ModelSet

class dysmalpy.models.ModelSet

Bases: object

Object that contains all model components, parameters, and settings

ModelSet does not take any arguments. Instead, it first should be initialized and then ModelSet.add_component() can be used to include specific model components. All included components can then be accessed through ModelSet.components which is a dictionary that has keys equal to the names of each component. The primary method of ModelSet is ModelSet.simulate_cube() which produces a model data cube of line emission that follows the full kinematics of given model.

Methods Summary

add_component(model[, name, light, ...])	Add a model component to the set
circular_velocity(r[, compute_baryon, ...])	Calculate the total circular velocity as a function of radius
enclosed_mass(r[, compute_baryon, ...])	Calculate the total enclosed mass
get_dlnrhogas_dlnr(r)	Calculate the composite derivative dln(rho,gas) / dlnr
get_dm_aper(r)	Calculate the enclosed dark matter fraction
get_dm_frac_r_ap()	Calculate the dark matter fraction within an aperture radius
get_encl_mass_r_ap()	Calculate the total enclosed mass within an aperture radius
get_free_parameter_keys()	Return the index within an array of each free parameter
get_free_parameters_values()	Return the current values of the free parameters
get_halo_alpha()	Return the alpha parameter value for a TwoPowerHalo
get_halo_rb()	Return the Burkert radius parameter value for a Burkert dark matter halo
get_log_prior()	Return the total log prior based on current values
get_mvirial()	Return the virial mass of the dark matter halo component
get_prior_transform(u)
get_vmax([r, tracer])	Calculate the peak velocity of the rotation curve
set_parameter_fixed(model_name, param_name, fix)	Change whether a specific parameter is fixed or not
set_parameter_value(model_name, param_name, ...)	Change the value of a specific parameter
simulate_cube([obs, dscale])	Simulate a line emission cube of this model set
update_parameters(theta)	Update all of the free and tied parameters of the model
vcirc_sq(r[, compute_baryon, compute_dm, step1d])	Calculate the square of the total circular velocity as a function of radius
velocity_profile(r[, tracer, compute_dm])	Calculate the rotational velocity as a function of radius
write_profile_file([r, filename, cols, ...])	Output various radial profiles of the ModelSet
write_vrot_vcirc_file([r, filename, tracer, ...])	Output the rotational and circular velocities to a file

Methods Documentation

add_component(model, name=None, light=False, geom_type='galaxy', disp_type='galaxy')

Add a model component to the set

Parameters:

• model (_DysmalModel) – Model component to be added to the model set

• name (str) – Name of the model component

• light (bool) – If True, use the mass profile of the model component in the calculation of the flux of the line, i.e. setting the mass-to-light ratio equal to 1.

• geom_type ({'galaxy', component name}) – Specify which model components the geometry applies to. Only used if model is a Geometry. If ‘galaxy’, then all included components except named components with other geometries will follow this geometry (i.e., those with a separate geometry included that has ‘geom_type’=the component name). Default is ‘galaxy’.

• disp_type ({'galaxy', component name}) – Specify which model components the dispersion applies to (by name, with the exception of the default profiles). Only used if model is a DispersionProfile. Default is ‘galaxy’.

circular_velocity(r, compute_baryon=False, compute_dm=False, step1d=0.2)

Calculate the total circular velocity as a function of radius

Parameters:

• r (float or array) – Radius or radii at which to calculate the circular velocity in kpc

• compute_baryon (bool) – If True, also return the circular velocity due to the baryons

• compute_dm (bool) – If True, also return the circular velocity due to the halo

• step1d (float, optional) – Step size in kpc to use during adiabatic contraction calculation

Returns:

• vel (float or array) – Total circular velocity in km/s

• vbaryon (float or array, only if compute_baryon = True) – Circular velocity due to the baryons

• vdm (float or array, only if compute_dm = True) – Circular velocity due to the halo

enclosed_mass(r, compute_baryon=False, compute_dm=False, step1d=0.2)

