def run(opt, args):
images = Images()
if opt.aneb:
opt.image_number = '-1'
if len(args) > 0:
from ase.io import string2index
try:
images.read(args, string2index(opt.image_number))
except IOError as e:
if len(e.args) == 1:
parser.error(e.args[0])
else:
parser.error(e.args[1] + ': ' + e.filename)
else:
images.initialize([Atoms()])
if opt.interpolate:
images.interpolate(opt.interpolate)
if opt.aneb:
images.aneb()
if opt.repeat != '1':
r = opt.repeat.split(',')
if len(r) == 1:
r = 3 * r
images.repeat_images([int(c) for c in r])
if opt.radii_scale:
images.set_radii(opt.radii_scale)
if opt.output is not None:
images.write(opt.output,
rotations=opt.rotations,
show_unit_cell=opt.show_unit_cell)
opt.terminal = True
if opt.terminal:
if opt.graph is not None:
data = images.graph(opt.graph)
for line in data.T:
for x in line:
print(x, end=' ')
print()
else:
from ase.gui.gui import GUI
import ase.gui.gtkexcepthook
ase
gui = GUI(images, opt.rotations, opt.show_unit_cell, opt.bonds)
gui.run(opt.graph)
def show_clusters(self):
from ase.gui.gui import GUI
from ase.gui.images import Images
all_clusters = []
self.tag_by_probability()
for uid in range(len(self.gaussians)):
cluster = self.atoms[self.cluster_id == uid]
cluster.info = {"name": "Cluster ID: {}".format(uid)}
all_clusters.append(cluster)
images = Images()
images.initialize(all_clusters)
gui = GUI(images)
gui.show_name = True
gui.run()
def run(args):
from ase.gui.images import Images
from ase.atoms import Atoms
images = Images()
if args.filenames:
images.read(args.filenames, args.image_number)
else:
images.initialize([Atoms()])
if args.interpolate:
images.interpolate(args.interpolate)
if args.repeat != '1':
r = args.repeat.split(',')
if len(r) == 1:
r = 3 * r
images.repeat_images([int(c) for c in r])
if args.radii_scale:
images.scale_radii(args.radii_scale)
if args.output is not None:
warnings.warn('You should be using "ase convert ..." instead!')
images.write(args.output, rotations=args.rotations)
args.terminal = True
if args.terminal:
if args.graph is not None:
data = images.graph(args.graph)
for line in data.T:
for x in line:
print(x, end=' ')
print()
else:
import os
from ase.gui.gui import GUI
backend = os.environ.get('MPLBACKEND', '')
if backend == 'module://ipykernel.pylab.backend_inline':
# Jupyter should not steal our windows
del os.environ['MPLBACKEND']
gui = GUI(images, args.rotations, args.bonds, args.graph)
gui.run()
def run(opt, args):
images = Images()
if opt.aneb:
opt.image_number = '-1'
if len(args) > 0:
from ase.io import string2index
images.read(args, string2index(opt.image_number))
else:
images.initialize([Atoms()])
if opt.interpolate:
images.interpolate(opt.interpolate)
if opt.aneb:
images.aneb()
if opt.repeat != '1':
r = opt.repeat.split(',')
if len(r) == 1:
r = 3 * r
images.repeat_images([int(c) for c in r])
if opt.radii_scale:
images.set_radii(opt.radii_scale)
if opt.output is not None:
images.write(opt.output, rotations=opt.rotations,
show_unit_cell=opt.show_unit_cell)
opt.terminal = True
if opt.terminal:
if opt.graph is not None:
data = images.graph(opt.graph)
for line in data.T:
for x in line:
print(x, end=' ')
print()
else:
from ase.gui.gui import GUI
import ase.gui.gtkexcepthook
ase
gui = GUI(images, opt.rotations, opt.show_unit_cell, opt.bonds)
gui.run(opt.graph)
def __init__(self,
images=None,
rotations='',
show_unit_cell=True,
show_bonds=False):
# Try to change into directory of file you are viewing
try:
os.chdir(os.path.split(sys.argv[1])[0])
# This will fail sometimes (e.g. for starting a new session)
except:
pass
if not images:
images = Images()
images.initialize([Atoms()])
self.images = images
self.config = read_defaults()
menu = self.get_menu_data(show_unit_cell, show_bonds)
self.window = ui.ASEGUIWindow(close=self.exit,
menu=menu,
config=self.config,
scroll=self.scroll,
scroll_event=self.scroll_event,
press=self.press,
move=self.move,
release=self.release,
resize=self.resize)
View.__init__(self, rotations)
Status.__init__(self)
self.graphs = [] # list of matplotlib processes
self.graph_wref = [] # list of weakrefs to Graph objects
self.movie_window = None
self.vulnerable_windows = []
self.simulation = {} # Used by modules on Calculate menu.
