# Journal Club 0730 Agenda

- Ruka's PN simulations.

https://astrobear.pas.rochester.edu/trac/astrobear/wiki/u/smurugan/pn2013

- Sink particle algorithm wrap up.

- Learning to code self-gravity solver (Poisson equation).

# Meeting Update 07/29/2013

- Still running binary global frame
- Running HSE + disk with tracers
- Final week paper stuff
- Trying to run simulation with FEDERRATH accretion

# Meeting update 7/29

- Attended teleconference with Bruce Balick
- Tried a few different runs to try and fix the issues with MHD runs, but a lot of those problems seem to have stemmed from a bug in the module that Martin has fixed.
- Re-running the constant ambient DW model at 64 zones/ radius

# Meeting Update 0729

- Krumholz accretion + Patch refinement worked with a factor added to the initial mass equation. I have done a run on Kraken with 320*192*192 base resolution + 2 level patch (effective resolution is 512 zones per clump radius) (with a factor of 0.25 added to drho). The rotating runs should look interesting with the increased resolution.

The star also grows to greater mass, not sure if it is because of the initial mass (with 0.25 factor, the initial mass is now about 10 units instead of 0.01) or increased resolution. We can try a factor > 0.25 to test the difference.

- Bluestreak has some compiling problem, and it seems I'm not on the new grant. Currently I can only use the old grant hours. Each of the high resolution runs takes about 2 days on 1080 cores on Kraken, therefore we need about 50000 cpu hours for each run. 6 runs (as planned) will cost about 10% of the new allocation.

- Currently working on merging 3.0 with thermal diffusion, will meet with LLE people this week.

# Meeting update

Please see my previous post for the appendix write up for the self-gravity TEST (https://astrobear.pas.rochester.edu/trac/astrobear/blog/erica07272013)

Please see my previous post for the different types of curve to visualize the growth rate of jeans instability https://astrobear.pas.rochester.edu/trac/astrobear/blog/erica07262013

I am working on my 2D code. I made a page here https://astrobear.pas.rochester.edu/trac/astrobear/wiki/u/erica/2D_Godunov

I don't anticipate it taking too long to finish, and will post the results there.

Also, I got this email last week and wonder if it should be looked into or ignored???

*Dear Erica Kaminski,
*

According to the University of Rochester's online repository you wrote a paper entitled "The effect of the ambient medium on the collapse of a bonnor-ebert sphere: deviation from the canonical outsidein collapse" during your studies.

I am an Editor of LAP LAMBERT Academic Publishing, an international publisher specialized in the publication of research papers.

We would be pleased to consider integrating the above mentioned work in our catalogue of printed books.

In case you are interested in our offer please contact me at your earliest convenience. I will be pleased to send you a detailed brochure for your perusal.

I am looking forward to hearing from you.

Kind regards

Irina Rusu Acquisition Editor

LAP LAMBERT Academic Publishing is a trademark of: AV Akademikerverlag GmbH & Co. KG

Heinrich-Böcking-Str. 6-8 66121, Saarbrücken, Germany

i.rusu@lap-publishing-house.com / www.lap-publishing-house.com

Handelsregister Amtsgericht Saarbrücken HRA 10356
Identification Number (Verkehrsnummer): 11868
Partner with unlimited liability: VDM Management GmbH
Handelsregister Amtsgericht Saarbrücken HRB 18918
Managing directors: Thorsten Ohm (CEO) *
*

# Meeting Update 07/29/2013 -- Baowei

- Tickets
- new: #304(Problem keeping hydro static equilibrium with sink particle)
- closed: none

- User
- Called Bruce. Schedule for the visit of Bruce's student?
- Student at Universidad de Chile asked to download 2.0

- Resources

# meeting 07/29/13 zhuo

- Read 1-12 chapters in "Statistical Physics" by Kerson Huang (I did this not just in one week but since the beginning of this summer). It is about ensembles, time-series analysis, stochastic process and thermal dynamics - all of them are very helpful in understanding astrophysics (diffusion, viscosity and heat conduction) and even cosmology (distribution and ensembles).
- Read chapter 5 and 6 in "Riemann Solver". After reading these, I feel that Fourier analysis can be powerful in Riemann solver, and could be even powerful when combined with AMR.
- Plan to read some numerical analysis books, a potential one is "Finite difference methods for ordinary and partial differential equations : steady-state and time-dependent problems" by Randall J. LeVeque, UW. It is best know both numerical stuff and physics stuff so that one may tell what is physical and what is unphysical in simulations.

