def __init__(self, systemtype, parent=None):
QtGui.QWidget.__init__(self)
self.ui = MainWindow.Ui_MainWindow()
self.ui.setupUi(self)
self.listMinima = [
self.ui.listWidget,
self.ui.listMinima1,
self.ui.listMinima2,
self.ui.listFrom
]
self.systemtype = systemtype
self.NewSystem()
self.transition=None
#try to load the pymol viewer.
self.usepymol = True
try:
from pymol_viewer import PymolViewer
self.pymolviewer = PymolViewer(self.system.load_coords_pymol)
except (ImportError or NotImplementedError):
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()
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 __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
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 pygmin 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()
# 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()
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, filename=":memory:"):
"""
connect to an existing database at location filename
"""
self.list_manager.clear()
db = self.system.create_database(db=filename)
self.system.database = db
#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)
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)
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)
# 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
from pygmin.gui.graph_viewer import GraphViewDialog
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()
self.graphview.widget.show_graph()
return
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]
self.normalmode_explorer.set_coords(min1.coords)
self.normalmode_explorer.show()
def get_selected_ts(self):
ts = self.ts_selected
if ts is None:
raise Exception("you must select a transition state first")
return ts
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.get_selected_ts()
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 on_btn_start_basinhopping_clicked(self, clicked=None):
if clicked is None: return
db = self.system.database
self.system.database = None
self.bhrunner = BHRunner(self.system)
self.bhrunner.start()
self.system.database = db
# def tsSearch(self):
# ts = self.system.findTS(self.ui.oglTS.coords[1])
# self.transition = [ts[1][0], ts[0][0], ts[2][0]]
# def showFrameTS(self, i):
# if self.transition:
# self.ui.oglTS.setCoords(self.transition[i])
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 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
def on_btn_connect_all_clicked(self, checked=None):
if checked is None: return
from pygmin.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()
class MyForm(QtGui.QMainWindow):
def __init__(self, systemtype, parent=None):
QtGui.QWidget.__init__(self)
self.ui = MainWindow.Ui_MainWindow()
self.ui.setupUi(self)
self.listMinima = [
self.ui.listWidget,
self.ui.listMinima1,
self.ui.listMinima2,
self.ui.listFrom
]
self.systemtype = systemtype
self.NewSystem()
self.transition=None
#try to load the pymol viewer.
self.usepymol = True
try:
from pymol_viewer import PymolViewer
self.pymolviewer = PymolViewer(self.system.load_coords_pymol)
except (ImportError or NotImplementedError):
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()
def NewSystem(self):
self.system = self.systemtype()
db = self.system.create_database()
self.system.database = db
self.system.database.onMinimumAdded=self.NewMinimum
self.system.database.onMinimumRemoved=self.RemoveMinimum
for l in self.listMinima:
l.clear()
def edit_params(self):
self.paramsdlg = DlgParams(self.system.params)
self.paramsdlg.show()
#def save(self):
# import pickle
# filename = QtGui.QFileDialog.getSaveFileName(self, 'Save File', '.')
# output = open(filename, "w")
# pickle.dump(self.system.storage, output)
def connect(self):
"""
connect to an existing database
"""
filename = QtGui.QFileDialog.getSaveFileName(self, 'Open File', '.')
self.connect_db(filename)
def connect_db(self, filename):
db = self.system.create_database(db=filename)
self.system.database = db
for minimum in self.system.database.minima():
self.NewMinimum(minimum)
self.system.database.onMinimumAdded=self.NewMinimum
self.system.database.onMinimumRemoved=self.RemoveMinimum
def SelectMinimum(self, item):
print "selecting minimum", item.minimum._id, item.minimum.energy
self.ui.widget.setSystem(self.system)
self.ui.widget.setCoords(item.coords)
self.ui.widget.setMinimum(item.minimum)
self.ui.oglTS.setSystem(self.system)
self.ui.oglTS.setCoords(item.coords)
if self.usepymol:
self.pymolviewer.update_coords([item.coords], index=1, delete_all=True)
def _SelectMinimum1(self, minimum):
"""by minimum"""
self.ui.oglPath.setSystem(self.system)
self.ui.oglPath.setCoords(minimum.coords, index=1)
self.ui.oglPath.setMinimum(minimum, index=1)
self.neb = None
if self.usepymol:
self.pymolviewer.update_coords([minimum.coords], index=1)
def SelectMinimum1(self, item):
