pysimm.apps.random_walk

Module Contents

Functions

displ_next_unit_default(m, s)	pysimm.apps.random_walk.displ_next_unit_default
find_last_backbone_vector(s, m)	pysimm.apps.random_walk.find_last_backbone_vector
copolymer(m, nmon, s_=None, **kwargs)	pysimm.apps.random_walk.copolymer
random_walk(m, nmon, s_=None, **kwargs)	pysimm.apps.random_walk.random_walk
find_last_tail_vector(s)	pysimm.apps.random_walk.find_last_tail_vector
rot_mat_about_axis(v, theta)	pysimm.apps.random_walk.rot_mat_about_axis
define_plane(a1, a2, a3)	pysimm.apps.random_walk.define_plane
reflect_coords_thru_plane(atom, plane)	pysimm.apps.random_walk.reflect_coords_thru_plane
scale_monomer(atom, origin, scale)	pysimm.apps.random_walk.scale_monomer
redo_monomer_insertion(s, m, i)	pysimm.apps.random_walk.redo_monomer_insertion
constrained_opt(s, m, active)	pysimm.apps.random_walk.constrained_opt
random_walk_tacticity(m, nmon, s_=None, **kwargs)	pysimm.apps.random_walk.random_walk_tacticity
__check_tags__(m, **kwargs)	pysimm.apps.random_walk.__check_tags__
check_tacticity(s, char_idxs, mon_len)	pysimm.apps.random_walk.check_tacticity

pysimm.apps.random_walk.displ_next_unit_default(m, s)

pysimm.apps.random_walk.displ_next_unit_default

Default implementation of displacement of next repetitive unit in random walk method for a polymer growth

Parameters

• m – System object – updated

• s – ItemContainer of ~pysimm.system.Particle objects

Returns

general placeholder for connectivity order of linker atoms; default implementation assumes work with polymers with a single linkage bond, thus no connectivity order is needed

Return type

empty list

pysimm.apps.random_walk.find_last_backbone_vector(s, m)

pysimm.apps.random_walk.find_last_backbone_vector

Finds vector between backbone atoms in terminal monomer. Requires current system s, and reference monomer m.

Parameters

• s – System object

• m – System object

Returns

list of vector components

pysimm.apps.random_walk.copolymer(m, nmon, s_=None, **kwargs)

pysimm.apps.random_walk.copolymer

Builds copolymer using random walk methodology using pattern

Parameters

• m – list of reference monomer :class:`~pysimm.system.System`s

• nmon – total number of monomers to add to chain

• s – System in which to build polymer chain (None)

• settings – dictionary of simulation settings

• density – density at which to build polymer (0.3)

• forcefield – Forcefield object to acquire new force field parameters

• capped – True/False if monomers are capped

• unwrap – True to unwrap final system

• traj – True to build xyz trajectory of polymer growth (True)

• pattern – list of pattern for monomer repeat units, should match length of m ([1 for _ in range(len(m))])

• limit – during MD, limit atomic displacement by this max value (LAMMPS ONLY)

• sim – Simulation object for relaxation between polymer growth

Returns

new copolymer System

pysimm.apps.random_walk.random_walk(m, nmon, s_=None, **kwargs)

pysimm.apps.random_walk.random_walk

Builds homopolymer using random walk methodology

Parameters

• m – reference monomer System

• nmon – total number of monomers to add to chain

• s – System in which to build polymer chain (None)

• extra_bonds – EXPERMINTAL, True if making ladder backbone polymer

• geometry_rule – a pointer to a method that orients series of atoms of the next repetitive unit in random run

• settings – dictionary of simulation settings

• density – density at which to build polymer (0.3)

• forcefield – Forcefield object to acquire new force field parameters

• capped – True/False if monomers are capped

• unwrap – True to unwrap final system

• traj – True to build xyz trajectory of polymer growth (True)

• limit – during MD, limit atomic displacement by this max value (LAMMPS ONLY)

• sim – Simulation object for relaxation between polymer growth

• debug – Boolean; print extra-output

Returns

new polymer System

pysimm.apps.random_walk.find_last_tail_vector(s)

pysimm.apps.random_walk.find_last_tail_vector Finds vector defined by bond in the system between the tail atom and its capping atom. Requires list of particles s that formed a monomer connected on previous step of the polymerisation.

Parameters

s – ItemContainer of Particle objects

Returns

list of vector components

pysimm.apps.random_walk.rot_mat_about_axis(v, theta)

pysimm.apps.random_walk.rot_mat_about_axis This function returns the matrix that represents a rotation about vector v by theta degrees. Used for isotactic insertions of monomers

Parameters

• v – vector about which to rotate

• theta – degrees to rotate

Returns

matrix representation of rotation

pysimm.apps.random_walk.define_plane(a1, a2, a3)

pysimm.apps.random_walk.define_plane This function returns the mathematical constants defining a plane containing three input particles

Parameters

• a1 – three atoms or particles

• a2 – three atoms or particles

• a3 – three atoms or particles

Returns

np.array containing a,b,c,d that define the plane a*x + b*y + c*z + d = 0 that contains the input particles

pysimm.apps.random_walk.reflect_coords_thru_plane(atom, plane)

pysimm.apps.random_walk.reflect_coords_thru_plane This function reflects an atom through a plane, and is used for implementing syndiotactic insertions of monomers

