def __init__(self, ycube, parent=None):
QtGui.QWidget.__init__(self, parent)
self.setWindowTitle('3D Data Visualization')
layout = QtGui.QVBoxLayout(self)
self.visualization = Visualization(ycube)
self.group_checkbox = QtGui.QGroupBox()
self.group_checkbox.setTitle("Display Objects")
self.checkbox_plane1 = QtGui.QCheckBox("Show Plane 1")
self.checkbox_plane1.setChecked(True)
self.checkbox_plane1.stateChanged.connect(self.show_plane1)
self.checkbox_plane2 = QtGui.QCheckBox("Show Plane 2")
self.checkbox_plane2.setChecked(True)
self.checkbox_plane2.stateChanged.connect(self.show_plane2)
self.checkbox_iso = QtGui.QCheckBox("Show Isometric Surface")
self.checkbox_iso.setChecked(True)
self.checkbox_iso.stateChanged.connect(self.show_iso)
hbox = QtGui.QHBoxLayout()
hbox.addWidget(self.checkbox_plane1)
hbox.addWidget(self.checkbox_plane2)
hbox.addWidget(self.checkbox_iso)
self.group_checkbox.setLayout(hbox)
self.ui = self.visualization.edit_traits(parent=self,
kind='subpanel').control
layout.addWidget(self.ui)
layout.addWidget(self.group_checkbox)
self.ui.setParent(self)
self.show()
def init(self, parent):
""" Finishes initializing the editor by creating the underlying toolkit
widget.
"""
self.control = QtGui.QCheckBox()
self.control.stateChanged.connect(self.update_object)
self.set_tooltip()
def rebuild_editor(self):
""" Rebuilds the editor after its definition is modified.
"""
while self._connections_to_rebuild:
signal, handler = self._connections_to_rebuild.pop()
signal.disconnect(handler)
# Clear any existing content:
self.clear_layout()
cur_value = parse_value(self.value)
# Create a sizer to manage the radio buttons:
labels = self.names
values = self.values
n = len(labels)
cols = self.factory.cols
rows = (n + cols - 1) // cols
# incr will keep track of how to increment index so that as we traverse
# the grid in row major order, the elements are added to appear in
# column major order
incr = [n // cols] * cols
rem = n % cols
for i in range(cols):
incr[i] += rem > i
incr[-1] = -sum(incr[:-1]) + 1
# e.g for a gird:
# 0 2 4
# 1 3 5
# incr should be [2, 2, -3]
# Add the set of all possible choices:
layout = self.control.layout()
index = 0
# populate the layout in row_major order
for i in range(rows):
for j in range(cols):
if n > 0:
cb = QtGui.QCheckBox(labels[index])
cb.value = values[index]
if cb.value in cur_value:
cb.setCheckState(QtCore.Qt.Checked)
else:
cb.setCheckState(QtCore.Qt.Unchecked)
cb.clicked.connect(self._mapper.map)
self._connections_to_rebuild.append(
(cb.clicked, self._mapper.map)
)
self._mapper.setMapping(cb, labels[index])
layout.addWidget(cb, i, j)
index += incr[j]
n -= 1
def rebuild_editor(self):
""" Rebuilds the editor after its definition is modified.
"""
while self._connections_to_rebuild:
signal, handler = self._connections_to_rebuild.pop()
signal.disconnect(handler)
# Clear any existing content:
self.clear_layout()
cur_value = parse_value(self.value)
# Create a sizer to manage the radio buttons:
labels = self.names
values = self.values
n = len(labels)
cols = self.factory.cols
rows = (n + cols - 1) // cols
incr = [n // cols] * cols
rem = n % cols
for i in range(cols):
incr[i] += rem > i
incr[-1] = -sum(incr[:-1]) + 1
# Add the set of all possible choices:
layout = self.control.layout()
index = 0
for i in range(rows):
for j in range(cols):
if n > 0:
cb = QtGui.QCheckBox(labels[index])
cb.value = values[index]
if cb.value in cur_value:
cb.setCheckState(QtCore.Qt.Checked)
else:
cb.setCheckState(QtCore.Qt.Unchecked)
cb.clicked.connect(self._mapper.map)
self._connections_to_rebuild.append(
(cb.clicked, self._mapper.map))
self._mapper.setMapping(cb, labels[index])
layout.addWidget(cb, i, j)
index += incr[j]
n -= 1
def rebuild_editor ( self ):
""" Rebuilds the editor after its definition is modified.
