<html>
<table width=“100%” cellspacing=0 cellpadding=2 border=0 summary=“heading”> <tr bgcolor=“#7799ee”> <td valign=bottom> <br> <font color=“#ffffff” face=“helvetica, arial”> <br><big><big><strong><a href=“ase.html”><font color=“#ffffff”>ase</font></a>.atom</strong></big></big></font></td
<td align=right valign=bottom
<font color=“#ffffff” face=“helvetica, arial”><a href=“.”>index</a><br><a href=“file:/usr/local/lib/python2.7/dist-packages/ase/atom.py”>/usr/local/lib/python2.7/dist-packages/ase/atom.py</a></font></td></tr></table><p><tt>This module defines the <a href="#Atom">Atom</a> <a href="__builtin__.html#object">object</a>.</tt></p><p>
<table width=“100%” cellspacing=0 cellpadding=2 border=0 summary=“section”> <tr bgcolor=“#aa55cc”> <td colspan=3 valign=bottom> <br> <font color=“#ffffff” face=“helvetica, arial”><big><strong>Modules</strong></big></font></td></tr>
<tr><td bgcolor=“#aa55cc”><tt> </tt></td><td> </td> <td width=“100%”><table width=“100%” summary=“list”><tr><td width=“25%” valign=top><a href=“numpy.html”>numpy</a><br> </td><td width=“25%” valign=top><a href=“warnings.html”>warnings</a><br> </td><td width=“25%” valign=top></td><td width=“25%” valign=top></td></tr></table></td></tr></table><p> <table width=“100%” cellspacing=0 cellpadding=2 border=0 summary=“section”> <tr bgcolor=“#ee77aa”> <td colspan=3 valign=bottom> <br> <font color=“#ffffff” face=“helvetica, arial”><big><strong>Classes</strong></big></font></td></tr>
<tr><td bgcolor=“#ee77aa”><tt> </tt></td><td> </td> <td width=“100%”><dl> <dt><font face=“helvetica, arial”><a href=“builtin.html#object”>builtin.object</a> </font></dt><dd> <dl> <dt><font face=“helvetica, arial”><a href=“ase.atom.html#Atom”>Atom</a> </font></dt></dl> </dd> </dl> <p> <table width=“100%” cellspacing=0 cellpadding=2 border=0 summary=“section”> <tr bgcolor=“#ffc8d8”> <td colspan=3 valign=bottom> <br> <font color=“#000000” face=“helvetica, arial”><a name=“Atom”>class <strong>Atom</strong></a>(<a href=“builtin.html#object”>builtin.object</a>)</font></td></tr>
<tr bgcolor=“#ffc8d8”><td rowspan=2><tt> </tt></td> <td colspan=2><tt>Class for representing a single atom.<br> <br> Parameters:<br> <br> symbol: str or int<br> Can be a chemical symbol (str) or an atomic number (int).<br> position: sequence of 3 floats<br> Atomi position.<br> tag: int<br> Special purpose tag.<br> momentum: sequence of 3 floats<br> Momentum for atom.<br> mass: float<br> Atomic mass in atomic units.<br> magmom: float or 3 floats<br> Magnetic moment.<br> charge: float<br> Atomic charge.<br> </tt></td></tr> <tr><td> </td> <td width=“100%”>Methods defined here:<br> <dl><dt><a name=“Atom-init”><strong>init</strong></a>(self, symbol<font color=“#909090”>='X'</font>, position<font color=“#909090”>=(0, 0, 0)</font>, tag<font color=“#909090”>=None</font>, momentum<font color=“#909090”>=None</font>, mass<font color=“#909090”>=None</font>, magmom<font color=“#909090”>=None</font>, charge<font color=“#909090”>=None</font>, atoms<font color=“#909090”>=None</font>, index<font color=“#909090”>=None</font>)</dt></dl>
<dl><dt><a name=“Atom-repr”><strong>repr</strong></a>(self)</dt></dl>
<dl><dt><a name=“Atom-cut_reference_to_atoms”><strong>cut_reference_to_atoms</strong></a>(self)</dt><dd><tt>Cut reference to atoms <a href=“builtin.html#object”>object</a>.</tt></dd></dl>
<dl><dt><a name=“Atom-delete”><strong>delete</strong></a>(self, name)</dt><dd><tt>Delete attribute.</tt></dd></dl>
<dl><dt><a name=“Atom-get”><strong>get</strong></a>(self, name)</dt><dd><tt>Get attribute, return default if not explicitely set.</tt></dd></dl>
<dl><dt><a name=“Atom-get_atomic_number”><strong>get_atomic_number</strong></a>(self)</dt></dl>
<dl><dt><a name=“Atom-get_charge”><strong>get_charge</strong></a>(self)</dt></dl>
<dl><dt><a name=“Atom-get_initial_magnetic_moment”><strong>get_initial_magnetic_moment</strong></a>(self)</dt></dl>
<dl><dt><a name=“Atom-get_mass”><strong>get_mass</strong></a>(self)</dt></dl>
