Martin's update, 4 Feb '13
CRL 618 paper submitted!!!
Poloidal collimation. Running the latest sims suggested by Andrea, where the BC force field lines to remain vertical (vr=0) at the bottom of the domain.
| Lines in this sim are bent but keep their end points free. Different from previous runs (https://clover.pas.rochester.edu/trac/astrobear/blog/poloidalCollimation) |
|
| The above set up plus fixing Bzboundary seems to show the most bent lines. |
|
Arbitrary EOS update
I have successfully moved nearly all references to gamma to the EOS module - and all uses of pressure get the pressure from the press functions which can be modified to handle arbitrary EOS.
Now I just need to modify the Riemann solvers to handle an arbitrary EOS - or build a new one.
- For hydrodynamics, the riemann problem has three waves
- left shock/rarefaction
- entropy/contact
- right shock/rarefaction
- Neither the pressure nor velocity changes across the entropy/contact wave, so we can define a p* and u* that connects to the left state across a shock/rarefaction and to the right state across a shock/rarefaction. We can calculate dP*/du* so that newton rhapson iteration can be used.
For arbitrary EOS, there are now two difficulties.
- First, since the density can change across the contact, we know have two more unknowns gamma*L and gamma*R and two more equations which must go into the solution.
- And we no longer can easily calculate dP*/du* so we must resort to the secant method.
The two new equations are
where
Unfortunately the above solution is designed around the exact Riemann solver - which does not work with MHD. What about approximate Riemann solvers like the HLL?
The HLL method does not require the solution for the pressure in the star region - but just uses the conservation law and the assumption of a constant uniform state between the left and right waves.
Then integrating around the entire volume we have
And then integrating around the right half we have
Or the left half
which we can solve F*
so the only modification would be in estimating the wave speeds - but this can be done using the sound speed (or fast speed) in the left and right states - so only modification would be to calculation of sound speed. Seems very straight forward.
What about the HLLC? Once we have U* from the HLL we can estimate the speed of the contact
and then the jump conditions can be solved for p* from either the right or left as:
which then give everything else - from jump conditions. No EOS assumed
What about HLLD? Same basic principle - everything derives from jump conditions… Should be trivial to modify all of these HLL type solvers to work with arbitrary EOS.
Science Outreach Update
I just met with April Luehmann about science outreach. Here is a distilled version of what I learned:
- The university does not have a centralized structure, and so many departments are disconnected and not well communicated. Any push for an outreach program between departments are usually made and then dissolve once group members change or move on.
- No science outreach department in the University
- April is the PI on research for scientific teaching. She has a group of doctoral students of varied research focus: girls in science, underprivileged urban students, technology in the classroom, neuroscience and psychology, etc. all with the main objective of teaching science in revolutionary (not limited to traditional methods) ways to students that need help.
- In the summer there are 2 sessions she oversees: A) prepares masters students for teaching science, B) has masters students teach students; students are from East High school and Freedom school.
- In the Fall and Spring semesters, there is an after school club called the Science STARS (Students Tackling Authentic and Relevant Science) at East High. This is an NSF funded effort to get girls involved in science. Here is the page discussing the grant and program: http://www.rochester.edu/news/show.php?id=3941.
- Throughout the academic year, the STARS leaders engage/mentor/hang out with the students.
Where do we fit into this model? Well, instead of starting up our own science outreach program (time, money, lots of effort to get connected to local schools), we can piggy back off of April's program. This means potentially the following a) this semester taking the kids to planetarium or out star observing with a telescope (I volunteered to do this with April), b) in April/May, we as a larger group can organize with April mini-lessons with the students, c) I may participate in research meetings with April's team occasionally, d) I may attend a few of her lessons in the summer session A on science teaching (and could distill information to the rest of the group).
2.5D Pulsed Jet Runs
My initial thought to inject a jet was to have a velocity profile that decreases with increasing radius, and have pressure and magnetic field be constant inside the jet. However, I decided to try it a different way following Lind 1998. They keep the jet velocity constant, and give the pressure and magnetic field a radial profile. Here is a first try at the run with very strong magnetic field (707.11 uG). I also changed the size of the grid to see more of the evolution of the jet.
