~grm08/fluidity/hilbert-for-pyop2 : revision 2249

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include "spud_base.rnc"

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include "adaptivity_options.rnc"

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include "diagnostic_algorithms.rnc"

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include "input_output.rnc"

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include "solvers.rnc"

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include "stabilisation.rnc"

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start =

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(

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## The root node of the options dictionary.

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element shallow_water_options {

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comment,

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## Model output files are named according to the simulation

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## name, e.g. [simulation_name]_0.vtu. Non-standard

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## characters in the simulation name should be avoided.

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element simulation_name {

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anystring

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},

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## Options dealing with the specification of geometry

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element geometry {

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## Dimension of the problem.

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## This can only be set once

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element dimension {

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attribute replaces {"NDIM"},

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element integer_value {

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attribute rank {"0"},

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("2"|"1")

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}

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},

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## The position mesh

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element mesh {

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attribute name { "CoordinateMesh" },

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mesh_info

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},

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## The velocity mesh

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element mesh {

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attribute name { "VelocityMesh" },

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mesh_info

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},

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## The pressure mesh

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element mesh {

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attribute name { "PressureMesh" },

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mesh_info

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},

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element mesh {

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attribute name { xsd:string },

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mesh_info,

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element exclude_from_mesh_adaptivity{empty}?

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}*,

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## Quadrature

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element quadrature {

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## Quadrature degree

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##

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## note: this specifies the degree of quadrature,

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## not the number of gauss points

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element degree {

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attribute replaces {"NGI"},

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integer

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},

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## Surface quadrature degree

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##

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## note: this specifies the degree of surface

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## quadrature not the number of surface gauss points

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element surface_degree {

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attribute replaces {"SNGI"},

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integer

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}?,

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## Select which family of quadrature rules to use.

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## The default is family_cools.

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## family_wandzura allows for degree up to 30

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## on triangular meshes.

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## family_grundmann_moeller allows for degree up to

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## 29 on simplicial meshes in arbitrary dimension.

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element quadrature_family {

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( "family_cools" | "family_grundmann_moeller" | "family_wandzura" )

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}?

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}

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},

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## Input/output options

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element io {

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## Format for dump files. Only vtk for now.

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element dump_format {

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element string_value{

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"vtk"

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}

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},

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(

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## Period between dumps in time units.

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##

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## Specifies the period between each dump of the solution to disk.

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## A value of 0.0 indicates that there would be a dump at every timestep.

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element dump_period {

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(

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element constant {

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attribute replaces {"TIMDUM"},

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real

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}|

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## Python function prescribing real input. Functions should be of the form:

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##

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## def val(t):

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## # Function code

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## return # Return value

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##

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##

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element python {

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attribute replaces {"TIMDUM"},

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python_code

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}

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)

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}|

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## Dump period, in timesteps.

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##

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## Specifies the number of timesteps between each dump of the solution to disk.

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## A value of 0 indicates a dump at every timestep.

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element dump_period_in_timesteps {

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(

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element constant {

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integer

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}|

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## Python function prescribing integer input. Functions should be of the form:

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##

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## def val(t):

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## # Function code

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## return # Return value

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##

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##

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element python {

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python_code

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}

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)

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}

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),

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# every CPUDUM seconds write results to disc.

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## This is usually disabled.

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element cpu_dump_period {

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attribute replaces {"CPUDUM"},

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real

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}?,

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## The period between dumps in walltime seconds. This is usually disabled.

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element wall_time_dump_period {

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attribute replaces {"WTIDUM"},

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real

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}?,

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(

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## The mesh on to which all the fields will be

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## interpolated for VTK output.

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element output_mesh {

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attribute name { "VelocityMesh" }

150

}|

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## The mesh on to which all the fields will be

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## interpolated for VTK output.

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element output_mesh {

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attribute name { "PressureMesh" }

155

}|

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## The mesh on to which all the fields will be

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## interpolated for VTK output.

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element output_mesh {

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attribute name { "CoordinateMesh" }

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}|

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## The mesh on to which all the fields will be

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## interpolated for VTK output.

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element output_mesh {

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attribute name { xsd:string }

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}

166

)

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},

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## Options dealing with time discretisation

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element timestepping {

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## Current simulation time. At the start of the simulation this

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## is the start time.

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element current_time {

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attribute replaces {"ACCTIM"},

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real,

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## The following excerpt from the Udunits

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## documentation explains the time unit encoding by

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## example:

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##

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## The specification:

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##

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## seconds since 1992-10-8 15:15:42.5 -6:00

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##

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## indicates seconds since October 8th, 1992 at 3

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## hours, 15 minutes and 42.5 seconds in the afternoon

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## in the time zone which is six hours to the west of

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## Coordinated Universal Time (i.e. Mountain Daylight

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## Time). The time zone specification can also be

188

## written without a colon using one or two-digits

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## (indicating hours) or three or four digits

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## (indicating hours and minutes).

191

##

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## Time units are particularly required in situations

193

## where the problem (time-varying) boundary conditions

194

## and/ initial conditions are a function of time as

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## defined by a calendar. Examples include atmospheric

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## forcing and climatology. The current time, specified

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## above, is zero at the reference data/time.

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element time_units{attribute date { xsd:string }}?

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},

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## The time step size. If adaptive time stepping is used

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## then this is the initial time step size.

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element timestep {

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attribute replaces {"DT"},

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real

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},

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## How many nonlinear iterations in the timestepping loop

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element nonlinear_iterations {

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attribute replaces {"ITINOI"},

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integer

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},

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## Simulation time at which the simulation should end.

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element finish_time {

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attribute replaces {"LTIME"},

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real

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},

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## Timestep after which the simulation should end.

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element final_timestep {

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integer

219

}?,

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## Maximum CPU time (secs) taken up before

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## simulation terminates writing results to disc.

222

##

223

## Manual suggests 1.E+20

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element cpu_time_limit {

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attribute replaces {"CPULIM"},

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real

227

}?,

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## Maximum wall time (secs) taken up before

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## simulation terminates writing results to disc.

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##

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## This is usually disabled.

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element wall_time_limit {

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attribute replaces {"WATIME"},

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real

235

}?

236

},

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## The physical parameters

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element physical_parameters {

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## Set a gravity to be included in the buoyancy term.

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element gravity {

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## Acceleration due to gravity. 9.8 m/s^2 on earth.

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element magnitude {

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attribute replaces { "GRAVTY" },

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real

245

}

246

}?,

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element coriolis {

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attribute replaces { "OPTOME" },

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(

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## f-plane approximation

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## This means the Coriolis force looks like:

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## f k x u

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## where k is the z unit vector

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## and u the velocity vector

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## and f is constant

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element f_plane {

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attribute replaces { "OPTOME = 0" },

258

## f-plane approximation

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## This means the Coriolis force looks like:

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## f k x u

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## where k is the z unit vector

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## and u the velocity vector

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## and f is constant

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element f {

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attribute replaces {"OMEGA" },

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real

267

}

268

}|

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## Beta-plane approximation

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## This means the Coriolis force looks like:

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## f k x u

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## where k is the z unit vector

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## and u the velocity vector

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## and f=f_0+beta . (x,y,z)

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element beta_plane {

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attribute replaces { "OPTOME = 1" },

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## Beta-plane approximation

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## This means the Coriolis force looks like:

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## f k x u

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## where k is the z unit vector

281

## and u the velocity vector

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## and f=f_0+beta . (x,y,z)

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element f_0 {

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attribute replaces {"OMEGA" },

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real

286

},

287

## Beta-plane approximation

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## This means the Coriolis force looks like:

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## f k x u

290

## where k is the z unit vector

291

## and u the velocity vector

292

## and f=f_0+beta . (x,y,z)

293

## usually only the y-component of beta is non-zero

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element beta {

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attribute replaces {"OMEGA1 OMEGA2 OMEGA3" },

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real_dim_vector

297

}

298

}

299

)

300

}?

301

},

302

## The material or phase options

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element material_phase {

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attribute name { "Fluid" },

305

(

306

## Velocity vector and momentum options

307

element vector_field {

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attribute rank { "1" },

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attribute name { "Velocity" },

310

## Field type

311

(

312

element prognostic {

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element mesh {

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attribute name { "VelocityMesh" }

315

},

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prognostic_velocity_field

317

}|

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element prescribed {

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element mesh {

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attribute name { "VelocityMesh" }

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},

322

prescribed_vector_field

323

}|

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element aliased {

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attribute material_phase_name { xsd:string },

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attribute field_name {"Velocity" }

327

}

328

)

329

},

330

## Free surface elevation

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element scalar_field {

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attribute rank { "0" },

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attribute name { "LayerThickness" },

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element prognostic {

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pressure_mesh_choice,

336

prognostic_layerthickness_field

337

}

338

},

339

scalar_field_choice*,

340

vector_field_choice*

341

#tensor_field_choice*

342

)

343

},

344

element mesh_adaptivity {

345

(

346

hr_adaptivity|

347

prescribed_adaptivity

348

)

349

}?,

350

## Debugging options

351

element debug {

352

element check_inverse_coriolis_matrix {

353

empty

354

}?,

355

element check_wave_matrix {

356

empty

357

}?,

358

element check_solution {

359

empty

360

}?

361

}?

362

}

363

)

364

365

scalar_field_choice =

366

(

367

# The first is a generic field, which may be used for any user-defined field

368

# that FLUIDITY knows nothing about, or a generic diagnostic

369

(

370

element scalar_field {

371

attribute rank { "0" },

372

attribute name { xsd:string },

373

## Field type

374

(

375

element prognostic {

376

velocity_mesh_choice,

377

prognostic_scalar_field

378

}|

379

element prescribed {

380

velocity_mesh_choice,

381

prescribed_scalar_field

382

}|

383

element diagnostic {

384

scalar_diagnostic_algorithms,

385

velocity_mesh_choice,

386

diagnostic_scalar_field

387

}

388

)

389

}|

390

## Passive Tracer

391

element scalar_field {

392

attribute rank { "0" },

393

attribute name { "Tracer" },

394

attribute replaces { "IDENT = 666" },

395

element prognostic {

396

velocity_mesh_choice,

397

prognostic_scalar_field

398

}

399

}|

400

## CFLNumber

401

##

402

## See http://amcg.ese.ic.ac.uk/index.php?title=Local:Diagnostics#CFL_Number

403

##

404

## Adapting to this field is not recommended

405

element scalar_field {

406

attribute rank { "0" },

407

attribute name { "CFLNumber" },

408

attribute replaces { "IDENT = -601" },

409

(

410

element diagnostic {

411

internal_algorithm,

412

velocity_mesh_choice,

413

diagnostic_scalar_field

414

}

415

)

416

}

417

)

418

)

419

420

# Choice of input method, e.g. for boundary conditions

421

input_choice_real =

422

(

423

input_choice_real_contents

424

)

425

426

input_choice_real_plus_boundary_forcing =

427

(

428

input_choice_real_contents|

429

element from_file {

430

element tidal {

431

attribute file_name { string },

432

attribute variable_name_amplitude { string },

433

attribute variable_name_phase { string },

434

## See E.W. Schwiderski - Rev. Geophys. Space

435

## Phys. Vol. 18 No. 1 pp. 243--268, 1980

436

## for details of these constituent.

437

attribute name {"M2"|"S2"|"N2"|"K2"|"K1"|"O1"|"P1"|"Q1"|"Mf"|"Mm"|"Ssa"}

438

}+

439

}

440

)

441

442

input_choice_real_plus_file =

443

(

444

input_choice_real_contents|

445

## Initialise the field from an existing file (indended primarily for picking up prescribed fields from previously run prognostic simulations). The file mesh must match the mesh of this field (except for piecewise constant fields which will be remapped back from the discontinuous nodal values).

446

##

447

## THIS WILL NOT WORK FOR PRESCRIBED FIELDS NOT DIRECTLY UNDERNEATH /material_phase

448

element from_file {

449

attribute file_name { xsd:string },

450

vtu_input_format,

451

comment

452

}

453

)

454

455

input_choice_real_contents =

456

## Constant value

457

element constant {

458

real

459

}|

460

## Python function prescribing real input. Functions should be of the form:

461

##

462

## def val(X, t):

463

## # Function code

464

## return # Return value

465

##

466

## where X is a tuple of length geometry dimension.

467

element python {

468

python_code

469

}

470

471

# Choice of input method for initial conditions

472

# Note: combine = "choice" should be used here to combine with input_choice_real, but Diamond doesn't support it

473

input_choice_initial_condition_real =

474

(

475

## Constant value

476

element constant {

477

real

478

}|

479

## Python function prescribing real input. Functions should be of the form:

480

##

481

## def val(X, t):

482

## # Function code

483

## return # Return value

484

##

485

## where X is a tuple of length geometry dimension.

486

element python {

487

python_code

488

}|

489

## Initialise the field from an existing file (indended

490

## primarily for use in checkpointing). The file mesh must match

491

## the mesh of this field (except for piecewise constant fields

492

## which will be remapped back from the discontinuous nodal values).

493

## In parallel the process number is

494

## appended to the filename, e.g. if the file_name attribute is

495

## set to "input.vtu", process 0 reads from "input-0.vtu".

496

element from_file {

497

attribute file_name { xsd:string },

498

(

499

vtu_input_format|

500

netcdf_input_format

501

),

502

comment

503

}

504

)

505

506

# Choice of input method, e.g. for boundary conditions

507

input_choice_real_dim_vector =

508

(

509

input_choice_real_dim_vector_contents

510

)

511

512

# Choice of input method, e.g. for prescribed fields

513

input_choice_real_dim_vector_plus_file =

514

(

515

input_choice_real_dim_vector_contents|

516

## Initialise the field from an existing file (indended primarily for picking up prescribed fields from previously run prognostic simulations). The file mesh must match the mesh of this field (except for piecewise constant fields which will be remapped back from the discontinuous nodal values).

517

##

518

## THIS WILL NOT WORK FOR PRESCRIBED FIELDS NOT DIRECTLY UNDERNEATH /material_phase

519

element from_file {

520

attribute file_name { xsd:string },

521

vtu_input_format,

522

comment

523

}

524

)

525

526

input_choice_real_dim_vector_contents =

527

## Constant value

528

element constant {

529

real_dim_vector

530

}|

531

## Python function prescribing dimensional vector input. Functions should be of the form:

532

##

533

## def val(X, t):

534

## # Function code

535

## return # Return value

536

##

537

## where X and the return value are tuples of length geometry dimension.

538

element python {

539

python_code

540

}

541

542

# Choice of input method, e.g. for boundary conditions

543

# this one specifies a vector field of dim minus one

544

input_choice_real_dim_minus_one_vector =

545

(

546

## Constant value

547

element constant {

548

real_dim_minus_one_vector

549

}|

550

## Python function prescribing dimensional vector input. Functions should be of the form:

551

##

552

## def val(X, t):

553

## # Function code

554

## return # Return value

555

##

556

## where X and the return value are tuples of length geometry dimension.

557

element python {

558

python_code

559

}

560

)

561

562

## Import data from NetCDF CF-1.x file.

563

input_choice_netcdf =

564

(

565

element from_file {

566

## The format of this file should conform to NetCDF CF 1.x

567

## (http://cf-pcmdi.llnl.gov/)

568

attribute file_name { xsd:string },

569

comment

570

}

571

)

572

573

# Choice of input method for initial conditions

574

# Note: combine = "choice" should be used here to combine with input_choice_real, but Diamond doesn't support it

575

input_choice_initial_condition_vector =

576

(

577

## Constant value

578

element constant {

579

real_dim_vector

580

}|

581

## Python function prescribing dimensional vector input. Functions should be of the form:

582

##

583

## def val(X, t):

584

## # Function code

585

## return # Return value

586

##

587

## where X and the return value are tuples of length geometry dimension.

588

element python {

589

python_code

590

}|

591

## Initialise the field from an existing file (indended primarily for use in checkpointing). The file mesh must match the mesh of this field (except for piecewise constant fields which will be remapped back from the discontinuous nodal values).

592

element from_file {

593

attribute file_name { xsd:string },

594

vtu_input_format,

595

comment

596

}|

597

## Set balanced velocity from height field

598

element balanced {

599

empty

600

}

601

)

602

603

# Choice of input method for initial/boundary conditions

604

# version for real symmetric tensor

605

input_choice_real_dim_symmetric_tensor =

606

(

607

## Constant symmetric tensor

608

element constant {

609

real_dim_symmetric_tensor

610

}|

611

## Python command prescribing symmetric tensor input.

612

##

613

## Note that it is for the python function to determine

614

## that the results it produces are, in fact, symmetric.

615

##

616

## An example that returns the three-dimensional identity:

617

##

618

## def val(X, t):

619

## return [[1, 0, 0],

620

## [0, 1, 0],

621

## [0, 0, 1]]

622

element python {

623

python_code

624

}

625

)

626

627

# Choice of input method for initial/boundary conditions

628

# version for real tensor

629

input_choice_real_dim_tensor =

630

(

631

## Constant tensor

632

element constant {

633

real_dim_tensor

634

}|

635

## Python command prescribing tensor input.

636

##

637

## An example that returns the three-dimensional identity:

638

##

639

## def val(X, t):

640

## return [[1, 0, 0],

641

## [0, 1, 0],

642

## [0, 0, 1]]

643

element python {

644

python_code

645

}

646

)

647

648

prognostic_velocity_field =

649

(

650

velocity_equation_choice,

651

## Spatial discretisation options

652

element spatial_discretisation {

653

(

654

## A new version of continuous galerkin assembly.

655

element continuous_galerkin {

656

## Stabilisation options for the galerkin discretisation

657

element stabilisation{

658

(

659

no_stabilisation|

660

su_stabilisation|

661

supg_stabilisation

662

)

663

},

664

## Discretisation options for the mass terms in the velocity equation.

665

element mass_terms{

666

## Lump the mass matrix - currently required if solving for pressure

667

element lump_mass_matrix {

668

## Lump on the submesh.

669

## This only works for simplex meshes and is only

670

## strictly valid on 2d meshes.

671

element use_submesh {

672

empty

673

}?

674

}?,

675

## Remove the mass terms from the equation.

676

element exclude_mass_terms {

677

empty

678

}?

679

},

680

## Discretisation options for the advection terms in the velocity equation.

681

element advection_terms {

682

## Integrate the advection terms of the momentum equation by parts.

683

## This allows for the imposition of weak boundary conditions.

684

## If activated the element advection matrix takes the form:

685

## / /

686

## - | (grad N_A dot nu) N_B rho dV - (1. - beta) | N_A ( div nu ) N_B rho dV

687

## / /

688

## otherwise it takes the standard form:

689

## / /

690

## | N_A (nu dot grad N_B) rho dV + beta | N_A ( div nu ) N_B rho dV

691

## / /

692

## where beta is set in conservative_advection, N is

693

## a shape function and nu is the relative nonlinear

694

## velocity.

695

element integrate_advection_by_parts {

696

empty

697

}?,

698

## Remove the advection terms (u.grad u rho + beta

699

## div u rho u) from the equation.

700

## This overrides any other advection term options

701

## (including conservative_advection below).

702

element exclude_advection_terms {

703

empty

704

}?

705

}

706

}|

707

## Discontinuous galerkin formulation. This causes Momentum_DG to be

708

## called instead of diff3d. Confusingly it is not necessary to provide

709

## a discontinuous velocity field for this to work!

710

element discontinuous_galerkin {

711

attribute replaces { "DISOPT" },

712

element advection_scheme {

713

(

714

## Disable advection

715

element none {

716

empty

717

}|

718

## Straightforward upwinding of the nonlinear velocity

719

element upwind {

720

empty

721

}

722

)

723

}

724

}

725

)

726

},

727

## Solver

728

element solver {

729

linear_solver_options_asym

730

},

731

(

732

## Initial condition for WholeMesh

733

##

734

## Only specify one condition if not using mesh regions.

735

## Otherwise select other initial_condition option, specify region_ids

736

## and distinct names. Then add extra intial conditions for other regions.

737

element initial_condition {

738

attribute name { "WholeMesh" },

739

input_choice_initial_condition_vector

740

}|

741

## Multiple initial_conditions are allowed if specifying

742

## different values in different

743

## regions of the mesh (defined by region_ids). In this case

744

## each initial_condition

745

## requires a distinct name for the options dictionary.

746

element initial_condition {

747

attribute name { string },

748

region_ids,

749

input_choice_initial_condition_vector

750

}

751

)+,

752

## Boundary conditions

753

element boundary_conditions {

754

attribute replaces { "boundary, TMPER1 TMPER2 TMPERI" },

755

attribute name { string },

756

## Surface id:

757

element surface_ids {

758

integer_vector

759

},

760

velocity_boundary_conditions

761

}*,

762

prognostic_vector_output_options,

763

prognostic_vector_stat_options,

764

vector_convergence_options,

765

prognostic_detector_options,

766

vector_steady_state_options,

767

adaptivity_options_prognostic_vector_field,

768

interpolation_algorithm_vector,

769

discrete_properties_algorithm_vector?

770

)

771

772

prognostic_layerthickness_field =

773

(

774

## Spatial discretisation options

775

element spatial_discretisation {

776

(

777

## Development continuous Galerkin formulation. This causes

778

## Advection_Diffusion_CG to be used instead of hart3d.

779

element continuous_galerkin {

780

## Discretisation options for the advection terms.

781

element advection_terms {

782

## Remove the advection terms from the equation.

783

## This overrides any other advection term options (including

784

## conservative_advection below).

785

element exclude_advection_terms {

786

comment

787

}?

