Monnier Group Research Wiki - User contributions [en]

Torus

2012-04-24T16:39:47Z

141.211.198.109: /* hydro */

=Preface=

TORUS is a three-dimensional radiative transfer code which uses an adaptive mesh refinement scheme and a Monte-Carlo method to solve for the radiative equilibrium, hydrostatic equilibrium, and dust sublimation in circumstellar discs around both low and high-mass pre-main-sequence stars. TORUS is either an acronym for Transport of Radiation Under Sobolev, or Transport of Radiation Using Stokes.

Much of this is covered in detail on the TORUS wiki at Exeter, [http://wiki.astro.ex.ac.uk/bin/view/TorusWeb/WebHome TorusWeb]. To gain access to that resource, you must make an account; if you have SVN access to the TORUS distribution, that username/password should also work for the wiki (I think..). Here, I will discuss TORUS from an example-driven perspective.

=Physics modules in TORUS=

==radeq==
perform a radiative equilibrium calculation

==stateq==

==photoionphysics==

==radiationhydro==

==hydro==

<nowiki>hydro T ! vertical hydrostatic eq. puffs up inner disk

nhydrothreads 17 ! number of hydro threads.. ehhh? 16+1 control.. see how this goes.

nhydro 4 ! max number of hydro iterations. i think default is 5

splitovermpi T</nowiki>

==dustphysics==

Use dust microphysics; this has to be on if you want a disk there!

=AMR grid=

==Grid setup==
amrgridsize

amrgridcentre[x/y]

amr2d

maxdepthamr

The volume of the smallest grid cell (your finest resolution in the grid) is:

Vol = (grid size / 2^(maxdepthamr))^3
So, for a grid 2000 AU across (1000 AU, radially speaking) and a max cell depth of 20, the smallest cell is 0.0019 AU to a side.

Here is a sample AMR mesh setup:

<nowiki>! AMR grid parameters

readgrid F ! we aren't reading a grid, we will set one up from scratch

! inputfile grid_out.dat ! if we did read in a grid, this is how to call it

writegrid T ! write the grid to file (this includes the grid cells, and the EOS in each cell)

outputfile grid_out.dat ! name of the output grid

amrgridsize 2.0e6 ! units of 10^10cm (here, I've made grid a little bigger than disk itself- the outermost cells will be huge and empty)

amrgridcentrex 1.0e6 ! the linear size of the top-level AMR mesh in units of 10^10 cm. This is useful if you use multiple sources

amr2d T ! this is a 2d (cylindical) model

maxdepthamr 22 ! capping the AMR mesh depth helps TORUS to converge faster, saves some CPU. Set this based on how fine a resolution you need in final model.</nowiki>

==Special grid options==

TORUS can smooth the grid, reducing large cell-to-cell variations in cell refinement and optical depth.

<nowiki>smoothgridtau T ! smooths the grid for optical depth, in order to resolve disc photosphere

dosmoothgrid T ! smooth the grid for jumps in cell refinement

smoothfactor 3.0 ! make sure that neighboring cells are not only one AMR depth apart

lambdasmooth 5500.0

taumax 1.

taumin 0.01
</nowiki>

=TORUS output=

Once your TORUS model has reached the criteria for convergence (more on this later), the final grid is written to a temporary output file, and then TORUS will calculate SEDs, images, and/or line profiles by sending however many photons you specify through the converged grid. If you don't calculate the SEDs/images/line profiles while running TORUS, fear not; change the lucy_grid_tmp.dat file to a different name and use it as an input to TORUS, turning off all the other physics modules. In this way, you can 'hot start' TORUS and calculate output data without re-running your model.

==Sample output calls==

===SEDs===

<nowiki>nphotons 100000 ! the number of photon packets in SED

! Output SEDs

spectrum T ! produce a spectrum

! SED parameters

ninc 2 ! number of inclinations

firstinc 1.0 ! the first inclination (degrees)

lastinc 48.0 ! the last inclination (degrees)

filename MWC275 ! the root of the output filename

sised T ! Write spectrum as lambda vs F lambda in SI units

sedlammin 0.12 ! minimum wavelength in SED file

sedlammax 2000 ! maximum wavelength in SED file

sedwavlin F ! Linear spacing in SED file?

sednumlam 1000 ! number of wavelength points in SED
</nowiki>

The comments make this fairly self-explanatory, but note: you must set nphotons for an SED or an image. In general, the SEDs need fewer photons than the images to get decent signal to noise (in the SED, divide the total number of photons by the number of wavelength points). I've found 50,000 photons or more for the SEDs works well. Also, if you don't specify sednumlam, the default is 200 wavelength points, and that can produce a jagged, noisy SED.

