total_species

shihab2196

Dec 10th, 2023 (edited)

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# -*- coding: utf-8 -*-
"""
Author: Shihab Ahmed
Created on Fri Dec 8 13:29:43 2023
"""
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import random
def get_species_count(speciesfile):
with open(speciesfile,'r') as sf:
species = {}
for line in sf:
if "Timestep" in line:
headers = line.strip().split()[1:] # not taking '#'
species_name = headers[3:] # skip Timestep, No_moles, No_Specs
else:
values = [int(x) for x in line.strip().split()]
timestep = values[0]
species_count = values[3:]
species[timestep]={}
for key,value in zip(species_name,species_count):
if key in species:
species[timestep][key]+=value
else:
species[timestep][key] = value
df = pd.DataFrame(species).fillna(0)
df.index.name = 'Timestep'
return df
base_oil = 'PAO4'
data = {}
for cutoff in np.array(range(30,76,5))/100:
commmon = r"C:\Users\arup2\OneDrive - University of California Merced\Desktop\LAMMPS\Base_Oil\{}\25_{}_200_O2_Soria\Production\1600".format(base_oil,base_oil)
sim_dir = ['\\Sim-1','\\Sim-2','\\Sim-3']
flag = True
for sim in sim_dir:
directory = commmon+sim
speciesfile = directory+f'\\species_{cutoff}.out'
if cutoff==0.30:
speciesfile = directory+'\\species.out'
current = get_species_count(speciesfile).T
if flag:
summed_species = current.copy()
flag = False
else:
summed_species = summed_species.add(current,fill_value=0)
exclude= ['O2', 'H62C30']
nsim = len(sim_dir) # number of simulation
species = (summed_species/nsim).drop(exclude,axis=1)
plt.style.use("classic")
plt.figure(figsize=(6.4, 4.8))
total_molecule = species.sum(axis=1)
last_value = total_molecule.iloc[-1:].mean()
data[cutoff]=last_value
plt.plot(data.keys(),data.values(),marker='s',c='r')
plt.xlim(0.29)
plt.xlabel('Bond order cutoff')
plt.ylabel('Total number of reaction products')
plt.savefig(r'C:\Users\arup2\OneDrive - University of California Merced\Desktop\LAMMPS\Post Processing\lammps_processing\python_outputs\species'+'\\species_speciesfile{}'.format(random.randint(0,10000000000)),dpi=400,bbox_inches='tight')

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