Physical System

Classes related to the physical System being modelled, which consists of Components.

API

Classes:

AxisymmetricVisibleComponent(**kwds)
BarDiskComponent([mge_pot, mge_lum, ...])	Rotating triaxial component with a MGE projected density (i.e.
BarDiskComponentAngles([mge_pot, mge_lum, ...])	Rotating triaxial component with a MGE projected density (i.e.
Component([name, visible, ...])	A component of the physical system
DarkComponent([density])	Any dark component of the sytem, with no observed MGE or kinemtics
GeneralisedNFW(**kwds)	A GeneralisedNFW halo
Hernquist(**kwds)	A Hernquist sphere
NFW(**kwds)	An NFW halo
NFW_m200_c(**kwds)	An NFW halo with m200-c relation from Dutton & Maccio 14
Plummer(**kwds)	A Plummer sphere
System(*args)	The physical system being modelled
TriaxialCoredLogPotential(**kwds)	A TriaxialCoredLogPotential
TriaxialVisibleComponent(**kwds)	Triaxial component with a MGE projected density
VisibleComponent([mge_pot, mge_lum])	Any visible component of the sytem, with an MGE

class physical_system.AxisymmetricVisibleComponent(**kwds)

Methods:

validate()

Validate the component

validate()

Validate the component

Ensure it has the required attributes and parameters. Also validates the parameter generator settings’ minstep value for non-fixed parameters.

Parameters:

para list with parameter names. Mandatory.

Returns:

None.

Raises:

ValueErrorif a required attribute is missing or the required

parameters do not exist

class physical_system.BarDiskComponent(mge_pot=None, mge_lum=None, disk_pot=None, disk_lum=None, **kwds)

Rotating triaxial component with a MGE projected density (i.e. a bar)

Note: all bar components are constrained to have the same omega.

class physical_system.BarDiskComponentAngles(mge_pot=None, mge_lum=None, disk_pot=None, disk_lum=None, **kwds)

Rotating triaxial component with a MGE projected density (i.e. a bar), with viewing angles specified.

Note: all bar components are constrained to have the same omega.

Methods:

validate_parset(par)

Validate the p, q, u parameters

validate_parset(par)

Validate the p, q, u parameters

Validates the triaxial component’s p, q, u parameters. Requires self.qobs to be set. A parameter set is valid if the resulting (theta, psi, phi) are not np.nan.

Parameters:

pardict

{ “p”:val, … } where “p” are the component’s parameters and val are their respective values

Returns:

bool

True if the parameter set is valid, False otherwise

class physical_system.Component(name=None, visible=None, contributes_to_potential=None, symmetry=None, kinematic_data=[], population_data=[], parameters=[])

A component of the physical system

e.g. the stellar component, black hole, or dark halo of a galaxy

Parameters:

namestring

a short but descriptive name of the component

visibleBool

whether this is visible <–> whether it has an associated MGE

contributes_to_potentialBool

whether this contributes_to_potential not currently used

symmetrystring

one of ‘spherical’, ‘axisymm’, or ‘triax’ not currently used

kinematic_datalist

a list of dyn.kinemtics.Kinematic data for this component

parameterslist

a list of dyn.parameter_space.Parameter objects for this component

population_datalist

a list of dyn.populations.Population data for this component not currently used

Methods:

get_par_by_name(n)	Get a parameter using its (unsuffixed) name.
get_parname(par)	Strip the component name suffix from the parameter name.
validate([par])	Validate the component
validate_parset(par)	Validates the component's parameter values.

get_par_by_name(n)

Get a parameter using its (unsuffixed) name.

Parameters:

nstr

The parameter name (without the component name suffix)

Returns:

pa dyn.parameter_space.Parameter object

The parameter in question.

get_parname(par)

Strip the component name suffix from the parameter name.

Parameters:

parstr

The full parameter name “parameter-component”.

Returns:

pure_parnamestr

The parameter name without the component name suffix.

validate(par=None)

Validate the component

Ensure it has the required attributes and parameters. Also validates the parameter generator settings’ minstep value for non-fixed parameters.

Parameters:

para list with parameter names. Mandatory.

Returns:

None.

Raises:

ValueErrorif a required attribute is missing or the required

parameters do not exist

validate_parset(par)

Validates the component’s parameter values.

Kept separate from the validate method to facilitate easy calling from the parameter generator class. This is a placeholder method which returns True if all parameters are non-negative, except for logarithmic parameters which are not checked. Specific validation should be implemented for each component subclass.

