# 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`](api/pylimer_tools_cpp.do_linear_walk_chain_from_to.html.md#pylimer_tools_cpp.do_linear_walk_chain_from_to)(box, ...[, ...]) | Get coordinates linearly interpolated from one point to another (both exclusive). | |-----------------------------------------------------------------------------------------------------------------------------------------------------|--------------------------------------------------------------------------------------------| | [`do_random_walk`](api/pylimer_tools_cpp.do_random_walk.html.md#pylimer_tools_cpp.do_random_walk)(chain_len[, bead_distance, ...]) | Do a random walk, return the coordinates of each point visited. | | [`do_random_walk_chain_from_to`](api/pylimer_tools_cpp.do_random_walk_chain_from_to.html.md#pylimer_tools_cpp.do_random_walk_chain_from_to)(box, ...[, ...]) | Do a random walk from one point to another. | | [`do_random_walk_chain_from_to_mc`](api/pylimer_tools_cpp.do_random_walk_chain_from_to_mc.html.md#pylimer_tools_cpp.do_random_walk_chain_from_to_mc)(box, ...[, ...]) | Do a random walk from one point to another. | | [`inverse_langevin`](api/pylimer_tools_cpp.inverse_langevin.html.md#pylimer_tools_cpp.inverse_langevin)(x) | A somewhat accurate (for $x \in (-1, 1)$) implementation of the inverse Langevin function. | | [`randomly_sample_entanglements`](api/pylimer_tools_cpp.randomly_sample_entanglements.html.md#pylimer_tools_cpp.randomly_sample_entanglements)(universe, ...) | Randomly find pairs of atoms that are close together and could be entanglements | | [`split_csv`](api/pylimer_tools_cpp.split_csv.html.md#pylimer_tools_cpp.split_csv)(file_path[, delimiter]) | Read a file containing a number of CSVs. | | [`version_information`](api/pylimer_tools_cpp.version_information.html.md#pylimer_tools_cpp.version_information)() | Returns a string of the the current version, incl. | ### Classes | [`Atom`](api/pylimer_tools_cpp.Atom.html.md#pylimer_tools_cpp.Atom)(\*args, \*\*kwargs) | A single bead or atom. | |-------------------------------------------------------------------------------------------------------------------------------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| | [`AtomPairEntanglements`](api/pylimer_tools_cpp.AtomPairEntanglements.html.md#pylimer_tools_cpp.AtomPairEntanglements)(self) | A struct to store pairs of atoms that are close together and could be entanglements. | | [`AtomStyle`](api/pylimer_tools_cpp.AtomStyle.html.md#pylimer_tools_cpp.AtomStyle)(\*values) | An enumeration of the LAMMPS atom styles. | | [`AveFileReader`](api/pylimer_tools_cpp.AveFileReader.html.md#pylimer_tools_cpp.AveFileReader)(self, file_path) | Alternative implementation of the data file reader implemented in [`pylimer_tools.io.read_lammps_output_file.read_averages_file()`](pylimer_tools.io.html.md#pylimer_tools.io.read_lammps_output_file.read_averages_file). | | [`BackTrackStatus`](api/pylimer_tools_cpp.BackTrackStatus.html.md#pylimer_tools_cpp.BackTrackStatus)(\*values) | Enum for controlling the strand linking process in linkStrandsCallback. | | [`Box`](api/pylimer_tools_cpp.Box.html.md#pylimer_tools_cpp.Box)(\*args, \*\*kwargs) | The box that the simulation is run in. | | [`ComputedDoubleValues`](api/pylimer_tools_cpp.ComputedDoubleValues.html.md#pylimer_tools_cpp.ComputedDoubleValues)(\*values) | Floating point output quantities | | [`ComputedIntValues`](api/pylimer_tools_cpp.ComputedIntValues.html.md#pylimer_tools_cpp.ComputedIntValues)(\*values) | Integer output quantities | | [`DPDSimulator`](api/pylimer_tools_cpp.DPDSimulator.html.md#pylimer_tools_cpp.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](acknowledgements.html.md#id11)] and Schneider *et al.