UPDATE: the new server address is 172.20.64.135 (only espresso 2.1.2j is installed)

A few polymer examples on ESPResSo for PHY-5320

Options:

1. Install ESPResSo (MacOSX, Linux, NOT windows)
   • ESPResSo 2 (RECOMMENDED)- PROS: Fast, Has Constraints (wall+tube), good documentation, CON: uses TCL
   • ESPResSo 3 - PROS: Uses python, CONS: Slow, no constraints, little documentation
2. Get an account on a server with a pre-installed version (RECOMMENDED)
3. Install another package, HOOMD, LAMMPS etc,

This version is only supported with TCL you can download it here: ESPResSo 2

or used the wget command

wget http://download.savannah.gnu.org/releases/espressomd/Espresso-2.1.2j.tar.gz

Unzip the archive and go in the dircectory it created

tar -zxf Espresso-2.1.2j.tar.gz 
cd espresso-2.1.2j

Copy the configuration file over,

wget http://web5.uottawa.ca/www5/p2uo/website/Espresso/myconfig.h

and run the configuration script with

./configure

If everything is fine (which should be if you have all dependencies), go ahead and compile with the make command

make

To test it, try to execute "Espresso"

./Espresso

which should print out something like this:

*******************************************************
*                                                     *
*                    - Espresso -                     *
*                    ============                     *
*      A MPI Parallel Molecular Dynamics Program      *
*                                                     *
*                                                     *
* (c) 2002-2006                                       *
* Max-Planck-Institute for Polymer Research           *
* Mainz, Germany                                      *
*                                                     *
*******************************************************

Get the source code: git clone https://github.com/espressomd/espresso.git go in the directory, and make a new directory called build, go into build and run cmake

cd espresso
mkdir build
cd build
cmake ../

You will see if you need dependencies, if everything seems fine, you can copy the config file here in the "build" directory and compile ESPResSo with "make"

wget  http://web5.uottawa.ca/www5/p2uo/website/Espresso/myconfig.hpp
make

Which hopefully completes successfully. Test by running pypresso

./pypresso

which should bring you to an interactive python shell

[GCC 4.2.1 Compatible Apple LLVM 7.3.0 (clang-703.0.31)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>>

##Installing ESPResSo dependencies

/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
brew update
brew install python
brew install cmake
brew install fftw
pip install numpy

For ESPResSo 3, you need openMPI, boost and cython

brew install open-mpi
brew install boost --with-mpi
brew install boost-python
pip install cython

apt-get install cython

etc etc, same for the other dependencies

I made user accounts on 172.20.64.135, which is only accessible from a UOttawa computer. The accounts name is taken the Univerity of Ottawa identifier are [email protected], and the password is the same thing, but written in capital letters. for example, my University email is [email protected].

This means that for me,

username: dsean092 password: DSEAN092

I can access it via ssh, from a command-line type:

ssh [email protected]

and type in the password when prompted. The first thing you should do is change the password using the command passwd ESPResSo is installed system-wide,

to use python (with espresso 3) use pypresso or use Espresso in which case opens a TCL session.