mesa-users — open list for mesa comments, questions, & answers

[mesa-users] Load model

[張世昕 <ss...@as...>]

Dear mesa-users,

I have problem about loading the saved model.

It shows that,
"finish_load_model: failed in set_vars
 failed in finish_load_model
 star_read_model ierr          -1
WARNING: allocate failed for eos tables
 do_load1_star ierr          -1
WARNING: allocate failed for eos tables"

I did nothing but edit the inlist file. (without touching the eos stuff)
Once the wrong message show up, mesa can't load
any saved model any more.
How do I fix it?

Cheers,
Shih-Hsin

Re: [mesa-users] new controls namelist variables

[Bill P. <pa...@ki...>]

On Mar 10, 2011, at 9:02 PM, Theodore Arthur Sande wrote:

> Dear mesa-users,
> 
> I have a simple question. I wish to define a new controls namelist variable,
> e.g. average_h1_min, that specifies the minimum value for average_h1, beyond
> which evolution should be terminated.
> 
> I assume this is simple to do. Should just experiment with the suggestions
> adumbrated in "8. Adding your own code to control MESA star"? Or must I make
> modifications somewhere else in the code requiring recompilation? The key point
> is that I wish to have the numeric value read from the controls namelist.

Hi,

Good question.  Looks like I better add "xa_average_upper_limit_species" in addition
to the current "xa_central_upper_limit_species" and "xa_surface_lower_limit_species".

But you don't have to wait for me to make a new release if you are willing to write a few
lines yourself.   In your work/src directory you'll find run_star_extras.f.   It has a line
      include 'standard_run_star_extras.dek'
that you now should replace by the contents of star/public/standard_run_star_extras.dek

Then find the 'extras_check_model' routine.   In that routine you'll find the following lines:

         if (.false. .and. s% star_mass_h1 < 0.35d0) then
            ! stop when star hydrogen mass drops to specified level
            extras_check_model = terminate
            write(*, *) 'have reached desired hydrogen mass'
            return
         end if

Replace by these:

         if (s% star_mass_h1/s% star_mass <= s% x_ctrl(1)) then
            ! stop when star hydrogen mass fraction drops to specified level
            extras_check_model = terminate
            write(*, *) 'have reached desired hydrogen mass fraction'
            return
         end if
 
In your inlist, you should set x_ctrl(1) to your desired limit.

Now do ./mk in your work directory and give it a try.

Let me know how it goes.

Cheers,
Bill

[mesa-users] new controls namelist variables

[Theodore A. S. <ta...@MI...>]

Dear mesa-users,

I have a simple question. I wish to define a new controls namelist variable,
e.g. average_h1_min, that specifies the minimum value for average_h1, beyond
which evolution should be terminated.

I assume this is simple to do. Should just experiment with the suggestions
adumbrated in "8. Adding your own code to control MESA star"? Or must I make
modifications somewhere else in the code requiring recompilation? The key point
is that I wish to have the numeric value read from the controls namelist.

Thanks!

Theodore Arthur Sande

MIT Department of Physics
ta...@mi...

[mesa-users] gravity?

[Manos C. <ma...@as...>]

Hi all,

 I recently started to use MESA to produce high mass evolved stellar 
models. One parameter that I want to check at each zone is the 
gravitational potential.
Do the output log files from a run give this information? I failed to 
locate one, but if there is a way to obtain it, it would be extremely 
useful to me.

Thanks a lot

Manos Chatzopoulos
UT Austin

[mesa-users] very thin shell burning

[Kent B. <kg...@la...>]

So I'm running some Population III calculations at the lower end of the
mass range, and the very thin shell burning on the giant branch is
taking *forever*. 

What's the latest thinking about mass loss in Population III? I know
it's thought to be rather low, but just how rather low?

What is the state of the art in modeling very thin shell burning? Brute
force seems, well, like brute force. Are there methods out there that
treat it as a front propagation problem?

Interested in any information anyone has.

-- Kent G. Budge
CCS-2, LANL

[mesa-users] MESA C++ Interface and Interactive Python Driver

[Bill P. <pa...@ki...>]

Hi,
Thanks to Kent Budge, a C++ interface for MESA is now available at MESA++. It features an interactive Python driver that you may find fun to play with.

There is a also new MESA release to go with it -- 3075.

Cheers,
Bill

Re: [mesa-users] Question about the MESA.

[Bill P. <pa...@ki...>]

Hi,

On Feb 28, 2011, at 11:08 PM, Takeshi Mikami wrote:

>>> I use r2987 and have a question about "/data/star_data/log_columns.list".
>>> There are items of "conv_mx*_top/bottom".
>>> Through editing it, Can it output another physical parameters (temperature,
>>> density, ...) at the top/bottom of convection to "star.log"?
>>> If it is possible, please teach me the method.
>>> 
>>> I know it is possible to do about radius ("conv_mx1_top" ->
>>> "conv_mx1_top_r").
>> 


Hi,

You can get information about the top and bottom of the largest convection zone
by using the following items in log_columns.list.

If you want things that are not provided here, it is possible to make small
modifications to your copy of run_star_extras (it is in your work/src directory).
Ask for help if you want to try that.

Good luck,
Bill

      
   ! conditions at base of largest convection zone (by mass)
      !cz_mass ! mass coordinate of base (Msun)
      !cz_log_xmass ! mass exterior to base (g)
      !cz_log_xmsun ! mass exterior to base (Msun)
      !cz_xm ! mass exterior to base (Msun)
      !cz_logT
      !cz_logRho
      !cz_logP
      !cz_radius ! Rsun
      !cz_log_column_depth
      !cz_log_radial_depth
      !cz_luminosity ! Lsun
      !cz_opacity
      !cz_log_tau
      !cz_eta
      !cz_log_eps_nuc ! log10(ergs/g/s)
      !cz_t_heat ! Cp*T/eps_nuc (seconds)
      
      !cz_csound
      !cz_scale_height
      !cz_grav
      
      !cz_omega
      !cz_omega_div_omega_crit
      
      !cz_zone
      
   ! mass fractions at base of largest convection zone (by mass)
      !cz_log_xa h1
      !cz_log_xa he4



