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From: Frank T. <fx...@ma...> - 2017-03-09 16:18:29
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> I would like to know where can I find information about the definition of these variables. from the top level mesa directory one could try something like grep -r -I "mixing types” * to sleuth where the various definitions are set. const/public/const_def.f90 looks like a promising start. > kinds of mixing MESA uses and how the code calculates them? the mesa instrument papers is the place to start for a description of the various mixing models. what the source actually does is far too big a topic for email. fxt > On Mar 9, 2017, at 2:30 AM, Gonçalo Andrade <gnm...@ho...> wrote: > > Hello > > > In the history_columns.list file there is a section about mixing regions with the following comments: > > ! mixing regions > > ! mx1 refers to the largest (by mass) convective region. > ! mx2 is the 2nd largest. > > ! conv_mx1_top and conv_mx1_bot are the region where mixing_type == convective_mixing. > ! mx1_top and mx1_bot are the extent of all kinds of mixing, convective and other. > > > > I would like to know where can I find information about the definition of these variables. > > The last line is my biggest problem, namely that it refers to "all kinds of mixing, convective and other". Where can I read what "other" kinds of mixing MESA uses and how the code calculates them? > > > Thank you for your help, > > Gonçalo Andrade > ------------------------------------------------------------------------------ > 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 |
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From: Josiah S. <jws...@uc...> - 2017-03-09 15:58:46
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Hi Gonçalo, > In the history_columns.list file there is a section about mixing > regions with the following comments: > > ! mixing regions > > ! mx1 refers to the largest (by mass) convective region. > ! mx2 is the 2nd largest. > > ! conv_mx1_top and conv_mx1_bot are the region where mixing_type == convective_mixing. > ! mx1_top and mx1_bot are the extent of all kinds of mixing, convective and other. > > I would like to know where can I find information about the definition > of these variables. The way to find out exactly how these variables are set is to go into star/private and look for the code that sets them :) > The last line is my biggest problem, namely that it refers to "all > kinds of mixing, convective and other". Where can I read what "other" > kinds of mixing MESA uses and how the code calculates them? An example of another kind of mixing is semiconvection. The "types" of mixing MESA knows about are listed in const/public/const_def.f. If you want more detail about the mixing, the history column "mixing_regions" will report the mixing_type of each mixing region. (Make sure to read its explanation in history_columns.defaults before using it.) To find out how these other types of mixing are implemented, you'll need to look at the MESA instrument papers and find the discussion of the mixing process of interest. It is worth mentioning that some of these mixing processes also have multiple implementations available. Hope that helps, Josiah |
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From: Gonçalo A. <gnm...@ho...> - 2017-03-09 10:31:01
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Hello
In the history_columns.list file there is a section about mixing regions with the following comments:
! mixing regions
! mx1 refers to the largest (by mass) convective region.
! mx2 is the 2nd largest.
! conv_mx1_top and conv_mx1_bot are the region where mixing_type == convective_mixing.
! mx1_top and mx1_bot are the extent of all kinds of mixing, convective and other.
I would like to know where can I find information about the definition of these variables.
The last line is my biggest problem, namely that it refers to "all kinds of mixing, convective and other". Where can I read what "other" kinds of mixing MESA uses and how the code calculates them?
