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fluidity_options.rnc
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include "spud_base.rnc"
include "adaptivity_options.rnc"
include "diagnostic_algorithms.rnc"
include "input_output.rnc"
include "solvers.rnc"
include "stabilisation.rnc"
include "mesh_options.rnc"
include "physical_parameters.rnc"
include "prognostic_field_options.rnc"
include "prescribed_field_options.rnc"
include "spatial_discretisation.rnc"
include "temporal_discretisation.rnc"
include "flredecomp.rnc"
include "multiphase_interaction.rnc"
include "equation_of_state.rnc"
start =
(
## The root node of the options dictionary.
element fluidity_options {
comment,
## Model output files are named according to the simulation
## name, e.g. [simulation_name]_0.vtu. Non-standard
## characters in the simulation name should be avoided.
element simulation_name {
anystring
},
## Option problem_type does not change the tree. It is just used for options checking.
element problem_type {
element string_value {
# Lines is a hint to the gui about the size of the text box.
# It is not an enforced limit on string length.
attribute lines { "1" },
( "fluids" | "oceans" | "multimaterial" | "stokes" | "large_scale_ocean_options" | "foams" | "multiphase" )
},
comment
},
geometry,
## Input/output options
element io {
## Format for dump files. Only vtk for now.
element dump_format {
element string_value{
"vtk"
}
},
(
## Period between dumps in time units.
##
## Specifies the period between each dump of the solution to disk.
## A value of 0.0 indicates that there would be a dump at every timestep.
element dump_period {
(
element constant {
real
}|
## Python function prescribing real input. Functions should be of the form:
##
## def val(t):
## # Function code
## return # Return value
##
##
element python {
python_code
}
)
}|
## Dump period, in timesteps.
##
## Specifies the number of timesteps between each dump of the solution to disk.
## A value of 0 indicates a dump at every timestep.
element dump_period_in_timesteps {
(
element constant {
integer
}|
## Python function prescribing integer input. Functions should be of the form:
##
## def val(t):
## # Function code
## return # Return value
##
##
element python {
python_code
}
)
}
),
## Disable dump at simulation start
element disable_dump_at_start {
comment
}?,
## Disable dump at simulation end
element disable_dump_at_end {
comment
}?,
# every CPUDUM seconds write results to disc.
## This is usually disabled.
element cpu_dump_period {
real
}?,
## The period between dumps in walltime seconds. This is usually disabled.
element wall_time_dump_period {
real
}?,
## Number of dumps before we overwrite previous dumps.
element max_dump_file_count {
integer
}?,
(
## The mesh on to which all the fields will be
## interpolated for VTK output.
element output_mesh {
attribute name { "VelocityMesh" }
}|
## The mesh on to which all the fields will be
## interpolated for VTK output.
element output_mesh {
attribute name { "PressureMesh" }
}|
## The mesh on to which all the fields will be
## interpolated for VTK output.
element output_mesh {
attribute name { "CoordinateMesh" }
}|
## The mesh on to which all the fields will be
## interpolated for VTK output.
element output_mesh {
attribute name { xsd:string }
}
),
## Options for convergence analysis.
element convergence {
## Whether to enable the creation of a convergence
## file, giving details of the convergence of each
## field over the global nonlinear iteration loop.
## The .convergence file is in the same format as the .stat file.
element convergence_file {
comment
}?,
## Write state to a vtu on every iteration.
##
## This is a useful debugging tool if things are not converging.
## To prevent an excessive number of files being accumulated previous
## timestep files will be overwritten hence it is best to use
## in conjunction with /timestepping/nonlinear_iterations/terminate_if_not_converged
element convergence_vtus {
comment
}?
