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¶
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Get coordinates linearly interpolated from one point to another (both exclusive). |
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Do a random walk, return the coordinates of each point visited. |
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Do a random walk from one point to another. |
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Do a random walk from one point to another. |
A somewhat accurate (for \(x \in (-1, 1)\)) implementation of the inverse Langevin function. |
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Randomly find pairs of atoms that are close together and could be entanglements |
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Read a file containing a number of CSVs. |
Returns a string of the the current version, incl. |
Classes¶
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A single bead or atom. |
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A struct to store pairs of atoms that are close together and could be entanglements. |
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An enumeration of the LAMMPS atom styles. |
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Alternative implementation of the data file reader implemented in |
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Enum for controlling the strand linking process in linkStrandsCallback. |
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The box that the simulation is run in. |
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Floating point output quantities |
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Integer output quantities |
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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]. |
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A reader for LAMMPS's write_data files. |
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A class to write a LAMMPS data file from a universe. |
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A reader for LAMMPS's dump files. |
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An enum representing the reason for exiting the simulation or optimization procedure. |
An iterator to iterate throught the universes in |
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For MC generation, converts the \(N\) to a maximum distance within which to sample. |
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How slip-links may act when they reach each-other or even a crosslink. |
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A |
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A small simulation tool for quickly minimizing the force between the crosslinker beads. |
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A small simulation tool for quickly minimizing the force between the crosslinker beads. |
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The base interface to change the way the force is evaluated during a MEHP run. |
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A small simulation tool for quickly minimizing the force between the crosslinker beads. |
A generic implementation of a class, that shall provide a maximum distance for the MC sampling. |
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An (ideally) connected series of atoms/beads. |
An iterator to iterate through the atoms in |
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An enum representing the type of molecule/chain/strand. |
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Gives access to somewhat fast queries on the neighbourhood of atoms. |
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For MC generation, to disable the neighbour list usage. |
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This is equal to a spring evaluator for Langevin chains. |
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Compute the normal modes and predict the loss/storage moduli. |
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A configuration object to configure the output values and frequency for simulation classes in this package. |
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Solver for sparse linear equation systems |
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This is equal to a spring evaluator for Gaussian chains. |
A more efficient structure of the network for use in |
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A more efficient structure of the network for use in MEHP force balance, namely |
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A more efficient structure of the network for use in MEHP, namely |
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How the structure shall be simplified during the optimization in order to remove non-trapped entanglement links. |
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Represents a full Polymer Network structure, a collection of molecules. |
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This class represents a sequence of Universes, with the Universe's data only being read on request. |
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For MC generation, converts the \(N\) to a maximum distance within which to sample. |
Variables¶
Stop the linking process |
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Track backward in the linking process |
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Continue linking forward |