Meeting Update Jan.28
- Did magneto-thermal instability runs to test implicit solver in astrobear. The magnetic pressure profile at 1 computational time (corresponding to 200 sound crossing time) is shown below.
- Made resistivity documentation page. The final section, "how to turn on resistivity" could be moved into user's guide. I'll make similar pages for viscosity and thermal conduction this week.
- Done revising the poster for the Cancun meeting.
Meeting update
- Meeting with April Luehmann this week for coffee to discuss possibilities for science outreach. April is a Professor at the Warner School in science education. She does research in and guides science outreach programs.
- Toro can't be copied by the UR copy center due to copy rights. I am looking into printing off some copies from an online source.
- https://clover.pas.rochester.edu/trac/astrobear/wiki/Tutorials - Added page on aasTex tips
- From the Uni's IT desk, have the following options for film production services:
Steve Fasone and two part-time professional staff based out of the Med Center, Rate: $50 per hour. They charge for the duration of the event plus 1 hour to account for prep, setup and strike. A DVD camera original is included. Additional copies, editing (such as adding titles) add additional charges. They provide other services outside of production, including: editing; graphics; dvd & cd authoring; creating web-friendly assets; duplication; print graphics; packaging; captioning (in the form of DVD subtitles, open-captions as part of the video, or web captions).Contact: Steve Fasone at steve_fasone@urmc.rochester.edu or 585-275-2540
Undergraduate Film Council: Rate: $20-25 per hour, depending on the amount of equipment needed to service the event. Contact: sstewar9@u.rochester.edu
and, URTV: Base fee: 25 per hour labor/equipment fee for additional services as needed. DVD production fee: $7 per DVD (please allow 2-3 weeks for processing). Contact: URTVmail@gmail.com
- Working on my paper, made headway with embedding figures (previous post on how to do convert to .eps formats efficiently with the software I was using), and on my methods/results section: https://clover.pas.rochester.edu/trac/astrobear/wiki/u/u/erica/BEPaper
Meeting Update - Jason and Ivan 0128
- Used remaining hours on Kraken to run a 3 Jupiter Mass sim for 4 orbits (no more time is available !)
- Still working on sim plots.
- Introduced AstroBEAR to Andrew, we are going to meet up again on Wednesday.
Meeting Update 01/28/2013 -- Baowei
- Users
- New users: Give the latest revision code to Tony Piro and Christian Ott from Caltech
- Yan asked questions about visit
- Wiki: tried to install AccountManagement plugins but failed
- Following writing your own problem module, worked on build modules: https://clover.pas.rochester.edu/trac/astrobear/blog/bliu01222013
- Working on testing and checking in 2D MUSCL code and installing AstroBEAR on Stampede
Meeting Update 1/28/2013
- Magnetized Colliding Flow run on BlueStreak running well after successful restart
- Worked on writing your own problem module and updated information on using magnetic fields
- Consolidating operations dealing with equation of state to EOS module - updated riemann solvers to use same ordering as Info%q (rho, p, E) instead of (rho, E, p) so that many of the same routines don't need to be duplicated.
- Plans for this week
- Scaling tests on Kraken for proposal
- Work on developer's guide as well as other wiki projects
- implement tabulated EOS
- Start on FLD solver
Meeting Update: Monday January 28, 2013
Have ruby framework for modifying existing module, compiling and running automatically.
Next I will learn how to write/run Visit scripts for automatic plotting.
Meeting Update 01/28/2013 - Eddie
1D Rad Shocks
Done with formatting plots for 1D radiative shock runs. Some of the models don't look quite right, so I have to investigate a little further as to why. Hopefully, it's just a plotting issue where I will have to adjust the yrange in gnuplot and perhaps the length scale of the simulation. Here are some examples (v=30 km/s, n=100 cm-3):
| B (uG) | Hydro Variables | Emission Lines |
|---|---|---|
| 1 | |
|
| 30 | |
|
2.5D Pulsed Jets
Coding and initial runs for the 2.5D pulsed jets are finished. Here are the parameters and a few movies of the H-alpha emission. Since AMR is on, the H-alpha emission calculated for each cell is multiplied by the cell area. The magnetic field is helical.
