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--- abinitio:ase_atoms_man [2022/08/24 11:36] – [Data] kimi
+++ abinitio:ase_atoms_man [2022/08/24 11:43] (現在) – [Examples] kimi
@@ 行 76: / 行 76: @@
 ===== Examples =====
-<html>
+  * These three are equivalent:<code python>
-:<br>
+>>> d = 1.104  # N2 bondlength
-&nbsp;<br>
+>>> a = Atoms('N2', [(0, 0, 0), (0, 0, d)])
-These&nbsp;three&nbsp;are&nbsp;equivalent:<br>
+>>> a = Atoms(numbers=[7, 7], positions=[(0, 0, 0), (0, 0, d)])
-&nbsp;<br>
+>>> a = Atoms([Atom('N', (0, 0, 0)), Atom('N', (0, 0, d)])</code>
-&gt;&gt;&gt;&nbsp;d&nbsp;=&nbsp;1.104&nbsp;&nbsp;#&nbsp;N2&nbsp;bondlength<br>
-&gt;&gt;&gt;&nbsp;a&nbsp;=&nbsp;<a href="#Atoms">Atoms</a>('N2',&nbsp;[(0,&nbsp;0,&nbsp;0),&nbsp;(0,&nbsp;0,&nbsp;d)])<br>
+  * FCC gold:<code python>
-&gt;&gt;&gt;&nbsp;a&nbsp;=&nbsp;<a href="#Atoms">Atoms</a>(numbers=[7,&nbsp;7],&nbsp;positions=[(0,&nbsp;0,&nbsp;0),&nbsp;(0,&nbsp;0,&nbsp;d)])<br>
+>>> a = 4.05  # Gold lattice constant
-&gt;&gt;&gt;&nbsp;a&nbsp;=&nbsp;<a href="#Atoms">Atoms</a>([Atom('N',&nbsp;(0,&nbsp;0,&nbsp;0)),&nbsp;Atom('N',&nbsp;(0,&nbsp;0,&nbsp;d)])<br>
+>>> b = a / 2
-&nbsp;<br>
+>>> fcc = Atoms('Au',
-FCC&nbsp;gold:<br>
+...             cell=[(0, b, b), (b, 0, b), (b, b, 0)],
-&nbsp;<br>
+...             pbc=True)</code>
-&gt;&gt;&gt;&nbsp;a&nbsp;=&nbsp;4.05&nbsp;&nbsp;#&nbsp;Gold&nbsp;lattice&nbsp;constant<br>
-&gt;&gt;&gt;&nbsp;b&nbsp;=&nbsp;a&nbsp;/&nbsp;2<br>
+  * Hydrogen wire:<code python>
-&gt;&gt;&gt;&nbsp;fcc&nbsp;=&nbsp;<a href="#Atoms">Atoms</a>('Au',<br>
+>>> d = 0.9  # H-H distance
-...&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;cell=[(0,&nbsp;b,&nbsp;b),&nbsp;(b,&nbsp;0,&nbsp;b),&nbsp;(b,&nbsp;b,&nbsp;0)],<br>
+>>> L = 7.0
-...&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;pbc=True)<br>
+>>> h = Atoms('H', positions=[(0, L / 2, L / 2)],
-&nbsp;<br>
+...           cell=(d, L, L),
-Hydrogen&nbsp;wire:<br>
+...           pbc=(1, 0, 0))</code>
-&nbsp;<br>
-&gt;&gt;&gt;&nbsp;d&nbsp;=&nbsp;0.9&nbsp;&nbsp;#&nbsp;H-H&nbsp;distance<br>
-&gt;&gt;&gt;&nbsp;L&nbsp;=&nbsp;7.0<br>
-&gt;&gt;&gt;&nbsp;h&nbsp;=&nbsp;<a href="#Atoms">Atoms</a>('H',&nbsp;positions=[(0,&nbsp;L&nbsp;/&nbsp;2,&nbsp;L&nbsp;/&nbsp;2)],<br>
-...&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;cell=(d,&nbsp;L,&nbsp;L),<br>
-...&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;pbc=(1,&nbsp;0,&nbsp;0))<br>&nbsp;</tt></td></tr>
-<tr><td>&nbsp;</td>
-</html>
