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
"""
if clicked is None: return
if not hasattr(self, "dgraph_dlg"):
self.dgraph_dlg = DGraphDialog(self.system.database, parent=self)
self.dgraph_dlg.dgraph_widget.minimum_selected.connect(
self.on_minimum_picked)
self.dgraph_dlg.dgraph_widget.minimum_selected.connect(
self.SelectMinimum)
self.dgraph_dlg.rebuild_disconnectivity_graph()
self.dgraph_dlg.show()
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
"""
if clicked is None: return
if not hasattr(self, "dgraph_dlg"):
self.dgraph_dlg = DGraphDialog(self.system.database, parent=self)
self.dgraph_dlg.dgraph_widget.minimum_selected.connect(self.on_minimum_picked)
self.dgraph_dlg.dgraph_widget.minimum_selected.connect(self.SelectMinimum)
self.dgraph_dlg.rebuild_disconnectivity_graph()
self.dgraph_dlg.show()
class MainGUI(QtGui.QMainWindow):
"""
this is the main class for the pele gui
Parameters
----------
app :
the application object returned by QtGui.QApplication()
systemtype : system class object
the system class
"""
def __init__(self, app, systemtype, parent=None):
QtGui.QWidget.__init__(self)
self.ui = Ui_MainWindow()
self.ui.setupUi(self)
self.systemtype = systemtype
self.transition = None
self.app = app
self.double_ended_connect_runs = []
self.pick_count = 0
self.minima_selection = MySelection()
self.on_minimum_1_selected = Signal()
self.on_minimum_2_selected = Signal()
# set up the list manager
self.list_manager = ListViewManager(self)
# define the system
self.NewSystem()
# finish setting up the list manager (this must be done after NewSystem() is called)
self.list_manager.finish_setup()
# try to load the pymol viewer.
try:
self.usepymol = self.system.params.gui.use_pymol
except (KeyError, AttributeError):
self.usepymol = config.getboolean("gui", "use_pymol")
if self.usepymol:
try:
from pymol_viewer import PymolViewer
self.pymolviewer = PymolViewer(self.system.load_coords_pymol)
except (ImportError or NotImplementedError):
self.usepymol = False
if self.usepymol == False:
# note: glutInit() must be called exactly once. pymol calls it
# during pymol.finish_launching(), so if we call it again it will
# give an error. On the other hand, if we're not using pymol we
# must call it.
from OpenGL.GLUT import glutInit
glutInit()
self.bhmanager = None
def NewSystem(self):
"""
this is called to initialize the system with a database
"""
self.system = self.systemtype()
self.connect_db()
def on_action_edit_params_triggered(self, checked=None):
if checked is None:
return
self.paramsdlg = DlgParams(self.system.params)
self.paramsdlg.show()
def processEvents(self):
self.app.processEvents()
def on_action_db_connect_triggered(self, checked=None):
"""
launch a file browser to connect to an existing database
"""
if checked is None:
return
filename = QtGui.QFileDialog.getSaveFileName(self, "Select database", ".")
if len(filename) > 0:
self.connect_db(filename)
def connect_db(self, database=":memory:"):
"""
connect to an existing database at location filename
"""
self.list_manager.clear()
# note: database can be either Database, or string, or QString
if isinstance(database, Database):
self.system.database = database
else:
self.system.database = self.system.create_database(db=database)
# add minima to listWidged. do sorting after all minima are added
for minimum in self.system.database.minima():
self.NewMinimum(minimum, sort_items=False)
self.list_manager._sort_minima()
self.NewTS(self.system.database.transition_states(order_energy=True))
self.list_manager.resize_columns_minima()
self.list_manager.resize_columns_ts()
self.system.database.on_minimum_added.connect(self.NewMinimum)
self.system.database.on_minimum_removed(self.RemoveMinimum)
self.system.database.on_ts_added.connect(self.NewTS)
self.system.database.on_ts_removed.connect(self.RemoveTS)
def SelectMinimum(self, minimum, set_selected=True):
"""when you click on a minimum in the basinhopping tab
"""
# print "selecting minimum", minimum._id, minimum.energy
if set_selected:
self.list_manager._select_main(minimum)
return
self.ui.ogl_main.setSystem(self.system)
self.ui.ogl_main.setCoords(minimum.coords)
self.ui.ogl_main.setMinimum(minimum)
self.ui.oglTS.setSystem(self.system)
if self.usepymol:
self.pymolviewer.update_coords([minimum.coords], index=1, delete_all=True)
def _SelectMinimum1(self, minimum, set_selected=True):
"""set the first minimum displayed in the connect tab"""
if set_selected:
self.list_manager._select1(minimum)
return
print "selecting minimum 1:", minimum._id, minimum.energy
self.ui.oglPath.setSystem(self.system)
self.ui.oglPath.setCoords(minimum.coords, index=1)
# self.ui.oglPath.setMinimum(minimum, index=1)
self.minima_selection.minimum1 = minimum
self.minima_selection.coords1 = minimum.coords
self.neb = None
if self.usepymol:
self.pymolviewer.update_coords([minimum.coords], index=1)
self.on_minimum_1_selected(minimum)
def _SelectMinimum2(self, minimum, set_selected=True):
"""set the second minimum displayed in the connect tab"""
if set_selected:
self.list_manager._select2(minimum)
return
print "selecting minimum 2:", minimum._id, minimum.energy
self.ui.oglPath.setSystem(self.system)
self.ui.oglPath.setCoords(minimum.coords, index=2)
# self.ui.oglPath.setMinimum(minimum, index=2)
self.minima_selection.minimum2 = minimum
self.minima_selection.coords2 = minimum.coords
self.neb = None
if self.usepymol:
self.pymolviewer.update_coords([minimum.coords], index=2)
self.on_minimum_2_selected(minimum)
def get_selected_minima(self):
"""return the two minima that have been chosen in the gui"""
m1, m2 = self.minima_selection.minimum1, self.minima_selection.minimum2
if m1 is None or m2 is None:
raise Exception("you must select two minima first")
return m1, m2
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
"""
coords1, coords2 = self.minima_selection.coords1, self.minima_selection.coords2
if coords1 is None or coords2 is None:
raise Exception("you must select two minima first")
return coords1, coords2
def show_TS(self, ts):
"""
show the transition state and the associated minima in the 3d viewer
"""
self.ui.oglTS.setSystem(self.system)
m1 = ts.minimum1
m2 = ts.minimum2
# put them in best alignment
mindist = self.system.get_mindist()
dist, m1coords, tscoords = mindist(m1.coords, ts.coords)
dist, m2coords, tscoords = mindist(m2.coords, ts.coords)
self.tscoordspath = np.array([m1coords, tscoords, m2coords])
labels = ["minimum: energy " + str(m1.energy) + " id " + str(m1._id)]
labels += ["ts: energy " + str(ts.energy)]
labels += ["minimum: energy " + str(m2.energy) + " id " + str(m2._id)]
self.ui.oglTS.setCoordsPath(self.tscoordspath, frame=1, labels=labels)
if self.usepymol:
self.pymolviewer.update_coords(self.tscoordspath, index=1, delete_all=True)
def on_btnAlign_clicked(self, clicked=None):
"""use mindist to align the minima.
