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

Re: [mesa-users] Suppress H burning

[RICHARD H D T. <tow...@as...>]

That would work. But as someone who has never played with the nuclear stuff in MESA, I’m at a loss how to start. Is there a tutorial on modifying nets that I could follow?

cheers,

Rich

> On Mar 18, 2017, at 1:27 PM, Josiah Schwab <jws...@uc...> wrote:
> 
> can you just take those reactions out of your net?
> 
> -j

Re: [mesa-users] Suppress H burning

[Josiah S. <jws...@uc...>]

can you just take those reactions out of your net?

-j

[mesa-users] Suppress H burning

[RICHARD H D T. <tow...@as...>]

Hi folks —

Is there a simple way to suppress hydrogen burning in MESA? By this, I mean set eps_pp and eps_cno to zero, but leave other reactions (e.g., 3a) untouched.

cheers,

Rich

Re: [mesa-users] Fwd: Wind loss in MESA

[Alessandro P. <pa...@st...>]

Hi Rob,

my inlist files don't have the .txt extension, I guess that was appended 
by the mail server upon forwarding.

Anyway, the problem is now solved, indeed I had to specify the wind 
scheme prescription in the &control.

Thanks for your help!

A.


On 03/18/2017 06:27 PM, Robert Farmer wrote:
> Hi
> My first guess is that mesa is not reading your inlists, all the files 
> you provided have .txt at the end but, mesa will look for the file 
> inlist (no .txt) first and use that to load the other inlist files
>
> Your inlists also do not specify any mass loss prescription thus mesa 
> will not turn on mass loss, you need to look at the options in:
>
> http://mesa.sourceforge.net/controls_defaults.html#mass_gain_or_loss
>
> and find those suitable for you model, i would suggest looking at the 
> _wind_scheme options
>
> Rob
>
> On Sat, Mar 18, 2017 at 10:13 AM, Bill Paxton <pa...@ki... 
> <mailto:pa...@ki...>> wrote:
>
>     Hi,
>
>     Glad to hear that you are using MESA again.
>
>     I'm forwarding your question to mesa-users -- there are lots of
>     experienced users who are happy to answer questions like this one.
>       Thanks for attaching the inlists; that's a big help.
>
>     Cheers,
>     Bill
>
>
>
>     Begin forwarded message:
>
>>     *Resent-From: *<pa...@ki... <mailto:pa...@ki...>>
>>     *From: *Alessandro Patruno <pa...@st...
>>     <mailto:pa...@st...>>
>>     *Date: *March 18, 2017 10:00:08 AM PDT
>>     *To: *pa...@ki... <mailto:pa...@ki...>
>>     *Subject: **Wind loss in MESA*
>>
>
>>     I am using the latest version (9575) and I am evolving a binary
>>     with a point mass and a low mass main sequence donor (say <1
>>     Msun). In my simulations I want the donor star to begin with a
>>     certain rotational velocity, synchronize with the orbit and emit
>>     wind (enhanced by tidal effects). I see that in this version of
>>     MESA all this is possible and so I want to take advantage of this.
>>
>>     However, I am having troubles to activate the wind loss in the
>>     low mass star. For some reason the code does not calculate any
>>     mass loss (wind) during the calculations and I do not know what I
>>     am doing wrong. The lg_wind_mdot_1 stays stuck at -99 throughout
>>     the simulation.
>>
>>     Do you know how to activate a de Jager type mass loss during the
>>     main sequence of low mass stars?
>>
>>
>
>
>
>
>
>
>
>     ------------------------------------------------------------------------------
>     Check out the vibrant tech community on one of the world's most
>     engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>     _______________________________________________
>     mesa-users mailing list
>     mes...@li...
>     <mailto:mes...@li...>
>     https://lists.sourceforge.net/lists/listinfo/mesa-users
>     <https://lists.sourceforge.net/lists/listinfo/mesa-users>
>
>

-- 

Dr. Alessandro Patruno -- NWO VIDI Fellow
Leiden Observatory
Huygens Laboratory
Leiden University
Niels Bohrweg 2
2333 CA Leiden, The Netherlands
Tel.: +31 (0)71 527 5813
Website: http://apatruno.wordpress.com
------------------------------------------

Re: [mesa-users] equally spaced grids

[Jing L. <jin...@gm...>]

Thank you very much, Robert :-)

Sincerely,
Jing

On Sat, Mar 18, 2017 at 10:34 AM, Robert Farmer <rjf...@as...> wrote:

> Hi
>
> >Is it possible to ask mesa to adopt an evenly spaced grid mesh please?
>
> No, mesa works by adjusting the mesh based on minimizing the change in
> certain quantities between the mesh points. This way it can optimize the
> problem to use the fewest mesh points as possible while still capturing the
> spatial variation.
>
> If you need constant grid as input for another code, then one option would
> be to generate more points than you need and then in a post processing step
> interpolate your profile output onto a constant grid. The max_dq control
> option is one way to specify the minimum resolution you need (but your
> likely to get a higher resolution in some parts of the model)
>
> Rob
>
>
>
> On Sat, Mar 18, 2017 at 10:17 AM, Jing Luan <jin...@gm...> wrote:
>
>> Dear mesa developers and users,
>>
>> Is it possible to ask mesa to adopt an evenly spaced grid mesh please?
>>
>> Many thanks :-)
>>
>> Sincerely,
>> Jing
>>
>> ------------------------------------------------------------
>> ------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> mesa-users mailing list
>> mes...@li...
>> https://lists.sourceforge.net/lists/listinfo/mesa-users
>>
>>
>

Re: [mesa-users] equally spaced grids

[Robert F. <rjf...@as...>]

Hi

>Is it possible to ask mesa to adopt an evenly spaced grid mesh please?

No, mesa works by adjusting the mesh based on minimizing the change in
certain quantities between the mesh points. This way it can optimize the
problem to use the fewest mesh points as possible while still capturing the
spatial variation.

If you need constant grid as input for another code, then one option would
be to generate more points than you need and then in a post processing step
interpolate your profile output onto a constant grid. The max_dq control
option is one way to specify the minimum resolution you need (but your
likely to get a higher resolution in some parts of the model)

Rob



On Sat, Mar 18, 2017 at 10:17 AM, Jing Luan <jin...@gm...> wrote:

> Dear mesa developers and users,
>
> Is it possible to ask mesa to adopt an evenly spaced grid mesh please?
>
> Many thanks :-)
>
> Sincerely,
> Jing
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> mesa-users mailing list
> mes...@li...
> https://lists.sourceforge.net/lists/listinfo/mesa-users
>
>

Re: [mesa-users] Fwd: Wind loss in MESA

[Robert F. <rjf...@as...>]

Hi
My first guess is that mesa is not reading your inlists, all the files you
provided have .txt at the end but, mesa will look for the file inlist (no
.txt) first and use that to load the other inlist files

Your inlists also do not specify any mass loss prescription thus mesa will
not turn on mass loss, you need to look at the options in:

http://mesa.sourceforge.net/controls_defaults.html#mass_gain_or_loss

and find those suitable for you model, i would suggest looking at the
_wind_scheme options

Rob

On Sat, Mar 18, 2017 at 10:13 AM, Bill Paxton <pa...@ki...> wrote:

> Hi,
>
> Glad to hear that you are using MESA again.
>
> I'm forwarding your question to mesa-users -- there are lots of
> experienced users who are happy to answer questions like this one.   Thanks
> for attaching the inlists; that's a big help.
>
> Cheers,
> Bill
>
>
>
> Begin forwarded message:
>
> *Resent-From: *<pa...@ki...>
> *From: *Alessandro Patruno <pa...@st...>
> *Date: *March 18, 2017 10:00:08 AM PDT
> *To: *pa...@ki...
> *Subject: **Wind loss in MESA*
>
>
> I am using the latest version (9575) and I am evolving a binary with a
> point mass and a low mass main sequence donor (say <1 Msun). In my
> simulations I want the donor star to begin with a certain rotational
> velocity, synchronize with the orbit and emit wind (enhanced by tidal
> effects). I see that in this version of MESA all this is possible and so I
> want to take advantage of this.
>
> However, I am having troubles to activate the wind loss in the low mass
> star. For some reason the code does not calculate any mass loss (wind)
> during the calculations and I do not know what I am doing wrong. The
> lg_wind_mdot_1 stays stuck at -99 throughout the simulation.
>
> Do you know how to activate a de Jager type mass loss during the main
> sequence of low mass stars?
>
>
>
>
>
>
>
>
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> mesa-users mailing list
> mes...@li...
> https://lists.sourceforge.net/lists/listinfo/mesa-users
>
>

[mesa-users] Fwd: Wind loss in MESA

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

Hi,

Glad to hear that you are using MESA again.