# Self-gravity test for appendix write up

I didn't write the implementation part of the appendix yet, as I think it may be easier once I learn a bit about the gravity solver techniques, and HYPRE (within the next month with my own code building). I made a short outline of what I think this appendix might include, and have built it into the pdf that is here:

http://www.pas.rochester.edu/~erica/BEsphere_AF_07.11.13.pdf

On the other hand, I did write up the test for self-gravity, using the Jeans instability growth rate stuff I have been talking about lately. That is built into the pdf as well. As far as the figures for the section go, I just thought to use both the perturbation vs. time graph and the slope graph from blog post:

https://astrobear.pas.rochester.edu/trac/astrobear/blog/erica07262013

This however, is up to wiser judgment than myself.

# A closer look at Jeans Instability plots

First is a plot of the total density at a peak (i.e., a peak is a region that is growing in density over simulation). The analytical function for the density is:

where

is the background density, is the density perturbation, and is the growth rate, calculated to be ~628.8 (in computational units).At the peak, the Cos(x) function is just 1, and so in scaled units, the function becomes:

Since this is not an exact exponential, it does not appear as a straight line on a log-linear plot (see for reference). Here is the data output from astrobear compared to the analytical function, on a linear-linear plot:

Now, since the perturbation

is just an exponential (given by above), it looks like this on a semi-log plot:The slope of this line, on a semi-log plot, gives the power 'e' is raised to. That is, since

, . Here the log is base 10, NOT e, so log(e) DNE 1. This is an equation of a line with slope = log(e)*628.8, or ~273. Thus, if one plots the perturbation on a semi-log plot, and calculates the slope — it should give back this number - m=273.
When calculating the average slope using log(y2)-log(y1)/x2-x1, I get a number very close to 273. This is good. But perhaps more descriptive is a plot of the *instantaneous* slope of this line - to see any deviations of astrobear's output from the analytical curve. To make this plot, I calculated the derivative of the log of the analytical function:

(as expected), and plotted this against the instantaneous derivative of the data (calculated using log(i+1)-log(i) / log(j+1) - log(j) in my spreadsheet). This is what I get:

As we see, initially the data from astrobear lines up very well with the analytical result, but over a couple of e-folding times, the rate of change increases compared to the analytical curve. By 5 e-folding times, the difference is ~10% (easily seen in the first plot). If we consider the error from the non-linear term to grow roughly as

, and take t = 5/628.8 (5 e-folding times), then the error is ~2%. This seems to match the data. This means that by a few e-folding times, the non-linear term becomes significant, and so we can no longer assume a linear perturbation to govern evolution.# Gammas and polytropes..

Is the gamma from the polytropic index, the same as gamma in astrobear. I think gamma in astrobear is the 'adiabatic index', a ratio of specific heats — but this is not the case for the polytrope according to this -

http://en.wikipedia.org/wiki/Polytropic_process#Notation

and here is a write up detailing the math

# Meeting Update 07/23/2013 - Eddie

- PPVI went really well: met a lot of new people, shared my poster, got my emission map movie in Adam's review talk, had a really good time in Germany!

- Haven't had too much opportunity to review the 3D pulsed jet stuff. I know Baowei and Jonathan have been working on it and updating the ticket, so I will check that out soon. I'll be in email and phone contact while I'm in California for the next two weeks, so I'll try to help out as much as I can.

- I re-ran some 1D radiative shock models, reformatted the data, and sent it to Pat. Hopefully, that is all he needs, but if he needs more I can probably do any additional work for this fairly quickly when I get back.