called when the align button is pressed
"""
if clicked is None:
return
coords1, coords2 = self.get_selected_coords()
align = self.system.get_mindist()
pot = self.system.get_potential()
print "energy before alignment", pot.getEnergy(coords1), pot.getEnergy(coords2)
dist, coords1, coords2 = align(coords1, coords2)
print "energy after alignment", pot.getEnergy(coords1), pot.getEnergy(coords2)
print "best alignment distance", dist
self.ui.oglPath.setCoords(coords1, index=1)
self.ui.oglPath.setCoords(coords2, index=2)
self.minima_selection.coords1 = coords1
self.minima_selection.coords2 = coords2
if self.usepymol:
self.pymolviewer.update_coords([coords1], index=1)
self.pymolviewer.update_coords([coords2], index=2)
def on_btnNEB_clicked(self, clicked=None):
"""do an NEB run (not a connect run). Don't find best alignment first"""
if clicked is None:
return
coords1, coords2 = self.get_selected_coords()
from neb_explorer import NEBExplorer
if not hasattr(self, "nebexplorer"):
self.nebexplorer = NEBExplorer(system=self.system, app=self.app, parent=self)
self.nebexplorer.show()
self.nebexplorer.new_neb(coords1, coords2, run=False)
# def showFrame(self, i):
# if hasattr(self, "nebcoords"):
# self.ui.oglPath.setCoords(self.nebcoords[i,:])
def on_minimum_picked(self, min1):
"""called when a minimimum is clicked on in the graph or disconnectivity graph"""
if (self.pick_count % 2) == 0:
self._SelectMinimum1(min1)
else:
self._SelectMinimum2(min1)
self.pick_count += 1
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
"""
if clicked is None:
return
if not hasattr(self, "dgraph_dlg"):
self.dgraph_dlg = DGraphDialog(self.system.database, parent=self)
self.dgraph_dlg.dgraph_widget.minimum_selected.connect(self.on_minimum_picked)
self.dgraph_dlg.dgraph_widget.minimum_selected.connect(self.SelectMinimum)
self.dgraph_dlg.rebuild_disconnectivity_graph()
self.dgraph_dlg.show()
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
"""
if clicked is None:
return
self.pick_count = 0
if not hasattr(self, "graphview"):
self.graphview = GraphViewDialog(self.system.database, parent=self, app=self.app)
self.graphview.widget.on_minima_picked.connect(self.on_minimum_picked)
self.graphview.widget.on_minima_picked.connect(self.SelectMinimum)
self.graphview.show()
self.graphview.widget.make_graph()
try:
m1, m2 = self.get_selected_minima()
self.graphview.widget._show_minimum_energy_path(m1, m2)
except:
self.graphview.widget.show_graph()
def on_pushNormalmodesMin_clicked(self, clicked=None):
if clicked is None:
return
if not hasattr(self, "normalmode_explorer"):
self.normalmode_explorer = NormalmodeBrowser(self, self.system, self.app)
min1 = self.ui.ogl_main.minima[1]
if min1 is None:
raise RuntimeError("you must select a minimum first")
self.normalmode_explorer.set_coords(min1.coords)
self.normalmode_explorer.show()
def on_pushNormalmodesTS_clicked(self, clicked=None):
if clicked is None:
return
if not hasattr(self, "normalmode_explorer"):
self.normalmode_explorer = NormalmodeBrowser(self, self.system, self.app)
ts = self.list_manager.get_selected_ts()
if ts is None:
raise RuntimeError("you must select a transition state first")
self.normalmode_explorer.set_coords(ts.coords)
self.normalmode_explorer.show()
def NewMinimum(self, minimum, sort_items=True):
""" add a new minimum to the system """
self.list_manager.NewMinimum(minimum, sort_items=sort_items)
def RemoveMinimum(self, minimum):
"""remove a minimum from self.minima_list_model"""
self.list_manager.RemoveMinimum(minimum)
def NewTS(self, ts, sort=True):
"""add new transition state, or list of transition states"""
self.list_manager.NewTS(ts, sort=sort)
def RemoveTS(self, ts):
"""remove transition state"""
raise Exception("removing transition states not implemented yet")
obj = self.ui.list_TS
tsid = id(ts)
itms = self.ui.list_TS.findItems("*", QtCore.Qt.MatchWildcard)
for i in itms:
if i.tsid == tsid:
obj.takeItem(obj.row(i))
def set_basinhopping_number_alive(self, nalive):
"""set the label that shows how many basinhopping processes are alive"""
self.ui.label_bh_nproc.setText("%d B.H. processes" % nalive)
def on_btn_start_basinhopping_clicked(self, clicked=None):
"""this is run when the start basinhopping button is clicked"""
if clicked is None:
return
# set up the basinhopping manager if not already done
if self.bhmanager is None:
self.bhmanager = BHManager(
self.system, self.system.database, on_number_alive_changed=self.set_basinhopping_number_alive
)
# get the number of steps from the input box
nstepsstr = self.ui.lineEdit_bh_nsteps.text()
nsteps = None
try:
nsteps = int(nstepsstr)
except ValueError:
# ignore the text if it is the default text
if "steps" not in nstepsstr:
sys.stderr.write("can't convert %s to integer\n" % nstepsstr)
# start a basinhopping run
self.bhmanager.start_worker(nsteps=nsteps)
def on_btn_stop_basinhopping_clicked(self, clicked=None):
if clicked is None:
return
self.bhmanager.kill_all_workers()
def on_action_delete_minimum_triggered(self, checked=None):
if checked is None:
return
min1 = self.ui.ogl_main.minima[1]
ret = QtGui.QMessageBox.question(
self,
"Deleting minima",
"Do you want to delete minima %d with energy %g" % (min1._id, min1.energy),
QtGui.QMessageBox.Ok,
QtGui.QMessageBox.Cancel,
)
if ret == QtGui.QMessageBox.Ok:
print "deleting minima"
print "deleting minimum", min1._id, min1.energy
self.RemoveMinimum(min1)
self.system.database.removeMinimum(min1)
def on_btnConnect_clicked(self, clicked=None):
if clicked is None:
return
return self._doubleEndedConnect(reconnect=False)
def on_btnReconnect_clicked(self, clicked=None):
if clicked is None:
return
return self._doubleEndedConnect(reconnect=True)
def _doubleEndedConnect(self, reconnect=False, min1min2=None):
"""
launch a double ended connect run to connect the two selected minima.
