Question about Creating an Automated Process in Python

[Supratik1234]

Hi everyone, I am very new to Python so I don't know a lot about coding whatsoever but I am a part of a research group involved in ab initio md. For this python script, we are trying to find O-H distance between two different molecules using a XYZ file with 50 time steps of a reaction run through NWChem. I had to individually type "OX" and "HX" to specify which oxygen and hydrogen atoms I wanted to use to measure the distance between them for each time step (50 total). So I had to write "OX" 50 times for the specific oxygen I wanted to use. Is there any way to automate this process, so I can just choose the oxygen I want in the first time step and that will apply to all of them? I have attached an image of the python script to show everyone what I have as of right now! Please let me know and thank you in advance.

import os
import os.path
import matplotlib.pyplot as plt
import time as ti
import numpy as np

def main(): 
    data_folder = os.path.join("OHNWCHEM")
    file_input = "T3Fmolecule copy.xyz"
    data_file = os.path.join(data_folder, file_input)
    
    ts = []
    Hs = []
    Os = []
    
    #Opens a file, goes through every line, and pulls the Ns and Os
    with open(data_file, "r") as f:
        f_lines = f.readlines()
        count = 0 
        Hcount = 0
        for line in f_lines:
            l=line.split()
            if l[0] == "HX":
                Hs.append(np.array((float(l[1]),float(l[2]),float(l[3]))))
            elif l[0] == "OX":
                Os.append(np.array((float(l[1]),float(l[2]),float(l[3]))))
            elif l[0].isnumeric() == True and len(l)>1:
                ts.append(float(l[0]))
    
                
    #Turns a vector position into a vector matrix (one big list)
    f.close()
    Hs = np.vstack(Hs)
    Os = np.vstack(Os)
   # print(ts)    #include when you want to see the number of timesteps
    
    #Going down the list for x,y,z for N and O and then plotting it
    r = distCalc(Hs[:,0],Hs[:,1],Hs[:,2],Os[:,0],Os[:,1],Os[:,2])
    float_ts = list(np.float_(ts)*0.242)
    plt.plot(float_ts,r)
    plt.xlabel("Time (fs)")
    plt.ylabel("O-H Distance (nm)")
    plt.grid()    
    plt.show()
    
    
#Performs the Distance Calculation for O-N
def distCalc (a1,b1,c1,a2,b2,c2):
    return pow(sum((pow((a2-a1)*0.1,2),pow((b2-b1)*0.1,2),pow((c2-c1)*0.1,2))),0.5)

main()

Larz60+ write Jan-14-2023, 01:03 AM:
Please post all code, output and errors (it it's entirety) between their respective tags. Refer to BBCode help topic on how to post. Use the "Preview Post" button to make sure the code is presented as you expect before hitting the "Post Reply/Thread" button.
Rather than attaching. I have done this for you this time. Please use bbcode tags on future posts. Thank you.