radmc3dPy package¶
Subpackages¶
- radmc3dPy.models package
- Submodules
- radmc3dPy.models.lines_nlte_lvg_1d_1 module
- radmc3dPy.models.ppdisk module
- radmc3dPy.models.ppdisk_acc module
- radmc3dPy.models.ppdisk_amr module
- radmc3dPy.models.simple_1 module
- radmc3dPy.models.spher1d_1 module
- radmc3dPy.models.spher2d_1 module
- radmc3dPy.models.template module
- radmc3dPy.models.test_scattering_1 module
- Module contents
Submodules¶
radmc3dPy.analyze module¶
This module contains functions to read and write input/output data for RADMC-3D and to do some simple analysis/diagnostics of the model.
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radmc3dPy.analyze.
findContainerLeafID
(cellCRD=None, cellHW=None, xi=None, yi=None, zi=None, childID=None, isLeaf=None, nChild=None, crd=None)¶ Function to find the tree index of a leaf cell containing a given point in space, i.e. if the following is true : xcell - dxcell <= xpoint < xcell + dxcell for each dimension. This function is to be used in multiprocessing.
Parameters: cellCRD : ndarray
Array with dimensions [ncell, 3] containing the cell centre coordiantes of the tree
cellHW : ndarray
Array with dimensions [ncell, 3] containing the half width of cells in the tree
xi : ndarray
Array of cell interface indices in the base grid in the first dimension
yi : ndarray
Array of cell interface indices in the base grid in the second dimension
zi : ndarray
Array of cell interface indices in the base grid in the third dimension
childID : ndarray
Child index array
isLeaf : ndarray
Boolean array containing the node type for each cell (True - leaf, False - branch)
nChild : int
Number of children (8,4,2 for 3,2,1 active dimensions)
crd : ndarray
Array of length 3 containing the coordinates of the point whose container leaf is to be found
Returns: Tree index of the container leaf if it is found. If the point is outside of the base grid -1 is returned.
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radmc3dPy.analyze.
findContainerLeafIDRec
(x=None, y=None, z=None, dx=None, dy=None, dz=None, childID=None, isLeaf=None, nChild=None, crd=(), cellID=None)¶ Recursive function to find the leaf cell in the tree that contains a given point in space
Parameters: x : ndarray
Tree cell center array in the first dimension
y : ndarray
Tree cell center array in the second dimension
z : ndarray
Tree cell center array in the tird dimension
dx : ndarray
Tree cell halfwidth array in the first dimension
dy : ndarray
Tree cell halfwidth array in the second dimension
dz : ndarray
Tree cell halfwidth array in the third dimension
childID : list
List of children indices. Each list element is an ndarray with nChild elements containing the child indices
isLeaf : ndarray
Boolean array for the cell type (True - leaf, False - branch)
nChild : int
Nr of children (i.e. 8, 4, or 2 for 3, 2, 1 active dimensions, respectively)
crd : ndarray
Three element list/tuple/array containing the point coordinates
cellID : int
Index of cell to be tested
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radmc3dPy.analyze.
gdensMinMax
(x=None, y=None, z=None, dx=None, dy=None, dz=None, model=None, ppar=None, **kwargs)¶ Example function to be used as decision function for resolving cells in tree building. It calculates the gas density at a random sample of coordinates within a given cell than take the ratio of the max/min density. If it is larger than a certain threshold value it will return True (i.e. the cell should be resolved) if the density variation is less than the threshold it returns False (i.e. the cell should not be resolved)
Parameters: x : ndarray
Cell centre coordinates of the cells in the first dimension
y : ndarray
Cell centre coordinates of the cells in the second dimension
z : ndarray
Cell centre coordinates of the cells in the third dimension
dx : ndarray
Half size of the cells in the first dimension
dy : ndarray
Half size of the cells in the second dimension
dz : ndarray
Half size of the cells in the third dimension
model : object
A radmc3dPy model (must contain a getGasDensity() function)
ppar : dictionary
All parameters of the problem (from the problem_params.inp file). It is not used here, but must be present for compatibility reasons.
**kwargs: dictionary
Parameters used to decide whether the cell should be resolved. It should the following keywords; ‘nsample’, which sets the number of random points the gas desity is sampled at within the cell and ‘threshold’ that sets the threshold value for max(gasdens)/min(gasdens) above which the cell should be resolved.
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radmc3dPy.analyze.
getDensVstruct
(data=None, vmean_temp=False, ispec_tgas=0, gsize=None, idust=None, mstar=None, mu=None)¶ Calculates the vertical hydrostatic equilibrium
Parameters: data : radmc3dData
An instance of the radmc3DData class containing the density structure of the model
vmean_temp : bool
If True (T(z) = T(-z) = 0.5*(T(z) + T(-z))) if False (T(z)!=T(-z))
idust : list
List of dust indices whose structure must be calculated
mstar : float
Stellar mass
ispec_tgas : int
Index of dust species whose temperature is taken to be the gas temperature
gsize : ndarray, optional
Dust grain sizes - If specified, the gas temperature is calculated as the average temperature of all dust grains in the grid cell weighted by the total surface area of dust grains with given size - NOTE: this approach assumes that all dust grains of a given size have the same bulk density
mu : float, optional
Mean molecular weight (default: 2.3)
Returns
——-
Returns an ndarray with the dust density
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radmc3dPy.analyze.
gmass
(x=None, y=None, z=None, dx=None, dy=None, dz=None, model=None, ppar=None, **kwargs)¶ Example function to be used as decision function for resolving cells in tree building. It calculates the gas density at a random sample of coordinates within a given cell than take the ratio of the max/min density. If it is larger than a certain threshold value it will return True (i.e. the cell should be resolved) if the density variation is less than the threshold it returns False (i.e. the cell should not be resolved)
Parameters: x : ndarray
Cell centre coordinates of the cells in the first dimension
y : ndarray
Cell centre coordinates of the cells in the second dimension
z : ndarray
Cell centre coordinates of the cells in the third dimension
dx : ndarray
Half size of the cells in the first dimension
dy : ndarray
Half size of the cells in the second dimension
dz : ndarray
Half size of the cells in the third dimension
model : object
A radmc3dPy model (must contain a getGasDensity() function)
ppar : dictionary
All parameters of the problem (from the problem_params.inp file). It is not used here, but must be present for compatibility reasons.
**kwargs: dictionary
Parameters used to decide whether the cell should be resolved. It should contain the following keywords; ‘nsample’, which sets the number of random points the gas desity is sampled at within the cell and ‘threshold’ that sets the threshold value for max(gasdens)/min(gasdens) above which the cell should be resolved.
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radmc3dPy.analyze.
interpolateOctree
(data=None, x=None, y=None, z=None, var=None, nproc=1)¶ Nearest neighbour inteprolation on an octree
- data : radmc3dData
- Data container
- x : ndarray
- Coordiantes of the point to be interpolated on in the first dimension
- y : ndarray
- Coordiantes of the point to be interpolated on in the second dimension
- z : ndarray
- Coordiantes of the point to be interpolated on in the third dimension
- var : list
- Name of the variables to be interpolated, supported names are: ddens, dtemp, gdens, ndens, gtemp, gvel, vturb
- nproc : int
- Number of processes to be used (for parallel computing)
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radmc3dPy.analyze.
plotDustOpac
(opac=None, var='kabs', idust=0, ax=None, xlabel=None, ylabel=None, fmt='', **kwargs)¶ Plots the dust opacity as a function of wavelength
Parameters: opac : radmc3dDustOpac
Dust opacity container
var : {‘kabs’, ‘ksca’, ‘kext’, ‘g’}
Variable to be plotted
idust : int, optional
Dust index in opac to be plotted (default=0)
ax : Axis, optional
Matplotlib axis to plot on. If not set the current axis will be used.
xlabel : str, optional
Label of the x-axis
ylabel : str, optional
Label of the y-axis
fmt : str, optional
Format of the plotted line. The same as the third non-keyword argument of matplotlib.pyplot.plot()
Keyword Arguments:
Any further keyword argument that will be passed to matplotlib.pyplot.plot()
Returns: The returned list by matplotlib.pyplot.plot()
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radmc3dPy.analyze.
plotScatmat
(opac=None, var='z11', idust=0, iwav=None, wav=None, xvar='ang', iang=None, ang=None, ax=None, xlabel=None, ylabel=None, title=None, fmt='', **kwargs)¶ Plots the scattering matrix elements either as a function of scattering angle at a specific wavelength (default) or as a function of wavelength at a specific scattering angle
Parameters: opac : radmc3dDustOpac
Dust opacity container
var : {‘kabs’, ‘ksca’, ‘kext’, ‘g’}
Variable to be plotted
idust : int, optional
Dust index in opac to be plotted (default=0)
iwav : int, optional
Wavelength index (used only if xvar=’ang’) to be plotted.
wav : float, optional
Wavelength at which the plot should be made (used only if xvar=’ang’). In practice, instead of interpolating to this wavelength, the nearest wavelength in the wavelength grid will be used.
xvar : {‘ang’, ‘wav’}
Variable for plotting the scattering matrix elements against (default=’ang’)
iang : int, optional
Scattering angle index (used only if xvar=’wav’)
ang : int, optional
Scattering angle in degrees at which the plot should be made (used only if xvar=’wav’). In practice, instead of interpolating to this scattering angle, the nearest angle in the angular grid will be used.
ax : Axis, optional
Matplotlib axis to plot on. If not set the current axis will be used.
xlabel : str, optional
Label of the x-axis
ylabel : str, optional
Label of the y-axis
title : str, optional
Title of the plot. If not set either the wavelength (for xvar=’ang’) or the scattering angle (for xvar=’wav’) the plot was made at.
fmt : str, optional
Format of the plotted line. The same as the third non-keyword argument of matplotlib.pyplot.plot()
Keyword Arguments:
Any further keyword argument that will be passed to matplotlib.pyplot.plot()
Returns: The returned list by matplotlib.pyplot.plot()
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radmc3dPy.analyze.
plotSlice2D
(data=None, var='ddens', plane='xy', crd3=0.0, icrd3=None, ispec=-1, xlim=(), ylim=(), log=False, linunit='cm', angunit='rad', nx=100, ny=100, showgrid=False, gridcolor='k', gridalpha=1.0, nproc=1, contours=False, clev=None, clmin=None, clmax=None, ncl=None, cllog=False, clcol='k', cllabel=False, cllabel_fontsize=10, cllabel_fmt='%.1f', clalpha=1.0, ax=None, lattitude=True, **kwargs)¶ Function to plot an axis-aligned 2D slice of the variables in the model. Any additional keyword argument above the listed ones will be passed on to matplotlib.pylab.pcolormesh(). For an octree grid the variables are interpolated onto a regular grid using nearest neighbour interpolation before plotting. The size and resolution of the regular image grid can be set at input.
Parameters: data : radmc3dData
Instance of radmc3dData containing the field variable to be displayed
var : {‘ddens’, ‘dtemp’, ‘gdens’, ‘ndens’, ‘gtemp’, ‘vturb’, ‘vx’, ‘vy’, ‘vz’, ‘taux’, ‘tauy’}
Variable to be displayed
plane : {‘xy’, ‘xz’, ‘yz’, ‘yx, ‘zx’, ‘yz’}
Plane to be displayed
crd3 : float
Coordinate of the third dimension (i.e. when plotting a slice in the x-y plane, crd3 is the z-coordinate)
icrd3 : int
Index of the third coordinate in the grid (only for regular grid!)
ispec : int
Dust species index. If negative dust densities will be summed up and the total cumulative density will be displayed
xlim : tuple
Coordinate boundaries in the first dimension of the plot (also the coordinate boundary of the regular grid data on AMR grids are interpolated to)
ylim : tuple
Coordinate boundaries in the second dimension of the plot (also the coordinate boundary of the regular grid data on AMR grids are interpolated to)
log : bool
If True the contour/image will be displayed on a logarithmic stretch
linunit : {‘cm’, ‘au’, ‘pc’, ‘rs’}
Unit selection for linear image coordinate axes.
nx : int
Number of horizontal pixels in the interpolated image if the data is defined in an Octree
ny : int
Number of vertical pixels in the interpolated image if the data is defined in an Octree
showgrid : bool
If True the spatial grid will be overlayed
gridcolor : str
Color of the spatial grid overlay
gridalpha : float
Opacity of the lines in the spatial grid overlay (0.0 - fully transparent, 1.0 - fully opaque)
angunit : {‘rad’, ‘deg’}
Unit selection for angular image coordinate axes (only if spherical coordinate system is used).
nproc : int
Number of parallel processes to be used for interpolation.
contours : bool
If True contour lines are plotted, if False a colorscale plot will be created
clev : ndarray
A numpy ndarray containing the levels to be displayed with contour lines. If clev is set then clmin, clmax and ncl are omitted
clmin : float
Min. contour level (for setting auto-contours between clmin and clmax at ncl values)
clmax : float
Max. contour level (for setting auto-contours between clmin and clmax at ncl values)
ncl : float
Number of contour levels (for setting auto-contours between clmin and clmax at ncl values)
cllog : bool
If clmin, clmax and ncl are used to generate the contour levels, then if cllog is True the contours will be log-scaled
clcol : str
Color-code for the contour lines for single color contours
cllabel : bool
If True the contour line values will be displayed, if False only the contour lines will be displayed (default = False)
cllabel_fontsize: int
Size of the font used to displaye the contour line values
cllabel_fmt : str
Format of the contour line labels (default “%.1f”)
clalpha : float
Transparency of the contour lines (1.0 fully opaque, 0.0 fully transparent)
lattitude : bool
If the coordinate sytem used in RADMC-3D is spherical, then the 2nd coordiante is the co-lattitude. If lattitude is set to True then the 2nd coordinate in the RADMC-3D grid will be transformet to true lattitude (i.e. pi/2.-colattitude). If set to false the original co-lattitude will be used.
ax : matplotlib.axes.Axes
Matplotlib axis to plot to
Keyword Arguments :
All other keyword arugments will be passed to pcolormesh() or countour()
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radmc3dPy.analyze.
plotSpectrum
(a, ev=False, kev=False, micron=False, jy=False, lsun=False, lnu=False, nulnu=False, fnu=False, nufnu=False, dpc=1.0, oplot=False, xlg=False, ylg=False, obs=False, mol=None, ilin=None)¶ Plot the spectrum / SED
Parameters: a : ndarray
A 2D array of size [Nfreq,2] returned by readSpectrum(). [:,0] - wavelength in micrometer, or for line data the velocity in km/s [:,1] - flux density in erg/s/cm/cm/Hz
ev : bool
True –> energy in electronvolt (default=Hz)
kev : bool
True –> energy in kiloelectronvolt (default=Hz)
micron : bool
True –> wavelength in micron (default=Hz)
jy : bool
True –> Flux in Jansky
lnu : bool
True –> L_nu (default L_nu)
fnu : bool
True –> F_nu in units of erg/s/cm^2/Hz(default L_nu)
nufnu : bool
True –> nu*F_nu in units of erg/s/cm^2 (default L_nu)
nulnu : bool
True –> nu*L_nu (default F_nu)
lsun : bool
True –> nu*L_nu in units of solar luminosity
dpc : bool
Distance of observer in units of parsec (Default: 1 pc)
oplot : bool
True –> Plot without refreshing subplot
xlg : bool
True –> logarithmic x-axis
ylg : bool
True –> logarithmic y-axis
obs : bool
- True –> Treat the spectrum as an observation
(i.e. do not scale with dpc^(-2))
mol : radmc3dMolecule
- (optional) Molecule data (see radmc3dMolecule class)
This is required if you want to plot a line spectrum with on the x-axis the radial velocity in km/s
ilin : bool
- (if set) the index of the line (of mol; starting,
as in RADMC-3D, with the index 1) which shall act as the 0 km/s wavelength reference. If ilin is set the x axis will be in km/s (overriding other settings)
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radmc3dPy.analyze.
readData
(ddens=False, dtemp=False, gdens=False, gtemp=False, gvel=False, ispec=None, vturb=False, grid=None, binary=True, old=False, octree=False)¶ Reads the physical variables of the model (e.g. density, velocity, temperature).