Parameters:

pardict

{ “p”:val, … } where “p” are the component’s parameters and val are their respective raw values

Returns:

isvalidbool

True if the parameter set is valid, False otherwise

class physical_system.DarkComponent(density=None, **kwds)

Any dark component of the sytem, with no observed MGE or kinemtics

This is an abstract layer and none of the attributes/methods are currently used.

Methods:

get_dh_legacy_strings(parset)

Generates and returns two strings needed for the legacy Fortran files.

get_dh_legacy_strings(parset)

Generates and returns two strings needed for the legacy Fortran files.

This method only applies to dark halo components.

Parameters:

parsetastropy table row

Holds the parameter set.

Returns:

specsstr

A string with the legacy code and the number of parameters, space separated.

par_valsstr

The parameter values in the sequence legacy Fortran expects them, space separated.

class physical_system.GeneralisedNFW(**kwds)

A GeneralisedNFW halo

from Zhao (1996) Defined with parameters: concentration [R200/NFW scale length], Mvir [Msol], inner_log_slope []

Methods:

validate()	Validate the component
validate_parset(par)	Validates the GeneralisedNFW's parameters.

validate()

Validate the component

Ensure it has the required attributes and parameters. Also validates the parameter generator settings’ minstep value for non-fixed parameters.

Parameters:

para list with parameter names. Mandatory.

Returns:

None.

Raises:

ValueErrorif a required attribute is missing or the required

parameters do not exist

validate_parset(par)

Validates the GeneralisedNFW’s parameters.

Requires c and Mvir >0, and gam leq 1

Parameters:

pardict

{ “p”:val, … } where “p” are the component’s parameters and val are their respective values

Returns:

bool

True if the parameter set is valid, False otherwise

class physical_system.Hernquist(**kwds)

A Hernquist sphere

Defined with parameters: rhoc [central density, Msun/km^3] and rc [scale length, km]

Methods:

validate()

Validate the component

validate()

Validate the component

Ensure it has the required attributes and parameters. Also validates the parameter generator settings’ minstep value for non-fixed parameters.

Parameters:

para list with parameter names. Mandatory.

Returns:

None.

Raises:

ValueErrorif a required attribute is missing or the required

parameters do not exist

class physical_system.NFW(**kwds)

An NFW halo

Defined with parameters: c [concentration, R200/scale] and f [dm-fraction, M200/total-stellar-mass]

Methods:

validate()

Validate the component

validate()

Validate the component

Ensure it has the required attributes and parameters. Also validates the parameter generator settings’ minstep value for non-fixed parameters.

Parameters:

para list with parameter names. Mandatory.

Returns:

None.

Raises:

ValueErrorif a required attribute is missing or the required

parameters do not exist

class physical_system.NFW_m200_c(**kwds)

An NFW halo with m200-c relation from Dutton & Maccio 14

The relation: log10(c200) = 0.905 - 0.101 * log10(M200/(1e12/h)). Component defined with parameter f [dm-fraction, M200/total-stellar-mass]

Methods:

get_c200(system, parset)	Calculates and returns c200 (see Dutton & Maccio 2014).
get_dh_legacy_strings(parset, system)	Generates and returns two strings needed for the legacy Fortran files.
validate()	Validate the component

get_c200(system, parset)

Calculates and returns c200 (see Dutton & Maccio 2014).

Parameters:

systema dyn.physical_system.System object

parsetastropy table row

Must contain dark matter fraction f-{self.name} and ml

Returns:

float

c200

get_dh_legacy_strings(parset, system)

Generates and returns two strings needed for the legacy Fortran files.

This method overrides the parent class’ method because for legacy Fortran purposes, NFW_m200_c has two parameters. Note that NFW_m200_c needs an addiional parameter system.

Parameters:

parsetastropy table row

Holds the parameter set.

Returns:

specsstr

A string with the legacy code and the number of parameters, space separated.

par_valsstr

The parameter values in the sequence legacy Fortran expects them, space separated.

validate()

Validate the component

Ensure it has the required attributes and parameters. Also validates the parameter generator settings’ minstep value for non-fixed parameters.

Parameters:

para list with parameter names. Mandatory.

Returns:

None.