self.module_state = {} # Used by modules to store their state.
self.arrowkey_mode = self.ARROWKEY_SCAN
self.move_atoms_mask = None
def run(opt, args):
images = Images()
if opt.aneb:
opt.image_number = '-1'
if len(args) > 0:
from ase.io import string2index
images.read(args, string2index(opt.image_number))
else:
images.initialize([Atoms()])
if opt.interpolate:
images.interpolate(opt.interpolate)
if opt.aneb:
images.aneb()
if opt.repeat != '1':
r = opt.repeat.split(',')
if len(r) == 1:
r = 3 * r
images.repeat_images([int(c) for c in r])
if opt.output is not None:
images.write(opt.output,
rotations=opt.rotations,
show_unit_cell=opt.show_unit_cell)
opt.terminal = True
if opt.terminal:
if opt.graph is not None:
data = images.graph(opt.graph)
for line in data.T:
for x in line:
print x,
print
else:
from ase.gui.gui import GUI
import ase.gui.gtkexcepthook
gui = GUI(images, opt.rotations, opt.show_unit_cell, opt.bonds)
gui.run(opt.graph)
def run(args):
from ase.gui.images import Images
from ase.atoms import Atoms
images = Images()
if args.filenames:
from ase.io import string2index
images.read(args.filenames, string2index(args.image_number))
else:
images.initialize([Atoms()])
if args.interpolate:
images.interpolate(args.interpolate)
if args.repeat != '1':
r = args.repeat.split(',')
if len(r) == 1:
r = 3 * r
images.repeat_images([int(c) for c in r])
if args.radii_scale:
images.set_radii(args.radii_scale)
if args.output is not None:
images.write(args.output,
rotations=args.rotations,
show_unit_cell=args.show_unit_cell)
args.terminal = True
if args.terminal:
if args.graph is not None:
data = images.graph(args.graph)
for line in data.T:
for x in line:
print(x, end=' ')
print()
else:
from ase.gui.gui import GUI
gui = GUI(images, args.rotations, args.show_unit_cell, args.bonds)
gui.run(args.graph)
def run(args):
from ase.gui.images import Images
from ase.atoms import Atoms
images = Images()
if args.filenames:
from ase.io import string2index
images.read(args.filenames, string2index(args.image_number))
else:
images.initialize([Atoms()])
if args.interpolate:
images.interpolate(args.interpolate)
if args.repeat != '1':
r = args.repeat.split(',')
if len(r) == 1:
r = 3 * r
images.repeat_images([int(c) for c in r])
if args.radii_scale:
images.set_radii(args.radii_scale)
if args.output is not None:
images.write(args.output, rotations=args.rotations,
show_unit_cell=args.show_unit_cell)
args.terminal = True
if args.terminal:
if args.graph is not None:
data = images.graph(args.graph)
for line in data.T:
for x in line:
print(x, end=' ')
print()
else:
from ase.gui.gui import GUI
gui = GUI(images, args.rotations, args.show_unit_cell, args.bonds)
gui.run(args.graph)
def __init__(self, images=None,
rotations='',
show_unit_cell=True,
show_bonds=False):
# Try to change into directory of file you are viewing
try:
os.chdir(os.path.split(sys.argv[1])[0])
# This will fail sometimes (e.g. for starting a new session)
except:
pass
if not images:
images = Images()
images.initialize([Atoms()])
self.images = images
self.config = read_defaults()
menu = self.get_menu_data(show_unit_cell, show_bonds)
self.window = ui.ASEGUIWindow(self.exit, menu, self.config,
self.scroll,
self.scroll_event,
self.press, self.move, self.release,
self.resize)
View.__init__(self, rotations)
Status.__init__(self)
self.graphs = [] # list of matplotlib processes
self.graph_wref = [] # list of weakrefs to Graph objects
self.movie_window = None
self.vulnerable_windows = []
self.simulation = {} # Used by modules on Calculate menu.
