Several pair styles, bond styles, and integration fixes for coarse-grainedmodelling of single- and double-stranded DNA and RNA based on the oxDNA andoxRNA model of Doye, Louis and Ouldridge. The package includes Langevin-typerigid-body integrators with improved stability.
Several extensions of the dissipative particle dynamics (DPD)method. Specifically, energy-conserving DPD (eDPD) that can modelnon-isothermal processes, many-body DPD (mDPD) for simulatingvapor-liquid coexistence, and transport DPD (tDPD) for modelingadvection-diffusion-reaction systems. The equations of motion of theseDPD extensions are integrated through a modified velocity-Verlet (MVV)algorithm.
A pair style for smoothed dissipative particle dynamics (SDPD), whichis an extension of smoothed particle hydrodynamics (SPH) to mesoscalewhere thermal fluctuations are important (see theSPH package).Also two fixes for moving and rigid body integration of SPH/SDPD particles(particles of atom_style meso).
A fix that wraps the Parallelizable Open source Efficient MultibodySoftware (POEMS) library, which is able to simulate the dynamics ofarticulated body systems. These are systems with multiple rigidbodies (collections of particles) whose motion is coupled byconnections at hinge points.
Fixes which enforce rigid constraints on collections of atoms orparticles. This includes SHAKE and RATTLE, as well as variousrigid-body integrators for a few large bodies or many small bodies.Also several computes which calculate properties of rigid bodies. 2b1af7f3a8