def test(self):
num_poly = 2
num_mono = 5
polymer.create_polymer(start_pos=[1, 1, 1],
N_P=num_poly,
bond_length=0.9,
bond=self.fene,
MPC=num_mono,
start_id=2)
# Was the start id considered
# bond=fene,start_id=2)
for i in 0, 1:
self.assertTrue(not self.system.part.exists(i))
# Were all other particles placed in the correct order
for i in range(2, 2 + num_mono * num_poly):
self.assertTrue(self.system.part.exists(i))
# Total number of particles
self.assertEqual(len(self.system.part), num_mono * num_poly)
# Start position
np.testing.assert_allclose(np.copy(self.system.part[2].pos),
[1., 1., 1.])
# Distance between consecutive particles
for i in range(num_poly):
first_particle = 2 + num_mono * i
for j in range(first_particle + 1, first_particle + num_mono):
print(first_particle, j)
self.assertAlmostEqual(self.system.distance(
self.system.part[j], self.system.part[j - 1]),
0.9,
places=5)
# Test polymer with specified pos2
self.system.part.clear()
polymer.create_polymer(start_pos=[1, 1, 1],
pos2=[1.9, 1, 1],
N_P=1,
bond_length=0.9,
bond=self.fene,
MPC=num_mono,
start_id=2,
angle2=1)
np.testing.assert_allclose(np.copy(self.system.part[2].pos),
[1., 1., 1.])
np.testing.assert_allclose(np.copy(self.system.part[3].pos),
[1.9, 1., 1.])
def setUpClass(self):
box_l = 20.0
# start with a small bo
self.system.box_l = np.array([box_l, box_l, box_l])
self.system.cell_system.set_n_square(use_verlet_lists=False)
fene = FeneBond(k=30, d_r_max=2)
self.system.bonded_inter.add(fene)
polymer.create_polymer(N_P=self.num_poly,
bond_length=0.9,
MPC=self.num_mono,
bond=fene)
# bring two polymers to opposite corners:
# far in centre cell, but mirror images are close
head_id = 0
tail_id = head_id + self.num_mono
cm = np.mean(self.system.part[head_id:tail_id].pos, axis=0)
self.system.part[head_id:tail_id].pos = self.system.part[
head_id:tail_id].pos - cm + self.system.box_l
head_id = self.num_mono + 1
tail_id = head_id + self.num_mono
cm = np.mean(self.system.part[head_id:tail_id].pos, axis=0)
self.system.part[head_id:tail_id].pos -= cm
def calc(var):
# AVB: Create an output directory for this to store the output files
outdir = "./Noelle/r01.5kBT4Ads/1000=3.2"
if not os.path.exists(outdir):
os.makedirs(outdir)
# Setup constant
time_step = 0.01
loops = 30
step_per_loop = 100
# AVB: the parameters (that I usually use)
a = 0.05
r0 = 2.0 * a
kBT = 4.0e-6
vwf_type = 0
collagen_type = 1
monomer_mass = 0.01
box_l = 32.0
#print("Shear velocity:")
#shear_velocity = float(input())
#vy = box_l*shear_velocity
vy = var
print(vy)
v = [0, vy, 0]
# System setup
system = 0
system = System(box_l=[box_l, box_l, box_l])
system.set_random_state_PRNG()
np.random.seed(seed=system.seed)
system.cell_system.skin = 0.4
mpc = 20 # The number of monomers has been set to be 20 as default
# Change this value for further simulations
# Fene interaction
fene = interactions.FeneBond(k=0.04, d_r_max=0.3)
system.bonded_inter.add(fene)
# Setup polymer of part_id 0 with fene bond
# AVB: Notice the mode, max_tries and shield parameters for pruned self-avoiding random walk algorithm
polymer.create_polymer(N_P=1,
MPC=mpc,
bond=fene,
bond_length=r0,
start_pos=[29.8, 16.0, 16.0],
mode=2,
max_tries=100,
shield=0.6 * r0)
# AVB: setting the type of particles and changing mass of each monomer to 0.01
system.part[:].type = vwf_type
system.part[:].mass = monomer_mass
# AVB: I suggest to add Lennard-Jones interaction between the monomers
# AVB: to reproduce hydrophobicity
# AVB: parameters for the potential (amplitude and cut-off redius)
amplVwfVwf = 4.0 * kBT # sometimes we change this to 2.0*kBT
rcutVwfVwf = 1.5 * r0
# AVB: the potential
system.non_bonded_inter[vwf_type, vwf_type].lennard_jones.set_params(
epsilon=amplVwfVwf,
sigma=r0 / 1.122,
shift="auto",
cutoff=rcutVwfVwf,
min=r0 * 0.6)
print("Warming up the polymer chain.")