self.module_state = {} # Used by modules to store their state.
self.moving = False
self.move_atoms_mask = None
def run(args):
from ase.gui.images import Images
from ase.atoms import Atoms
images = Images()
if args.filenames:
images.read(args.filenames, args.image_number)
else:
images.initialize([Atoms()])
if args.interpolate:
images.interpolate(args.interpolate)
if args.repeat != '1':
r = args.repeat.split(',')
if len(r) == 1:
r = 3 * r
images.repeat_images([int(c) for c in r])
if args.radii_scale:
images.scale_radii(args.radii_scale)
if args.output is not None:
warnings.warn('You should be using "ase convert ..." instead!')
images.write(args.output, rotations=args.rotations)
args.terminal = True
if args.terminal:
if args.graph is not None:
data = images.graph(args.graph)
for line in data.T:
for x in line:
print(x, end=' ')
print()
else:
from ase.gui.gui import GUI
gui = GUI(images, args.rotations, args.bonds, args.graph)
gui.run()
class KMC_ViewBox(threading.Thread, View, Status, FakeUI):
"""The part of the viewer GUI that displays the model's
current configuration.
"""
def __init__(self,
queue,
signal_queue,
vbox,
window,
rotations='',
show_unit_cell=True,
show_bonds=False):
threading.Thread.__init__(self)
self.image_queue = queue
self.signal_queue = signal_queue
self.configured = False
self.ui = FakeUI.__init__(self)
self.images = Images()
self.aseGui = GUI()
#self.aseGui.images.initialize([ase.atoms.Atoms()])
self.images.initialize([ase.atoms.Atoms()])
self.killed = False
self.paused = False
self.vbox = vbox
self.window = window
self.vbox.connect('scroll-event', self.scroll_event)
self.window.connect('key-press-event', self.on_key_press)
rotations = '0.0x,0.0y,0.0z' #[3,3,3]#np.zeros(3)
self.config = {
'force_vector_scale': None,
'velocity_vector_scale': None,
'swap_mouse': False
}
View.__init__(self, rotations)
Status.__init__(self)
self.vbox.show()
if os.name == 'posix':
self.live_plot = True
else:
self.live_plot = False
#self.drawing_area.realize()
self.scaleA = 3.0
self.center = np.array([8, 8, 8])
#self.set_colors()
#self.set_coordinates(0)
self.center = np.array([0, 0, 0])
self.tofs = get_tof_names()
# history tracking arrays
self.times = []
self.tof_hist = []
self.occupation_hist = []
# prepare diagrams
self.data_plot = plt.figure()
#plt.xlabel('$t$ in s')
self.tof_diagram = self.data_plot.add_subplot(211)
self.tof_diagram.set_yscale('log')
#self.tof_diagram.get_yaxis().get_major_formatter().set_powerlimits(
#(3, 3))
self.tof_plots = []
for tof in self.tofs:
self.tof_plots.append(self.tof_diagram.plot([], [], label=tof)[0])
self.tof_diagram.legend(loc='lower left')
self.tof_diagram.set_ylabel(
'TOF in $\mathrm{s}^{-1}\mathrm{site}^{-1}$')
self.occupation_plots = []
self.occupation_diagram = self.data_plot.add_subplot(212)
for species in sorted(settings.representations):
self.occupation_plots.append(
self.occupation_diagram.plot([], [], label=species)[0], )
self.occupation_diagram.legend(loc=2)
self.occupation_diagram.set_xlabel('$t$ in s')
self.occupation_diagram.set_ylabel('Coverage')
def update_vbox(self, atoms):
"""Update the ViewBox."""
