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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
- import magnolia.speciesfile_parser as sfp
- base_oil = 'PAO4'
- data = {}
- all_data = {}
- total_species = {}
- 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 = sfp.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.count(axis=1)
- total_species[cutoff] = len(species.columns)
- last_value = total_molecule.iloc[-10:].mean()
- data[cutoff]=last_value
- all_data[cutoff]=species
- #%%
- plt.plot(total_species.keys(),total_species.values(),marker='s',c='r')
- plt.xlim(0.29)
- plt.xlabel('Bond order cutoff')
- plt.ylabel('Total number of different species')
- 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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