<commit_before>ENVISIoN: Electronic Structure Visualization Studio
===================================================

ENVISIoN is an open source tool/toolkit for electron visualization.

ENVISIoN is implemented using (a modified version of) the Inviwo visualization framework, developed at the Scientific Visualization Group at Linköping University (LiU).

The initial version was developed as part of the course TFYA75: Applied Physics - Bachelor Project, given at Linköping University, Sweden (LiU) spring term 2017. The title of the final report was: "Design och implementing av en interakiv visualisering av elektronstrukturdata". Authors: <NAME>, <NAME>, <NAME>, <NAME>, <NAME>. The project was supervised by <NAME> (main supervisor), <NAME> (expert and client), and <NAME> (expert). The course examinator was <NAME>.

The main part of ENVISoN is built using Python scripting in Inviwo. It provides a set of python 
routines that allows a user with just a few simple commands to:

- Read and parse output from electronic structure codes (presently VASP, and some support for Elk is implemented), storing the result in a structured HDF5 file.
- Generate interactive Inviwo visualization networks for
  tasks common when analyzing electronic structure calculations. 
  Presently there is (to varying degree) support for crystal structures, 
  ab-inito molecular dynamics, charge density, ELF, DOS/pDOS and 
  band structure visualization.

How to build and run ENVISIoN on Ubuntu Linux 17.10
---------------------------------------------------

Requirements: Ubuntu 17.10 with working graphics acceleration.

Create working directory
~~~~~~~~~~~~~~~~~~~~~~~~
::

  mkdir -p ~/ENVISIoN
  cd ~/ENVISIoN

Install dependencies
~~~~~~~~~~~~~~~~~~~~

Git::

  sudo apt-get install git 

Dependencies for Inviwo::

  sudo apt-get install build-essential
  sudo apt-get install cmake cmake-qt-gui cmake-curses-gui
  sudo apt-get install libpython3-dev libpython3-dbg 
  sudo apt-get install mesa-common-dev libglu1-mesa-dev
  sudo apt-get install libxcursor-dev libxinerama-dev libxrandr-dev

Qt5 (Using specifically Qt5.6.1 is highly recommended)::

  wget http://download.qt.io/official_releases/qt/5.6/5.6.1/qt-opensource-linux-x64-5.6.1.run
  chmod +x qt-opensource-linux-x64-5.6.1.run
  [ "$XDG_SESSION_TYPE" == "wayland" ] && xhost si:localuser:root # enable sudo with gui if on Wayland
  sudo ./qt-opensource-linux-x64-5.6.1.run
  [ "$XDG_SESSION_TYPE" == "wayland" ] && xhost -si:localuser:root 
  qtchooser -install Qt5.6.1 /opt/Qt5.6.1/5.6/gcc_64/bin/qmake
  export QT_SELECT=Qt5.6.1

Dependencies for ENVISIoN::

  sudo apt-get install doxygen python-sphinx-rtd-theme
  sudo apt-get install python3-h5py python3-regex

Download ENVISIoN
~~~~~~~~~~~~~~~~~
::

  git clone https://github.com/rartino/ENVISIoN 
<commit_msg>Add python3-numpy to ENVISIoN dependencies<commit_after>ENVISIoN: Electronic Structure Visualization Studio
===================================================

ENVISIoN is an open source tool/toolkit for electron visualization.

ENVISIoN is implemented using (a modified version of) the Inviwo visualization framework, developed at the Scientific Visualization Group at Linköping University (LiU).

The initial version was developed as part of the course TFYA75: Applied Physics - Bachelor Project, given at Linköping University, Sweden (LiU) spring term 2017. The title of the final report was: "Design och implementing av en interakiv visualisering av elektronstrukturdata". Authors: <NAME>, <NAME>, <NAME>, <NAME>, <NAME>. The project was supervised by <NAME> (main supervisor), <NAME> (expert and client), and <NAME> (expert). The course examinator was <NAME>.

The main part of ENVISoN is built using Python scripting in Inviwo. It provides a set of python 
routines that allows a user with just a few simple commands to:

- Read and parse output from electronic structure codes (presently VASP, and some support for Elk is implemented), storing the result in a structured HDF5 file.
- Generate interactive Inviwo visualization networks for
  tasks common when analyzing electronic structure calculations. 
  Presently there is (to varying degree) support for crystal structures, 
  ab-inito molecular dynamics, charge density, ELF, DOS/pDOS and 
  band structure visualization.

How to build and run ENVISIoN on Ubuntu Linux 17.10
---------------------------------------------------

Requirements: Ubuntu 17.10 with working graphics acceleration.

Create working directory
~~~~~~~~~~~~~~~~~~~~~~~~
::

  mkdir -p ~/ENVISIoN
  cd ~/ENVISIoN

Install dependencies
~~~~~~~~~~~~~~~~~~~~

Git::

  sudo apt-get install git 

Dependencies for Inviwo::

  sudo apt-get install build-essential
  sudo apt-get install cmake cmake-qt-gui cmake-curses-gui
  sudo apt-get install libpython3-dev libpython3-dbg 
  sudo apt-get install mesa-common-dev libglu1-mesa-dev
  sudo apt-get install libxcursor-dev libxinerama-dev libxrandr-dev

Qt5 (Using specifically Qt5.6.1 is highly recommended)::

  wget http://download.qt.io/official_releases/qt/5.6/5.6.1/qt-opensource-linux-x64-5.6.1.run
  chmod +x qt-opensource-linux-x64-5.6.1.run
  [ "$XDG_SESSION_TYPE" == "wayland" ] && xhost si:localuser:root # enable sudo with gui if on Wayland
  sudo ./qt-opensource-linux-x64-5.6.1.run
  [ "$XDG_SESSION_TYPE" == "wayland" ] && xhost -si:localuser:root 
  qtchooser -install Qt5.6.1 /opt/Qt5.6.1/5.6/gcc_64/bin/qmake
  export QT_SELECT=Qt5.6.1

Dependencies for ENVISIoN::

  sudo apt-get install doxygen python-sphinx-rtd-theme
  sudo apt-get install python3-h5py python3-regex python3-numpy

Download ENVISIoN
~~~~~~~~~~~~~~~~~
::

  git clone https://github.com/rartino/ENVISIoN 

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