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

Re: [mesa-users] EoS & partial ionization

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

Hi Ken,

>From eos/public/eos_lib.f:

      ! The MESA EOS is based on the OPAL, SCVH, and HELM EOS's.
      ! The OPAL-SCVH values are used for approximately
      !     Z < 0.04, logRho < 3.3, and logT < 7.7
      ! HELM is used for all other cases.

Since you're in pure "Z" territory, you're accessing the HELM EoS which
assumes full ionization  (Frank, correct me if I am wrong).

Aaron



On Wed, Aug 3, 2011 at 8:20 PM, Ken Shen <ke...@as...> wrote:

> Hi all.  I've got a question about how the MESA EoS handles partial
> ionization.  In particular, are the changes in free electron fraction
> taken into account when the EoS returns, e.g., chiT and chiRho?  As a
> test, here are the results for two calls to the EoS for X_12C = X_16O
> = 0.5 and rho = 2e-8 g/cm^3:
>
> T = 6.5e4 K
> P = 9.022e4 dyne/cm^2
> free_e = 0.3463
> chiT = 2.499
> mu = 1.745
>
> T = 6.4e4 K
> P = 8.577e4 dyne/cm^2
> free_e = 0.3364
> chiT = 2.482
> mu = 1.745
>
> A crude calculation from these two calls gives dlnP/dlnT = 3.26, which
> is significantly different from the returned value of chiT = 2.5.
> Also, the mean molecular weight that is returned seems to assume full
> ionization; it should be 2.39 for the first call and 2.44 for the
> second.
>
>
> Thanks,
> Ken
>
>
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[mesa-users] EoS & partial ionization

[Ken S. <ke...@as...>]

Hi all.  I've got a question about how the MESA EoS handles partial
ionization.  In particular, are the changes in free electron fraction
taken into account when the EoS returns, e.g., chiT and chiRho?  As a
test, here are the results for two calls to the EoS for X_12C = X_16O
= 0.5 and rho = 2e-8 g/cm^3:

T = 6.5e4 K
P = 9.022e4 dyne/cm^2
free_e = 0.3463
chiT = 2.499
mu = 1.745

T = 6.4e4 K
P = 8.577e4 dyne/cm^2
free_e = 0.3364
chiT = 2.482
mu = 1.745

A crude calculation from these two calls gives dlnP/dlnT = 3.26, which
is significantly different from the returned value of chiT = 2.5.
Also, the mean molecular weight that is returned seems to assume full
ionization; it should be 2.39 for the first call and 2.44 for the
second.


Thanks,
Ken

Re: [mesa-users] MESA is hydrodynamic mode

[Jean-Claude P. <jc...@gm...>]

Problem solved ! Sorry for the spam.

JC

On 29/07/11 15:14, Jean-Claude Passy wrote:
> Hi all,
>
> could someone please tell me how to turn on the hydrodynamic mode ?
>
> Thanks a lot,
>
> JC
>

[mesa-users] MESA is hydrodynamic mode

[Jean-Claude P. <jc...@gm...>]

Hi all,

could someone please tell me how to turn on the hydrodynamic mode ?

Thanks a lot,

JC

[mesa-users] net module

[harikrishnan r. <hr...@ic...>]

Hi all,
I am a grad student at stony brook university working in the astronomy dept.
I am working on some reaction networks and would love to use your module
"net" to evolve density and temperature using the reaction network. I am
having a little difficulty understanding and implementing the functions in
net. I would be really grateful if someone could point me to an earlier
thread where this is discussed. Could i get a code snippet of the net module
being used separately?
Sincerely
Harikrishnan

Re: [mesa-users] irradiation

[Jean-Claude P. <jc...@gm...>]

Hi,

no you need both. The 'relax_irradiation' helps you getting started by
relaxing the star as you turn on irradiation progressively. The section
in your inlist should look like:

----------------------------------------------------
set_irradiation = .true.

relax_irradiation = .true.
relax_irradiation_min_steps = 200
relax_irradiation_max_yrs_dt = 1d-1

new_irrad_flux = 1d7 ! erg s^-1 cm^-2
new_irrad_col_depth = 1 ! g cm^-2
----------------------------------------------------