## For longer chains (>100) an extensive
## warmup is neccessary ...
system.time_step = 0.002
system.thermostat.set_langevin(kT=4.0e-6, gamma=1.0)
# AVB: Here the Langevin thermostat is needed, because we have not yet initialized the LB-fluid.
# AVB: And somehow it is necessary so that the polymer adopts the equilibrium conformation of the globule.
# AVB: you may skip this step
for i in range(100):
system.force_cap = float(i) + 1
system.integrator.run(100)
print("Warmup finished.")
system.force_cap = 0
system.integrator.run(100)
system.time_step = time_step
system.integrator.run(500)
# AVB: the following command turns the Langevin thermostat on in line 49
system.thermostat.turn_off()
# AVB: This command sets the velocities of all particles to zero
system.part[:].v = [0, 0, 0]
# AVB: The density was too small here. I have set 1.0 for now.
# AVB: It would be necessary to recalculate, but the density of the liquid should not affect the movements of the polymer (this is how our physical model works).
lbf = espressomd.lb.LBFluid(agrid=1,
dens=1.0,
visc=1.0e2,
tau=time_step,
fric=0.01)
system.actors.add(lbf)
system.thermostat.set_lb(kT=4.0e-6)
# Setup boundaries
walls = [lbboundaries.LBBoundary() for k in range(2)]
walls[0].set_params(shape=shapes.Wall(normal=[1, 0, 0], dist=1.5),
velocity=v)
walls[1].set_params(shape=shapes.Wall(normal=[-1, 0, 0], dist=-30.5))
for wall in walls:
system.lbboundaries.add(wall)
print("Warming up the system with LB fluid.")
system.integrator.run(5000)
print("LB fluid warming finished.")
# AVB: after this you should have a completely collapsed polymer globule
# AVB: If you want to watch the process of globule formation in Paraview, just change 5000 to 0 in line 100
N = 25
x_coord = np.array([30] * N)
y_coord = np.arange(14, 24, 5 / N)
z_coord = np.arange(14, 24, 5 / N)
for i in range(N):
for j in range(N):
system.part.add(id=i * N + j + 100,
pos=np.array([x_coord[i], y_coord[j], z_coord[i]]),
v=np.array([0, 0, 0]),
type=i * N + j + 100)
all_collagen = range(100, (N - 1) * N + (N - 1) + 100)
system.comfixed.types = all_collagen
for i in range(100, (N - 1) * N + (N - 1) + 100):
system.non_bonded_inter[vwf_type,
i].lennard_jones.set_params(epsilon=amplVwfVwf,
sigma=r0 / 1.122,
shift="auto",
cutoff=rcutVwfVwf,
min=r0 * 0.6)
# configure correlators
com_pos = ComPosition(ids=(0, ))
c = Correlator(obs1=com_pos,
tau_lin=16,
tau_max=loops * step_per_loop,
delta_N=1,
corr_operation="square_distance_componentwise",
compress1="discard1")
system.auto_update_accumulators.add(c)
print("Sampling started.")
