#!/usr/bin/env python
# coding: utf-8

# # Birth-Death
# 
# This is for an integrated test of E-Cell4. Here, we test a simple birth-death process in volume.

# In[1]:


get_ipython().run_line_magic('matplotlib', 'inline')
from ecell4.prelude import *


# Parameters are given as follows. `D` and `radius` mean a diffusion constant and a radius of molecules, respectively. Dimensions of length and time are assumed to be micro-meter and second.

# In[2]:


D = 1  # 0.01
radius = 0.005


# In[3]:


N = 20  # a number of samples


# In[4]:


y0 = {} # {'A': 60}
duration = 3
V = 8


# Make a model for all algorithms. No birth reaction with more than one product is accepted.

# In[5]:


with species_attributes():
    A | {'radius': radius, 'D': D}

with reaction_rules():
    ~A > A | 45.0
    A > ~A | 1.5

m = get_model()


# Save a result with `ode` as `obs`, and plot it:

# In[6]:


ret1 = run_simulation(duration, y0=y0, volume=V, model=m)
ret1


# Simulating with `gillespie` (Bars represent standard error of the mean):

# In[7]:


ret2 = ensemble_simulations(duration, ndiv=20, y0=y0, volume=V, model=m, solver='gillespie', repeat=N)
ret2.plot('o', ret1, '-')


# Simulating with `meso`:

# In[8]:


ret2 = ensemble_simulations(
    duration, ndiv=20, y0=y0, volume=V, model=m, solver=('meso', Integer3(3, 3, 3), 0.25), repeat=N)
ret2.plot('o', ret1, '-')


# Simulating with `spatiocyte`:

# In[9]:


ret2 = ensemble_simulations(
    duration, ndiv=20, y0=y0, volume=V, model=m, solver=('spatiocyte', radius), repeat=N)
ret2.plot('o', ret1, '-')


# Simulating with `egfrd`:

# In[10]:


ret2 = ensemble_simulations(
    duration, ndiv=20, y0=y0, volume=V, model=m, solver=('egfrd', Integer3(8, 8, 8)), repeat=N)
ret2.plot('o', ret1, '-')


# Simulating with `bd`:

# In[11]:


ret2 = ensemble_simulations(
    duration, ndiv=20, y0=y0, volume=V, model=m, solver=('bd', Integer3(8, 8, 8), 0.1), repeat=N)
ret2.plot('o', ret1, '-')