Loading binarycpython/utils/#functions.py#deleted 100644 → 0 +0 −198 Original line number Diff line number Diff line from collections import defaultdict import binary_c from binarycpython.binaryc_python_utils from binaryc_python_utils.custom_logging_functions import ( create_and_load_logging_function, ) def create_arg_string(arg_dict): """ Function that creates the arg string """ arg_string = "" for key in arg_dict.keys(): arg_string += "{key} {value} ".format(key=key, value=arg_dict[key]) arg_string = arg_string.strip() return arg_string def get_defaults(): """ Function that calls the binaryc get args function and cast it into a dictionary All the values are strings """ default_output = binary_c.return_arglines() default_dict = {} for default in default_output.split("\n"): if not default in ["__ARG_BEGIN", "__ARG_END", ""]: key, value = default.split(" = ") # Filter out NULLS (not compiled anyway) if not value in ["NULL", "Function"]: if not value == "": default_dict[key] = value return default_dict def get_arg_keys(): """ Function that return the list of possible keys to give in the arg string """ return get_defaults().keys() def run_system(**kwargs): """ Wrapper to run a system with settings This function determines which underlying python-c api function will be called based upon the arguments that are passed via kwargs. - if custom_logging_code or custom_logging_dict is included in the kwargs then it will - if """ # Load default args args = get_defaults() if "custom_logging_code" in kwargs: # Use kwarg value to override defaults and add new args for key in kwargs.keys(): if not key == "custom_logging_code": args[key] = kwargs[key] # Generate library and get memaddr func_memaddr = create_and_load_logging_function(kwargs["custom_logging_code"]) # Construct arguments string and final execution string arg_string = create_arg_string(args) arg_string = "binary_c {}".format(arg_string) # Run it and get output output = binary_c.run_binary_custom_logging(arg_string, func_memaddr) return output elif "log_filename" in kwargs: # Use kwarg value to override defaults and add new args for key in kwargs.keys(): args[key] = kwargs[key] # Construct arguments string and final execution string arg_string = create_arg_string(args) arg_string = "binary_c {}".format(arg_string) # Run it and get output output = binary_c.run_binary_with_logfile(arg_string) return output else: # run the plain basic type # Use kwarg value to override defaults and add new args for key in kwargs.keys(): args[key] = kwargs[key] # Construct arguments string and final execution string arg_string = create_arg_string(args) arg_string = "binary_c {}".format(arg_string) # Run it and get output output = binary_c.run_binary(arg_string) return output def run_system_with_log(**kwargs): """ Wrapper to run a system with settings AND logs the files to a designated place defined by the log_filename parameter. """ # Load default args args = get_defaults() # args = {} # For example # physics_args['M_1'] = 20 # physics_args['separation'] = 0 # 0 = ignored, use period # physics_args['orbital_period'] = 100000000000 # To make it single # Use kwarg value to override defaults and add new args for key in kwargs.keys(): args[key] = kwargs[key] # Construct arguments string and final execution string arg_string = create_arg_string(args) arg_string = "binary_c {}".format(arg_string) # print(arg_string) # Run it and get output buffer = "" output = binary_c.run_binary_with_log(arg_string) return output def parse_output(output, selected_header): """ Function that parses output of binary_c: This function works in two cases: if the caught line contains output like 'example_header time=12.32 mass=0.94 ..' or if the line contains output like 'example_header 12.32 0.94' You can give a 'selected_header' to catch any line that starts with that. Then the values will be put into a dictionary. TODO: Think about exporting to numpy array or pandas instead of a defaultdict """ value_dicts = [] val_lists = [] # split output on newlines for i, line in enumerate(output.split("\n")): # Skip any blank lines if not line == "": split_line = line.split() # Select parts header = split_line[0] values_list = split_line[1:] # print(values_list) # Catch line starting with selected header if header == selected_header: # Check if the line contains '=' symbols: value_dict = {} if all('=' in el for el in values_list): for el in values_list: key, val = el.split("=") value_dict[key.strip()] = val.strip() value_dicts.append(value_dict) else: if any('=' in el for el in values_list): raise ValueError('Caught line contains some = symbols but not all of them do. aborting run') else: for i, val in enumerate(values_list): value_dict[i] = val value_dicts.append(value_dict) if len(value_dicts) == 0: print( "Sorry, didnt find any line matching your header {}".format(selected_header) ) return None keys = value_dicts[0].keys() # Construct final dict. final_values_dict = defaultdict(list) for value_dict in value_dicts: for key in keys: final_values_dict[key].append(value_dict[key]) return final_values_dict examples/notebooks/.ipynb_checkpoints/workshop_example_notebook-checkpoint.ipynb +32 −33 Original line number Diff line number Diff line %% Cell type:markdown id: tags: # Binary_c and python example notebook The following notebook servers as an example of how the binary_c python wrapper works and how it could be used. By: David Hendriks 30 nov 2019 %% Cell type:code id: tags: ``` python import binarycpython import binary_c_python_api ``` %% Cell type:markdown id: tags: ## Core api wrapper functions: %% Cell type:markdown id: tags: ### run_binary() %% Cell type:code id: tags: ``` python m1 = 15.0 # Msun m2 = 14.0 # Msun separation = 0 # 0 = ignored, use period orbital_period = 4530.0 # days eccentricity = 0.0 metallicity = 0.02 max_evolution_time = 15000 # You need to set this! argstring = "binary_c M_1 {0:g} M_2 {1:g} separation {2:g} orbital_period {3:g} eccentricity {4:g} metallicity {5:g} max_evolution_time {6:g} ".format( m1, m2, separation, orbital_period, eccentricity, metallicity, max_evolution_time, ) output = binary_c_python_api.run_binary(argstring) print("\n\nBinary_c output:\n\n") print('\n'.join(output.split('\n')[:10])) ``` %% Output Binary_c output: example_header_1 time=0 mass_1=15 mass_2=14 st1=1 st2=1 sep=3540.3 ecc=0 example_header_2 0 15 14 1 1 3540.3 0 INITIAL_GRID 15 14 4530 0.02 1 0 example_header_1 time=0 mass_1=15 mass_2=14 st1=1 st2=1 sep=3540.3 ecc=0 example_header_2 0 15 14 1 1 3540.3 0 INITIAL_GRID 15 14 4530 0.02 1 0 example_header_1 time=1e-07 mass_1=15 mass_2=14 st1=1 st2=1 sep=3540.3 ecc=0 example_header_2 1e-07 15 14 1 1 3540.3 0 example_header_1 time=2e-07 mass_1=15 mass_2=14 st1=1 st2=1 sep=3540.3 ecc=0 example_header_2 2e-07 15 14 1 1 3540.3 0 %% Cell type:markdown id: tags: ### run_binary_with_log %% Cell type:code id: tags: ``` python import tempfile import os m1 = 15.0 # Msun m2 = 14.0 # Msun separation = 0 # 0 = ignored, use period orbital_period = 4530.0 # days eccentricity = 0.0 metallicity = 0.02 max_evolution_time = 15000 # You need to set this! log_filename=tempfile.gettempdir() + "/test_log.txt" argstring = "binary_c M_1 {0:g} M_2 {1:g} separation {2:g} orbital_period {3:g} eccentricity {4:g} metallicity {5:g} max_evolution_time {6:g} log_filename {7} ".format( m1, m2, separation, orbital_period, eccentricity, metallicity, max_evolution_time, log_filename, ) output = binary_c_python_api.run_binary(argstring) print(os.path.exists(log_filename)) with open(log_filename, 'r') as f: print(f.read()) # print("\n\nBinary_c output:\n\n") # print(output) ``` %% Output True TIME M1 M2 K1 K2 SEP ECC R1/ROL1 R2/ROL2 TYPE RANDOM_SEED=1748 RANDOM_COUNT=0 0.0000 10.000 20.000 1 1 2.8176e+08 0.00 0.000 0.000 INITIAL 8.8656 9.980 19.203 1 2 2.8966e+08 0.00 0.000 0.000 TYPE_CHNGE 8.8814 9.980 19.185 1 4 2.8983e+08 0.00 0.000 0.000 TYPE_CHNGE 9.8724 9.977 10.122 1 5 4.2066e+08 0.00 0.000 0.000 TYPE_CHNGE 9.8834 9.977 9.974 1 5 4.2379e+08 0.00 0.000 0.000 q-inv 9.8901 9.977 1.621 1 13 -125.89 -1.00 0.000 0.000 Randbuf=42123 - d48r(0)=0.976476 - d48r(1)=0.214027 - d48r(2)=0.638803 - d48r(3)=0.00325497 - d48r(4)=0.931833 9.8901 9.977 1.621 1 13 -125.89 -1.00 0.000 0.000 SN kick II (SN type 12 12, pre-explosion M=8.50996 Mc=6.81718 type=5) -> kick 1(190) vk=132.601 vr=0.0878271 omega=5.85488 phi=-1.45663 -> vn=132.592 ; final sep -125.894 ecc -1 (random count 0) - Runaway v=(0,0,0) |v|=0 : companion v=(0,0,0), |v|=0 ; 9.8901 9.977 1.621 1 13 -125.89 -1.00 0.000 0.000 TYPE_CHNGE 9.8901 9.977 1.621 1 13 -125.89 -1.00 0.000 0.000 DISRUPT 9.8901 9.977 1.621 1 13 -125.89 -1.00 0.000 0.000 SN 24.4615 9.890 1.621 2 13 -125.89 -1.00 0.000 0.000 OFF_MS 24.4615 9.890 1.621 2 13 -125.89 -1.00 0.000 0.000 TYPE_CHNGE 24.5257 9.887 1.621 3 13 -125.89 -1.00 0.000 0.000 TYPE_CHNGE 24.5353 9.886 1.621 4 13 -125.89 -1.00 0.000 0.000 TYPE_CHNGE 27.3558 9.424 1.621 5 13 -125.89 -1.00 0.000 0.000 TYPE_CHNGE 27.4616 1.338 1.621 13 13 -125.89 -1.00 0.000 0.000 d48r(5)=0.99127 - d48r(6)=0.231093 - d48r(7)=0.881928 - d48r(8)=0.603217 27.4616 1.338 1.621 13 13 -125.89 -1.00 0.000 0.000 SN kick II (SN type 12 12, pre-explosion M=9.30206 Mc=2.87012 type=5) -> kick 1(190) vk=663.531 vr=0 omega=3.79013 phi=0.869266 -> vn=663.531 ; final sep -125.894 ecc -1 (random count 5) - Runaway v=(0,0,0) |v|=0 : companion v=(0,0,0), |v|=0 ; 27.4616 1.338 1.621 13 13 -125.89 -1.00 0.000 0.000 TYPE_CHNGE 27.4616 1.338 1.621 13 13 -125.89 -1.00 0.000 0.000 q-inv 27.4616 1.338 1.621 13 13 -125.89 -1.00 0.000 0.000 SN 15000.0000 1.338 1.621 13 13 -125.89 -1.00 0.000 0.000 MAX_TIME TIME M1 M2 K1 K2 SEP ECC R1/ROL1 R2/ROL2 TYPE RANDOM_SEED=7106 RANDOM_COUNT=0 0.0000 15.000 14.000 1 1 2.786e+08 0.00 0.000 0.000 INITIAL 12.7509 14.645 13.776 2 1 2.8427e+08 0.00 0.000 0.000 TYPE_CHNGE 12.7773 14.639 13.775 4 1 2.8435e+08 0.00 0.000 0.000 TYPE_CHNGE 13.1380 13.748 13.758 4 1 2.9373e+08 0.00 0.000 0.000 q-inv 14.0900 10.830 13.705 4 2 3.2934e+08 0.00 0.000 0.000 OFF_MS 14.0900 10.830 13.705 4 2 3.2934e+08 0.00 0.000 0.000 TYPE_CHNGE 14.1204 10.726 13.700 4 4 3.3081e+08 0.00 0.000 0.000 TYPE_CHNGE 14.2118 10.410 13.566 5 4 3.3702e+08 0.00 0.000 0.000 TYPE_CHNGE 14.2646 1.472 13.462 13 4 -31.236 -1.00 0.000 0.000 Randbuf=34421 - d48r(0)=0.0570946 - d48r(1)=0.458272 - d48r(2)=0.13108 - d48r(3)=0.562029 - d48r(4)=0.924056 14.2646 1.472 13.462 13 4 -31.236 -1.00 0.000 0.000 SN kick II (SN type 12 12, pre-explosion M=9.89211 Mc=4.78817 type=5) -> kick 1(190) vk=302.148 vr=0.113492 omega=5.80602 phi=0.124379 -> vn=302.048 ; final sep -31.2365 ecc -1 (random count 0) - Runaway v=(0,0,0) |v|=0 : companion v=(0,0,0), |v|=0 ; 14.2646 1.472 13.462 13 4 -31.236 -1.00 0.000 0.000 TYPE_CHNGE 14.2646 1.472 13.462 13 4 -31.236 -1.00 0.000 0.000 DISRUPT 14.2646 1.472 13.462 13 4 -31.236 -1.00 0.000 0.000 SN 15.7087 1.472 10.210 13 5 -31.236 -1.00 0.000 0.000 TYPE_CHNGE 15.7695 1.472 1.444 13 13 -31.236 -1.00 0.000 0.000 d48r(5)=0.608402 - d48r(6)=0.696003 - d48r(7)=0.796455 - d48r(8)=0.0834973 15.7695 1.472 1.444 13 13 -31.236 -1.00 0.000 0.000 SN kick II (SN type 12 12, pre-explosion M=9.85661 Mc=4.3914 type=5) -> kick 1(190) vk=392.156 vr=0 omega=0.524629 phi=0.634667 -> vn=392.156 ; final sep -31.2365 ecc -1 (random count 5) - Runaway v=(0,0,0) |v|=0 : companion v=(0,0,0), |v|=0 ; 15.7695 1.472 1.444 13 13 -31.236 -1.00 0.000 0.000 TYPE_CHNGE 15.7695 1.472 1.444 13 13 -31.236 -1.00 0.000 0.000 q-inv 15.7695 1.472 1.444 13 13 -31.236 -1.00 0.000 0.000 SN 15000.0000 1.472 1.444 13 13 -31.236 -1.00 0.000 0.000 MAX_TIME Probability : 1 %% Cell type:markdown id: tags: ### run binary with custom logging line %% Cell type:code id: tags: ``` python from binarycpython.utils import custom_logging_functions # generate logging lines. Here you can choose whatever you want to have logged, and with what header # this generates working print statements logging_line = custom_logging_functions.autogen_C_logging_code( {"MY_STELLAR_DATA": ["model.time", "star[0].mass"],} ) # OR # You can also decide to `write` your own logging_line, which allows you to write a more complex logging statement with conditionals. logging_line = 'Printf("MY_STELLAR_DATA time=%g mass=%g\\n", stardata->model.time, stardata->star[0].mass)' # Generate entire shared lib code around logging lines custom_logging_code = custom_logging_functions.binary_c_log_code(logging_line) # print(custom_logging_code) # Make this code into a shared library and the function into memory func_memaddr = custom_logging_functions.create_and_load_logging_function(custom_logging_code) # Run system with custom logging code m1 = 15.0 # Msun m2 = 14.0 # Msun separation = 0 # 0 = ignored, use period orbital_period = 4530.0 # days eccentricity = 0.0 metallicity = 0.02 max_evolution_time = 15000 # You need to set this! argstring = "binary_c M_1 {0:g} M_2 {1:g} separation {2:g} orbital_period {3:g} eccentricity {4:g} metallicity {5:g} max_evolution_time {6:g} ".format( m1, m2, separation, orbital_period, eccentricity, metallicity, max_evolution_time, ) output = binary_c_python_api.run_binary_custom_logging(argstring, func_memaddr) print('\n'.join(output.split('\n')[:20])) ``` %% Output example_header_1 time=0 mass_1=15 mass_2=14 st1=1 st2=1 sep=3540.3 ecc=0 example_header_2 0 15 14 1 1 3540.3 0 INITIAL_GRID 15 14 4530 0.02 1 0 MY_STELLAR_DATA time=0 mass=15 example_header_1 time=0 mass_1=15 mass_2=14 st1=1 st2=1 sep=3540.3 ecc=0 example_header_2 0 15 14 1 1 3540.3 0 INITIAL_GRID 15 14 4530 0.02 1 0 MY_STELLAR_DATA time=0 mass=15 example_header_1 time=1e-07 mass_1=15 mass_2=14 st1=1 st2=1 sep=3540.3 ecc=0 example_header_2 1e-07 15 14 1 1 3540.3 0 MY_STELLAR_DATA time=1e-07 mass=15 example_header_1 time=2e-07 mass_1=15 mass_2=14 st1=1 st2=1 sep=3540.3 ecc=0 example_header_2 2e-07 15 14 1 1 3540.3 0 MY_STELLAR_DATA time=2e-07 mass=15 example_header_1 time=3e-07 mass_1=15 mass_2=14 st1=1 st2=1 sep=3540.3 ecc=0 example_header_2 3e-07 15 14 1 1 3540.3 0 MY_STELLAR_DATA time=3e-07 mass=15 example_header_1 time=4e-07 mass_1=15 mass_2=14 st1=1 st2=1 sep=3540.3 ecc=0 example_header_2 4e-07 15 14 1 1 3540.3 0 MY_STELLAR_DATA time=4e-07 mass=15 %% Cell type:markdown id: tags: ## Using utils functions In the utils.functions there are some functions that make it easier to interact with the core api functions. %% Cell type:markdown id: tags: ### run_system() This function serves as an example on the function run_system and parse_output. There is more functionality with this method and several tasks are done behind the scene. Requires pandas, numpy to run. run_system: mostly just makes passing arguments to the function easier. It also loads all the necessary defaults in the background parse_output: Takes the raw output of binary_c and selects those lines that start with the given header. Note, if you dont use the custom_logging functionality binary_c should be configured to have output that starts with that given header The parsing of the output only works correctly if either all of the values are described inline like `mass=<number>' or none of them are. %% Cell type:code id: tags: ``` python from binarycpython.utils.functions import run_system, parse_output import pandas as pd import numpy as np # Run system. all arguments can be given as optional arguments. output = run_system(M_1=10, M_2=20, separation=0, orbital_period=100000000000) print('\n'.join(output.split('\n')[:10])) # Catch results that start with a given header. (Mind that binary_c has to be configured to print them if your not using a custom logging function) result_example_header_1 = parse_output(output, selected_header="example_header_1") result_example_header_2 = parse_output(output, selected_header="example_header_2") # print(result_example_header_1) #### Now do whatever you want with it: # Or put them into a pandas array # Cast the data into a dataframe. # This example automatically catches the column names because the binary_c output line is constructed as 'example_header_1 time=<number>..' print('\n\n') df = pd.DataFrame.from_dict(result_example_header_1, dtype=np.float64) print(df) # This example has column headers which are numbered, but we can override that with custom headers. df2 = pd.DataFrame.from_dict(result_example_header_2, dtype=np.float64) df2.columns=['time', 'mass_1', 'mass_2', 'st1', 'st2', 'sep', 'ecc'] print(df2) ``` %% Output example_header_1 time=0 mass_1=10 mass_2=20 st1=1 st2=1 sep=2.81762e+08 ecc=0 example_header_2 0 10 20 1 1 2.81762e+08 0 INITIAL_GRID 10 20 1e+11 0.02 1 0 example_header_1 time=0 mass_1=10 mass_2=20 st1=1 st2=1 sep=2.81762e+08 ecc=0 example_header_2 0 10 20 1 1 2.81762e+08 0 INITIAL_GRID 10 20 1e+11 0.02 1 0 example_header_1 time=1e-07 mass_1=10 mass_2=20 st1=1 st2=1 sep=2.81762e+08 ecc=0 example_header_2 1e-07 10 20 1 1 2.81762e+08 0 example_header_1 time=2e-07 mass_1=10 mass_2=20 st1=1 st2=1 sep=2.81762e+08 ecc=0 example_header_2 2e-07 10 20 1 1 2.81762e+08 0 time mass_1 mass_2 st1 st2 sep ecc 0 0.000000e+00 10.00000 20.00000 1.0 1.0 2.817620e+08 0.0 1 0.000000e+00 10.00000 20.00000 1.0 1.0 2.817620e+08 0.0 2 1.000000e-07 10.00000 20.00000 1.0 1.0 2.817620e+08 0.0 3 2.000000e-07 10.00000 20.00000 1.0 1.0 2.817620e+08 0.0 4 3.000000e-07 10.00000 20.00000 1.0 1.0 2.817620e+08 0.0 ... ... ... ... ... ... ... ... 3927 1.102750e+04 1.33817 1.62124 13.0 13.0 -1.705700e+01 -1.0 3928 1.202750e+04 1.33817 1.62124 13.0 13.0 -1.705700e+01 -1.0 3929 1.302750e+04 1.33817 1.62124 13.0 13.0 -1.705700e+01 -1.0 3930 1.402750e+04 1.33817 1.62124 13.0 13.0 -1.705700e+01 -1.0 3931 1.500000e+04 1.33817 1.62124 13.0 13.0 -1.705700e+01 -1.0 3927 1.102750e+04 1.33817 1.62124 13.0 13.0 -4.896110e+01 -1.0 3928 1.202750e+04 1.33817 1.62124 13.0 13.0 -4.896110e+01 -1.0 3929 1.302750e+04 1.33817 1.62124 13.0 13.0 -4.896110e+01 -1.0 3930 1.402750e+04 1.33817 1.62124 13.0 13.0 -4.896110e+01 -1.0 3931 1.500000e+04 1.33817 1.62124 13.0 13.0 -4.896110e+01 -1.0 [3932 rows x 7 columns] time mass_1 mass_2 st1 st2 sep ecc 0 0.000000e+00 10.00000 20.00000 1.0 1.0 2.817620e+08 0.0 1 0.000000e+00 10.00000 20.00000 1.0 1.0 2.817620e+08 0.0 2 1.000000e-07 10.00000 20.00000 1.0 1.0 2.817620e+08 0.0 3 2.000000e-07 10.00000 20.00000 1.0 1.0 2.817620e+08 0.0 4 3.000000e-07 10.00000 20.00000 1.0 1.0 2.817620e+08 0.0 ... ... ... ... ... ... ... ... 