MoabSkinner

Re-generate the OpenMC geometry on-the-fly according to changes in the mesh geometry and/or contours in temperature and density

Description

This user object bins the spatial domain according to three characteristics:

temperature (by grouping elements into n_temperature_bins with equal spacing between temperature_min and temperature_max
density (by grouping elements into n_density_bins with equal spacing between density_min and density_max)
subdomain

For example, suppose the domain consists of two subdomains, with temperature and density distributions as shown in the top row of Figure 1. The elements are then grouped into individualized bins, according to unique combinations of the temperature bin, the density bin, and the subdomain bin. In the lower right of Figure 1 is then shown the surface skins produced internally, which can be used to define the boundaries of new regions on which to track particles.

Figure 1: Mesh skinning operation

tip

You can visualize this user object (i.e., the bin indices) using a SpatialUserObjectAux.

Example Input Syntax

Below is an example input file that skins a mesh, generating the bin distributions shown in Figure 1.

[UserObjects<<<{"href": "../../syntax/UserObjects/index.html"}>>>]
  [moab]
    type = MoabSkinner<<<{"description": "Re-generate the OpenMC geometry on-the-fly according to changes in the mesh geometry and/or contours in temperature and density", "href": "MoabSkinner.html"}>>>
    verbose<<<{"description": "Whether to print diagnostic information"}>>> = true
    material_names<<<{"description": "List of names for each subdomain to use for naming the new volumes created in MOAB. You only need to set this if using this skinner independent of OpenMC; otherwise, these names are auto-deduced from OpenMC"}>>> = "mat mat"

    temperature<<<{"description": "Temperature variable by which to bin elements"}>>> = temp
    n_temperature_bins<<<{"description": "Number of temperature bins"}>>> = 3
    temperature_min<<<{"description": "Lower bound of temperature bins"}>>> = 445.0
    temperature_max<<<{"description": "Upper bound of temperature bins"}>>> = 655.0

    density<<<{"description": "Density variable by which to bin elements"}>>> = rho
    n_density_bins<<<{"description": "Number of density bins"}>>> = 5
    density_min<<<{"description": "Lower bound of density bins"}>>> = 445.0
    density_max<<<{"description": "Upper bound of density bins"}>>> = 655.0

    output_skins<<<{"description": "Whether the skinned MOAB mesh (skins generated from the libMesh [Mesh]) should be written to a file. The files will be named moab_skins_<n>.h5m, where <n> is the time step index. You can then visualize these files by running 'mbconvert'."}>>> = true
  []
[]

The binning, colored on a per-element basis as shown in Figure 1 can be visualized with the SkinnedBins auxiliary kernel.

Input Parameters

n_temperature_binsNumber of temperature bins
C++ Type:unsigned int
Controllable:No
Description:Number of temperature bins
temperatureTemperature variable by which to bin elements
C++ Type:std::string
Controllable:No
Description:Temperature variable by which to bin elements
temperature_maxUpper bound of temperature bins
C++ Type:double
Unit:(no unit assumed)
Controllable:No
Description:Upper bound of temperature bins

