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--- abinitio:ase_atoms_man [2022/08/24 11:25] – kimi
+++ abinitio:ase_atoms_man [2022/08/24 11:43] (現在) – [Examples] kimi
@@ 行 11: / 行 11: @@
 In order to calculate energies, forces and stresses, a calculator
 object has to attached to the atoms object.
+===== Parameters =====
 <html>
- <p>
-<table summary="section" border="0" cellpadding="2" cellspacing="0" width="100%">
+:<br>
-<tbody><tr bgcolor="#ffc8d8">
-<td colspan="3" valign="bottom">&nbsp;<br>
-<font color="#000000" face="helvetica, arial"><a name="Atoms"></a>(<a href="__builtin__.html#object">__builtin__.object</a>)</font></td></tr>
-<tr bgcolor="#ffc8d8"><td rowspan="2"><tt>&nbsp;&nbsp;&nbsp;</tt></td>
-<td colspan="2"><tt><a href="#Atoms">Atoms</a>&nbsp;<a href="__builtin__.html#object">object</a>.<br>
-&nbsp;<br>
-The&nbsp;<a href="#Atoms">Atoms</a>&nbsp;<a href="__builtin__.html#object">object</a>&nbsp;can&nbsp;represent&nbsp;an&nbsp;isolated&nbsp;molecule,&nbsp;or&nbsp;a<br>
-periodically&nbsp;repeated&nbsp;structure.&nbsp;&nbsp;It&nbsp;has&nbsp;a&nbsp;unit&nbsp;cell&nbsp;and<br>
-there&nbsp;may&nbsp;be&nbsp;periodic&nbsp;boundary&nbsp;conditions&nbsp;along&nbsp;any&nbsp;of&nbsp;the&nbsp;three<br>
-unit&nbsp;cell&nbsp;axes.<br>
-&nbsp;<br>
-Information&nbsp;about&nbsp;the&nbsp;atoms&nbsp;(atomic&nbsp;numbers&nbsp;and&nbsp;position)&nbsp;is<br>
-stored&nbsp;in&nbsp;ndarrays.&nbsp;&nbsp;Optionally,&nbsp;there&nbsp;can&nbsp;be&nbsp;information&nbsp;about<br>
-tags,&nbsp;momenta,&nbsp;masses,&nbsp;magnetic&nbsp;moments&nbsp;and&nbsp;charges.<br>
-&nbsp;<br>
-In&nbsp;order&nbsp;to&nbsp;calculate&nbsp;energies,&nbsp;forces&nbsp;and&nbsp;stresses,&nbsp;a&nbsp;calculator<br>
-<a href="__builtin__.html#object">object</a>&nbsp;has&nbsp;to&nbsp;attached&nbsp;to&nbsp;the&nbsp;atoms&nbsp;<a href="__builtin__.html#object">object</a>.<br>
-&nbsp;<br>
-Parameters:<br>
 &nbsp;<br>
 symbols:&nbsp;str&nbsp;(formula)&nbsp;or&nbsp;list&nbsp;of&nbsp;str<br>&nbsp;&nbsp;&nbsp;&nbsp;Can&nbsp;be&nbsp;a&nbsp;string&nbsp;formula,&nbsp;a&nbsp;list&nbsp;of&nbsp;symbols&nbsp;or&nbsp;a&nbsp;list&nbsp;of<br>
@@ 行 90: / 行 73: @@
 &nbsp;&nbsp;&nbsp;&nbsp;not&nbsp;make&nbsp;any&nbsp;assumptions&nbsp;about&nbsp;the&nbsp;existence&nbsp;of&nbsp;keys.<br>
 &nbsp;<br>
-Examples:<br>
+</html>
-&nbsp;<br>
-These&nbsp;three&nbsp;are&nbsp;equivalent:<br>
+===== Examples =====
-&nbsp;<br>
+  * These three are equivalent:<code python>
-&gt;&gt;&gt;&nbsp;d&nbsp;=&nbsp;1.104&nbsp;&nbsp;#&nbsp;N2&nbsp;bondlength<br>
+>>> d = 1.104  # N2 bondlength
-&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>
+>>> a = Atoms('N2', [(0, 0, 0), (0, 0, d)])
-&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 = Atoms(numbers=[7, 7], positions=[(0, 0, 0), (0, 0, d)])
-&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>
+>>> a = Atoms([Atom('N', (0, 0, 0)), Atom('N', (0, 0, d)])</code>
-&nbsp;<br>
-FCC&nbsp;gold:<br>
+  * FCC gold:<code python>
-&nbsp;<br>
