curvedSpaceSim: A framework for simulating particles interacting along geodesics

Abstract

A large number of powerful, high-quality, and open-source simulation packages exist to efficiently perform molecular dynamics simulations, and their prevalence has greatly accelerated discoveries across a wide range of scientific domains. These packages typically simulate particles in flat (Euclidean) space, with options to specify a variety of boundary conditions. While more exotic, many physical systems are constrained to and interact across curved surfaces, such as organisms moving across the landscape, colloids pinned at curved fluid-fluid interfaces, and layers of epithelial cells forming highly curved tissues. The calculation of distances and the updating of equations of motion in idealized geometries (namely, on surfaces of constant curvature) can be done analytically, but it is much more challenging to efficiently perform molecular-dynamics-like simulations on arbitrarily curved surfaces. This article discusses a simulation framework which combines tools from particle-based simulations with recent work in discrete differential geometry to model particles that interact via geodesic distances and move on an arbitrarily curved surface. We present computational cost estimates for a variety of surface complexities with and without various algorithmic specializations (e.g., restrictions to short-range interaction potentials, or multi-threaded parallelization). Our flexible and extensible framework is set up to easily handle both equilibrium and non-equilibrium dynamics, and will enable researchers to access time- and particle-number-scales previously inaccessible.

Program summary

Program Title: curvedSpaceSim

CPC Library link to program files: https://doi.org/10.17632/wc7nxf93ym.1

Developer's repository link: https://github.com/sussmanLab/curvedSpaceSim

Licensing provisions: GPLv3

Programming language: C++

Nature of problem: Molecular-dynamics-like simulations of degrees of freedom evolving on a curved two-dimensional manifold according to standard equilibrium or non-equilibrium equations of motion and interacting via geodesics.

Solution method: We discretize both time and space, using modern tools from discrete differential geometry to efficiently find geodesic paths and distances. MPI parallelization is implemented to access large system sizes, and where appropriate (e.g., when dealing with short-ranged inter-particle potentials) we implement the ability to aggressively prune data structures, greatly decreasing the computational cost of our many-particle simulations.