.. module:: basics

=======================================
ase-gui basics and command line options
=======================================

General use
-----------

Visualizing a system with ase-gui is straight-forward using a regular
mouse. The scroll function allows to change the magnification, the
left mouse button selects atoms, the right mouse button allows to
rotate, and the middle button allows to translate the system on the
screen.

Depending on the number of selected atoms, ase-gui automatically measures
different quantities:

================================= ======================================
Selection                         measurement
================================= ======================================
single atom                       xyz position and atomic symbol
two atoms                         interatomic distance and symbols
three atoms                       all three internal angles and
                                  symbols
four atoms, selected sequentially Measures the dihedral angle,
                                  e.g. the angle between bonds 12 and 34
more than four atoms              chemical composition of selection.
================================= ======================================

ase-gui can save the following file formats:

=========== =================================
File format Comment
=========== =================================
xyz         XYZ file
traj        ASE trajectory
pdb         PDB file
cube        Gaussian cube file
py          Python script
vnl         VNL file
png         Portable Network Graphics
pov         Persistance of Vision
eps         Encapsulated PostScript
in          FHI-aims geometry input
POSCAR      VASP geometry input
bundle      ASE bundle trajectory
cif         Crystallographic Information File
=========== =================================

Files
-----

The :ref:`ase-gui` program can read all the file formats the ASE's
:func:`~ase.io.read` function can understand.

::
  
  $ ase-gui N2Fe110-path.traj


Selecting part of a trajectory
------------------------------
  
A Python-like syntax for selecting a subset of configurations can be
used.  Instead of the Python syntax ``list[start:stop:step]``, you use
:file:`filaname@start:stop:step`::

  $ ase-gui x.traj@0:10:1  # first 10 images
  $ ase-gui x.traj@0:10    # first 10 images
  $ ase-gui x.traj@:10     # first 10 images
  $ ase-gui x.traj@-10:    # last 10 images
  $ ase-gui x.traj@0       # first image
  $ ase-gui x.traj@-1      # last image
  $ ase-gui x.traj@::2     # every second image

If you want to select the same range from many files, the you can use
the :option:`-n` or :option:`--image-number` option::

  $ ase-gui -n -1 *.traj   # last image from all files
  $ ase-gui -n 0 *.traj    # first image from all files

.. tip::

  Type :command:`ase-gui -h` for a description of all command line options.


Writing files
-------------

::

  $ ase-gui -n -1 a*.traj -o new.traj

Possible formats are: ``traj``, ``xyz``, ``cube``, ``pdb``, ``eps``,
``png``, and ``pov``.  For details, see the :mod:`~ase.io` module
documentation.

Interactive use
---------------

The :ref:`ase-gui` program can also be launched directly from a Python
script or interactive session:

>>> from ase import *
>>> atoms = ...
>>> view(atoms)

or

>>> view(atoms, repeat=(3, 3, 2))

or, to keep changes to your atoms:

>>> atoms.edit()


NEB calculations
----------------

Use :menuselection:`Tools --> NEB` to plot energy barrier.

::
  
  $ ase-gui --interpolate 3 initial.xyz final.xyz -o interpolated_path.traj


Plotting data from the command line
-----------------------------------
Plot the energy relative to the energy of the first image as a
function of the distance between atom 0 and 5::

  $ ase-gui -g "d(0,5),e-E[0]" x.traj
  $ ase-gui -t -g "d(0,5),e-E[0]" x.traj > x.dat  # No GUI, write data to stdout

The symbols are the same as used in the plotting data function.


Defaults for ase-gui
--------------------

Using a file ``~/.ase/gui.py``, certain defaults can be set. If it exists,
this file is executed after initializing the variables and colours
normally used in ase-gui. One can change the default graphs that are
plotted, and the default radii for displaying specific atoms. This
example will display the energy evolution and the maximal force in a
graph and also display Cu atoms (Z=29) with a radius of 1.6 Angstrom.

::

  gui_default_settings['gui_graphs_string'] = "i, e - min(E), fmax"
  gui_default_settings['covalent_radii'] = [[29,1.6]]


.. _high contrast:

High contrast settings for ase-gui
----------------------------------

In revision 2600 or later, it is possible to change the foreground and
background colors used to draw the atoms, for instance to draw white
graphics on a black background. This can be done in ``~/.ase/gui.py``.

::

  gui_default_settings['gui_foreground_color'] = '#ffffff' #white
  gui_default_settings['gui_background_color'] = '#000000' #black

To change the color scheme of graphs it is necessary to change the
default behaviour of Matplotlib in a similar way by using a file
``~/.matplotlib/matplotlibrc``.

::

  patch.edgecolor  : white
  text.color       : white
  axes.facecolor   : black
  axes.edgecolor   : white
  axes.labelcolor  : white
  axes.color_cycle : b, g, r, c, m, y, w
  xtick.color      : white
  ytick.color      : white
  grid.color       : white
  figure.facecolor : 0.1
  figure.edgecolor : black

Finally, the color scheme of the windows themselves (i.e. menus, buttons
and text etc.) can be changed by choosing a different desktop theme. In
Ubuntu it is possible to get white on a dark background by selecting the
theme HighContrastInverse under Appearances in the system settings dialog.