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libMobility

Documentation is available at libmobility.readthedocs.io

This repository contains several GPU solvers that can compute the action of the hydrodynamic mobility (at the RPY/FCM level) of a group of particles (in different geometries) with forces acting on them.

In particular, given a group of forces, $\boldsymbol{F}$, and torques, $\boldsymbol{\tau}$, acting on a group of positions, $\boldsymbol{X}$ and directions $\boldsymbol{\tau}$, the libMobility solvers can compute:

$$\begin{bmatrix}d\boldsymbol{X}\\ d\boldsymbol{\tau}\end{bmatrix} = \boldsymbol{\mathcal{\Omega}}\begin{bmatrix}\boldsymbol{F}\\ \boldsymbol{T}\end{bmatrix}dt + \text{prefactor}\sqrt{2 k_B T \boldsymbol{\mathcal{\Omega}}}d\boldsymbol{W}$$

Where $d\boldsymbol{X}$ are the linear displacements, $\boldsymbol{d\tau}$ are the angular displacements, $\boldsymbol{\mathcal{\Omega}}$ is the grand mobility tensor, $\boldsymbol{F}$ are the forces, $\boldsymbol{T}$ are the torques, $\text{prefactor}$ is an user provided prefactor and $d\boldsymbol{W}$ is a collection of i.i.d Weinner processes and $T$ is the temperature.

Each solver in libMobility allows to compute either the deterministic term, the stochastic term, or both at the same time.

For each solver, a python and a C++ interface are provided. All solvers have the same interface, although some input parameters might change (an open boundaries solver does not accept a box size as a parameter).

Repository Structure

This repository is organized into the following directories:

  • solvers/: This directory hosts a subfolder for each solver module. Each subfolder contains the implementation of the libMobility interface specific to that solver.

  • examples/: Contains examples on how to use the library from Python and C++.

  • include/: Includes the essential C++ base classes and utility files needed to construct the modules.

  • devtools/: Contains dev specific scripts and files, like a meta.yaml file to build a conda package for libMobility using conda-build.

  • docs/: Contains the source files for the documentation.

  • tests/: Contains the tests for the library.

Installation

You can install libMobility latest release through our conda channel:

$ conda install -c conda-forge -c stochasticHydroTools libmobility

Check the documentation for additional information on installation, such as how to compile from source.

Python Usage

Importing libMobility will make available any module under "solvers".

An usage example is available in python/example.py.
Calling

	help(SolverName)

will provide more in depth information about the solver.

C++ Usage

In order to use a module called SolverName, the header solvers/SolverName/mobility.h must be included.
If the module has been compiled correctly the definitions required for the functions in mobility.h will be available at solvers/SolverName/mobility.so.
An example is available in cpp/example.cpp.