I created a page dealing with Thermally induced collapse of clouds…

I added several new plots showing cooling lengths, jeans lengths, destruction times, etc… to the CollidingFlows page.

I've created a project page for CollidingFlows with low resolution studies to try and find the parameter regime that creates sink particles…

2011. This page is a continuation of

​http://www.pas.rochester.edu/~martinhe/magneticTOWERS.html

Aug

More progress on the paper(​http://www.pas.rochester.edu/~martinhe/2011/magTOWER/paper.pdf). New azimuthal forces plot, Figure 8. Estimate 1st draft to be ready in a few weeks (before I go to Poland).

Here's the poster I'll present in Poland (​http://www.oa.uj.edu.pl/mfu2011/):

​http://www.pas.rochester.edu/~martinhe/2011/magTOWER/poster.pdf

Also, for the curious folks, here's the latex poster source code (compile with pdflatex poster.tex):

​http://www.pas.rochester.edu/~martinhe/2011/magTOWER/poster.tar

July.

Writing the first short paper about our magnetic tower simulations. Latest draft: ​http://www.pas.rochester.edu/~martinhe/2011/magTOWER/paper.pdf Currently writing the results sections.

New movies. Field line movies only show 4 lines in the central part of the tower. This makes them much clearer; using more lines make movies confusing.

Adiabatic:

• dens vs beta:

​http://www.pas.rochester.edu/~martinhe/2011/magTOWER/summer/densVSbeta-slow.gif

• field lines lateral view:

​http://www.pas.rochester.edu/~martinhe/2011/magTOWER/summer/adiabat-side-slower.gif

• field lines upper view:

​http://www.pas.rochester.edu/~martinhe/2011/magTOWER/summer/adiabat-up-slower.gif

• Three tower cases:

field lines lateral view (I tried showing the towers closer to each other and larger, but visiti does not follow my commands. I'd have to do it by hand): ​http://www.pas.rochester.edu/~martinhe/2011/magTOWER/summer/3towers-slow.gif

I will talk about my progress in the following projets (2011).

29 nov

• Magnetic tower paper. Writing the conclusions. Should have it ready for Adam's and Eric's final revision by the end of the week.

• CRL 618. The new 4 runs, with AMR (i.e. no particle grids), are in bluegene's queue. I've experienced some code running problems there, but Jonathan and I are working to solve them. In addition, Bin and I are running two of the sims in bluehive. Finish time estimation of 4 day/sim.

• Binary.

-Setup comparison:

​http://www.pas.rochester.edu/~martinhe/2011/binary/diffSETUPS.gif

I've been working on two simulations: one with an initial Keplerian disk and the other one with the orbiting binaries.

-Initial Keplerian Disks, gamma=1.001.

+5amr, no ambient wind, the disk is unstable and tilts. I'mm still running this sim further:

​http://www.pas.rochester.edu/~martinhe/2011/binary/29nov-densCONTOURS-pole.gif

​http://www.pas.rochester.edu/~martinhe/2011/binary/29nov-densCONTOURS-edge.gif

​http://www.pas.rochester.edu/~martinhe/2011/binary/29nov-densCONTOURS-angle.gif

Now trying 6amr but keeping the same gravity soft radius than in the 5amr sim.

+The disk is embedded in an abient medium with dens=dens_disk/1000 and v_x= 20kms^-1:

​http://www.pas.rochester.edu/~martinhe/2011/binary/29nova.gif

Currently running one without any wind and 5 amr levels.

-Binaries. I've ran a test simulation with the primary injecting the wind, while the secondary pulls gas form t=0 with 4amr levels. I see that a disk forms and tilts (apologies for the ugly image, the orbital plane is the XY one):

​http://www.pas.rochester.edu/~martinhe/2011/binary/29nova.png

Currently running one with 5 amr levels and a secondary's gravity field which will be tunned on once the primary's wind goes beyond the grid boundaries. Snapshot:

​http://www.pas.rochester.edu/~martinhe/2011/binary/29novf.png

21 nov

• CRL 618. New runs with diffusion and artificial viscosity seem to get rid of carbuncles. Also, seems that, as expected, 5amr, 64 cells/r_clump are necessary to resolve the clumps properly. The two movies below show runs with a density contrast of 100 and a particle grid which follows the clump or the jet.