788

},

789

comment

790

}

791

)

792

},

793

## Temporal discretisation options

794

element temporal_discretisation {

795

## Implicit/explicit control (THETA)

796

## =0. -- explicit

797

## =0.5 -- Crank-Nicolson

798

## =1. -- implicit

799

element theta {

800

attribute replaces {"THETA"},

801

real

802

},

803

## Non-linear relaxation term

804

## =0. -- previous timestep velocity solution used in non-linear terms of momentum equations

805

## =1. -- previous iteration velocity solution used in non-linear terms of momentum equations

806

## 0. < ITHETA < 1.

807

element relaxation {

808

attribute replaces {"ITHETA"},

809

real

810

}

811

},

812

## Solver

813

element solver {

814

linear_solver_options_asym

815

},

816

(

817

## Initial condition for WholeMesh

818

##

819

## Only specify one condition if not using mesh regions.

820

## Otherwise select other initial_condition option, specify region_ids

821

## and distinct names. Then add extra intial conditions for other regions.

822

element initial_condition {

823

attribute name { "WholeMesh" },

824

input_choice_initial_condition_real

825

}|

826

## Multiple initial_conditions are allowed if specifying

827

## different values in different

828

## regions of the mesh (defined by region_ids). In this case

829

## each initial_condition

830

## requires a distinct name for the options dictionary.

831

element initial_condition {

832

attribute name { string },

833

region_ids,

834

input_choice_initial_condition_real

835

}

836

),

837

## Mean value of thickness to use in wave equation solver

838

## Will be replaced by a field in due course

839

element mean_layer_thickness {

840

real

841

},

842

prognostic_scalar_output_options,

843

prognostic_scalar_stat_options,

844

adaptivity_options_prognostic_scalar_field,

845

interpolation_algorithm_scalar

846

)

847

848

849

prognostic_scalar_field =

850

(

851

## Solver

852

element solver {

853

linear_solver_options_sym

854

},

855

(

856

## Initial condition for WholeMesh

857

##

858

## Only specify one condition if not using mesh regions.

859

## Otherwise select other initial_condition option, specify region_ids

860

## and distinct names. Then add extra intial conditions for other regions.

861

element initial_condition {

862

attribute name { "WholeMesh" },

863

input_choice_initial_condition_real

864

}|

865

## Multiple initial_conditions are allowed if specifying

866

## different values in different

867

## regions of the mesh (defined by region_ids). In this case

868

## each initial_condition

869

## requires a distinct name for the options dictionary.

870

element initial_condition {

871

attribute name { string },

872

region_ids,

873

input_choice_initial_condition_real

874

}

875

),

876

## Diffusivity for field

877

element tensor_field {

878

attribute name { "Diffusivity" },

879

attribute rank { "2" },

880

attribute replaces { "TMUXX TMUYY TMUZZ TMUYZ TMUXZ TMUXY TALLMU TCONMU" },

881

element prescribed {

882

mesh_choice?,

883

prescribed_values_tensor_field

884

}

885

}?,

886

prognostic_scalar_output_options,

887

prognostic_scalar_stat_options

888

)

889

890

# Default child of diagnostic scalar field

891

diagnostic_scalar_field =

892

(

893

diagnostic_output_options,

894

diagnostic_scalar_stat_options,

895

scalar_convergence_options,

896

diagnostic_detector_options,

897

scalar_steady_state_options,

898

adaptivity_options_scalar_field,

899

recalculation_options?

900

)

901

902

# Default child of diagnostic scalar field without adaptivity options

903

diagnostic_scalar_field_no_adapt =

904

(

905

diagnostic_output_options,

906

diagnostic_scalar_stat_options,

907

diagnostic_detector_options

908

)

909

910

# Default child of diagnostic scalar field

911

diagnostic_scalar_field_tidal_range =

912

(

913

diagnostic_output_options,

914

diagnostic_scalar_stat_options,

915

diagnostic_detector_options,

916

adaptivity_options_scalar_field,

917

(

918

element spin_up_time {

919

real

920

}

921

)

922

)

923

924

# Default child of prescribed scalar field

925

# This is a choice of ways of inputing the prescribed field

926

prescribed_scalar_field =

927

(

928

prescribed_scalar_field_no_adapt,

929

adaptivity_options_scalar_field,

930

interpolation_algorithm_scalar?,

931

discrete_properties_algorithm_scalar?,

932

recalculation_options?

933

)

934

935

# Default child of prescribed scalar field without adaptivity options

936

# This is a choice of ways of inputing the prescribed field

937

prescribed_scalar_field_no_adapt =

938

(

939

prescribed_values_scalar_field,

940

prescribed_output_options,

941

prescribed_scalar_stat_options,

942

prescribed_detector_options

943

)

944

945

prescribed_values_scalar_field =

946

(

947

(

948

## Value for WholeMesh

949

## Only specify one value if not using mesh regions.

950

## Otherwise select other value option, specify region_ids

951

## and distinct names. Then add extra values for other regions.

952

element value {

953

attribute name { "WholeMesh" },

954

input_choice_real_plus_file

955

}|

956

## Multiple values are now allowed if using different value assignments

957

## in different regions of the mesh (specified by region_ids).

958

## In this case each value requires a distinct name for the options dictionary.

959

element value {

960

attribute name { string },

961

region_ids,

962

input_choice_real_plus_file

963

}

964

)+

965

)

966

967

# Default child of diagnostic vector field

968

# Currently, this is empty, but in future this might include

969

# options that are general to all diagnostic vector fields

970

diagnostic_vector_field =

971

(

972

diagnostic_output_options,

973

diagnostic_vector_stat_options,

974

vector_convergence_options,

975

diagnostic_detector_options,

976

vector_steady_state_options,

977

adaptivity_options_vector_field,

978

recalculation_options?

979

)

980

981

982

diagnostic_vector_field_bed_shear_stress =

983

(

984

(

985

element density {

986

real

987

}

988

),

989

(

990

element drag_coefficient {

991

real

992

}

993

),

994

diagnostic_output_options,

995

diagnostic_vector_stat_options,

996

diagnostic_detector_options,

997

adaptivity_options_vector_field

998

)

999

1000

1001

1002

# Default child of prescribed vector field

1003

# This is a choice of ways of inputing the prescribed field

1004

prescribed_vector_field =

1005

(

1006

prescribed_vector_field_no_adapt,

1007

adaptivity_options_vector_field,

1008

interpolation_algorithm_vector?,

1009

discrete_properties_algorithm_vector?,

1010

recalculation_options?

1011

)

1012

1013

# Default child of prescribed vector field without adaptivity options

1014

# This is a choice of ways of inputing the prescribed field

1015

prescribed_vector_field_no_adapt =

1016

(

1017

prescribed_values_vector_field,

1018

prescribed_output_options,

1019

prescribed_vector_stat_options,

1020

prescribed_detector_options

1021

)

1022

1023

prescribed_values_vector_field =

1024

(

1025

(

1026

## Value for WholeMesh

1027

##

1028

## Only specify one value if not using mesh regions.

1029

## Otherwise select other value option, specify region_ids

1030

## and distinct names. Then add extra values for other regions.

1031

element value {

1032

attribute name { "WholeMesh" },

1033

input_choice_real_dim_vector_plus_file

1034

}|

1035

## Multiple values are now allowed if using different value assignments

1036

## in different regions of the mesh (specified by region_ids).

1037

## In this case each value requires a distinct name for the options dictionary.

1038

element value {

1039

attribute name { string },

1040

region_ids,

1041

input_choice_real_dim_vector_plus_file

1042

}

1043

)+

1044

)

1045

1046

# Default child of diagnostic tensor field

1047

# Currently, this is empty, but in future this might include

1048

# options that are general to all diagnostic tensor fields

1049

diagnostic_tensor_field =

1050

(

1051

diagnostic_output_options,

1052

adaptivity_options_tensor_field

1053

)

1054

1055

# Default child of prescribed vector field

1056

# This is a choice of ways of inputing the prescribed tensor field

1057

# If the field is constant then a symmetric, or asymmetric tensor may be entered

1058

prescribed_tensor_field =

1059

(

1060

prescribed_values_tensor_field,

1061

adaptivity_options_tensor_field

1062

)

1063

1064

prescribed_values_tensor_field =

1065

(

1066

(

1067

## Value for WholeMesh

1068

##

1069

## Only specify one value if not using mesh regions.

1070

## Otherwise select other value option, specify region_ids

1071

## and distinct names. Then add extra values for other regions.

1072

element value {

1073

attribute name { "WholeMesh" },

1074

input_choice_tensor_field

1075

}|

1076

## Multiple values are now allowed if using different value assignments

1077

## in different regions of the mesh (specified by region_ids).

1078

## In this case each value requires a distinct name for the options dictionary.

1079

element value {

1080

attribute name { string },

1081

region_ids,

1082

input_choice_tensor_field

1083

}

1084

)+

1085

)

1086

1087

1088

velocity_components_choice =

1089

(

1090

(

1091

# rotated bcs are not implemented... this is where they should go when they are

1092

# element align_bc_with_surface {

1093

# element normal_component {

1094

# input_choice_real

1095

# }?,

1096

# element tangent_component_1 {

1097

# input_choice_real

1098

# }?,

1099

# element tangent_component_2 {

1100

# input_choice_real

1101

# }?,

1102

# rotation_matrix_components

1103

# }|

1104

element align_bc_with_cartesian {

1105

element x_component {

1106

input_choice_real_bc_component

1107

}?,

1108

element y_component {

1109

input_choice_real_bc_component

1110

}?,

1111

element z_component {

1112

input_choice_real_bc_component

1113

}?

1114

}

1115

)

1116

)

1117

1118

input_choice_real_bc_component =

1119

(

1120

input_choice_real|

1121

element synthetic_eddy_method {

1122

## use a large number to ensure Gaussian

1123

## behaviour of the fluctuating component

1124

element number_of_eddies {

1125

integer

1126

},

1127

element turbulence_lengthscale {

1128

input_choice_real

1129

},

1130

## mean profile

1131

##

1132

## usually a function of height,

1133

## for ABL simulations use a log profile

1134

element mean_profile {

1135

input_choice_real

1136

},

1137

## Reynolds stresses profile

1138

##

1139

## usually a function of height,

1140

## assumes that the remaining stresses are negligible

1141

element Re_stresses_profile {

1142

input_choice_real

1143

}

1144

}

1145

)

1146

1147

# and again for robin b.c.s

1148

robin_velocity_components_choice =

1149

(

1150

(

1151

# element align_bc_with_surface {

1152

# element normal_component {

1153

# element order_zero_coefficient {

1154

# input_choice_real

1155

# },

1156

# element order_one_coefficient {

1157

# input_choice_real

1158

# }

1159

# }?,

1160

# element tangent_component_1 {

1161

# element order_zero_coefficient {

1162

# input_choice_real

1163

# },

1164

# element order_one_coefficient {

1165

# input_choice_real

1166

# }

1167

# }?,

1168

# element tangent_component_2 {

1169

# element order_zero_coefficient {

1170

# input_choice_real

1171

# },

1172

# element order_one_coefficient {

1173

# input_choice_real

1174

# }

1175

# }?,

1176

# rotation_matrix_components

1177

# }|

1178

element align_bc_with_cartesian {

1179

element x_component {

1180

element order_zero_coefficient {

1181

input_choice_real

1182

},

1183

element order_one_coefficient {

1184

input_choice_real

1185

}

1186

}?,

1187

element y_component {

1188

element order_zero_coefficient {

1189

input_choice_real

1190

},

1191

element order_one_coefficient {

1192

input_choice_real

1193

}

1194

}?,

1195

element z_component {

1196

element order_zero_coefficient {

1197

input_choice_real

1198

},

1199

element order_one_coefficient {

1200

input_choice_real

1201

}

1202

}?

1203

}

1204

)

1205

)

1206

1207

velocity_boundary_conditions =

1208

(

1209

(

1210

element type {

1211

attribute name { "dirichlet" },

1212

## Apply the dirichlet bc weakly. Available automatically

1213

## with a discontinuous_galerkin Velocity

1214

## spatial_discretisation. Available if you

1215

## integrate_continuity_by_parts with a

1216

## continuous_galerkin Pressure or use a control_volume

1217

## Pressure spatial_discretisation and/or

1218

## integrate_advection_by_parts under Velocity

1219

## spatial_discretisation with continuous_galerkin.

1220

##

1221

## If not selected boundary conditions are applied strongly.

1222

element apply_weakly {

1223

## If the initial condition and boundary conditions

1224

## differ, setting this option will cause the initial

1225

## condition on the boundary to be overwritten with

1226

## the boundary condition. Since you are applying the

1227

## boundary condition weakly, you probably do *not*

1228

## want this.

1229

element boundary_overwrites_initial_condition {

1230

empty

1231

}?

1232

}?,

1233

velocity_components_choice

1234

}|

1235

element type {

1236

attribute name { "neumann" },

1237

velocity_components_choice

1238

}|

1239

element type {

1240

attribute name { "robin" },

1241

robin_velocity_components_choice

1242

}|

1243

element type {

1244

attribute name { "free_surface" }

1245

}|

1246

## Apply quadratic drag. Specify drag coefficient. If you

1247

## want to exactly replicate results from using the OCEDRA

1248

## option, set this to 0.003 and remember to apply to both

1249

## bottom and sides.

1250

element type {

1251

attribute name { "drag" },

1252

input_choice_real,

1253

(

1254

## Use a quadratic drag.

1255

##

1256

## This means that the drag coefficient is nondimensional.

1257

element quadratic_drag {

1258

empty

1259

}|

1260

## Use a linear drag (basically just a surface absorption term).

1261

##

1262

## This means that the drag coefficient has units of momentum.

1263

element linear_drag {

1264

empty

1265

}

1266

)

1267

}|

1268

1269

## Apply wind forcing specified by stress or wind velocity.

1270

## Replaces windy.dat and windy.py

1271

element type {

1272

attribute name { "wind_forcing" },

1273

(

1274

## Wind forcing with user specified wind stress

1275

##

1276

## Note that the stress needs to be specified

1277

## using the same density units as the reference_density

1278

## under equation of state.So if you use the recommended

1279

## non-dimensional value of 1.0 for reference_density and

1280

## your calculated stress is in kg m^-1s^-2 and the dimensional

1281

## reference_density is 1000.0 kg m^-3, you need to divide

1282

## the calculated stress in SI units by 1000.0.

1283

element wind_stress {

1284

input_choice_real_dim_minus_one_vector|

1285

element from_netcdf {

1286

## The format of this file should conform to NetCDF CF 1.x

1287

## (http://cf-pcmdi.llnl.gov/).

1288

attribute file_name { xsd:string },

1289

attribute east_west { xsd:string },

1290

attribute north_south { xsd:string },

1291

comment

1292

}

1293

}|

1294

## Wind forcing with user specified 10m wind velocity

1295

element wind_velocity {

1296

## Specify wind drag coefficient (dimensionless)

1297

## Suggested value: 4.0e-4

1298

element wind_drag_coefficient {

1299

input_choice_real

1300

},

1301

## Density of air.

1302

##

1303

## Note that you have to specify

1304

## this density in the same units as the

1305

## reference_density under equation of state.

1306

## So with a typicial value of rho_air=1.3 kgm^-3

1307

## and rho_water=1000 kgm^-3, if you fill in the

1308

## recommended (non-dimensional) value of 1.0 for

1309

## reference_density, this field needs to be 1.3e-3.

1310

element density_air {

1311

real

1312

},

1313

## Specify wind velocity

1314

element wind_velocity {

1315

input_choice_real_dim_minus_one_vector|

1316

element from_netcdf {

1317

## The format of this file should conform to NetCDF CF 1.x

1318

## (http://cf-pcmdi.llnl.gov/)

1319

attribute file_name { xsd:string },

1320

attribute east_west { xsd:string },

1321

attribute north_south { xsd:string },

1322

comment

1323

}

1324

}

1325

}

1326

)

1327

}|

1328

1329

## When using control_volumes under Pressure

1330

## spatial_discretisation or when using

1331

## integrate_continuity_by_parts with continuous_galerkin

1332

## Pressure and continuous_galerkin Velocity this

1333

## boundary condition type imposes a weak no normal flow

1334

## boundary condition on the surface_ids specified.

1335

element type {

1336

attribute name { "no_normal_flow" },

1337

empty

1338

}|

1339

1340

## Implements a penalty function for the near wall region.

1341

## Using this option coarse meshes can

1342

## be used in the near wall region.

1343

##

1344

## Should be used in combination with a no_normal_flow condition.

1345

##

1346

## See Bazilevs et al. 2007

1347

element type{

1348

attribute name { "near_wall_treatment" },

1349

element tolerance {real}

1350

}|

1351

## Log law of the wall

1352

##

1353

## Should be used in combination with a no_normal_flow condition.

1354

element type{

1355

attribute name { "log_law_of_wall" },

1356

element surface_roughness {real}

1357

}

1358

)

1359

)

1360

1361

# Output options for prognostic fields

1362

prognostic_scalar_output_options =

1363

(

1364

## Specify what is written to vtu dump files

1365

element output {

1366

## By default each field in the options file is written to vtu.

1367

## Select this option to exclude this field.

1368

element exclude_from_vtu {

1369

empty

1370

}?,

1371

## Select this option to also write the values of this field

1372

## on the previous timestep.

1373

## (included under the name: Old<field_name> )

1374

element include_previous_time_step {

1375

empty

1376

}?,

1377

## Select this option to also write the values of this field

1378

## used in the nonlinear iteration.

1379

## (included under the name: Nonlinear<field_name> )

1380

element include_nonlinear_field {

1381

empty

1382

}?,

1383

## Output a file details the convergence (or otherwise) of

1384

## this field with every advective nonlinear

1385

## iteration.

1386

## ONLY WORKS FOR PURE CONTROL VOLUME DISCRETISATIONS.

1387

element convergence_file {

1388

comment

1389

}?

1390

}

1391

)

1392

1393

# Output options for pressure (can't have a convergence file)

1394

pressure_output_options =

1395

(

1396

## Specify what is written to vtu dump files

1397

element output {

1398

## By default each field in the options file is written to vtu.

1399

## Select this option to exclude this field.

1400

element exclude_from_vtu {

1401

empty

1402

}?,

1403

## Select this option to also write the values of this field

1404

## on the previous timestep.

1405

## (included under the name: Old<field_name> )

1406

element include_previous_time_step {

1407

empty

1408

}?,

1409

## Select this option to also write the values of this field

1410

## used in the nonlinear iteration.

1411

## (included under the name: Nonlinear<field_name> )

1412

element include_nonlinear_field {

1413

empty

1414

}?,

1415

## Write out some extra debugging vtu files that can be used

1416

## to analyse what goes on in the pressure projection steps.

1417

## WARNING: this may create a huge amount of vtu files, as

1418

## multiple files are written per nonlinear iteration.

1419

element debugging_vtus {

1420

empty

1421

}?

1422

}

1423

)

1424

1425

# Output options for prognostic fields

1426

prognostic_vector_output_options =

1427

(

1428

## Specify what is written to vtu dump files

1429

element output {

1430

## By default each field in the options file is written to vtu.

1431

## Select this option to exclude this field.

1432

element exclude_from_vtu {

1433

empty

1434

}?,

1435

## Select this option to also write the values of this field

1436

## on the previous timestep.

1437

## (included under the name: Old<field_name> )

1438

element include_previous_time_step {

1439

empty

1440

}?,

1441

## Select this option to also write the values of this field

1442

## used in the nonlinear iteration.

1443

## (included under the name: Nonlinear<field_name> )

1444

element include_nonlinear_field {

1445

empty

1446

}?

1447

}

1448

)

1449

1450

# Output options for all other fields

1451

field_output_options =

1452

(

1453

## Specify what is written to vtu dump files

1454

element output {

1455

## By default each field in the options file is written to vtu.

1456

## Select this option to exclude this field.

1457

element exclude_from_vtu {

1458

empty

1459

}?

1460

}

1461

)

1462

1463

diagnostic_output_options = field_output_options

1464

prescribed_output_options = field_output_options

1465

1466

# Options for inclusion/exclusion of standard field statistics from the .stat

1467

# file

1468

include_stat =

1469

(

1470

## Include this field in the .stat file (magnitude and components)

1471

element include_in_stat {

1472

comment

1473

}

1474

)

1475

exclude_components_from_stat =

1476

(

1477

## Include just the magnitude of this field in the .stat file

1478

## (excluding the components)

1479

element exclude_components_from_stat {

1480

comment

1481

}

1482

)

1483

exclude_stat =

1484

(

1485

## Exclude this field from the .stat file.

1486

element exclude_from_stat {

1487

comment

1488

}

1489

)

1490

1491

# Diagnostic statistics options for prognostic scalar fields

1492

prognostic_scalar_stat_options =

1493

(

1494

## Specify what is added to .stat files

1495

element stat {

1496

prognostic_scalar_stat_options.stat

1497

}

1498

)

1499

1500

# Diagnostic statistics for all other scalar fields

1501

prognostic_scalar_stat_no_old_or_nonlinear_options =

1502

(

1503

## Specify what is added to .stat files

1504

element stat {

1505

prognostic_scalar_stat_no_old_or_nonlinear_options.stat

1506

1507

}

1508

)

1509

1510

diagnostic_scalar_stat_options = prognostic_scalar_stat_no_old_or_nonlinear_options

1511

prescribed_scalar_stat_options = prognostic_scalar_stat_no_old_or_nonlinear_options

1512

1513

# Combining of stat elements for scalar fields

1514

prognostic_scalar_stat_options.stat = prognostic_scalar_stat_no_old_or_nonlinear_options.stat

1515

prognostic_scalar_stat_options.stat &=

1516

(

1517

## Enable to include the previous timestep value of this field in the .stat file.

1518

element include_previous_time_step {

1519

comment

1520

}?,

1521

## Enable to include the values of this field in the nonlinear

1522

## iteration in the .stat file.

1523

element include_nonlinear_field {

1524

comment

1525

}?

