def test_respect_constraints_wall(self):
"""
Check that constraints are respected.
"""
num_poly = 20
num_mono = 5
bond_length = 1.19
w = espressomd.shapes.Wall(normal=[0., 0., 1.], dist=0.5 * self.box_l)
wall_constraint = espressomd.constraints.ShapeBasedConstraint(shape=w)
c = self.system.constraints.add(wall_constraint)
positions = polymer.positions(
n_polymers=num_poly, beads_per_chain=num_mono,
bond_length=bond_length, respect_constraints=True, seed=self.seed)
positions %= self.box_l
z_components = positions[:, :, 2][0]
for z in z_components:
print(z)
self.assertGreaterEqual(z, 0.5 * self.box_l)
# assert that illegal start position raises error
with self.assertRaisesRegex(Exception, 'Invalid start positions.'):
illegal_start = np.array([[1., 1., 0.2 * self.box_l]])
positions = polymer.positions(
n_polymers=1,
beads_per_chain=10,
start_positions=illegal_start,
bond_length=bond_length,
respect_constraints=True, seed=self.seed)
self.system.constraints.remove(wall_constraint)
def test_start_positions(self):
"""
Check that setting start positions behaves correctly.
"""
num_poly = 90
num_mono = 25
bond_length = 0.83
start_positions = np.random.random((num_poly, 3)) * self.box_l
# make sure that incorrect size leads to error
with self.assertRaises(ValueError):
positions = polymer.positions(n_polymers=num_poly + 1,
beads_per_chain=num_mono,
start_positions=start_positions,
bond_length=bond_length,
seed=self.seed)
# check that start positions are actually used
positions = polymer.positions(n_polymers=num_poly,
beads_per_chain=num_mono,
start_positions=start_positions,
bond_length=bond_length,
seed=self.seed)
self.assertListEqual(start_positions.tolist(), positions[:,
0].tolist())
def setUpClass(cls):
box_l = 20.0
# start with a small box
cls.system.box_l = np.array([box_l, box_l, box_l])
cls.system.cell_system.set_n_square(use_verlet_lists=False)
fene = FeneBond(k=30, d_r_max=2)
cls.system.bonded_inter.add(fene)
positions = polymer.positions(n_polymers=cls.num_poly,
bond_length=0.9,
beads_per_chain=cls.num_mono,
seed=42)
for p in positions:
for ndx, m in enumerate(p):
part_id = len(cls.system.part)
cls.system.part.add(id=part_id, pos=m)
if ndx > 0:
cls.system.part[part_id].add_bond((fene, part_id - 1))
# bring two polymers to opposite corners:
# far in cell centre, but mirror images are close
head_id = 0
tail_id = head_id + cls.num_mono
cm = np.mean(cls.system.part[head_id:tail_id].pos, axis=0)
cls.system.part[head_id:tail_id].pos = cls.system.part[
head_id:tail_id].pos - cm + cls.system.box_l
head_id = cls.num_mono + 1
tail_id = head_id + cls.num_mono
cm = np.mean(cls.system.part[head_id:tail_id].pos, axis=0)
cls.system.part[head_id:tail_id].pos -= cm
def test_bond_lengths(self):
"""
Check that distance between neighboring monomers is indeed bond_length.
"""
bond_lengths = [0.735, 1.459]
num_poly = 10
num_mono = 25
for bond_length in bond_lengths:
positions = polymer.positions(
n_polymers=num_poly, beads_per_chain=num_mono,
bond_length=bond_length, seed=self.seed)
self.assertShape(positions, num_poly, num_mono)
self.assertBondLength(positions, bond_length)
def test_min_dist(self):
"""
Check that min_dist is respected.
"""
num_poly = 5
num_mono = 150
bond_length = 0.945
positions = polymer.positions(
n_polymers=num_poly, beads_per_chain=num_mono,
bond_length=bond_length, min_distance=bond_length,
seed=self.seed)
self.assertBondLength(positions, bond_length)
self.assertMinDistGreaterEqual(positions, bond_length - 1e-10)
def test_bond_angles(self):
"""
Check that bond_angle is obeyed.