Parameters: ddens : bool
If True dust density will be read (all dust species and grain sizes)
dtemp : bool
If True dust temperature will be read (all dust species and grain sizes)
gdens : bool
If True gas density will be read (NOTE: the gas density will be number density in 1/cm^3)
gtemp : bool
If True gas temperature will be read (all dust species and grain sizes)
gvel : bool
If True the velocity field will be read
ispec : str
Name of the molecule in the ‘molecule_ispec.inp’ filename
vturb : bool
If True the microturbulent velocity field will be read
grid : radmc3dGrid
An instance of radmc3dGrid containing the spatial and frequency grid of the model. If the grid is passed to the function it will not be read again from file. This can be useful for octree models to save time.
old : bool, optional
If set to True the file format of the previous, 2D version of radmc will be used
binary: bool
Set it to True for C-style binary and False for formatted ASCII files
octree: bool
True for models with octree AMR and False for models with regular grid
Returns: Returns an instance of the radmc3dData class
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radmc3dPy.analyze.
readGrid
(sgrid=True, wgrid=True, sgrid_fname=None, wgrid_fname=None, old=False)¶ Reads the spatial and frequency grid. This function is an interface to radmc3dGrid.readGrid().
Parameters: sgrid : bool
If True the spatial grid will be read
wgrid : bool
If True the wavelength grid will be read
sgrid_fname : str
File containing the spatial grid (default: amr_grid.inp)
wgrid_fname : str
File containing the wavelength grid (default: wavelength_micron.inp)
old : bool
If True the format of the old 2D version of radmc3d (radmc) will be used
Returns
——-
Returns an instance of the radmc3dGrid (for regular grid) or radmc3dOctree (for octree AMR) class
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radmc3dPy.analyze.
readMol
(mol=None, fname=None)¶ Wrapper around the radmc3dMolecule.read() method
Parameters: mol : str
molecule name (e.g. ‘co’) if the file name is in the form of ‘molecule_<mol>.inp’
fname : str
full file name
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radmc3dPy.analyze.
readOpac
(ext=None, idust=None, scatmat=None, old=False)¶ Reads the dust opacity files. This function is an interface to radmc3dDustOpac.readOpac()
Parameters: ext : list
Each element of the list is be a string, the file name extension (file names should look like ‘dustkappa_ext.inp’)
idust : list
Each element of the list is an integer, the index of the dust species in the master opacity file (dustopac.inp’)
scatmat: list
If specified, its elements should be booleans indicating whether the opacity file contains also the full scattering matrix (True) or only dust opacities (False)
old : bool, optional
If set to True the file format of the previous, 2D version of radmc will be used
Returns: Returns an instance of the radmc3dDustOpac class
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radmc3dPy.analyze.
readParams
()¶ Reads the problem_params.inp file. This function is an interface to radmc3dPar.readPar().
Returns: Returns an instance of the radmc3dPar class
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radmc3dPy.analyze.
readSpectrum
(fname='', old=False)¶ Reads the spectrum / SED
Parameters: fname : str, optional
Name of the file to be read
old : bool, optional
If set to True the file format of the previous, 2D version of radmc will be used
Returns: Returns an ndarray with [Nwavelength, 2] dimensions
[Nwavelength,0] is the wavelength / velocity and [Nwavelength,1] is the flux density
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radmc3dPy.analyze.
readStars
(fname='')¶ Reads the data (mass, radius, temperature, spectrum) of discrete stellar sources
Parameters: fname : str
Name of the file to be read (if omitted the default value is stars.inp)
Returns: An instance of radmc3dRadSources containing the stellar data
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radmc3dPy.analyze.
writeDefaultParfile
(model='', fname='')¶ Writes a parameter file (problem_params.inp) with default parameters for a given model.
Parameters: model : str
Name of the model whose parameter should be written to the file
fname : str, optional
Name of the parameter file to be written (if omitted problem_params.inp will be used)
radmc3dPy.conf module¶
radmc3dPy.crd_trans module¶
This module contains functions for coordinate transformations (e.g. rotation). For help on the syntax or functionality of each function see the help of the individual functions
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radmc3dPy.crd_trans.
csrot
(crd=None, ang=None, xang=0.0, yang=0.0, zang=0.0, deg=False)¶ Performs coordinate system rotation.
Parameters: crd : numpy ndarray
Three element vector containing the coordinates of a given point in a cartesian system
ang : list, ndarray
Three element list/ndarray describing the rotation angles around the x, y and z axes, respectively
xang: float
Rotation around the x-axis
yang: float
Rotation around the y-axis
zang: float
Rotation around the z-axis
deg : float, optional
If True angles should be given in degree instead of radians (as by default)
Returns: list
Returns a three element list with the rotated coordinates
Notes
Rotation matrices
Around the x-axis:
\[\begin{split}\left(\begin{matrix} 1 & 0 & 0 \\ 0 & cos(\alpha) & -sin(\alpha)\\ 0 & sin(\alpha) & cos(\alpha) \end{matrix}\right)\end{split}\]Around the y-axis:
\[\begin{split}\left(\begin{matrix} cos(\beta) & 0 & -sin(\beta) \\ 0 & 1 & 0\\ sin(\beta)& 0 & cos(\beta) \end{matrix}\right)\end{split}\]Around the z-axis
\[\begin{split}\left(\begin{matrix} cos(\gamma) & -sin\gamma) & 0 \\ sin(\gamma) & cos(\gamma) & 0 \\ 0 & 0 & 1 \end{matrix}\right)\end{split}\]
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radmc3dPy.crd_trans.
ctransSph2Cart
(crd=None, reverse=False)¶ Transform coordinates between spherical to cartesian systems
Parameters: crd : ndarray
Three element array containing the input coordinates [x,y,z] or [r,theta,phi] by default the coordinates assumed to be in the cartesian system
reverse : bool
If True calculates the inverse transformation (cartesian -> spherical). In this case crd should be [r,theta,phi]
Returns: Returns a three element array containig the output coordinates [r,theta,phi] or [x,y,z]
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radmc3dPy.crd_trans.
vrot
(crd=None, v=None, ang=None)¶ Rotates a vector in spherical coordinate system. First transforms the vector to cartesian coordinate system, then does the rotation then makes the inverse transformation
Parameters: crd : ndarray
Three element array containing the coordinates of a given point in the cartesian system
v : ndarray
Three element array, angles of rotation around the x,y,z axes
ang : ndarray
Three element arrray containing the angles to rotate around the x, y, z, axes, respectively
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radmc3dPy.crd_trans.
vtransSph2Cart
(crd=None, v=None, reverse=False)¶ Transform velocities between spherical to cartesian systems
Parameters: crd : ndarray
Three element array containing the input coordinates [x,y,z] or [r,theta,phi] by default the coordinates assumed to be in the cartesian system
v : ndarray
Three element array containing the input velocities in the same coordinate system as crd
reverse : bool
If True it calculates the inverse trasnformation (cartesian -> spherical)
Returns: Returns a three element array containg the output velocities [vr,vphi,vtheta] or [vx,vy,vz]
radmc3dPy.data module¶
This module contains a class for handling variable data in radmc-3d
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class
radmc3dPy.data.
radmc3dData
(grid=None)¶ Bases:
object
- RADMC-3D data class.
- Reading and writing dust density/temperature, gas density/temperature/velocity, generating a legacy vtk file for visualization.
Attributes
grid (radmc3dGrid, radmc3dOctree) Instance of the radmc3dGrid class, contains the spatial and frequency grids rhodust (ndarray) Dust density in g/cm^3 dusttemp (ndarray) Dust temperature in K rhogas (ndarray) Gas density in g/cm^3 ndens_mol (ndarray) Number density of the molecule [molecule/cm^3] ndens_cp (ndarray) Number density of the collisional partner [molecule/cm^3] gasvel (ndarray) Gas velocity in cm/s gastemp (ndarray) Gas temperature in K vturb (ndarray) Mictroturbulence in cm/s taux (ndarray) Optical depth along the x (cartesian) / r (cylindrical) / r (spherical) dimension tauy (ndarray) Optical depth along the y (cartesian) / theta (cylindrical) / theta (spherical) dimension tauz (ndarray) Optical depth along the z (cartesian) / z (cylindrical) / phi (spherical) dimension sigmadust (ndarray) Dust surface density in g/cm^2 sigmagas (ndarray) Gas surface density in molecule/cm^2 (or g/cm^2 depending on the dimension of rhogas) Methods
getDustMass
([idust])Calculates the dust mass in radmc3dData.rhodust getGasMass
([mweight, rhogas])Calculates the gas mass in radmc3dData.ndens_mol or radmc3dData.rhogas getSigmaDust
([idust])Calculates the dust surface density. getSigmaGas
()Calculates the gas surface density. getTau
([idust, axis, wav, kappa, old])Calculates the optical depth along any given combination of the axes. getTauOneDust
([idust, axis, kappa])Calculates the optical depth of a single dust species along any given combination of the axes. readDustDens
([fname, binary, old, octree])Reads the dust density. readDustTemp
([fname, binary, octree, old])Reads the dust temperature. readGasDens
([fname, ispec, binary, octree])Reads the gas density. readGasTemp
([fname, binary, octree])Reads the gas temperature. readGasVel
([fname, binary, octree])Reads the gas velocity. readVTurb
([fname, binary, octree])Reads the turbulent velocity field. writeDustDens
([fname, binary, old, octree])Writes the dust density. writeDustTemp
([fname, binary, octree])Writes the dust density. writeGasDens
([fname, ispec, binary, octree])Writes the gas density. writeGasTemp
([fname, binary, octree])Writes the gas temperature. writeGasVel
([fname, binary, octree])Writes the gas velocity. writeVTK
([vtk_fname, ddens, dtemp, idust, ...])Writes physical variables to a legacy vtk file. writeVTurb
([fname, binary, octree])Writes the microturbulence file. -
getDustMass
(idust=-1)¶ Calculates the dust mass in radmc3dData.rhodust
Parameters: idust : int
Dust index whose dust should be calculated. If it is set to -1 (default) the total dust mass is calculated summing up all dust species
Returns: A single float being the dust mass in gramm
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getGasMass
(mweight=2.3, rhogas=False)¶ Calculates the gas mass in radmc3dData.ndens_mol or radmc3dData.rhogas
Parameters: mweight : float
Molecular weight [atomic mass unit / molecule, i.e. same unit as mean molecular weight]
- rhogas : bool, optional
If True the gas mass will be calculated from radmc3dData.rhogas, while if set to False the gas mass will be calculated from radmc3dData.ndens_mol. The mweight parameter is only required for the latter.
Returns: A single float being the gas mass in gramm
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getSigmaDust
(idust=-1)¶ Calculates the dust surface density.
Parameters: idust : int, optional
Index of the dust species for which the surface density should be calculated if omitted the calculated surface density will be the sum over all dust species
-
getSigmaGas
()¶ Calculates the gas surface density. This method uses radmc3dData.rhogas to calculate the surface density, thus the unit of surface density depends on the unit of radmc3dData.rhogas (g/cm^2 or molecule/cm^2)
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getTau
(idust=None, axis='xy', wav=0.0, kappa=None, old=False)¶ Calculates the optical depth along any given combination of the axes.
Parameters: idust : list
List of dust component indices whose optical depth should be calculated If multiple indices are set the total optical depth is calculated summing over all dust species in idust
axis : str
Name of the axis/axes along which the optical depth should be calculated (e.g. ‘x’ for the first dimension or ‘xyz’ for all three dimensions)
wav : float
Wavelength at which the optical depth should be calculated
kappa : list, tuple
If set it should be a list of mass extinction coefficients at the desired wavelength The number of elements in the list should be equal to that in the idust keyword
old : bool, optional
If set to True the file format of the previous, 2D version of radmc will be used
-
getTauOneDust
(idust=0, axis='', kappa=0.0)¶ Calculates the optical depth of a single dust species along any given combination of the axes.
Parameters: idust : int
Index of the dust species whose optical depth should be calculated
axis : str
Name of the axis/axes along which the optical depth should be calculated (e.g. ‘x’ for the first dimension or ‘xyz’ for all three dimensions)
kappa : float
Mass extinction coefficients of the dust species at the desired wavelength
Returns: Returns a dictionary with the following keys
- taux : ndarray
optical depth along the first dimension
- tauy : ndarray
optical depth along the second dimension
(tauz is not yet implemented)
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readDustDens
(fname=None, binary=True, old=False, octree=False)¶ Reads the dust density.
Parameters: fname : str, optional
Name of the file that contains the dust density. If omitted ‘dust_density.inp’ is used (or if binary=True the ‘dust_density.binp’ is used).
binary : bool, optional
If true the data will be read in binary format, otherwise the file format is ascii
old : bool, optional
If set to True the file format of the previous, 2D version of radmc will be used
octree : bool, optional
If the data is defined on an octree-like AMR
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readDustTemp
(fname=None, binary=True, octree=False, old=False)¶ Reads the dust temperature.
Parameters: fname : str, optional
Name of the file that contains the dust temperature.
binary : bool, optional
If true the data will be read in binary format, otherwise the file format is ascii
octree : bool, optional
If the data is defined on an octree-like AMR
old : bool, optional
If True dust temperature will be written in the old RADMC format
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readGasDens
(fname=None, ispec='', binary=True, octree=False)¶ Reads the gas density.
Parameters: ispec : str
File name extension of the ‘numberdens_ispec.inp’ (or if binary=True ‘numberdens_ispec.binp’) file.
binary : bool
If true the data will be read in binary format, otherwise the file format is ascii
octree : bool, optional
If the data is defined on an octree-like AMR
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readGasTemp
(fname=None, binary=True, octree=False)¶ Reads the gas temperature.
Parameters: fname : str,optional
Name of the file that contains the gas temperature. If omitted ‘gas_temperature.inp’ (or if binary=True ‘gas_tempearture.binp’) is used.
binary : bool
If true the data will be read in binary format, otherwise the file format is ascii
octree : bool, optional
If the data is defined on an octree-like AMR
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readGasVel
(fname=None, binary=True, octree=False)¶ Reads the gas velocity.
Parameters: fname : str, optional
Name of the file that contains the gas velocity If omitted ‘gas_velocity.inp’ (if binary=True ‘gas_velocity.binp’)is used.
binary : bool
If true the data will be read in binary format, otherwise the file format is ascii
octree : bool, optional
If the data is defined on an octree-like AMR
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readVTurb
(fname=None, binary=True, octree=False)¶ Reads the turbulent velocity field.
