Posts for the month of July 2014

Fall back shell

Green line indicates the local escape velocity. Raleigh-Taylor Instability happens at last stage. Temperature is 100K so that wind are all super sonic (low as 8 Mach speed high as 28 Mach speed).

From theoretical calculation, the dense shell should stop at r=7.4AU, in sim, the shell stop around r=6.2AU

test1.gif

rho.gif

Meeting Update 07/28

Now in full control of Erica's CollidingFlows data on Bluestreak. Completed first reservation (5 days) today. Can see our progress here (CFRunStatsHighRes).

  • E-mailed Carl about the soonest I can get another reservation (4-7 days on BS). (Update 14:47: Got our reservation extended to next Monday at 8am).
  • Erica is working on what is necessary to get us up on Stampede.

Currently:

  • scp-ing files from BS to /grassdata/madams/.
  • Post-processing on Bamboo.
  • Running B10S30 on our extended reservation on BS at 512 nodes for 48 hours (07-28-2014 14:49).
  • Submitted B10S60 to the standard queue on BS at 128 nodes for 24 hours… pending, but we'll see what happens.

Some highlights from CFRunStatsHighRes Page:

Beta Shear Machine, Path Frames Completed / Left Filling Fracs Walltime Taken / Left (1-2) Info, (3) Message allocations Framerate (hrs/frame), No. cores Notes
1 60 BS, /scratch/madams15/CollidingFlows/Beta1/Shear60/Restart/ 122/200 0.106 0.559 0.631 0.321 0.467 16.8days/0days 282.5 gb, 197.6 mb, 64.0 mb ~5hr/frame, 2048 cores Reservation. Stayed with 128 nodes. Started with 48 hours left on reservation.
10 15 BS, /scratch/madams15/CollidingFlows/Beta10/Shear15/Restart 139/200 0.386 0.698 0.616 0.496 0.468 22.1days/0days 422.4 gb, 296.5 mb, 64.0 mb 7hr/frame, 2048 cores Reservation. Restarted with 128 nodes on 07/26.
10 30 BS, /scratch/madams15/CollidingFlows/Beta10/Shear30 128/200 0.136 0.587 0.601 0.465 0.418 1.2mo/0days 377.0 gb, 252.4 mb, 64.0 mb 9hr/frame, 2048 cores Reservation. Started Jul 24 08:46, cancelled to test other runs, started again at Jul 26 16:41.
10 60 BS, /scratch/madams15/CollidingFlows/Beta10/Shear60/Restart/ 151/200 0.180 0.547 0.544 0.318 0.269 6.7days/0days 305.3 gb, 211.8 mb, 64.0 mb ~4hr/frame, 2048 cores Reservation.

Going Forward:

No. Nodes Case frames/hr frames/day Chombos Left Days to Complete Weeks to Complete
128 B1S60 0.2 4.8 78 16 2.29
B10S15 0.143 3.5 61 17 2.43
B10S30 0.111 2.67 72 27 3.9
B10S60 0.25 6 49 8 1.14

No. Nodes Case frames/hr frames/day Chombos Left Days to Complete Weeks to Complete
256 B1S60 0.4 9.6 78 8.1 1.16
B10S15 0.29 6.96 61 8.7 1.24
B10S30 0.22 5.28 72 13 1.86
B10S60 0.5 12 49 4 0.57

No. Nodes Case frames/hr frames/day Chombos Left Days to Complete Weeks to Complete
512 B1S60 0.8 19.2 78 4 0.57
B10S15 0.57 13.68 61 4.5 0.643
B10S30 0.44 10.56 72 7 1
B10S60 1 24 49 2 0.29
  • Depending on how quickly we can get onto Stampede, I am estimating that we'll be done with these in 2 weeks if we do this most efficiently.

Meeting Update 7/28/2014

Anisotropic Windflows from close in Exo-planets (Stone & Proga 2009)

  • Close-in EGP's: a < 0.1 AU. Because of tidal locking and irradiation on only one side, the assumption of spherical symmetry no longer holds.
  • The paper investigates the effect of anisotropic heating on winds in 2D.

Method: Take hydrodynamic equations in polar coordinates. Introduce anisotropy by making internal energy a function of theta on the surface of the planet.

  • Hydrodynamic escape parameter.

-Adiabatic Index.

Some results:

-Evidence of non-radial outflow.

-Inflow on the night side

-Shock front as the wind flows from the day side to night side.

-Only radial outflow at large radii.

-Nearly isothermal.

-Sonic surface at 0.5R. Decelerating wind on the night side?

