[mesa-users] mesa-users Digest, Vol 38, Issue 13
Zhao Guo
guo at chara.gsu.edu
Tue Oct 23 10:33:30 EDT 2012
Hi,everyone
I'm newbie.And I have intalled and run the Appetizer on mesa-getting
started successfully.Then I go to star/work
and edit inlist_project to set the 'mesa_dir' parameters, then
./mk
it seems OK
./rn
THe following pop up in terminal:
-----------------------------------
Revision: 4589
Tue Oct 23 10:15:35 EDT 2012
saved initial &star_job inlist values: star_job_namelist.out
version_number 4589
read inlist_project
The terminal output contains the following information
'step' is the number of steps since the start of the run,
'lg_dt_yr' is log10 timestep in years,
'age_yr' is the simulated years since the start run,
'lg_Tcntr' is log10 center temperature (K),
'lg_Dcntr' is log10 center density (g/cm^3),
'lg_Pcntr' is log10 center pressure (ergs/cm^3),
'Teff' is the surface temperature (K),
'lg_R' is log10 surface radius (Rsun),
'lg_L' is log10 surface luminosity (Lsun),
'lg_LH' is log10 total PP and CNO hydrogen burning power (Lsun),
'lg_L3a' is log10 total triple-alpha helium burning power (Lsun),
'lg_LZ' is log10 total burning power excluding LH and L3a and
photodisintegrations (Lsun),
'lg_LNuc' is log10 nuclear power excluding photodisintegration (Lsun),
'lg_LNeu' is log10 total neutrino power (Lsun),
'lg_Psurf' is log10 surface pressure (gas + radiation),
'Mass' is the total stellar baryonic mass (Msun),
'lg_Mdot' is log10 magnitude of rate of change of mass (Msun/year),
'lg_Dsurf' is log10 surface density (g/cm^3),
'H_rich' is the remaining mass outside of the hydrogen poor core,
'H_poor' is the core mass where hydrogen abundance is <= 0.10E-03
'He_poor' is the core mass where helium abundance is <= 0.10E-03
'H_cntr' is the center H1 mass fraction,
'He_cntr' is the center He4 mass fraction,
'C_cntr' is the center C12 mass fraction,
'N_cntr' is the center N14 mass fraction,
'O_cntr' is the center O16 mass fraction,
'Ne_cntr' is the center Ne20 mass fraction,
'X_avg' is the star average hydrogen mass fraction,
'Y_avg' is the star average helium mass fraction,
'Z_avg' is the star average metallicity,
'gam_cntr' is the center plasma interaction parameter,
'eta_cntr' is the center electron degeneracy parameter,
'pts' is the number of grid points in the current model,
'iters' is the number of newton iterations for the current step,
'retry' is the number of step retries required during the run,
'bckup' is the number of step backups required during the run,
'dt_limit' is an indication of what limited the timestep.
All this and more are saved in the LOGS directory during the run.
create pre-main-sequence model
xa(i) 4
-1.0074784592947262D-18
failed in build_pre_ms_model
star_create_pre_ms_model ierr -1
do_load1_star ierr -1
-------------------------------------
Why I get errors like this? Could anyone help me?
I am using mesa 4589 version.
My linux version info:
Linux version 2.6.18-238.19.1.el5PAE (mockbuild at builder10.centos.org) (gcc
version 4.1.2 20080704 (Red Hat 4.1.2-50)) #1 SMP Fri Jul 15 08:15:44 EDT
2011
Thank you very much!
