OOPSE-3.0/doc/SelectionExpression.html

<html>

<head>

<title>Select Commands in OOPSE</title>

</head>


<body bgcolor=white>

<basefont size=3>


<div align=center>

  <p><font size="+2"><b>Select Commands in </b></font><b><font size="+2">OOPSE</font></b></p>
  <h2 align="left"><a name="introduction" id="introduction"> Introduction </a></h2>
  <p align="left">&nbsp;</p>
  <p align="center"><img src="classoopse_1_1StuntDouble.png" width="292" height="136"></p>
  <p align="left"><b><a name="stuntdouble" id="stuntdouble"></a> Stuntdouble </b> stands in for some object that can be manipulated by the Integrators or Minimizers. </p>
  <p align="left"><b><a name="atom" id="atom"></a> Atom </b>is a fundamental unit in OOPSE</p>
  <p align="left"><b><a name="datom" id="datom"></a> DirectionalAtom </b>is a special atom</p>
  <p align="left"><b><a name="rigidbody" id="rigidbody"></a> Rigid-body </b>is a collection of atoms or directional atoms. </p>
  <p align="left"> Every molecule, atom and directional atom in OOPSE have their own name which are given by .md file. In contrast, the name of rigid-body, which is [MoleculeName]_RB_[index] (the content inside the brackets will be replaced), is generated automatically. For example, the name of the first rigi-body of DMPC molecule is DMPC_RB_0. <br>
  </p>
</div>

<a name="syntax" id="syntax">

<h2>

Syntax of the select command

</h2>

</a>


The most general form of the select command is: <b>select <i>expression</i>

</b>

<p>The expression represents an arbitrary set of stuntdoubles (atoms or rigid-bodies) in OOPSE. Expressions are composed of either name expressions, index expression, predefined sets, user define expression, comparison operators, within expressions, or logical combinations of the above expression types.  Expression can be combined with parentheses and the Boolean operators</p>

<p><b><a name="logic"></a> Logical expression. </b> </p>

<p>The logical operators allow complex queries to be constructed out of simpler ones using the standard boolean connectives <b>and, or, not</b>. Parentheses can be used to alter the precedence of the operators.

<ul>

  <table width="441" border=1 cellpadding=5 bgcolor="#FFFFFF">

    <tr bgcolor="#FFCCFF">

      <td width="174"><div align="left">logical operator </div></td>

      <td width="241"><div align="left">equivalent operator</div></td>

    </tr>

    <tr bgcolor="#FFCCFF">

      <td><div align="left">and</div></td>

      <td><div align="left">&quot;&amp;&quot;, &quot;&amp;&amp;&quot; </div></td>

    </tr>

    <tr bgcolor="#FFCCFF">

      <td><div align="left">or</div></td>

      <td><div align="left">&quot;|&quot;, &quot;||&quot;, &quot;,&quot; </div></td>

    </tr>

    <tr bgcolor="#FFCCFF">

      <td><div align="left">not</div></td>

      <td><div align="left">&quot;!&quot;</div></td>

    </tr>

  </table>

  <p>&nbsp;</p>

</ul>

<p><a name="name"><b> Name expression.

</b></a> </p>

<ul>

<table width="886" border="1" bordercolor="#6B7683" bgcolor="#FFFFCC">

  <tr>

    <td colspan="2"><div align="center">expression</div></td>

    <td width="434"><div align="center">description</div></td>

  </tr>

  <tr>

    <td width="183" rowspan="3">expression without &quot;.&quot; </td>

    <td width="247"><div align="left">select DMPC</div></td>

    <td>select all stuntdoubles belong to DMPC molecule </td>

  </tr>

  <tr>

    <td><div align="left">select C*</div></td>

    <td>select all carbon atoms </td>

  </tr>

  <tr>

    <td><div align="left">select DMPC_RB_*</div></td>

    <td>select all rigid-bodies (only select rigid-bodies, not include the atoms belong to them)</td>

  </tr>

  <tr>

    <td rowspan="3">expression has one &quot;.&quot; </td>

    <td>select TIP3P.O_TIP3P</td>

    <td>select stuntdoubles belong to molecule </td>

  </tr>

  <tr>

    <td>select DMPC_RB_0.PO4</td>

    <td>select atoms belong to rigid-bodies</td>

  </tr>

  <tr>

    <td>select DMPC.20</td>

    <td>select stuntdoubles by their internal indices inside the molecules </td>

  </tr>

  <tr>

    <td>expression has two &quot;.&quot;</td>

    <td>select DMPC.DMPC_RB_?.*</td>

    <td>select all atoms belong to rigid-bodies within DMPC molecule</td>

  </tr>

</table>

<p>&nbsp;</p>

</ul>

<p><a name="index" id="index"><b> Index expression </b></a></p>

<ul>

<table width="894" border=1 cellpadding=5 bgcolor="#FFFFFF"><tr bgcolor="#FFFFCC">