===Images===

<nowiki>nphotons 10000000 ! the number of photon packets in image

image T ! produce images

nimage 4 ! how many images?

imageaxisunits AU

imagesize 20 ! Size of your image across each side in AU. divide this by your npixels to get desired AU/pixel resolution.

imagefile1 kband_20AU.fits ! name of first image file

lambdaimage1 21590. ! monochromatic wavelength in Angstroms

npixels1 256 ! number of pixels. I generally don't adjust this (the more pixels, the more photons you need)

inclination1 0 ! inclination of the system; if unknown, try a few different values in multiple images

imagetype1 dustonly ! choose freefree, forbidden, recombination, or dustonly

imagefile2 nband_1_20AU.fits

lambdaimage2 77000 ! 7.7

npixels2 256

inclination2 0

imagetype2 dustonly

imagefile3 nband_2_20AU.fits

lambdaimage3 99000 ! 9.9um

npixels3 256

inclination3 0

imagetype3 dustonly

imagefile4 nband_3_20AU.fits

lambdaimage4 126000 ! 12.6um

npixels4 256

inclination4 0

imagetype4 dustonly

</nowiki>
===Line profiles===

To calculate line profiles, you must run the TORUS model with the comoving frame option enabled.

<nowiki>cmf T ! comoving frame (vs sobolev approx)</nowiki>

also, specify the atomic physics option and its parameters:

<nowiki>atomicphysics T ! Include atomic physics
natom 1 ! One model atom
atom1 H.atm ! Hydrogen
xabundance 1.0 ! Pure hydrogen
yabundance 0. ! no helium

vturb 20. ! microturbulence in km/s

TORUS will output a velocity space data cube per your input parameters:

! output a datacube

datacube T ! produce a fits datacube
inclination 1. ! viewing angle
positionangle 0. ! position angle
datacubefile cmf_i1_ha.fits ! title of fits output
imageside 1500. ! size of image in 10^10cm
npixels 200 ! number of pixels
nv 200 ! number of velocity bins
maxVel 800.d0 ! -800 to +800 km/s
distance 140. ! distance to object in pc
lamline 6563. ! wavelength in Angstroms</nowiki>

=The nitty-gritty: input parameters=

==Source parameters==

Awesomely, TORUS can handle multiple input sources; to add additional sources, simply change the numerical value after each parameter, and set nsource to whatever value greater than 1 applies.

<nowiki>! Source parameters

nsource 1 ! there is just one source

radius1 2.0 ! it has a radius of 1 solar radius

teff1 10000. ! the source effective temperature

contflux1 kurucz ! the continuum flux (other option is blackbody)

mass1 2.5 ! the source has a mass of one solar mass

sourcepos1 0. 0. 0 ! it is located at the grid cntre

distance 150. ! Distance to observer, pc</nowiki>

==Disk geometries==

These are the input options for the geometry parameter:

===benchmark===
A Pascucci benchmark disk

===shakara===

This is a sample pulled from an MWC 275 parameter file.

<nowiki>geometry shakara ! flared protostellar disk

rinner 0.22 ! inner disc radius (AU) --this is from ajay's paper

router 200. ! outer disc radius (AU)

height 10. ! disc scaleheight at 100 AU (in AU)

mdisc 0.01 ! Msun

alphadisc 1.0 ! this is from ajay's paper

betadisc 1.125 ! disc scaleheight goes as r^beta</nowiki>

===ttauri===

===Options that apply to any disk geometry===

<nowiki>smoothinneredge T ! exponential density decay at inner disk edge

gasopacity T</nowiki>

The gasopacity switch is, I believe, the only way that gas is applied in TORUS: the gas is a source of opacity, and it is a radiation source (probably mostly emission), but it isn't coupled to the gas (i.e., doesn't play a role in the hydrostatic equilibrium of the disk).

==Dust options==

These dust parameters apply when dustphysics T.