| Density (cm-3) | Velocity (km/s) | Temperature (K) | |
|---|---|---|---|
| Ambient | 500 | 0 | 8000 |
| Jet | 5000 | 60 (initial), 20-100 (random pulses) | 10000 |
| B (uG) | Image (frame 80) | movie |
|---|---|---|
| 7.07 | | Halpha_b7.gif |
| 21.21 | | Halpha_b21.gif |
| 70.71 | | Halpha_b70.gif |
| 212.13 | | Halpha_b212.gif |
| 707.11 | | Halpha_b707.gif |
Documentation
Had a documentation meeting last Friday (ehansen01252013) to discuss new group organization and updates that still need to be done for the wiki. Will make a more detailed table of things that need to be done and who should be doing them.
Documentation Meeting - 01/25/2013
Last Time
- Jonathan's post from last time: johannjc01092013
User Guide
- Erica's new user's guide: UserGuide
Teams and Leaders
- new group organization: Teams
Blog Categories
- cleaned up some of the redundant/unnecessary blog categories. Using these will be nice for team meetings. Is there a way to have a drop down menu of the most commonly used categories (say top 5) when creating a new post?
Discussion Plugin
- discussion plugin is not working at the moment, but I had also cleaned that up and there is a newer forum (created by Erica) for discussing wiki documentation.
To-Do List
| Task | Member |
|---|---|
| Update objects pages | Eddie |
| Update specifics within User Guide | Eddie, Erica |
| Update multi-physics pages | Shule, Eddie |
| Debug Team Page | Baowei |
| Education Team Page | Erica |
| Development Team Page | Jonathan |
| Organize Developer Guide | Jonathan |
Martin's update, 28 Jan '13
CRL618. I sent Section 4 (numerics) of the paper back to Bruce.
Poloidal Collimation. Talked to Andrea Ciardi, we discussed about new BC (more resolution, vr=0) for the sim,
https://clover.pas.rochester.edu/trac/astrobear/blog/poloidalCollimation
Saving a .eps image from libre calc in libre draw --
Found this in the forum: http://ask.libreoffice.org/en/question/37/how-do-i-export-a-chart-in-an-image-format-from/ and it was super duper helpful.
- In Calc, left-click once on the chart to select it.
- Right-click and select "Position and Size…"
- Write down the values of Width and Height for the chart.
- Open a new drawing in Draw (from Calc select File > New > Drawing).
- In Draw, select Format > Page…, and set all margins to zero. Then, in the Paper Format section, select "user" as Format, and set the page Width and Height to the values of the chart.
- Go to the Calc window, select the chart and copy it.
- Go back to the Draw window and paste the chart. It should occupy the whole page.
- Now you can export the drawing (File > Export…) to several different formats. You can even choose a vector format if that is the best option for later use.
Build Problem Module
Following the User Guide: https://clover.pas.rochester.edu/trac/astrobear/wiki/ModulesOnAstroBear , I built two problem modules
- Simple Clump Module (with objects)
- Documentation is very clear and easy to follow. The code is straightforward — maybe need a little bit background knowledge: Ghost zones (Parallel programming), gamma7=1.0/(gamma-1)(Energy and pressure relations), Namelist (Fortran) and data files
- code compiled with AstroBEAR
- Need to update the "problem.data" from template to get it run — with "rho=, radius=, velocity=…."
- data files for user to try and run?
- Result:ClumpMovie_0AMR
- Simple Clump Module (without objects)
- Result with 4 nodes: Result:ClumpOld_0AMR
- Result with 4 nodes: Result:ClumpOld_0AMR
- RTInstability
- Fixed grids: Movie_NoAMR
- 1 level AMR: Movie1LevelAMR
- Fixed grids: Movie_NoAMR
- Clump with Toroidal magnetic field
- Result:rhoBxMovie
- Result:rhoBxMovie
- Clump with Rotation
Martin's update, 21 Jan '13
Binary disks working on Noam's corrections. Finished with all fast corrections. Missing:
- specific angular momentum
- ram pressure stripping
- impact parameter
http://www.pas.rochester.edu/~martinhe/disk.pdf
CRL618 got comments back from Bruce, and will have a chat today or tomorrow. Paper very close to publications, he says.
Poloidal collimation, will have a skype call with Andrea soon.
