[mesa-users] mesa-users Digest, Vol 36, Issue 13
Agnes Kim
agnesbischoff at gmail.com
Sun Aug 26 11:59:36 EDT 2012
Thanks, Bill for the new release and the helpful notes. While thinking
of the best place to save this information on my computer, it occurred
to me that the best place to keep these notes was actually the Mesa
FAQ and tutorial page. I took the liberty to upload a copy there. On
second thoughts it occurs to me that I should have created a folder
and placed it in that folder to leave room notes on future releases,
but I can't figure out how to move or delete the file.
For those of you who have not been to the Mesa FAQ page yet, here is the link:
http://mesastar.org/documentation
Agnes
> Message: 5
> Date: Sun, 26 Aug 2012 08:34:26 -0700
> From: Bill Paxton <paxton at kitp.ucsb.edu>
> Subject: [mesa-users] mesa 4411 -- R&R release
> To: "mesa-users at lists.sourceforge.net ?[mesa-users at lists.sourceforge"
> <mesa-users at lists.sourceforge.net>
> Message-ID: <831741C0-F9DB-47B3-8BBB-0793D2B460E1 at kitp.ucsb.edu>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi,
>
> This release has lots of R&R -- Reorganizing and Renaming.
>
> In addition to that, there are lots of new features and one important bug fix.
>
> Details follow.
>
> Cheers,
> Bill
>
>
>
>
> The motivation for this upheaval came from the MESA Summer School
> where it was pointed out that while most of the naming and
> organization in mesa is rational, there are a few glaring exceptions
> that make it more difficult for new users to get started.
> Of course experienced users, like yourself, have become accustomed
> to the current scheme with warts and all, and for you it will be a pain to have
> things change. Sorry about that, but I hope it will be a fairly minor
> inconvenience and a major improvement for future users.
>
>
> REORGANIZING
>
> As you know, mesa is organized as a set of "modules" such as num, eos, star, etc.
> Each module creates a library that has an interface defined in its "public"
> directory and an implementation defined in its "private" directory.
> In the case of star, the library provides routines to do basic operations
> of stellar evolution such as read or initialize a model, evolve a model for
> a single step, write a model profile, etc. But we need more than that
> in order to run a full stellar evolution job. In the past, all of the extra
> things were dumped into star/public along with the library routines.
> Now we have added separate directories for the extra files so that
> the files in star/public are limited to the actual star library interface.
>
> Here's the new directory structure for mesa/star:
>
> star/public interface to the star library
> star_lib.f library procedures for star
> star_def.f definitions of data for star
> star_def.inc the extension "dek" has been changed to "inc" for "include"
> star_data.inc
> star_controls.inc
>
>
> star/other user definable routines for modifying and extending the star library
> other_am_mixing.f transport of angular momemtum
> other_atm.f surface atmosphere boundary conditions
> other_cgrav.f variable "constant" G
> other_diffusion.f gravitational settling and chem diffusion
> other_energy_implicit.f extra energy source with timescale <= step size
> other_energy.f extra energy source with timescale >> step size
> other_eos.f alternative equation of state routine
> other_kap.f alternative opacities routine
> other_mesh_functions.f experiments with new criteria for mesh refinement
> other_mixing.f alternative routine for setting mixing diffusion coeffs
> other_mlt.f alternative implementation of mixing length theory
> other_torque.f extra torque source
> other_wind.f alternative recipes for wind mass loss
> other_pgstar_plots.f user defined plots for screen or file using pgstar
> sample_pgstar_plot.f sample using the other_pgstar_plots function
> inlist_pgstar_other inlist for sample_pgstar_plot
>
>
> star/job routines for controlling stellar evolution jobs
> run_star.f top level routine called by users to run star jobs
> run_star_support.f job control routines for single star evolution
> standard_run_star_extras.inc templates for user defined routines called by run star
>
>
> star/defaults parameters for star public and star job
> controls.defaults defaults for &controls namelist
> star_job.defaults defaults for &star_job namelist
> pgstar.defaults defaults for &pgstar namelist
> history_columns.list previously located in mesa/data/star_data
> profile_columns.list previously located in mesa/data/star_data
>
>
> star/work a sample work directory for using mesa/star
> inlist
> inlist_project
> LOGS
> make
> photos
> src
> ...
>
>
> star/binary_systems routines for controlling jobs such as Roche Lobe overflow
> [NOTE: expect changes here in the not-too-distant future.]
> rlo_routines.inc
> rlo_binary_routines.inc
> rlo_data.inc
> tide_routines.inc
>
>
> star/astero_adipls routines for jobs doing asteroseismology using star and adipls
> [NOTE: this used to live in mesa/astero]
> makefile
> astero_search_controls.defaults
> astero_pgstar_controls.defaults
> run_star_extras_adipls.f
> extras_support.f
> star_adipls_support.f
> star_adipls_support_procs.f
> pgstar_echelle_plot.f
> pgstar_echelle_plot_stub.f
>
>
> star/astero_adipls/work/ a sample work directory for using astero_adipls
> inlist_astero_search_controls
> adipls.c.pruned.in
> redistrb.c.pruned.in
> make
> src
> ...