      
   ! conditions at top of largest convection zone (by mass)
      !cz_top_mass ! mass coordinate of top (Msun)
      !cz_top_log_xmass ! mass exterior to top (g)
      !cz_top_log_xmsun ! mass exterior to top (Msun)
      !cz_top_xm ! mass exterior to top (Msun)
      !cz_top_logT
      !cz_top_logRho
      !cz_top_logP
      !cz_top_radius ! Rsun
      !cz_top_log_column_depth
      !cz_top_log_radial_depth
      !cz_top_luminosity ! Lsun
      !cz_top_opacity
      !cz_top_log_tau
      !cz_top_eta
      !cz_top_log_eps_nuc ! log10(ergs/g/s)
      !cz_top_t_heat ! Cp*T/eps_nuc (seconds)
      
      !cz_top_csound
      !cz_top_scale_height
      !cz_top_grav
      
      !cz_top_omega
      !cz_top_omega_div_omega_crit
      
      !cz_top_zone
      
   ! mass fractions at top of largest convection zone (by mass)
      !cz_top_log_xa h1
      !cz_top_log_xa he4

[mesa-users] make that 3065

[Bill P. <pa...@ki...>]

Hi,

new release is 3065 -- poor old 3062 didn't last long!

-B

Re: [mesa-users] [mesa] would someone please give me help in using pgstar?

[Bill P. <pa...@ki...>]

On Feb 27, 2011, at 6:03 PM, Y.R. Zeng wrote:

> 
> Hello:
> I am learning how to use mesa now.
> I use the fedora 14 and ifort 12.0.and i install pgplot follow the mesa/utilities/pgplot/readme.Then i  can draw pictures by using ./demo etc. After having installed mesa by changing makefile_header as "USE_PGSTAR = YES
> LOAD_PGPLOT = -L/usr/local/lib -lpgplot -L/usr/lib -lX11 -lpng"
> the install process is very smooth.then i test some example,such as star/test_suite/solar etc. nothing goes wrong. However,when i use star /work, files are written only in LOGS and photos,No picture is drawed and no file is written in pgstar and pgstar_out.,and I don't know how to use pgstar to draw pictures.would someone please give me help?I am a new user to pgplot.
>                                    Yours Zeng
> 


Hi,

I wonder if the problem could be something simple like not setting pgstar_flag = .true. in the &star_job section of your inlist?

If that isn't the problem, then please send more details including the inlists from the work directory you are using.

Good luck!

Bill

[mesa-users] mesa 3062 is available

[Bill P. <pa...@ki...>]

Hi,

A new release is now out there.  It fixes the gfortran compiler problem we had with the last release.

Also some inlist changes:
	dX_nuc timestep limits deprecated; use dX_nuc_drop limits instead
	removed obsolete controls for CO enhanced opacities (CO_full_on and CO_full_off) 
		and require explicit setting for base_Z
		to enable enhanced opacities, just set use_CO_enhanced_opacities to .true.

There is now a one_zone_ns_burst_jina example in star/exercises.

And I've enhanced the one zone burn application in jina and added one to net.

Cheers,
Bill

[mesa-users] [mesa] would someone please give me help in using pgstar?

[Y.R. Z. <yr...@ya...>]

Hello:
I am learning how to use mesa now.
I use the fedora 14 and ifort 12.0.and i install pgplot follow the mesa/utilities/pgplot/readme.Then i  can draw pictures by using ./demo etc. After having installed mesa by changing makefile_header as "USE_PGSTAR = YES
LOAD_PGPLOT = -L/usr/local/lib -lpgplot -L/usr/lib -lX11 -lpng"
the install process is very smooth.then i test some example,such as star/test_suite/solar etc. nothing goes wrong. However,when i use star /work, files are written only in LOGS and photos,No picture is drawed and no file is written in pgstar and pgstar_out.,and I don't know how to use pgstar to draw pictures.would someone please give me help?I am a new user to pgplot.
                                   Yours Zeng
 


      

Re: [mesa-users] Possible numerical instability

[Aaron D. <aar...@gm...>]

Hi Matwey,

You're likely running into a real challenge with stellar physics, rather
than MESA.  However, it's impossible to help you diagnose your problem
without more information.

Please try the following: save a model near where the problem occurs but
sufficiently far away that the model hasn't already arrived at logdt=-1.
 Verify that this model eventually dies at the same place as the run that
starts at the pre-MS.  Then, you can send us the saved model, your inlist,
and the last few lines from the terminal output.  This will make it possible
for us to understand what you're experiencing and then we may be able to
help you.

Best wishes,
Aaron



On Sun, Feb 27, 2011 at 2:35 AM, Matwey V. Kornilov <
mat...@gm...> wrote:

> Hi,
>
> I am trying to tune `1M_pre_ms_to_wd` test (which works excellently)
> for star whose mass is 2M. I faced with strange behavior after H-He
> pulses at AGB. logdt dropped down to -1.0 and less. The track on
> logL-logT looks to be numerically noisy (at least for me, so tell me
> if I'm wrong).
> My version is r2987. I need help to overcome this thing.
>
> Thanks in advance.
>
> --
> With best regards,
> Matwey V. Kornilov
> http://0x2207.blogspot.com
> xmpp:0x...@ja...
>
>
> ------------------------------------------------------------------------------
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> _______________________________________________
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>
>

[mesa-users] Possible numerical instability

[Matwey V. K. <mat...@gm...>]

Hi,

I am trying to tune `1M_pre_ms_to_wd` test (which works excellently)
for star whose mass is 2M. I faced with strange behavior after H-He
pulses at AGB. logdt dropped down to -1.0 and less. The track on
logL-logT looks to be numerically noisy (at least for me, so tell me
if I'm wrong).
My version is r2987. I need help to overcome this thing.

Thanks in advance.

-- 
With best regards,
Matwey V. Kornilov
http://0x2207.blogspot.com
xmpp:0x...@ja...

Re: [mesa-users] Question about the MESA.

