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https://github.com/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
https://github.com/piti-diablotin/agate
abinit dft phonon simulations
Last synced: about 2 months ago
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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
- Host: GitHub
- URL: https://github.com/piti-diablotin/agate
- Owner: piti-diablotin
- License: gpl-3.0
- Created: 2017-09-17T13:50:15.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2024-08-15T17:19:24.000Z (4 months ago)
- Last Synced: 2024-08-15T19:33:46.490Z (4 months ago)
- Topics: abinit, dft, phonon, simulations
- Language: C++
- Homepage:
- Size: 48.9 MB
- Stars: 7
- Watchers: 2
- Forks: 9
- Open Issues: 0
-
Metadata Files:
- Readme: README
- Changelog: ChangeLog
- License: COPYING
- Authors: AUTHORS
Awesome Lists containing this project
README
[](https://travis-ci.com/piti-diablotin/agate)
[](https://github.com/piti-diablotin/agate/releases/latest)
[](https://zenodo.org/badge/latestdoi/103832429)
# 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](www.abinit.org "Abinit website") DFT code. However, it can perfectly read some [VASP](www.vasp.at "VASP website") 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](https://github.com/piti-diablotin/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](https://github.com/piti-diablotin/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](https://github.com/piti-diablotin/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
```