}?,
## Whether to enable dumping of checkpointing output.
##
## See http://amcg.ese.ic.ac.uk/index.php?title=Local:Checkpointing_from_new_options
element checkpointing {
## Checkpointing period, in dumps. Non-negative value
## required. A value of zero indicates that checkpoints
## should be created at every dump. If
## /io/max_dumpfile_count is exceeded then earlier
## checkpoints may be overwritten.
element checkpoint_period_in_dumps {
integer
},
## Enable to checkpoint at simulation start.
element checkpoint_at_start {
comment
}?,
## Enable to force a checkpoint at simulation end.
element checkpoint_at_end {
comment
}?,
comment
}?,
## Diagnostic output (.stat file) options
element stat {
## Enable to write diagnostic output at simulation start
element output_at_start {
comment
}?,
## Enable to write diagnostic output immediately before mesh adapts
element output_before_adapts {
comment
}?,
## Enable to write diagnostic output immediately after mesh adapts
element output_after_adapts {
comment
}?,
comment
},
## Specification of detectors. Note that when running in parallel the detector output is in binary format even if binary_output is not enabled. When running in serial, although the output is in principle still generated in ascii format if binary_output is not enabled, it is not certain that it is working well. Hence, it is recommended to enable binary_output and work with binary files.
element detectors {
(
## A single static detector
element static_detector {
attribute name { xsd:string },
(
element location {
real_dim_vector
}|
## File containing the detectors positions in binary form
element from_checkpoint_file {
attribute file_name { xsd:string },
## The format of the input file containing field data.
element format {
element string_value {
"binary"
}
}
}
)
}|
## A single lagrangian detector
element lagrangian_detector {
attribute name { xsd:string },
(
## This is the initial location of a detector that moves with the fluid velocity.
element location {
real_dim_vector
}|
## File containing the detectors positions in binary form
element from_checkpoint_file {
attribute file_name { xsd:string },
## The format of the input file containing field data.
element format {
element string_value {
"binary"
}
}
}
)
}|
## Detectors with their locations specified via a python function or from a file. Allows detector arrays to be added.
element detector_array {
attribute name { xsd:string },
## The number of detectors prescribed by the python function.
element number_of_detectors {
integer
},
(
## Create fixed detectors.
element static {
empty
}|
## Create detectors which move with the fluid velocity.
element lagrangian {
empty
}
),
(
## Python function prescribing dimensional vector input. Functions should be of the form:
##
## def val(t):
## # Function code
## return # Return value
##
## The return value must have length number_of_detectors.
##
## *** IMPORTANT NOTE ***
##
## The t argument is for future use only - currently detector locations are only set at simulation start.
element python {
python_code
}|
## File containing the detectors positions in binary form
element from_file {
attribute file_name { xsd:string },
## The format of the input file containing field data.
element format {
element string_value {
"binary"
}
}
}|
## File containing the detectors positions in binary form
element from_checkpoint_file {
attribute file_name { xsd:string },
## The format of the input file containing field data.
element format {
element string_value {
"binary"
}
}
}
)
}
)*,
(
## By default Fluidity will fail if a detector has left the domain.
element fail_outside_domain {
empty
}|
## Enable to write NaN values to detector output if a detector has left the domain.
element write_nan_outside_domain {
empty
}
),
## Enable to write detector output in ascii format. This output format will not work in parallel, if not enabled format defaults to binary.
element ascii_output {
comment
}?,
## Enable to let detectors move with the domain if mesh_movement is enabled.
element move_with_mesh {
empty
}?,
lagrangian_timestepping?
}?,
## Options to create even more output in the logs:
##
## Note that the main option to control the log output is given on the command line:
##
## -v0 only output error and warnings
##
## -v1 also give "navigational information", to indicate where in the code we currently are
##
## -v2 also give any additional information (mins and maxes of fields, etc.)
##
element log_output {
## Log all allocates and deallocates done for meshes, fields, sparsities and matrices.
##
## NOTE: Requires -v2
element memory_diagnostics {
empty
}?
}?,
## include time as VTK FieldData with the name "TimeValue".
## Paraview versions >= 5.5 will automatically use this to
## set the time level.
element time_as_metadata {
empty
}?