1526

)

1527

prognostic_scalar_stat_no_old_or_nonlinear_options.stat =

1528

(

1529

exclude_stat?,

1530

cv_stats?,

1531

surface_integral_stats_scalar*,

1532

mixing_stats*

1533

)

1534

1535

# Diagnostic statistics options for vector fields, with enabled by default

1536

vector_field_stat_options_enabled_default = include_stat

1537

vector_field_stat_options_enabled_default |= exclude_components_from_stat

1538

vector_field_stat_options_enabled_default |= exclude_stat

1539

1540

# Diagnostic statistics options for vector fields, with enabled by default

1541

vector_field_stat_options_disabled_default = exclude_stat

1542

vector_field_stat_options_disabled_default |= exclude_components_from_stat

1543

vector_field_stat_options_disabled_default |= include_stat

1544

1545

# Diagnostic statistics for prognostic vector fields

1546

prognostic_vector_stat_options =

1547

(

1548

## Specify what is added to .stat files

1549

element stat {

1550

(

1551

prognostic_vector_stat_options.stat

1552

)

1553

}

1554

)

1555

1556

# Diagnostic statistics for all other vector fields

1557

prognostic_vector_stat_no_old_or_nonlinear_options =

1558

(

1559

## Specify what is added to .stat files

1560

element stat {

1561

prognostic_vector_stat_no_old_or_nonlinear_options.stat

1562

}

1563

)

1564

diagnostic_vector_stat_options = prognostic_vector_stat_no_old_or_nonlinear_options

1565

prescribed_vector_stat_options = prognostic_vector_stat_no_old_or_nonlinear_options

1566

1567

# Combining of stat elements for vector fields

1568

prognostic_vector_stat_options.stat = prognostic_vector_stat_no_old_or_nonlinear_options.stat

1569

prognostic_vector_stat_options.stat &=

1570

(

1571

## Specify how the previous timestep value of this field is added to the .stat file.

1572

element previous_time_step {

1573

vector_field_stat_options_disabled_default

1574

},

1575

## Specify how the values of this field used in the nonlinear iteration are added to the .stat file.

1576

element nonlinear_field {

1577

vector_field_stat_options_disabled_default

1578

},

1579

## What surface IDs do you want to do the calculation over?

1580

element compute_body_forces_on_surfaces {

1581

integer_vector

1582

}?

1583

)

1584

prognostic_vector_stat_no_old_or_nonlinear_options.stat =

1585

(

1586

vector_field_stat_options_enabled_default,

1587

surface_integral_stats_vector*

1588

)

1589

1590

# Convergence options for prognostic scalar fields

1591

scalar_convergence_options =

1592

(

1593

## Decide whether this field is tested for convergence

1594

## during nonlinear iterations

1595

## (if /timestepping/nonlinear_iterations and

1596

## /timestepping/nonlinear_iterations/tolerance are

1597

## enabled).

1598

## Also specifies whether the field is added to the

1599

## convergence file (if /io/convergence_file is enabled).

1600

element convergence {

1601

(

1602

## Include this field in convergence testing

1603

## (if /timestepping/nonlinear_iterations and

1604

## /timestepping/nonlinear_iterations/tolerance are

1605

## enabled) and file (if /io/convergence_file is enabled)

1606

element include_in_convergence {

1607

comment

1608

}|

1609

## Exclude this field from convergence testing and file

1610

element exclude_from_convergence {

1611

comment

1612

}

1613

)

1614

}

1615

)

1616

1617

# Convergence statistics options for prognostic vector fields (velocity)

1618

vector_convergence_options =

1619

(

1620

## Decide whether this field is tested for convergence

1621

## during nonlinear iterations

1622

## (if /timestepping/nonlinear_iterations and

1623

## /timestepping/nonlinear_iterations/tolerance are

1624

## enabled).

1625

## Also specifies whether the field is added to the

1626

## convergence file (if /io/convergence_file is enabled).

1627

element convergence {

1628

(

1629

## Include this field (magnitude and components)

1630

## in convergence testing

1631

## (if /timestepping/nonlinear_iterations and

1632

## /timestepping/nonlinear_iterations/tolerance are

1633

## enabled) and file (if /io/convergence_file is enabled)

1634

element include_in_convergence {

1635

comment

1636

}|

1637

## Include just the magnitude of this field

1638

## in convergence testing

1639

## (if /timestepping/nonlinear_iterations and

1640

## /timestepping/nonlinear_iterations/tolerance are

1641

## enabled) and file (if /io/convergence_file is enabled)

1642

## i.e. excluding the components

1643

element exclude_components_from_convergence {

1644

comment

1645

}|

1646

## Exclude this field entirely from convergence testing and file

1647

element exclude_from_convergence {

1648

comment

1649

}

1650

)

1651

}

1652

)

1653

1654

# Steady state options for prognostic scalar fields

1655

scalar_steady_state_options =

1656

(

1657

## Decide whether this field is tested for a steady state

1658

## between timesteps

1659

## (if /timestepping/steady_state is

1660

## enabled).

1661

element steady_state {

1662

(

1663

## Include this field in steady state testing

1664

## (if /timestepping/steady_state is

1665

## enabled)

1666

element include_in_steady_state {

1667

comment

1668

}|

1669

## Exclude this field from steady state testing

1670

element exclude_from_steady_state {

1671

comment

1672

}

1673

)

1674

}

1675

)

1676

1677

# Steady state statistics options for prognostic vector fields (velocity)

1678

vector_steady_state_options =

1679

(

1680

## Decide whether this field is tested for a steady state

1681

## between timesteps

1682

## (if /timestepping/steady_state is

1683

## enabled).

1684

element steady_state {

1685

(

1686

## Include this field (magnitude and components)

1687

## in steady state testing

1688

## (if /timestepping/steady_state is enabled)

1689

element include_in_steady_state {

1690

comment

1691

}|

1692

## Include just the magnitude of this field

1693

## in steady state testing

1694

## (if /timestepping/steady_state is

1695

## enabled)

1696

## i.e. excluding the components

1697

element exclude_components_from_steady_state {

1698

comment

1699

}|

1700

## Exclude this field entirely from convergence testing and file

1701

element exclude_from_steady_state {

1702

comment

1703

}

1704

)

1705

}

1706

)

1707

1708

# Options for whether a field is to be included in detector output.

1709

detector_options_enabled_default =

1710

(

1711

## Specify what is added to detector files

1712

element detectors {

1713

(

1714

## This field is output at each detector location.

1715

element include_in_detectors {

1716

comment

1717

}|

1718

## This field is not output at detector locations.

1719

element exclude_from_detectors {

1720

comment

1721

}

1722

)

1723

}

1724

)

1725

1726

# Options for whether a field is to be included in detector output.

1727

detector_options_disabled_default =

1728

(

1729

## Specify what is added to detector files

1730

element detectors {

1731

(

1732

## This field is not output at detector locations.

1733

element exclude_from_detectors {

1734

comment

1735

}|

1736

## This field is output at each detector location.

1737

element include_in_detectors {

1738

comment

1739

}

1740

)

1741

}

1742

)

1743

1744

# Detector output defaults on for prognostic and diagnostic fields,

1745

# off for prescribed.

1746

prognostic_detector_options = detector_options_enabled_default

1747

diagnostic_detector_options = detector_options_enabled_default

1748

prescribed_detector_options = detector_options_disabled_default

1749

1750

adaptivity_preprocessing =

1751

## Occasionally, it is desirable to apply operations or filters

1752

## to fields before using them for the purposes of adaptivity.

1753

element preprocessing {

1754

(

1755

## Invert a helmholtz operator to smooth out the field

1756

## before using it to adapt. This can help with noisy

1757

## fields.

1758

element helmholtz_smoother {

1759

element smoothing_length_scale {

1760

real_dim_symmetric_tensor

1761

},

1762

element solver {

1763

linear_solver_options_sym

1764

}

1765

}

1766

)

1767

}?

1768

1769

generic_aliased_field =

1770

(

1771

attribute material_phase_name { xsd:string },

1772

attribute field_name { xsd:string }

1773

)

1774

1775

# Most common mesh choices

1776

mesh_choice =

1777

(

1778

element mesh {

1779

attribute name { xsd:string }

1780

}|

1781

element mesh {

1782

attribute name { "CoordinateMesh" }

1783

}|

1784

element mesh {

1785

attribute name { "VelocityMesh" }

1786

}|

1787

element mesh {

1788

attribute name { "PressureMesh" }

1789

}

1790

)

1791

1792

# Not really a choice, for fields that have to be on the velocity mesh

1793

# currently that's all scalar fields, except pressure

1794

# and of course velocity itself

1795

# If you want to implement scalar fields on other meshes, feel free to do so

1796

# but bare in mind you need to make sure the field stays outside RMEM.

1797

# Currently all scalar fields are packed in RMEM with length nonods

1798

velocity_mesh_choice =

1799

(

1800

(

1801

element mesh {

1802

attribute name { "VelocityMesh" }

1803

}|

1804

element mesh {

1805

attribute name { "PressureMesh" }

1806

}|

1807

element mesh {

1808

attribute name { "CoordinateMesh" }

1809

}|

1810

element mesh {

1811

attribute name { string }

1812

}

1813

)

1814

)

1815

1816

pressure_mesh_choice =

1817

(

1818

(

1819

element mesh {

1820

attribute name { "PressureMesh" }

1821

}|

1822

element mesh {

1823

attribute name { "VelocityMesh" }

1824

}|

1825

element mesh {

1826

attribute name { "CoordinateMesh" }

1827

}|

1828

element mesh {

1829

attribute name { string }

1830

}

1831

)

1832

)

1833

1834

# This is the choice of additional scalar field to be solved for

1835

scalar_field_choice =

1836

(

1837

# The first is a generic field, which may be used for any user-defined field

1838

# that FLUIDITY knows nothing about, or a generic diagnostic

1839

(

1840

element scalar_field {

1841

attribute rank { "0" },

1842

attribute name { xsd:string },

1843

## Field type

1844

(

1845

element prognostic {

1846

velocity_mesh_choice,

1847

prognostic_scalar_field

1848

}|

1849

element prescribed {

1850

velocity_mesh_choice,

1851

prescribed_scalar_field

1852

}|

1853

element diagnostic {

1854

scalar_diagnostic_algorithms,

1855

velocity_mesh_choice,

1856

diagnostic_scalar_field

1857

}|

1858

element aliased {

1859

generic_aliased_field

1860

}

1861

)

1862

}|

1863

## Prognostic scalar fields below this

1864

element ___Prognostic_Fields_Below___ {

1865

empty

1866

}|

1867

1868

# This is the long list of fields that FLUIDITY knows about

1869

# -- First is a list of fields that are primarily prognostic,

1870

# but can be set to prescribed, or aliased...

1871

# -- The list is in order of most frequently used.

1872

1873

## Salinity

1874

element scalar_field {

1875

attribute rank { "0" },

1876

attribute name { "Salinity" },

1877

attribute replaces { "IDENT = 42" },

1878

(

1879

element prognostic {

1880

velocity_mesh_choice,

1881

prognostic_scalar_field

1882

}|

1883

element prescribed {

1884

velocity_mesh_choice,

1885

prescribed_scalar_field

1886

}|

1887

element aliased {

1888

generic_aliased_field

1889

}

1890

)

1891

}|

1892

## Temperature

1893

element scalar_field {

1894

attribute rank { "0" },

1895

attribute name { "Temperature" },

1896

attribute replaces { "IDENT = -1" },

1897

(

1898

element prognostic {

1899

velocity_mesh_choice,

1900

prognostic_scalar_field

1901

}|

1902

element prescribed {

1903

velocity_mesh_choice,

1904

prescribed_scalar_field

1905

}|

1906

element aliased {

1907

generic_aliased_field

1908

}

1909

)

1910

}|

1911

## Background Temperature

1912

element scalar_field {

1913

attribute rank { "0" },

1914

attribute name { "BackgroundTemperature" },

1915

(

1916

element prescribed {

1917

velocity_mesh_choice,

1918

prescribed_scalar_field

1919

}

1920

)

1921

}|

1922

## Passive Tracer

1923

element scalar_field {

1924

attribute rank { "0" },

1925

attribute name { "Tracer" },

1926

attribute replaces { "IDENT = 666" },

1927

(

1928

element prognostic {

1929

velocity_mesh_choice,

1930

prognostic_scalar_field

1931

}|

1932

element prescribed {

1933

velocity_mesh_choice,

1934

prescribed_scalar_field

1935

}|

1936

element aliased {

1937

generic_aliased_field

1938

}

1939

)

1940

}|

1941

## Free Surface

1942

## NOTE: the prognostic FreeSurface field only works with the

1943

## legacy_continuous_galerkin code path

1944

## NOTE: if you are using the free_surface boundary condition

1945

## applied to the Velocity field (recommended), you should not

1946

## use the prognostic FreeSurface field. In this case you may

1947

## (optionally) add a diagnostic FreeSurface field.

1948

element scalar_field {

1949

attribute rank { "0" },

1950

attribute name { "FreeSurface" },

1951

(

1952

## Free Surface

1953

## NOTE: the prognostic FreeSurface field only works with the

1954

## legacy_continuous_galerkin code path

1955

element prognostic {

1956

## Note that this is not the quadratic mesh balance pressure is

1957

## actually calculated on, but the linear mesh it is projected back

1958

## on for output purposes.

1959

element mesh {

1960

attribute name { "VelocityMesh" }

1961

},

1962

prognostic_free_surface_field

1963

}|

1964

## Free Surface

1965

## NOTE: the diagnostic FreeSurface field only works in combination

1966

## with the free_surface boundary condition applied to the Velocity

1967

## field. It gives you a 3D field (constant over the vertical)

1968

## of the free surface elevation.

1969

element diagnostic {

1970

internal_algorithm,

1971

# this is hard-coded on the PressureMesh as long as the Pressure is

1972

# if this is no longer true, it should be option-checked to be on the

1973

# same mesh as Pressure

1974

## Must be on the same mesh as Pressure

1975

element mesh {

1976

attribute name { "PressureMesh" }

1977

},

1978

diagnostic_scalar_field

1979

}

1980

1981

)

1982

}|

1983

## Second Fluid

1984

element scalar_field {

1985

attribute rank { "0" },

1986

attribute name { "SecondFluid" },

1987

attribute replaces { "IDENT = 56" },

1988

(

1989

element prognostic {

1990

velocity_mesh_choice,

1991

prognostic_scalar_field

1992

}|

1993

element prescribed {

1994

velocity_mesh_choice,

1995

prescribed_scalar_field

1996

}|

1997

element aliased {

1998

generic_aliased_field

1999

}

2000

)

2001

}|

2002

## Diffuse Interface

2003

element scalar_field {

2004

attribute rank { "0" },

2005

attribute name { "DiffuseInterface" },

2006

attribute replaces { "IDENT = 57" },

2007

(

2008

element prognostic {

2009

velocity_mesh_choice,

2010

prognostic_scalar_field

2011

}|

2012

element prescribed {

2013

velocity_mesh_choice,

2014

prescribed_scalar_field

2015

}|

2016

element aliased {

2017

generic_aliased_field

2018

}

2019

)

2020

}|

2021

## If enabled, decomposes Pressure by solving for the balanced part of

2022

## Pressure using a "geopressure" solver:

2023

##

2024

## f = - grad p_gp + g

2025

##

2026

## By choosing an appropriate mesh (typically velocity mesh order + 1)

2027

## for the balanced part of pressure, physical balance can be

2028

## represented to a higher degree of accuracy.

2029

element scalar_field {

2030

attribute rank { "0" },

2031

attribute name { "GeostrophicPressure" },

2032

attribute replaces { "IDENT = -2003" },

2033

(

2034

element prognostic {

2035

## The GeostrophicPressure mesh

2036

##

2037

## WARNING: It is usual for this to be a higher degree

2038

## mesh than the velocity mesh

2039

element mesh {

2040

attribute name { xsd:string },

2041

comment

2042

},

2043

prognostic_geostrophic_pressure_field

2044

}

2045

)

2046

}|

2047

element scalar_field {

2048

attribute rank { "0" },

2049

attribute name { "VerticalBalancePressure" },

2050

(

2051

element prognostic {

2052

## This needs to be a quadratic DG mesh

2053

mesh_choice,

2054

prognostic_vertical_balance_pressure_field

2055

}

2056

)

2057

}|

2058

## MaterialVolumeFraction field:

2059

##

2060

## Volume fraction of this material.

2061

## Required in multimaterial simulations.

2062

## - if prognostic solves for the volume fraction

2063

## - if prescribed uses a specified volume fraction

2064

## - if diagnostic solves for the final material volume fraction

2065

## Only 1 diagnostic MaterialVolumeFraction field allowed per

2066

## simulation or solves for all the volume fractions based on

2067

## the SumMaterialVolumeFractions field.

2068

##

2069

## A diagnostic MaterialVolumeFraction field is currently required for

2070

## compressible multimaterial simulations (even if only 1 material).

2071

## Generally also requires a MaterialDensity field.

2072

element scalar_field {

2073

attribute rank { "0" },

2074

attribute name { "MaterialVolumeFraction" },

2075

(

2076

element prognostic {

2077

velocity_mesh_choice,

2078

prognostic_scalar_field,

2079

cap_option?,

2080

surface_tension_option?

2081

}|

2082

element diagnostic {

2083

internal_algorithm,

2084

velocity_mesh_choice,

2085

diagnostic_scalar_field,

2086

cap_option?

2087

}|

2088

element prescribed {

2089

velocity_mesh_choice,

2090

prescribed_scalar_field,

2091

cap_option?

2092

}|

2093

element aliased {

2094

generic_aliased_field

2095

}

2096

)

2097

}|

2098

## MaterialDensity field:

2099

##

2100

## Field for the density of this material.

2101

## Required in multimaterial simulations.

2102

## - prescribed if an incompressible simulation

2103

## - diagnostic if using a linear equation of state

2104

## - prognostic if a compressible simulation

2105

## (note that if you set a multimaterial

2106

## equation of state and this field is

2107

## prognostic then its initial condition

2108

## will be overwritten by the density that

2109

## satisfies the initial pressure and

2110

## the equation of state)

2111

element scalar_field {

2112

attribute rank { "0" },

2113

attribute name { "MaterialDensity" },

2114

(

2115

element prognostic {

2116

velocity_mesh_choice,

2117

prognostic_scalar_field

2118

}|

2119

element diagnostic {

2120

internal_algorithm,

2121

velocity_mesh_choice,

2122

diagnostic_scalar_field

2123

}|

2124

element prescribed {

2125

velocity_mesh_choice,

2126

prescribed_scalar_field

2127

}|

2128

element aliased {

2129

generic_aliased_field

2130

}

2131

)

2132

}|

2133

## MaterialInternalEnergy field:

2134

##

2135

## Field for the internal energy of this material.

2136

## Required in multimaterial compressible simulations

2137

## with full miegrunneisen (perfect gas) eos.

2138

element scalar_field {

2139

attribute rank { "0" },

2140

attribute name { "MaterialInternalEnergy" },

2141

(

2142

element prognostic {

2143

velocity_mesh_choice,

2144

prognostic_scalar_field

2145

}|

2146

element aliased {

2147

generic_aliased_field

2148

}

2149

)

2150

}|

2151

## SumMaterialVolumeFractions field:

2152

##

2153

## Sums the prognostic MaterialVolumeFraction fields.

2154

## - diagnostic: sums all the volume fractions in the other

2155

## material phases

2156

element scalar_field {

2157

attribute rank { "0" },

2158

attribute name { "SumMaterialVolumeFractions" },

2159

(

2160

element diagnostic {

2161

internal_algorithm,

2162

velocity_mesh_choice,

2163

diagnostic_scalar_field

2164

}|

2165

element aliased {

2166

generic_aliased_field

2167

}

2168

)

2169

}|

2170

## CopiedField - This field copies the previous timesteps

2171

## values from another (specified) field at every iteration

2172

## and then solves the field using different (again, specified)

2173

## scheme and solution options.

2174

## For instance, this field can be used to create a diffused

2175

## field to adapt to.

2176

## Unless someone requests otherwise this is only currently possible

2177

## for fields within the same material_phase.

2178

element scalar_field {

2179

attribute rank { "0" },

2180

attribute name { "CopiedField" },

2181

(

2182

element prognostic {

2183

velocity_mesh_choice,

2184

attribute copy_from_field { string },

2185

prognostic_scalar_field

2186

}

2187

)

2188

}|

2189

## Calculate the stream function of 2D incompressible flow. Note

2190

## that this *only* makes sense for proper 2D (not pseudo-2D) simulations.

2191

## Requires a continuous mesh.

2192

element scalar_field {

2193

attribute rank { "0" },

2194

attribute name { "StreamFunction" },

2195

(

2196

element prognostic {

2197

mesh_choice,

2198

prognostic_stream_function_field

2199

}

2200

)

2201

}|

2202

## Phytoplankton

2203

element scalar_field {

2204

attribute rank { "0" },

2205

attribute name { "Phytoplankton" },

2206

(

2207

element prognostic {

2208

velocity_mesh_choice,

2209

prognostic_scalar_field

2210

}|

2211

element prescribed {

2212

velocity_mesh_choice,

2213

prescribed_scalar_field

2214

}

2215

)

2216

}|

2217

## Zooplankton

2218

element scalar_field {

2219

attribute rank { "0" },

2220

attribute name { "Zooplankton" },

2221

(

2222

element prognostic {

2223

velocity_mesh_choice,

2224

prognostic_scalar_field

2225

}|

2226

element prescribed {

2227

velocity_mesh_choice,

2228

prescribed_scalar_field

2229

}

2230

)

2231

}|

2232

## Nutrient

2233

element scalar_field {

2234

attribute rank { "0" },

2235

attribute name { "Nutrient" },

2236

(

2237

element prognostic {

2238

velocity_mesh_choice,

2239

prognostic_scalar_field

2240

}|

2241

element prescribed {

2242

velocity_mesh_choice,

2243

prescribed_scalar_field

2244

}

2245

)

