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- # -*- coding: utf-8 -*-
- """
- Author: Shihab Ahmed
- Created on Wed Jan 10 23:26:09 2024
- """
- import numpy as np
- import matplotlib.pyplot as plt
- import random
- import magnolia.speciesfile_parser as sfp
- dirrs = [r"C:\Users\arup2\OneDrive - University of California Merced\Desktop\LAMMPS\Antioxidants\ABCDE\D\D_300_O2\Production\1000K",
- r"C:\Users\arup2\OneDrive - University of California Merced\Desktop\LAMMPS\Antioxidants\ABCDE\B\B_300_O2\Production\1150"]
- fig, ax = plt.subplots()
- labels = ['Molecule A', 'Molecule B']
- markers = ['s','^']
- for i, dirr in enumerate(dirrs):
- 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:
- 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)
- ax.plot(total_species.keys(),total_species.values(),marker=markers[i],
- label=labels[i])
- ax.set_xlim(0.29)
- ax.legend(loc='upper left')
- ax.set_xlabel('Bond order cutoff')
- ax.set_ylabel('Total number of different species')
- fig.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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