cheers,
Zhao
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> Today's Topics:
>
> 1. Re: nugrid-mesa.py (Falk Herwig)
> 2. An error with rotation initialization (Ehsan Moravveji)
> 3. Re: An error with rotation initialization (Ehsan Moravveji)
> 4. Installation error and solution on Mac OS X 10.8 (Aaron Dotter)
> 5. Re: Installation error and solution on Mac OS X 10.8
> (Richard Townsend)
> 6. Re: nugrid-mesa.py (Chris Mankovich)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 20 Oct 2012 15:42:27 -0700
> From: Falk Herwig <fherwig at uvic.ca>
> Subject: Re: [mesa-users] nugrid-mesa.py
> To: Josiah Schwab <jwschwab at berkeley.edu>
> Cc: "mesa-users at lists.sourceforge.net users"
> <mesa-users at lists.sourceforge.net>
> Message-ID: <3397E8CB-5D89-4F0D-AF16-1E3DEFF2E486 at uvic.ca>
> Content-Type: text/plain; charset=iso-8859-1
>
> After some more testing, documenting and cleaning up, please try again:
> http://www.mesastar.org/tools-utilities/python-based-stuff/nugrids-mesa.py-1
>
> In addition to the mesa.py file another file data_plot.py is needed. This
> is now all directly available from mesastars.org.
>
> Presently these files live on the NuGrid svn server.
>
> Falk.
>
>
> On 2012-10-19, at 7:00 PM, Josiah Schwab wrote:
>
>> This tool requires the files from nugrid_pylib. Are you trying to just
>> use the mesa.py file all by itself? (Or if you have those, some path
>> may be set incorrectly.)
>>
>> Josiah
>>
>> On 10/19/2012 04:46 PM, Chris Mankovich wrote:
>>> Hi Falk,
>>>
>>> I'm eager to give this a shot, but I'm failing at the import step:
>>>
>>> In [2]: import mesa
>>> ---------------------------------------------------------------------------
>>> ImportError Traceback (most recent call
>>> last)
>>> /home/chris/he/<ipython-input-2-6c94b0867429> in <module>()
>>> ----> 1 import mesa
>>>
>>> /home/chris/he/mesa.py in <module>()
>>> 113 '''
>>> 114 import numpy as np
>>> --> 115 from data_plot import *
>>> 116 import numpy as np
>>> 117 import matplotlib
>>>
>>> ImportError: No module named data_plot
>>>
>>>
>>> This is running "ipython --pylab --profile=numpy". python version
>>> 2.7.3, ipython version 0.12.1. What am I missing?
>>>
>>> Chris
>>>
>>> On Wed, Oct 17, 2012 at 8:32 PM, Falk Herwig <fherwig at uvic.ca
>>> <mailto:fherwig at uvic.ca>> wrote:
>>>
>>> NuGrid's mesa.py update available to deal with new naming scheme:
>>> http://mesastar.org/tools-utilities/python-based-stuff/nugrids-mesa.py
>>> Contributions, improvements and bug fixes welcome.
>>> Falk.
>>>
>>> --
>>> Falk Herwig
>>> Dept of Physics & Astronomy, U of Victoria
>>> fherwig at uvic.ca <mailto:fherwig at uvic.ca>, tel: +1 (250) 721-7743
>>> <tel:%2B1%20%28250%29%20721-7743>
>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Everyone hates slow websites. So do we.
>>> Make your web apps faster with AppDynamics
>>> Download AppDynamics Lite for free today:
>>> http://p.sf.net/sfu/appdyn_sfd2d_oct
>>> _______________________________________________
>>> mesa-users mailing list
>>> mesa-users at lists.sourceforge.net
>>> <mailto:mesa-users at lists.sourceforge.net>
>>> https://lists.sourceforge.net/lists/listinfo/mesa-users
>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Everyone hates slow websites. So do we.
>>> Make your web apps faster with AppDynamics
>>> Download AppDynamics Lite for free today:
>>> http://p.sf.net/sfu/appdyn_sfd2d_oct
>>>
>>>
>>>
>>> _______________________________________________
>>> mesa-users mailing list
>>> mesa-users at lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/mesa-users
>>>
>
> --
> Falk Herwig
> Dept of Physics & Astronomy, U of Victoria
> fherwig at uvic.ca, tel: +1 (250) 721-7743
>
>
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Sun, 21 Oct 2012 11:40:17 +0330
> From: "Ehsan Moravveji" <moravveji at iasbs.ac.ir>
> Subject: [mesa-users] An error with rotation initialization
> To: mesa-users at lists.sourceforge.net
> Message-ID:
> <0149130e3dc33b5e66960040527631b0.squirrel at mail.iasbs.ac.ir>
> Content-Type: text/plain;charset=utf-8
>
> Hello All.