2246

}|

2247

## Detritus

2248

element scalar_field {

2249

attribute rank { "0" },

2250

attribute name { "Detritus" },

2251

(

2252

element prognostic {

2253

velocity_mesh_choice,

2254

prognostic_scalar_field

2255

}|

2256

element prescribed {

2257

velocity_mesh_choice,

2258

prescribed_scalar_field

2259

}

2260

)

2261

}|

2262

2263

## PhaseVolumeFraction:

2264

## Required in porous_media problem type

2265

element scalar_field {

2266

attribute rank { "0" },

2267

attribute name { "PhaseVolumeFraction" },

2268

(

2269

element prognostic {

2270

velocity_mesh_choice,

2271

prognostic_scalar_field

2272

}|

2273

element prescribed {

2274

velocity_mesh_choice,

2275

prescribed_scalar_field

2276

}

2277

)

2278

}|

2279

2280

## Electrical Potential:

2281

## Required in electrokinetic, electrothermal

2282

## and electrochemical problems

2283

## (sub-option of porous_media problem type)

2284

element scalar_field {

2285

attribute rank { "0" },

2286

attribute name { "ElectricalPotential" },

2287

(

2288

element prognostic {

2289

velocity_mesh_choice,

2290

prognostic_scalar_field

2291

}

2292

)

2293

}|

2294

2295

# Insert new prognostic scalar fields here using the template:

2296

# element scalar_field {

2297

# attribute rank { "0" },

2298

# attribute name { "NewFieldName" },

2299

# (

2300

# element prognostic {

2301

# velocity_mesh_choice,

2302

# prognostic_scalar_field

2303

# }|

2304

# element prescribed {

2305

# velocity_mesh_choice,

2306

# prescribed_scalar_field

2307

# }|

2308

# element aliased {

2309

# generic_aliased_field

2310

# }

2311

# )

2312

# }

2313

2314

# -- Second is a list of fields that are primarily prescribed,

2315

# but can be aliased. An example is wind velocity.

2316

# -- The list is in order of most frequently used.

2317

2318

## Prescribed scalar fields below this

2319

element ___Prescribed_fields_below___ {

2320

empty

2321

}|

2322

element scalar_field {

2323

attribute rank { "0" },

2324

attribute name { "DistanceToSideBoundaries" },

2325

attribute replaces { "IDENT = -144" },

2326

(

2327

element prescribed {

2328

velocity_mesh_choice,

2329

prescribed_scalar_field

2330

}|

2331

element aliased {

2332

generic_aliased_field

2333

}

2334

)

2335

}|

2336

## MaterialFrictionAngle for multimaterial

2337

## plasticity problems

2338

##

2339

## Requires a diagnostic bulk FrictionAngle field

2340

## - not tested yet

2341

element scalar_field {

2342

attribute rank { "0" },

2343

attribute name { "MaterialFrictionAngle" },

2344

(

2345

element prescribed {

2346

velocity_mesh_choice,

2347

prescribed_scalar_field

2348

}|

2349

element aliased {

2350

generic_aliased_field

2351

}

2352

)

2353

}|

2354

## MaterialCohesion for multimaterial

2355

## plasticity problems

2356

##

2357

## Requires a diagnostic bulk Cohesion field

2358

## - not tested yet

2359

element scalar_field {

2360

attribute rank { "0" },

2361

attribute name { "MaterialCohesion" },

2362

(

2363

element prescribed {

2364

velocity_mesh_choice,

2365

prescribed_scalar_field

2366

}|

2367

element aliased {

2368

generic_aliased_field

2369

}

2370

)

2371

}|

2372

#

2373

# Insert new prescribed scalar fields here using the template:

2374

# element scalar_field {

2375

# attribute rank { "0" },

2376

# attribute name { "NewFieldName" },

2377

# (

2378

# element prescribed {

2379

# velocity_mesh_choice,

2380

# prescribed_scalar_field

2381

# }|

2382

# element aliased {

2383

# generic_aliased_field

2384

# }

2385

# )

2386

# }

2387

#

2388

# -- Last is a list of fields that are primarily diagnostic,

2389

# but can be aliased. An example is Tidal Range.

2390

# -- The list is in order of most frequently used.

2391

#

2392

## Diagnostic scalar fields below this

2393

element ___Diagnostic_Fields_Below___ {

2394

empty

2395

}|

2396

element scalar_field {

2397

attribute rank { "0" },

2398

attribute name { "PerturbationDensity" },

2399

attribute replaces { "IDENT = -143" },

2400

(

2401

element diagnostic {

2402

internal_algorithm,

2403

velocity_mesh_choice,

2404

diagnostic_scalar_field

2405

}|

2406

element aliased {

2407

generic_aliased_field

2408

}

2409

)

2410

}|

2411

## ControlVolumeDivergence:

2412

##

2413

## div field

2414

##

2415

## Divergence of the velocity field where

2416

## the divergence operator is defined using

2417

## the control volume C^T matrix.

2418

## This assumes that the test space is discontinuous

2419

## control volumes.

2420

element scalar_field {

2421

attribute rank { "0" },

2422

attribute name { "ControlVolumeDivergence" },

2423

(

2424

element diagnostic {

2425

internal_algorithm,

2426

attribute field_name { string },

2427

velocity_mesh_choice,

2428

diagnostic_cv_divergence_scalar_field

2429

}|

2430

element aliased {

2431

generic_aliased_field

2432

}

2433

)

2434

}|

2435

## Diffusive dissipation

2436

element scalar_field {

2437

attribute rank { "0" },

2438

attribute name { "DiffusiveDissipation" },

2439

(

2440

element diagnostic {

2441

internal_algorithm,

2442

velocity_mesh_choice,

2443

diagnostic_scalar_field

2444

}|

2445

element aliased {

2446

generic_aliased_field

2447

}

2448

)

2449

}|

2450

## Viscous dissipation

2451

element scalar_field {

2452

attribute rank { "0" },

2453

attribute name { "ViscousDissipation" },

2454

(

2455

element diagnostic {

2456

internal_algorithm,

2457

velocity_mesh_choice,

2458

diagnostic_scalar_field

2459

}|

2460

element aliased {

2461

generic_aliased_field

2462

}

2463

)

2464

}|

2465

## Richardson Number:

2466

##

2467

## Ri = \frac{N^2}{(\frac{\partial u}{\partial z})^2 + (\frac{\partial u}{\partial z})^2}

2468

## with

2469

## N^2 = -\frac{g}{\rho_0}\frac{\partial \rho}{\partial z}

2470

##

2471

## Limitations:

2472

## - Gravity must be constant.

2473

## - Assumes gravity is in -ve final coordinate direction.

2474

element scalar_field {

2475

attribute rank { "0" },

2476

attribute name { "RichardsonNumber" },

2477

attribute depends { "Velocity,PerturbationDensity" },

2478

(

2479

element diagnostic {

2480

internal_algorithm,

2481

velocity_mesh_choice,

2482

diagnostic_richardson_number_field

2483

}|

2484

element aliased {

2485

generic_aliased_field

2486

}

2487

)

2488

}|

2489

## CFLNumber

2490

##

2491

## See http://amcg.ese.ic.ac.uk/index.php?title=Local:Diagnostics#CFL_Number

2492

##

2493

## Adapting to this field is not recommended

2494

element scalar_field {

2495

attribute rank { "0" },

2496

attribute name { "CFLNumber" },

2497

attribute replaces { "IDENT = -601" },

2498

(

2499

element diagnostic {

2500

internal_algorithm,

2501

velocity_mesh_choice,

2502

diagnostic_scalar_field

2503

}|

2504

element aliased {

2505

generic_aliased_field

2506

}

2507

)

2508

}|

2509

## ControlVolumeCFLNumber

2510

##

2511

## Courant Number as defined on a control volume mesh

2512

##

2513

## Adapting to this field is not recommended

2514

element scalar_field {

2515

attribute rank { "0" },

2516

attribute name { "ControlVolumeCFLNumber" },

2517

(

2518

element diagnostic {

2519

internal_algorithm,

2520

velocity_mesh_choice,

2521

diagnostic_scalar_field

2522

}|

2523

element aliased {

2524

generic_aliased_field

2525

}

2526

)

2527

}|

2528

## DG_CourantNumber

2529

##

2530

## Courant Number as defined on a DG mesh

2531

##

2532

## Adapting to this field is not recommended

2533

element scalar_field {

2534

attribute rank { "0" },

2535

attribute name { "DG_CourantNumber" },

2536

(

2537

element diagnostic {

2538

internal_algorithm,

2539

velocity_mesh_choice,

2540

diagnostic_scalar_field

2541

}|

2542

element aliased {

2543

generic_aliased_field

2544

}

2545

)

2546

}|

2547

## CVMaterialDensityCFLNumber

2548

##

2549

## Courant Number as defined on a control volume mesh and

2550

## incorporating the MaterialDensity.

2551

## Requires a MaterialDensity field!

2552

##

2553

## Adapting to this field is not recommended

2554

element scalar_field {

2555

attribute rank { "0" },

2556

attribute name { "CVMaterialDensityCFLNumber" },

2557

(

2558

element diagnostic {

2559

internal_algorithm,

2560

velocity_mesh_choice,

2561

diagnostic_scalar_field

2562

}|

2563

element aliased {

2564

generic_aliased_field

2565

}

2566

)

2567

}|

2568

element scalar_field {

2569

attribute rank { "0" },

2570

attribute name { "SolidConcentration" },

2571

(

2572

element diagnostic {

2573

internal_algorithm,

2574

velocity_mesh_choice,

2575

diagnostic_scalar_field

2576

}|

2577

element aliased {

2578

generic_aliased_field

2579

}

2580

)

2581

}|

2582

## This scalar field is meant to replace DENTRAF.

2583

## Basically, if you use new options, DENTRAF is no longer needed

2584

## No repointing is done from this field to DENTRAF.

2585

element scalar_field {

2586

attribute rank { "0" },

2587

attribute name { "CopyofDensity" },

2588

attribute replaces { "DENTRAF" },

2589

(

2590

element diagnostic {

2591

internal_algorithm,

2592

velocity_mesh_choice,

2593

diagnostic_scalar_field

2594

}

2595

)

2596

}|

2597

## Add field to be used by Solid_configuration to

2598

## Visualize the solids and MaterialVolumeFraction together

2599

element scalar_field {

2600

attribute rank { "0" },

2601

attribute name { "VisualizeSolidFluid" },

2602

(

2603

element diagnostic {

2604

internal_algorithm,

2605

velocity_mesh_choice,

2606

diagnostic_scalar_field

2607

}

2608

)

2609

}|

2610

## Add field to be used by Solid_configuration to

2611

## Visualize the solid_Concentration

2612

element scalar_field {

2613

attribute rank { "0" },

2614

attribute name { "VisualizeSolid" },

2615

(

2616

element diagnostic {

2617

internal_algorithm,

2618

velocity_mesh_choice,

2619

diagnostic_scalar_field

2620

}

2621

)

2622

}|

2623

## Add field to be used by Solid_configuration to

2624

## map the solid_Concentration from particle mesh to

2625

## the fluid mesh.

2626

element scalar_field {

2627

attribute rank { "0" },

2628

attribute name { "ParticleScalar" },

2629

(

2630

element diagnostic {

2631

internal_algorithm,

2632

mesh_choice,

2633

diagnostic_scalar_field

2634

}

2635

)

2636

}|

2637

## Add field to be used by Explicit_ALE to

2638

## visualize functional values before iterations start.

2639

element scalar_field {

2640

attribute rank { "0" },

2641

attribute name { "FunctionalBegin" },

2642

(

2643

element diagnostic {

2644

internal_algorithm,

2645

mesh_choice,

2646

diagnostic_scalar_field

2647

}

2648

)

2649

}|

2650

## Add field to be used by Explicit_ALE to

2651

## visualize functional values at each iteration.

2652

element scalar_field {

2653

attribute rank { "0" },

2654

attribute name { "FunctionalIter" },

2655

(

2656

element diagnostic {

2657

internal_algorithm,

2658

mesh_choice,

2659

diagnostic_scalar_field

2660

}

2661

)

2662

}|

2663

## add a MaterialVolume scalar_field to calculate the spatially varying

2664

## volume of a material (requires a MaterialVolumeFraction)

2665

element scalar_field {

2666

attribute rank { "0" },

2667

attribute name { "MaterialVolume" },

2668

(

2669

element diagnostic {

2670

internal_algorithm,

2671

velocity_mesh_choice,

2672

diagnostic_scalar_field

2673

}|

2674

element aliased {

2675

generic_aliased_field

2676

}

2677

)

2678

}|

2679

## add a MaterialMass scalar_field to calculate the spatially varying

2680

## mass of a material (requires a MaterialVolumeFraction and a MaterialDensity)

2681

element scalar_field {

2682

attribute rank { "0" },

2683

attribute name { "MaterialMass" },

2684

(

2685

element diagnostic {

2686

internal_algorithm,

2687

velocity_mesh_choice,

2688

diagnostic_scalar_field

2689

}|

2690

element aliased {

2691

generic_aliased_field

2692

}

2693

)

2694

}|

2695

## Calculates the MaterialDensity based on the bulk Pressure

2696

## (and MaterialInternalEnergy if appropriate) for the equation

2697

## of state of this material.

2698

element scalar_field {

2699

attribute rank { "0" },

2700

attribute name { "MaterialEOSDensity" },

2701

(

2702

element diagnostic {

2703

internal_algorithm,

2704

velocity_mesh_choice,

2705

diagnostic_scalar_field

2706

}|

2707

element aliased {

2708

generic_aliased_field

2709

}

2710

)

2711

}|

2712

## Calculates the MaterialPressure based on the MaterialDensity

2713

## (and MaterialInternalEnergy if appropriate) for the equation

2714

## of state of this material.

2715

element scalar_field {

2716

attribute rank { "0" },

2717

attribute name { "MaterialPressure" },

2718

(

2719

element diagnostic {

2720

internal_algorithm,

2721

velocity_mesh_choice,

2722

diagnostic_scalar_field

2723

}|

2724

element aliased {

2725

generic_aliased_field

2726

}

2727

)

2728

}|

2729

## Calculates the BulkMaterialPressure based on the MaterialDensity

2730

## and MaterialVolumeFraction (and MaterialInternalEnergy if appropriate)

2731

## for the equation of state of all materials.

2732

element scalar_field {

2733

attribute rank { "0" },

2734

attribute name { "BulkMaterialPressure" },

2735

(

2736

element diagnostic {

2737

internal_algorithm,

2738

velocity_mesh_choice,

2739

diagnostic_scalar_field

2740

}|

2741

element aliased {

2742

generic_aliased_field

2743

}

2744

)

2745

}|

2746

## Grid Reynolds number

2747

element scalar_field {

2748

attribute rank { "0" },

2749

attribute name { "GridReynoldsNumber" },

2750

(element diagnostic {

2751

internal_algorithm,

2752

element mesh {

2753

attribute name { "VelocityMesh" }

2754

},

2755

diagnostic_scalar_field

2756

}

2757

| element aliased { generic_aliased_field })

2758

}|

2759

## GridPecletNumber

2760

##

2761

## Peclet Number Pe = U*dx/2*diffusivity

2762

##

2763

## Also see the test case 'grid_peclet_number'

2764

## if you wish to see the effect of changing the

2765

## diffusivity on a 1D, cg-discretised tracer-field

2766

##

2767

## Adapting to this field is not recommended

2768

element scalar_field {

2769

attribute rank { "0" },

2770

attribute name { "GridPecletNumber" },

2771

(

2772

element diagnostic {

2773

internal_algorithm,

2774

## Mesh on which to calculate dx

2775

mesh_choice,

2776

## This is the name of the scalar field

2777

## to calculate the Peclet number for

2778

## Note this field needs to have a diffusivity

2779

element field_name { string },

2780

diagnostic_scalar_field

2781

}|

2782

element aliased {

2783

generic_aliased_field

2784

}

2785

)

2786

}|

2787

## Horizontal velocity divergence:

2788

##

2789

## div_H velocity

2790

##

2791

## Uses the gravity field direction to determine the horizontal plane.

2792

element scalar_field {

2793

attribute rank { "0" },

2794

attribute name { "HorizontalVelocityDivergence" },

2795

(

2796

element diagnostic {

2797

internal_algorithm,

2798

velocity_mesh_choice,

2799

diagnostic_scalar_field

2800

}|

2801

element aliased {

2802

generic_aliased_field

2803

}

2804

)

2805

}|

2806

2807

## Velocity divergence:

2808

##

2809

## div velocity

2810

##

2811

element scalar_field {

2812

attribute rank { "0" },

2813

attribute name { "VelocityDivergence" },

2814

(

2815

element diagnostic {

2816

internal_algorithm,

2817

velocity_mesh_choice,

2818

diagnostic_scalar_field

2819

}|

2820

element aliased {

2821

generic_aliased_field

2822

}

2823

)

2824

}|

2825

2826

## Vorticity for a 2D field:

2827

##

2828

## du dv

2829

## -- - --

2830

## dy dx

2831

element scalar_field {

2832

attribute rank { "0" },

2833

attribute name { "Vorticity2D" },

2834

(

2835

element diagnostic {

2836

internal_algorithm,

2837

mesh_choice,

2838

diagnostic_scalar_field

2839

}|

2840

element aliased {

2841

generic_aliased_field

2842

}

2843

)

2844

}|

2845

2846

## Kinetic energy density:

2847

##

2848

## 1/2 rho_0*|u|^2

2849

##

2850

## where rho_0 is the (reference) density

2851

##

2852

## Limitations:

2853

## - The Density, PerturbationDensity, KineticEnergyDensity and Velocity fields must be on the same mesh.

2854

element scalar_field {

2855

attribute rank { "0" },

2856

attribute name { "KineticEnergyDensity" },

2857

(

2858

element diagnostic {

2859

internal_algorithm,

2860

velocity_mesh_choice,

2861

diagnostic_scalar_field

2862

}|

2863

element aliased {

2864

generic_aliased_field

2865

}

2866

)

2867

}|

2868

2869

## Gravitational potential energy density:

2870

##

2871

## rho_0*(1.0 + rho')*(g dot (r - r_0))

2872

##

2873

## where rho_0 is the (reference) density, rho' is the perturbation density and r_0 is the potential energy zero point.

2874

##

2875

## Limitations:

2876

## - Requires a constant gravity direction.

2877

## - The Density, PerturbationDensity and GravitationalPotentialEnergyDensity fields must be on the same mesh.

2878

element scalar_field {

2879

attribute rank { "0" },

2880

attribute name { "GravitationalPotentialEnergyDensity" },

2881

(

2882

element diagnostic {

2883

internal_algorithm,

2884

velocity_mesh_choice,

2885

diagnostic_scalar_field,

2886

## Coordinate of a point with a potential energy of zero.

2887

element zero_point {

2888

real_dim_vector

2889

}

2890

}|

2891

element aliased {

2892

generic_aliased_field

2893

}

2894

)

2895

}|

2896

## Isopycnal coordinate

2897

##

2898

## z_star(x,t) = 1/A int_V' H(rho(x',t)-rho(x,t)) dV'

2899

##

2900

## where rho is the density, A is the width/area of the domain

2901

##

2902

## Limitations:

2903

## - You need to specify a (fine) mesh to redistribute the PerturbationDensity onto

2904

## - Requires a constant gravity direction.

2905

## - The Density, PerturbationDensity and GravitationalPotentialEnergyDensity fields must be on the same mesh.

2906

element scalar_field {

2907

attribute rank { "0" },

2908

attribute name { "IsopycnalCoordinate" },

2909

(

2910

element diagnostic {

2911

internal_algorithm,

2912

velocity_mesh_choice,

2913

## This is the mesh onto which we redistribute the PerturbationDensity

2914

element fine_mesh {

2915

attribute name { string }

2916

},

2917

diagnostic_scalar_field

2918

}|

2919

element aliased {

2920

generic_aliased_field

2921

}

2922

)

2923

}|

2924

## Background potential energy density:

2925

##

2926

## PE_b = rho*z_star

2927

##

2928

## where rho is the density, z_star is the isopycnal coordinate

2929

##

2930

## Limitations:

2931

## - Requires a constant gravity direction.

2932

## - The Density, PerturbationDensity and

2933

## GravitationalPotentialEnergyDensity fields must be on the

2934

## same mesh.

2935

element scalar_field {

2936

attribute rank { "0" },

2937

attribute name { "BackgroundPotentialEnergyDensity" },

2938

(

2939

element diagnostic {

2940

internal_algorithm,

2941

velocity_mesh_choice,

2942

diagnostic_scalar_field

2943

}|

2944

element aliased {

2945

generic_aliased_field

2946

}

2947

)

2948

}|

2949

2950

## Ertel potential vorticity:

2951

##

2952

## (f + curl u) dot grad rho'

2953

##

2954

## Limitations:

2955

## - Requires a geometry dimension of 3.

2956

element scalar_field {

2957

attribute rank { "0" },

2958

attribute name { "PotentialVorticity" },

2959

attribute depends { "Velocity,PerturbationDensity" },

2960

(

2961

element diagnostic {

2962

internal_algorithm,

2963

velocity_mesh_choice,

2964

diagnostic_scalar_field

2965

}|

2966

element aliased {

2967

generic_aliased_field

2968

}

2969

)

2970

}|

2971

## Relative potential vorticity:

2972

##

2973

## curl u dot grad rho'

2974

element scalar_field {

2975

attribute rank { "0" },

2976

attribute name { "RelativePotentialVorticity" },

2977

attribute depends { "Velocity,PerturbationDensity" },

2978

(

2979

element diagnostic {

2980

internal_algorithm,

2981

velocity_mesh_choice,

2982

diagnostic_scalar_field

2983

}|

2984

element aliased {

2985

generic_aliased_field

2986

}

2987

)

2988

}|

2989

## Local average mesh edge lengths

2990

element scalar_field {

2991

attribute rank { "0" },

2992

attribute name { "MeshEdgeLengths" },

2993

(

2994

element diagnostic {

2995

internal_algorithm,

2996

element mesh {

2997

attribute name { "CoordinateMesh" }

2998

},

2999

diagnostic_scalar_field

3000

}|

3001

element aliased {

3002

generic_aliased_field

3003

}

3004

)

3005

}|

3006

## Calculate the horizontal stream function psi where:

3007

## \partial_x \psi = -v

3008

## \partial_y \psi = u

3009

## where u and v are perpendicular to the gravity direction. Applies a

3010

## strong Dirichlet boundary condition of 0 on all boundaries.

3011

element scalar_field {

3012

attribute rank { "0" },

3013

attribute name { "HorizontalStreamFunction" },

3014

attribute depends { "Velocity" },

3015

(

3016

element diagnostic {

3017

internal_algorithm,

3018

velocity_mesh_choice,

3019

## Solver

3020

element solver {

3021

linear_solver_options_sym

3022

},

3023

diagnostic_scalar_field

3024

}|

3025

element aliased {

3026

generic_aliased_field

3027

}

3028

)

3029

}|

3030

## Speed:

3031

##

3032

## |u|

3033

##

3034

## Limitations:

3035

## - The Speed and Velocity fields must be on the same mesh.

3036

element scalar_field {

3037

attribute rank { "0" },

3038

attribute name { "Speed" },

3039

(

3040

element diagnostic {

3041

internal_algorithm,

3042

velocity_mesh_choice,

3043

diagnostic_scalar_field

3044

}|

3045

element aliased {

3046

generic_aliased_field

3047

}

3048

)

3049

}|

3050

3051

## Volume of the vehicles

3052

##

3053

## used in Traffic Modelling

3054

element scalar_field {

3055

attribute rank { "0" },

3056

attribute name { "SolidPhase" },

3057

attribute raplaces { "IDENT = -42"},

3058

(

3059

element diagnostic {

3060

internal_algorithm,

3061

velocity_mesh_choice,

3062

diagnostic_scalar_field

3063

}|

3064

element aliased {

3065

generic_aliased_field

3066

}

3067

)

3068

}|

3069

## Absolute Difference between two scalar fields.

3070

##

3071

## Both fields must be in this material_phase.

3072

## Assumes both fields are on the same mesh as the AbsoluteDifference field.

3073

element scalar_field {

3074

attribute rank { "0" },

3075

attribute name { "AbsoluteDifference" },

3076

(

3077

element diagnostic {

3078

internal_algorithm,

3079

attribute field_name_a { string },

3080

attribute field_name_b { string },

3081

mesh_choice,

3082

diagnostic_scalar_field,

3083

## Evaluate the absolute difference once the average difference has been removed?

3084

element relative_to_average {

3085

empty

3086

}?,

3087

## Ignore boundary nodes (i.e. zero them when calculating the difference)

3088

element ignore_boundaries {

3089

empty

3090

}?