>
>
>
>
> RENAMING
>
>
> in the LOGS directory, the nth profile is now called profile<n>.data rather than the old name log<n>.data,
> and the history file is now called history.data instead of the old name star.log
>
> there is now a default to write the current set of &controls at the same time as the profile.
> the file containing the controls for the nth profile is in LOGS/controls<n>.data
> note that there is already an option to save the &star_job controls to a file: save_star_job_namelist
>
> the options for the history.data file are now called "history_columns.list" instead of "log_columns.list"
> the optiions for profiles is still called "profile_columns.list"
>
> there are a bunch of changes related to calling the history "history" rather than calling it "log",
> and a bunch more for using "profile<n>.data" instead of "star<n>.log"
>
> in run_star_extras,
> new old
> how_many_extra_history_columns how_many_extra_log_columns
> data_for_extra_history_columns data_for_extra_log_columns
>
> in &star_job,
> new old
> history_columns_file log_columns_file
>
> in &controls,
> new old
> do_history_file do_log_files
> history_interval log_cnt
> trace_history_value_name trace_log_value_name
> num_trace_history_values num_trace_log_values
> maxlen_history_column_name maxlen_log_column_name
> star_history_name star_log_name
> star_history_header_name star_log_header_name
> star_history_..._format star_log_..._format
>
> profile_data_prefix log_data_prefix
> profile_data_suffix log_data_suffix
> profile_data_header_suffix log_data_header_suffix
> write_profiles_flag do_profiles
>
> write_controls_info_with_profile
> controls_data_prefix
> controls_data_suffix
>
>
> MESA_DIR environment variable
>
> In &star_job, the control "mesa_data_dir" has been replaced by "mesa_dir".
> If the value given for mesa_dir in your inlist is the string of length 0,
> then the code uses the value of the MESA_DIR environment variable.
> This lets you set mesa_dir = '' in all of your work directories and change
> to a new installation of mesa just be changing an environment variable.
>
>
> In summary, here's an incomplete list of things you'll probably need to do
>
> 1) change mesa_data_dir to mesa_dir in inlist &star_job
> 2) replace "log_column" by "history_column" in run_star_extras
> 3) replace "log_column" by "history_column" in inlist &star_job
> 4) replace "log_cnt" by "history_interval" in inlist &controls
> 5) rename log_columns.list to history_columns.list
> 6) change "equitorial" to "equatorial" in profile_columns.list
>
>
>
> A bug fix you might really care about
>
> I just found and fixed a bug that has been blocking the effect of the special rate factors.
> Turns out that the special factor was correctly set to the requested value --
> but unfortunately that was happening before another routine came along
> and "initialized" the array of factors to all 1's. So if you were you setting
> a rate factor, it wasn't having an effect.
>
>
> Other changes
>
> there is now a "max_wind" in the controls along with "min_wind"
>
> the net 1 zone burn tool includes an option to show_Qs for the the reactions
>
> run.f now passes the name 'inlist' to do_run_star so you can change the "root" inlist name if desired.
>
> change in work_standard_makefile for new location of run_star -- now in star/job, was in star/test/src.
>
> added l=3 option to astero.
>
> astero chi^2 as weighted sum of chi^2 for spectro and seismic
>
> add echelle plot to astero (using the other_pgstar_plots function in star)
>
> add pgstar plot for logg vs. logTeff
>
> change astero to save controls to file at start of run
>
> change astero to save best model information to file at end of run
>
> add option for astero to take series of parameter settings from file (for follow to scan grid)
>
> revise diffusion timestep selection to make it more robust (but this still needs more work)
>
> decrease default value for mesh_delta_coeff from 1.0 to 0.7 to give better spatial resolution
>
> fix spelling of "equatorial" (it was misspelled as "equitorial")
>
> have removed seulex from num because of problems with 1 zone burn; recommend using rodas4 instead
>
> rename star test_suite case from "astero" to "example_astero"
>
>
>
> History window for PGSTAR
>
> this is similar to Cntr_Hist and Surf_Hist, but you get to select the things to plot.
> the Hist plot has 4 panels, each with different left and right y axes.
> the yaxis choices are given as names that are valid as entries in history_columns.list.
> see "Hist window" in star/defaults/pgstar.defaults
>
> Here's an example -- just edit your inlist to change the values to be plotted.
>
>
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> End of mesa-users Digest, Vol 36, Issue 13
> ******************************************
--
Assistant Professor of Physics
Department of Chemistry, Physics and Astronomy
Georgia College & State University
Milledgeville, GA 31061
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