Meeting Update: Monday January 21, 2013
- Created singleton classes for data files in template module:
- GlobalData.rb
- PhysicsData.rb
- ProblemData.rb
- ScalesData.rb
- SolverData.rb
- Each class can have one instance.
- <file>.data is written automatically when a change is made to any instance variable.
- The instance variables will be modified by the user through a GUI or simple interface.
- Example
Code highlighting:
#ProblemData.rb
require 'singleton'
class ProblemData
include Singleton
def self.attr_accessor(*names)
names.each { |name|
module_eval %Q{
attr_reader :#{name}
def #{name}= (value)
@#{name} = value
self.print
end
}
}
end
attr_accessor :density, :pressure, :velocity
def initialize
@density = 1
@pressure = 1
@velocity = [0,0,0]
self.print
end
def print(filename="problem.data")
File.new(filename,"w").puts %Q{
&AmbientData
density = #{@density}
pressure = #{@pressure}
velocity = #{@velocity.join(",")}
/
}
end
end
Meeting Update 01/21/2013 - Eddie
- I finished the script that automatically runs astrobear through the entire parameter space for my 1D radiative shocks AND creates the plots. It is kind of awesome that I can do 87 runs and 2 plots per run in about an hour.
- The plots of the higher shock velocities do not look as good. It might be that it takes a couple of more cells to resolve the shock, but I want to investigate a bit to make sure the shock is steady.
- I will finish coding and start running the 2.5D pulsed jet today and tomorrow. Expect images later this week.
- I did a little bit of work on documentation for the wiki. Mostly just moving/renaming a few pages and creating teams and leaders. Should have a documentation meeting later this week.
Meeting Update Jan.21
Made movies for Gianluca's visit. Resistive images Here's a list for paper figures:
- density cut-through with field lines (black&white and color)
- field pressure cut-through (normalized to the initial field pressure therefore tells us amplification)
- total field energy evolution line plot (tells whether the stretching amplification dominates or field diffusion dominates?)
- bright spot: maximum field pressure amplification line plot (corresponding to Gianluca's Zeeman measuring idea)
submitted a set of jobs that test fixed grid thermal conduction in 3D by running 3D RT instability. The cases and domain resolutions are:
| non-conductive | weakly conductive | strongly conductive |
| 32*32*160 | 32*32*160 | 32*32*160 |
| 64*64*320 | 64*64*320 | 64*64*320 |
| 128*128*640 | 128*128*640 | 128*128*640 |
Each simulation contains 1 wavelength on x and y direction, 5 wavelengths on z direction. This set of simulations will be run on bluehive 64 cores.
Finished the Cancun poster:
poster
They informed me that they have put me on the waiting list for oral presentation in case someone withdrawing. So I also prepared a ppt for the oral presentation. The talk is likely to be twice as long as the HEDLA one so I added more stuff from the clump paper (instabilities, magnetic field and mixing ratio evolution, mathematical modeling).
Meeting update
I have updated the figures with colors and in units of sound crossing time for the various BE runs. Also, have been reading for ApJ submission stuff - found some helpful sources will post on the wiki later today. Couldn't find anything on naming sections on the official submission websites — any criterion here? Last week I read chapter 5 in Toro, too. https://clover.pas.rochester.edu/trac/astrobear/wiki/u/erica/BERunsFigures
Meeting Update 1/21/2013
Worked with Christine in setting up her problem module.
- Uses AmbientObjects, DiskObjects, RefinementObjects, ProjectionObjects, ProfileObjects, and implements the stream the ol' fashioned way - though we may want to make a StreamObjects or a JetObjects to do 'jets' from a boundary.
- Ran into problems with the boundaries due to cooling time scales being short and DM Cooling has no equilibrium temps.
- Solution was to have very high density contrast between disk (1e-7 g/cc) and outer edge of ambient (1e-20 g/cc).
- Also wanted to have hydrostatic equilibrium without requiring temperature extremes - so set up isothermal solution…
- First we added a constant pressure to p_inf to get the desired pressure at the disk edge - but since the density changes, this makes the ambient no longer isothermal.
- IF we try to solve for to give pressure matching at the disk edge we end up with a transcendental equation
- If instead we fix T or and solve for we get an easier equation to solve.
