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