  <td width="113">select 20 </td>

    <td width="520">select all of the stuntdoubles of molecule 20</td>

</tr>

  <tr bgcolor="#FFFFCC">

    <td>select 20 to 30      </td>

    <td>select all of the stuntdoubles of molecules  which global indices are between 20 (inclusive) and 30 (exclusive) </td>

  </tr>

</table>

</ul>


<p>&nbsp; </p>

<p><a name="predefine" id="predefine"><b> Predefine set </b></a></p>

<ul>

  <table width="449" border=1 cellpadding=5 bgcolor="#FFFFFF">

    <tr bgcolor="#FFCCFF">

      <td width="91"><div align="left">keyword</div></td>

      <td width="332"><div align="left">description</div></td>

    </tr>

    <tr bgcolor="#FFCCFF">

      <td><div align="left">all</div></td>

      <td><div align="left">select all stuntdoubles</div></td>

    </tr>

    <tr bgcolor="#FFCCFF">

      <td><div align="left">none</div></td>

      <td><div align="left">select none of the stuntdoubles </div></td>

    </tr>

  </table>

</ul>

<p>&nbsp;</p>

<p><a name="user" id="user"><b> User define expression.</b></a></p>

<p> User can define arbitrary terms to represent groups of stuntdoubles, and then use the terms you have defined in select commands. The general form for the define command is: <strong>define <em>term expression</em></strong></p>

<p> Once defined, user can use such terms in boolean expressions </p>

<ul>

  <table width="659" border=1 cellpadding=5 bgcolor="#FFFFFF">

    <tr bgcolor="#FFFFCC">

      <td><p>define SSDWATER SSD or SSD1 or SSDRF</p>

      <p>select SSDWATER  </p>      <div align="left"></div></td>

    </tr>

  </table>

</ul>

<p><a name="comparison" id="comparison"> <b>Comparison expression.</b></a></p>

<p>Stuntdoubles can be distinguished using comparision operators on their properties. The general form for the comparison command is: a property name, followed by a comparision operator and then a number.</p>

<ul>

  <table width="668" border=1 cellpadding=5 bgcolor="#FFFFFF">

    <tr bgcolor="#FFCCFF">

      <td width="305"><div align="left">property</div></td>

      <td width="331"><div align="left">mass, dipole, charge </div></td>

    </tr>

    <tr bgcolor="#FFCCFF">

      <td><div align="left">comparision operator</div></td>

      <td><div align="left">&quot;&gt;&quot;, &quot;&lt;&quot;, &quot;=&quot;, &quot;&gt;=&quot;, &quot;&lt;=&quot;, &quot;!=&quot; </div></td>

    </tr>

  </table>

</ul>

<ul>

  <table width="672" border=1 cellpadding=5 bgcolor="#FFFFFF">

    <tr bgcolor="#FFFFCC">

      <td width="302">select mass &gt; 16.0 and charge &lt; -2 </td>

      <td width="338">select stuntdoubles which mass is great than 16.0 and charge is less than -2 </td>

    </tr>

  </table>

</ul>

<p>&nbsp;</p>

<p><b> <a name="within"></a>    Within expression.</b>

<p> Within selection selects all stuntdoubles within the specified distance (in ?) from a selection, including the selection itself. The general form for within selection is: <b>select within(<i>distance, expression</i>) </b>

<ul>

  <table width="681" border=1 cellpadding=5 bgcolor="#FFFFFF">

    <tr bgcolor="#FFFFCC">

      <td width="306">select within(2.5, PO4 or NC4) </td>

      <td width="343"><blockquote>select stunntdoules which are within 2.5 ? from either PO4 or NC4 </blockquote></td>

