GriddedData Class Reference

Container for holding a function defined on a grid of arbitrary dimension. More...

#include <GriddedData.h>

Public Types
typedef MooseUtils::SemidynamicVector< Real, 4 >	GridPoint
typedef MooseUtils::SemidynamicVector< ADReal, 4 >	ADGridPoint
typedef MooseUtils::SemidynamicVector< unsigned int, 4 >	GridIndex

Public Member Functions
	GriddedData (std::string file_name)
	Construct with a file name. More...
virtual	~GriddedData ()=default
unsigned int	getDim ()
	Returns the dimensionality of the grid. More...
void	getAxes (std::vector< int > &axes)
	Yields axes information. More...
void	getGrid (std::vector< std::vector< Real >> &grid)
	Yields the grid. More...
void	getFcn (std::vector< Real > &fcn)
	Yields the values defined at the grid points. More...
Real	evaluateFcn (const GridIndex &ijk)
	Evaluates the function at a given grid point. More...

Static Public Member Functions
static void	parse (unsigned int &dim, std::vector< int > &axes, std::vector< std::vector< Real >> &grid, std::vector< Real > &f, std::vector< unsigned int > &step, std::string file_name)
	parse the file_name extracting information. More...

Private Member Functions
void	updateGrid (unsigned int &dim, const std::vector< Real > &axis_i, const int axis_index)

Static Private Member Functions
static bool	getSignificantLine (std::ifstream &file_stream, std::string &line)
	Extracts the next line from file_stream that is: More...
static void	splitToRealVec (const std::string &input_string, std::vector< Real > &output_vec)
	Splits an input_string using space as the separator Converts the resulting items to Real, and adds these to the end of output_vec. More...

Private Attributes
unsigned int	_dim
std::vector< int >	_axes
std::vector< std::vector< Real > >	_grid
std::vector< Real >	_fcn
std::vector< unsigned int >	_step

Detailed Description

Container for holding a function defined on a grid of arbitrary dimension.

Information is read from a file. The file contains the grid, which has dimension _dim, and consists of _dim vectors of Reals. The file also contains the function values at each grid point. The file also contains information on how to embed the grid into a MOOSE simulation. This is achieved through specifying the MOOSE direction that each grid axis corresponds to. For instance, the first grid axis might correspond to the MOOSE "y" direction, the second grid axis might correspond to the MOOSE "t" direction, etc.

Definition at line 32 of file GriddedData.h.

Member Typedef Documentation

ADGridPoint

typedef MooseUtils::SemidynamicVector<ADReal, 4> GriddedData::ADGridPoint

Definition at line 43 of file GriddedData.h.

GridIndex

typedef MooseUtils::SemidynamicVector<unsigned int, 4> GriddedData::GridIndex

Definition at line 44 of file GriddedData.h.

GridPoint

typedef MooseUtils::SemidynamicVector<Real, 4> GriddedData::GridPoint

Definition at line 42 of file GriddedData.h.

Constructor & Destructor Documentation

GriddedData()

GriddedData::GriddedData

(

std::string

file_name

)

Construct with a file name.

Creates a GriddedData object by reading info from file_name A grid is defined in _grid.

For example, if grid[0] = {1, 2, 3} and grid[1] = {-1, 1} this defines a 2D grid (_dim = 2), with points (1,-1), (2,-1), (3,-1), (1,1), (2,1), (3,1) The i_th axis of the grid corresponds to the axes[i] axis of the simulation: see the function getAxes Values at each grid point are stored in _fcn. They are ordered as in the example above. _step is just a quantity used in evaluateFcn The file must have the following format: All blank lines and lines starting with # are ignored The first significant line (not blank or starting with #) should be either AXIS X or AXIS Y or AXIS Z or AXIS T The next significant line should be a space-separated array of real numbers defining the grid along that axis direction. Any number of AXIS and subsequent space-separated arrays can be defined, but if using this in conjunction with PiecewiseMultilinear, a maximum of 4 should be defined. The AXIS lines define the grid in the MOOSE simulation reference frame, and is used by PiecewiseMultilinear, for instance. The next significant line should be DATA All significant lines after DATA should be the function values at each grid point, on any number of lines of the file, but each line must be space separated. The ordering is such that when the function is evaluated, f[i,j,k,l] corresponds to the i + j*Ni + k*Ni*Nj + l*Ni*Nj*Nk data value. Here i>=0 corresponds to the index along the first AXIS, and Ni is the number of grid points along that axis, etc. See the function parse for an example.

