Torus - Revision history

141.211.97.9: /* Makefile */

2017-07-07T14:48:55Z

Makefile

← Older revision		Revision as of 14:48, 7 July 2017
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	[[media: alicia_torus_makefile.txt]] My makefile (cropped down to just my SYSTEM selection). Within the TORUS folder, this is just called Makefile.		[[media: alicia_torus_makefile.txt]] My makefile (cropped down to just my SYSTEM selection). Within the TORUS folder, this is just called Makefile.

			[[media: Alicia_torus.makefile]] My makefile (cropped down to just my SYSTEM selection). Within the TORUS folder, this is just called Makefile.

	==Version info==		==Version info==

Monnierast: /* stateq */

2012-04-24T21:57:00Z

stateq

← Older revision		Revision as of 21:57, 24 April 2012
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	Statistical equilibrium calculation by solving the rate equations. If atomicphysics T then a comoving frame algorithm or the Sobolev approximation are employed (I think now, by default, TORUS uses the comoving frame algorithm exclusively by default.. back in 2010, you had to set cmf T to do a comoving frame calculation).		Statistical equilibrium calculation by solving the rate equations. If atomicphysics T then a comoving frame algorithm or the Sobolev approximation are employed (I think now, by default, TORUS uses the comoving frame algorithm exclusively by default.. back in 2010, you had to set cmf T to do a comoving frame calculation).

	Effectively, these are both ray-tracing algorithms (as implemented in TORUS, based on [http://adsabs.harvard.edu/abs/2000A%26A...362..697H Hogerheijde and van der Tak, 2000]), they just differ in how the photon tracer is assumed to interact with the medium. The Sobolev approximation assumes <math>\Delta r</math> (the line width, or range of velocities that can interact wind+line) is negligibly small. In the case of a slower, or less accelerating wind, the Sobolev approximation breaks down because <math>\Delta r</math> is too large. The comoving frame algorithm gets around that (the photon changes its local comoving frame frequency as it goes, so the velocities sampled are typical of the local flow).		Effectively, these are both ray-tracing algorithms (as implemented in TORUS, based on [http://adsabs.harvard.edu/abs/2000A%26A...362..697H Hogerheijde and van der Tak, 2000]), they just differ in how the photon tracer is assumed to interact with the medium. The Sobolev approximation assumes <math>\Delta r</math> (the line width, or range of velocities that can interact wind+line) is negligibly small. In the case of a slower, or less accelerating wind, the Sobolev approximation breaks down because <math>\Delta r</math> is too large. The comoving frame algorithm gets around that (the photon changes its local comoving frame frequency as it goes, so the velocities sampled are typical of the local flow). <br>
			(This google book excerpt explains this much better than my notes do.. [http://books.google.com/books?id=J48PULzdgSgC&lpg=PA122&ots=clT0ecflye&dq=sobolev%20approximation&pg=PA123#v=onepage&q=sobolev%20approximation&f=false])

	The speed of this calculation depends on the optical depth of a given line; H<math>\alpha</math> runs more slowly than Br<math>\gamma</math>, for instance.		The speed of this calculation depends on the optical depth of a given line; H<math>\alpha</math> runs more slowly than Br<math>\gamma</math>, for instance.

Monnierast: /* shakara */

2012-04-24T21:54:44Z

shakara

@@ Line 521: / Line 521: @@
 ===shakara===
 This is a sample pulled from an MWC 275 parameter file.
@@ Line 545: / Line 547: @@
   |betadisc 1.125
   |! disc scaleheight goes as r^beta</nowiki>
   |}

Monnierast: /* benchmark */

2012-04-24T21:50:27Z

benchmark

← Older revision		Revision as of 21:50, 24 April 2012
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	===benchmark===		===benchmark===

	A Pascucci (2004) benchmark disk		A [http://adsabs.harvard.edu/abs/2004A%26A...417..793P Pascucci (2004)] benchmark disk

	===shakara===		===shakara===

Monnierast: /* TORUS output */

2012-04-24T21:42:54Z

TORUS output

← Older revision		Revision as of 21:42, 24 April 2012
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	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.		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.

			TORUS writes SEDs to .dat files, and images/velocity data cubes are fits format. Grid visualization files are in .vtk format; these can be viewed with VisIt (see Auxiliary Software, above).

