moved some files around and created examples directory containing some examples

README.md

@@ -37,9 +37,16 @@ Then to test the Python module:
 ```
 You will require whatever libraries with which binary_c was compiled, as well as the compiler with which Python was built (usually gcc, which is easily installed on most systems).
 
+If you want to be able to import the binary_c module correctly for child directories (or anywhere for that matter), execute or put the following code in your .bashrc/.zshrc: 
+```
+export LD_LIBRARY_PATH=<full path to directory containing libbinary_c_api.so>
+```
+
 TODO 
 ---------------------
-- ?Put the header and src files in a dedicated directory
+- ?Put the header and src files in a dedicated directory. 
 - ?Have the compiled files be written into build
 - Use sphinx for auto generation of docs
 - Use queueing system/asynchronous task queue
+- Make some parse-data that can be easily used
+- Make some simple script to assign probabilities

examples/full_evolution_with_plot.py

+import os, sys
+import matplotlib.pyplot as plt
+
+import binary_c
+
+# Append root dir of this project to include functionality
+sys.path.append(os.path.dirname(os.getcwd()))
+from utils.defaults import physics_defaults
+from utils.functions import create_arg_string
+
+
+
+
+def example_with_loading_default_args():
+    """
+    Example function loading the default physics args for a binary_c system. Got
+    it from the binary_grid2 perl module
+
+    This function works if binary_c is set to log something every timestep so that we can plot the evolution of a system
+    """
+
+    # Load args
+    physics_args = physics_defaults.copy()
+
+    # Manually set M_1, M_2, orbital_period and separation values:
+    physics_args['M_1'] = 20
+    physics_args['M_2'] = 15
+    physics_args['separation'] = 0 # 0 = ignored, use period
+    physics_args['orbital_period'] = 4530.0
+
+    arg_string = create_arg_string(physics_args)
+
+    arg_string = f'binary_c {arg_string}' 
+
+    buffer = ""
+
+    output = binary_c.run_binary(arg_string)
+
+    # Make some 
+    results = {}
+    time_arr = []
+    mass_arr = []
+    mass_2_arr = []
+
+    # split output on newlines
+    for line in output.split('\n'):
+        # Skip any blank lines
+        if not line=='':
+            split_line = line.split()
+            header = split_line[0]
+            value_array = split_line[1:]
+
+            # Use parse data here:
+            if header=='TESTLOG':
+                # Add values to lists
+                time_arr.append(float(value_array[0]))
+                mass_arr.append(float(value_array[1]))
+                mass_2_arr.append(float(value_array[4]))
+
+    # Save in results dir
+    results['time'] = time_arr
+    results['mass'] = mass_arr
+    results['mass2'] = mass_2_arr
+
+    return results
+
+results = example_with_loading_default_args()
+
+# Plot some stuff
+plt.plot(results['time'], results['mass'])
+plt.plot(results['time'], results['mass2'])
+plt.xscale('log')
+plt.show()
\ No newline at end of file

python_API_test.py

@@ -7,8 +7,6 @@ import binary_c
 # module.
 ############################################################
 
-
-
 def run_test_binary():
     m1 = 15.0 # Msun
     m2 = 14.0 # Msun

test_david.py

 #!/usr/bin/python3
 import os
 import binary_c
+import matplotlib.pyplot as plt
 
 from defaults import physics_defaults
 
@@ -27,9 +28,9 @@ def run_test_binary():
     # print ("Binary_c output:\n\n")
     print (output)
 
-
 def run_simple_loop_binary():
     # Some simple function with a loop
+    # This function assumes a single output line
 
     m2 = 14.0 # Msun
     separation = 0 # 0 = ignored, use period
@@ -77,30 +78,6 @@ def run_simple_loop_binary():
     print('zams_mass1:' ,initial_m1)
     print('time:', time)
 
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 # print("Current binary_c object class functions: ")
 # print(dir(binary_c))
 
@@ -119,41 +96,4 @@ def run_simple_loop_binary():
 # run_test_binary()
 
 # Test grid-like
-# run_simple_loop_binary()
-
+# run_simple_loop_binary()
\ No newline at end of file
-def create_arg_string(arg_dict):
-    """
-    Function that creates the arg string
-    """
-
-    arg_string = '' 
-    for key in arg_dict.keys():
-        arg_string += f'{key} {arg_dict[key]} '
-    arg_string = arg_string.strip()
-    return arg_string
-
-def example_with_loading_default_args():
-    """
-    Example function loading the default physics args for a binary_c system. Got
-    it from the binary_grid2 perl module
-    """
-
-    # Load args
-    physics_args = physics_defaults.copy()
-
-    # Manually set M_1, M_2, orbital_period and separation values:
-    physics_args['M_1'] = 20
-    physics_args['M_2'] = 15
-    physics_args['separation'] = 0 # 0 = ignored, use period
-    physics_args['orbital_period'] = 4530.0
-
-    arg_string = create_arg_string(physics_args)
-
-    arg_string = f'binary_c {arg_string}' 
-
-    output = binary_c.run_binary(arg_string)
-    print (output)
-
-
-
-example_with_loading_default_args()
\ No newline at end of file

utils/functions.py

+def create_arg_string(arg_dict):
+    """
+    Function that creates the arg string
+    """
+
+    arg_string = '' 
+    for key in arg_dict.keys():
+        arg_string += f'{key} {arg_dict[key]} '
+    arg_string = arg_string.strip()
+    return arg_string
\ No newline at end of file

utils/stellar_types.py

+stellar_type = {
+    0: 'low mass main sequence', 
+    1: 'Main Sequence',
+    2: 'Hertzsprung Gap',
+    3: 'First Giant Branch', 
+    4: 'Core Helium Burning',
+    5: 'Early Asymptotic Giant Branch',
+    6: 'Thermally Pulsing', 
+    7: 'NAKED_MAIN_SEQUENCE_HELIUM_STAR',
+    8: 'NAKED_HELIUM_STAR_HERTZSPRUNG_GAP',
+    9: 'NAKED_HELIUM_STAR_GIANT_BRANCH',
+    10: 'HELIUM_WHITE_DWARF', 
+    11: 'CARBON_OXYGEN_WHITE_DWARF',
+    12: 'OXYGEN_NEON_WHITE_DWARF',
+    13: 'NEUTRON_STAR', 
+    14: 'BLACK_HOLE', 
+    15: 'MASSLESS REMNANT'
+}
\ No newline at end of file