piti-diablotin / agate

Open-source software to post-process Abinit (https://www.abinit.org) data and more ! See qAgate (https://github.com/piti-diablotin/qAgate) for more advanced Graphical User Interface

Presentation

Agate is a tool engine to visualize and post-process data from ab-initio codes. It 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 you're 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.

A new Qt GUI is available and is called qAgate.

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.

Some features

Here is a small list of quantities that you can extract with agate from a 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
  • Phonons band structures (if tdep from abinit is available)

  And 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

How to install

Altough the package is available on Windows, MacOS and Linux, only the Linux and MacOS under Hombrew procedures will be presented.

Ubuntu

Personal Repository

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 agate

and you are done ! Simply execute agate in a terminal.

From sources

First you need to install some dependancies. On Ubuntu == 14.04

sudo apt-get install g++ autotools-dev automake autoconf m4 libtool libncurses5-dev libjpeg8-dev libpng3-dev libnetcdf-dev libcurl3-dev libfreetype6-dev libglfw-dev libeigen3-dev fontconfig ttf-ubuntu-font-family libxml2-dev gnuplot-qt libyaml-cpp-dev libfftw3-dev libssh-dev libreadline-dev cxxtest git

On Ubuntu >= 16.04 (LTS versions and last non-LTS)

sudo apt install g++ autotools-dev automake autoconf m4 libtool libncurses5-dev libjpeg8-dev libpng-dev libnetcdf-dev libcurl3-dev libfreetype6-dev libglfw3-dev libeigen3-dev fontconfig ttf-ubuntu-font-family libxml2-dev gnuplot-qt libyaml-cpp-dev libfftw3-dev libssh-dev libreadline-dev cxxtest git

Then the procedure is the same. Compile agate with

git clone https://github.com/piti-diablotin/agate.git
cd agate 
./autogen.sh
mkdir build
cd build
../configure 
make
sudo make install

That's it. Note that agate will be installed in /usr/local/ (prefix to use to compile qAgate).

Debian 10

The procedure is the same as for ubuntu with 2 modifications: the dependencies and the configure steps

su
apt install g++ autotools-dev automake autoconf m4 libtool libncurses5-dev libjpeg62-turbo-dev libpng-dev libnetcdf-dev libcurl3-dev libfreetype6-dev libglfw3-dev libeigen3-dev fontconfig libxml2-dev gnuplot-qt libyaml-cpp-dev libfftw3-dev libssh-dev libreadline-dev cxxtest git make
git clone https://github.com/piti-diablotin/agate.git
cd agate
./autogen.sh
mkdir build
cd build
../configure --disable-dependency-tracking
make
make install

Note that agate will be installed in /usr/local/ (prefix to use to compile qAgate).

Fedora

It is exactly the same as for Ubuntu with the following packages (Fedora 22)

sudo su
yum install autoconf automake m4 libjpeg-turbo-devel libpng-devel netcdf-devel libcurl-devel freetype-devel glfw-devel eigen3-devel fontconfig wget unzip libxml2-devel yaml-cpp-devel fftw-devel libssh-devel readline-devel cxxtest git gcc-c++ gnuplot
git clone https://github.com/piti-diablotin/agate.git
cd agate 
./autogen.sh
mkdir build
cd build
../configure
make
make install

MacOS X

Homebrew

A tap formula is available. You need first to had the tap. You can add the tap from piti-diablotin which is the most up-to-date, or the one from abinit.

brew tap piti-diablotin/tap
# or
brew tap abinit/tap

Then just run

brew install agate

You can now run agate from your terminal.

From sources

The procedure has been tested on MacOS only with Homebrew. Macport should work too.

brew install automake autoconf curl cxxtest eigen fftw freetype git glfw gnuplot jpeg libpng libssh libtool libxml2 netcdf yaml-cpp readline
git clone https://github.com/piti-diablotin/agate.git
cd agate 
./autogen.sh
mkdir build
cd build
../configure
make
sudo make install

agate's Issues

error: 'pi' was not declared in this scope

Compiler: gcc version 7.3.0 (crosstool-NG 1.23.0.452-d158)

make[2]: Entering directory '$SRC_DIR/src/window'
CXX window.lo
window.cpp: In member function 'virtual void Window::loopStep()':
window.cpp:464:86: error: 'pi' was not declared in this scope
this->lookAt(paral_proj? totalfactor : totalfactor/tan(_optionf["perspective"] * pi/(2.*180.)),0,0,0);
^~
window.cpp:464:86: note: suggested alternative:
In file included from ../../include/io/configparser.hxx:35:0,
from ../../include/io/configparser.hpp:163,
from ../../include/window/window.hpp:44,
from window.cpp:27:
../../include/base/phys.hpp:54:16: note: 'phys::pi'
const double pi = 3.1415926535897932384626433832795; ///< pi ...
^~
make[2]: *** [Makefile:401: window.lo] Error 1
make[2]: Leaving directory '$SRC_DIR/src/window'
make[1]: *** [Makefile:488: all-recursive] Error 1
make[1]: Leaving directory '$SRC_DIR'
make: *** [Makefile:399: all] Error 2