			'''Important!''' The most recent versions of TORUS write binary xml files; my system does not support these files, so I include binaryxml F in my parameters files.

	==Sample output calls==		==Sample output calls==

Monnierast: /* Options that apply to any disk geometry */

2012-04-24T21:35:46Z

Options that apply to any disk geometry

← Older revision		Revision as of 21:35, 24 April 2012
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	\|}		\|}

	As far as I know, you can only change this within the lucy_mod.F90 file (don't forget to re-build TORUS after editing that file!). You can limit the number of hydro iterations on top of these Lucy iterations by setting the nhydro keyword. The default is 5 hydro iterations.		As far as I know, you can only change this within the lucy_mod.F90 file (don't forget to re-build TORUS after editing that file!). You can limit the number of hydro iterations on top of these Lucy iterations by setting the nhydro keyword. The default is 5 hydro iterations (with 9 Lucy iterations per hydro iteration).

	==Dust options==		==Dust options==

Monnierast: /* ttauri */

2012-04-24T21:34:04Z

ttauri

← Older revision		Revision as of 21:34, 24 April 2012
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	===ttauri===		===ttauri===

	~~(so many~~ parameters ~~here~~.. ~~coming soon~~.)		The ttauri geometry includes a magnetosphere, disk, and disk wind. Each of these separately has its own parameters; I have yoinked these images directly from the TORUS wiki:

			[[Image:ttmagpars.jpg]]
			[[Image:ttdiscpars.jpg]]
			[[Image:ttdwpars.jpg]]

			A hot ring is generated on the star (near the pole); the temperature of this hot ring depends on the accretion rate, mdotpar1.

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

Monnierast at 21:26, 24 April 2012

2012-04-24T21:26:33Z

← Older revision		Revision as of 21:26, 24 April 2012
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	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. In this mini-manual, I'm not going to address any molecular capabilities of TORUS, and I am leaving out a lot of TORUS' functionality I don't personally use.		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. In this mini-manual, I'm not going to address any molecular capabilities of TORUS, and I am leaving out a lot of TORUS' functionality I don't personally use.


	=Building TORUS=		=Building TORUS=
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	Tim and the Exeter group use [https://wci.llnl.gov/codes/visit/ VisIt] and [http://www.atnf.csiro.au/computing/software/karma/ kvis] to display TORUS outputs. VisIt will plot the .vtk output, and kvis plots fits outputs (dust continuum images as well as the velocity data cubes and line profiles therein). I posted a tutorial to the Exeter wiki regarding how to generate specific plots with these tools; pdf here: [[media:Plottingtorusdata.pdf]].		Tim and the Exeter group use [https://wci.llnl.gov/codes/visit/ VisIt] and [http://www.atnf.csiro.au/computing/software/karma/ kvis] to display TORUS outputs. VisIt will plot the .vtk output, and kvis plots fits outputs (dust continuum images as well as the velocity data cubes and line profiles therein). I posted a tutorial to the Exeter wiki regarding how to generate specific plots with these tools; pdf here: [[media:Plottingtorusdata.pdf]].


	=Physics modules in TORUS=		=Physics modules in TORUS=
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	==atomicphysics==		==atomicphysics==

	This module must be enabled to do line transfer calculations. This module can either perform a comoving frame calculation (computationally expensive) or use the Sobolev approximation.		This module must be enabled to do line transfer calculations. This module can either perform a comoving frame calculation (computationally expensive) or use the Sobolev approximation (Sobolev may be disabled as of 2012?).

	Example from the literature of implementation of this function of TORUS- [http://adsabs.harvard.edu/abs/2006MNRAS.370..580K Kurosawa, Harries & Symington (2006)]. In this paper, the authors were distinguishing which parameters would generate Halpha line profiles like those in [http://adsabs.harvard.edu/abs/1996A%26AS..120..229R Bo Reipurth's classification].		Example from the literature of implementation of this function of TORUS- [http://adsabs.harvard.edu/abs/2006MNRAS.370..580K Kurosawa, Harries & Symington (2006)]. In this paper, the authors were distinguishing which parameters would generate Halpha line profiles like those in [http://adsabs.harvard.edu/abs/1996A%26AS..120..229R Bo Reipurth's classification].
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	\|grid split into 64 plus 1 control thread		\|grid split into 64 plus 1 control thread
	\|}		\|}


