[mesa-users] negative age and rotation values in "OSC" file

Juan Carlos Suárez jcsuarez at iaa.es
Thu Feb 16 10:54:15 EST 2017 

Dear Richard and all,

Thank you very much for your valuable help. 
Now we are able to construct a complete evolutionary track from PMS to TAMS (we are indeed interested in 
keeping the PMS models), with around 4K for the number of shells, and using the Eddington atmosphere.
Taking a look to the OSC files, it seems that now everything is OK except for the effective temperature (corresponding
to glob(14) which is now 0.00000 for all the models in the track).

We have used the inlist attached to this email.

JC
> On 11 Feb 2017, at 23:17, RICHARD H D TOWNSEND <townsend at astro.wisc.edu> wrote:
> 
> Hi Juan Carlos —
> 
> In your email below, I can spot quite a few different problems you’re running into. In each case I’ll try to explain what’s going on
> 
>> On Feb 10, 2017, at 12:26 PM, Juan Carlos Suárez <jcsuarez at iaa.es> wrote:
>> 
>> Dear Richard,
>> 
>> We have modified a little bit the previous “inlist” in order to include some atmosphere (the default simple atmosphere)
>> since we are interested in working with the photosphere radius. So we decided to include the following options in the
>> inlist (attached)
>> ! if true, write atmosphere to pulse files
>> 
>> add_atmosphere_to_pulse_info = .TRUE.
> 
> Although it’s not the main cause of your problems below, I should mention that In MESA 8845 (and previous releases) there is a bug in the atmosphere writing routine. The code should output the same atmosphere as selected by the ‘which_atm_option’ parameter; however, in many cases (including the default ‘simple_photosphere’ atmosphere), the atmosphere written out is actually the ‘Paczynski_grey’ atmosphere. This bug is fixed in the development version of MESA, but only for a restricted set of atmosphere choices:
> 
> Eddington_grey
> Paczynski_grey
> solar_Hopf_grey
> Krishna_Swamy
> grey_and_kap
> 
> For other atmosphere options the code now halts — because there is insufficient information to construct the atmosphere structure.
> 
>> ! if true, add point for r=0 to pulse files
>> 
>> add_center_point_to_pulse_info = .FALSE.
> 
> In fact, it’s setting this flag to .FALSE. that ‘fixed’ the problem with age and rotation rate being overwritten (as discussed in the previous email) — the central second derivative data only gets calculated when add_center_point_to_pulse_info = .TRUE. (which itself is a bug — again, fixed in the development version)
> 
>> ! if true, add k=1 cell to pulse files
>> 
>> keep_surface_point_for_pulse_info = .false.
>> ! add double points at discontinuities
>> 
>> add_double_points_to_pulse_info = .TRUE.
> 
> This is what’s causing the (approximate) doubling of the number of points in the OSC files. This flag causes MESA to write out a double points when it detects a density discontinuity. The threshold for recognizing density discontinuities is set by the threshold_dlnrho_for_double_point flag. Since this flag defaults to zero, *every* pair of adjacent cells in the model is producing a double point!
> 
> The fix is to set add_double_points_to_pulse_info = .FALSE., or to specify a non-zero value for threshold_dlnrho_for_double_point — e.g., 10.
> 
>> 
>> Curiously, it seems that now the problem of the negative ages and rotation values is solved, but we
>> do not know why. 
>> 
> 
> See above!
> 
>> On the other hand unfortunately the computation halted with an error 
>> 
>> failed to open LOGS/profile686.data
>> star_finish_step ierr          28
>> after_step_loop ierr          28
>> 
>> That is, it halted at model 686, while without the above options MESA reached the 905 models with no errors.
>> 
> 
> I imagine the program halted because it ran out of disk space. You are writing out a profile *and* an OSC file after each timestep. Each profile file is ~15MB, and each OSC file is ~5MB. After 686 models, you have used up well over 10 GB of disk space.