Hope that helps.
Good luck,

JC


On 22/07/11 21:59, ztt wrote:
> Hi Jean,
>
> Thanks for your reply. My mail box didn't get your email but I saw it
> on the mailing list.
> So is this the correct procedure example for turning on irradiation??
> 1. do relax with:
> relax_irradiation = .true.
> relax_irradiation_min_steps = 200
> relax_irradiation_max_yrs_dt = 1d-1
>
> new_irrad_flux = 1d7 ! erg s^-1 cm^-2
> new_irrad_col_depth = 1 ! g cm^-2
> with 'set_irradiation = .true.' commented;
> 2. turn on irradiation with:
> set_irradiation = .true.
> new_irrad_flux = 1d7 ! erg s^-1 cm^-2
> new_irrad_col_depth = 1 ! g cm^-2
> but with all the relax_* commented now;
>
> while keep the setup for tau & atmosphere all the time:
> set_tau_factor = .true. ! change tau_factor without reconverging.
> set_to_this_tau_factor = 100
>
> which_atm_option = 'grey_and_kap'
> !which_atm_option = 'grey_irradiated'
>
> atm_grey_irradiated_atol = 1d-4
> atm_grey_irradiated_rtol = 1d-4
> atm_grey_irradiated_T_eq = 1000 ! equilibrium temperature based on
> irradiation
> ! e.g., might use T_eq = Teff_star*(R_star/(2*Distance_to_star))^(1/2)
> atm_grey_irradiated_kap_nu = 4d-3 ! opacity for irradiation
> atm_grey_irradiated_P_surf = 1d6 ! 1 bar in cgs units
> &nb! sp; ; atm_grey_irradiated_max_tries = 50 ! limit on iterations
> trace_atm_grey_irradiated = .false.
>
> Thank you very much!
>
> Best wishes, Tingtao
>
>

[mesa-users] irradiation

[ztt <ztt...@12...>]

  Hi Jean,

Thanks for your reply. My mail box didn't get your email but I saw it on the mailing list.
So is this the correct procedure example for turning on irradiation??
1. do relax with:
      relax_irradiation = .true.
      relax_irradiation_min_steps = 200
      relax_irradiation_max_yrs_dt = 1d-1

      new_irrad_flux = 1d7 ! erg s^-1 cm^-2
      new_irrad_col_depth = 1 ! g cm^-2
with 'set_irradiation = .true.' commented;
2. turn on irradiation with:
      set_irradiation = .true.
      new_irrad_flux = 1d7 ! erg s^-1 cm^-2
      new_irrad_col_depth = 1 ! g cm^-2
but with all the relax_* commented now;

while keep the setup for tau & atmosphere all the time:
      set_tau_factor = .true. ! change tau_factor without reconverging.
      set_to_this_tau_factor = 100

      which_atm_option = 'grey_and_kap'
      !which_atm_option = 'grey_irradiated'

            atm_grey_irradiated_atol = 1d-4
            atm_grey_irradiated_rtol = 1d-4
            atm_grey_irradiated_T_eq = 1000 ! equilibrium temperature based on irradiation
               ! e.g., might use T_eq = Teff_star*(R_star/(2*Distance_to_star))^(1/2)
            atm_grey_irradiated_kap_nu = 4d-3 ! opacity for irradiation
            atm_grey_irradiated_P_surf = 1d6 ! 1 bar in cgs units
            atm_grey_irradiated_max_tries = 50 ! limit on iterations
            trace_atm_grey_irradiated = .false.

Thank you very much!

Best wishes, Tingtao

Re: [mesa-users] irradiation

[Jean-Claude P. <jc...@gm...>]

Hi Tingtao,

you have to remove the exclamation mark before 'set_irradiation = .true.'

Best,

JC

On 21/07/11 21:54, ztt wrote:
> Dear Mesa users,
>
> Do you have experience with the irradiated_planet test_suite? I tried
> with 2 different inlist:
> !set_irradiation = .true.
> ! relax_irradiation = .true.
> ! relax_irradiation_min_steps = 200
> ! relax_irradiation_max_yrs_dt = 1d-1
>
> ! new_irrad_flux = 1d7 ! erg s^-1 cm^-2
> ! new_irrad_col_depth = 1 ! g cm^-2
>
> and the other one:
> !set_irradiation = .true.
> relax_irradiation = .true.
> relax_irradiation_min_steps = 200
> relax_irradiation_max_yrs_dt = 1d-1
> new_irrad_flux = 1d7 ! erg s^-1 cm^-2
> new_irrad_col_depth = 1 ! g cm^-2
>
> both use which_atm_option = 'grey_and_kap'
>
> then do ./star_irrad, and the results are the same.
> Could you give me some hints about how to make irradiation work??
> Thank you!
>
> Best wishes, Tingtao
>
>

[mesa-users] how to restart svn

[阿亮 <chl...@gm...>]

how to restart svn?
thank you!