 ===== Method =====
@@ 行 504: / 行 496: @@
 </html>
 ===== Data =====
-<html>
+^calc |Calculator object. |
+^cell |Attribute for direct manipulation of the unit cell. |
+^constraints |Constraints of the atoms. |
+^numbers |Attribute for direct manipulation of the atomic numbers. |
+^pbc |Attribute for direct manipulation of the periodic boundary condition flags. |
+^positions |Attribute for direct manipulation of the positions. |
-descriptors defined here:<br>
+Data and other attributes defined here:
-<dl><dt><strong>__dict__</strong></dt>
-<dd><tt>dictionary&nbsp;for&nbsp;instance&nbsp;variables&nbsp;(if&nbsp;defined)</tt></dd>
-</dl>
-<dl><dt><strong>__weakref__</strong></dt>
-<dd><tt>list&nbsp;of&nbsp;weak&nbsp;references&nbsp;to&nbsp;the&nbsp;object&nbsp;(if&nbsp;defined)</tt></dd>
-</dl>
-<dl><dt><strong>calc</strong></dt>
-<dd><tt>Calculator&nbsp;object.</tt></dd>
-</dl>
-<dl><dt><strong>cell</strong></dt>
-<dd><tt>Attribute&nbsp;for&nbsp;direct&nbsp;manipulation&nbsp;of&nbsp;the&nbsp;unit&nbsp;cell.</tt></dd>
-</dl>
-<dl><dt><strong>constraints</strong></dt>
-<dd><tt>Constraints&nbsp;of&nbsp;the&nbsp;atoms.</tt></dd>
-</dl>
-<dl><dt><strong>numbers</strong></dt>
-<dd><tt>Attribute&nbsp;for&nbsp;direct&nbsp;manipulation&nbsp;of&nbsp;the&nbsp;atomic&nbsp;numbers.</tt></dd>
-</dl>
-<dl><dt><strong>pbc</strong></dt>
-<dd><tt>Attribute&nbsp;for&nbsp;direct&nbsp;manipulation&nbsp;of&nbsp;the&nbsp;periodic&nbsp;boundary&nbsp;condition&nbsp;flags.</tt></dd>
-</dl>
-<dl><dt><strong>positions</strong></dt>
-<dd><tt>Attribute&nbsp;for&nbsp;direct&nbsp;manipulation&nbsp;of&nbsp;the&nbsp;positions.</tt></dd>
-</dl>
-<hr>
-Data and other attributes defined here:<br>
-<dl><dt><strong>__hash__</strong> = None</dt></dl>
-</td></tr></tbody></table></p></td></tr></tbody></table></p><p>
-<table summary="section" border="0" cellpadding="2" cellspacing="0" width="100%">
-<tbody><tr bgcolor="#55aa55">
-<td colspan="3" valign="bottom">&nbsp;<br>
-</html>
 ==== Data ====
 <code python>
-atomic_masses= array([   0.     ,    1.00794,    4.0026 ,    6....        nan,        nan,        nan,        nan])
+atomic_masses= array([0., 1.00794, 4.0026, 6. ... nan, nan, nan, nan])
 atomic_numbers = {'Ac': 89, 'Ag': 47, 'Al': 13, 'Am': 95, 'Ar': 18, 'As': 33, 'At': 85, 'Au': 79, 'B': 5, 'Ba': 56, ...}
 chemical_symbols = ['X', 'H', 'He', 'Li', 'Be', 'B', 'C', 'N', 'O', 'F', 'Ne', 'Na', 'Mg', 'Al', 'Si', 'P', 'S', 'Cl', 'Ar', 'K', ...]
+</code>