def view(atoms, data=None, viewer='ag', repeat=None, block=False):
# Ignore for parallel calculations:
if parallel.size != 1:
return
if hasattr(atoms, 'GetUnitCell'):
# Convert old ASE ListOfAtoms to new style.
atoms = OldASEListOfAtomsWrapper(atoms).copy()
vwr = viewer.lower()
if vwr == 'ag':
format = 'traj'
if repeat is None:
command = 'ag'
else:
command = 'ag --repeat=%d,%d,%d' % tuple(repeat)
repeat = None
elif vwr == 'vmd':
format = 'cube'
command = 'vmd'
elif vwr == 'rasmol':
format = 'pdb'
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
else:
raise RuntimeError('Unknown viewer: ' + viewer)
fd, filename = tempfile.mkstemp('.' + format, 'ase-')
fd = os.fdopen(fd, 'w')
if repeat is not None:
atoms = atoms.repeat()
if data is None:
write(fd, atoms, format=format)
else:
write(fd, atoms, format=format, data=data)
fd.close()
if block:
os.system('%s %s' % (command, filename))
os.remove(filename)
else:
if os.name in ['ce', 'nt']: # Win
# XXX: how to make it non-blocking?
os.system('%s %s' % (command, filename))
os.remove(filename)
else:
os.system('%s %s & ' % (command, filename))
os.system('(sleep 60; rm %s) &' % filename)
def view(atoms,
data=None,
viewer='ase-gui',
repeat=None,
block=False,
colors={}):
# Ignore for parallel calculations:
if parallel.size != 1:
return
vwr = viewer.lower()
if vwr == 'ase-gui':
format = 'traj'
if repeat is None:
command = 'ase-gui'
else:
command = 'ase-gui --repeat=%d,%d,%d' % tuple(repeat)
repeat = None
elif vwr == 'vmd':
format = 'cube'
command = 'vmd'
elif vwr == 'rasmol':
format = 'pdb'
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 == 'custom':
ag.main(colors)
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, filename])
os.remove(filename)
else:
subprocess.Popen([command, filename])
subprocess.Popen(['sleep 60; rm {0}'.format(filename)], shell=True)
def view(atoms, data=None, viewer='ase-gui', repeat=None, block=False):
# Ignore for parallel calculations:
if parallel.size != 1:
return
vwr = viewer.lower()
if vwr == 'ase-gui':
format = 'traj'
if repeat is None:
command = 'ase-gui'
else:
command = 'ase-gui --repeat=%d,%d,%d' % tuple(repeat)
repeat = None
elif vwr == 'vmd':
format = 'cube'
command = 'vmd'
elif vwr == 'rasmol':
format = 'pdb'
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
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, filename])
os.remove(filename)
else:
subprocess.Popen([command, filename])
subprocess.Popen(['sleep 60; rm {0}'.format(filename)], shell=True)
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)
def sage(self, atoms):
from ase.visualize.sage import view_sage_jmol
return view_sage_jmol(atoms)