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 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
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 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()
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')])]
win = ui.MainWindow('Test', menu=menu)
win.add(ui.Label('Hello'))
win.add(ui.Button('Hello', hello))
r = ui.Rows([ui.Label(x * 7) for x in 'abcd'])
win.add(r)
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)
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."""))
