1. MICCoM
  2. COPSS
  3. COPSS-Polarization-public

Overview

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COPSS

COPSS (Continuum Particle Simulation Suite) is an open source, libMesh based, software for continuum-particle simulations. The package is designed to be easy to use, extensible, and scalable. It currently includes two modules, COPSS-Hydrodynamics to solve hydrodynamic interactions in colloidal suspensions and COPSS-Polarization to solve electrostatic interactions in heterogeneous dielectric media. The algorithms beneath COPSS have been published or under-review, but the code framework, user-interface, etc., are still rough. We are working on improving COPSS and appreciate your contributions.

COPSS-Polarization

COPSS-Polarization solves the electrostatic interactions in charged systems that exhibit sharp discontinuous changes in dielectric permittivity. It is based on an efficient $O(N)$ computational approach to model arbitrary-shaped sharp interfaces separating dielectrics with spatially different dielectric permittivities. A parallel boundary element Poisson solver is the center of the algorithm.

Installation

COPSS is written using libMesh framework. It also requires PETSc for parallel linear equation solvers and ScalFMM for fast multipole computations. Before installing COPSS, you need to install PETSc, libMesh, and ScalFMM. To achieve the best parallel performance of COPSS, we suggest install it on a Linux cluster environment.

0. System environment prep

You should have the following software loaded or compiled

  • CMAKE (version 2.8.12 or later)
  • GCC (version 4.8.4 or later)
  • PYTHON (python 2)
  • OPENMPI (version 1.10.4 or later) or MVAPICH (version mvapich2 2.2b or later)

1. Install PETSc

  • Download PETSC's latest release ( version 3.7.4 or later ) from PETSc download, or git clone PETSc repository:

    mkdir $HOME/projects/

    cd $HOME/projects/

    git clone -b maint https://bitbucket.org/petsc/petsc petsc

  • Configure PETSc:

    cd $HOME/projects/petsc

    ./configure --with-cc=mpicc --with-cxx=mpicxx --with-mpiexec=mpiexec --with-fc=mpif90 –download-fblaslapack --download-scalapack --download-mumps --download-superlu_dist --download-hypre --download-ml --download-parmetis --download-metis --download-triangle --download-chaco --with-debugging=0

    Then follow the instructions on screen to install and test the package.

  • Export environment variables:

    export PETSC_DIR=*/path/to/PETSC* export PETSC_ARCH=*PETSC_ARCH_NAME*

    Add the above codes to ~/.bashrc and source ~/.bashrc before next step. (*/path/to/PETSC* and *PETSC_ARCH_NAME* can be found on the screen after installation.)

    If you meet any trouble, please refer to PETSC installation, or reach out to PETSc community for help.

2. Install libMesh

  • Download libMesh's latest release ( version 1.1.0 or later ) from libMesh download, or git clone libMesh repository:

    cd $HOME/projects/

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

  • Build libMesh:

    cd $HOME/projects/libmesh

    ./configure -prefix=$HOME/projects/libmesh/libmesh-opt --enable-optional --enable-vtk --enable-gzstream --enable-trilinos --disable-strict-lgpl --enable-laspack --enable-capnproto --enable-nodeconstraint --enable-perflog --enable-ifem --enable-petsc --enable-blocked-storage --enable-unique-id --enable-unique-ptr --enable-parmesh 2>&1 | tee my_config_output_opt.txt

    (Read the configuration output, make sure PETSC is enabled).

  • Export environment variables:

    export LIBMESH_DIR=*/path/to/LIBMESH*

    **Add the above codes to ~/.bashrc and source ~/.bashrc before next step.

    If you meet any trouble, please refer to libMesh installation, or reach out to libMesh community for help.

3. Install ScalFMM

  • COPSS-Polarization houses its own version of ScalFMM that is specifically modified for the polarization problem. Download the latest version

    cd /path/to/where/you/want/to/install/copss

    git clone https://bitbucket.org/COPSS/copss-polarization-public.git

    cd copss/contrib/scalfmm/

  • Configure ScalFMM:

    cd scalfmm/

    mkdir Build

    cd Build

    cmake .. -DSCALFMM_USE_MPI=ON -DSCALFMM_USE_FFT=OFF -DSCALFMM_USE_SSE=OFF -DSCALFMM_USE_AVX=OFF -DCMAKE_INSTALL_PREFIX=../Install

    make

    make install

    If you meet any trouble, please refer to ScalFMM Build, or reach out to ScalFMM community for help.

4. Install COPSS-Polarization

  • Compile the codes

    cd /path/to/copss/src/

    make

  • Run the system

    cp /path/to/copss/examples/sphere/2_spheres

    python run.py (You can define how many cores you want to run on in run.py)

    You need to set up your system in control.in and interfaces.in. More details can be found in our documentation.

Build documentation

After you have build COPSS-Polarization you can further build the documentation from doxygen/ directory. Make sure you have Doxygen ready:

doxygen Doxyfile.bak

Then you can view the documentation in IE browser:

google-chrome html.index.html

What's next

  • Coupling COPSS with molecular dynamics package LAMMPS
  • Coupling COPSS with hydrodynamics calculations (COPSS-Hydrodynamics developed by COPSS team).
  • More user friendly interface.
  • etc...

Contribution

Hydrodynamic and electrostatic interactions are ubiquitous in nature and technology, including but not limited to colloidal, biological, granular systems, etc. COPSS is trying to solve these problems in a efficient and scalable manner. Contributions on the code structure, parallel-performance, applications are much appreciated.

Contact

Algorithm

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

Main contributors

License

  • The codes are open-source and distributed under the GNU GPL license, and may not be used for any commercial or for-profit purposes without our permission.