I'm forwarding your question to mesa-users -- there are lots of experienced users who are happy to answer questions like this one.   Thanks for attaching the inlists; that's a big help.

Cheers,
Bill



Begin forwarded message:

> Resent-From: <pa...@ki...>
> From: Alessandro Patruno <pa...@st...>
> Date: March 18, 2017 10:00:08 AM PDT
> To: pa...@ki...
> Subject: Wind loss in MESA
> 

> I am using the latest version (9575) and I am evolving a binary with a point mass and a low mass main sequence donor (say <1 Msun). In my simulations I want the donor star to begin with a certain rotational velocity, synchronize with the orbit and emit wind (enhanced by tidal effects). I see that in this version of MESA all this is possible and so I want to take advantage of this.
> 
> However, I am having troubles to activate the wind loss in the low mass star. For some reason the code does not calculate any mass loss (wind) during the calculations and I do not know what I am doing wrong. The lg_wind_mdot_1 stays stuck at -99 throughout the simulation.
> 
> Do you know how to activate a de Jager type mass loss during the main sequence of low mass stars?
> 
> 

[mesa-users] equally spaced grids

[Jing L. <jin...@gm...>]

Dear mesa developers and users,

Is it possible to ask mesa to adopt an evenly spaced grid mesh please?

Many thanks :-)

Sincerely,
Jing

Re: [mesa-users] remote pgplot

[Martin C. <mar...@gm...>]

ahh the win_flags.. forgot about those.
I can just set them to false, then everything works the way I want it to.

thanks so much guys.

Martin

On Fri, Mar 17, 2017 at 7:00 PM, Robert Farmer <rjf...@as...> wrote:

> When i run things on a cluster i usually get this error message (probably
> from leaving the win_flags=.true.)
>
> PGPLOT /xw: cannot connect to X server []
> PGPLOT /xw: cannot connect to X server []
>
> but file saving still runs fine, I think as along as X is running you'll
> be okay. This is without me doing anything special, though maybe the
> sysadmins configured things differently.
>
> Rob
>
> On Fri, Mar 17, 2017 at 3:55 PM, RICHARD H D TOWNSEND <
> tow...@as...> wrote:
>
>> I wonder if pgplot will still try to create a remote X session when you
>> start up, even if no windows are opened.
>>
>> If this occurs, you can make the X session local to the (remote) server
>> by setting the DISPLAY environment variable to localhost:0.0
>>
>> But you’ll need appropriate permissions to access the X server, and may
>> have to play with xhost and/or .Xauthority files. It’s a bit messy.
>>
>> cheers,
>>
>> Rich
>>
>> > On Mar 17, 2017, at 3:51 PM, Robert Farmer <rjf...@as...> wrote:
>> >
>> > Hi
>> > All the pgplots have the option to save a png with the _file_ flags,
>> for instance for the abundance plots:
>> >
>> >          Abundance_file_flag = .true.
>> >          Abundance_file_dir = 'png'
>> >          Abundance_file_prefix = 'abund_'
>> >          Abundance_file_interval = 5 ! output when
>> mod(model_number,Abundance_file_interval)==0
>> >
>> > writes an abundance plot to file every 5 steps to a folder called png
>> >
>> > The options
>> >
>> >          file_device = 'png'
>> >          file_extension = 'png'
>> >
>> > can be used to output either png or ps (for postscript files).
>> >
>> > Rob
>> >
>> >
>> >
>> > On Fri, Mar 17, 2017 at 3:42 PM, Martin C. <mar...@gm...>
>> wrote:
>> > Hi all,
>> >
>> > I'm running MESA on a remote server. I'd like to run PGPLOT so I can
>> output png files so that I can later make videos from them.
>> >
>> > I can use
>> > ssh -Y ...
>> > but that forces me to stream the plots to my local computer which I
>> don't want.
>> > So how can I run PGLOT remotely only.
>> > Any tips?
>> >
>> > thanks,
>> >
>> > Martin
>> > --
>> > Martin C.
>> >
>> > ------------------------------------------------------------
>> ------------------
>> > Check out the vibrant tech community on one of the world's most
>> > engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> > _______________________________________________
>> > mesa-users mailing list
>> > mes...@li...
>> > https://lists.sourceforge.net/lists/listinfo/mesa-users
>> >
>> >
>> > ------------------------------------------------------------
>> ------------------
>> > Check out the vibrant tech community on one of the world's most
>> > engaging tech sites, Slashdot.org! http://sdm.link/slashdot______
>> _________________________________________
>> > mesa-users mailing list
>> > mes...@li...
>> > https://lists.sourceforge.net/lists/listinfo/mesa-users
>>
>>
>


-- 
Martin C.

Re: [mesa-users] remote pgplot

[Robert F. <rjf...@as...>]

When i run things on a cluster i usually get this error message (probably
from leaving the win_flags=.true.)

PGPLOT /xw: cannot connect to X server []
PGPLOT /xw: cannot connect to X server []

but file saving still runs fine, I think as along as X is running you'll be
okay. This is without me doing anything special, though maybe the sysadmins
configured things differently.

Rob

On Fri, Mar 17, 2017 at 3:55 PM, RICHARD H D TOWNSEND <
tow...@as...> wrote:

> I wonder if pgplot will still try to create a remote X session when you
> start up, even if no windows are opened.
>
> If this occurs, you can make the X session local to the (remote) server by
> setting the DISPLAY environment variable to localhost:0.0
>
> But you’ll need appropriate permissions to access the X server, and may
> have to play with xhost and/or .Xauthority files. It’s a bit messy.
>
> cheers,
>
> Rich
>
> > On Mar 17, 2017, at 3:51 PM, Robert Farmer <rjf...@as...> wrote:
> >
> > Hi
> > All the pgplots have the option to save a png with the _file_ flags, for
> instance for the abundance plots:
> >
> >          Abundance_file_flag = .true.
> >          Abundance_file_dir = 'png'
> >          Abundance_file_prefix = 'abund_'
> >          Abundance_file_interval = 5 ! output when
> mod(model_number,Abundance_file_interval)==0
> >
> > writes an abundance plot to file every 5 steps to a folder called png
> >
> > The options
> >
> >          file_device = 'png'
> >          file_extension = 'png'
> >
> > can be used to output either png or ps (for postscript files).
> >
> > Rob
> >
> >
> >
> > On Fri, Mar 17, 2017 at 3:42 PM, Martin C. <mar...@gm...> wrote:
> > Hi all,
> >
> > I'm running MESA on a remote server. I'd like to run PGPLOT so I can
> output png files so that I can later make videos from them.
> >
> > I can use
> > ssh -Y ...
> > but that forces me to stream the plots to my local computer which I
> don't want.
> > So how can I run PGLOT remotely only.
> > Any tips?
> >
> > thanks,
> >
> > Martin
> > --
> > Martin C.
> >
> > ------------------------------------------------------------
> ------------------
> > Check out the vibrant tech community on one of the world's most
> > engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> > _______________________________________________
> > mesa-users mailing list
> > mes...@li...
> > https://lists.sourceforge.net/lists/listinfo/mesa-users
> >
> >
> > ------------------------------------------------------------
> ------------------
> > Check out the vibrant tech community on one of the world's most
> > engaging tech sites, Slashdot.org! http://sdm.link/slashdot______
> _________________________________________
> > mesa-users mailing list
> > mes...@li...
> > https://lists.sourceforge.net/lists/listinfo/mesa-users
>
>

Re: [mesa-users] remote pgplot

[RICHARD H D T. <tow...@as...>]

I wonder if pgplot will still try to create a remote X session when you start up, even if no windows are opened.

