.. _openmx_viewer:

:orphan:

Using OpenMX Viewer to visualize the molecular dynamics
=======================================================

Molecules and crystals can be visualized using softwares such as `XCrySDen <http://www.xcrysden.org>`_, `VESTA <https://jp-minerals.org/vesta/en/>`_ and `VMD <http://www.ks.uiuc.edu/Research/vmd/>`_, but sometimes there are difficulties in installing these softwares into the computer we are using, say during a workshop like the CMD workshop. In such a circumstance, it is quite useful to use web-based tools. Among others, I find `OpenMX Viewer <http://www.openmx-square.org/viewer/index.html>`_ very useful. Below, I describe how to use OpenMX Viewer by using the C\ :sub:`2`\H\ :sub:`4`\  as an example.

Visit the `OpenMX Viewer <http://www.openmx-square.org/viewer/index.html>`_ site:

.. image:: ../../../img/omxwp.png
   :scale: 25%
   :align: center

Download your trajectory file, say, ``traj.xyz`` to your local computer, and then drag and drop your trajectory file as suggested in the web page (see below):

.. image:: ../../../img/dtomxwp.png
   :scale: 65%
   :align: center


Then you can see the following image:

.. image:: ../../../img/omxwpc2h4p.png
   :scale: 25%
   :align: center


By clicking the ``>>`` botton, you can see the atoms moving.