if not self.center.any():
self.center = atoms.cell.diagonal() * .5
#self.images = Images([atoms])
#self.images.filenames = ['kmcos GUI - %s' % settings.model_name]
#self.set_colors()
#self.set_coordinates(0)
#self.set_atoms(atoms)
self.scale = self.scaleA
self.aseGui.scale = self.scale
atoms.center(vacuum=3.0)
self.aseGui.images.initialize([atoms])
self.aseGui.images.center()
self.aseGui.set_frame()
#self.draw()
#self.label.set_label('%.3e s (%.3e steps)' % (atoms.kmc_time,
# atoms.kmc_step))
def update_plots(self, atoms):
"""Update the coverage and TOF plots."""
# fetch data piggy-backed on atoms object
new_time = atoms.kmc_time
occupations = atoms.occupation.sum(axis=1) / lattice.spuck
tof_data = atoms.tof_data
# store locally
while len(self.times) > getattr(settings, 'hist_length', 30):
self.tof_hist.pop(0)
self.times.pop(0)
self.occupation_hist.pop(0)
self.times.append(atoms.kmc_time)
self.tof_hist.append(tof_data)
self.occupation_hist.append(occupations)
# plot TOFs
for i, tof_plot in enumerate(self.tof_plots):
tof_plot.set_xdata(self.times)
tof_plot.set_ydata([tof[i] for tof in self.tof_hist])
self.tof_diagram.set_xlim(self.times[0], self.times[-1])
self.tof_diagram.set_ylim(
1e-3, 10 * max([tof[i] for tof in self.tof_hist]))
# plot occupation
for i, occupation_plot in enumerate(self.occupation_plots):
occupation_plot.set_xdata(self.times)
occupation_plot.set_ydata([occ[i] for occ in self.occupation_hist])
max_occ = max(occ[i] for occ in self.occupation_hist)
self.occupation_diagram.set_ylim([0, max(1, max_occ)])
self.occupation_diagram.set_xlim([self.times[0], self.times[-1]])
self.data_plot.canvas.draw_idle()
manager = plt.get_current_fig_manager()
if hasattr(manager, 'toolbar'):
toolbar = manager.toolbar
if hasattr(toolbar, 'set_visible'):
toolbar.set_visible(False)
plt.show()
# [:] is necessary so that it copies the
# values and doesn't reinitialize the pointer
self.time = new_time
return False
def kill(self):
self.killed = True
def run(self):
time.sleep(1.)
while not self.killed:
time.sleep(1)
if not self.image_queue.empty():
atoms = self.image_queue.get()
gobject.idle_add(self.update_vbox, atoms)
if self.live_plot:
gobject.idle_add(self.update_plots, atoms)
def on_key_press(self, _widget, event):
"""Process key press event on view box."""
