pele.gui.run

pele.gui.run.excepthook()

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def excepthook(ex_type, ex_value, traceback_obj):

redirected exception handler

class pele.gui.run.MySelection

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class MySelection:

keep track of which minima have been selected and whether those coordinates have been modified

class pele.gui.run.MainGUI

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class MainGUI(QtWidgets.QMainWindow):

this is the main class for the pele gui

Parameters:

app

the application object returned by QtWidgets.QApplication()

systemtypesystem class object

the system class

MainGUI.NewSystem()

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def NewSystem(self):

this is called to initialize the system with a database

MainGUI.on_action_db_connect_triggered()

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def on_action_db_connect_triggered(self, checked=None):

launch a file browser to connect to an existing database

MainGUI.connect_db()

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def connect_db(self, database=":memory:"):

connect to an existing database at location filename

MainGUI.SelectMinimum()

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def SelectMinimum(self, minimum, set_selected=True):

when you click on a minimum in the basinhopping tab

MainGUI.get_selected_minima()

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def get_selected_minima(self):

return the two minima that have been chosen in the gui

MainGUI.get_selected_coords()

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def get_selected_coords(self):

return the two sets of coordinates that have been chosen in the gui

note, that these may not be the same as what is stored in the minimum. E.g. they may be the aligned structures

MainGUI.show_TS()

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def show_TS(self, ts):

show the transition state and the associated minima in the 3d viewer

MainGUI.on_btnAlign_clicked()

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def on_btnAlign_clicked(self, clicked=None):

use mindist to align the minima.

called when the align button is pressed

MainGUI.on_btnNEB_clicked()

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def on_btnNEB_clicked(self, clicked=None):

do an NEB run (not a connect run). Don’t find best alignment first

MainGUI.on_minimum_picked()

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def on_minimum_picked(self, min1):

called when a minimimum is clicked on in the graph or disconnectivity graph

MainGUI.on_btnDisconnectivity_graph_clicked()

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def on_btnDisconnectivity_graph_clicked(self, clicked=None):

show the disconnectivity graph

it is interactive, so that when you click on an end point that minima is selected

MainGUI.on_btnShowGraph_clicked()

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def on_btnShowGraph_clicked(self, clicked=None):

show the graph of minima and transition states

make it interactive, so that when you click on a point that minima is selected

MainGUI.NewMinimum()

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def NewMinimum(self, minimum, sort_items=True):

add a new minimum to the system

MainGUI.RemoveMinimum()

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def RemoveMinimum(self, minimum):

remove a minimum from self.minima_list_model

MainGUI.NewTS()

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def NewTS(self, ts, sort=True):

add new transition state, or list of transition states

MainGUI.RemoveTS()

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def RemoveTS(self, ts):

remove transition state

MainGUI.set_basinhopping_number_alive()

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def set_basinhopping_number_alive(self, nalive):

set the label that shows how many basinhopping processes are alive

MainGUI.on_btn_start_basinhopping_clicked()

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def on_btn_start_basinhopping_clicked(self, clicked=None):

this is run when the start basinhopping button is clicked

MainGUI.on_btn_connect_in_optim_clicked()

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def on_btn_connect_in_optim_clicked(self, clicked=None):

spawn an OPTIM job and retrieve the minima and transition states it finds

MainGUI.compute_thermodynamic_information()

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def compute_thermodynamic_information(self, on_finish=None):

compute thermodynamic information for minima and ts in the background

call on_finish when the calculation is done

pele.gui.run.run_gui()

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def run_gui(system, db=None, application=None):

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

Parameters:

systemSystem class

A pele system, derived from BaseSystem. All information about the system is in this class.

dbpele database or string, optional

connect to this database or the database at this file location

applicationQApplication

Use this QApplication object rather than creating a new one