• Clump, rho_amb=const, 4amr

​http://www.pas.rochester.edu/~martinhe/2011/crl/21nova.gif

• Clump, rho_amb=r^-1, 4amr

​http://www.pas.rochester.edu/~martinhe/2011/crl/21novd.gif

• Jet, rho_amb=const, 5amr

​http://www.pas.rochester.edu/~martinhe/2011/crl/21novb.gif

(in this test the particle is a bit offset relatie to the jet's head, this will be corrected for future runs).

• Jet, rho_amb=r^-1, 4amr. The bowshock seems too thick. I'll reduce the diffusion for the next run.

​http://www.pas.rochester.edu/~martinhe/2011/crl/21novc.gif

• Disks. I found that the latest datasets yield a stable disk at the centra of the grid with a Keplerian vel profile fir both gamma=1.001 and 1.667. I've defer a simulation which will include an inflowing wind because I want to get the binary simulations running soon for my aas talk. The binary implementation is almost ready. My tests are not long enough to see any potential disk tilt.

• Magnetic towers. New paragraph and plot (which substitutes the one I showed during the last meeting) where I quantitatively show that our towers are PFD,

see pages 21 and 23 of the latest draft:

​http://www.pas.rochester.edu/~martinhe/2011/magTOWER/paper.pdf

I plan to have the paper ready by the beginning of next week?

• PN paper. I've not yet let the other co-authors know about the latest referee's response.

What now?

Are we submitting the paper as it is now to MNRAS or New Astronomy?

• Students. Ruka has given me the 1st draft of his report.

16nov

• Students. Ruka's Bondi module is now working! (see his post). Matt's final part of the testing scripts seem to be working too. We're ready to start testing (Matt ?). We've included new tests to catch bugs related to Hypre and threading compilation flags.

• Accretion disks. My implementation keeps showing disk tilt, but velocity plots suggest it is caused by material that flows along the disk poles and collides at the centre. Even with a disk to ambient density contrast of 100 and gravity potential softening. I also tried gamma=5/3, but the disk ended up launching some sort of jet, very early in its evo.

I'm now working with Jonathan's implementation. Differences:

I see a stable disk. I'm now running two sims: one with the disk alone and one with an incoming wind too. I'll next couple Jonathan's implementation with my binary one. I expect to have this in a week time.

• Magnetic towers. New plot: Poyting to kinetic fluxes:

​http://www.pas.rochester.edu/~martinhe/2011/magTOWER/pfd.pdf

Andrea: "The pictures look fine indeed and pretty convincing. However be aware that the 1/ (beta M^{2) relation is only (very) approximative and may not apply everywhere. The only way to really show it is PDF is to calculate the Poynitng flux and kinetic flux along the jet at different height/radii and compare. I really think it is worth the effort, even for future work.".}

I'll so some plots of the ratio of Poyting to kinetic flux: [ B_z²/(8pi) ] v_z / ( .5 rho v_z³ )

• AGN jet truncation due to stellar winds. Tests keep going well. The following show an AGN radio jet with an opening angle of 20^o, and a star with a strong wind, but not so to truncate the jet.

​http://www.pas.rochester.edu/~martinhe/2011/agn/2d-dens-10nov11.gif ← small grid

​http://www.pas.rochester.edu/~martinhe/2011/agn/2d-dens-16nov11.gif ← large grid

We expect larger opening angles close to the host galaxy (​http://www.cita.utoronto.ca/~everett/agnOverview/31xopmon.jpg) and we also want the star to have some velocity and a stronger wind. Coming up soon.

• CRL 618. New implementation to follow the clump faster and see the effect of artificial viscosity, difusion and the code's limiters on the spurious features that we saw (along the head of the clump) before (see Bin's blog).

