Recent changes to Home

Home modified by Dr Pierre Maxted

Dr Pierre Maxted — Thu, 31 Jul 2014 18:33:14 -0000

--- v3
+++ v4
@@ -1,4 +1,3 @@
-
  This is the README file for version 1.0 of bagemass.

 ***************
@@ -167,9 +166,9 @@
 star to be studied. See Maxted et al. 2014 for a description of these 4
 observed quantities.

-> Enter T_eff \[K\] [6000.,   100.,  -100.] > 
+> Enter T_eff \[K\] \[6000.,   100.,  -100.\] > 
 > Enter log L/Lsun \[0.0,  5.0, -5.0\] > 
-> Enter observed metalicity, \[Fe/H\]_s [0.0,  0.1, -0.1] > 
+> Enter observed metalicity, \[Fe/H\]_s \[0.0,  0.1, -0.1\] > 
 > Enter observed density, rho/rho_Sun \[1.00,  0.01, -0.01\] > 

  Observations are entered in the format
@@ -195,7 +194,7 @@
 example, you can add a prior constraint that the age of star must be less than
 the age of the Galactic disc (10 +/- 1 Gyr) using the following input.

-$  Enter prior on age \[Gyr\] [0.0,   0.0,  17.5,   0.0] >  0.0 0.0 10 1
+$  Enter prior on age \[Gyr\] \[0.0,   0.0,  17.5,   0.0\] >  0.0 0.0 10 1

  If hilim=0 then all trial chain points greater than hilim are rejected, and
 similarly for lolim.

Home modified by Dr Pierre Maxted

Dr Pierre Maxted — Thu, 31 Jul 2014 18:32:17 -0000

--- v2
+++ v3
@@ -50,8 +50,6 @@

  Commands entered on the command line are preceeded by "$".

- Output from the program is preceeded by ">".
-
  1. Download the compressed tar file bagemass.tar.gz from sourceforge

      http://sourceforge.net/projects/bagemass/
@@ -87,7 +85,7 @@
      share/
      share/bagemass/

-6. [Optional] Remove object files
+6. \[Optional\] Remove object files

     $ make clean

@@ -108,7 +106,7 @@
 >   1    1.78    0.00
 >   2    1.50    0.00
 >   3    1.78    0.02
->  Enter model grid number [1] > 
+>  Enter model grid number \[1\] > 

  If you hit return at all the prompts you should see lots of numbers printed to
@@ -118,7 +116,7 @@
 >  
 > Mean age         =    1.788 +/-    1.238
 > Mean mass        =    1.075 +/-    0.045
-> Mean [Fe/H]_init =    0.019 +/-    0.084
+> Mean \[Fe/H\]_init =    0.019 +/-    0.084
 >   
 >  --
 >   
@@ -157,7 +155,7 @@
 >  1    1.78    0.00
 >  2    1.50    0.00
 >  3    1.78    0.02
-> Enter model grid number [1] > 
+> Enter model grid number \[1\] > 

  The default grid number is shown in square brackets. Hit return to accept the
 default or enter the grid number desired and then hit return.
@@ -169,10 +167,10 @@
 star to be studied. See Maxted et al. 2014 for a description of these 4
 observed quantities.

-> Enter T_eff [K] [6000.,   100.,  -100.] > 
-> Enter log L/Lsun [0.0,  5.0, -5.0] > 
-> Enter observed metalicity, [Fe/H]_s [0.0,  0.1, -0.1] > 
-> Enter observed density, rho/rho_Sun [1.00,  0.01, -0.01] > 
+> Enter T_eff \[K\] [6000.,   100.,  -100.] > 
+> Enter log L/Lsun \[0.0,  5.0, -5.0\] > 
+> Enter observed metalicity, \[Fe/H\]_s [0.0,  0.1, -0.1] > 
+> Enter observed density, rho/rho_Sun \[1.00,  0.01, -0.01\] > 

  Observations are entered in the format

@@ -197,7 +195,7 @@
 example, you can add a prior constraint that the age of star must be less than
 the age of the Galactic disc (10 +/- 1 Gyr) using the following input.

-$  Enter prior on age [Gyr] [0.0,   0.0,  17.5,   0.0] >  0.0 0.0 10 1
+$  Enter prior on age \[Gyr\] [0.0,   0.0,  17.5,   0.0] >  0.0 0.0 10 1

  If hilim=0 then all trial chain points greater than hilim are rejected, and
 similarly for lolim.
@@ -213,8 +211,8 @@

  First there are 2 scaling factors that can be adjusted.

