/usr/share/pyshared/ase/atom.py is in python-ase 3.6.0.2515-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 | """This module defines the Atom object."""
import warnings
import numpy as np
from ase.data import atomic_numbers, chemical_symbols, atomic_masses
# 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': ('magmoms', 0.0),
'charge': ('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 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')
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
Atomi 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, str):
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 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 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 attribute."""
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 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', 'Atomic charge')
x = xyzproperty(0)
y = xyzproperty(1)
z = xyzproperty(2)
def _get(self, name):
"""Helper function for deprecated get methods."""
warnings.warn('Use atom.%s' % name, stacklevel=3)
return getattr(self, name)
def _set(self, name, value):
"""Helper function for deprecated set methods."""
warnings.warn('Use atom.%s = ...' % name, stacklevel=3)
setattr(self, name, value)
def get_symbol(self): return self._get('symbol')
def get_atomic_number(self): return self._get('number')
def get_position(self): return self._get('position')
def get_tag(self): return self._get('tag')
def get_momentum(self): return self._get('momentum')
def get_mass(self): return self._get('mass')
def get_initial_magnetic_moment(self): return self._get('magmom')
def get_charge(self): return self._get('charge')
def set_symbol(self, value): self._set('symbol', value)
def set_atomic_number(self, value): self._set('number', value)
def set_position(self, value): self._set('position', value)
def set_tag(self, value): self._set('tag', value)
def set_momentum(self, value): self._set('momentum', value)
def set_mass(self, value): self._set('mass', value)
def set_initial_magnetic_moment(self, value): self._set('magmom', value)
def set_charge(self, value): self._set('charge', value)
|