Parameters

• atom – either an atom or an array containing x,y,z coordinates for an atom, to be reflected through the plane

• plane – np.array containing a,b,c,d that define a plane, a*x + b*y + c*z + d = 0

Returns

new coordinates after reflection through plane

pysimm.apps.random_walk.scale_monomer(atom, origin, scale)

pysimm.apps.random_walk.scale_monomer This function scales the atom–origin vector. It is used by redo_monomer_insertion to scale the last monomer relative to its attachment point to the polymer chain

Parameters

• atom – either an atom or an array containing x,y,z coordinates for an atom, to be scaled relative to the origin

• origin – either an atom or an array containing x,y,z coordinates for where the “atom” argument should be scaled to

• scale – the factor by which the atom–origin vector should be scaled.

Returns

scaled atom–origin vector

pysimm.apps.random_walk.redo_monomer_insertion(s, m, i)

pysimm.apps.random_walk.redo_monomer_insertion This function is called by random_walk_tacticity if the latest capped monomer insertion resulted in hardcore overlaps. 1) The hardcore overlap is resolved by shrinking the last monomer by a factor of 0.8, iteratively, until there are no more hardcore overlaps. 2) Then the shrunken last monomer is frozen while the rest of the polymer chain is optimized, and the last monomer is scaled in size by 1.05 3) Cycles of contrainedOptimization and regrowth are alternated until a reasonable structure is obtained

Parameters

• s – System is a polymer chain in which the last monomer insertion has generated a hardcore overlap

• m – reference monomer System. Must be a capped monomer, with headCap and tail_cap as the first and last atoms in the .mol file.

• i – number of the offending monomer, used for labelling diagnostic .xyz output files

Returns

nothing; all changes to the polymer chain are written to the argument s_

pysimm.apps.random_walk.constrained_opt(s, m, active)

pysimm.apps.random_walk.constrained_opt This function is called by redo_monomer_insertion and optimizes polymer chain s while keeping the last monomer fixed.

Parameters

• s – System is a polymer chain in which the last monomer insertion has generated a hardcore overlap

• m – reference monomer System. Must be a capped monomer, with headCap and tail_cap as the first and last atoms in the .mol file.

Returns

nothing; all changes to the polymer chain are written to the argument s_

pysimm.apps.random_walk.random_walk_tacticity(m, nmon, s_=None, **kwargs)

pysimm.apps.random_walk.random_walk_tacticity Builds homopolymer with controllable tacticity from capped monomer structure

Parameters

• m – reference monomer System. Must be a capped monomer, with headCap and tail_cap

• file. (as the first and last atoms in the .mol) –

• nmon – total number of monomers to add to chain

• s – System in which to build polymer chain (None)

• extra_bonds – EXPERMINTAL, True if making ladder backbone polymer

• settings – dictionary of simulation settings

• density – density at which to build polymer (0.3)

• forcefield – Forcefield object to acquire new force field parameters

• unwrap – True to unwrap final system

• debug – Boolean; print extra-output (False)

• traj – True to build xyz trajectory of polymer growth (True)

• limit – during MD, limit atomic displacement by this max value (LAMMPS ONLY)

• sim – Simulation object for relaxation between polymer growth

• tacticity – float between 0 and 1. 1 = 100% isotactic insertions 0 = 100% syndiotactic insertions 0.5 = equal changes of isotactic or syndiotactic insertions (i.e. atactic)

• rotation – degrees to rotate monomer per insertion

• md_spacing – how many monomer insertion steps to perform between MD relaxation steps (1)

• error_check – True/False for if monomers should be checked for hardcore overlaps after insertion

Returns

new polymer System

pysimm.apps.random_walk.__check_tags__(m, **kwargs)

pysimm.apps.random_walk.__check_tags__ private method to assert the polymerisation-related decorators assigned to the system ‘m’ that represents the next repetitive unit

pysimm.apps.random_walk.check_tacticity(s, char_idxs, mon_len)

pysimm.apps.random_walk.check_tacticity Method evaluates the local geometry of the polymer System. correct input includes :param char_idxs: characteristic indexes that define the structure of repetetive unit of the monomer. :type char_idxs: list of int :param It is supposed to have 4 elements which define index of: :type It is supposed to have 4 elements which define index of: 1) first atom in backbone; (2 :param backbone;: :type backbone;: 3) closest to backbone atom on the fisrt side chain; (4 :param side chain: :param mon_len: number of atoms in uncapped rep. unit :type mon_len: int

Note: currentely it is assumed that polymerisation does not change local indexing so indexes of corresponding characteristic atoms of the chain can be found by adding a number multiple of mon_len

Returns

angles (in deg) between corresponding pairs of backbone vector (1-2) and normal to the plane produced by to side chains (2-3 x 2-4). Those vectors can be either on one half-space of (3-2-4) plane, so the angle will be >90 (deg) or on the opposite half-spaces of the plane, so the angle <90 (deg). orientations (list of boolean): sequence that tracks local geometry of a chain: records True if two consecutive rep.units form a meso dyad, and False if they form a racemo dyad

Return type

angles (list of float)