[Aaron D. <aar...@gm...>]

Hi Takeshi,

There are a couple of options to access the information you require.  If
you're only interested in the largest convection zone, search the default
log_columns.list (in mesa/data/star_data/) and search for

   ! conditions at base of largest convection zone (by mass)

and

   ! conditions at top of largest convection zone (by mass)

where you will information on lots of quantities at the top and bottom of
the largest convection zone.

If you want more information about all of the convection zones, you'll have
to write some code (or use the profile at every step).  In order to do this,
you'll use some of the "extra" routines that Bill has kindly made available.
 To figure out how to do the calculation, grep for conv_mx2_bot_r in
mesa/star/private/.  The example you're looking for is in report.f.

Then, you need to set up the extra information in
mesa/star/test/src/run_star_extras.f.  The first thing you'll find is that
this file just 'includes' standard_run_star_extras.dek, which is in
mesa/star/public/.  When I've needed to use one of these functions in the
past, I've commented out that include line and then copied the full contents
of standard_run_star_extras.dek into my run_star_extras.f.  Once you've done
that, you need to edit the functions/subroutines that will be used to write
extra information to the log files.

There are two of these:

      integer function how_many_extra_log_columns(s, id, id_extra)
         type (star_info), pointer :: s
         integer, intent(in) :: id, id_extra
         how_many_extra_log_columns = 0
      end function how_many_extra_log_columns


      subroutine data_for_extra_log_columns(s, id, id_extra, n, names, vals,
ierr)
         type (star_info), pointer :: s
         integer, intent(in) :: id, id_extra, n
         character (len=maxlen_log_column_name) :: names(n)
         double precision :: vals(n)
         integer, intent(out) :: ierr
         ierr = 0
      end subroutine data_for_extra_log_columns

If you wanted to add two extra columns to your log file, you'd
change how_many_extra_log_columns from 0 to 2.  Then edit 2 values of the
arrays in the next subroutine.  For example,

names(1) = 'conv_mx1_top_t'
names(2) = 'conv_mx1_bot_t'

vals(1) = s% value_you_want_1
vals(2) = s% value_you_want_2


Then recompile the code and see what happens.  I hope this is useful as a
guide for how to proceed.  Please let us know if you have more questions.

Aaron

Re: [mesa-users] Brunt Vaisala Frequency

[Bill P. <pa...@ki...>]

On Feb 26, 2011, at 11:52 AM, Jim Fuller wrote:

> Hey everybody,
> 
> I've been using mesa to calculate the Brunt-Vaisala frequency in main sequence stars of various masses. Since the brunt freq. is proportional to the force of gravity, it should go to zero at the center of the star, regardless of mass. However, in the models I am generating, it approaches some finite positive value near the center of my stars (for stars of various masses and ages). Has anybody run into this problem or can point me to the location in the code where the brunt frequency is calculated? Thanks,
> 


Hi Jim,

Good question -- I wonder if it might be an artifact of smoothing.  
Here's how to track down the place in the code where brunt is calculated.

In star/private, do

grep brunt *

among a bunch of output, you'll find that micro.f has what we want.

subroutine do_brunt_N2_for_cell
         g = s% grav(k)
         r = s% r(k)
         csound = interp_val_to_pt(s% csound,k,s% dq)
         s% brunt_N2(k) = (g/r)*(-g*r/csound**2 - s% dlnRho_dlnR(k))

the call on interp_val_to_pt is because mesa calculates csound at cell centers,
but we need a value at the cell boundary for use in Brunt.
The other things, g, r, and dlnRho_dlnR are defined at cell boundaries already.

we next need to see how dlnRho_dlnR is calculated, so back to grep where we find
subroutine do_brunt_N2
         dlnd(:) = s% lnd(:)
         dlnr(:) = s% lnr(:)
         call make_delta(dlnd,s% brunt_nsmooth,nz,.false.)
         call make_delta(dlnr,s% brunt_nsmooth,nz,.false.)
         s% dlnRho_dlnR(:) = dlnd(:)/dlnr(:)

the routine make_delta is defined in the same place.
it smooths the "raw" values of lnd and lnr before taking differences.
the amount of smoothing is controlled by 'brunt_nsmooth'

checking star_defaults.dek shows that the default for brunt_nsmooth is 50,
so there is quite a bit of smoothing happening.  

You might want to try smaller values for brunt_nsmooth and see what happens.

Alternatively, you might want a different smoothing scheme --
the one in the code now is very crude.  If you find something that
works well, please let me know and we'll put it into mesa!

Hope that helps.

Cheers,
Bill


p.s., I also see that there is a bug in the calculation of dlnRho_dlnR!
The code in do_brunt_N2 should actually be using cell centered lnr.
I'll fix that for the next release.   If you'd like to try changing it sooner,
here's a modified version of the routine -- just replace the current
definition in micro.f and then do

	cd star/test; ./mk ; ./ck ; ./export


      subroutine do_brunt_N2(s,nzlo,nzhi,ierr)
         type (star_info), pointer :: s         
         integer, intent(in) :: nzlo, nzhi
         integer, intent(out) :: ierr
         logical, parameter :: use_omp = .true.
         integer :: nz
         double precision, pointer :: dlnd(:), dlnr(:)
         ierr = 0
         if (dbg) write(*,*) 'do_brunt_N2 call foreach_cell', nzlo, nzhi
         nz = s% nz
         allocate(dlnd(nz), dlnr(nz))
         dlnd(:) = s% lnd(:)
         dlnr(:) = s% lnr(:)
         call make_delta_lnd(dlnd,s% brunt_nsmooth,nz)
         call make_delta_lnr(dlnr,s% brunt_nsmooth,nz)
         s% dlnRho_dlnR(:) = dlnd(:)/dlnr(:)
         deallocate(dlnd,dlnr)
         call make_smooth(s% dlnRho_dlnR,s% brunt_nsmooth,nz)
         call foreach_cell(s,nzlo,nzhi,use_omp,do_brunt_N2_for_cell,ierr)
         