-Density variations b/w opposite sides are only significant very close to the planet.

-Polar velocity increasing as you go from day to night side; discontinuity at the shock.

-Effect of increasing gamma. Cooling.

-Mass loss rate decreased by a factor of 2.

-Model not valid at very large distances. Effect of including stellar winds?

-Met Jonathan for a walk-through of the 3D outflow routine.

Figures for the HEDLA paper, more TSF shock study

Here are the figures for the hedla paper. The magnetized tsf has poloidal field axis aligned with beta = 12. The beta = 6 and toroidal beta = 12 data are not yet visualized.

Fig1: slice through the disk (side on view). Left panel: pseudo color = density, contour = magnetic pressure. Right panel: contour = density, grey streamlines: field lines.

Fig2: slice through the disk (top down view). Left panel: pseudo color = density, contour = magnetic pressure. Right panel: contour = density, grey streamlines: field lines.

Fig3: 3D view of the disk and the jet. (a) and (b) are the same frame (t = 0.36 Myrs), but with different opacity schemes to show: (a) jet feature (b) overall morphology including the disk obscured by the cloud material surrounding it.

Fig4: line plots of stellar mass, accretion rate, mixing ratio, circumstellar bound mass.

The following are the triggering runs with new shock structure, with shell speed = 20 km/s and wind speed = 20 km/s, no stars formed: http://www.pas.rochester.edu/~shuleli/tsf_0728/images/tsf_0728B_0050.png

movie

Here is a comparison between shell = 10 km/s wind = 100 km/s and shell = 10 km/s wind = 10 km/s:

http://www.pas.rochester.edu/~shuleli/tsf_0728/images/tsf_0728A_0017.png

movie

fall back shell

I lowered the temperature of the wind by a factor of 20, now it is only 100K - freezing cold. So every wind is now super super sonic wind now. The dense shell stopped at r=10AU, from theoretical calculation, it should stop at r=8AU.

rho.gif

Logrho.gif

v.gif

The program stopped there with:

High CFL - restarting step. 0.22934E+03 > 0.10000E+03

forrtl: severe (174): SIGSEGV, segmentation fault occurred

fall back

Wind parameter as time dependent variables

If there is no pressure, the second wind should halt at r=4.7AU.

Logrho.gif

v.gif

The velocity=0 happens at r=4AU, which seems meet the theoretical result.

rhov.gif

Adjusting Gravity in 3D Ablative RT module

Gravity value with different bottom heat flux for the current code

Heat flux at the bottom seems too low. Tried randomly bigger flux. Gravity increases first then drops. Seems something very wrong.

flb=6.0E+21 (calculated) flb=6.8E+21 flb=7.13E+21
gravity & total mass http://www.pas.rochester.edu/~bliu/AblativeRT/3Dcase/checkGravity/3dgravity_thin_6.0.png http://www.pas.rochester.edu/~bliu/AblativeRT/3Dcase/checkGravity/3dgravity_thin6.8.png http://www.pas.rochester.edu/~bliu/AblativeRT/3Dcase/checkGravity/3dgravity_thin7.13.png
Int(P+rho*V2) http://www.pas.rochester.edu/~bliu/AblativeRT/3Dcase/checkGravity/3d_integralsurface_thin_6.0.png http://www.pas.rochester.edu/~bliu/AblativeRT/3Dcase/checkGravity/3d_integralsurface_thin_6.8.png http://www.pas.rochester.edu/~bliu/AblativeRT/3Dcase/checkGravity/3d_integralsurface_thin_7.13.png

Compare with 2D Case

1. Initial Profile

Initial profile are close enough except the momentum along the gravity direction.

Rho&T http://www.pas.rochester.edu/~bliu/AblativeRT/3Dcase/2DCompare/initPro2D3DCompare.png
py or pz http://www.pas.rochester.edu/~bliu/AblativeRT/3Dcase/2DCompare/initialMomentumCompare.png

2. heat diffusion check

Turn hydro off. Compare the 2D (gravity along -y direction) and 3D (gravity along -z direction). The solver seems OK.

2D, flb=0 2D, flb=6E21
3D, flb=0 3D, flb=6E21

3. Pure hydro test

Turn off the heat diffusion off. Compare the density and the momentum along gravity direction -py for 2D and pz for 3D — plots are along the center line.

2D rho 2D, momentum 2D, pressure
3D rho 3D, momentum 3D, pressure

Here's a picture to compare the py (2D) and pz (3D) — both along the center line at time=1.345E-5 (cu) http://www.pas.rochester.edu/~bliu/AblativeRT/3Dcase/2DCompare/Momemtum_tf.png

4. compare top and bottom integral of P+Rho*V2

The integrals (pressure + rho*v2) were calculated with queries of integrate (2D) and weighted variable sum (3D) in visit.