<dl><dt><a name=“Atom-get_momentum”><strong>get_momentum</strong></a>(self)</dt></dl>
<dl><dt><a name=“Atom-get_position”><strong>get_position</strong></a>(self)</dt></dl>
<dl><dt><a name=“Atom-get_raw”><strong>get_raw</strong></a>(self, name)</dt><dd><tt>Get attribute, return None if not explicitely set.</tt></dd></dl>
<dl><dt><a name=“Atom-get_symbol”><strong>get_symbol</strong></a>(self)</dt></dl>
<dl><dt><a name=“Atom-get_tag”><strong>get_tag</strong></a>(self)</dt></dl>
<dl><dt><a name=“Atom-set”><strong>set</strong></a>(self, name, value)</dt><dd><tt>Set attribute.</tt></dd></dl>
<dl><dt><a name=“Atom-set_atomic_number”><strong>set_atomic_number</strong></a>(self, value)</dt></dl>
<dl><dt><a name=“Atom-set_charge”><strong>set_charge</strong></a>(self, value)</dt></dl>
<dl><dt><a name=“Atom-set_initial_magnetic_moment”><strong>set_initial_magnetic_moment</strong></a>(self, value)</dt></dl>
<dl><dt><a name=“Atom-set_mass”><strong>set_mass</strong></a>(self, value)</dt></dl>
<dl><dt><a name=“Atom-set_momentum”><strong>set_momentum</strong></a>(self, value)</dt></dl>
<dl><dt><a name=“Atom-set_position”><strong>set_position</strong></a>(self, value)</dt></dl>
<dl><dt><a name=“Atom-set_symbol”><strong>set_symbol</strong></a>(self, value)</dt></dl>
<dl><dt><a name=“Atom-set_tag”><strong>set_tag</strong></a>(self, value)</dt></dl>
<hr> Data descriptors defined here:<br> <dl><dt><strong>atoms</strong></dt> </dl> <dl><dt><strong>charge</strong></dt> <dd><tt>Atomic charge</tt></dd> </dl> <dl><dt><strong>data</strong></dt> </dl> <dl><dt><strong>index</strong></dt> </dl> <dl><dt><strong>magmom</strong></dt> <dd><tt>Initial magnetic moment</tt></dd> </dl> <dl><dt><strong>mass</strong></dt> <dd><tt>Atomic mass</tt></dd> </dl> <dl><dt><strong>momentum</strong></dt> <dd><tt>XYZ-momentum</tt></dd> </dl> <dl><dt><strong>number</strong></dt> <dd><tt>Atomic number</tt></dd> </dl> <dl><dt><strong>position</strong></dt> <dd><tt>XYZ-coordinates</tt></dd> </dl> <dl><dt><strong>symbol</strong></dt> <dd><tt>Chemical symbol</tt></dd> </dl> <dl><dt><strong>tag</strong></dt> <dd><tt>Integer tag</tt></dd> </dl> <dl><dt><strong>x</strong></dt> <dd><tt>X-coordinate</tt></dd> </dl> <dl><dt><strong>y</strong></dt> <dd><tt>Y-coordinate</tt></dd> </dl> <dl><dt><strong>z</strong></dt> <dd><tt>Z-coordinate</tt></dd> </dl> </td></tr></table></td></tr></table><p> <table width=“100%” cellspacing=0 cellpadding=2 border=0 summary=“section”> <tr bgcolor=“#eeaa77”> <td colspan=3 valign=bottom> <br> <font color=“#ffffff” face=“helvetica, arial”><big><strong>Functions</strong></big></font></td></tr>
<tr><td bgcolor=“#eeaa77”><tt> </tt></td><td> </td> <td width=“100%”><dl><dt><a name=“-atomproperty”><strong>atomproperty</strong></a>(name, doc)</dt><dd><tt>Helper function to easily create <a href=“#Atom”>Atom</a> attribute property.</tt></dd></dl> <dl><dt><a name=“-xyzproperty”><strong>xyzproperty</strong></a>(index)</dt><dd><tt>Helper function to easily create <a href=“#Atom”>Atom</a> XYZ-property.</tt></dd></dl> </td></tr></table><p> <table width=“100%” cellspacing=0 cellpadding=2 border=0 summary=“section”> <tr bgcolor=“#55aa55”> <td colspan=3 valign=bottom> <br> <font color=“#ffffff” face=“helvetica, arial”><big><strong>Data</strong></big></font></td></tr>
<tr><td bgcolor=“#55aa55”><tt> </tt></td><td> </td> <td width=“100%”><strong>atomic_masses</strong> = array([ 0. , 1.00794, 4.0026 , 6…. nan, nan, nan, nan])<br> <strong>atomic_numbers</strong> = {'Ac': 89, 'Ag': 47, 'Al': 13, 'Am': 95, 'Ar': 18, 'As': 33, 'At': 85, 'Au': 79, 'B': 5, 'Ba': 56, …}<br> <strong>chemical_symbols</strong> = ['X', 'H', 'He', 'Li', 'Be', 'B', 'C', 'N', 'O', 'F', 'Ne', 'Na', 'Mg', 'Al', 'Si', 'P', 'S', 'Cl', 'Ar', 'K', …]<br> <strong>names</strong> = {'charge': ('charges', 0.0), 'magmom': ('magmoms', 0.0), 'mass': ('masses', None), 'momentum': ('momenta', array([ 0., 0., 0.])), 'number': ('numbers', 0), 'position': ('positions', array([ 0., 0., 0.])), 'tag': ('tags', 0)}</td></tr></table></html>