If the minima are not connected, or reconnect is True, launch a connect browser
in a separate window. Else just show the path in the OGL viewer
"""
# determine which minima to connect
if min1min2 is None:
min1, min2 = self.get_selected_minima()
else:
min1, min2 = min1min2
database = self.system.database
if not reconnect:
# check if the minima are already connected
double_ended_connect = self.system.get_double_ended_connect(
min1, min2, database, fresh_connect=False, verbosity=0
)
if double_ended_connect.graph.areConnected(min1, min2):
print "minima are already connected. loading smoothed path in viewer"
mints, S, energies = double_ended_connect.returnPath()
clist = [m.coords for m in mints]
smoothpath = self.system.smooth_path(clist)
coords = np.array(smoothpath)
self.nebcoords = coords
self.nebenergies = np.array(energies)
print "setting path in oglPath"
self.ui.oglPath.setCoordsPath(coords) # , labels)
# self.ui.oglPath.setCoords(coords[0,:], 1)
# self.ui.oglPath.setCoords(None, 2)
# self.ui.sliderFrame.setRange(0, coords.shape[0]-1)
if self.usepymol:
self.pymolviewer.update_coords(self.nebcoords, index=1, delete_all=True)
return
# make the connect viewer
decviewer = ConnectViewer(self.system, self.system.database, min1, min2, parent=self, app=self.app)
print "starting double ended"
decviewer.show()
decviewer.start()
# store pointers
self.double_ended_connect_runs.append(decviewer)
def on_btn_connect_in_optim_clicked(self, clicked=None):
"""spawn an OPTIM job and retrieve the minima and transition states
it finds"""
if clicked is None:
return
min1, min2 = self.get_selected_minima()
# existing_minima = set(self.system.database.minima())
spawner = self.system.get_optim_spawner(min1.coords, min2.coords)
spawner.run()
db = self.system.database
newminima, newts = spawner.load_results(self.system.database)
# for m in newminima:
# if m not in existing_minima:
# self.NewMinimum(m)
# now use DoubleEndedConnect to test if they are connected
graph = TSGraph(db)
if graph.areConnected(min1, min2):
# use double ended connect to draw the interpolated path
# this is ugly
self._doubleEndedConnect(reconnect=False, min1min2=(min1, min2))
def _merge_minima(self, min1, min2):
mindist = self.system.get_mindist()
dist, x1, x2 = mindist(min1.coords, min2.coords)
query = "Do you want to merge minimum %d with energy %g" % (min1._id, min1.energy)
query += " with minimum %d with energy %g" % (min2._id, min2.energy)
query += " separated by distance %g" % (dist)
ret = QtGui.QMessageBox.question(self, "Merging minima", query, QtGui.QMessageBox.Ok, QtGui.QMessageBox.Cancel)
if ret == QtGui.QMessageBox.Ok:
m1, m2 = min1, min2
if m1._id > m2._id:
m1, m2 = m2, m1
print "merging minima", m1._id, m2._id # , ": minimum", m2._id, "will be deleted"
self.system.database.mergeMinima(m1, m2)
self.RemoveMinimum(m2)
def on_action_merge_minima_triggered(self, checked=None):
if checked is None:
return
min1, min2 = self.get_selected_minima()
self._merge_minima(min1, min2)
def on_action_compute_thermodynamic_info_triggered(self, checked=None):
if checked is None:
return
def on_done():
print "done computing thermodynamic info"
self._on_done = on_done # because on_finish stores a weak reference
self.compute_thermodynamic_information(on_finish=self._on_done)
# def launch_connect_explorer(self):
# coords1, coords2 = self.get_selected_coords()
#
# if not hasattr(self, "local_connect_explorer"):
# self.local_connect_explorer = ConnectExplorerDialog(self.system)
# self.local_connect_explorer.nebwgt.process_events.connect(self.processEvents)
# self.local_connect_explorer.show()
# self.local_connect_explorer.createNEB(coords1, coords2)
# self.local_connect_explorer.runNEB()
def on_btn_close_all_clicked(self, checked=None):
if checked is None:
return
print "closing all windows"
for dv in self.double_ended_connect_runs:
dv.hide()
# del dv
self.double_ended_connect_runs = []
try:
self.local_connect_explorer.hide()
del self.local_connect_explorer
except AttributeError:
pass
try:
self.dgraph_dlg.hide()
del self.dgraph_dlg
except AttributeError:
pass
try:
self.nebexplorer.hide()
del self.nebexplorer
except AttributeError:
pass
try:
self.rate_viewer.hide()
del self.rate_viewer
except AttributeError:
pass
def on_btn_connect_all_clicked(self, checked=None):
if checked is None:
return
from pele.gui.connect_all import ConnectAllDialog
# if hasattr(self, "connect_all"):
# if not self.connect_all.isVisible():
# self.connect_all.show()
# if not self.connect_all.is_running()
self.connect_all = ConnectAllDialog(self.system, self.system.database, parent=self, app=self.app)
self.connect_all.show()
self.connect_all.start()
def on_pushTakestepExplorer_clicked(self):
if not hasattr(self, "takestep_explorer"):
self.takestep_explorer = TakestepExplorer(
parent=self, system=self.system, app=self.app, database=self.system.database
)
self.takestep_explorer.show()
def on_btn_heat_capacity_clicked(self, clicked=None):
if clicked is None:
return
self.cv_viewer = HeatCapacityViewer(self.system, self.system.database, parent=self)
self.cv_viewer.show()
self.cv_viewer.rebuild_cv_plot()
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
"""