If this occurs, you can make the X session local to the (remote) server by setting the DISPLAY environment variable to localhost:0.0

But you’ll need appropriate permissions to access the X server, and may have to play with xhost and/or .Xauthority files. It’s a bit messy.

cheers,

Rich

> On Mar 17, 2017, at 3:51 PM, Robert Farmer <rjf...@as...> wrote:
> 
> Hi
> All the pgplots have the option to save a png with the _file_ flags, for instance for the abundance plots:
> 
>          Abundance_file_flag = .true.
>          Abundance_file_dir = 'png'
>          Abundance_file_prefix = 'abund_'
>          Abundance_file_interval = 5 ! output when mod(model_number,Abundance_file_interval)==0
> 
> writes an abundance plot to file every 5 steps to a folder called png 
> 
> The options
> 
>          file_device = 'png'
>          file_extension = 'png'
> 
> can be used to output either png or ps (for postscript files).
> 
> Rob
> 
> 
> 
> On Fri, Mar 17, 2017 at 3:42 PM, Martin C. <mar...@gm...> wrote:
> Hi all,
> 
> I'm running MESA on a remote server. I'd like to run PGPLOT so I can output png files so that I can later make videos from them. 
> 
> I can use
> ssh -Y ...
> but that forces me to stream the plots to my local computer which I don't want. 
> So how can I run PGLOT remotely only.
> Any tips?
> 
> thanks,
> 
> Martin
> -- 
> Martin C.
> 
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> mesa-users mailing list
> mes...@li...
> https://lists.sourceforge.net/lists/listinfo/mesa-users
> 
> 
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot_______________________________________________
> mesa-users mailing list
> mes...@li...
> https://lists.sourceforge.net/lists/listinfo/mesa-users

Re: [mesa-users] remote pgplot

[Robert F. <rjf...@as...>]

Hi
All the pgplots have the option to save a png with the _file_ flags, for
instance for the abundance plots:

         Abundance_file_flag = .true.
         Abundance_file_dir = 'png'
         Abundance_file_prefix = 'abund_'
         Abundance_file_interval = 5 ! output when
mod(model_number,Abundance_file_interval)==0

writes an abundance plot to file every 5 steps to a folder called png

The options

         file_device = 'png'
         file_extension = 'png'

can be used to output either png or ps (for postscript files).

Rob



On Fri, Mar 17, 2017 at 3:42 PM, Martin C. <mar...@gm...> wrote:

> Hi all,
>
> I'm running MESA on a remote server. I'd like to run PGPLOT so I can
> output png files so that I can later make videos from them.
>
> I can use
> ssh -Y ...
> but that forces me to stream the plots to my local computer which I don't
> want.
> So how can I run PGLOT remotely only.
> Any tips?
>
> thanks,
>
> Martin
> --
> Martin C.
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> mesa-users mailing list
> mes...@li...
> https://lists.sourceforge.net/lists/listinfo/mesa-users
>
>

[mesa-users] remote pgplot

[Martin C. <mar...@gm...>]

Hi all,

I'm running MESA on a remote server. I'd like to run PGPLOT so I can output
png files so that I can later make videos from them.

I can use
ssh -Y ...
but that forces me to stream the plots to my local computer which I don't
want.
So how can I run PGLOT remotely only.
Any tips?

thanks,

Martin
-- 
Martin C.

Re: [mesa-users] calculate reaction flows

[Oriol A. <ori...@gm...>]

Hi,

You have to install the package. One option is to use pip:
$ pip install periodictable
You can find more information about the periodictable package (or download
it) here https://pypi.python.org/pypi/periodictable

Oriol Abril
Group of Astronomy and Astrophysics, UPC-BarcelonaTech


2017-03-16 9:25 GMT+01:00 ertaoLee <ert...@gm...>:

> Dear Michael Zingale，
>
> Thank you for your help!
>
> When I try to run the code, I cannot find the "periodictable". Could you
> tell me where to get it.
>
> ------------------------------
> Er-Tao Li(李二涛)
> Institute of Nuclear Technology，College of Physics & Energy, Shenzhen
> University
> Nanhai Ave 3688, Shenzhen, Guangdong, P.R.China, 518060
> Tel: 86-755-26536232. Fax: 86-755-26534374
>
> *From:* Michael Zingale <mic...@st...>
> *Date:* 2017-03-15 20:33
> *To:* ertaoLee <ert...@gm...>
> *CC:* mesa-users <mes...@li...>
> *Subject:* Re: [mesa-users] calculate reaction flows
> Hi, this isn't MESA-specific, but we've written some python routines to
> interface with the reaclib rates and allow you to explore this (I think
> MESA uses some of these same rates).  Basically, you feed it a set of rates
> and it constructs a network and then in a Jupyter notebook, you can
> visualize it to show the flow and allow you to vary the temperature /
> density with sliders to see how rates change with conditions.  It is still
> a bit rough around the edges, and quite new, so things could break, but the
> code is here:
>
> https://github.com/pyreaclib/pyreaclib
>
> and a sample notebook that allows for the interactive exploration of rates
> is here:
> https://github.com/pyreaclib/pyreaclib/blob/development/
> examples/interactive-example.ipynb
>
> (in the live notebook version, there will be a temperature and density
> slider to allow you to change the conditions).
>
> Note, this functionality is only available on the 'development' branch, so
> you'll need to work there if you want to play.
>
> This notebook describes some of the data structures;
> https://github.com/pyreaclib/pyreaclib/blob/development/
> examples/pyreaclib-examples.ipynb
>
>
> On Tue, Mar 14, 2017 at 11:20 PM, ertaoLee <ert...@gm...> wrote:
>
>> Dear MESA users,
>>
>> I am trying to find out which reactions are more important than others.
>> So, I need to calculate the reaction forward and reverse flows for each
>> reaction and draw a flow diagram.
>>
>> How do I do that?
>>
>> Thanks in advance for any help that you can offer!
>>
>>
>> ------------------------------
>> Er-Tao Li(李二涛)
>> Institute of Nuclear Technology，College of Physics & Energy, Shenzhen
>> University
>> Nanhai Ave 3688, Shenzhen, Guangdong, P.R.China, 518060
>> Tel: 86-755-26536232. Fax: 86-755-26534374
>>
>> ------------------------------------------------------------
>> ------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> mesa-users mailing list
>> mes...@li...
>> https://lists.sourceforge.net/lists/listinfo/mesa-users
>>
>>
>
>
> --
> Michael Zingale
> Associate Professor
>
> Dept. of Physics & Astronomy • Stony Brook University • Stony Brook, NY
> 11794-3800
> *phone*:  631-632-8225 <(631)%20632-8225>
> *e-mail*: Mic...@st...
> *web*: http://www.astro.sunysb.edu/mzingale
> github: http://github.com/zingale
>
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> mesa-users mailing list
> mes...@li...
> https://lists.sourceforge.net/lists/listinfo/mesa-users
>
>

Re: [mesa-users] calculate reaction flows

[ertaoLee <ert...@gm...>]

Dear Michael Zingale，

Thank you for your help!

