Merge pull request #563 from reinhold-willcox/directory_reorganization

Directory reorganization

Author: themikelau

demo/demo_plot.png

@@ -124,18 +124,18 @@ If you do not have python3 installed, install it by following the instructions b
 
 
 ## 2. Evolving your first binary
-To start using COMPAS, you will need the python script pythonSubmit.py, which specifies all the program options (physics assumptions, output types) and runs COMPAS in the terminal. Although the primary functionality of COMPAS is to evolve a whole population of binary stars rapidly, for now, let's focus on evolving a single stellar system and examining the detailed output.
+To start using COMPAS, you will need the python script `pythonSubmitDemo.py`, which specifies all the program options (physics assumptions, output types) and runs COMPAS in the terminal. Although the primary functionality of COMPAS is to evolve a whole population of binary stars rapidly, for now, let's focus on evolving a single stellar system and examining the detailed output.
 
-To start, change to the `demo` directory:
+To start, change to the `examples/methods_paper_plots/detailed_evolution/` directory:
 
-    cd $COMPAS_ROOT_DIR/demo
+    cd $COMPAS_ROOT_DIR/examples/methods_paper_plots/detailed_evolution/
 
-Here, you will find the script pythonSubmitDemo.py for this demo.
+Here, you will find the script `pythonSubmitDemo.py` for this demo.
 
 ### 2.1 Running COMPAS from a grid file
 In population synthesis, the initial stellar population is usually generated by drawing the primary mass, secondary mass, semi-major axis, and eccentricity from their respective distributions specified in the program options. However, we illustrate COMPAS's ability to specify a grid of initial values for single and binary star evolution using COMPAS's grid functionality.
 
-An example grid file, `Grid_demo.txt`, has been included in the `demo` directory. Open it with a text editor to view it:
+An example grid file, `Grid_demo.txt`, has been included in the current `detailed_evolution` directory. Open it with a text editor to view it:
 
     # Demo BSE Grid file
 
@@ -144,7 +144,7 @@ An example grid file, `Grid_demo.txt`, has been included in the `demo` directory
 
 It should be clear that this grid file specifies a binary of zero-age main sequence stars with primary mass 35.4 Msol, secondary mass 29.3 Msol, metallicity 0.001, zero eccentricity, and semi-major axis of 1.02 AU. For more detailed documentation of COMPAS's grid functionality for both single and binary stars, please see [Specifications](./COMPAS_Doc.pdf).
 
-To tell the python submit script to take its input from this grid file, you need to open `pythonSubmit.py` with a text editor, and specify the grid filename `grid_filename = 'Grid_demo.txt'`.  And to print the time evolution of binary properties, we need to turn on detailed output: `detailed_output = True`.  COMPAS can produce logfiles of different types: HDF5, CSV, TSV, and TXT, which can be chosen by editing the line `logfile_type = 'HDF5'` (the default type is HDF5).  For this demo, this has all been done for you in the file `pythonSubmitDemo.py`.
+To tell the python submit script to take its input from this grid file, you usually need to open `$COMPAS_ROOT_DIR/preProcessing/pythonSubmit.py` with a text editor, and specify the grid filename `grid_filename = 'Grid_demo.txt'`.  And to print the time evolution of binary properties, we need to turn on detailed output: `detailed_output = True`.  COMPAS can produce logfiles of different types: HDF5, CSV, TSV, and TXT, which can be chosen by editing the line `logfile_type = 'HDF5'` (the default type is HDF5).  For this demo, this has all been done for you in the file `pythonSubmitDemo.py` found in the current directory.
 
 Now let's run COMPAS!
 
@@ -181,10 +181,10 @@ The COMPAS run just now produces a new directory `COMPAS_Output`, inside which y
 
 We examine `BSE_Detailed_Output_0.h5` to look at the evolution of the two stars. A default python plotting script has been included to visualise the data. Let's run the script:
 
-    python3 $COMPAS_ROOT_DIR/demo/single_sys_plotter.py
+    python3 single_sys_plotter.py
 
 This should produce the following plot:  
-![demo_plot](../demo/demo_plot.png)
+![demo_plot](../examples/methods_paper_plots/detailed_evolution/gw151226evol.png)
 
 
 COMPAS provides many tools for analysing and post-processing the data. Please view the post-processing documentation in `COMPAS/postProcessing`. 

docs/getting_started.md

@@ -17,7 +17,7 @@ If you have not already, you will need to install Stroopwafel. If you have admin
 
 ---------------
 
-To use Stroopwafel sampling, copy `defaults/stroopwafelInterface.py` into your working directory. 
+To use Stroopwafel sampling, copy `preProcessing/stroopwafelInterface.py` into your working directory. 
 
 
 ### Settings
@@ -30,7 +30,7 @@ If you have many non-default COMPAS arguments, you may want to set them in the
 `pythonSubmit.py` file in the same directory. For now, the file must be named this way 
 and placed in the same directory as the `stroopwafelInterface.py` file. 
 
-A configurable pythonSubmit file can be found in the `defaults/` directory.
+A configurable pythonSubmit file can be found in the `preProcessing/` directory.
 
 Set your desired options, then set the `usePythonSubmit` parameter to `True` 
 in the `stroopwafelInterface.py`.

docs/sampling.md

@@ -85,6 +85,7 @@ def main():
     fig.subplots_adjust(left=0.05)  #adjusting boundaries of the plotter
     fig.subplots_adjust(wspace=.3)
     plt.savefig('gw151226evol.eps', format='eps') 
+    plt.savefig('gw151226evol.png', format='png') 
     plt.show()