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

Robert Farmer rjfarmer at asu.edu
Tue Nov 8 12:40:35 EST 2016 

hi
So things work fine for me (once i put the test_nuclear_rates_tables into
the test_nuclear folder as its missing from there)

quick test, do:
rm $MESA_DIR/data/rates_data/cache/*

to remove MESA's cached version of the rate tables, then try your code
again, otherwise try re-downloading mesa and installing it again to clean
up any changes you might of made.

Rob

On Mon, Nov 7, 2016 at 5:20 PM, Gonçalo Andrade <gnmandrade at hotmail.com>
wrote:

> Hi
>
>
>
> That's really weird. I've been trying those 3 nets that appear in the
> inlist. They all work if I don't include my rates' tables and the last one
> I used was my modified net.
>
> I attached my working folder and my rates_tables folder
> (test_nuclear_rates_tables) that I had to put in
>
>
> $MESA_DIR/data/rates_data/
>
>
> Also, referring to the last email, I can generate the rates_tables based
> on modified S-factors. My objective is to use them but right I'm just
> trying to run the code and making sure he uses my tables instead of the
> pre-defined ones, so I hadn't that much care choosing the values. I'll try
> to follow your advice and add some points with lower rates at smaller
> temperatures, but it shouldn't matter that much since it works on your
> system.
>
>
>
>
> Gonçalo Andrade
>
>
> ------------------------------
> *De:* Robert Farmer <rjfarmer at asu.edu>
> *Enviado:* 7 de novembro de 2016 23:42
>
> *Para:* Gonçalo Andrade
> *Cc:* mesa-users at lists.sourceforge.net
> *Assunto:* Re: [mesa-users] [MESA]: Question Astrophysical Factor
>
> 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/pr
>>>>>>>> operties-of-carbon-oxygen-white-dwarfs-from-monte-carlo-stel
>>>>>>>> lar-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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