Calculate the total enclosed mass

Parameters:

• r (float or array) – Radius or radii at which to calculate the enclosed mass in kpc

• compute_baryon (bool) – If True, also return the enclosed mass of the baryons

• compute_dm (bool) – If True, also return the enclosed mass of the halo

• step1d (float, optional) – Step size in kpc to use during adiabatic contraction calculation

Returns:

• enc_mass (float or array) – Total enclosed mass in Msun

• enc_bary (float or array, only if compute_baryon = True) – Enclosed mass of the baryons, in Msun

• enc_dm (float or array, only if compute_dm = True) – Enclosed mass of the halo, in Msun

get_dlnrhogas_dlnr(r)

Calculate the composite derivative dln(rho,gas) / dlnr

** Assumes gas follows same distribution as total baryons.

Based on slope, so do not need to rescale for fgas/Mgas under this assumption.**

Parameters:

r (float or array) – Radius or radii in kpc

Returns:

dlnrhogas_dlnr

Return type:

float or array

get_dm_aper(r)

Calculate the enclosed dark matter fraction

Parameters:

r (float or array) – Radius or radii in kpc within which to calculate the dark matter fraction. Assumes a DarkMatterHalo component is included in the ModelSet.

Returns:

dm_frac – Enclosed dark matter fraction at r

Return type:

array

get_dm_frac_r_ap()

Calculate the dark matter fraction within an aperture radius

Uses the method self._model_aperture_r to get the defined apeture radius. By default this function seturns the disk effective radius (i.e., self.components[‘disk+bulge’].__getattribute__[‘r_eff_disk’].value )

Returns:

dm_frac – Dark matter fraction within the specified effective radius

Return type:

float

get_encl_mass_r_ap()

Calculate the total enclosed mass within an aperture radius

Uses the method self._model_aperture_r to get the defined apeture radius. By default this function seturns the disk effective radius (i.e., self.components[‘disk+bulge’].__getattribute__[‘r_eff_disk’].value )

Returns:

menc – Total enclosed mass within the specified effective radius

Return type:

float

Notes

(OLD: This method uses the total circular velocity to determine the enclosed mass based on v^2 = GM/r.)

get_free_parameter_keys()

Return the index within an array of each free parameter

Returns:

pfree_keys – Dictionary of all model components with their parameters. If a model parameter is free, then it lists its index within p. Otherwise, -99.

Return type:

dictionary

get_free_parameters_values()

Return the current values of the free parameters

Returns:

pfree – Values of the free parameters

Return type:

array

get_halo_alpha()

Return the alpha parameter value for a TwoPowerHalo

Returns:

alpha – Value of the alpha parameter. Returns None if the correct component does not exist.

Return type:

float or None

get_halo_rb()

Return the Burkert radius parameter value for a Burkert dark matter halo

Parameters:

model_key_halo (list) – One element list with the name of the Burkert model component

Returns:

rb – Value of the Burkert radius. Returns None if the correct component does not exist.

Return type:

float or None

get_log_prior()

Return the total log prior based on current values

Returns:

log_prior_model – Summed log prior

Return type:

float

get_mvirial()

Return the virial mass of the dark matter halo component

Returns:

mvir – Virial mass of the dark matter halo in log(Msun)

Return type:

float

get_prior_transform(u)

get_vmax(r=None, tracer=None)

Calculate the peak velocity of the rotation curve

Parameters:

• r (array, optional) – Radii to sample to find the peak. If None, then a linearly spaced array from 0 to 25 kpc with 251 points will be used

• tracer (string) – Name of the dynamical tracer (used to determine which is the appropriate dispersion profile).

Returns:

vmax – Peak velocity of the rotation curve in km/s

Return type:

float

Notes

This simply finds the maximum of the rotation curve which is calculated at discrete radii, r.

set_parameter_fixed(model_name, param_name, fix)

Change whether a specific parameter is fixed or not

Parameters:

• model_name (str) – Name of the model component the parameter belongs to.