3091

}|

3092

element aliased {

3093

generic_aliased_field

3094

}

3095

)

3096

}|

3097

3098

## Absolute Difference between two scalar fields.

3099

##

3100

## Both fields must be in this material_phase.

3101

## Assumes both fields are on the same mesh as the AbsoluteDifference field.

3102

element scalar_field {

3103

attribute rank { "0" },

3104

attribute name { "ScalarAbsoluteDifference" },

3105

(

3106

element diagnostic {

3107

internal_algorithm,

3108

attribute field_name_a { string },

3109

attribute field_name_b { string },

3110

mesh_choice,

3111

diagnostic_scalar_field,

3112

## Evaluate the absolute difference once the average difference has been removed?

3113

element relative_to_average {

3114

empty

3115

}?,

3116

## Ignore boundary nodes (i.e. zero them when calculating the difference)

3117

element ignore_boundaries {

3118

empty

3119

}?

3120

}|

3121

element aliased {

3122

generic_aliased_field

3123

}

3124

)

3125

}|

3126

## Galerkin projection of one field onto another mesh.

3127

##

3128

## The field must be in this material_phase.

3129

##

3130

## NOTE: you need the solver options if the mesh

3131

## of this field is continuous.

3132

element scalar_field {

3133

attribute rank { "0" },

3134

attribute name { "GalerkinProjection" },

3135

(

3136

element diagnostic {

3137

internal_algorithm,

3138

element source_field_name { string },

3139

mesh_choice,

3140

## Lump the mass matrix of the galerkin projection

3141

## less accurate but faster and might give smoother result.

3142

element lump_mass {

3143

empty

3144

}?,

3145

element solver {

3146

linear_solver_options_sym

3147

}?,

3148

diagnostic_scalar_field

3149

}|

3150

element aliased {

3151

generic_aliased_field

3152

}

3153

)

3154

}|

3155

## Primary production of Phytoplankton. This is calculated by

3156

## the ocean biology module and will not be calculated unless

3157

## ocean biology is being simulated.

3158

element scalar_field {

3159

attribute rank { "0" },

3160

attribute name { "PrimaryProduction" },

3161

(

3162

element diagnostic {

3163

internal_algorithm,

3164

velocity_mesh_choice,

3165

diagnostic_scalar_field

3166

}|

3167

element aliased {

3168

generic_aliased_field

3169

}

3170

)

3171

}|

3172

## Grazing of Phytoplankton by Zooplankton. This is calculated by

3173

## the ocean biology module and will not be calculated unless

3174

## ocean biology is being simulated.

3175

element scalar_field {

3176

attribute rank { "0" },

3177

attribute name { "PhytoplanktonGrazing" },

3178

(

3179

element diagnostic {

3180

internal_algorithm,

3181

velocity_mesh_choice,

3182

diagnostic_scalar_field

3183

}|

3184

element aliased {

3185

generic_aliased_field

3186

}

3187

)

3188

3189

}|

3190

element scalar_field {

3191

attribute rank { "0" },

3192

attribute name { "TidalRange" },

3193

attribute replaces { "IDENT = -32" },

3194

(

3195

element diagnostic {

3196

internal_algorithm,

3197

velocity_mesh_choice,

3198

diagnostic_scalar_field_tidal_range

3199

}|

3200

element aliased {

3201

generic_aliased_field

3202

}

3203

)

3204

}|

3205

element scalar_field {

3206

attribute rank { "0" },

3207

attribute name { "MaxFreeSurface" },

3208

attribute replaces { "IDENT = -33" },

3209

(

3210

element diagnostic {

3211

internal_algorithm,

3212

velocity_mesh_choice,

3213

diagnostic_scalar_field

3214

}|

3215

element aliased {

3216

generic_aliased_field

3217

}

3218

)

3219

}|

3220

element scalar_field {

3221

attribute rank { "0" },

3222

attribute name { "MinFreeSurface" },

3223

attribute replaces { "IDENT = -34" },

3224

(

3225

element diagnostic {

3226

internal_algorithm,

3227

velocity_mesh_choice,

3228

diagnostic_scalar_field

3229

}|

3230

element aliased {

3231

generic_aliased_field

3232

}

3233

)

3234

}|

3235

element scalar_field {

3236

attribute rank { "0" },

3237

attribute name { "HarmonicAmplitudeM2" },

3238

(

3239

element diagnostic {

3240

internal_algorithm,

3241

velocity_mesh_choice,

3242

diagnostic_scalar_field

3243

}|

3244

element aliased {

3245

generic_aliased_field

3246

}

3247

)

3248

}|

3249

element scalar_field {

3250

attribute rank { "0" },

3251

attribute name { "HarmonicPhaseM2" },

3252

(

3253

element diagnostic {

3254

internal_algorithm,

3255

velocity_mesh_choice,

3256

diagnostic_scalar_field

3257

}|

3258

element aliased {

3259

generic_aliased_field

3260

}

3261

)

3262

}|

3263

element scalar_field {

3264

attribute rank { "0" },

3265

attribute name { "HarmonicAmplitudeS2" },

3266

(

3267

element diagnostic {

3268

internal_algorithm,

3269

velocity_mesh_choice,

3270

diagnostic_scalar_field

3271

}|

3272

element aliased {

3273

generic_aliased_field

3274

}

3275

)

3276

}|

3277

element scalar_field {

3278

attribute rank { "0" },

3279

attribute name { "HarmonicPhaseS2" },

3280

(

3281

element diagnostic {

3282

internal_algorithm,

3283

velocity_mesh_choice,

3284

diagnostic_scalar_field

3285

}|

3286

element aliased {

3287

generic_aliased_field

3288

}

3289

)

3290

}|

3291

element scalar_field {

3292

attribute rank { "0" },

3293

attribute name { "HarmonicAmplitudeN2" },

3294

(

3295

element diagnostic {

3296

internal_algorithm,

3297

velocity_mesh_choice,

3298

diagnostic_scalar_field

3299

}|

3300

element aliased {

3301

generic_aliased_field

3302

}

3303

)

3304

}|

3305

element scalar_field {

3306

attribute rank { "0" },

3307

attribute name { "HarmonicPhaseN2" },

3308

(

3309

element diagnostic {

3310

internal_algorithm,

3311

velocity_mesh_choice,

3312

diagnostic_scalar_field

3313

}|

3314

element aliased {

3315

generic_aliased_field

3316

}

3317

)

3318

}|

3319

element scalar_field {

3320

attribute rank { "0" },

3321

attribute name { "HarmonicAmplitudeK2" },

3322

(

3323

element diagnostic {

3324

internal_algorithm,

3325

velocity_mesh_choice,

3326

diagnostic_scalar_field

3327

}|

3328

element aliased {

3329

generic_aliased_field

3330

}

3331

)

3332

}|

3333

element scalar_field {

3334

attribute rank { "0" },

3335

attribute name { "HarmonicPhaseK2" },

3336

(

3337

element diagnostic {

3338

internal_algorithm,

3339

velocity_mesh_choice,

3340

diagnostic_scalar_field

3341

}|

3342

element aliased {

3343

generic_aliased_field

3344

}

3345

)

3346

}|

3347

element scalar_field {

3348

attribute rank { "0" },

3349

attribute name { "HarmonicAmplitudeK1" },

3350

(

3351

element diagnostic {

3352

internal_algorithm,

3353

velocity_mesh_choice,

3354

diagnostic_scalar_field

3355

}|

3356

element aliased {

3357

generic_aliased_field

3358

}

3359

)

3360

}|

3361

element scalar_field {

3362

attribute rank { "0" },

3363

attribute name { "HarmonicPhaseK1" },

3364

(

3365

element diagnostic {

3366

internal_algorithm,

3367

velocity_mesh_choice,

3368

diagnostic_scalar_field

3369

}|

3370

element aliased {

3371

generic_aliased_field

3372

}

3373

)

3374

}|

3375

element scalar_field {

3376

attribute rank { "0" },

3377

attribute name { "HarmonicAmplitudeO1" },

3378

(

3379

element diagnostic {

3380

internal_algorithm,

3381

velocity_mesh_choice,

3382

diagnostic_scalar_field

3383

}|

3384

element aliased {

3385

generic_aliased_field

3386

}

3387

)

3388

}|

3389

element scalar_field {

3390

attribute rank { "0" },

3391

attribute name { "HarmonicPhaseO1" },

3392

(

3393

element diagnostic {

3394

internal_algorithm,

3395

velocity_mesh_choice,

3396

diagnostic_scalar_field

3397

}|

3398

element aliased {

3399

generic_aliased_field

3400

}

3401

)

3402

}|

3403

element scalar_field {

3404

attribute rank { "0" },

3405

attribute name { "HarmonicAmplitudeP1" },

3406

(

3407

element diagnostic {

3408

internal_algorithm,

3409

velocity_mesh_choice,

3410

diagnostic_scalar_field

3411

}|

3412

element aliased {

3413

generic_aliased_field

3414

}

3415

)

3416

}|

3417

element scalar_field {

3418

attribute rank { "0" },

3419

attribute name { "HarmonicPhaseP1" },

3420

(

3421

element diagnostic {

3422

internal_algorithm,

3423

velocity_mesh_choice,

3424

diagnostic_scalar_field

3425

}|

3426

element aliased {

3427

generic_aliased_field

3428

}

3429

)

3430

}|

3431

element scalar_field {

3432

attribute rank { "0" },

3433

attribute name { "HarmonicAmplitudeQ1" },

3434

(

3435

element diagnostic {

3436

internal_algorithm,

3437

velocity_mesh_choice,

3438

diagnostic_scalar_field

3439

}|

3440

element aliased {

3441

generic_aliased_field

3442

}

3443

)

3444

}|

3445

element scalar_field {

3446

attribute rank { "0" },

3447

attribute name { "HarmonicPhaseQ1" },

3448

(

3449

element diagnostic {

3450

internal_algorithm,

3451

velocity_mesh_choice,

3452

diagnostic_scalar_field

3453

}|

3454

element aliased {

3455

generic_aliased_field

3456

}

3457

)

3458

}|

3459

element scalar_field {

3460

attribute rank { "0" },

3461

attribute name { "HarmonicAmplitudeMf" },

3462

(

3463

element diagnostic {

3464

internal_algorithm,

3465

velocity_mesh_choice,

3466

diagnostic_scalar_field

3467

}|

3468

element aliased {

3469

generic_aliased_field

3470

}

3471

)

3472

}|

3473

element scalar_field {

3474

attribute rank { "0" },

3475

attribute name { "HarmonicPhaseMf" },

3476

(

3477

element diagnostic {

3478

internal_algorithm,

3479

velocity_mesh_choice,

3480

diagnostic_scalar_field

3481

}|

3482

element aliased {

3483

generic_aliased_field

3484

}

3485

)

3486

}|

3487

element scalar_field {

3488

attribute rank { "0" },

3489

attribute name { "HarmonicAmplitudeMm" },

3490

(

3491

element diagnostic {

3492

internal_algorithm,

3493

velocity_mesh_choice,

3494

diagnostic_scalar_field

3495

}|

3496

element aliased {

3497

generic_aliased_field

3498

}

3499

)

3500

}|

3501

element scalar_field {

3502

attribute rank { "0" },

3503

attribute name { "HarmonicPhaseMm" },

3504

(

3505

element diagnostic {

3506

internal_algorithm,

3507

velocity_mesh_choice,

3508

diagnostic_scalar_field

3509

}|

3510

element aliased {

3511

generic_aliased_field

3512

}

3513

)

3514

}|

3515

element scalar_field {

3516

attribute rank { "0" },

3517

attribute name { "HarmonicAmplitudeSSa" },

3518

(

3519

element diagnostic {

3520

internal_algorithm,

3521

velocity_mesh_choice,

3522

diagnostic_scalar_field

3523

}|

3524

element aliased {

3525

generic_aliased_field

3526

}

3527

)

3528

}|

3529

## Output the universal numbering of the mesh on which this field is based.

3530

element scalar_field {

3531

attribute rank { "0" },

3532

attribute name { "UniversalNumber" },

3533

(

3534

element diagnostic {

3535

internal_algorithm,

3536

mesh_choice,

3537

diagnostic_scalar_field

3538

}|

3539

element aliased {

3540

generic_aliased_field

3541

}

3542

)

3543

}|

3544

## Output the processors which own the nodes of the mesh on which this field is based.

3545

element scalar_field {

3546

attribute rank { "0" },

3547

attribute name { "NodeOwner" },

3548

(

3549

element diagnostic {

3550

internal_algorithm,

3551

mesh_choice,

3552

diagnostic_scalar_field

3553

}|

3554

element aliased {

3555

generic_aliased_field

3556

}

3557

)

3558

}|

3559

## Output the processors which own the elements of the mesh on which this field is based.

3560

element scalar_field {

3561

attribute rank { "0" },

3562

attribute name { "ElementOwner" },

3563

(

3564

element diagnostic {

3565

internal_algorithm,

3566

mesh_choice,

3567

diagnostic_scalar_field

3568

}|

3569

element aliased {

3570

generic_aliased_field

3571

}

3572

)

3573

}|

3574

## Primary production of Phytoplankton. This is calculated by

3575

## the ocean biology module and will not be calculated unless

3576

## ocean biology is being simulated.

3577

element scalar_field {

3578

attribute rank { "0" },

3579

attribute name { "HarmonicPhaseSSa" },

3580

(

3581

element diagnostic {

3582

internal_algorithm,

3583

velocity_mesh_choice,

3584

diagnostic_scalar_field

3585

}|

3586

element aliased {

3587

generic_aliased_field

3588

}

3589

)

3590

}

3591

3592

# Insert new diagnostic scalar fields here using the template:

3593

# element scalar_field {

3594

# attribute rank { "0" },

3595

# attribute name { "NewFieldName" },

3596

# (

3597

# element diagnostic {

3598

# internal_algorithm,

3599

# velocity_mesh_choice,

3600

# diagnostic_scalar_field

3601

# }|

3602

# element aliased {

3603

# generic_aliased_field

3604

# }

3605

# )

3606

# }

3607

)

3608

)

3609

3610

# This is the choice of additional vector field to be solved for

3611

vector_field_choice =

3612

(

3613

# The first is a generic field, which may be used for any user-defined field

3614

# that FLUIDITY knows nothing about, or a generic diagnostic

3615

# Prognostic vector fields are not possible (other than velocity and those known fields below).

3616

(

3617

## Generic field variable (vector)

3618

element vector_field {

3619

attribute rank { "1" },

3620

attribute name { xsd:string },

3621

## Field type

3622

(

3623

element prescribed {

3624

mesh_choice,

3625

prescribed_vector_field

3626

}|

3627

element aliased {

3628

generic_aliased_field

3629

}|

3630

element diagnostic {

3631

vector_diagnostic_algorithms,

3632

velocity_mesh_choice,

3633

diagnostic_vector_field

3634

}

3635

)

3636

}|

3637

#

3638

# -- List of fields that are primarily prognostic,

3639

# but can be aliased.

3640

# -- The list is in order of most frequently used.

3641

#

3642

## Prescribed vector fields below this

3643

element ___Prognostic_fields_below___ {

3644

empty

3645

}|

3646

3647

#

3648

# -- List of fields that are primarily prescribed,

3649

# but can be aliased. An example is Maximum bed shear stress.

3650

# -- The list is in order of most frequently used.

3651

#

3652

## Prescribed vector fields below this

3653

element ___Prescribed_fields_below___ {

3654

empty

3655

}|

3656

#

3657

# Insert new prescribed vector fields here using the template:

3658

# element vector_field {

3659

# attribute rank { "1" },

3660

# attribute name { "NewFieldName" },

3661

# (

3662

# element prescribed {

3663

# mesh_choice,

3664

# prescribed_vector_field

3665

# }|

3666

# element aliased {

3667

# generic_aliased_field

3668

# }

3669

# )

3670

# }

3671

#

3672

# -- Last is a list of fields that are primarily diagnostic,

3673

# but can be aliased. An example is Tidal Range.

3674

# -- The list is in order of most frequently used.

3675

#

3676

## Diagnostic vector fields below this

3677

element ___Diagnostic_Fields_Below___ {

3678

empty

3679

}|

3680

3681

## Gradient of a scalar field evaluated using the C gradient

3682

## matrix constructed using finite elements.

3683

## Field must be in this material_phase.

3684

element vector_field {

3685

attribute rank { "1" },

3686

attribute name { "FiniteElementGradient" },

3687

(

3688

element diagnostic {

3689

internal_algorithm,

3690

attribute field_name { string },

3691

mesh_choice,

3692

element integrate_gradient_by_parts {

3693

empty

3694

}?,

3695

diagnostic_gradient_vector_field

3696

}|

3697

element aliased {

3698

generic_aliased_field

3699

}

3700

)

3701

}|

3702

3703

## Gradient of a scalar field evaluated using the transpose

3704

## of the C^T divergence matrix constructed using finite

3705

## elements.

3706

## Field must be in this material_phase.

3707

element vector_field {

3708

attribute rank { "1" },

3709

attribute name { "FiniteElementDivergenceTransposed" },

3710

(

3711

element diagnostic {

3712

internal_algorithm,

3713

attribute field_name { string },

3714

mesh_choice,

3715

element integrate_divergence_by_parts {

3716

empty

3717

}?,

3718

diagnostic_gradient_vector_field

3719

}|

3720

element aliased {

3721

generic_aliased_field

3722

}

3723

)

3724

}|

3725

3726

## Relative vorticity field - curl of the velocity field

3727

element vector_field {

3728

attribute rank { "1" },

3729

attribute name { "Vorticity" },

3730

(

3731

element diagnostic {

3732

internal_algorithm,

3733

### Relative vorticity

3734

#element algorithm {

3735

# attribute name { "curl" },

3736

# attribute material_phase_support { "single" },

3737

# attribute source_field_name { "Velocity" }

3738

#},

3739

element mesh {

3740

attribute name { "VelocityMesh" }

3741

},

3742

diagnostic_vector_field

3743

}|

3744

element aliased {

3745

generic_aliased_field

3746

}

3747

)

3748

}|

3749

## Planetary vorticity

3750

##

3751

## Limitations:

3752

## - Requires geometry dimension of 3.

3753

element vector_field {

3754

attribute rank { "1" },

3755

attribute name { "PlanetaryVorticity" },

3756

(

3757

element diagnostic {

3758

internal_algorithm,

3759

velocity_mesh_choice,

3760

diagnostic_vector_field

3761

}|

3762

element aliased {

3763

generic_aliased_field

3764

}

3765

)

3766

}|

3767

## Absolute vorticity:

3768

##

3769

## f + curl u

3770

##

3771

## Limitations:

3772

## - Requires a geometry dimension of 3.

3773

element vector_field {

3774

attribute rank { "1" },

3775

attribute name { "AbsoluteVorticity" },

3776

attribute depends { "Velocity" },

3777

(

3778

element diagnostic {

3779

internal_algorithm,

3780

velocity_mesh_choice,

3781

diagnostic_vector_field

3782

}|

3783

element aliased {

3784

generic_aliased_field

3785

}

3786

)

