {'Dragcoefficient'} ||
|| counter ||  || DELETED ||
|| dakotadat || || DELETED||
|| dakotain || || DELETED||
|| dakotaout || ||DELETED ||
|| dakotaresults || qmu.results || ||
|| deltaH || ||DELETED ||
|| DeltaH || || DELETED||
|| DeltaT || || DELETED ||
|| deltaT || ||DELETED ||
|| deviatoricstress || || DELETED (moved to results) ||
|| dhdt || balancethickness.thickening_rate || ||
|| diagnostic_ref || diagnostic.referential || ||
|| dim || mesh.dimension || ||
|| domainoutline || || DELETED ||
|| drag_coefficient || friction.coefficient || ||
|| drag_p || friction.p || ||
|| drag_q || friction.q || ||
|| drag_type || ||DELETED ||
|| dt ||  timestepping.time_step || ||
|| dummy || miscellaneous.dummy || ||
|| edges || mesh.edges || ||
|| element_debug || || DELETED||
|| element_debugid || ||DELETED ||
|| elementconnectivity || mesh.elementconnectivity || ||
|| elementonbed || mesh.elementonbed || ||
|| elementonhutter ||  || DELETED ||
|| elementonicesheet || mask.elementongroundedice || ||
|| elementoniceshelf || mask.elementonfloatingice || ||
|| elementonmacayeal ||  || DELETED ||
|| elementonpattyn || || DELETED ||
|| elementonstokes || || DELETED ||
|| elementonsurface || mesh.elementonsurface || ||
|| elementonwater || mask.elementonwater || ||
|| elements || mesh.elements || ||
|| elements2d || mesh.elements2d || ||
|| elements_type || flowequation.element_equation || new numbering||
|| elements_type2d || || DELETED||
|| eps_abs || diagnostic.abstol || ||
|| eps_cm || inversion.cost_function_threshold || ||
|| eps_rel || diagnostic.reltol || ||
|| eps_rel || steadystate.reltol || One convergence criterion per type of solution ||
|| eps_res || diagnostic.restol || ||
|| epsvel || || DELETED ||
|| errlog || ||moved to results ||
|| extractedelements || mesh.extractedelements || ||
|| extractednodes || mesh.extractedvertices || ||
|| extrusionexponent || || DELETED||
|| firn_layer || || DELETED||
|| fm_criterion || flaim.criterion || ||
|| fm_flightreqs || flaim.flightreqs || ||
|| fm_gridsatequator || flaim.gridsatequator || ||
|| fm_quality || flaim.quality || ||
|| fm_solution || flaim.solution || ||
|| fm_split_antimeridian || flaim.split_antimeridian || ||
|| fm_tracks || flaim.tracks || ||
|| fm_usevalueordering || flaim.usevalueordering || ||
|| forcings || || DELETED||
|| g || constants.g || ||
|| geothermalflux || basalforcings.geothermalflux || ||
|| gprof || debug.gprof || ||
|| groundingline_melting_rate || groundingline.melting_rate || ||
|| groundingline_migration || groundingline.migration || no more enums, strings instead i.e. 'SoftMigration',... ||
|| heatcapacity || materials.heatcapacity || ||
|| hemisphere || mesh.hemisphere || ||
|| hydro_CR || hydrology.CR || ||
|| hydro_kn || hydrology.kn || ||
|| hydro_n || hydrology.n || ||
|| hydro_p || hydrology.p || ||
|| hydro_q || hydrology.q || ||
|| hydrostatic_adjustment || prognostic.hydrostatic_adjustment || ||
|| icesheetoutline || || DELETED||
|| iceshelfoutline || ||DELETED ||
|| inputfilename || || DELETED||
|| io_gather || settings.io_gather || ||
|| isdiagnostic || transient.isdiagnostic || ||
|| ishutter || flowequation.ishutter || ||
|| ismacayealpattyn || flowequation.ismacayealpattyn || ||
|| isprognostic || transient.isprognostic || ||
|| isstokes || flowequation.isstokes || ||
|| isthermal || transient.isthermal || ||
|| lat || mesh.lat || ||
|| latentheat || materials.latentheat || ||
|| loadresults || || DELETED (now an option of solve.m) ||
|| long || mesh.long || ||
|| lowerelements || mesh.lowerelements || ||
|| lowernodes || mesh.lowervertex || ||
|| lowmem || settings.lowmem || ||
|| mask || || DELETED||
|| max_nonlinear_iterations || diagnostic.maxiter || ||
|| max_nonlinear_iterations || thermal.maxiter || One maxiter per type of solution ||