Parameters: fname : str, optional
Name of the file that contains the turbulent velocity field If omitted ‘microturbulence.inp’ (if binary=True ‘microturbulence.binp’) is used.
binary : bool
If true the data will be read in binary format, otherwise the file format is ascii
octree : bool, optional
If the data is defined on an octree-like AMR
-
writeDustDens
(fname='', binary=True, old=False, octree=False)¶ Writes the dust density.
Parameters: fname : str, optional
Name of the file into which the dust density should be written. If omitted ‘dust_density.inp’ is used.
binary : bool
If true the data will be written in binary format, otherwise the file format is ascii
old : bool, optional
If set to True the file format of the previous, 2D version of radmc will be used
octree : bool, optional
If the data is defined on an octree-like AMR
-
writeDustTemp
(fname='', binary=True, octree=False)¶ Writes the dust density.
Parameters: fname : str, optional
Name of the file into which the dust density should be written. If omitted ‘dust_density.inp’ is used.
binary : bool
If true the data will be written in binary format, otherwise the file format is ascii
octree : bool, optional
If the data is defined on an octree-like AMR
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writeGasDens
(fname=None, ispec='', binary=True, octree=False)¶ Writes the gas density.
Parameters: fname : str, optional
Name of the file into which the data will be written. If omitted “numberdens_xxx.inp” and “numberdens_xxx.binp” will be used for ascii and binary format, respectively (xxx is the name of the molecule).
ispec : str
File name extension of the ‘numberdens_ispec.inp’ (if binary=True ‘numberdens_ispec.binp’) file into which the gas density should be written
binary : bool
If true the data will be written in binary format, otherwise the file format is ascii
octree : bool, optional
If the data is defined on an octree-like AMR
-
writeGasTemp
(fname='', binary=True, octree=False)¶ Writes the gas temperature.
Parameters: fname : str, optional
Name of the file into which the gas temperature should be written. If omitted ‘gas_temperature.inp’ (if binary=True ‘gas_tempearture.binp’) is used.
binary : bool
If true the data will be written in binary format, otherwise the file format is ascii
octree : bool, optional
If the data is defined on an octree-like AMR
-
writeGasVel
(fname='', binary=True, octree=False)¶ Writes the gas velocity.
Parameters: fname : str, optional
Name of the file into which the gas temperature should be written. If omitted ‘gas_velocity.inp’ (if binary=True ‘gas_velocity.binp’) is used.
binary : bool
If true the data will be written in binary format, otherwise the file format is ascii
octree : bool, optional
If the data is defined on an octree-like AMR
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writeVTK
(vtk_fname='', ddens=False, dtemp=False, idust=None, gdens=False, gvel=False, gtemp=False)¶ Writes physical variables to a legacy vtk file.
Parameters: vtk_fname : str
Name of the file to be written, if not specified ‘radmc3d_data.vtk’ will be used
ddens : bool
If set to True the dust density will be written to the vtk file
dtemp : bool
If set to True the dust temperature will be written to the vtk file
idust : list
List of indices that specifies which dust component should be written if not set then the first dust species (zero index) will be used
gdens : bool
If set to True the gas density will be written to the vtk file
gtemp : bool
If set to True the gas temperature will be written to the vtk file
gvel : bool
If set to True the gas velocity will be written to the vtk file
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writeVTurb
(fname='', binary=True, octree=False)¶ Writes the microturbulence file.
Parameters: fname : str, optional
Name of the file into which the turubulent velocity field should be written. If omitted ‘microturbulence.inp’ (if binary=True ‘microturbuulence.binp’) is used.
binary : bool
If true the data will be written in binary format, otherwise the file format is ascii
octree : bool, optional
If the data is defined on an octree-like AMR
radmc3dPy.dustopac module¶
This module contains classes for handling dust opacities
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radmc3dPy.dustopac.
computeDustOpacMie
(fname='', matdens=None, agraincm=None, lamcm=None, theta=None, logawidth=None, wfact=3.0, na=20, chopforward=0.0, errtol=0.01, verbose=False, extrapolate=False, return_type=1)¶ Compute dust opacity with Mie theory based on the optical constants in the optconst_file. Optionally also the scattering phase function in terms of the Mueller matrix elements can be computed. To smear out the resonances that appear due to the perfect sphere shape, you can optionally smear out the grain size distribution a bit with setting the width of a Gaussian grain size distribution.
Parameters: fname : str
File name of the optical constants file. This file should contain three columns: first the wavelength in micron, then the n-coefficient and then the k-coefficient. See Jena optical constants database: http://www.astro.uni-jena.de/Laboratory/Database/databases.html
matdens : float
Material density in g/cm^3
agraincm : float
Grain radius in cm
lamcm : ndarray
Wavelength grid in cm
theta : ndarray, optional
Angular grid (a numpy array) between 0 and 180 which are the scattering angle sampling points at which the scattering phase function is computed.
logawidth : float, optional
If set, the size agrain will instead be a sample of sizes around agrain. This helps to smooth out the strong wiggles in the phase function and opacity of spheres at an exact size. Since in Nature it rarely happens that grains all have exactly the same size, this is quite natural. The value of logawidth sets the width of the Gauss in ln(agrain), so for logawidth<<1 this give a real width of logawidth*agraincm.
wfact : float
Grid width of na sampling points in units of logawidth. The Gauss distribution of grain sizes is cut off at agrain * exp(wfact*logawidth) and agrain * exp(-wfact*logawidth). Default = 3
na : int
Number of size sampling points (if logawidth set, default=20)
chopforward : float
If >0 this gives the angle (in degrees from forward) within which the scattering phase function should be kept constant, essentially removing the strongly peaked forward scattering. This is useful for large grains (large ratio 2*pi*agraincm/lamcm) where the forward scattering peak is extremely strong, yet extremely narrow. If we are not interested in very forward-peaked scattering (e.g. only relevant when modeling e.g. the halo around the moon on a cold winter night), this will remove this component and allow a lower angular grid resolution for the theta grid.
errtol : float
Tolerance of the relative difference between kscat and the integral over the zscat Z11 element over angle. If this tolerance is exceeded, a warning is given.
verbose : bool
If set to True, the code will give some feedback so that one knows what it is doing if it becomes slow.
extrapolate : bool
If set to True, then if the wavelength grid lamcm goes out of the range of the wavelength grid of the optical constants file, then it will make a suitable extrapolation: keeping the optical constants constant for lamcm < minimum, and extrapolating log-log for lamcm > maximum.
return_type : {0, 1}
If 0 a dictionary is returned (original return type) if 1 an instance of radmc3dDustOpac will be returned
Returns: A dictionary with the following keys:
- kabs : ndarray
Absorption opacity kappa_abs_nu (a numpy array) in units of cm^2/gram
- ksca : ndarray
Scattering opacity kappa_abs_nu (a numpy array) in units of cm^2/gram
- gsca : ndarray
The <cos(theta)> g-factor of scattering
- theta : ndarray (optional, only if theta is given at input)
The theta grid itself (just a copy of what was given)
- zscat : ndarray (optional, only if theta is given at input)
The components of the scattering Mueller matrix Z_ij for each wavelength and each scattering angel. The normalization of Z is such that kscat can be reproduced (as can be checked) by the integral: 2*pi*int_{-1}^{+1}Z11(mu)dmu=kappa_scat. For symmetry reasons only 6 elements of the Z matrix are returned: Z11, Z12, Z22, Z33, Z34, Z44. Note that Z21 = Z12 and Z43 = -Z34. The scattering matrix is normalized such that if a plane wave with Stokes flux
Fin = (Fin_I,Fin_Q,Fin_U,Fin_V)
hits a dust grain (which has mass mgrain), then the scattered flux
Fout = (Fout_I,Fout_Q,Fout_U,Fout_V)
at distance r from the grain at angle theta is given by
Fout(theta) = (mgrain/r^2) * Zscat . Fin
where . is the matrix-vector multiplication. Note that the Stokes components must be such that the horizontal axis in the “image” is pointing in the scattering plane. This means that radiation with Fin_Q < 0 is scattered well, because it is vertically polarized (along the scattering angle axis), while radiation with Fin_Q > 0 is scatterd less well because it is horizontally polarized (along the scattering plane).
- kscat_from_z11 : ndarray (optional, only if theta is given at input)
The kscat computed from the (above mentioned) integral of Z11 over all angles. This should be nearly identical to kscat if the angular grid is sufficiently fine. If there are strong differences, this is an indication that the angular gridding (the theta grid) is not fine enough. But you should have then automatically gotten a warning message as well (see errtol).
- wavmic : ndarray (optional, only if extrapolate is set to True)
The original wavelength grid from the optical constants file, with possibly an added extrapolated
- ncoef : ndarray (optional, only if extrapolate is set to True)
The optical constant n at that grid
- kcoef : ndarray (optional, only if extrapolate is set to True)
The optical constant k at that grid
- agr : ndarray (optional, only if logawidth is not None)
Grain sizes
- wgt : ndarray (optional, only if logawidth is not None)
The averaging weights of these grain (not the masses!) The sum of wgt.sum() must be 1.
- zscat_nochop : ndarray (optional, only if chopforward > 0)
The zscat before the forward scattering was chopped off
- kscat_nochop : ndarray (optional, only if chopforward > 0)
The kscat originally from the bhmie code
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class
radmc3dPy.dustopac.
radmc3dDustOpac
¶ Bases:
object
Class to handle dust opacities.
Attributes
wav (list) Each element of the list contains an ndarray with the wavelength grid freq (list) Each element of the list contains an ndarray with the frequency grid nwav (list) Each element of the list contains an integer with the number of wavelengths kabs (list) Each element of the list contains an ndarray with the absorption coefficient per unit mass ksca (list) Each element of the list contains an ndarray with the scattering coefficient per unit mass phase_g (list) Each element of the list contains an ndarray with the hase function ext (list) Each element of the list contains a string wht the file name extension of the duskappa_ext.Kappa file therm (list) Each element of the list contains a bool, if it is set to False the dust grains are quantum-heated (default: True) idust (lisintt) Each element of the list contains an integer with the index of the dust species in the dust density distribution array scatmat (list) Each element is a boolean indicating whether the dust opacity table includes (True) the full scattering matrix or not (False) nang (list) Each element is a string, containing the number of scattering angles in the scattering matrix if its given scatang (list) Each element is a numpy ndarray containing the scattering angles in the scattering matrix if its given z11 (list) Each element is a numpy ndarray containing the (1,1) element of the scattering angles in the scattering matrix if its given z12 (list) Each element is a numpy ndarray containing the (1,2) element of the scattering angles in the scattering matrix if its given z22 (list) Each element is a numpy ndarray containing the (2,2) element of the scattering angles in the scattering matrix if its given z33 (list) Each element is a numpy ndarray containing the (3,3) element of the scattering angles in the scattering matrix if its given z34 (list) Each element is a numpy ndarray containing the (3,4) element of the scattering angles in the scattering matrix if its given z44 (list) Each element is a numpy ndarray containing the (4,4) element of the scattering angles in the scattering matrix if its given Methods
makeOpac
([ppar, wav, old, code, theta, ...])Createst the dust opacities using a Mie code distributed with RADMC-3D. makeopacRadmc2D
([ext])Creates dust opacities (dustopac_*.inp files) for the previous 2D version of radmc mixOpac
([ppar, mixnames, mixspecs, mixabun, ...])Mixes dust opacities. readMasterOpac
()Reads the master opacity file ‘dustopac.inp’. readOpac
([ext, idust, scatmat, old])Reads the dust opacity files. runMakedust
([freq, gmin, gmax, ngs, ...])Interface function to the F77 code makedust to calculate mass absorption coefficients. writeMasterOpac
([ext, therm, ...])Writes the master opacity file ‘dustopac.inp’. writeOpac
([fname, ext, idust, scatmat])Writes dust opacities to file -
makeOpac
(ppar=None, wav=None, old=False, code='python', theta=None, logawidth=None, wfact=3.0, na=20, chopforward=0.0, errtol=0.01, verbose=False, extrapolate=False)¶ Createst the dust opacities using a Mie code distributed with RADMC-3D.
Parameters: ppar : dictionary
Parameters of the simulations
wav : ndarray, optional
Wavelength grid on which the mass absorption coefficients should be calculated
code : {‘python’, ‘fortran’}
Version of the mie scattering code BHMIE to be used. ‘fortran’ - use the original fortran77 code of Bruce Drain (should be downloaded separately, compiled and its path added to the PATH environment variable), ‘python’ a python version of BHMIE by Kees Dullemond (radmc3dPy.miescat).
theta : ndarray, optional
Angular grid (a numpy array) between 0 and 180 which are the scattering angle sampling points at which the scattering phase function is computed.
logawidth : float, optional
If set, the size agrain will instead be a sample of sizes around agrain. This helps to smooth out the strong wiggles in the phase function and opacity of spheres at an exact size. Since in Nature it rarely happens that grains all have exactly the same size, this is quite natural. The value of logawidth sets the width of the Gauss in ln(agrain), so for logawidth<<1 this give a real width of logawidth*agraincm.
wfact : float
Grid width of na sampling points in units of logawidth. The Gauss distribution of grain sizes is cut off at agrain * exp(wfact*logawidth) and agrain * exp(-wfact*logawidth). Default = 3
na : int
Number of size sampling points (if logawidth set, default=20)
chopforward : float
If >0 this gives the angle (in degrees from forward) within which the scattering phase function should be kept constant, essentially removing the strongly peaked forward scattering. This is useful for large grains (large ratio 2*pi*agraincm/lamcm) where the forward scattering peak is extremely strong, yet extremely narrow. If we are not interested in very forward-peaked scattering (e.g. only relevant when modeling e.g. the halo around the moon on a cold winter night), this will remove this component and allow a lower angular grid resolution for the theta grid.
errtol : float
Tolerance of the relative difference between kscat and the integral over the zscat Z11 element over angle. If this tolerance is exceeded, a warning is given.
verbose : bool
If set to True, the code will give some feedback so that one knows what it is doing if it becomes slow.
extrapolate : bool
If set to True, then if the wavelength grid lamcm goes out of the range of the wavelength grid of the optical constants file, then it will make a suitable extrapolation: keeping the optical constants constant for lamcm < minimum, and extrapolating log-log for lamcm > maximum.
old : bool, optional
If set to True the file format of the previous, 2D version of radmc will be used
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makeopacRadmc2D
(ext=None)¶ Creates dust opacities (dustopac_*.inp files) for the previous 2D version of radmc It takes the input dust opacity files and interpolates them onto the used frequency grid
Parameters: ext : list
List of dustkappa file name extensions, i.e. the input file name has to be named as dustkappa_ext[i].inp
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static
mixOpac
(ppar=None, mixnames=None, mixspecs=None, mixabun=None, writefile=True)¶ Mixes dust opacities.
Parameters: ppar : dictionary, optional
All parameters of the actual model setup.
mixnames : list, optional
Names of the files into which the mixed dust opacities will be written (not needed if writefile=False)
mixspecs : list, optional
Names of the files from which the dust opacities are read (not needed if readfile=False)
mixabun : list, optional
Abundances of different dust species
writefile : bool
If False the mixed opacities will not be written out to files given in mixnames.
NOTE, either ppar or mixname, mixspecs, and mixabun should be set.