# TODO: deal carefuly with what will happen if this is called again
# before the first calculation is done. if self.thermo_worker is overwritten will
# the first calculation stop?
from pele.gui._cv_viewer import GetThermodynamicInfoParallelQT
self.thermo_worker = GetThermodynamicInfoParallelQT(self.system, self.system.database, npar=1)
if on_finish is not None:
self.thermo_worker.on_finish.connect(on_finish)
self.thermo_worker.start()
njobs = self.thermo_worker.njobs
print "calculating thermodynamics for", njobs, "minima and transition states"
# def _compute_rates(self, min1, min2, T=1.):
# """compute rates without first calculating thermodynamics
# """
# print "computing rates at temperature T =", T
# tslist = [ts for ts in self.system.database.transition_states()
# if ts.fvib is not None]
# rcalc = RateCalculation(tslist, [min1], [min2], T=T)
# r12, r21 = rcalc.compute_rates()
# print "rate from", min1._id, "to", min2._id, "=", r12
# print "rate from", min2._id, "to", min1._id, "=", r21
#
# def compute_rates(self, min1, min2, T=1.):
# """compute the transition rate from min1 to min2 and vice versa"""
# def on_finish():
# print "thermodynamic calculation finished"
# self._compute_rates(min1, min2)
# self._on_finish_thermo_reference = on_finish # so it doeesn't get garbage collected
# self.compute_thermodynamic_information(on_finish=on_finish)
def on_btn_rates_clicked(self, clicked=None):
if clicked is None:
return
if not hasattr(self, "rate_viewer"):
m1, m2 = self.minima_selection.minimum1, self.minima_selection.minimum2
self.rate_viewer = RateViewer(self.system, self.system.database, parent=self)
if m1 is not None:
self.rate_viewer.update_A(m1)
if m2 is not None:
self.rate_viewer.update_B(m2)
self.on_minimum_1_selected.connect(self.rate_viewer.update_A)
self.on_minimum_2_selected.connect(self.rate_viewer.update_B)
self.rate_viewer.show()
class MainGUI(QtGui.QMainWindow):
"""
this is the main class for the pele gui
Parameters
----------
app :
the application object returned by QtGui.QApplication()
systemtype : system class object
the system class
"""
def __init__(self, app, systemtype, parent=None):
QtGui.QWidget.__init__(self)
self.ui = Ui_MainWindow()
self.ui.setupUi(self)
self.systemtype = systemtype
self.transition = None
self.app = app
self.double_ended_connect_runs = []
self.pick_count = 0
self.minima_selection = MySelection()
self.on_minimum_1_selected = Signal()
self.on_minimum_2_selected = Signal()
# set up the list manager
self.list_manager = ListViewManager(self)
# define the system
self.NewSystem()
# finish setting up the list manager (this must be done after NewSystem() is called)
self.list_manager.finish_setup()
# try to load the pymol viewer.
try:
self.usepymol = self.system.params.gui.use_pymol
except (KeyError, AttributeError):
self.usepymol = config.getboolean("gui", "use_pymol")
if self.usepymol:
try:
from .pymol_viewer import PymolViewer
self.pymolviewer = PymolViewer(self.system.load_coords_pymol)
except (ImportError or NotImplementedError):
self.usepymol = False
if not self.usepymol:
# note: glutInit() must be called exactly once. pymol calls it
# during pymol.finish_launching(), so if we call it again it will
# give an error. On the other hand, if we're not using pymol we
# must call it.
from OpenGL.GLUT import glutInit
glutInit()
self.bhmanager = None
def NewSystem(self):
"""
this is called to initialize the system with a database
"""
self.system = self.systemtype()
self.connect_db()
def on_action_edit_params_triggered(self, checked=None):
if checked is None: return
self.paramsdlg = DlgParams(self.system.params)
self.paramsdlg.show()
def processEvents(self):
self.app.processEvents()
def on_action_db_connect_triggered(self, checked=None):
"""
launch a file browser to connect to an existing database
"""
if checked is None: return
filename = QtGui.QFileDialog.getSaveFileName(self, 'Select database',
'.')