},
## Particle options. Particles, like Lagrangian detectors, move with a specified velocity field.
## In addition, particles can carry attributes, being properties of the particles. These attributes
## can be constant, or based on a python expression that depends on other attribute values, at the end
## of the previous timestep, or field values interpolated at the particle location. Planned future
## functionality includes the ability to spawn and delete particles to ensure sufficient particles are
## present in every region, and the ability to interpolate from particles back to the (Eulerian) mesh.
element particles {
(
## Particles groups containing multiple particle arrays or subgroups. The particle group specifies
## which velocity field is used, as well as attributes carried and (eventually) spawning
## and deleting options.
element particle_group {
attribute name { xsd:string },
element velocity_field {
attribute name { xsd:string }
},
## Particle subgroups arrays specified within a particle group. All subgroups utilize the same velocity field
## and carry the same attributes. Subgroups can have different initial positions specified via a python
## function of from a file.
element particle_subgroup {
attribute name { xsd:string },
## The number of particles prescribed by the python function.
element number_of_particles {
integer
},
(
##Initial position of particles
element initial_position {
## Python function prescribing dimensional vector input. Functions should be of the form:
##
## def val(t):
## # Function code
## return # Return value
##
## The return value must have length number_of_particles.
##
## *** IMPORTANT NOTE ***
##
## The t argument is for future use only - currently particle locations are only set at simulation start.
element python {
python_code
}|
## File containing the particle positions in binary form
element from_file {
attribute file_name { xsd:string },
## The format of the input file containing field data.
element format {
element string_value {
"binary"
}
}
}
}
),
(
##Define particle attributes
element attributes {
element attribute {
attribute name { xsd:string },
generic_particle_attribute_choice
}+
}?
)
}+
}+
)*,
(
## By default Fluidity will fail if a particle has left the domain.
element fail_outside_domain {
empty
}|
## Enable to write NaN values to particle output if a particle has left the domain.
element write_nan_outside_domain {
empty
}
),
## Enable to write particle output in ascii format
element ascii_output {
comment
}?,
## Enable to let particles move with the domain if mesh_movement is enabled.
element move_with_mesh {
empty
}?,
lagrangian_timestepping
}?,
## Options dealing with time discretisation
element timestepping {
## Current simulation time. At the start of the simulation this
## is the start time.
element current_time {
real,
## The following excerpt from the Udunits
## documentation explains the time unit encoding by
## example:
##
## The specification:
##
## seconds since 1992-10-8 15:15:42.5 -6:00
##
## indicates seconds since October 8th, 1992 at 3
## hours, 15 minutes and 42.5 seconds in the afternoon
## in the time zone which is six hours to the west of
## Coordinated Universal Time (i.e. Mountain Daylight
## Time). The time zone specification can also be
## written without a colon using one or two-digits
## (indicating hours) or three or four digits
## (indicating hours and minutes).
##
## Time units are particularly required in situations
## where the problem (time-varying) boundary conditions
## and/ initial conditions are a function of time as
## defined by a calendar. Examples include atmospheric
## forcing and climatology. The current time, specified
## above, is zero at the reference data/time.
element time_units{attribute date { xsd:string }}?
},
## The time step size. If adaptive time stepping is used
## then this is the initial time step size.
element timestep {
real
},
## Simulation time at which the simulation should end.
element finish_time {
real
},
## Timestep after which the simulation should end.
element final_timestep {
integer
}?,
## Maximum CPU time (in seconds) before the simulation terminates
element cpu_time_limit {
real
}?,
## Maximum wall time (secs) taken up before
## simulation terminates writing results to disc.
##
## This is usually disabled.
element wall_time_limit {
real
}?,
## maximum number of non-linear iterations.
##
## Manual suggests 2
element nonlinear_iterations {
integer,
## tolerance for non-linear iteration.
## Manual suggests 1.0E-12
element tolerance {
real,
(
## Select the norm with which you want the tolerance to be tested.
##
## The infinity norm.
element infinity_norm {
empty
}|
## Select the norm with which you want the tolerance to be tested.
##
## The l2 norm.
element l2_norm {
empty
}|
## Select the norm with which you want the tolerance to be tested.
##
## The l2 norm evaluated on a control volume mesh.
element cv_l2_norm {
empty
}
)
}?,
## Terminate the simulation if the number of
## nonlinear_iterations is reached
## and the tolerance criterion is not met.
## This is mostly useful as a debugging option if you
## suspect the solution is not converging.
element terminate_if_not_converged {
empty
}?,
## Number of non-linear iterations for the first time step after adapting the mesh.
## This option will work only if the mesh_adaptivity is switched on.
element nonlinear_iterations_at_adapt {
integer
}?