"""
# Clear any existing content:
self.clear_layout()
cur_value = parse_value( self.value )
# Create a sizer to manage the radio buttons:
labels = self.names
values = self.values
n = len( labels )
cols = self.factory.cols
rows = (n + cols - 1) / cols
incr = [ n / cols ] * cols
rem = n % cols
for i in range( cols ):
incr[i] += (rem > i)
incr[-1] = -(reduce( lambda x, y: x + y, incr[:-1], 0 ) - 1)
# Add the set of all possible choices:
layout = self.control.layout()
index = 0
for i in range( rows ):
for j in range( cols ):
if n > 0:
cb = QtGui.QCheckBox(labels[index])
cb.value = values[index]
if cb.value in cur_value:
cb.setCheckState(QtCore.Qt.Checked)
else:
cb.setCheckState(QtCore.Qt.Unchecked)
QtCore.QObject.connect(cb,
QtCore.SIGNAL('clicked()'),
self._mapper,
QtCore.SLOT('map()'))
self._mapper.setMapping(cb, labels[index])
layout.addWidget(cb, i, j)
index += incr[j]
n -= 1
def __init__(self, parent=None):
super(TaskBarLayout, self).__init__(parent)
self.load_scan_button = QtGui.QPushButton("Load Scan")
self.define_leads_button = QtGui.QPushButton("Define Leads")
self.define_leads_button.setEnabled(False)
self.load_coord_button = QtGui.QPushButton("Load Coordinates")
self.load_coord_button.setEnabled(False)
self.clean_button = QtGui.QPushButton("Clean scan")
self.save_button=QtGui.QPushButton("Save as...")
self.save_button.setEnabled(False)
self.bipolar_box = QtGui.QCheckBox("Include Bipolar Pairs")
save_layout = QtGui.QVBoxLayout()
save_layout.addWidget(self.save_button)
save_layout.addWidget(self.bipolar_box)
self.addWidget(self.load_scan_button)
self.addWidget(self.define_leads_button)
self.addWidget(self.load_coord_button)
self.addLayout(save_layout)
self.addWidget(self.clean_button)
def __init__(self, controller, config, parent=None):
"""
Panel that displays and interacts with localized contacts
:param controller: The PylocControl for the app
:param config: The loaded config dict for the app
:param parent: A parent widget
"""
super(ContactPanelWidget, self).__init__(parent)
self.config = config
self.controller = controller
layout = QtGui.QVBoxLayout(self)
lead_layout = QtGui.QHBoxLayout()
layout.addLayout(lead_layout)
self.labels = OrderedDict()
self.label_dropdown = NoScrollComboBox()
self.label_dropdown.setMaximumWidth(75)
add_labeled_widget(lead_layout,
"Label :", self.label_dropdown)
self.contact_name = QtGui.QLineEdit()
lead_layout.addWidget(self.contact_name)
loc_layout = QtGui.QHBoxLayout()
layout.addLayout(loc_layout)
self.x_lead_loc = QtGui.QLineEdit()
self.x_loc_max = QtGui.QLabel('')
add_labeled_widget(loc_layout,
"Lead x:", self.x_lead_loc,self.x_loc_max)
self.y_lead_loc = QtGui.QLineEdit()