Raises:

ValueErrorif a required attribute is missing or the required

parameters do not exist

class physical_system.Plummer(**kwds)

A Plummer sphere

Defined with parameters: M [mass, Msol] and a [scale length, arcsec]

Methods:

validate()

Validate the component

validate()

Validate the component

Ensure it has the required attributes and parameters. Also validates the parameter generator settings’ minstep value for non-fixed parameters.

Parameters:

para list with parameter names. Mandatory.

Returns:

None.

Raises:

ValueErrorif a required attribute is missing or the required

parameters do not exist

class physical_system.System(*args)

The physical system being modelled

e.g. system is a galaxy. A system is composed of Components e.g. the galaxy is composed of stars, black hole, dark matter halo. This object is automatically created when the configuration file is read.

Methods:

add_component(cmp)	add a component to the system
get_all_bar_components()	Get all components which are rotating MGEs (i.e.
get_all_dark_components()	Get all components which are Dark
get_all_dark_non_plummer_components()	Get all Dark components which are not plummer
get_all_kinematic_data()	Loop over all components, extract their kinemtics into a list.
get_all_mge_components()	Get all components which contain MGEs
get_component_from_class(cmp_class)	Parameters:
get_component_from_name(cmp_name)	Parameters:
get_par_by_name(n)	Get a parameter using its name.
get_unique_bar_component()	Return the unique rotating bar component (raises an error if there are zero or multiple such components)
get_unique_triaxial_visible_component()	Return the unique non-bar MGE component (raises an error if there are zero or multiple such components)
is_bar_disk_system()	Check if the system contains at least one bar component and at least one disk component.
is_bar_disk_system_with_angles()	Check if the system is a bar-disk with phi, psi, theta specified directly in the configuration file.
validate()	Validate the system
validate_parset(par)	Validates the system's parameter values

add_component(cmp)

add a component to the system

Parameters:

cmpa dyn.physical_system.Component object

Returns:

None

updated the system componenent attributes

get_all_bar_components()

Get all components which are rotating MGEs (i.e. bars)

Returns:

list

a list of Component objects, keeping only the rotating MGE components

get_all_dark_components()

Get all components which are Dark

Returns:

list

a list of Component objects, keeping only the dark components

get_all_dark_non_plummer_components()

Get all Dark components which are not plummer

Useful in legacy orbit libraries for finding the dark halo component. For legacy models, the black hole is always a plummer, so any Dark but non plummer components must represent the dark halo.

Returns:

list

a list of Component objects, keeping only the dark components

get_all_kinematic_data()

Loop over all components, extract their kinemtics into a list.

Returns:

list

all_kinematics in a list

get_all_mge_components()

Get all components which contain MGEs

Returns:

list

a list of Component objects

get_component_from_class(cmp_class)

Parameters:

cmp_classstring

name of the component type/class

Returns:

a dyn.physical_system.Component object

Raises:

ValueErrorif there are more than one component of the same class.

# TODO: remove this limit, e.g. if we had two MGE-based components one for stars, one for gas

get_component_from_name(cmp_name)

Parameters:

cmp_namestring

component name (as specified in the congi file)

Returns:

a dyn.physical_system.Component object

get_par_by_name(n)

Get a parameter using its name.

Parameters:

nstr

The parameter name.

Returns:

pa dyn.parameter_space.Parameter object

The parameter in question.

get_unique_bar_component()

Return the unique rotating bar component (raises an error if there are zero or multiple such components)

Returns:

a dyn.physical_system.BarDiskComponent object

get_unique_triaxial_visible_component()

Return the unique non-bar MGE component (raises an error if there are zero or multiple such components)

Returns:

a dyn.physical_system.TriaxialVisibleComponent object

is_bar_disk_system()

Check if the system contains at least one bar component and at least one disk component.

Returns:

isbardiskBool

System contains a bar and a disk.

is_bar_disk_system_with_angles()

Check if the system is a bar-disk with phi, psi, theta specified directly in the configuration file.

Returns:

hasanglesBool

System is specified by angles.

validate()

Validate the system

Ensures the System has the required attributes: at least one component, no duplicate component names, and the ml parameter, and that the sformat string for the ml parameter is set. Also validates the parameter generator settings’ minstep value for ml if it is a non-fixed parameter.

Returns:

None.

Raises:

ValueErrorif required attributes or components are missing, or if

there is no ml parameter

validate_parset(par)

Validates the system’s parameter values

Kept separate from the validate method to facilitate easy calling from the ParameterGenerator class. Returns True if all parameters are non-negative, except for logarithmic parameters which are not checked.