• param_name (str) – Name of the parameter

• fix (bool) – If True, the parameter will be fixed to its current value. If False, it will be a free parameter allowed to vary during fitting.

set_parameter_value(model_name, param_name, value, skip_updated_tied=False)

Change the value of a specific parameter

Parameters:

• model_name (str) – Name of the model component the parameter belongs to.

• param_name (str) – Name of the parameter

• value (float) – Value to change the parameter to

simulate_cube(obs=None, dscale=None)

Simulate a line emission cube of this model set

Parameters:

• obs (Observation class) – Instance holding the observation information

• dscale (float) – Conversion from sky to physical coordinates in arcsec/kpc

Returns:

• cube_final (3D array) – Line emission cube that incorporates all of the kinematics due to the components of the current ModelSet

• spec (1D array) – Values of the spectral channels as determined by spec_type, spec_start, spec_step, nspec, and spec_unit

update_parameters(theta)

Update all of the free and tied parameters of the model

Parameters:

theta (array with length = ModelSet.nparams_free) – New values for the free parameters

Notes

The order of the values in theta is important. Use ModelSet.get_free_parameter_keys() to determine the correct order.

vcirc_sq(r, compute_baryon=False, compute_dm=False, step1d=0.2)

Calculate the square of the total circular velocity as a function of radius

Parameters:

• r (float or array) – Radius or radii at which to calculate the circular velocity in kpc

• compute_baryon (bool) – If True, also return the circular velocity due to the baryons

• compute_dm (bool) – If True, also return the circular velocity due to the halo

• step1d (float, optional) – Step size in kpc to use during adiabatic contraction calculation

Returns:

• vel (float or array) – Total circular velocity in km/s

• vbaryon (float or array, only if compute_baryon = True) – Circular velocity due to the baryons

• vdm (float or array, only if compute_dm = True) – Circular velocity due to the halo

velocity_profile(r, tracer=None, compute_dm=False)

Calculate the rotational velocity as a function of radius

Parameters:

• r (float or array) – Radius or radii at which to calculate the velocity in kpc

• tracer (string) – Name of the dynamical tracer (used to determine which is the appropriate dispersion profile).

• compute_dm (bool) – If True also return the circular velocity due to the dark matter halo

Returns:

• vel (float or array) – Rotational velocity as a function of radius in km/s

• vdm (float or array) – Circular velocity due to the dark matter halo in km/s Only returned if compute_dm = True

write_profile_file(r=None, filename=None, cols=None, prettycolnames=None, colunits=None, tracer=None, overwrite=False)

Output various radial profiles of the ModelSet

Parameters:

• r (array, optional) – Radii to sample to find the peak. If None, then a linearly spaced array from 0 to 10 kpc with a stepsize of 0.1 will be used

• filename (str, optional) – Output filename to write to. Will be written as ascii, w/ space delimiter. Default is ‘rprofiles.txt’

• cols (list, optional) – Names of ModelSet methods that will be called as function of r, and to be saved as a column in the output file. Default is [‘velocity_profile’, ‘circular_velocity’, ‘get_dm_aper’].

• prettycolnames (list, optional) – Alternate column names for output in file header (eg, ‘vrot’ not ‘velocity_profile’) Default is cols.

• colunits (list, optional) – Units of each column. r is added by hand, and will always be in kpc.

• tracer (string) – Name of the dynamical tracer (used to determine which is the appropriate dispersion profile).

write_vrot_vcirc_file(r=None, filename=None, tracer=None, overwrite=False)

Output the rotational and circular velocities to a file

Parameters:

• r (array, optional) – Radii to sample to find the peak. If None, then a linearly spaced array from 0 to 25 kpc with 251 points will be used

• filename (str, optional) – Name of file to output velocities to. Default is ‘vout.txt’

• tracer (string) – Name of the dynamical tracer (used to determine which is the appropriate dispersion profile).