FBIM

Fluctuating Boundary Integral Method (FBIM) by Yuanxun Bao, Manas Rachh, Eric E. Keaveny, Leslie Greengard and Aleksandar Donev

This repository contains demo codes for simulating the overdamped Brownian Dynamics of suspension of rigid particles using boundary integral method.

For details of the method, see the paper: A fluctuating boundary integral method for Brownian suspensions, Y. Bao, M. Rachh, E. Keaveny, L. Greengard and A. Donev, J. Comp. Phys., 374:1094–1119, 2018 arXiv

Table of Contents

• libFBEM: contains routines needed for FBIM

• libMatCode: contains routines for exporting matrices needed for FBIM

• SingQuad: codes for exporting singular quadrature as a matrix

• SingleBodyTest: demo codes for BD simulation of a single body (disk, ellipse, starfish)

Instructions

1. First, open MATLAB and compile mex codes:

• cd libFBEM and mex -v fastgridding2d_mex.c.
• cd libMatCode and mex -v expint_eone.C -I/usr/local/include/ -lgsl.

2. Then run BD_EM_onedisk_precompute.m, copy the value paramEwald_ref.xi, and paste it to XI= in makendiskMsing_alpert.

3. Go to SingleBodyTest, in command line, run make -f makendiskMsing_alpert to export Alpert quadrature as a matrix.

4. Run BD_EM_onedisk_precompute.m again to finish precomputation. Repeat 2-4 if you change the parameters.

5. Run BD_EM_onedisk.m for simulating free diffusion of a single disk.