Required Parameters

build_graveyardFalseWhether to build a graveyard around the geometry
Default:False
C++ Type:bool
Controllable:No
Description:Whether to build a graveyard around the geometry
densityDensity variable by which to bin elements
C++ Type:std::string
Controllable:No
Description:Density variable by which to bin elements
density_maxUpper bound of density bins
C++ Type:double
Unit:(no unit assumed)
Controllable:No
Description:Upper bound of density bins
density_min0Lower bound of density bins
Default:0
C++ Type:double
Unit:(no unit assumed)
Controllable:No
Description:Lower bound of density bins
faceting_tol0.0001Faceting tolerance for DagMC
Default:0.0001
C++ Type:double
Unit:(no unit assumed)
Controllable:No
Description:Faceting tolerance for DagMC
geom_tol1e-06Geometry tolerance for DagMC
Default:1e-06
C++ Type:double
Unit:(no unit assumed)
Controllable:No
Description:Geometry tolerance for DagMC
graveyard_scale_inner1.01Multiplier on mesh bounding box to form inner graveyard surface
Default:1.01
C++ Type:double
Unit:(no unit assumed)
Controllable:No
Description:Multiplier on mesh bounding box to form inner graveyard surface
graveyard_scale_outer1.1Multiplier on mesh bounding box to form outer graveyard surface
Default:1.1
C++ Type:double
Unit:(no unit assumed)
Controllable:No
Description:Multiplier on mesh bounding box to form outer graveyard surface
material_namesList of names for each subdomain to use for naming the new volumes created in MOAB. You only need to set this if using this skinner independent of OpenMC; otherwise, these names are auto-deduced from OpenMC
C++ Type:std::vector<std::string>
Controllable:No
Description:List of names for each subdomain to use for naming the new volumes created in MOAB. You only need to set this if using this skinner independent of OpenMC; otherwise, these names are auto-deduced from OpenMC
n_density_binsNumber of density bins
C++ Type:unsigned int
Controllable:No
Description:Number of density bins
output_fullFalseWhether the MOAB mesh (copied from the libMesh [Mesh]) should be written to a file. The files will be named moab_full_.h5m, where is the time step index. You can then visualize these files by running 'mbconvert'.
Default:False
C++ Type:bool
Controllable:No
Description:Whether the MOAB mesh (copied from the libMesh [Mesh]) should be written to a file. The files will be named moab_full_.h5m, where is the time step index. You can then visualize these files by running 'mbconvert'.
output_skinsFalseWhether the skinned MOAB mesh (skins generated from the libMesh [Mesh]) should be written to a file. The files will be named moab_skins_.h5m, where is the time step index. You can then visualize these files by running 'mbconvert'.
Default:False
C++ Type:bool
Controllable:No
Description:Whether the skinned MOAB mesh (skins generated from the libMesh [Mesh]) should be written to a file. The files will be named moab_skins_.h5m, where is the time step index. You can then visualize these files by running 'mbconvert'.
temperature_min0Lower bound of temperature bins
Default:0
C++ Type:double
Unit:(no unit assumed)
Controllable:No
Description:Lower bound of temperature bins
verboseFalseWhether to print diagnostic information
Default:False
C++ Type:bool
Controllable:No
Description:Whether to print diagnostic information

Optional Parameters

allow_duplicate_execution_on_initialFalseIn the case where this UserObject is depended upon by an initial condition, allow it to be executed twice during the initial setup (once before the IC and again after mesh adaptivity (if applicable).
Default:False
C++ Type:bool
Controllable:No
Description:In the case where this UserObject is depended upon by an initial condition, allow it to be executed twice during the initial setup (once before the IC and again after mesh adaptivity (if applicable).
execute_onTIMESTEP_ENDThe list of flag(s) indicating when this object should be executed. For a description of each flag, see https://mooseframework.inl.gov/source/interfaces/SetupInterface.html.
Default:TIMESTEP_END
C++ Type:ExecFlagEnum
Options:NONE, INITIAL, LINEAR, LINEAR_CONVERGENCE, NONLINEAR, NONLINEAR_CONVERGENCE, POSTCHECK, TIMESTEP_END, TIMESTEP_BEGIN, MULTIAPP_FIXED_POINT_END, MULTIAPP_FIXED_POINT_BEGIN, MULTIAPP_FIXED_POINT_CONVERGENCE, FINAL, CUSTOM
Controllable:No
Description:The list of flag(s) indicating when this object should be executed. For a description of each flag, see https://mooseframework.inl.gov/source/interfaces/SetupInterface.html.
execution_order_group0Execution order groups are executed in increasing order (e.g., the lowest number is executed first). Note that negative group numbers may be used to execute groups before the default (0) group. Please refer to the user object documentation for ordering of user object execution within a group.
Default:0
C++ Type:int
Controllable:No
Description:Execution order groups are executed in increasing order (e.g., the lowest number is executed first). Note that negative group numbers may be used to execute groups before the default (0) group. Please refer to the user object documentation for ordering of user object execution within a group.
force_postauxFalseForces the UserObject to be executed in POSTAUX
Default:False
C++ Type:bool
Controllable:No
Description:Forces the UserObject to be executed in POSTAUX
force_preauxFalseForces the UserObject to be executed in PREAUX
Default:False
C++ Type:bool
Controllable:No
Description:Forces the UserObject to be executed in PREAUX
force_preicFalseForces the UserObject to be executed in PREIC during initial setup
Default:False
C++ Type:bool
Controllable:No
Description:Forces the UserObject to be executed in PREIC during initial setup

