magritte.core module

core.__version__ = '0.5.8': Current version of Magritte.

Core module of Magritte: a modern software library for 3D radiative transfer.

class magritte.core.Boundary

Bases: pybind11_builtins.pybind11_object

Class containing the model boundary.

get_boundary_condition(self: magritte.core.Boundary, arg0: int) → magritte.core.BoundaryCondition: Getter for the boundary condition.

read(self: magritte.core.Boundary, arg0: magritte.core.Io) → None: Read object from file.

set_boundary_condition(self: magritte.core.Boundary, arg0: int, arg1: magritte.core.BoundaryCondition) → magritte.core.BoundaryCondition: Setter for the boundary condition.

write(self: magritte.core.Boundary, arg0: magritte.core.Io) → None: Write object to file.

property boundary2point: Array with point index for each boundary point.

property boundary_temperature: Array with radiative temperature for each boundary point (only relevant for thermal boundary conditions).

property point2boundary: Array with boundary index for each point.

class magritte.core.Chemistry

Bases: pybind11_builtins.pybind11_object

Class containing the chemistry.

read(self: magritte.core.Chemistry, arg0: magritte.core.Io) → None: Read object from file.

write(self: magritte.core.Chemistry, arg0: magritte.core.Io) → None: Write object to file.

property species: Species object.

class magritte.core.CollisionPartner

Bases: pybind11_builtins.pybind11_object

Class containing collision partner data.

read(self: magritte.core.CollisionPartner, arg0: magritte.core.Io, arg1: int, arg2: int) → None: Read object from file.

write(self: magritte.core.CollisionPartner, arg0: magritte.core.Io, arg1: int, arg2: int) → None: Write object to file.

property Cd: Array with collisional de-excitation rates.

property Ce: Array with collisional excitation rates.

property icol: Array with upper levels of the collisional transitions.

property jcol: Array with lower levels of the collisional transitions.

property ncol: Number of collisional transitions.

property ntmp: Number of temperatures at which data is given.

property num_col_partner: Number of the species corresponding to the collision partner.

property orth_or_para_H2: In case the collision partner is H2, this indicates whether it is ortho (o) or para (p).

property tmp: Array with temperatures corresponding to the collisional data.

class magritte.core.Frequencies

Bases: pybind11_builtins.pybind11_object

Class containing the (local) frequency bins.

read(self: magritte.core.Frequencies, arg0: magritte.core.Io) → None: Read object from file.

write(self: magritte.core.Frequencies, arg0: magritte.core.Io) → None: Write object to file.

property nu: Array of frequency bins for each point in the model.

class magritte.core.Geometry

Bases: pybind11_builtins.pybind11_object

Class containing the model geometry.

read(self: magritte.core.Geometry, arg0: magritte.core.Io) → None: Read object from file.

write(self: magritte.core.Geometry, arg0: magritte.core.Io) → None: Write object to file.

property boundary: Boundary object

property lengths: Array containing the lengths of the rays for each direction and point.

property points: Points object.

property rays: Rays object.

class magritte.core.Image

Bases: pybind11_builtins.pybind11_object

Image class, 2D point cloud of intensities for each frequency bin.

property I: Intensity of the points in the image (for each frequency bin).

property ImX: X-coordinates of the points in the image plane.

property ImY: Y-coordinates of the points in the image plane.

property freqs: Frequency bins of the image.

property imagePointPosition: Position of image points (model points or projection surface).

property imageType: Type of image (intensity or optical depth).

property image_direction_x: coordinate of image x direction in a 3D general geometry.

property image_direction_y: coordinate of image y direction in a 3D general geometry.

property image_direction_z: direction in which the image is taken.

property nfreqs: Number of frequency bins in the image.

property ray_nr: Number of the ray along which the image is taken.

class magritte.core.ImagePointPosition

Bases: pybind11_builtins.pybind11_object

Members:

AllModelPoints

ProjectionSurface

property name

class magritte.core.ImageType

Bases: pybind11_builtins.pybind11_object

Members:

Intensity

OpticalDepth

property name

class magritte.core.Io

Bases: pybind11_builtins.pybind11_object

Abstract input/output base class.

class magritte.core.IoPython

Bases: magritte.core.Io

Input/output class for io, implemented in Python.

property implementation: Type of input/output. Either “hdf5” or “text”.

property io_file: Name of the folder or file to read from or write to.