    </tr>
  </table>

</ul>

<p>

<h2><a name="syntax" id="syntax"> Tools using selection command </a></h2>
<p><b><a name="within"></a> Dump2XYZ</b>
<p>Dump2XYZ can transform an OOPSE dump file into a xyz file which could be opened by other molecular viewers, such as Jmol and VMD. 
<ul>
  <table width="890" border=1 cellpadding=5 bgcolor="#FFFFFF">
    <tr bgcolor="#6699FF">
      <td width="191"><blockquote>
          <p>--selection</p>
      </blockquote></td>
      <td width="667">Specifying --selection=&quot;selection command&quot; with Dump2XYZ, user can select an arbitrary set of stuntdoubles to be converted. </td>
    </tr>
    <tr bgcolor="#CCFF99">
      <td><blockquote>
          <p>--originsele</p>
      </blockquote></td>
      <td rowspan="2">In order to rotate the system, --originsele and --refselec must be given to define the new coordinate set. A stuntdouble with a dipole, which direction is always (0, 0, 1) in body frame, is specified by --originsele. The new x-z plane is defined by the direction of dipole and the stuntdouble specified by --refsele. </td>
    </tr>
    <tr bgcolor="#CCFF99">
      <td><blockquote>
          <p>--refsele</p>
      </blockquote></td>
    </tr>
  </table>
</ul>
<p>
<p><b><a name="within"></a> StaticProps</b>
<p> 
<p align="center"><img src="definition.jpg" width="720" height="540">
<p align="left">There are five seperate radial distribution functions availiable in OOPSE. Since every radial distrbution function invlove the calculation between a pair, --sele1 and --sele2 must be given.
<ul>
  <table width="890" border=1 cellpadding=5 bgcolor="#FFFFFF">
    <tr bgcolor="#CCFFCC">
      <td width="191"><blockquote>
        <p>option</p>
      </blockquote></td>
      <td width="667"><blockquote>
          <div align="center">description</div>
      </blockquote></td>
    </tr>
    <tr bgcolor="#CCFFCC">
      <td><blockquote>
        <p>--gofr</p>
      </blockquote></td>
      <td>normal pair distribution function.</td>
    </tr>
    <tr bgcolor="#CCFFCC">
      <td><blockquote>
        <p>--r_theta</p>
      </blockquote></td>
      <td>Calculate angle dependent pair distribution function. The angle is defined by r and A's dipole moment. </td>
    </tr>
    <tr bgcolor="#CCFFCC">
      <td><blockquote>
        <p>--r_omega</p>
      </blockquote></td>
      <td>Calculate angle dependent pair distribution function. The angle is defined by A's dipole moment and B's dipole moment . </td>
    </tr>
    <tr bgcolor="#CCFFCC">
      <td><blockquote>
        <p>--theta_omega</p>
      </blockquote></td>
      <td>Calculate the two dimension distribution of two angles.</td>
    </tr>
    <tr bgcolor="#CCFFCC">
      <td><blockquote>
        <p>--gxyz</p>
      </blockquote></td>
      <td>Calculate the three dimension distribution of the particle B in the body frame of particle A. Therefore, --originsele and --refsele must be given to define A's internal coordinate set. </td>
    </tr>
  </table>
</ul>
<p>&nbsp; </p>
<p><b><a name="within"></a> DynamicProps </b>
<ul>
  <table width="890" border=1 cellpadding=5 bgcolor="#FFFFFF">
    <tr bgcolor="#CCFFCC">
      <td width="191">        <p align="center">option</p></td>
      <td width="667"><blockquote>
          <div align="center">description</div>
      </blockquote></td>
    </tr>
    <tr bgcolor="#CCFFCC">
      <td>        <p align="center">--rcorr</p></td>
      <td>mean square displacement </td>
    </tr>
    <tr bgcolor="#CCFFCC">
      <td>        <p align="center">--vcorr</p></td>
      <td>velocity correlation function</td>
    </tr>
    <tr bgcolor="#CCFFCC">
      <td>        <p align="center">--dcorr</p></td>
      <td>dipole correlation function </td>
    </tr>
  </table>
</ul>
<p>
</body>

