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Merge pull request #1673 from helvrud/create_polymer

Create polymer
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fweik committed Dec 4, 2017
2 parents 3d4b341 + f0a6bca commit 29189a154185be99d2cfcb18fcebb041de29aa04
Showing with 46 additions and 28 deletions.
  1. +1 −1 src/python/espressomd/interactions.pyx
  2. +45 −27 src/python/espressomd/polymer.pyx
@@ -1650,7 +1650,7 @@ class BondedInteractionNotDefined(object):
class FeneBond(BondedInteraction):
def __init__(self, *args, **kwargs):
"""
FeneBond initializer. Used to instatiate a FeneBond identifier
@@ -71,51 +71,69 @@ def validate_params(_params, default):
# wrapper function to expose to the user interface
def create_polymer(**kwargs):
"""
Wrapper function to setup polymers.
""" Generators have a ``Yields`` section instead of a ``Returns`` section.
Parameters
----------
n : :obj:`intd`
The upper limit of the range to generate, from 0 to `n` - 1.
N_P : :obj:`int`
Number of polymer chains
Number of polymer chains
MPC : :obj:`int`
Number of monomers per chain
Number of monomers per chain
bond_length : :obj:`float`
distance between adjacent monomers in a chain
distance between adjacent monomers in a chain
bond : :obj:`espressomd.interactions.BondedInteraction`
The bonded interaction to be set up between the monomers.
start_id : :obj:`int`, optional
Particle ID of the first monomer, all other particles will have larger IDs
start_pos : array_like :obj:`float`
Position of the first monomer
Particle ID of the first monomer, all other particles will have larger IDs. Defaults to 0
start_pos : array_like :obj:`float`. Defaults to numpy.array([0, 0, 0])
Position of the first monomer
mode : :obj:`int`, optional
Selects a specific random walk procedure for the
polymer setup mode = 1 uses a common random walk,
mode = 2 produces a pruned self-avoiding random walk,
and mode = 0 a self-avoiding random walk. Note that
mode = 2 does not produce a true self- avoiding
random walk distribution but is much faster than mode = 0
Selects a specific random walk procedure for the
polymer setup mode = 1 uses a common random walk,
mode = 2 produces a pruned self-avoiding random walk,
and mode = 0 a self-avoiding random walk. Note that
mode = 2 does not produce a true self-avoiding
random walk distribution but is much faster than mode = 0. Defaults to 1
shield : :obj:`float`, optional
Shielding radius for the pruned self-avoiding walk mode
Shielding radius for the pruned self-avoiding walk mode. Defaults to 0
max_tries : :obj:`int`, optional
Maximal number of attempts to set up a polymer,
default value is 30,000. Depending on the random walk
mode and the polymer length this value needs to be
adapted.
Maximal number of attempts to set up a polymer,
default value is 1,000. Depending on the random walk
mode and the polymer length this value needs to be
adapted.
val_poly : :obj:`float`, optional
Valency of the monomers, default is 0.0
Valency of the monomers, default is 0.0
charge_distance : :obj:`int`, optional
Distance between charged monomers along the chain.
Distance between charged monomers along the chain. Default is 1
type_poly_neutral : :obj:`int`, optional
Particle type of neutal monomers
Particle type of neutal monomers, default is 0.
type_poly_charged : :obj:`int`, optional
Particle type for charged monomers
Particle type for charged monomers, default is 1
angle : :obj:`float`, optional
angle2 : :obj:`float`, optional
The both angles angle and angle2 allow to set up
planar or helical polymers, they fix the angles
between adjacent bonds.
The both angles angle and angle2 allow to set up
planar or helical polymers, they fix the angles
between adjacent bonds.
pos2 : array_like, optional
Sets the position of the second monomer.
Sets the position of the second monomer. Defaults to numpy.array([0, 0, 0]).
constraints : :obj:`int`, optional
Either 0 or 1, default is 0. If 1, the particle setup-up tries to obey previously defined constraints.
Examples
--------
This example sets 2 polyelectrolyte chains of the length 10. Beads are connected by FENE potential.
>>> fene = interactions.FeneBond(k=10, d_r_max=2)
>>> polymer.create_polymer(
N_P = 2,
MPC = 10,
bond_length = 1,
bond = fene,
val_poly = -1.0)
"""
params=dict()
default_params=dict()
default_params["N_P"] = 0

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