if len(filename) > 0:
self.connect_db(filename)
def connect_db(self, database=":memory:"):
"""
connect to an existing database at location filename
"""
self.list_manager.clear()
# note: database can be either Database, or string, or QString
if isinstance(database, Database):
self.system.database = database
else:
self.system.database = self.system.create_database(db=database)
# add minima to listWidged. do sorting after all minima are added
for minimum in self.system.database.minima():
self.NewMinimum(minimum, sort_items=False)
self.list_manager._sort_minima()
self.NewTS(self.system.database.transition_states(order_energy=True))
self.list_manager.resize_columns_minima()
self.list_manager.resize_columns_ts()
self.system.database.on_minimum_added.connect(self.NewMinimum)
self.system.database.on_minimum_removed(self.RemoveMinimum)
self.system.database.on_ts_added.connect(self.NewTS)
self.system.database.on_ts_removed.connect(self.RemoveTS)
def SelectMinimum(self, minimum, set_selected=True):
"""when you click on a minimum in the basinhopping tab
"""
# print "selecting minimum", minimum._id, minimum.energy
if set_selected:
self.list_manager._select_main(minimum)
return
self.ui.ogl_main.setSystem(self.system)
self.ui.ogl_main.setCoords(minimum.coords)
self.ui.ogl_main.setMinimum(minimum)
self.ui.oglTS.setSystem(self.system)
if self.usepymol:
self.pymolviewer.update_coords([minimum.coords],
index=1,
delete_all=True)
def _SelectMinimum1(self, minimum, set_selected=True):
"""set the first minimum displayed in the connect tab"""
if set_selected:
self.list_manager._select1(minimum)
return
print("selecting minimum 1:", minimum._id, minimum.energy)
self.ui.oglPath.setSystem(self.system)
self.ui.oglPath.setCoords(minimum.coords, index=1)
# self.ui.oglPath.setMinimum(minimum, index=1)
self.minima_selection.minimum1 = minimum
self.minima_selection.coords1 = minimum.coords
self.neb = None
if self.usepymol:
self.pymolviewer.update_coords([minimum.coords], index=1)
self.on_minimum_1_selected(minimum)
def _SelectMinimum2(self, minimum, set_selected=True):
"""set the second minimum displayed in the connect tab"""
if set_selected:
self.list_manager._select2(minimum)
return
print("selecting minimum 2:", minimum._id, minimum.energy)
self.ui.oglPath.setSystem(self.system)
self.ui.oglPath.setCoords(minimum.coords, index=2)
# self.ui.oglPath.setMinimum(minimum, index=2)
self.minima_selection.minimum2 = minimum
self.minima_selection.coords2 = minimum.coords
self.neb = None
if self.usepymol:
self.pymolviewer.update_coords([minimum.coords], index=2)
self.on_minimum_2_selected(minimum)
def get_selected_minima(self):
"""return the two minima that have been chosen in the gui"""
m1, m2 = self.minima_selection.minimum1, self.minima_selection.minimum2
if m1 is None or m2 is None:
raise Exception("you must select two minima first")
return m1, m2
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
"""
coords1, coords2 = self.minima_selection.coords1, self.minima_selection.coords2
if coords1 is None or coords2 is None:
raise Exception("you must select two minima first")
return coords1, coords2
def show_TS(self, ts):
"""
show the transition state and the associated minima in the 3d viewer
"""
self.ui.oglTS.setSystem(self.system)
m1 = ts.minimum1
m2 = ts.minimum2
# put them in best alignment
mindist = self.system.get_mindist()
dist, m1coords, tscoords = mindist(m1.coords, ts.coords)
dist, m2coords, tscoords = mindist(m2.coords, ts.coords)
self.tscoordspath = np.array([m1coords, tscoords, m2coords])
labels = ["minimum: energy " + str(m1.energy) + " id " + str(m1._id)]
labels += ["ts: energy " + str(ts.energy)]
labels += ["minimum: energy " + str(m2.energy) + " id " + str(m2._id)]
self.ui.oglTS.setCoordsPath(self.tscoordspath, frame=1, labels=labels)
if self.usepymol:
self.pymolviewer.update_coords(self.tscoordspath,
index=1,
delete_all=True)
def on_btnAlign_clicked(self, clicked=None):
"""use mindist to align the minima.
called when the align button is pressed
"""
if clicked is None: return
coords1, coords2 = self.get_selected_coords()
align = self.system.get_mindist()
pot = self.system.get_potential()
print("energy before alignment", pot.getEnergy(coords1),
pot.getEnergy(coords2))
dist, coords1, coords2 = align(coords1, coords2)
print("energy after alignment", pot.getEnergy(coords1),
pot.getEnergy(coords2))
print("best alignment distance", dist)
self.ui.oglPath.setCoords(coords1, index=1)
self.ui.oglPath.setCoords(coords2, index=2)
self.minima_selection.coords1 = coords1
self.minima_selection.coords2 = coords2
if self.usepymol:
self.pymolviewer.update_coords([coords1], index=1)
self.pymolviewer.update_coords([coords2], index=2)
def on_btnNEB_clicked(self, clicked=None):
"""do an NEB run (not a connect run). Don't find best alignment first"""
if clicked is None: return
coords1, coords2 = self.get_selected_coords()
from .neb_explorer import NEBExplorer
if not hasattr(self, "nebexplorer"):
self.nebexplorer = NEBExplorer(system=self.system,
app=self.app,
parent=self)
self.nebexplorer.show()
self.nebexplorer.new_neb(coords1, coords2, run=False)
# def showFrame(self, i):
# if hasattr(self, "nebcoords"):
# self.ui.oglPath.setCoords(self.nebcoords[i,:])
def on_minimum_picked(self, min1):
"""called when a minimimum is clicked on in the graph or disconnectivity graph"""
if (self.pick_count % 2) == 0:
self._SelectMinimum1(min1)
else:
self._SelectMinimum2(min1)
self.pick_count += 1