Execution Scheduling Parameters

control_tagsAdds user-defined labels for accessing object parameters via control logic.
C++ Type:std::vector<std::string>
Controllable:No
Description:Adds user-defined labels for accessing object parameters via control logic.
enableTrueSet the enabled status of the MooseObject.
Default:True
C++ Type:bool
Controllable:Yes
Description:Set the enabled status of the MooseObject.
use_displaced_meshFalseWhether the skinned mesh should be generated from a displaced mesh
Default:False
C++ Type:bool
Controllable:No
Description:Whether the skinned mesh should be generated from a displaced mesh

Advanced Parameters

prop_getter_suffixAn optional suffix parameter that can be appended to any attempt to retrieve/get material properties. The suffix will be prepended with a '_' character.
C++ Type:MaterialPropertyName
Unit:(no unit assumed)
Controllable:No
Description:An optional suffix parameter that can be appended to any attempt to retrieve/get material properties. The suffix will be prepended with a '_' character.
use_interpolated_stateFalseFor the old and older state use projected material properties interpolated at the quadrature points. To set up projection use the ProjectedStatefulMaterialStorageAction.
Default:False
C++ Type:bool
Controllable:No
Description:For the old and older state use projected material properties interpolated at the quadrature points. To set up projection use the ProjectedStatefulMaterialStorageAction.

Material Property Retrieval Parameters

(cardinal/test/tests/userobjects/moab_skinner/all_bins.i)

[Mesh]
  [cube]
    type = FileMeshGenerator
    file = ../../neutronics/meshes/tet_cube.e
  []
  [id1]
    type = ParsedSubdomainMeshGenerator
    input = cube
    combinatorial_geometry = 'z < 0.0'
    block_id = 1
    epsilon = 1e-8
  []
  [id2]
    type = ParsedSubdomainMeshGenerator
    input = id1
    combinatorial_geometry = 'z >= 0.0'
    block_id = 3
    epsilon = 1e-8
  []
[]

[Problem]
  type = FEProblem
  solve = false
[]

[AuxVariables]
  [rho]
    family = MONOMIAL
    order = CONSTANT
  []
  [temp]
    family = MONOMIAL
    order = CONSTANT
  []
  [rho_bins]
    family = MONOMIAL
    order = CONSTANT
  []
  [temp_bins]
    family = MONOMIAL
    order = CONSTANT
  []
  [subdomain_bins]
    family = MONOMIAL
    order = CONSTANT
  []
  [bins]
    family = MONOMIAL
    order = CONSTANT
  []
[]

[AuxKernels]
  [rho]
    type = FunctionAux
    variable = rho
    function = rho
    execute_on = timestep_begin
  []
  [temp]
    type = FunctionAux
    variable = temp
    function = temp
    execute_on = timestep_begin
  []
  [rho_bins]
    type = SkinnedBins
    variable = rho_bins
    skinner = moab
    skin_by = density
  []
  [temp_bins]
    type = SkinnedBins
    variable = temp_bins
    skinner = moab
    skin_by = temperature
  []
  [subdomain_bins]
    type = SkinnedBins
    variable = subdomain_bins
    skinner = moab
    skin_by = subdomain
  []
  [bins]
    type = SkinnedBins
    variable = bins
    skinner = moab
  []
[]

[Functions]
  [temp]
    type = ParsedFunction
    expression = 400+x*100+100*t
  []
  [rho]
    type = ParsedFunction
    expression = 400+y*100+100*t
  []
[]

[UserObjects]
  [moab]
    type = MoabSkinner
    verbose = true
    material_names = "mat mat"

    temperature = temp
    n_temperature_bins = 3
    temperature_min = 445.0
    temperature_max = 655.0

    density = rho
    n_density_bins = 5
    density_min = 445.0
    density_max = 655.0

    output_skins = true
  []
[]

[Executioner]
  type = Transient
  num_steps = 2
[]

[Outputs]
  exodus = true
  hide = 'temp rho'
[]

Description
Example Input Syntax
Input Parameters