In [1]:

    

%load_ext ipyext.writeandexecute


    

    




'writeandexecute' magic loaded.

In [2]:

    

%%writeandexecute -i cg_hexane cg_hexane.py
import mbuild as mb

from mbuild.examples.alkane.alkane import Alkane


class Propane(mb.Compound):
    def __init__(self):
        super(Propane, self).__init__()

        c = Alkane(n=3, cap_front=True, cap_end=False)
        self.add(c, 'propane')

        self.add(c['down'], 'down', containment=False)

class Hexane(mb.Compound):
    def __init__(self):
        super(Hexane, self).__init__()

        self.add(Propane(), 'propane1')
        self.add(Propane(), 'propane2')

        mb.force_overlap(self['propane1'], 
                         self['propane1']['down'], 
                         self['propane2']['down'])


    

In [3]:

    

hexane = Hexane()
print(hexane)
hexane.visualize()


    

    




<Hexane 20 particles, non-periodic, 19 bonds, id: 4370839032>

In [4]:

    

particles = [Propane]
cg = mb.coarse_grain(hexane, particle_classes=particles)
print(cg)
cg.visualize()


    

    




<Hexane (proxy)  2 particles, non-periodic, 0 bonds, id: 4524679408>

In [ ]: