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- # -*- coding: utf-8 -*-
- """
- Author: Shihab Ahmed
- Created on Fri Dec 29 03:52:55 2023
- """
- import numpy as np
- import matplotlib.pyplot as plt
- import random
- import magnolia.speciesfile_parser as sfp
- data = {}
- all_data = {}
- total_species = {}
- for cutoff in np.array(range(30,80,5))/100:
- total_species[cutoff]=0
- for cutoff in np.array(range(30,80,5))/100:
- dirr = r"C:\Users\arup2\OneDrive - University of California Merced\Desktop\LAMMPS\Antioxidants\ABCDE\D\D_300_O2\Production\1000K"
- sim_dir = ['\\Sim-1','\\Sim-2','\\Sim-3']
- flag = True
- for sim in sim_dir:
- directory = dirr+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', 'H26C34O4']
- 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)
- #%%
- 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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