self.y_loc_max = QtGui.QLabel('')
add_labeled_widget(loc_layout,
" y:", self.y_lead_loc,self.y_loc_max)
self.lead_group = QtGui.QLineEdit("0")
add_labeled_widget(loc_layout,
" group:", self.lead_group)
vox_layout = QtGui.QHBoxLayout()
layout.addLayout(vox_layout)
self.r_voxel = QtGui.QLineEdit()
add_labeled_widget(vox_layout,
"R:", self.r_voxel)
self.a_voxel = QtGui.QLineEdit()
add_labeled_widget(vox_layout,
"A:", self.a_voxel)
self.s_voxel = QtGui.QLineEdit()
add_labeled_widget(vox_layout,
"S:", self.s_voxel)
self.axes_checkbox = QtGui.QCheckBox("Show RAS Tags")
self.axes_checkbox.setChecked(True)
vox_layout.addWidget(self.axes_checkbox)
self.submit_button = QtGui.QPushButton("Submit")
layout.addWidget(self.submit_button)
contact_label = QtGui.QLabel("Contacts:")
layout.addWidget(contact_label)
self.contacts = []
self.contact_list = QtGui.QListWidget()
self.contact_list.setSelectionMode(QtGui.QAbstractItemView.ContiguousSelection)
layout.addWidget(self.contact_list)
self.interpolate_button = QtGui.QPushButton("Interpolate")
layout.addWidget(self.interpolate_button)
self.seed_button = QtGui.QPushButton("Seeding")
self.seed_button.setCheckable(True)
layout.addWidget(self.seed_button)
self.micro_button = QtGui.QPushButton("Add Micro-Contacts")
layout.addWidget(self.micro_button)
self.assign_callbacks()
def __init__(self, xyz_file, dyson_file=None):
super(Main, self).__init__()
self.settings = Settings({
"Continuum Orbital": {
"Ionization transitions":
[0, ["only intra-atomic", "inter-atomic"]]
},
"Averaging": {
"Euler angle grid points": 5,
"polar angle grid points": 1000,
"sphere radius Rmax": 300.0,
},
"Scan": {
"nr. points": 20
},
"Cube": {
"extra space / bohr": 15.0,
"points per bohr": 3.0
}
})
# perform DFTB calculation
# BOUND ORBITAL = H**O
self.atomlist = XYZ.read_xyz(xyz_file)[0]
# shift molecule to center of mass
print "shift molecule to center of mass"
pos = XYZ.atomlist2vector(self.atomlist)
masses = AtomicData.atomlist2masses(self.atomlist)
pos_com = MolCo.shift_to_com(pos, masses)
self.atomlist = XYZ.vector2atomlist(pos_com, self.atomlist)
self.tddftb = LR_TDDFTB(self.atomlist)
self.tddftb.setGeometry(self.atomlist, charge=0)
options = {"nstates": 1}
try:
self.tddftb.getEnergies(**options)
except DFTB.Solver.ExcitedStatesNotConverged:
pass
self.valorbs, radial_val = load_pseudo_atoms(self.atomlist)
if dyson_file == None:
# Kohn-Sham orbitals are taken as Dyson orbitals
self.H**O, self.LUMO = self.tddftb.dftb2.getFrontierOrbitals()
self.bound_orbs = self.tddftb.dftb2.getKSCoefficients()
self.orbe = self.tddftb.dftb2.getKSEnergies()
orbital_names = []
norb = len(self.orbe)
for o in range(0, norb):
if o < self.H**O:
name = "occup."