# Meeting update

Here is the new Jeans instability calculation of the growth rate

- periodic boundary conditions, both physical and elliptical
- using expressions given here: https://astrobear.pas.rochester.edu/trac/astrobear/wiki/u/erica/JeansTest
- tfinal = 5 e-folding times
- isothermal EOS

I see that the code reproduces the growth rate well up until ~4 e-folding times. But by 5 e-folding times, the difference is ~10% in the perturbation. This is much better than it's been: https://astrobear.pas.rochester.edu/trac/astrobear/blog/erica06262013

I could fidget around with the code a bit more, if necessary - Is this good enough for a test of self-gravity for the paper?

Also, here are fun plots showing the velocity and density perturbations on the same graph

t = 0:

Vx is in red, rho is in green. The density peaks at the zero's of Cos(kx). E.g., a local max is at 1. The vx perturbation is a Sin(x) function, and it has minima that corresponds with the density maxima. This produces converging flows at the max in density, as you would expect you need to develop the Jeans instability.

t = tfinal:

By the end of the sim, the density perturbation has grown a little, but velocity has grown a lot.

# Meeting Update 7/23/13 -Erini

- polytrope wiki current version u/Polytropes

- I have been working on my ticket #303

- I had some confusion in terms of various global.data parameters that I have cleaned through, thus the following two gifs represent my issues

n=3 res:80^3 comp cell size: 2's - notice the asymmetry n=1.5 res:80^3 comp cell size: 2's

-beginning to think that some of the issues might actually be with the numerics http://adsabs.harvard.edu/full/2000PASJ...52..217H

Horedt lists that the density ratio is a dependent criteria in the stability equation for embedded polytropes - perhaps the density ratio being used is too high, e-mailed prof blackman and perhaps he can provide some insight on the usefulness of the paper

# Meeting Update 0723

- Attended PPVI meeting. The poster is very successful, also talked to many colleagues.

- Received Kraken token from NICS. I've sent out the activation form, the newly allocated hours can be used for the Triggering project once my account is activated.

- Met with LLE folks. Currently working on merging the diffusion solver with AstroBEAR 3.0 of which the tested in dev version I just received from Baowei.

- Chris Mckee mentioned to me his earlier Triggering work with Nakamura. He was talking about this 2005 paper:

http://arxiv.org/pdf/astro-ph/0511016v1.pdf

It has some interesting points. I may do a journal club presentation on it in the coming weeks.

- Meetings before the end of this year?

# Meeting Update July 23

- All of the basic runs for the PN page are done!
- Added two new sections to the planetary nebulae wiki page
- Trying to figure out what could be the cause of the "bubbles" in the MHD runs
- Trying different parameters for the torus case, as it seems to be very similar to the constant ambient.

# Meeting Update 07/23/2013 - Dan

I've been trying to fix the problem of my star not being in hydro static equilibrium. I tried the HydroStaticStar module in the latest AstroBEAR and it worked until I tried adding a sink particle.

No Sink Particle | Sink Particle |
---|---|

Martin's code ran on bluehive and needed more time so it's now running with more time. I've also started writing reports for the REU program.

# Meeting Update 07/23/2013 -- Baowei

- Tickets

- Users
- Met with LLE folks: will merge AstroBEAR3.0 with Shule's work and give to Rui
- Ian installed AstroBEAR2.0 on Pleiades. Asked for reference.
- Gave Bruce the materials he needed for Teragrid proposal

- Resources
- Computing time: Kraken old grant 51% (585,530 SUs) remaining, new grant %100 (3,422,821 SUs) remaining, Stampede 15%(65,694 SUs) remaining. Update the page https://astrobear.pas.rochester.edu/trac/astrobear/wiki/ProjectRuns
- Archive the data: local machines are pretty full. For the first archiving, move to bluehive and zip the data files there?

- Code management
- AstroBEAR3.0 is on its way and will pull into the current scrambler folder
- current scrambler will move to branch 2.0

# Meeting Update 07/23/2013 Zhuo

- Finished programming complete Riemann solver, it is correct.
- attended HEDP summer school, discovered a lot of fun in fusion technology, high energy density physics, astrophysics and computational science.

