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:
- 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
- Get an account on a server with a pre-installed version (RECOMMENDED)
- 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:
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.