         contains
         
         subroutine make_smooth(z,nsmooth,nz)
            double precision, pointer :: z(:)
            integer, intent(in) :: nz, nsmooth
            integer :: j, k
            do j=1,nsmooth
               z(1) = (3*z(1) + z(2))*0.25d0
               do k=2,nz-1
                  z(k) = (z(k-1) + 2*z(k) + z(k+1))*0.25d0
               end do
               z(nz) = (z(nz-1) + 3*z(nz))*0.25d0
               do k=nz-1,2,-1
                  z(k) = (z(k-1) + 2*z(k) + z(k+1))*0.25d0
               end do
            end do
         end subroutine make_smooth
         
         subroutine make_delta_lnd(z,nsmooth,nz)
            double precision, pointer :: z(:)
            integer, intent(in) :: nz, nsmooth
            integer :: j, k
            call make_smooth(z,nsmooth,nz)
            do k=2,nz
               z(k-1) = z(k-1) - z(k)
            end do
            z(nz) = z(nz-1)
         end subroutine make_delta_lnd
         
         subroutine make_delta_lnr(z,nsmooth,nz)
            double precision, pointer :: z(:)
            integer, intent(in) :: nz, nsmooth
            integer :: j, k
            call make_smooth(z,nsmooth,nz)
            do k=2,nz-1
               z(k-1) = 0.5d0*(z(k-1) - z(k+1))
            end do
            z(nz) = z(nz-1)
            z(1) = z(2)
         end subroutine make_delta_lnr
         
      end subroutine do_brunt_N2

[mesa-users] Brunt Vaisala Frequency

[Jim F. <sla...@gm...>]

Hey everybody,

I've been using mesa to calculate the Brunt-Vaisala frequency in main
sequence stars of various masses. Since the brunt freq. is proportional to
the force of gravity, it should go to zero at the center of the star,
regardless of mass. However, in the models I am generating, it approaches
some finite positive value near the center of my stars (for stars of various
masses and ages). Has anybody run into this problem or can point me to the
location in the code where the brunt frequency is calculated? Thanks,

-Jim

Re: [mesa-users] PGPSTAR, problem in pgstar_controls.dek during compilation with gfortran

[Maxime V. <via...@gm...>]

Hi,

I just upgraded to gfortran 4.5.1, for revision 2987 I got the same error than Mike but for revision 3039 the compilation was successful. I just ran mesa star with the parameter test file and I got the nice pgplot ouput, so it seems to be working now.

Many thanks !
Maxime

On Feb 24, 2011, at 8:49 PM, Bill Paxton wrote:

> Hi,
> 
> Damn compilers anyway!    It seems that gfortran 4.5.1 (but not 4.6) has a nonstandard rule for deciding between local vs. external definitions of a symbol.  Everyone else uses the local, but gfortran 4.5.1 uses the external one.  In this case, we have a local definition of show_convective_section as a logical function (that's the one we want), but gfortran is instead using a definition of show_convective_section as a subroutine in a module that is being "use"d in pgstar_trho_profile.   
> 
> I should have caught this before the release.  Sorry for missing it.  
> There will be a new release very soon (I hope!).   And it will be fixed in that.
> 
> If you are feeling lucky and don't want to wait, you can update to 3039.
> I think it is okay, but it has been put through the entire test_suite.
> 
> -Bill
> 
> 
> 
> 
> 
> On Feb 24, 2011, at 11:44 AM, Mike Zingale wrote:
> 
>> Hi Bill/Maxine, I am also having trouble compiling the latest MESA with pgstar.  I am using gfortran 4.5.1 on Fedora 14, and I get past the pgstar_ctrls_io.f compilation, but die a bit later with:
>> 
>> gfortran -fno-range-check  -fopenmp  -I../public -I../private -I../../include -Wunused-value -Werror -W -fimplicit-none   -O2 -c -ffree-form ../private/pgstar_trho_profile.f
>> ../private/pgstar_trho_profile.f:698.49:
>> 
>>        has_convection = show_convective_section()
>>                                                1
>> Error: Unexpected use of subroutine name 'show_convective_section' at (1)
>> ../private/pgstar_trho_profile.f:699.47:
>> 
>>        has_overshoot = show_overshoot_section()
>>                                              1
>> Error: Unexpected use of subroutine name 'show_overshoot_section' at (1)
>> ../private/pgstar_trho_profile.f:700.57:
>> 
>>        has_semiconvection = show_semiconvective_section()
>>                                                        1
>> Error: Unexpected use of subroutine name 'show_semiconvective_section' at (1)
>> ../private/pgstar_trho_profile.f:701.55:
>> 