|| max_steadystate_iterations || steadystate.maxiter || ||
|| maxiter || inversion.maxiter_per_step || ||
|| meanvel || || DELETED ||
|| meltingpoint || materials.meltingpoint || ||
|| mem_debug || debug.valgrind || ||
|| memoryleaks ||  || DELETED ||
|| mesh_domainoutline || ||DELETED ||
|| mesh_resolution || || DELETED||
|| mesh_riftoutline || || DELETED ||
|| min_mechanical_constraints || diagnostic.rift_penalty_threshold || ||
|| min_thermal_constraints || thermal.penalty_threshold || ||
|| minh ||  || DELETED ||
|| mixed_layer_capacity || materials.mixed_layer_capacity || ||
|| name || miscellaneous.name || ||
|| ndt ||  timestepping.final_time || ||
|| nodeconnectivity || mesh.vertexconnectivity || ||
|| nodeonbed || mesh.vertexonbed || ||
|| nodeonboundary || mesh.vertexonboundary || ||
|| nodeonhutter || || DELETED ||
|| nodeonicesheet || mask.vertexongroundedice || ||
|| nodeoniceshelf || mask.vertexonfloatingice || ||
|| nodeonmacayeal || flowequation.bordermacayeal || ||
|| nodeonpattyn || flowequation.borderpattyn || ||
|| nodeonstokes || flowequation.borderstokes || ||
|| nodeonsurface || mesh.vertexonsurface || ||
|| nodeonwater || mask.vertexonwater || ||
|| notes || miscellaneous.notes || ||
|| npart || qmu.numberofpartitions || ||
|| nsteps || inversion.nsteps || ||
|| num_cm_responses || inversion.num_cost_functions || ||
|| num_control_type || inversion.num_control_parameters || ||
|| numberofelements || mesh.numberofelements || ||
|| numberofelements2d || mesh.numberofelements2d || ||
|| numberofnodes || mesh.numberofvertices || ||
|| numberofnodes2d || mesh.numberofvertices2d || ||
|| numberofresponses || qmu.numberofresponses || ||
|| numberofvariables || ||DELETED ||
|| numlayers || mesh.numlayers || ||
|| numrifts || rifts.numrifts || ||
|| observed_temperature || || DELETED (use temperature field instead) ||
|| optscal || inversion.gradient_scaling || ||
|| outlog || || moved to results||
|| output_frequency || settings.output_frequency || ||
|| outputfilename || || DELETED||
|| parameterfile || ||DELETED ||
|| part || qmu.partition || ||
|| penalties || diagnostic.vertex_pairing || ||
|| penalties || prognostic.vertex_pairing || One pairing option per solution ||
|| penalty_lock || diagnostic.rift_penalty_lock || ||
|| penalty_melting || ||DELETED ||
|| penalty_offset || diagnostic.penalty_factor || ||
|| penalty_offset || thermal.penalty_factor || One factor per type of solution ||
|| penalty_offset || prognostic.penalty_factor || One factor per type of solution ||
|| petscoptions || solver || ||
|| pressure || initialization.pressure || ||
|| pressure_elem || ||DELETED ||
|| pressureload || diagnostic.icefront || no more Enums - 0:Air 1:Water 2:Ice ||
|| prognostic_DG ||  || DELETED (prognostic.stabilization=3 instead) ||
|| qmu_analysis || qmu.isqmu || ||
|| qmu_mass_flux_profile_directory || qmu.mass_flux_profile_directory || ||
|| qmu_mass_flux_profiles || qmu.mass_flux_profiles || ||
|| qmu_mass_flux_segments || qmu.mass_flux_segments || ||
|| qmu_method || qmu.method || ||
|| qmu_params || qmu.params || ||
|| qmu_relax || || DELETED ||
|| qmu_save_femmodel || ||DELETED (debugging feature) ||
|| repository || || DELETED (removed the out of core capability) ||
|| requested_outputs || diagnostic.requested_outputs || One type of outputs per solution ||
|| requested_outputs || prognostic.requested_outputs || One type of outputs per solution ||
|| requested_outputs || thermal.requested_outputs || One type of outputs per solution ||
|| requested_outputs || balancethickness.requested_outputs || One type of outputs per solution ||
|| requested_outputs || steadystate.requested_outputs || One type of outputs per solution ||
