[Mesa-users] Resolved Mesastar Question re Setting Initial CO Abudance Enhancements

Tue Aug 6 03:12:14 UTC 2024

HI Warrick (and all),

That indeed solved the issue! Thank you very much.

Just in case anyone else ends up facing this issue: I ended up taking the
mass fraction values for h1, h2, he3, and he4 for the sun from Lodders
(2009), which are given inside data/chem_data/lodders09.data, and altering
the values to match my required X and Y fractions. I note that this
approach works since the stars I am working on have near-solar X and Y mass
fractions (i.e., X=0.732, Y=0.26), so the modifications to the H and He
isotope mass fractions were only minor.

Thank you to all who have responded to my initial email and helped me solve
this issue.

Kind regards,
Kayla.

On Mon, Aug 5, 2024 at 7:26 PM Warrick Ball <W.H.Ball at bham.ac.uk> wrote:

> Hi Kayla,
>
> I haven't been following this conversation closely but at a glance it
> looks like the issue is that the `&star_job` part of your inlist has:
>
>        initial_h1 = -1
>        initial_h2 = -1
>        initial_he3 = -1
>        initial_he4 = -1
>
> and that's what the model is using for the initial H and He abundances.
> You mentioned that you're trying to create a model with X=0.732 and Y=0.26,
> so presumably you want `initial_h1` and `initial_h2` to add up to 0.732 and
> `initial_he3` and `initial_he4` to add up to 0.26.
>
> I can't remember offhand where to look (and won't have time until much
> later today) but IIRC the defaults to give reasonable values of the
> relative quantities of each isotope to use.
>
> Regards,
> Warrick
>
> ___________
>
> Warrick Ball
> Senior Research Software Engineer
> University of Birmingham
> W.H.Ball at bham.ac.uk
>
> On Mon, 5 Aug 2024, KAYLA MARTIN via Mesa-users wrote:
>
> > CAUTION: This email originated from outside the organisation. Do not
> click links or open attachments unless you recognise the sender and know
> the content is safe.
> > Hi Lynn, Evan,
> > I am wondering if I could get your help with problem solving for the
> method you suggested.
> >
> > As far as I can tell, I am implementing the z_fraction_* settings
> correctly. However, when I try to run my model it only just gets past
> relax_to_radiative_core before throwing an error(?) about the custom
> composition. Based on O_cntr and other
> > similar values printed to the terminal before the error, the
> z_fraction_* specifications seem to have worked... so, I am not sure why
> the model is not then continuing to evolve past this point -- I am not even
> certain if the pre-MS model is created
> > before the error occurs.
> >
> > I have attached a text log of the terminal output (incl. the error at
> the end), as well as a copy of my inlist. Are you able to take a brief look
> and let me know what I may be missing? Any suggestions on how to get past
> this point? I am having no
> > luck.
> >
> > Kind regards,
> >
> > Kayla Martin --
> > PhD Candidate (Astronomy & Astrophysics)
> > Administration Assistant, Association for Astronomy
> > Desk 504, 12 Wally’s Walk (Level 5), Macquarie University
> >
> >
> > On Fri, Aug 2, 2024 at 12:48 AM Buchele, Lynn <lynn.buchele at h-its.org>
> wrote:
> >
> >       Dear Kayla (sending this again as I forgot to cc the mailing list)
> ,
> >       I can give an initial answer to your questions, although others on
> the list may have more details to add. For setting the composition, I'm
> guessing that your composition changes are at the level of elements, not
> isotopes.
> >       In this case (and assuming you create your model with either
> create_pre_main_sequence_model or create_initial_model), you can set
> >       set_uniform_initial_composition = .true. and
> >       initial_zfracs = 0 in star jobs and set the element abundances
> using
> >       z_fraction_* in the controls section (
> https://docs.mesastar.org/en/release-r24.03.1/reference/controls.html#accretion-dump-missing-metals-into-heaviest
> this points to a section about accretion but the z_fraction_* controls are
> also used
> >       in generating an initial model). For this, you need to set all the
> elements and have them sum to one.
> >
> >       If you want to make changes to the abundance of isotopes (rather
> than elements) you can use set_uniform_initial_xa_from_file, see
> https://docs.mesastar.org/en/release-r24.03.1/reference/star_job.html#set-uniform-initial-xa-from-file
> .
> >
> > As for custom opacity tables, you are correct that AESOPUS only provides
> low temperature opacity tables. It looks like the webpage for generating
> custom OPAL tables is down, but you might be able to use OP tables which
> you can generate here:
> > http://op-opacity.obspm.fr/opacity/
> > The caveat is that these only generate type 1 tables, which won't
> account for changes in the C/O ratio. If you're only dealing with hydrogen
> burning, this shouldn't be a problem. You can look at when MESA (by
> default) starts using type 2 tables
> > here:
> https://docs.mesastar.org/en/release-r24.03.1/kap/defaults.html#use-type2-opacities
> > If you do need type 2 tables, perhaps someone else on the mailing list
> has a suggestion for how to generate them.
> > I think the preprocessor instructions given in the README should work
> (you can use the inlist_OP_* as a template since your custom files should
> be in the same format). The inlists discussed here are inlists for the
> opacity preprocessor, not the
> > star kap insists, so they will have different options available.
> Otherwise, you can provide information about the structure of the tables in
> the kap inlist using the controls described here:
> >
> https://docs.mesastar.org/en/release-r24.03.1/kap/defaults.html#custom-tables
> .
> > For the lowT AESOPUS tables, you only need to use the inlist parameter
> AESOPUS_filename.
> >
> > Hopefully this helps!
> >
> >
> > Best,
> > Lynn
> >
> >
> __________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________
> > From: Mesa-users <mesa-users-bounces at lists.mesastar.org> on behalf of
> KAYLA MARTIN via Mesa-users <mesa-users at lists.mesastar.org>
> > Sent: Thursday, August 1, 2024 9:48:50 AM
> > To: mesa-users at lists.mesastar.org
> > Subject: [Mesa-users] Mesastar Question: Setting Initial CO Abudance
> Enhancements
> >
> > This email originates from an external sender. Please verify the
> sender's identity carefully before opening any attachments or links!
> >
> > Hi,
> > This is my first post on the mesa user list.
> >
> > I am creating a model with X=0.732, Y=0.26, and Z=0.008, with the
> chemical composition mixture of Grevesse & Sauval (1998). In this model, I
> need to set [O/Fe]=+0.2 (equivalent to [O/H]=-0.1 or X(O)=0.0042), though I
> cannot see a clear way to
> > implement this in my model.
> >
> > I have attempted to create an opacity table using the AESOPUS tool,
> though it seems this only applies at 'low temperatures' (the tool won't let
> me set higher than Teff=log3.7)? Further, the implementation of the tables
> generated from this tool
> > are unclear -- the related instructions in mesa have outdated
> information (last updates ~2013), and contains variables that no longer
> exist in more recent mesa versions (e.g.,
> $MESA_DIR/kap/preprocessor/README_creating_OPAL_type2_tables notes
> > inlist variables such as Zfrac_O).
> >
> > Any guidance on how to correctly specify the initial oxygen abundance in
> my model with a gs98 reference solar composition will be very helpful.
> >
> > Thanks!
> >
> >
> >
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