[mesa-users] [MESA]: Question Astrophysical Factor

Robert Farmer rjfarmer at asu.edu
Mon Nov 7 13:35:18 EST 2016 

Hi

Does having the rates_table option as:
rate_tables_dir = './rates_tables'  (put a ./ in front of the folder name)
Work for you? for loading the rates from a local folder called rates_table

Convergence issues are hard to fix normally and even harder to do during
the pre-MS.

First test, does the model work okay without the new rates, given all the
other options you have set?

Some options that may or may not work for you:

Don't make your own pre-MS star, (create_pre_main_sequence_model = .false.)
MESA will load a pre-built model and then continue the evolution with your
inlist options

set pre_ms_relax_num_steps = 100 this makes MESA take more steps during the
pre-MS so the change per-step is smaller and it might be easier to converge
the results

Make a pre-MS model with the rate changes off, save a photo, stop the run
then restart from the photo with the rates on (a more complicated and
manual way of running the first option)

Change mixing_length_alpha (again you can always change it after the pre-MS
has finished by stopping the run, changing the file and restarting from a
photo)

Rob


On Sun, Nov 6, 2016 at 4:45 PM, Gonçalo Andrade <gnmandrade at hotmail.com>
wrote:

> Hi Robert
>
>
> Since our last email I've been trying to solve this problem.
> I've fixed some errors but others have appeared.
>
>
> 1) I was misunderstanding how MESA uses the nuclear tables directory. By
> looking at the error messages I saw that MESA instead of using the folder
> inside the working directory (where I have my inlists and stuff like that),
> it ads whatever I put as argument in the
>
> rate_tables_dir = 'rates_tables'
>
> to the folder
>
> $MESA_DIR/data/rates_data/
>
> So I need to place my tables in this directory.
>
>
>
>
> 2) After "solving" this problem, the code stopped ignoring my tables and
> started to output error messages saying "segmentation fault". This was easy
> to solve, it was only due to errors in the files' names.
>
>
>
> 3) I now think I've managed to get the code reading the tables, but each
> time I change a reaction the code doesn't run because it has convergence
> problems. I've already tried a wide range of values in the rate files.
> I've changed some things, so I send you as an attachment my current inlist
> files, my rate files and a print of the error message.
>
>
> Thank you,
> Gonçalo
>
>
> ------------------------------
> *De:* Robert Farmer <rjfarmer at asu.edu>
> *Enviado:* 1 de novembro de 2016 17:35
>
> *Para:* Gonçalo Andrade
> *Cc:* mesa-users at lists.sourceforge.net users
> *Assunto:* Re: [mesa-users] [MESA]: Question Astrophysical Factor
>
> Hi
>
> So looking over your files
>
> When the run starts you see MESA prints out a list of isotopes and
> abundances, there is no h2 printed at all, this means there is no h2 in
> your nuclear networks. You need to remove the comment in you
> add_test_nuclear file on the add_isos(h2) file.
>
> Also maybe just a copy error, but in the rate file the temperature should
> be in units of 10^8 not 10^9 as your comment in the file suggests
>
> Rob
>
>
> On Tue, Nov 1, 2016 at 3:59 AM, Gonçalo Andrade <gnmandrade at hotmail.com>
> wrote:
>
>> Hi
>>
>>
>>
>> I've fixed that detail on the rates_list.txt, but the result was the
>> same. It doesn't change a bit and I've put some really big numbers on the
>> rates of the pp reaction so I think it should have a major impact on the
>> model.
>>
>>
>> I now tried changing the first line of rpp_to_he3.txt from low rate to
>> high rate, but I'm still waiting for the results.
>>
>>
>>
>> Thank you,
>>
>> Gonçalo
>>
>>
>> ------------------------------
>> *De:* Robert Farmer <rjfarmer at asu.edu>
>> *Enviado:* 31 de outubro de 2016 20:06
>>
>> *Para:* Gonçalo Andrade
>> *Cc:* mesa-users at lists.sourceforge.net users
>> *Assunto:* Re: [mesa-users] [MESA]: Question Astrophysical Factor
>>
>> Hi
>>
>> your rates_list.txt has the line
>>
>> r_pp_to_he3     'rpp_tp_he3.txt'
>>
>> guessing it should be:
>>
>> r_pp_to_he3     'rpp_to_he3.txt'
