def __init__(self, poly=None, melt_id=1):
"""Define empty lists.
Inputs:
poly: polymer object with set values.
melt_id: id number of current melt object.
"""
# box sizes
self.sidelen = [100, 100, 100]
self.build_sidelen = [100, 100, 100]
# id number
self.melt_id = melt_id
# polymer instance
if poly != None:
self.p = poly
else:
self.p = polymer()
# final arrays for writing
self.coeff = None
self.value = {"atom": [], "bond": [], "angle": [], "dihedral": [], "improper": []}
# set build parameters
self.set_build_number(1, 1, 1)
# dihedral properties
di_e = [0.7003,0.4995,-6.501,-13.002]
di_d = [1,1,1,1]
di_n = [3,2,2,2]
# improper properties
im_e = [4.995,4.995]
im_d = [1,1]
im_n = [2,3]
# set nmonomers
nmonomers = 10
# make an instance of the molecule
c = polymer(nmonomers)
# set box dimensions
c.set_box_size(100)
# set range (which monomers to set
mtype1 = range(1,nmonomers+1)
# define atom, bond, and dihedral types
for i in range(4):
c.define_type('atom',[mass[i]],mtype1)
c.define_type('bond',[bond_e[i],bond_d[i],aspaces[i]],mtype1)
c.define_type('dihedral',[di_e[i],di_d[i],di_n[i]],mtype1)
# define pair types
for j in range(i,4):
def move(self, obstacles, monomers,fixed, polymers, num):
obs=0
v1=0
v2=0
#if the monomer is not in a polymer
if self.ispoly==0:
for i in xrange(constant.NB_OBS):
if self.near(obstacles[i], constant.CONTACT_OBS)==1:
v1=v1+obstacles[i].v1-self.v1
v2=v2+obstacles[i].v2-self.v2
obs+=1
for y in xrange(constant.NB_MONO):
if y!=num:
# if self.near(monomers[y], CONTACT_MONO)==1:
# v1=v1+monomers[y].v1-self.v1
# v2=v2+monomers[y].v2-self.v2
# obs+=1
if self.near(monomers[y], constant.CONTACT_POL)==1:
#if the monomer self hits is already the head of a polymer
if monomers[y].ishead==1:
polymers[monomers[y]].add(monomers[num],polymers)
#print "HAAAAAAAAA"
# new=polymers[y]
# new.append(y)
# polymers[num]=new
# del polymers[y]
# self.ispoly=1
# monomers[y].ishead=num
#if the monomer self hits is alone
elif monomers[y].ispoly==0:
polymers[monomers[num]]=polymer.polymer(monomers[num],monomers[y],polymers)
#print monomers[num].ishead
#print polymers.has_key(monomers[num])
else:
v1=v1+monomers[y].v1-self.v1
v2=v2+monomers[y].v2-self.v2
obs+=1
#if the monomer didn't hit anything, then random movment
if obs==0:
self.move_random()
#else, take into consideration objects hit
elif obs!=0:
self.v1_next=v1/obs
self.v2_next=v2/obs
# norm=math.sqrt(self.v1_next*self.v1_next+self.v2_next*self.v2_next)
# self.v1_next=self.v1_next*(constant.SPEED+10)/norm
# self.v2_next=self.v2_next*(constant.SPEED+10)/norm
# if fix!=0:
# norm=math.sqrt(self.v1*self.v1+self.v2*self.v2)
# self.v1_next=self.v1_next*(constant.SPEED+10)/norm
# self.v2_next=self.v2_next*(constant.SPEED+10)/norm
fix=0
for j in xrange(constant.NB_FIX):
if self.near(fixed[j],constant.CONTACT_FIX)==1:
self.v1_next=-self.v1
self.v2_next=-self.v2
fix=1
self.wind()
