pylimer_tools_cpp package

Module contents

pylimer_tools_cpp Module

pylimer_tools_cpp

A collection of utility python functions for handling LAMMPS output and polymers in Python.

Functions

do_linear_walk_chain_from_to(box, ...[, ...])	Get coordinates linearly interpolated from one point to another (both exclusive).
do_random_walk(chain_len[, bead_distance, ...])	Do a random walk, return the coordinates of each point visited.
do_random_walk_chain_from_to(box, ...[, ...])	Do a random walk from one point to another.
do_random_walk_chain_from_to_mc(box, ...[, ...])	Do a random walk from one point to another.
inverse_langevin(x)	A somewhat accurate (for \(x \in (-1, 1)\)) implementation of the inverse Langevin function.
randomly_sample_entanglements(universe, ...)	Randomly find pairs of atoms that are close together and could be entanglements
split_csv(file_path[, delimiter])	Read a file containing a number of CSVs.
version_information()	Returns a string of the the current version, incl.

Classes

Atom(*args, **kwargs)	A single bead or atom.
AtomPairEntanglements(self)	A struct to store pairs of atoms that are close together and could be entanglements.
AtomStyle(self, value)	An enumeration of the LAMMPS atom styles.
AveFileReader(self, file_path)	Alternative implementation of the data file reader implemented in pylimer_tools.read_lammps_output_file.read_averages_file().
BackTrackStatus(self, value)	Enum for controlling the strand linking process in linkStrandsCallback.
Box(*args, **kwargs)	The box that the simulation is run in.
ComputedDoubleValues(self, value)	Floating point output quantities
ComputedIntValues(self, value)	Integer output quantities
DPDSimulator(self, universe[, ...])	A quick-and-dirty implementation of the dissipative particle dynamics (DPD) simulation with slip-springs as presented by Langeloth et al. [LMBohmMullerPlathe13] and Schneider et al. [SFKarimiVarzanehMullerPlathe21].
DataFileReader(self)	A reader for LAMMPS's write_data files.
DataFileWriter(self, universe)	A class to write a LAMMPS data file from a universe.
DumpFileReader(self, path_of_file_to_read)	A reader for LAMMPS's dump files.
ExitReason(self, value)	An enum representing the reason for exiting the simulation or optimization procedure.
LazyUniverseSequenceIterator	An iterator to iterate throught the universes in UniverseSequence.
LinearMaxDistanceProvider(self, ...)	For MC generation, converts the \(N\) to a maximum distance within which to sample.
LinkSwappingMode(self, value)	How slip-links may act when they reach each-other or even a crosslink.
MCUniverseGenerator(self[, lx, ly, lz])	A pylimer_tools_cpp.Universe generator using a Monte-Carlo procedure.
MEHPForceBalance(self, universe[, ...])	A small simulation tool for quickly minimizing the force between the crosslinker beads.
MEHPForceBalance2(*args, **kwargs)	A small simulation tool for quickly minimizing the force between the crosslinker beads.
MEHPForceEvaluator(self)	The base interface to change the way the force is evaluated during a MEHP run.
MEHPForceRelaxation(self, universe[, ...])	A small simulation tool for quickly minimizing the force between the crosslinker beads.
MaxDistanceProvider	A generic implementation of a class, that shall provide a maximum distance for the MC sampling.
Molecule(self, arg0, arg1, arg2, arg3)	An (ideally) connected series of atoms/beads.
MoleculeIterator	An iterator to iterate through the atoms in Molecule.
MoleculeType(self, value)	An enum representing the type of molecule/chain/strand.
NeighbourList(self, atoms, box, cutoff)	Gives access to somewhat fast queries on the neighbourhood of atoms.
NoMaxDistanceProvider(self)	For MC generation, to disable the neighbour list usage.
NonGaussianSpringForceEvaluator(self[, ...])	This is equal to a spring evaluator for Langevin chains.
NormalModeAnalyzer(self, spring_from, spring_to)	Compute the normal modes and predict the loss/storage moduli.
OutputConfiguration(self)	A configuration object to configure the output values and frequency for simulation classes in this package.
SLESolver(self, value)	Solver for sparse linear equation systems
SimpleSpringMEHPForceEvaluator(self[, kappa])	This is equal to a spring evaluator for Gaussian chains.
SimplifiedBalance2Network	A more efficient structure of the network for use in MEHPForceBalance2.
SimplifiedBalanceNetwork	A more efficient structure of the network for use in MEHP force balance, namely MEHPForceBalance, though also passable to namely MEHPForceBalance2.
SimplifiedNetwork	A more efficient structure of the network for use in MEHP, namely MEHPForceRelaxation.
StructureSimplificationMode(self, value)	How the structure shall be simplified during the optimization in order to remove non-trapped entanglement links.
Universe(self, Lx, Ly, Lz)	Represents a full Polymer Network structure, a collection of molecules.
UniverseSequence(self)	This class represents a sequence of Universes, with the Universe's data only being read on request.
ZScoreMaxDistanceProvider(self, ...)	For MC generation, converts the \(N\) to a maximum distance within which to sample.

Variables

STOP	Enum for controlling the strand linking process in linkStrandsCallback.
TRACK_BACKWARD	Enum for controlling the strand linking process in linkStrandsCallback.
TRACK_FORWARD	Enum for controlling the strand linking process in linkStrandsCallback.