Coverage for ase / atom.py: 94.44%
126 statements
« prev ^ index » next coverage.py v7.13.5, created at 2026-03-30 08:22 +0000
1# fmt: off
3"""This module defines the Atom object."""
5import numpy as np
7from ase.data import atomic_masses, atomic_numbers, chemical_symbols
9# Singular, plural, default value:
10names = {'position': ('positions', np.zeros(3)),
11 'number': ('numbers', 0),
12 'tag': ('tags', 0),
13 'momentum': ('momenta', np.zeros(3)),
14 'mass': ('masses', None),
15 'magmom': ('initial_magmoms', 0.0),
16 'charge': ('initial_charges', 0.0)}
19def atomproperty(name, doc):
20 """Helper function to easily create Atom attribute property."""
22 def getter(self):
23 return self.get(name)
25 def setter(self, value):
26 self.set(name, value)
28 def deleter(self):
29 self.delete(name)
31 return property(getter, setter, deleter, doc)
34def abcproperty(index):
35 """Helper function to easily create Atom ABC-property."""
37 def getter(self):
38 return self.scaled_position[index]
40 def setter(self, value):
41 # We can't just do self.scaled_position[i] = value
42 # because scaled_position is a new buffer, not a view into
43 # something we can write back to.
44 # This is a clear bug!
45 spos = self.scaled_position
46 spos[index] = value
47 self.scaled_position = spos
49 return property(getter, setter, doc='ABC'[index] + '-coordinate')
52def xyzproperty(index):
53 """Helper function to easily create Atom XYZ-property."""
55 def getter(self):
56 return self.position[index]
58 def setter(self, value):
59 self.position[index] = value
61 return property(getter, setter, doc='XYZ'[index] + '-coordinate')
64class Atom:
65 """Class for representing a single atom.
67 Parameters
68 ----------
70 symbol: str or int
71 Can be a chemical symbol (str) or an atomic number (int).
72 position: sequence of 3 floats
73 Atomic position.
74 tag: int
75 Special purpose tag.
76 momentum: sequence of 3 floats
77 Momentum for atom.
78 mass: float
79 Atomic mass in atomic units.
80 magmom: float or 3 floats
81 Magnetic moment.
82 charge: float
83 Atomic charge.
84 """
85 __slots__ = ['data', 'atoms', 'index']
87 def __init__(self, symbol='X', position=(0, 0, 0),
88 tag=None, momentum=None, mass=None,
89 magmom=None, charge=None,
90 atoms=None, index=None):
92 self.data = d = {}
94 if atoms is None:
95 # This atom is not part of any Atoms object:
96 if isinstance(symbol, str):
97 d['number'] = atomic_numbers[symbol]
98 else:
99 d['number'] = symbol
100 d['position'] = np.array(position, float)
101 d['tag'] = tag
102 if momentum is not None:
103 momentum = np.array(momentum, float)
104 d['momentum'] = momentum
105 d['mass'] = mass
106 if magmom is not None:
107 magmom = np.array(magmom, float)
108 d['magmom'] = magmom
109 d['charge'] = charge
111 self.index = index
112 self.atoms = atoms
114 @property
115 def scaled_position(self):
116 pos = self.position
117 spos = self.atoms.cell.scaled_positions(pos[np.newaxis])
118 return spos[0]
120 @scaled_position.setter
121 def scaled_position(self, value):
122 pos = self.atoms.cell.cartesian_positions(value)
123 self.position = pos
125 def __repr__(self):
126 s = f"Atom('{self.symbol}', {list(self.position)}"
127 for name in ['tag', 'momentum', 'mass', 'magmom', 'charge']:
128 value = self.get_raw(name)
129 if value is not None:
130 if isinstance(value, np.ndarray):
131 value = value.tolist()
132 s += f', {name}={value}'
133 if self.atoms is None:
134 s += ')'
135 else:
136 s += ', index=%d)' % self.index
137 return s
139 def cut_reference_to_atoms(self):
140 """Cut reference to atoms object."""
141 for name in names:
142 self.data[name] = self.get_raw(name)
143 self.index = None
144 self.atoms = None
146 def get_raw(self, name):
147 """Get name attribute, return None if not explicitly set."""
148 if name == 'symbol':
149 return chemical_symbols[self.get_raw('number')]
151 if self.atoms is None:
152 return self.data[name]
154 plural = names[name][0]
155 if plural in self.atoms.arrays:
156 return self.atoms.arrays[plural][self.index]
157 else:
158 return None
160 def get(self, name):
161 """Get name attribute, return default if not explicitly set."""
162 value = self.get_raw(name)
163 if value is None:
164 if name == 'mass':
165 value = atomic_masses[self.number]
166 else:
167 value = names[name][1]
168 return value
170 def set(self, name, value):
171 """Set name attribute to value."""
172 if name == 'symbol':
173 name = 'number'
174 value = atomic_numbers[value]
176 if self.atoms is None:
177 assert name in names
178 self.data[name] = value
179 else:
180 plural, default = names[name]
181 if plural in self.atoms.arrays:
182 array = self.atoms.arrays[plural]
183 if name == 'magmom' and array.ndim == 2:
184 assert len(value) == 3
185 array[self.index] = value
186 else:
187 if name == 'magmom' and np.asarray(value).ndim == 1:
188 array = np.zeros((len(self.atoms), 3))
189 elif name == 'mass':
190 array = self.atoms.get_masses()
191 else:
192 default = np.asarray(default)
193 array = np.zeros((len(self.atoms),) + default.shape,
194 default.dtype)
195 array[self.index] = value
196 self.atoms.new_array(plural, array)
198 def delete(self, name):
199 """Delete name attribute."""
200 assert self.atoms is None
201 assert name not in ['number', 'symbol', 'position']
202 self.data[name] = None
204 symbol = atomproperty('symbol', 'Chemical symbol')
205 number = atomproperty('number', 'Atomic number')
206 position = atomproperty('position', 'XYZ-coordinates')
207 tag = atomproperty('tag', 'Integer tag')
208 momentum = atomproperty('momentum', 'XYZ-momentum')
209 mass = atomproperty('mass', 'Atomic mass')
210 magmom = atomproperty('magmom', 'Initial magnetic moment')
211 charge = atomproperty('charge', 'Initial atomic charge')
212 x = xyzproperty(0)
213 y = xyzproperty(1)
214 z = xyzproperty(2)
216 a = abcproperty(0)
217 b = abcproperty(1)
218 c = abcproperty(2)