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

Thu May 23 19:57:32 UTC 2024

 Kaili, I believe you are unaffected by a rate floor when reading in an
external rate file as you are supplying the rate in this circumstance. I
was mistaken in initially suggesting there was a rate floor here.

-EbF

On Thu, May 23, 2024 at 11:58 AM Ebraheem Farag <ekfarag at asu.edu> wrote:

> It is present, but it only affects generalized networks with reactions
> that aren't contained within the standard scope of the hardwired networks
> such as "pp_and_cno_extras.net" or "co_burn.net" etc.. I believe all the
> core pp and cno reactions (not including be9 burning) are unaffected and
> are evaluated separately without a rate floor. This includes 'r_h2_pg_he3'.
> The floor exists because certain reactions coming out of the JINA reaclib
> database result in numerical issues in the cold regions of post-main
> sequence stars with very large general reaction networks. Hence, a rate
> floor was implemented for reactions which do not normally dominate the
> energy budget of the model. We're working to remove this, but you're always
> welcome to lower the floor to capture the other reactions if your model
> is unaffected. : &starjob 'jina_reaclib_min_T9 = '
>
> If you're curious which reactions are hardcoded, see
> $MESA_DIR/rates/raw_rates.f90.
>
> -EbF
>
> On Thu, May 23, 2024 at 11:16 AM Marc Pinsonneault <
> mhpinsonneault at gmail.com> wrote:
>
>> Is this reaction floor present for all reactions, or only for late stage
>> burning? We have seen reports on this list of Be9 burning being set to zero
>> below 10^7 K; how is p+d (critical for the pre-MS) treated?
>>
>> cheers
>>
>> marc
>>
>> On Wed, May 22, 2024 at 3:36 PM Ebraheem Farag via Mesa-users <
>> mesa-users at lists.mesastar.org> wrote:
>>
>>> 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
>>> $MESA_DIR/rates/private/rates_support.f90 to see how the rates are
>>> tabulated. The only course of action I can see at the moment is to rewrite
>>> this portion of the rates module which appears to interpolate over the rate
>>> in linear-log space, i.e. the raw/screened rate vs logT.
>>>
>>> I don't have any immediate solution for you, but this is a great issue
>>> for the MESAhub github
>>> <https://urldefense.com/v3/__https://github.com/MESAHub/mesa/issues__;!!IKRxdwAv5BmarQ!cwA7vnByCpKUIQ8GCMc_uq6jZysiv3RDUzCW-mYeOE4w5aSA9WolZvYDpG3zY3ixf0Gjr6WPUYamTDYpDt0-Mn1fV_Ys$>,
>>> 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$>,
>>>> NACRE II nuclear reaction rates are smooth functions of the temperature in
>>>> log-log space. However, MESA's interpolation scheme seems to be "wavy"
>>>> (best shown in the interval between first two NACRE II nodes).
>>>>
>>>> Are there scientifical justifications for the above choices? If not,
>>>> have these issues been addressed in r23.05.1, r24.03.1, or the development
>>>> version? Or do you have suggestions to make the results closer to what one
>>>> would expect from published tables and figures? Thank you.
>>>>
>>>> Cheers,
>>>> Kaili
>>>>
>>>>
>>>> ------------------------------
>>>> *From:* Mesa-users <mesa-users-bounces at lists.mesastar.org> on behalf
>>>> of Cao, Kaili via Mesa-users <mesa-users at lists.mesastar.org>
>>>> *Sent:* Saturday, May 18, 2024 9:43 AM
>>>> *To:* Ebraheem Farag <ekfarag at asu.edu>
>>>> *Cc:* mesa-users at lists.mesastar.org <mesa-users at lists.mesastar.org>
>>>> *Subject:* Re: [Mesa-users] [EXT] How to check a nuclear reaction rate?
>>>>
>>>> This Message Is From an External Sender
>>>> This message came from outside your organization.
>>>> Report Suspicious
>>>> <https://us-phishalarm-ewt.proofpoint.com/EWT/v1/KGKeukY!vIQcEWaND6YARRdwH-4E9wlFBBf_XzPeL4iwrAAzMJWVX_H1yXjAuZJtTvX8rXtCw1Ax1KTJsplG1ROx9KwsLQammciCxiJBWRSlOiJFnSzOTpJbPc0zTuD3-3NLmoI7ZnwMxG2TMqxXY31zQmg$>
>>>>
>>>> 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$>
>>>> Assistant Professor
>>>> University of Arizona & Steward Observatory
>>>> _______________________________________________
>>>> mesa-users at lists.mesastar.org
>>>>
>>>> https://urldefense.com/v3/__https://lists.mesastar.org/mailman/listinfo/mesa-users__;!!IKRxdwAv5BmarQ!foyQi1VBFivv-y4at5IxR0HkoxALt1Rstta9UwJqBMM8kJ_UfaXxwO9Qrm5MyeMiMleRNa7811_iIG1mJbHjW5zrweVEBw$
>>>>
>>>> _______________________________________________
>>>> mesa-users at lists.mesastar.org
>>>>
>>>> https://urldefense.com/v3/__https://lists.mesastar.org/mailman/listinfo/mesa-users__;!!IKRxdwAv5BmarQ!c4bjDS3MpzcYVlEzXF7wJX2bZDe29vLOaOhgvrkOWW5Wzf3oXksUkagITelOKylEOSB-tKTF-DhiqX-uzktLbt4SVH-O2A$
>>>>
>>>> _______________________________________________
>>> mesa-users at lists.mesastar.org
>>> https://lists.mesastar.org/mailman/listinfo/mesa-users
>>> <https://urldefense.com/v3/__https://lists.mesastar.org/mailman/listinfo/mesa-users__;!!IKRxdwAv5BmarQ!cwA7vnByCpKUIQ8GCMc_uq6jZysiv3RDUzCW-mYeOE4w5aSA9WolZvYDpG3zY3ixf0Gjr6WPUYamTDYpDt0-MrfF8QWm$>
>>>
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