3787

}|

3788

3789

## Gradient of a scalar field evaluated using the transpose

3790

## of the C^T matrix constructed using control volumes.

3791

## Field must be in this material_phase.

3792

element vector_field {

3793

attribute rank { "1" },

3794

attribute name { "ControlVolumeDivergenceTransposed" },

3795

(

3796

element diagnostic {

3797

internal_algorithm,

3798

attribute field_name { string },

3799

velocity_mesh_choice,

3800

diagnostic_cv_gradient_vector_field

3801

}|

3802

element aliased {

3803

generic_aliased_field

3804

}

3805

)

3806

}|

3807

## Full velocity in an

3808

## inner element SGS treatment of momentum

3809

##

3810

## Limitations:

3811

## - Requires a geometry dimension of 3.

3812

## - Requires inner element active for momentum

3813

element vector_field {

3814

attribute rank { "1" },

3815

attribute name { "InnerElementFullVelocity" },

3816

(

3817

element diagnostic {

3818

internal_algorithm,

3819

element mesh {

3820

attribute name { "InnerElementMesh" }

3821

},

3822

diagnostic_vector_field

3823

}|

3824

element aliased {

3825

generic_aliased_field

3826

}

3827

)

3828

}|

3829

## Vorticity of the full velocity in an

3830

## inner element SGS treatment of momentum

3831

##

3832

## Limitations:

3833

## - Requires a geometry dimension of 3.

3834

## - Requires inner element active for momentum

3835

element vector_field {

3836

attribute rank { "1" },

3837

attribute name { "InnerElementFullVorticity" },

3838

(

3839

element diagnostic {

3840

internal_algorithm,

3841

element mesh {

3842

attribute name { "InnerElementMesh" }

3843

},

3844

diagnostic_vector_field

3845

}|

3846

element aliased {

3847

generic_aliased_field

3848

}

3849

)

3850

}|

3851

## Vorticity of the SGS velocity in an

3852

## inner element SGS treatment of momentum

3853

##

3854

## Limitations:

3855

## - Requires a geometry dimension of 3.

3856

## - Requires inner element active for momentum

3857

element vector_field {

3858

attribute rank { "1" },

3859

attribute name { "InnerElementVorticity" },

3860

(

3861

element diagnostic {

3862

internal_algorithm,

3863

element mesh {

3864

attribute name { "InnerElementMesh" }

3865

},

3866

diagnostic_vector_field

3867

}|

3868

element aliased {

3869

generic_aliased_field

3870

}

3871

)

3872

}|

3873

## The continuous solution mapped to a discontinuous mesh

3874

##

3875

## Limitations:

3876

## - Requires a geometry dimension of 3.

3877

## - Requires inner element active for momentum

3878

element vector_field {

3879

attribute rank { "1" },

3880

attribute name { "DgMappedVelocity" },

3881

(

3882

element diagnostic {

3883

internal_algorithm,

3884

element mesh {

3885

attribute name { "InnerElementMesh" }

3886

},

3887

diagnostic_vector_field

3888

}|

3889

element aliased {

3890

generic_aliased_field

3891

}

3892

)

3893

}|

3894

## Vorticity of the DG mapped Velocity

3895

## Note vorticity is actually calculated over a DG field

3896

##

3897

## Limitations:

3898

## - Requires a geometry dimension of 3.

3899

## - Requires inner element active for momentum

3900

element vector_field {

3901

attribute rank { "1" },

3902

attribute name { "DgMappedVorticity" },

3903

(

3904

element diagnostic {

3905

internal_algorithm,

3906

element mesh {

3907

attribute name { "InnerElementMesh" }

3908

},

3909

diagnostic_vector_field

3910

}|

3911

element aliased {

3912

generic_aliased_field

3913

}

3914

)

3915

}|

3916

## Solid Velocity field. Used to generate the momentum source

3917

element vector_field {

3918

attribute rank { "1" },

3919

attribute replaces {"UTRAF,VTRAF,WTRAF"},

3920

attribute name { "SolidVelocity" },

3921

(

3922

element diagnostic {

3923

internal_algorithm,

3924

mesh_choice,

3925

diagnostic_vector_field

3926

}

3927

)

3928

}|

3929

## Same as Solid Velocity field but it is on the Particle mesh.

3930

## It is used to map the velocities coming from an external program like

3931

## FEMDEM or DEM to the fluid mesh.

3932

element vector_field {

3933

attribute rank { "1" },

3934

attribute name { "ParticleVector" },

3935

(

3936

element diagnostic {

3937

internal_algorithm,

3938

mesh_choice,

3939

diagnostic_vector_field

3940

}

3941

)

3942

}|

3943

## Same as Solid Velocity field but it is on the Particle mesh.

3944

## It is used to map the velocities coming from an external program like

3945

## FEMDEM or DEM to the fluid mesh.

3946

element vector_field {

3947

attribute rank { "1" },

3948

attribute name { "ParticleForce" },

3949

(

3950

element diagnostic {

3951

internal_algorithm,

3952

mesh_choice,

3953

diagnostic_vector_field

3954

}

3955

)

3956

}|

3957

3958

## Same as Solid Velocity field but it is on the Particle mesh.

3959

## It is used to map the velocities coming from an external program like

3960

## FEMDEM or DEM to the fluid mesh.

3961

element vector_field {

3962

attribute rank { "1" },

3963

attribute name { "SolidForce" },

3964

(

3965

element diagnostic {

3966

internal_algorithm,

3967

velocity_mesh_choice,

3968

diagnostic_vector_field

3969

}

3970

)

3971

}|

3972

element vector_field {

3973

attribute rank { "1" },

3974

attribute name { "VelocityPlotForSolids" },

3975

(

3976

element diagnostic {

3977

internal_algorithm,

3978

velocity_mesh_choice,

3979

diagnostic_vector_field

3980

}

3981

)

3982

}|

3983

## Same as Solid Velocity field but it is on the Particle mesh.

3984

## It is used to map the velocities coming from an external program like

3985

## FEMDEM or DEM to the fluid mesh.

3986

element vector_field {

3987

attribute rank { "1" },

3988

attribute name { "FunctionalGradient" },

3989

(

3990

element diagnostic {

3991

internal_algorithm,

3992

velocity_mesh_choice,

3993

diagnostic_vector_field

3994

}

3995

)

3996

}|

3997

## LinearMomentum field.

3998

## p = \rho*u

3999

## (where p is the linear momentum, \rho the density and u the velocity)

4000

element vector_field {

4001

attribute rank { "1" },

4002

attribute name { "LinearMomentum" },

4003

(

4004

element diagnostic {

4005

internal_algorithm,

4006

velocity_mesh_choice,

4007

diagnostic_vector_field

4008

}|

4009

element aliased {

4010

generic_aliased_field

4011

}

4012

)

4013

}|

4014

## Calculate the control volume auxiliary gradient for a particular field.

4015

## The related field must be a scalar field in this material_phase.

4016

element vector_field {

4017

attribute rank { "0" },

4018

attribute name { "ControlVolumeAuxiliaryGradient" },

4019

(

4020

element diagnostic {

4021

internal_algorithm,

4022

velocity_mesh_choice,

4023

attribute gradient_of_field { string },

4024

diagnostic_vector_field

4025

}|

4026

element aliased {

4027

generic_aliased_field

4028

}

4029

)

4030

}|

4031

## Calculate the dg (Bassi Rebay) auxiliary gradient for a particular field.

4032

## The related field must be a scalar field in this material_phase.

4033

element vector_field {

4034

attribute rank { "0" },

4035

attribute name { "DGAuxiliaryGradient" },

4036

(

4037

element diagnostic {

4038

internal_algorithm,

4039

velocity_mesh_choice,

4040

attribute gradient_of_field { string },

4041

diagnostic_vector_field

4042

}|

4043

element aliased {

4044

generic_aliased_field

4045

}

4046

)

4047

}|

4048

## Experimental geostrophic source field to be used in combination with

4049

## a free surface. Does not solve a vertical balance yet.

4050

element vector_field {

4051

attribute rank { "1" },

4052

attribute name { "GeostrophicSource" },

4053

(

4054

element diagnostic {

4055

internal_algorithm,

4056

mesh_choice,

4057

diagnostic_vector_field

4058

}

4059

)

4060

}|

4061

4062

## Absolute Difference between two vector fields.

4063

##

4064

## Both fields must be in this material_phase.

4065

## Assumes both fields are on the same mesh as the AbsoluteDifference field.

4066

element vector_field {

4067

attribute rank { "1" },

4068

attribute name { "AbsoluteDifference" },

4069

(

4070

element diagnostic {

4071

internal_algorithm,

4072

attribute field_name_a { string },

4073

attribute field_name_b { string },

4074

mesh_choice,

4075

diagnostic_vector_field

4076

}|

4077

element aliased {

4078

generic_aliased_field

4079

}

4080

)

4081

}|

4082

4083

## Absolute Difference between two vector fields.

4084

##

4085

## Both fields must be in this material_phase.

4086

## Assumes both fields are on the same mesh as the AbsoluteDifference field.

4087

element vector_field {

4088

attribute rank { "1" },

4089

attribute name { "VectorAbsoluteDifference" },

4090

(

4091

element diagnostic {

4092

internal_algorithm,

4093

attribute field_name_a { string },

4094

attribute field_name_b { string },

4095

mesh_choice,

4096

diagnostic_vector_field

4097

}|

4098

element aliased {

4099

generic_aliased_field

4100

}

4101

)

4102

}|

4103

4104

## Bed Shear Stress = density*drag_coeff*|u|*u

4105

##

4106

## at the moment this assumes the density and drag coefficients are constants.

4107

## This diagnostic vector field is only calculated over surface elements/nodes,

4108

## interior nodes will have zero value.

4109

element vector_field {

4110

attribute rank { "1" },

4111

attribute name { "BedShearStress" },

4112

(

4113

element diagnostic {

4114

internal_algorithm,

4115

velocity_mesh_choice,

4116

diagnostic_vector_field_bed_shear_stress

4117

}|

4118

element aliased {

4119

generic_aliased_field

4120

}

4121

)

4122

}|

4123

## Max Bed Shear Stress.

4124

##

4125

## Note that you need BedShearStress turned on for this to work.

4126

element vector_field {

4127

attribute rank { "1" },

4128

attribute name { "MaxBedShearStress" },

4129

(

4130

element diagnostic {

4131

internal_algorithm,

4132

velocity_mesh_choice

4133

#diagnostic_vector_field_max_bed_shear_stress

4134

}|

4135

element aliased {

4136

generic_aliased_field

4137

}

4138

),

4139

## This is the time after which the max operator is

4140

## applied to the bed shear stress.

4141

element spin_up_time {

4142

real

4143

}

4144

}|

4145

4146

## Displacement

4147

element vector_field {

4148

attribute rank { "1" },

4149

attribute name { "Displacement" },

4150

(

4151

element diagnostic {

4152

internal_algorithm,

4153

velocity_mesh_choice,

4154

diagnostic_vector_field

4155

}|

4156

element aliased {

4157

generic_aliased_field

4158

}

4159

)

4160

}|

4161

## Galerkin projection of one field onto another mesh.

4162

##

4163

## The field must be in this material_phase.

4164

##

4165

## NOTE: you need the solver options if the mesh

4166

## of this field is continuous.

4167

element vector_field {

4168

attribute rank { "1" },

4169

attribute name { "GalerkinProjection" },

4170

(

4171

element diagnostic {

4172

internal_algorithm,

4173

element source_field_name { string },

4174

mesh_choice,

4175

## Lump the mass matrix of the galerkin projection

4176

## less accurate but faster and might give smoother result.

4177

element lump_mass {

4178

empty

4179

}?,

4180

element solver {

4181

linear_solver_options_sym

4182

}?,

4183

diagnostic_vector_field

4184

}|

4185

element aliased {

4186

generic_aliased_field

4187

}

4188

)

4189

}|

4190

## Projects the Coriolis term onto the mesh of this diagnostic field.

4191

## Note that multiple projection methods are available (under the

4192

## algorithm option).

4193

element vector_field {

4194

attribute rank { "1" },

4195

attribute name { "Coriolis" },

4196

(

4197

element diagnostic {

4198

coriolis_algorithm,

4199

velocity_mesh_choice,

4200

diagnostic_vector_field

4201

}

4202

)

4203

}

4204

4205

# Insert new diagnostic vector field here using the template:

4206

# element vector_field {

4207

# attribute rank { "1" },

4208

# attribute name { "NewFieldName" },

4209

# (

4210

# element diagnostic {

4211

# internal_algorithm,

4212

# mesh_choice,

4213

# diagnostic_vector_field

4214

# }|

4215

# element aliased {

4216

# generic_aliased_field

4217

# }

4218

# )

4219

# }

4220

)

4221

)

4222

4223

# This is the choice of additional tensor fields

4224

tensor_field_choice =

4225

(

4226

# The first is a generic field, which may be used for any user-defined field

4227

# that FLUIDITY knows nothing about, or a generic diagnostic

4228

# Prognostic tensor fields are not possible.

4229

(

4230

## Generic field variable (tensor)

4231

element tensor_field {

4232

attribute rank { "2" },

4233

attribute name { xsd:string },

4234

## Field type

4235

(

4236

element prescribed {

4237

mesh_choice,

4238

prescribed_tensor_field

4239

}|

4240

element aliased {

4241

generic_aliased_field

4242

}|

4243

element diagnostic {

4244

tensor_diagnostic_algorithms,

4245

velocity_mesh_choice,

4246

python_diagnostic_field_code?,

4247

diagnostic_tensor_field

4248

}

4249

)

4250

}|

4251

#

4252

# -- Second is a list of tensor fields that are primarily prescribed,

4253

# but can be aliased.

4254

# -- The list is in order of most frequently used.

4255

#

4256

## Prescribed scalar fields below this

4257

element ___Prescribed_fields_below___ {

4258

empty

4259

}|

4260

4261

## MaterialViscosity field:

4262

##

4263

## Field for the viscosity of this material.

4264

## Required if using a diagnostic bulk viscosity

4265

## in a multimaterial simulation.

4266

element tensor_field {

4267

attribute rank { "2" },

4268

attribute name { "MaterialViscosity" },

4269

(

4270

element prescribed {

4271

mesh_choice,

4272

prescribed_tensor_field

4273

}|

4274

element aliased {

4275

generic_aliased_field

4276

}

4277

)

4278

}|

4279

4280

element tensor_field {

4281

attribute rank { "2" },

4282

attribute name { "MaterialElasticity" },

4283

(

4284

element prescribed {

4285

mesh_choice,

4286

prescribed_tensor_field

4287

}|

4288

element aliased {

4289

generic_aliased_field

4290

}

4291

)

4292

}|

4293

4294

#

4295

# Insert new prescribed tensor fields here using the template:

4296

# element tensor_field {

4297

# attribute rank { "2" },

4298

# attribute name { "NewFieldName" },

4299

# (

4300

# element prescribed {

4301

# mesh_choice,

4302

# prescribed_tensor_field

4303

# }|

4304

# element aliased {

4305

# generic_aliased_field

4306

# }

4307

# )

4308

# }|

4309

#

4310

# -- Last is a list of fields that are primarily diagnostic,

4311

# but can be aliased.

4312

# -- The list is in order of most frequently used.

4313

#

4314

## Diagnostic tensor fields below this

4315

element ___Diagnostic_Fields_Below___ {

4316

empty

4317

}|

4318

## From a field on a mesh, diagnose the anisotropic

4319

## interpolation weight that would give the mesh back.

4320

## It is computed as:

4321

## \Eps = M^-1 |H|

4322

element tensor_field {

4323

attribute rank { "2" },

4324

attribute name { "FieldTolerance" },

4325

(

4326

element diagnostic {

4327

internal_algorithm,

4328

element source_field_name { string },

4329

velocity_mesh_choice,

4330

diagnostic_tensor_field

4331

}|

4332

element aliased {

4333

generic_aliased_field

4334

}

4335

)

4336

}

4337

4338

# Insert new diagnostic tensor field here using the template:

4339

# element tensor_field {

4340

# attribute name { "NewFieldName" },

4341

# (

4342

# element diagnostic {

4343

# internal_algorithm,

4344

# mesh_choice,

4345

# diagnostic_tensor_field

4346

# }|

4347

# element aliased {

4348

# generic_aliased_field

4349

# }

4350

# )

4351

# }

4352

)

4353

)

4354

4355

mesh_info =

4356

(

4357

## Read mesh from file.

4358

element from_file {

4359

(

4360

## Triangle mesh format.

4361

##

4362

## Enter the base name without the .edge .ele, .face or

4363

## .node extensions, and without process numbers.

4364

element format {

4365

attribute name { "triangle" },

4366

comment

4367

}|

4368

## Read the mesh from a vtu. Note that the mesh will have no surface

4369

## or region IDs.

4370

element format {

4371

attribute name { "vtu" },

4372

comment

4373

}|

4374

## CGNS mesh format (not yet implemented)

4375

element format {

4376

attribute name { "cgns" },

4377

comment

4378

}

4379

),

4380

attribute file_name { xsd:string },

4381

from_file_mesh_stat_options,

4382

comment

4383

}|

4384

## Make mesh from existing mesh. The existing mesh cannot itself

4385

## be made from an existing mesh (i.e. it must be read from a

4386

## file).

4387

element from_mesh {

4388

mesh_choice,

4389

element mesh_shape {

4390

element polynomial_degree {

4391

integer

4392

}

4393

}?,

4394

element mesh_continuity {

4395

element string_value{

4396

"continuous" | "discontinuous"

4397

}

4398

}?,

4399

## Make mesh periodic

4400

element periodic_boundary_conditions {

4401

attribute name { xsd:string },

4402

## List of boundary ids that are aliased to

4403

element physical_boundary_ids {

4404

integer_vector

4405

},

4406

## List of boundary ids that are aliased

4407

element aliased_boundary_ids {

4408

integer_vector

4409

},

4410

## Python code which takes coordinate of an aliased

4411

## boundary node and returns the coordinate of a physical

4412

## boundary node

4413

element coordinate_map {

4414

python_code

4415

}

4416

}*,

4417

## Extrude a horizontal (1D or 2D) mesh in the vertical

4418

element extrude {

4419

## Depth over which to extrude

4420

## top will be at z=0

4421

## bottom will be at z=-bottom_depth

4422

element bottom_depth {

4423

real

4424

},

4425

## Constant or function to specify the depth of the

4426

## layers. The function is a function of all coordinates

4427

## (so in 2+1D: x,y and z) to specify a layer depth that

4428

## varies both in the horizontal as in the vertical.

4429

element sizing_function {

4430

input_choice_real

4431

},

4432

## surface_id to assign to the top of the extruded mesh

4433

element top_surface_id {

4434

integer

4435

}?,

4436

## surface_id to assign to the bottom of the extruded mesh

4437

element bottom_surface_id {

4438

integer

4439

}?

4440

}?,

4441

derived_mesh_stat_options,

4442

comment

4443

}

4444

)

4445

4446

# Options for inclusion/exclusion of mesh statistics from the .stat file

4447

include_mesh_in_stat =

4448

(

4449

## Include this mesh in the .stat file

4450

element include_in_stat {

4451

comment

4452

}

4453

)

4454

exclude_mesh_from_stat =

4455

(

4456

## Exclude this mesh from the .stat file

4457

element exclude_from_stat {

4458

comment

4459

}

4460

)

4461

4462

# Diagnostic statistics options for meshed, with enabled by default

4463

mesh_stat_options_enabled_default = include_mesh_in_stat

4464

mesh_stat_options_enabled_default |= exclude_mesh_from_stat

4465

4466

# Diagnostic statistics options for meshed, with disabled by default

4467

mesh_stat_options_disabled_default = exclude_mesh_from_stat

4468

mesh_stat_options_disabled_default |= include_mesh_in_stat

4469

4470

from_file_mesh_stat_options =

4471

(

4472

## Specify what is added to .stat files

4473

element stat {

4474

mesh_stat_options_enabled_default

4475

}

4476

)

4477

derived_mesh_stat_options =

4478

(

4479

## Specify what is added to .stat files

4480

element stat {

4481

mesh_stat_options_disabled_default

4482

}

4483

)

4484

4485

input_choice_tensor_field =

4486

(

4487

(

4488

## An isotropic tensor, i.e.

4489

## one with no directional variation.

4490

## Can be represented as a scalar real.

4491

element isotropic {

4492

input_choice_real

4493

}|

4494

## A symmetric tensor, i.e.

4495

## A^T = A

4496

element anisotropic_symmetric {

4497

input_choice_real_dim_symmetric_tensor

4498

}|

4499

## A general asymmetric tensor.

4500

element anisotropic_asymmetric {

4501

input_choice_real_dim_tensor

4502

}

4503

)

4504

)

4505

4506

constitutive_laws =

4507

(

4508

(

4509

## Constitutive laws for fluids

4510

element constitutive_law {

4511

attribute name { "fluid" }

4512

}|

4513

## Constitutive laws for solids

4514

element constitutive_law {

4515

attribute name { "solid" }

4516

}

4517

)

4518

)

4519

4520

region_ids =

4521

(

4522

## Optional region ids to associate different values

4523

## to different regions of the mesh.

4524

## Leave unselected if you`re not using multiple regions or

4525

## region_ids.

4526

## Currently only works with triangle files created by gmsh2triangle.

4527

element region_ids {

4528

integer_vector

4529

}?

4530

)

4531

4532

temporal_control_volume_options =

4533

(

4534

## Temporal discretisation options that are only relevant if a control volume or mixed control volume - continuous galerkin spatial discretisation is selected for this field.