# Convert animated gif file to videos on bamboo

- Command lines converting animated gif to different video formats

Example: : gif —Eddie's 2.5D emission Jets

New formats: avi, mp4, mov, mpeg/mpg

- Convert
**gif**to**jpg**files firstconvert old.gif old%05d.jpg

- Convert
**jpg**files to**avi**avconv -i old-%d.jpg new.avi

- Convert
**avi**to**mp4**,**mov**avconv -i new.avi new.mp4 avconv -i new.avi new.mov

- Convert
**mp4**to**mpeg/mpg**

# Meeting Update 07/15/2013 Zhuo

- I will leave for OSU to attend HEDP summer school from July 14th - July 20th
- I have finished programming Riemann solver, i.e. 1D shock tube. It is correct. But I did not consider the vacuum case.

# Fixing latex tags

Thought this might be handy if we ever want to do any batch editing of wiki pages.

#!/bin/bash for i in `trac-admin ./ wiki list | tail -n +4 | head -n -1 | awk -F ' ' '{print $1}'` do trac-admin ./ wiki export $i | perl -pe 's/\[\[latex\(([^\$])(.*?)\)]]/\[\[latex\(\$$1$2\$\)]]/g' | trac-admin ./ wiki import $i done

It basically selects all of the wiki pages and then parses them through a perl regex parser that replaces

[[latex($<some stuff>$)]]

with

[[latex($<some stuff>$)]]

but leaves

[[latex($<some_otherstuff>$)]]

alone. This should fix most things - though it may miss things like

[[latex($ $a=b$$)]]

And here is a script for batch-editing blog posts. Since the blog posts are managed through a plugin they have their own table - and trac-admin does not provide any easy front end… So you should only modify the trac database after shutting down the web server.

#!/bin/bash #make sure to shut down wiki server sqlite3 db/trac.db << EOF .out fullblog_dump .dump fullblog_posts .exit EOF perl -p -i -e 's/\[\[latex\(([^\$])(.*?)\)]]/\[\[latex\(\$$1$2\$\)]]/g' fullblog_dump sqlite3 db/trac.db << EOF DROP TABLE fullblog_posts; .read fullblog_dump .exit EOF

This will unfortunately modify this blog post as well

# PPVI poster

Final revision of PPVI poster (attached).

# Poster

Attached to this blog post

# Journal Club Meeting 0709

**Agenda**

In this week's journal club, we'll have:

- Discuss the poster format.

http://www.pas.rochester.edu/~shuleli/tsf_project/poster.pdf

- Adam discussing a paper.

http://adsabs.harvard.edu/abs/2012ApJ...747...22H

http://adsabs.harvard.edu/abs/2010ApJ...709...27W

http://adsabs.harvard.edu/abs/2010ApJ...720L..26L

- Jonathan's post on evanescent solutions to self-gravity:

https://astrobear.pas.rochester.edu/trac/astrobear/blog/johannjc07042013

# Procedures for backing up your data

- Procedures for backing up your old computing data
- create a folder on /media/tmp070813 and name it with username_date. For example:
**bliu_07092013** **MOVE — NOT COPY**the data you want to back up to the folder you created- Make detailed notes about what these data are and save it as username_date.txt. For example:
**bliu_07092013.txt** - I will tar these data to the 4TB hard drive once everybody is done moving their data. And I will clean everything on /media/tmp070813 after that.
- Old data will be backed-up & cleaned
**twice**every year. Our first backup date is**Aug 1st 2013**

- create a folder on /media/tmp070813 and name it with username_date. For example:

**
**

# Meeting Update July 8

My project for the last week has been writing scripts to run/make movies of all of the planetary nebulae cases at once.

- Still working on getting the make movies part to work properly.
- This will be useful when testing how changing one parameter will affect all of the runs/ make organization a lot easier.

MHD is now working, there is a new table for it at the bottom of the PN Page.

# Shock triggered star formation rotational vs nonrotatinoal, different mach

We have the following runs:

Krumholz accretion:

Mach = 1.5: non-rotational (case NR), rotation axis along the shock normal (case RA), rotation axis perp to shock normal (case RP). For the rotational cases, K = Omega*tff = 0.1.