When I try to run the code, I cannot find the "periodictable". Could you tell me where to get it.




Er-Tao Li(李二涛)
Institute of Nuclear Technology，College of Physics & Energy, Shenzhen University
Nanhai Ave 3688, Shenzhen, Guangdong, P.R.China, 518060 
Tel: 86-755-26536232. Fax: 86-755-26534374 

From: Michael Zingale
Date: 2017-03-15 20:33
To: ertaoLee
CC: mesa-users
Subject: Re: [mesa-users] calculate reaction flows
Hi, this isn't MESA-specific, but we've written some python routines to interface with the reaclib rates and allow you to explore this (I think MESA uses some of these same rates).  Basically, you feed it a set of rates and it constructs a network and then in a Jupyter notebook, you can visualize it to show the flow and allow you to vary the temperature / density with sliders to see how rates change with conditions.  It is still a bit rough around the edges, and quite new, so things could break, but the code is here:


https://github.com/pyreaclib/pyreaclib



and a sample notebook that allows for the interactive exploration of rates is here:
https://github.com/pyreaclib/pyreaclib/blob/development/examples/interactive-example.ipynb



(in the live notebook version, there will be a temperature and density slider to allow you to change the conditions).


Note, this functionality is only available on the 'development' branch, so you'll need to work there if you want to play.


This notebook describes some of the data structures;
https://github.com/pyreaclib/pyreaclib/blob/development/examples/pyreaclib-examples.ipynb





On Tue, Mar 14, 2017 at 11:20 PM, ertaoLee <ert...@gm...> wrote:

Dear MESA users,

I am trying to find out which reactions are more important than others. 
So, I need to calculate the reaction forward and reverse flows for each reaction and draw a flow diagram.

How do I do that?

Thanks in advance for any help that you can offer!





Er-Tao Li(李二涛)
Institute of Nuclear Technology，College of Physics & Energy, Shenzhen University
Nanhai Ave 3688, Shenzhen, Guangdong, P.R.China, 518060 
Tel: 86-755-26536232. Fax: 86-755-26534374 

------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
mesa-users mailing list
mes...@li...
https://lists.sourceforge.net/lists/listinfo/mesa-users







-- 

Michael Zingale
Associate Professor


Dept. of Physics & Astronomy • Stony Brook University • Stony Brook, NY 11794-3800
phone:  631-632-8225
e-mail: Mic...@st...
web: http://www.astro.sunysb.edu/mzingale
github: http://github.com/zingale

[mesa-users] JINA-CEE workshop: Forging Connections: From Nuclei to the Cosmic Web

[Falk H. <fh...@uv...>]

Forging Connections: From Nuclei to the Cosmic Web
A JINA-CEE workshop
June 26-29, 2017 (welcome reception evening on June 25th)
Michigan State University Kellogg Conference Center
East Lansing, MI, USA

Workshop website: http://indico.fnal.gov/event/connections

Abstract / discussion panel / breakout session proposal deadline: March 20th, 2017
Registration deadline: May 12th, 2017

Motivation
Roughly half of the elements in the universe that are heavier than helium are in stars and the interstellar medium, and the rest is in the circumgalactic and intergalactic medium.  All of these elements are produced in stars or their remnants, and they are critical to both structure formation (i.e., star and galaxy formation) and stellar evolution.  The purpose of this workshop is to bring together observers, experimentalists, and theorists whose expertise spans the range of subjects necessary to understand the full life cycle of the baryonic content of the universe, and to forge connections to address the challenges relating to studying chemical enrichment in the era of large stellar and intergalactic medium surveys.  Specific focus areas of this workshop include:

- Nucleosynthesis and nuclear reaction rates
- Stellar evolution and explosions
- Local Group stellar surveys and targeted observations
- Asteroseismology and abundances
- Mixing of stellar ejecta into the ambient gas
- Circumgalactic and intergalactic medium observations
- Chemical evolution modeling in the era of large surveys

This workshop is organized by the JINA Center for the Evolution of the Elements and will have a participant-driven component, and will include a mixture of talks, panel discussions, and breakout sessions.  To facilitate a high level of interactivity, the workshop will be capped at a maximum of 80 participants.

Invited Speakers and Scientific Advisors*
Almudena Arcones* (U. Darmstadt, Germany)
Timothy Beers* (U. Notre Dame, USA)
Joss Bland-Hawthorn* (U. Sydney, Australia)
Rongmon Bordoloi (MIT, USA)
Charlie Conroy* (Harvard U., USA)
Iris Dillmann (TRIUMF, Canada)
Marius Eichler (U. Darmstadt, Germany)
Anna Frebel* (MIT, USA)
Christopher Fryer* (LANL, USA)
Brad Gibson* (U. Hull, UK)
Gerry Gilmore* (Cambridge U., UK)
Alexander Heger (Monash U., Australia)
Amanda Karakas* (ANU, Australia)
Lars Mattsson (Stockholm U., Sweden)
Melissa Ness (MPIA, Germany)
Molly Peeples* (STScI, USA)
Marco Pignatari* (U. Hull, UK)
Jason Tumlinson (STScI, USA)
Michael Wiescher (U. Notre Dame, USA)

Organizing Committee
Brian O’Shea (MSU - Chair)
Benoit Côté (MSU/U. Victoria - Co-Chair)
Falk Herwig (U. Victoria, Canada)
Hendrik Schatz (MSU/NSCL, USA)
Devin Silvia (MSU, USA)
Lena Simon (JINA-CEE, USA)
Artemis Spyrou (MSU/NSCL, USA)
Frank Timmes (ASU, USA)
Dawn Welch (JINA-CEE, USA)

Contact
con...@ns...<mailto:con...@ns...>
--
Dr Falk Herwig, Professor
Dept of Physics & Astronomy
University of Victoria
fh...@uv...<mailto:fh...@uv...>, tel: +1 (250) 721-7743

Re: [mesa-users] calculate reaction flows

[Michael Z. <mic...@st...>]

Hi, this isn't MESA-specific, but we've written some python routines to
interface with the reaclib rates and allow you to explore this (I think
MESA uses some of these same rates).  Basically, you feed it a set of rates
and it constructs a network and then in a Jupyter notebook, you can
visualize it to show the flow and allow you to vary the temperature /
density with sliders to see how rates change with conditions.  It is still
a bit rough around the edges, and quite new, so things could break, but the
code is here:

https://github.com/pyreaclib/pyreaclib

and a sample notebook that allows for the interactive exploration of rates
is here:
https://github.com/pyreaclib/pyreaclib/blob/development/examples/interactive-example.ipynb

(in the live notebook version, there will be a temperature and density
slider to allow you to change the conditions).

Note, this functionality is only available on the 'development' branch, so
you'll need to work there if you want to play.