4535

element control_volumes {

4536

## Number of iterations within an advection solve.

4537

## This increases the accuracy of the face values and ensures that

4538

## the pivoted solution is cancelled out.

4539

## Defaults to 1 if unselected.

4540

element number_advection_iterations {

4541

attribute replaces { "INT(ABS(NDISOT)/10)" },

4542

integer,

4543

## Cut short advection_iterations if the specified tolerance

4544

## is reached.

4545

## This only works for pure control volume discretisations.

4546

element tolerance {

4547

real,

4548

(

4549

## Select the norm with which you want the tolerance to be tested.

4550

##

4551

## The infinity norm.

4552

element infinity_norm {

4553

empty

4554

}|

4555

## Select the norm with which you want the tolerance to be tested.

4556

##

4557

## The l2 norm.

4558

element l2_norm {

4559

empty

4560

}|

4561

## Select the norm with which you want the tolerance to be tested.

4562

##

4563

## The l2 norm evaluated on a control volume mesh.

4564

element cv_l2_norm {

4565

empty

4566

}

4567

)

4568

}?

4569

}?,

4570

(

4571

## Use timestep subcycling to solve this equation.

4572

## Specify the maximum courant number per subcycle.

4573

## This only works for pure control volume discretisations.

4574

element maximum_courant_number_per_subcycle {

4575

real,

4576

field_based_cfl_number_options

4577

}|

4578

## Use timestep subcycling to solve this equation.

4579

## Specify the number of subcycles.

4580

## This only works for pure control volume discretisations.

4581

element number_advection_subcycles {

4582

integer

4583

}

4584

)?,

4585

## Only works if a control volume or mixed control volume -

4586

## continuous galerkin spatial discretisation is selected.

4587

## If not active then the theta specified above will be used.

4588

## Otherwise use variable limited theta on individual faces.

4589

element limit_theta {

4590

attribute replaces { "MOD(INT(ABS(NDISOT)/1),10) = 1,3,5,7,9 (odd)" },

4591

empty

4592

}?,

4593

## Only works if a control volume or mixed control volume -

4594

## continuous galerkin spatial discretisation is selected.

4595

## Time discretisation of upwind discretisation off which the

4596

## higher order solution is pivotted.

4597

## - pivot_theta = 1 - implicit pivot (default if not set and

4598

## best choice if not intentionally modifying

4599

## scheme to be explicit)

4600

## - pivot_theta = 0 - explicit pivot

4601

element pivot_theta {

4602

real

4603

}?

4604

}

4605

)

4606

4607

temporal_discontinuous_galerkin_options =

4608

(

4609

## This enables DG-specific timestepping options, such as

4610

## explicit advection subcycling.

4611

element discontinuous_galerkin {

4612

(

4613

## Use timestep subcycling to solve this equation.

4614

## Specify the maximum courant number per subcycle.

4615

element maximum_courant_number_per_subcycle {

4616

real

4617

}|

4618

## Use timestep subcycling to solve this equation.

4619

## Specify the number of subcycles.

4620

element number_advection_subcycles {

4621

integer

4622

}

4623

)?

4624

}

4625

)

4626

4627

pure_cv_options =

4628

(

4629

## Use a pure control volume discretisations.

4630

## Follows a new control volume code path.

4631

element control_volumes {

4632

spatial_control_volume_options,

4633

(

4634

## Use the gradient of the field constructed using the

4635

## basis functions of the parent finite element mesh to

4636

## form the divergence.

4637

##

4638

## DOES NOT CURRENTLY WORK WITH ROBIN OR WEAK DIRICHLET BOUNDARY CONDITIONS!

4639

##

4640

## Based on schemes in Handbook of Numerical Analysis,

4641

## P.G. Ciarlet, J.L. Lions eds, vol 7, pp 713-1020

4642

element diffusion_scheme {

4643

attribute name{"ElementGradient"}

4644

}|

4645

## Use an auxiliary gradient equation to find the gradient of the field.

4646

##

4647

## DOES NOT CURRENTLY WORK WITH ROBIN BOUNDARY CONDITIONS!

4648

##

4649

## Based on scheme proposed in Bassi, F. & Rebay, S., A

4650

## high-order accurate discontinuous finite element method

4651

## for the numerical solution of the compressible

4652

## Navier-Stokes equations, Journal Of Computational

4653

## Physics, 1997, 131, 267-279

4654

element diffusion_scheme {

4655

attribute name{"BassiRebay"}

4656

}

4657

)

4658

}

4659

)

4660

4661

spatial_control_volume_options = standard_control_volume_options

4662

spatial_control_volume_options |= compressive_control_volume_options

4663

4664

standard_control_volume_options =

4665

(

4666

## First Order Upwind face value discretisation

4667

## face_value = donor_value,

4668

## where

4669

## donor_value = income*val_1 + (1.-income)*val_2,

4670

## where val_i is the value on the ith node neighbouring the face and

4671

## income = [0, 1] depending on whether the flow is coming from node 1 or 2

4672

## First order upwinding is monotonic so no limiting is ever required

4673

element face_value {

4674

attribute name { "FirstOrderUpwind" },

4675

attribute replaces { "MOD(INT(ABS(NDISOT)/1),10) = 0,1" },

4676

empty

4677

}|

4678

## Trapezoidal face value discretisation

4679

## face_value = 0.5*(val_1 + val_2),

4680

## where

4681

## val_i is the value on the ith node neighbouring the face

4682

##

4683

## Trapezoidal discretisation is unbounded so limiting is compulsory

4684

element face_value {

4685

attribute name { "Trapezoidal" },

4686

attribute replaces { "MOD(INT(ABS(NDISOT)/1),10) = 2,3" },

4687

limiter_options

4688

}|

4689

## Finite Element face value discretisation

4690

## face_value = finite element interpolation from surrounding nodes

4691

##

4692

## Finite element discretisation may become unbounded so limiting is often necessary.

4693

element face_value {

4694

attribute name { "FiniteElement" },

4695

attribute replaces { "MOD(INT(ABS(NDISOT)/1),10) = 4,5,6,7" },

4696

limiter_options?

4697

}

4698

)

4699

4700

coupled_spatial_control_volume_options = coupled_control_volume_options

4701

coupled_spatial_control_volume_options |= compressive_control_volume_options

4702

4703

# coupled control volume options are the same as the standard ones (annoyingly copied and pasted)

4704

# except that firstorderupwind gets limiter options

4705

coupled_control_volume_options =

4706

(

4707

## First Order Upwind face value discretisation

4708

## face_value = donor_value,

4709

## where

4710

## donor_value = income*val_1 + (1.-income)*val_2,

4711

## where val_i is the value on the ith node neighbouring the face and

4712

## income = [0, 1] depending on whether the flow is coming from node 1 or 2

4713

## First order upwinding is monotonic so no limiting is ever required

4714

element face_value {

4715

attribute name { "FirstOrderUpwind" },

4716

attribute replaces { "MOD(INT(ABS(NDISOT)/1),10) = 0,1" },

4717

limiter_options?

4718

}|

4719

## Trapezoidal face value discretisation

4720

## face_value = 0.5*(val_1 + val_2),

4721

## where

4722

## val_i is the value on the ith node neighbouring the face

4723

##

4724

## Trapezoidal discretisation is unbounded so limiting is compulsory

4725

element face_value {

4726

attribute name { "Trapezoidal" },

4727

attribute replaces { "MOD(INT(ABS(NDISOT)/1),10) = 2,3" },

4728

limiter_options

4729

}|

4730

## Finite Element face value discretisation

4731

## face_value = finite element interpolation from surrounding nodes

4732

##

4733

## Finite element discretisation may become unbounded so limiting is often necessary.

4734

element face_value {

4735

attribute name { "FiniteElement" },

4736

attribute replaces { "MOD(INT(ABS(NDISOT)/1),10) = 4,5,6,7" },

4737

limiter_options?

4738

}

4739

)

4740

4741

compressive_control_volume_options =

4742

(

4743

## HyperC face value discretisation

4744

##

4745

## face_value calculated from upper bound of explicit TVD zone of NVD diagram

4746

## Normally used for MaterialVolumeFraction fields

4747

element face_value {

4748

attribute name { "HyperC" },

4749

attribute replaces { "MOD(INT(ABS(NDISOT)/1),10) = 8,9" },

4750

upwind_value_options?,

4751

cv_face_cfl_number_options

4752

}|

4753

## UltraC face value discretisation

4754

##

4755

## face_value calculated from extended upper bound of

4756

## explicit TVD zone of NVD diagram assuming

4757

## values bounded by target_maximum and target_minimum.

4758

element face_value {

4759

attribute name { "UltraC" },

4760

attribute replaces { "MOD(INT(ABS(NDISOT)/1),10) = 8,9, with ULTRAC = TRUE from solidity_options.inp" },

4761

## Specifiy the upper bound which UltraC will use to

4762

## calculate the maximum flux.

4763

element target_maximum {

4764

real

4765

},

4766

## Specifiy the lower bound which UltraC will use to

4767

## calculate the minimum flux.

4768

element target_minimum {

4769

real

4770

},

4771

upwind_value_options?,

4772

cv_face_cfl_number_options

4773

}|

4774

## **UNDER TESTING**

4775

##

4776

## PotentialUltraC face value discretisation

4777

##

4778

## face_value calculated from extended upper bound of

4779

## explicit TVD zone of NVD diagram if potential

4780

## value of field is sufficient (as specified by

4781

## target_maximum) to ensure the correct front advection

4782

## velocity.

4783

##

4784

## If not then either switch to HyperC or use a modified flux

4785

## based on the potential function.

4786

element face_value {

4787

attribute name { "PotentialUltraC" },

4788

## Specifiy the upper bound which PotentialUltraC will use

4789

## to calculate the maximum flux if the potential function

4790

## value is sufficient to maintain the correct front

4791

## advection velocity.

4792

element target_maximum {

4793

real

4794

},

4795

## Specifiy the lower bound which PotentialUltraC will use to calculate the minimum flux.

4796

element target_minimum {

4797

real

4798

},

4799

(

4800

## Select what PotentialUltraC should do if the

4801

## potential function value does not reach the required

4802

## value specified by the target_maximum.

4803

##

4804

## Switch to using HyperC face values. This ensures

4805

## that the advection velocity is correct however may

4806

## create isolated regions beneath the target_maximum.

4807

element switch_to_hyperc {

4808

empty

4809

}|

4810

## Select what PotentialUltraC should do if the

4811

## potential function value does not reach the required

4812

## value specified by the target_maximum.

4813

##

4814

## Modify the maximum nodal values (both downwind and

4815

## upwind) so that the fluxes are at their maximum

4816

## possible without affecting the front advection

4817

## velocity.

4818

element use_potential_flux {

4819

empty

4820

}

4821

),

4822

upwind_value_options?,

4823

cv_face_cfl_number_options

4824

}

4825

)

4826

4827

#Select the type of dynamic control to be used

4828

#Note: DEM and FEMDEM require the respective libraries

4829

#to be compiled.

4830

input_solid_dynamics_choice =

4831

(

4832

## Obtain values from point and radius file.

4833

##

4834

## First line of file is free to use (for comments)

4835

## Second line must contain the number of particles

4836

## Third and fourth line are again for comments.

4837

## Following lines include 10 columns, corresponding to

4838

## the particle's x, y, and z positions, followed by the radius, then

4839

## velocities in x, y, and z directions, followed by angular velocities

4840

## in the x, y, and z directions.

4841

element dynamic_type {

4842

attribute name {"from_input_file"},

4843

attribute file_name {xsd:string}

4844

}|

4845

## Two python scripts must be provided. The script is cycled over each particle.

4846

## One script for particle position (output is tuple of position coords)

4847

## Second script is for particle radius (output is tuple of position coords)

4848

## Third script is for particle translational velocity.

4849

## Fourth script is for particle angular velocity. (Note: particles

4850

## have a no slip boundary condition at the surface, so this angular velocity

4851

## WILL matter to the flow.)

4852

## Python functions should be of the form:

4853

## def val(X, t):

4854

## Function code

4855

## return # Return value

4856

## where X is a tuple of length geometry dimension.

4857

## X[0] contains the number of the particle (in real format)

4858

element dynamic_type {

4859

attribute name {"python_script"}

4860

}|

4861

element dynamic_type {

4862

attribute name {"use_simple_dynamics"},

4863

element set_bottom{real},

4864

element set_xmin{real},

4865

element set_ymin{real},

4866

element set_zmin{real},

4867

element set_xmax{real},

4868

element set_ymax{real},

4869

element set_zmax{real}

4870

}|

4871

## Using y3D to model dynamics. Filename of input file for y3D must

4872

## be specified.

4873

element dynamic_type {

4874

attribute name {"use_y3D"},

4875

attribute file_name {xsd:string}

4876

}|

4877

## Using femdem 2D to model dynamics. Filename of input file must

4878

## be specified.

4879

element dynamic_type {

4880

attribute name {"use_2Dfemdem"},

4881

attribute file_name {xsd:string}

4882

}|

4883

## Using femdem 3D to model dynamics. Filename of input file must

4884

## be specified.

4885

element dynamic_type {

4886

attribute name {"use_3Dfemdem"},

4887

attribute file_name {xsd:string},

4888

element quad2lin {

4889

attribute file_name {xsd:string}

4890

}

4891

}

4892

)

4893

4894

cap_option =

4895

(

4896

## Cap the min and max values of this field when using

4897

## it as a volume fraction to work out bulk material

4898

## properties.

4899

## No capping used if not selected.

4900

element cap_values {

4901

## Set the upper bound on the field.

4902

## Defaults to huge(0.0)*epsilon(0.0) if not set.

4903

element upper_cap {

4904

real

4905

}?,

4906

## Set the lower bound on the field.

4907

## Defaults to -huge(0.0)*epsilon(0.0) if not set.

4908

element lower_cap {

4909

real

4910

}?

4911

}

4912

)

4913

4914

surface_tension_option =

4915

(

4916

element surface_tension {

4917

## Surface tension coefficient

4918

element surface_tension_coefficient {

4919

real

4920

},

4921

## The equilibrium contact angle (in radians) with the boundaries identified by the surface ids

4922

element equilibrium_contact_angle {

4923

real,

4924

## Surface ids:

4925

element surface_ids {

4926

integer_vector

4927

}

4928

}?

4929

}

4930

)

4931

4932

limiter_options =

4933

(

4934

## Limit the face value to satisfy a boundedness criterion.

4935

element limit_face_value{

4936

(

4937

sweby_limiter|

4938

ultimate_limiter

4939

)

4940

}

4941

)

4942

4943

sweby_limiter =

4944

## See "High-Resolution Schemes Using Flux Limiters for

4945

## Hyperblic Conservation-Laws", P. K. Sweby, 1984, Siam

4946

## Journal on Numerical Analysis, 21, 995-1011

4947

element limiter {

4948

attribute replaces { "MOD(INT(ABS(NDISOT)/1),10) = 2,3,4,5" },

4949

attribute name {"Sweby"},

4950

slope_options?,

4951

upwind_value_options?

4952

}

4953

4954

ultimate_limiter =

4955

## See "The Ultimate Conservative Difference Scheme Applied

4956

## to Unsteady One-Dimensional Advection", B. P. Leonard,

4957

## 1991, Computer Methods in Applied Mechanics and

4958

## Engineering, 88, 17-74

4959

element limiter {

4960

attribute name {"Ultimate"},

4961

field_based_cfl_number_options,

4962

upwind_value_options?

4963

}

4964

4965

slope_options =

4966

(

4967

## Control the upper and lower slopes of the NVD limiter

4968

element slopes {

4969

## Defaults to Sweby, 1984 limiter (= 1.0) if unselected

4970

element lower {

4971

real

4972

}?,

4973

## Defaults to Sweby, 1984 limiter (= 2.0) if unselected

4974

element upper {

4975

real

4976

}?

4977

}

4978

)

4979

4980

upwind_value_options =

4981

(

4982

(

4983

## Select the method to be used for calculating the upwind value.

4984

## If not selected will default to project_upwind_value_from_point for

4985

## simplex element meshes and to a locally_bound_upwind_value for cube

4986

## element meshes.

4987

##

4988

## This method projects the upwind value from a point in the element just

4989

## upwind of the node pair straddling the face. It is otherwise known as

4990

## anisotropic limiting.

4991

## This is only available on simplex meshes as it involes a search around

4992

## the donor node to find the upwind element.

4993

element project_upwind_value_from_point {

4994

attribute replaces { "NDISOT > 0 on simplex meshes" },

4995

## When the donor node is on a domain boundary reflect the projection

4996

## back into the mesh.

4997

element reflect_off_domain_boundaries {

4998

empty

4999

}?,

5000

## Constrain the projected value to be between the min and max of the

5001

## element values which it was found from.

5002

element bound_projected_value_locally {

5003

empty

5004

}?,

5005

## Store the locations of the elements where the upwind values

5006

## are projected from for each node pair.

5007

## This inserts an integer csr matrix into state so is memory expensive but

5008

## saves a significant amount of time (searching around the neighbouring elements).

5009

## This is unsafe for moving meshes but should be ok for adaptive meshes.

5010

element store_upwind_elements {

5011

attribute replaces { "ABS(NDISOT) >= 1000" },

5012

## Store the quadrature locations within the elements

5013

## where the upwind values

5014

## are projected from for each node pair.

5015

## This inserts a real block csr matrix into state so is even more memory

5016

## expensive than just storing the upwind elements and

5017

## only saves a comparitively

5018

## marginal amount of time (as actually searching the

5019

## neighbouring elements is the

5020

## slowest bit, finding the quadrature is relatively easy).

5021

element store_upwind_quadrature {

5022

attribute replaces { "ABS(NDISOT) >= 1000" },

5023

empty

5024

}?

5025

}?

5026

}|

5027

## Select the method to be used for calculating the upwind value.

5028

## If not selected will default to project_upwind_value_from_point for

5029

## simplex element meshes and to a locally_bound_upwind_value for cube

5030

## element meshes.

5031

##

5032

## Projects the value of the advected variable from the downwind or donor node

5033

## using the interpolated gradient at the donor node in the

5034

## direction of the vector

5035

## connecting the node pair straddling the face.

5036

## This is available on all meshes (except if bounding the values).

5037

element project_upwind_value_from_gradient {

5038

(

5039

## Select which node to project from:

5040

## Project from the downwind node (Jasak et al., 1999) so that:

5041

## upwind_value = downwind_value - 2*gradient.vector

5042

element project_from_downwind_value {

5043

comment

5044

}|

5045

## Select which node to project from:

5046

## Project from the donor node so that:

5047

## upwind_value = donor_value - gradient.vector

5048

element project_from_donor_value {

5049

comment

5050

}

5051

),

5052

## When the donor node is on a domain boundary reflect the projection

5053

## back into the mesh.

5054

element reflect_off_domain_boundaries {

5055

empty

5056

}?,

5057

## Constrain the projected value to be between the min and max of the

5058

## element values which surround it.

5059

## This is only available on simplex meshes as it involes a search around

5060

## the donor node to find the upwind element.

5061

element bound_projected_value_locally {

5062

## Store the locations of the elements closest to the project value.

5063

## This inserts an integer csr matrix into state so is

5064

## memory expensive but

5065

## saves a significant amount of time (searching around

5066

## the neighbouring elements).

5067

## This is unsafe for moving meshes but should be ok for adaptive meshes.

5068

element store_upwind_elements {

5069

comment

5070

}?

5071

}?

5072

}|

5073

## Select the method to be used for calculating the upwind value.

5074

## If not selected will default to project_upwind_value_from_point for

5075

## simplex element meshes and to a locally_bound_upwind_value for cube

5076

## element meshes.

5077

##

5078

## Chooses an upwind value by selecting the maximum or minimum of the neighbouring

5079

## nodes depending on the local slope of the donor and downwind values.

5080

## Otherwise known as isotropic limiting.

5081

## This is available on all meshes.

5082

element locally_bound_upwind_value {

5083

attribute replaces { "all cube elements, NDISOT < 0 on simplex elements" },

5084

empty

5085

}|

5086

## Select the method to be used for calculating the upwind value.

5087

## If not selected will default to project_upwind_value_from_point for

5088

## simplex element meshes and to a locally_bound_upwind_value for cube

5089

## element meshes.

5090

##

5091

## Chooses an upwind value by selecting the value at the node most directy

5092

## upwind from the vector connecting the donor and downwind nodes.

5093

## This is available on all meshes.

5094

element pseudo_structured_upwind_value {

5095

empty

5096

}

5097

)

5098

)

5099

5100

field_based_cfl_number_options =

5101

(

5102

(

5103

## Select the Courant Number definition to be used.

5104

##

5105

## This uses the control volume definition of the CFL Number.

5106

element courant_number {

5107

attribute name { "ControlVolumeCFLNumber" },

5108

empty

5109

}|

5110

## ***UNDER TESTING***

5111

##

5112

## Select the Courant Number definition to be used.

5113

##

5114

## This uses the control volume definition of the CFL Number.

5115

element courant_number {

5116

attribute name { "CVMaterialDensityCFLNumber" },

5117

empty

5118

}|

5119

## Select the Courant Number definition to be used.

5120

##

5121

## This uses the finite element approximation of the CFL Number.

5122

element courant_number {

5123

attribute name { "CFLNumber" },

5124

empty

5125

}|

5126

## Select the Courant Number definition to be used.

5127

element courant_number {

5128

attribute name { string },

5129

empty

5130

}

5131

)

5132

)

5133

5134

cv_face_cfl_number_options =

5135

(

5136

(

5137

## Select the Courant Number definition to be used in the slope of

5138

## the NVD diagram upper bound.

5139

## This uses the finite difference definition of the CFL Number

5140

## consistent with the 1D version of HyperC (Leonard, 1981).

5141

## This is the default that reproduces old behaviour.

5142

## All others are under testing or construction.

5143

element courant_number {

5144

attribute name { "FiniteDifferenceCFLNumber" },

5145

empty

5146

}|

5147

## Select the Courant Number definition to be used in the slope of

5148

## the NVD diagram upper bound.

5149

## This uses the control volume definition of the CFL Number.

5150

element courant_number {

5151

attribute name { "ControlVolumeCFLNumber" },

5152

empty

5153

}|

5154

## ***UNDER TESTING***

5155

##

5156

## Select the Courant Number definition to be used in the slope of

5157

## the NVD diagram upper bound.

5158

## This uses a control volume definition of the CFL Number

5159

## that incorporates the MaterialDensity.

5160

## Requires a MaterialDensity field in this material_phase!

5161

element courant_number {

5162

attribute name { "CVMaterialDensityCFLNumber" },

5163

empty

5164

}|

5165

## ***UNDER TESTING***

5166

##

5167

## Select the Courant Number definition to be used in the slope of

5168

## the NVD diagram upper bound.

5169

## This uses the finite element approximation of the CFL Number.

5170

element courant_number {

5171

attribute name { "CFLNumber" },

5172

empty

5173

}|

5174

## ***UNDER TESTING***

5175

##

5176

## Select the Courant Number definition to be used in the slope of

5177

## the NVD diagram upper bound.

5178

element courant_number {

5179

attribute name { string },

5180

empty

5181

}

5182

)

5183

)

5184

5185

timestep_cfl_number_options =

5186

(

5187

(

5188

## Select the Courant Number definition to be used for adaptive timestepping.

5189

## This uses the finite element approximation of the CFL Number.

5190

element courant_number {

5191

attribute name { "CFLNumber" },

5192

## Select the mesh on which you wish to evaluate the CFLNumber.

5193

velocity_mesh_choice

5194

}|

5195

## Select the Courant Number definition to be used for adaptive timestepping.

5196

## This uses the control volume definition of the CFL Number.

5197

element courant_number {

5198

attribute name { "ControlVolumeCFLNumber" },

5199

## Select the mesh on which you wish to evaluate the ControlVolumeCFLNumber.

5200

velocity_mesh_choice

5201

}

5202

)

5203

)

5204

5205

mixing_stats =

5206

(

5207

## Enable to include in the .stat file the fractions of the

5208

## scalar field contained in

5209

## bins specified by the user. This allows mixing of the field to be quantified.

5210

## Replaces and expands upon the old heaviside.dat file

5211

element include_mixing_stats{

5212

attribute name { xsd:string },

5213

attribute replaces { "heaviside.dat file" },

5214

(

5215

## Select whether to evaluate the volume fraction over the finite element

5216

## (continuous galerkin) or within the control volume (control_volumes).

5217

##

5218

## NOTE: continuous_galerkin only works with linear tets

5219

##

5220

## NOTE: continuous_galerkin is not fully validated yet

5221

element continuous_galerkin {

5222

## if select normalise the volume fractions will be

5223

## divided by the total volume of the domain

5224

element normalise {

5225

empty

5226

}?