​http://www.pas.rochester.edu/~martinhe/2011/crl/16nov.png

Note that the time figures are larger by a factor of ~10 because these runs have been compiled with check flags on. Future simulations will run ~10 times faster.

Running with a massless particle allows us to make full sims in a coupe of days. Once we're happy with the diffusion setup and the morphology of the clumps, we can either switch to the gradients AMR or combine it with the particle's, in order to capture the clump/jets' cavity with higher resolution.

8nov

• Magnetic tower paper, sent to all co-authors. Got responses from Andrea and Pat. Waiting for comments from Adam, Eric and Sergey.

• Binary. 6amr run has almost completed 20 orbits, like the 5 amr one. 5+6amr run is still running.

*Disk tests. These are set up as flat (radius/height=4) cylinders at the center of the grid, with a constant disk to ambient density ratio of 10 and a Keplerian azimuthal velocity about the central, static, point gravity particle. The rest of the setup (gamma=1.001, mass_particle, grid size, scales, etc.) are as in the binary simulations (see previous posts). No wind is injected, and the duration of the movie is equivalent to 2 orbital periods of the binary simulations.

-The disk does not reach a stable state, at least for the simulations' times explored, but I'm still running these tests.

-The link below shows logarithmic density maps, upper view, of a 5amr (left part) and a 6amr (right part) disk.

​http://www.pas.rochester.edu/~martinhe/2011/binary/8nov11.5amrVS6amr.gif

-The link below shows logarithmic 3d density iso-coutours. 5amr (top) and a 6amr (bottom). Edge-on (left) and pole-on (right). The viewing position is the same in all panels; the bottom ones actually show a smaller disk. The beginning of the simulations is particularly surprising (left column) for I see oscillations of the gas that is in the central most orbits.

​http://www.pas.rochester.edu/~martinhe/2011/binary/8nov11.5amrVS6amr.3d.gif

-The initial oscillations are likely due to ambient medium which is nor rotating about the central gravity particle and is thus pulled by gravity along the poles. Also, the ambient medium and the disk have temperatures of 100 and 10 K, respectively. The idea was to have pressure equilibrium as initial conditions. Yet, may be the low temperature of the disk is such that the scale defined by the contrast of Keplerian to sound speeds is rather small and so I do not resolve it, even with 6 amr levels. This is motivated by the fact that I see the inner part of the disk very rapidly collapses in to a 2 cell thick structure. I'm now working to improve the implementation.

• CRL618. Bin and I have the new setup which includes diffusion and carbuncles prevention. Our runs (jet/clump to ambient density ratio of 100 with a constant, and stratified, density ambient) are waiting in bluehive's queue.

• AGN jet truncation due to stellar winds. Tests are going well:

​http://www.pas.rochester.edu/~martinhe/2011/agn/agn.8nov.gif

​http://www.pas.rochester.edu/~martinhe/2011/agn/agn.8nov.2.gif

This is a logarithmic false colour map of the grid gas density. The jet enters the grid on the left vertical face. The star has a spherical wind (Mdot~5e-6, v~500km/s) and is at the intersection of the three planes, at the middle of the grid. The flow structure after the collision of the stellar wind and the jet is very interesting, potentially observationally distinctive.

1 nov

* Binary.

• Tests with a simple disk about one star (only) are running (see link below, 2d slice, left: the disk just before interacting with the wind; right: the disk just after interacting with the wind). Results soon.

​http://www.pas.rochester.edu/~martinhe/2011/binary/1nov11a.png

• Soothed plots: Angm. mom. projection, mass and accretion rate (which seem to be rather high) vs time, for 5 and 6 amr levels:

​http://www.pas.rochester.edu/~martinhe/2011/binary/1nov11.pdf

25 oct

• Magnetic tower project.

*Hydro comparison: ​http://www.pas.rochester.edu/~martinhe/2011/magTOWER/25oct11.pdf.

*Working on Andrea's comments.

• Binary project.