Thank you for your help,
Gonçalo Andrade
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From: Earl B. <ear...@gm...> - 2017-03-08 18:58:28
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Thanks Aaron! Good suggestion: I have added that line to the top of both scripts. Best regards, Earl Bellinger --- www.earlbellinger.com Department of Astronomy, Yale University Stellar Ages & Galactic Evolution Group, Max Planck Institute On Wed, Mar 8, 2017 at 1:54 PM, Bill Wolf <wm...@ph...> wrote: > Thanks for the nifty tool, Earl! > > For what it’s worth, a similar feature (though currently missing the SDK > installation feature) is available for bash users through my mesa command > line interface: > > GitHub.com/wmwolf/mesa_cli > > It also provides a number of other features from the command line, but is > still under active development. > > Bill > > ________________________ > William Wolf > wm...@ph... > > UCSB Department of Physics > > On March 8, 2017 at 10:46:35 AM, Earl Bellinger (ear...@gm...) > wrote: > > Dear mesa-users, > > In order to expedite/streamline the installation and setting up of > MESA, I have put together a short script that installs the latest > (64-bit Linux) versions of both the mesasdk and MESA, and additionally > stores the relevant environment variables in the `bash_profile` so > that everything will be loaded properly in each new terminal session. > > Here is the script: > > https://github.com/earlbellinger/asteroseismology/blob/master/scripts/install_MESA.sh > > You can run it totally automatically by downloading it, making it > executable with > chmod +x install_MESA.sh > and then calling it from the command line in the place you would like > to install MESA with > ./install_MESA.sh > Prior to running it however I would recommend for people to read each > line carefully and understand what operations are being performed. > > I've tested it on a few different machines and they all seemed to work > without a hitch. > > If the distribution of such a script is unwelcome, please feel free to > delete this post! > > > P. S. Since I study asteroseismology, here is a similar script for > (independently) installing GYRE: > > https://github.com/earlbellinger/asteroseismology/blob/master/scripts/install_GYRE.sh > > Best regards, > Earl Bellinger > > --- > www.earlbellinger.com > Department of Astronomy, Yale University > Stellar Ages & Galactic Evolution Group, Max Planck Institute > > ------------------------------------------------------------------------------ > 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 |
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From: Bill W. <wm...@ph...> - 2017-03-08 18:54:41
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Thanks for the nifty tool, Earl! For what it’s worth, a similar feature (though currently missing the SDK installation feature) is available for bash users through my mesa command line interface: GitHub.com/wmwolf/mesa_cli It also provides a number of other features from the command line, but is still under active development. Bill ________________________ William Wolf wm...@ph... UCSB Department of Physics On March 8, 2017 at 10:46:35 AM, Earl Bellinger (ear...@gm...) wrote: Dear mesa-users, In order to expedite/streamline the installation and setting up of MESA, I have put together a short script that installs the latest (64-bit Linux) versions of both the mesasdk and MESA, and additionally stores the relevant environment variables in the `bash_profile` so that everything will be loaded properly in each new terminal session. Here is the script: https://github.com/earlbellinger/asteroseismology/blob/master/scripts/install_MESA.sh You can run it totally automatically by downloading it, making it executable with chmod +x install_MESA.sh and then calling it from the command line in the place you would like to install MESA with ./install_MESA.sh Prior to running it however I would recommend for people to read each line carefully and understand what operations are being performed. I've tested it on a few different machines and they all seemed to work without a hitch. If the distribution of such a script is unwelcome, please feel free to delete this post! P. S. Since I study asteroseismology, here is a similar script for (independently) installing GYRE: https://github.com/earlbellinger/asteroseismology/blob/master/scripts/install_GYRE.sh Best regards, Earl Bellinger --- www.earlbellinger.com Department of Astronomy, Yale University Stellar Ages & Galactic Evolution Group, Max Planck Institute ------------------------------------------------------------------------------ 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 |
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From: Aaron D. <aar...@gm...> - 2017-03-08 18:52:33