>>        has_thermo_haline = show_thermo_haline_section()
>>                                                      1
>> Error: Unexpected use of subroutine name 'show_thermo_haline_section' at (1)
>> ../private/pgstar_trho_profile.f:763.57:
>> 
>>           show_convective_section = show_mixing_section(convective_mixing, cl
>>                                                        1
>> Error: Unexpected use of subroutine name 'show_mixing_section' at (1)
>> ../private/pgstar_trho_profile.f:769.61:
>> 
>>           show_semiconvective_section = show_mixing_section(semiconvective_mi
>>                                                            1
>> Error: Unexpected use of subroutine name 'show_mixing_section' at (1)
>> ../private/pgstar_trho_profile.f:775.60:
>> 
>>           show_thermo_haline_section = show_mixing_section(thermo_haline_mixi
>>                                                           1
>> Error: Unexpected use of subroutine name 'show_mixing_section' at (1)
>> ../private/pgstar_trho_profile.f:781.56:
>> 
>>           show_overshoot_section = show_mixing_section(overshoot_mixing, clr_
>>                                                       1
>> Error: Unexpected use of subroutine name 'show_mixing_section' at (1)
>> make: *** [pgstar_trho_profile.o] Error 1
>> 
>> /home/zingale/development/mesa/star/make
>> FAILED
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> On Thu, 24 Feb 2011, Bill Paxton wrote:
>> 
>>> Hi Maxime,
>>> 
>>> I suggest upgrading to 4.5.1 -- you can do that easily at this website:
>>> 
>>> http://gcc.gnu.org/wiki/GFortranBinaries
>>> 
>>> Good luck!
>>> 
>>> -Bill
>>> 
>>> 
>>> 
>>> 
>>> On Feb 24, 2011, at 10:29 AM, Maxime Viallet wrote:
>>> 
>>>> 
>>>> 	Hello Mesa-people,
>>>> 
>>>> I have successfully compiled and run mesa (rev. 2987) using gfortran 4.5.0 on mac os X 10.6.6
>>>> Now I am trying to get the PGPLOT interface working and I am running into this puzzling error while compiling the "star" module:
>>>> 
>>>> gfortran -fno-range-check  -fopenmp  -I../public -I../private -I../../include -Wunused-value -Werror -W -fimplicit-none   -O2 -c -ffree-form ../private/pgstar_ctrls_io.f
>>>> pgstar_controls.dek:5.74:
>>>>  Included at ../private/pgstar_ctrls_io.f:33:
>>>> 
>>>>    type (pgstar_win_file_data) :: pgstar_win_file_ptr(num_pgstar_plots)
>>>>                                                                        1
>>>> Error: Object 'pgstar_win_file_ptr' at (1) must have the SAVE attribute for default initialization of a component
>>>> make: *** [pgstar_ctrls_io.o] Error 1
>>>> 
>>>> /Users/viallet/postdoc/mesa/star/make
>>>> FAILED
>>>> 
>>>> 
>>>> Of course I naively tried to add by hand the "save" statement but then the file star/public/star_def.f would not compile anymore.
>>>> 
>>>> Has somebody already encountered this problem ?
>>>> 
>>>> Thanks !
>>>> Maxime
>>>> ------------------------------------------------------------------------------
>>>> Free Software Download: Index, Search & Analyze Logs and other IT data in
>>>> Real-Time with Splunk. Collect, index and harness all the fast moving IT data
>>>> generated by your applications, servers and devices whether physical, virtual
>>>> or in the cloud. Deliver compliance at lower cost and gain new business
>>>> insights. http://p.sf.net/sfu/splunk-dev2dev
>>>> _______________________________________________
>>>> mesa-users mailing list
>>>> mes...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/mesa-users
>>> 
>>> 
>>> ------------------------------------------------------------------------------
>>> Free Software Download: Index, Search & Analyze Logs and other IT data in
>>> Real-Time with Splunk. Collect, index and harness all the fast moving IT data
>>> generated by your applications, servers and devices whether physical, virtual
>>> or in the cloud. Deliver compliance at lower cost and gain new business
>>> insights. http://p.sf.net/sfu/splunk-dev2dev
>>> _______________________________________________
>>> mesa-users mailing list
>>> mes...@li...
>>> https://lists.sourceforge.net/lists/listinfo/mesa-users
>>> 
>> 
>> 
>> ----------------------------------------------------------------------------
>> Michael Zingale (mzi...@ma...)
>> Assistant Professor
>> 
>> Dept. of Physics and Astronomy    office: ESS 440
>> Stony Brook University            phone:  631-632-8225
>> Stony Brook, NY 11794-3800        web: http://www.astro.sunysb.edu/mzingale
>> ----------------------------------------------------------------------------
>> 
> 