Mach = 3.16: non-rotational

Federrath accretion:

Mach = 1.5, 2.5, 3.16 non-rotational

Mach = 1.5, beta = 4 magnetized (field perpendicular to shock normal)

The shock compression phase prior to the formation of the star all look very similar. The initial formation of the star is at about 2 cloud crushing time for Mach = 1.5, 1.6 cloud crushing time for Mach = 3.16. Initially, the cloud with a newly formed star embedded looks like this:

For Mach = 1.5, different rotation cases at 2 crushing time:

For Mach = 1.5, different rotation cases at 2.5 crushing time:

For Mach = 1.5, different rotation cases at 3.6 crushing time:

Comparison of Star Mass evolution for different rotations:

Comparison of Accretion Rate for different rotations:

Comparison of Wind Material Mixing evolution for different rotations:

**Movies**

case NR:see previous post

case RA:

http://www.pas.rochester.edu/~shuleli/tsf_project/tsf_rot1.gif

case RP:

http://www.pas.rochester.edu/~shuleli/tsf_project/tsf_rot2.gif

Mach = 3.16:

http://www.pas.rochester.edu/~shuleli/tsf_project/mach3.gif

Mach = 1.5, K = 1 (lateral expansion too strong to be contained by the shock):

http://www.pas.rochester.edu/~shuleli/tsf_project/K1.gif

Comparison of Star Mass evolution for different Mach:

Comparison of Accretion Rate for different Mach:

Comparison of Wind Material Mixing evolution for different Mach:

# Meeting Update 07/08/2013

Did some runs of the HS disk with a de-resolved center. The red line is the accretion rate for the disk in HS equilibrium with an ambient. The other lines are the accretion rates but when the density of the ambient is an order of magnitude less then the previous line. The red curve has an accretion rate of about .0019 solar masses/yr and the green one has .00748 solar masses/yr, both of these are taken from the 40th cycle and onward.

There are also a few videos (mpeg) attached showing the density and radial flux during a run.

I've also did a small run with the wind driven disk on bluehive, but need to increase the bounds of it to be able to see anything.

# Meeting Update 07/08/2013 - Eddie

Just got back into the swing of things today, so not much to report in terms of results. Here's where I'm at now with my various projects:

### Pulsed Jets Paper

The paper is coming along fine. I can only work on the 2.5D parts, since the 3D runs are still blowing up.

### 3D Jets (precessing)

Implemented a precessing injection velocity and tried running a few simulations. I have low resolution runs for theta = 3 and 1 deg. The precessing period is 1/3 of the pulsation period. The resolution is 24 x 120 x 24 + 1.

I tried a higher resolution (3 levels) on kraken for theta = 2, 1, and 0.1 deg, but they failed to complete. I backed down to 2 levels and am trying the theta = 1 deg run again.

### 3D Jets (testing minimum temperature)

At the meeting two weeks ago, Jonathan mentioned that some of my simulations had these "flashes" in the temperature plot. We suspected it might be pressure protections, so I tried a run where I increased the minimum temperature. That run completed and the data is on Kraken waiting to be visualized.

### 3D Jets (fixing the explosions)

We still don't know for sure what caused the explosions, but we've seen some interesting grid effects at the injection boundary. Today and tomorrow, I am going to implement a sub-sampling routine into my problem module. This should be a much more accurate way of initializing radial profiles on a Cartesian grid.

### 3D Jets (colliding)

We heard back from Sergei and Andrea, and they are going to give me some initial parameters soon that I can use to run some comparable simulations.

### 1D Radiative Shocks

Just got an email from Pat today. He needs the data in a specific format to make plots, so I will work on reproducing that stuff for him soon.

# Meeting Update 07/08/2013 Zhuo

- I know what is chapter 1-4 of Riemann Solver talking about now, and I roughly know the flow chart of shock tube problem program.
- Learnt how to write f90 program, I can use f90 now.
- Ran several CorotatingBinary on bluehive, the density at stationary point is higher than the companion which is not very reasonable.

# Meeting update for 07/08/2013

- Reformatted poster. Adam - does this look ok?
- Modified open mp calls to launch 1 to split threads once per grid update. Line label refers to the total number of threads in use per node. The solid lines are times for forking the threads at every do loop - while the dotted lines are times for 1 fork at the start of a grid update.