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Hi Earl, Neat! Thanks for sharing this. Just a suggestion for those who don't use bash as their shell, to put a line such as #!/bin/bash at the top of the script. Alternatively, you can instruct people to run it as bash install_MESA.sh Cheers, Aaron On Wed, Mar 8, 2017 at 1:44 PM, Earl Bellinger <ear...@gm...> wrote: > Dear mesa-users, > > In order to expedite/streamline the installation and setting up of > MESA, I have put together a short script that installs the latest > (64-bit Linux) versions of both the mesasdk and MESA, and additionally > stores the relevant environment variables in the `bash_profile` so > that everything will be loaded properly in each new terminal session. > > Here is the script: > > https://github.com/earlbellinger/asteroseismology/blob/master/ > scripts/install_MESA.sh > > You can run it totally automatically by downloading it, making it > executable with > chmod +x install_MESA.sh > and then calling it from the command line in the place you would like > to install MESA with > ./install_MESA.sh > Prior to running it however I would recommend for people to read each > line carefully and understand what operations are being performed. > > I've tested it on a few different machines and they all seemed to work > without a hitch. > > If the distribution of such a script is unwelcome, please feel free to > delete this post! > > > P. S. Since I study asteroseismology, here is a similar script for > (independently) installing GYRE: > > https://github.com/earlbellinger/asteroseismology/blob/master/ > scripts/install_GYRE.sh > > Best regards, > Earl Bellinger > > --- > www.earlbellinger.com > Department of Astronomy, Yale University > Stellar Ages & Galactic Evolution Group, Max Planck Institute > > ------------------------------------------------------------ > ------------------ > 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 > |
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From: Earl B. <ear...@gm...> - 2017-03-08 18:44:54
|
Dear mesa-users, In order to expedite/streamline the installation and setting up of MESA, I have put together a short script that installs the latest (64-bit Linux) versions of both the mesasdk and MESA, and additionally stores the relevant environment variables in the `bash_profile` so that everything will be loaded properly in each new terminal session. Here is the script: https://github.com/earlbellinger/asteroseismology/blob/master/scripts/install_MESA.sh You can run it totally automatically by downloading it, making it executable with chmod +x install_MESA.sh and then calling it from the command line in the place you would like to install MESA with ./install_MESA.sh Prior to running it however I would recommend for people to read each line carefully and understand what operations are being performed. I've tested it on a few different machines and they all seemed to work without a hitch. If the distribution of such a script is unwelcome, please feel free to delete this post! P. S. Since I study asteroseismology, here is a similar script for (independently) installing GYRE: https://github.com/earlbellinger/asteroseismology/blob/master/scripts/install_GYRE.sh Best regards, Earl Bellinger --- www.earlbellinger.com Department of Astronomy, Yale University Stellar Ages & Galactic Evolution Group, Max Planck Institute |
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From: Robert F. <rjf...@as...> - 2017-03-08 17:54:09
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>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 > > |
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From: amber l. <amb...@gm...> - 2017-03-08 17:19:12
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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 |
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From: Frank T. <fxt...@gm...> - 2017-03-08 17:14:44
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hi amber, the values depend on one’s purpose and need. if one has no idea what the nuclear flows are going to be, then use small min Xs so that the network expands and contracts in A or Z at the tiniest provocation. once the flows are learned, one can craft a suitable softwired network or guide the adaptive network with suitable controls on the Xs, As, and Zs. in this sense small min Xs can be a useful exploration tool. if one is only interested in the major abundances in a particular experiment, then use large min Xs. if one cares, say, about trace radionuclides like al26 or ti44, then one should use smaller min Xs like 1-e6. from an efficiency point of view, the time saved by starting with a small network and expanding to large is usually minuscule as the vast bulk of the compute time is spent during the more advanced burning stages when the number of isotopes is larger. i agree with rob on changing the default settings to more modest general-purpose values. fxt > On Mar 8, 2017, at 8:33 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 |
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From: Robert F. <rjf...@as...> - 2017-03-08 16:33:48
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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 > > |
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From: amber l. <amb...@gm...> - 2017-03-08 16:00:48
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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 |
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From: Warrick B. <wb...@bi...> - 2017-03-08 08:45:01
