File coordinates.hxx¶

Defines

DERIV_FUNC_REGION_ENUM_TO_STRING(func, T)¶

GRAD_FUNC_REGION_ENUM_TO_STRING(func, T)¶

class Coordinates¶

#include <coordinates.hxx>

Represents a coordinate system, and associated operators

This is a container for a collection of metric tensor components

Public Functions

Coordinates(Mesh *mesh, Options *options = nullptr)¶: Standard constructor from input.

Coordinates(Mesh *mesh, Options *options, const CELL_LOC loc, const Coordinates *coords_in, bool force_interpolate_from_centre = false)¶: Constructor interpolating from another Coordinates object By default attempts to read staggered Coordinates from grid data source, interpolating from CELL_CENTRE if not present. Set force_interpolate_from_centre argument to true to always interpolate (useful if CELL_CENTRE Coordinates have been changed, so reading from file would not be correct).

Coordinates(Mesh *mesh, Field2D dx, Field2D dy, BoutReal dz, Field2D J, Field2D Bxy, Field2D g11, Field2D g22, Field2D g33, Field2D g12, Field2D g13, Field2D g23, Field2D g_11, Field2D g_22, Field2D g_33, Field2D g_12, Field2D g_13, Field2D g_23, Field2D ShiftTorsion, Field2D IntShiftTorsion, bool calculate_geometry = true)¶: A constructor useful for testing purposes. To use it, inherit from Coordinates. If calculate_geometry is true (default), calculate the non-uniform variables, Christoffel symbols

Coordinates &operator=(Coordinates&&)¶

~Coordinates()¶

void outputVars(Datafile &file)¶

Adds variables to the output file, for post-processing

Must be a better way so that Coordinates doesn’t depend on Datafile

BoutReal zlength() const¶: Length of the Z domain. Used for FFTs.

int geometry(bool recalculate_staggered = true, bool force_interpolate_from_centre = false)¶: Calculate differential geometry quantities from the metric tensor.

int calcCovariant(const std::string &region = "RGN_ALL")¶: Invert contravatiant metric to get covariant components.

int calcContravariant(const std::string &region = "RGN_ALL")¶: Invert covariant metric to get contravariant components.

int jacobian()¶: Calculate J and Bxy.

void setParallelTransform(std::unique_ptr<ParallelTransform> pt)¶: Set the parallel (y) transform for this mesh. Mostly useful for tests.

ParallelTransform &getParallelTransform()¶: Return the parallel transform.

Field2D DDX(const Field2D &f, CELL_LOC outloc = CELL_DEFAULT, const std::string &method = "DEFAULT", const std::string &region = "RGN_NOBNDRY")¶

Field2D DDX(const Field2D &f, CELL_LOC outloc, const std::string &method, REGION region)¶

Field2D DDX(const Field2D &f, CELL_LOC outloc, DIFF_METHOD method, REGION region = RGN_NOBNDRY)¶

Field2D DDY(const Field2D &f, CELL_LOC outloc = CELL_DEFAULT, const std::string &method = "DEFAULT", const std::string &region = "RGN_NOBNDRY")¶

Field2D DDY(const Field2D &f, CELL_LOC outloc, const std::string &method, REGION region)¶

Field2D DDY(const Field2D &f, CELL_LOC outloc, DIFF_METHOD method, REGION region = RGN_NOBNDRY)¶

Field2D DDZ(const Field2D &f, CELL_LOC outloc = CELL_DEFAULT, const std::string &method = "DEFAULT", const std::string &region = "RGN_NOBNDRY")¶

Field2D DDZ(const Field2D &f, CELL_LOC outloc, const std::string &method, REGION region)¶

Field2D DDZ(const Field2D &f, CELL_LOC outloc, DIFF_METHOD method, REGION region = RGN_NOBNDRY)¶

Field2D Grad_par(const Field2D &var, CELL_LOC outloc = CELL_DEFAULT, const std::string &method = "DEFAULT")¶: Gradient along magnetic field b.Grad(f)

Field2D Grad_par(const Field2D &f, CELL_LOC outloc, DIFF_METHOD method)¶

Field3D Grad_par(const Field3D &var, CELL_LOC outloc = CELL_DEFAULT, const std::string &method = "DEFAULT")¶

Field3D Grad_par(const Field3D &f, CELL_LOC outloc, DIFF_METHOD method)¶

Field2D Vpar_Grad_par(const Field2D &v, const Field2D &f, CELL_LOC outloc = CELL_DEFAULT, const std::string &method = "DEFAULT")¶: Advection along magnetic field V*b.Grad(f)