* [[SFKarimiVarzanehMullerPlathe21](acknowledgements.html.md#id10)]. | | [`DataFileReader`](api/pylimer_tools_cpp.DataFileReader.html.md#pylimer_tools_cpp.DataFileReader)(self) | A reader for LAMMPS's write_data files. | | [`DataFileWriter`](api/pylimer_tools_cpp.DataFileWriter.html.md#pylimer_tools_cpp.DataFileWriter)(self, universe) | A class to write a LAMMPS data file from a universe. | | [`DumpFileReader`](api/pylimer_tools_cpp.DumpFileReader.html.md#pylimer_tools_cpp.DumpFileReader)(self, path_of_file_to_read) | A reader for LAMMPS's dump files. | | [`ExitReason`](api/pylimer_tools_cpp.ExitReason.html.md#pylimer_tools_cpp.ExitReason)(\*values) | An enum representing the reason for exiting the simulation or optimization procedure. | | [`LazyUniverseSequenceIterator`](api/pylimer_tools_cpp.LazyUniverseSequenceIterator.html.md#pylimer_tools_cpp.LazyUniverseSequenceIterator) | An iterator to iterate throught the universes in [`UniverseSequence`](api/pylimer_tools_cpp.UniverseSequence.html.md#pylimer_tools_cpp.UniverseSequence). | | [`LinearMaxDistanceProvider`](api/pylimer_tools_cpp.LinearMaxDistanceProvider.html.md#pylimer_tools_cpp.LinearMaxDistanceProvider)(self, ...) | For MC generation, converts the $N$ to a maximum distance within which to sample. | | [`LinkSwappingMode`](api/pylimer_tools_cpp.LinkSwappingMode.html.md#pylimer_tools_cpp.LinkSwappingMode)(\*values) | How slip-links may act when they reach each-other or even a crosslink. | | [`MCUniverseGenerator`](api/pylimer_tools_cpp.MCUniverseGenerator.html.md#pylimer_tools_cpp.MCUniverseGenerator)(self[, lx, ly, lz]) | A [`pylimer_tools_cpp.Universe`](api/pylimer_tools_cpp.Universe.html.md#pylimer_tools_cpp.Universe) generator using a Monte-Carlo procedure. | | [`MEHPForceBalance`](api/pylimer_tools_cpp.MEHPForceBalance.html.md#pylimer_tools_cpp.MEHPForceBalance)(self, universe[, ...]) | A small simulation tool for quickly minimizing the force between the crosslinker beads. | | [`MEHPForceBalance2`](api/pylimer_tools_cpp.MEHPForceBalance2.html.md#pylimer_tools_cpp.MEHPForceBalance2)(\*args, \*\*kwargs) | A small simulation tool for quickly minimizing the force between the crosslinker beads. | | [`MEHPForceEvaluator`](api/pylimer_tools_cpp.MEHPForceEvaluator.html.md#pylimer_tools_cpp.MEHPForceEvaluator)(self) | The base interface to change the way the force is evaluated during a MEHP run. | | [`MEHPForceRelaxation`](api/pylimer_tools_cpp.MEHPForceRelaxation.html.md#pylimer_tools_cpp.MEHPForceRelaxation)(self, universe[, ...]) | A small simulation tool for quickly minimizing the force between the crosslinker beads. | | [`MaxDistanceProvider`](api/pylimer_tools_cpp.MaxDistanceProvider.html.md#pylimer_tools_cpp.MaxDistanceProvider) | A generic implementation of a class, that shall provide a maximum distance for the MC sampling. | | [`Molecule`](api/pylimer_tools_cpp.Molecule.html.md#pylimer_tools_cpp.Molecule)(self, arg0, arg1, arg2, arg3) | An (ideally) connected series of atoms/beads. | | [`MoleculeIterator`](api/pylimer_tools_cpp.MoleculeIterator.html.md#pylimer_tools_cpp.MoleculeIterator) | An iterator to iterate through the atoms in [`Molecule`](api/pylimer_tools_cpp.Molecule.html.md#pylimer_tools_cpp.Molecule). | | [`MoleculeType`](api/pylimer_tools_cpp.MoleculeType.html.md#pylimer_tools_cpp.MoleculeType)(\*values) | An enum representing the type of molecule/chain/strand. | | [`NeighbourList`](api/pylimer_tools_cpp.NeighbourList.html.md#pylimer_tools_cpp.NeighbourList)(self, atoms, box, cutoff) | Gives access to somewhat fast queries on the neighbourhood of atoms. | | [`NoMaxDistanceProvider`](api/pylimer_tools_cpp.NoMaxDistanceProvider.html.md#pylimer_tools_cpp.NoMaxDistanceProvider)(self) | For