5227

}|

5228

## Select whether to evaluate the volume fraction over the finite element

5229

## (continuous galerkin) or within the control volume (control_volumes).

5230

element control_volumes {

5231

## if select normalise the volume fractions will be divided by the total volume of the domain

5232

element normalise {

5233

empty

5234

}?

5235

}

5236

),

5237

## The values of the bounds of the bins

5238

## e.g. the values 0 1 2 3 will return 4 bins

5239

## and the fraction of the field in each bin with,

5240

## 0<=field<1, 1<=field<2, 2<=field<3, 3<=field,

5241

## will be calculated.

5242

element mixing_bin_bounds {

5243

real_vector

5244

},

5245

## Define the tolerance beneath the specified bins that should be included.

5246

## Defaults to zero at machine tolerance (epsilon(0.0)) if not selected.

5247

element tolerance {

5248

real

5249

}?

5250

}

5251

)

5252

5253

cv_stats =

5254

(

5255

## Include statistics evaluated on the control volume mesh.

5256

element include_cv_stats {

5257

empty

5258

}

5259

)

5260

5261

# Options for inclusion of calculations of surface integrals in the .stat file

5262

surface_integral_stats_base.surface_integral =

5263

(

5264

attribute name { xsd:string },

5265

## Surface IDs defining the surface over which to integrate. If disabled, integrates over the whole surface.

5266

element surface_ids {

5267

integer_vector

5268

}?,

5269

## Enable to normalise the integral by dividing by the surface area

5270

element normalise {

5271

comment

5272

}?

5273

)

5274

surface_integral_stats_scalar =

5275

(

5276

## Surface integral calculations. The following integral types are available:

5277

## value: Integrates the field

5278

## gradient_normal: Integrates the normal component of the gradient of the field

5279

element surface_integral {

5280

surface_integral_stats_scalar.surface_integral

5281

}

5282

)

5283

surface_integral_stats_scalar.surface_integral = surface_integral_stats_base.surface_integral

5284

surface_integral_stats_scalar.surface_integral &=

5285

(

5286

attribute type { "value" | "gradient_normal" }

5287

)

5288

surface_integral_stats_vector =

5289

(

5290

## Surface integral calculations. The following integral types are available:

5291

## normal: Integrates the normal component of the field

5292

element surface_integral {

5293

surface_integral_stats_vector.surface_integral

5294

}

5295

)

5296

surface_integral_stats_vector.surface_integral = surface_integral_stats_base.surface_integral

5297

surface_integral_stats_vector.surface_integral &=

5298

(

5299

attribute type { "normal" }

5300

)

5301

5302

velocity_equation_choice =

5303

(

5304

## Select the equation used to solve for velocity.

5305

element equation {

5306

attribute name { "ShallowWater" }

5307

}

5308

)

5309

5310

scalar_equation_choice =

5311

(

5312

(

5313

## Select the equation used to solve for this field.

5314

## Advection Diffusion is the norm for scalar fields.

5315

## Works for all discretisation types.

5316

element equation {

5317

attribute name { "AdvectionDiffusion" }

5318

}|

5319

## ***UNDER TESTING***

5320

##

5321

## Select the equation used to solve for this field.

5322

## Conservation of Mass equation - requires the selection of a Density field.

5323

## ONLY WORKS FOR CONTROL VOLUME DISCRETISATIONS WITHOUT A

5324

## DIFFUSIVITY, SOURCE OR ABSORPTION.

5325

element equation {

5326

attribute name { "ConservationOfMass" },

5327

(

5328

## Select density to use in the Conservation of Mass Equation

5329

## Use the MaterialDensity - useful for multimaterial simulations

5330

## Clearly this requires a MaterialDensity field to be present

5331

element density {

5332

attribute name { "MaterialDensity" }

5333

}|

5334

## Select density to use in the Conservation of Mass Equation

5335

## Use the bulk Density

5336

## Clearly this requires a Density field to be present

5337

element density {

5338

attribute name { "Density" }

5339

}|

5340

## Select density to use in the Conservation of Mass Equation

5341

element density {

5342

attribute name { string }

5343

}

5344

)

5345

}|

5346

## ***UNDER TESTING***

5347

##

5348

## Select the equation used to solve for this field.

5349

## Reduced Conservation of Mass equation - requires the selection of a Density field.

5350

##

5351

## ONLY WORKS FOR CONTROL VOLUME DISCRETISATIONS WITHOUT A

5352

## DIFFUSIVITY, SOURCE OR ABSORPTION.

5353

##

5354

## This equation is very similar to a standard conservation of mass equation

5355

## except that the time discretisation uses only a single time level of density.

5356

## This enables consistency between the

5357

## MaterialVolumeFraction (ReducedConservationOfMass) and

5358

## MaterialDensity (Advection) equations in compressible multimaterial simulations.

5359

element equation {

5360

attribute name { "ReducedConservationOfMass" },

5361

(

5362

## Select density to use in the Reduced Conservation of Mass Equation

5363

## Use the MaterialDensity - useful for multimaterial simulations

5364

## Clearly this requires a MaterialDensity field to be present

5365

element density {

5366

attribute name { "MaterialDensity" }

5367

}|

5368

## Select density to use in the Reduced Conservation of Mass Equation

5369

## Use the bulk Density

5370

## Clearly this requires a Density field to be present

5371

element density {

5372

attribute name { "Density" }

5373

}|

5374

## Select density to use in the Reduced Conservation of Mass Equation

5375

element density {

5376

attribute name { string }

5377

}

5378

)

5379

}|

5380

## ***UNDER TESTING***

5381

##

5382

## Select the equation used to solve for this field.

5383

## Internal Energy equation - requires the selection of a Density field.

5384

## ONLY WORKS FOR CONTROL VOLUME DISCRETISATIONS WITHOUT A

5385

## DIFFUSIVITY, SOURCE OR ABSORPTION.

5386

## Solve the internal energy equation for this field.

5387

## Requires pressure and velocity fields to be present.

5388

## Uses a nonconservative time discretisation.

5389

element equation {

5390

attribute name { "InternalEnergy" },

5391

(

5392

## Select density to use in the Internal Energy Equation

5393

## Use the MaterialDensity - useful for multimaterial simulations

5394

## Clearly this requires a MaterialDensity field to be present

5395

## Whatever field is selected must be present.

5396

element density {

5397

attribute name { "MaterialDensity" }

5398

}|

5399

## Select density to use in the Internal Energy Equation

5400

## Use the bulk Density

5401

## Clearly this requires a Density field to be present

5402

## Whatever field is selected must be present.

5403

element density {

5404

attribute name { "Density" }

5405

}|

5406

## Select density to use in the Internal Energy Equation

5407

## Whatever field is selected must be present.

5408

element density {

5409

attribute name { string }

5410

}

5411

)

5412

}|

5413

## Option to solve for electrical potential from

5414

## electrokinetic, electrochemical or electrothermal sources

5415

element equation {

5416

attribute name { "ElectricalPotential" }

5417

}

5418

)

5419

)

5420

5421

inner_element_scalar =

5422

(

5423

## Inner element sub-grid scale model (Candy and Pain)

5424

## Requires continuous galerkin selected above.

5425

element inner_element {

5426

attribute replaces { "NSUBTLOC, NSUBNTLOC" },

5427

## Inner element solution of the scalar field.

5428

element scalar_field {

5429

attribute rank { "0" },

5430

attribute name { "InnerElement" },

5431

element prognostic {

5432

element mesh {

5433

attribute name { "InnerElementMesh" }

5434

},

5435

prognostic_scalar_output_options,

5436

prognostic_scalar_stat_options,

5437

prognostic_detector_options

5438

}

5439

}

5440

}

5441

)

5442

5443

inner_element_velocity =

5444

(

5445

## Inner element sub-grid scale model (Candy and Pain)

5446

## Requires continuous galerkin selected above.

5447

element inner_element {

5448

attribute replaces { "NSUBVLOC, NSUBNVLOC" },

5449

## SGS velocity in an inner element SGS treatment of momentum

5450

##

5451

## Limitations:

5452

## - Requires a geometry dimension of 3.

5453

## - Requires inner element active for momentum

5454

element vector_field {

5455

attribute rank { "1" },

5456

attribute name { "InnerElement" },

5457

element prognostic {

5458

element mesh {

5459

attribute name { "InnerElementMesh" }

5460

},

5461

prognostic_vector_output_options,

5462

prognostic_vector_stat_options,

5463

vector_convergence_options

5464

}

5465

},

5466

## A filter for the sub-grid scale equations

5467

## Add diffusion to matrix D of the Inner Element model

5468

element use_filter {

5469

## Strength of the diffusion term

5470

## Suggested value: 0.01

5471

element strength {

5472

real

5473

},

5474

empty

5475

}?,

5476

element use_quadratic_pressure {

5477

attribute replaces { "PREOPT=PREOPT+1000" }

5478

}?,

5479

element apply_full_discontinuous_Galerkin {

5480

attribute replaces { "PREOPT=PREOPT+10000" }

5481

}?

5482

}?

5483

)

5484

forcing =

5485

(

5486

## Add forcing from ocean data

5487

## If you enable this you MUST enable the /geometry/ocean_boundaries option too

5488

element ocean_forcing{

5489

## The netCDF data file downloaded from ERA-40 reanalysis

5490

element input_file {

5491

attribute file_name {xsd:string}

5492

},

5493

element mesh_choice {

5494

velocity_mesh_choice

5495

},

5496

element surface_stress {

5497

empty

5498

}?,

5499

element temperature_flux {

5500

empty

5501

}?,

5502

element salinity_flux {

5503

empty

5504

}?,

5505

element solar_radiation {

5506

empty

5507

}?

5508

}

5509

)

5510

5511

biology =

5512

(

5513

## Model of biological processes in the ocean.

5514

element ocean_biology{

5515

## A simple model of phytoplankton, zooplankton, general nutrient and detritus.

5516

element pznd {

5517

(

5518

## Python code specifying the source and sink relationships

5519

## between the biological tracers. This is usually achieved by

5520

## importing fluidity.ocean_biology and calling a scheme from there.

5521

element source_and_sink_algorithm {

5522

python_code

5523

}|

5524

## Do not calculate sources and sinks.

5525

## This option is generally only useful for testing.

5526

element disable_sources_and_sinks {

5527

empty

5528

}

5529

),

5530

# ## Phytoplankton

5531

# element scalar_field {

5532

# attribute rank { "0" },

5533

# attribute name { "Phytoplankton" },

5534

# (

5535

# element prognostic {

5536

# velocity_mesh_choice,

5537

# prognostic_scalar_field

5538

# }|

5539

# element prescribed {

5540

# velocity_mesh_choice,

5541

# prescribed_scalar_field

5542

# }

5543

# )

5544

# },

5545

# ## Zooplankton

5546

# element scalar_field {

5547

# attribute rank { "0" },

5548

# attribute name { "Zooplankton" },

5549

# (

5550

# element prognostic {

5551

# velocity_mesh_choice,

5552

# prognostic_scalar_field

5553

# }|

5554

# element prescribed {

5555

# velocity_mesh_choice,

5556

# prescribed_scalar_field

5557

# }

5558

# )

5559

# },

5560

# ## Nutrient

5561

# element scalar_field {

5562

# attribute rank { "0" },

5563

# attribute name { "Nutrient" },

5564

# (

5565

# element prognostic {

5566

# velocity_mesh_choice,

5567

# prognostic_scalar_field

5568

# }|

5569

# element prescribed {

5570

# velocity_mesh_choice,

5571

# prescribed_scalar_field

5572

# }

5573

# )

5574

# },

5575

# ## Detritus

5576

# element scalar_field {

5577

# attribute rank { "0" },

5578

# attribute name { "Detritus" },

5579

# (

5580

# element prognostic {

5581

# velocity_mesh_choice,

5582

# prognostic_scalar_field

5583

# }|

5584

# element prescribed {

5585

# velocity_mesh_choice,

5586

# prescribed_scalar_field

5587

# }

5588

# )

5589

# },

5590

## Photosynthetically Active Radiation (PAR)

5591

element scalar_field {

5592

attribute rank { "0" },

5593

attribute name { "PhotosyntheticRadiation" },

5594

(

5595

element prognostic {

5596

velocity_mesh_choice,

5597

prognostic_photosynthetic_radiation

5598

}|

5599

element prescribed {

5600

velocity_mesh_choice,

5601

prescribed_scalar_field

5602

}

5603

)

5604

}

5605

}

5606

}

5607

)

5608

5609

5610

prognostic_photosynthetic_radiation =

5611

(

5612

## PAR equation.

5613

element equation {

5614

attribute name { "PhotosyntheticRadiation" }

5615

},

5616

## Spatial discretisation options

5617

element spatial_discretisation {

5618

(

5619

## Discontinuous galerkin formulation. You can also use this

5620

## formulation with a continuous field in which case a simple

5621

## galerkin formulation will result.

5622

element discontinuous_galerkin {

5623

empty

5624

}

5625

)

5626

},

5627

(

5628

## Solver

5629

element solver {

5630

linear_solver_options_asym

5631

}

5632

),

5633

## Coefficients of absorption of photosynthetically active

5634

## radiation for water and phytoplankton.

5635

element absorption_coefficients {

5636

## Photosynthetically active radiation absorption coefficient for water.

5637

element water {

5638

real

5639

},

5640

## Photosynthetically active radiation absorption coefficient for water.

5641

element phytoplankton {

5642

real

5643

}

5644

},

5645

## Boundary conditions

5646

element boundary_conditions {

5647

attribute replaces { "boundary, TTPER1 TTPER2 TTPERI" },

5648

attribute name { string },

5649

## Surface id:

5650

element surface_ids {

5651

integer_vector

5652

},

5653

## Type

5654

(

5655

element type {

5656

attribute name { "dirichlet" },

5657

## Apply the dirichlet bc weakly. Only available with

5658

## discontinuous_galerkin, control_volume and

5659

## legacy_mixed_cv_cg spatial_discretisations.

5660

##

5661

## If not selected boundary conditions are applied strongly.

5662

element apply_weakly {

5663

empty

5664

},

5665

input_choice_real

5666

}|

5667

element type {

5668

attribute name { "neumann" },

5669

input_choice_real

5670

}|

5671

element type {

5672

attribute name { "robin" },

5673

element order_zero_coefficient {

5674

input_choice_real

5675

},

5676

element order_one_coefficient {

5677

input_choice_real

5678

}

5679

}

5680

)

5681

}+,

5682

prognostic_scalar_output_options,

5683

prognostic_scalar_stat_options,

5684

scalar_convergence_options,

5685

prognostic_detector_options,

5686

scalar_steady_state_options,

5687

adaptivity_options_scalar_field,

5688

## Set the priority of this field

5689

## This determines the order in which scalar_fields are solved for:

5690

## - higher numbers have the highest priority

5691

## - lower numbers (including negative) have the lowest priority

5692

## - default if not set is 0

5693

element priority {

5694

integer

5695

}?

5696

)

5697

5698

recalculation_options =

5699

(

5700

## Prevent this field from being recalculated at every timestep.

5701

## This is cheaper especially if you are enforcing discrete properties on the field.

5702

element do_not_recalculate {

5703

empty

5704

}

5705

)

5706

5707

discrete_properties_algorithm_scalar =

5708

(

5709

## Select discrete properties to enforce on the field

5710

## either after being prescribed or interpolated

5711

element enforce_discrete_properties {

5712

## Update this field using the lagrangian multiplier

5713

## calculated in the solenoidal projection of a

5714

## scalar field.

5715

##

5716

## Note this field must be specified as the update field

5717

## underneath that vector field too.

5718

##

5719

## Note also this only really makes sense for coupled

5720

## fields like velocity and pressure.

5721

element solenoidal_lagrange_update {

5722

empty

5723

}?

5724

}

5725

)

5726

5727

discrete_properties_algorithm_vector =

5728

(

5729

## Select discrete properties to enforce on the field

5730

## either after being prescribed or interpolated

5731

element enforce_discrete_properties {

5732

solenoidal_options?

5733

}

5734

)

5735

5736

solenoidal_options =

5737

## Constrained divergence-free projection.

5738

## This adds an additional constraint that ensures that the field

5739

## is solenoidal, i.e. divergence-free.

5740

## This is equivalent in cost to a pressure solve.

5741

## This is expensive, and thus best left until

5742

## needed.

5743

##

5744

## Note well: this only makes sense for nondivergent

5745

## vector fields, such as incompressible velocity!

5746

element solenoidal {

5747

## Options for the mass matrix of the field being interpolated

5748

element interpolated_field {

5749

(

5750

element continuous {

5751

## Lump the mass matrix for the assembly of the projection matrix

5752

## (not for the initial galerkin projection)

5753

##

5754

## Required when using interpolating continuous fields

5755

element lump_mass_matrix {

5756

## Lump on the submesh.

5757

## This only works for simplex meshes and is only

5758

## strictly valid on 2d meshes.

5759

element use_submesh {

5760

empty

5761

}?

5762

}

5763

}|

5764

element discontinuous {

5765

## Lump the mass matrix for the assembly of the projection matrix

5766

## (not for the initial galerkin projection)

5767

element lump_mass_matrix {

5768

empty

5769

}?

5770

}

5771

)

5772

},

5773

## Options for the lagrange multiplier

5774

##

5775

## Must be on a continuous mesh!

5776

element lagrange_multiplier {

5777

pressure_mesh_choice,

5778

element spatial_discretisation {

5779

(

5780

element continuous_galerkin {

5781

## Remove the stabilisation term from the projection operator.

5782

##

5783

## Automatic when not using P1P1.

5784

element remove_stabilisation_term {

5785

empty

5786

}?,

5787

## Integrate the divergence operator by parts.

5788

##

5789

## Automatic when projecting a discontinuous field

5790

element integrate_divergence_by_parts {

5791

empty

5792

}?

5793

}|

5794

element control_volumes {

5795

empty

5796

}

5797

)

5798

},

5799

element reference_node {

5800

integer

5801

}?,

5802

(

5803

## Update a scalar field using the lagrange multiplier from

5804

## the divergence free projection of this field. The selected

5805

## scalar field must have solenoidal selected in its interpolation

5806

## options too and it must be on the same mesh as used for the

5807

## solenoidal projection above.

5808

##

5809

## Note well: this only really makes sense for scalar fields linked to nondivergent

5810

## vector fields, such as pressure to incompressible velocity!

5811

element update_scalar_field {

5812

attribute name { "Pressure" },

5813

empty

5814

}|

5815

## Update a scalar field using the lagrange multiplier from

5816

## the divergence free projection of this field. The selected

5817

## scalar field must have solenoidal selected in its interpolation

5818

## options too and it must be on the same mesh as used for the

5819

## solenoidal projection above.

5820

##

5821

## Note well: this only really makes sense for scalar fields linked to nondivergent

5822

## vector fields, such as pressure to incompressible velocity!

5823

element update_scalar_field {

5824

attribute name { string },

5825

empty

5826

}

5827

)?,

5828

## Solver options for the linear solve.

5829

## This method requires the inversion of a projection matrix.

5830

element solver {

5831

linear_solver_options_sym

5832

}

5833

}

5834

}

5835

5836

represcribe_before_interpolation =

5837

## Represcribe the field before interpolation.

5838

##

5839

## This means the interpolation will not be conservative from the previous mesh so be careful what you're trying to achieve!

5840

element represcribe_before_interpolation {

5841

empty

5842

}

5843