[Mesa-users] Why does MESA interpret nuclear reaction rates this way?

Wed May 22 19:35:36 UTC 2024

Hi Kaili,

Thanks for raising this issue! As far as I'm aware, the rates are not
interpolated in log-log space as you've identified. This is the same case
for  the latest MESA release version. You can look into
$MESA_DIR/rates/private/rates_support.f90 to see how the rates are
tabulated. The only course of action I can see at the moment is to rewrite
this portion of the rates module which appears to interpolate over the rate
in linear-log space, i.e. the raw/screened rate vs logT.

I don't have any immediate solution for you, but this is a great issue for
the MESAhub github <https://github.com/MESAHub/mesa/issues>, if you'd like
to open an issue there, we can take a closer look and see what can be done
to address this in the near term and ultimately in a future MESA releases.

As for "C12(a,g)O16", this is a helium burning nuclear reaction rate which
only dominates near the end of Helium burning to set the C/O ratio for
later phases of evolution. This is to say the rate floor being at T8 = 0.6
should be a non-issue, although not ideal.

-EbF

On Tue, May 21, 2024 at 8:43 AM Cao, Kaili via Mesa-users <
mesa-users at lists.mesastar.org> wrote:

> Dear MESA developers and users,
>
> Thanks again to Mathieu (Renzo) for teaching me how to check nuclear
> reaction rates in MESA.
>
> Employing $MESA_DIR/rates/test/show_rates, I managed to visualize how MESA
> interprets NACRE II rates. Using h2_he3_to_h1_he4 as an example, the plot
> below compares MESA's interpretation (black curve; I have been using
> release/r22.11.1) with its underlying NACRE II data (red crosses) shipped
> with MESA ($MESA_DIR/data/rates_data/rate_tables/r_*_nacreII.dat).
>
> I find the results quite unsettling, principally for two reasons:
> - For temperatures below the first node or above the last one, it seems
> that MESA uses a nearest-neighbor extrapolator. For some reactions, e.g.,
> C12(a,g)O16, for which NACRE II starts at T8 = 0.6, this indicates that
> MESA assumes the rate at solar surface is identical to that at solar center.
> - As can be seen on http://www.astro.ulb.ac.be/nacreii/index.html
> <https://urldefense.com/v3/__http://www.astro.ulb.ac.be/nacreii/index.html__;!!IKRxdwAv5BmarQ!c4bjDS3MpzcYVlEzXF7wJX2bZDe29vLOaOhgvrkOWW5Wzf3oXksUkagITelOKylEOSB-tKTF-DhiqX-uzktLbt5ZPrySVg$>,
> NACRE II nuclear reaction rates are smooth functions of the temperature in
> log-log space. However, MESA's interpolation scheme seems to be "wavy"
> (best shown in the interval between first two NACRE II nodes).
>
> Are there scientifical justifications for the above choices? If not, have
> these issues been addressed in r23.05.1, r24.03.1, or the development
> version? Or do you have suggestions to make the results closer to what one
> would expect from published tables and figures? Thank you.
>
> Cheers,
> Kaili
>
>
> ------------------------------
> *From:* Mesa-users <mesa-users-bounces at lists.mesastar.org> on behalf of
> Cao, Kaili via Mesa-users <mesa-users at lists.mesastar.org>
> *Sent:* Saturday, May 18, 2024 9:43 AM
> *To:* Ebraheem Farag <ekfarag at asu.edu>
> *Cc:* mesa-users at lists.mesastar.org <mesa-users at lists.mesastar.org>
> *Subject:* Re: [Mesa-users] [EXT] How to check a nuclear reaction rate?
>
> This Message Is From an External Sender
> This message came from outside your organization.
> Report Suspicious
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>
> Hello Eb,
>
> Thanks. I removed reactions not in pp_and_cno_extras and it worked. The