3927 1.102750e+04 1.33817 1.62124 13.0 13.0 -1.705700e+01 -1.0 3928 1.202750e+04 1.33817 1.62124 13.0 13.0 -1.705700e+01 -1.0 3929 1.302750e+04 1.33817 1.62124 13.0 13.0 -1.705700e+01 -1.0 3930 1.402750e+04 1.33817 1.62124 13.0 13.0 -1.705700e+01 -1.0 3931 1.500000e+04 1.33817 1.62124 13.0 13.0 -1.705700e+01 -1.0 3927 1.102750e+04 1.33817 1.62124 13.0 13.0 -4.896110e+01 -1.0 3928 1.202750e+04 1.33817 1.62124 13.0 13.0 -4.896110e+01 -1.0 3929 1.302750e+04 1.33817 1.62124 13.0 13.0 -4.896110e+01 -1.0 3930 1.402750e+04 1.33817 1.62124 13.0 13.0 -4.896110e+01 -1.0 3931 1.500000e+04 1.33817 1.62124 13.0 13.0 -4.896110e+01 -1.0 [3932 rows x 7 columns] %% Cell type:markdown id: tags: ### run_system() and custom logging Function that will use a automatically generated piece of logging code. Compile it, load it into memory and run a binary system. See run_system on how several things are done in the background here. %% Cell type:code id: tags: ``` python from binarycpython.utils.custom_logging_functions import ( autogen_C_logging_code, binary_c_log_code, ) import pandas as pd import numpy as np # generate logging lines. Here you can choose whatever you want to have logged, and with what header # this generates working print statements logging_line = autogen_C_logging_code( {"MY_STELLAR_DATA": ["model.time", "star[0].mass"],} ) # OR # You can also decide to `write` your own logging_line, which allows you to write a more complex logging statement with conditionals. logging_line = 'Printf("MY_STELLAR_DATA time=%g mass=%g\\n", stardata->model.time, stardata->star[0].mass)' # Generate entire shared lib code around logging lines custom_logging_code = binary_c_log_code(logging_line) # Run system. all arguments can be given as optional arguments. the custom_logging_code is one of them and will be processed automatically. output = run_system( M_1=1, metallicity=0.002, M_2=0.1, separation=0, orbital_period=100000000000, custom_logging_code=custom_logging_code, ) # Catch results that start with a given header. (Mind that binary_c has to be configured to print them if your not using a custom logging function) # DOESNT WORK YET if you have the line autogenerated. result_example_header = parse_output(output, "MY_STELLAR_DATA") # Cast the data into a dataframe. df = pd.DataFrame.from_dict(result_example_header, dtype=np.float64) # Do whatever you like with the dataframe. print(df) ``` %% Output time mass 0 0.000000e+00 1.000000 1 0.000000e+00 1.000000 2 1.000000e-07 1.000000 3 2.000000e-07 1.000000 4 3.000000e-07 1.000000 ... ... ... 3630 1.131680e+04 0.627748 3631 1.231680e+04 0.627748 3632 1.331680e+04 0.627748 3633 1.431680e+04 0.627748 3634 1.500000e+04 0.627748 [3635 rows x 2 columns] %% Cell type:markdown id: tags: ## Other example Checking how much mass stars lose on the main sequence. %% Cell type:code id: tags: ``` python def run_and_calc_mass(**kwargs): """ Function to run a given system and look at the mass lost in the main sequence of the star """ # start = time.time() output = run_system(**kwargs) result = parse_output(output, 'example_header_1') # stop = time.time() # print("Took {:.2f}s to run single system".format(stop-start)) # print("The following keys are present in the results:\n{}".format(result.keys())) # print(len(result)) #### Now do whatever you want with it: # Cast the data into a dataframe. df = pd.DataFrame.from_dict(result, dtype=np.float64) # Get last change moment last_st = df['st1'].unique()[-1] last_stellar_type_change_time_1 = df[df.st1==last_st]['time'].iloc[0] # slice to get that last time sliced_df = df[df.time < last_stellar_type_change_time_1] # Cut off late parts of evolution main_sequence = sliced_df[sliced_df.st1==1] initial_mass = main_sequence.iloc[0].mass_1 final_mass = main_sequence.iloc[-1].mass_1 initial_time = main_sequence.iloc[0].time final_time = main_sequence.iloc[-1].time mass_lost = initial_mass - final_mass fraction = mass_lost/initial_mass # Return the mass fraction (wrt initial mass) return fraction ``` %% Cell type:code id: tags: ``` python import time metallicity_002 = 0.02 metallicity_001 = 0.01 metallicity_0002 = 0.002 mass_range = np.arange(1, 25, .5) start = time.time() fractions_z002 = [run_and_calc_mass(M_1=mass, M_2=10, separation=0, orbital_period=100000000000, metallicity=metallicity_002, effective_metallicity=metallicity_002) for mass in mass_range] fractions_z001 = [run_and_calc_mass(M_1=mass, M_2=10, separation=0, orbital_period=100000000000, metallicity=metallicity_001, effective_metallicity=metallicity_001) for mass in mass_range] fractions_z0002 = [run_and_calc_mass(M_1=mass, M_2=10, separation=0, orbital_period=100000000000, metallicity=metallicity_0002, effective_metallicity=metallicity_0002) for mass in mass_range] stop = time.time() print("Took {}s".format(stop-start)) ``` %% Output Took 12.005768775939941s Took 14.214274644851685s %% Cell type:code id: tags: ``` python import matplotlib.pyplot as plt fig, ax = plt.subplots(nrows=1, ncols=1, figsize=(12,8)) ax.plot(mass_range, fractions_z002, '--', label='Z=0.02') ax.plot(mass_range, fractions_z001, '-.', label='Z=0.01') ax.plot(mass_range, fractions_z0002, '-', label='Z=0.002') ax.set_xlabel(r'Initial Mass ($M_{\odot}$)', fontsize=18) ax.set_ylabel(r'Fraction of total initial mass lost on main sequence', fontsize=18) ax.set_title('Fraction of total initial mass lost during main sequence for different metallicities', fontsize=18) ax.legend() ax.set_yscale('log') #save_loop(name='plots/mass_loss_MS.{format}', formats=['pdf', 'png', 'eps'], bbox_inches='tight') plt.show() ``` %% Output %% Cell type:code id: tags: ``` python ``` examples/notebooks/workshop_example_notebook.ipynb +48 −49 File changed.Preview size limit exceeded, changes collapsed. 