*Run with 6amr levels is still running and it has gotten up to time=14.8 orbits. The disk tilts; I see and angle ~ 10^o-50^o between the orbital ang. mom. vector (vertical direction) and that of the disk.

*Run with 5amr unitl time=3 orbits, and then restart with 6amr levels is running too. It is rather slow though. I'm working to fix this.

*Run with 7amr unpractically slow; quite a bit of fractional steps between every level 0 step. I'm now:

*updating my implementation to use threading *running with a slightly large gravity softening radius (which will make the conditions at the inner disk less dramatic)

to see if it helps.

• CRL618 project.

*bear2fix and shape are now working. Bin's in charge of producing the synthetic emission and PV diagrams.

*Also running another clump-no rings case with more resolution at the flow behind the clump, as requested by Bruce via email.

• AGN jet truncation project. Implementing it.

18 oct

• I worked on the 3 proceeding from the magnetic fields in the universe 3 conference. I submitted them yesterday. Will post them in astro-ph this week.

• Magnetic tower. I've been writing the intro and Andrea's comments. The hydro-rotating run is in bluegene's queue. I expect to have the data in a few days time.

• Binary. We have a 5 amr and a 6amr runs. Both have completed about 10 orbits.
  • r_disk(6amr) < r_disk(5amr).
  • 6amr disk shows a rather moderate tilt, whereas the 5amr disk, as we saw before, tilts all the way to the orbital plane.
  • Projected angular momentum plots (something's wrong): ​http://www.pas.rochester.edu/~martinhe/2011/binary/18oct11.pdf
  • Density movies: ​http://www.pas.rochester.edu/~martinhe/2011/binary/18oct11.gif

Meeting resolutions: (i) continue running the 6 amr run (ii) run a 7amr version (iii) run a 5 amr until orbit 3, and then restart with 6amr (iiii) revise the angular momentum projection angles plots routine.

• CRL 618. I'm working on the synthetic maps. First test of the jet with ambient rings: ​http://www.pas.rochester.edu/~martinhe/2011/18ocr11-crl.jpg

• AGN jet truncation. I met with Eric yesterday to discuss simulations to explore ​http://adsabs.harvard.edu/abs/2006MNRAS.371.1717H. We agreed in a couple of test I'll run soon, in which a light 3D hydro jet will run into a sink particle with a spherical wind of M^.~10^-6 M_suny^-1 and v_wind~100 km s^-1.

• I'll be out of town this friday.

11 oct

• Binary wind capture problem. I've finished the Tenerife proceedings and registereed to the aas meeting in January, at TX. Since it's close to the holidays I was planning to change my plane tickets so I can aslo give some seminars at Mexico's Institutes of astronomy and astroph.

High resolution run is still running. I've found that the disk that forms has a radius about 4 times smaller than disks we've seen so far. Here's a 3D dens iso-contour snapshot after 3.5 orbits:

​http://www.pas.rochester.edu/~martinhe/2011/binary/11oct11a.png

There's a slight tilt of the disk.

Previous run: angular momentum vector projection angle plots:

​http://www.pas.rochester.edu/~martinhe/2011/binary/11oct11b.png

movie:

​http://www.pas.rochester.edu/~martinhe/2011/binary/11oct11b.gif

• Magnetic tower. I've been working on the intro of the paper. I'll then work on the rotation section to include Andrea's comments, and we should then be ready to submit.

We have enough data to make a second paper that analyses the hydro vs. PFD regimes further, as Eric has been suggesting. We should talk about that with him. i.e. how would that affect the current text. Also, I want to use the data to do some statistical analysis on synthetic polarimetry for a third paper.

I've also been writing the Poland's proceedings about the mag tower+ experiments talk. The one about the tower poster is ready.

• AGN: I've been writing the proceedings about the AGN poster that I took to Poland (​http://www.pas.rochester.edu/~martinhe/AGNposter.pdf). Ready for submission too.

• CRL 618: I've been trying to make shape synthetic emission, and PV, images. They are not ready yet, but I estimate another week for it.