This notebook describes some of the data structures;
https://github.com/pyreaclib/pyreaclib/blob/development/examples/pyreaclib-examples.ipynb


On Tue, Mar 14, 2017 at 11:20 PM, ertaoLee <ert...@gm...> wrote:

> Dear MESA users,
>
> I am trying to find out which reactions are more important than others.
> So, I need to calculate the reaction forward and reverse flows for each
> reaction and draw a flow diagram.
>
> How do I do that?
>
> Thanks in advance for any help that you can offer!
>
>
> ------------------------------
> Er-Tao Li(李二涛)
> Institute of Nuclear Technology，College of Physics & Energy, Shenzhen
> University
> Nanhai Ave 3688, Shenzhen, Guangdong, P.R.China, 518060
> Tel: 86-755-26536232. Fax: 86-755-26534374
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> mesa-users mailing list
> mes...@li...
> https://lists.sourceforge.net/lists/listinfo/mesa-users
>
>


-- 
Michael Zingale
Associate Professor

Dept. of Physics & Astronomy • Stony Brook University • Stony Brook, NY
11794-3800
*phone*:  631-632-8225
*e-mail*: Mic...@st...
*web*: http://www.astro.sunysb.edu/mzingale
github: http://github.com/zingale

Re: [mesa-users] calculate reaction flows

[Ian F. <ifo...@gm...>]

Hi,

Last year I spent quite a bit of time trying to find an intermediate sized
reaction net that would give simulations with accurate composition history
especially for stars 8Msun's and above. That meant trying to identify
isotopes and reactions that had the biggest impact. Part of the problem I
found (excluding my general lack of understanding) was that different
isotopes and reactions varied in importance at different temperatures and
compositions. Especially for stars that go through huge temperature changes
and densities, unless you have precise knowledge about the reaction, it
would be near impossible to isolate those that mattered. In some runs, even
including or omitting one reaction could make huge differences with the
effect only emerging at a specific temperature. On top of that our
knowledge of reaction rates still needs much research, so there can be
quite large differences in simulations depending on the rates chosen.

For now, I have resigned to just specifying the isotopes and let Mesa
identify all the reactions for larger stars otherwise my simulations can
produce unreliable results. For smaller stars however, the simpler reaction
nets supplied with mesa work pretty well because the temperature range and
density change is far less. Thus for the 1M pre_ms_to wd test suite
example, I was able to show that the o18_and_ne22 net (which has key
isotopes up to mg24) produced a result very similar to a net which had all
the reactions in a net with most of the isotopes up to mg24.

kind regards
ian

On 15 March 2017 at 15:43, Robert Farmer <rjf...@as...> wrote:

> Hi
>
> There is no direct way to do this, to work out the important reactions you
> could look at the abundances as well as adding
> add_reaction_categories to your profile columns to get a summary of the
> energy per reaction category (for example burn_fe shows the total energy
> from all fe based reactions)
>
> You could also look in the net/test code which does 1-zone burns which
> might be easier to get the flow rates and the individual forward/reverse
> rates
>
> Rob
>
> On Tue, Mar 14, 2017 at 8:20 PM, ertaoLee <ert...@gm...> wrote:
>
>> Dear MESA users,
>>
>> I am trying to find out which reactions are more important than others.
>> So, I need to calculate the reaction forward and reverse flows for each
>> reaction and draw a flow diagram.
>>
>> How do I do that?
>>
>> Thanks in advance for any help that you can offer!
>>
>>
>> ------------------------------
>> Er-Tao Li(李二涛)
>> Institute of Nuclear Technology，College of Physics & Energy, Shenzhen
>> University
>> Nanhai Ave 3688, Shenzhen, Guangdong, P.R.China, 518060
>> Tel: 86-755-26536232. Fax: 86-755-26534374
>>
>> ------------------------------------------------------------
>> ------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> mesa-users mailing list
>> mes...@li...
>> https://lists.sourceforge.net/lists/listinfo/mesa-users
>>
>>
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> mesa-users mailing list
> mes...@li...
> https://lists.sourceforge.net/lists/listinfo/mesa-users
>
>

Re: [mesa-users] calculate reaction flows

[Robert F. <rjf...@as...>]

Hi

There is no direct way to do this, to work out the important reactions you
could look at the abundances as well as adding
add_reaction_categories to your profile columns to get a summary of the
energy per reaction category (for example burn_fe shows the total energy
from all fe based reactions)

You could also look in the net/test code which does 1-zone burns which
might be easier to get the flow rates and the individual forward/reverse
rates

Rob

On Tue, Mar 14, 2017 at 8:20 PM, ertaoLee <ert...@gm...> wrote:

> Dear MESA users,
>
> I am trying to find out which reactions are more important than others.
> So, I need to calculate the reaction forward and reverse flows for each
> reaction and draw a flow diagram.
>
> How do I do that?
>
> Thanks in advance for any help that you can offer!
>
>
> ------------------------------
> Er-Tao Li(李二涛)
> Institute of Nuclear Technology，College of Physics & Energy, Shenzhen
> University
> Nanhai Ave 3688, Shenzhen, Guangdong, P.R.China, 518060
> Tel: 86-755-26536232. Fax: 86-755-26534374
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> mesa-users mailing list
> mes...@li...
> https://lists.sourceforge.net/lists/listinfo/mesa-users
>
>

[mesa-users] calculate reaction flows

[ertaoLee <ert...@gm...>]

Dear MESA users,

I am trying to find out which reactions are more important than others. 
So, I need to calculate the reaction forward and reverse flows for each reaction and draw a flow diagram.

How do I do that?

Thanks in advance for any help that you can offer!





Er-Tao Li(李二涛)
Institute of Nuclear Technology，College of Physics & Energy, Shenzhen University
Nanhai Ave 3688, Shenzhen, Guangdong, P.R.China, 518060 
Tel: 86-755-26536232. Fax: 86-755-26534374 

Re: [mesa-users] minimum mass fraction values

[Jon B. <jon...@gm...>]

    

"FWIW, my experience with MESA as well as in other general computing is that increasing memory gives more speedup than increasing cores.   There's probably documentation for this effect, maybe someone more CS trained than I has a reference."
For more cores to be helpful, there have to be multiple pieces of work to do that don't depend on the results of work not already done (CS shorthand for this is "the task must be parallelizable"). An analogy often given is "one woman can produce a baby in 9 months,  and 9 women can produce 9 babies in 9 months,  but 9 women can't produce one baby in a month".
RAM doesn't provide any speedup by itself, but if the information a program is working on doesn't fit in memory,  the operating system will start writing stuff in memory to disk in order to pretend that it has more RAM. Disk access is slow compared to memory access, so this tends to slow things down significantly: If your program needs only a little more RAM than is available, and most other processes in the machine aren't doing anything at the moment,  things will be done almost as quickly as if everything fit in RAM,  but if you need a lot more memory than you have, and/or other programs are active and fighting yours for memory,  performance will fall sharply. Analogously, on an open book quiz,  students that have everything memorized will be done faster than those who have to check their notes,  and someone who can do multi-digit arithmetic in their head will be done with a math problem faster than someone who has to write it out on paper. CPU cache size can impact performance in a similar way to RAM size,  fir similar reasons. 

-------- Original message --------
From: amber lauer <amb...@gm...> 
Date: 3/9/2017  23:07  (GMT-06:00) 
To: Robert Farmer <rjf...@as...> 
Cc: mes...@li... 
Subject: Re: [mesa-users] minimum mass fraction values 

Whenever I run with the adaptive net, the nets in the "nets" folder usually have 70-100 species in my experience. I don't know if that's typical. I am still doing XRB, as well as other models. Generally I run with Max Z, N, and A turned off and use Min_X values ~10e-11. The 10e-21 run was for benchmarking and to see if there was any significant difference, I had the elapsed time column added but I didn't check it the total run time, but I can if you are interested. It was really just a one off. The machine I'm speaking of has 48Gb of memory and it can run that 
adaptive net case with mesa_67.net as the initial net in a day. FWIW, my experience with MESA as well as in other general computing is that increasing memory gives more speedup than increasing cores.   There's probably documentation for this effect, maybe someone more CS trained than I has a reference. 