Definition at line 55 of file GriddedData.C.

{
  parse(_dim, _axes, _grid, _fcn, _step, file_name);
}

~GriddedData()

virtual GriddedData::~GriddedData ( )

virtualdefault

Member Function Documentation

evaluateFcn()

Real GriddedData::evaluateFcn

(

const GridIndex &

ijk

)

Evaluates the function at a given grid point.

For instance, evaluateFcn({n,m}) = value at (grid[0][n], grid[1][m]), for a function defined on a 2D grid

Definition at line 92 of file GriddedData.C.

{
  if (ijk.size() != _dim)
    mooseError(
        "Gridded data evaluateFcn called with ", ijk.size(), " arguments, but expected ", _dim);
  unsigned int index = ijk[0];
  for (unsigned int i = 1; i < _dim; ++i)
    index += ijk[i] * _step[i];
  if (index >= _fcn.size())
    mooseError("Gridded data evaluateFcn attempted to access index ",
               index,
               " of function, but it contains only ",
               _fcn.size(),
               " entries");
  return _fcn[index];
}

getAxes()

void GriddedData::getAxes

(

std::vector< int > &

axes

)

Yields axes information.

If axes[i] == 0 then the i_th axis in the grid data corresponds to the x axis in the simulation If axes[i] == 1 then the i_th axis in the grid data corresponds to the y axis in the simulation If axes[i] == 2 then the i_th axis in the grid data corresponds to the z axis in the simulation If axes[i] == 3 then the i_th axis in the grid data corresponds to the time in the simulation

Definition at line 67 of file GriddedData.C.

{
  axes.resize(_dim);
  std::copy(_axes.begin(), _axes.end(), axes.begin());
}

getDim()

unsigned int GriddedData::getDim

(

)

Returns the dimensionality of the grid.

This may have nothing to do with the dimensionality of the simulation. Eg, a 2D grid with axes (Y,Z) (so dim=2) be used in a 3D simulation.

Definition at line 61 of file GriddedData.C.

{
  return _dim;
}

getFcn()

void GriddedData::getFcn

(

std::vector< Real > &

fcn

)

Yields the values defined at the grid points.

Definition at line 85 of file GriddedData.C.

{
  fcn.resize(_fcn.size());
  std::copy(_fcn.begin(), _fcn.end(), fcn.begin());
}

getGrid()

void GriddedData::getGrid

(

std::vector< std::vector< Real >> &

grid

)

Yields the grid.

grid[i] = a vector of Reals that define the i_th axis of the grid.

Definition at line 74 of file GriddedData.C.

{
  grid.resize(_dim);
  for (unsigned int i = 0; i < _dim; ++i)
  {
    grid[i].resize(_grid[i].size());
    std::copy(_grid[i].begin(), _grid[i].end(), grid[i].begin());
  }
}

getSignificantLine()

bool GriddedData::getSignificantLine ( std::ifstream &  file_stream, std::string &  line  )

staticprivate

Extracts the next line from file_stream that is:

• not empty
• does not start with # Returns true if such a line was found, otherwise returns false

Definition at line 209 of file GriddedData.C.

Referenced by parse().

{
  while (std::getline(file_stream, line))
  {
    if (line.size() == 0) // empty line: read next line from file
      continue;
    if (line[0] == '#') // just a comment: read next line from file
      continue;
    // have got a significant line
    return true;
  }
  // have run out of file
  return false;
}

parse()

void GriddedData::parse ( unsigned int &  dim, std::vector< int > &  axes, std::vector< std::vector< Real >> &  grid, std::vector< Real > &  f, std::vector< unsigned int > &  step, std::string  file_name  )

static

parse the file_name extracting information.

Here is an example file:

this is a comment line at start of file

AXIS Y -1.5 0

there is no reason why the x axis can't be second

AXIS X 1 2 3

This example has a 3D grid, but the 3rd direction is time

AXIS T 0 199

now some data

DATA

following for x=1, t=0

1 2

following for x=2, t=0

2 3

following for x=3, t=0

2 3

following for x=1, t=199

89 900

following for x=2, t=199, and x=3, t=199

1 -3 -5 -6.898

end of file

Definition at line 110 of file GriddedData.C.

