Index: /issm/trunk/template =================================================================== --- /issm/trunk/template (revision 9413) +++ /issm/trunk/template (revision 9414) @@ -1,152 +1,307 @@ 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 + 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 + segments + segmentmarkers + connectivity }}} Projection{{{ -lat -long -hemisphere + lat + long + hemisphere }}} Geometry {{{ -bed_slopex -bed_slopey -surface_slopex -surface_slopey -surface -thickness -thickness_coeff -> delete or rename ? -bed -bathymetry + bed_slopex + bed_slopey + surface_slopex + surface_slopey + surface + thickness + thickness_coeff -> delete or rename ? + bed + bathymetry +}}} +geography{{{ -> rename mask? + elementoniceshelf + elementonicesheet + elementonwater + nodeoniceshelf + nodeonicesheet + nodeonwater + mask -> delete? }}} Miscelaneous {{{ -notes -name + notes + name + dummy }}} Private {{{ -runtimename -counter -runmefile + counter + runtimename + runmefile + inputfilename + outputfilename + solution_type -> rename solution }}} flowapproximation{{{ -elements_type -vertices_type -ishutter -ismacayealpattyn -isstokes -elementonhutter -elementonmacayeal -elementonpattyn -elementonstokes -nodeonhutter -nodeonmacayeal -nodeonpattyn -nodeonstokes -borderstokes -elements_type2d -> remove -vertices_type2d -> remove + 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 + 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 + isdiagnostic + vx + vy + vz + vel + spcvx + spcvy + spcvz + stokesreconditioning + shelf_dampening + viscosity_overshoot + min_mechanical_constraints + pressureload -> rename icefront? + diagnostic_ref -> rename referential? + penalties + pressure + eps_res -> rename following PETSc: restol + eps_rel -> rename following PETSc: rtol + eps_abs-> rename following PETSc: atol + max_nonlinear_iterations -> rename maxiter +}}} +thermal{{{ + isthermal + temperature + spctemperature + penalty_melting + min_thermal_constraints + geothermalflux + waterfraction + artificial_diffusivity -> rename stabilization + max_nonlinear_iterations -> rename maxiter + stabilize_constraints -> rename (not clear) +}}} +prognostic{{{ + isprognostic + hydrostatic_adjustment + artificial_diffusivity -> rename stabilization + prognostic_DG -> should be merged with stabilization + penalties +}}} +balancethickness{{{ + spcthickness -> duplicate from prognostic? + thickness_obs + dhdt + artificial_diffusivity -> rename stabilization +}}} +steadystate{{{ + eps_rel -> rename following PETSc: rtol + max_steadystate_iterations -> rename maxiter +}}} +hydrology{{{ + hydro_n + hydro_CR + hydro_p + hydro_q + hydro_kn + spwatercolumn + watercolumn }}} friction{{{ -drag_type -drag_coefficient -drag_p -drag_q + drag_type + drag_coefficient + drag_p + drag_q + spcthickness }}} control{{{ -cm_responses -tolx -optscal -eps_cm -cm_min -cm_max -cm_jump -cm_gradient -epsvel -meanvel -num_control_type -num_cm_responses + control_analysis + control_type + weights + nsteps + maxiter + cm_responses + tolx + optscal + eps_cm + cm_min + cm_max + cm_jump + cm_gradient + epsvel + meanvel + num_control_type + num_cm_responses + vx_obs + vy_obs + vel_obs }}} 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 + 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 + fm_tracks + fm_flightreqs + fm_criterion + fm_gridsatequator + fm_usevalueordering + fm_split_antimeridian + fm_solution + fm_quality +}}} +verbose {{{ + -> already exists +}}} +cluster{{{ + waitonlock -> cluster dependent + -> already exists +}}} +rifts{{{ + rifts + numrifts + riftinfo -> should be removed (constructed by marshall) + riftproperties +}}} +smb{{{ + surface_accumulation_rate + surface_ablation_rate + surface_mass_balance +}}} +basalmelting{{{ + basal_melting_rate + basal_melting_rate_correction + basal_melting_rate_correction_apply -> remove (correction 0 has the same effect) +}}} +timestepping{{{ + dt + ndt + time_adapt + cfl_coefficient + adaptative_cfl +}}} +radar{{{ +sarpwr +sarxm +sarym +}}} +partitioning{{{ +adjacency +vwgt +}}} +goundingline {{{ + groundingline_migration + groundingline_melting_rate +}}} +results{{{ + requested_outputs + results_on_vertices + output_frequency + outlog + errlog + + all model results ??? +}}} +solver{{{ +petscoptions +}}} +debug{{{ + gprof + mem_debug -> rename valgrind + memoryleaks -> never used }}} +io_gather +penalty_offset +penalty_lock +g +yts +sparsity +lowmem +mesh_domainoutline -> remove +mesh_riftoutline -> remove +mesh_resolution -> remove +vx_obs_raw -> remove (should be in dummy) +vy_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) +vel_obs_raw -> remove (should be in dummy) domainoutline -> remove riftoutline -> remove @@ -155,169 +310,24 @@ wateroutline -> remove parameterfile -> remove - -io_gather - -stokesreconditioning -shelf_dampening -penalties -penalty_offset -penalty_melting -penalty_lock -segments -segmentmarkers -rifts -riftinfo -riftproperties -numrifts +forcings -> delete 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 +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