"""
bond_angles = [0.436 * np.pi, np.pi / 3., np.pi / 5.]
num_poly = 10
num_mono = 25
bond_length = 1.34
for bond_angle in bond_angles:
positions = polymer.positions(
n_polymers=num_poly, beads_per_chain=num_mono,
bond_angle=bond_angle, bond_length=bond_length,
seed=self.seed)
self.assertShape(positions, num_poly, num_mono)
self.assertBondLength(positions, bond_length)
self.assertBondAngle(positions, bond_angle, bond_length)
from espressomd import polymer
from espressomd import interactions
system = espressomd.System(box_l=[100.0, 100.0, 100.0])
system.set_random_state_PRNG()
#system.seed = system.cell_system.get_state()['n_nodes'] * [1234]
system.time_step = 0.01
system.thermostat.set_langevin(kT=1.0, gamma=1.0, seed=42)
system.cell_system.skin = 0.4
fene = interactions.FeneBond(k=10, d_r_max=2)
system.bonded_inter.add(fene)
positions = polymer.positions(n_polymers=5,
beads_per_chain=50,
bond_length=1.0,
seed=1234)
for polymer in positions:
for i, pos in enumerate(polymer):
id = len(system.part)
system.part.add(id=id, pos=pos)
if i > 0:
system.part[id].add_bond((fene, id - 1))
system.integrator.run(steps=0)
h5_file = h5md.H5md(filename="sample.h5",
write_pos=True,
write_vel=True,
write_force=True,
write_species=True,
write_mass=False,
c2 = system.constraints.add(particle_type=0,
penetrable=False,
only_positive=False,
shape=ceil)
# create stiff FENE bonds
fene = interactions.FeneBond(k=30, d_r_max=2)
system.bonded_inter.add(fene)
# start it next to the wall to test it!
start = np.array([1, 1, 1 + wall_offset])
# polymer.positions will avoid violating the constraints
positions = polymer.positions(n_polymers=1,
beads_per_chain=50,
bond_length=1.0,
seed=1234,
min_distance=0.9,
respect_constraints=True)
for i, pos in enumerate(positions[0]):
id = len(system.part)
system.part.add(id=id, pos=pos)
if i > 0:
system.part[id].add_bond((fene, id - 1))
# Warmup
#############################################################
minimize_steps = 20
minimize_n_times = 10
min_dist = 0.9
# bonding interaction parameter
bond_l = 1.2 # bond length
kbond = 100 # force constant for harmonic bond
harmonic_bond = interactions.HarmonicBond(k=kbond, r_0=bond_l)
system.bonded_inter.add(harmonic_bond)
# non-bonding interactions (LJ)
lj_eps = 1.0
lj_sig = 1.0
lj_cut = 1.12246
lj_shift = 0.0
# setting up the polymer
positions = polymer.positions(n_polymers=N_P,
beads_per_chain=MPC,
bond_length=bond_l,
seed=13)
for polymer in positions:
for i, pos in enumerate(polymer):
id = len(system.part)
system.part.add(id=id, pos=pos, type=type_A, q=charges[type_A])
if i > 0:
system.part[id].add_bond((harmonic_bond, id - 1))
# setting up counterions
for i in range(N0):
system.part.add(pos=np.random.random(3) * system.box_l,
type=type_H,
q=charges[type_H])
# setting up other ions
# - Na+ and OH-
box_v = n_part / density
Box_l = (box_v**(1. / 3.)) * np.ones(3)
system.change_volume_and_rescale_particles(d_new=Box_l[0])
#system.thermostat.set_langevin(kT=1, gamma=1, seed=88)
system.time_step = 0.01
system.cell_system.skin = 0.1
print("The Vol. of Box Simulation is", box_v, "\n")
############################################
###### initializing polymers #######
############################################
for k in frac_range:
polymers = polymer.positions(n_polymers=n_polymers,
beads_per_chain=beads_per_chain,
bond_length=1.,
seed=88)
frac_phobic = k
polymers_list = []
c = 0 ## unnecessary list. creates a list that gonna contains others lists.
for p in polymers:
polymers_list.append(
[x for x in range(c, c + beads_per_chain)]
) ## inserts a list(numbered from c to c+beads_per_chain) into polymers_list for each polymer p in polymers
c += beads_per_chain
for i, m in enumerate(p):
if i < beads_per_chain * frac_phobic:
id = len(system.part)
system.part.add(id=id, type=0, pos=m)
if i > 0:
cs.set_domain_decomposition(True)
cs.set_domain_decomposition(use_verlet_lists=True)
system.thermostat.set_langevin(kT=1.0, gamma=1.0, seed=42)
system.time_step = 0.01
# Create a minimal polymer
system.non_bonded_inter[0, 0].lennard_jones.set_params(epsilon=1,
sigma=1,
cutoff=2**(1. / 6),
shift="auto")
fene = interactions.FeneBond(k=10, d_r_max=1.5)
system.bonded_inter.add(fene)
positions = polymer.positions(n_polymers=1,
beads_per_chain=100,
bond_length=0.97,
seed=1234,
min_distance=0.969)
for i, pos in enumerate(positions[0]):
id = len(system.part)
system.part.add(id=id, pos=pos)
if i > 0:
system.part[id].add_bond((fene, id - 1))
n_steps = 1000
print("Testing without verlet lists...")
cs.set_domain_decomposition(use_verlet_lists=False)
for skin in np.arange(5, 15, 1):
profile()