Meeting Update 01/21/2013 -- Baowei
- Trac backup & Blue Streak Queue
- Trac backup got conflicts with the new NameTag plugin which is required by Discussion. Trac backup back to normal after the plugin was removed but the forum is down.
- Blue Streak queue system works now ?
- MUSCL and sweep schemes in AstroBEAR presentation
- Working on moving from Ranger to Stampede (#273)
Meeting Update - Jason and Ivan 0121
I've worked on a few plots yesterday (plots), radial measurements of density and temperatures, I need to discuss them in detail with Jason.
I am meeting with Andrew Lipnicky on Wednesday and introducing the code to him.
Andrew will probably need access to the repository to download new AstroBEAR revisions in the future.
The search for amino acids in space
If it can be here, does that implicate an affinity for connectedness and purpose? If amino acids here are the building blocks of DNA and hence life, do they possess a natural affinity for this elsewhere?
Teams and Leaders
This table also has its own page at Teams. There are now team pages for each team where the leaders can organize useful long-term information. Information for meetings will probably still be handled by the blog, but it's up to the leader to decide how he/she wants to use their team page.
| Team | Leader | Description |
|---|---|---|
| Documentation | Eddie | review updated wiki pages, discuss outdated sections and organizational issues |
| Debug | Baowei/Martin | tickets: review closed, check progress of active, assign new. tests: check current, discuss need for new |
| Development | Jonathan/Shule | check status of enhancements in progress, discuss new ideas and what changed in recent code revisions |
| Education | Erica | code mini-lessons, seminal paper discussions, community outreach |
Meeting Update: Monday January 14, 2013
- Familiarized with contents of global.data (with Erica's help)
- Thoughts for GUI
- Choose existing module
- Set up directory on host machine where code can be modified through web GUI
- Compiled, run, and plotted on web host
- Images or videos are then served to browser
- Set up directory on host machine where code can be modified through web GUI
- Choose existing module
- Ruby on rails ?
- Existing U of R "Webwork" server ?
- Barebones server (starting from something I wrote) ?
Meeting Update Jan.14
Not much to update since I was visiting relatives/traveling most of the time last week. Here's a recap on where I'm at for the ongoing projects.
Heat conduction solver: The conduction front and RT(not quantitative) tests are done. 3D compatibility is added. Next up is a 3D RT test to check the things I've added. After that, our collaborators can step in and play with the code on their own problems. Remaining task is putting in 1D compatibility (probably not relevant for the collaboration, but good to have). I will also touch base with Jonathan about the heat flux conservation routine he suggested me to add.
Triggered star formation: Last time I got a stable cloud with 1/100 pc in radius and 1 solar mass. I will submit some jobs with this cloud + shock to bluestreak this week.
Resistive clump: I'm currently preparing the first draft. For this week, I will make a short presentation from the draft (several pages pdf) for Gianluca's visit.
Meeting Update 01/14/13 - Eddie
1D MHD Radiative Shocks
I made some modifications to my problem module and generated some plots with my gnuplot script. Every run that I do will have these two plots (or something very close to these). The first is of the hydro variables: log(number density), log(temperature), and ionization fraction. The second is emission lines. Pat gave me some useful feedback, so I just have to tweak these a bit.
I already made the hydro plot look much better. I instead plotted computational number density and temperature, and I made the y-axis a log scale.
Wiki Documentation
We had a useful meeting last week about wiki organization and documentation. Erica has already made significant progress on the User Guide. I have only done a few minor things, but I will be in charge of updating some introductory things within the User Guide, as well as object pages and multiphysics pages.
We briefly discussed the possibility of having leaders and/or teams. We might not necessarily need teams if everyone is part of every team. However, I think it would be useful to have a leader to run a meeting maybe every other week or once a month. This format would also work for debugging, code development, public relations, etc.
Martin's update, 14 Jan '13
Binary formed disks Will work on the referee's comments this week.
CRL 618 Wrote the "methodology, implementation and results" part of section 4 in the paper, and sent it back to Bruce. He seemed happy with the text and said he will work with it.
HELDA Did some more referee corrections (the second round !!!) to the proceedings, sent them back to the editor, and they finally got accepted.