	=Types of calculations done in TORUS=		=Types of calculations done in TORUS=
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	In a monte carlo way, the wavenumber of the photon packet is randomly chosen from a set of integers, and the photon packet is sent off in a random direction. Photon packets undergo scattering and absorption/re-emission following bound-free and free-free processes. If the packet escapes to infinity or is deflected backwards, the loop ends. Within a given spherical shell, the photon packet's path depends on the optical depth in that shell; if the photon's mean free path takes it into the next shell, a new optical depth is calculated, and the photon packet is followed through that shell. If the packet's mean free path is short enough that it stays in a shell, it is then either scattered or absorbed. If absorbed, the photon packet is assigned a new frequency dependent upon the shell's emissivity; if scattered, a new direction is assigned at the point of scattering. The monte carlo estimators detect departures from equilibrium; when the rate of absorption and rate of emission are balanced, equilibrium is reached.		In a monte carlo way, the wavenumber of the photon packet is randomly chosen from a set of integers, and the photon packet is sent off in a random direction. Photon packets undergo scattering and absorption/re-emission following bound-free and free-free processes. If the packet escapes to infinity or is deflected backwards, the loop ends. Within a given spherical shell, the photon packet's path depends on the optical depth in that shell; if the photon's mean free path takes it into the next shell, a new optical depth is calculated, and the photon packet is followed through that shell. If the packet's mean free path is short enough that it stays in a shell, it is then either scattered or absorbed. If absorbed, the photon packet is assigned a new frequency dependent upon the shell's emissivity; if scattered, a new direction is assigned at the point of scattering. The monte carlo estimators detect departures from equilibrium; when the rate of absorption and rate of emission are balanced, equilibrium is reached.


	==photoion eq==		==photoion eq==
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	=~~Troubleshooting~~=		=Running TORUS=

			Guess I'd be remiss if I didn't include how to run TORUS! Generally, I create a folder for the object I'm running, and keep the parameters file in there. From that directory, call the torus executable and give your parameter file as an input:

			torus/torus.intelmac parameters.dat

			Running over an ssh connection, I use nohup (no hangup) so logging out doesn't kill the job:

			nohup torus/torus.intelmac parameters.dat >& screendump.txt &

			The >& sends stdout to a text file. That way if TORUS prints messages to screen, you can check the output file later.

			==Benchmarks==

			To start with, I recommend benchmarking your version of TORUS. In the torus folder is a directory called benchmarks/. Within that directory are examples of different models the Exeter group always runs after each change to TORUS modules to make sure things didn't get inadvertently broken.

			{\|
			\|Pascucci+(2004) 2D benchmark
			\|benchmarks/disc/
			\|-
			\|Pascucci+2004 3D benchmark
			\|benchmarks/disc_cylindrical/
			\|-
			\|40,000 K star with gas envelope
			\|benchmarks/image_fluxMPI/
			\|}

			At this time, there aren't any ttauri or shakara geometry benchmark models. )I'll upload some working parameters files for those soon)

			After you've checked the outputs and are happy that your version of TORUS built properly and is working as it should, move on to create your own parameters files.

			==Creating parameters files==

	~~In the most common application of TORUS, performing~~ a ~~radiative equilibrium calculation, output is generated after each Lucy iteration. The~~ file ~~convergence_lucy~~.~~dat documents each Lucy iteration-~~ the ~~iteration number, mean temperature change in~~ the ~~disk, minimum/maximum temperature changes within~~ the ~~grid cells, percentage of bad cells (<50 photon packets through~~ a ~~given cell)~~, ~~dust emissivity/stellar emissivity~~, ~~total emissivity, maximum fractional change in temperature across all cells, and nMonte, the number of photon packets~~.		I recommend beginning with a template; copy a benchmark parameters file and adapt it from there. Consider the physics modules you need to perform the calculations you want. TORUS is very good about letting the user know when a keyword is missing, conflicts with another, or is unnecessary altogether.


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	\|		\|
	\|}		\|}


	=TORUS output=		=TORUS output=
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	TORUS can calculate very simple disk configurations, or as complicated a disk (plus magnetosphere, in the ttauri case) as you want. If you talk to Ilse, she can tell you about her own disk geometry modules. Since TORUS is written in a modular way, creating whatever geometry you'd like is more straightforward than one might think.		TORUS can calculate very simple disk configurations, or as complicated a disk (plus magnetosphere, in the ttauri case) as you want. If you talk to Ilse, she can tell you about her own disk geometry modules. Since TORUS is written in a modular way, creating whatever geometry you'd like is more straightforward than one might think.