> When I just run the star/test_suite/multimass/ with default
> run_star_extra.f, I get the following error because of failure in
> initializing rotation:
>
> turn on velocities
> turn on rotation
> new_surface_rotation_v =
> 4.5000000000000000D+01
> 3.5583680158225128D-06
> STOP dm_sum 441
> 3.4950878204674813D+26
> debugging: set1_omega
> new_point_dmbar 441
> 3.4950878419316793D+26
>
> Of course, when I suppress it, the evolution runs normally.
> I use SDK + v. 4589 + 3 threads on Lion 10.7
> How can I fix this?
> I guess the fix should also apply to the test_suite as well.
>
> Thanks folks.
> ehsan.
>
>
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 22 Oct 2012 11:29:04 +0330
> From: "Ehsan Moravveji" <moravveji at iasbs.ac.ir>
> Subject: Re: [mesa-users] An error with rotation initialization
> To: "Ehsan Moravveji" <moravveji at iasbs.ac.ir>
> Cc: mesa-users at lists.sourceforge.net
> Message-ID:
> <ed28f8776b8dce47b605e8f9d3204c18.squirrel at mail.iasbs.ac.ir>
> Content-Type: text/plain;charset=utf-8
>
> Ok, let me respond to myself, as I figured out the issue.
> The starting kick of rotation better be close to the ZAMS. So, mesa is not
> really happy when it wants to contract a cloud
> (create_pre_main_sequence_model = .true.) and at the same time rotate it.
> So, the best option is to postpone it as late as the star reaches a more
> stable configuration. I do it through the run_star_extras, when the model
> reaches ZAMS.
> So, just wrote it for those who might be possibly interested.
>
> Best to all.
> Ehsan.
>
>> Hello All.
>> When I just run the star/test_suite/multimass/ with default
>> run_star_extra.f, I get the following error because of failure in
>> initializing rotation:
>>
>> turn on velocities
>> turn on rotation
>> new_surface_rotation_v =
>> 4.5000000000000000D+01
>> 3.5583680158225128D-06
>> STOP dm_sum 441
>> 3.4950878204674813D+26
>> debugging: set1_omega
>> new_point_dmbar 441
>> 3.4950878419316793D+26
>>
>> Of course, when I suppress it, the evolution runs normally.
>> I use SDK + v. 4589 + 3 threads on Lion 10.7
>> How can I fix this?
>> I guess the fix should also apply to the test_suite as well.
>>
>> Thanks folks.
>> ehsan.
>>
>>
>> --
>> This message has been scanned for viruses and
>> dangerous content by MailScanner, and is
>> believed to be clean.
>>
>>
>> ------------------------------------------------------------------------------
>> Everyone hates slow websites. So do we.
>> Make your web apps faster with AppDynamics
>> Download AppDynamics Lite for free today:
>> http://p.sf.net/sfu/appdyn_sfd2d_oct
>> _______________________________________________
>> mesa-users mailing list
>> mesa-users at lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/mesa-users
>>
>
>
> --
> This message has been scanned for viruses and
> dangerous content by MailScanner, and is
> believed to be clean.
>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 23 Oct 2012 11:32:28 +1100
> From: Aaron Dotter <aaron.dotter at gmail.com>
> Subject: [mesa-users] Installation error and solution on Mac OS X 10.8
> To: mesa-users <mesa-users at lists.sourceforge.net>
> Message-ID:
> <CAN5--jOjAKD2TKjS0X_PSZua+hZ6W3uQhGmrJ9QFZdf=_XFHCA at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,
>
> In attempting to install MESA r4589 on new Macs running OS X 10.8.2 with
> 64-bit SDK version 20120728, Thomas Puzia and I found errors suggesting
> that the linker could not find some specific dynamic library. This showed
> up as a run-time error: it came in the output file tmp.txt in
> mesa/const/test.