AGN Finished the proceedings for the Milan meeting (http://www.pas.rochester.edu/~martinhe/2012/AGNprocs.pdf), which I'll submit and post in astro-ph. Also implementing the new MHD runs.
Poloidal collimation. Waiting for Andrea's comments on the latest sim. Produced 3D renderings for the Nature paper (https://clover.pas.rochester.edu/trac/astrobear/blog/poloidalCollimation, bottom).
Meeting update
I began typing up the paper in Latex. This was a bit of a learning experience, but seems to be fine now- progress here: http://www.pas.rochester.edu/~erica/BEsphere
There were some things I learned about getting images in the correct form for an ApJ draft, and posted on a previous wiki.
Worked on New Users stuff, like organizing the User's Guide, etc. It still needs to be edited I think— it can be smoother and cleaner than it is already. Other things on my plate as far documentation: FAQ, Discussion Boards, Additional Physics.. Also - what is the New User's lesson plan - should they be directed to go through the user's guide in order (I think this is best).. Do we want to re-arrange the tree-structure in the wiki by renaming pages accordingly?
In other news, I am reading the Gudonov chapter in Toro now.
Jason and Ivan - Meeting Update 0114
Came back from the AAS meeting!
Resuming analysis of Kraken runs today.
Should make a blog post on new plots towards the end of the week.
Meeting Update 01/14/2013 -- Baowei
- Wiki & Machines
- wiki documentation
- Trac backup failing
- Blue Streak: currently has issues with job submitting and scheduling
- 2D: nan errors and segmentation fault, working on it …..
- working on 1D Euler Solver with MUSCL Scheme (Sod Shock Tube, Lax-Friedrichs / Riemann solver for fluxes):
Meeting update 1/13/2013
PPM now converges to 3rd order using the new less-restrictive limiters.
Still getting oscillations in BrioWu Shock tube
Not sure what is going on - though probably not a bug with PPM - as that would ruin convergence.
Christina's run
Went 20 or so frames during the 24 hour reservation on bluestreak without difficulties. System has been down - so I've been unable to restart and run further.
FLD
Still waiting on working implicit thermal diff solver…
Things to do:
- Try to nail down source of oscillations in BrioWu shock tube
- Continue to work on documentation issues (Props to Erica for New Users Guide)
- Write up basic differences between directional split schemes (ie MUSCL-Hancock) with unsplit schemes (ie CTU) and the use of the Sweep algorithm to do unsplit updates for developer's guide and to go over briefly at next week's group meeting?
- Work with Christine to setup problem module
A new user's perspective
So after talking with Jake it seems like the following need improvement for the New User:
-A big picture summary of astrobear would be nice to start the absolute new user off (computational domain, cell-centered fluid variables, spatio/temporal solution of Euler equations, data files, refinement, objects, etc)
-Setting up the mesh manually in the "writing your module" page, i.e. coding up the domain and a shape to put within it manually
-Then doing the same thing but this time with the ambient object and shapes
Also, should the new user ALWAYS go through chs 1-4 sequentially? As for Jake, he skipped to Ch.4 - Writing your own module, and as such, I think it hurt his intuition and understanding of the code. I think it would be best for everyone to go through the basics of compiling, running, visualization, data files first before writing a module. Else, it could be really unclear what the module's purpose is. .
Schedule of topics for Christine's visualization lesson:
Have a BE sphere collapse run directory ready to go - here: grassdata/erica/NewUserLessons/Visualization/run_dir
Explain briefly what we are setting up, 3D BE sphere at (0,0,0) that is perturbed to collapse, 3 levels of refinement
Run the simulation
Open files in visit
Make a pseudocolor plot of rho, slice it
Show the mesh
Step through the time states
Add a title, and a time state
Make a movie
Lineout
Make a movie
Query options
Selection options (clip)
Query options with a clip
Expressions
Updated User's Guide under "New Users" -- Check it out!
The wiki is beginning to look better. Please refer to the updated New User's Guide to see if you like where things are going. I organized this page into a flow that seems most efficient and logical for a new user to follow. Note I have only really moved things around, and have not went through and checked/edited content of any of these pages. I will be meeting with Jake today to help him with module writing, and have asked him to note any problems with the module writing help page that he may find.
