def __init__(self,
system,
database,
min1=None,
min2=None,
parent=None,
app=None):
QtGui.QMainWindow.__init__(self, parent=parent)
self.ui = UI()
self.ui.setupUi(self)
self.ui.centralwidget.hide()
self.app = app
self.system = system
self.database = database
self.ogl = self.ui.ogl
self.ogl.setSystem(system)
self.textEdit = self.ui.textEdit
self.textEdit.setReadOnly(True)
self.textEdit_writer = OutLog(self.textEdit)
self.view_log = self.ui.view_Log
self.ui.actionLog.setChecked(True)
if min1 is not None and min2 is not None:
self.decrunner = DECRunner(system,
database,
min1,
min2,
outstream=self.textEdit_writer)
self.decrunner.on_finished.connect(self.on_finished)
self.view_3D = self.ui.view_ogl
self.ui.action3D.setChecked(True)
self.wgt_energies = ConnectEnergyWidget(parent=self)
self.view_energies = self.new_view("Energies", self.wgt_energies,
QtCore.Qt.TopDockWidgetArea)
self.ui.actionEnergy.setChecked(True)
self.wgt_graphview = GraphViewWidget(database=self.database,
parent=self,
app=app)
self.view_graphview = self.new_view("Graph View", self.wgt_graphview,
QtCore.Qt.TopDockWidgetArea)
self.view_graphview.hide()
self.ui.actionGraph.setChecked(False)
self.ui.actionPause.setVisible(False)
self.ui.actionD_Graph.setVisible(False)
self.ui.actionSummary.setVisible(False)
self.ui.actionSummary.setChecked(False)
self.ui.actionRandom_connect.setChecked(False)
self.ui.actionRandom_connect.setVisible(False)
self.smoothed_path = None
def do_one_connection(self, min1, min2):
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 do_one_connection(self, min1, min2):
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 __init__(self, system, database, min1=None, min2=None, parent=None, app=None):
QtGui.QMainWindow.__init__(self, parent=parent)
self.ui = UI()
self.ui.setupUi(self)
self.ui.centralwidget.hide()
self.app = app
self.system = system
self.database = database
self.ogl = self.ui.ogl
self.ogl.setSystem(system)
self.textEdit = self.ui.textEdit
self.textEdit.setReadOnly(True)
self.textEdit_writer = OutLog(self.textEdit)
self.view_log = self.ui.view_Log
self.ui.actionLog.setChecked(True)
if min1 is not None and min2 is not None:
self.decrunner = DECRunner(system, database, min1, min2, outstream=self.textEdit_writer)
self.decrunner.on_finished.connect(self.on_finished)
self.view_3D = self.ui.view_ogl
self.ui.action3D.setChecked(True)
self.wgt_energies = ConnectEnergyWidget(parent=self)
self.view_energies = self.new_view("Energies", self.wgt_energies, QtCore.Qt.TopDockWidgetArea)
self.ui.actionEnergy.setChecked(True)
self.wgt_graphview = GraphViewWidget(database=self.database, parent=self, app=app)
self.view_graphview = self.new_view("Graph View", self.wgt_graphview, QtCore.Qt.TopDockWidgetArea)
self.view_graphview.hide()
self.ui.actionGraph.setChecked(False)
self.ui.actionPause.setVisible(False)
self.ui.actionD_Graph.setVisible(False)
self.ui.actionSummary.setVisible(False)
self.ui.actionSummary.setChecked(False)
self.ui.actionRandom_connect.setChecked(False)
self.ui.actionRandom_connect.setVisible(False)
self.smoothed_path = None
class ConnectAllDialog(ConnectViewer):
def __init__(self, system, database, parent=None, app=None):
super(ConnectAllDialog, self).__init__(system,
database,
app=app,
parent=parent)
self.wgt_dgraph = DGraphWidget(database=self.database, parent=self)
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.actionRandom_connect.setVisible(True)
self.ui.actionRandom_connect.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()
def do_one_connection(self, min1, min2):
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_next_pair_gmin(self):
minima = self.database.minima()
min1 = minima[0]
graph = TSGraph(self.database)
all_connected = True
for m2 in minima[1:]:
if not graph.areConnected(min1, m2):
if (min1, m2) in self.failed_pairs or (
m2, min1) in self.failed_pairs:
continue
all_connected = False
break
if all_connected:
print "minima are all connected, ending"
self.textEdit_summary.insertPlainText(
"minima are all connected, ending\n")
return None, None
return min1, m2
def get_next_pair_random(self):
''' get a new connect job '''
query = self.database.session.query(Minimum)
# if self.Emax is not None:
# query.filter(Minimum.energy < self.Emax)
while True:
min1 = query.order_by(sqlalchemy.func.random()).first()
min2 = query.order_by(sqlalchemy.func.random()).first()
if (min1, min2) not in self.failed_pairs and (
min2, min1) not in self.failed_pairs:
return min1, min2
def do_next_connect(self):
self.is_running = True
if self.ui.actionRandom_connect.isChecked():
self.min1, self.min2 = self.get_next_pair_random()
else:
self.min1, self.min2 = self.get_next_pair_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):
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):
if self.view_dgraph.isVisible():
self.wgt_dgraph.rebuild_disconnectivity_graph()
def update_summary_view(self):
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 ConnectViewer(QtGui.QMainWindow):
"""
external viewer for connect runs
This viewer will use DECRunner to run a connect job in parallel.