print("lenth after warmup")
print(
system.analysis.calc_re(chain_start=0,
number_of_chains=1,
chain_length=mpc - 1)[0])
lengths = []
ylengths = []
for i in range(loops):
system.integrator.run(step_per_loop)
system.analysis.append()
lengths.append(
system.analysis.calc_re(chain_start=0,
number_of_chains=1,
chain_length=mpc - 1)[0])
lbf.print_vtk_velocity(outdir + "/" + str(vy) + "%04i.vtk" % i)
system.part.writevtk(outdir + "/" + str(vy) + "vwf_all%04i.vtk" % i,
types=all_collagen)
system.part.writevtk(outdir + "/" + str(vy) + "vwf_poly%04i.vtk" % i,
types=[0])
cor = list(system.part[:].pos)
y = []
for l in cor:
y.append(l[1])
ylengths.append(max(y) - min(y))
sys.stdout.write("\rSampling: %05i" % i)
sys.stdout.flush()
walls[0].set_params(shape=shapes.Wall(normal=[1, 0, 0], dist=1.5))
walls[1].set_params(shape=shapes.Wall(normal=[-1, 0, 0], dist=-30.5))
for i in range(100):
system.integrator.run(step_per_loop)
lengths.append(
system.analysis.calc_re(chain_start=0,
number_of_chains=1,
chain_length=mpc - 1)[0])
system.part.writevtk(outdir + "/" + str(vy) +
"vwf_all[r0=2,kBT=4]intheEND.vtk")
with open(outdir + "/lengths" + str(vy) + ".dat", "a") as datafile:
datafile.write("\n".join(map(str, lengths)))
with open(outdir + "/lengthsY" + str(vy) + ".dat", "a") as datafile:
datafile.write("\n".join(map(str, ylengths)))
mean_vy = [(vy * 10000) / 32, sum(ylengths) / len(ylengths)]
print("mean_vy")
print(mean_vy)
with open(outdir + "/mean_vy" + "2kBT_2r0" + ".dat", "a") as datafile:
datafile.write(" ".join(map(str, mean_vy)))
c.finalize()
corrdata = c.result()
corr = zeros((corrdata.shape[0], 2))
corr[:, 0] = corrdata[:, 0]
corr[:, 1] = (corrdata[:, 2] + corrdata[:, 3] + corrdata[:, 4]) / 3
savetxt(outdir + "/msd_nom" + str(mpc) + ".dat", corr)
with open(outdir + "/rh_out.dat", "a") as datafile:
rh = system.analysis.calc_rh(chain_start=0,
number_of_chains=1,
chain_length=mpc - 1)
datafile.write(str(mpc) + " " + str(rh[0]) + "\n")
mpc = int(sys.argv[1])
except:
raise ValueError("First argument cannot be transformed into integer!")
# Lennard-Jones interaction
system.non_bonded_inter[0,0].lennard_jones.set_params(
epsilon=1.0, sigma=1.0,
shift=0.25, cutoff=1.226)
# Fene interaction
fene = interactions.FeneBond(k=7, d_r_max=2)
system.bonded_inter.add(fene)
# Setup polymer of part_id 0 with fene bond
polymer.create_polymer(N_P=1, MPC=mpc, bond=fene, bond_length=1)
print("Warming up the polymer chain.")
## For longer chains (>100) an extensive
## warmup is neccessary ...
system.time_step = 0.002
system.thermostat.set_langevin(kT=1.0, gamma=10)
for i in range(100):
system.force_cap = i
system.integrator.run(1000)
print("Warmup finished.")
system.force_cap = 0
system.integrator.run(10000)
system.thermostat.set_langevin(kT=1.0, gamma=1.0)
system.cell_system.set_n_square(use_verlet_lists=False)
outfile = open('polymer.vtf', 'w')
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=2)
system.bonded_inter.add(fene)
polymer.create_polymer(N_P=1,
bond_length=1.0,
type_poly_neutral=0,
type_poly_charged=0,
MPC=50,
bond=fene,
start_pos=[0., 0., 0.])
vtf.writevsf(system, outfile)
#############################################################
# Warmup #
#############################################################
warm_steps = 10
lj_cap = 1
system.force_cap = lj_cap
i = 0
act_min_dist = system.analysis.min_dist()
system.box_l = [100, 100, 100]
system.thermostat.set_langevin(kT=1.0, gamma=1.0)
system.cell_system.set_n_square(use_verlet_lists=False)
outfile = open('polymer.vtf', 'w')
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=2)
system.bonded_inter.add(fene)
polymer.create_polymer(N_P=1,
bond_length=1.0,
type_poly_neutral=0,
type_poly_charged=0,
MPC=50,
bond=fene)
vtf.writevsf(system, outfile)
#############################################################
# Warmup #
#############################################################
warm_steps = 10
lj_cap = 1
system.force_cap = lj_cap
i = 0
act_min_dist = system.analysis.min_dist()
# warmp with zero temperature to remove overlaps
# domain decomposition with verlet list: three equivalent commands
cs.set_domain_decomposition()
cs.set_domain_decomposition(True)
cs.set_domain_decomposition(use_verlet_lists=True)
system.thermostat.set_langevin(kT=1.0, gamma=1.0)
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)
polymer.create_polymer(
N_P=1, bond_length=0.97, MPC=100, bond=fene, start_pos=[0, 0, 0])
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()
print("Testing with verlet lists...")
cs.set_domain_decomposition(use_verlet_lists=True)
for skin in np.arange(5, 15, 1):
profile()
cs.set_n_square(True)
print("Testing with N-squared ...")