|| requested_outputs || transient.requested_outputs || One type of outputs per solution ||
|| responsedescriptors || qmu.responsedescriptors || ||
|| responses || qmu.responses || ||
|| results || results || ||
|| results_on_vertices || settings.results_on_vertices || ||
|| rheology_B || materials.rheology_B || ||
|| rheology_law || materials.rheology_law ||no more enum: 'None','Paterson','Arrhenius' ||
|| rheology_n || materials.rheology_n || ||
|| rho_firn || ||DELETED ||
|| rho_ice || materials.rho_ice || ||
|| rho_water || materials.rho_water || ||
|| riftinfo || ||DELETED ||
|| riftoutline || || DELETED||
|| riftproperties || rifts.riftproperties || ||
|| rifts || rifts.riftstruct || ||
|| runmefile || ||DELETED ||
|| sarpwr || radaroverlay.pwr || ||
|| sarxm || radaroverlay.x || ||
|| sarym || radaroverlay.y || ||
|| segmentmarkers || mesh.segmentmarkers || ||
|| segments || mesh.segments || ||
|| shelf_dampening || diagnostic.shelf_dampening || ||
|| solution_type || private.solution_type || ||
|| sparsity || ||DELETED ||
|| spctemperature || thermal.spctemperature || ||
|| spcthickness || prognostic.spcthickness || One field per type of solution ||
|| spcthickness || balancethickness.spcthickness || One field per type of solution ||
|| spcvx || diagnostic.spcvx || ||
|| spcvy || diagnostic.spcvy || ||
|| spcvz || diagnostic.spcvz || ||
|| spcwatercolumn || hydrology.spcwatercolumn || ||
|| stabilize_constraints || thermal.penalty_lock || ||
|| stokesreconditioning || diagnostic.stokesreconditioning || ||
|| strainrate || || DELETED (moved to results) ||
|| stress || || DELETED (moved to results)||
|| stress_bed || || DELETED (moved to results) ||
|| stress_surface || || DELETED (moved to results) ||
|| surface ||  geometry.surface || ||
|| surface_ablation_rate || surfaceforcings.ablation_rate || ||
|| surface_accumulation_rate || surfaceforcings.accumulation_rate || ||
|| surface_mass_balance || surfaceforcings.mass_balance || ||
|| surface_slopex || || DELETED (moved to results)  ||
|| surface_slopey || || DELETED (moved to results)  ||
|| temperature || initialization.temperature || ||
|| thermal_exchange_velocity || materials.thermal_exchange_velocity || ||
|| thermalconductivity || materials.thermalconductivity || ||
|| thickness ||  geometry.thickness || ||
|| thickness_coeff ||  geometry.hydrostatic_ratio || ||
|| thickness_obs ||  inversion.thickness_obs || ||
|| time_adapt ||  timestepping.time_adapt || ||
|| timeacc || ||DELETED ||
|| timedec || || DELETED||
|| tolx || || DELETED ||
|| upperelements || mesh.upperelements || ||
|| uppernodes || mesh.uppervertex || ||
|| variabledescriptors || qmu.variabledescriptors || ||
|| variables || qmu.variables || ||
|| vel || initialization.vel || ||
|| vel_bal || || DELETED||
|| vel_obs ||  inversion.vel_obs || ||
|| vel_obs_raw || ||DELETED ||
|| verbose || verbose || ||
|| vertices_type || flowequation.vertex_equation || new numbering ||
|| vertices_type2d || || DELETED||
|| viscosity_overshoot || diagnostic.viscosity_overshoot || ||
|| viscousheating || ||DELETED ||
|| vwgt || qmu.vertex_weight || ||
|| vx || initialization.vx || ||
|| vx_bal || || DELETED||
|| vx_obs || inversion.vx_obs || ||
|| vx_obs_raw || || DELETED||
|| vy || initialization.vy || ||
|| vy_bal || ||DELETED ||
|| vy_obs ||  inversion.vy_obs || ||
|| vy_obs_raw || ||DELETED ||
|| vz || initialization.vz || ||
|| waitonlock || settings.waitonlock || ||
|| watercolumn || initialization.watercolumn || ||
|| waterfraction || initialization.waterfraction || ||
|| wateroutline || ||DELETED ||
|| weights || inversion.cost_functions_coefficients || ||
|| x || mesh.x || ||
|| x2d || mesh.x2d || ||
|| y || mesh.y || ||
|| y2d || mesh.y2d || ||
|| yts || constants.yts || ||
|| z || mesh.z || ||
|| z2d || ||DELETED ||