• Testing: We've been having regular meetings. The RT module, data files and testing page (​https://clover.pas.rochester.edu/trac/astrobear/wiki/TestSuite/RayleighTaylor2D) are ready. Edd has also been working in documenting the FieldLoopAdvention one. Bin is working on her radiative shock bear2fix data files and in updating their documentation. Ruka's now fluently playing with the code and has started the implementation of the 2.5D hydro Bondi accretion test. Matt is working on the testing scripts. We should have the 1st version of the suite ready very soon now.

4 oct

• I've been writing the NSF proposal.

• All crl616 run complete. We should have a telecom with Bruce.

• Binary-formed accretion disk. I ran the latest simulation from longer. Another one, with an extra refinement level, is running now.

• I'm writing the Tenerife proceedings. Want to send them by Friday.

• I'm writing the AAS, TX, abstract about the binary problem.

• How's the magnetic tower paper going?

27 sep

• CRL 618. Problem: jet run is much slower than the clump one. The chombos show maxDens_clump~97, but maxDens_jet(head)~900, at t_comp~0.0084. Problem in the module. Fixed and running both jet with and without rings. Quick ugly density plots:

​http://www.pas.rochester.edu/~martinhe/27sep-crl618jets.png

• Advances in the binary problem. See Accretion-disc post.

• Working on the NSF proposal and different proceedings we have.

• Updates to the testing wiki page. Matt and I will get our hands on the testing scripts and related bear2fix routines this week.

• The hydro cooling case of the magnetic tower has completed:

​http://www.pas.rochester.edu/~martinhe/2011/magTOWER/27sep.png. The next one is the hydro rotating which I'll run soon.

20 sep

• Binary simulations. The new run, which has a grid twice as large -in every direction- than the previous run, in on going. Should have a movie for the research meeting.

• CRL 618. The clump run, with and without ambient rings, have completed (see Bin's blog). The jet runs, with and without ambient rings, are slowly on going. We should have data to show to Bruce Balick in a week time.

• Magnetic tower. Waiting for Sergey's and Andrea's comments. Writing the talk proceedings. Running (gbene) the hydro+cooling case, as requested by Eric.

• Writing the Tenerife and Poland (AGN) proceedings.

13 Sep.

• Tenerife PN proceedings?
• I have been working on:

• Binary problem, bear2fix plots of mean angular momentum vector direction vs time

• Updating testing documentation and scripts

• Matt?

6 Sep.

-Present a summary of the MfuThree meeting, and discuss about some potential collaborations with people I saw there.

-Possibly related to the magnetic tower sims:

-​http://arxiv.org/abs/0804.1871

-​http://arxiv.org/abs/0903.5340

-Discus some ideas about the binary, wind capture, accretion disk formation simulations.

-Discus about Bin's and Ruka's (the new undergrad) projects.

15 aug New initial conditions for the binary problem which seem to affect the inclination of the disk found before.

I'll present a preview of my jet Poland talk at the journal club. I'll leave this Friday and will be back on Tuesday the 30th.

Still working on the magnetic tower paper. Plan to give the 1st draft to Adam and Eric this Thursday.

27 June

Accretion disk formation ​https://clover.pas.rochester.edu/trac/astrobear/blog/category/Accretion-disk. Do the resolution and outflow radius affect the average orientation of the disk?

Magnetic tower. Paper results analysis.

Bin and I have been working on the new CRL-618 runs with velocities of 200 and 500km/s.

This page is continuation of ​http://www.pas.rochester.edu/~martinhe/2011/binary/binary.html.

Sep 27

Find movie of the disk density at ​http://www.pas.rochester.edu/~martinhe/2011/binary/27sep.gif. Top - logarithmic density maps of the orbital plane. Bottom - 3-D logarithmic density iso-contours viewed edge-on (left); y (vetical) - z (horizontal) plane -perpendicular to the orbital plane- showing linear maps of the Vz velocity component (right). The bottom right panel maintains its blue-red colors close to the left and right boundaries, hence no inflow.

The disk tilts (see bottom left panel). And the tilt angle sem to increase in time. Could this be torques from the AGB wind on the disk?