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
"""
if clicked is None: return
if not hasattr(self, "dgraph_dlg"):
self.dgraph_dlg = DGraphDialog(self.system.database, parent=self)
self.dgraph_dlg.dgraph_widget.minimum_selected.connect(
self.on_minimum_picked)
self.dgraph_dlg.dgraph_widget.minimum_selected.connect(
self.SelectMinimum)
self.dgraph_dlg.rebuild_disconnectivity_graph()
self.dgraph_dlg.show()
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
"""
if clicked is None: return
self.pick_count = 0
if not hasattr(self, "graphview"):
self.graphview = GraphViewDialog(self.system.database,
parent=self,
app=self.app)
self.graphview.widget.on_minima_picked.connect(
self.on_minimum_picked)
self.graphview.widget.on_minima_picked.connect(self.SelectMinimum)
self.graphview.show()
self.graphview.widget.make_graph()
try:
m1, m2 = self.get_selected_minima()
self.graphview.widget._show_minimum_energy_path(m1, m2)
except Exception:
self.graphview.widget.show_graph()
def on_pushNormalmodesMin_clicked(self, clicked=None):
if clicked is None: return
if not hasattr(self, "normalmode_explorer"):
self.normalmode_explorer = NormalmodeBrowser(
self, self.system, self.app)
min1 = self.ui.ogl_main.minima[1]
if min1 is None:
raise RuntimeError("you must select a minimum first")
self.normalmode_explorer.set_coords(min1.coords)
self.normalmode_explorer.show()
def on_pushNormalmodesTS_clicked(self, clicked=None):
if clicked is None: return
if not hasattr(self, "normalmode_explorer"):
self.normalmode_explorer = NormalmodeBrowser(
self, self.system, self.app)
ts = self.list_manager.get_selected_ts()
if ts is None:
raise RuntimeError("you must select a transition state first")
self.normalmode_explorer.set_coords(ts.coords)
self.normalmode_explorer.show()
def NewMinimum(self, minimum, sort_items=True):
""" add a new minimum to the system """
self.list_manager.NewMinimum(minimum, sort_items=sort_items)
def RemoveMinimum(self, minimum):
"""remove a minimum from self.minima_list_model"""
self.list_manager.RemoveMinimum(minimum)
def NewTS(self, ts, sort=True):
"""add new transition state, or list of transition states"""
self.list_manager.NewTS(ts, sort=sort)
def RemoveTS(self, ts):
"""remove transition state"""
raise Exception("removing transition states not implemented yet")
obj = self.ui.list_TS
tsid = id(ts)
itms = self.ui.list_TS.findItems('*', QtCore.Qt.MatchWildcard)
for i in itms:
if i.tsid == tsid:
obj.takeItem(obj.row(i))
def set_basinhopping_number_alive(self, nalive):
"""set the label that shows how many basinhopping processes are alive"""
self.ui.label_bh_nproc.setText("%d B.H. processes" % nalive)
def on_btn_start_basinhopping_clicked(self, clicked=None):
"""this is run when the start basinhopping button is clicked"""
if clicked is None: return
# set up the basinhopping manager if not already done
if self.bhmanager is None:
self.bhmanager = BHManager(
self.system,
self.system.database,
on_number_alive_changed=self.set_basinhopping_number_alive)
# get the number of steps from the input box
nstepsstr = self.ui.lineEdit_bh_nsteps.text()
nsteps = None
try:
nsteps = int(nstepsstr)
except ValueError:
# ignore the text if it is the default text
if "steps" not in nstepsstr:
sys.stderr.write("can't convert %s to integer\n" % nstepsstr)
# start a basinhopping run
self.bhmanager.start_worker(nsteps=nsteps)
def on_btn_stop_basinhopping_clicked(self, clicked=None):
if clicked is None: return
self.bhmanager.kill_all_workers()
def on_action_delete_minimum_triggered(self, checked=None):
if checked is None: return
min1 = self.ui.ogl_main.minima[1]
ret = QtGui.QMessageBox.question(
self, "Deleting minima",
"Do you want to delete minima %d with energy %g" %
(min1._id, min1.energy), QtGui.QMessageBox.Ok,
QtGui.QMessageBox.Cancel)
if ret == QtGui.QMessageBox.Ok:
print("deleting minima")
print("deleting minimum", min1._id, min1.energy)
self.RemoveMinimum(min1)
self.system.database.removeMinimum(min1)
def on_btnConnect_clicked(self, clicked=None):
if clicked is None: return
return self._doubleEndedConnect(reconnect=False)
def on_btnReconnect_clicked(self, clicked=None):
if clicked is None: return
return self._doubleEndedConnect(reconnect=True)
def _doubleEndedConnect(self, reconnect=False, min1min2=None):
"""
launch a double ended connect run to connect the two selected minima.
If the minima are not connected, or reconnect is True, launch a connect browser
in a separate window. Else just show the path in the OGL viewer
"""
# determine which minima to connect
if min1min2 is None:
min1, min2 = self.get_selected_minima()
else:
min1, min2 = min1min2
database = self.system.database
if not reconnect:
# check if the minima are already connected
double_ended_connect = self.system.get_double_ended_connect(
min1, min2, database, fresh_connect=False, verbosity=0)
if double_ended_connect.graph.areConnected(min1, min2):
print(
"minima are already connected. loading smoothed path in viewer"
)
mints, S, energies = double_ended_connect.returnPath()
clist = [m.coords for m in mints]
smoothpath = self.system.smooth_path(clist)
coords = np.array(smoothpath)
self.nebcoords = coords
self.nebenergies = np.array(energies)
print("setting path in oglPath")
self.ui.oglPath.setCoordsPath(coords)
# self.ui.oglPath.setCoords(coords[0,:], 1)
# self.ui.oglPath.setCoords(None, 2)
# self.ui.sliderFrame.setRange(0, coords.shape[0]-1)
if self.usepymol:
self.pymolviewer.update_coords(self.nebcoords,
index=1,
delete_all=True)
return
