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Given the following text description, write Python code to implement the functionality described below step by step
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Description:
 Examples for epoxpy molecule library
Particle A
Particles B and C are exactly the same as particle A
Step1:  Particle C10
C10 is just a chain of 10 C's. It has two parameters to set the position and orientation of the first particle. The position and orientation of the other 9 particles depend on this first one.
Step2:  Epoxy blend (10 A's, 20 B's and 2 C10's)
The blend can be given a box size. The default is [1,1,1].
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Python Code:
import epoxpy
from epoxpy.lib import A
a = A()
a.visualize(show_ports=True)
Explanation: Examples for epoxpy molecule library
Particle A
Particles B and C are exactly the same as particle A
End of explanation
from epoxpy.lib import C10
c10 = C10()
c10.visualize(show_ports=True)
Explanation: Particle C10
C10 is just a chain of 10 C's. It has two parameters to set the position and orientation of the first particle. The position and orientation of the other 9 particles depend on this first one.
End of explanation
from epoxpy.lib import Epoxy_A_10_B_20_C10_2_Blend
import mbuild as mb
import random
random.seed(1024)
blend = Epoxy_A_10_B_20_C10_2_Blend()
#blend.visualize()
mix_box = mb.packing.fill_box(blend,1,box=[3,3,3])
print(mix_box.n_bonds)
print(mix_box.n_particles)
mix_box.visualize(show_ports=False)
from foyer import Forcefield
mix_box.save('blend.gsd', write_ff=False)
mix_box.save('blend.hoomdxml')
%matplotlib inline
import matplotlib.pyplot as plt
import epoxpy.epoxy_simulation as es
import epoxpy.job as jb
import epoxpy.temperature_profile_builder as tpb
print('\n# Test1: Running the simulation in a single job')
# This simulation should run a total of 700 time steps because the default dt of the HOOMD engine is 1e-2
mix_time = 3e4
md_time = 4e4
mix_kt = 2.0
time_scale = 1e4
temp_scale = 1
type_A_md_temp_profile = tpb.LinearTemperatureProfileBuilder(initial_temperature=mix_kt, initial_time=mix_time)
type_A_md_temp_profile.add_state_point(60 * time_scale, 4.5 * temp_scale)
type_A_md_temp_profile.add_state_point(190 * time_scale, 4.5 * temp_scale)
type_A_md_temp_profile.add_state_point(240 * time_scale, 1.0 * temp_scale)
fig = type_A_md_temp_profile.get_figure()
plt.show()
fig.savefig("type_A_temp_profile.png")
myEpoxySim = es.EpoxySimulation('epoxy_test_mbuild', mix_time=mix_time, mix_kt=mix_kt,
                                temp_prof=type_A_md_temp_profile, n_mul=1.0, bond=True, bond_period=1*time_scale)
mySingleJobForEpoxy = jb.SingleJob(myEpoxySim)
mySingleJobForEpoxy.execute()
Explanation: Epoxy blend (10 A's, 20 B's and 2 C10's)
The blend can be given a box size. The default is [1,1,1].
End of explanation
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