class magritte.core.IoText

Bases: magritte.core.Io

Intput/output class for text-based io, implemented in C++.

property io_file: Name of the folder or file to read from or write to.

class magritte.core.LineProducingSpecies

Bases: pybind11_builtins.pybind11_object

Class containing a line producing species.

index(self: magritte.core.LineProducingSpecies, arg0: int, arg1: int) → int

read(self: magritte.core.LineProducingSpecies, arg0: magritte.core.Io, arg1: int) → None: Read object from file.

write(self: magritte.core.LineProducingSpecies, arg0: magritte.core.Io, arg1: int) → None: Write object to file.

property J: Isotropic radiation field.

property J2_0: Anisotropic radiation field tensor element 0

property J2_1_Im: Anisotropic radiation field tensor element 1 (imaginary part)

property J2_1_Re: Anisotropic radiation field tensor element 1 (real part)

property J2_2_Im: Anisotropic radiation field tensor element 2 (imaginary part)

property J2_2_Re: Anisotropic radiation field tensor element 2 (real part)

property Jeff: Array with effective mean intensities in the lines.

property linedata: Linedata object.

property population: Array with level populations for each point.

property population_tot: Array with the sum of all level populations at each point. (Should be equal to the abundance of the species.)

property quadrature: Quadrature object.

class magritte.core.Linedata

Bases: pybind11_builtins.pybind11_object

Class containing line data.

read(self: magritte.core.Linedata, arg0: magritte.core.Io, arg1: int) → None: Read object from file.

write(self: magritte.core.Linedata, arg0: magritte.core.Io, arg1: int) → None: Write object to file.

property A: Array with Einstein A coefficients.

property Ba: Array with Einstein B (absorption) coeficients.

property Bs: Array with Einstsin B (stimulated emission) coefficients.

property colpar: Vector of collision partner objects.

property energy: Array with the energy for each level.

property frequency: Array with frequencies of the line transitions.

property inverse_mass: Inverse mass (1/mass) of the species.

property irad: Array with upper levels of the radiative transitions.

property jrad: Array with lower levels of the radiative transitions.

property ncolpar: Number of collision partners.

property nlev: Number of energy levels.

property nrad: Number of radiative transitions.

property num: Number of the species corresponding the line data.

property sym: Chemical symbol of the species.

property weight: Array with the statistical weight for each level.

class magritte.core.Lines

Bases: pybind11_builtins.pybind11_object

Class containing the lines and their data.

read(self: magritte.core.Lines, arg0: magritte.core.Io) → None: Read object from file.

resize_LineProducingSpecies(self: magritte.core.Lines, arg0: int) → None: Resize the vector LineProducingSpecies.

set_emissivity_and_opacity(self: magritte.core.Lines) → None: Set the emissivity and opacity arrays.

write(self: magritte.core.Lines, arg0: magritte.core.Io) → None: Write object to file.

property emissivity: Array with emissivities for each point and frequency bin.

property inverse_width: Array with the inverse widths for each line at each point.

property line: Array with the line (centre) frequencies.

property lineProducingSpecies: Vector of LineProducingSpecies.

property opacity: Array with opacities for each point and frequency bin.

class magritte.core.Model

Bases: pybind11_builtins.pybind11_object

Class containing the Magritte model.

compute_Jeff(self: magritte.core.Model) → int: Compute the effective mean intensity in the line.

compute_LTE_level_populations(self: magritte.core.Model) → int: Compute the level populations for the model assuming local thermodynamic equilibrium (LTE).

compute_image(self: magritte.core.Model, arg0: int) → int: Compute an image for the model along the given ray.

compute_image_for_point(self: magritte.core.Model, arg0: int, arg1: int) → int: Compute image (single pixel) for a single point.

compute_image_new(*args, **kwargs)

Overloaded function.

compute_image_new(self: magritte.core.Model, arg0: int) -> int

Compute an image of the model along the given ray direction, using the new imager.

compute_image_new(self: magritte.core.Model, arg0: int, arg1: int, arg2: int) -> int

Compute an image of the model along the given ray direction, using the new imager, specifying the image resolution.

compute_image_new(self: magritte.core.Model, arg0: float, arg1: float, arg2: float, arg3: int, arg4: int) -> int

Compute an image of the model along the given ray direction, using the new imager, specifying the ray direction and image resolution.

compute_image_optical_depth(self: magritte.core.Model, arg0: int) → int: Compute an image of the optical depth for the model along the given ray.

compute_image_optical_depth_new(*args, **kwargs)

Overloaded function.

compute_image_optical_depth_new(self: magritte.core.Model, arg0: int) -> int

Compute an image of the optical depth for the model along the given ray direction, using the new imager.

compute_image_optical_depth_new(self: magritte.core.Model, arg0: int, arg1: int, arg2: int) -> int

Compute an image of the optical depth for the model along the given ray direction, using the new imager, specifying the image resolution.

compute_image_optical_depth_new(self: magritte.core.Model, arg0: float, arg1: float, arg2: float, arg3: int, arg4: int) -> int

Compute an image of the optical depth for the model along the given ray direction, using the new imager, specifying the ray direction and image resolution.

compute_inverse_line_widths(self: magritte.core.Model) → int: Compute the inverse line widths for the model. (Needs to be recomputed whenever the temperature of turbulence changes.)

compute_level_populations(self: magritte.core.Model, arg0: bool, arg1: int) → int: Compute the level populations for the model assuming statistical equilibrium until convergence, optionally using Ng-acceleration, and for the given maximum number of iterations.

compute_level_populations_from_stateq(self: magritte.core.Model) → int: Compute the level populations for the model assuming statistical equilibrium.

compute_level_populations_shortchar(self: magritte.core.Model, arg0: bool, arg1: int) → int: Compute the level populations using the short-characteristics solver for the model assuming statistical equilibrium until convergence, optionally using Ng-acceleration, and for the given maximum number of iterations.

compute_level_populations_sparse(self: magritte.core.Model, arg0: bool, arg1: int) → int: Compute the level populations for the model assuming statistical equilibrium until convergence, optionally using Ng-acceleration, and for the given maximum number of iterations. (Memory sparse option.)

compute_radiation_field_feautrier_order_2(self: magritte.core.Model) → int: Compute the radiation field for the modle using the 2nd-order Feautrier solver.

compute_radiation_field_feautrier_order_2_anis(self: magritte.core.Model) → int: Compute the radiation field for the modle using the 2nd-order Feautrier solver, anisotropic case.

compute_radiation_field_feautrier_order_2_sparse(self: magritte.core.Model) → int: Compute the radiation field for the modle using the 2nd-order Feautrier solver.

compute_radiation_field_shortchar_order_0(self: magritte.core.Model) → int: Compute the radiation field for the modle using the 0th-order short-characteristics methods.

compute_spectral_discretisation(*args, **kwargs)

Overloaded function.

compute_spectral_discretisation(self: magritte.core.Model) -> int

Compute the spectral discretisation for the model tailored for line (Gauss-Hermite) quadrature.

compute_spectral_discretisation(self: magritte.core.Model, arg0: float) -> int

Compute the spectral discretisation for the model tailored for images with the given spectral width.

compute_spectral_discretisation(self: magritte.core.Model, arg0: float, arg1: float) -> int

Compute the spectral discretisation for the model tailored for images with the given min and max frequency.

compute_spectral_discretisation(self: magritte.core.Model, arg0: float, arg1: float, arg2: int) -> int

Compute the spectral discretisation for the model tailored for images with the given min and max frequency. Can also specify the amount of frequency bins to use (instead of defaulting to parameters.nfreqs).

read(*args, **kwargs)

Overloaded function.

read(self: magritte.core.Model) -> None

Read model file (using the hdf5 implementation of IoPython and using the model name specified in parameters.)

read(self: magritte.core.Model, arg0: magritte.core.Io) -> None

Read model file using the given Io object.

read(self: magritte.core.Model, arg0: str) -> None

Read model file (assuming HDF5 file format).

set_boundary_condition(self: magritte.core.Model) → int: Set boundary condition (internally).

set_column(self: magritte.core.Model) → int: Set column (internally).

set_eta_and_chi(self: magritte.core.Model, arg0: int) → int: Set latest emissivity and opacity for the model in the eta and chi variables respectively.

write(*args, **kwargs)

Overloaded function.

write(self: magritte.core.Model) -> None

Write model file (using the hdf5 implementation of IoPython and using the model name specified in parameters.)

write(self: magritte.core.Model, arg0: magritte.core.Io) -> None

Write model file using the given Io object.

write(self: magritte.core.Model, arg0: str) -> None

Write model file (assuming HDF5 file format).

property error_max: Max relative error in the level populaitons.

property error_mean: Mean relative error in the level populations.