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binarycpython/utils/#functions.py#deleted 100644 → 0 +0 −198 Original line number Diff line number Diff line from collections import defaultdict import binary_c from binarycpython.binaryc_python_utils from binaryc_python_utils.custom_logging_functions import ( create_and_load_logging_function, ) def create_arg_string(arg_dict): """ Function that creates the arg string """ arg_string = "" for key in arg_dict.keys(): arg_string += "{key} {value} ".format(key=key, value=arg_dict[key]) arg_string = arg_string.strip() return arg_string def get_defaults(): """ Function that calls the binaryc get args function and cast it into a dictionary All the values are strings """ default_output = binary_c.return_arglines() default_dict = {} for default in default_output.split("\n"): if not default in ["__ARG_BEGIN", "__ARG_END", ""]: key, value = default.split(" = ") # Filter out NULLS (not compiled anyway) if not value in ["NULL", "Function"]: if not value == "": default_dict[key] = value return default_dict def get_arg_keys(): """ Function that return the list of possible keys to give in the arg string """ return get_defaults().keys() def run_system(**kwargs): """ Wrapper to run a system with settings This function determines which underlying python-c api function will be called based upon the arguments that are passed via kwargs. - if custom_logging_code or custom_logging_dict is included in the kwargs then it will - if """ # Load default args args = get_defaults() if "custom_logging_code" in kwargs: # Use kwarg value to override defaults and add new args for key in kwargs.keys(): if not key == "custom_logging_code": args[key] = kwargs[key] # Generate library and get memaddr func_memaddr = create_and_load_logging_function(kwargs["custom_logging_code"]) # Construct arguments string and final execution string arg_string = create_arg_string(args) arg_string = "binary_c {}".format(arg_string) # Run it and get output output = binary_c.run_binary_custom_logging(arg_string, func_memaddr) return output elif "log_filename" in kwargs: # Use kwarg value to override defaults and add new args for key in kwargs.keys(): args[key] = kwargs[key] # Construct arguments string and final execution string arg_string = create_arg_string(args) arg_string = "binary_c {}".format(arg_string) # Run it and get output output = binary_c.run_binary_with_logfile(arg_string) return output else: # run the plain basic type # Use kwarg value to override defaults and add new args for key in kwargs.keys(): args[key] = kwargs[key] # Construct arguments string and final execution string arg_string = create_arg_string(args) arg_string = "binary_c {}".format(arg_string) # Run it and get output output = binary_c.run_binary(arg_string) return output def run_system_with_log(**kwargs): """ Wrapper to run a system with settings AND logs the files to a designated place defined by the log_filename parameter. """ # Load default args args = get_defaults() # args = {} # For example # physics_args['M_1'] = 20 # physics_args['separation'] = 0 # 0 = ignored, use period # physics_args['orbital_period'] = 100000000000 # To make it single # Use kwarg value to override defaults and add new args for key in kwargs.keys(): args[key] = kwargs[key] # Construct arguments string and final execution string arg_string = create_arg_string(args) arg_string = "binary_c {}".format(arg_string) # print(arg_string) # Run it and get output buffer = "" output = binary_c.run_binary_with_log(arg_string) return output def parse_output(output, selected_header): """ Function that parses output of binary_c: This function works in two cases: if the caught line contains output like 'example_header time=12.32 mass=0.94 ..' or if the line contains output like 'example_header 12.32 0.94' You can give a 'selected_header' to catch any line that starts with that. Then the values will be put into a dictionary. TODO: Think about exporting to numpy array or pandas instead of a defaultdict """ value_dicts = [] val_lists = [] # split output on newlines for i, line in enumerate(output.split("\n")): # Skip any blank lines if not line == "": split_line = line.split() # Select parts header = split_line[0] values_list = split_line[1:] # print(values_list) # Catch line starting with selected header if header == selected_header: # Check if the line contains '=' symbols: value_dict = {} if all('=' in el for el in values_list): for el in values_list: key, val = el.split("=") value_dict[key.strip()] = val.strip() value_dicts.append(value_dict) else: if any('=' in el for el in values_list): raise ValueError('Caught line contains some = symbols but not all of them do. aborting run') else: for i, val in enumerate(values_list): value_dict[i] = val value_dicts.append(value_dict) if len(value_dicts) == 0: print( "Sorry, didnt find any line matching your header {}".format(selected_header) ) return None keys = value_dicts[0].keys() # Construct final dict. final_values_dict = defaultdict(list) for value_dict in value_dicts: for key in keys: final_values_dict[key].append(value_dict[key]) return final_values_dict
