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 get_atoms(self):
atoms = OldASEListOfAtomsWrapper(self.loa).copy()
atoms.set_calculator(self)
return atoms
def __init__(self, symbols=None,
positions=None, numbers=None,
tags=None, momenta=None, masses=None,
magmoms=None, charges=None,
scaled_positions=None,
cell=None, pbc=None,
constraint=None,
calculator=None):
atoms = None
if hasattr(symbols, 'GetUnitCell'):
from ase.old import OldASEListOfAtomsWrapper
atoms = OldASEListOfAtomsWrapper(symbols)
symbols = None
elif hasattr(symbols, "get_positions"):
atoms = symbols
symbols = None
elif (isinstance(symbols, (list, tuple)) and
len(symbols) > 0 and isinstance(symbols[0], Atom)):
# Get data from a list or tuple of Atom objects:
data = zip(*[atom.get_data() for atom in symbols])
atoms = Atoms(None, *data)
symbols = None
if atoms is not None:
# Get data from another Atoms object:
if scaled_positions is not None:
raise NotImplementedError
if symbols is None and numbers is None:
numbers = atoms.get_atomic_numbers()
if positions is None:
positions = atoms.get_positions()
if tags is None and atoms.has('tags'):
tags = atoms.get_tags()
if momenta is None and atoms.has('momenta'):
momenta = atoms.get_momenta()
if magmoms is None and atoms.has('magmoms'):
magmoms = atoms.get_initial_magnetic_moments()
if masses is None and atoms.has('masses'):
masses = atoms.get_masses()
if charges is None and atoms.has('charges'):
charges = atoms.get_charges()
if cell is None:
cell = atoms.get_cell()
if pbc is None:
pbc = atoms.get_pbc()
if constraint is None:
constraint = [c.copy() for c in atoms.constraints]
self.arrays = {}
if symbols is None:
if numbers is None:
if positions is not None:
natoms = len(positions)
elif scaled_positions is not None:
natoms = len(scaled_positions)
else:
natoms = 0
numbers = np.zeros(natoms, int)
self.new_array('numbers', numbers, int)
else:
if numbers is not None:
raise ValueError(
'Use only one of "symbols" and "numbers".')
else:
self.new_array('numbers', symbols2numbers(symbols), int)
if cell is None:
cell = np.eye(3)
self.set_cell(cell)
if positions is None:
if scaled_positions is None:
positions = np.zeros((len(self.arrays['numbers']), 3))
else:
positions = np.dot(scaled_positions, self._cell)
else:
if scaled_positions is not None:
raise RuntimeError, 'Both scaled and cartesian positions set!'
self.new_array('positions', positions, float, (3,))
self.set_constraint(constraint)
self.set_tags(default(tags, 0))
self.set_momenta(default(momenta, (0.0, 0.0, 0.0)))
self.set_masses(default(masses, None))
self.set_initial_magnetic_moments(default(magmoms, 0.0))
self.set_charges(default(charges, 0.0))
if pbc is None:
pbc = False
self.set_pbc(pbc)
self.adsorbate_info = {}
self.set_calculator(calculator)
def __init__(self,
symbols=None,
positions=None,
numbers=None,
tags=None,
momenta=None,
masses=None,
magmoms=None,
charges=None,
scaled_positions=None,
cell=None,
pbc=None,
constraint=None,
calculator=None):
atoms = None
if hasattr(symbols, 'GetUnitCell'):
from ase.old import OldASEListOfAtomsWrapper
atoms = OldASEListOfAtomsWrapper(symbols)
symbols = None
elif hasattr(symbols, 'get_positions'):
atoms = symbols
symbols = None
elif (isinstance(symbols, (list, tuple)) and len(symbols) > 0
and isinstance(symbols[0], Atom)):
# Get data from a list or tuple of Atom objects:
data = zip(*[atom.get_data() for atom in symbols])
atoms = self.__class__(None, *data)
symbols = None
if atoms is not None:
# Get data from another Atoms object:
if scaled_positions is not None:
raise NotImplementedError
if symbols is None and numbers is None:
numbers = atoms.get_atomic_numbers()
if positions is None:
positions = atoms.get_positions()
if tags is None and atoms.has('tags'):
tags = atoms.get_tags()
if momenta is None and atoms.has('momenta'):
momenta = atoms.get_momenta()
if magmoms is None and atoms.has('magmoms'):
magmoms = atoms.get_initial_magnetic_moments()
if masses is None and atoms.has('masses'):
masses = atoms.get_masses()
if charges is None and atoms.has('charges'):
charges = atoms.get_charges()
if cell is None:
cell = atoms.get_cell()
if pbc is None:
pbc = atoms.get_pbc()
if constraint is None:
constraint = [c.copy() for c in atoms.constraints]
if calculator is None:
calculator = atoms.get_calculator()
self.arrays = {}
if symbols is None:
if numbers is None:
if positions is not None:
natoms = len(positions)
elif scaled_positions is not None:
natoms = len(scaled_positions)
else:
natoms = 0
numbers = np.zeros(natoms, int)
self.new_array('numbers', numbers, int)
else:
if numbers is not None:
raise ValueError('Use only one of "symbols" and "numbers".')
else:
self.new_array('numbers', symbols2numbers(symbols), int)
if cell is None:
cell = np.eye(3)
self.set_cell(cell)
if positions is None:
if scaled_positions is None:
positions = np.zeros((len(self.arrays['numbers']), 3))
else:
positions = np.dot(scaled_positions, self._cell)
else:
if scaled_positions is not None:
raise RuntimeError, 'Both scaled and cartesian positions set!'
self.new_array('positions', positions, float, (3, ))
self.set_constraint(constraint)
self.set_tags(default(tags, 0))
self.set_momenta(default(momenta, (0.0, 0.0, 0.0)))
self.set_masses(default(masses, None))
self.set_initial_magnetic_moments(default(magmoms, 0.0))
self.set_charges(default(charges, 0.0))
if pbc is None:
pbc = False
self.set_pbc(pbc)
self.adsorbate_info = {}
self.set_calculator(calculator)
def get_atoms(self):
atoms = OldASEListOfAtomsWrapper(self.loa).copy()
atoms.set_calculator(self)
return atoms
