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.
  1. View the normal modes of each structure.
  1. Find transition states between minima using the double ended connect algorithm
  1. Compare the structures of minima.
  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.
  1. Run the nudged elastic band algorithm interactively.

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

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)

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.

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