signal_dict = {
'a': 'ACCUM_RATE_SUMMATION',
'c': 'COVERAGE',
'd': 'DOUBLE',
'h': 'HALVE',
's': 'SWITCH_SURFACE_PROCESSS_OFF',
'S': 'SWITCH_SURFACE_PROCESSS_ON',
'w': 'WRITEOUT',
}
if event.string in [' ', 'p']:
if not self.paused:
self.signal_queue.put('PAUSE')
self.paused = True
else:
self.signal_queue.put('START')
self.paused = False
elif event.string in ['?']:
for key, command in list(signal_dict.items()):
print('%4s %s' % (key, command))
elif event.string in signal_dict:
self.signal_queue.put(signal_dict.get(event.string, ''))
def scroll_event(self, _window, event):
"""Zoom in/out when using mouse wheel"""
x = 1.0
if event.direction == gtk.gdk.SCROLL_UP:
x = 1.2
elif event.direction == gtk.gdk.SCROLL_DOWN:
x = 1.0 / 1.2
self._do_zoom(x)
def _do_zoom(self, x):
"""Utility method for zooming"""
self.scaleA *= x
try:
atoms = self.image_queue.get()
except Exception as e:
atoms = ase.atoms.Atoms()
print(e)
self.update_vbox(atoms)
class KMC_ViewBox(threading.Thread, View, Status, FakeUI):
"""The part of the viewer GUI that displays the model's
current configuration.
"""
def __init__(self, queue, signal_queue, vbox, window,
rotations='', show_unit_cell=True, show_bonds=False):
threading.Thread.__init__(self)
self.image_queue = queue
self.signal_queue = signal_queue
self.configured = False
self.ui = FakeUI.__init__(self)
self.images = Images()
self.images.initialize([ase.atoms.Atoms()])
self.killed = False
self.paused = False
self.vbox = vbox
self.window = window
self.vbox.connect('scroll-event', self.scroll_event)
self.window.connect('key-press-event', self.on_key_press)
View.__init__(self, self.vbox, rotations)
Status.__init__(self, self.vbox)
self.vbox.show()
if os.name == 'posix':
self.live_plot = True
else:
self.live_plot = False
self.drawing_area.realize()
self.scale = 10.0
self.center = np.array([8, 8, 8])
self.set_colors()
self.set_coordinates(0)
self.center = np.array([0, 0, 0])
self.tofs = get_tof_names()
# history tracking arrays
self.times = []
self.tof_hist = []
self.occupation_hist = []
# prepare diagrams
self.data_plot = plt.figure()
#plt.xlabel('$t$ in s')
self.tof_diagram = self.data_plot.add_subplot(211)
self.tof_diagram.set_yscale('log')
#self.tof_diagram.get_yaxis().get_major_formatter().set_powerlimits(
#(3, 3))
self.tof_plots = []
for tof in self.tofs:
self.tof_plots.append(self.tof_diagram.plot([], [], label=tof)[0])
self.tof_diagram.legend(loc='lower left')
self.tof_diagram.set_ylabel(
'TOF in $\mathrm{s}^{-1}\mathrm{site}^{-1}$')
self.occupation_plots = []
self.occupation_diagram = self.data_plot.add_subplot(212)
for species in sorted(settings.representations):
self.occupation_plots.append(
self.occupation_diagram.plot([], [], label=species)[0],)
self.occupation_diagram.legend(loc=2)
self.occupation_diagram.set_xlabel('$t$ in s')
self.occupation_diagram.set_ylabel('Coverage')
def update_vbox(self, atoms):
"""Update the ViewBox."""
if not self.center.any():
self.center = atoms.cell.diagonal() * .5
self.images = Images([atoms])
self.images.filenames = ['kmos GUI - %s' % settings.model_name]
self.set_colors()
self.set_coordinates(0)
self.draw()
self.label.set_label('%.3e s (%.3e steps)' % (atoms.kmc_time,
atoms.kmc_step))
def update_plots(self, atoms):
"""Update the coverage and TOF plots."""