			===benchmark===

	~~===benchmark===~~		A Pascucci (2004) benchmark disk
	A Pascucci benchmark disk

	===shakara===		===shakara===
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	===ttauri===		===ttauri===

			(so many parameters here.. coming soon.)

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

	'Important!' If you set variable dust sublimation, vertical hydrostatic equilibrium must be on (hydro T) to allow the inner disk to puff up!! This will add the secondary convergence criterion that convergence can only be reached if the number of Lucy iterations is greater than 9- this is an excerpt from lucy_mod.F90:		'''Important!''' If you set variable dust sublimation, vertical hydrostatic equilibrium must be on (hydro T) to allow the inner disk to puff up!! This will add the secondary convergence criterion that convergence can only be reached if the number of Lucy iterations is greater than 9- this is an excerpt from lucy_mod.F90:

	{\|		{\|
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	\|! torus assumes this value, even if you don't explicitly define it.		\|! torus assumes this value, even if you don't explicitly define it.
	\|}		\|}


			=Troubleshooting=

			In the most common application of TORUS, performing a radiative equilibrium calculation, output is generated after each Lucy iteration. The file convergence_lucy.dat documents each Lucy iteration- the iteration number, mean temperature change in the disk, minimum/maximum temperature changes within the grid cells, percentage of bad cells (<50 photon packets through a given cell), dust emissivity/stellar emissivity, total emissivity, maximum fractional change in temperature across all cells, and nMonte, the number of photon packets.

Monnierast at 21:06, 24 April 2012

2012-04-24T21:06:17Z

← Older revision		Revision as of 21:06, 24 April 2012
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	Generally, what happens in TORUS is that the disk begins cold. Photons are first absorbed, and then escape (~mm re-radiation, the disk is optically thin to it). The first Lucy iteration goes quickly, and each successive iteration takes longer and longer as the disk becomes optically thick to its own radiation. Usually, convergence (radiative equilibrium only, not hydrostatic) is reached in 5-10 Lucy iterations. The primary criterion for convergence is that the change in total emissivity is less than 1% (with respect to the previous iteration). If you include hydro calculations, a secondary convergence criterion is forced that TORUS run through at least 5 hydro iterations (within each hydro iteration, there are however many radiative equilibrium iterations necessary to reach convergence). These criteria can be relaxed by editing lucy_mod.F90 (not recommended unless you're very comfortable with what you're doing!!! See [[editing lucy_mod.F90]] for an example). Between iterations, if convergence is not met and the fraction of bad cells (<50 photon packets through the cell) is nonzero, the number of source photons doubles. The initial number of photons is ~10x the number of cells, but this can be adjusted with the nlucy parameter.		Generally, what happens in TORUS is that the disk begins cold. Photons are first absorbed, and then escape (~mm re-radiation, the disk is optically thin to it). The first Lucy iteration goes quickly, and each successive iteration takes longer and longer as the disk becomes optically thick to its own radiation. Usually, convergence (radiative equilibrium only, not hydrostatic) is reached in 5-10 Lucy iterations. The primary criterion for convergence is that the change in total emissivity is less than 1% (with respect to the previous iteration). If you include hydro calculations, a secondary convergence criterion is forced that TORUS run through at least 5 hydro iterations (within each hydro iteration, there are however many radiative equilibrium iterations necessary to reach convergence). These criteria can be relaxed by editing lucy_mod.F90 (not recommended unless you're very comfortable with what you're doing!!! See [[editing lucy_mod.F90]] for an example). Between iterations, if convergence is not met and the fraction of bad cells (<50 photon packets through the cell) is nonzero, the number of source photons doubles. The initial number of photons is ~10x the number of cells, but this can be adjusted with the nlucy parameter.


	==dustphysics==		==dustphysics==

			This includes dust emission/absorption processes and must be T if radiative transfer in the disk is being calculated.