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static
readMasterOpac
()¶ Reads the master opacity file ‘dustopac.inp’. It reads the dustkappa filename extensions (dustkappa_ext.inp) corresponding to dust species indices
Returns: Returns a dictionary with the following keys:
-
readOpac
(ext=None, idust=None, scatmat=None, old=False)¶ Reads the dust opacity files.
Parameters: ext : list
File name extension (file names should look like ‘dustkappa_ext.inp’)
idust: list
Indices of the dust species in the master opacity file (dustopac.inp’) - starts at 0
scatmat: list
If specified, its elements should be booleans indicating whether the opacity file contains also the full scattering matrix (True) or only dust opacities (False)
old : bool, optional
If set to True the file format of the previous, 2D version of radmc will be used
-
static
runMakedust
(freq=None, gmin=None, gmax=None, ngs=None, lnk_fname=None, gdens=None)¶ Interface function to the F77 code makedust to calculate mass absorption coefficients.
Parameters: freq : ndarray
Contains the frequency grid on which the opacities should be calculated
gmin : float
Minimum grain size
gmax : float
Maximum grain size
ngs : int
Number of grain sizes
gdens : float
Density of the dust grain in g/cm^3
lnk_fname : str
Name of the file in which the optical constants are stored
Returns: Returns an ndarray with [nfreq,ngs] dimensions containing the resulting opacities
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static
writeMasterOpac
(ext=None, therm=None, scattering_mode_max=1, old=False)¶ Writes the master opacity file ‘dustopac.inp’.
Parameters: ext : list
List of dustkappa file name extensions
therm : list
List of integers specifying whether the dust grain is thermal or quantum heated (0-thermal, 1-quantum)
scattering_mode_max : int
Scattering mode code in radmc3d : 0 - no scattering, 1 - isotropic scattering, 2 - anisotropic scattering with Henyei-Greenstein phase function, 5 - anisotropic scattering using the full scattering matrix and stokes vectors.
old : bool, optional
If set to True the file format of the previous, 2D version of radmc will be used
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writeOpac
(fname=None, ext=None, idust=None, scatmat=False)¶ Writes dust opacities to file
Parameters: fname : str
Name of the file to write the dust opacties into
ext : str
If fname is not specified, the output file name will be generated as dustkappa_EXT.inp or dustkapscatmat_EXT.inp depending on the file format
idust : int
Dust species index whose opacities should be written to file
scatmat : bool
If True the full scattering matrix will be written to file on top of the opacities (i.e. the file name should be dustkapscatmat_EXT.inp). If False only the dust opacities and the asymmetry parameter (if present) will be written to file (dustkappa_EXT.inp type files)
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radmc3dPy.image module¶
This module contains classes/functions to create and read images with RADMC-3D and to calculate interferometric visibilities and write fits files For help on the syntax or functionality of each function see the help of the individual functions
-
radmc3dPy.image.
cmask
(im=None, rad=0.0, au=False, arcsec=False, dpc=None)¶ - Simulates a coronographic mask.
- Sets the image values to zero within circle of a given radius around the image center.
Parameters: im : radmc3dImage
A radmc3dImage class containing the image
rad : float
The raadius of the mask
au : bool
If true the radius is taken to have a unit of AU
arcsec : bool
If true the radius is taken to have a unit of arcsec (dpc should also be set)
dpc : float
Distance of the source (required if arcsec = True)
NOTE if arcsec=False and au=False rad is taken to have a unit of pixel
Returns: Returns a radmc3dImage class containing the masked image
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radmc3dPy.image.
getPSF
(nx=None, ny=None, psfType='gauss', pscale=None, fwhm=None, pa=None, tdiam_prim=8.2, tdiam_sec=0.94, wav=None)¶ Calculates a two dimensional Gaussian PSF.
Parameters: nx : int
Image size in the first dimension
ny : int
Image size in the second dimension
psfType : {‘gauss’, ‘airy’}
Shape of the PSF. If psfType=’gauss’, fwhm and pa should also be given. If psfType=’airy’, the tdiam_prim, tdiam_sec and wav parameters should also be specified.
pscale : list
Pixelscale of the image, if set fwhm should be in the same unit, if not set unit of fwhm is pixels
fwhm : list, optional
Full width at half maximum of the psf along the two axis (should be set only if psfType=’gauss’)
pa : float, optional
Position angle of the gaussian if the gaussian is not symmetric (should be set only if psfType=’gauss’)
tdiam_prim : float, optional
Diameter of the primary aperture of the telescope in meter. (should be set only if psfType=’airy’)
tdiam_sec : float, optional
Diameter of the secondary mirror (central obscuration), if there is any, in meter. If no secondary mirror/obscuration is present, this parameter should be set to zero. (should be set only if psfType=’airy’)
wav : float, optional
Wavelength of observation in micrometer (should be set only if psfType=’airy’)
Returns: Returns a dictionary with the following keys:
- psf : ndarray
- The two dimensional psf
- x : ndarray
- The x-axis of the psf
- y : ndarray
- The y-axis of the psf
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radmc3dPy.image.
makeImage
(npix=None, incl=None, wav=None, sizeau=None, phi=None, posang=None, pointau=None, fluxcons=True, nostar=False, noscat=False, widthkms=None, linenlam=None, vkms=None, iline=None, lambdarange=None, nlam=None, stokes=False, binary=False)¶ Calculates a rectangular image with RADMC-3D
Parameters: npix : int
Number of pixels on the rectangular images
sizeau : float
Diameter of the image in au
incl : float
Inclination angle of the source
wav : float
Wavelength of the image in micron
phi : float, optional
Azimuthal rotation angle of the source in the model space
posang : float, optional
Position angle of the source in the image plane
pointau : Float, optional
Three elements list of the cartesian coordinates of the image center
widthkms : float, optional
Width of the frequency axis of the channel maps
linenlam : int, optional
Number of wavelengths to calculate images at
vkms : float, optional
A single velocity value at which a channel map should be calculated
iline : int, optional
Line transition index
lambdarange : list, optional
Two element list with the wavelenght boundaries between which multiwavelength images should be calculated
nlam : int, optional
Number of wavelengths to be calculated in lambdarange
fluxcons : bool, optional
This should not even be a keyword argument, it ensures flux conservation (adaptive subpixeling) in the rectangular images
nostar : bool, optional
If True the calculated images will not contain stellar emission
noscat : bool, optional
- If True, scattered emission will be neglected in the source function, however,
extinction will contain scattering if kappa_scat is not zero.
stokes : bool, optional
If True, images in all four stokes parameters (IQUV) will be calculated, if False only the intensity will be calculated
binary : bool, optional
If True the output image will be written in a C-style binary format, if False the image format will be ASCII
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radmc3dPy.image.
plotImage
(image=None, arcsec=False, au=False, log=False, dpc=None, maxlog=None, saturate=None, bunit='norm', ifreq=0, cmask_rad=None, interpolation='nearest', cmap=<matplotlib.colors.LinearSegmentedColormap object>, stokes='I', fig=None, ax=None, projection='polar', deg=True, rmax=None, rlog=True, **kwargs)¶ Plots a radmc3d image.
Parameters: image : radmc3dImage
A radmc3dImage class returned by readimage
arcsec : bool
If True image axis will have the unit arcsec (NOTE: dpc keyword should also be set!)
au : bool
If True image axis will have the unit AU
log : bool
If True image scale will be logarithmic, otherwise linear
dpc : float
Distance to the source in parsec (This keywords should be set if arcsec=True, or bunit!=’norm’)
maxlog : float
Logarithm of the lowest pixel value to be plotted, lower pixel values will be clippde
saturate : float
Highest pixel values to be plotted in terms of the peak value, higher pixel values will be clipped
bunit : {‘norm’, ‘inu’, ‘snu’, ‘jy/beam’, ‘jy/pixel’}
Unit of the image, (‘norm’ - Inu/max(Inu), ‘inu’ - Inu, ‘snu’ - Jy/pixel, ‘jy/pixel’ - Jy/pixel, ‘jy/beam’ - Jy/beam), default is ‘norm’. The ‘snu’ keyword value is kept for backward compatibility as it is fully equivalent with the ‘jy/pixel’ keyword value.
ifreq : int
If the image file/array consists of multiple frequencies/wavelengths ifreq denotes the index of the frequency/wavelength in the image array to be plotted
cmask_rad : float
Simulates coronographyic mask : sets the image values to zero within this radius of the image center The unit is the same as the image axis (au, arcsec, cm) NOTE: this works only on the plot, the image array is not changed (for that used the cmask() function)
interpolation : str
interpolation keyword for imshow (e.g. ‘nearest’, ‘bilinear’, ‘bicubic’)
cmap : matplotlib color map
stokes : {‘I’, ‘Q’, ‘U’, ‘V’, ‘PI’, ‘P’}
What to plot for full stokes images, Stokes I/Q/U/V, PI - polarised intensity (PI = sqrt(Q^2 + U^2 + V^2)) P - polarisation fraction (i.e. sqrt(Q^2 + U^2 + V^2) / I) PIL - polarised intensity (PI = sqrt(Q^2 + U^2)) PL - fraction of linear polarisation (i.e. sqrt(Q^2 + U^2) / I)
fig : matplotlig.figure.Figure, optional
An instance of a matplotlib Figure. If not provided a new Figure will be generated. If provided plotImage will add a single Axes to the Figure, using add_subplots() with the appropriate projection. If the desired plot is to be made for a multi-panel plot, the appropriate Axes instance can be passed to the ax keyword. This keyword is only used for circular images.
ax : matplotlib.axes.Axes, optional
An instance of a matplotlib Axes to draw the plot on. Note, that the projection of the axes should be the same as the projection keyword passed to plotImage. This keyword is only used for circular images.
projection : {‘polar’, ‘cartesian’}
Projection of the plot. For cartesian plots a rectangular plot will be drawn, with the horizontal axis being the azimuth angle, and the vertical axis the radius.
deg : bool
If True the unit of the azimuthal coordinates will degree, if False it will be radian. Used only for circular images and for cartesian projection.
rmax : float
Maximum value of the radial coordinate for polar projection. Used only for circular images.
rlog : bool
If True the radial coordiante axis will be set to logarithmic for cartesian projection. Used only for circular images.
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radmc3dPy.image.
plotPolDir
(image=None, arcsec=False, au=False, dpc=None, ifreq=0, cmask_rad=None, color='w', nx=20, ny=20)¶ Function to plot the polarisation direction for full stokes images
Parameters: image : radmc3dImage
A radmc3dImage class returned by readimage
arcsec : bool
If True image axis will have the unit arcsec (NOTE: dpc keyword should also be set!)
au : bool
If True image axis will have the unit AU
dpc : float
Distance to the source in parsec (This keywords should be set if arcsec=True, or bunit!=’norm’)
ifreq : int
If the image file/array consists of multiple frequencies/wavelengths ifreq denotes the index of the frequency/wavelength in the image array to be plotted
cmask_rad : float
Simulates coronographyic mask : sets the image values to zero within this radius of the image center The unit is the same as the image axis (au, arcsec, cm) NOTE: this works only on the plot, the image array is not changed (for that used the cmask() function)
color : str
Color for the polarisation direction plot
nx : int
Number of grid points along the horizontal axis at which the direction should be displayed
ny : int
Number of grid points along the vertical axis at which the direction should be displayed
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class
radmc3dPy.image.
radmc3dCircimage
¶ Bases:
object
RADMC-3D circular image class
Attributes
image (ndarray) The image as calculated by radmc3d (the values are intensities in erg/s/cm^2/Hz/ster) rc (ndarray) Radial cell center coordinate of the image [cm] ri (ndarray) Radial cell interface coordinate of the image [cm] phic (ndarray) Azimuthal cell center coordinate of the image [rad] phii (ndarray) Azimuthal cell interface coordinate of the image [rad] nr (int) Number of pixels in the radial direction nphi (int) Number of pixels in the azimuthal direction nfreq (int) Number of frequencies in the image cube freq (ndarray) Frequency grid in the image cube nwav (int) Number of wavelengths in the image cube (same as nfreq) wav (ndarray) Wavelength grid in the image cube filename (str) Name of the file the image data was read from stokes (bool) If True the image data contain the full stokes vector (I,Q,U,V) Methods
getPixelSize
()Calculates the pixel size readImage
([filename, old])Reads a circular image -
getPixelSize
()¶ Calculates the pixel size
Returns: The pixel size in cm^2
-
readImage
(filename='circimage.out', old=False)¶ Reads a circular image
Parameters: filename : str
Name of the file to be read.
old : bool
If True the image format of the old 2D code (radmc) will be used. If False (default) the RADMC-3D format is used.
-
-
class
radmc3dPy.image.
radmc3dImage
¶ Bases:
object
RADMC-3D image class
Attributes
image (ndarray) The image as calculated by radmc3d (the values are intensities in erg/s/cm^2/Hz/ster) imageJyppix (ndarray) The image with pixel units of Jy/pixel x (ndarray) x coordinate of the image [cm] y (ndarray) y coordinate of the image [cm] nx (int) Number of pixels in the horizontal direction ny (int) Number of pixels in the vertical direction sizepix_x (float) Pixel size in the horizontal direction [cm] sizepix_y (float) Pixel size in the vertical direction [cm] nfreq (int) Number of frequencies in the image cube freq (ndarray) Frequency grid in the image cube nwav (int) Number of wavelengths in the image cube (same as nfreq) wav (ndarray) Wavelength grid in the image cube Methods
getClosurePhase
([bl, pa, dpc])Calculates clusure phases for a given model image for any arbitrary baseline triplet. getMomentMap
([moment, nu0, wav0])Calculates moment maps. getVisibility
([bl, pa, dpc])Calculates visibilities for a given set of projected baselines and position angles with Discrete Fourier Transform. imConv
([dpc, psfType, fwhm, pa, tdiam_prim, ...])Convolves a RADMC-3D image with a two dimensional Gaussian psf. plotMomentMap
([moment, nu0, wav0, dpc, au, ...])Plots moment maps readImage
([fname, binary, old])Reads an image calculated by RADMC-3D writeFits
([fname, dpc, coord, bandwidthmhz, ...])Writes out a RADMC-3D image data in fits format. -
getClosurePhase
(bl=None, pa=None, dpc=None)¶ Calculates clusure phases for a given model image for any arbitrary baseline triplet.
Parameters: bl : list/ndarray
A list or ndrray containing the length of projected baselines in meter.
pa : list/ndarray
A list or Numpy array containing the position angles of projected baselines in degree.
dpc : distance of the source in parsec
Returns: Returns a dictionary with the following keys:
- bl : projected baseline in meter
- pa : position angle of the projected baseline in degree
- nbl : number of baselines
- u : spatial frequency along the x axis of the image
- v : spatial frequency along the v axis of the image
- vis : complex visibility at points (u,v)
- amp : correlation amplitude
- phase : Fourier phase
- cp : closure phase
- wav : wavelength
- nwav : number of wavelengths
Notes
bl and pa should either be an array with dimension [N,3] or if they are lists each element of the list should be a list of length 3, since closure phases are calculated only for closed triangles
-
getMomentMap
(moment=0, nu0=None, wav0=None)¶ Calculates moment maps.
Parameters: moment : int
Moment of the channel maps to be calculated
nu0 : float
Rest frequency of the line in Hz
wav0 : float
Rest wavelength of the line in micron
Returns: Ndarray with the same dimension as the individual channel maps
-
getVisibility
(bl=None, pa=None, dpc=None)¶ Calculates visibilities for a given set of projected baselines and position angles with Discrete Fourier Transform.