Re: [mesa-users] PGPSTAR, problem in pgstar_controls.dek during compilation with gfortran

[Bill P. <pa...@ki...>]

Hi,

Damn compilers anyway!    It seems that gfortran 4.5.1 (but not 4.6) has a nonstandard rule for deciding between local vs. external definitions of a symbol.  Everyone else uses the local, but gfortran 4.5.1 uses the external one.  In this case, we have a local definition of show_convective_section as a logical function (that's the one we want), but gfortran is instead using a definition of show_convective_section as a subroutine in a module that is being "use"d in pgstar_trho_profile.   

I should have caught this before the release.  Sorry for missing it.  
There will be a new release very soon (I hope!).   And it will be fixed in that.

If you are feeling lucky and don't want to wait, you can update to 3039.
I think it is okay, but it has been put through the entire test_suite.

-Bill





On Feb 24, 2011, at 11:44 AM, Mike Zingale wrote:

> Hi Bill/Maxine, I am also having trouble compiling the latest MESA with pgstar.  I am using gfortran 4.5.1 on Fedora 14, and I get past the pgstar_ctrls_io.f compilation, but die a bit later with:
> 
> gfortran -fno-range-check  -fopenmp  -I../public -I../private -I../../include -Wunused-value -Werror -W -fimplicit-none   -O2 -c -ffree-form ../private/pgstar_trho_profile.f
> ../private/pgstar_trho_profile.f:698.49:
> 
>         has_convection = show_convective_section()
>                                                 1
> Error: Unexpected use of subroutine name 'show_convective_section' at (1)
> ../private/pgstar_trho_profile.f:699.47:
> 
>         has_overshoot = show_overshoot_section()
>                                               1
> Error: Unexpected use of subroutine name 'show_overshoot_section' at (1)
> ../private/pgstar_trho_profile.f:700.57:
> 
>         has_semiconvection = show_semiconvective_section()
>                                                         1
> Error: Unexpected use of subroutine name 'show_semiconvective_section' at (1)
> ../private/pgstar_trho_profile.f:701.55:
> 
>         has_thermo_haline = show_thermo_haline_section()
>                                                       1
> Error: Unexpected use of subroutine name 'show_thermo_haline_section' at (1)
> ../private/pgstar_trho_profile.f:763.57:
> 
>            show_convective_section = show_mixing_section(convective_mixing, cl
>                                                         1
> Error: Unexpected use of subroutine name 'show_mixing_section' at (1)
> ../private/pgstar_trho_profile.f:769.61:
> 
>            show_semiconvective_section = show_mixing_section(semiconvective_mi
>                                                             1
> Error: Unexpected use of subroutine name 'show_mixing_section' at (1)
> ../private/pgstar_trho_profile.f:775.60:
> 
>            show_thermo_haline_section = show_mixing_section(thermo_haline_mixi
>                                                            1
> Error: Unexpected use of subroutine name 'show_mixing_section' at (1)
> ../private/pgstar_trho_profile.f:781.56:
> 
>            show_overshoot_section = show_mixing_section(overshoot_mixing, clr_
>                                                        1
> Error: Unexpected use of subroutine name 'show_mixing_section' at (1)
> make: *** [pgstar_trho_profile.o] Error 1
> 
> /home/zingale/development/mesa/star/make
> FAILED
> 
> 
> 
> 
> 
> 
> 
> On Thu, 24 Feb 2011, Bill Paxton wrote:
> 
>> Hi Maxime,
>> 
>> I suggest upgrading to 4.5.1 -- you can do that easily at this website:
>> 
>> http://gcc.gnu.org/wiki/GFortranBinaries
>> 
>> Good luck!
>> 
>> -Bill
>> 
>> 
>> 
>> 
>> On Feb 24, 2011, at 10:29 AM, Maxime Viallet wrote:
>> 
>>> 
>>> 	Hello Mesa-people,
>>> 
>>> I have successfully compiled and run mesa (rev. 2987) using gfortran 4.5.0 on mac os X 10.6.6
>>> Now I am trying to get the PGPLOT interface working and I am running into this puzzling error while compiling the "star" module:
>>> 
>>> gfortran -fno-range-check  -fopenmp  -I../public -I../private -I../../include -Wunused-value -Werror -W -fimplicit-none   -O2 -c -ffree-form ../private/pgstar_ctrls_io.f
>>> pgstar_controls.dek:5.74:
>>>   Included at ../private/pgstar_ctrls_io.f:33:
>>> 
>>>     type (pgstar_win_file_data) :: pgstar_win_file_ptr(num_pgstar_plots)
>>>                                                                         1
>>> Error: Object 'pgstar_win_file_ptr' at (1) must have the SAVE attribute for default initialization of a component
>>> make: *** [pgstar_ctrls_io.o] Error 1
>>> 
>>> /Users/viallet/postdoc/mesa/star/make
>>> FAILED
>>> 
>>> 
>>> Of course I naively tried to add by hand the "save" statement but then the file star/public/star_def.f would not compile anymore.
>>> 
>>> Has somebody already encountered this problem ?
>>> 
>>> Thanks !
>>> Maxime
>>> ------------------------------------------------------------------------------
>>> Free Software Download: Index, Search & Analyze Logs and other IT data in
>>> Real-Time with Splunk. Collect, index and harness all the fast moving IT data
>>> generated by your applications, servers and devices whether physical, virtual
>>> or in the cloud. Deliver compliance at lower cost and gain new business
>>> insights. http://p.sf.net/sfu/splunk-dev2dev
>>> _______________________________________________
>>> mesa-users mailing list
>>> mes...@li...
>>> https://lists.sourceforge.net/lists/listinfo/mesa-users
>> 
>> 
>> ------------------------------------------------------------------------------
>> Free Software Download: Index, Search & Analyze Logs and other IT data in
>> Real-Time with Splunk. Collect, index and harness all the fast moving IT data
>> generated by your applications, servers and devices whether physical, virtual
>> or in the cloud. Deliver compliance at lower cost and gain new business
>> insights. http://p.sf.net/sfu/splunk-dev2dev
>> _______________________________________________
>> mesa-users mailing list
>> mes...@li...
>> https://lists.sourceforge.net/lists/listinfo/mesa-users
>> 
> 
> 
> ----------------------------------------------------------------------------
> Michael Zingale (mzi...@ma...)
> Assistant Professor
> 
> Dept. of Physics and Astronomy    office: ESS 440
> Stony Brook University            phone:  631-632-8225
> Stony Brook, NY 11794-3800        web: http://www.astro.sunysb.edu/mzingale
> ----------------------------------------------------------------------------
> 

Re: [mesa-users] PGPSTAR, problem in pgstar_controls.dek during compilation with gfortran 4.5.0

[Mike Z. <mzi...@sc...>]

Hi Bill/Maxine, I am also having trouble compiling the latest MESA with 
pgstar.  I am using gfortran 4.5.1 on Fedora 14, and I get past the 
pgstar_ctrls_io.f compilation, but die a bit later with:

gfortran -fno-range-check  -fopenmp  -I../public -I../private 
-I../../include -Wunused-value -Werror -W -fimplicit-none   -O2 -c 
-ffree-form ../private/pgstar_trho_profile.f
../private/pgstar_trho_profile.f:698.49:

          has_convection = show_convective_section()
                                                  1
Error: Unexpected use of subroutine name 'show_convective_section' at (1)
../private/pgstar_trho_profile.f:699.47:

          has_overshoot = show_overshoot_section()
                                                1
Error: Unexpected use of subroutine name 'show_overshoot_section' at (1)
../private/pgstar_trho_profile.f:700.57:

          has_semiconvection = show_semiconvective_section()
                                                          1
Error: Unexpected use of subroutine name 'show_semiconvective_section' at (1)
../private/pgstar_trho_profile.f:701.55:

          has_thermo_haline = show_thermo_haline_section()
                                                        1
Error: Unexpected use of subroutine name 'show_thermo_haline_section' at (1)
../private/pgstar_trho_profile.f:763.57:

             show_convective_section = show_mixing_section(convective_mixing, cl
                                                          1
Error: Unexpected use of subroutine name 'show_mixing_section' at (1)
../private/pgstar_trho_profile.f:769.61:

             show_semiconvective_section = show_mixing_section(semiconvective_mi
                                                              1
Error: Unexpected use of subroutine name 'show_mixing_section' at (1)
../private/pgstar_trho_profile.f:775.60:

             show_thermo_haline_section = show_mixing_section(thermo_haline_mixi
                                                             1
Error: Unexpected use of subroutine name 'show_mixing_section' at (1)
../private/pgstar_trho_profile.f:781.56:

             show_overshoot_section = show_mixing_section(overshoot_mixing, clr_
                                                         1
Error: Unexpected use of subroutine name 'show_mixing_section' at (1)
make: *** [pgstar_trho_profile.o] Error 1

/home/zingale/development/mesa/star/make
FAILED







On Thu, 24 Feb 2011, Bill Paxton wrote:

