def __init__(self, parent=None, system=None, app=None):
QtGui.QMainWindow.__init__(self, parent=parent)
self.ui = UI()
self.ui.setupUi(self)
self.ui.view3D.setSystem(system)
self.system = system
self._params = dict()
self._params["amplitude"]=1.0
self._params["remove_known_zeroev"]=True
export = self._params["export"] = dict()
export["nframes"]=100
self._params["nframes"] = 30
self.app = app
self.current_selection = None
self.ui.actionShow_energies.setChecked(False)
self.ui.mplwidget.hide()
self.ui.actionRun.setVisible(False)
def __init__(self, parent=None, system=None, app=None):
QtGui.QMainWindow.__init__(self, parent=parent)
self.ui = UI()
self.ui.setupUi(self)
self.ui.view3D.setSystem(system)
self.system = system
self._params = dict()
self._params["amplitude"] = 1.0
self._params["remove_known_zeroev"] = True
export = self._params["export"] = dict()
export["nframes"] = 100
self._params["nframes"] = 30
self.app = app
self.current_selection = None
self.ui.actionShow_energies.setChecked(False)
self.ui.mplwidget.hide()
self.ui.actionRun.setVisible(False)
class NormalmodeBrowser(QtGui.QMainWindow):
"""
the GUI for exploring normal modes
"""
def __init__(self, parent=None, system=None, app=None):
QtGui.QMainWindow.__init__(self, parent=parent)
self.ui = UI()
self.ui.setupUi(self)
self.ui.view3D.setSystem(system)
self.system = system
self._params = dict()
self._params["amplitude"]=1.0
self._params["remove_known_zeroev"]=True
export = self._params["export"] = dict()
export["nframes"]=100
self._params["nframes"] = 30
self.app = app
self.current_selection = None
self.ui.actionShow_energies.setChecked(False)
self.ui.mplwidget.hide()
self.ui.actionRun.setVisible(False)
def set_coords(self, coords, normalmodes=None):
"""
set the coordinates for which the normal modes will be computed
"""
self.coords = coords
self.normalmodes = normalmodes
if normalmodes is None:
self._calculate_normalmodes()
self._fill_normalmodes()
self.ui.view3D.setCoords(coords)
def _calculate_normalmodes(self):
"""
compute the normal modes
"""
# pot = self.system.get_potential()
# E, g, hess = pot.getEnergyGradientHessian(self.coords)
# metric = self.system.get_metric_tensor(self.coords)
# freq, mode = normalmodes(hess, metric = metric)
freq, mode = self.system.get_normalmodes(self.coords)
mode=np.real(mode.transpose())
self.normalmodes = []
#self.normalmodes.append((fre[0], m.flatten()))
for f, m in zip(freq, mode):
self.normalmodes.append((f, m)) #np.dot(metric, m)))
def _fill_normalmodes(self):
"""
populate the list of normal modes
"""
self.ui.listNormalmodes.clear()
for n in self.normalmodes:
self.ui.listNormalmodes.addItem(NormalmodeItem(n))
def on_listNormalmodes_currentItemChanged(self, newsel):
"""
change which normal mode we're looking at
"""
if newsel is None:
self.currentmode = None
return
orthogopt = self.system.get_orthogonalize_to_zero_eigenvectors()
mode = newsel.get_mode().copy()
if self._params["remove_known_zeroev"]:
mode = orthogopt(mode, self.coords)
self.currentmode = mode
self.current_selection = newsel
# generate the configurations from the normal mode
amp = self._params["amplitude"]
vector = self.currentmode
nframes = self._params["nframes"]
dxlist = [amp * float(i) / nframes for i in xrange(-nframes/2,nframes/2)]
coordspath = [self.coords + dx * vector for dx in dxlist]
coordspath = np.array(coordspath)
self.dxlist = dxlist
self.coordspath = coordspath
self.ui.view3D.setCoordsPath(coordspath)#, labels=labels)
# self.ui.view3D.ui.btn_animate.hide()
if self.ui.actionShow_energies.isChecked():
self.draw_energy_plot()
def draw_energy_plot(self):
"""
make a plot of the energies and the energies from the harmonic approximation
"""
if self.current_selection is None: return
dxlist = self.dxlist
coordspath = self.coordspath
# get the energies of the configurations
pot = self.system.get_potential()
energies = [pot.getEnergy(coords) for coords in coordspath]
# get the energies of the harmonic approximation
freq = self.current_selection.get_freq()
expected_energies = np.array([ 0.5*(freq)*(dx)**2 for dx in dxlist])
expected_energies += pot.getEnergy(self.coords)
# make the plot
ax = self.ui.mplwidget.axes
ax.clear()
ax.plot(dxlist, energies, label="energy")
ax.plot(dxlist, expected_energies, label="harmonic approximation")
ax.legend(loc='best')
ax.set_xlabel("displacement")
self.ui.mplwidget.draw()
def on_actionRun_toggled(self, checked=None):
if checked is None: return
if checked:
self.ui.view3D.start_animation()
else:
self.ui.view3D.stop_animation()
def on_actionShow_energies_toggled(self, checked=None):
if checked is None: return
if checked:
self.ui.mplwidget.show()
self.draw_energy_plot()
else:
self.ui.mplwidget.hide()
def on_actionSave_triggered(self, checked=None):
"""
save the normal modes to disk
"""
if checked is None:
return
dialog = QtGui.QFileDialog(self)
dialog.setFileMode(QtGui.QFileDialog.AnyFile)
dialog.selectFile("mode.pickle")
dialog.setAcceptMode(QtGui.QFileDialog.AcceptSave);
if(not dialog.exec_()):
return