[mesa-users] irradiation

[ztt <ztt...@12...>]

  Dear Mesa users,

Do you have experience with the irradiated_planet test_suite? I tried with 2 different inlist:
      !set_irradiation = .true.
!      relax_irradiation = .true.
!      relax_irradiation_min_steps = 200
!      relax_irradiation_max_yrs_dt = 1d-1

!      new_irrad_flux = 1d7 ! erg s^-1 cm^-2
!      new_irrad_col_depth = 1 ! g cm^-2

and the other one:
      !set_irradiation = .true.
      relax_irradiation = .true.
      relax_irradiation_min_steps = 200
      relax_irradiation_max_yrs_dt = 1d-1
      new_irrad_flux = 1d7 ! erg s^-1 cm^-2
      new_irrad_col_depth = 1 ! g cm^-2

both use which_atm_option = 'grey_and_kap'

then do ./star_irrad, and the results are the same.
Could you give me some hints about how to make irradiation work??
Thank you!

Best wishes, Tingtao

Re: [mesa-users] create a profile from .mod file ?

[Jean-Claude P. <jc...@gm...>]

Got it, just had to change the inlist actually.

JC

On 20/07/11 14:46, Jean-Claude Passy wrote:
> Bonus question: is it possible to restart MESA (either using a photo or
> a mod file) AND change some logistics parameters, for instance
> 'profile_interval' ?
>
> Thanks a ton,
>
> JC
>
> On 20/07/11 10:53, Jean-Claude Passy wrote:
>> Hi all,
>>
>> I may have asked this already but I cannot remember the answer: is it
>> possible to create an object profile from a restart file (*.mod) ?
>>
>> Thanks a lot,
>>
>> JC
>>
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Re: [mesa-users] create a profile from .mod file ?

[Jean-Claude P. <jc...@gm...>]

Bonus question: is it possible to restart MESA (either using a photo or 
a mod file) AND change some logistics parameters, for instance 
'profile_interval' ?

Thanks a ton,

JC

On 20/07/11 10:53, Jean-Claude Passy wrote:
> Hi all,
>
> I may have asked this already but I cannot remember the answer: is it
> possible to create an object profile from a restart file (*.mod) ?
>
> Thanks a lot,
>
> JC
>
> ------------------------------------------------------------------------------
> 10 Tips for Better Web Security
> Learn 10 ways to better secure your business today. Topics covered include:
> Web security, SSL, hacker attacks&  Denial of Service (DoS), private keys,
> security Microsoft Exchange, secure Instant Messaging, and much more.
> http://www.accelacomm.com/jaw/sfnl/114/51426210/
> _______________________________________________
> mesa-users mailing list
> mes...@li...
> https://lists.sourceforge.net/lists/listinfo/mesa-users

[mesa-users] create a profile from .mod file ?

[Jean-Claude P. <jc...@gm...>]

Hi all,

I may have asked this already but I cannot remember the answer: is it 
possible to create an object profile from a restart file (*.mod) ?

Thanks a lot,

JC

Re: [mesa-users] use pgstar

[ztt <ztt...@12...>]

Dear Frank,

I installed pgplot in mesa/utils/pgplot again, and the demos work well. Then I change the .bashrc like
'export PGPLOT_DIR=~/mesa/utils/pgplot' and sourced it.
but I came back to mesa directory and do './mk', it gave me this error:

home/ztt/mesa/star
building star package.

make: `libstar.a' is up to date.
make: `libstar.a' is up to date.
gfortran -fno-range-check  -fopenmp  -o ../star \
    run_star_extras.o run_star.o  run.o -L../../make -lstar -L../../../lib -lpulse -ldiffusion -lionization -lmlt -latm -lkaro -lcolors -leos -lkap -lweak -lnet -lscreen -lrates -lreaclib -lneu -lchem -linterp_2d -linterp_1d -lnum -lutils -lalert -lconst -lmtx    -lmesalapack -lmesablas -L~/mesa/utils/pgplot  -lpgplot -L/usr/X11R6/lib -lX11                                             
/usr/bin/ld: cannot find -lpgplot
collect2: ld returned 1 exit status
make: *** [star] Error 1

FAILED


Do you think it's some problem with the environment variables I set??
Thank you a lot.