> Hi Maxime,
>
> I suggest upgrading to 4.5.1 -- you can do that easily at this website:
>
> http://gcc.gnu.org/wiki/GFortranBinaries
>
> Good luck!
>
> -Bill
>
>
>
>
> On Feb 24, 2011, at 10:29 AM, Maxime Viallet wrote:
>
>>
>> 	Hello Mesa-people,
>>
>> I have successfully compiled and run mesa (rev. 2987) using gfortran 4.5.0 on mac os X 10.6.6
>> Now I am trying to get the PGPLOT interface working and I am running into this puzzling error while compiling the "star" module:
>>
>> gfortran -fno-range-check  -fopenmp  -I../public -I../private -I../../include -Wunused-value -Werror -W -fimplicit-none   -O2 -c -ffree-form ../private/pgstar_ctrls_io.f
>> pgstar_controls.dek:5.74:
>>    Included at ../private/pgstar_ctrls_io.f:33:
>>
>>      type (pgstar_win_file_data) :: pgstar_win_file_ptr(num_pgstar_plots)
>>                                                                          1
>> Error: Object 'pgstar_win_file_ptr' at (1) must have the SAVE attribute for default initialization of a component
>> make: *** [pgstar_ctrls_io.o] Error 1
>>
>> /Users/viallet/postdoc/mesa/star/make
>> FAILED
>>
>>
>> Of course I naively tried to add by hand the "save" statement but then the file star/public/star_def.f would not compile anymore.
>>
>> Has somebody already encountered this problem ?
>>
>> Thanks !
>> Maxime
>> ------------------------------------------------------------------------------
>> Free Software Download: Index, Search & Analyze Logs and other IT data in
>> Real-Time with Splunk. Collect, index and harness all the fast moving IT data
>> generated by your applications, servers and devices whether physical, virtual
>> or in the cloud. Deliver compliance at lower cost and gain new business
>> insights. http://p.sf.net/sfu/splunk-dev2dev
>> _______________________________________________
>> mesa-users mailing list
>> mes...@li...
>> https://lists.sourceforge.net/lists/listinfo/mesa-users
>
>
> ------------------------------------------------------------------------------
> Free Software Download: Index, Search & Analyze Logs and other IT data in
> Real-Time with Splunk. Collect, index and harness all the fast moving IT data
> generated by your applications, servers and devices whether physical, virtual
> or in the cloud. Deliver compliance at lower cost and gain new business
> insights. http://p.sf.net/sfu/splunk-dev2dev
> _______________________________________________
> mesa-users mailing list
> mes...@li...
> https://lists.sourceforge.net/lists/listinfo/mesa-users
>


----------------------------------------------------------------------------
Michael Zingale (mzi...@ma...)
Assistant Professor

Dept. of Physics and Astronomy    office: ESS 440
Stony Brook University            phone:  631-632-8225
Stony Brook, NY 11794-3800        web: http://www.astro.sunysb.edu/mzingale
----------------------------------------------------------------------------

Re: [mesa-users] PGPSTAR, problem in pgstar_controls.dek during compilation with gfortran 4.5.0

[Bill P. <pa...@ki...>]

Hi Maxime,

I suggest upgrading to 4.5.1 -- you can do that easily at this website:

http://gcc.gnu.org/wiki/GFortranBinaries

Good luck!

-Bill




On Feb 24, 2011, at 10:29 AM, Maxime Viallet wrote:

> 
> 	Hello Mesa-people,
> 
> I have successfully compiled and run mesa (rev. 2987) using gfortran 4.5.0 on mac os X 10.6.6
> Now I am trying to get the PGPLOT interface working and I am running into this puzzling error while compiling the "star" module:
> 
> gfortran -fno-range-check  -fopenmp  -I../public -I../private -I../../include -Wunused-value -Werror -W -fimplicit-none   -O2 -c -ffree-form ../private/pgstar_ctrls_io.f
> pgstar_controls.dek:5.74:
>    Included at ../private/pgstar_ctrls_io.f:33:
> 
>      type (pgstar_win_file_data) :: pgstar_win_file_ptr(num_pgstar_plots)
>                                                                          1
> Error: Object 'pgstar_win_file_ptr' at (1) must have the SAVE attribute for default initialization of a component
> make: *** [pgstar_ctrls_io.o] Error 1
> 
> /Users/viallet/postdoc/mesa/star/make
> FAILED
> 
> 
> Of course I naively tried to add by hand the "save" statement but then the file star/public/star_def.f would not compile anymore.
> 
> Has somebody already encountered this problem ?
> 
> Thanks !
> Maxime
> ------------------------------------------------------------------------------
> Free Software Download: Index, Search & Analyze Logs and other IT data in 
> Real-Time with Splunk. Collect, index and harness all the fast moving IT data 
> generated by your applications, servers and devices whether physical, virtual
> or in the cloud. Deliver compliance at lower cost and gain new business 
> insights. http://p.sf.net/sfu/splunk-dev2dev 
> _______________________________________________
> mesa-users mailing list
> mes...@li...
> https://lists.sourceforge.net/lists/listinfo/mesa-users

[mesa-users] PGPSTAR, problem in pgstar_controls.dek during compilation with gfortran 4.5.0

[Maxime V. <via...@gm...>]

	Hello Mesa-people,

I have successfully compiled and run mesa (rev. 2987) using gfortran 4.5.0 on mac os X 10.6.6
Now I am trying to get the PGPLOT interface working and I am running into this puzzling error while compiling the "star" module:

gfortran -fno-range-check  -fopenmp  -I../public -I../private -I../../include -Wunused-value -Werror -W -fimplicit-none   -O2 -c -ffree-form ../private/pgstar_ctrls_io.f
pgstar_controls.dek:5.74:
    Included at ../private/pgstar_ctrls_io.f:33:

      type (pgstar_win_file_data) :: pgstar_win_file_ptr(num_pgstar_plots)
                                                                          1
Error: Object 'pgstar_win_file_ptr' at (1) must have the SAVE attribute for default initialization of a component
make: *** [pgstar_ctrls_io.o] Error 1

/Users/viallet/postdoc/mesa/star/make
FAILED


Of course I naively tried to add by hand the "save" statement but then the file star/public/star_def.f would not compile anymore.

Has somebody already encountered this problem ?

Thanks !
Maxime

[mesa-users] Question about the MESA.