elif o == self.H**O:
name = "H**O"
elif o == self.LUMO:
name = "LUMO "
else:
name = "virtual"
name = name + " " + str(o).rjust(4) + (
" %+10.3f eV" % (self.orbe[o] * 27.211))
orbital_names.append(name)
initially_selected = self.H**O
else:
# load coefficients of Dyson orbitals from file
names, ionization_energies, self.bound_orbs = load_dyson_orbitals(
dyson_file)
self.orbe = np.array(ionization_energies) / 27.211
orbital_names = []
norb = len(self.orbe)
for o in range(0, norb):
name = names[o] + " " + str(o).rjust(4) + (
" %4.2f eV" % (self.orbe[o] * 27.211))
orbital_names.append(name)
initially_selected = 0
self.photo_kinetic_energy = slako_tables_scattering.energies[0]
self.epol = np.array([15.0, 0.0, 0.0])
# Build Graphical User Interface
main = QtGui.QWidget()
mainLayout = QtGui.QHBoxLayout(main)
#
selectionFrame = QtGui.QFrame()
selectionFrame.setSizePolicy(QtGui.QSizePolicy.Fixed,
QtGui.QSizePolicy.Preferred)
mainLayout.addWidget(selectionFrame)
selectionLayout = QtGui.QVBoxLayout(selectionFrame)
#
label = QtGui.QLabel(selectionFrame)
label.setText("Select bound MO:")
selectionLayout.addWidget(label)
# bound orbitals
self.orbitalSelection = QtGui.QListWidget(selectionFrame)
self.orbitalSelection.itemSelectionChanged.connect(
self.selectBoundOrbital)
norb = len(self.orbe)
self.orbital_dict = {}
for o in range(0, norb):
name = orbital_names[o]
self.orbital_dict[name] = o
item = QtGui.QListWidgetItem(name, self.orbitalSelection)
if o == initially_selected:
selected_orbital_item = item
selectionLayout.addWidget(self.orbitalSelection)
### VIEWS
center = QtGui.QWidget()
mainLayout.addWidget(center)
centerLayout = QtGui.QGridLayout(center)
#
boundFrame = QtGui.QFrame()
centerLayout.addWidget(boundFrame, 1, 1)
boundLayout = QtGui.QVBoxLayout(boundFrame)
# "Bound Orbital"
label = QtGui.QLabel(boundFrame)
label.setText("Bound Orbital")
boundLayout.addWidget(label)
#
self.boundOrbitalViewer = QCubeViewerWidget(boundFrame)
boundLayout.addWidget(self.boundOrbitalViewer)
# continuum orbital
continuumFrame = QtGui.QFrame()
centerLayout.addWidget(continuumFrame, 1, 2)
continuumLayout = QtGui.QVBoxLayout(continuumFrame)
# "Dipole-Prepared Continuum Orbital"
label = QtGui.QLabel(continuumFrame)
label.setText("Dipole-Prepared Continuum Orbital")
continuumLayout.addWidget(label)
self.continuumOrbitalViewer = QCubeViewerWidget(continuumFrame)
continuumLayout.addWidget(self.continuumOrbitalViewer)
self.efield_objects = []
self.efield_actors = []
self.selected = None
# picker
self.picker = self.continuumOrbitalViewer.visualization.scene.mayavi_scene.on_mouse_pick(
self.picker_callback)
self.picker.tolerance = 0.01
# PHOTO KINETIC ENERGY
sliderFrame = QtGui.QFrame(continuumFrame)
continuumLayout.addWidget(sliderFrame)
sliderLayout = QtGui.QHBoxLayout(sliderFrame)
# label
self.pke_label = QtGui.QLabel()
self.pke_label.setText("PKE: %6.4f eV" %
(self.photo_kinetic_energy * 27.211))
sliderLayout.addWidget(self.pke_label)
# Slider for changing the PKE
self.pke_slider = QtGui.QSlider(QtCore.Qt.Horizontal)
self.pke_slider.setMinimum(0)