Angles plot: ​http://www.pas.rochester.edu/~martinhe/2011/binary/27sep-angles.png

Sep 23

Case with V_AGB=5km/s. This is slightly less than the scape velocity from the secondary which, thus, dominates the wind dynamics after a few orbital periods after its gravity is switched on.

Sep 22

a=25AU, V_AGB=10km/s (twice as fast as in old sims), l_grid=200AU (twice as long as the old sims), outflow_only BC. I do not see inflow from the boundaries. I see a varying tilt angle (10^o-45^o) between the disk and the orbital angular momentum vectors. ​http://www.pas.rochester.edu/~martinhe/2011/binary/22sep.png

Angular momentum projection angles plot is coming soon.

Sep 14

Some corrections to the bear2fix angular momentum projection routines. The still plots in the two links below have been updated accordingly. Mild changes. I've resumed the simulation that corresponds to the links below (a=25 AU, v_AGB=5km/s), it's running in bluehive and should go three times further.

Sep 13

Plot of the mean angular momentum direction as a function of radius and time: ​http://www.pas.rochester.edu/~martinhe/2011/binary/plot.pdf

Plot of the mean angular momentum direction as a function of time: ​http://www.pas.rochester.edu/~martinhe/2011/binary/13sep.html

Aug

a=25AU, Vagb=5km/s, "sandwich grid" (-5:5,-5:5,-2.5:2.5) AU. This simulation has two phases. During the 1st one, the binaries orbit each other twice, the AGB primary has its slow wind and the secondary only affects the orbit of the primary, but not the gas. This allows the grid to be filled with the AGB wind condition before the disk formation begins. The 2nd simulation phase begins next, when I turn on the gravity between the secondary and the gas. The system orbits 4 times.

2D pole-one logarithmic density map:

​http://www.pas.rochester.edu/~martinhe/2011/binary/25-5-fullAGB-2Ddens.gif

3D, 2 panels: pole-on and edge-on views. The disk that forms is not significantly tilted.

​http://www.pas.rochester.edu/~martinhe/2011/binary/25-5-fullAGB-2panels-3Ddens.gif

Also ran the same simulation but in a cubic grid. I see significant differences in the disks:

​http://www.pas.rochester.edu/~martinhe/2011/binary/25-5-2panels-3Ddens-sandwichVScubicGRIDS.gif

Here's a good still shot too:

​http://www.pas.rochester.edu/~martinhe/2011/binary/2panels-3Ddens-sandwichVScubicGRIDS-0180.png

A cubic grid version also with an AGB wind which has filled the grid and a=25AU, but with Vagb=30km/s, is running now. Should have the movie in a few days (before my trip).

Next simulation: a=25AU, Vagb=5km/s. The initial conditions for the disk should be an AGB wind which has expanded beyond the grid boundaries.

The simulation of a=25AU and Vagb=5km/s has run up to 5.7 orbits. Here's a number density [cm^-3] logarithmic grayscale map, and an opaque dark-blue map of the grid:

​http://www.pas.rochester.edu/~martinhe/2011/binary/25-5-2Ddens.gif (A)

The grid in this simulation is [-5:5,-5:5,-2.5:2.5], "a sandwich", and each computational length unit=10AU. This makes the simulation faster without compromising disk formation dynamics. I see complex flow patterns. The rotation of the diks is synchronous with the orbital one.

Here a 3D view of the number density of this simulation:

​http://www.pas.rochester.edu/~martinhe/2011/binary/25-5-2panels-3Ddens.gif (B)

The left panel is a perspective view. The AGB primary is the red particle. The orbital plane is opaque, in the middle of the figures. This is a viewing angle of about 10 degrees. Disk material below the orbital plane is shaded. The right panel shows the same simulations but normal to the orbital plane and from bottom to top relative to the left panel.