MC generation, to disable the neighbour list usage. | | [`NonGaussianSpringForceEvaluator`](api/pylimer_tools_cpp.NonGaussianSpringForceEvaluator.html.md#pylimer_tools_cpp.NonGaussianSpringForceEvaluator)(self[, ...]) | This is equal to a spring evaluator for Langevin chains. | | [`NormalModeAnalyzer`](api/pylimer_tools_cpp.NormalModeAnalyzer.html.md#pylimer_tools_cpp.NormalModeAnalyzer)(self, spring_from, spring_to) | Compute the normal modes and predict the loss/storage moduli. | | [`NormalModeSolver`](api/pylimer_tools_cpp.NormalModeSolver.html.md#pylimer_tools_cpp.NormalModeSolver)(\*values) | Solver algorithms for normal mode analysis | | [`OutputConfiguration`](api/pylimer_tools_cpp.OutputConfiguration.html.md#pylimer_tools_cpp.OutputConfiguration)(self) | A configuration object to configure the output values and frequency for simulation classes in this package. | | [`SLESolver`](api/pylimer_tools_cpp.SLESolver.html.md#pylimer_tools_cpp.SLESolver)(\*values) | Solver for sparse linear equation systems | | [`SimpleSpringMEHPForceEvaluator`](api/pylimer_tools_cpp.SimpleSpringMEHPForceEvaluator.html.md#pylimer_tools_cpp.SimpleSpringMEHPForceEvaluator)(self[, kappa]) | This is equal to a spring evaluator for Gaussian chains. | | [`SimplifiedBalance2Network`](api/pylimer_tools_cpp.SimplifiedBalance2Network.html.md#pylimer_tools_cpp.SimplifiedBalance2Network) | A more efficient structure of the network for use in [`MEHPForceBalance2`](api/pylimer_tools_cpp.MEHPForceBalance2.html.md#pylimer_tools_cpp.MEHPForceBalance2). | | [`SimplifiedBalanceNetwork`](api/pylimer_tools_cpp.SimplifiedBalanceNetwork.html.md#pylimer_tools_cpp.SimplifiedBalanceNetwork) | A more efficient structure of the network for use in MEHP force balance, namely [`MEHPForceBalance`](api/pylimer_tools_cpp.MEHPForceBalance.html.md#pylimer_tools_cpp.MEHPForceBalance), though also passable to namely [`MEHPForceBalance2`](api/pylimer_tools_cpp.MEHPForceBalance2.html.md#pylimer_tools_cpp.MEHPForceBalance2). | | [`SimplifiedNetwork`](api/pylimer_tools_cpp.SimplifiedNetwork.html.md#pylimer_tools_cpp.SimplifiedNetwork) | A more efficient structure of the network for use in MEHP, namely [`MEHPForceRelaxation`](api/pylimer_tools_cpp.MEHPForceRelaxation.html.md#pylimer_tools_cpp.MEHPForceRelaxation). | | [`StructureSimplificationMode`](api/pylimer_tools_cpp.StructureSimplificationMode.html.md#pylimer_tools_cpp.StructureSimplificationMode)(\*values) | How the structure shall be simplified during the optimization in order to remove non-trapped entanglement links. | | [`Universe`](api/pylimer_tools_cpp.Universe.html.md#pylimer_tools_cpp.Universe)(self, Lx, Ly, Lz) | Represents a full Polymer Network structure, a collection of molecules. | | [`UniverseSequence`](api/pylimer_tools_cpp.UniverseSequence.html.md#pylimer_tools_cpp.UniverseSequence)(self) | This class represents a sequence of Universes, with the Universe's data only being read on request. | | [`ZScoreMaxDistanceProvider`](api/pylimer_tools_cpp.ZScoreMaxDistanceProvider.html.md#pylimer_tools_cpp.ZScoreMaxDistanceProvider)(self, ...) | For MC generation, converts the $N$ to a maximum distance within which to sample. | ### Variables | [`STOP`](api/pylimer_tools_cpp.STOP.html.md#pylimer_tools_cpp.STOP) | Stop the linking process | |--------------------------------------------------------------------------------------------------|---------------------------------------| | [`TRACK_BACKWARD`](api/pylimer_tools_cpp.TRACK_BACKWARD.html.md#pylimer_tools_cpp.TRACK_BACKWARD) | Track backward in the linking process | | [`TRACK_FORWARD`](api/pylimer_tools_cpp.TRACK_FORWARD.html.md#pylimer_tools_cpp.TRACK_FORWARD) | Continue linking forward |