Pre-processing Utilities¶

PreProcessDriver¶

class sierra::nalu::PreProcessDriver¶

A driver that runs all preprocessor tasks.

This class is responsible for reading the input file, parsing the user-requested list of tasks, initializing the task instances, executing them, and finally writing out the updated Exodus database with changed inputs.

Public Functions

PreProcessDriver(stk::ParallelMachine &comm, const std::string filename)¶

Parameters

comm: MPI Communicator reference
filename: Name of the YAML input file

void run()¶: Run all tasks and output the updated Exodus database.

PreProcessingTask¶

class sierra::nalu::PreProcessingTask¶

An abstract implementation of a PreProcessingTask.

This class defines the interface for a pre-processing task and contains the infrastructure to allow concrete implementations of pre-processing tasks to register themselves for automatic runtime discovery. Derived classes must implement two methods:

initialize - Perform actions on STK MetaData before processing BulkData
run - All actions on BulkData and other operations on mesh after it has been loaded from the disk.

For automatic class registration, the derived classes must implement a constructor that takes two arguments: a CFDMesh reference, and a const reference to YAML::Node that contains the inputs necessary for the concrete task implementation. It is the derived class’ responsibility to process the input dictionary and perform error checking. No STK mesh manipulations must occur in the constructor.

Subclassed by sierra::nalu::ABLFields, sierra::nalu::BdyIOPlanes, sierra::nalu::NDTW2D, sierra::nalu::RotateMesh, sierra::nalu::SamplingPlanes

Public Functions

PreProcessingTask(CFDMesh &mesh)¶

Parameters

mesh: A CFDMesh instance

Public Static Functions

PreProcessingTask *create(CFDMesh &mesh, const YAML::Node &node, std::string lookup)¶: Runtime creation of concrete task instance.

Protected Attributes

CFDMesh &mesh_¶: Reference to the CFDMesh instance.

ABLFields¶

class sierra::nalu::ABLFields¶

Initialize velocity and temperature fields for ABL simulations.

This task is activated by using the init_abl_fields task in the preprocessing input file. It requires a section init_abl_fields in the nalu_preprocess section with the following parameters:

init_abl_fields:
  fluid_parts: [Unspecified-2-HEX]

  temperature:
    heights: [    0, 650.0, 750.0, 10750.0]
    values:  [280.0, 280.0, 288.0,   318.0]

  velocity:
    heights: [0.0, 10.0, 30.0, 70.0, 100.0, 650.0, 10000.0]
    values:
      - [ 0.0, 0.0, 0.0]
      - [4.81947, -4.81947, 0.0]
      - [5.63845, -5.63845, 0.0]
      - [6.36396, -6.36396, 0.0]
      - [6.69663, -6.69663, 0.0]
      - [8.74957, -8.74957, 0.0]
      - [8.74957, -8.74957, 0.0]

The sections temperature and velocity are optional, allowing the user to initialize only the temperature or the velocity as desired. The heights are in meters, the temperature is the potential temperature in Kelvin, and the velocity is the actual vector in m/s. Currently, the code does not include the ability to automatically convert (mangitude, direction) to velocity vectors.

Inherits from sierra::nalu::PreProcessingTask

Public Functions

void initialize()¶: Declare velocity and temperature fields and register them for output.

void run()¶: Initialize the velocity and/or temperature fields by linear interpolation.

Private Functions

void load(const YAML::Node &abl)¶: Parse the YAML file and initialize parameters.

void load_velocity_info(const YAML::Node &abl)¶: Helper function to parse and initialize velocity inputs.

void load_temperature_info(const YAML::Node &abl)¶: Helper function to parse and initialize temperature inputs.

void init_velocity_field()¶: Initialize the velocity field through linear interpolation.

void init_temperature_field()¶: Intialize the temperature field through linear interpolation.

Private Members

stk::mesh::MetaData &meta_¶: STK Metadata object.

stk::mesh::BulkData &bulk_¶: STK Bulkdata object.

stk::mesh::PartVector fluid_parts_¶: Parts of the fluid mesh where velocity/temperature is initialized.

std::vector<double> vHeights_¶: List of heights where velocity is defined.

Array2D<double> velocity_¶: List of velocity (3-d components) at the user-defined heights.

std::vector<double> THeights_¶: List of heights where temperature is defined.

std::vector<double> TValues_¶: List of temperatures (K) at user-defined heights (THeights_)

int ndim_¶: Dimensionality of the mesh.

bool doVelocity_¶: Flag indicating whether velocity is initialized.

bool doTemperature_¶: Flag indicating whether temperature is initialized.

BdyIOPlanes¶

class sierra::nalu::BdyIOPlanes¶

Extract boundary planes for I/O mesh.

Given an ABL precursor mesh, this utility extracts the specified boundaries and creates a new IO Transfer mesh for use with ABL precursor simulations.

Inherits from sierra::nalu::PreProcessingTask

Public Functions

void initialize()¶

Register boundary parts and attach coordinates to the parts.