Bottom Top
http://www.pas.rochester.edu/~bliu/AblativeRT/3Dcase/2DCompare/Bottom_int_PplusRhoV2.png http://www.pas.rochester.edu/~bliu/AblativeRT/3Dcase/2DCompare/Top_int_PplusRhoV2.png

Check the derivative of momentum

2D 3D
http://www.pas.rochester.edu/~bliu/AblativeRT/3Dcase/2DCompare/dTotalPydt_2D.png http://www.pas.rochester.edu/~bliu/AblativeRT/3Dcase/2DCompare/dTotalPzdt_3D.png

Single star

Very low res, star radius only consist of 8 cells, but the result is good. The zigzags are due to boundary. Red is from Parker's solution.

X axis is the radius, 1 CU = 2.5 AU

The outburst is very obscure. There is no significant shock in linear plot.

rho.gif

Meeting update

Last week,

  • Horizons program with kids — we went over our cosmic address and the cosmic calendar (with Neil Tyson's Cosmos), and had a lab demo with Craig.
  • Working on my ticket for restarts
  • Ran the sims out for 4 days on Bluestreak reservation, Marissa is set to start them up again on a 7 day reservation there starting Thursday.
  • Read Hennebelle's 'CF successes and limits' - attached to this blog post
  • Working with UNC to get access to their machines

Meeting Update 07-21

Objectives

  • I know it is about time, but now attempting to make low-res fly-throughs of the .bov files that we already have for our colliding flows visualizations. Plan is once we get all of the high-res data from our production runs, I'll make some nice fly-throughs of those?
    • cp'd code, global.data, profile.data, and physics.data to /bamboodata/erica/CollidingFlows/CollidingFlows/MHD_3D/ to /bamboodata/madams/CollidingFlows/FlyThru/
    • Referencing ProjectionObjects wikipage.
    • Need problem.f90.
  • Continuing to make .bov gifs for the files as we get them.
    • Bluestreak is currently down until Thursday this week at 8am, in time for my reservation to pick up on Erica's restarts.
    • Erica, Baowei and myself think it will be good to get some code up on Stampede, and run some jobs there. Erica says it'll probably be even faster. I'll have to familiarize myself with how to run jobs there.
    • Having computer issues with Clover and my own personal macbook. Making 3D Box CDM plots is very computationally intensive for these machines…

Mass-1 Column Density Maps

Beta 1

GIF

Beta 10

GIF

GIF

GIF

So what are different about these than those posted in my last blog post? I found the coloring to be too weak on the ones I previously posted. I also did not consider the ratio between GmX and the GxBounds when determining the maximum and minimum. So after going through and visualizing all of the mass-1 .bov sets for Beta 1 and 10 for our production runs, I have decided max = 1000 and min = 190 will be appropriate. This implies, given the size of the box (looked up in global.data), for all beta 10 cases, the mass2 and mass 3 will have max = 639 and min = 121.4. I think Beta 1 has a different box size, but I need to double check.

Again, it seems like I'll only be able to focus on fly-throughs, enhancement, somethings I noticed previously about bovs, and getting on Stampede until I can ssh to BGQ.

Meeting Update 07/21/2014 -- Baowei

  • Ablative RT
    1. Thick Target:
Initial profile http://www.pas.rochester.edu/~bliu/AblativeRT/3Dcase/initialProfile/init_Profile.png
Movies Rho; RhoPlot;TPlot
Gravity http://www.pas.rochester.edu/~bliu/AblativeRT/3Dcase/checkGravity/3dgravity_thick.png
  1. Thin Target
Initial profile http://www.pas.rochester.edu/~bliu/AblativeRT/3Dcase/ThinTarget/initialProfile_thin/init_Profile_thinTarget.png
Movies RhoPlot;TPlot
Gravity http://www.pas.rochester.edu/~bliu/AblativeRT/3Dcase/checkGravity/3dgravity_thin.png
  1. 2D Gravity

http://www.pas.rochester.edu/~bliu/AblativeRT/3Dcase/checkGravity/2dgravity_st.png

Meeting Update 0721

I have run three triggering runs with different shock velocity and realistic shock structure. The shocks below are only different in velocity. However, the density and temperature structures used here is based on the Vs = 150 km/s shock therefore they are not accurate for the other two runs.

