New Wind Opacity Calculations
18Nov05 - with new versions of code

Goal: 1-D with realistic wind density profile, external photospheric BBdy field plus embedded x-rays: accurate ph-ix cross-sections for zeta Pup is the ultimate goal...

Step 1: make atomic models for just hydrogen, carbon, and iron - g.s. only (atomic model builder 2.7.4 and atbase v.5.1)

Step 2: do a test run in PrismSpect (v.3.2.0) (for comparison with Spect3d) - calc1_3elem.psi: key parameter is zero-width (1-sided external field, steady state, abund ratio .0001:.001:1...) - first simulation using this workspace = calc1_3elem_runA (ran in a few seconds - looking at ionization: HII, CV, FeV - opacity values seem reasonable: see plot below)

Step 3: very similar PrismSpect run, but with 1-D plasma rather than zero D: only changes were "planar, DeltaL, 1e11 cm" - calc1_3elem_runB - OK, results look very similar and it only took a few seconds to run

Step 4: run essentially the same calculation, but in Spect3D (v.5.3)

Spect3d questions for Joe: 

- First screen: hydrocode or single cell - I want multicell but not hydrocode (...no new plasma grid generator?) (later: OK, Joe answered these questions for me, will try using the plasma grid generator and export a exo file)

- "Plasma" panel - no ion/cc option (I used 1.67e-14 g/cc)...and 1.67e-3 g/cm2 for 'characteristic size' to get DeltaL=1e11cm; set mean atomic wt by hand (to 1.012)

- Kinetics Model panel - how should I set the C-R options? 

OK, basic workspace saved as calc1_3elem; first run *runSPa

First run took only a few seconds, but how to view ionization fractions and opacity (used spectral viewer to look at spectrum...)

 Joe says, need to use the drilldown option in the visualizer (not activated for a single-zone calc - PrismSpect is more sophisticated for single zone stuff)

Step 5: running plasma grid generator (v.2.1.1): made a one zone spherical object (after talking with Joe: save via file>export netCDF - it creates an exo file, which spect3d can just treat the same as a helios output file)

Step 6: running Spect3d with this exo file (but it's single zone, so...)

- Plasma tab is confusing ("material fractions"...)

- External Rad Source - only seems to allow it at Rmax (maybe that's because Rmin is zero in this case)

> simulation ran, but spectrum was flat.  

*maybe should first try to do a 1-D planar simulation, so it's comparable to the PrismSpect calc

21Nov05: 

Making a cartesian grid using the plasma grid generator (some questions about parameter choices for object properties...)

For spect3d, copied calc2_3elem workspace...changed input file... 
In the "plasma" tab of spect3d, I changed the "plasma properties" to "vol_fraction..." for both T and density (No, got error message that T and dens are both the same...)

First run from this workspace: calc2_cartesian1_3elem_runSPa

OK, ran without complaining and produced a reasonable looking spectrum; 
Now using "drilldown" option in visualizer to look at ionization fractions... 

Optical depth plot was automatically generated, and it looks reasonable: 

I'm wondering about the grid points, which I set to 3 in plasma grid gen... look at this: 

Where are the mass depth values coming from?  Why aren't properties uniform (all the other things - density, etc. look like this); in fact, here's the C ionization fractions:

...I thought that I'd set areal mass to 1.67e-3 (and I did set spatial extent of grid to 1e11 in pgg)

CIII and Fe IV are dominant (but Fe V was dominant in PrismSpect calc, I believe)

...conditions may be a little different due to temp specs in eV; I didn't convert them carefully.  Note also that the spatial (and other physical) properties of the grid are all specified in the exo file (thus by pgg), not in Spect3D input/params. 

28Nov05:

Setting up new exo file - cartesian grid still - everything the same, except more points within the grid

OK, now modifying the spect3d workspace to handle this new exo file: calc2_cartesian1_3elem_11gridpoints.spw

This run is called: calc2_cartesian1_3elem_runSPb

Hmmm... the drilldown output still doesn't look sensible (e.g. material properties like temperature that are *defined* to be constant aren't):

29Nov05

Heard back from Pam – the (or just “a”) problem is the detector settings.  I basically didn’t set them – there’s a third dimension that has to agree with the grid… Here’s Pam’s screenshot: 

I’m modifying my (same) workspace in accord with this… and running a new run from it: 

calc2_cartesian1_3elem_11gridpoints.spw

output: calc2_cartesian1_3elem_runSPc

(sent email to Pam…) 

Trying another run (same workspace, output *runSPd) with only change being a higher external rad temp (5.0 vs 3.2 eV). 

30Nov05

(Pam responded – see her email for expl of how to deal with coordinate systems, etc.)

Next step – do a Cartesian calc with a second, narrow and hot region : set up a new PGG workspace (modified from the current one), write out an exo file, and make a modified Spect3d workspace to run it. 

plasmagrid_cartesian1_1zone_11gridpoints.pgw > plasmagrid_cartesian1_2zones.pgw

Two objects – here are the three screens governing the properties of the original, larger object:

And here are the same screens for the second object: 

And here’s the main PGG interface:

plasmagrid_cartesian1_2zones.exo

calc2_cartesian1_3elem_2zones.spw

calc2_cartesian1_2zones_runA

(see also a new notes .doc)… 

{And I’d like to go back and test the sensitivity of the external radiation field temperature on the ionization balance}