The parts are created as SHELL elements to as needed by the Nalu Transfer class.

void run()¶: Copy user specified boundaries and save the IO Transfer mesh.

Private Functions

void load(const YAML::Node &node)¶: Parse user inputs from the YAML file.

void create_boundary(const std::string bdyName)¶: Copy the boundary from Fluid mesh to the IO Xfer mesh.

Private Members

CFDMesh &mesh_¶: Original mesh DB information.

CFDMesh iomesh_¶: IO Mesh db STK meta and bulk data.

std::vector<std::string> bdyNames_¶: User specified list of boundaries to be extracted.

std::string output_db_ = {""}¶: Name of the I/O db where the boundaries are written out.

SamplingPlanes¶

class sierra::nalu::SamplingPlanes¶

Generate 2-D grids/planes for data sampling.

Currently only generates horizontal planes at user-defined heights.

Requires a section generate_planes in the input file within the nalu_preprocess section:

generate_planes:
  fluid_part: Unspecified-2-hex

  heights: [ 70.0 ]
  part_name_format: "zplane_%06.1f"

  dx: 12.0
  dy: 12.0

With the above input definition, it will use the bounding box of the fluid_part to determine the bounding box of the plane to be generated. This will provide coordinate axis aligned sapling planes in x and y directions. Alternately, the user can specify boundary_type to be quad_vertices and provide the vertices of the quadrilateral that is used to generate the sampling plane as shown below:

generate_planes:
  boundary_type: quad_vertices
  fluid_part: Unspecified-2-hex

  heights: [ 50.0, 70.0, 90.0 ]
  part_name_format: "zplane_%06.1f"

  nx: 25  # Number of divisions along (1-2) and (4-3) vertices
  ny: 25  # Number of divisions along (1-4) and (2-3) vertices
  vertices:
    - [250.0, 0.0]
    - [500.0, -250.0]
    - [750.0, 0.0]
    - [500.0, 250.0]

part_name_format is a printf-like format specification that takes one argument - the height as a floating point number. The user can use this to tailor how the nodesets or the shell parts are named in the output Exodus file.

Inherits from sierra::nalu::PreProcessingTask

Public Types

enum PlaneBoundaryType¶

Sampling Plane boundary type.

Values:

BOUND_BOX = 0¶: Use bounding box of the fluid mesh defined.

QUAD_VERTICES¶: Use user-defined vertex list for plane boundary.

Private Functions

void calc_bounding_box()¶: Use fluid Realm mesh to estimate the x-y bounding box for the sampling planes.

void generate_zplane(const double zh)¶: Generate entities and update coordinates for a given sampling plane.

Private Members

stk::mesh::MetaData &meta_¶: STK Metadata object.

stk::mesh::BulkData &bulk_¶: STK Bulkdata object.

std::vector<double> heights_¶: Heights where the averaging planes are generated.

std::array<std::array<double, 3>, 2> bBox_¶: Bounding box of the original mesh.

std::string name_format_¶: Format specification for the part name.

std::vector<std::string> fluidPartNames_¶: Fluid realm parts (to determine mesh bounding box)

stk::mesh::PartVector fluidParts_¶: Parts of the fluid mesh (to determine mesh bounding box)

double dx_¶: Spatial resolution in x and y directions.

double dy_¶: Spatial resolution in x and y directions.

size_t nx_¶: Number of nodes in x and y directions.

size_t mx_¶: Number of elements in x and y directions.

int ndim_¶: Dimensionality of the mesh.

PlaneBoundaryType bdyType_ = {BOUND_BOX}¶: User defined selection of plane boundary type.

RotateMesh¶

class sierra::nalu::RotateMesh¶

Rotate a mesh.

rotate_mesh:
  mesh_parts:
    - unspecified-2-hex

  angle: 45.0
  origin: [500.0, 0.0, 0.0]
  axis: [0.0, 0.0, 1.0]

Inherits from sierra::nalu::PreProcessingTask

Private Members

stk::mesh::MetaData &meta_¶: STK Metadata object.

stk::mesh::BulkData &bulk_¶: STK Bulkdata object.

std::vector<std::string> meshPartNames_¶: Part names of the mesh that needs to be rotated.

stk::mesh::PartVector meshParts_¶: Parts of the mesh that need to be rotated.

double angle_¶: Angle of rotation.

std::vector<double> origin_¶: Point about which rotation is performed.

std::vector<double> axis_¶: Axis around which the rotation is performed.

int ndim_¶: Dimensionality of the mesh.

NDTW2D¶

class sierra::nalu::NDTW2D¶

2-D Nearest distance to wall calculator

Calculates a new field NDTW containing the wall distance for 2-D airfoil-like applications used in RANS wall models.

Inherits from sierra::nalu::PreProcessingTask

Public Functions

void initialize()¶: Initialize the NDTW field and register for output.

void run()¶: Calculate wall distance and update NDTW field.