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Hi Anne and Evan, Thanks very much for the quick and useful replies. I had already tried the diffusion_do_thermal_diffusion option but saw no change, which is obvious if it isn't implemented yet. I'll stick to the implementation from Thoul et al. (1994), as advised. Also, my apologies to Evan: I did search the forum archive but my choice of keywords (or a lack of coffee) must've made me miss your post. Cheers, Warrick ------------ Warrick Ball Postdoc, School of Physics and Astronomy University of Birmingham, Edgbaston, Birmingham B15 2TT wb...@bi... +44 (0)121 414 4552 On Tue, 7 Mar 2017, Evan Bauer wrote: > You beat me to it. The “cgs” solver does not include thermal diffusion terms from the Burgers equations (yet). So far, I’ve mostly been using it for the degenerate interior of WDs where those terms are > unimportant/wrong. Of course, they’re quite important on the main sequence, and Warrick’s plot shows about the difference I would expect from neglecting them. The Thoul et al. (1994) solver is certainly the > correct one to use in this circumstance. I’ve attempted to address the current status and motivation for different diffusion solver options in the notes attached to this mailing list > post: https://sourceforge.net/p/mesa/mailman/message/35626929/. > > As you point out, there is an option that allows setting diffusion_do_thermal_diffusion = .true., however it doesn’t actually do anything right now. That’s why it’s false by default. I haven’t yet finished > adding the code to include the thermal diffusion terms in the Burgers equations. I should clarify that in the comments in the defaults file… > > Cheers, > Evan > > > On Mar 7, 2017, at 9:47 AM, ann...@ul... wrote: > > Question: Does the cgs solver include the heat diffusion terms in Burger’s equation? > If not, it could explain the difference. > As I understand the default values, you have to set diffusion_do_thermal_diffusion = .true. to include the heat terms when using the cgs solver. Default value is .false. > > Anne > > > Le 7 mars 2017 à 08:53, Warrick Ball <wb...@bi...> a écrit : > > Hi everyone, > > I've been playing around with calibrating solar models and found myself surprised at how much difference the different formulations of gravitational settling can make. I've attached a plot > showing the surface oxygen abundance as a function of age for four 1.25 Msun models using a standard work folder in r9575 and a choice of either: > > 1. no diffusion (do_element_diffusion = .false.) > > 2. the Thoul et al. (1994) formulation (do_element_diffusion = .true., > everything else default), > > 3. the cgs solver (diffusion_use_cgs_solver = .true.), or > > 4. the Thoul et al. (1994) formulation with Iben & Macdonald (1985) > coefficients (instead of Paquette et al. 1986). > > An example inlist is also attached. > > What surprised me was that switching from the Thoul et al. (1994) formulation to the direct solution of the Burgers equations (the cgs solver, if I understood correctly) changed the maximum > depletion by more than 60%. Is there a simple reason for this? Are there good reasons to use one formulation rather than the other for Sun-like stars? I'm not very familiar with the > literature on the subject so I'm going to start looking into it (and the code) in more detail now. But I'm hoping the vast collective wisdom of this forum might steer me in the right > direction... > > Cheers, > Warrick > > > ------------ > Warrick Ball > Postdoc, School of Physics and Astronomy > University of Birmingham, Edgbaston, Birmingham B15 2TT > wb...@bi... > +44 (0)121 414 4552<t_XO_diffusion.png><inlist_project.txt>------------------------------------------------------------------------------ > 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 > > > > |
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From: Evan B. <eb...@ph...> - 2017-03-07 17:59:46
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You beat me to it. The “cgs” solver does not include thermal diffusion terms from the Burgers equations (yet). So far, I’ve mostly been using it for the degenerate interior of WDs where those terms are unimportant/wrong. Of course, they’re quite important on the main sequence, and Warrick’s plot shows about the difference I would expect from neglecting them. The Thoul et al. (1994) solver is certainly the correct one to use in this circumstance. I’ve attempted to address the current status and motivation for different diffusion solver options in the notes attached to this mailing list post: https://sourceforge.net/p/mesa/mailman/message/35626929/ <https://sourceforge.net/p/mesa/mailman/message/35626929/>. As you point out, there is an option that allows setting diffusion_do_thermal_diffusion = .true., however it doesn’t actually do anything right now. That’s why it’s false by default. I haven’t yet finished adding the code to include the thermal diffusion terms in the Burgers equations. I should clarify that in the comments in the defaults file… Cheers, Evan > On Mar 7, 2017, at 9:47 AM, ann...@ul... wrote: > > Question: Does the cgs solver include the heat diffusion terms in Burger’s equation? > If not, it could explain the difference. > As I understand the default values, you have to set diffusion_do_thermal_diffusion = .true. to include the heat terms when using the cgs solver. Default value is .false. > > Anne > > >> Le 7 mars 2017 à 08:53, Warrick Ball <wb...@bi...