On Thu, Mar 9, 2017 at 2:30 PM, Robert Farmer <rjf...@as...> wrote:
>So 17Gb is the max mesa can use for the nuc nets matrix solver? 

this is the combination of nuclear network plus structure equations (they are solved simultaneously) matrix,  you may use more memory overall as this doesn't include things like the eos files that are loaded etc

Are you still doing xray bursts? what did you have for the other adaptive net options?

Rob

On Thu, Mar 9, 2017 at 1:21 PM, amber lauer <amb...@gm...> wrote:
So 17Gb is the max mesa can use for the nuc nets matrix solver? I just finished a run with an adaptive net with my min Z set at 10e-21, and I used a starting model with an abundance profile containing roughly 20 species. I just checked the profile in the region of interest for my research, and even with those settings the net only has about 70 species. So it works out OK, at least in my case. 

On Wed, Mar 8, 2017 at 11:53 AM, Robert Farmer <rjf...@as...> wrote:
>Unfortunately in my case, this can be as low as 10e-9. For more final 
models, I have a machine built specially for this purpose with 16 cores,
 so I can dedicate a bit more time for the larger networks. 

There are limits on how big the matrix mesa can solve based on memory limits. Mesa memory scales as ~num_isos**2 * num_zones, with an upper limit based of the size of the 4-byte int used to index the matrix array (2^31-1 which is about ~17GB of memory for double precision numbers). This is about 400 isos with 1000 zones, so if you want more isotopes you will need to reduce your spatial resolution.

>What about when starting from an abundance profile? If I have an isotope
 with abundance of 10e-13, but min x for keep is set at 10e-9, for 
example, will it eliminate it immediately? Or after a few steps?

Immediately, though it might get re-added if there is a reaction that makes it. This is the problem i find with the adaptive nets is once you add an isotope it gets quite hard to remove it, given all the possible reactions that could make it, so the nets never get smaller.

Rob



On Wed, Mar 8, 2017 at 10:18 AM, amber lauer <amb...@gm...> wrote:
Yeah, we've all experienced that vicious slowdown. However when trying to match observables, you have to at least use the values from observation as a lower bound. Unfortunately in my case, this can be as low as 10e-9. For more final models, I have a machine built specially for this purpose with 16 cores, so I can dedicate a bit more time for the larger networks. 

What about when starting from an abundance profile? If I have an isotope with abundance of 10e-13, but min x for keep is set at 10e-9, for example, will it eliminate it immediately? Or after a few steps?

On Wed, Mar 8, 2017 at 10:33 AM, Robert Farmer <rjf...@as...> wrote:
Hi

Those values come from the cited Woosley, Heger, et al, ApJSS, 151:75-102, 2004 paper. I would advise against using them for mesa, in fact i'm going to go change them. If you look in the MESA3 paper at the x-ray burst section, I use much larger values for the different controls, 10**-6 to 10**-3, the smaller the number for xmin the more isotopes you get in the net and you can very quickly get more than mesa can cope with.

Rob

On Wed, Mar 8, 2017 at 9:00 AM, amber lauer <amb...@gm...> wrote:
I'm trying to decide on a good min X, not just for the adaptive net, but also for inclusion in abundance profiles. I see that the 'standard' values in star_job.defaults are 10e-23 and ~10e-18. Is there a numerical/computational argument for a relevant threshold? 

-- 
Amber Lauer. M.S. Physics
PhD Candidate,
Graduate School of Physics,Louisiana State University


------------------------------------------------------------------------------

Announcing the Oxford Dictionaries API! The API offers world-renowned

dictionary content that is easy and intuitive to access. Sign up for an

account today to start using our lexical data to power your apps and

projects. Get started today and enter our developer competition.

http://sdm.link/oxford
_______________________________________________

mesa-users mailing list

mes...@li...

https://lists.sourceforge.net/lists/listinfo/mesa-users





------------------------------------------------------------------------------

Announcing the Oxford Dictionaries API! The API offers world-renowned

dictionary content that is easy and intuitive to access. Sign up for an

account today to start using our lexical data to power your apps and

projects. Get started today and enter our developer competition.

http://sdm.link/oxford
_______________________________________________

mesa-users mailing list

mes...@li...

https://lists.sourceforge.net/lists/listinfo/mesa-users





-- 
Amber Lauer. M.S. Physics
PhD Candidate,
Graduate School of Physics,Louisiana State University


------------------------------------------------------------------------------

Announcing the Oxford Dictionaries API! The API offers world-renowned

dictionary content that is easy and intuitive to access. Sign up for an

account today to start using our lexical data to power your apps and

projects. Get started today and enter our developer competition.

http://sdm.link/oxford
_______________________________________________

mesa-users mailing list

mes...@li...

https://lists.sourceforge.net/lists/listinfo/mesa-users







-- 
Amber Lauer. M.S. Physics
PhD Candidate,
Graduate School of Physics,Louisiana State University






-- 
Amber Lauer. M.S. Physics
PhD Candidate,
Graduate School of Physics,Louisiana State University

Re: [mesa-users] minimum mass fraction values

[amber l. <amb...@gm...>]

Whenever I run with the adaptive net, the nets in the "nets" folder usually
have 70-100 species in my experience. I don't know if that's typical. I am
still doing XRB, as well as other models. Generally I run with Max Z, N,
and A turned off and use Min_X values ~10e-11. The 10e-21 run was for
benchmarking and to see if there was any significant difference, I had the
elapsed time column added but I didn't check it the total run time, but I
can if you are interested. It was really just a one off. The machine I'm
speaking of has 48Gb of memory and it can run that adaptive net case with
mesa_67.net as the initial net in a day. FWIW, my experience with MESA as
well as in other general computing is that increasing memory gives more
speedup than increasing cores.   There's probably documentation for this
effect, maybe someone more CS trained than I has a reference.

On Thu, Mar 9, 2017 at 2:30 PM, Robert Farmer <rjf...@as...> wrote:

