def __init__(self, system, database, parent=None, app=None):
ConnectViewer.__init__(self, system, database, app=app, parent=parent)
self.setWindowTitle("Connect all")
self.wgt_dgraph = DGraphWidget(database=self.database, parent=self)
self.connect_manager = ConnectManager(database)
self.view_dgraph = self.new_view("Disconnectivity Graph",
self.wgt_dgraph,
QtCore.Qt.TopDockWidgetArea)
self.view_dgraph.hide()
self.ui.actionD_Graph.setVisible(True)
self.ui.actionD_Graph.setChecked(False)
self.textEdit_summary = QtGui.QTextEdit(parent=self)
self.textEdit_summary.setReadOnly(True)
self.view_summary = self.new_view("Summary",
self.textEdit_summary,
pos=QtCore.Qt.TopDockWidgetArea)
self.connect_summary = _ConnectAllSummary()
self.ui.actionSummary.setVisible(True)
self.view_summary.hide()
self.ui.actionSummary.setChecked(False)
self.ui.action3D.setChecked(False)
self.view_3D.hide()
self.ui.actionEnergy.setChecked(False)
self.view_energies.hide()
self.ui.actionPause.setVisible(True)
self.is_running = False
self.failed_pairs = set()
# add combo box to toolbar
self.combobox = Qt.QComboBox()
self.ui.toolBar.addWidget(self.combobox)
self.combobox.addItems(
["connect strategy:", "random", "global min", "untrap", "combine"])
self.combobox.setToolTip(
"the strategy used to select which minima to connect")
def __init__(self, system, database, parent=None, app=None):
ConnectViewer.__init__(self, system, database, app=app, parent=parent)
self.setWindowTitle("Connect all")
self.wgt_dgraph = DGraphWidget(database=self.database, parent=self)
self.connect_manager = ConnectManager(database)
self.view_dgraph = self.new_view("Disconnectivity Graph", self.wgt_dgraph, QtCore.Qt.TopDockWidgetArea)
self.view_dgraph.hide()
self.ui.actionD_Graph.setVisible(True)
self.ui.actionD_Graph.setChecked(False)
self.textEdit_summary = QtGui.QTextEdit(parent=self)
self.textEdit_summary.setReadOnly(True)
self.view_summary = self.new_view("Summary", self.textEdit_summary, pos=QtCore.Qt.TopDockWidgetArea)
self.connect_summary = _ConnectAllSummary()
self.ui.actionSummary.setVisible(True)
self.view_summary.hide()
self.ui.actionSummary.setChecked(False)
self.ui.action3D.setChecked(False)
self.view_3D.hide()
self.ui.actionEnergy.setChecked(False)
self.view_energies.hide()
self.ui.actionPause.setVisible(True)
self.is_running = False
self.failed_pairs = set()
# add combo box to toolbar
self.combobox = Qt.QComboBox()
self.ui.toolBar.addWidget(self.combobox)
self.combobox.addItems(["connect strategy:",
"random",
"global min",
"untrap",
"combine"])
self.combobox.setToolTip("the strategy used to select which minima to connect")
class ConnectAllDialog(ConnectViewer):
"""define the Connect All dialog
This class manages connecting minima in the database. It selects which
minima to connect and submits the job in a separate process. It deals with
any messages (such as new minima and transition states) sent from that process.
When the process ends it starts a new one.
"""
def __init__(self, system, database, parent=None, app=None):
ConnectViewer.__init__(self, system, database, app=app, parent=parent)
self.setWindowTitle("Connect all")
self.wgt_dgraph = DGraphWidget(database=self.database, parent=self)
self.connect_manager = ConnectManager(database)
self.view_dgraph = self.new_view("Disconnectivity Graph", self.wgt_dgraph, QtCore.Qt.TopDockWidgetArea)
self.view_dgraph.hide()
self.ui.actionD_Graph.setVisible(True)
self.ui.actionD_Graph.setChecked(False)
self.textEdit_summary = QtGui.QTextEdit(parent=self)
self.textEdit_summary.setReadOnly(True)
self.view_summary = self.new_view("Summary", self.textEdit_summary, pos=QtCore.Qt.TopDockWidgetArea)
self.connect_summary = _ConnectAllSummary()
self.ui.actionSummary.setVisible(True)
self.view_summary.hide()
self.ui.actionSummary.setChecked(False)
self.ui.action3D.setChecked(False)
self.view_3D.hide()
self.ui.actionEnergy.setChecked(False)
self.view_energies.hide()
self.ui.actionPause.setVisible(True)
self.is_running = False
self.failed_pairs = set()
# add combo box to toolbar
self.combobox = Qt.QComboBox()
self.ui.toolBar.addWidget(self.combobox)
self.combobox.addItems(["connect strategy:",
"random",
"global min",
"untrap",
"combine"])
self.combobox.setToolTip("the strategy used to select which minima to connect")