Newest runs (as fas as they've gotten). a=binary separation [AU] , v=AGB [km/s] wind velocity.

a=5, v=5. ​http://www.pas.rochester.edu/~martinhe/2011/binary/summer/18jul-densISOCONTOURS-a.gif

a=5, v=30. ​http://www.pas.rochester.edu/~martinhe/2011/binary/summer/18jul-densISOCONTOURS-b.gif

a=25, v=5. Tired to run with lScale=10AU and the same grid size as the tow simulations above (just at the post of 13 june, ​http://www.pas.rochester.edu/~martinhe/2011/binary/binary.html). This setup, however, produced wrongly high v, because the code's velocity scale only depends on tempScale (i.e. velscale \propto tempscale and not to lscale). Easy solution would be to reduce tempscale and rerun. Yet, I decided to change as little parameters as possible between different runs (a=5 and a=25), so I'm now running this case (a=25 v=5) with lscale =1AU and a 4 times larger grid than in the a=5 case. Progress, about .5 orbit.

a=25, v=30. Very problematic run. Need to adjust AR to follow the wind while it travels between the stars. Currently running in bluehive with the above described setup. Progress, I only have 3 chombos, ~ ¼ of the 1st orbit.

Difficult to get much further before the Tenerife conference.

New stuff:

I wanted to document the process of inserting a new module (i.e. one that is not yet built into the astrobear architecture) into the makefile, and thought this would be a good place to do so.

In the astrobear main directory, open the makefile (lower case m). This lists the dependencies of everything in a hierarchy of files, from those that are more "global" to those that are not.

Look for the obj_files = list. It is there that you should insert your module object file name. It should be listed after the dependencies it uses, but before the problem module (or any other module for that matter) that calls it. Be sure to use the same syntax of other elements in the list, namely end it with ".o/". Once this is done, you are ready to make.

So for the past couple weeks the new users' group has been playing around with the Field Loop Advection problem. I've looked at a lot of the data files, just trying to understand what each one is for. In my most recent run of the problem I changed it to 2D and ran for 20 frames instead of the default 10. We've also been doing some intro to visit. For this run, I created this simple movie that shows the magnetic field vectors: ​Bvec_movie

I realize this entry is not too exciting, but it's also helpful just for getting used to editing the Wiki, posting blogs, linking different pages, etc…

Hi all. I tried stepping on the boundaries using nWinds taken from the true love problem.f90 to see if that fixed the noise from the previous movie:

This, I think, looks worse… I am attaching the data files I am using as well as the problem module. I see that the word "chombo" that indicates the current frame, shrinks when going from frame 0 to 1. I thought this may be an indication that the frame was old, or they are from a mismatched data set. But, this is not the case. . .

I am currently running the simul with my original boundary conditions to make sure I can duplicate the previous run. I am also attempting to run with periodic boundary conditions everywhere… but this is reporting a looong string of high cfl warnings.. From the first frames it produced, though, 0, 1, and 2, everything looks good..

So here is a quick comparison of the 2 different simuls (my first run, described in prev. post, and the new one with winds turned on)…

Set up:

3D Simulation: -Mass = 0.18 Solar Mass -At = 4km/s -Temp = 0.29 K -Crossing Time = 1.3 cu -Rho_c = 3x10^-21

My equations are cast in CGS. Their output then must be divided by appropriate scales before being read into the q-arrays.

For the BE problem I am following the table in this presentation for some parameter values —

​http://astro1.physics.utoledo.edu/~megeath/ph6820/lecture6_ph6820.pdf

The input vars are central density (10d3 - 10d4 g/cc), xi (nondimensional radius), and r (~1 pc). The crossing time is ~5myr.

Referring to pg. 244 of Stahler, xi should be chosen by the p/rho_central<(1/14.1) criterion. This looks to correspond to a xi less then 5…

In physics.data I am setting rscale, lscale, and … TempScale???

So it seems, the units of the scales read in by astrobear and defined as "rscale" and the like have pre-set unit(s). I.e. rho scale (rscale) is in g/cc. lscale in cm., etc.

These scales are divided into your problem variables (that have the same units of the scales) to create scale-less quantities called computational units (c.u.) that are compatible with astrobear.