-> Enter initial step size scale [0.500] > 
-> Enter MCMC step size scaling factor [1.00] > 
+> Enter initial step size scale \[0.500\] > 
+> Enter MCMC step size scaling factor \[1.00\] > 

  These can generally be left at their default values, but you can experiment
 with these values if you are having trouble getting your Markov chain to
@@ -225,8 +223,8 @@

  The last two prompts set the lengths of the two Markov chains.

-> Number of steps for MCMC burn-in [1000] > 
-> Number of MCMC steps [10000] > 
+> Number of steps for MCMC burn-in \[1000\] > 
+> Number of MCMC steps \[10000\] > 

  The default values are ok for test runs, but for proper analysis you will
 probably want to use values of 50-100,000 for both chains.
@@ -251,17 +249,17 @@

  The following output files should also be created every time bagemass is run.
   chain.dat          - Second Markov chain. 
-  zams.dat           - zero-age main sequence at best-fit [Fe/H]
-  track.dat          - evolution file for best-fit mass and [Fe/H]
+  zams.dat           - zero-age main sequence at best-fit \[Fe/H\]
+  track.dat          - evolution file for best-fit mass and \[Fe/H\]
   track_mlo.dat      - evolution track for best-fit mass - error, and 
-                       best-fit [Fe/H] 
+                       best-fit \[Fe/H\] 
   track_mhi.dat      - evolution track for best-fit mass + error, and 
-                       best-fit [Fe/H] 
-  isochrone.dat      - isochrone for best-fit age and [Fe/H]
+                       best-fit \[Fe/H\] 
+  isochrone.dat      - isochrone for best-fit age and \[Fe/H\]
   isochrone_alo.dat  - isochrone for best-fit age - error,  and
-                       best-fit [Fe/H] 
+                       best-fit \[Fe/H\] 
   isochrone_ahi.dat  - isochrone for best-fit age + error,  and
-                       best-fit [Fe/H] 
+                       best-fit \[Fe/H\] 

  These are ascii files with comments in the headers preceeded with '#' that
 describe the content of the file and give the variable names for each column.
@@ -271,11 +269,11 @@
 Step     - Markov chain step number
 Age      - Age in Gyr
 Mass     - Stellar mass in solar units
-[Fe/H]_i - Initial metallicity 
+\[Fe/H\]_i - Initial metallicity 
 DeltaR   - Undocumented/disabled feature (should always by 0.0)
 Teff     - Effective temperature in Kelvin
 LogL     - Logarithm of the luminosity in solar units
-[Fe/H]_s - Surface metallicity
+\[Fe/H\]_s - Surface metallicity
 rho      - Stellar density in solar units.
 Xc       - Central hydrogen abundance per unit mass
 loglike  - Logarithm of the likelihood 
@@ -290,5 +288,3 @@
  Some variables appear twice in these files under column headings Radius_0,
 Teff_0, etc. 