Best wishes, Tingtao

At 2011-07-12 17:36:36，"Frank Timmes" <fx...@ma...> wrote:

dear tingtao,


cd mesa/utils
tar -xjf pgplot.tbz
cd pgplot


and follow the README


fxt






On Jul 12, 2011, at 1:06 AM, ztt wrote:

Dear Mesa users,

I'm trying to get pgstar working for onscreen snapshot plot. Since my laptop is running with Ubuntu11.04, I downloaded the package and installed pgplot5.2 according to T.J.Pearson's instructions. So I have /usr/local/src/pgplot directory which contains everything extracted from the downloaded pgplot5.2 package, and /usr/local/pgplot directory where I installed it and compiled the files(so now it also contains demos and all the *.o files).
I also set the environment variables in ~/.bashrc like this:
export PGPLOT_DIR=/usr/local/pgplot
export PGPLOT_DEV=/Xserve

Then in mesa/utils/makefile_header I also set this :
# for Ubuntu, Philip Pinto found these libraries to be necessary:                                                                      
LOAD_PGPLOT = -L${PGPLOT_DIR} -lpgplot  -lX11 -lxcb -lXau -lXdmcp -lXext  -lz                                          

But when I do './clean' then './mk' in the mesa directory, it still report errors:
(below is only a small fraction of the report, others are similar)


/home/ztt/mesa/star/make/../private/pgstar_trho_profile.f:424: undefined reference to `pgunsa_'
../../make/libstar.a(pgstar_trho_profile.o): In function `do_kap_regions':
/home/ztt/mesa/star/make/../private/pgstar_trho_profile.f:237: undefined reference to `pgsave_'
/home/ztt/mesa/star/make/../private/pgstar_trho_profile.f:239: undefined reference to `pgsci_'
/home/ztt/mesa/star/make/../private/pgstar_trho_profile.f:240: undefined reference to `pgsls_'
/home/ztt/mesa/star/make/../private/pgstar_trho_profile.f:251: undefined reference to `pgsci_'
/home/ztt/mesa/star/make/../private/pgstar_trho_profile.f:258: undefined reference to `pgsci_'
/home/ztt/mesa/star/make/../private/pgstar_trho_profile.f:259: undefined reference to `pgmove_'
/home/ztt/mesa/star/make/../private/pgstar_trho_profile.f:260: undefined reference to `pgdraw_'
/home/ztt/mesa/star/make/../private/pgstar_trho_profile.f:261: undefined reference to `pgdraw_'
/home/ztt/mesa/star/make/../private/pgstar_trho_profile.f:262: undefined reference to `pgdraw_'
/home/ztt/mesa/star/make/../private/pgstar_trho_profile.f:263: undefined reference to `pgdraw_'
/home/ztt/mesa/star/make/../private/pgstar_trho_profile.f:264: undefined reference to `pgdraw_'
../../make/libstar.a(pgstar_trho_profile.o):/home/ztt/mesa/star/make/../private/pgstar_trho_profile.f:265: more undefined references to `pgdraw_' follow
../../make/libstar.a(pgstar_trho_profile.o): In function `do_kap_regions':
/home/ztt/mesa/star/make/../private/pgstar_trho_profile.f:268: undefined reference to `pgsci_'
/home/ztt/mesa/star/make/../private/pgstar_trho_profile.f:277: undefinedan reference to `pgsci_'
/home/ztt/mesa/star/make/../private/pgstar_trho_profile.f:279: undefined reference to `pgsci_'
/home/ztt/mesa/star/make/../private/pgstar_trho_profile.f:286: undefined reference to `pgsci_'
/home/ztt/mesa/star/make/../private/pgstar_trho_profile.f:287: undefined reference to `pgsls_'

Do you have any experience about this problem? I don't know if this is about the manual installation of pgplot.
Thank you a lot.

Best wishes, Tingtao


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[mesa-users] Chosing reaction networks

[Roni W. <ron...@gm...>]

Dear MESA users,

 

I am trying to get mesa run with a more elaborate reaction network.

 

I did the following:

 

&star_job 

      change_net = .true. ! switch nuclear reaction network

      new_net_name = 'ns_he.net'

 

where ns_he.net is one of the networks present in mesa/data/net_data/nets.

 

The code keeps running with the basic net.

 

What am I missing?