> test rates (r1 to r9) and those for al26 isomers are also not included, so
> I thought redundant rates were fine, but I was wrong.
>
> Cheers,
> Kaili
> ------------------------------
> *From:* Ebraheem Farag <ekfarag at asu.edu>
> *Sent:* Saturday, May 18, 2024 4:16 AM
> *To:* Cao, Kaili <cao.1191 at buckeyemail.osu.edu>
> *Cc:* mesa-users at lists.mesastar.org <mesa-users at lists.mesastar.org>
> *Subject:* Re: [Mesa-users] [EXT] How to check a nuclear reaction rate?
>
> Hello Kaili,
>
> The isotope li6 is not contained in the 'pp_and_cno_extras.net
> <https://urldefense.com/v3/__http://pp_and_cno_extras.net__;!!KGKeukY!wRpNUs2FYL9xM-l5TQ68oEWuZPWUU2fsjtBKO3aUGUFGOn32_m3SRislwndYL2tTCECDplkDSyamxc4P899l8CxNO3dG$>',
> let alone that reaction rate. You'll have to decide whether this is a
> reaction you need for your science or not. If so, you can make your own
> network to include it.
>
> -EbF
>
> On Fri, May 17, 2024 at 7:15 AM Cao, Kaili <cao.1191 at buckeyemail.osu.edu>
> wrote:
>
> Hello Eb,
>
> Thank you for your previous help regarding nuclear reaction rates and
> local cache directories.
>
> Following your instructions, specifically your method 3, I made a local
> copy of rate_tables/, and added lines like:
> r_h1_h1_ag_li6         'r_h1_h1_ag_li6_nacreII.dat'
> into rate_list.txt therein.
>
> However, when I tried to ./rn the model, I got:
> add_reaction_for_handle failed in reaclib_parse_handle r_h1_h1_ag_li6
>  invalid rate file r_h1_h1_ag_li6
>  rates_init failed in init_raw_rates_records
>  read_raw_rates_records failed in net_setup_tables
>  set_net failed in net_tables
>  failed in set_net
>
> I have been using MESA release/r22.11.1, and
>       change_net = .true.
>       new_net_name = 'pp_and_cno_extras.net
> <https://urldefense.com/v3/__http://pp_and_cno_extras.net__;!!KGKeukY!wRpNUs2FYL9xM-l5TQ68oEWuZPWUU2fsjtBKO3aUGUFGOn32_m3SRislwndYL2tTCECDplkDSyamxc4P899l8CxNO3dG$>
> '
>
> Is there anything else I need to do if I want to use NACRE II rates?
> Please let me know if you need additional information. Thanks.
>
> Cheers,
> Kaili
> ------------------------------
> *From:* Mesa-users <mesa-users-bounces at lists.mesastar.org> on behalf of
> Cao, Kaili via Mesa-users <mesa-users at lists.mesastar.org>
> *Sent:* Thursday, March 28, 2024 9:32 AM
> *To:* Ebraheem Farag <ekfarag at asu.edu>
> *Cc:* mesa-users at lists.mesastar.org <mesa-users at lists.mesastar.org>
> *Subject:* Re: [Mesa-users] [EXT] How to check a nuclear reaction rate?
>
> Hello Eb,
>
> Thank you for sharing these approaches, and sorry for the delay. I think
> your method 3 is especially good for running models in parallel.
>
> Cheers,
> Kaili
> ------------------------------
> *From:* Ebraheem Farag <ekfarag at asu.edu>
> *Sent:* Tuesday, March 26, 2024 9:08 PM
> *To:* Cao, Kaili <cao.1191 at buckeyemail.osu.edu>
> *Cc:* Mathieu Renzo <mrenzo at arizona.edu>; mesa-users at lists.mesastar.org <
> mesa-users at lists.mesastar.org>
> *Subject:* Re: [Mesa-users] [EXT] How to check a nuclear reaction rate?
>
> Hello Kaili,
>
> Yes, it's probably wise to always clear the cache if you are going to
> regenerate new rates, just in case.
>
> 1- Setting those controls in the inlists is one approach, especially if
> you want to provide a special rate factor.
> 2- Another approach is to change the global default in MESA by navigating
> to $MESA_DIR/star/data/rate_tables/rate_list.txt and adding a line that
> says 'r_n14_pg_o15     r_n14_pg_o15_nacreII.dat'.
> 3- One more approach (that I personally opt for in most cases) is to
> repeat 2 but with a local copy of /rate_tables in your MESA model folder.