-
-

Home modified by Dr Pierre Maxted

Dr Pierre Maxted — Thu, 31 Jul 2014 18:28:36 -0000

--- v1
+++ v2
@@ -1,8 +1,294 @@
-Welcome to your wiki!
-
-This is the default page, edit it as you see fit. To add a new page simply reference it within brackets, e.g.: [SamplePage].
-
-The wiki uses [Markdown](/p/bagemass/wiki/markdown_syntax/) syntax.
-
-[[members limit=20]]
-[[download_button]]
+
+ This is the README file for version 1.0 of bagemass.
+
+***************
+VERSION HISTORY
+***************
+
+ 1.0 - First export version.
+       31 Jul 2014, p.maxted@keele.ac.uk
+
+ This software is distributed under the terms of the GNU General Public
+License GPLv3 (https://www.gnu.org/licenses/gpl.html).
+
+ Please cite the following publication if you publish results based on this
+software.
+ 
+ P. F. L. Maxted, A. M. Serenelli and J. Southworth
+ 2014, MNRAS, submitted.
+
+Index:
+   1. CONTENTS
+   2. INSTALLATION
+   3. RUNNING THE PROGRAM
+   4. OUTPUT FILES
+
+***********
+1. CONTENTS
+***********
+
+README:  This file. 
+
+Makefile: Used by GNU make to compile and install the software.
+
+data/: Directory containing spline fits to grids of stellar models stored as
+      FITS files.
+
+src/: Source code 
+
+***************
+2. INSTALLATION
+***************
+
+ This software should compile without much trouble on any modern linux system, 
+the only package you may need to install is cfitsio:
+
+  http://heasarc.gsfc.nasa.gov/fitsio/fitsio.html
+
+Step-by-step instructions 
+-------------------------
+
+ Commands entered on the command line are preceeded by "$".
+
+ Output from the program is preceeded by ">".
+
+ 1. Download the compressed tar file bagemass.tar.gz from sourceforge
+ 
+     http://sourceforge.net/projects/bagemass/
+
+ 2. Unpack the archive 
+
+     $ tar xzvf bagemass-1.0.tar.gz
+
+    This will create a directory bagemass-1.0
+
+ 3. Move to the directory created in the previous step.
+
+    $ cd bagemass-1.0
+
+ 4. Use any text editor to edit the file Makefile, e.g., 
+
+    $ pico Makefile
+
+     Change the values of the variables INSTALL, LCFITSIO, F77 and FFLAGS as
+    needed. 
+
+ 5. Compile and install
+
+    $ make
+
+     You may see some warnings when src/herm2ev.f and src/herm3ev.f are 
+    compiled - these can be ignored.
+
+     The following directories will be created in the installation directory
+    if they do not already exist.
+
+     bin/
+     share/
+     share/bagemass/
+
+6. [Optional] Remove object files
+
+    $ make clean
+
+7. If the "bin" sub-directory in the installation directory is not already in 
+   the PATH system variable of your shell, add it now (and "rehash" if needed).
+
+8. Test run bagemass
+
+   $ bagemass
+
+ You should see the following output on your terminal
+
+>   
+> This is bagemass version 1.0
+> (p.maxted@keele.ac.uk)
+>   
+>   Available alpha_MLT and He-enhancement values are ...
+>   1    1.78    0.00
+>   2    1.50    0.00
+>   3    1.78    0.02
+>  Enter model grid number [1] > 
+
+   
+ If you hit return at all the prompts you should see lots of numbers printed to
+screen, finishing with the following output. (The actual values printed will be
+slightly different to this example.)
+
+>  
+> Mean age         =    1.788 +/-    1.238
+> Mean mass        =    1.075 +/-    0.045
+> Mean [Fe/H]_init =    0.019 +/-    0.084
+>   
+>  --
+>   
+>   Please cite the following paper if you publish the 
+>   results of this analysis.
+>   P. F. L. Maxted, A. M. Serenelli and J. Southworth
+>   2014, MNRAS, submitted.
+>   
+ 
+ The following output files should also be created every time bagemass is run.
+  zams.dat
+  track_mlo.dat
+  track_mhi.dat
+  track.dat
+  isochrone_alo.dat
+  isochrone_ahi.dat
+  isochrone.dat
+  chain.dat
+
+
+
+**********************
+3. RUNNING THE PROGRAM
+**********************
+
+ First read the description of the method and models in Maxted et al., 2014.
+
+ The program is run using the following command
+
+ $ bagemass
+
+ The version number of the program is printed and the user is offered a choice
+of model grids, e.g., 
+
+>  Available alpha_MLT and He-enhancement values are ...
+>  1    1.78    0.00
+>  2    1.50    0.00
+>  3    1.78    0.02
+> Enter model grid number [1] > 
+
+ The default grid number is shown in square brackets. Hit return to accept the
+default or enter the grid number desired and then hit return.
+
+ The full path to the model grid is displayed and the models are loaded (this
+can take a few seconds).
+
+ The next set of prompts enable the user to enter the observed data for the
+star to be studied. See Maxted et al. 2014 for a description of these 4
+observed quantities.
+
+> Enter T_eff [K] [6000.,   100.,  -100.] > 
+> Enter log L/Lsun [0.0,  5.0, -5.0] > 
+> Enter observed metalicity, [Fe/H]_s [0.0,  0.1, -0.1] > 
+> Enter observed density, rho/rho_Sun [1.00,  0.01, -0.01] > 
+
+ Observations are entered in the format
+
+  value +error -error 
+
+ This enables the user to use asymmetrical error bars if needed. If the
+measurements has symmetrical error bars, simply enter this value twice, once
