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

[Robert Farmer]

So i just ran your inlists as is and everything works fine (did you change
the nets since you last sent them?), mesa picked up the new rate in the
local folder and there where no convergence issues getting out of the
pre-MS.

can you do a:
rm -rf LOGS photos
to get rid of any data files (or move them to another if you want to keep
them) and then send a zipped copy of your work folder with your inlists and
everything else in, so i can see exactly what you have.

Rob


On Mon, Nov 7, 2016 at 4:21 PM, Robert Farmer <rjfarmer at asu.edu> wrote:

> Hi
>
> A convergence problem is not a bug. What its telling you is that MESA has
> struggled and failed to find a way to satisfy all the stellar structure
> equations given the constraints that your inlist sets. Updating to a new
> version may help, and is worth a shot, as changes are made to the code but
> i don't know of anything particular that will has been fixed that would help
>
> >This might work, but then I cannot specify the mass and the Z right?
> You can specify mass but not Z, that is pre-set to solar for the pre
> created pre-MS models
>
> The next thing to think about is, are your rates sensible? If we look at
> MESA's rate for rpp_he3, to do this we need to look at the cached data mesa
> written out:
>
> cd $MEA_DIR/rates/test
> ./show_rates $MESA_DIR/data/rates_data/cache/rpp_to_he3_1.bin >
> rpp_to_he3_1.txt
>
> Then inspecting rpp_to_he3_1.txt shows that for T<10**7K the rates are
> ~<10^-20. So maybe a trial for you would be to add some more low
> temperature data points, with a very small rate factors such that the
> rpp_he3 rate is almost 0 for the temperatures on the pre-MS and early
> evolution until the star gets hotter. This is the E (experiment) part of
> MESA.
>
> Why the rates folder isn't working properly i'll have a look into.
>
> Rob
>
>
>
> On Mon, Nov 7, 2016 at 3:52 PM, Gonçalo Andrade <gnmandrade at hotmail.com>
> wrote:
>
>> 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
>> ------
>>
>>
>> I've tried that, the code looks for the tables in the non existing
>> directory
>>
>> $MESA_DIR/data/rates_data/./rates_tables
>>
>> So I gave up on that and added my tables on a "test_nuclear_rates_tables"
>> folder inside rates_data, using then
>>
>> rate_tables_dir = 'test_nuclear_rates_tables'
>>
>>
>> ----------
>>
>> First test, does the model work okay without the new rates, given all the
>> other options you have set?
>>
>> ----------
>>
>>
>> If I use the same inlist but comment just the line
>>
>>   rate_tables_dir = 'test_nuclear_rates_tables'
>>
>> It runs without any problem.
>>
>>
>> -----------
>>
>> 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
>>
>> -----------
>>
>> This might work, but then I cannot specify the mass and the Z right? I
>> needed to model a real observable star, so it would be useful to have
>> freedom in these parameters.
>>
>> -----------
>>
>> 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
>>
>> -----------
>>
>>
>> I've tried it at 100, and in several values as high as 25000, still
>> doesn't converge.
>>
>>
>> -----------
>>
>> 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)
>>
>> -----------
>>
>> I've tried this. I used the same inlist commenting the line that calls my
>> tables and using the comands
>>
>>     Lnuc_div_L_zams_limit = 0.99d0
>>     stop_near_zams = .true.
>>
>> to stop and save the ZAMS model.
>>
>> When I restart with the new reactions on the last photo it has the same
>> convergence problem, but with an even smaller dt.
>>
>>
>>
>> -----------
>>
>>
>> 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)
>>
>>
>> -----------
>>
>>
>> I've tried a wide variety of values, between 0.005 and 500, they all had
>> the same convergence problem.
>>
>>
>>
>>
>>
>> Having tried all the suggestions, is it possible that this is a bug that
>> has been fixed in more recent versions?
>> My MESA version is the 8118. Current version is the 8845. Is it worth to
>> try installing it all again with the new version?
>>
>>
>>
>> Gonçalo Andrade
>>
>>
>> ------------------------------
>> *De:* Robert Farmer <rjfarmer at asu.edu>
>> *Enviado:* 7 de novembro de 2016 18:35
>> *Para:* Gonçalo Andrade
>> *Cc:* mesa-users at lists.sourceforge.net
>> *Assunto:* Re: [mesa-users] [MESA]: Question Astrophysical Factor
>>
>> 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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