# domain decomposition with verlet list: three equivalent commands
cs.set_domain_decomposition()
cs.set_domain_decomposition(True)
cs.set_domain_decomposition(use_verlet_lists=True)
system.thermostat.set_langevin(kT=1.0, gamma=1.0)
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)
polymer.create_polymer(N_P=1, bond_length=0.97, MPC=100, bond=fene)
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()
print("Testing with verlet lists...")
cs.set_domain_decomposition(use_verlet_lists=True)
for skin in np.arange(5, 15, 1):
profile()
cs.set_n_square(True)
print("Testing with N-squared ...")
import espressomd # pylint: disable=import-error
from espressomd.io.writer import h5md # pylint: disable=import-error
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)
system.cell_system.skin = 0.4
fene = interactions.FeneBond(k=10, d_r_max=2)
system.bonded_inter.add(fene)
polymer.create_polymer(N_P=5, bond_length=1.0, MPC=50, bond=fene)
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,
write_charge=True,
write_ordered=True)
for i in range(1):
h5_file.write()
h5_file.flush()
h5_file.close()
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)
system.cell_system.skin = 0.4
fene = interactions.FeneBond(k=10, d_r_max=2)
system.bonded_inter.add(fene)
polymer.create_polymer(N_P=5,
bond_length=1.0,
MPC=50,
bond=fene,
start_pos=[1., 1., 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,
write_charge=True,
write_ordered=True)
for i in range(1):
h5_file.write()
h5_file.flush()
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
polymer.create_polymer(N_P=N_P,
bond_length=bond_l,
MPC=MPC,
start_id=0,
bond=harmonic_bond,
type_poly_neutral=type_HA,
type_poly_charged=type_A,
mode=0,
val_poly=charges[type_A])
# 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-
for i in range(nNaOH):
system.part.add(pos=np.random.random(3) * system.box_l,
type=type_OH,
# Lennard-Jones interaction
#system.non_bonded_inter[0,0].lennard_jones.set_params(
# epsilon=0.01, sigma=1.0,
# shift="auto", cutoff=2.0**(1.0/6.0))
# Fene interaction
fene = interactions.FeneBond(k=0.4, d_r_max=0.3)
system.bonded_inter.add(fene)
# Setup polymer of part_id 0 with fene bond
# AVB: Notice the mode, max_tries and shield parameters for pruned self-avoiding random walk algorithm
polymer.create_polymer(N_P=1,
MPC=mpc,
bond=fene,
bond_length=r0,
start_pos=[16.0, 16.0, 16.0],
mode=2,
max_tries=100,
shield=0.6 * r0)
# AVB: setting the type of particles and changing mass of each monomer to 0.01
system.part[:].type = vwf_type
system.part[:].mass = monomer_mass
# AVB: I suggest to add Lennard-Jones interaction between the monomers
# AVB: to reproduce hydrophobicity
# AVB: parameters for the potential (amplitude and cut-off redius)
amplVwfVwf = 4.0 * kBT # sometimes we change this to 2.0*kBT
rcutVwfVwf = 2.0 * r0
# AVB: the potential
system.non_bonded_inter[vwf_type,
type_counter += 1
system.non_bonded_inter[type_mono, type_mono].lennard_jones.set_params(
epsilon=1., sigma=1., cutoff=2.**(1. / 6.), shift="auto")
# See PRL-A, Volume 33, number 5, May 1986, Gary S. Grest and Kurt Kremer
k_fene = (30. * epsilon) / (sigma * sigma)
r_fene = 1.5 * sigma
fene = interactions.FeneBond(k=k_fene, d_r_max=r_fene)
system.bonded_inter.add(fene)
poly_start = 0
polymer.create_polymer(N_P=1,
bond_length=0.97,
MPC=n_mono,
start_id=poly_start,
bond=fene,
type_poly_neutral=type_mono,
type_poly_charged=type_mono,
mode=1)
poly_end = poly_start + n_mono
# this is to init a polymer a s straight line
#for p in range(0,n_mono):
# system.part.add(id=p, pos=[p+0.5, 1,1], type=type_mono )
#for p in range(1,n_mono):
# system.part[p].add_bond((fene,p-1))
print("\t** Placed {} monomers\n".format(n_mono))
cap = 1
system.non_bonded_inter.set_force_cap(cap)
print("Warming up... ", )