>
> We were able to solve the problem by adding both $MESASDK_ROOT/lib and
> /usr/local/lib at the front of DYLD_LIBRARY_PATH in that order.
>
> I've added an entry under the mesa forum FAQ under Compiling / Platform
> Specific Issues - Mac OS X at
> http://mesastar.org/documentation/frequently-asked-questions
>
>
> Aaron
> -------------- next part --------------
> An HTML attachment was scrubbed...
>
> ------------------------------
>
> Message: 5
> Date: Mon, 22 Oct 2012 19:36:03 -0500
> From: Richard Townsend <townsend at astro.wisc.edu>
> Subject: Re: [mesa-users] Installation error and solution on Mac OS X
> 10.8
> To: Aaron Dotter <aaron.dotter at gmail.com>
> Cc: mesa-users <mesa-users at lists.sourceforge.net>
> Message-ID: <88744FE8-22DB-49C1-A350-662DF33773B2 at astro.wisc.edu>
> Content-Type: text/plain; charset=iso-8859-1
>
> Hi Aaron --
>
> Setting DYLD_LIBRARY_PATH is generally a bad idea, and can break other
> parts of OS X (ask Bill about this; he's experienced the problems
> directly).
>
> Can I ask what errors the linker was producing?
>
> cheers,
>
> Rich
>
> On Oct 22, 2012, at 7:32 PM, Aaron Dotter wrote:
>
>> Hi,
>>
>> In attempting to install MESA r4589 on new Macs running OS X 10.8.2 with
>> 64-bit SDK version 20120728, Thomas Puzia and I found errors suggesting
>> that the linker could not find some specific dynamic library. This
>> showed up as a run-time error: it came in the output file tmp.txt in
>> mesa/const/test.
>>
>> We were able to solve the problem by adding both $MESASDK_ROOT/lib and
>> /usr/local/lib at the front of DYLD_LIBRARY_PATH in that order.
>>
>> I've added an entry under the mesa forum FAQ under Compiling / Platform
>> Specific Issues - Mac OS X at
>> http://mesastar.org/documentation/frequently-asked-questions
>>
>>
>> Aaron
>> ------------------------------------------------------------------------------
>> Everyone hates slow websites. So do we.
>> Make your web apps faster with AppDynamics
>> Download AppDynamics Lite for free today:
>> http://p.sf.net/sfu/appdyn_sfd2d_oct_______________________________________________
>> mesa-users mailing list
>> mesa-users at lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/mesa-users
>
>
>
>
> ------------------------------
>
> Message: 6
> Date: Mon, 22 Oct 2012 17:56:49 -0700
> From: Chris Mankovich <cmankovich at umail.ucsb.edu>
> Subject: Re: [mesa-users] nugrid-mesa.py
> To: Falk Herwig <fherwig at uvic.ca>
> Cc: "mesa-users at lists.sourceforge.net users"
> <mesa-users at lists.sourceforge.net>
> Message-ID:
> <CAFGiHn2ZZfateFh+sYLwe3Bj21pfV33hdV_zA=tCRBSJVcJoMw at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi everyone,
>
> I'm up and running now. Thanks for attending to this!
>
> Chris
>
> On Sat, Oct 20, 2012 at 3:42 PM, Falk Herwig <fherwig at uvic.ca> wrote:
>
>> After some more testing, documenting and cleaning up, please try again:
>>
>> http://www.mesastar.org/tools-utilities/python-based-stuff/nugrids-mesa.py-1
>>
>> In addition to the mesa.py file another file data_plot.py is needed.
>> This
>> is now all directly available from mesastars.org.