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Revision:	2102
Committed:	Thu Mar 10 16:14:07 2005 UTC (19 years, 4 months ago) by tim
Content type:	text/html
File size:	11874 byte(s)
Log Message:	minor change
#	User	Rev	Content
1	tim	2061	<html>
2	tim	2063
3	tim	2061	<head>
4	tim	2063
5	tim	2061	<title>Select Commands in OOPSE</title>
6	tim	2063
7	tim	2061	</head>
8
9	tim	2063
10
11	tim	2061	<body bgcolor=white>
12	tim	2063
13	tim	2061	<basefont size=3>
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15	tim	2063
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17	tim	2061	<div align=center>
18	tim	2063
19			<p><font size="+2"><b>Select Commands in </b></font><b><font size="+2">OOPSE</font></b></p>
20			<h2 align="left"><a name="introduction" id="introduction"> Introduction </a></h2>
21			<p align="left"> </p>
22			<p align="center"><img src="classoopse_1_1StuntDouble.png" width="292" height="136"></p>
23			<p align="left"><b><a name="stuntdouble" id="stuntdouble"></a> Stuntdouble </b> stands in for some object that can be manipulated by the Integrators or Minimizers. </p>
24			<p align="left"><b><a name="atom" id="atom"></a> Atom </b>is a fundamental unit in OOPSE</p>
25			<p align="left"><b><a name="datom" id="datom"></a> DirectionalAtom </b>is a special atom</p>
26			<p align="left"><b><a name="rigidbody" id="rigidbody"></a> Rigid-body </b>is a collection of atoms or directional atoms. </p>
27			<p align="left"> Every molecule, atom and directional atom in OOPSE have their own name which are given by .md file. In contrast, the name of rigid-body, which is [MoleculeName]_RB_[index] (the content inside the brackets will be replaced), is generated automatically. For example, the name of the first rigi-body of DMPC molecule is DMPC_RB_0. <br>
28			</p>
29	tim	2061	</div>
30	tim	2063
31	tim	2061	<a name="syntax" id="syntax">
32	tim	2063
33	tim	2061	<h2>
34	tim	2063
35	tim	2061	Syntax of the select command
36	tim	2063
37	tim	2061	</h2>
38	tim	2063
39	tim	2061	</a>
40
41	tim	2063
42
43	tim	2061	The most general form of the select command is: <b>select <i>expression</i>
44	tim	2063
45	tim	2061	</b>
46	tim	2063
47	tim	2061	<p>The expression represents an arbitrary set of stuntdoubles (atoms or rigid-bodies) in OOPSE. Expressions are composed of either name expressions, index expression, predefined sets, user define expression, comparison operators, within expressions, or logical combinations of the above expression types. Expression can be combined with parentheses and the Boolean operators</p>
48	tim	2063
49	tim	2061	<p><b><a name="logic"></a> Logical expression. </b> </p>
50	tim	2063
51	tim	2061	<p>The logical operators allow complex queries to be constructed out of simpler ones using the standard boolean connectives <b>and, or, not</b>. Parentheses can be used to alter the precedence of the operators.
52	tim	2063
53	tim	2061	<ul>
54	tim	2063
55	tim	2061	<table width="441" border=1 cellpadding=5 bgcolor="#FFFFFF">
56	tim	2063
57	tim	2061	<tr bgcolor="#FFCCFF">
58	tim	2063
59	tim	2061	<td width="174"><div align="left">logical operator </div></td>
60	tim	2063
61	tim	2061	<td width="241"><div align="left">equivalent operator</div></td>
62	tim	2063
63	tim	2061	</tr>
64	tim	2063
65	tim	2061	<tr bgcolor="#FFCCFF">
66	tim	2063
67	tim	2061	<td><div align="left">and</div></td>
68	tim	2063
69	tim	2061	<td><div align="left">"&", "&&" </div></td>
70	tim	2063
71	tim	2061	</tr>
72	tim	2063
73	tim	2061	<tr bgcolor="#FFCCFF">
74	tim	2063
75	tim	2061	<td><div align="left">or</div></td>
76	tim	2063
77			<td><div align="left">"\|", "\|\|", "," </div></td>
78
79	tim	2061	</tr>
80	tim	2063
81	tim	2061	<tr bgcolor="#FFCCFF">
82	tim	2063
83	tim	2061	<td><div align="left">not</div></td>
84	tim	2063
85	tim	2061	<td><div align="left">"!"</div></td>
86	tim	2063
87	tim	2061	</tr>
88	tim	2063
