Flux diagram

Flux diagram/README.md

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+# Flux diagram
+This script simulates your Shock Tube system through different time intervals and creates flux diagrams with species molecule images.
+
+- Clone these scripts to a new folder: `Flux diagram`  <br><br>
+- In the Cantera environment in terminal, install `conda install -c conda-forge pdf2image` <br><br>
+- Copy from your RMG run the Cantera output `chem_annotated.cti` and paste it in the folder, (the given file is for running a test, so you can just rename it). <br><br>
+- Same with the species dictionary `species_dictionary.txt`, (the given file is for running a test, so you can just rename it).<br><br>
+- In the first code block in `cte_replace_labels_to_smiles v2.ipynb` change the 4 paths to your files' location. <br><br>
+- Change the initial operating conditions of your Shock Tube system in the first code block in `cte_replace_labels_to_smiles v2.ipynb`.<br><br>
+- Put attention to your system's elements. Cantera lables them as one thing and Smiles as another thing, you should consider that in the code itself.<br><br>
+For instance, Argon's label in `cti` file is `Ar`, but in Smiles its label is `[Ar]`. For elements, you should consider Cantera's notation. Two cases are considered in the script: `Ar` and `Ne`.<br><br>
+- Run the script `cte_replace_labels_to_smiles v2.ipynb` under Cantera environmemt.
+
+## Output:<br>
+Ignition delay time plot in the folder:<br><br>
+![Idt](idt_plot.png)<br><br>
+
+11 folder for 11 different times intervals: 
+0.5tau, 0.6tau...tau, 1.1tau,...1.5tau<br>
+In each folder you will find a `png` file which contains the flux diagram specified in theat time. <br><br>
+For example:<br><br> 
+![rxn_diagram_tau](ReactionPathDiagram.png)<br><br>

Flux diagram/background_script.py

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+import argparse
+import os
+import yaml
+
+from rmgpy.chemkin import load_species_dictionary
+from rmgpy.molecule.draw import MoleculeDrawer
+
+def parse_command_line_arguments(command_line_args=None):
+    """
+    Parse command-line arguments.
+
+    Args:
+        command_line_args: The command line arguments.
+
+    Returns:
+        The parsed command-line arguments by key words.
+    """
+
+    parser = argparse.ArgumentParser(description='desc')
+    parser.add_argument('file', metavar='FILE', type=str, nargs=1,
+                        help='a file describing the job to execute')
+
+    args = parser.parse_args(command_line_args)
+    args.file = args.file[0]
+
+    return args
+
+
+def dict_species(path_species_dict):
+    """
+    This fucn creates an output.yml file of cantera_labels as keys
+    and smiles as values.
+    After that, it creates a folder of images of the species of pdf format (high resolution)
+    The name of the images are {smiles}.pdf
+    """
+    #######output.yml#######
+    dir_name=os.path.dirname(path_species_dict)
+    species_dict=load_species_dictionary(path_species_dict)
+    #generate_resonance_structures=False)
+    dict_label_smiles={species.label: species.molecule[0].to_smiles() for species in species_dict.values()}
+
+    path_output_yml=os.path.join(dir_name,"output.yml")
+    yaml_str = yaml.dump(data=dict_label_smiles)
+    with open(path_output_yml, 'w') as f:
+        f.write(yaml_str)
+
+    #######species images#######
+    if not os.path.exists(os.path.join(os.path.abspath(''),"images")): #check whether images folder exists
+        images_path=os.path.join(os.path.abspath(''),'images')
+        os.mkdir(images_path)
+        os.chdir(images_path)
+
+    else: #images folder exists
+        if "images" not in os.getcwd(): #can be Flux diagram folder or species_dictionary.txt file inside Flux folder -> check the 2 options
+            if "species_dictionary" in os.getcwd():
+                os.chdir(os.path.join(os.chdir("../"),"images"))
+            else:
+                os.chdir(os.path.join(os.getcwd(),"images"))
+        else:
+            pass #we are probably in the right filder of images
+
+    print("the images path: ",os.path.abspath(''))
+
+    for specie in species_dict.values():
+        molecule=specie.molecule[0]
+        smiles=molecule.to_smiles() 
+        if smiles != "[Ne]" and smiles != "[Ar]": #avoid parenthesis for elements - keep convention with Cantera
+            MoleculeDrawer().draw(molecule, file_format='pdf', target=f'{smiles}.pdf')
+        else:
+            if smiles=="[Ne]":
+                MoleculeDrawer().draw(molecule, file_format='pdf', target='Ne.pdf')
+            else:
+                MoleculeDrawer().draw(molecule, file_format='pdf', target='Ar.pdf')
+
+
+def main():
+    """
+    The main ARC executable function
+    """
+    args = parse_command_line_arguments()
+
+    if "images" in os.getcwd():
+        os.chdir("../") #go back one folder back in current working dir path
+
+    path=os.path.normpath(os.getcwd() )
+    path_species_dict = os.path.join(path,'species_dictionary.txt')
+
+    dict_species(path_species_dict)
+
+if __name__ == '__main__':
+    main()