> MESA should by default use this local rate_tables directory over the main
> default.
>
> In fact, in most of my inlists, I place the following in star_job so that
> my rate_tables and rates_cache are stored locally with some other caches
> and not bound to MESA's default rates or other data folders. (useful for
> running on a cluster)
>
> ! local directories data
>       mesa_dir =''
>       eosDT_cache_dir      = './eosDT_cache'
>       kap_cache_dir        = './kap_cache'
>       rate_tables_dir      = './rate_tables'
>       rates_cache_dir      = './rates_cache'
>
> > Would this be due to different forms of fitting functions?
> Possibly, MESA constructs its own piecewise monotonic cubic spline
> functions to interpolate and tabulate the rate. You can find the calls that
> do this in the same raw_rates.f90 file I referred to previously.
>
> -EbF
>
> On Tue, Mar 26, 2024 at 5:44 PM Cao, Kaili <cao.1191 at buckeyemail.osu.edu>
> wrote:
>
> Hello Eb,
>
>
> Thanks a lot for this information.
>
>
> Following the changelog, I suppose if I want to replace the default 14N
> proton capture rate with the NACRE II value shipped with MESA, I should
> write:
>
> num_special_rate_factors = 1
>
> reaction_for_special_factor(1) = 'r_n14_pg_o15'
>
> special_rate_factor(1) = 1
>
> filename_of_special_rate(1) = 'r_n14_pg_o15_nacreII.dat'
>
> in my inlists, and run $MESA_DIR/empty_caches before running my models;
> and if I want to replace multiple rates, I set num_special_rate_factors to
> the number I want and define other entries in a similar way. Please tell me
> if this is wrong, thank you.
>
>
> I have not changed nuclear reaction rates before, so I should have been
> using the defaults. I used `show_rates` to convert r_n14_pg_o15_1.bin, and
> the txt file tells me that:
>
> when T8 = 1.0000690699539715E-01, rate = 2.0247671654597788E-022.
>
> However, this is slightly (about 3.3%) below the NACRE rate provided by
> REACLIB Database
>
> https://reaclib.jinaweb.org/n14(p,g)o15/nacr/
> <https://urldefense.com/v3/__https://reaclib.jinaweb.org/n14(p,g)o15/nacr/__;!!IKRxdwAv5BmarQ!Z-CvDte8VjT4Inevmze_uCwVFvUjK3D6-CqjkxLALmrWBnmcVoiN3LIAbdO7AujD4bq5F0RgnDTghEqcs_gG6NChnPveJPM$>
>
> which claims: when T9 = 1.0000690699539715E-02, rate = 2.09489965936E-22.
>
> Could this be due to different forms of fitting functions? Thanks.
>
>
> Cheers,
>
> Kaili
> ------------------------------
> *From:* Ebraheem Farag <ekfarag at asu.edu>
> *Sent:* Tuesday, March 26, 2024 6:58 PM
> *To:* Cao, Kaili <cao.1191 at buckeyemail.osu.edu>
> *Cc:* Mathieu Renzo <mrenzo at arizona.edu>; mesa-users at lists.mesastar.org <
> mesa-users at lists.mesastar.org>
> *Subject:* Re: [Mesa-users] [EXT] How to check a nuclear reaction rate?
>
> Hello Kaili and thanks Mathieu,
>
> Be careful that you are sure which rate you are reading in. The default
> n14pg rate in MESA is from NACRE1, and is set in
> $MESA_DIR/rates/private/raw_rates.f90
> <https://urldefense.com/v3/__https://github.com/MESAHub/mesa/blob/5992b8ed6c3033a560ee4361f4cc86335c2bb6f4/rates/private/raw_rates.f90*L239__;Iw!!KGKeukY!zVv5mOzul0tRIDw0i-sHh034ARffwLjtJr6Dx4ry-uN7hRx4Tqorb_93tx9KO1RmpSUQcSGJSwue5kueu_2eyYbXs7cD$>
> :
> 239            case(ir_n14_pg_o15)
> 240               call do1(rate_n14pg_nacre)
>
> The controls for changing which n14_pg rate you adopt have been removed,
> but you can still adopt the rate by placing it in your local ./rate_tables
> directory or the global one that lives in
> $MESA_DIR/data/rates_data/rate_tables. See the changelog for rates in
> version r22.05.1