Parameters: bl : list/ndarray
A list or ndrray containing the length of projected baselines in meter.
pa : list/ndarray
A list or Numpy array containing the position angles of projected baselines in degree.
dpc : distance of the source in parsec
Returns: Returns a dictionary with the following keys:
- bl : projected baseline in meter
- pa : position angle of the projected baseline in degree
- nbl : number of baselines
- u : spatial frequency along the x axis of the image
- v : spatial frequency along the v axis of the image
- vis : complex visibility at points (u,v)
- amp : correlation amplitude
- phase : Fourier phase
- wav : wavelength
- nwav : number of wavelengths
-
imConv
(dpc=1.0, psfType='gauss', fwhm=None, pa=None, tdiam_prim=8.2, tdiam_sec=0.94)¶ Convolves a RADMC-3D image with a two dimensional Gaussian psf. The output images will have the same brightness units as the input images.
Parameters: dpc : float
Distance of the source in pc.
psfType : {‘gauss’, ‘airy’}
Shape of the PSF. If psfType=’gauss’, fwhm and pa should also be given. If psfType=’airy’, the tdiam_prim, tdiam_sec and wav parameters should also be specified.
fwhm : list, optional
A list of two numbers; the FWHM of the two dimensional psf along the two principal axes. The unit is assumed to be arcsec. (should only be set if psfType=’gauss’)
pa : float, optional
Position angle of the psf ellipse (counts from North counterclockwise, should only be set if psfType=’gauss’)
tdiam_prim : float, optional
Diameter of the primary aperture of the telescope in meter. (should be set only if psfType=’airy’)
tdiam_sec : float, optional
Diameter of the secondary mirror (central obscuration), if there is any, in meter. If no secondary mirror/obscuration is present, this parameter should be set to zero. (should only be set if psfType=’airy’)
Returns: Returns a radmc3dImage
-
plotMomentMap
(moment=0, nu0=None, wav0=None, dpc=1.0, au=False, arcsec=False, cmap=None, vclip=None)¶ Plots moment maps
Parameters: moment : int
Moment of the channel maps to be calculated
nu0 : float
Rest frequency of the line in Hz
wav0 : float
Rest wavelength of the line in micron
dpc : float
Distance of the source in pc
au : bool
If True displays the image with AU as the spatial axis unit
arcsec : bool
If True displays the image with arcsec as the spatial axis unit (dpc should also be set!)
cmap : matplotlib colormap
Color map to be used to display the moment map
vclip : list/ndarray
- Two element list / Numpy array containin the lower and upper limits for the values in the moment
map to be displayed
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readImage
(fname=None, binary=False, old=False)¶ Reads an image calculated by RADMC-3D
Parameters: fname : str, optional
File name of the radmc3d output image (if omitted ‘image.out’ is used)
old : bool
If set to True it reads old radmc-2d style image
binary : bool, optional
False - the image format is formatted ASCII if True - C-compliant binary (omitted if old=True)
-
writeFits
(fname='', dpc=1.0, coord='03h10m05s -10d05m30s', bandwidthmhz=2000.0, casa=False, nu0=0.0, stokes='I', fitsheadkeys=[], ifreq=None)¶ Writes out a RADMC-3D image data in fits format.
Parameters: fname : str
File name of the radmc3d output image (if omitted ‘image.fits’ is used)
dpc : float
Distance of the source in pc
coord : str
Image center coordinates
bandwidthmhz : float
Bandwidth of the image in MHz (equivalent of the CDELT keyword in the fits header)
casa : bool
If set to True a CASA compatible four dimensional image cube will be written
nu0 : float
Rest frequency of the line (for channel maps)
stokes : {‘I’, ‘Q’, ‘U’, ‘V’, ‘PI’}
Stokes parameter to be written if the image contains Stokes IQUV (possible choices: ‘I’, ‘Q’, ‘U’, ‘V’, ‘PI’ -Latter being the polarized intensity)
fitsheadkeys : dictionary
Dictionary containing all (extra) keywords to be added to the fits header. If the keyword is already in the fits header (e.g. CDELT1) it will be updated/changed to the value in fitsheadkeys, if the keyword is not present the keyword is added to the fits header.
ifreq : int
Frequency index of the image array to write. If set only this frequency of a multi-frequency array will be written to file.
-
-
radmc3dPy.image.
readImage
(fname=None, binary=False, old=False)¶ - Reads an image calculated by RADMC-3D.
- This function is an interface to radmc3dImage.readImage().
Parameters: fname : str, optional
File name of the radmc3d output image (if omitted ‘image.out’ is used)
- old : bool
If set to True it reads old radmc-2d style image
- binary : bool, optional
False - the image format is formatted ASCII if True - C-compliant binary (omitted if old=True)
-
radmc3dPy.image.
readcircimage
(filename='circimage.out', old=False)¶ A convenience function to read circular images
Parameters: filename : str
Name of the file to be read.
old : bool
If True the image format of the old 2D code (radmc) will be used. If False (default) the RADMC-3D format is used.
radmc3dPy.miescat module¶
This module contains functions for Mie-scattering and to write dust opacity files
-
radmc3dPy.miescat.
bhmie
(x=None, refrel=None, theta=None)¶ The famous Bohren and Huffman Mie scattering code. This version was ported to Python from the f77 code from Bruce Draine, which can be downloaded from:
The code originates from the book by Bohren & Huffman (1983) on “Absorption and Scattering of Light by Small Particles”. This python version was created by Cornelis Dullemond, February 2017.
Parameters: x : ndarray
Size parameter (2*pi*radius_grain/lambda)
refrel : complex
Complex index of refraction (example: 1.5 + 0.01*1j)
theta : ndarray
Scattering angles between 0 and 180 deg
Returns: A list with the following elements:
- [0] S1 : ndarray
- Complex phase function S1 (E perpendicular to scattering plane) as a function of theta
- [1] S2 : ndarray
- Complex phase function S1 (E parallel to scattering plane) as a function of theta
- [2] Qext : ndarray
- Efficiency factor for extinction (C_ext/pi*a**2)
- [3] Qsca : ndarray
- Efficiency factor for scatterin(C_sca/pi*a**2)
- [4] Qback : ndarray
- Backscattering efficiency ((dC_sca/domega)/pi*a**2 ) Note, this is (1/4*pi) smaller than the “radar backscattering efficiency” - see Bohren & Huffman 1983 pp. 120-123]
- [5] gsca : <cos(theta)> for scattering
-
radmc3dPy.miescat.
compute_opac_mie
(fname='', matdens=None, agraincm=None, lamcm=None, theta=None, logawidth=None, wfact=3.0, na=20, chopforward=0.0, errtol=0.01, verbose=False, extrapolate=False)¶ Compute dust opacity with Mie theory based on the optical constants in the optconst_file. Optionally also the scattering phase function in terms of the Mueller matrix elements can be computed. To smear out the resonances that appear due to the perfect sphere shape, you can optionally smear out the grain size distribution a bit with setting the width of a Gaussian grain size distribution.
Parameters: fname : str
File name of the optical constants file. This file should contain three columns: first the wavelength in micron, then the n-coefficient and then the k-coefficient. See Jena optical constants database: http://www.astro.uni-jena.de/Laboratory/Database/databases.html
matdens : float
Material density in g/cm^3
agraincm : float
Grain radius in cm
lamcm : ndarray
Wavelength grid in cm
theta : ndarray, optional
Angular grid (a numpy array) between 0 and 180 which are the scattering angle sampling points at which the scattering phase function is computed.
logawidth : float, optional
If set, the size agrain will instead be a sample of sizes around agrain. This helps to smooth out the strong wiggles in the phase function and opacity of spheres at an exact size. Since in Nature it rarely happens that grains all have exactly the same size, this is quite natural. The value of logawidth sets the width of the Gauss in ln(agrain), so for logawidth<<1 this give a real width of logawidth*agraincm.
wfact : float
Grid width of na sampling points in units of logawidth. The Gauss distribution of grain sizes is cut off at agrain * exp(wfact*logawidth) and agrain * exp(-wfact*logawidth). Default = 3
na : int
Number of size sampling points (if logawidth set, default=20)
chopforward : float
If >0 this gives the angle (in degrees from forward) within which the scattering phase function should be kept constant, essentially removing the strongly peaked forward scattering. This is useful for large grains (large ratio 2*pi*agraincm/lamcm) where the forward scattering peak is extremely strong, yet extremely narrow. If we are not interested in very forward-peaked scattering (e.g. only relevant when modeling e.g. the halo around the moon on a cold winter night), this will remove this component and allow a lower angular grid resolution for the theta grid.
errtol : float
Tolerance of the relative difference between kscat and the integral over the zscat Z11 element over angle. If this tolerance is exceeded, a warning is given.
verbose : bool
If set to True, the code will give some feedback so that one knows what it is doing if it becomes slow.
extrapolate : bool
If set to True, then if the wavelength grid lamcm goes out of the range of the wavelength grid of the optical constants file, then it will make a suitable extrapolation: keeping the optical constants constant for lamcm < minimum, and extrapolating log-log for lamcm > maximum.
Returns: A dictionary with the following keys:
- kabs : ndarray
Absorption opacity kappa_abs_nu (a numpy array) in units of cm^2/gram
- ksca : ndarray
Scattering opacity kappa_abs_nu (a numpy array) in units of cm^2/gram
- gsca : ndarray
The <cos(theta)> g-factor of scattering
- theta : ndarray (optional, only if theta is given at input)
The theta grid itself (just a copy of what was given)
- zscat : ndarray (optional, only if theta is given at input)
The components of the scattering Mueller matrix Z_ij for each wavelength and each scattering angel. The normalization of Z is such that kscat can be reproduced (as can be checked) by the integral: 2*pi*int_{-1}^{+1}Z11(mu)dmu=kappa_scat. For symmetry reasons only 6 elements of the Z matrix are returned: Z11, Z12, Z22, Z33, Z34, Z44. Note that Z21 = Z12 and Z43 = -Z34. The scattering matrix is normalized such that if a plane wave with Stokes flux
Fin = (Fin_I,Fin_Q,Fin_U,Fin_V)
hits a dust grain (which has mass mgrain), then the scattered flux
Fout = (Fout_I,Fout_Q,Fout_U,Fout_V)
at distance r from the grain at angle theta is given by
Fout(theta) = (mgrain/r^2) * Zscat . Fin
where . is the matrix-vector multiplication. Note that the Stokes components must be such that the horizontal axis in the “image” is pointing in the scattering plane. This means that radiation with Fin_Q < 0 is scattered well, because it is vertically polarized (along the scattering angle axis), while radiation with Fin_Q > 0 is scatterd less well because it is horizontally polarized (along the scattering plane).
- kscat_from_z11 : ndarray (optional, only if theta is given at input)
The kscat computed from the (above mentioned) integral of Z11 over all angles. This should be nearly identical to kscat if the angular grid is sufficiently fine. If there are strong differences, this is an indication that the angular gridding (the theta grid) is not fine enough. But you should have then automatically gotten a warning message as well (see errtol).
- wavmic : ndarray (optional, only if extrapolate is set to True)
The original wavelength grid from the optical constants file, with possibly an added extrapolated
- ncoef : ndarray (optional, only if extrapolate is set to True)
The optical constant n at that grid
- kcoef : ndarray (optional, only if extrapolate is set to True)
The optical constant k at that grid
- agr : ndarray (optional, only if logawidth is not None)
Grain sizes
- wgt : ndarray (optional, only if logawidth is not None)
The averaging weights of these grain (not the masses!) The sum of wgt.sum() must be 1.
- zscat_nochop : ndarray (optional, only if chopforward > 0)
The zscat before the forward scattering was chopped off
- kscat_nochop : ndarray (optional, only if chopforward > 0)
The kscat originally from the bhmie code
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radmc3dPy.miescat.
write_radmc3d_kappa_file
(package=None, name=None)¶ - The RADMC-3D radiative transfer package
- http://www.ita.uni-heidelberg.de/~dullemond/software/radmc-3d/
can perform dust continuum radiative transfer for diagnostic purposes. It is designed for astronomical applications. The code needs the opacities in a particular form. This subroutine writes the opacities out in that form. It will write it to the file dustkappa_<name>.inp. This is the simpler version of the opacity files, containing only kabs, kscat, gscat as a function of wavelength.
-
radmc3dPy.miescat.
write_radmc3d_scatmat_file
(package=None, name=None, comment=False)¶ - The RADMC-3D radiative transfer package
- http://www.ita.uni-heidelberg.de/~dullemond/software/radmc-3d/
can perform dust continuum radiative transfer for diagnostic purposes. It is designed for astronomical applications. The code needs the opacities in a particular form. This subroutine writes the opacities out in that form. It will write it to the file dustkapscatmat_<name>.inp.
radmc3dPy.molecule module¶
This module contains classes to handle molecular data
-
class
radmc3dPy.molecule.
radmc3dMolecule
¶ Bases:
object
RADMC-3D molecule class Based on the Leiden LAMDA database, but is in principle generic
- NOTE: For now only the levels and lines are included, not the
- collision rates.
Attributes
name (str) The name as listed in the molecule file molweight (float) Molecular weight in units of proton mass nlev (int) Nr of energy levels nlin (int) Nr of lines energycminv (float) Energy[ilev] of level ilev in 1/cm energy (float) Energy[ilev] of level ilev in erg wgt (float) Statistical weight[ilev] of level ilev jrot (float) Quantum rotational J[ilev] of level ilev iup (int) ilev of upper level of line ilin (starting with 0) ilow (int) ilev of lower level of line ilin (starting with 0) aud (float) Einstein A up low of line ilin in 1/second freq (float) Frequency of line ilin in Hz lam (float) Wavelength of line ilin in micron temp (ndarray) Temperature grid of the partition function pfunc (ndarray) Partition function Methods
getPartitionFunction
([temp, tmin, tmax, ...])Calculates the partition function at a grid of temperatures read
([mol, fname])Read the molecule_<mol>.inp file -
getPartitionFunction
(temp=None, tmin=None, tmax=None, ntemp=None, tlog=True)¶ Calculates the partition function at a grid of temperatures
Parameters: temp : list,ndarray
Temperature(s) in Kelvin to calculate the partition function at
tmin : float, optional
Minimum temperature in the grid (if temp is None)
tmax : float, optional
Maximum temperature in the grid (if temp is None)
ntemp : int, optional
Number of temperature in the grid (if temp is None)
tlog : bool
If True the generated temperature grid will be logarithmic. If False the grid will be linear.
