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 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 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()