# make the connect viewer
decviewer = ConnectViewer(self.system,
self.system.database,
min1,
min2,
parent=self,
app=self.app)
print("starting double ended")
decviewer.show()
decviewer.start()
# store pointers
self.double_ended_connect_runs.append(decviewer)
def on_btn_connect_in_optim_clicked(self, clicked=None):
"""spawn an OPTIM job and retrieve the minima and transition states
it finds"""
if clicked is None: return
min1, min2 = self.get_selected_minima()
# existing_minima = set(self.system.database.minima())
spawner = self.system.get_optim_spawner(min1.coords, min2.coords)
spawner.run()
db = self.system.database
newminima, newts = spawner.load_results(self.system.database)
# for m in newminima:
# if m not in existing_minima:
# self.NewMinimum(m)
# now use DoubleEndedConnect to test if they are connected
graph = TSGraph(db)
if graph.areConnected(min1, min2):
# use double ended connect to draw the interpolated path
# this is ugly
self._doubleEndedConnect(reconnect=False, min1min2=(min1, min2))
def _merge_minima(self, min1, min2):
mindist = self.system.get_mindist()
dist, x1, x2 = mindist(min1.coords, min2.coords)
query = "Do you want to merge minimum %d with energy %g" % (
min1._id, min1.energy)
query += " with minimum %d with energy %g" % (
min2._id, min2.energy)
query += " separated by distance %g" % dist
ret = QtGui.QMessageBox.question(self, "Merging minima", query,
QtGui.QMessageBox.Ok,
QtGui.QMessageBox.Cancel)
if ret == QtGui.QMessageBox.Ok:
m1, m2 = min1, min2
if m1._id > m2._id:
m1, m2 = m2, m1
print("merging minima", m1._id, m2._id)
self.system.database.mergeMinima(m1, m2)
self.RemoveMinimum(m2)
def on_action_merge_minima_triggered(self, checked=None):
if checked is None: return
min1, min2 = self.get_selected_minima()
self._merge_minima(min1, min2)
def on_action_compute_thermodynamic_info_triggered(self, checked=None):
if checked is None: return
def on_done():
print("done computing thermodynamic info")
self._on_done = on_done # because on_finish stores a weak reference
self.compute_thermodynamic_information(on_finish=self._on_done)
def on_btn_close_all_clicked(self, checked=None):
if checked is None: return
print("closing all windows")
for dv in self.double_ended_connect_runs:
dv.hide()
# del dv
self.double_ended_connect_runs = []
try:
self.local_connect_explorer.hide()
del self.local_connect_explorer
except AttributeError:
pass
try:
self.dgraph_dlg.hide()
del self.dgraph_dlg
except AttributeError:
pass
try:
self.nebexplorer.hide()
del self.nebexplorer
except AttributeError:
pass
try:
self.rate_viewer.hide()
del self.rate_viewer
except AttributeError:
pass
def on_btn_connect_all_clicked(self, checked=None):
if checked is None: return
from pele.gui.connect_all import ConnectAllDialog
# if hasattr(self, "connect_all"):
# if not self.connect_all.isVisible():
# self.connect_all.show()
# if not self.connect_all.is_running()
self.connect_all = ConnectAllDialog(self.system,
self.system.database,
parent=self,
app=self.app)
self.connect_all.show()
self.connect_all.start()
def on_pushTakestepExplorer_clicked(self):
if not hasattr(self, "takestep_explorer"):
self.takestep_explorer = TakestepExplorer(
parent=self,
system=self.system,
app=self.app,
database=self.system.database)
self.takestep_explorer.show()
def on_btn_heat_capacity_clicked(self, clicked=None):
if clicked is None: return
self.cv_viewer = HeatCapacityViewer(self.system,
self.system.database,
parent=self)
self.cv_viewer.show()
self.cv_viewer.rebuild_cv_plot()
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
"""
# TODO: deal carefuly with what will happen if this is called again
# before the first calculation is done. if self.thermo_worker is overwritten will
# the first calculation stop?
from pele.gui._cv_viewer import GetThermodynamicInfoParallelQT
self.thermo_worker = GetThermodynamicInfoParallelQT(
self.system, self.system.database, npar=1)
if on_finish is not None:
self.thermo_worker.on_finish.connect(on_finish)
self.thermo_worker.start()
njobs = self.thermo_worker.njobs
print("calculating thermodynamics for", njobs,
"minima and transition states")
# def _compute_rates(self, min1, min2, T=1.):
# """compute rates without first calculating thermodynamics
# """
# print "computing rates at temperature T =", T
# tslist = [ts for ts in self.system.database.transition_states()
# if ts.fvib is not None]
# rcalc = RateCalculation(tslist, [min1], [min2], T=T)
# r12, r21 = rcalc.compute_rates()
# print "rate from", min1._id, "to", min2._id, "=", r12
# print "rate from", min2._id, "to", min1._id, "=", r21
#
# def compute_rates(self, min1, min2, T=1.):
# """compute the transition rate from min1 to min2 and vice versa"""
# def on_finish():
# print "thermodynamic calculation finished"
# self._compute_rates(min1, min2)
# self._on_finish_thermo_reference = on_finish # so it doeesn't get garbage collected
# self.compute_thermodynamic_information(on_finish=on_finish)
def on_btn_rates_clicked(self, clicked=None):
if clicked is None: return
if not hasattr(self, "rate_viewer"):
m1, m2 = self.minima_selection.minimum1, self.minima_selection.minimum2
self.rate_viewer = RateViewer(self.system,
self.system.database,
parent=self)
if m1 is not None:
self.rate_viewer.update_A(m1)
if m2 is not None:
self.rate_viewer.update_B(m2)
self.on_minimum_1_selected.connect(self.rate_viewer.update_A)
self.on_minimum_2_selected.connect(self.rate_viewer.update_B)
self.rate_viewer.show()
def main():
if len(sys.argv) < 2:
usage()
exit(1)
