[mesa-users] MESA code Questions!!
Francis Timmes
fxt44 at mac.com
Fri Jul 10 20:21:23 EDT 2015
also consider carefully going through the pgstar tutorial at
http://mesa.sourceforge.net/pgstar.html
as it will help shine a light on several items that currently appear mysterious.
fxt
> On Jul 10, 2015, at 3:10 PM, Chris Mankovich <cmankovich at ucsc.edu> wrote:
>
> Hi Ebraheem,
>
> I've come to the conclusion that the profile_column.list has something to do with making you're own information text in a plot or something of that sort.
>
> The output and pgstar portions pages of the sourceforge site describe what profile_columns.list and history_columns.list actually do -- they allow the user to specify which columns mesa star will write to output files during runtime. Once a given column has been enabled, it's available to pgstar for real-time plotting. (Here "plotting" here also includes a simple text display as in the Text_Summary windows, which are also integrated into some of the combination Grid* plots by default.)
>
> You must
> • add the names of the columns you want to your history_columns.list or profile_columns.list. You're interested in the surface abundance of some set of isotopes; each one of those is a global property of the star. Hence they are history variables, not profile variables, so you need to edit your local copy of history_columns.list. (Profiles are for quantities that vary from zone to zone, like density.) Look in that file to find the relevant lines to uncomment or add.
> • Tell pgstar to then plot (or print) this quantity. All the options live within star/defaults/pgstar.defaults. (This file also contains the answer to your earlier question about the Grid8 window.) As an example you could enable the Text_Summary1 window and change the columns that it prints to the columns you're interested in. If you want them on a plot versus time or any other history variable, you might try the History_Track* windows.
>
> To see how to fully utilize the pgstar namelist, I recommend going through Frank Timmes' lab material from the last MESA Summer School. Hands-on experience is the only way any of us ever got comfortable with these tools, so understand that if our suggestions come across as vague, it's because we'd rather help you figure out what to do than tell you which lines to put where. That way you get to know how things work, which empowers you to help yourself or others in the future.
>
>
> Chris
>
>
>
> On Fri, Jul 10, 2015 at 2:26 PM, Farag, Ebraheem Khaled <farag.11 at lanl.gov> wrote:
> I've read every inlist you've sent and compared every detail.
> to be specific: I want a plot that will show surface abundances of all the element isotopes i choose. I don't want a default plot because they just don't do that. I've come to the conclusion that the profile_column.list has something to do with making you're own information text in a plot or something of that sort. Please tell me if you are fully understanding my ultimate goal, and if you could possible help out with showing how i can use profile_column.list to create the type of plot I'm looking for. I'm not sure how to put it into my inlist. it's very vague in the directions. I just says a command to type in an inlist with no truth value and has to information as to which or what inlist to put it into.
> ___
> p.s. I've read every topic pertaining to this question in all defaults on the source forge and there are no similar topics I've found o the forum. There is also no explanation at all, as far as I've seen on how to fully utilize the profile_column.list and history_column.list
>
>
> Thanks,
> -Ebraheem
>
> ________
>
>
> _____________________________
> From: Willie Strickland [cwskas at gmail.com]
> Sent: Friday, July 10, 2015 2:39 PM
> To: Farag, Ebraheem Khaled
> Cc: mesa-users
> Subject: Re: [mesa-users] MESA code Questions!!
>
> The default inlist_pgstar is found at $MESA_DIR/star/defaults/pgstar.defaults
>
> You may make a copy of that in your working directory and change it any way you like. The one I sent is the basic one that I use and I just add and remove items as necessary. Unless I am studying someone else’s inlists or one of the test cases. Then there may be a specific inlist_pgstar for that case.
>
> Did you look at the other inlists I sent? It is very helpful to look at the various options in other inlists and determine what results you get from the various options. All of the options are annotated in $MESA_DIR/star/defaults/
>
> Willie
>
>
> > On Jul 10, 2015, at 8:18 AM, Farag, Ebraheem Khaled <farag.11 at lanl.gov> wrote:
> >
> > I don't see how you received all that text information about abundances etc. at the bottom of the .png you linked? I looked in your pgstar and just about everything is commented out except plots to show. Does that grid 8 layout just come stock displaying those four columns of information>?