Returns: The temperature grid and partition function will be put in the temp and pfunc data attributes of the class
-
read
(mol=None, fname=None)¶ Read the molecule_<mol>.inp file
The file format is the format of the Leiden LAMDA molecular database
Parameters: mol : str
molecule name (e.g. ‘co’) if the file name is in the form of ‘molecule_<mol>.inp’
fname : str
full file name
radmc3dPy.natconst module¶
This module contains natural constants in CGS units
Translated from RADMC’s IDL function problem_natconst.pro
List of natural constants:
| Name | Description |
|---|---|
| gg | Gravitational constant |
| mp | Mass of proton [g] |
| me | Mass of electron [g] |
| kk | Bolzmann’s constant [erg/K] |
| hh | Planck’s constant [erg.s] |
| ee | Unit charge |
| cc | Light speed [cm/s] |
| st | Thmpson cross-section [cm^2] |
| ss | Stefan-Boltzmann const [erg/cm^2/K^4/s] |
| aa | 4 * ss / cc |
| muh2 | Mean molecular weight (H2 + He + metals) |
| ev | Electronvolt [erg] |
| kev | Kilo electronvolt [erg] |
| micr | Micron [cm] |
| km | Kilometer [cm] |
| angs | Angstrom [cm] |
| ls | Solar luminosity [erg/s] |
| rs | Solar radius [cm] |
| ms | Solar mass [g] |
| ts | Solar effective temperature [K] |
| au | Astronomical unit [cm] |
| pc | Parsec [cm] |
| mea | Mass of Earth [g] |
| rea | Equatorila radius of Earth [cm] |
| mmo | Mass of Moon [g] |
| rmo | Radius of Moon [cm] |
| dmo | Distance earth-moon (center-to-center) [cm] |
| mju | Mass of Jupiter |
| rju | Equatorial radius of Jupiter [cm] |
| dju | Distance Jupiter-Sun [cm] |
| year | Year [s] |
| hour | Hour [s] |
| day | Day [s] |
radmc3dPy.octree module¶
This module contains a class for handling Octree mesh
-
class
radmc3dPy.octree.
radmc3dOctree
¶ Bases:
object
Octree-like object with switchable resolution in each dimension
Attributes
xi (ndarray) Base grid cell interface grid in the first dimension yi (ndarray) Base grid cell interface grid in the second dimension zi (ndarray) Base grid cell interface grid in the third dimension xc (ndarray) Base grid cell center grid in the first dimension yc (ndarray) Base grid cell center grid in the second dimension zc (ndarray) Base grid cell center grid in the third dimension x (ndarray) Tree cell center array in the first dimension y (ndarray) Tree cell center array in the second dimension z (ndarray) Tree cell center array in the third dimension dx (ndarray) Tree cell halfwidth array in the first dimension dy (ndarray) Tree cell halfwidth array in the second dimension dz (ndarray) Tree cell halfwidth array in the third dimension leafID (ndarray) Leaf index array, mapping between a full tree and an array containing only the leaves isLeaf (ndarray) Boolean array for the cell type (True - leaf, False - branch) level (ndarray) Level array (base grid is level 0) parentID (ndarray) Array containing the index of the parent cell (currently unused, only needed if we go up in the tree) childID (list) List of children indices. Each list element is an ndarray with nChild elements containing the child indices act_dim (list) A three element array to indicate which dimension is active, i.e. which dimensions are the cells resolved (0 - inactive, 1 - active) nCell (int) Nr of cells (both branch and leaf) in the tree nxRoot (int) Nr of cells in the base grid in the first dimension nyRoot (int) Nr of cells in the base grid in the second dimension nzRoot (int) Nr of cells in the base grid in the third dimension nLeaf (int) Nr of leaf cells (i.e. true, unresolved grid cells) nBranch (int) Nr of branches (i.e. resolved cells) nChild (int) Nr of children (i.e. 8, 4, or 2 for 3, 2, 1 active dimensions, respectively) levelMax (int) Highest actual level in the tree (Base grid has a level of 0 and the level increases) levelMaxLimit (int) Highest allowed level in the tree (only used in tree building) crd_sys ({‘car’, ‘sph’}) Coordinate system type cartesian or spherical Methods
convArrLeaf2Tree
([var])Converts a leaf array to full tree size. convArrTree2Leaf
([var])Converts a data array to leaf size. generateLeafID
()Function to generate the cell index mapping from arrays containing the full tree and those containing getCellVolume
([fullTree])Calculates the grid cell volume getContainerLeafID
([crd])Finds the tree index of a leaf that contains a given coordinate makeSpatialGrid
([ppar, levelMaxLimit, ...])Function to create an octree-like AMR grid makeWavelengthGrid
([wbound, nw, ppar])Creates the wavelength/frequency grid. putNode
([crd, cellsize, level, parentID, cellID])Function to put the data of a single node into the tree. readGrid
()Reads the spatial and wavelength grids from files readSpatialGrid
([fname])Reads the spatial grid from amr_grid.inp readWavelengthGrid
([fname])Function to read the wavelength/frequency grid resolveNodes
([rsIDs])Resolve multiple nodes simultaneously and add the children of the resolved node to the tree arrays extending selfCheck
()Performs a self-check of the tree allocation and report it to the screen setModel
([model])Sets the model to be used for tree building writeSpatialGrid
([fname])Writes the wavelength grid to a file (e.g. writeWavelengthGrid
([fname, old])Wriites the wavelength grid to a file (e.g. -
convArrLeaf2Tree
(var=None)¶ Converts a leaf array to full tree size.
Parameters: var : ndarray
A one or two dimensional ndarray with the first dimension is the size of the full tree
Returns: A one or two dimensional ndarray with size of of the full tree in the first dimension
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convArrTree2Leaf
(var=None)¶ Converts a data array to leaf size. The input is a scalar or vector variable defined at all nodes and the returned variable will only represent values at leaf nodes thereby reduced in length compared to the input.
Parameters: var : ndarray
A one or two dimensional ndarray with the first dimension is the size of the full tree
Returns: A one or two dimensional ndarray with size of nLeaf in the first dimension
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generateLeafID
()¶ Function to generate the cell index mapping from arrays containing the full tree and those containing only the leaves
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getCellVolume
(fullTree=False)¶ Calculates the grid cell volume
Parameters: fullTree : bool, optional
If True the cell volumes of the full tree (including both branches and leaves) will be calculated, while if set to False (default) the volume of only the leaf cells will be calculated
Returns: An linear ndarray containing the cell volumes
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getContainerLeafID
(crd=())¶ Finds the tree index of a leaf that contains a given coordinate
Parameters: crd : tuple
List/tuple/ndarray containing the tree dimensional coordinates of the point
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makeSpatialGrid
(ppar=None, levelMaxLimit=None, dfunc=None, model='', **kwargs)¶ Function to create an octree-like AMR grid
Parameters: ppar : dictionary
Dictionary containing all input parameters of the model (from the problem_params.inp file)
model : str
Name of the model to be used in the tree building
dfunc : function
A user defined function that decides whether an AMR grid cell should be refined
levelMaxLimit : int, optional
Highest allowable level of the tree. This keyword is optional. If not specified at input as a separate keyword, levelMaxLimit should be present in the problem_params.inp file.
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makeWavelengthGrid
(wbound=None, nw=None, ppar=None)¶ Creates the wavelength/frequency grid.
Parameters: wbound : list
Contains the wavelength boundaries of the wavelength grid (should contain at least two elements)
nw : list
Contains len(wbound)-1 elements containing the number of wavelengths between the bounds set by wbound
ppar : dictionary, optional
Contains all input parameters with the parameter names as keys
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putNode
(crd=(), cellsize=(), level=None, parentID=-1, cellID=None)¶ Function to put the data of a single node into the tree. This funcion assumes that all the arrays have already been allocated for the tree so input cell indices must refer to already existing array elements.
Parameters: crd : tuple
Cell center coordinates of the node
cellsize : tuple
Full size of the cell in each dimension
level : int
Level of the cell in the tree
parentID : int
Tree index of the parent cell
cellID : int
Tree index of the cell to be added
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readGrid
()¶ Reads the spatial and wavelength grids from files
-
readSpatialGrid
(fname='')¶ Reads the spatial grid from amr_grid.inp
Parameters: fname : str, optional
File name from which the spatial grid should be read. If omitted ‘amr_grid.inp’ will be used.
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readWavelengthGrid
(fname='wavelength_micron.inp')¶ Function to read the wavelength/frequency grid
Parameters: fname : str, optional
Name of the file to read the wavelength grid from (if not specified wavelenth_micron.inp will be used)
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resolveNodes
(rsIDs=None)¶ Resolve multiple nodes simultaneously and add the children of the resolved node to the tree arrays extending the tree array
Parameters: rsIDs : list
List/tuple/array of indices of the resolvable cell in the tree array
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selfCheck
()¶ Performs a self-check of the tree allocation and report it to the screen
-
setModel
(model='')¶ Sets the model to be used for tree building
Parameters: model : str
Name of the model
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writeSpatialGrid
(fname='')¶ Writes the wavelength grid to a file (e.g. amr_grid.inp).
Parameters: fname : str, optional
File name into which the spatial grid should be written. If omitted ‘amr_grid.inp’ will be used.
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writeWavelengthGrid
(fname='', old=False)¶ Wriites the wavelength grid to a file (e.g. wavelength_micron.inp).
Parameters: fname : str, optional
File name into which the wavelength grid should be written. If omitted ‘wavelength_micron.inp’ will be used
old : bool, optional
If set to True the file format of the previous, 2D version of radmc will be used
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radmc3dPy.params module¶
This module contains classes for handling of parameters of the model setup and for file I/O
-
class
radmc3dPy.params.
radmc3dPar
¶ Bases:
object
Parameter class for a RADMC-3D model.
Attributes
ppar (dictionary) Contains parameter values with parameter names as keys pdesc (dictionary) Contains parameter description (comments in the parameter file) with parameter names as keys pblock (dictionary) Contains the block names in the parameter file and parameter names as values pvalstr: dictionary Contains parameter values as strings with parameter names as keys Methods
loadDefaults
([model, ppar, reset])Sets all parameters to default values. printPar
()Prints the parameters of the current model. readPar
([fname])Reads a parameter file. setPar
([parlist])Sets a parameter in the radmc3DPar class. writeParfile
([fname])Writes a parameter file. -
loadDefaults
(model='', ppar=None, reset=True)¶ Sets all parameters to default values.
Parameters: model : str
Model name whose paraemters should also be loaded
ppar : dictionary
Contains parameter values as string and parameter names as keys Default values will be re-set to the values in this dictionary
reset : bool
If True the all class attributes will be re-initialized before the default values would be loaded. I.e. it will remove all entries from the dictionary that does not conain default values either in this function or in the optional ppar keyword argument
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printPar
()¶ Prints the parameters of the current model.
-
readPar
(fname='')¶ Reads a parameter file. The parameters in the files should follow python syntax
Parameters: fname : str, optional
File name to be read (if omitted problem_params.inp is used)
Returns: Returns a dictionary with the parameter names as keys
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setPar
(parlist=None)¶ Sets a parameter in the radmc3DPar class. If the paramter is already defined its value will be modified
Parameters: parlist : list
If the parameter is already defined parlist should be a two element list 1) parameter name, 2) parameter expression/value as a string
If the parameter is not yet defined parlist should be a four element list 1) parameter name, 2) parameter expression/value as a string 3) Parameter description (= comment field in the parameter file)
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writeParfile
(fname='')¶ Writes a parameter file.
Parameters: fname : str, optional
File name to be read (if omitted problem_params.inp is used)
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radmc3dPy.radsources module¶
This module contains classes for radiation sources
-
class
radmc3dPy.radsources.
radmc3dRadSources
(ppar=None, grid=None)¶ Bases:
object
Class of the radiation sources. Currently discrete stars and continuous starlike source, the latter only in spherical coordinates.
Attributes
wav (ndarray) Wavelength for the stellar spectrum freq (ndarray) Frequency for the stellar spectrum nwav (int) Number of wavelenghts in the stellar spectrum nfreq (int) Number of frequencies in the stellar spectrum mstar (list) List of stellar masses tstar (list) List of stellar effective temperatures rstar (list) List of stellar radii lstar (list) List of stellar luminosities nstar (int) Number of stars pstar (list) Each element of the list contains a three element list, the cartesian coordinates of the stars fnustar (ndarray) Stellar spectrum (flux@1pc in erg/s/cm/cm/Hz) csdens (ndarray) Stellar density for continuous starlike source csntemplate (int) Number of stellar templates cstemp (ndarray) Stellar template cstemptype (int) Stellar template type 1 - Blackbody given by the effective temperature 2 - Frequency dependent spectrum cststar (ndarray) Stellar effective temperature csmstar (ndarray) Stellar mass csrstar (ndarray) Stellar radius tacc (ndarray) Effective temperature of a viscous accretion disk as a function of cylindrical radius accrate (float) Accretion rate of the viscous accretion disk [g/s] fnuaccdisk (ndarray) Spatially integrated frequency-dependent flux density of the accretion disk @ 1pc distance tspot (float) Temperature of the hot spot / boundary layer on the stellar surface starsurffrac (float) Fraction of the stellar surface covered by the hot spot / boundary layer fnustpot (ndarray) Frequency-dependent flux density of the hot spot / boundary layer @ 1pc distance Methods
findPeakStarspec
()Calculates the peak wavelength of the stellar spectrum. getAccdiskSpectra
([ppar, grid, incl])Calculates the emergent spectra of an optically thick accretion disk at face-on orientation (incl=0deg). getAccdiskStellarDensity
([grid])Calculates the stellar density for continuous starlike sources for modeling a viscous accretion disk. getAccdiskStellarTemplates
([ppar, grid])Calculates the stellar template for continuous starlike sources for modeling a viscous accretion disk. getAccdiskTemperature
([ppar, grid])Calculates the effective temperature of a viscous accretion disk. getSpotSpectrum
([ppar, grid])Calculates the spectrum of a hot spot / boundary layer on the stellar surface getStarSpectrum
([tstar, rstar, lstar, ...])Calculates a blackbody stellar spectrum. getTotalLuminosities
([readInput])Calcultes the frequency integrated luminosities of all radiation sources. readStarsinp
([fname])Reads the data of discrete stellar sources from the stars.inp file. readStellarsrcDensity
([fname, binary])Reads the stellar density of a continuous starlike source. readStellarsrcTemplates
([fname])Reads the stellar template of a continuous starlike source. writeStarsinp
([ppar, wav, freq, old])Writes the input file for discrete stellar sources (stars.inp). writeStellarsrcDensity
([fname, binary])Writes the stellar density of a continuous starlike source. writeStellarsrcTemplates
([fname])Writes the stellar template of a continuous starlike source. -
findPeakStarspec
()¶ Calculates the peak wavelength of the stellar spectrum.
Returns: The peak wavelength of the stellar spectrum in nu*Fnu for all
stars as a list
-
getAccdiskSpectra
(ppar=None, grid=None, incl=0.0)¶ Calculates the emergent spectra of an optically thick accretion disk at face-on orientation (incl=0deg).
Parameters: ppar : dictionary
Dictionary containing all input parameters keys should include * mstar : stellar mass * rstar : stellar radius * accrate : accretion rate
NOTE, that for the calculation of the effective disk temperature only the first star is used if more than one values are given in mstar and rstar.
incl : float, optional
Inclination angle in degrees at which the spectrum be calculated (default - 0deg)
grid : radmc3dGrid, optional
An instance of a radmc3dGrid class containing the spatial and wavelength grid
-
getAccdiskStellarDensity
(grid=None)¶ Calculates the stellar density for continuous starlike sources for modeling a viscous accretion disk.
Parameters: grid : radmc3dGrid, optional
An instance of a radmc3dGrid class containing the spatial and wavelength grid
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getAccdiskStellarTemplates
(ppar=None, grid=None)¶ Calculates the stellar template for continuous starlike sources for modeling a viscous accretion disk.