filename = dialog.selectedFiles()[0]
path = []
nframes = self._params["export"]["nframes"]
for i in xrange(nframes):
t = np.sin(i/float(nframes)*2.*np.pi)
path.append(self.coords + self._params["amplitude"]*t*self.currentmode)
pickle.dump(path, open(filename, "w"))
def on_actionParameters_triggered(self, checked=None):
"""
open a dialog box to change the parameters
"""
if checked is None:
return
if not hasattr(self, "_paramsdlg"):
self._paramsdlg = DlgParams(self._params, parent=self)
self._paramsdlg.show()
class NormalmodeBrowser(QtGui.QMainWindow):
"""
the GUI for exploring normal modes
"""
def __init__(self, parent=None, system=None, app=None):
QtGui.QMainWindow.__init__(self, parent=parent)
self.ui = UI()
self.ui.setupUi(self)
self.ui.view3D.setSystem(system)
self.system = system
self._params = dict()
self._params["amplitude"] = 1.0
self._params["remove_known_zeroev"] = True
export = self._params["export"] = dict()
export["nframes"] = 100
self._params["nframes"] = 30
self.app = app
self.current_selection = None
self.ui.actionShow_energies.setChecked(False)
self.ui.mplwidget.hide()
self.ui.actionRun.setVisible(False)
def set_coords(self, coords, normalmodes=None):
"""
set the coordinates for which the normal modes will be computed
"""
self.coords = coords
self.normalmodes = normalmodes
if normalmodes is None:
self._calculate_normalmodes()
self._fill_normalmodes()
self.ui.view3D.setCoords(coords)
def _calculate_normalmodes(self):
"""
compute the normal modes
"""
# pot = self.system.get_potential()
# E, g, hess = pot.getEnergyGradientHessian(self.coords)
# metric = self.system.get_metric_tensor(self.coords)
# freq, mode = normalmodes(hess, metric = metric)
freq, mode = self.system.get_normalmodes(self.coords)
mode = np.real(mode.transpose())
self.normalmodes = []
#self.normalmodes.append((fre[0], m.flatten()))
for f, m in zip(freq, mode):
self.normalmodes.append((f, m)) #np.dot(metric, m)))
def _fill_normalmodes(self):
"""
populate the list of normal modes
"""
self.ui.listNormalmodes.clear()
for n in self.normalmodes:
self.ui.listNormalmodes.addItem(NormalmodeItem(n))
def on_listNormalmodes_currentItemChanged(self, newsel):
"""
change which normal mode we're looking at
"""
if newsel is None:
self.currentmode = None
return
orthogopt = self.system.get_orthogonalize_to_zero_eigenvectors()
mode = newsel.get_mode().copy()
if self._params["remove_known_zeroev"] and orthogopt is not None:
mode = orthogopt(mode, self.coords)
self.currentmode = mode
self.current_selection = newsel
# generate the configurations from the normal mode
amp = self._params["amplitude"]
vector = self.currentmode
nframes = self._params["nframes"]
dxlist = [
amp * float(i) / nframes for i in xrange(-nframes / 2, nframes / 2)
]
coordspath = [self.coords + dx * vector for dx in dxlist]
coordspath = np.array(coordspath)
self.dxlist = dxlist
self.coordspath = coordspath
self.ui.view3D.setCoordsPath(coordspath) #, labels=labels)
# self.ui.view3D.ui.btn_animate.hide()
if self.ui.actionShow_energies.isChecked():
self.draw_energy_plot()
def draw_energy_plot(self):
"""
make a plot of the energies and the energies from the harmonic approximation
"""
if self.current_selection is None: return
dxlist = self.dxlist
coordspath = self.coordspath
# get the energies of the configurations
pot = self.system.get_potential()
energies = [pot.getEnergy(coords) for coords in coordspath]
# get the energies of the harmonic approximation
freq = self.current_selection.get_freq()
expected_energies = np.array([0.5 * (freq) * (dx)**2 for dx in dxlist])
expected_energies += pot.getEnergy(self.coords)
# make the plot
ax = self.ui.mplwidget.axes
ax.clear()
ax.plot(dxlist, energies, label="energy")
ax.plot(dxlist, expected_energies, label="harmonic approximation")
ax.legend(loc='best')
ax.set_xlabel("displacement")
self.ui.mplwidget.draw()
def on_actionRun_toggled(self, checked=None):
if checked is None: return
if checked:
self.ui.view3D.start_animation()
else:
self.ui.view3D.stop_animation()
def on_actionShow_energies_toggled(self, checked=None):
if checked is None: return
if checked:
self.ui.mplwidget.show()
self.draw_energy_plot()
else:
self.ui.mplwidget.hide()
def on_actionSave_triggered(self, checked=None):
"""
save the normal modes to disk
"""
if checked is None:
return
dialog = QtGui.QFileDialog(self)
dialog.setFileMode(QtGui.QFileDialog.AnyFile)
dialog.selectFile("mode.pickle")
dialog.setAcceptMode(QtGui.QFileDialog.AcceptSave)
if (not dialog.exec_()):
return
filename = dialog.selectedFiles()[0]
path = []
nframes = self._params["export"]["nframes"]
for i in xrange(nframes):
t = np.sin(i / float(nframes) * 2. * np.pi)
path.append(self.coords +
self._params["amplitude"] * t * self.currentmode)
pickle.dump(path, open(filename, "w"))
def on_actionParameters_triggered(self, checked=None):
"""
open a dialog box to change the parameters
"""
if checked is None:
return
if not hasattr(self, "_paramsdlg"):
self._paramsdlg = DlgParams(self._params, parent=self)
self._paramsdlg.show()