}?,
## Vary the timestep according to the courant number.
element adaptive_timestep {
## The timestep will be adjusted (within the tolerance
## and bounds specified) to target this courant
## number. Timestep adapts occur at the end of each
## timestep and after a mesh adapt.
element requested_cfl {
real
},
timestep_cfl_number_options,
## Minimum time step size.
## Manual suggests 0.0
element minimum_timestep {
## If enabled, signals model termination if a timestep less
## than or equal to the minimum_timestep is requested. The
## model will stop at the end of the timestep in order to
## allow for the latest output to be written.
element terminate_if_reached {
comment
}?,
real
}?,
## Maximum time step size.
## Manual suggests 1.E+10
element maximum_timestep {
real
}?,
## The maximum ratio by which the timestep is allowed
## to increase in a timestep adapt. e.g., a value of
## 1.1 indicates that the timestep may be increased by
## at most 10%.
element increase_tolerance {
real
}?,
## Specify whether you want to calculate a new timestep
## at the first timestep or not.
element at_first_timestep {
empty
}?
}?,
## Activate if you want to terminate the simulation once a
## steady state is reached.
##
## Enable/disable fields in this check under each field in
## steady_state options.
# Preprocessor legacy: STEDER = 0. is equivalent to inactive.
element steady_state {
## Enter the tolerance to which you want a steady state to be judged.
element tolerance {
real,
(
## Select the norm with which you want the tolerance to be tested.
##
## The infinity norm.
element infinity_norm {
empty
}|
## Select the norm with which you want the tolerance to be tested.
##
## The l2 norm.
element l2_norm {
empty
}|
## Select the norm with which you want the tolerance to be tested.
##
## The l2 norm evaluated on a control volume mesh.
element cv_l2_norm {
empty
}
)
},
## If activated compare the above tolerance to the rate
## of change of the fields. Otherwise compare it
## directly to the change in the field.
element acceleration_form {
empty
}?,
## Write out the changes in the tested fields to a .steady_state
## file.
element steady_state_file {
(
## Write steady state output in binary format
element binary_output {
comment
}|
## Write steady state output in plain text format
element plain_text_output {
comment
}
),
comment
}?
}?
},
physical_parameter_options?,
## The material or phase options
element material_phase {
attribute name { xsd:string },
equation_of_state_options?,
## Subgridscale parameterisations
element subgridscale_parameterisations {
## Lagrangian-averaged Navier-Stokes equations
element LANS {
(
## smoothing length specified as isotropic homogeneous
element alpha_isotropic_homogeneous {
real
}|
element alpha_anisotropic_homogeneous_cartesian {
real_dim_symmetric_tensor
}
)
