Source code for ase.atom

"""This module defines the Atom object."""

import numpy as np

from ase.data import atomic_numbers, chemical_symbols, atomic_masses
from ase.utils import basestring

# Singular, plural, default value:
names = {'position': ('positions', np.zeros(3)),
         'number': ('numbers', 0),
         'tag': ('tags', 0),
         'momentum': ('momenta', np.zeros(3)),
         'mass': ('masses', None),
         'magmom': ('initial_magmoms', 0.0),
         'charge': ('initial_charges', 0.0)}


def atomproperty(name, doc):
    """Helper function to easily create Atom attribute property."""

    def getter(self):
        return self.get(name)

    def setter(self, value):
        self.set(name, value)

    def deleter(self):
        self.delete(name)

    return property(getter, setter, deleter, doc)


def abcproperty(index):
    """Helper function to easily create Atom ABC-property."""

    def getter(self):
        spos = self.atoms.get_scaled_positions()
        return spos[self.index][index]

    def setter(self, value):
        spos = self.atoms.get_scaled_positions()
        spos[self.index][index] = value
        self.atoms.set_scaled_positions(spos)

    return property(getter, setter, doc='ABC'[index] + '-coordinate')


def xyzproperty(index):
    """Helper function to easily create Atom XYZ-property."""

    def getter(self):
        return self.position[index]

    def setter(self, value):
        self.position[index] = value

    return property(getter, setter, doc='XYZ'[index] + '-coordinate')


[docs]class Atom(object): """Class for representing a single atom. Parameters: symbol: str or int Can be a chemical symbol (str) or an atomic number (int). position: sequence of 3 floats Atomic position. tag: int Special purpose tag. momentum: sequence of 3 floats Momentum for atom. mass: float Atomic mass in atomic units. magmom: float or 3 floats Magnetic moment. charge: float Atomic charge. """ __slots__ = ['data', 'atoms', 'index'] def __init__(self, symbol='X', position=(0, 0, 0), tag=None, momentum=None, mass=None, magmom=None, charge=None, atoms=None, index=None): self.data = d = {} if atoms is None: # This atom is not part of any Atoms object: if isinstance(symbol, basestring): d['number'] = atomic_numbers[symbol] else: d['number'] = symbol d['position'] = np.array(position, float) d['tag'] = tag if momentum is not None: momentum = np.array(momentum, float) d['momentum'] = momentum d['mass'] = mass if magmom is not None: magmom = np.array(magmom, float) d['magmom'] = magmom d['charge'] = charge self.index = index self.atoms = atoms def __repr__(self): s = "Atom('%s', %s" % (self.symbol, list(self.position)) for name in ['tag', 'momentum', 'mass', 'magmom', 'charge']: value = self.get_raw(name) if value is not None: if isinstance(value, np.ndarray): value = value.tolist() s += ', %s=%s' % (name, value) if self.atoms is None: s += ')' else: s += ', index=%d)' % self.index return s def cut_reference_to_atoms(self): """Cut reference to atoms object.""" for name in names: self.data[name] = self.get_raw(name) self.index = None self.atoms = None def get_raw(self, name): """Get name attribute, return None if not explicitely set.""" if name == 'symbol': return chemical_symbols[self.get_raw('number')] if self.atoms is None: return self.data[name] plural = names[name][0] if plural in self.atoms.arrays: return self.atoms.arrays[plural][self.index] else: return None def get(self, name): """Get name attribute, return default if not explicitely set.""" value = self.get_raw(name) if value is None: if name == 'mass': value = atomic_masses[self.number] else: value = names[name][1] return value def set(self, name, value): """Set name attribute to value.""" if name == 'symbol': name = 'number' value = atomic_numbers[value] if self.atoms is None: assert name in names self.data[name] = value else: plural, default = names[name] if plural in self.atoms.arrays: array = self.atoms.arrays[plural] if name == 'magmom' and array.ndim == 2: assert len(value) == 3 array[self.index] = value else: if name == 'magmom' and np.asarray(value).ndim == 1: array = np.zeros((len(self.atoms), 3)) elif name == 'mass': array = self.atoms.get_masses() else: default = np.asarray(default) array = np.zeros((len(self.atoms),) + default.shape, default.dtype) array[self.index] = value self.atoms.new_array(plural, array) def delete(self, name): """Delete name attribute.""" assert self.atoms is None assert name not in ['number', 'symbol', 'position'] self.data[name] = None symbol = atomproperty('symbol', 'Chemical symbol') number = atomproperty('number', 'Atomic number') position = atomproperty('position', 'XYZ-coordinates') tag = atomproperty('tag', 'Integer tag') momentum = atomproperty('momentum', 'XYZ-momentum') mass = atomproperty('mass', 'Atomic mass') magmom = atomproperty('magmom', 'Initial magnetic moment') charge = atomproperty('charge', 'Initial atomic charge') x = xyzproperty(0) y = xyzproperty(1) z = xyzproperty(2) scaled_position = atomproperty('scaled_position', 'ABC-coordinates') a = abcproperty(0) b = abcproperty(1) c = abcproperty(2)