> a écrit : >> >> Hi everyone, >> >> I've been playing around with calibrating solar models and found myself surprised at how much difference the different formulations of gravitational settling can make. I've attached a plot showing the surface oxygen abundance as a function of age for four 1.25 Msun models using a standard work folder in r9575 and a choice of either: >> >> 1. no diffusion (do_element_diffusion = .false.) >> >> 2. the Thoul et al. (1994) formulation (do_element_diffusion = .true., >> everything else default), >> >> 3. the cgs solver (diffusion_use_cgs_solver = .true.), or >> >> 4. the Thoul et al. (1994) formulation with Iben & Macdonald (1985) >> coefficients (instead of Paquette et al. 1986). >> >> An example inlist is also attached. >> >> What surprised me was that switching from the Thoul et al. (1994) formulation to the direct solution of the Burgers equations (the cgs solver, if I understood correctly) changed the maximum depletion by more than 60%. Is there a simple reason for this? Are there good reasons to use one formulation rather than the other for Sun-like stars? I'm not very familiar with the literature on the subject so I'm going to start looking into it (and the code) in more detail now. But I'm hoping the vast collective wisdom of this forum might steer me in the right direction... >> >> Cheers, >> Warrick >> >> >> ------------ >> Warrick Ball >> Postdoc, School of Physics and Astronomy >> University of Birmingham, Edgbaston, Birmingham B15 2TT >> wb...@bi... >> +44 (0)121 414 4552<t_XO_diffusion.png><inlist_project.txt>------------------------------------------------------------------------------ >> 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 |
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From: <ann...@ul...> - 2017-03-07 17:47:40
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Question: Does the cgs solver include the heat diffusion terms in Burger’s equation? If not, it could explain the difference. As I understand the default values, you have to set diffusion_do_thermal_diffusion = .true. to include the heat terms when using the cgs solver. Default value is .false. Anne > Le 7 mars 2017 à 08:53, Warrick Ball <wb...@bi...> a écrit : > > Hi everyone, > > I've been playing around with calibrating solar models and found myself surprised at how much difference the different formulations of gravitational settling can make. I've attached a plot showing the surface oxygen abundance as a function of age for four 1.25 Msun models using a standard work folder in r9575 and a choice of either: > > 1. no diffusion (do_element_diffusion = .false.) > > 2. the Thoul et al. (1994) formulation (do_element_diffusion = .true., > everything else default), > > 3. the cgs solver (diffusion_use_cgs_solver = .true.), or > > 4. the Thoul et al. (1994) formulation with Iben & Macdonald (1985) > coefficients (instead of Paquette et al. 1986). > > An example inlist is also attached. > > What surprised me was that switching from the Thoul et al. (1994) formulation to the direct solution of the Burgers equations (the cgs solver, if I understood correctly) changed the maximum depletion by more than 60%. Is there a simple reason for this? Are there good reasons to use one formulation rather than the other for Sun-like stars? I'm not very familiar with the literature on the subject so I'm going to start looking into it (and the code) in more detail now. But I'm hoping the vast collective wisdom of this forum might steer me in the right direction... > > Cheers, > Warrick > > > ------------ > Warrick Ball > Postdoc, School of Physics and Astronomy > University of Birmingham, Edgbaston, Birmingham B15 2TT > wb...@bi... > +44 (0)121 414 4552<t_XO_diffusion.png><inlist_project.txt>------------------------------------------------------------------------------ > 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 |
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From: Bill P. <pa...@ki...> - 2017-03-07 17:10:14
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Wouldn't it be great if there were "hooks" in pgstar plots for doing things like this? Just a general "add_decorations" hook might do the trick. -bill On Mar 7, 2017, at 9:00 AM, Robert Farmer wrote: > Hi > > Not directly, you would need to write your own custom pgstar plot, then you could any number of boxes/shapes you want > > Rob > > On Mon, Mar 6, 2017 at 9:48 PM, amber lauer <al...@ls...> wrote: > Is there any way to add multiple, non-concentric target boxes to the HR plot? > > > -- > 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 |
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From: Robert F. <rjf...@as...> - 2017-03-07 17:00:29
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Hi Not directly, you would need to write your own custom pgstar plot, then you could any number of boxes/shapes you want Rob On Mon, Mar 6, 2017 at 9:48 PM, amber lauer <al...@ls...> wrote: > Is there any way to add multiple, non-concentric target boxes to the HR > plot? > > > -- > 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 > > |
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From: Warrick B. <wb...@bi...> - 2017-03-07 16:54:05
|
Hi everyone,
I've been playing around with calibrating solar models and found myself
surprised at how much difference the different formulations of
gravitational settling can make. I've attached a plot showing the surface
oxygen abundance as a function of age for four 1.25 Msun models using a
standard work folder in r9575 and a choice of either:
1. no diffusion (do_element_diffusion = .false.)