The log messages from that run will be redirected into a GUI text viewer.
When the run is finished, the completed path will be shown in an OGL viewer
Parameters
----------
system :
database :
min1, min2 : Minimum objects
the minima to try to connect
parent :
the parent window
app :
the application
See Also
--------
DECRunner
"""
def __init__(self,
system,
database,
min1=None,
min2=None,
parent=None,
app=None):
QtGui.QMainWindow.__init__(self, parent=parent)
self.ui = UI()
self.ui.setupUi(self)
self.ui.centralwidget.hide()
self.app = app
self.system = system
self.database = database
self.ogl = self.ui.ogl
self.ogl.setSystem(system)
self.textEdit = self.ui.textEdit
self.textEdit.setReadOnly(True)
self.textEdit_writer = OutLog(self.textEdit)
self.view_log = self.ui.view_Log
self.ui.actionLog.setChecked(True)
if min1 is not None and min2 is not None:
self.decrunner = DECRunner(system,
database,
min1,
min2,
outstream=self.textEdit_writer)
self.decrunner.on_finished.connect(self.on_finished)
self.view_3D = self.ui.view_ogl
self.ui.action3D.setChecked(True)
self.wgt_energies = ConnectEnergyWidget(parent=self)
self.view_energies = self.new_view("Energies", self.wgt_energies,
QtCore.Qt.TopDockWidgetArea)
self.ui.actionEnergy.setChecked(True)
self.wgt_graphview = GraphViewWidget(database=self.database,
parent=self,
app=app)
self.view_graphview = self.new_view("Graph View", self.wgt_graphview,
QtCore.Qt.TopDockWidgetArea)
self.view_graphview.hide()
self.ui.actionGraph.setChecked(False)
self.ui.actionPause.setVisible(False)
self.ui.actionD_Graph.setVisible(False)
self.ui.actionSummary.setVisible(False)
self.ui.actionSummary.setChecked(False)
self.ui.actionRandom_connect.setChecked(False)
self.ui.actionRandom_connect.setVisible(False)
self.smoothed_path = None
def start(self):
self.decrunner.start()
def on_finished(self):
print "success", self.decrunner.success
# print "success", self.decrunner.smoothed_path
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
# show the smoothed path in the ogl viewer
self.show_path()
# plot the energies
self.make_energy_plot()
# plot the graph of minima
self.make_graph()
def make_energy_plot(self):
if self.wgt_energies.isVisible() and self.decrunner.success:
self.wgt_energies.update_gui(self.S, self.energies)
def show_path(self):
if self.ogl.isVisible() and self.smoothed_path is not None:
self.ogl.setCoordsPath(self.smoothed_path)
def make_graph(self):
if self.wgt_graphview.isVisible() and self.decrunner.success:
self.wgt_graphview.make_graph(database=self.decrunner.database,
minima=self.decrunner.newminima)
self.wgt_graphview.show_graph()
def new_view(self, title, widget, pos=QtCore.Qt.RightDockWidgetArea):
child = QtGui.QDockWidget(title, self)
child.setWidget(widget)
self.addDockWidget(pos, child)
return child
def toggle_view(self, view, show):
if show:
view.show()
else:
view.hide()
def on_actionEnergy_toggled(self, checked):
self.toggle_view(self.view_energies, checked)
self.make_energy_plot()
def on_actionGraph_toggled(self, checked):
self.toggle_view(self.view_graphview, checked)
self.make_graph()
def on_action3D_toggled(self, checked):
self.toggle_view(self.view_3D, checked)
self.show_path()
def on_actionLog_toggled(self, checked):
self.toggle_view(self.view_log, checked)
def on_actionKill_triggered(self, checked=None):
sys.stderr.write("kill toggled, terminating early\n")
if checked is None: return
self.decrunner.terminate_early()
def closeEvent(self, event):
self.on_actionKill_triggered(True)
super(ConnectViewer, self).closeEvent(event)
class ConnectViewer(QtGui.QMainWindow):
"""
external viewer for connect runs
This viewer will use DECRunner to run a connect job in parallel.
The log messages from that run will be redirected into a GUI text viewer.
