system.non_bonded_inter[0, 0].lennard_jones.set_params(epsilon=1,
sigma=1,
cutoff=2**(1. / 6),
shift="auto")
system.non_bonded_inter[0, 1].lennard_jones.set_params(epsilon=1,
sigma=1,
cutoff=2**(1. / 6),
shift="auto")
system.non_bonded_inter[1, 1].lennard_jones.set_params(epsilon=1,
sigma=1,
cutoff=2**(1. / 6),
shift="auto")
fene = interactions.FeneBond(k=30, d_r_max=1.5)
system.bonded_inter.add(fene)
# The call to diamond.Diamond() creates 16 connected polymers.
# These polymers are initialized in a straight line connected to crosslink nodes
# Furthermore they are connected to one another across simulation boxes in a periodic fashion.
# It is crucial that the simulation box, chain length and a-parameters be
# chosen such that the arrangement will not break bonds.
# monomers per chain
MPC = 15
# length for Kremer-Grest chain
bond_length = 0.966
# The physical distance beween nodes such that a line of monomers "fit" needs to be worked out.
import numpy as np
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, 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",
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")
class CommonTests(ut.TestCase):
"""
Class that holds common test methods.
"""
system = espressomd.System(box_l=[1.0, 1.0, 1.0])
# avoid particles to be set outside of the main box, otherwise particle
# positions are folded in the core when writing out and we cannot directly
# compare positions in the dataset and where particles were set. One would
# need to unfold the positions of the hdf5 file.
system.box_l = [npart, npart, npart]
system.cell_system.skin = 0.4
system.time_step = 0.01
written_pos = None
written_bonds = None
written_atoms = None
types_to_write = None
for i in range(npart):
system.part.add(id=i,
pos=np.array([float(i), float(i),
float(i)]),
v=np.array([1.0, 2.0, 3.0]),
type=1 + (-1)**i)
system.bonded_inter.add(interactions.FeneBond(k=1., d_r_max=10.0))
system.part[0].add_bond((0, 1))
system.part[0].add_bond((0, 2))
system.part[0].add_bond((0, 3))
system.integrator.run(steps=0)
def test_pos(self):
"""Test if positions have been written properly."""
if self.types_to_write == 'all':
simulation_pos = np.array([((i), float(i), float(i), float(i))
for i in range(npart)])
elif (2 in self.types_to_write):
simulation_pos = np.array([((i * 2), float(i * 2), float(i * 2),
float(i * 2))
for i in range(npart // 2)])
self.assertTrue(np.allclose(simulation_pos[:, 1:],
self.written_pos[:, 1:]),
msg="Positions not written correctly by writevcf!")
def test_bonds(self):
"""Test if bonds have been written properly: just look at number of bonds"""
if self.types_to_write == 'all':
simulation_bonds = np.array([1, 2, 3]) # the two bonded particles
elif (2 in self.types_to_write):
types = [2]
simulation_bonds = np.array(2) # only this one is type 2
self.assertTrue(np.allclose(np.shape(simulation_bonds),
np.shape(self.written_bonds)),
msg="Bonds not written correctly by writevsf!")
def test_atoms(self):
"""Test if atom declarations have been written properly."""
if self.types_to_write == 'all':
simulation_atoms = np.array([((i), (1 + (-1)**i))
for i in range(npart)])
elif (2 in self.types_to_write):
simulation_atoms = np.array([((i * 2), 2)
for i in range(npart // 2)])
self.assertTrue(np.allclose(simulation_atoms[:, 1],
self.written_atoms[:, 1]),
msg="Atoms not written correctly by writevsf!")
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
"""
This sample illustrates how bond information can be stored.
"""
from __future__ import print_function
import espressomd
from espressomd import interactions
system = espressomd.System(box_l=[10.0, 10.0, 10.0])
f = interactions.FeneBond(k=1, d_r_max=1)
f2 = interactions.FeneBond(k=2, d_r_max=1.5)
h = interactions.HarmonicBond(r_0=0, k=1)
# Pickle data
###########################################################
try:
import cPickle as pickle
except ImportError:
import pickle
system.bonded_inter.add(f)
system.bonded_inter.add(f2)
system.bonded_inter.add(h)
output_filename = "bonded_inter_save.pkl"
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
print("The number of monomers")
mpc = float(input()) # The number of monomers has been set to be 20 as default
# Change this value for further simulations
# 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.cell_system.skin = skin
system.box_l = [box_l, box_l, box_l]
system.thermostat.set_langevin(kT=1.0, gamma=1.0)
### Particle types
type_counter = 0
type_mono = type_counter
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):