def do_one_connection(self, min1, min2):
"""start one connect job with the given minima"""
self.textEdit.insertPlainText("\n\n")
self.textEdit_summary.insertPlainText("\nNow connecting minima %d %d\n" % (self.min1._id, self.min2._id))
self.decrunner = DECRunner(self.system, self.database, min1, min2, outstream=self.textEdit_writer,
return_smoothed_path=True)
self.decrunner.on_finished.connect(self.on_finished)
self.tstart = time.clock()
self.decrunner.start()
def _get_connect_strategy(self):
"""read from the combobox which connect strategy to use"""
text = self.combobox.currentText()
if "random" in text:
return "random"
elif "global" in text:
return "gmin"
elif "untrap" in text:
return "untrap"
elif "combine" in text:
return "combine"
else:
return "random"
def do_next_connect(self):
"""do another connect job"""
self.is_running = True
strategy = self._get_connect_strategy()
self.min1, self.min2 = self.connect_manager.get_connect_job(strategy=strategy)
# if self.ui.actionRandom_connect.isChecked():
# else:
# self.min1, self.min2 = self.connect_manager.get_connect_job(strategy="gmin")
if self.min1 is None or self.min2 is None:
self.is_running = False
return
self.do_one_connection(self.min1, self.min2)
def start(self):
"""this is called to start submitting jobs again"""
self.do_next_connect()
def update_energy_view(self):
"""plot the energies"""
if self.view_energies.isVisible():
self.wgt_energies.update_gui(self.S, self.energies)
def update_graph_view(self):
"""show the graph view"""
if self.view_graphview.isVisible():
self.wgt_graphview.make_graph()
self.wgt_graphview.show_graph()
def update_3D_view(self):
"""show the smoothed path in the ogl viewer"""
if self.view_3D.isVisible():
self.ogl.setCoordsPath(self.smoothed_path)
def update_dgraph_view(self):
"""update the disconnectivity graph"""
if self.view_dgraph.isVisible():
self.wgt_dgraph.rebuild_disconnectivity_graph()
def update_summary_view(self):
"""update the summary text"""
self.textEdit_summary.clear()
summary = self.connect_summary.get_summary()
self.textEdit_summary.insertPlainText(summary)
def on_finished(self):
print "finished connecting", self.min1._id, "and", self.min2._id
tend = time.clock()
elapsed_time = tend - self.tstart
# print "\n"
# add this run to the summary
self.connect_summary.add(self.min1, self.min2, self.decrunner.success,
self.decrunner.newminima, self.decrunner.newtransition_states, elapsed_time=elapsed_time)
if not self.isVisible():
self.is_running = False
return
if self.decrunner.success:
# get the path data
self.smoothed_path = np.array(self.decrunner.smoothed_path)
self.S = np.array(self.decrunner.S)
self.energies = np.array(self.decrunner.energies)
# print self.smoothed_path.shape
self.update_3D_view()
self.update_energy_view()
self.update_graph_view()
self.update_dgraph_view()
else:
print "connection run failed"
# summary "connection run failed"
if not self.decrunner.killed_early:
self.failed_pairs.add( (self.min1, self.min2) )
self.update_summary_view()
if self.ui.actionPause.isChecked():
self.is_running = False
return
self.do_next_connect()
def on_actionEnergy_toggled(self, checked):
self.toggle_view(self.view_energies, checked)
self.update_energy_view()
def on_actionGraph_toggled(self, checked):
self.toggle_view(self.view_graphview, checked)
self.update_graph_view()
def on_action3D_toggled(self, checked):
self.toggle_view(self.view_3D, checked)
self.update_3D_view()
def on_actionD_Graph_toggled(self, checked):
self.toggle_view(self.view_dgraph, checked)
self.update_dgraph_view()
def on_actionSummary_toggled(self, checked):
self.toggle_view(self.view_summary, checked)
def on_actionPause_toggled(self, checked):
if checked is None: return
if not checked:
if not self.is_running:
self.start()
def on_actionKill_triggered(self, checked=None):
if checked is None: return
self.ui.actionPause.setChecked(True)
self.is_running = False
self.decrunner.terminate_early()
class ConnectAllDialog(ConnectViewer):
"""define the Connect All dialog
This class manages connecting minima in the database. It selects which
minima to connect and submits the job in a separate process. It deals with
any messages (such as new minima and transition states) sent from that process.
When the process ends it starts a new one.