self.pke_slider.setMaximum(len(slako_tables_scattering.energies) - 1)
self.pke_slider.setValue(0)
self.pke_slider.sliderReleased.connect(self.changePKE)
self.pke_slider.valueChanged.connect(self.searchPKE)
sliderLayout.addWidget(self.pke_slider)
#
# molecular frame photoangular distribution
mfpadFrame = QtGui.QFrame()
centerLayout.addWidget(mfpadFrame, 2, 1)
mfpadLayout = QtGui.QVBoxLayout(mfpadFrame)
mfpadLayout.addWidget(QtGui.QLabel("Molecular Frame PAD"))
mfpadTabs = QtGui.QTabWidget()
mfpadLayout.addWidget(mfpadTabs)
# 2D map
mfpadFrame2D = QtGui.QFrame()
mfpadTabs.addTab(mfpadFrame2D, "2D")
mfpadLayout2D = QtGui.QVBoxLayout(mfpadFrame2D)
self.MFPADfig2D = Figure()
self.MFPADCanvas2D = FigureCanvas(self.MFPADfig2D)
mfpadLayout2D.addWidget(self.MFPADCanvas2D)
self.MFPADCanvas2D.draw()
NavigationToolbar(self.MFPADCanvas2D, mfpadFrame2D, coordinates=True)
# 3D
mfpadFrame3D = QtGui.QFrame()
mfpadTabs.addTab(mfpadFrame3D, "3D")
mfpadLayout3D = QtGui.QVBoxLayout(mfpadFrame3D)
self.MFPADfig3D = Figure()
self.MFPADCanvas3D = FigureCanvas(self.MFPADfig3D)
mfpadLayout3D.addWidget(self.MFPADCanvas3D)
self.MFPADCanvas3D.draw()
NavigationToolbar(self.MFPADCanvas3D, mfpadFrame3D, coordinates=True)
# orientation averaged photoangular distribution
avgpadFrame = QtGui.QFrame()
centerLayout.addWidget(avgpadFrame, 2, 2)
avgpadLayout = QtGui.QVBoxLayout(avgpadFrame)
self.activate_average = QtGui.QCheckBox("Orientation Averaged PAD")
self.activate_average.setToolTip(
"Check this box to start averaging of the molecular frame PADs over all orientations. This can take a while."
)
self.activate_average.setCheckState(QtCore.Qt.Unchecked)
self.activate_average.stateChanged.connect(self.activateAveragedPAD)
avgpadLayout.addWidget(self.activate_average)
avgpadTabs = QtGui.QTabWidget()
avgpadLayout.addWidget(avgpadTabs)
# 1D map
avgpadFrame1D = QtGui.QFrame()
avgpadTabs.addTab(avgpadFrame1D, "1D")
avgpadLayout1D = QtGui.QVBoxLayout(avgpadFrame1D)
self.AvgPADfig1D = Figure()
self.AvgPADCanvas1D = FigureCanvas(self.AvgPADfig1D)
avgpadLayout1D.addWidget(self.AvgPADCanvas1D)
self.AvgPADCanvas1D.draw()
NavigationToolbar(self.AvgPADCanvas1D, avgpadFrame1D, coordinates=True)
# 2D map
avgpadFrame2D = QtGui.QFrame()
avgpadFrame2D.setToolTip(
"The averaged PAD should have no phi-dependence anymore. A phi-dependence is a sign of incomplete averaging."
)
avgpadTabs.addTab(avgpadFrame2D, "2D")
avgpadLayout2D = QtGui.QVBoxLayout(avgpadFrame2D)
self.AvgPADfig2D = Figure()
self.AvgPADCanvas2D = FigureCanvas(self.AvgPADfig2D)
avgpadLayout2D.addWidget(self.AvgPADCanvas2D)
self.AvgPADCanvas2D.draw()
NavigationToolbar(self.AvgPADCanvas2D, avgpadFrame2D, coordinates=True)
# Table
avgpadFrameTable = QtGui.QFrame()
avgpadTabs.addTab(avgpadFrameTable, "Table")
avgpadLayoutTable = QtGui.QVBoxLayout(avgpadFrameTable)
self.avgpadTable = QtGui.QTableWidget(0, 6)
self.avgpadTable.setToolTip(
"Activate averaging and move the PKE slider above to add a new row with beta values. After collecting betas for different energies you can save the table or plot a curve beta(PKE) for the selected orbital."