 

Thanks,

Roni 

 

[mesa-users] use pgstar

[ztt <ztt...@12...>]

Dear Mesa users,

I'm trying to get pgstar working for onscreen snapshot plot. Since my laptop is running with Ubuntu11.04, I downloaded the package and installed pgplot5.2 according to T.J.Pearson's instructions. So I have /usr/local/src/pgplot directory which contains everything extracted from the downloaded pgplot5.2 package, and /usr/local/pgplot directory where I installed it and compiled the files(so now it also contains demos and all the *.o files).
I also set the environment variables in ~/.bashrc like this:
export PGPLOT_DIR=/usr/local/pgplot
export PGPLOT_DEV=/Xserve

Then in mesa/utils/makefile_header I also set this :
# for Ubuntu, Philip Pinto found these libraries to be necessary:                                                                      
LOAD_PGPLOT = -L${PGPLOT_DIR} -lpgplot  -lX11 -lxcb -lXau -lXdmcp -lXext  -lz                                          

But when I do './clean' then './mk' in the mesa directory, it still report errors:
(below is only a small fraction of the report, others are similar)


/home/ztt/mesa/star/make/../private/pgstar_trho_profile.f:424: undefined reference to `pgunsa_'
../../make/libstar.a(pgstar_trho_profile.o): In function `do_kap_regions':
/home/ztt/mesa/star/make/../private/pgstar_trho_profile.f:237: undefined reference to `pgsave_'
/home/ztt/mesa/star/make/../private/pgstar_trho_profile.f:239: undefined reference to `pgsci_'
/home/ztt/mesa/star/make/../private/pgstar_trho_profile.f:240: undefined reference to `pgsls_'
/home/ztt/mesa/star/make/../private/pgstar_trho_profile.f:251: undefined reference to `pgsci_'
/home/ztt/mesa/star/make/../private/pgstar_trho_profile.f:258: undefined reference to `pgsci_'
/home/ztt/mesa/star/make/../private/pgstar_trho_profile.f:259: undefined reference to `pgmove_'
/home/ztt/mesa/star/make/../private/pgstar_trho_profile.f:260: undefined reference to `pgdraw_'
/home/ztt/mesa/star/make/../private/pgstar_trho_profile.f:261: undefined reference to `pgdraw_'
/home/ztt/mesa/star/make/../private/pgstar_trho_profile.f:262: undefined reference to `pgdraw_'
/home/ztt/mesa/star/make/../private/pgstar_trho_profile.f:263: undefined reference to `pgdraw_'
/home/ztt/mesa/star/make/../private/pgstar_trho_profile.f:264: undefined reference to `pgdraw_'
../../make/libstar.a(pgstar_trho_profile.o):/home/ztt/mesa/star/make/../private/pgstar_trho_profile.f:265: more undefined references to `pgdraw_' follow
../../make/libstar.a(pgstar_trho_profile.o): In function `do_kap_regions':
/home/ztt/mesa/star/make/../private/pgstar_trho_profile.f:268: undefined reference to `pgsci_'
/home/ztt/mesa/star/make/../private/pgstar_trho_profile.f:277: undefinedan reference to `pgsci_'
/home/ztt/mesa/star/make/../private/pgstar_trho_profile.f:279: undefined reference to `pgsci_'
/home/ztt/mesa/star/make/../private/pgstar_trho_profile.f:286: undefined reference to `pgsci_'
/home/ztt/mesa/star/make/../private/pgstar_trho_profile.f:287: undefined reference to `pgsls_'

Do you have any experience about this problem? I don't know if this is about the manual installation of pgplot.
Thank you a lot.

Best wishes, Tingtao

Re: [mesa-users] Printing planet profile properties

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

Hello,

On Jul 11, 2011, at 8:58 PM, Gabriel-Dominique Marleau wrote:

> Dear MESA/star users,
> 
> With in mind the modeling of giant gas planets (which seems to be garnering a healthy amount of attention in this mailing list), would someone know how to:
> 
> 1. Print log*.data files of the "on-the-side" models calculated while adding a core with relax_M_center and relax_R_center on (as explained in star/public/run_star_defaults.dek)?

I didn't anticipate anyone wanting to do that!  As you've seen, the standard "relax" routines turn off logging.   I can think of 2 things you might do.   You can find the relevant code in star/private/relax.f.   The routine do_internal_evolve is the place where logging is turned off by the following 2 lines:
         s% do_log_files = .false.
         s% do_profiles = .false.
You could try just commenting those out and remaking star by doing
	cd star/test
	./mk;./export
An alternative method that doesn't involve modifying the code would be to write your own versions of the relax routines that you want to follow.
For example, you could copy the routines do_relax_R_center, before_evolve_relax_R_center, relax_R_center_check_model, and do1_relax_R_center.
Replace the call on do_internal_evolve in do_relax_R_center by a call on star_evolve_to_check_point (see star/public/star_lib).


> 
> 2. Add to the log files the composition in terms of the H, H_2, He mass fractions, i.e. track their dissociation and ionisation fractions within the star? I could not find a relevant column name in mesa/data/star_data/profile_columns.list but I may be missing something simple.

