[mesa-users] MESA code Questions!!

Wed Jul 15 15:20:32 EDT 2015

Hi Ebraheem,

You may have found these, but for any other new users following the 
thread...

Profiles are saved as text files in the LOGS subdirectory.  They include 
the things that you specify in your profile_columns.list. The format is 
mostly self-explanatory, but basically is two lines of header about that 
timeslice (age, total stellar mass, etc) followed by a blank line, 
followed by two lines of header of what the columns are, followed by the 
profile with one zone per line.

If you are wondering which profile goes with which timestep, you should 
look in LOGS/profiles.index, which gives a list of which file number 
("profile number") corresponds to which timeslice, ("model number" in 
mesa parlance).

There are parameters that control when profile files are created. You 
can read about them here:
  http://mesa.sourceforge.net/controls_defaults.html#controls_for_output
For example, the profile write interval in number of models is 
"profile_interval".

Also there are a few controls also in
http://mesa.sourceforge.net/star_job_defaults.html#output
like for writing a profile outside the LOGS on termination or writing a 
profile at a specific model number.

Since you have already put the sound speed in your profile_columns.list 
so that you can use it in pgstar, and radius is in there by default, I 
think you should already have the data that you want sitting it a 
profile file.

Hope that helps,
Dean

On 07/13/2015 04:38 PM, Farag, Ebraheem Khaled wrote:
> thanks again, that was very helpful. I was wondering about one more 
> thing. How should i go about outputting the sound speed vs radius into 
> a .data file? I probed the pgstar defaults for some answers about 
> possibly saving models and how they might relate but I'm not sure i 
> found anything useful in relation to my goals
> ------------------------------------------------------------------------
> *From:* Bill Paxton [paxton at kitp.ucsb.edu]
> *Sent:* Monday, July 13, 2015 12:11 PM
> *To:* Farag, Ebraheem Khaled
> *Cc:* mesa-users group
> *Subject:* Re: [mesa-users] MESA code Questions!!
>
> take a look at star/test_suite/example_solar_model/inlist_solar_model. 
>   it does this
>       ! atomic diffusion
>       do_element_diffusion = .true. ! determines whether or not we do 
> diffusion
>       diffusion_dt_limit = 7d11 ! no element diffusion if dt < this 
> limit (in seconds)
>       diffusion_T_full_on = 1d3
>       diffusion_T_full_off = 1d3
>       diffusion_calculates_ionization = .true.
>
>       diffusion_num_classes = 4 ! number of classes of species for 
> diffusion calculations
>       diffusion_class_representative(1) = 'h1'
>       diffusion_class_representative(2) = 'he4'
>       diffusion_class_representative(3) = 'o16'
>       diffusion_class_representative(4) = 'fe56'
>       ! in ascending order.  species goes into 1st class with A_max >= 
> species A
>       diffusion_class_A_max(1) = 2
>       diffusion_class_A_max(2) = 4
>       diffusion_class_A_max(3) = 16
>       diffusion_class_A_max(4) = 10000
>       diffusion_use_isolve = .true.
>       diffusion_rtol_for_isolve = 1d-4
>       diffusion_atol_for_isolve = 1d-5
>       diffusion_maxsteps_for_isolve = 1000
>       diffusion_isolve_solver = 'ros2_solver'
>
> b
>
>
> On Jul 13, 2015, at 11:06 AM, Farag, Ebraheem Khaled wrote:
>
>> how exactly do i turn it on?
>> ------------------------------------------------------------------------
>> *From:*Josiah W. Schwab [jwschwab at berkeley.edu]
>> *Sent:*Monday, July 13, 2015 12:06 PM
>> *To:*Bill Paxton
>> *Cc:*Farag, Ebraheem Khaled; mesa-users group
>> *Subject:*Re: [mesa-users] MESA code Questions!!
>>
>> No, Ebraheem has not turned on diffusion.  Perhaps my reply was too 
>> oblique of a hint to do so :)
>>
>> Josiah
>>
>> On Mon, Jul 13, 2015 at 10:59 AM, Bill Paxton<paxton at kitp.ucsb.edu 
>> <mailto:paxton at kitp.ucsb.edu>>wrote:
>>
>>     diffusion is not turned on by default, but I assume you have
>>     turned it on as in the sample solar model test case.
>>     even with diffusion on, the surface layers may be mixed into the
>>     convective region, so you'll only see changes in abundances that
>>     impact the entire convective region.  such things might happen --
>>     but only if the burning effects are getting into the convective
>>     region somehow.  i'm not an expert of that question, but I
>>     believe there are some folks on mesa-users who have considered
>>     this (Matteo?).
>>
>>     b
>>
>>
>>
>>
>>     On Jul 13, 2015, at 10:46 AM, Farag, Ebraheem Khaled wrote:
>>
>>     > The other models, I've seen from lanl pulsation codes are using
>>     Burgers' diffusion treatment as implemented by cox et al.(1989)
>>     and nuclear reaction rates from Angulo et al.(1999) with
>>     correction to the N14 rate from FOrmicola et al.(2004)
>>     >
>>     > -I'm trying to mirror these abundance models through MESA by
>>     using unreleased Opacity tables
>>     >
>>     > does this provide any info?
>>     > ________________________________________
>>     > From: Josiah Schwab [jwschwab at berkeley.edu
>>     <mailto:jwschwab at berkeley.edu>]
>>     > Sent: Monday, July 13, 2015 11:30 AM
>>     > To: Farag, Ebraheem Khaled
>>     > Cc: Francis Timmes; mesa-users
>>     > Subject: Re: [mesa-users] MESA code Questions!!
>>     >
>>     > Hi Ebraheem,
>>     >
>>     >> I'm only having one small strange problem.
>>     >>
>>     >> my surface abundances are exactly the same over the whole
>>     lifespan of
>>     >> the sun. is there something wrong with my model?
>>     >>
>>     >> This is very saddening to see. A fix would be greatly appreciated!
>>     >
>>     > What physics do you think will cause them to change?
>>     >
>>     > Josiah
>>     >
>>     >
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