# (
# element leray {
# empty
# }|
# element LANS_momentum_form {
# empty
# }|
# element LANS_stress_form {
# empty
# }
# )
}?,
## This is the generic length scale (vertical turbulence mixed layer) model,
## based here on Warner et al 2005, Ocean Modelling 8:81-113,
## which is itself based on the works of Umlauf and Burchard 2003.
##
## The GLS model encodes four individual turbulence closure models which can be chosen via 'option' below.
##
## You will need to make sure that DistanceToTop and DistanceToBottom fields (under geometry/ocean_boundaries)
## are switched on, as well as PerturbationDensity.
element GLS {
## The base GLS option:
## 1. k-kl which is a variant of Mellor-Yamada 2.5
## 2. k-epsilon
## 3. k-omega
## 4. 'gen' from Warner et al 2005
##
## k-epsilon is recommended.
element option {
element string_value {
"k-kl"|"k-epsilon"|"k-omega"|"gen"
}
},
## The stability function choice:
## 1. KanthaClayson-94 which corresponds to Kantha and Clayson 1994
## 2. Galperin-88 which corresponds to Galperin et al 1988
## 3. Canuto-01-A which corresponds to choice A from Canuto et al 2001
## 4. Canuto-01-B which corresponds to choice B from Canuto et al 2001
##
## Canuto A or B are recommended.
element stability_function {
element string_value {
"KanthaClayson-94"|"GibsonLaunder-78"|"Canuto-01-A"|"Canuto-01-B"
}
},
## The wall function choice:
## 1. None - pick this unless you're using k-kl
## 2. Mellor and Yamada (1980) - parabolic shape
## 3. Burchard (1998) - symmetric linear shape
## 4. Burchard (2001) - Used for infinitely deep basins
## 5. Blumberg et al (1992) - open channel flow
##
## See manual for equations.
element wall_function {
element string_value {
"none"|"MellorYamda"|"Burchard98"|"Burchard01"|"Blumberg"
}
}?,
## Smooth buoyancy frequency before using it?
element smooth_buoyancy{
empty
}?,
## Smooth velocity shear before using it?
element smooth_shear{
empty
}?,
## Do you want the boundary conditions to be set automatically?
## Make sure the ocean geometry settings are enabled for this option
element calculate_boundaries {
element string_value {
"neumann"|"dirichlet"
},
element top_surface_ids {
integer_vector
},
element bottom_surface_ids {
integer_vector
}
}?,
## Perform relaxation of the diffusivity and viscosity in the GLS model.
## Value should be >=0 and < 1. 0 is no relaxation (i.e. always use the
## most up-to-date value) and 0.9 would represent making the current value
## be 0.9*old_value + 0.1*new_value. Default is 0.0
## If being used with adaptivity, ensure you switch on interpolation of the
## GLSVerticalDiffusivity and GLSVerticalViscosity fields. You will seg fault
## otherwise.
element relax_diffusivity {
real
}?,
## Add extra parameterisation for internal wave breaking at base of MLD. This
## is based on the same parameterisation in NEMO and smooths the TKE down
## the water column based on an exponential function
## Set the two parameters: % of TKE to smooth down and length scale to do this over
element ocean_parameterisation {
element lengthscale {
real
},
element percentage {
real
}
}?,
## Turbulent kinetic energy. Make sure that the Diffusivity tensor field in here is set to diagnostic/internal.
element scalar_field {
attribute rank { "0" },
attribute name { "GLSTurbulentKineticEnergy" },
(
element prognostic {
velocity_mesh_choice,
prognostic_scalar_field,
## Minimum value of TKE in m2s2. A typical value will be around 1e-6
element minimum_value {
real
}
}|
element aliased {
generic_aliased_field
}
)
},
## Generic second equation used in GLS.
## Make sure that the Diffusivity tensor field in here is set to diagnostic/internal.
element scalar_field {
attribute rank { "0" },
attribute name { "GLSGenericSecondQuantity" },
(
element prognostic {
velocity_mesh_choice,
prognostic_scalar_field
}|
element aliased {
generic_aliased_field
}
)
},
## Background viscosity
element tensor_field {
attribute rank { "2" },
attribute name { "GLSBackgroundViscosity" },
(
element prescribed {
mesh_choice,
prescribed_tensor_field
}|
element diagnostic {
mesh_choice,
(
sediment_concentration_dependent_viscosity_algorithm
),
diagnostic_tensor_field
}
)
},
## Background diffusivity
element tensor_field {
attribute rank { "2" },
attribute name { "GLSBackgroundDiffusivity" },
(
element prescribed {
mesh_choice,
prescribed_tensor_field
}
)
},
## Eddy viscosity K_M
element tensor_field {
attribute rank { "2" },
attribute name { "GLSEddyViscosityKM" },
(
element diagnostic {
internal_algorithm,
velocity_mesh_choice,
diagnostic_scalar_field
}|
element aliased {
generic_aliased_field
}
)
},
## Eddy diffusivity K_H
element tensor_field {
attribute rank { "2" },
attribute name { "GLSEddyDiffusivityKH" },
(
element diagnostic {
internal_algorithm,
velocity_mesh_choice,
diagnostic_scalar_field
}|
element aliased {
generic_aliased_field
}
)
},
## Length scale (a diagnostic with GLS)
element scalar_field {
attribute rank { "0" },
attribute name { "GLSLengthScale" },
(
element diagnostic {
internal_algorithm,
velocity_mesh_choice,
diagnostic_scalar_field
}|
element aliased {
generic_aliased_field
}
)