The mesa/eos doesn't provide the ionization fractions; that's why you didn't find them.  If you'd like to provide a routine to return the ionization fractions for H and He, I'd be delighted.


> 3. Get the following columns to print?   


if you don't find what you want in mesa/data/star_data/profile_columns.list, you can add columns in your run_star_extras using how_many_extra_profile_columns and data_for_extra_profile_columns.

here are a few things related to Brunt and mixing that are already available:

> - chiY ! dlnP/dlnY used in calculate of brunt_B term
> - dlnY_dlnP ! the actual dlnY/dlnP in the model as used in brunt_B

      !brunt_N2 ! brunt-vaisala frequency squared
      !brunt_A ! = N^2*r/g
      !brunt_N2_dimensionless ! N2 in units of 3GM/R^3
      !brunt_N_dimensionless ! N in units of sqrt(3GM/R^3)
      !brunt_frequency ! cycles per day
      !brunt_N ! sqrt(abs(brunt_N2))
      !log_brunt_N ! log10(brunt_N)
      !log_brunt_N2 ! log10(brunt_N2)
      !sign_brunt_N2 ! sign of brunt_N2 (+1 for Ledoux stable; -1 for Ledoux unstable)
      !lamb_S2 ! for l=1: S = 2*(csound/r)^2
      !lamb_S ! for l=1: S = sqrt(2)*csound/r
      !brunt_dlnRho_dlnR ! smoothed numerical difference

> - dlnmu_dr ! for salt-finger mixing
> - semiconvection_criterion ! positive means stable
> Including them in profile_columns.list with "use_Ledoux_criterion = .true." and values for alpha_semiconvection and thermo_haline_coeff yields for each a "failed to recognize item" error.

   !gradL ! gradient for Ledoux criterion for convection
   !gradL_composition_term ! = composition term in gradL.  negative means thermohaline instability.
   !sch_stable ! 1 if grada > gradr, 0 otherwise
   !ledoux_stable ! 1 if gradL > gradr, 0 otherwise
   !stability_type ! values same as defined in mlt_def for mixing types


Good luck!
Bill

[mesa-users] Printing planet profile properties

[Gabriel-Dominique M. <gab...@ma...>]

Dear MESA/star users,

With in mind the modeling of giant gas planets (which seems to be garnering a healthy amount of attention in this mailing list), would someone know how to:

1. Print log*.data files of the "on-the-side" models calculated while adding a core with relax_M_center and relax_R_center on (as explained in star/public/run_star_defaults.dek)?

2. Add to the log files the composition in terms of the H, H_2, He mass fractions, i.e. track their dissociation and ionisation fractions within the star? I could not find a relevant column name in mesa/data/star_data/profile_columns.list but I may be missing something simple.

3. Get the following columns to print?
- chiY ! dlnP/dlnY used in calculate of brunt_B term
- dlnY_dlnP ! the actual dlnY/dlnP in the model as used in brunt_B
- dlnmu_dr ! for salt-finger mixing
- semiconvection_criterion ! positive means stable
Including them in profile_columns.list with "use_Ledoux_criterion = .true." and values for alpha_semiconvection and thermo_haline_coeff yields for each a "failed to recognize item" error.

Thank you for any help,

Gabriel-Dominique Marleau
Department of Physics
McGill University

[mesa-users] Irradiated Planet Atmospheres

[Konstantin B. <kba...@gp...>]

Dear MESA users,

when using the "which_atm_option = 'grey_irradiated' ," is there a way to
force the radius that corresponds to a lower pressure than the default 1bar?
Is this done by changing atm_grey_irradiated_P_surf ? I tried changing this
and immediately ran into convergence issues....

Thanks,
Konstantin

Re: [mesa-users] Yet about Brunt calculation ...

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

Hi Ehsan,

Thanks for your email and your thoughts on how we might make progress getting mesa to be able to support asteroseismology.  As you know, that's a high priority and lots of people are helping, yourself included.  

At this point it is too early to predict where the problems lie or how they will be solved, and we welcome input and participation in figuring things out.  Happily mesa is modular!  So you might try writing a routine to call the eos to calculate the brunt the way you suggest.  You can get all the things you need in the profile output from star to be able to calculate a brunt profile using a different scheme and compare it what we're doing now.  That would be very interesting to see.

I'm confident we'll get there -- but there's still some hard work to be done.