> 
> To get around this issue, you should consider the following approaches:
> 
> *) Don’t set mesh_delta_coeff so small — you use 0.15, which results in very high resolution models (some might say over-resolved). 0.5 might be a better choice for this parameter.
> 
> *) Only write out every N’th profile/OSC file, rather than all of them. To do this, set profile_interval = N
> 
> *) Don’t bother writing out the pre-MS models, if you don’t need them. This can be achieved by doing two separate runs — an initial run with no profile/OSC file output, which terminates at the ZAMS. Then, do a restart and write out profiles/OSC files as necessary.
> 
>> In addition to this, with the above options it seems that MESA has doubled the number
>> of mesh points (from 4K to 8K). Is that what we should expect? The 4K additional 
>> points are located at the atmosphere?
>> 
> 
> No, as I mentioned above, every single model point is being written as a double point — not what you want!
> 
> So, to sum up:
> 
> *) Upgrade to the development version of MESA.
> 
> *) Set add_atmosphere_to_pulse_data = .FALSE., or set which_atm_option to one of the atmosphere choices listed above.
> 
> *) Set add_double_points_to_pulse_data = .FALSE., or specify a non-zero value for threshold_dlnrho_for_double_point.
> 
> *) Adjust mesh_delta_coeff, set_profile_interval to reduce size of files, or run the pre-MS and MS parts separately.
> 
> (Note also that some of the parameter names have changed, with the phrase ‘pulse_info’ changed to ‘pulse_data’)
> 
> Hope that helps!
> 
> cheers,
> 
> Rich
> 
> 
>> Thanks!
>> JC
>> 
>> 
>>> On 9 Feb 2017, at 20:38, Juan Carlos Suárez <jcsuarez at iaa.es> wrote:
>>> 
>>> Yes here it is!
>>> JC
>>>> On 9 Feb 2017, at 20:05, RICHARD H D TOWNSEND <townsend at astro.wisc.edu> wrote:
>>>> 
>>>> Hi Juan —
>>>> 
>>>> Can you post the inlist file(s) that you’re using?
>>>> 
>>>> Many thanks,
>>>> 
>>>> Rich
>>>> 
>>>>> On Feb 9, 2017, at 12:43 PM, Juan Carlos Suárez <jcsuarez at iaa.es> wrote:
>>>>> 
>>>>> Dear colleagues
>>>>> 
>>>>> I am trying to compute a 1.5 Msun evolutionary model (with solar metallicity) from PMS to TAMS approx.
>>>>> We have set the options to obtain the .OSC files to be read by our oscillation codes. 
>>>>> 
>>>>> We found that for all the models the age provided has negative values.
>>>>> 
>>>>> Moreover, although no option for rotation was included in the inlist (i.e. rotation should be zero)
>>>>> we obtain some models with rotation 0 but others with negative non-zero values
>>>>> 
>>>>> Any idea?
>>>>> 
>>>>> Thanks in advance!
>>>>> 
>> 
>> --------------------------------------------------------------------------------------------------------------------
>> Dr. Juan Carlos Suárez 
>>    Ramon y Cajal fellow at Física Teórica y del Cosmos Dept. University of Granada 
>>    Facultad de Ciencias. 18071. Granada. Spain
>>  jcsuarez at ugr.es | +34 958249056 | www.ugr.es/~fqm292/ 
>>    Associate researcher at Stellar Physics Dept. IAA-CSIC
>>  Glorieta de la Astronomia s/n. 18008. Granada. Spain
>>  jcsuarez at iaa.es | +34 958230619 | www.iaa.es
>> --------------------------------------------------------------------------------------------------------------------
>> 
>> 
>> 
>> <inlist_project>
> 

--------------------------------------------------------------------------------------------------------------------
Dr. Juan Carlos Suárez 
    Ramon y Cajal fellow at Física Teórica y del Cosmos Dept. University of Granada 
    Facultad de Ciencias. 18071. Granada. Spain
	  jcsuarez at ugr.es | +34 958249056 | www.ugr.es/~fqm292/ 
    Associate researcher at Stellar Physics Dept. IAA-CSIC
	  Glorieta de la Astronomia s/n. 18008. Granada. Spain
	  jcsuarez at iaa.es | +34 958230619 | www.iaa.es
--------------------------------------------------------------------------------------------------------------------
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