When the run is finished, the completed path will be shown in an OGL viewer
Parameters
----------
system :
database :
min1, min2 : Minimum objects
the minima to try to connect
parent :
the parent window
app :
the application
See Also
--------
DECRunner
"""
def __init__(self, system, database, min1=None, min2=None, parent=None, app=None):
QtGui.QMainWindow.__init__(self, parent=parent)
self.ui = UI()
self.ui.setupUi(self)
self.ui.centralwidget.hide()
self.app = app
self.system = system
self.database = database
self.ogl = self.ui.ogl
self.ogl.setSystem(system)
self.textEdit = self.ui.textEdit
self.textEdit.setReadOnly(True)
self.textEdit_writer = OutLog(self.textEdit)
self.view_log = self.ui.view_Log
self.ui.actionLog.setChecked(True)
if min1 is not None and min2 is not None:
self.decrunner = DECRunner(system, database, min1, min2, outstream=self.textEdit_writer)
self.decrunner.on_finished.connect(self.on_finished)
self.view_3D = self.ui.view_ogl
self.ui.action3D.setChecked(True)
self.wgt_energies = ConnectEnergyWidget(parent=self)
self.view_energies = self.new_view("Energies", self.wgt_energies, QtCore.Qt.TopDockWidgetArea)
self.ui.actionEnergy.setChecked(True)
self.wgt_graphview = GraphViewWidget(database=self.database, parent=self, app=app)
self.view_graphview = self.new_view("Graph View", self.wgt_graphview, QtCore.Qt.TopDockWidgetArea)
self.view_graphview.hide()
self.ui.actionGraph.setChecked(False)
self.ui.actionPause.setVisible(False)
self.ui.actionD_Graph.setVisible(False)
self.ui.actionSummary.setVisible(False)
self.ui.actionSummary.setChecked(False)
self.ui.actionRandom_connect.setChecked(False)
self.ui.actionRandom_connect.setVisible(False)
self.smoothed_path = None
def start(self):
self.decrunner.start()
def on_finished(self):
print "success", self.decrunner.success
# print "success", self.decrunner.smoothed_path
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
# show the smoothed path in the ogl viewer
self.show_path()
# plot the energies
self.make_energy_plot()
# plot the graph of minima
self.make_graph()
def make_energy_plot(self):
if self.wgt_energies.isVisible() and self.decrunner.success:
self.wgt_energies.update_gui(self.S, self.energies)
def show_path(self):
if self.ogl.isVisible() and self.smoothed_path is not None:
self.ogl.setCoordsPath(self.smoothed_path)
def make_graph(self):
if self.wgt_graphview.isVisible() and self.decrunner.success:
self.wgt_graphview.make_graph(database=self.decrunner.database, minima=self.decrunner.newminima)
self.wgt_graphview.show_graph()
def new_view(self, title, widget, pos=QtCore.Qt.RightDockWidgetArea):
child = QtGui.QDockWidget(title, self)
child.setWidget(widget)
self.addDockWidget(pos, child)
return child
def toggle_view(self, view, show):
if show:
view.show()
else:
view.hide()
def on_actionEnergy_toggled(self, checked):
self.toggle_view(self.view_energies, checked)
self.make_energy_plot()
def on_actionGraph_toggled(self, checked):
self.toggle_view(self.view_graphview, checked)
self.make_graph()
def on_action3D_toggled(self, checked):
self.toggle_view(self.view_3D, checked)
self.show_path()
def on_actionLog_toggled(self, checked):
self.toggle_view(self.view_log, checked)
def on_actionKill_triggered(self, checked=None):
sys.stderr.write( "kill toggled, terminating early\n")
if checked is None: return
self.decrunner.terminate_early()
def closeEvent(self, event):
self.on_actionKill_triggered(True)
super(ConnectViewer, self).closeEvent(event)
class ConnectAllDialog(ConnectViewer):
def __init__(self, system, database, parent=None, app=None):
super(ConnectAllDialog, self).__init__(system, database, app=app, parent=parent)
self.wgt_dgraph = DGraphWidget(database=self.database, parent=self)
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()
def do_one_connection(self, min1, min2):
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 do_next_connect(self):
self.is_running = True
minima = self.database.minima()
self.min1 = minima[0]
graph = Graph(self.database)
all_connected = True
for m2 in minima[1:]:
if not graph.areConnected(self.min1, m2):
if (self.min1, m2) in self.failed_pairs or (m2, self.min1) in self.failed_pairs:
continue
all_connected = False
break
if all_connected:
print "minima are all connected, ending"
self.textEdit_summary.insertPlainText("minima are all connected, ending\n")
self.is_running = False
return
self.min2 = m2
self.do_one_connection(self.min1, m2)
def start(self):
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):
if self.view_dgraph.isVisible():
self.wgt_dgraph.rebuild_disconnectivity_graph()
def update_summary_view(self):
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()