[mesa-users] optical_depth -- and a message for MESA BLACK BELT USERS
paxton at kitp.ucsb.edu
Fri Mar 23 13:35:27 EDT 2012
Let's see if there are any black belts out there who can help on this.
But first you need to provide enough info to make it possible for them.
Make a saved model a few steps before the bad one.
Make a modified inlist that starts by loading that newly saved model.
Confirm that the problem still happens when you run with the new inlist.
Send the starting model and the modified inlist.
If possible, provide a plot to show where things are bad.
explain what is wrong in enough detail so someone else can see the problem.
Include the log file for that model.
include version number info for mesa, the compiler, and the operating system.
On Mar 23, 2012, at 10:18 AM, jingluan at caltech.edu wrote:
> Dear Bill,
> Thank you so much for guiding me. Although I have not yet figured out what
> specific problem causes the strange tau(:), I will try to follow yours to
> I still have one question. If this weird tau were caused by
> non-convergence, I would NOT be able to find it out if I did not
> accidentally check the tau values. MESA does not report err information
> like 'convergence problem', normally I would accept this model as a
> converged one and trust the outputs by mesa, e.g. the figures plotted by
> pgplot. But actually there is something wrong in the model (e.g. the tau
> in this case) which is NOT revealed. I feel that in practice people do not
> check every variable's value in s to see whether it makes sense if MESA
> does not report error.
> Thank you so much!
>>>>> MESA USERS
>> Please consider that if you are publishing papers using mesa,
>> it might be a good idea to be able to poke around inside the code enough
>> to get an idea of what is going on. If you can do that, you are a mesa
>> black belt!
>> Are you a black belt yet? Do you want to become one?
>> If so, take a moment to see if you could have answered this email
>> On Mar 23, 2012, at 9:00 AM, jingluan at caltech.edu wrote:
>>> At the kth shell where it satisfies s% R(k)/rsol==s% photosphere_r, I
>>> found that s% tau(k)=361 in a model by mesa2664;
>>> Then I calculate a variable called tau_phot by summing s% opacity(j)*s%
>>> rho(j)*(s% R(j)-s% R(j+1)) over j=1,..,k; and I got tau_phot=5184;
>>> It is pretty weird. What could be the problem? The model has not yet
>>> converged well? But mesa does not report any ierr information though.
>> Hi Jing,
>> Good question! Rather than just giving an answer, let's go through
>> the process of discovering how things work (which is what I just did!).
>> Question: why do I find weird value for tau before the model has
>> 1st step: grep to find where tau is set.
>> cd star/private
>> grep tau *.f -n > lst
>> open the file lst and don't panic when you see a lot of lines
>> we don't care about places that are reading tau;
>> we want to find where it is being set.
>> this looks like the best bet:
>> star_utils.f:566: tau(k) = tau(k-1) + dtau
>> that is in a routine called "get_tau" which is a sign that we're on the
>> right track.
>> open star_utils and take a look at get_tau -- bingo!
>> 2nd step: find where and when get_tau is being called.
>> grep 'call get_tau' * -n
>> report.f:203: call get_tau(s, s% tau)
>> open report and find the call on get_tau. it is in a routine called
>> 3rd step: find where and when do_report is being called.
>> grep 'call do_report' * -n
>> evolve.f:285: call do_report(s, ierr)
>> read_model.f:67: call do_report(s, ierr)
>> we find 2 places: one in evolve and the other in read_model.
>> since we're doing evolution rather than reading, we want the one in
>> open evolve.f and find the call on do_report.
>> turns out that it is called from do_evolve_step,
>> after the model has converged (in do_struct_burn_mix) .
>> understanding the order of events in do_evolve_step is the hard part of
>> there's a lot of extra things in there for error checks and timekeeping,
>> fundamentally here's the order in which things are done:
>> prepare_for_new_step -- does remesh
>> prepare_for_new_try -- save stuff in case need to do retry or backup
>> do_winds -- calculate mdot for this step
>> do_adjust_mass -- add or remove material according to mdot
>> do_set_vars -- set variables for new mesh and mass
>> do_element_diffusion -- optional
>> save_pre_hydro_values -- save starting values for solver
>> do_struct_burn_mix -- solve for new model
>> smooth_newly_non_conv -- optionally smooth abundances
>> do_brunt_N2 -- optionally calculate brunt N^2 at each cell
>> do_report -- calculate information for logs and profiles
>> One more subtle point that "black belt" mesa user's should know:
>> the diffusion coefficients for convective mixing, overshooting,
>> thermohaline mixing are calculated in the call on do_set_vars from
>> do_evolve_step and remain fixed during the rest of the calls from
>> in particular, they are not updated between iterations of the solver, so
>> are not being treated in a fully implicit manner. this is done for
>> numerical reasons only.
>> Okay --- now I expect that there will be lots of mesa users out there
>> in the future who'll be able to dig out the answers to questions like
>> Consider it part of your qualification for getting a mesa black belt. ;-)
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