Core Utilities

CFDMesh

class CFDMesh

STK Mesh interface.

This class provides a thin wrapper around the STK mesh objects (MetaData, BulkData, and StkMeshIoBroker) for use with various preprocessing utilities.

Public Functions

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

Create a CFD mesh instance from an existing mesh database.

Parameters

  • comm: MPI Communicator object

  • filename: Exodus database filename

CFDMesh(stk::ParallelMachine &comm, const int ndim)

Create a CFD mesh instance from scratch.

Parameters

  • comm: MPI Communicator object

  • ndim: Dimensionality of mesh

~CFDMesh()
void init(stk::io::DatabasePurpose db_purpose = stk::io::READ_MESH)

Initialize the mesh database.

If an input DB is provided, the mesh is read from the file. The MetaData is committed and the BulkData is ready for use/manipulation.

stk::ParallelMachine &comm()

Reference to the MPI communicator object.

stk::mesh::MetaData &meta()

Reference to the stk::mesh::MetaData instance.

stk::mesh::BulkData &bulk()

Reference to the stk::mesh::BulkData instance.

stk::io::StkMeshIoBroker &stkio()

Reference to the STK mesh I/O instance.

void add_output_field(const std::string field)

Register a field for output during write.

Parameters

  • field: Name of the field to be output

size_t open_database(std::string output_db)

Open a database for writing time series data.

Return

A valid file handle for use with write_database

See

write_database, write_timesteps

Parameters

  • output_db: Pathname to the output ExodusII database

void write_database(size_t fh, double time)

Write time series data to an open database.

See

open_database, write_timesteps

Parameters

  • fh: Valid file handle

  • time: Time to write

void write_database(std::string output_db, double time = 0.0)

Write the Exodus results database with modifications.

See

write_database_with_fields

Parameters

  • output_db: Pathname to the output ExodusII database

  • time: Timestep to write

Parameters

  • output_db: Filename for the output Exodus database

  • time: (Optional) time to write (default = 0.0)

void write_database_with_fields(std::string output_db)

Write database with restart fields.

Copies the restart data fields from the input Exodus database to the output database.

Parameters

  • output_db: Pathname to the output ExodusII database

template<typename Functor>
void write_timesteps(std::string output_db, int num_steps, Functor lambdaFunc)

Write time-history to database.

This method accepts a functor that takes one integer argument (timestep) and returns the time (double) that must be written to the database. The functor should update the fields that are being written to the database. An example would be to simulate mesh motion by updating the mesh_displacement field at every timestep.

The following example shows the use with a C++ lambda function:

double deltaT = 0.01;  // Timestep size

write_timesteps("inflow_history.exo", 100,
  [&](int tstep) {
      double time = tstep * deltaT;

      // Update velocity and coordinates

      return time;
});

BoxType calc_bounding_box(const stk::mesh::Selector selector, bool verbose = true)

Calculate the bounding box of the mesh.

The selector can pick parts that are not contiguous. However, the bounding box returned will be the biggest box that encloses all parts selected.

Return

An stk::search::Box instance containing the min and max points (3-D).

Parameters

  • selector: An instance of stk::mesh::Selector to filter parts of the mesh where bounding box is calculated.

  • verbose: If true, then print out the bounding box to standard output.

void set_decomposition_type(std::string decompType)

Set automatic mesh decomposition property.

Valid decomposition types are: rcb, rib, block, linear

Parameters

  • decompType: The decomposition type

void set_64bit_flags()

Force output database to use 8-bit integers.

bool db_modified()

Flag indicating whether the DB has been modified.

void set_write_flag(bool flag = true)

Force output of the results DB.

const std::unordered_set<std::string> &output_fields()

Return a reference to the registered output fields.

Interpolation utilities

struct OutOfBounds

Flags and actions for out-of-bounds operation.

Public Types

enum boundLimits

Out of bounds limit types.

Values:

LOWLIM = -2

xtgt < xarray[0]

UPLIM = -1

xtgt > xarray[N]

VALID = 0

xarray[0] <= xtgt <= xarray[N]

enum OobAction

Flags indicating action to perform on Out of Bounds situation.

Values:

ERROR = 0

Raise runtime error.

WARN

Warn and then CLAMP.

CLAMP

Clamp values to the end points.

EXTRAPOLATE

Extrapolate linearly based on end point.

template<typename T>
InterpTraits<T>::index_type sierra::nalu::utils::check_bounds(const Array1D<T> &xinp, const T &x)

Determine whether the given value is within the limits of the interpolation table.

Return

A std::pair containing the OutOfBounds flag and the index (0 or MAX)

Parameters

  • xinp: 1-D array of monotonically increasing values

  • x: The value to check for

template<typename T>
InterpTraits<T>::index_type sierra::nalu::utils::find_index(const Array1D<T> &xinp, const T &x)

Return an index object corresponding to the x-value based on interpolation table.

Return

The std::pair returned contains two values: the bounds indicator and the index of the element in the interpolation table such that xarray[i] <= x < xarray[i+1]

Parameters

  • xinp: 1-D array of monotonically increasing values

  • x: The value to check for

template<typename T>
void sierra::nalu::utils::linear_interp(const Array1D<T> &xinp, const Array1D<T> &yinp, const T &xout, T &yout, OutOfBounds::OobAction oob = OutOfBounds::CLAMP)

Perform a 1-D linear interpolation.

Parameters

  • xinp: A 1-d vector of monotonically increasing x-values

  • yinp: Corresponding 1-d vector of y-values

  • xout: Target x-value for interpolation

  • yout: Interpolated value at xout

  • oob: (Optional) Out-of-bounds handling (default: CLAMP)

YAML utilities

Miscellaneous utilities for working with YAML C++ library.

namespace sierra
namespace nalu
namespace wind_utils

Functions

template<typename T>
bool get_optional(const YAML::Node &node, const std::string &key, T &result)

Fetch an optional entry from the YAML dictionary if it exists.

The result parameter is unchanged if the entry is not found in the YAML dictionary.

Parameters

  • node: The YAML::Node instance to be examined

  • key: The name of the variable to be extracted

  • result: The variable that is updated with the value if it exists

template<typename T>
bool get_optional(const YAML::Node &node, const std::string &key, T &result, const T &default_value)

Fetch an optional entry from the YAML dictionary if it exists.

The result parameter is updated with the value from the dictionary if it exists, otherwise it is initialized with the default value provided.

Parameters

  • node: The YAML::Node instance to be examined

  • key: The name of the variable to be extracted

  • result: The variable that is updated with the value if it exists

  • default_value: The default value to be used if the parameter is not found in the dictionary.

Performance Monitoring Utilities

namespace sierra
namespace nalu

Functions

Teuchos::RCP<Teuchos::Time> get_timer(const std::string &name)

Return a timer identified by name.

If an existing timer is found, then the timer is returned. Otherwise a new timer is created. The user will have to manually start/stop the timer. For most use cases, it might be preferable to use get_stopwatch function instead.

Teuchos::TimeMonitor get_stopwatch(const std::string &name)

Return a stopwatch identified by name.

The clock starts automatically upon invocation and will be stopped once the Teuchos::Timemonitor instance returned by this function goes out of scope.