Referenced by GriddedData().

{
  // initialize
  dim = 0;
  axes.resize(0);
  grid.resize(0);
  f.resize(0);

  // open file and initialize quantities
  std::ifstream file(file_name.c_str());
  if (!file.good())
    mooseError("Error opening file '" + file_name + "' from GriddedData.");
  std::string line;
  bool reading_grid_data = false;
  bool reading_value_data = false;

  // read file line-by-line extracting data
  while (getSignificantLine(file, line))
  {
    // look for AXIS keywords
    reading_grid_data = false;
    if (line.compare("AXIS X") == 0)
    {
      dim += 1;
      reading_grid_data = true;
      axes.push_back(0);
    }
    else if (line.compare("AXIS Y") == 0)
    {
      dim += 1;
      reading_grid_data = true;
      axes.push_back(1);
    }
    else if (line.compare("AXIS Z") == 0)
    {
      dim += 1;
      reading_grid_data = true;
      axes.push_back(2);
    }
    else if (line.compare("AXIS T") == 0)
    {
      dim += 1;
      reading_grid_data = true;
      axes.push_back(3);
    }

    // just found an AXIS keyword
    if (reading_grid_data)
    {
      grid.resize(dim); // add another dimension to the grid
      grid[dim - 1].resize(0);
      if (getSignificantLine(file, line))
        splitToRealVec(line, grid[dim - 1]);
      continue; // read next line from file
    }

    // previous significant line must have been DATA
    if (reading_value_data)
      splitToRealVec(line, f);

    // look for DATA keyword
    if (line.compare("DATA") == 0)
      reading_value_data = true;

    // ignore any other lines - if we get here probably the data file is corrupt
  }

  // check that some axes have been defined
  if (dim == 0)
    mooseError("No valid AXIS lines found by GriddedData");

  // step is useful in evaluateFcn
  step.resize(dim);
  step[0] = 1; // this is actually not used
  for (unsigned int i = 1; i < dim; ++i)
    step[i] = step[i - 1] * grid[i - 1].size();

  // perform some checks
  unsigned int num_data_points = 1;
  for (unsigned int i = 0; i < dim; ++i)
  {
    if (grid[i].size() == 0)
      mooseError("Axis ", i, " in your GriddedData has zero size");
    num_data_points *= grid[i].size();
  }
  if (num_data_points != f.size())
    mooseError("According to AXIS statements in GriddedData, number of data points is ",
               num_data_points,
               " but ",
               f.size(),
               " function values were read from file");
}

splitToRealVec()

void GriddedData::splitToRealVec ( const std::string &  input_string, std::vector< Real > &  output_vec  )

staticprivate

Splits an input_string using space as the separator Converts the resulting items to Real, and adds these to the end of output_vec.

Definition at line 225 of file GriddedData.C.

Referenced by parse().

{
  std::vector<Real> values;
  bool status = MooseUtils::tokenizeAndConvert<Real>(input_string, values, " ");

  if (!status)
    mooseError("GriddedData: Failed to convert string into Real when reading line ", input_string);

  for (auto val : values)
    output_vec.push_back(val);
}

updateGrid()

void GriddedData::updateGrid ( unsigned int &  dim, const std::vector< Real > &  axis_i, const int  axis_index  )

private

Member Data Documentation

_axes

std::vector<int> GriddedData::_axes

private

Definition at line 117 of file GriddedData.h.

Referenced by getAxes(), and GriddedData().

_dim

unsigned int GriddedData::_dim

private

Definition at line 116 of file GriddedData.h.

Referenced by evaluateFcn(), getAxes(), getDim(), getGrid(), and GriddedData().

_fcn

std::vector<Real> GriddedData::_fcn

private

Definition at line 119 of file GriddedData.h.

Referenced by evaluateFcn(), getFcn(), and GriddedData().

_grid

std::vector<std::vector<Real> > GriddedData::_grid

private

Definition at line 118 of file GriddedData.h.

Referenced by getGrid(), and GriddedData().

_step

std::vector<unsigned int> GriddedData::_step

private

Definition at line 120 of file GriddedData.h.

Referenced by evaluateFcn(), and GriddedData().

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The documentation for this class was generated from the following files:

• include/utils/GriddedData.h
• src/utils/GriddedData.C