> >So 17Gb is the max mesa can use for the nuc nets matrix solver?
>
> this is the combination of nuclear network plus structure equations (they
> are solved simultaneously) matrix,  you may use more memory overall as this
> doesn't include things like the eos files that are loaded etc
>
> Are you still doing xray bursts? what did you have for the other adaptive
> net options?
>
> Rob
>
> On Thu, Mar 9, 2017 at 1:21 PM, amber lauer <amb...@gm...> wrote:
>
>> So 17Gb is the max mesa can use for the nuc nets matrix solver? I just
>> finished a run with an adaptive net with my min Z set at 10e-21, and I used
>> a starting model with an abundance profile containing roughly 20 species. I
>> just checked the profile in the region of interest for my research, and
>> even with those settings the net only has about 70 species. So it works out
>> OK, at least in my case.
>>
>> On Wed, Mar 8, 2017 at 11:53 AM, Robert Farmer <rjf...@as...> wrote:
>>
>>> >Unfortunately in my case, this can be as low as 10e-9. For more final
>>> models, I have a machine built specially for this purpose with 16 cores, so
>>> I can dedicate a bit more time for the larger networks.
>>>
>>> There are limits on how big the matrix mesa can solve based on memory
>>> limits. Mesa memory scales as ~num_isos**2 * num_zones, with an upper limit
>>> based of the size of the 4-byte int used to index the matrix array (2^31-1
>>> which is about ~17GB of memory for double precision numbers). This is about
>>> 400 isos with 1000 zones, so if you want more isotopes you will need to
>>> reduce your spatial resolution.
>>>
>>> >What about when starting from an abundance profile? If I have an
>>> isotope with abundance of 10e-13, but min x for keep is set at 10e-9, for
>>> example, will it eliminate it immediately? Or after a few steps?
>>>
>>> Immediately, though it might get re-added if there is a reaction that
>>> makes it. This is the problem i find with the adaptive nets is once you add
>>> an isotope it gets quite hard to remove it, given all the possible
>>> reactions that could make it, so the nets never get smaller.
>>>
>>> Rob
>>>
>>>
>>>
>>> On Wed, Mar 8, 2017 at 10:18 AM, amber lauer <amb...@gm...>
>>> wrote:
>>>
>>>> Yeah, we've all experienced that vicious slowdown. However when trying
>>>> to match observables, you have to at least use the values from observation
>>>> as a lower bound. Unfortunately in my case, this can be as low as 10e-9.
>>>> For more final models, I have a machine built specially for this purpose
>>>> with 16 cores, so I can dedicate a bit more time for the larger networks.
>>>>
>>>> What about when starting from an abundance profile? If I have an
>>>> isotope with abundance of 10e-13, but min x for keep is set at 10e-9, for
>>>> example, will it eliminate it immediately? Or after a few steps?
>>>>
>>>> On Wed, Mar 8, 2017 at 10:33 AM, Robert Farmer <rjf...@as...>
>>>> wrote:
>>>>
>>>>> Hi
>>>>>
>>>>> Those values come from the cited Woosley, Heger, et al, ApJSS,
>>>>> 151:75-102, 2004 paper. I would advise against using them for mesa, in fact
>>>>> i'm going to go change them. If you look in the MESA3 paper at the x-ray
>>>>> burst section, I use much larger values for the different controls, 10**-6
>>>>> to 10**-3, the smaller the number for xmin the more isotopes you get in the
>>>>> net and you can very quickly get more than mesa can cope with.
>>>>>
>>>>> Rob
>>>>>
>>>>> On Wed, Mar 8, 2017 at 9:00 AM, amber lauer <amb...@gm...>
>>>>> wrote:
>>>>>
>>>>>> I'm trying to decide on a good min X, not just for the adaptive net,
>>>>>> but also for inclusion in abundance profiles. I see that the 'standard'
>>>>>> values in star_job.defaults are 10e-23 and ~10e-18. Is there a
>>>>>> numerical/computational argument for a relevant threshold?
>>>>>>
>>>>>> --
>>>>>> Amber Lauer. M.S. Physics
>>>>>> PhD Candidate,
>>>>>> Graduate School of Physics,
>>>>>> Louisiana State University
>>>>>>
>>>>>> ------------------------------------------------------------
>>>>>> ------------------
>>>>>> Announcing the Oxford Dictionaries API! The API offers world-renowned
>>>>>> dictionary content that is easy and intuitive to access. Sign up for
>>>>>> an
>>>>>> account today to start using our lexical data to power your apps and
>>>>>> projects. Get started today and enter our developer competition.
>>>>>> http://sdm.link/oxford
>>>>>> _______________________________________________
>>>>>> mesa-users mailing list
>>>>>> mes...@li...
>>>>>> https://lists.sourceforge.net/lists/listinfo/mesa-users
>>>>>>
>>>>>>
>>>>>
>>>>> ------------------------------------------------------------
>>>>> ------------------
>>>>> Announcing the Oxford Dictionaries API! The API offers world-renowned
>>>>> dictionary content that is easy and intuitive to access. Sign up for an
>>>>> account today to start using our lexical data to power your apps and
>>>>> projects. Get started today and enter our developer competition.
>>>>> http://sdm.link/oxford
>>>>> _______________________________________________
>>>>> mesa-users mailing list
>>>>> mes...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/mesa-users
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> Amber Lauer. M.S. Physics
>>>> PhD Candidate,
>>>> Graduate School of Physics,
>>>> Louisiana State University
>>>>
>>>> ------------------------------------------------------------
>>>> ------------------
>>>> Announcing the Oxford Dictionaries API! The API offers world-renowned
>>>> dictionary content that is easy and intuitive to access. Sign up for an
>>>> account today to start using our lexical data to power your apps and
>>>> projects. Get started today and enter our developer competition.
>>>> http://sdm.link/oxford
>>>> _______________________________________________
>>>> mesa-users mailing list
>>>> mes...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/mesa-users
>>>>
>>>>
>>>
>>
>>
>> --
>> Amber Lauer. M.S. Physics
>> PhD Candidate,
>> Graduate School of Physics,
>> Louisiana State University
>>
>
>


-- 
Amber Lauer. M.S. Physics
PhD Candidate,
Graduate School of Physics,
Louisiana State University

Re: [mesa-users] minimum mass fraction values

[Robert F. <rjf...@as...>]

>So 17Gb is the max mesa can use for the nuc nets matrix solver?

this is the combination of nuclear network plus structure equations (they
are solved simultaneously) matrix,  you may use more memory overall as this
doesn't include things like the eos files that are loaded etc

Are you still doing xray bursts? what did you have for the other adaptive
net options?

Rob

On Thu, Mar 9, 2017 at 1:21 PM, amber lauer <amb...@gm...> wrote:

> So 17Gb is the max mesa can use for the nuc nets matrix solver? I just
> finished a run with an adaptive net with my min Z set at 10e-21, and I used
> a starting model with an abundance profile containing roughly 20 species. I
> just checked the profile in the region of interest for my research, and
> even with those settings the net only has about 70 species. So it works out
> OK, at least in my case.
>
> On Wed, Mar 8, 2017 at 11:53 AM, Robert Farmer <rjf...@as...> wrote:
>
>> >Unfortunately in my case, this can be as low as 10e-9. For more final
>> models, I have a machine built specially for this purpose with 16 cores, so
>> I can dedicate a bit more time for the larger networks.
>>
>> There are limits on how big the matrix mesa can solve based on memory
>> limits. Mesa memory scales as ~num_isos**2 * num_zones, with an upper limit
>> based of the size of the 4-byte int used to index the matrix array (2^31-1
>> which is about ~17GB of memory for double precision numbers). This is about
>> 400 isos with 1000 zones, so if you want more isotopes you will need to
>> reduce your spatial resolution.
>>
>> >What about when starting from an abundance profile? If I have an isotope
>> with abundance of 10e-13, but min x for keep is set at 10e-9, for example,
>> will it eliminate it immediately? Or after a few steps?
>>
>> Immediately, though it might get re-added if there is a reaction that
>> makes it. This is the problem i find with the adaptive nets is once you add
>> an isotope it gets quite hard to remove it, given all the possible
>> reactions that could make it, so the nets never get smaller.
>>
>> Rob
>>
>>
>>
>> On Wed, Mar 8, 2017 at 10:18 AM, amber lauer <amb...@gm...>
>> wrote:
>>
>>> Yeah, we've all experienced that vicious slowdown. However when trying
>>> to match observables, you have to at least use the values from observation
>>> as a lower bound. Unfortunately in my case, this can be as low as 10e-9.
>>> For more final models, I have a machine built specially for this purpose
>>> with 16 cores, so I can dedicate a bit more time for the larger networks.
>>>
>>> What about when starting from an abundance profile? If I have an isotope
>>> with abundance of 10e-13, but min x for keep is set at 10e-9, for example,
>>> will it eliminate it immediately? Or after a few steps?
>>>
>>> On Wed, Mar 8, 2017 at 10:33 AM, Robert Farmer <rjf...@as...> wrote:
>>>
>>>> Hi
>>>>
>>>> Those values come from the cited Woosley, Heger, et al, ApJSS,
>>>> 151:75-102, 2004 paper. I would advise against using them for mesa, in fact
>>>> i'm going to go change them. If you look in the MESA3 paper at the x-ray
>>>> burst section, I use much larger values for the different controls, 10**-6
>>>> to 10**-3, the smaller the number for xmin the more isotopes you get in the
>>>> net and you can very quickly get more than mesa can cope with.
>>>>
>>>> Rob
>>>>
>>>> On Wed, Mar 8, 2017 at 9:00 AM, amber lauer <amb...@gm...>
>>>> wrote:
>>>>
>>>>> I'm trying to decide on a good min X, not just for the adaptive net,
>>>>> but also for inclusion in abundance profiles. I see that the 'standard'
>>>>> values in star_job.defaults are 10e-23 and ~10e-18. Is there a
>>>>> numerical/computational argument for a relevant threshold?
>>>>>
>>>>> --
>>>>> Amber Lauer. M.S. Physics
>>>>> PhD Candidate,
>>>>> Graduate School of Physics,
>>>>> Louisiana State University
>>>>>
>>>>> ------------------------------------------------------------
>>>>> ------------------
>>>>> Announcing the Oxford Dictionaries API! The API offers world-renowned
>>>>> dictionary content that is easy and intuitive to access. Sign up for an
>>>>> account today to start using our lexical data to power your apps and
>>>>> projects. Get started today and enter our developer competition.
>>>>> http://sdm.link/oxford
>>>>> _______________________________________________
>>>>> mesa-users mailing list
>>>>> mes...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/mesa-users
>>>>>
>>>>>
>>>>
>>>> ------------------------------------------------------------
>>>> ------------------
>>>> Announcing the Oxford Dictionaries API! The API offers world-renowned
>>>> dictionary content that is easy and intuitive to access. Sign up for an
>>>> account today to start using our lexical data to power your apps and
>>>> projects. Get started today and enter our developer competition.
>>>> http://sdm.link/oxford
>>>> _______________________________________________
>>>> mesa-users mailing list
>>>> mes...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/mesa-users
>>>>
>>>>
>>>
>>>
>>> --
>>> Amber Lauer. M.S. Physics
>>> PhD Candidate,
>>> Graduate School of Physics,
>>> Louisiana State University
>>>
>>> ------------------------------------------------------------
>>> ------------------
>>> Announcing the Oxford Dictionaries API! The API offers world-renowned
>>> dictionary content that is easy and intuitive to access. Sign up for an
>>> account today to start using our lexical data to power your apps and
>>> projects. Get started today and enter our developer competition.
>>> http://sdm.link/oxford
>>> _______________________________________________
>>> mesa-users mailing list
>>> mes...@li...
>>> https://lists.sourceforge.net/lists/listinfo/mesa-users
>>>
>>>
>>
>
>
> --
> Amber Lauer. M.S. Physics
> PhD Candidate,
> Graduate School of Physics,
> Louisiana State University
>