# fetch data piggy-backed on atoms object
new_time = atoms.kmc_time
occupations = atoms.occupation.sum(axis=1) / lattice.spuck
tof_data = atoms.tof_data
# store locally
while len(self.times) > getattr(settings, 'hist_length', 30):
self.tof_hist.pop(0)
self.times.pop(0)
self.occupation_hist.pop(0)
self.times.append(atoms.kmc_time)
self.tof_hist.append(tof_data)
self.occupation_hist.append(occupations)
# plot TOFs
for i, tof_plot in enumerate(self.tof_plots):
tof_plot.set_xdata(self.times)
tof_plot.set_ydata([tof[i] for tof in self.tof_hist])
self.tof_diagram.set_xlim(self.times[0], self.times[-1])
self.tof_diagram.set_ylim(1e-3,
10 * max([tof[i] for tof in self.tof_hist]))
# plot occupation
for i, occupation_plot in enumerate(self.occupation_plots):
occupation_plot.set_xdata(self.times)
occupation_plot.set_ydata(
[occ[i] for occ in self.occupation_hist])
self.occupation_diagram.set_xlim([self.times[0], self.times[-1]])
self.data_plot.canvas.draw_idle()
manager = plt.get_current_fig_manager()
if hasattr(manager, 'toolbar'):
toolbar = manager.toolbar
if hasattr(toolbar, 'set_visible'):
toolbar.set_visible(False)
plt.show()
# [:] is necessary so that it copies the
# values and doesn't reinitialize the pointer
self.time = new_time
return False
def kill(self):
self.killed = True
def run(self):
time.sleep(1.)
while not self.killed:
time.sleep(0.05)
if not self.image_queue.empty():
atoms = self.image_queue.get()
gobject.idle_add(self.update_vbox, atoms)
if self.live_plot:
gobject.idle_add(self.update_plots, atoms)
def on_key_press(self, _widget, event):
"""Process key press event on view box."""
if event.string in [' ', 'p']:
if not self.paused:
self.signal_queue.put('PAUSE')
self.paused = True
else:
self.signal_queue.put('START')
self.paused = False
elif event.string == 'd':
self.signal_queue.put('DOUBLE')
elif event.string == 'h':
self.signal_queue.put('HALVE')
elif event.string == 's':
self.signal_queue.put('SWITCH_SURFACE_PROCESSES_OFF')
elif event.string == 'S':
self.signal_queue.put('SWITCH_SURFACE_PROCESSES_ON')
def scroll_event(self, _window, event):
"""Zoom in/out when using mouse wheel"""
x = 1.0
if event.direction == gtk.gdk.SCROLL_UP:
x = 1.2
elif event.direction == gtk.gdk.SCROLL_DOWN:
x = 1.0 / 1.2
self._do_zoom(x)
def _do_zoom(self, x):
"""Utility method for zooming"""
self.scale *= x
try:
atoms = self.image_queue.get()
except Exception, e:
atoms = ase.atoms.Atoms()
print(e)
self.update_vbox(atoms)
class KMC_ViewBox(threading.Thread, View, Status, FakeUI):
def __init__(self,
queue,
signal_queue,
vbox,
window,
rotations='',
show_unit_cell=True,
show_bonds=False):
threading.Thread.__init__(self)
self.image_queue = queue
self.signal_queue = signal_queue
self.configured = False
self.ui = FakeUI.__init__(self)
self.images = Images()
self.images.initialize([ase.atoms.Atoms()])
self.killed = False
self.paused = False
self.vbox = vbox
self.window = window
self.vbox.connect('scroll-event', self.scroll_event)
self.window.connect('key-press-event', self.on_key_press)
View.__init__(self, self.vbox, rotations)
Status.__init__(self, self.vbox)
self.vbox.show()
self.drawing_area.realize()
self.scale = 10.0
self.center = np.array([8, 8, 8])
self.set_colors()
self.set_coordinates(0)
self.center = np.array([0, 0, 0])
self.tofs = get_tof_names()
# history tracking arrays
self.times = []
