MICCoM COPSS - Electrostatic Polarization Code

This code solves the electrostatic polarization problem involving arbitrary-shaped polarizable dielectric objects embeded in a dielectric continuum using a boundary element method (BEM). It runs in parallel and utilizes iterative solver GMRES accelerated by a kernel-independent Fast Multipole Method (FMM) with O(N) computational complexity. The code is being developed using libMesh (finite-element library) and ScalFMM (FMM library). The outputs of this code are body forces on each dielectric object and the Exodus file that can be used to visualize the distribution of surface charge densities on each object using e.g. Paraview.

Our method paper has details on the implementation and tests of this code: An O(N) and parallel approach to integral problems by a kernel-independent fast multipole method: Application to polarization and magnetization of interacting particles. If you find our work helpful, we humbly ask you to include a citation of the paper, as a means to support our continuous development of the code.

0. Access the source code

Please fill the form so we can add you as a user to this repository.

1. Install PETSc

You should have a working parallel compiler (OpenMPI or MPICH) on your machine or cluster.
Download PETSc's latest release at this link

We install PETSc by executing the following commands, then follow PETSc's on-screen instructions to finish installation.

./configure --download-hypre=1 --with-ssl=0 --with-debugging=no --with-pic=1 --with-shared-libraries=1 --with-cc=mpicc --with-cxx=mpicxx --with-fc=mpif90 --download-fblaslapack=1 --download-cmake=1 --download-metis=1 --download-parmetis=1 --download-superlu_dist=1 --download-mumps=1 --download-scalapack=1 --CC=mpicc --CXX=mpicxx --FC=mpif90 --F77=mpif77 --F90=mpif90 --CFLAGS='-fPIC -fopenmp' --CXXFLAGS='-fPIC -fopenmp' --FFLAGS='-fPIC -fopenmp' --FCFLAGS='-fPIC -fopenmp' --F90FLAGS='-fPIC -fopenmp' --F77FLAGS='-fPIC -fopenmp'

Be sure to set environmental variables PETSC_DIR and PETSC_ARCH, for example in your .bashrc file

#!bash
export PETSC_DIR=/Users/xikai/Softwares/petsc-3.7.4
export PETSC_ARCH=arch-darwin-c-opt

2. Install libMesh

Download libMesh source code into your machine, for example

cd Softwares
git clone git://github.com/libMesh/libmesh.git

Install libMesh

cd libmesh
mkdir source
mv * source
mkdir build
cd build
../source/configure --prefix=/Users/xikai/Softwares/libmesh/build --with-methods=opt --enable-silent-rules --enable-unique-id --disable-warnings --enable-unique-ptr --enable-openmp --disable-maintainer-mode --enable-petsc-required --disable-timestamps
make
make install

Set the environment variable for libMesh: in your bash profile, add the libMesh directory, for example:
```
#!bash

export LIBMESH_DIR=~/Softwares/libmesh/build
```

3. Install ScalFMM

Follow instructions in the README file in /contrib/scalfmm

4. Compile the application code

Type make in the /src folder. It will generate the executable file.
```
#!linux

make
```

5. Run simulations

Test drive examples here. Instructions for running the application are in README in each specific example's folder.

Wiki

Polarization / Home