def __init__(self, box=[1, 1, 1]):
super(Epoxy_A_10_B_20_C10_2_Blend, self).__init__()
if len(box) is not 3:
raise ValueError('box shape should be 3. You passed in {}'.format(
len(box)))
num_a = 10
num_b = 20
num_c10 = 2
for index in range(0, num_a):
self.add(A(), label='A[$]')
x = random.uniform(-box[0] / 2, box[0] / 2)
y = random.uniform(-box[1] / 2, box[1] / 2)
z = random.uniform(-box[2] / 2, box[2] / 2)
mb.translate(self['A'][-1], [x, y, z])
for index in range(0, num_b):
self.add(B(), label='B[$]')
x = random.uniform(-box[0] / 2, box[0] / 2)
y = random.uniform(-box[1] / 2, box[1] / 2)
z = random.uniform(-box[2] / 2, box[2] / 2)
mb.translate(self['B'][-1], [x, y, z])
for index in range(0, num_c10):
self.add(C10(), label='C10[$]')
x = random.uniform(-box[0] / 2, box[0] / 2)
y = random.uniform(-box[1] / 2, box[1] / 2)
z = random.uniform(-box[2] / 2, box[2] / 2)
mb.translate(self['C10'][-1], [x, y, z])
def set_initial_structure(self):
print('========INITIAIZING FOR DPD FENE==========')
desired_box_volume = ((A.mass * self.num_a) + (B.mass * self.num_b) +
(C10.mass * self.num_c10)) / self.density
desired_box_dim = (desired_box_volume**(1. / 3.))
self.box = [desired_box_dim, desired_box_dim, desired_box_dim]
if self.old_init == True:
print("\n\n ===USING OLD INIT=== \n\n")
As = my_init.Bead(btype="A", mass=A.mass)
Bs = my_init.Bead(btype="B", mass=B.mass)
C10s = my_init.PolyBead(btype="C", mass=1.0,
N=10) # Hardcode C10, with mon-mass 1.0
snap = my_init.init_system(
{
As: int(self.num_a),
Bs: int(self.num_b),
C10s: int(self.num_c10)
}, self.density / 10)
self.system = hoomd.init.read_snapshot(snap)
else:
if self.shrink is True:
print('Packing {} A particles ..'.format(self.num_a))
mix_box = mb.packing.fill_box(A(), self.num_a,
box=self.box) #,overlap=0.5)
mix_box = mb.packing.solvate(mix_box,
B(),
self.num_b,
box=self.box) #,overlap=0.5)
print('Packing {} B particles ..'.format(self.num_b))
mix_box = mb.packing.solvate(mix_box,
C10(),
self.num_c10,
box=self.box) #,overlap=0.5)
print('Packing {} C10 particles ..'.format(self.num_c10))
else:
blend = Epoxy_A_10_B_20_C10_2_Blend()
mix_box = mb.packing.fill_box(blend,
self.n_mul,
box=self.box,
overlap=0.050)
if self.init_file_name.endswith('.hoomdxml'):
mix_box.save(self.init_file_name)
elif self.init_file_name.endswith('.gsd'):
mix_box.save(self.init_file_name, write_ff=False)
if self.init_file_name.endswith('.hoomdxml'):
self.system = hoomd.deprecated.init.read_xml(
self.init_file_name)
elif self.init_file_name.endswith('.gsd'):
self.system = hoomd.init.read_gsd(self.init_file_name)
print('Initial box dimension: {}'.format(
self.system.box.dimensions))
snapshot = self.system.take_snapshot(bonds=True)
for p_id in range(snapshot.particles.N):
p_types = snapshot.particles.types
p_type = p_types[snapshot.particles.typeid[p_id]]
if p_type == 'A':
snapshot.particles.mass[p_id] = A.mass
if p_type == 'B':
snapshot.particles.mass[p_id] = B.mass
if p_type == 'C':
snapshot.particles.mass[p_id] = C.mass
print(snapshot.bonds.types)
snapshot.bonds.types = ['C-C', 'A-B']
self.system.restore_snapshot(snapshot)
if self.shrink is True:
self.nl = self.get_non_bonded_neighbourlist()
self.setup_force_fields(stage=cmn.Stages.MIXING)
size_variant = variant.linear_interp([(0, self.system.box.Lx),
(self.shrink_time,
desired_box_dim)])
md.integrate.mode_standard(dt=self.mix_dt)
md.integrate.langevin(group=hoomd.group.all(),
kT=self.shrinkT,
seed=1223445) #self.seed)
resize = hoomd.update.box_resize(L=size_variant)
hoomd.run(self.shrink_time)
snapshot = self.system.take_snapshot()
print('Initial box dimension: {}'.format(snapshot.box))
if self.init_file_name.endswith('.hoomdxml'):
deprecated.dump.xml(group=hoomd.group.all(),
filename=self.init_file_name,
all=True)
elif self.init_file_name.endswith('.gsd'):
hoomd.dump.gsd(group=hoomd.group.all(),
filename=self.init_file_name,
overwrite=True,
period=None)
def c10_new_position(self):
from epoxpy.lib import C10
return C10(c1_pos=[10, 0, 0], rotate_random=False)
def c10(self):
from epoxpy.lib import C10
return C10(rotate_random=False)