>>
>> Rob
>>
>>
>> On Mon, Oct 31, 2016 at 1:00 PM, Gonçalo Andrade <gnmandrade at hotmail.com>
>> wrote:
>>
>>> Hi
>>>
>>>
>>> >So you have a modified network, does this network include the reaction
>>> you want? you have the list_net_reactions = .true. so check that list to
>>> see if your desired reaction is there.
>>>
>>> I've tried with the other networks (commented) and It seemed not to
>>> work, so I tried modifying it but the result was practically the same.
>>>
>>>
>>> > What does rate_tables/rates_list.txt look like? What does the rates
>>> file you are using look like? What does your network look like?
>>>
>>> I think I attached all the relevant files. I created a folder called
>>> "nets" for the networks.
>>>
>>> Gonçalo
>>>
>>> ------------------------------
>>> *De:* Robert Farmer <rjfarmer at asu.edu>
>>> *Enviado:* 31 de outubro de 2016 19:50
>>> *Para:* Gonçalo Andrade
>>> *Cc:* mesa-users at lists.sourceforge.net users
>>>
>>> *Assunto:* Re: [mesa-users] [MESA]: Question Astrophysical Factor
>>>
>>> Hi
>>>
>>> >new_net_name = 'mod_cno_extras_o18_and_ne22.net'
>>>
>>> So you have a modified network, does this network include the reaction
>>> you want? you have the list_net_reactions = .true. so check that list to
>>> see if your desired reaction is there.
>>>
>>> What does rate_tables/rates_list.txt look like? What does the rates file
>>> you are using look like? What does your network look like?
>>>
>>> Rob
>>>
>>>
>>> On Mon, Oct 31, 2016 at 12:28 PM, Gonçalo Andrade <
>>> gnmandrade at hotmail.com> wrote:
>>>
>>>> Hi
>>>>
>>>>
>>>> > Please keep replies on the mesa users list, others may be able to
>>>> help and may be helped by any response.
>>>>
>>>> Thanks for you advice!
>>>>
>>>> > Did you alter your star_job inlist to point to the rates folder? I
>>>> would need to see your inlists, folder structure and rates files to see
>>>> whats gone wrong.
>>>>
>>>> I think I did. I added the line:
>>>>
>>>>   rate_tables_dir = './rate_tables'
>>>>
>>>> on my inlist and put the files on that folder.
>>>>
>>>> I send my inlist as an attachment, maybe that helps.
>>>> It also has a commented section using the special rate factor command,
>>>> I tried it because of another member's advice, but I think it doesn't allow
>>>> me to test the astrophysical  as I need.
>>>>
>>>>
>>>> Thanks for the rest of the information.
>>>>
>>>> Gonçalo Andrade
>>>>
>>>>
>>>> ------------------------------
>>>> *De:* Robert Farmer <rjfarmer at asu.edu>
>>>> *Enviado:* 31 de outubro de 2016 18:18
>>>> *Para:* Gonçalo Andrade; mesa-users at lists.sourceforge.net users
>>>>
>>>> *Assunto:* Re: [mesa-users] [MESA]: Question Astrophysical Factor
>>>>
>>>> Hi
>>>> Please keep replies on the mesa users list, others may be able to help
>>>> and may be helped by any response.
>>>>
>>>> >I've created the rate_tables directory and put the files there as you
>>>> said but the code seems to ignore my tables.
>>>>
>>>> Did you alter your star_job inlist to point to the rates folder? I
>>>> would need to see your inlists, folder structure and rates files to see
>>>> whats gone wrong.
>>>>
>>>> >1) If I do what you said for an existing reaction, like rpp_to_he3,
>>>> the code is supposed to ignore the default tables and use mine right? Or it
>>>> adds a new reaction with my tables?
>>>>
>>>> It should use yours, if its been set up correctly
>>>>
>>>> >2) On the table files (txt), what are the units of the "Rates" column?
>>>>
>>>> Reactions per second
>>>>
>>>> Rob
>>>>
>>>> On Sun, Oct 30, 2016 at 10:59 AM, Gonçalo Andrade <
>>>> gnmandrade at hotmail.com> wrote:
>>>>
>>>>> Hi Rob
>>>>>
>>>>>
>>>>>
>>>>> Thank you for your help. It took me a long time to produce properly
>>>>> the rate tables from the s-factor so I could only try your method a few
>>>>> weeks ago.
>>>>>
>>>>>
>>>>>
>>>>> I've created the rate_tables directory and put the files there as you
>>>>> said but the code seems to ignore my tables. I even tried to put really big
>>>>> numbers just to check if it was using the tables and the result was no
>>>>> different from what I had before.
>>>>>