class magritte.core.Parameters

Bases: pybind11_builtins.pybind11_object

Class containing the model parameters.

adaptive_ray_tracing(self: magritte.core.Parameters) → bool: Whether or not to use adaptive ray tracing.

dimension(self: magritte.core.Parameters) → int: Spatial dimension of the model.

hnrays(self: magritte.core.Parameters) → int: Half the number of rays.

model_name(self: magritte.core.Parameters) → str: Model name.

nboundary(self: magritte.core.Parameters) → int: Number of boundary points.

nfreqs(self: magritte.core.Parameters) → int: Number of frequency bins.

nlines(self: magritte.core.Parameters) → int: Number of lines.

nlspecs(self: magritte.core.Parameters) → int: Number of line producing species.

npoints(self: magritte.core.Parameters) → int: Number of points.

nquads(self: magritte.core.Parameters) → int: Number of quadrature points.

nrays(self: magritte.core.Parameters) → int: Number of rays.

nspecs(self: magritte.core.Parameters) → int: Number of species.

read(self: magritte.core.Parameters, arg0: magritte.core.Io) → None: Rread object from file.

set_adaptive_ray_tracing(self: magritte.core.Parameters, arg0: bool) → None: Set whether or not to use adaptive ray tracing.

set_dimension(self: magritte.core.Parameters, arg0: int) → None: Set spatial dimension of the model.

set_hnrays(self: magritte.core.Parameters, arg0: int) → None: Set the half of the number of rays.

set_model_name(self: magritte.core.Parameters, arg0: str) → None: Set model name.

set_nboundary(self: magritte.core.Parameters, arg0: int) → None: Set number of boundary points.

set_nfreqs(self: magritte.core.Parameters, arg0: int) → None: Set number of frequency bins.

set_nlines(self: magritte.core.Parameters, arg0: int) → None: Set number of lines.

set_nlspecs(self: magritte.core.Parameters, arg0: int) → None: Set number of line producing species.

set_npoints(self: magritte.core.Parameters, arg0: int) → None: Set number of points.

set_nquads(self: magritte.core.Parameters, arg0: int) → None: Set number of quadrature points.

set_nrays(self: magritte.core.Parameters, arg0: int) → None: Set number of rays.

set_nspecs(self: magritte.core.Parameters, arg0: int) → None: Set number of species.

set_spherical_symmetry(self: magritte.core.Parameters, arg0: bool) → None: Set whether or not to use spherical symmetry

set_use_scattering(self: magritte.core.Parameters, arg0: bool) → None: Set whether or not to use scattering.

spherical_symmetry(self: magritte.core.Parameters) → bool: Whether or not to use spherical symmetry.

use_scattering(self: magritte.core.Parameters) → bool: Whether or not to use scattering.

version(self: magritte.core.Parameters) → str: Magritte version number.

write(self: magritte.core.Parameters, arg0: magritte.core.Io) → None: Write object to file.

property Ng_acceleration_mem_limit: Memory limit for ng acceleration.

property Ng_acceleration_remove_N_its: Number of iterations to ignore when using ng-acceleration

property adaptive_Ng_acceleration_min_order: Minimal order of ng acceleration when using adaptive Ng acceleration. Has to be larger than 1.

property adaptive_Ng_acceleration_use_max_criterion: Whether of not to use the maximum relative change as criterion for the adaptive ng-acceleration

property convergence_fraction: Fraction of levels that should obey the convergence criterion.

property max_distance_opacity_contribution: The distance (scaled to line width) at which we ignore the opacity/emissivity contribution.

property max_width_fraction: Max tolerated Doppler shift as fraction of line width (default=0.5).

property min_dtau: Minimum optical depth increment that will be assumed in the solver.

property min_opacity: Minimum opacity that will be assumed in the solver.

property min_rel_pop_for_convergence: Minimum relative level population to be considered in the convergence criterion.

property n_off_diag: Bandwidth of the ALO (0=diagonal, 1=tri-diaginal, 2=penta-diagonal, …)

property one_line_approximation: Whether or not to use one line approximation.

property pop_prec: Required precision for ALI.

property population_inversion_fraction: Threshold factor for population inversion required for LTE to be used; set this higher than 1

property store_intensities: Whether or not to store intensities.

property sum_opacity_emissivity_over_all_lines: Whether or not to sum the opacity, emissivity over all lines (including the zero contributions).

property use_adaptive_Ng_acceleration: Whether to use adaptive Ng acceleration.