Best wishes,
Bill




On Jul 9, 2011, at 11:35 AM, Ehsan Moravveji wrote:

> Dear Bill and mesa friends,
> Hi.
> I'm totally aware that implimentation of Brunt-Vaisala is challenging for you, and you made a lot of efforts to implement Brassard et al. receipe into MESA. Great ...
> 
> But, 
> I read the first 4 pages of the paper. They clearly state in a paragraph above Eq. 14 that "We thus may use Y ... as a unique indicator of composition change" and indeed they are true for a model of white dwarf, which is quite simple star. One can even model a white dwarf with a composite polytrope of varying n and still succeed to explain many phenomena. But, in my opinion this cannot be the case for evolved stars off the main sequence.
> 
> Here, I have attached a plot of the abundance profile variations within a model of Rigel. We are all familiar with similar plots.
> 
> 1- The H profile variation could be quite profound outside the core.
> 2- For other heavier species, their abundances are small, but the differential of their logarithm may still contribute appreciably to the last term in Eq. 13 of Brassard et al. at least for the first few abundant species in normal stars.
> 3- caling multiple times to EOS could be demanding and CPU expensive, but in my opinion, a better evaluation of N2 is by considering Eq. 13 and letting the sum over just few species, say those that are followed by the rates.
> 4- I admit that I might be totally wrong, but need to be justified.
> 5- I have no idea how difficult it might be to implement numerically the more "standard" (in the sense of literature) N^2 using \nabla_\mu rather than B term in Brassard et al. 
> Physically, \nabla_\mu is very meaningful; it carries the weighted presence of all species in each layer, plus electrons! Not only He.
> 6- Unfortunately, I'm not familiar with the Lars formula called "simple". But, what I intend to do is to scape from free parameters once a quantity is free from this, and N^2 is. I'm really annoyed when I have to decide upon brunt_H_frac and test the effects of this keeping all parameters fixed, and repeating and repeating. And even after that, being yet worried of it's potential effects with the changes in the model. Of course, this is my problem and comes from my lack of knowledge.
> 
> N^2 has a very critical role in asteroseismology, and that's indeed why it is worth to discuss. Specially, it is an input to pulsation codes, and when N^2 profile has some spikes, it makes the solution of pulsation equations tough.
> 
> With kind regards.
> 
> Moravveji, Ehsan.

Re: [mesa-users] Using MESA on a 16 core machine

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

Hi Nathan,

MESA will use OpenMP by default, and OpenMP will use the number of threads specified by the environment variable OMP_NUM_THREADS.
So you can do setenv or export to control how many threads are used.

My impression has been that the ifort implementation of OpenMP was significantly better than the gfortran one, but I haven't done a careful comparison.

But if you are interested in improved performance, you should see if there is any way to get ifort.   You might at least try a "free sample period" to compare.

Getting mesa/star to make good use of more than 3 or 4 cores is a challenge that I'm working on, but we're not there yet.

Cheers,
Bill




 


On Jul 9, 2011, at 2:22 PM, Nathan Thompson wrote:

> Hello, 
> 
> My name is Nathan Thompson and I am a graduate student at Wichita State University. I have been using MESA on my personal computer for about a year to do computations. It is an Intel i7 860 machine (four cores) and does well with the computations.
> 
> Recently, I was given an account on a university computer in order to use that to do computations, a 16 core machine of which I am not 100% sure of the processor type, but I was assured that each of its cores were faster than my i7. However, when I ran the same model in MESA on both boxes, my PC did the computations twice as quickly as the university machine (and I had full use of all 16 cores). Both versions of MESA were compiled using gfortran.
> 
> I know the MESA is "thread safe" as stated by the website, but performance is noted to not increase with additional processors. Is there an option that I need to set in MESA to activate the use of OpenMP for multiple threads, or is this enabled "out of the box?" Also, is there a way to limit the number of cores MESA has access to, so that I can test to see if one of these cores is indeed faster than my i7?
> 
> Thanks,
> Nathan Thompson
> Wichita State University
> 
> 
> ------------------------------------------------------------------------------
> All of the data generated in your IT infrastructure is seriously valuable.
> Why? It contains a definitive record of application performance, security 
> threats, fraudulent activity, and more. Splunk takes this data and makes 
> sense of it. IT sense. And common sense.
> http://p.sf.net/sfu/splunk-d2d-c2_______________________________________________
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Re: [mesa-users] Using MESA on a 16 core machine

[Jeremy S. <j.a...@da...>]

Hi Nathan,

I run MESA here on the COSMOS super computer here in Cambridge and found it 
significantly faster. On 2 cores I can get a 1M from pre ms to WD in 1.5 
hours. The technician helped me a lot and we found that three cores is the 
most efficient (gaining only a small boost with 4).