<nowiki>iso_scatter T ! Assume isotropic scattering (assumed by benchmark)

ndusttype 1

graintype1 sil_dl ! Drain and Lee silicates

amin1 0.01 ! minimum grain size (microns)

amax1 0.25 ! maximum grain size (microns)

qdist1 1.5 ! power law index (a^-qdist)

dusttogas 0.01 ! torus assumes this value, even if you don't explicitly define it.

vardustsub T</nowiki>

Important! If you set variable dust sublimation, vertical hydrostatic equilibrium must be on (hydro T) to allow the inner disk to puff up!!

Torus

2012-04-24T16:39:12Z

141.211.198.109:

Torus

2012-04-24T16:24:11Z

141.211.198.109:

Main Page

2012-04-23T19:18:37Z

141.211.198.109: /* Welcome to the Internal Wiki Site for the Monnier Group at the University of Michigan */

[[Image:PR_epsAur.jpg|900px|{4-epochs of Epsilon Aurigae}]]

== '''Welcome to the Internal Wiki Site for the Monnier Group at the University of Michigan''' ==

Please click on the Project Links below to find more information

[[MIRC]] Michigan Infrared Combiner

[[CHAMP]] Chara-Michigan Phasetracker

[[SMART]] Single-mode Asymmetric Recombination

[[NASACAM]] L-band integrated optics

[[LabControl]] Lab Control with iPad

[[CHARA AO]] CHARA Adaptive Optics

[[torus]] TORUS 3-dimensional radiative transfer code

[[MIKE]] Optical echelle spectroscopy of YSOs, rapid rotators
----

[[Observing History and Target Files]]

----

[[Reduced data]]

----

[[Collaboration on Papers]]

----

[[Code Snapshots]]

----

[[DOCUSHARE MIGRATION|Migration Pages]] (needs attention to integrate into this new wiki)

----

-----

[[Some wiki help]]

[[Algol 2010 materials]]

[[2010 July Magellan Run Materials]]

[[2011 February Magellan Run Materials]]

[[2011 March Magellan Run Materials]]

[[MIRC 6T upgrade]]

Main Page

2011-02-04T23:37:08Z

141.211.198.109: /* Welcome to the Internal Wiki Site for the Monnier Group at the University of Michigan */

[[Image:PR_epsAur.jpg|900px|{4-epochs of Epsilon Aurigae}]]

== '''Welcome to the Internal Wiki Site for the Monnier Group at the University of Michigan''' ==

Please click on the Project Links below to find more information

[[MIRC]] Michigan Infrared Combiner

[[CHAMP]] Chara-Michigan Phasetracker

[[SMART]] Single-mode Asymmetric Recombination

[[NASACAM]] L-band integrated optics

[[LabControl]] Lab Control with iPad

[[torus]] TORUS 3-dimensional radiative transfer code
----

[[Observing History and Target Files]]

----

[[Reduced data]]

----

[[Collaboration on Papers]]

----

[[Code Snapshots]]

----

[[DOCUSHARE MIGRATION|Migration Pages]] (needs attention to integrate into this new wiki)

----
Quick Links

[[Engineering 2011JanFeb]] *** NEW ! ***

[[CHAMP todo list]]

[[Some wiki help]]

[[Algol 2010 materials]]

[[2010 July Magellan Run Materials]]

[[2011 February Magellan Run Materials]]

[[MIRC 6T upgrade]]

Main Page

2011-02-04T23:36:52Z

141.211.198.109: /* Welcome to the Internal Wiki Site for the Monnier Group at the University of Michigan */

[[Image:PR_epsAur.jpg|900px|{4-epochs of Epsilon Aurigae}]]

== '''Welcome to the Internal Wiki Site for the Monnier Group at the University of Michigan''' ==

Please click on the Project Links below to find more information

[[MIRC]] Michigan Infrared Combiner

[[CHAMP]] Chara-Michigan Phasetracker

[[SMART]] Single-mode Asymmetric Recombination

[[NASACAM]] L-band integrated optics

[[LabControl]] Lab Control with iPad

[[torus]] TORUS 3-dimensional radiative transfer code
----

[[Observing History and Target Files]]

----

[[Reduced data]]

----

[[Collaboration on Papers]]

----

[[Code Snapshots]]

----

[[DOCUSHARE MIGRATION|Migration Pages]] (needs attention to integrate into this new wiki)

----
Quick Links

[[Engineering 2011JanFeb]] *** NEW ! ***

[[CHAMP todo list]]

[[Some wiki help]]

[[Algol 2010 materials]]

[[2010 July Magellan Run Materials]]
[[2011 February Magellan Run Materials]]

[[MIRC 6T upgrade]]