SolutionRasterizer

Process an XYZ file of atomic coordinates and filter atoms via threshold or map variable values.

Mesoscale microstructure simulations using the phase field method can be utilized to generate initial structures for large scale molecular dynamics simulations. One application is the construction of nano-foam atomistic samples from simulations of spinodal decomposition.

Nano foam atomistic configuration generated using the SolutionRasterizer.

MOOSE provides a built in system to template an atomic coordinate file in the .xyz format from the simulation result in a given mesh file. The workflow is as follows

  1. Set up a phase field simulation and output a finite element mesh file

  2. Create a bulk .xyz input file with the desired underlying lattice and crystal structure

  3. Use the minimal input file shown below to load the mesh and .xyz input

MOOSE will load the .xyz input and finite element mesh superpose both and use thresholding to carve out _rejected_ atoms while retaining _accepted_ atoms. Finally a new .xyz output is written containing only the _accepted_ atoms, generating a porous microstructure.

The SolutionRasterizer user object is derived from the SolutionUserObject and inherits its input parameters. It takes the following additional input parameters:

Input ParameterDescription
xyz_inputAn .xyz file as an input file. This input file should contain an atomistic simulation cell completely filled with atoms of a chosen crystal structure (a polycrystalline sample can be supplied).
xyz_outputOutput .xyz file containing the filtered (or mapped) atomic coordinate file.
raster_mode = FILTERIn FILTER mode the SolutionRasterizer uses thresholding on a specified non-linear variable to reject or accept atom from the input file to pass to the output .xyz file.
raster_mode = MAPIn MAP mode the SolutionRasterizer takes the atoms from the input file and add an additional column to the data set containing the value of a specified non-linear variable.
thresholdValue of the selected non-linear variable to use in FILTER mode used to _accept_ or _reject_ atoms from the xyz_input file.

Minimal working input file

The following input can be executed with the MOOSE Phase Field module executable and will

  • load the mesh file diffuse_out.e

  • load the atomic coordinate file in.xyz

  • accept all atoms at the coordinates where the value of the non-linear variable c is above a value of 0.5

  • write out the atomic coordinate file out.xyz

[Mesh]
  type = GeneratedMesh
  dim = 3
[]

[Problem]
  kernel_coverage_check = false
  solve = false
[]

[Executioner]
  type = Steady
[]

[UserObjects]
  [./soln]
    type = SolutionRasterizer
    system_variables = 'c'
    mesh = diffuse_out.e
    execute_on = timestep_begin

    variable = c
    xyz_input = in.xyz
    xyz_output = out.xyz

    # raster_mode = MAP
    raster_mode = FILTER
    threshold = 0.5
  [../]
[]
(moose/modules/phase_field/test/tests/solution_rasterizer/raster.i)

Input Parameters

  • meshThe name of the mesh file (must be xda/xdr or exodusII file).

    C++ Type:MeshFileName

    Unit:(no unit assumed)

    Controllable:No

    Description:The name of the mesh file (must be xda/xdr or exodusII file).

  • variableVariable from the mesh file to use for mapping to or filtering of the atoms.

    C++ Type:std::string

    Unit:(no unit assumed)

    Controllable:No

    Description:Variable from the mesh file to use for mapping to or filtering of the atoms.

  • xyz_inputXYZ input file.

    C++ Type:FileName

    Unit:(no unit assumed)

    Controllable:No

    Description:XYZ input file.

  • xyz_outputXYZ output file.

    C++ Type:FileName

    Unit:(no unit assumed)

    Controllable:No

    Description:XYZ output file.

Required Parameters

  • esThe name of the file holding the equation system info in xda/xdr format (xda/xdr only).

    Default:

    C++ Type:FileName

    Unit:(no unit assumed)

    Controllable:No

    Description:The name of the file holding the equation system info in xda/xdr format (xda/xdr only).

  • 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

    Unit:(no unit assumed)

    Options:NONE, INITIAL, LINEAR, NONLINEAR_CONVERGENCE, NONLINEAR, POSTCHECK, TIMESTEP_END, TIMESTEP_BEGIN, MULTIAPP_FIXED_POINT_END, MULTIAPP_FIXED_POINT_BEGIN, 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.

  • 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.

  • raster_modeMAPRasterization mode (MAP|FILTER).

    Default:MAP

    C++ Type:MooseEnum

    Unit:(no unit assumed)

    Options:MAP, FILTER

    Controllable:No

    Description:Rasterization mode (MAP|FILTER).

  • rotation1_vector0 0 1Vector about which to rotate points of the simulation.

    Default:0 0 1

    C++ Type:libMesh::VectorValue<double>

    Unit:(no unit assumed)

    Controllable:No

    Description:Vector about which to rotate points of the simulation.