"""
def __init__(self, system, database, parent=None, app=None):
ConnectViewer.__init__(self, system, database, app=app, parent=parent)
self.setWindowTitle("Connect all")
self.wgt_dgraph = DGraphWidget(database=self.database, parent=self)
self.connect_manager = ConnectManager(database)
self.view_dgraph = self.new_view("Disconnectivity Graph", self.wgt_dgraph, QtCore.Qt.TopDockWidgetArea)
self.view_dgraph.hide()
self.ui.actionD_Graph.setVisible(True)
self.ui.actionD_Graph.setChecked(False)
self.textEdit_summary = QtGui.QTextEdit(parent=self)
self.textEdit_summary.setReadOnly(True)
self.view_summary = self.new_view("Summary", self.textEdit_summary, pos=QtCore.Qt.TopDockWidgetArea)
self.connect_summary = _ConnectAllSummary()
self.ui.actionSummary.setVisible(True)
self.view_summary.hide()
self.ui.actionSummary.setChecked(False)
self.ui.action3D.setChecked(False)
self.view_3D.hide()
self.ui.actionEnergy.setChecked(False)
self.view_energies.hide()
self.ui.actionPause.setVisible(True)
self.is_running = False
self.failed_pairs = set()
# add combo box to toolbar
self.combobox = Qt.QComboBox()
self.ui.toolBar.addWidget(self.combobox)
self.combobox.addItems(["connect strategy:",
"random",
"global min",
"untrap",
"combine"])
self.combobox.setToolTip("the strategy used to select which minima to connect")
def do_one_connection(self, min1, min2):
"""start one connect job with the given minima"""
self.textEdit.insertPlainText("\n\n")
self.textEdit_summary.insertPlainText("\nNow connecting minima %d %d\n" % (self.min1._id, self.min2._id))
self.decrunner = DECRunner(self.system, self.database, min1, min2, outstream=self.textEdit_writer,
return_smoothed_path=True)
self.decrunner.on_finished.connect(self.on_finished)
self.tstart = time.process_time()
self.decrunner.start()
def _get_connect_strategy(self):
"""read from the combobox which connect strategy to use"""
text = self.combobox.currentText()
if "random" in text:
return "random"
elif "global" in text:
return "gmin"
elif "untrap" in text:
return "untrap"
elif "combine" in text:
return "combine"
else:
return "random"
def do_next_connect(self):
"""do another connect job"""
self.is_running = True
strategy = self._get_connect_strategy()
self.min1, self.min2 = self.connect_manager.get_connect_job(strategy=strategy)
# if self.ui.actionRandom_connect.isChecked():
# else:
# self.min1, self.min2 = self.connect_manager.get_connect_job(strategy="gmin")
if self.min1 is None or self.min2 is None:
self.is_running = False
return
self.do_one_connection(self.min1, self.min2)
def start(self):
"""this is called to start submitting jobs again"""
self.do_next_connect()
def update_energy_view(self):
"""plot the energies"""
if self.view_energies.isVisible():
self.wgt_energies.update_gui(self.S, self.energies)
def update_graph_view(self):
"""show the graph view"""
if self.view_graphview.isVisible():
self.wgt_graphview.make_graph()
self.wgt_graphview.show_graph()
def update_3D_view(self):
"""show the smoothed path in the ogl viewer"""
if self.view_3D.isVisible():
self.ogl.setCoordsPath(self.smoothed_path)
def update_dgraph_view(self):
"""update the disconnectivity graph"""
if self.view_dgraph.isVisible():
self.wgt_dgraph.rebuild_disconnectivity_graph()
def update_summary_view(self):
"""update the summary text"""
self.textEdit_summary.clear()
summary = self.connect_summary.get_summary()
self.textEdit_summary.insertPlainText(summary)
def on_finished(self):
print("finished connecting", self.min1._id, "and", self.min2._id)
tend = time.process_time()
elapsed_time = tend - self.tstart
# print "\n"
# add this run to the summary
self.connect_summary.add(self.min1, self.min2, self.decrunner.success,
self.decrunner.newminima, self.decrunner.newtransition_states, elapsed_time=elapsed_time)
if not self.isVisible():
self.is_running = False
return
if self.decrunner.success:
# get the path data
self.smoothed_path = np.array(self.decrunner.smoothed_path)
self.S = np.array(self.decrunner.S)
self.energies = np.array(self.decrunner.energies)
# print self.smoothed_path.shape
self.update_3D_view()
self.update_energy_view()
self.update_graph_view()
self.update_dgraph_view()
else:
print("connection run failed")
# summary "connection run failed"
if not self.decrunner.killed_early:
self.failed_pairs.add( (self.min1, self.min2) )
self.update_summary_view()
if self.ui.actionPause.isChecked():
self.is_running = False
return
self.do_next_connect()
def on_actionEnergy_toggled(self, checked):
self.toggle_view(self.view_energies, checked)
self.update_energy_view()
def on_actionGraph_toggled(self, checked):
self.toggle_view(self.view_graphview, checked)
self.update_graph_view()
def on_action3D_toggled(self, checked):
self.toggle_view(self.view_3D, checked)
self.update_3D_view()
def on_actionD_Graph_toggled(self, checked):
self.toggle_view(self.view_dgraph, checked)
self.update_dgraph_view()
def on_actionSummary_toggled(self, checked):
self.toggle_view(self.view_summary, checked)
def on_actionPause_toggled(self, checked):
if checked is None: return
if not checked:
if not self.is_running:
self.start()
def on_actionKill_triggered(self, checked=None):
if checked is None: return
self.ui.actionPause.setChecked(True)
self.is_running = False
self.decrunner.terminate_early()
