File coordinates.hxx#

class Coordinates#

#include <coordinates.hxx>

Represents a coordinate system, and associated operators

This is a container for a collection of metric tensor components

Public Types

using FieldMetric = Field3D #

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, FieldMetric dx, FieldMetric dy, FieldMetric dz, FieldMetric J, FieldMetric Bxy, FieldMetric g11, FieldMetric g22, FieldMetric g33, FieldMetric g12, FieldMetric g13, FieldMetric g23, FieldMetric g_11, FieldMetric g_22, FieldMetric g_33, FieldMetric g_12, FieldMetric g_13, FieldMetric g_23, FieldMetric ShiftTorsion, FieldMetric IntShiftTorsion)#: 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&&) = default#

~Coordinates() = default#

void outputVars(Options &output_options)#: Add variables to output_options, for post-processing.

const Field2D &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.

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

inline ParallelTransform &getParallelTransform()#: Return the parallel transform.

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

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

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

Field3D DDX(const Field3D &f, CELL_LOC outloc = CELL_DEFAULT, const std::string &method = "DEFAULT", const std::string &region = "RGN_NOBNDRY")#

Field3D DDY(const Field3D &f, CELL_LOC outloc = CELL_DEFAULT, const std::string &method = "DEFAULT", const std::string &region = "RGN_NOBNDRY") const#

Field3D DDZ(const Field3D &f, CELL_LOC outloc = CELL_DEFAULT, const std::string &method = "DEFAULT", const std::string &region = "RGN_NOBNDRY")#

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

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

FieldMetric 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)

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

FieldMetric 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)

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

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

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

FieldMetric 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)#

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

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

FieldMetric Laplace(const Field2D &f, CELL_LOC outloc = CELL_DEFAULT, const std::string &dfdy_boundary_conditions = "free_o3", const std::string &dfdy_dy_region = "")#

Field3D Laplace(const Field3D &f, CELL_LOC outloc = CELL_DEFAULT, const std::string &dfdy_boundary_conditions = "free_o3", const std::string &dfdy_dy_region = "")#

Field2D Laplace_perpXY(const Field2D &A, const Field2D &f)#

Public Members

FieldMetric dx#

FieldMetric dy#

FieldMetric dz#: Mesh spacing in x, y and z.

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

FieldMetric d1_dx#: 2nd-order correction for non-uniform meshes d/di(1/dx), d/di(1/dy) and d/di(1/dz)

FieldMetric d1_dy#

FieldMetric d1_dz#

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

FieldMetric Bxy#: Magnitude of B = nabla z times nabla x.

FieldMetric g11#: Contravariant metric tensor (g^{ij})

FieldMetric g22#

FieldMetric g33#

FieldMetric g12#

FieldMetric g13#

FieldMetric g23#

FieldMetric g_11#: Covariant metric tensor.

FieldMetric g_22#

FieldMetric g_33#

FieldMetric g_12#

FieldMetric g_13#

FieldMetric g_23#

FieldMetric G1_11#: Christoffel symbol of the second kind (connection coefficients)

FieldMetric G1_22#

FieldMetric G1_33#

FieldMetric G1_12#

FieldMetric G1_13#

FieldMetric G1_23#

FieldMetric G2_11#

FieldMetric G2_22#

FieldMetric G2_33#

FieldMetric G2_12#

FieldMetric G2_13#

FieldMetric G2_23#

FieldMetric G3_11#

FieldMetric G3_22#

FieldMetric G3_33#

FieldMetric G3_12#

FieldMetric G3_13#

FieldMetric G3_23#

FieldMetric G1#

FieldMetric G2#

FieldMetric G3#

FieldMetric ShiftTorsion#: d pitch angle / dx. Needed for vector differentials (Curl)

FieldMetric 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.

const FieldMetric &invSg() const#

const FieldMetric &Grad2_par2_DDY_invSg(CELL_LOC outloc, const std::string &method) const#

void checkCovariant()#

void checkContravariant()#

Private Members

int nz#

Mesh *localmesh#

CELL_LOC location#

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

mutable std::unique_ptr<Field2D> zlength_cache = {nullptr}#: Cache variable for zlength. Invalidated when Coordinates::geometry is called

mutable std::map<std::string, std::unique_ptr<FieldMetric>> Grad2_par2_DDY_invSgCache#: Cache variable for Grad2_par2.

mutable std::unique_ptr<FieldMetric> invSgCache = {nullptr}#