self.tof_hist = []
self.occupation_hist = []
# prepare diagrams
self.data_plot = plt.figure()
#plt.xlabel('$t$ in s')
self.tof_diagram = self.data_plot.add_subplot(211)
self.tof_diagram.get_yaxis().get_major_formatter().set_powerlimits(
(3, 3))
self.tof_plots = []
for tof in self.tofs:
self.tof_plots.append(self.tof_diagram.plot([], [], label=tof)[0])
self.tof_diagram.legend(loc='lower left')
self.tof_diagram.set_ylabel(
'TOF in $\mathrm{s}^{-1}\mathrm{site}^{-1}$')
self.occupation_plots = []
self.occupation_diagram = self.data_plot.add_subplot(212)
for species in sorted(settings.representations):
self.occupation_plots.append(
self.occupation_diagram.plot([], [], label=species)[0], )
self.occupation_diagram.legend(loc=2)
self.occupation_diagram.set_xlabel('$t$ in s')
self.occupation_diagram.set_ylabel('Coverage')
#print('initialized viewbox')
def update_vbox(self, atoms):
if not self.center.any():
self.center = atoms.cell.diagonal() * .5
self.images = Images([atoms])
self.images.filenames = ['kmos GUI - %s' % settings.model_name]
self.set_colors()
self.set_coordinates(0)
self.draw()
self.label.set_label('%.3e s (%.3e steps)' %
(atoms.kmc_time, atoms.kmc_step))
def update_plots(self, atoms):
# fetch data piggy-backed on atoms object
new_time = atoms.kmc_time
new_procstat = atoms.procstat
occupations = atoms.occupation.sum(axis=1) / lattice.spuck
tof_data = atoms.tof_data
# store locally
while len(self.times) > 30:
self.tof_hist.pop(0)
self.times.pop(0)
self.occupation_hist.pop(0)
self.times.append(atoms.kmc_time)
self.tof_hist.append(tof_data)
self.occupation_hist.append(occupations)
# plot TOFs
for i, tof_plot in enumerate(self.tof_plots):
self.tof_plots[i].set_xdata(self.times)
self.tof_plots[i].set_ydata([tof[i] for tof in self.tof_hist])
self.tof_diagram.set_xlim(self.times[0], self.times[-1])
self.tof_diagram.set_ylim(0,
max([tof[i] for tof in self.tof_hist]))
# plot occupation
for i, occupation_plot in enumerate(self.occupation_plots):
self.occupation_plots[i].set_xdata(self.times)
self.occupation_plots[i].set_ydata(
[occ[i] for occ in self.occupation_hist])
self.occupation_diagram.set_xlim([self.times[0], self.times[-1]])
self.data_plot.canvas.draw_idle()
plt.show()
# [:] is necessary so that it copies the
# values and doesn't reinitialize the pointer
self.time = new_time
return False
def kill(self):
self.killed = True
#print(' ... viewbox received kill')
def run(self):
time.sleep(1.)
while not self.killed:
time.sleep(0.05)
if not self.image_queue.empty():
atoms = self.image_queue.get()
gobject.idle_add(self.update_vbox, atoms)
gobject.idle_add(self.update_plots, atoms)
def on_key_press(self, window, event):
if event.string in [' ', 'p']:
if not self.paused:
self.signal_queue.put('PAUSE')
self.paused = True
else:
self.signal_queue.put('START')
self.paused = False
elif event.string == 'd':
self.signal_queue.put('DOUBLE')
elif event.string == 'h':
self.signal_queue.put('HALVE')
def scroll_event(self, window, event):
"""Zoom in/out when using mouse wheel"""
x = 1.0
if event.direction == gtk.gdk.SCROLL_UP:
x = 1.2
elif event.direction == gtk.gdk.SCROLL_DOWN:
x = 1.0 / 1.2
self._do_zoom(x)
def _do_zoom(self, x):
"""Utility method for zooming"""
self.scale *= x
try:
atoms = self.image_queue.get()
except Exception, e:
atoms = ase.atoms.Atoms()
print(e)
self.update_vbox(atoms)