Re: [mesa-users] minimum mass fraction values

[amber l. <amb...@gm...>]

So 17Gb is the max mesa can use for the nuc nets matrix solver? I just
finished a run with an adaptive net with my min Z set at 10e-21, and I used
a starting model with an abundance profile containing roughly 20 species. I
just checked the profile in the region of interest for my research, and
even with those settings the net only has about 70 species. So it works out
OK, at least in my case.

On Wed, Mar 8, 2017 at 11:53 AM, Robert Farmer <rjf...@as...> wrote:

> >Unfortunately in my case, this can be as low as 10e-9. For more final
> models, I have a machine built specially for this purpose with 16 cores, so
> I can dedicate a bit more time for the larger networks.
>
> There are limits on how big the matrix mesa can solve based on memory
> limits. Mesa memory scales as ~num_isos**2 * num_zones, with an upper limit
> based of the size of the 4-byte int used to index the matrix array (2^31-1
> which is about ~17GB of memory for double precision numbers). This is about
> 400 isos with 1000 zones, so if you want more isotopes you will need to
> reduce your spatial resolution.
>
> >What about when starting from an abundance profile? If I have an isotope
> with abundance of 10e-13, but min x for keep is set at 10e-9, for example,
> will it eliminate it immediately? Or after a few steps?
>
> Immediately, though it might get re-added if there is a reaction that
> makes it. This is the problem i find with the adaptive nets is once you add
> an isotope it gets quite hard to remove it, given all the possible
> reactions that could make it, so the nets never get smaller.
>
> Rob
>
>
>
> On Wed, Mar 8, 2017 at 10:18 AM, amber lauer <amb...@gm...> wrote:
>
>> Yeah, we've all experienced that vicious slowdown. However when trying to
>> match observables, you have to at least use the values from observation as
>> a lower bound. Unfortunately in my case, this can be as low as 10e-9. For
>> more final models, I have a machine built specially for this purpose with
>> 16 cores, so I can dedicate a bit more time for the larger networks.
>>
>> What about when starting from an abundance profile? If I have an isotope
>> with abundance of 10e-13, but min x for keep is set at 10e-9, for example,
>> will it eliminate it immediately? Or after a few steps?
>>
>> On Wed, Mar 8, 2017 at 10:33 AM, Robert Farmer <rjf...@as...> wrote:
>>
>>> Hi
>>>
>>> Those values come from the cited Woosley, Heger, et al, ApJSS,
>>> 151:75-102, 2004 paper. I would advise against using them for mesa, in fact
>>> i'm going to go change them. If you look in the MESA3 paper at the x-ray
>>> burst section, I use much larger values for the different controls, 10**-6
>>> to 10**-3, the smaller the number for xmin the more isotopes you get in the
>>> net and you can very quickly get more than mesa can cope with.
>>>
>>> Rob
>>>
>>> On Wed, Mar 8, 2017 at 9:00 AM, amber lauer <amb...@gm...>
>>> wrote:
>>>
>>>> I'm trying to decide on a good min X, not just for the adaptive net,
>>>> but also for inclusion in abundance profiles. I see that the 'standard'
>>>> values in star_job.defaults are 10e-23 and ~10e-18. Is there a
>>>> numerical/computational argument for a relevant threshold?
>>>>
>>>> --
>>>> Amber Lauer. M.S. Physics
>>>> PhD Candidate,
>>>> Graduate School of Physics,
>>>> Louisiana State University
>>>>
>>>> ------------------------------------------------------------
>>>> ------------------
>>>> Announcing the Oxford Dictionaries API! The API offers world-renowned
>>>> dictionary content that is easy and intuitive to access. Sign up for an
>>>> account today to start using our lexical data to power your apps and
>>>> projects. Get started today and enter our developer competition.
>>>> http://sdm.link/oxford
>>>> _______________________________________________
>>>> mesa-users mailing list
>>>> mes...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/mesa-users
>>>>
>>>>
>>>
>>> ------------------------------------------------------------
>>> ------------------
>>> Announcing the Oxford Dictionaries API! The API offers world-renowned
>>> dictionary content that is easy and intuitive to access. Sign up for an
>>> account today to start using our lexical data to power your apps and
>>> projects. Get started today and enter our developer competition.
>>> http://sdm.link/oxford
>>> _______________________________________________
>>> mesa-users mailing list
>>> mes...@li...
>>> https://lists.sourceforge.net/lists/listinfo/mesa-users
>>>
>>>
>>
>>
>> --
>> Amber Lauer. M.S. Physics
>> PhD Candidate,
>> Graduate School of Physics,
>> Louisiana State University
>>
>> ------------------------------------------------------------
>> ------------------
>> Announcing the Oxford Dictionaries API! The API offers world-renowned
>> dictionary content that is easy and intuitive to access. Sign up for an
>> account today to start using our lexical data to power your apps and
>> projects. Get started today and enter our developer competition.
>> http://sdm.link/oxford
>> _______________________________________________
>> mesa-users mailing list
>> mes...@li...
>> https://lists.sourceforge.net/lists/listinfo/mesa-users
>>
>>
>


-- 
Amber Lauer. M.S. Physics
PhD Candidate,
Graduate School of Physics,
Louisiana State University