2. the Thoul et al. (1994) formulation (do_element_diffusion = .true.,
everything else default),
3. the cgs solver (diffusion_use_cgs_solver = .true.), or
4. the Thoul et al. (1994) formulation with Iben & Macdonald (1985)
coefficients (instead of Paquette et al. 1986).
An example inlist is also attached.
What surprised me was that switching from the Thoul et al. (1994)
formulation to the direct solution of the Burgers equations (the cgs
solver, if I understood correctly) changed the maximum depletion by more
than 60%. Is there a simple reason for this? Are there good reasons to
use one formulation rather than the other for Sun-like stars? I'm not
very familiar with the literature on the subject so I'm going to start
looking into it (and the code) in more detail now. But I'm hoping the
vast collective wisdom of this forum might steer me in the right
direction...
Cheers,
Warrick
------------
Warrick Ball
Postdoc, School of Physics and Astronomy
University of Birmingham, Edgbaston, Birmingham B15 2TT
wb...@bi...
+44 (0)121 414 4552 |
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From: amber l. <al...@ls...> - 2017-03-07 06:23:57
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Is there any way to add multiple, non-concentric target boxes to the HR plot? -- Amber Lauer. M.S. Physics PhD Candidate, Graduate School of Physics, Louisiana State University |
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From: Robert F. <rjf...@as...> - 2017-03-07 01:43:08
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Hi So the issue is your model end up with some very low density material at the surface which leads to the atm_by_integration breaking as it cant find a solution and returns an error which stops things like lnT_surf from being set. So your best option in this case is to pick a different atm option. I'll also work on getting a better error message in there for future users who might hit this issue. Rob On Sat, Mar 4, 2017 at 6:24 PM, Mathieu Renzo <m....@uv...> wrote: > Hi all, > > I have found an issue with the outer boundary condition/ EOS when running > a 30 solar mass pure helium star (no metals). Find attached the inlist and > starting pure helium model, and a model only a few steps away from the > issue for convenience. > > The file out_Edd has the very last part of the output when the models > fails, which seem to indicate that the outer atmosphere boundary condition > returns NaNs, which results in the code hitting a STOP statement. > > I have also found that using a different atmosphere boundary condition > (e.g. grey_and_kap) this problem is avoided. > > Bests, > > Mathieu > > -- > Mathieu Renzo <https://staff.fnwi.uva.nl/m.renzo/> > PhD student/KITP grad fellow > Anton Pannekoek Institute, > University of Amsterdam > > Contacts: > > Address: PO Box 94249, 1090 GE Amsterdam > Office: C4.128a > Telephone: (+31) 020-5258352 <+31%2020%20525%208352> > Skype name: m4thr3n > Mail: m....@uv... > > ------------------------------------------------------------ > ------------------ > 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 > > |
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From: Umberto B. <umb...@un...> - 2017-03-06 12:43:51
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Hello Aaron, thanks a lot for this! My top 5 wish-list is: 1) create a solar model 2) create a white dwarf 3) how to add a custom reaction rate. 4) how to make and use a custom opacity table. 5) binaries 101 Cheers, Umberto ________________________________ From: Aaron Dotter [aar...@gm...] Sent: Monday, March 06, 2017 3:19 AM To: mesa-users Subject: [mesa-users] video tutorials Hi MESA users, We'd like your input on a series of MESA video tutorials, hosted on youtube (or similar), starting with how to install MESA. What would you like to see? We have a list below but you can also suggest other subjects. Alternatively, if you've made your own video, let us know where it is and what it's about. Thanks, Aaron 1) walk through http://mesa.sourceforge.net/starting.html 2) walk through http://mesa.sourceforge.net/run_star_extras.html 3) create a solar model 4) create a white dwarf 5) mesa & python for plotting 6) how to make and use a custom input composition (non-solar). 7) how to add a custom reaction rate. 8) how to make and use a custom opacity table. 9) how to user ADIPLS with MESA 10) how to use GYRE with MESA 11) binaries 101 |