Parameters: ppar : dictionary
Dictionary containing all input parameters keys should include: * mstar : stellar mass * rstar : stellar radius * accrate : accretion rate
NOTE, that for the calculation of the effective disk temperature only the first star is used if more than one values are given in mstar and rstar.
grid : radmc3dGrid, optional
An instance of a radmc3dGrid class containing the spatial and wavelength grid
-
getAccdiskTemperature
(ppar=None, grid=None)¶ Calculates the effective temperature of a viscous accretion disk.
Parameters: ppar : dictionary
Dictionary containing all input parameters keys should include * mstar : stellar mass * rstar : stellar radius * accrate : accretion rate
NOTE, that for the calculation of the effective disk temperature only the first star is used if more than one values are given in mstar and rstar.
grid : radmc3dGrid, optional
An instance of a radmc3dGrid class containing the spatial and wavelength grid
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getSpotSpectrum
(ppar=None, grid=None)¶ Calculates the spectrum of a hot spot / boundary layer on the stellar surface
Parameters: ppar : dictionary
Dictionary containing all input parameters keys should include * mstar : stellar mass * rstar : stellar radius * accrate : accretion rate
NOTE, that for the calculation of the effective disk temperature only the first star is used if more than one values are given in mstar and rstar.
grid : radmc3dGrid, optional
An instance of a radmc3dGrid class containing the spatial and wavelength grid
-
getStarSpectrum
(tstar=None, rstar=None, lstar=None, mstar=None, ppar=None, grid=None)¶ Calculates a blackbody stellar spectrum.
Parameters: tstar : list
Effective temperature of the stars in [K]
rstar : list
Radius of the stars in [cm]
lstar : list
Bolometric luminosity of the star [erg/s] (either rstar or lstar should be given)
mstar : list
Stellar mass in [g] (only required if an atmosphere model is used to calculate logg)
ppar : dictionary
Dictionary containing all input parameters
grid : radmc3dGrid, optional
An instance of a radmc3dGrid class containing the spatial and wavelength grid
-
getTotalLuminosities
(readInput=True)¶ Calcultes the frequency integrated luminosities of all radiation sources.
Parameters: readInput : bool, optional
If true the input files of the radiation sources are read and the the total luminosities are calculated from them. If readInput is set to False, the luminosities are calculated by semi-analytic spectra.
Returns: Returns a dictionary with the following keys
- lnu_star : Luminosity of the discrete stars
- lnu_accdisk : Luminosity of the accretion disk
- lnu_spot : Luminosity of the hot spot / boundary layer on the stellar surface
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readStarsinp
(fname='')¶ Reads the data of discrete stellar sources from the stars.inp file.
Parameters: fname : str, optional
File name of the file that should be read (if omitted stars.inp will be used)
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readStellarsrcDensity
(fname=None, binary=False)¶ Reads the stellar density of a continuous starlike source.
Parameters: fname : str, optional
Name of the file from which the stellar templates will be read. If omitted the default ‘stellarsrc_templates.inp’ will be used.
binary : bool, optional
If True the file should contain a C-style binary stream, if False the file should be written as formatted ASCII
-
readStellarsrcTemplates
(fname='stellarsrc_templates.inp')¶ Reads the stellar template of a continuous starlike source.
Parameters: fname : str, optional
Name of the file from which the stellar templates will be read. If omitted the default ‘stellarsrc_templates.inp’ will be used.
-
writeStarsinp
(ppar=None, wav=None, freq=None, old=False)¶ Writes the input file for discrete stellar sources (stars.inp).
Parameters: ppar : dictionary
Dictionary containing all parameters of the model (only mandatory if accretion is switched on)
wav : ndarray, optional
Wavelength grid for the stellar spectrum
freq : ndarray, optional
Frequency grid for the stellar spectrum (either freq or wav should be set)
old : bool, optional
If set to True the file format of the previous, 2D version of radmc will be used
-
writeStellarsrcDensity
(fname='', binary=False)¶ Writes the stellar density of a continuous starlike source.
Parameters: fname : str, optional
Name of the file into which the stellar templates will be written. If omitted the default ‘stellarsrc_templates.inp’ will be used.
binary : bool, optional
If True the output will be written in a C-style binary stream, if False the output will be formatted ASCII
-
writeStellarsrcTemplates
(fname='stellarsrc_templates.inp')¶ Writes the stellar template of a continuous starlike source.
Parameters: fname : str, optional
Name of the file into which the stellar templates will be written. If omitted the default ‘stellarsrc_templates.inp’ will be used.
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radmc3dPy.reggrid module¶
This module contains a class for handling regular wavelength and spatial grids
-
class
radmc3dPy.reggrid.
radmc3dGrid
¶ Bases:
object
Class for spatial and frequency grid used by RADMC-3D.
Attributes
act_dim (ndarray) A three element vector the i-th element is 1 if the i-th dimension is active, otherwize the i-th element is zero crd_sys ({‘sph’, ‘cyl’, ‘car’}) coordinate system of the spatial grid nx (int) Number of grid points in the x (cartesian) / r (cylindrical) / r (spherical) dimension ny (int) Number of grid points in the y (cartesian) / theta (cylindrical) / theta (spherical) dimension nz (int) Number of grid points in the z (cartesian) / z (cylindrical) / phi (spherical) dimension nxi (int) Number of cell interfaces in the x (cartesian) / r (cylindrical) / r (spherical) dimension nyi (int) Number of cell interfaces in the y (cartesian) / theta (cylindrical) / theta (spherical) dimension nzi (int) Number of cell interfaces in the z (cartesian) / z (cylindrical) / phi (spherical) dimension nwav (int) Number of wavelengths in the wavelength grid nfreq (int) Number of frequencies in the grid (equal to nwav) x (ndarray) Cell centered x (cartesian) / r (cylindrical) / r (spherical) grid points y (ndarray) Cell centered y (cartesian) / theta (cylindrical) / theta (spherical) grid points z (ndarray) Cell centered z (cartesian) / z (cylindrical) / phi (spherical) grid points xi (ndarray) Cell interfaces in the x (cartesian) / r (cylindrical) / r (spherical) dimension yi (ndarray) Cell interfaces in the y (cartesian) / theta (cylindrical) / theta (spherical) dimension zi (ndarray) Cell interfaces in the z (cartesian) / z (cylindrical) / phi (spherical) dimension wav (ndarray) Wavelengh grid freq (ndarray) Frequency grid Methods
getCellVolume
()Calculates the volume of grid cells. makeSpatialGrid
([crd_sys, xbound, ybound, ...])Calculates the spatial grid. makeWavelengthGrid
([wbound, nw, ppar])Creates the wavelength/frequency grid. readGrid
([old])Reads the spatial (amr_grid.inp) and frequency grid (wavelength_micron.inp). readSpatialGrid
([fname, old])Reads the spatial grid readWavelengthGrid
([fname, old])Reads the wavelength grid writeSpatialGrid
([fname, old])Writes the wavelength grid to a file (e.g. writeWavelengthGrid
([fname, old])Wriites the wavelength grid to a file (e.g. -
getCellVolume
()¶ Calculates the volume of grid cells.
-
makeSpatialGrid
(crd_sys=None, xbound=None, ybound=None, zbound=None, nxi=None, nyi=None, nzi=None, ppar=None)¶ Calculates the spatial grid.
Parameters: crd_sys : {‘sph’,’car’}
Coordinate system of the spatial grid
xbound : list
(with at least two elements) of boundaries for the grid along the first dimension
ybound : list
(with at least two elements) of boundaries for the grid along the second dimension
zbound : list
(with at least two elements) of boundaries for the grid along the third dimension
nxi : int
Number of grid points along the first dimension. List with len(xbound)-1 elements with nxi[i] being the number of grid points between xbound[i] and xbound[i+1]
nyi : int
Same as nxi but for the second dimension
nzi : int
Same as nxi but for the third dimension
ppar : Dictionary containing all input parameters of the model (from the problem_params.inp file)
if ppar is set all keyword arguments that are not set will be taken from this dictionary
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makeWavelengthGrid
(wbound=None, nw=None, ppar=None)¶ Creates the wavelength/frequency grid.
Parameters: wbound : list
Contains the wavelength boundaries of the wavelength grid (should contain at least two elements)
nw : list
Contains len(wbound)-1 elements containing the number of wavelengths between the bounds set by wbound
ppar : dictionary, optional
Contains all input parameters with the parameter names as keys
-
readGrid
(old=False)¶ Reads the spatial (amr_grid.inp) and frequency grid (wavelength_micron.inp).
Parameters: old : bool, optional
If set to True the file format of the previous, 2D version of radmc will be used
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readSpatialGrid
(fname='', old=False)¶ Reads the spatial grid
Parameters: fname : str, optional
File name from which the spatial grid should be read. If omitted ‘amr_grid.inp’ will be used.
old : bool, optional
If set to True the file format of the previous, 2D version of radmc will be used
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readWavelengthGrid
(fname=None, old=False)¶ Reads the wavelength grid
Parameters: fname : str, optional
File name from which the spatial grid should be read. If omitted ‘wavelength_micron.inp’ will be used.
old : bool, optional
If set to True the file format of the previous, 2D version of radmc will be used
-
writeSpatialGrid
(fname='', old=False)¶ Writes the wavelength grid to a file (e.g. amr_grid.inp).
Parameters: fname : str, optional
File name into which the spatial grid should be written. If omitted ‘amr_grid.inp’ will be used.
old : bool, optional
If set to True the file format of the previous, 2D version of radmc will be used
-
writeWavelengthGrid
(fname='', old=False)¶ Wriites the wavelength grid to a file (e.g. wavelength_micron.inp).
Parameters: fname : str, optional
File name into which the wavelength grid should be written. If omitted ‘wavelength_micron.inp’ will be used
old : bool, optional
If set to True the file format of the previous, 2D version of radmc will be used
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radmc3dPy.setup module¶
This module contains functions to set up a RADMC-3D model for dust and/or line simulations. For help on the syntax or functionality of each function see the help of the individual functions
-
radmc3dPy.setup.
problemSetupDust
(model=None, binary=True, writeDustTemp=False, old=False, dfunc=None, dfpar=None, **kwargs)¶ Function to set up a dust model for RADMC-3D
Parameters: model : str
Name of the model that should be used to create the density structure. The file should be in a directory from where it can directly be imported (i.e. the directory should be in the PYTHON_PATH environment variable or it should be in the current working directory) and the file name should be ‘model_xxx.py’, where xxx stands for the string that should be specified in this variable
binary : bool, optional
If True input files will be written in binary format, if False input files are written as formatted ascii text.
writeDustTemp : bool, optional
If True a separate dust_temperature.inp/dust_tempearture.binp file will be written under the condition that the model contains a function getDustTemperature()
old : bool, optional
If set to True the input files for the old 2D version of radmc will be created
dfunc : function, optional
Decision function for octree-like amr tree building. It should take linear arrays of cell centre coordinates (x,y,z) and cell half-widhts (dx,dy,dz) in all three dimensions, a radmc3d model, a dictionary with all parameters from problem_params.inp and an other keyword argument (**kwargs). It should return a boolean ndarray of the same length as the input coordinates containing True if the cell should be resolved and False if not. An example for the implementation of such decision function can be found in radmc3dPy.analyze module (radmc3dPy.analyze.gdensMinMax()).
dfpar : dictionary
**kwargs : Any varible name in problem_params.inp can be used as a keyword argument.
At first all variables are read from problem_params.in to a dictionary called ppar. Then if there is any keyword argument set in the call of problem_setup_dust the ppar dictionary is searched for this key. If found the value belonging to that key in the ppar dictionary is changed to the value of the keyword argument. If no such key is found then the dictionary is simply extended by the keyword argument. Finally the problem_params.inp file is updated with the new parameter values.
Notes
Files written by problemSetupDust() for RADMC-3D
- dustopac.inp : Dust opacity master file.
- wavelength_micron.inp : Wavelength grid.
- amr_grid.inp : Spatial grid.
- stars.inp : Input radiation field (discrete stellar sources).
- stellarsrc_density.inp : Input radiation field (continuous stellar sources).
- stellarsrc_templates.inp : Input radiation field (continuous stellar sources).
- dust_density.inp : Dust density distribution.
- radmc3d.inp : Parameters for RADMC-3D (e.g. Nr of photons to be used, scattering type, etc).
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radmc3dPy.setup.
problemSetupGas
(model=None, fullsetup=False, binary=True, writeGasTemp=False, dfunc=None, dfpar=None, **kwargs)¶ Function to set up a gas model for RADMC-3D
Parameters: model : str
Name of the model that should be used to create the density structure the file should be in a directory from where it can directly be imported (i.e. the directory should be in the PYTHON_PATH environment variable, or it should be the current working directory) and the file name should be ‘MODELNAME.py’, where MODELNAME stands for the string that should be specified in this variable
fullsetup : bool, optional
If False only the files related to the gas simulation is written out (i.e. no grid, stellar parameter file and radmc3d master command file is written) assuming that these files have already been created for a previous continuum simulation. If True the spatial and wavelength grid as well as the input radiation field and the radmc3d master command file will be (over)written.
binary : bool, optional
If True input files will be written in binary format, if False input files are written as formatted ascii text.
writeGasTemp : bool, optional
If True a separate gas_temperature.inp/gas_tempearture.binp file will be written under the condition that the model contains a function get_gas_temperature()
dfunc : function, optional
Decision function for octree-like amr tree building. It should take linear arrays of cell centre coordinates (x,y,z) and cell half-widhts (dx,dy,dz) in all three dimensions, a radmc3d model, a dictionary with all parameters from problem_params.inp and an other keyword argument (**kwargs). It should return a boolean ndarray of the same length as the input coordinates containing True if the cell should be resolved and False if not. An example for the implementation of such decision function can be found in radmc3dPy.analyze module (radmc3dPy.analyze.gdensMinMax()).
dfpar : dictionary
**kwargs : Any varible name in problem_params.inp can be used as a keyword argument.
At first all variables are read from problem_params.in to a dictionary called ppar. Then if there is any keyword argument set in the call of problem_setup_gas the ppar dictionary is searched for such key. If found the value belonging to that key in the ppar dictionary is changed to the value of the keyword argument. If no such key is found then the dictionary is simply extended by the keyword argument. Finally the problem_params.inp file is updated with the new parameter values. Any additional keyword argument for the octree AMR mesh generation should also be passed here.
Notes
Files written by problemSetupGas()
- lines.inp : Line mode master command file.
- numberdens_xxx.inp : Number density of molecule/atomic species ‘xxx’
- gas_velocity.inp : Gas velocity
- microturbulence.inp : The standard deviation of the Gaussian line profile caused by turbulent
- broadening.
- gas_temperature.inp : Gas temperature (which may be different from the dust temperature). If
- tgas_eq_tdust is set to zero in radmc3d.inp the gas temperature in this file will be used instead of the dust temperature.
If fullsetup is set to True the following additional files will be created
- amr_grid.inp : Spatial grid.
- wavelength_micron.inp : Wavelength grid.
- stars.inp : Input radiation field.
- radmc3d.inp : Parameters for RADMC-3D (e.g. Nr of photons to be used, scattering type, etc).
