How to use the Atomic Lab code

Download the Atomic Lab source code. Open the solution in MonoDevelop, monodevelop Atomic.sln. Compile and run by pressing F5. Alternatively, use the xbuild tool to compile the project:

xbuild Atomic.sln
mono Atomic.Samples/bin/Debug/Atomic.exe


The exe file contains CLR bytecode and is not a Windows executable despite the name. It's recommended to add your own code to a console project in the solution file. This project must have a reference to the Atomic project.

Prerequisites

On Debian/Ubuntu the following packages must be installed to use all components of the library:

apt-get install mono-complete monodevelop gawk libgsl0-dev coinor-libipopt-dev libmumps-seq-4.10.0


Assuming the directory ~/local in the home directory contains local binary and library files, the following steps installs all prerequisites. Make sure to update global variables in .bash_profile:

export PATH=$HOME/bin:$HOME/local/bin:$HOME/local/vesta:$PATH
export LD_LIBRARY_PATH=$HOME/local/lib:$LD_LIBRARY_PATH


If using MonoDevelop from Debian/Ubuntu it's necessary to create a local monodevelop script,
~/bin/monodevelop, otherwise LD_LIBRARY_PATH will be overwritten:

#!/bin/bash
source ~/.bash_profile
/usr/bin/monodevelop

Building Mono manually

To build Mono from the source on a Linux cluster:

cd ~/local
wget http://download.mono-project.com/sources/mono/mono-2.11.4.tar.bz2
tar -xjvf mono-2.11.4.tar.bz2
cd mono-2.11.4
./configure --prefix=$HOME/local
make
make install

VESTA

Used for atomic structure visualization.

cd ~/local
wget http://www.geocities.jp/kmo_mma/crystal/download/VESTA-x86_64.tar.bz2
tar -xjvf VESTA-x86_64.tar.bz2
mv VESTA-x86_64 vesta


Make sure it's added to PATH by added the following to ~/.bashrc:

export PATH=$HOME/local/vesta:$PATH

ATAT

Cluster expansion tool.

cd ~/local
wget http://www.brown.edu/Departments/Engineering/Labs/avdw/atat/atat3_00.tar.gz
tar -xzvf atat3_00.tar.gz
cd atat
./foolproof BINDIR=$HOME/local/bin
make BINDIR=$HOME/local/bin
make install BINDIR=$HOME/local/bin

IPOPT

Required to do non-linear numerical optimization. Install the Debian/Ubuntu package above or download and compile IPOPT source code.

Run the makeipopt script in Atomic Lab root directory to build the libipoptw.so shared object wrapper.

Spglib

Space group library used to determine symmetries. This is only needed of the SpaceGroup property of the Structure class is used. Determines space group number and space group symmetries.

cd ~/local
wget http://downloads.sourceforge.net/project/spglib/spglib/spglib-1.4/spglib-1.4.1.tar.gz
tar -xzvf spglib-1.4.1.tar.gz
cd spglib-1.4.1
./configure --prefix=$HOME/local
make
make install

Phonopy

Phonopy is used to compute phonon dispersion curves and thermal properties from VASP linear-response code. Additional Debian/Ubuntu packages:

apt-get install python-dev python-numpy python-matplotlib python-tk python-lxml python-yaml python-scipy


cd ~/local
wget http://downloads.sourceforge.net/project/phonopy/phonopy/phonopy-1.7/phonopy-1.7.3.tar.gz
tar -xzvf phonopy-1.7.3.tar.gz
cd phonopy-1.7.3
python setup.py install --home=$HOME/local


Update ~/.bash_profile:

export PYTHONPATH=$HOME/local/lib/python:$PYTHONPATH

Last edited Sep 25, 2013 at 10:24 PM by bakkedal, version 6