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From: <wfd...@ho...> - 2017-03-06 10:47:44
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Hi,all I'm doing grid modelling using inlist_astero_search_control. I can save the fgong file when i using the commend of write_fgong_for_each_model = .true. then i apply my script to run gyre and get oscillation frequencies. I know that the program has calculate the oscillation frequencies but didn't save it.Originally, i thought the commend of write_gyre_for_each_model = .true. maybe work but it didn't. So i wonder how can i save the oscillation frequencies file directly. Can some one help me on this ? Cheers, DuMinghao |
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From: CARLOS V. V. <cvi...@uc...> - 2017-03-06 05:26:34
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Excellent idea!!! Thanks!!! 2017-03-06 4:19 GMT+02:00 Aaron Dotter <aar...@gm...>: > Hi MESA users, > > We'd like your input on a series of MESA video tutorials, hosted on > youtube (or similar), starting with how to install MESA. > > What would you like to see? We have a list below but you can also suggest > other subjects. > > Alternatively, if you've made your own video, let us know where it is and > what it's about. > > Thanks, > Aaron > > 1) walk through http://mesa.sourceforge.net/starting.html > > 2) walk through http://mesa.sourceforge.net/run_star_extras.html > > 3) create a solar model > > 4) create a white dwarf > > 5) mesa & python for plotting > > 6) how to make and use a custom input composition (non-solar). > > 7) how to add a custom reaction rate. > > 8) how to make and use a custom opacity table. > > 9) how to user ADIPLS with MESA > > 10) how to use GYRE with MESA > > 11) binaries 101 > > > ------------------------------------------------------------ > ------------------ > 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 > > -- Carlos Viscasillas MSc. Astronomy & Astrophysics. Tel. +37062731519 |
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From: Aaron D. <aar...@gm...> - 2017-03-06 02:19:36
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Hi MESA users, We'd like your input on a series of MESA video tutorials, hosted on youtube (or similar), starting with how to install MESA. What would you like to see? We have a list below but you can also suggest other subjects. Alternatively, if you've made your own video, let us know where it is and what it's about. Thanks, Aaron 1) walk through http://mesa.sourceforge.net/starting.html 2) walk through http://mesa.sourceforge.net/run_star_extras.html 3) create a solar model 4) create a white dwarf 5) mesa & python for plotting 6) how to make and use a custom input composition (non-solar). 7) how to add a custom reaction rate. 8) how to make and use a custom opacity table. 9) how to user ADIPLS with MESA 10) how to use GYRE with MESA 11) binaries 101 |
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From: Mathieu R. <m....@uv...> - 2017-03-05 01:25:26
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Hi all, I have found an issue with the outer boundary condition/ EOS when running a 30 solar mass pure helium star (no metals). Find attached the inlist and starting pure helium model, and a model only a few steps away from the issue for convenience. The file out_Edd has the very last part of the output when the models fails, which seem to indicate that the outer atmosphere boundary condition returns NaNs, which results in the code hitting a STOP statement. I have also found that using a different atmosphere boundary condition (e.g. grey_and_kap) this problem is avoided. Bests, Mathieu -- Mathieu Renzo <https://staff.fnwi.uva.nl/m.renzo/> PhD student/KITP grad fellow Anton Pannekoek Institute, University of Amsterdam Contacts: Address: PO Box 94249, 1090 GE Amsterdam Office: C4.128a Telephone: (+31) 020-5258352 Skype name: m4thr3n Mail: m....@uv... <mailto:m....@uv...> |
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