>>>>> Is there any step missing? I always do "./clean && ./mk && ./rn" when
>>>>> running the code.
>>>>>
>>>>>
>>>>> Two more questions:
>>>>>
>>>>> 1) If I do what you said for an existing reaction, like rpp_to_he3,
>>>>> the code is supposed to ignore the default tables and use mine right? Or it
>>>>> adds a new reaction with my tables?
>>>>>
>>>>>
>>>>> 2) On the table files (txt), what are the units of the "Rates" column?
>>>>>
>>>>>
>>>>> Thanks a lot for your help.
>>>>>
>>>>>
>>>>> Gonçalo Andrade
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> ------------------------------
>>>>> *De:* Robert Farmer <rjfarmer at asu.edu>
>>>>> *Enviado:* 16 de setembro de 2016 00:59
>>>>> *Para:* Gonçalo Andrade
>>>>> *Cc:* mesa-users at lists.sourceforge.net
>>>>> *Assunto:* Re: [mesa-users] [MESA]: Question Astrophysical Factor
>>>>>
>>>>> Hi
>>>>> You cant change the s-factor directly, however you can give mesa a
>>>>> file with a customized set of nuclear reaction rates where you have changed
>>>>> the s-factor yourself.
>>>>>
>>>>> What you need to do (and example inlists and rate files can be found
>>>>> here http://mesastar.org/results/properties-of-carbon-oxygen-whit
>>>>> e-dwarfs-from-monte-carlo-stellar-models) follows:
>>>>>
>>>>>
>>>>> Add this to the star_job section of your inlists
>>>>>
>>>>> rate_tables_dir = './rate_tables'
>>>>>
>>>>> Then make a folder rate_tables in your mesa work directory. Inside
>>>>> that folder make a file rates_list.txt file with the following line:
>>>>>
>>>>> r_h1_pg_h2     'r_h1_pg_h2.txt'
>>>>>
>>>>> This says we want to alter the reaction h1+h1 -> h2 by looking for a
>>>>> file called r_h1_pg_h2.txt where we will specify the rate as a function of
>>>>> temperature
>>>>>
>>>>> Then make a file called r_h1_pg_h2.txt in (rate_tables), where the
>>>>> first two lines are:
>>>>> #  r_h1_pg_h2 low rate:
>>>>> # T8            RATE
>>>>>
>>>>> Then you need to add a line with the number of rate points you have.
>>>>> Then give the temperature in units of 10**8 K and a rate with one rate per
>>>>> line. An example file might look like this though you will want many more
>>>>> rate points than this:
>>>>>
>>>>> #  r_h1_pg_h2 low rate:
>>>>> # T8            RATE
>>>>> 5
>>>>> 0.01    0.0
>>>>> 0.5      1.0
>>>>> 1.0      2.0
>>>>> 10.5    3.0
>>>>> 100.0 10.0
>>>>>
>>>>> Then run mesa and it should be using your new nuclear rate.
>>>>>
>>>>> Rob
>>>>>
>>>>>
>>>>>
>>>>> On Thu, Sep 15, 2016 at 4:25 PM, Gonçalo Andrade <
>>>>> gnmandrade at hotmail.com> wrote:
>>>>>
>>>>>> Dear Sir or Madam,
>>>>>>
>>>>>>
>>>>>>
>>>>>> I'm a MSc student and I'm doing my master thesis on asteroseismology
>>>>>> of red giant stars. I'm using MESA to do models of these stars.
>>>>>>
>>>>>>
>>>>>> I found this email on the MESA community website and I decided to try
>>>>>> it as a last resource.
>>>>>>
>>>>>>
>>>>>> The thing I need to do now in my project is to change the
>>>>>> Astrophysical Factor (S-Factor) from the pp nuclear reaction to try to find
>>>>>> out what changes does it have in the star and if these can be measured
>>>>>> using seismology. The problem is I've been been searching online for some
>>>>>> weeks and I can't find out how to change this factor. I've tried several
>>>>>> things, the closest to what I wanted, I think, was to change the value on
>>>>>> the file $MESA_DIR/rates/private/ratelib.f90 , but after that change
>>>>>> the code no longer compiles...
>>>>>>
>>>>>>
>>>>>> I a few words, I just need to change the S-Factor of the pp reaction.
>>>>>>
>>>>>>
>>>>>>
>>>>>> I thank you in advance and hope I'm not being inconvenient.
>>>>>>
>>>>>>
>>>>>> Yours faithfully,
>>>>>>
>>>>>> Gonçalo Andrade
>>>>>>
>>>>>>
>>>>>>
>>>>>> ------------------------------------------------------------
>>>>>> ------------------
>>>>>>
>>>>>> _______________________________________________
>>>>>> mesa-users mailing list
>>>>>> mesa-users at lists.sourceforge.net
>>>>>> https://lists.sourceforge.net/lists/listinfo/mesa-users
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
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