Would be nice to have this all spiffed up for Christine's upcoming visit, but seems like it will be a continual project of updating, adding, and editing information on these pages. Also, we may want to rename pages so to be more organized as Eddie and me were thinking about on the discussion forum. . .
A few wiki documentation things to sort out
- contact us link on Download Page does not work if not logged in
- Instructions for installing AstroBEAR discuss using mercurial but don't mention where to check out the official 'repo' – which would of course only work for local folks anyways…
- AstroBearStandardOut needs to be updated to describe elliptic time usage. It would be helpful to also show some common errors that are seen.
- ModulesOnAstroBear
does not discuss the ProblemBeforeGlobalStep subroutineSimulation data section should not encourage the use of numerical indices for things like px, or Energy as these will be dependent on equation of state, lMHD, nTracers, etc…Dimensions section should be updated since 1D problems are possibleDimensions section should also encourage the use of CellPos function to get (x,y,z from i,j,k)Units and scaling section should mention scales.data file that is dumped by codeAlso worth mentioning that value of info%q should technically be average of physical solution over cell… Motivation for sub-cycling/smoothing etc…Also perhaps setting up a clump would be a good example - since you could then show how to rewrite the problem module using the ambient and clumps objects.Units and scaling section should not encourage the changing of physical scalesInitializing a Grid says that each infodef has a %dx which is not trueInitializing a grid has an incorrect expression for the number of ghost zonesFlagging cells for refinement implies that the errflag array extends into ghost zones – which it doesn'tAdditionalPhysics should probably be a separate pageAdditionalPhysics says that MaintainAuxArrays needs to be set to true which is no longer correct- AdditionalPhysics should discuss equation of state options as well.
Aux fields only need to be initialized if lMaintainAuxArrays is true (in 1D MHD it is false)Also an example that shows how to calculate the location of aux field entries would be good – as well as an example showing how to initialize a divergence free auxfield using a vector potential.- It would be nice to stop storing the Cooling Objects in the chombo file – which would simplify the problem module.
- Not sure if selfgravity still has a problem with a uniform density field… this should be checked – and it would only be a problem with peridiodic BC's for the potential – also a discussion (or link to a discussion) about what needs to bet set in global.data for self-gravity to work.
- I believe you can have sink particles without self-gravity (ie just point gravity)
- This should also be updated with viscosity/resistivity/thermal conduction stuff…
- AstroBearObjects
- Disks need to be added to Initial conditions documentation
- VectorPerturbations needs to be added to the Sub-Objects and documented
- All of the individual object pages need to be (created) or updated to reflect changes made by Ivan and others
- ScramblerIntro
- Need to decide what to do about refinement objects etc…
- How to setup a properly posed problem should probably be linked from somewhere else…
- DataFileTutorial
- io.data, communication.data, modules.data, and process.data are depracated
Data File Tutorials should be moved inside of ScramblerIntro and the 'Getting Started with AstroBEAR' should be renamed to 'AstroBEAR user's guide' or something… and linked below the Download link on the main wiki page.Then Tutorials will have information on things besides AstroBEAR - though the visit tutorial could be linked from the visualization page.The link to Code on the main wiki page is essentially a link to a developers guideMeeting pages are depracatedCollaborators & Projects, Publications, and Image Gallery probably don't belong under 'NewUsers'
Getting Images from Libre Calc to ApJ Latex Pre-print
I made plots for the BE paper in Libre Office Calc spreadsheets. ApJ pre-prints should include plots that are in .eps format. To save an image from Calc, one must do a work around:
- Make a copy of the plot, and paste in Libre Draw — Calc can't save images
- Format page so to eliminate margins
- Size your picture to match that of the page — if the margins aren't set to 0, there could be data cut off from the picture if the plot isn't correctly aligned to the page… frustrating :/
- Save your image as .eps, with size = size of picture
This image is now in the right format to be called in the latex file.
Making copies at UR copy center
One could drop a book off to Meliora Hall and they will send it over to the hospital's copy shop, where they could make copies and bind them for us.
