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<span class="target" id="module-ase.atom"></span><section id="the-atom-object">

<h1>The Atom object<a class=“headerlink” href=“#the-atom-object” title=“Permalink to this headline”>¶</a></h1> ASE defines a python class called <a class=“reference internal” href=“#ase.atom.Atom” title=“ase.atom.Atom”>

py py-class docutils literal notranslate"

<span class="pre">Atom</span>

</a> to setup and handle atoms in electronic structure and molecular simulations. From a python script, atoms can be created like this: <div class=“doctest highlight-default notranslate”><div class=“highlight”><pre>>>> from ase import Atom >>> a1 = Atom('Si', (0, 0, 0)) >>> a2 = Atom('H', (1.3, 0, 0), mass=2) >>> a3 = Atom(14, position=(0, 0, 0)) # same as a1 </pre></div> </div> <dl class=“py class”> <dt class=“sig sig-object py” id=“ase.atom.Atom”> class ase.atom.Atom(symbol='X', position=(0, 0, 0), tag=None, momentum=None, mass=None, magmom=None, charge=None, atoms=None, index=None)<a class=“reference internal” href=“../_modules/ase/atom.html#Atom”>[source]</a><a class=“headerlink” href=“#ase.atom.Atom” title=“Permalink to this definition”>¶</a></dt> <dd>Class for representing a single atom. Parameters: <dl class=“simple”> <dt>symbol: str or int</dt><dd>Can be a chemical symbol (str) or an atomic number (int). </dd> <dt>position: sequence of 3 floats</dt><dd>Atomic position. </dd> <dt>tag: int</dt><dd>Special purpose tag. </dd> <dt>momentum: sequence of 3 floats</dt><dd>Momentum for atom. </dd> <dt>mass: float</dt><dd>Atomic mass in atomic units. </dd> <dt>magmom: float or 3 floats</dt><dd>Magnetic moment. </dd> <dt>charge: float</dt><dd>Atomic charge. </dd> </dl> </dd></dl>

The first argument to the constructor of an <a class=“reference internal” href=“#ase.atom.Atom” title=“ase.atom.Atom”>

py py-class docutils literal notranslate"

<span class="pre">Atom</span>

</a> object is the chemical symbol, and the second argument is the position in Å units (see <a class=“reference internal” href=“units.html#module-ase.units” title=“ase.units”>

py py-mod docutils literal notranslate"

<span class="pre">ase.units</span>

</a>). The position can be any numerical sequence of length three. The properties of an atom can also be set using keywords like it is done in the a2 and a3 examples above. More examples: <div class=“doctest highlight-default notranslate”><div class=“highlight”><pre>>>> a = Atom('O', charge=-2) >>> b = Atom(8, charge=-2) >>> c = Atom('H', (1, 2, 3), magmom=1) >>> print(a.charge, a.position) -2 [ 0. 0. 0.] >>> c.x = 0.0 >>> c.position array([ 0., 2., 3.]) >>> b.symbol 'O' >>> c.tag = 42 >>> c.number 1 >>> c.symbol = 'Li' >>> c.number 3 </pre></div> </div> If the atom object belongs to an Atoms object, then assigning values to the atom attributes will change the corresponding arrays of the atoms object: <div class=“doctest highlight-default notranslate”><div class=“highlight”><pre>>>> from ase import Atoms >>> OH = Atoms('OH') >>> OH[0].charge = -1 >>> OH.get_initial_charges() array([-1., 0.]) </pre></div> </div> Another example: <div class=“doctest highlight-default notranslate”><div class=“highlight”><pre>>>> for atom in bulk: … if atom.symbol == 'Ni': … atom.magmom = 0.7 # set initial magnetic moment </pre></div> </div> The different properties of an atom can be obtained and changed via attributes (

literal notranslate"

<span class="pre">position</span>

,

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<span class="pre">number</span>

,

literal notranslate"

<span class="pre">tag</span>

,

literal notranslate"

<span class="pre">momentum</span>

,

literal notranslate"

<span class="pre">mass</span>

,

literal notranslate"

<span class="pre">magmom</span>

,

literal notranslate"

<span class="pre">charge</span>

,

literal notranslate"

<span class="pre">x</span>

,

literal notranslate"

<span class="pre">y</span>

,

literal notranslate"

<span class="pre">z</span>

): <div class=“doctest highlight-default notranslate”><div class=“highlight”><pre>>>> a1.position = [1, 0, 0] >>> a1.position [1, 0, 0] >>> a1.z = 2.5 >>> a1.position [1, 0, 2.5] >>> a2.magmom = 1.0 </pre></div> </div> That last line will set the initial magnetic moment that some calculators use (similar to the <a class=“reference internal” href=“atoms.html#ase.Atoms.set_initial_magnetic_moments” title=“ase.Atoms.set_initial_magnetic_moments”>

py py-meth docutils literal notranslate"

<span class="pre">set_initial_magnetic_moments()</span>

</a> method). <div class=“admonition note”> Note The

literal notranslate"

<span class="pre">position</span>

and

literal notranslate"

<span class="pre">momentum</span>

attributes refer to mutable objects, so in some cases, you may want to use

literal notranslate"

<span class="pre">a1.position.copy()</span>

in order to avoid changing the position of

literal notranslate"

<span class="pre">a1</span>

by accident. </div> <section id=“getting-an-atom-from-an-atoms-object”> <h2>Getting an Atom from an Atoms object<a class=“headerlink” href=“#getting-an-atom-from-an-atoms-object” title=“Permalink to this headline”>¶</a></h2> Indexing an <a class=“reference internal” href=“atoms.html#ase.Atoms” title=“ase.Atoms”>

py py-class docutils literal notranslate"

<span class="pre">Atoms</span>

</a> object returns an <a class=“reference internal” href=“#ase.atom.Atom” title=“ase.atom.Atom”>

py py-class docutils literal notranslate"

<span class="pre">Atom</span>

</a> object still remembering that it belongs to the collective <a class=“reference internal” href=“atoms.html#ase.Atoms” title=“ase.Atoms”>

py py-class docutils literal notranslate"

<span class="pre">Atoms</span>

</a>: Modifying it will also change the atoms object: <div class=“doctest highlight-default notranslate”><div class=“highlight”><pre>>>> from ase.build import molecule >>> atoms = molecule('CH4') >>> atoms.get_positions() array(0. , 0. , 0. ], [ 0.629118, 0.629118, 0.629118], [-0.629118, -0.629118, 0.629118], [ 0.629118, -0.629118, -0.629118], [-0.629118, 0.629118, -0.629118) >>> a = atoms[2] >>> a Atom('H', [-0.62911799999999996, -0.62911799999999996, 0.62911799999999996], index=2) >>> a.x = 0 >>> atoms.get_positions() array(0. , 0. , 0. ], [ 0.629118, 0.629118, 0.629118], [ 0. , -0.629118, 0.629118], [ 0.629118, -0.629118, -0.629118], [-0.629118, 0.629118, -0.629118) </pre></div> </div> <div class=“admonition seealso”> See also <dl class=“simple”> <dt><a class=“reference internal” href=“atoms.html#module-ase” title=“ase”>

py py-mod docutils literal notranslate"

<span class="pre">ase</span>

</a>:</dt><dd>More information about how to use collections of atoms. </dd> <dt><a class=“reference internal” href=“calculators/calculators.html#module-ase.calculators” title=“ase.calculators: Energy, force and stress calculators.”>

py py-mod docutils literal notranslate"

<span class="pre">ase.calculators</span>

</a>:</dt><dd>Information about how to calculate forces and energies of atoms. </dd> </dl> </div> </section> </section>

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