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ESPResSo++

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ESPResSo++ is an extensible, flexible, fast and parallel simulation software for soft matter research. It is a highly versatile software package for the scientific simulation and analysis of coarse-grained atomistic or bead-spring models as they are used in soft matter research. ESPResSo and ESPResSo++ have common roots and share parts of the developer/user community. However their development is independent and they are different software packages. ESPResSo++ is free, open-source software published under the GNU General Public License (GPL).

Quick start:

To get a copy of the developer version (most recent version) of ESPResSo++, you can use git or docker. Using docker will give you a binary release (nothing to compile, but performance may not be optimal). If you use git clone or download a tarball, you will have to compile ESPResSo+ yourself, which might lead to better performance.

Using docker:

$ docker pull espressopp/espressopp
$ docker run -it espressopp/espressopp /bin/bash

Using git:

$ git clone https://github.com/espressopp/espressopp.git

Alternatively, you can download a tarball or zip file of previous release versions of ESPResSo++.

Dependencies

C++ Dependencies

  • Boost ( >= 1.69.0)
  • MPI
  • FFTW3
  • GROMACS (required when WITH_XTC flag is enabled)
  • HDF5

Python Dependencies

ESPResSo++ requires Python 3.7 or newer. All required Python packages are listed in requirements.txt. You can install them via: pip3 install -r requirements.txt

Quick install:

$ cd espressopp
$ cmake -DCMAKE_INSTALL_PREFIX=/where/to/install/espressopp .
$ make -j2
$ make install
$ export PYTHONPATH=/where/to/install/espressopp/lib/python3*/site-packages:${PYTHONPATH}

After building go to the examples directory and have a look at the Python scripts.

You can also use Pipenv, simply after compilation call in the root directory

$ pipenv install
$ pipenv shell

then you can go to examples and have a look at the Python scripts.

CMake options

You can customize the build process by applying following CMake flags

  • WITH_XTC - build E++ with support of dumping trajectory to GROMACS xtc files (default: OFF).
  • CMAKE_INSTALL_PREFIX - where the E++ should be installed.
  • CMAKE_CXX_FLAGS - put specific compilation flags.

Then, the flags can be used in cmake

$ cmake . -DWITH_XTC=ON -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_CXX_FLAGS=-O3
$ make

How to install E++ in some Linux distributions

Ubuntu

$ apt-get -qq install -y build-essential openmpi-bin libfftw3-dev python3-dev libboost-all-dev git python3-mpi4py cmake wget python3-numpy ipython3 clang llvm ccache python3-pip doxygen sphinx-common python3-matplotlib graphviz texlive-latex-base texlive-latex-extra texlive-latex-recommended ghostscript libgromacs-dev clang-format curl latexmk libhdf5-dev python3-h5py sudo

$ cd espressopp
$ cmake .
$ make

Fedora

$ dnf install -y make cmake wget git gcc-c++ doxygen python-devel openmpi-devel environment-modules python-pip clang llvm compiler-rt ccache findutils boost-devel boost-python3-devel python-sphinx fftw-devel python-matplotlib texlive-latex-bin graphviz boost-openmpi-devel ghostscript python3-mpi4py-openmpi texlive-hyphen-base texlive-cm texlive-cmap texlive-ucs texlive-ec gromacs-devel hwloc-devel lmfit-devel ocl-icd-devel hdf5-devel python-h5py atlas hdf5 liblzf python-six python-nose python-numpy
$ cd espressopp
$ cmake .
$ make

Documentation

http://espressopp.github.io

Reporting issues

Report bugs on the GitHub issues site