examples/notebooks/.ipynb_checkpoints/workshop_example_notebook-checkpoint.ipynb +32 −33 Original line number Diff line number Diff line %% Cell type:markdown id: tags: # Binary_c and python example notebook The following notebook servers as an example of how the binary_c python wrapper works and how it could be used. By: David Hendriks 30 nov 2019 %% Cell type:code id: tags: ``` python import binarycpython import binary_c_python_api ``` %% Cell type:markdown id: tags: ## Core api wrapper functions: %% Cell type:markdown id: tags: ### run_binary() %% Cell type:code id: tags: ``` python m1 = 15.0 # Msun m2 = 14.0 # Msun separation = 0 # 0 = ignored, use period orbital_period = 4530.0 # days eccentricity = 0.0 metallicity = 0.02 max_evolution_time = 15000 # You need to set this! argstring = "binary_c M_1 {0:g} M_2 {1:g} separation {2:g} orbital_period {3:g} eccentricity {4:g} metallicity {5:g} max_evolution_time {6:g} ".format( m1, m2, separation, orbital_period, eccentricity, metallicity, max_evolution_time, ) output = binary_c_python_api.run_binary(argstring) print("\n\nBinary_c output:\n\n") print('\n'.join(output.split('\n')[:10])) ``` %% Output Binary_c output: example_header_1 time=0 mass_1=15 mass_2=14 st1=1 st2=1 sep=3540.3 ecc=0 example_header_2 0 15 14 1 1 3540.3 0 INITIAL_GRID 15 14 4530 0.02 1 0 example_header_1 time=0 mass_1=15 mass_2=14 st1=1 st2=1 sep=3540.3 ecc=0 example_header_2 0 15 14 1 1 3540.3 0 INITIAL_GRID 15 14 4530 0.02 1 0 example_header_1 time=1e-07 mass_1=15 mass_2=14 st1=1 st2=1 sep=3540.3 ecc=0 example_header_2 1e-07 15 14 1 1 3540.3 0 example_header_1 time=2e-07 mass_1=15 mass_2=14 st1=1 st2=1 sep=3540.3 ecc=0 example_header_2 2e-07 15 14 1 1 3540.3 0 %% Cell type:markdown id: tags: ### run_binary_with_log %% Cell type:code id: tags: ``` python import tempfile import os m1 = 15.0 # Msun m2 = 14.0 # Msun separation = 0 # 0 = ignored, use period orbital_period = 4530.0 # days eccentricity = 0.0 metallicity = 0.02 max_evolution_time = 15000 # You need to set this! log_filename=tempfile.gettempdir() + "/test_log.txt" argstring = "binary_c M_1 {0:g} M_2 {1:g} separation {2:g} orbital_period {3:g} eccentricity {4:g} metallicity {5:g} max_evolution_time {6:g} log_filename {7} ".format( m1, m2, separation, orbital_period, eccentricity, metallicity, max_evolution_time, log_filename, ) output = binary_c_python_api.run_binary(argstring) print(os.path.exists(log_filename)) with open(log_filename, 'r') as f: print(f.read()) # print("\n\nBinary_c output:\n\n") # print(output) ``` %% Output True TIME M1 M2 K1 K2 SEP ECC R1/ROL1 R2/ROL2 TYPE RANDOM_SEED=1748 RANDOM_COUNT=0 0.0000 10.000 20.000 1 1 2.8176e+08 0.00 0.000 0.000 INITIAL 8.8656 9.980 19.203 1 2 2.8966e+08 0.00 0.000 0.000 TYPE_CHNGE 8.8814 9.980 19.185 1 4 2.8983e+08 0.00 0.000 0.000 TYPE_CHNGE 9.8724 9.977 10.122 1 5 4.2066e+08 0.00 0.000 0.000 TYPE_CHNGE 9.8834 9.977 9.974 1 5 4.2379e+08 0.00 0.000 0.000 q-inv 9.8901 9.977 1.621 1 13 -125.89 -1.00 0.000 0.000 Randbuf=42123 - d48r(0)=0.976476 - d48r(1)=0.214027 - d48r(2)=0.638803 - d48r(3)=0.00325497 - d48r(4)=0.931833 9.8901 9.977 1.621 1 13 -125.89 -1.00 0.000 0.000 SN kick II (SN type 12 12, pre-explosion M=8.50996 Mc=6.81718 type=5) -> kick 1(190) vk=132.601 vr=0.0878271 omega=5.85488 phi=-1.45663 -> vn=132.592 ; final sep -125.894 ecc -1 (random count 0) - Runaway v=(0,0,0) |v|=0 : companion v=(0,0,0), |v|=0 ; 9.8901 9.977 1.621 1 13 -125.89 -1.00 0.000 0.000 TYPE_CHNGE 9.8901 9.977 1.621 1 13 -125.89 -1.00 0.000 0.000 DISRUPT 9.8901 9.977 1.621 1 13 -125.89 -1.00 0.000 0.000 SN 24.4615 9.890 1.621 2 13 -125.89 -1.00 0.000 0.000 OFF_MS 24.4615 9.890 1.621 2 13 -125.89 -1.00 0.000 0.000 TYPE_CHNGE 24.5257 9.887 1.621 3 13 -125.89 -1.00 0.000 0.000 TYPE_CHNGE 24.5353 9.886 1.621 4 13 -125.89 -1.00 0.000 0.000 TYPE_CHNGE 27.3558 9.424 1.621 5 13 -125.89 -1.00 0.000 0.000 TYPE_CHNGE 27.4616 1.338 1.621 13 13 -125.89 -1.00 0.000 0.000 d48r(5)=0.99127 - d48r(6)=0.231093 - d48r(7)=0.881928 - d48r(8)=0.603217 27.4616 1.338 1.621 13 13 -125.89 -1.00 0.000 0.000 SN kick II (SN type 12 12, pre-explosion M=9.30206 Mc=2.87012 type=5) -> kick 1(190) vk=663.531 vr=0 omega=3.79013 phi=0.869266 -> vn=663.531 ; final sep -125.894 ecc -1 (random count 5) - Runaway v=(0,0,0) |v|=0 : companion v=(0,0,0), |v|=0 ; 27.4616 1.338 1.621 13 13 -125.89 -1.00 0.000 0.000 TYPE_CHNGE 27.4616 1.338 1.621 13 13 -125.89 -1.00 0.000 0.000 q-inv 27.4616 1.338 1.621 13 13 -125.89 -1.00 0.000 0.000 SN 15000.0000 1.338 1.621 13 13 -125.89 -1.00 0.000 0.000 MAX_TIME TIME M1 M2 K1 K2 SEP ECC R1/ROL1 R2/ROL2 TYPE RANDOM_SEED=7106 RANDOM_COUNT=0 0.0000 15.000 14.000 1 1 2.786e+08 0.00 0.000 0.000 INITIAL 12.7509 14.645 13.776 2 1 2.8427e+08 0.00 0.000 0.000 TYPE_CHNGE 12.7773 14.639 13.775 4 1 2.8435e+08 0.00 0.000 0.000 TYPE_CHNGE 13.1380 13.748 13.758 4 1 2.9373e+08 0.00 0.000 0.000 q-inv 14.0900 10.830 13.705 4 2 3.2934e+08 0.00 0.000 0.000 OFF_MS 14.0900 10.830 13.705 4 2 3.2934e+08 0.00 0.000 0.000 TYPE_CHNGE 14.1204 10.726 13.700 4 4 3.3081e+08 0.00 0.000 0.000 TYPE_CHNGE 14.2118 10.410 13.566 5 4 3.3702e+08 0.00 0.000 0.000 TYPE_CHNGE 14.2646 1.472 13.462 13 4 -31.236 -1.00 0.000 0.000 Randbuf=34421 - d48r(0)=0.0570946 - d48r(1)=0.458272 - d48r(2)=0.13108 - d48r(3)=0.562029 - d48r(4)=0.924056 14.2646 1.472 13.462 13 4 -31.236 -1.00 0.000 0.000 SN kick II (SN type 12 12, pre-explosion M=9.89211 Mc=4.78817 type=5) -> kick 1(190) vk=302.148 vr=0.113492 omega=5.80602 phi=0.124379 -> vn=302.048 ; final sep -31.2365 ecc -1 (random count 0) - Runaway v=(0,0,0) |v|=0 : companion v=(0,0,0), |v|=0 ; 14.2646 1.472 13.462 13 4 -31.236 -1.00 0.000 0.000 TYPE_CHNGE 14.2646 1.472 13.462 13 4 -31.236 -1.00 0.000 0.000 DISRUPT 14.2646 1.472 13.462 13 4 -31.236 -1.00 0.000 0.000 SN 15.7087 1.472 10.210 13 5 -31.236 -1.00 0.000 0.000 TYPE_CHNGE 15.7695 1.472 1.444 13 13 -31.236 -1.00 0.000 0.000 d48r(5)=0.608402 - d48r(6)=0.696003 - d48r(7)=0.796455 - d48r(8)=0.0834973 15.7695 1.472 1.444 13 13 -31.236 -1.00 0.000 0.000 SN kick II (SN type 12 12, pre-explosion M=9.85661 Mc=4.3914 type=5) -> kick 1(190) vk=392.156 vr=0 omega=0.524629 phi=0.634667 -> vn=392.156 ; final sep -31.2365 ecc -1 (random count 5) - Runaway v=(0,0,0) |v|=0 : companion v=(0,0,0), |v|=0 ; 15.7695 1.472 1.444 13 13 -31.236 -1.00 0.000 0.000 TYPE_CHNGE 15.7695 1.472 1.444 13 13 -31.236 -1.00 0.000 0.000 q-inv 15.7695 1.472 1.444 13 13 -31.236 -1.00 0.000 0.000 SN 15000.0000 1.472 1.444 13 13 -31.236 -1.00 0.000 0.000 MAX_TIME Probability : 1 %% Cell type:markdown id: tags: ### run binary with custom logging line %% Cell type:code id: tags: ``` python from binarycpython.utils import custom_logging_functions # generate logging lines. Here you can choose whatever you want to have logged, and with what header # this generates working print statements logging_line = custom_logging_functions.autogen_C_logging_code( {"MY_STELLAR_DATA": ["model.time", "star[0].mass"],} ) # OR # You can also decide to `write` your own logging_line, which allows you to write a more complex logging statement with conditionals. logging_line = 'Printf("MY_STELLAR_DATA time=%g mass=%g\\n", stardata->model.time, stardata->star[0].mass)' # Generate entire shared lib code around logging lines custom_logging_code = custom_logging_functions.binary_c_log_code(logging_line) # print(custom_logging_code) # Make this code into a shared library and the function into memory func_memaddr = custom_logging_functions.create_and_load_logging_function(custom_logging_code) # Run system with custom logging code m1 = 15.0 # Msun m2 = 14.0 # Msun separation = 0 # 0 = ignored, use period orbital_period = 4530.0 # days eccentricity = 0.0 metallicity = 0.02 max_evolution_time = 15000 # You need to set this! argstring = "binary_c M_1 {0:g} M_2 {1:g} separation {2:g} orbital_period {3:g} eccentricity {4:g} metallicity {5:g} max_evolution_time {6:g} ".format( m1, m2, separation, orbital_period, eccentricity, metallicity, max_evolution_time, ) output = binary_c_python_api.run_binary_custom_logging(argstring, func_memaddr) print('\n'.join(output.split('\n')[:20])) ``` %% Output example_header_1 time=0 mass_1=15 mass_2=14 st1=1 st2=1 sep=3540.3 ecc=0 example_header_2 0 15 14 1 1 3540.3 0 INITIAL_GRID 15 14 4530 0.02 1 0 MY_STELLAR_DATA time=0 mass=15 example_header_1 time=0 mass_1=15 mass_2=14 st1=1 st2=1 sep=3540.3 ecc=0 example_header_2 0 15 14 1 1 3540.3 0 INITIAL_GRID 15 14 4530 0.02 1 0 MY_STELLAR_DATA time=0 mass=15 example_header_1 time=1e-07 mass_1=15 mass_2=14 st1=1 st2=1 sep=3540.3 ecc=0 example_header_2 1e-07 15 14 1 1 3540.3 0 MY_STELLAR_DATA time=1e-07 mass=15 example_header_1 time=2e-07 mass_1=15 mass_2=14 st1=1 st2=1 sep=3540.3 ecc=0 example_header_2 2e-07 15 14 1 1 3540.3 0 MY_STELLAR_DATA time=2e-07 mass=15 example_header_1 time=3e-07 mass_1=15 mass_2=14 st1=1 st2=1 sep=3540.3 ecc=0 example_header_2 3e-07 15 14 1 1 3540.3 0 MY_STELLAR_DATA time=3e-07 mass=15 example_header_1 time=4e-07 mass_1=15 mass_2=14 st1=1 st2=1 sep=3540.3 ecc=0 example_header_2 4e-07 15 14 1 1 3540.3 0 MY_STELLAR_DATA time=4e-07 mass=15 %% Cell type:markdown id: tags: ## Using utils functions In the utils.functions there are some functions that make it easier to interact with the core api functions. %% Cell type:markdown id: tags: ### run_system() This function serves as an example on the function run_system and parse_output. There is more functionality with this method and several tasks are done behind the scene. Requires pandas, numpy to run. run_system: mostly just makes passing arguments to the function easier. It also loads all the necessary defaults in the background parse_output: Takes the raw output of binary_c and selects those lines that start with the given header. Note, if you dont use the custom_logging functionality binary_c should be configured to have output that starts with that given header The parsing of the output only works correctly if either all of the values are described inline like `mass=<number>' or none of them are. %% Cell type:code id: tags: ``` python from binarycpython.utils.functions import run_system, parse_output import pandas as pd import numpy as np # Run system. all arguments can be given as optional arguments. output = run_system(M_1=10, M_2=20, separation=0, orbital_period=100000000000) print('\n'.join(output.split('\n')[:10])) # Catch results that start with a given header. (Mind that binary_c has to be configured to print them if your not using a custom logging function) result_example_header_1 = parse_output(output, selected_header="example_header_1") result_example_header_2 = parse_output(output, selected_header="example_header_2") # print(result_example_header_1) #### Now do whatever you want with it: # Or put them into a pandas array # Cast the data into a dataframe. # This example automatically catches the column names because the binary_c output line is constructed as 'example_header_1 time=<number>..' print('\n\n') df = pd.DataFrame.from_dict(result_example_header_1, dtype=np.float64) print(df) # This example has column headers which are numbered, but we can override that with custom headers. df2 = pd.DataFrame.from_dict(result_example_header_2, dtype=np.float64) df2.columns=['time', 'mass_1', 'mass_2', 'st1', 'st2', 'sep', 'ecc'] print(df2) ``` %% Output example_header_1 time=0 mass_1=10 mass_2=20 st1=1 st2=1 sep=2.81762e+08 ecc=0 example_header_2 0 10 20 1 1 2.81762e+08 0 INITIAL_GRID 10 20 1e+11 0.02 1 0 example_header_1 time=0 mass_1=10 mass_2=20 st1=1 st2=1 sep=2.81762e+08 ecc=0 example_header_2 0 10 20 1 1 2.81762e+08 0 INITIAL_GRID 10 20 1e+11 0.02 1 0 example_header_1 time=1e-07 mass_1=10 mass_2=20 st1=1 st2=1 sep=2.81762e+08 ecc=0 example_header_2 1e-07 10 20 1 1 2.81762e+08 0 example_header_1 time=2e-07 mass_1=10 mass_2=20 st1=1 st2=1 sep=2.81762e+08 ecc=0 example_header_2 2e-07 10 20 1 1 2.81762e+08 0 time mass_1 mass_2 st1 st2 sep ecc 0 0.000000e+00 10.00000 20.00000 1.0 1.0 2.817620e+08 0.0 1 0.000000e+00 10.00000 20.00000 1.0 1.0 2.817620e+08 0.0 2 1.000000e-07 10.00000 20.00000 1.0 1.0 2.817620e+08 0.0 3 2.000000e-07 10.00000 20.00000 1.0 1.0 2.817620e+08 0.0 4 3.000000e-07 10.00000 20.00000 1.0 1.0 2.817620e+08 0.0 ... ... ... ... ... ... ... ... 3927 1.102750e+04 1.33817 1.62124 13.0 13.0 -1.705700e+01 -1.0 3928 1.202750e+04 1.33817 1.62124 13.0 13.0 -1.705700e+01 -1.0 3929 1.302750e+04 1.33817 1.62124 13.0 13.0 -1.705700e+01 -1.0 3930 1.402750e+04 1.33817 1.62124 13.0 13.0 -1.705700e+01 -1.0 3931 1.500000e+04 1.33817 1.62124 13.0 13.0 -1.705700e+01 -1.0 3927 1.102750e+04 1.33817 1.62124 13.0 13.0 -4.896110e+01 -1.0 3928 1.202750e+04 1.33817 1.62124 13.0 13.0 -4.896110e+01 -1.0 3929 1.302750e+04 1.33817 1.62124 13.0 13.0 -4.896110e+01 -1.0 3930 1.402750e+04 1.33817 1.62124 13.0 13.0 -4.896110e+01 -1.0 3931 1.500000e+04 1.33817 1.62124 13.0 13.0 -4.896110e+01 -1.0 [3932 rows x 7 columns] time mass_1 mass_2 st1 st2 sep ecc 0 0.000000e+00 10.00000 20.00000 1.0 1.0 2.817620e+08 0.0 1 0.000000e+00 10.00000 20.00000 1.0 1.0 2.817620e+08 0.0 2 1.000000e-07 10.00000 20.00000 1.0 1.0 2.817620e+08 0.0 3 2.000000e-07 10.00000 20.00000 1.0 1.0 2.817620e+08 0.0 4 3.000000e-07 10.00000 20.00000 1.0 1.0 2.817620e+08 0.0 ... ... ... ... ... ... ... ... 