"""called by the ui"""
return self._SelectMinimum1(item.minimum)
def _SelectMinimum2(self, minimum):
"""by minimum"""
self.ui.oglPath.setSystem(self.system)
self.ui.oglPath.setCoords(minimum.coords, index=2)
self.ui.oglPath.setMinimum(minimum, index=2)
self.neb = None
if self.usepymol:
self.pymolviewer.update_coords([minimum.coords], index=2)
def SelectMinimum2(self, item):
"""called by the ui"""
return self._SelectMinimum2(item.minimum)
def Invert(self):
coords2 = self.ui.oglPath.coords[2]
self.ui.oglPath.setCoords(-coords2, 2)
if self.usepymol:
self.pymolviewer.update_coords([-coords2], index=2)
def AlignMinima(self):
coords1 = self.ui.oglPath.coords[1]
coords2 = self.ui.oglPath.coords[2]
align = self.system.get_mindist()
dist, coords1, coords2 = align(coords1, coords2)
self.ui.oglPath.setCoords(coords1, 1)
self.ui.oglPath.setCoords(coords2, 2)
if self.usepymol:
self.pymolviewer.update_coords([coords1], index=1)
self.pymolviewer.update_coords([coords2], index=2)
print "best alignment distance", dist
pass
def ConnectMinima(self):
self.neb = self.system.createNEB(self.ui.oglPath.coords[1], self.ui.oglPath.coords[2])
self.neb.optimize()
self.nebcoords = self.neb.coords
self.nebenergies = self.neb.energies
self.ui.oglPath.setCoords(self.neb.coords[0,:], 1)
self.ui.oglPath.setCoords(None, 2)
self.ui.sliderFrame.setRange(0,self.neb.coords.shape[0]-1)
if self.usepymol:
self.pymolviewer.update_coords(self.nebcoords, index=1, delete_all=True)
def showFrame(self, i):
if hasattr(self, "nebcoords"):
self.ui.oglPath.setCoords(self.nebcoords[i,:])
def show_disconnectivity_graph(self):
import pylab as pl
pl.ion()
pl.clf()
ax = pl.gca()
fig = pl.gcf()
graphwrapper = Graph(self.system.database)
dg = DisconnectivityGraph(graphwrapper.graph, subgraph_size=2)
dg.calculate()
#draw minima as points
xpos, minima = dg.get_minima_layout()
energies = [m.energy for m in minima]
points = ax.scatter(xpos, energies, picker=5)
#draw line segments connecting minima
line_segments = dg.line_segments
for x, y in line_segments:
ax.plot(x, y, 'k')
#define what happens when a point is clicked on
global pick_count
pick_count = 0
def on_pick(event):
if event.artist != points:
# print "you clicked on something other than a node"
return True
thispoint = event.artist
ind = event.ind[0]
min1 = minima[ind]
print "you clicked on minimum with id", min1._id, "and energy", min1.energy
global pick_count
#print pick_count
pick_count += 1
if (pick_count % 2) == 0:
self._SelectMinimum1(min1)
else:
self._SelectMinimum2(min1)
fig = pl.gcf()
cid = fig.canvas.mpl_connect('pick_event', on_pick)
pl.show()
def show_graph(self):
import pylab as pl
import networkx as nx
pl.ion()
pl.clf()
ax = pl.gca()
fig = pl.gcf()
#get the graph object, eliminate nodes without edges
graphwrapper = Graph(self.system.database)
graph = graphwrapper.graph
degree = graph.degree()
nodes = [n for n, nedges in degree.items() if nedges > 0]
graph = graph.subgraph(nodes)
#get the layout of the nodes from networkx
layout = nx.spring_layout(graph)
layoutlist = layout.items()
xypos = np.array([xy for n, xy in layoutlist])
#color the nodes by energy
e = np.array([m.energy for m, xy in layoutlist])
#plot the nodes
points = ax.scatter(xypos[:,0], xypos[:,1], picker=5,
s=8**2, c=e, cmap=pl.cm.autumn)
fig.colorbar(points)
#label the nodes
ids = [n._id for n, xy in layoutlist]
for i in range(len(ids)):
ax.annotate( ids[i], xypos[i] )
#plot the edges as lines
for u, v in graph.edges():
line = np.array([layout[u], layout[v]])
ax.plot(line[:,0], line[:,1], '-k')
#scale the axes so the points are not cutoff
xmin, ymin = np.min(xypos, 0)
xmax, ymax = np.max(xypos, 0)
dx = (xmax - xmin)*.1
dy = (ymax - ymin)*.1
ax.set_xlim([xmin-dx, xmax+dx])
ax.set_ylim([ymin-dy, ymax+dy])
global pick_count
pick_count = 0
def on_pick(event):
if event.artist != points:
# print "you clicked on something other than a node"
return True
thispoint = event.artist
ind = event.ind[0]
min1 = layoutlist[ind][0]
print "you clicked on minimum with id", min1._id, "and energy", min1.energy
global pick_count
#print pick_count
pick_count += 1
if (pick_count % 2) == 0:
self._SelectMinimum1(min1)
else:
self._SelectMinimum2(min1)
fig = pl.gcf()
cid = fig.canvas.mpl_connect('pick_event', on_pick)
#ids = dict([(n, n._id) for n in nodes])
#nx.draw(graph, labels=ids, nodelist=nodes)
#ax.draw()
# pl.draw()
pl.show()
def showEnergies(self):
#note: this breaks if pylab isn't a local import. I don't know why
import pylab as pl
pl.ion()
pl.plot(self.nebenergies, "o-", label="energies")
if False: #show climbing images
neb = self.neb
cl=[]
en=[]
for i in xrange(len(neb.energies)):
if(neb.isclimbing[i]):
print "climbing image :", i, neb.energies[i]
cl.append(i)
en.append(neb.energies[i])
