pele GUI#

pele is primarily designed to be used as a library, but there is an extensive GUI as well. The gui can be used to explore almost everything implemented in pele. An example workflow might be:

  1. Run basinhopping to find the global minimum structure.

  2. See a list of minima found and view the structure in 3D using openGL.

_images/gui_main.png

  1. View the normal modes of each structure.

_images/gui_normalmodes.png

  1. Find transition states between minima using the double ended connect algorithm

_images/gui_connect_all.png

  1. Compare the structures of minima.

_images/gui_ts.png

  1. See a list of all known transition states, view the 3d structure, and look at the normal modes.

  2. Create an interactive disconnectivity graph. Clicking on a minimum in the disconnectivity graph will bring up the minimum in the main window for 3D viewing and analysis.

_images/gui_dgraph.png

  1. Run the nudged elastic band algorithm interactively.

_images/gui_NEB.png

pele GUI (pele.gui)#

This module contains all the necessary components for running the gui.

run_gui(system[, db, application])

The top level function that will launch the gui for a given system

Simply initialize your system and pass it to run_gui:

from pele.systems import LJCluster
from pele.gui import run_gui
mysystem = LJCluster(13)
run_gui(mysystem)

if you pass a database file name it will connect to an existing database or create a new one at that location:

run_gui(mysystem, db="database.sqlite")

Preparing my System for use in the gui#

If you have written your own system class and want to run it in the gui, there are a few additional member functions must be defined:

mysystem.draw(coords, index)
mysystem.smooth_path(images)

Both of these are used for displaying your system in a 3D OpenGL renderer. See BaseSystem and existing derived classes like LJCluster and BLJCluster for more information and examples of how to implement these.