This package contains 2 mains utilities.
The first one is agate which a glfw based UI and qagate which offers the same functionnalities with a Qt UI.
Agate is mainly designed to work with the Abinit DFT code. However, it can perfectly read some VASP files and other commonly used format.
Agate should help you to visualize in a glance any input file to make sure the structure your simulating is the one you want. You can in some ways modify the structure and save it into a new file with the format you want.
At the moment the most remarkable functionnalities are for molecular dynamics (MD) simulations and phonon analysis. Agate allows you to extract information of a trajectory to interpret the physics on the system. Several tools are included to make life easier.
Here is a small list of quantities that you can extract with agate from an MD simulation:
- OpenGL capabilities
- Extract images to make a movie
- Concatenate several simulations in one
- PIMD aware : centroid, gyration
- NEB/String methode
- Plot functions :
-
Temperature
-
Pression
-
Volume
-
Lattice parameters
- Stress tensor
-
Electronic energy (DFT energy)
- Electronic entropy
- Kinetic energy
- Positions
- Pair Distribution Function
- Mean Square displacements
- Positions autocorrelation
- Velocities autocorrelation
- Phonon density of states
Ans some phonon related capabilities:
- Visualize indivual or combined mode(s)
- Extract dominant q vectors
- Extract indivual mode amplitude
- Construct your own structure with condensed phonons
Altough the abiout package is available on Windows, MacOS and Linux, only the linux installation procedure will be presented here. For MacOS, you can almost follow the From the source procedure.
The PPA contains package for all maintained Ubuntu distributions. Simply run
sudo add-apt-repository ppa:piti-diablotin/abiout
sudo apt-get update
sudo apt-get install abiout
and you are done !
Simply execute agate or qagate in a terminal.
First you need to install some dependancies. On Ubuntu <= 15.04
sudo apt-get install debhelper autotools-dev automake autoconf m4 libjpeg8-dev libpng3-dev libnetcdf-dev libnetcdfc++4 libcurl3-dev libfreetype6-dev libglfw-dev libeigen3-dev fontconfig libglu1-mesa-dev wget unzip cmake xorg-dev ttf-ubuntu-font-family libxml2-dev gnuplot-qt libyaml-cpp-dev libboost-dev qtbase5-dev qt5-qmake qt5-default libqt5opengl5-dev libfftw3-dev
On Ubuntu >= 16.04 (15.10 not maintained anymore)
debhelper (>= 8.0.0), autotools-dev, automake, autoconf, m4, libjpeg8-dev, libpng-dev, libnetcdf-dev, libnetcdf-c++4-dev, libcurl3-dev, libfreetype6-dev, libglfw3-dev, libeigen3-dev, fontconfig, libglu1-mesa-dev, ttf-ubuntu-font-family, libxml2-dev, gnuplot-qt, libyaml-cpp-dev, libboost-dev, qtbase5-dev, qt5-qmake, qt5-default, libqt5opengl5-dev, libfftw3-dev
Then the procedure is the same. Compile spglib if desired with
tar xfz spglib-1.9.9.tar.gz
cd spglib-1.9.9 && mkdir build && cd build && ../configure && make && sudo make install
Finally compile abiout with
./autogent.sh
./configure --with-qt
make
sudo make install
That's it.
You will find in the Win_x86 and OSX directories a .exe for windows and a .dmg for MacOS that will install everything needed
WARNING: Thoses 2 versions are 2 years old and completely outdated !!! Use at your own risk. (WIP for new versions)