Each double-sided page = 5cents (2.5 cents for a single sided page) Cover binding ranges between $2.5-4.5
For the relevant chapters in Toro - chapter's 1-8, I priced it out to be ~$18.00
Meeting Update 01/07/13 - Eddie
progress since last meeting
- completed about half of the runs for 1D rad shocks with B field
- started writing module for a 2D/2.5D pulsed jet
to do list
- write a gnuplot script to create plots for the 1D rad shocks. This will make plotting for all the runs easy, and also allow Anna to generate comparable plots with her data.
- use new Al cooling table to run lab simulation of jet (Francisco)
on the back burner
- implement cylindrical coordinates
Meeting Update 01/08/2013
- Things I worked on over break…
- MHD convergence - done
- PPM convergence - almost
- Things to work on this week…
- FLD solver
- Documentation ???
- Developer's manual ???
- Christina's MHD run got to frame 3 in 24 hours on 4000 cpus with refining up to 4 levels. Frame 3 was 11 GB! Resubmitted with 3 levels of AMR except where jeans criterion triggers 4 levels - and it has been in queue for 6 days.
THIS WEEK'S SCOOP
Over the break, I finished the exact Reimann solver program. The results are here: https://clover.pas.rochester.edu/trac/astrobear/wiki/u/erica/ExactRiemannSolver
Next I will be learning about approximate reimann solvers. I will begin reading Toro chapter 5 this week.
I also finished paper figures, here:
https://clover.pas.rochester.edu/trac/astrobear/wiki/u/erica/BERunsFigures
I had to adjust the old script to make the plots look better - sampling from smaller sized zones as the resolution increased over the sim. The script now samples shells of the same radius as the smallest dx on the grid at any time. This is much more accurate. The plots look pretty good, but the BP is still wonkey despite the radial averaging. I wonder if here I should just fit a smooth curve to the data?
The Intro for the paper is nearly done:
https://clover.pas.rochester.edu/trac/astrobear/wiki/u/u/erica/BEPaper
Would like to begin moving this wiki material into a latex pdf this week as well.
Meeting Update 01/07/2013 -- Baowei
- Christine's visit
- Jan 14th (Monday): office, account, group meeting(?), lunch(?)
- Volunteers?
- Golden Version — Current revision: 1201:72d442594ac2, includes
- updated scripts for routine test suites running on blue hive and blue streak
- MHD convergence tests
- The routine test running of MHDWaves failed on blue streak
- Project runs for Teragrid
- Machines:
- AstroBEAR and required libraries installed on LLE cyclone. Tested with RTInstability by Rui
- checking local machines (bamboo unreachable, clover trac backup failed). will restart if necessary.
- Wiki
- installed Discussion plugin
- Working on MUSCL
Exact Reimann Solver finished
I have finished the Exact Riemann Solver program and have tested it against Toro's and it works well. The code basically uses the different wave speeds in the grid to determine any position on the grid (x,t). This was a really neat concept. Using relative wave speeds, one can determine at which point in solution space you are, and thus the fluid variables at that point are given analytically. This is because there are essentially 5 possibilities - pre- or post- shock, ahead, behind, or within rarefaction fan. The waves spread out from the contact discontinuity - (although, not sure why this would be a strict condition from the equations) - and so the algorithm checks the relative pressures ahead and behind the waves to determine whether the wave is a shock or rarefaction. A shock has simple expressions for the post shock region, given by the jump conditions, and so the pre-shock region would just be the initial data state, and the post shock would be given by the jump condition. The post-shock region is aka "the star region" and its pressure and velocity are constant through-out. This region is where the initial discontinuity of the Reimann problem exists as well, later to travel through the grid as the contact discontinuity. What I am trying to get at is that behind any wave, the rho is given by either the jump condition or the isentropic condition for a rarefaction. This is a constant value until the contact is reached. Once the sampling point passes the contact, the same is true on the other side. So in this sense there are 4 regions - 1. Left state, 2. Left star region (with p, u given by the Reimann solver, and rho determined by the left state's post wave solution), 3. Right star state (same situation as 2, but with reference to right wave solution, 4. Right state.
Here is my progress page that links to my code and shows the results of the Toro tests: https://clover.pas.rochester.edu/trac/astrobear/wiki/u/erica/ExactRiemannSolver
The directory is here: grassdata/erica/ExactRiemannSolver
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