)
self.avgpadTable.setHorizontalHeaderLabels(
["PKE / eV", "sigma", "beta1", "beta2", "beta3", "beta4"])
avgpadLayoutTable.addWidget(self.avgpadTable)
# Buttons
buttonFrame = QtGui.QFrame()
avgpadLayoutTable.addWidget(buttonFrame)
buttonLayout = QtGui.QHBoxLayout(buttonFrame)
deleteButton = QtGui.QPushButton("Delete")
deleteButton.setToolTip("clear table")
deleteButton.clicked.connect(self.deletePADTable)
buttonLayout.addWidget(deleteButton)
buttonLayout.addSpacing(3)
scanButton = QtGui.QPushButton("Scan")
scanButton.setToolTip(
"fill table by scanning automatically through all PKE values")
scanButton.clicked.connect(self.scanPADTable)
buttonLayout.addWidget(scanButton)
saveButton = QtGui.QPushButton("Save")
saveButton.setToolTip("save table as a text file")
saveButton.clicked.connect(self.savePADTable)
buttonLayout.addWidget(saveButton)
plotButton = QtGui.QPushButton("Plot")
plotButton.setToolTip("plot beta2 column as a function of PKE")
plotButton.clicked.connect(self.plotPADTable)
buttonLayout.addWidget(plotButton)
"""
# DOCKS
self.setDockOptions(QtGui.QMainWindow.AnimatedDocks | QtGui.QMainWindow.AllowNestedDocks)
#
selectionDock = QtGui.QDockWidget(self)
selectionDock.setWidget(selectionFrame)
selectionDock.setFeatures(QtGui.QDockWidget.DockWidgetFloatable | QtGui.QDockWidget.DockWidgetMovable)
self.addDockWidget(QtCore.Qt.DockWidgetArea(1), selectionDock)
#
boundDock = QtGui.QDockWidget(self)
boundDock.setWidget(boundFrame)
boundDock.setFeatures(QtGui.QDockWidget.DockWidgetFloatable | QtGui.QDockWidget.DockWidgetMovable)
boundDock.setSizePolicy(QtGui.QSizePolicy.Preferred, QtGui.QSizePolicy.Preferred)
self.addDockWidget(QtCore.Qt.DockWidgetArea(2), boundDock)
#
continuumDock = QtGui.QDockWidget(self)
continuumDock.setWidget(continuumFrame)
continuumDock.setFeatures(QtGui.QDockWidget.DockWidgetFloatable | QtGui.QDockWidget.DockWidgetMovable)
continuumDock.setSizePolicy(QtGui.QSizePolicy.Preferred, QtGui.QSizePolicy.Preferred)
self.addDockWidget(QtCore.Qt.DockWidgetArea(2), continuumDock)
"""
self.setCentralWidget(main)
self.status_bar = QtGui.QStatusBar(main)
self.setStatusBar(self.status_bar)
self.default_message = "Click on the tip of the green arrow in the top right figure to change the orientation of the E-field"
self.statusBar().showMessage(self.default_message)
# Menu bar
menubar = self.menuBar()
exitAction = QtGui.QAction('&Exit', self)
exitAction.setShortcut('Ctrl+Q')
exitAction.setStatusTip('Exit program')
exitAction.triggered.connect(exit)
fileMenu = menubar.addMenu('&File')
fileMenu.addAction(exitAction)
settingsMenu = menubar.addMenu('&Edit')
settingsAction = QtGui.QAction('&Settings...', self)
settingsAction.setStatusTip('Edit settings')
settingsAction.triggered.connect(self.editSettings)
settingsMenu.addAction(settingsAction)
self.loadContinuum()
# select H**O
selected_orbital_item.setSelected(True)