It is useful to assign a value to these scales that will result in a small computational unit after division.

This means, choose physically appropriate scales, here is an lscale that might be relevant to your problem:

lscale = 7.4d15 !cm

Here, 1 c.u. (computational unit) of length is equivalent to 7.4 x 10^{15 cm.}

So if you have a clump say that has a length on the order of this scale, you can divide it's length by this scale to get something close to 1 that astrobear uses.

If you want to use units other than CGS, you may personalize them in problem.data, as long as you convert them to CGS before dividing by the scales (remember the goal is non-dimensionalization) The flow of info. should go something like:

vars in problem.data → read into problem.f90 → populate q-arrays with var/varScale

Radius of circle = 1 pc. Central density = 1000 g/cc

r=5cu (in visit) —> 5*lscale = 1Pc rho=1cu (in visit) —> 1*rscale = 1000g/cc

I placed a new physics module called BE_module.f90 in the physics/ folder of astrobear which calculates the density profile of a Bonner-ebert sphere. Here is a preliminary result:

Blog posts should be used by folks to log their work for meetings etc… Rarely should any actual work or documentation be put directly into a blog. Instead try to find a home on the wiki for the information be it in a ticket, project page, discussion page, or in the general wiki documentation on the code and then link to the work from the blog (or just embed the work in the blog using the Image macro) Below are some examples of linking/embedding images from discussion topics, wiki pages, or tickets…

Discussion topics

[attachment:AdvanceTimes_1.jpg:discussion:topic/23 SampleImage]
[[Image(discussion:topic/23:AdvanceTimes_1.jpg, 50%)]]

Wiki pages

[attachment:StrongScalingEfficiencies.png:wiki:OptimizingScrambler SampleImage]
[[Image(wiki:OptimizingScrambler:StrongScalingEfficiencies.png, 50%)]]

Tickets

[attachment:bug.png:ticket:126 TicketAttachment]
[[Image(ticket:126:bug.png, width=50%)]]

Hi everyone. I put a circle on the grid:

I learned a bit about the global.data file that I think I will share here (unless there might be a better place to do so)…

So in global.data, Gmx controls the number of cells on the grid. This must be in agreement with Domain%mGlobal, that is, mGlobal is a domain-by-domain decomposition of the number of cells per domain. It must run from AT LEAST 1 to the max number of cells in each dimension (i.e. mx). I ran into issues when mGlobal did not match mx. If I increased the number of cells in my domain, with out a concomitant increase in mGlobal, the cells were squeezed into a smaller and smaller region… Both mGlobal and mx refer to indices of the cells. They therefore cannot be real or floating point numbers; they must be integers. Also, they can't have values below 1 (a negative or 0 value for a cell index does not make sense). On the other hand, there is GxBounds. This refers to the actual spatial coords of the grid. These can run from negative to positive numbers. To convert between the cell indices and their spatial location, I wrote this into my module:

Do k=1-zrmbc, mz+zrmbc

Do j=1-rmbc, my+rmbc

Do i=1-rmbc, mx+rmbc

x=(xlower + (REAL(i, xPrec)-half)*dx) y=(ylower + (REAL(j, xPrec)-half)*dx) z=(zlower + (REAL(k, xPrec)-half)*dx)

Visit does not produce a grid with negative values. So if you have your domain running from -10 to 10, Visit will produce a grid from 0 to 20. This is relevant to keep in mind when visualizing output.

Okay, lastly, when one writes the grid init subroutine in their problem module, it is useful to assign an alias for certain variables that are assigned elsewhere in the astrobear "net". For instance:

mx=Info%mx(1); xlower=Info%Xbounds(1,1) my=Info%mx(2); ylower=Info%Xbounds(2,1) mz=Info%mx(3); zlower=Info%Xbounds(3,1)

Here we are calling a local variable, mx, and giving it the value Info%mx(1). Info%mx(1), however, is populated in another module, receiving its value from global.data — gmx. mGlobal is discrete, cell-centered indices. xBounds are contiguous, spatial coords.

Test (redundant, I know..)