pl.plot(cl, en, "s", label="climbing images", markersize=10, markerfacecolor="none", markeredgewidth=2)
pl.legend(loc='best')
pl.show()
def NewMinimum(self, minimum):
E=minimum.energy
minid=id(minimum)
coords=minimum.coords
for obj in self.listMinima:
item = QMinimumInList('%.4f'%E)
item.setCoords(coords)
item.setMinimum(minimum)
obj.addItem(item)
obj.sortItems(1)
def RemoveMinimum(self, minimum):
minid = id(minimum)
for obj in self.listMinima:
itms = obj.findItems('*', QtCore.Qt.MatchWildcard)
for i in itms:
if(i.minid == minid):
obj.takeItem(obj.row(i))
def StartBasinHopping(self):
db = self.system.database
self.system.database = None
self.bhrunner = bhrunner.BHRunner(self.system)
self.bhrunner.start()
self.system.database = db
def tsSearch(self):
import numpy as np
ts = self.system.findTS(self.ui.oglTS.coords[1])
self.transition = [ts[1][0], ts[0][0], ts[2][0]]
def showFrameTS(self, i):
if(self.transition):
self.ui.oglTS.setCoords(self.transition[i])
def selectTransition(self):
pass
def delete_minimum(self):
min1 = self.ui.widget.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)
#this is currently not used. it may be used later though
# def LocalConnect(self):
# self.local_connect = self.system.create_local_connect()
#
# min1 = self.ui.listMinima1.selectedItems()[0].minimum
# min2 = self.ui.listMinima2.selectedItems()[0].minimum
# res = self.local_connect.connect(min1, min2)
# ntriplets = len(res.new_transition_states)
#
# path = []
# for i in range(ntriplets):
# tsret, m1ret, m2ret = res.new_transition_states[i]
# local_path = []
# local_path.append(m1ret[0])
# local_path.append(tsret.coords)
# local_path.append(m2ret[0])
# smoothpath = self.system.smooth_path(local_path)
# path += list(smoothpath)
#
# coords = np.array(path)
# self.nebcoords = coords
# self.ui.oglPath.setCoords(coords[0,:], 1)
# self.ui.oglPath.setCoords(None, 2)
# self.ui.sliderFrame.setRange(0, coords.shape[0]-1)
def doubleEndedConnect(self):
return self._doubleEndedConnect(reconnect=False)
def doubleEndedReConnect(self):
return self._doubleEndedConnect(reconnect=True)
def _doubleEndedConnect(self, reconnect=False):
# min1 = self.ui.listMinima1.selectedItems()[0].minimum
# min2 = self.ui.listMinima2.selectedItems()[0].minimum
# min1 = self.ui.
min1 = self.ui.oglPath.minima[1]
min2 = self.ui.oglPath.minima[2]
database = self.system.database
double_ended_connect = self.system.get_double_ended_connect(min1, min2, database,
fresh_connect=reconnect)
double_ended_connect.connect()
mints, S, energies = double_ended_connect.returnPath()
clist = [m.coords for m in mints]
print "done finding path, now just smoothing path. This can take a while"
smoothpath = self.system.smooth_path(clist)
print "done"
coords = np.array(smoothpath)
self.nebcoords = coords
self.nebenergies = np.array(energies)
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)
class MainGUI(QtGui.QMainWindow):
"""
this is the main class for the pygmin 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()
# 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()
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, filename=":memory:"):
"""
connect to an existing database at location filename
"""
self.list_manager.clear()
db = self.system.create_database(db=filename)
self.system.database = db
#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)
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)
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)
# 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
from pygmin.gui.graph_viewer import GraphViewDialog
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()
self.graphview.widget.show_graph()
return
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]
self.normalmode_explorer.set_coords(min1.coords)
self.normalmode_explorer.show()
def get_selected_ts(self):
ts = self.ts_selected
if ts is None:
raise Exception("you must select a transition state first")
return ts
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.get_selected_ts()
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 on_btn_start_basinhopping_clicked(self, clicked=None):
if clicked is None: return
db = self.system.database
self.system.database = None
self.bhrunner = BHRunner(self.system)
self.bhrunner.start()
self.system.database = db
# def tsSearch(self):
# ts = self.system.findTS(self.ui.oglTS.coords[1])
# self.transition = [ts[1][0], ts[0][0], ts[2][0]]
# def showFrameTS(self, i):
# if self.transition:
# self.ui.oglTS.setCoords(self.transition[i])
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 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
def on_btn_connect_all_clicked(self, checked=None):
if checked is None: return
from pygmin.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()
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()