1) Vs = 150 km/s, run to 37 kyrs (about 4.5 crushing time), no collapse. This is understandable as the shell we use has lower density and thinner than Boss'. If their shell need < 80 km/s to trigger, we may need even smaller shock speed.

http://www.pas.rochester.edu/~shuleli/realistic_shock/images/newshock1_0400.png

movie

2) Vs = 50 km/s, run to 100 kyrs (about 4 crushing time), no collapse. This is different than Boss' < 80 km/s criterion. But again, the shock structure is wildly different.

http://www.pas.rochester.edu/~shuleli/realistic_shock/images/newshock2_0300.png

movie

3) Vs = 10 km/s, run to just past the first crushing time, collapse triggered at the last frame. This is similar to our previous Mach 3 simulation, but with a very different shock structure.

http://www.pas.rochester.edu/~shuleli/realistic_shock/images/newshock3_0010.png

movie

Our next step should be trying to pin down the exact threshold velocity for collapse to happen, and research on how the shock structure should change when such velocity is reached. This means triggering can only happen outside of the 1~2 pc range we have assumed before, but actually much farther from the source of the shock.

Science Meeting Update 07/20/2014 - Eddie

For reference: ClumpClump/Morphology

Mainly just working on the Mach stem paper for the HEDLA proceedings. I hope to have it done within the next few days. I did some analysis on the shapes of the bow shocks from my simulations to confirm that they agree with the theory about Mach stem formation…

From analyzing the density maps, I was able to get a functional form for the bow shocks which end up looking like this:

Then, I can figure out what angle they would make if they intersected another bow shock. The theory of Mach stem formation says that they form at and above a critical angle which depends on gamma. For the values of gamma that I have used, these angles are:

gamma phi crit
5/3 74.75
1.4 83.31
1.2 95.34
1.01 137.46

Now, going back to the bow shock shape, I was able to pinpoint where these critical angles would occur. In other words, I figured out the critical separation distance for the 2 clumps at which Mach stems should begin to form. These are approximately:

gamma d crit
5/3 12.5
1.4 6.2
1.2 4.6
1.01 ?

I can't figure out d crit for the gamma = 1.01 case because the bow shock is unstable. The simulations are consistent with the theory because of which simulations we see Mach stems:

gamma d Mach stem?
5/3 15 no
5/3 10 yes
5/3 5 yes
1.4 10 no
1.4 5 yes
1.2 5 no

All simulated models not listed in the table above did not show evidence of a Mach stem.

Fall back for a single star

fall back for single star

Meeting Update 07-17-2014

Visualizations

  • Transferring files from Bluestreak to grassdata as we get them.
  • Some of the more recent .bov files have been corrupted. Moving the chombos for those to my scratch space so we can do post processing again. Here is what we have so far:

GIF GIF

GIF GIF


Outreach

  • PREP Visit: I was invited by PREP (Pre-College Experience in Physics for Girls) to have lunch with the students, and come give a talk on what I had been working on this summer. Titled the talk, "Your Computer: The unexpected frontier in star formation." Covered what we do know about star formation, how colliding flows, and AstroBEAR contributes to the field. We derived the Jeans mass as done in Derek Ward-Thompson's book (i.e. it was not intimidating, just some variable manipulation), and gave them a problem where they can just plug in some numbers and determine whether a proto-star will collapse to a star. I promised them brownies if I got 10 answers by Friday this week. Showed them some simulations Erica and I had done, how we use computers to run code. They seemed most blown away by terminal and that your computer doesn't need to just be used for writing essays for AP English and using Facebook. A lot of good questions, very smart students. Someone from the group should visit them every year.
  • Horizons: Erica and I shared the lesson last week (Thursday, July 10th). We had 5 students: one kindergartener, one in third grade, and three who were in middle school. Erica tells me that we only had three this past Tuesday. Today I am hosting the session in collaboration with some graduate students in Optics. We're going to talk about the Sun and telescopes. Hoping if the weather permits (sadly it is expected to be partly cloudy around that time) we'll use a sun-scope and check out some sunspots. Optics is bring some pinhole cameras and telescope demos as they get a lot of this stuff via donation from Edmund Optics.

Bug? Bubbles in wind object

I tried to run a 2D simulation where a Wind passes by a Wire surrounded by a cylindrical magnetic field embedded inside an Ambient medium. Wire object extends Clump object to a cylindrical shape.

For this run,

the grid consists of a square of 2.5 mm; magnetic field at the wire surface is 7.5 T; Wind and Ambient temperature is 300 K; Wire temperature is 3e-3 K; Wind density is 1e-5 g/cc; Wire density is 7.5e-2 g/cc; Ambient density is 7.5e-7 g/cc; Wind velocity is 150 km/s.

sigma = 10 at surface of wire

Description of bug: bubbles inside the wind appear and grow to dominate the simulation.

