"""Molecules that form a cluster. Similar to cluster3D.txt.
"""

__author__ = "Steve Andrews"
__date__ = "2020-11-23"

# Smoldyn simulation of molecule clustering
import smoldyn
import matplotlib.pyplot as plt
import numpy as np
s=smoldyn.Simulation(low=[-10,-10,-10],high=[10,10,10])
B=s.addSpecies('B',color='blue',difc=1,display_size=0.3)
R=s.addSpecies('R',color='red',difc=0,display_size=0.3)
B.addToSolution(200)
R.addToSolution(1,pos=[0,0,0])
rxn=s.addReaction(name='r',subs=[B,R],prds=[R,R],rate=20)
rxn.productPlacement(method='bounce',param=0.6)
s.addOutputData('counts')
s.addCommand(cmd='molcount counts',cmd_type='E')
s.setGraphics('opengl_good',1)
s.run(200,dt=0.1)
data = s.getOutputData('counts', 0)
dataT = np.array(data).T.tolist()
plt.plot(dataT[0],dataT[2],"r")
plt.xlabel("time")
plt.ylabel("cluster size")
plt.show()