	==atomicphysics==		==atomicphysics==
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	==stateq==		==stateq==

	Statistical equilibrium calculation by solving the rate equations. If atomicphysics T then a comoving frame algorithm is ~~employed~~.		Statistical equilibrium calculation by solving the rate equations. If atomicphysics T then a comoving frame algorithm or the Sobolev approximation are employed (I think now, by default, TORUS uses the comoving frame algorithm exclusively by default.. back in 2010, you had to set cmf T to do a comoving frame calculation).

			Effectively, these are both ray-tracing algorithms (as implemented in TORUS, based on [http://adsabs.harvard.edu/abs/2000A%26A...362..697H Hogerheijde and van der Tak, 2000]), they just differ in how the photon tracer is assumed to interact with the medium. The Sobolev approximation assumes <math>\Delta r</math> (the line width, or range of velocities that can interact wind+line) is negligibly small. In the case of a slower, or less accelerating wind, the Sobolev approximation breaks down because <math>\Delta r</math> is too large. The comoving frame algorithm gets around that (the photon changes its local comoving frame frequency as it goes, so the velocities sampled are typical of the local flow).

			The speed of this calculation depends on the optical depth of a given line; H<math>\alpha</math> runs more slowly than Br<math>\gamma</math>, for instance.

	==radeq==		==radeq==

	This requires that dustphysics T and uses the Monte-Carlo radiative equilibrium method of [http://adsabs.harvard.edu/abs/1999A%26A...344..282L Lucy (1999)]		This requires that dustphysics T and uses the Monte-Carlo radiative equilibrium method of [http://adsabs.harvard.edu/abs/1999A%26A...344..282L Lucy (1999)].

			===The Lucy algorithm===

			I'm going to go into a lot of depth describing this, as the Lucy algorithm is the heart of the radiative equilibrium part of TORUS. These are my transcribed notes on the Lucy (1999) paper.

			Lucy's method calculates temperature stratification and the emergent spectrum of an extended, non-grey (i.e., opacity is a function of wavelength) medium in LTE. The method avoids following single photons, but rather uses packets of constant energy:<br>
			<math>\epsilon(\nu)=nh\nu</math> <br>
			When a packet is absorbed, it is re-emitted in accordance with the emissivity of the medium:<br>
			<math>\epsilon(\nu_{emitted})=\epsilon(\nu_{absorbed})</math> <br>
			This constrains the radiation field to be divergence free at every iteration.

			Lucy's example is a stellar atmosphere, a blackbody of temperature <math>T_{b}</math> isotropically emitting at the innermost spherical shell, radiating out into concentric spherical shells. The shell's radii are defined such that <math>R_{J+1}/R_{J}</math> is constant. Within each shell, <math>\rho</math>, T, <math>\sigma</math>, and <math>k_{\nu}</math> are constant.

			In a monte carlo way, the wavenumber of the photon packet is randomly chosen from a set of integers, and the photon packet is sent off in a random direction. Photon packets undergo scattering and absorption/re-emission following bound-free and free-free processes. If the packet escapes to infinity or is deflected backwards, the loop ends. Within a given spherical shell, the photon packet's path depends on the optical depth in that shell; if the photon's mean free path takes it into the next shell, a new optical depth is calculated, and the photon packet is followed through that shell. If the packet's mean free path is short enough that it stays in a shell, it is then either scattered or absorbed. If absorbed, the photon packet is assigned a new frequency dependent upon the shell's emissivity; if scattered, a new direction is assigned at the point of scattering. The monte carlo estimators detect departures from equilibrium; when the rate of absorption and rate of emission are balanced, equilibrium is reached.


	==photoion eq==		==photoion eq==

	Solves photoionization equilibrium including thermal equilibrium using a method similar to that of Ercolano ~~xxxx~~. Dust may be included.		Solves photoionization equilibrium including thermal equilibrium using a method similar to that of [http://adsabs.harvard.edu/abs/2005MNRAS.362.1038E Ercolano (2005)]. Dust may be included.

	==hydrodynamics==		==hydrodynamics==

Monnierast at 20:28, 24 April 2012

2012-04-24T20:28:12Z

← Older revision		Revision as of 20:28, 24 April 2012
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	==~~radeq~~==		==dustphysics==
	~~perform a radiative equilibrium calculation~~

	~~[http://adsabs.harvard.edu/abs/1999A%26A...344..282L Lucy (1999)]~~
	~~[http://adsabs.harvard.edu/abs/2006MNRAS.370..580K Kurosawa, Harries & Symington (2006)]~~

	~~==stateq==~~

	==atomicphysics==		==atomicphysics==

	This module must be enabled to do line transfer calculations. This module can either perform a comoving frame calculation (computationally expensive) or use the Sobolev approximation.		This module must be enabled to do line transfer calculations. This module can either perform a comoving frame calculation (computationally expensive) or use the Sobolev approximation.