MPEG attached.

Maximum time of movie does not exceed 0.6 ns. Left side: log density Right side: log energy

Intersecting Bow Shocks: Extended Boundaries

This is the gamma = 5/3, d = 15 model. I extended the left and right boundaries to be 20 clump radii away from each clump, and this was enough to ensure that the bow shocks do not hit those boundaries.

movie

I am in the process of making side by side comparisons of all the other models. I will post them to this page: ClumpClump/Morphology

Binary

The plot of isosurface of density. The disk is a little tilted.

isotopview.gif

isosideview.gif

Disk Space Usage

  • Local Machines
Machine Size Jonathan Shule Baowei Martin Eddie Erica
bambooData 12 TB 4 TB 3.4 TB 1.8 TB 1.2 TB ? 0.5 TB
alfalfaData 4.2 TB 1.8 TB 0.7 TB 0.06TB 1.1 TB 0.4 TB 0.2 TB
grassData currently unaccessible
  • CIRC 200GB ~1TB GB per user
  • XSEDE
    1. Ranch ( archival, only a single copy ): 12 TB
    2. Oasis (mounted, Data will be retained for three months beyond the end of the project): 3TB

Meeting update

Machines are almost full.

Here is an updated page of CF run stats:

http://astrobear.pas.rochester.edu/trac/wiki/u/erica/CFRunStatsHighRes

Meeting Update 07/07/2014 -- Baowei

  • Ablative RT
    1. Gave 2D text data to Rui. Haven't got update from him.
    2. Still debugging on 3D code.
  • Users
    1. Worked with Guilherme of SUNY Oswego installing openmpi and hypre.

Meeting Update 0707

  • Finished revising the triggering paper, sent to Adam and Eric earlier today.
  • Running the triggering test run with realistic setup according to Chevalier et al. The initial setup is shown below, the cloud is the same as before, centered at x = 3. Currently at frame 50 (100 frames total).

http://www.pas.rochester.edu/~shuleli/tsf_new_shock/images/shockstucture2_0000.png

Single and Binary

Start with single star. The mass loss rate vary wish time as (increase to 10 times at time=1.5 and reduce to 1/10 at time=3.0):

and I fix the velocity at certain radius so that mass loss rate is proportional to wind density. The velocity at exact radius is obtained by solving:

numerically. From isothermal condition(2000 K throughout space) we can get the velocity that certain radius.

Under these conditions, the single star simulation become:

(Picture on the left is rho + vector v, picture on the right is speed + vector v)

single.gif

Pick out the magnitude of velocity on x axis:

lineout.gif

The relative difference of final velocity to the solution from Parker's stellar wind model is around 5%.

Problem 1: It is not symmetric.

Problem 2: When the star has relatively low mass loss rate, the wind speed profile does not meet the Parker's solution and the stellar structure behaves like a bubble. Either there is some threshold for this boundary condition or something worse is out there.

Problem 3: The speed profile plot of x axis does not match the color plot at small radius.

Phenomenon: It already has some fall back behavior.

Then we put a secondary star near the primary star and let they do circular motion. Their separation is 3.999 AU. The mass of them are and respectively.

zoomout.gif

zoomin.gif

Problem: The CFL number blow up.

High CFL - restarting step. 0.43877E+07 > 0.10000E+03

forrtl: severe (174): SIGSEGV, segmentation fault occurred

When there is only the primary star, this does not occur, but when I add the secondary, it does.

The fall back phenomenon is not obvious at this time frame.

Meeting update for 07/03/2014

High Resolution CDM for Beta 10 cases 15, 60(ish)

Our high resolution colliding flows simulations are starting to come in. Erica went through post-processing and here are some CDM. Grass ended up crashing while I was making the Beta 10 Shear 60 gif, so I only have frames up to 64.

GIF

GIF

Binary and Accretion Disk

This is a zoomed in simulation. There is a disk around the secondary star. I did not make the point particle to actually accrete material. Please pay attention to Time>3 when mass loss rate drop again, it seems there is a fall back process.

Binary.gif

But I still encounter this (thus the program stuck here at Time=4):

High CFL - restarting step. 0.33520E+03 > 0.10000E+02

forrtl: severe (174): SIGSEGV, segmentation fault occurred

Is my physical resolution too high?

Mass loss rate vary with time as:

while v is constant thus density changes like Mass loss rate with time.