> <https://urldefense.com/v3/__https://docs.mesastar.org/en/release-r24.03.1/changelog.html*id10__;Iw!!KGKeukY!zVv5mOzul0tRIDw0i-sHh034ARffwLjtJr6Dx4ry-uN7hRx4Tqorb_93tx9KO1RmpSUQcSGJSwue5kueu_2eyZmYtvWT$>
> which describes all of this in detail.
>
> The default $MESA_DIR/data/rates_data/rate_tables directory also provides
> the n14_pg rate from cf88 as well as NACREII if you want to give those a
> try.
>
> Cheers,
> EbF
>
> On Tue, Mar 26, 2024 at 2:25 PM Cao, Kaili via Mesa-users <
> mesa-users at lists.mesastar.org> wrote:
>
> Dear Mathieu,
>
> Thank you very much for your quick reply! The `show_rates` script is very
> handy.
>
> For those who are interested, I checked several values and found a slight
> disagreement between MESA and JINALAB. I will think more about this.
>
> Cheers,
> Kaili
>
> ------------------------------
> *From:* Mathieu Renzo <mrenzo at arizona.edu>
> *Sent:* Tuesday, March 26, 2024 4:47 PM
> *To:* mesa-users at lists.mesastar.org <mesa-users at lists.mesastar.org>
> *Cc:* Cao, Kaili <cao.1191 at buckeyemail.osu.edu>
> *Subject:* Re: [EXT][Mesa-users] How to check a nuclear reaction rate?
>
> Dear Kaili,
>
> there is a way to have MESA print out in a txt file the value of the rate
> used for a specific reaction as a function of T. This requires using a
> small script called `show_rates` to convert rates cached in binary format
> into a human-readable format. The script is available in
> $MESA_DIR/rates/test, see also the relevant section in the documentation
> <https://urldefense.com/v3/__https://docs.mesastar.org/en/latest/net/nets.html*inspect-the-temperature-dependence-of-used-rates__;Iw!!KGKeukY!0QlmTdnJvC0E1CaZrSUz7TvYvpiV-rjmVoz9yx6tnS8Bq_rNHy-Qb3j8dCKZJbXvYMrjHylRUXvL-uRn3JfLrjyeo4yp7N0$>
> .
>
> Hope this helps!
> Mathieu (with many thanks to Rob Farmer who taught me how to do this)
>
>
> On 3/26/24 13:41, Cao, Kaili via Mesa-users wrote:
>
> *External Email*
>
> Dear MESA Users,
>
>
>
> Thank you for reading this email.
>
>
>
> I would like to ask about how to check a nuclear reaction rate used in
> MESA, specifically the proton capture rate of 14N, which was halved in
> 2006 and is important for my purposes.
>
>
>
> I understand that the jina_reaclib_filename control is default to "current
> standard version," but I find the corresponding file
> (jina_reaclib_results_20171020_default) hard to decipher, and I wish to
> make a direct comparison to:
>
> https://reaclib.jinaweb.org/n14(p,g)o15/im05/
> <https://urldefense.com/v3/__https://reaclib.jinaweb.org/n14(p,g)o15/im05/__;!!KGKeukY!0QlmTdnJvC0E1CaZrSUz7TvYvpiV-rjmVoz9yx6tnS8Bq_rNHy-Qb3j8dCKZJbXvYMrjHylRUXvL-uRn3JfLrjyefN_wm2c$>
>
>
>
> Can someone please confirm that this rate is up to date, or instruct me
> how to check it? Thanks a lot.
>
>
>
> Best regards,
>
> Kaili Cao
>
> _______________________________________________mesa-users at lists.mesastar.orghttps://lists.mesastar.org/mailman/listinfo/mesa-users <https://urldefense.com/v3/__https://lists.mesastar.org/mailman/listinfo/mesa-users__;!!KGKeukY!0QlmTdnJvC0E1CaZrSUz7TvYvpiV-rjmVoz9yx6tnS8Bq_rNHy-Qb3j8dCKZJbXvYMrjHylRUXvL-uRn3JfLrjye3_SwXpY$>
>
>
> --
> Mathieu Renzo
> <https://urldefense.com/v3/__https://users.flatironinstitute.org/*mrenzo/__;fg!!KGKeukY!0QlmTdnJvC0E1CaZrSUz7TvYvpiV-rjmVoz9yx6tnS8Bq_rNHy-Qb3j8dCKZJbXvYMrjHylRUXvL-uRn3JfLrjyeqnLyNwI$>
> Assistant Professor
> University of Arizona & Steward Observatory
> _______________________________________________
> mesa-users at lists.mesastar.org
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>
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