/ABP_LAMMPS

custom fixes to model active Brownian particles in LAMMPS

Primary LanguageC++

ABP_LAMMPS

A collection of custom scripts to modify LAMMPS for the modelling of active Brownian particles

Contents

  1. fix_activeBD
  2. fix_active3D

The models

Active Brownian Particles in 3D (fix_active3D)

We model active colloids as active Brownian particles, which propel with a constant velocity vp, along their individual direction vectors e, which in turn are subject to rotational diffusion. We implement this model through molecular dynamics simulations using a customised version of the open source LAMMPS package, which integrates the following equations of motion:

Here is the particle velocity, is the magnitude of the constant applied active velocity, and F is the inter-particle force. The thermal fluctuations promoting translational diffusion are included in the Gaussian white-noise term , where , and DT is the translational diffusion coefficient. Thermal noise driving rotational diffusion of the direction vector e is represented by , where , and DR is the rotational diffusion coefficient. The two diffusion coefficients are related via .

Induced-charge electrophoresis (ICEP) Janus particles as active Brownian particles (fix_activeBD)

We model active ICEP Janus colloids as active Brownian particles. Assuming the external field driving particle motion is in the z direction, the particles undergo active motion in the xy plane and are diffusive in the z plane. For a particle being driven at a velocity , the particle velocity evolves according to:

and the orientation of the active propulsion is given by:

Adding code to LAMMPS

There are two ways to do this: make and CMAKE.

Adding code to LAMMPS with make

  • Download script and paste into the /src/ directory of your copy of LAMMPS. For example:
cp fix_activeBD.* mylammps/src
  • For activeBd and active3D we need the DIPOLE package. To add these packages to your build of LAMMPS, type the following in the LAMMPS /src/ directory.
make yes-dipole
  • Now we can build. For running on a single processor you can use serial, for parrallel you need mpi:
make serial
make mpi

This will produce the LAMMPS executable lmp_serial and lmp_mpi in lammps/src.

Adding code to LAMMPS with CMAKE

  • Download script and paste into the /src/ directory of your copy of LAMMPS. For example:
cp fix_activeBD.* mylammps/src
  • set up the build directory:
cd mylammps
mkdir build
cd build
  • For activeBD and active3D we need the DIPOLE package:
cmake -D PKG_DIPOLE=on ../cmake
  • Now build:
cmake --build .
  • This will create the lmp executable in the mylammps/build directory. You can install this executable to your system with:
make install