def test_x3d():
pytest.importorskip('IPython')
from IPython.display import HTML
from ase.visualize import x3d
atoms = bulk('Cu', cubic=True)
my_obj = x3d.view_x3d(atoms)
assert isinstance(my_obj, HTML)
def test_x3d():
import warnings
from unittest.case import SkipTest
from ase import Atoms
try:
with warnings.catch_warnings():
warnings.simplefilter('ignore', DeprecationWarning)
from IPython.display import HTML
from ase.visualize import x3d
except ImportError:
raise SkipTest('cannot import HTML from IPython.displacy')
else:
print('Testing x3d...')
a = 3.6
b = a / 2
atoms = Atoms('Cu4',
positions=[(0, 0, 0), (0, b, b), (b, 0, b), (b, b, 0)],
cell=(a, a, a),
pbc=True)
my_obj = x3d.view_x3d(atoms)
assert isinstance(my_obj, HTML)
def view(atoms, data=None, viewer='ase', repeat=None, block=False):
# Ignore for parallel calculations:
if parallel.size != 1:
return
vwr = viewer.lower()
if vwr == 'ase':
format = 'traj'
command = sys.executable + ' -m ase gui'
if repeat is not None:
command += ' --repeat={},{},{}'.format(*repeat)
repeat = None
elif vwr == 'vmd':
format = 'cube'
command = 'vmd'
elif vwr == 'rasmol':
format = 'proteindatabank'
command = 'rasmol -pdb'
elif vwr == 'xmakemol':
format = 'xyz'
command = 'xmakemol -f'
elif vwr == 'gopenmol':
format = 'xyz'
command = 'rungOpenMol'
elif vwr == 'avogadro':
format = 'cube'
command = 'avogadro'
elif vwr == 'sage':
from ase.visualize.sage import view_sage_jmol
view_sage_jmol(atoms)
return
elif vwr in ('ngl', 'nglview'):
from ase.visualize.nglview import view_ngl
return view_ngl(atoms)
elif vwr == 'x3d':
from ase.visualize.x3d import view_x3d
return view_x3d(atoms)
elif vwr == 'paraview':
# macro for showing atoms in paraview
macro = """\
from paraview.simple import *
version_major = servermanager.vtkSMProxyManager.GetVersionMajor()
source = GetActiveSource()
renderView1 = GetRenderView()
atoms = Glyph(Input=source,
GlyphType='Sphere',
# GlyphMode='All Points',
Scalars='radii',
ScaleMode='scalar',
)
RenameSource('Atoms', atoms)
atomsDisplay = Show(atoms, renderView1)
if version_major <= 4:
atoms.SetScaleFactor = 0.8
atomicnumbers_PVLookupTable = GetLookupTableForArray( "atomic numbers", 1)
atomsDisplay.ColorArrayName = ('POINT_DATA', 'atomic numbers')
atomsDisplay.LookupTable = atomicnumbers_PVLookupTable
else:
atoms.ScaleFactor = 0.8
ColorBy(atomsDisplay, 'atomic numbers')
atomsDisplay.SetScalarBarVisibility(renderView1, True)
Render()
"""
script_name = os.path.join(tempfile.gettempdir(), 'draw_atoms.py')
with open(script_name, 'w') as f:
f.write(macro)
format = 'vtu'
command = 'paraview --script=' + script_name
else:
raise RuntimeError('Unknown viewer: ' + viewer)
fd, filename = tempfile.mkstemp('.' + format, 'ase-')
if repeat is not None:
atoms = atoms.repeat()
if data is None:
write(filename, atoms, format=format)
else:
write(filename, atoms, format=format, data=data)
if block:
subprocess.call(command.split() + [filename])
os.remove(filename)
else:
subprocess.Popen(command.split() + [filename])
subprocess.Popen(['sleep 60; rm {0}'.format(filename)], shell=True)
import warnings
from unittest.case import SkipTest
from ase import Atoms
try:
with warnings.catch_warnings():
warnings.simplefilter('ignore', DeprecationWarning)
from IPython.display import HTML
from ase.visualize import x3d
except ImportError:
raise SkipTest('cannot import HTML from IPython.displacy')
else:
print('Testing x3d...')
a = 3.6
b = a / 2
atoms = Atoms('Cu4',
positions=[(0, 0, 0), (0, b, b), (b, 0, b), (b, b, 0)],
cell=(a, a, a),
pbc=True)
my_obj = x3d.view_x3d(atoms)
assert isinstance(my_obj, HTML)
def x3d(self, atoms):
from ase.visualize.x3d import view_x3d
return view_x3d(atoms)