Field2D Vpar_Grad_par(const Field2D &v, const Field2D &f, CELL_LOC outloc, DIFF_METHOD method)¶

Field3D Vpar_Grad_par(const Field3D &v, const Field3D &f, CELL_LOC outloc = CELL_DEFAULT, const std::string &method = "DEFAULT")¶

Field3D Vpar_Grad_par(const Field3D &v, const Field3D &f, CELL_LOC outloc, DIFF_METHOD method)¶

Field2D Div_par(const Field2D &f, CELL_LOC outloc = CELL_DEFAULT, const std::string &method = "DEFAULT")¶: Divergence along magnetic field Div(b*f) = B.Grad(f/B)

Field2D Div_par(const Field2D &f, CELL_LOC outloc, DIFF_METHOD method)¶

Field3D Div_par(const Field3D &f, CELL_LOC outloc = CELL_DEFAULT, const std::string &method = "DEFAULT")¶

Field3D Div_par(const Field3D &f, CELL_LOC outloc, DIFF_METHOD method)¶

Field2D Grad2_par2(const Field2D &f, CELL_LOC outloc = CELL_DEFAULT, const std::string &method = "DEFAULT")¶

Field2D Grad2_par2(const Field2D &f, CELL_LOC outloc, DIFF_METHOD method)¶

Field3D Grad2_par2(const Field3D &f, CELL_LOC outloc = CELL_DEFAULT, const std::string &method = "DEFAULT")¶

Field3D Grad2_par2(const Field3D &f, CELL_LOC outloc, DIFF_METHOD method)¶

Field2D Delp2(const Field2D &f, CELL_LOC outloc = CELL_DEFAULT, bool useFFT = true)¶

Field3D Delp2(const Field3D &f, CELL_LOC outloc = CELL_DEFAULT, bool useFFT = true)¶

FieldPerp Delp2(const FieldPerp &f, CELL_LOC outloc = CELL_DEFAULT, bool useFFT = true)¶

Field2D Laplace_par(const Field2D &f, CELL_LOC outloc = CELL_DEFAULT)¶

Field3D Laplace_par(const Field3D &f, CELL_LOC outloc = CELL_DEFAULT)¶

Field2D Laplace(const Field2D &f, CELL_LOC outloc = CELL_DEFAULT)¶

Field3D Laplace(const Field3D &f, CELL_LOC outloc = CELL_DEFAULT)¶

Public Members

Field2D dx¶

Field2D dy¶: Mesh spacing in x and y.

BoutReal dz¶: Mesh spacing in Z.

bool non_uniform¶: True if corrections for non-uniform mesh spacing should be included in operators.

Field2D d1_dx¶

Field2D d1_dy¶: 2nd-order correction for non-uniform meshes d/di(1/dx) and d/di(1/dy)

Field2D J¶: Coordinate system Jacobian, so volume of cell is J*dx*dy*dz.

Field2D Bxy¶: Magnitude of B = nabla z times nabla x.

Field2D g11¶: Contravariant metric tensor (g^{ij})

Field2D g22¶

Field2D g33¶

Field2D g12¶

Field2D g13¶

Field2D g23¶

Field2D g_11¶: Covariant metric tensor.

Field2D g_22¶

Field2D g_33¶

Field2D g_12¶

Field2D g_13¶

Field2D g_23¶

Field2D G1_11¶: Christoffel symbol of the second kind (connection coefficients)

Field2D G1_22¶

Field2D G1_33¶

Field2D G1_12¶

Field2D G1_13¶

Field2D G1_23¶

Field2D G2_11¶

Field2D G2_22¶

Field2D G2_33¶

Field2D G2_12¶

Field2D G2_13¶

Field2D G2_23¶

Field2D G3_11¶

Field2D G3_22¶

Field2D G3_33¶

Field2D G3_12¶

Field2D G3_13¶

Field2D G3_23¶

Field2D G1¶

Field2D G2¶

Field2D G3¶

Field2D ShiftTorsion¶: d pitch angle / dx. Needed for vector differentials (Curl)

Field2D IntShiftTorsion¶: Integrated shear (I in BOUT notation)

Private Functions

void setParallelTransform(Options *options)¶: Set the parallel (y) transform from the options file. Used in the constructor to create the transform object.

Private Members

int nz¶

Mesh *localmesh¶

CELL_LOC location¶

std::unique_ptr<ParallelTransform> transform = {nullptr}¶: Handles calculation of yup and ydown.