Parameters:

pardict

{ “p”:val, … } where “p” are the system’s parameters and val are their respective raw values

Returns:

isvalidbool

True if the parameter set is valid, False otherwise

class physical_system.TriaxialCoredLogPotential(**kwds)

A TriaxialCoredLogPotential

see e.g. Binney & Tremaine second edition p.171 Defined with parameters: p [B/A], q [C/A], Rc [core radius, kpc], Vc [asympt. circular velovity, km/s]

Methods:

validate()

Validate the component

validate()

Validate the component

Ensure it has the required attributes and parameters. Also validates the parameter generator settings’ minstep value for non-fixed parameters.

Parameters:

para list with parameter names. Mandatory.

Returns:

None.

Raises:

ValueErrorif a required attribute is missing or the required

parameters do not exist

class physical_system.TriaxialVisibleComponent(**kwds)

Triaxial component with a MGE projected density

Has parameters (p,q,u) = (b/a, c/a, sigma_obs/sigma_intrinsic) used for deprojecting the MGE. A given (p,q,u) correspond to a fixed set of viewing angles for the triaxial ellipsoid.

Methods:

find_grid_of_valid_pqu([n_grid])	Find valid values of the parameters (p,q,u)
suggest_parameter_values([target_u])	Suggest valid values of the parameters (p,q,u)
triax_pqu2tpp(p, q, u)	transform axis ratios to viewing angles
validate()	Validate the TriaxialVisibleComponent
validate_parset(par)	Validate the p, q, u parameters

find_grid_of_valid_pqu(n_grid=200)

Find valid values of the parameters (p,q,u)

Creates a grid of all values of 0<(p,q,u)<=1, and finds those which have a valid deprojection subject to the fulfilment of all three criteria: 1. 0 < q <= p <=1 2. max(q/qobs, p) < u 3. u< min(p/qobs, 1) where qobs is the smallest value of q for the MGE.

Parameters:

n_gridint

grid size used for p,q,u

Returns:

(p,q,u), valid

3d grids of p,q,u values, and boolen array valid which is True for valid values

suggest_parameter_values(target_u=0.9)

Suggest valid values of the parameters (p,q,u)

Find valid values using the mehtod find_grid_of_valid_pqu. Then for each of (p,q,u), we suggest values: - lo/hi : the min/max of all valid values - value : u=target_u, and p/q = mean of all valid p/q values where u is close to target value - step/minstep : a fifth/twentieth of the range of valid values

Parameters:

target_ufloat

Desired value of the parameter u

Returns:

string

text to print out suggesting quantities for (p,q,u)

triax_pqu2tpp(p, q, u)

transform axis ratios to viewing angles

transfer (p, q, u) to the three viewing angles (theta, psi, phi) with known flatting self.qobs. Taken from schw_basics, same as in vdB et al. 2008, MNRAS 385,2,647 We should possibly revisit the expressions later

validate()

Validate the TriaxialVisibleComponent

Validates parameter names and sets self.qobs (minimal flattening from mge data).

Returns:

None.

validate_parset(par)

Validate the p, q, u parameters

Validates the triaxial component’s p, q, u parameters. Requires self.qobs to be set. A parameter set is valid if the resulting (theta, psi, phi) are not np.nan.

Parameters:

pardict

{ “p”:val, … } where “p” are the component’s parameters and val are their respective values

Returns:

bool

True if the parameter set is valid, False otherwise

class physical_system.VisibleComponent(mge_pot=None, mge_lum=None, **kwds)

Any visible component of the sytem, with an MGE

Parameters:

mge_pota dyn.mges.MGE object

describing the (projected) surface-mass density

mge_luma dyn.mges.MGE object

describing the (projected) surface-luminosity density

Methods:

get_M_stars_tot(distance, parset)	Calculates and returns the total stellar mass via the mge.
validate(**kwds)	Validate the component

get_M_stars_tot(distance, parset)

Calculates and returns the total stellar mass via the mge.

Parameters:

distancefloat

Distance of the system in MPc

parsetastropy table row

must contain mass-to-light ratio ml

Returns:

float

Total stellar mass

validate(**kwds)

Validate the component

Ensure it has the required attributes and parameters. Also validates the parameter generator settings’ minstep value for non-fixed parameters.

Parameters:

para list with parameter names. Mandatory.

Returns:

None.

Raises:

ValueErrorif a required attribute is missing or the required

parameters do not exist

Inheritance Diagram