> >
> > thanks,
> > Ebraheem
> > From: Willie Strickland [cwskas at gmail.com]
> > Sent: Wednesday, July 08, 2015 2:01 PM
> > To: Farag, Ebraheem Khaled
> > Cc: mesa-users
> > Subject: Re: [mesa-users] MESA code Questions!!
> >
> > I forgot my inlists. They are attached, as well as history_columns.list & profile_columns.list.
> >
> > You can add additional abundances to your history.data by added one or more of the following to history_columns.list
> >
> > ! the following add all of the isos that are in the current net
> >
> > ! add_center_abundances
> > ! add_surface_abundances
> > ! add_average_abundances
> > ! add_log_center_abundances
> > ! add_log_surface_abundances
> > ! add_log_average_abundances
> >
> > Willie
> >
> >
> >
> >
> > > On Jul 8, 2015, at 1:49 PM, Willie Strickland <cwskas at gmail.com> wrote:
> > >
> > > It is recommended to use one of the test_suite cases as a starting point. For example.
> > >
> > > cp -R $MESA_DIR/star/test_suite/solar_calibration ~/documents/mymesa/ags05
> > > cd ~/documents/mymesa/ags05
> > >
> > > Read the info in ~/documents/mymesa/ags05
> > >
> > > I normally will run a test case as is, only changing the stopping conditions or other basic control options to make sure that works and I have a basic understanding of what is happening. Then I begin to make modifications to the inlists, one at a time, and re-run to make sure that works, repeat ….
> > >
> > > If the solar_calibration option does not fit, take a look at test_suite/1M_pre_ms_to_wd or other test_suite examples I have not done the solar_calibration except in testing so it may not be what you are looking for.
> > >
> > > I often will use $MESA_DIR/star/work as a starting point. It is pretty much bare bones. Then add to it the other choices you want. I used the approx21.net in this example, that may not be best for you, it is just an example of how to use one of the other nets found in $MESA_DIR/data/net_data/nets. The solar_calibration test case uses a different adjustment.
> > >
> > > After making sure it is working, then make further adjustments to your inlist_project to refine or change your results.
> > >
> > > For example.
> > >
> > > cp -R $MESA_DIR/star/work ~/documents/mymesa/ags05
> > > cd ~/documents/mymesa/ags05
> > >
> > > Using your preferred editor make the following changes
> > >
> > > change &controls
> > >
> > > initial_mass = 1 ! in Msun units
> > >
> > > add to &star_job
> > >
> > > set_uniform_initial_composition = .true.
> > >
> > > ! uniform initial composition of AGS05 abundances
> > > set_uniform_initial_composition = .true.
> > > initial_h1 = 0.7295
> > > initial_h2 = 0
> > > initial_he3 = 0
> > > initial_he4 = 0.25700
> > > initial_zfracs = 5
> > >
> > > change_net = .true.
> > > new_net_name = 'approx21.net'
> > >
> > > show_net_species_info = .true.
> > >
> > > add to &controls
> > >
> > > max_age = 4.57d9
> > >
> > > ./mk
> > > ./rn
> > >
> > >
> > > And I get the following results.
> > >
> > > <grid8_000001.png>
> > >
> > >
> > > Willie
> > >
> > >> On Jul 8, 2015, at 12:03 PM, Farag, Ebraheem Khaled <farag.11 at lanl.gov> wrote:
> > >>
> > >> Well I am basically trying to model the sun as well as possible so i can use altered opacity tables to see their affect on the resulting abundances.
> > >>
> > >>
> > >> -I asked previously how to achieve a sun like model, and the response i got gave no information at all...
> > >> -In turn i spoke to another student who used the mesa code and he told me to just use the tutorial and modify it with the specific parameters I wanted my "Sun" to fill.
> > >
>
>
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