def edit(self):
"""Modify atoms interactively through ag viewer.
Conflicts leading to undesirable behviour might arise
when matplotlib has been pre-imported with certain
incompatible backends and while trying to use the
plot feature inside the interactive ag. To circumvent,
please set matplotlib.use('gtk') before calling this
method.
"""
from ase.gui.images import Images
from ase.gui.gui import GUI
images = Images([self])
gui = GUI(images)
gui.run()
# use atoms returned from gui:
# (1) delete all currently available atoms
self.set_constraint()
for z in range(len(self)):
self.pop()
edited_atoms = gui.images.get_atoms(0)
# (2) extract atoms from edit session
self.extend(edited_atoms)
self.set_constraint(edited_atoms._get_constraints())
self.set_cell(edited_atoms.get_cell())
self.set_initial_magnetic_moments(edited_atoms.get_magnetic_moments())
self.set_tags(edited_atoms.get_tags())
return
def gui(display):
orig_ui_error = ui.error
try:
ui.error = Error()
gui = GUI()
yield gui
gui.exit()
finally:
ui.error = orig_ui_error
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 _set_reactive_indexes(self, filename):
'''
Manually set the molecule reactive atoms from the ASE GUI, imposing
constraints on the desired atoms.
'''
from ase import Atoms
from ase.gui.gui import GUI
from ase.gui.images import Images
data = read_xyz(filename)
coords = data.atomcoords[0]
labels = ''.join([pt[i].symbol for i in data.atomnos])
atoms = Atoms(labels, positions=coords)
while atoms.constraints == []:
print((
'\nPlease, manually select the reactive atom(s) for molecule %s.'
'\nRotate with right click and select atoms by clicking. Multiple selections can be done by Ctrl+Click.'
'\nWith desired atom(s) selected, go to Tools -> Constraints -> Constrain, then close the GUI.'
) % (filename))
GUI(images=Images([atoms]), show_bonds=True).run()
return list(atoms.constraints[0].get_indices())
def ase_view(mol):
'''
Display an Hypermolecule instance from the ASE GUI
'''
from ase import Atoms
from ase.gui.gui import GUI
from ase.gui.images import Images
if hasattr(mol, 'reactive_atoms_classes_dict'):
images = []
for c, coords in enumerate(mol.atomcoords):
centers = np.vstack([
atom.center
for atom in mol.reactive_atoms_classes_dict[c].values()
])
atomnos = np.concatenate((mol.atomnos, [0 for _ in centers]))
totalcoords = np.concatenate((coords, centers))
images.append(Atoms(atomnos, positions=totalcoords))
else:
images = [
Atoms(mol.atomnos, positions=coords) for coords in mol.atomcoords
]
try:
GUI(images=Images(images), show_bonds=True).run()
except TclError:
print(
'--> GUI not available from command line interface. Skipping it.')
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(args):
f1 = ase.io.read(args[0])
f2 = ase.io.read(args[1])
i1 = Images([f1])
i2 = Images([f2])
gui1 = GUI(i1, '', 1, False)
gui1.run(None)
gui2 = GUI(i2, '', 1, False)
gui2.run(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.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 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 show_configs():
db = dataset.connect(DB_NAME)
vac_tbl = db[VAC]
sol_tbl = db[SOL]
# Find unique runIDs
ids = sol_tbl.distinct('runID')
images = []
for runRes in ids:
positions = []
symbols = []
charges = []
runID = runRes['runID']
for item in sol_tbl.find(runID=runID):
symbols.append(item['symbol'])
pos = [item['X'], item['Y'], item['Z']]
positions.append(pos)
charges.append(None)
# Extract vacancy positions
for item in vac_tbl.find(runID=runID):
e = item['energy']
charges.append(e)
pos = [item['X'], item['Y'], item['Z']]
positions.append(pos)
symbols.append('X')
max_charge = max([c for c in charges if c is not None])
charges = [c - max_charge if c is not None else 0.0 for c in charges]
images.append(
Atoms(symbols=symbols, positions=positions, charges=charges))
from ase.gui.images import Images
from ase.gui.gui import GUI
images = Images(images)
images.covalent_radii[0] = covalent_radii[12]
gui = GUI(images)
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:
from ase.gui.gui import GUI
gui = GUI(images, args.rotations, args.bonds, args.graph)
gui.run()
def _set_leaving_group(self, mol, neighbors_indexes):
'''
Manually set the molecule leaving group from the ASE GUI, imposing
a constraint on the desired atom.
'''
if self.leaving_group_index is None:
from ase import Atoms
from ase.gui.gui import GUI
from ase.gui.images import Images
atoms = Atoms(mol.atomnos, positions=mol.atomcoords[0])
while True:
print(('\nPlease, manually select the leaving group atom for molecule %s'
'\nbonded to the sp3 reactive atom with index %s.'
'\nRotate with right click and select atoms by clicking.'
'\nThen go to Tools -> Constraints -> Constrain, and close the GUI.') % (mol.name, self.index))
GUI(images=Images([atoms]), show_bonds=True).run()
if atoms.constraints != []:
if len(list(atoms.constraints[0].get_indices())) == 1:
if list(atoms.constraints[0].get_indices())[0] in neighbors_indexes:
self.leaving_group_index = list(atoms.constraints[0].get_indices())[0]
break
else:
print('\nSeems that the atom you selected is not bonded to the reactive center or is the reactive atom itself.\nThis is probably an error, please try again.')
atoms.constraints = []
else:
print('\nPlease only select one leaving group atom.')
atoms.constraints = []
return self.others[neighbors_indexes.index(self.leaving_group_index)]
if __name__ == '__main__':
args = p.parse_args()
else:
# We are running inside the test framework: ignore sys.args
args = p.parse_args([])
for name in args.tests or alltests:
for n in alltests:
if n.startswith(name):
name = n
break
else:
1 / 0
print(name)
test = globals()[name]
gui = GUI()
def f():
test(gui)
if not args.pause:
gui.exit()
gui.run(test=f)
def window():
def hello(event=None):
print('hello', event)
menu = [('Hi', [ui.MenuItem('_Hello', hello, 'Ctrl+H')]),
('Hell_o', [ui.MenuItem('ABC', hello, choices='ABC')])]
def factory(images):
gui = GUI(images)
guis.append(gui)
return gui
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)
import traceback
try:
run(opt, args)
except KeyboardInterrupt:
pass
except Exception:
traceback.print_exc()
print(_("""
An exception occurred! Please report the issue to
[email protected] - thanks! Please also report this if
it was a user error, so that a better error message can be provided
next time."""))
gui.open(filename='h2o.json')
save_dialog(gui, 'h2o.cif@-1')
p = argparse.ArgumentParser()
p.add_argument('tests', nargs='*')
p.add_argument('-p', '--pause', action='store_true')
if __name__ == '__main__':
args = p.parse_args()
else:
# We are running inside the test framework: ignore sys.args
args = p.parse_args([])
for name in args.tests or alltests:
for n in alltests:
if n.startswith(name):
name = n
break
else:
1 / 0
print(name)
test = globals()[name]
gui = GUI()
def f():
test(gui)
if not args.pause:
gui.exit()
gui.run(test=f)
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)
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')
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)
import traceback
try:
run(opt, args)
except KeyboardInterrupt:
pass
except Exception:
traceback.print_exc()
print(_("""
An exception occurred! Please report the issue to
[email protected] - thanks! Please also report this if
it was a user error, so that a better error message can be provided
next time."""))