class magritte.core.Points

Bases: pybind11_builtins.pybind11_object

Class containing the spatial points.

read(self: magritte.core.Points, arg0: magritte.core.Io) → None: Read object from file.

write(self: magritte.core.Points, arg0: magritte.core.Io) → None: Write object to file.

property cum_n_neighbors: Cumulative number of neighbours of each point.

property n_neighbors: Number of neighbours of each point.

property neighbors: Linearised array of neighbours of each point.

property position: Array with position vectors of the points.

property velocity: Array with velocity vectors of the points (as a fraction of the speed of light).

class magritte.core.Quadrature

Bases: pybind11_builtins.pybind11_object

Class containing the data for Gauss-Hermite quadrature.

read(self: magritte.core.Quadrature, arg0: magritte.core.Io, arg1: int) → None: Read object from file.

write(self: magritte.core.Quadrature, arg0: magritte.core.Io, arg1: int) → None: Write object to file.

property roots: Array containing the roots for the Gauss-Hermite quadrature.

property weights: Array containing the weights for the Gauss-Hermite quadrature.

class magritte.core.Radiation

Bases: pybind11_builtins.pybind11_object

Class containing the radiation field.

read(self: magritte.core.Radiation, arg0: magritte.core.Io) → None: Read object from file.

write(self: magritte.core.Radiation, arg0: magritte.core.Io) → None: Write object to file.

property I: Array containing the intensity for each ray, point, and frequency bin.

property J: Array containing the mean intensity for each point and frequency bin.

property frequencies: Frequencies object.

property u: Array containing the mean intensity up and down a ray for each ray pair, point, and frequency bin.

property v: Array containing the flux up and down a ray for each ray pair, point, and frequency bin.

class magritte.core.Rays

Bases: pybind11_builtins.pybind11_object

Class containing the (light) rays (directional discretisation).

read(self: magritte.core.Rays, arg0: magritte.core.Io) → None: Read object from file.

write(self: magritte.core.Rays, arg0: magritte.core.Io) → None: Write object to file.

property antipod: Array with the number of the antipodal ray for each ray.

property direction: Array with direction vector of each ray.

property weight: Array with the weights that each ray contributes in integrals over directions.

class magritte.core.Species

Bases: pybind11_builtins.pybind11_object

Class containing the chemical species.

read(self: magritte.core.Species, arg0: magritte.core.Io) → None: Read object from file.

write(self: magritte.core.Species, arg0: magritte.core.Io) → None: Write object to file.

property abundance: Array with the abundances at each point.

property symbol: Symbol of the species.

class magritte.core.Temperature

Bases: pybind11_builtins.pybind11_object

Class containing the temperature.

read(self: magritte.core.Temperature, arg0: magritte.core.Io) → None: Read object from file.

write(self: magritte.core.Temperature, arg0: magritte.core.Io) → None: Write object to file.

property gas: Kinetic temperature of the gas.

class magritte.core.Thermodynamics

Bases: pybind11_builtins.pybind11_object

Class containing the thermodynamics.

read(self: magritte.core.Thermodynamics, arg0: magritte.core.Io) → None: Read object from file.

write(self: magritte.core.Thermodynamics, arg0: magritte.core.Io) → None: Write object to file.

property temperature: Temperature object.

property turbulence: Turbulence object.

class magritte.core.Turbulence

Bases: pybind11_builtins.pybind11_object

Class containing the (micro) turbulence.

read(self: magritte.core.Turbulence, arg0: magritte.core.Io) → None: Read object from file.

write(self: magritte.core.Turbulence, arg0: magritte.core.Io) → None: Write object to file.

property vturb2: Square of the micro turbulence as a fraction of the speed of light.

magritte.core.pcmp_comm_rank() → int: Get the rank of the current process (using MPI).

magritte.core.pcmp_comm_size() → int: Get the size of the current communicator (using MPI).

magritte.core.pcmp_length(arg0: int) → int: Get the size of an array with given length that is given to the current process (using MPI).

magritte.core.pcmp_start(arg0: int) → int: Get the first index of an array with given length that will be given to this process (using MPI).

magritte.core.pcmp_stop(arg0: int) → int: Get the last index of an array with given length that will be given to this process (using MPI).

magritte.core.pcmt_n_threads_avail() → int: Get the number of available threads (using OpenMP).

magritte.core.pcmt_set_n_threads_avail(arg0: int) → None: Set the number of available threads (using OpenMP).