-
class
radmc3dPy.setup.
radmc3dModel
(model=None, binary=None, old=False, dfunc=None, dfpar=None, parfile_update=True, **kwargs)¶ Bases:
object
Parameters: model : str
Name of the model that should be used to create the density structure. The file should be in a directory from where it can directly be imported (i.e. the directory should be in the PYTHON_PATH environment variable or it should be in the current working directory) and the file name should be ‘model_xxx.py’, where xxx stands for the string that should be specified in this variable
binary : bool, optional
If True input files will be written in binary format, if False input files are written as formatted ascii text.
old : bool, optional
If set to True the input files for the old 2D version of radmc will be created
dfunc : function, optional
Decision function for octree-like amr tree building. It should take linear arrays of cell centre coordinates (x,y,z) and cell half-widhts (dx,dy,dz) in all three dimensions, a radmc3d model, a dictionary with all parameters from problem_params.inp and an other keyword argument (**kwargs). It should return a boolean ndarray of the same length as the input coordinates containing True if the cell should be resolved and False if not. An example for the implementation of such decision function can be found in radmc3dPy.analyze module (radmc3dPy.analyze.gdensMinMax()).
dfpar : dictionary
parfile_update : bool
If True the parameter file (problem_params.inp) will be updated / overwritten with any parameters that are possibly passed as keyword arguments. For False the problem_params.inp file will not be overwritten irrespectively of the parameter values the data members of the radmc3dModel instance would contain.
Keyword Arguments :
Any varible name in problem_params.inp can be used as a keyword argument. At first all variables are read from problem_params.in to a dictionary called ppar. Then if there is any keyword argument set in the call of problem_setup_dust the ppar dictionary is searched for this key. If found the value belonging to that key in the ppar dictionary is changed to the value of the keyword argument. If no such key is found then the dictionary is simply extended by the keyword argument. Finally the problem_params.inp file is updated with the new parameter values.
Attributes
binary (bool) If True, it sets the data file format to binary (overwriting also the rto_style parameter!), if False the file format will be formatted ascii data (radmc3dData) Container for physical variables in the mode grid (radmc3dGrid) Container for spatial and wavelength grid model (str) Name of the model that has callable functions to generate physical variables for the model old (bool) If True the model is meant to be for radmc, the pre-decessor code of radmc-3d. opac (radmc3dOpac) Container for dust opacities par (radmc3dPar) Container for the parameters of the model (i.e. the content of the problem_params.inp file) radsources (radmc3dRadsources) Container for the radiation sources in the model Methods
makeDustOpac
()Generates dust opacities and writes them to file makeGrid
([sgrid, wgrid, writeToFile])Generates a spatial and/or wavelength grid makeRadSources
([writeToFile])Parameters: makeVar
([ddens, dtemp, gdens, gtemp, gvel, ...])Generates variables and possibly writes them to file readParams
()setupDust
([sgrid, wgrid, radsources, ...])Set up a model for RADMC-3D. setupGas
([sgrid, wgrid, radsources, gdens, ...])Set up a model for RADMC-3D. writeLinesInp
()Writes the lines.inp master command file for line simulation in RADMC-3D writeRadmc3dInp
()Writes the radmc3d.inp master command file for RADMC-3D -
makeDustOpac
()¶ Generates dust opacities and writes them to file
-
makeGrid
(sgrid=True, wgrid=True, writeToFile=False, **kwargs)¶ Generates a spatial and/or wavelength grid
Parameters: wgrid : bool
Set to True to generate the wavelength grid
sgrid : bool
Set to True to generate the spatial grid
writeToFile : bool
If True the grid will be written to amr_grid.inp and/or wavelength_micron.inp
**kwargs : Any varible name in problem_params.inp can be used as a keyword argument.
At first all variables are read from problem_params.in to a dictionary called ppar. Then if there is any keyword argument set in the call of problem_setup_dust the ppar dictionary is searched for this key. If found the value belonging to that key in the ppar dictionary is changed to the value of the keyword argument. If no such key is found then the dictionary is simply extended by the keyword argument. Finally the problem_params.inp file is updated with the new parameter values.
-
makeRadSources
(writeToFile=True)¶ Parameters: writeToFile : bool
If True the radiation will be written to stars.inp and or stellarsrc_density.inp, stellarsrc_templates.inp
-
makeVar
(ddens=False, dtemp=False, gdens=False, gtemp=False, gvel=False, vturb=False, writeToFile=False)¶ Generates variables and possibly writes them to file
Parameters: ddens : bool, optional
If True generates the dust density
dtemp : bool, optional
- If True generates the dust temperature (normally this would be calculated by RADMC-3D, but
in some cases, e.g. debugging, it might come handy)
gdens : bool, optional
If True generates the gas density
gtemp : bool, optional
If True generates the gas temperature
gvel : bool, optional
If True generates the gas velocity
vturb : bool, optional
If True generates the microturbulent velocity field
writeToFile : bool, optional
If True the generated variable(s) will be written to file
-
readParams
()¶
-
setupDust
(sgrid=True, wgrid=True, radsources=True, dustopac=True, ddens=True, dtemp=False)¶ Set up a model for RADMC-3D.
Parameters: sgrid : bool
Should the spatial grid be generated? (default=True)
wgrid : bool
Should the wavelength grid be generated? (default=True)
radsources : bool
Should the radiation sources be generated? (default=True)
dustopac : bool
Should dust opacities be generated? (default=True)
ddens : bool
Should the dust density be generated? (default=True)
dtemp : bool
Should the dust temperature be generated (default=False)
Note, that by default all generated data will be written to files immediately. In case you wish to generate
the files but not write the data to files but only keep them instead in data attributes, please use the individual generator functions methods (e.g. makeGrid, makeRadSources, makeVar, etc)
-
setupGas
(sgrid=False, wgrid=False, radsources=False, gdens=True, gtemp=True, gvel=True, vturb=True)¶ Set up a model for RADMC-3D.
Parameters: sgrid : bool
Should the spatial grid be generated? (default=False)
wgrid : bool
Should the wavelength grid be generated? (default=False)
radsources : bool
Should the radiation sources be generated? (default=False)
gdens : bool
Should the gas density be generated? (default=True)
gtemp : bool
Should the gas temperature be generated (default=False)
gvel : bool
Should the gas veloctiy be generated (default=False)
vturb : bool
Should the turbulent velocity field be generated (default=False)
Note, that by default all generated data will be written to files immediately. In case you wish to generate
the files but not write the data to files but only keep them instead in data attributes, please use the individual generator functions methods (e.g. makeGrid, makeRadSources, makeVar, etc)
-
writeLinesInp
()¶ Writes the lines.inp master command file for line simulation in RADMC-3D
-
writeRadmc3dInp
()¶ Writes the radmc3d.inp master command file for RADMC-3D
-
-
radmc3dPy.setup.
validateModel
(model='', dustModel=False, gasModel=False, writeDustTemp=False, octree=False)¶ Function to validate a model. It checks three things: 1) whether or not the model can be imported, 2) whether the model has all the function to be used as dust and/or gas model, 3) if it has the right number of arguments. The function names tested are getDefaultParams, getDustDensity, getGasDensity, getGasAbundance, getVTurb, getVelocity, getDustTempearture (optional).
Parameters: model : str
Name of the model to be tested
dustModel : bool
If True the existence of functions getDustDensity() and getDustTemperature() will be checked. The latter is only checked if writeDustTemp is set to True.
gasModel : bool
If True the existence of functions getGasDensity(), getGasAbundance(), getVTurb(), getVelocity() will be checked.
writeDustTemp: bool
If True the existence of the function getDustTemperature() will be checked.
octree : bool
If True the number of argument of the model functions will be checked. For regular grids only two arguments should be present for the grid instance and for the parameter dictionary (grid, ppar). For a model to be used with octree AMR three additional arguments for the three spatial coordiantes (x,y,z) should be present. The argument sequence should then be x, y, z, grid, ppar.
Returns: A boolean True if the model is valid and False if it is not.
-
radmc3dPy.setup.
writeLinesInp
(ppar=None)¶ Writes the lines.inp master command file for line simulation in RADMC-3D
Parameters: ppar : dictionary,
Contains all parameters of a RADMC-3D run
-
radmc3dPy.setup.
writeRadmc3dInp
(modpar=None)¶ Writes the radmc3d.inp master command file for RADMC-3D
Parameters: modpar : radmc3dPar
Contains all parameters of a RADMC-3D run.
-
radmc3dPy.setup.
writeRadmcInp
(modpar=None, nphot=None)¶ Writes the radmc.inp master command file for the 2D version of radmc
Parameters: modpar : radmc3dPar
Contains all parameters of a radmc run.
nphot : int
Number of photons used for the MC simulation
radmc3dPy.staratm module¶
This module contains functions to get various radiation sources in RADMC-3D. For help on the syntax or functionality of each function see the help of the individual functions
-
radmc3dPy.staratm.
getAtmModel
(teff=0.0, logg=None, mstar=None, lstar=None, rstar=None, iwav=None, model='kurucz', modeldir=None, wmax=7.0)¶ Interpolates the stellar model atmosphere on a pre-defined wavelength grid The model atmospheres are interpolated in logg and Teff and rebinned in wavelength to the input wavelength grid and scaled to have the same luminosity as specified
Parameters: teff : float
Effective temperature of the star
logg : float
Logarithm of the surface gravity of the star
mstar : float
Mass of the star in gramm
lstar : float, optional
Luminosity of the star (either lstar or rstar should be specified)
rstar : float, optional
Radius of the star (either lstar or rstar should be specified)
iwav : ndarray
Wavelength grid for which the stellar atmosphere model should be calculated
model : {‘kurucz’, ‘nextgen’, ‘ames-dusty’}
Name of the model atmosphere family
modeldir : str
Path to the atmosphere models
wmax : float
Maximum wavelength until the model atmosphere is used on the interpolated grid Longwards of this wavelength the Rayleigh-Jeans approximation (lambda^(-2)) is used.
Returns: Returns a dictionary with the following keys:
- wav : ndarray
- Wavelength in micron (same as the input iwav keyword)
- lnu : ndarray
- Monochromatic luminosity of the stellar atmosphere in erg/s/Hz
-
radmc3dPy.staratm.
getSpectrumAmesDusty
(teff=None, logg=None, mstar=None, lstar=None, rstar=None, modeldir=None, wav=None)¶ Interpolates the Ames-Dusty model atmospheres in logg and Teff
Parameters: teff : float
Effective temperature of the star
logg : float
Logarithm of the surface gravity of the star
mstar : float, optional
Stellar mass in g (either logg or mstar and rstar should be specified)
lstar : float, optional
Luminosity of the star (either lstar or rstar should be specified)
rstar : float, optional
Radius of the star (either lstar or rstar should be specified)
modeldir : str
Path to the AmesDusty atmosphere model grid
wav : ndarray
Wavelength grid for which the stellar atmosphere model should be calculated
Returns: Returns a dictionary with the following keys:
- wav : ndarray
- Wavelength in micron (same as the input wav keyword)
- lnu : ndarray
- Monochromatic luminosity of the stellar atmosphere in erg/s/Hz
- bnu : ndarray
- Monochromatic luminosity of a blackbody stellar atmosphere with the same luminosity and effective temperature as the stellar model in erg/s/Hz
-
radmc3dPy.staratm.
getSpectrumKurucz
(teff=None, logg=None, mstar=None, lstar=None, rstar=None, modeldir=None, wav=None)¶ Interpolates the Kurucz model atmospheres in logg and Teff
Parameters: teff : float
Effective temperature of the star
logg : float
Logarithm of the surface gravity of the star
mstar : float, optional
Stellar mass in g (either logg or mstar and rstar should be specified)
lstar : float, optional
Luminosity of the star (either lstar or rstar should be specified)
rstar : float, optional
Radius of the star (either lstar or rstar should be specified)
modeldir : str
Path to the Kurucz atmosphere model grid
wav : ndarray
Wavelength grid for which the stellar atmosphere model should be calculated
Returns: Returns a dictionary with the following keys:
- wav : ndarray
- Wavelength in micron (same as the input wav keyword)
- lnu : ndarray
- Monochromatic luminosity of the stellar atmosphere in erg/s/Hz
- lnucont : ndarray
- Monochromatic luminosity of the continuum stellar atmosphere in erg/s/Hz
-
radmc3dPy.staratm.
getSpectrumNextGen
(teff=None, logg=None, mstar=None, lstar=None, rstar=None, modeldir=None, wav=None)¶ Interpolates the NextGen model atmospheres in logg and Teff
Parameters: teff : float
Effective temperature of the star
logg : float
Logarithm of the surface gravity of the star
mstar : float, optional
Stellar mass in g (either logg or mstar and rstar should be specified)
lstar : float, optional
Luminosity of the star (either lstar or rstar should be specified)
rstar : float, optional
Radius of the star (either lstar or rstar should be specified)
modeldir : str
Path to the NextGen atmosphere model grid
wav : ndarray
Wavelength grid for which the stellar atmosphere model should be calculated
Returns: Returns a dictionary with the following keys:
- wav : ndarray
- Wavelength in micron (same as the input wav keyword)
- lnu : ndarray
- Monochromatic luminosity of the stellar atmosphere in erg/s/Hz
- bnu : ndarray
- Monochromatic luminosity of a blackbody stellar atmosphere with the same luminosity and effective temperature as the stellar model in erg/s/Hz
-
radmc3dPy.staratm.
readAmesDustySpectrum
(fname='')¶ Reads the Ames-Dusty model atmosphere
Parameters: fname : str
File name containing the Ames-Dusty model atmosphere (e.g. lte30-3.5-0.0.AMES-dusty.7)
Returns: Returns a dictionary with the following keys:
- wav : ndarray
- Wavelength in micron
- nwav : int
- Number of wavelength points
- inu : ndarray
- Specific intensity of the stellar model atmosphere in erg/s/cm/cm/Hz/ster
- bnu : list
- Specific intensity of a blackbody stellar model atmosphere with the same luminosity and the same effective temperature in erg/s/cm/cm/Hz/ster
- teff : float
- Effective temperature of the model
- logg : float
- Logarithm of the surface gravity of the model
- mph : float
- Metallicity of the atmosphere model
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radmc3dPy.staratm.
readKuruczGrid
(fname='')¶ Reads the Kurucz model atmosphere grid. It reads a whole file from the Kurucz grid that contains a 2D grid of atmosphere models for Teff and logg.
Parameters: fname : str
File name containing the Kurucz model atmosphere (e.g. fp00k2.pck)
Returns: Returns a dictionary with the following keys:
- wav : ndarray
- Wavelength in micron
- nwav : int
- Number of wavelength points
- inu : list
- Each element of the list contains an ndarray with the specific intensity of the stellar model atmosphere in erg/s/cm/cm/Hz/ster
- inucont : list
- Each element of the list contains an ndarray with the specific intensity of the stellar model atmosphere continuum in erg/s/cm/cm/Hz/ster
- teff : list
- Contains the Teff grid of the model grid
- logg : list
- Contains the logg grid of the model grid
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radmc3dPy.staratm.
readNextGenSpectrum
(fname='')¶ Reads the NextGen model atmosphere.
Parameters: fname : str
File name containing the NextGen model atmosphere (e.g. nlte98-4.5-2.5.NextGen.spec)
Returns: Returns a dictionary with the following keys:
- wav : ndarray
- Wavelength in micron
- nwav : int
- Number of wavelength points
- inu : ndarray