# The default is to use the largest connected component of the graph,
# rather than the component which includes the global minimum.
kwargs = {"include_gmin":False, "center_gmin":False}
outfile, colourfile, groupcolourfile, idfile = None, None, None, None
aspect = 6.0/7.0
width = 6
OPTIM = False
opts, args = getopt.gnu_getopt(sys.argv[1:], "ho:",
["help", "nlevels=", "subgraph_size=", "OPTIM",
"order_by_basin_size", "order_by_energy",
"include_gmin",
"center_gmin",
"Emax=",
"colourfile=",
"groupcolourfile=",
"idfile=",
"shape=",
"width="
])
for o, a in opts:
if o == "-h" or o == "--help":
usage()
exit(1)
if o == "-o":
outfile = a
elif o == "--nlevels":
kwargs["nlevels"] = int(a)
elif o == "--Emax":
kwargs["Emax"] = float(a)
elif o == "--subgraph_size":
kwargs["subgraph_size"] = int(a)
elif o == "--order_by_basin_size":
kwargs["order_by_basin_size"] = True
elif o == "--order_by_energy":
kwargs["order_by_energy"] = True
elif o == "--include_gmin":
kwargs["include_gmin"] = True
elif o == "--center_gmin":
kwargs["center_gmin"] = True
elif o == "--OPTIM":
OPTIM = True
elif o == "--colourfile":
colourfile = a
print "Setting colourfile to ", colourfile
elif o == "--groupcolourfile":
if colourfile:
raise AttributeError("Can't specify both colourfile and groupcolourfile")
groupcolourfile = a
elif o == '--idfile':
idfile = a
elif o == '--shape':
aspect = float(a)
elif o == '--width':
width = float(a)
else:
print "don't understand", o, a
print ""
usage()
exit(1)
groups = None
if OPTIM:
#make database from min.data ts.data
db = Database()
converter = OptimDBConverter(db)
converter.convert_no_coords()
groups = read_AB(db)
else:
if len(args) == 0:
print "you must specify database file"
print ""
usage()
exit()
dbfile = args[0]
if not os.path.exists(dbfile):
print "database file doesn't exist", dbfile
exit()
db = Database(dbfile)
if outfile is None and use_gui:
app = QApplication(sys.argv)
kwargs["show_minima"] = False
md = DGraphDialog(db, params=kwargs)
md.rebuild_disconnectivity_graph()
if groups is not None:
md.dgraph_widget.dg.color_by_group(groups)
md.dgraph_widget.redraw_disconnectivity_graph()
md.show()
sys.exit(app.exec_())
# make graph from database
t0 = time.time()
if "Emax" in kwargs and use_gui:
graph = reduced_db2graph(db, kwargs['Emax'])
else:
graph = dg.database2graph(db)
t1 = time.time()
print "loading the data into a transition state graph took", t1-t0, "seconds"
# do the disconnectivity graph analysis
mydg = dg.DisconnectivityGraph(graph, **kwargs)
print "doing disconnectivity graph analysis"
sys.stdout.flush()
t1 = time.time()
mydg.calculate()
t2 = time.time()
print "d-graph analysis finished in", t2-t1, "seconds"
print "number of minima:", mydg.tree_graph.number_of_leaves()
print "plotting disconnectivity graph"
sys.stdout.flush()
if colourfile:
print "Colouring tree according to file ", colourfile
colourfetcher = get_colours_from_file(db, colourfile)
colouredtree = dg.ColorDGraphByValue(mydg.tree_graph,colourfetcher,normalize_values=True)
print "tree set up"
colouredtree.run()
print "Finished colouring"
elif groupcolourfile:
print "Colouring tree according to file ", colourfile
grouplists = get_group_lists(groupcolourfile)
colouredtree = dg.ColorDGraphByGroups(mydg.tree_graph,grouplists)
colouredtree.run()
print "Finished colouring"
if idfile:
labelminima = []
labels = {}
fin = open(idfile,'r')
for line in fin:
minID = line.split()[0]
labelminima.append(db.getMinimum(minID))
# labels[labelminima[-1]]=str(labelminim
fin.close()
print "Labelling ", len(labelminima), "minima"
print "Creating axes with dimensions ", width, width/aspect
fig = plt.figure(figsize=(width, width/aspect))
fig.set_facecolor('white')
ax = fig.add_subplot(111, adjustable='box')
# make the figure and save it
mydg.plot(axes=ax)
if idfile:
print "Going into draw_minima"
mydg.draw_minima(labelminima,labels=True)
if outfile is None:
plt.show()
else:
plt.savefig(outfile)
t3 = time.time()
print "plotting finished in", t3-t2, "seconds"
def main():
if len(sys.argv) < 2:
usage()
exit(1)
kwargs = {}
outfile = None
OPTIM = False
opts, args = getopt.gnu_getopt(sys.argv[1:], "ho:",
["help", "nlevels=", "subgraph_size=", "OPTIM",
"order_by_basin_size", "order_by_energy",
"include_gmin",
"center_gmin",
"Emax=",
])
for o, a in opts:
if o == "-h" or o == "--help":
usage()
exit(1)
if o == "-o":
outfile = a
elif o == "--nlevels":
kwargs["nlevels"] = int(a)
elif o == "--Emax":
kwargs["Emax"] = float(a)
elif o == "--subgraph_size":
kwargs["subgraph_size"] = int(a)
elif o == "--order_by_basin_size":
kwargs["order_by_basin_size"] = True
elif o == "--order_by_energy":
kwargs["order_by_energy"] = True
elif o == "--includer_gmin":
kwargs["includer_gmin"] = True
elif o == "--center_gmin":
kwargs["center_gmin"] = True
elif o == "--OPTIM":
OPTIM = True
else:
print "don't understand", o, a
print ""
usage()
exit(1)
groups = None
if OPTIM:
#make database from min.data ts.data
db = Database()
converter = OptimDBConverter(db)
converter.convert_no_coords()
groups = read_AB(db)
else:
if len(args) == 0:
print "you must specify database file"
print ""
usage()
exit()
dbfile = args[0]
if not os.path.exists(dbfile):
print "database file doesn't exist", dbfile
exit()
db = Database(dbfile)
if outfile is None and use_gui:
app = QApplication(sys.argv)
kwargs["show_minima"] = False
md = DGraphDialog(db, params=kwargs)
md.rebuild_disconnectivity_graph()
if groups is not None:
md.dgraph_widget.dg.color_by_group(groups)
md.dgraph_widget.redraw_disconnectivity_graph()
md.show()
sys.exit(app.exec_())
# make graph from database
t0 = time.time()
if "Emax" in kwargs and use_gui:
graph = reduced_db2graph(db, kwargs['Emax'])
else:
graph = dg.database2graph(db)
t1 = time.time()
print "loading the data into a transition state graph took", t1-t0, "seconds"
# do the disconnectivity graph analysis
mydg = dg.DisconnectivityGraph(graph, **kwargs)
print "doing disconnectivity graph analysis"
sys.stdout.flush()
t1 = time.time()
mydg.calculate()
t2 = time.time()
print "d-graph analysis finished in", t2-t1, "seconds"
print "number of minima:", mydg.tree_graph.number_of_leaves()
print "plotting disconnectivigy graph"
sys.stdout.flush()
# make the figure and save it
mydg.plot()
if outfile is None:
plt.show()
else:
plt.savefig(outfile)
t3 = time.time()
print "plotting finished in", t3-t2, "seconds"