  • systemnl0The name of the system to pull values out of (xda/xdr only). The default name for the nonlinear system is 'nl0', auxiliary system is 'aux0'

    Default:nl0

    C++ Type:std::string

    Unit:(no unit assumed)

    Controllable:No

    Description:The name of the system to pull values out of (xda/xdr only). The default name for the nonlinear system is 'nl0', auxiliary system is 'aux0'

  • system_variablesThe name of the nodal and elemental variables from the file you want to use for values

    C++ Type:std::vector<std::string>

    Unit:(no unit assumed)

    Controllable:No

    Description:The name of the nodal and elemental variables from the file you want to use for values

  • thresholdAccept atoms with a variable value above this threshold in FILTER mode.

    C++ Type:double

    Unit:(no unit assumed)

    Controllable:No

    Description:Accept atoms with a variable value above this threshold in FILTER mode.

  • timestepIndex of the single timestep used or "LATEST" for the last timestep (exodusII only). If not supplied, time interpolation will occur.

    C++ Type:std::string

    Unit:(no unit assumed)

    Controllable:No

    Description:Index of the single timestep used or "LATEST" for the last timestep (exodusII only). If not supplied, time interpolation will occur.

  • 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

    Unit:(no unit assumed)

    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.

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

    Unit:(no unit assumed)

    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).

  • control_tagsAdds user-defined labels for accessing object parameters via control logic.

    C++ Type:std::vector<std::string>

    Unit:(no unit assumed)

    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

    Unit:(no unit assumed)

    Controllable:Yes

    Description:Set the enabled status of the MooseObject.

  • 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

    Unit:(no unit assumed)

    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

    Unit:(no unit assumed)

    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

    Unit:(no unit assumed)

    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

    Unit:(no unit assumed)

    Controllable:No

    Description:Forces the UserObject to be executed in PREIC during initial setup

  • use_displaced_meshFalseWhether or not this object should use the displaced mesh for computation. Note that in the case this is true but no displacements are provided in the Mesh block the undisplaced mesh will still be used.

    Default:False

    C++ Type:bool

    Unit:(no unit assumed)

    Controllable:No

    Description:Whether or not this object should use the displaced mesh for computation. Note that in the case this is true but no displacements are provided in the Mesh block the undisplaced mesh will still be used.

Advanced Parameters

  • rotation0_angle0Anticlockwise rotation angle (in degrees) to use for rotation about rotation0_vector.

    Default:0

    C++ Type:double

    Unit:(no unit assumed)

    Controllable:No

    Description:Anticlockwise rotation angle (in degrees) to use for rotation about rotation0_vector.

  • rotation0_vector0 0 1Vector about which to rotate points of the simulation.

    Default:0 0 1

    C++ Type:libMesh::VectorValue<double>

    Unit:(no unit assumed)

    Controllable:No

    Description:Vector about which to rotate points of the simulation.

  • rotation1_angle0Anticlockwise rotation angle (in degrees) to use for rotation about rotation1_vector.

    Default:0

    C++ Type:double

    Unit:(no unit assumed)

    Controllable:No

    Description:Anticlockwise rotation angle (in degrees) to use for rotation about rotation1_vector.

  • scale1 1 1 Scale factor for points in the simulation

    Default:1 1 1

    C++ Type:std::vector<double>

    Unit:(no unit assumed)

    Controllable:No

    Description:Scale factor for points in the simulation

  • scale_multiplier1 1 1 Scale multiplying factor for points in the simulation

    Default:1 1 1

    C++ Type:std::vector<double>

    Unit:(no unit assumed)

    Controllable:No

    Description:Scale multiplying factor for points in the simulation

  • transformation_ordertranslation scaleThe order to perform the operations in. Define R0 to be the rotation matrix encoded by rotation0_vector and rotation0_angle. Similarly for R1. Denote the scale by s, the scale_multiplier by m, and the translation by t. Then, given a point x in the simulation, if transformation_order = 'rotation0 scale_multiplier translation scale rotation1' then form p = R1*(R0*x*m - t)/s. Then the values provided by the SolutionUserObject at point x in the simulation are the variable values at point p in the mesh.

    Default:translation scale

    C++ Type:MultiMooseEnum

    Unit:(no unit assumed)

    Options:rotation0, translation, scale, rotation1, scale_multiplier

    Controllable:No

    Description:The order to perform the operations in. Define R0 to be the rotation matrix encoded by rotation0_vector and rotation0_angle. Similarly for R1. Denote the scale by s, the scale_multiplier by m, and the translation by t. Then, given a point x in the simulation, if transformation_order = 'rotation0 scale_multiplier translation scale rotation1' then form p = R1*(R0*x*m - t)/s. Then the values provided by the SolutionUserObject at point x in the simulation are the variable values at point p in the mesh.

  • translation0 0 0 Translation factors for x,y,z coordinates of the simulation

    Default:0 0 0

    C++ Type:std::vector<double>

    Unit:(no unit assumed)

    Controllable:No

    Description:Translation factors for x,y,z coordinates of the simulation

Coordinate System Transformation Parameters