Jeremy

On Jul 9 2011, Nathan Thompson wrote:

>Hello,
>
> My name is Nathan Thompson and I am a graduate student at Wichita State 
> University. I have been using MESA on my personal computer for about a 
> year to do computations. It is an Intel i7 860 machine (four cores) and 
> does well with the computations.
>
>Recently, I was given an account on a university computer in order to use
>that to do computations, a 16 core machine of which I am not 100% sure of
>the processor type, but I was assured that each of its cores were faster
>than my i7. However, when I ran the same model in MESA on both boxes, my PC
>did the computations twice as quickly as the university machine (and I had
>full use of all 16 cores). Both versions of MESA were compiled using
>gfortran.
>
> I know the MESA is "thread safe" as stated by the website, but 
> performance is noted to not increase with additional processors. Is there 
> an option that I need to set in MESA to activate the use of OpenMP for 
> multiple threads, or is this enabled "out of the box?" Also, is there a 
> way to limit the number of cores MESA has access to, so that I can test 
> to see if one of these cores is indeed faster than my i7?
>
>Thanks,
>Nathan Thompson
>Wichita State University
>

[mesa-users] Using MESA on a 16 core machine

[Nathan T. <nlt...@wi...>]

Hello,

My name is Nathan Thompson and I am a graduate student at Wichita State
University. I have been using MESA on my personal computer for about a year
to do computations. It is an Intel i7 860 machine (four cores) and does well
with the computations.

Recently, I was given an account on a university computer in order to use
that to do computations, a 16 core machine of which I am not 100% sure of
the processor type, but I was assured that each of its cores were faster
than my i7. However, when I ran the same model in MESA on both boxes, my PC
did the computations twice as quickly as the university machine (and I had
full use of all 16 cores). Both versions of MESA were compiled using
gfortran.

I know the MESA is "thread safe" as stated by the website, but performance
is noted to not increase with additional processors. Is there an option that
I need to set in MESA to activate the use of OpenMP for multiple threads, or
is this enabled "out of the box?" Also, is there a way to limit the number
of cores MESA has access to, so that I can test to see if one of these cores
is indeed faster than my i7?

Thanks,
Nathan Thompson
Wichita State University

[mesa-users] Sharing some modeling questions with YOU ...

[Ehsan M. <mor...@ia...>]

<html><div>
Dear MESA users,
Hi. I'm Ehsan, a PhD student from Iran. It is more
than a year I'm trying to find a suitable model from MESA that fits
simultaneously all the (exhaustive list of) observed properties of the
blue supergiant Rigel (beta Ori). This model would serve as an input to a
non-adiabatic pulsation code.
The reason I write this message to MESA
community is that I'm sure there are many experts that read this. I'm just
asking for your ideas regarding some points:

1- As usual, the
"standard" MESA models that I calculate cannot explain properly
the pulsational modes of Rigel. Hence, I have to try other possibilities.


2- The first point is that Rigel has surface He abundance
Ys=0.32+/-0.04, and vsini = 25+/-3 at solar metalicity. The only way I
found to enhance surface He is just by rotation, but when my model of
M=19Msun terminates at Teff = 12100+/-150 K, the surface velocity is
around 80 km/s, much higher than the observed one. This Ys has substanial
effect in driving radial modes, that I'm seeking to find.
If you have
any idea to mix He to the surface (even Ys=0.36) and keeping surface
rotation low, I'd be really appreciating.

3- Secondly, I also
like to increase the effect of kappa mechanism at the Iron bump of
opacity, but would like to know some "rational" ways to do so,
so that the refree of the paper would not argue !
Any idea on how to
enhance metals around this zone (logT=5.2) and increase the bump height is
the most welcome.

With kind regards.

Moravveji,
Ehsan.
Ph.D student of Astrophysics.
Department of Physics,
Institute for Advanced Studies in Basic Sciences (IASBS), GavaZang Road,

Zanjan 45137-66731, Iran.

Office: (+98)241-415 2118
Fax:    (+98)241-415 2104
http://iasbs.ac.ir/students/moravveji

-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.

Re: [mesa-users] understand the output of mesa/star

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

Hi,

On Jul 4, 2011, at 11:11 PM, ztt wrote:

> So I also would like to know if doubly-diffusive convection physics is already implemented in mesa.

Mesa now supports a wider range of options for convection than it did when the instrument paper was published.

Schwarzschild and Ledoux options are both included now, and semiconvection and thermohaline have also been added.

See the following items in the mesa/star/test_suite
	1M_thermohaline
	semiconvection

Good luck,
Bill