+as a positive value and once as a negative value. All three numbers must be
+entered on the same line, followed by return.
+
+ The next three prompts enable the user to enter priors on the age, initial 
+metallicity and mass of the star. 
+
+ For the age and metallicity, the default values are a flat distribution over
+the valid model range. Priors values are entered in the format
+
+  loerr lolim hilim hierr
+  
+ For chain values between lolim and hilim, the prior has a value of 1. If
+hierr is >0 and the chain value is >hilim, then the prior has a value
+exp(-0.5*(value-hilim)^2/hierr^2), and similarly for lolim and loerr. For
+example, you can add a prior constraint that the age of star must be less than
+the age of the Galactic disc (10 +/- 1 Gyr) using the following input.
+
+$  Enter prior on age [Gyr] [0.0,   0.0,  17.5,   0.0] >  0.0 0.0 10 1
+
+ If hilim=0 then all trial chain points greater than hilim are rejected, and
+similarly for lolim.
+
+ The prior on the mass is given by 
+
+  log(Likelihood) = alpha*Mass
+ 
+ The default is to use a flat prior prior for mass, i.e.,alpha=0. For a
+Salpeter distribution use alpha=-2.35.
+
+ The following prompts control the behaviour of Markov Chain calculation.
+
+ First there are 2 scaling factors that can be adjusted.
+
+> Enter initial step size scale [0.500] > 
+> Enter MCMC step size scaling factor [1.00] > 
+
+ These can generally be left at their default values, but you can experiment
+with these values if you are having trouble getting your Markov chain to
+converge. The first value scales the step size calculated by perturbing each
+of the parameters in-turn prior to the first Markov chain. The second value
+sets the step size in the two Markov chains as a factor of the standard
+deviation of each jump parameter.
+
+ The last two prompts set the lengths of the two Markov chains.
+
+> Number of steps for MCMC burn-in [1000] > 
+> Number of MCMC steps [10000] > 
+
+ The default values are ok for test runs, but for proper analysis you will
+probably want to use values of 50-100,000 for both chains.
+
+ The calculation starts as soon as the last prompt is completed.
+
+ The output to screen summarizes the progress of the calculation. This is
+self-explanatory once you have read and understood the description of the
+method in Maxted et al. (2014) and the description of the various output 
+variables in the following section.
+ 
+ One value of interest is the mean acceptance rate for the 2nd MCMC chain.
+This will generally have a value of 0.5+-0.1 for a well-mixed chain, perhaps
+slightly lower for complex cases. Values of the acceptance rate lower than
+about 0.2 may suggest that the MCMC chain has not converged.
+
+
+***************
+4. OUTPUT FILES
+***************
+
+ 
+ The following output files should also be created every time bagemass is run.
+  chain.dat          - Second Markov chain. 
+  zams.dat           - zero-age main sequence at best-fit [Fe/H]
+  track.dat          - evolution file for best-fit mass and [Fe/H]
+  track_mlo.dat      - evolution track for best-fit mass - error, and 
+                       best-fit [Fe/H] 
+  track_mhi.dat      - evolution track for best-fit mass + error, and 
+                       best-fit [Fe/H] 
+  isochrone.dat      - isochrone for best-fit age and [Fe/H]
+  isochrone_alo.dat  - isochrone for best-fit age - error,  and
+                       best-fit [Fe/H] 
+  isochrone_ahi.dat  - isochrone for best-fit age + error,  and
+                       best-fit [Fe/H] 
+
+ These are ascii files with comments in the headers preceeded with '#' that
+describe the content of the file and give the variable names for each column.
+
+The variables in chain.dat are as follows.
+
+Step     - Markov chain step number
+Age      - Age in Gyr
+Mass     - Stellar mass in solar units
+[Fe/H]_i - Initial metallicity 
+DeltaR   - Undocumented/disabled feature (should always by 0.0)
+Teff     - Effective temperature in Kelvin
+LogL     - Logarithm of the luminosity in solar units
+[Fe/H]_s - Surface metallicity
+rho      - Stellar density in solar units.
+Xc       - Central hydrogen abundance per unit mass
+loglike  - Logarithm of the likelihood 
+Chisq    - chi-squared.
+
+ The content  of the files zams.dat, etc. is similar, but it addition the
+following variables are provided.
+ 
+Radius   - Radius in solar units
+logg     - Logarithm of the surface gravity in units of cm.s^-2
+
+ Some variables appear twice in these files under column headings Radius_0,
+Teff_0, etc. 
+
+
+

Discussion for Home page

Dr Pierre Maxted — Thu, 31 Jul 2014 18:27:11 -0000

Please read Maxted et al. (2014) "Bayesian mass and age estimates for transiting planet host stars" (MNRAS submitted) for a complete description of the algorithm and models used in this software.

Home modified by Dr Pierre Maxted

Dr Pierre Maxted — Thu, 31 Jul 2014 18:03:52 -0000

Welcome to your wiki!

This is the default page, edit it as you see fit. To add a new page simply reference it within brackets, e.g.: [SamplePage].

The wiki uses Markdown syntax.

Project Members:

Dr Pierre Maxted (admin)