			Example from the literature of implementation of this function of TORUS- [http://adsabs.harvard.edu/abs/2006MNRAS.370..580K Kurosawa, Harries & Symington (2006)]. In this paper, the authors were distinguishing which parameters would generate Halpha line profiles like those in [http://adsabs.harvard.edu/abs/1996A%26AS..120..229R Bo Reipurth's classification].

	Right now, only H is fully implemented (He is in "beta" mode, so to speak). We've lobbied Tim to add Ca, Na, O next.		Right now, only H is fully implemented (He is in "beta" mode, so to speak). We've lobbied Tim to add Ca, Na, O next.
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	\|}		\|}

	==~~radiationhydro~~==		=Types of calculations done in TORUS=

			Which type of calculation TORUS does depends on the star+disk geometry and physics chosen by the user. Once those are defined, TORUS will do the necessary combinations of the following:

			==stateq==

			Statistical equilibrium calculation by solving the rate equations. If atomicphysics T then a comoving frame algorithm is employed.

			==radeq==

			This requires that dustphysics T and uses the Monte-Carlo radiative equilibrium method of [http://adsabs.harvard.edu/abs/1999A%26A...344..282L Lucy (1999)]

	This module combines photoionization and hydrodynamics; the evolution of the radiation field and the material dynamics are coupled. TORUS begins with a radiative transfer iteration, then the following iterations alternate between hydrodynamics and radiative transfer. To use this physics, the following modules must be enabled:		==photoion eq==

	{\|		Solves photoionization equilibrium including thermal equilibrium using a method similar to that of Ercolano xxxx. Dust may be included.
	~~\|radiationhydro T~~
	\|-
	~~\|hydrodynamics T~~
	\|-
	~~\|splitovermpi T~~
	\|-
	~~\|photoionphysics T~~
	\|}

	==hydrodynamics==		==hydrodynamics==
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	My usage of this module is somewhat limited to just making sure the inner edge of the disk puffs up; for more detailed discussion of the defaults (artificial viscosity, the flux limiting algorithm used, etc), see the [http://wiki.astro.ex.ac.uk/bin/view/TorusWeb/Hydrodynamics Exeter hydrodynamics wiki page].		My usage of this module is somewhat limited to just making sure the inner edge of the disk puffs up; for more detailed discussion of the defaults (artificial viscosity, the flux limiting algorithm used, etc), see the [http://wiki.astro.ex.ac.uk/bin/view/TorusWeb/Hydrodynamics Exeter hydrodynamics wiki page].

	==~~dustphysics~~==		==radiationhydro==

			This module combines photoionization and hydrodynamics; the evolution of the radiation field and the material dynamics are coupled. TORUS begins with a radiative transfer iteration, then the following iterations alternate between hydrodynamics and radiative transfer. To use this physics, the following modules must be enabled:

			{\|
			\|radiationhydro T
			\|-
			\|hydrodynamics T
			\|-
			\|splitovermpi T
			\|-
			\|photoionphysics T
			\|}

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

	==Troubleshooting==		=Troubleshooting=

	~~While~~ TORUS ~~is running~~, ~~some~~ output is generated after each Lucy iteration. The file convergence_lucy.dat documents each Lucy iteration- the iteration number, mean temperature change in the disk, minimum/maximum temperature changes within the grid cells, percentage of bad cells (<50 photon packets through a given cell), dust emissivity/stellar emissivity, total emissivity, maximum fractional change in temperature across all cells, and nMonte, the number of photon packets.		In the most common application of TORUS, performing a radiative equilibrium calculation, output is generated after each Lucy iteration. The file convergence_lucy.dat documents each Lucy iteration- the iteration number, mean temperature change in the disk, minimum/maximum temperature changes within the grid cells, percentage of bad cells (<50 photon packets through a given cell), dust emissivity/stellar emissivity, total emissivity, maximum fractional change in temperature across all cells, and nMonte, the number of photon packets.