>>
>> Presently these files live on the NuGrid svn server.
>>
>> Falk.
>>
>>
>> On 2012-10-19, at 7:00 PM, Josiah Schwab wrote:
>>
>> > This tool requires the files from nugrid_pylib. Are you trying to
>> just
>> use the mesa.py file all by itself? (Or if you have those, some path
>> may
>> be set incorrectly.)
>> >
>> > Josiah
>> >
>> > On 10/19/2012 04:46 PM, Chris Mankovich wrote:
>> >> Hi Falk,
>> >>
>> >> I'm eager to give this a shot, but I'm failing at the import step:
>> >>
>> >> In [2]: import mesa
>> >>
>> ---------------------------------------------------------------------------
>> >> ImportError Traceback (most recent call
>> last)
>> >> /home/chris/he/<ipython-input-2-6c94b0867429> in <module>()
>> >> ----> 1 import mesa
>> >>
>> >> /home/chris/he/mesa.py in <module>()
>> >> 113 '''
>> >> 114 import numpy as np
>> >> --> 115 from data_plot import *
>> >> 116 import numpy as np
>> >> 117 import matplotlib
>> >>
>> >> ImportError: No module named data_plot
>> >>
>> >>
>> >> This is running "ipython --pylab --profile=numpy". python version
>> >> 2.7.3, ipython version 0.12.1. What am I missing?
>> >>
>> >> Chris
>> >>
>> >> On Wed, Oct 17, 2012 at 8:32 PM, Falk Herwig <fherwig at uvic.ca
>> >> <mailto:fherwig at uvic.ca>> wrote:
>> >>
>> >> NuGrid's mesa.py update available to deal with new naming scheme:
>> >>
>> http://mesastar.org/tools-utilities/python-based-stuff/nugrids-mesa.py
>> >> Contributions, improvements and bug fixes welcome.
>> >> Falk.
>> >>
>> >> --
>> >> Falk Herwig
>> >> Dept of Physics & Astronomy, U of Victoria
>> >> fherwig at uvic.ca <mailto:fherwig at uvic.ca>, tel: +1 (250) 721-7743
>> >> <tel:%2B1%20%28250%29%20721-7743>
>> >>
>> >>
>> >>
>> >>
>> >>
>> ------------------------------------------------------------------------------
>> >> Everyone hates slow websites. So do we.
>> >> Make your web apps faster with AppDynamics
>> >> Download AppDynamics Lite for free today:
>> >> http://p.sf.net/sfu/appdyn_sfd2d_oct
>> >> _______________________________________________
>> >> mesa-users mailing list
>> >> mesa-users at lists.sourceforge.net
>> >> <mailto:mesa-users at lists.sourceforge.net>
>> >> https://lists.sourceforge.net/lists/listinfo/mesa-users
>> >>
>> >>
>> >>
>> >>
>> >>
>> ------------------------------------------------------------------------------
>> >> Everyone hates slow websites. So do we.
>> >> Make your web apps faster with AppDynamics
>> >> Download AppDynamics Lite for free today:
>> >> http://p.sf.net/sfu/appdyn_sfd2d_oct
>> >>
>> >>
>> >>
>> >> _______________________________________________
>> >> mesa-users mailing list
>> >> mesa-users at lists.sourceforge.net
>> >> https://lists.sourceforge.net/lists/listinfo/mesa-users
>> >>
>>
>> --
>> Falk Herwig
>> Dept of Physics & Astronomy, U of Victoria
>> fherwig at uvic.ca, tel: +1 (250) 721-7743
>>
>>
>>
>>
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> ------------------------------
>
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_sfd2d_oct
>
> ------------------------------
>
> _______________________________________________
> mesa-users mailing list
> mesa-users at lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/mesa-users
>
>
> End of mesa-users Digest, Vol 38, Issue 13
> ******************************************
>
Zhao Guo
Astronomy Program
Georgia State University
1+6789003094
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