}?,
## Unedited TKE. The TKE filed has the upper and lower surfaces
## altered with Dirichlet conditions for ouput. This is the
## unedited surface.
element scalar_field {
attribute rank { "0" },
attribute name { "GLSTurbulentKineticEnergyOriginal" },
(
element diagnostic {
internal_algorithm,
velocity_mesh_choice,
diagnostic_scalar_field
}|
element aliased {
generic_aliased_field
}
)
}?,
## Buoyancy frequency
element scalar_field {
attribute rank { "0" },
attribute name { "GLSBuoyancyFrequency" },
(
element diagnostic {
internal_algorithm,
velocity_mesh_choice,
diagnostic_scalar_field
}|
element aliased {
generic_aliased_field
}
)
}?,
## Velocity shear
element scalar_field {
attribute rank { "0" },
attribute name { "GLSVelocityShear" },
(
element diagnostic {
internal_algorithm,
velocity_mesh_choice,
diagnostic_scalar_field
}|
element aliased {
generic_aliased_field
}
)
}?,
## Shear production P
element scalar_field {
attribute rank { "0" },
attribute name { "GLSShearProduction" },
(
element diagnostic {
internal_algorithm,
velocity_mesh_choice,
diagnostic_scalar_field
}|
element aliased {
generic_aliased_field
}
)
}?,
## Buoyancy production B
element scalar_field {
attribute rank { "0" },
attribute name { "GLSBuoyancyProduction" },
(
element diagnostic {
internal_algorithm,
velocity_mesh_choice,
diagnostic_scalar_field
}|
element aliased {
generic_aliased_field
}
)
}?,
## Dissipation epsilon
element scalar_field {
attribute rank { "0" },
attribute name { "GLSDissipationEpsilon" },
(
element diagnostic {
internal_algorithm,
velocity_mesh_choice,
diagnostic_scalar_field
}|
element aliased {
generic_aliased_field
}
)
}?,
## Stability function S_M
element scalar_field {
attribute rank { "0" },
attribute name { "GLSStabilityFunctionSM" },
(
element diagnostic {
internal_algorithm,
velocity_mesh_choice,
diagnostic_scalar_field
}|
element aliased {
generic_aliased_field
}
)
}?,
## Stability function S_H
element scalar_field {
attribute rank { "0" },
attribute name { "GLSStabilityFunctionSH" },
(
element diagnostic {
internal_algorithm,
velocity_mesh_choice,
diagnostic_scalar_field
}|
element aliased {
generic_aliased_field
}
)
}?,
## Source1 - TKE source term
element scalar_field {
attribute rank { "0" },
attribute name { "GLSSource1" },
(
element diagnostic {
internal_algorithm,
velocity_mesh_choice,
diagnostic_scalar_field
}|
element aliased {
generic_aliased_field
}
)
}?,
## Source2 - Second Quantity source term
element scalar_field {
attribute rank { "0" },
attribute name { "GLSSource2" },
(
element diagnostic {
internal_algorithm,
velocity_mesh_choice,
diagnostic_scalar_field
}|
element aliased {
generic_aliased_field
}
)
}?,
## Absorption1 - TKE absorption term
element scalar_field {
attribute rank { "0" },
attribute name { "GLSAbsorption1" },
(
element diagnostic {
internal_algorithm,
velocity_mesh_choice,
diagnostic_scalar_field
}|