3927 1.102750e+04 1.33817 1.62124 13.0 13.0 -1.705700e+01 -1.0 3928 1.202750e+04 1.33817 1.62124 13.0 13.0 -1.705700e+01 -1.0 3929 1.302750e+04 1.33817 1.62124 13.0 13.0 -1.705700e+01 -1.0 3930 1.402750e+04 1.33817 1.62124 13.0 13.0 -1.705700e+01 -1.0 3931 1.500000e+04 1.33817 1.62124 13.0 13.0 -1.705700e+01 -1.0 3927 1.102750e+04 1.33817 1.62124 13.0 13.0 -4.896110e+01 -1.0 3928 1.202750e+04 1.33817 1.62124 13.0 13.0 -4.896110e+01 -1.0 3929 1.302750e+04 1.33817 1.62124 13.0 13.0 -4.896110e+01 -1.0 3930 1.402750e+04 1.33817 1.62124 13.0 13.0 -4.896110e+01 -1.0 3931 1.500000e+04 1.33817 1.62124 13.0 13.0 -4.896110e+01 -1.0 [3932 rows x 7 columns] %% Cell type:markdown id: tags: ### run_system() and custom logging Function that will use a automatically generated piece of logging code. Compile it, load it into memory and run a binary system. See run_system on how several things are done in the background here. %% Cell type:code id: tags: ``` python from binarycpython.utils.custom_logging_functions import ( autogen_C_logging_code, binary_c_log_code, ) import pandas as pd import numpy as np # generate logging lines. Here you can choose whatever you want to have logged, and with what header # this generates working print statements logging_line = autogen_C_logging_code( {"MY_STELLAR_DATA": ["model.time", "star[0].mass"],} ) # OR # You can also decide to `write` your own logging_line, which allows you to write a more complex logging statement with conditionals. logging_line = 'Printf("MY_STELLAR_DATA time=%g mass=%g\\n", stardata->model.time, stardata->star[0].mass)' # Generate entire shared lib code around logging lines custom_logging_code = binary_c_log_code(logging_line) # Run system. all arguments can be given as optional arguments. the custom_logging_code is one of them and will be processed automatically. output = run_system( M_1=1, metallicity=0.002, M_2=0.1, separation=0, orbital_period=100000000000, custom_logging_code=custom_logging_code, ) # Catch results that start with a given header. (Mind that binary_c has to be configured to print them if your not using a custom logging function) # DOESNT WORK YET if you have the line autogenerated. result_example_header = parse_output(output, "MY_STELLAR_DATA") # Cast the data into a dataframe. df = pd.DataFrame.from_dict(result_example_header, dtype=np.float64) # Do whatever you like with the dataframe. print(df) ``` %% Output time mass 0 0.000000e+00 1.000000 1 0.000000e+00 1.000000 2 1.000000e-07 1.000000 3 2.000000e-07 1.000000 4 3.000000e-07 1.000000 ... ... ... 3630 1.131680e+04 0.627748 3631 1.231680e+04 0.627748 3632 1.331680e+04 0.627748 3633 1.431680e+04 0.627748 3634 1.500000e+04 0.627748 [3635 rows x 2 columns] %% Cell type:markdown id: tags: ## Other example Checking how much mass stars lose on the main sequence. %% Cell type:code id: tags: ``` python def run_and_calc_mass(**kwargs): """ Function to run a given system and look at the mass lost in the main sequence of the star """ # start = time.time() output = run_system(**kwargs) result = parse_output(output, 'example_header_1') # stop = time.time() # print("Took {:.2f}s to run single system".format(stop-start)) # print("The following keys are present in the results:\n{}".format(result.keys())) # print(len(result)) #### Now do whatever you want with it: # Cast the data into a dataframe. df = pd.DataFrame.from_dict(result, dtype=np.float64) # Get last change moment last_st = df['st1'].unique()[-1] last_stellar_type_change_time_1 = df[df.st1==last_st]['time'].iloc[0] # slice to get that last time sliced_df = df[df.time < last_stellar_type_change_time_1] # Cut off late parts of evolution main_sequence = sliced_df[sliced_df.st1==1] initial_mass = main_sequence.iloc[0].mass_1 final_mass = main_sequence.iloc[-1].mass_1 initial_time = main_sequence.iloc[0].time final_time = main_sequence.iloc[-1].time mass_lost = initial_mass - final_mass fraction = mass_lost/initial_mass # Return the mass fraction (wrt initial mass) return fraction ``` %% Cell type:code id: tags: ``` python import time metallicity_002 = 0.02 metallicity_001 = 0.01 metallicity_0002 = 0.002 mass_range = np.arange(1, 25, .5) start = time.time() fractions_z002 = [run_and_calc_mass(M_1=mass, M_2=10, separation=0, orbital_period=100000000000, metallicity=metallicity_002, effective_metallicity=metallicity_002) for mass in mass_range] fractions_z001 = [run_and_calc_mass(M_1=mass, M_2=10, separation=0, orbital_period=100000000000, metallicity=metallicity_001, effective_metallicity=metallicity_001) for mass in mass_range] fractions_z0002 = [run_and_calc_mass(M_1=mass, M_2=10, separation=0, orbital_period=100000000000, metallicity=metallicity_0002, effective_metallicity=metallicity_0002) for mass in mass_range] stop = time.time() print("Took {}s".format(stop-start)) ``` %% Output Took 12.005768775939941s Took 14.214274644851685s %% Cell type:code id: tags: ``` python import matplotlib.pyplot as plt fig, ax = plt.subplots(nrows=1, ncols=1, figsize=(12,8)) ax.plot(mass_range, fractions_z002, '--', label='Z=0.02') ax.plot(mass_range, fractions_z001, '-.', label='Z=0.01') ax.plot(mass_range, fractions_z0002, '-', label='Z=0.002') ax.set_xlabel(r'Initial Mass ($M_{\odot}$)', fontsize=18) ax.set_ylabel(r'Fraction of total initial mass lost on main sequence', fontsize=18) ax.set_title('Fraction of total initial mass lost during main sequence for different metallicities', fontsize=18) ax.legend() ax.set_yscale('log') #save_loop(name='plots/mass_loss_MS.{format}', formats=['pdf', 'png', 'eps'], bbox_inches='tight') plt.show() ``` %% Output %% Cell type:code id: tags: ``` python ```
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