[takeshi m. <mi...@as...>]

Dear Dr.Dotter and Prof.Paxton,

It has been a long time. I am Takeshi Mikami in Hokkaido university.

I use r2987 and have a question about "/data/star_data/log_columns.list".
There are items of "conv_mx*_top/bottom".
Through editing it, Can it output another physical parameters (temperature, 
density, ...) at the top/bottom of convection to "star.log"?
If it is possible, please teach me the method.

I know it is possible to do about radius ("conv_mx1_top" -> 
"conv_mx1_top_r").


With best regards,
Takeshi

---
Takeshi Mikami, MC2.
Department of Cosmosciences, Graduate School of Science,
Hokkaido University.
e-mail:mi...@as... 

Re: [mesa-users] Chemical diffusion and white dwarf atmospheres

[Bill P. <pa...@ki...>]

Hi Chris,

Excellent questions!  diffusion with gamma > 1 is on the list, but isn't currently be worked on (at least not be me!).
Lars may have something to add since that's a topic of interest for him.

Concerning atmosphere effects -- the default behavior of mesa is to place the outer edge of the star model at the photosphere.
The atm module then deals with tau smaller than that and returns a surface pressure at that boundary.
The star module deals with tau > photosphere by means of the usual eos and opacities.
The boundary condition at the surface is that atm and star agree on T and P for the outer boundary of the star model.

If that's is your mode of operation, then at tau abound 25, you are below the photosphere, so mesa star is calcuating things.
Then it is a question of whether the eos and kap modules are going to produce good results for that part of the star.

For cases where you really need a non-grey atmosphere (such as brown dwarfs or giant planets), then we move
the outer boundary for mesa star to a larger optical depth and use a special atm option.  An example is the
 comparison in the paper with the Baraffe et al results.  For that we put the outer edge at tau=100 and use
the atm option to use the COND tables.  However those tables for great for brown dwarfs and planets, but
they stop at log(g) << what you need.

As far as other things not in mesa yet that might be relevant, I'm not the one to comment, but I'll certainly
be interested in what you learn!!!

Cheers,
Bill



On Feb 22, 2011, at 10:03 AM, Chris Richardson wrote:

> Hello all,
> 
> I don't have much experience with MESA but I've been exploring WD  
> cooling with it. I was curious if anyone has plans in the works to  
> incorporate chemical diffusion and gravitational settling where the  
> Coulomb coupling parameter is greater than unity.  Also, does MESA  
> implement non-ideal effects of gas EOS and chemical equilibrium into  
> atmospheric calculations at large gravities (say log(g) = 6.0 to 9.0)  
> at optical depths around tau = 25? What other treatments besides  
> crystallization (which is uncertain in all codes) currently hinder  
> MESA from reproducing accurate early and late time WD evolution? Any  
> insights would be greatly appreciated. Many thanks!
> 
> ------------------------------------------------------------------------------
> Free Software Download: Index, Search & Analyze Logs and other IT data in 
> Real-Time with Splunk. Collect, index and harness all the fast moving IT data 
> generated by your applications, servers and devices whether physical, virtual
> or in the cloud. Deliver compliance at lower cost and gain new business 
> insights. http://p.sf.net/sfu/splunk-dev2dev 
> _______________________________________________
> mesa-users mailing list
> mes...@li...
> https://lists.sourceforge.net/lists/listinfo/mesa-users

[mesa-users] Chemical diffusion and white dwarf atmospheres

[Chris R. <ric...@ms...>]

Hello all,

I don't have much experience with MESA but I've been exploring WD  
cooling with it. I was curious if anyone has plans in the works to  
incorporate chemical diffusion and gravitational settling where the  
Coulomb coupling parameter is greater than unity.  Also, does MESA  
implement non-ideal effects of gas EOS and chemical equilibrium into  
atmospheric calculations at large gravities (say log(g) = 6.0 to 9.0)  
at optical depths around tau = 25? What other treatments besides  
crystallization (which is uncertain in all codes) currently hinder  
MESA from reproducing accurate early and late time WD evolution? Any  
insights would be greatly appreciated. Many thanks!

[mesa-users] mesa 2987 has beta release of magnetic rotation plus thermohaline & semiconvective mixing

[Bill P. <pa...@ki...>]

Hello,

There has been wonderful progress on magnetic rotating start in mesa!
The big break was when Norbert Langer kindly let me have access to his code.
Matteo Cantiello, currently a post-doc with Langer, helped me get it running on my mac.
[And, good news, Matteo will be coming to KITP as a post doc soon,
so I'm looking forward to lots more mesa help from him over the coming years.]
With the ability to run the code and edit it to reveal details of internals, I was able
to get mesa to produce very similar results in a short time.    In addition to the Langer code,
Alex Heger independently let me have the routine from KEPLER that implements
the Spruit-Taylor magnetic dynamo, and Evert Glebbeek helped me with the rotation potential routine.
So we got important assistance from several sources -- all of it is very much appreciated!!!

This is a "beta" release for magnetic rotation plus thermohaline & semiconvective mixing.
"Beta" because it is not fully tested and verified, and it hasn't had enough use to reveal low frequency bugs.
But my preliminary "pre-verification" testing suggests that we are in good shape, 
both for the lower mass cases as in this paper by Cantiello & Langer

and for the 15 Msun case from Heger 2005


If you'd like to check it out, I suggest looking at the new test_suite cases:
	15M_dynamo
	1M_thermohaline
	semiconvection
And of course, don't hesitate to email mesa-users to ask for clarification and help.

Here are some other changes since the last release (2941)

add option to build eos tables without irradiation -- and option to get eos results without irradiation

allow png output from pgstar without requiring window open

add pgstar plots for mixing+dynamo and abundance+power

add sample_pgstar_plot (shows how to add your own plot windows to pgstar)

add Asplund, Grevesse, Sauval, and Scott 2009 solar abundances to chem. also add element atomic weights

add pgstar plots for abund+pwr+mix and abund+pwr+mix+dyn

new kap tables with better blending of Freedman opacities

add one_zone_burn_jina to star/exercises

add 15M_dynamo to star/test_suite

add 1M_thermohaline to star test_suite

add semiconvection to star test_suite

Cheers,
Bill