# Meeting update

Last week was spent revising the paper and designing my poster. I am trying to get the poster ready in the next day or so, but am having difficulty with the template Shule sent out. I can't get it to compile without a load of errors, and the .dvi is a crumpled mess of text. I am hoping to get some help with this today or tomorrow so to expedite things. Once this is done, I'd like to finish up the Jeans code this week before leaving town for PPVI.

# Meeting Update 07/08/2013 -- Baowei

- Tickets

- Users
- Trying to arrange a meeting with LLE
- Wrote to Ian

- Storage issue/Equipment
- Working with Dave to get 1 TB extra space on bamboo for Shule to move his stuff to local: /media/tmp070813/ on bamboo
- Looking for an easy way to back up the data to the new 4TB harddrive
- Poster tubes have been shipped to Adam. Hopefully will get them before Friday.

# Thinking about evanescent solutions to self-gravity...

So we start with the linearized differential equations

which we Fourier transform in physical space and solve the third equation for

and substitute it into the second.which gives us a matrix equation for the time evolution operator. Now we just need to find eigenvalues and eigenvectors.

The characteristic equation is

and we have

with eigen vectors

However given the presence of self-gravity we see that

can be real as well as imaginary.So for stable waves we have

where is real and positive. And there are two solutions… (a left and right going gravity-modified sound wave. Gravo-accoustic modes)And if

where is real - then we have two solutions as well.these correspond to an exponentially increasing collapse and an exponentially decreasing decay (which is just the time reversed version of the 1st) Note the velocity field is phase shifted.

# Journal Club Meeting 0702

**Agenda**

- Computation resources.

- Kraken (old grant):
**1,138,234 SUs**, 923,481 SUs remaining - Kraken (new grant):
**3,422,821 SUs**, 3,422,821 SUs remaining - Stampede:
**416,000 SUs**, 65,694 SUs remaining

https://astrobear.pas.rochester.edu/trac/astrobear/wiki/ProjectRuns

- Discuss sink particle in the code:

Federrath (section 2):

http://arxiv.org/pdf/1001.4456v2.pdf

Krumholz (section 2.2 to 2.4):

http://www.ucolick.org/~krumholz/papers/krumholz04.pdf

- Adam's talk.

# Meeting Update July 1

- Been working on adding MHD, lots of new things to learn!
- Module will compile, but gives errors when trying to run MHD…still works with all of the hydro runs
- Re-ran all of the hydro runs with most current version of module
- VisIt is being buggy. Apparently we don't usually run VisIt on bluehive? Trying to figure out how to get it to work locally

The compute engine running on hay.pas.rochester.edu has exited abnormally. Shortly thereafter, the following occured... VisIt could not find a compute engine to use for the plot on host hay.pas.rochester.edu. VisIt will try to launch a compute engine on that host.

- The Planetary Nebula page looks a little prettier now.

# Erini - Meeting Update - July 1st 2013

- updated a couple of wiki pages LE_Module

- polytrope is on grid

- Parameters:

grid resolution: 64 cubed

domain: -2d0 -2d0 2d0 2d0 2d0

final times used: (.001, .01)

frames used: (10,20)

timescale: 7655157.60438493

→ so for the .01 final time, we have 76551.57…yikes too small

→ so for the .01 t final time and 20 frames case we get the following

# Meeting update

- Working through some 2D theory/numerics on Euler equations

- Working through Jeans instability mods. Updates soon. Trying to get the right form of the perturbation expressions, as well as debugging

# Meeting Update 07/01/2013 -- Baowei

- Tickets
- New: #294(Refinement Artifacts), #295(Global Co-rotating Frame module stops running), #296(Self-Gravity Needs Investigation), #297(code terminates on Kraken immediately after starting when self gravity is turned on), #298(Problem running on Bluehive), #299(astrobear successfully compiled on bluehive but can't run by using PBS)
- Closed: #293(Problem running Hydro Static Disk)

- Users
- Ian: Install AstroBEAR on Pleiades

- Equipment
- Got the hard drive dock + 4TB hard disk.