+>>> a = 4.05  # Gold lattice constant
-&gt;&gt;&gt;&nbsp;a&nbsp;=&nbsp;4.05&nbsp;&nbsp;#&nbsp;Gold&nbsp;lattice&nbsp;constant<br>
+>>> b = a / 2
-&gt;&gt;&gt;&nbsp;b&nbsp;=&nbsp;a&nbsp;/&nbsp;2<br>
+>>> fcc = Atoms('Au',
-&gt;&gt;&gt;&nbsp;fcc&nbsp;=&nbsp;<a href="#Atoms">Atoms</a>('Au',<br>
+...             cell=[(0, b, b), (b, 0, b), (b, b, 0)],
-...&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>
+...             pbc=True)</code>
-...&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;pbc=True)<br>
-&nbsp;<br>
+  * Hydrogen wire:<code python>
-Hydrogen&nbsp;wire:<br>
+>>> d = 0.9  # H-H distance
-&nbsp;<br>
+>>> L = 7.0
-&gt;&gt;&gt;&nbsp;d&nbsp;=&nbsp;0.9&nbsp;&nbsp;#&nbsp;H-H&nbsp;distance<br>
+>>> h = Atoms('H', positions=[(0, L / 2, L / 2)],
-&gt;&gt;&gt;&nbsp;L&nbsp;=&nbsp;7.0<br>
+...           cell=(d, L, L),
-&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>
+...           pbc=(1, 0, 0))</code>
-...&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;cell=(d,&nbsp;L,&nbsp;L),<br>
+===== Method =====
-...&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>
-<td width="100%">Methods defined here:<br>
 <dl><dt><a name="Atoms-__add__"><strong>__add__</strong></a>(self, other)</dt></dl>
@@ 行 512: / 行 494: @@
 <hr>
-Data descriptors defined here:<br>
+</html>
-<dl><dt><strong>__dict__</strong></dt>
+===== Data =====
-<dd><tt>dictionary&nbsp;for&nbsp;instance&nbsp;variables&nbsp;(if&nbsp;defined)</tt></dd>
+^calc |Calculator object. |
-</dl>
+^cell |Attribute for direct manipulation of the unit cell. |
-<dl><dt><strong>__weakref__</strong></dt>
+^constraints |Constraints of the atoms. |
-<dd><tt>list&nbsp;of&nbsp;weak&nbsp;references&nbsp;to&nbsp;the&nbsp;object&nbsp;(if&nbsp;defined)</tt></dd>
+^numbers |Attribute for direct manipulation of the atomic numbers. |
-</dl>
+^pbc |Attribute for direct manipulation of the periodic boundary condition flags. |
-<dl><dt><strong>calc</strong></dt>
+^positions |Attribute for direct manipulation of the positions. |
-<dd><tt>Calculator&nbsp;object.</tt></dd>
-</dl>
+Data and other attributes defined here:
-<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>
+==== Data ====
-<table summary="section" border="0" cellpadding="2" cellspacing="0" width="100%">
+<code python>
-<tbody><tr bgcolor="#55aa55">
+atomic_masses= array([0., 1.00794, 4.0026, 6. ... nan, nan, nan, nan])
-<td colspan="3" valign="bottom">&nbsp;<br>
+atomic_numbers = {'Ac': 89, 'Ag': 47, 'Al': 13, 'Am': 95, 'Ar': 18, 'As': 33, 'At': 85, 'Au': 79, 'B': 5, 'Ba': 56, ...}
-<font color="#ffffff" face="helvetica, arial"><big><strong>Data</strong></big></font></td></tr>
+chemical_symbols = ['X', 'H', 'He', 'Li', 'Be', 'B', 'C', 'N', 'O', 'F', 'Ne', 'Na', 'Mg', 'Al', 'Si', 'P', 'S', 'Cl', 'Ar', 'K', ...]
+</code>
-<tr><td bgcolor="#55aa55"><tt>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</tt></td><td>&nbsp;</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', ...]</td></tr></tbody></table>
-</p></body></html>