89	tim	2061	</table>
90	tim	2063
91	tim	2061	<p> </p>
92	tim	2063
93	tim	2061	</ul>
94	tim	2063
95	tim	2061	<p><a name="name"><b> Name expression.
96	tim	2063
97	tim	2061	</b></a> </p>
98	tim	2063
99	tim	2061	<ul>
100	tim	2063
101	tim	2061	<table width="886" border="1" bordercolor="#6B7683" bgcolor="#FFFFCC">
102	tim	2063
103	tim	2061	<tr>
104	tim	2063
105	tim	2061	<td colspan="2"><div align="center">expression</div></td>
106	tim	2063
107	tim	2061	<td width="434"><div align="center">description</div></td>
108	tim	2063
109	tim	2061	</tr>
110	tim	2063
111	tim	2061	<tr>
112	tim	2063
113	tim	2061	<td width="183" rowspan="3">expression without "." </td>
114	tim	2063
115	tim	2061	<td width="247"><div align="left">select DMPC</div></td>
116	tim	2063
117	tim	2061	<td>select all stuntdoubles belong to DMPC molecule </td>
118	tim	2063
119	tim	2061	</tr>
120	tim	2063
121	tim	2061	<tr>
122	tim	2063
123	tim	2061	<td><div align="left">select C*</div></td>
124	tim	2063
125	tim	2061	<td>select all carbon atoms </td>
126	tim	2063
127	tim	2061	</tr>
128	tim	2063
129	tim	2061	<tr>
130	tim	2063
131	tim	2061	<td><div align="left">select DMPC_RB_*</div></td>
132	tim	2063
133	tim	2061	<td>select all rigid-bodies (only select rigid-bodies, not include the atoms belong to them)</td>
134	tim	2063
135	tim	2061	</tr>
136	tim	2063
137	tim	2061	<tr>
138	tim	2063
139	tim	2061	<td rowspan="3">expression has one "." </td>
140	tim	2063
141	tim	2061	<td>select TIP3P.O_TIP3P</td>
142	tim	2063
143	tim	2061	<td>select stuntdoubles belong to molecule </td>
144	tim	2063
145	tim	2061	</tr>
146	tim	2063
147	tim	2061	<tr>
148	tim	2063
149	tim	2061	<td>select DMPC_RB_0.PO4</td>
150	tim	2063
151	tim	2061	<td>select atoms belong to rigid-bodies</td>
152	tim	2063
153	tim	2061	</tr>
154	tim	2063
155	tim	2061	<tr>
156	tim	2063
157	tim	2061	<td>select DMPC.20</td>
158	tim	2063
159	tim	2061	<td>select stuntdoubles by their internal indices inside the molecules </td>
160	tim	2063
161	tim	2061	</tr>
162	tim	2063
163	tim	2061	<tr>
164	tim	2063
165	tim	2061	<td>expression has two "."</td>
166	tim	2063
167	tim	2061	<td>select DMPC.DMPC_RB_?.*</td>
168	tim	2063
169	tim	2061	<td>select all atoms belong to rigid-bodies within DMPC molecule</td>
170	tim	2063
171	tim	2061	</tr>
172	tim	2063
173	tim	2061	</table>
174	tim	2063
175	tim	2061	<p> </p>
176	tim	2063
177	tim	2061	</ul>
178	tim	2063
179	tim	2061	<p><a name="index" id="index"><b> Index expression </b></a></p>
180	tim	2063
181	tim	2061	<ul>
182	tim	2063
183	tim	2061	<table width="894" border=1 cellpadding=5 bgcolor="#FFFFFF"><tr bgcolor="#FFFFCC">
184	tim	2063
185	tim	2061	<td width="113">select 20 </td>
186	tim	2063
187	tim	2102	<td width="520">select all of the stuntdoubles of molecule 20</td>
188	tim	2063
189	tim	2061	</tr>
190	tim	2063
191	tim	2061	<tr bgcolor="#FFFFCC">
192	tim	2063
193	tim	2061	<td>select 20 to 30 </td>
194	tim	2063
195	tim	2102	<td>select all of the stuntdoubles of molecules which global indices are between 20 (inclusive) and 30 (exclusive) </td>
196	tim	2063
197	tim	2061	</tr>
198	tim	2063
199	tim	2061	</table>
200	tim	2063
201	tim	2061	</ul>
202
203	tim	2063
204
205	tim	2061	<p>  </p>
206	tim	2063
207	tim	2061	<p><a name="predefine" id="predefine"><b> Predefine set </b></a></p>
208	tim	2063
209	tim	2061	<ul>
210	tim	2063
211	tim	2061	<table width="449" border=1 cellpadding=5 bgcolor="#FFFFFF">
212	tim	2063
213	tim	2061	<tr bgcolor="#FFCCFF">
214	tim	2063
215	tim	2061	<td width="91"><div align="left">keyword</div></td>
216	tim	2063
217	tim	2061	<td width="332"><div align="left">description</div></td>
218	tim	2063
219	tim	2061	</tr>
220	tim	2063
221	tim	2061	<tr bgcolor="#FFCCFF">
222	tim	2063
223	tim	2061	<td><div align="left">all</div></td>
224	tim	2063
225	tim	2061	<td><div align="left">select all stuntdoubles</div></td>
226	tim	2063
227	tim	2061	</tr>
228	tim	2063
229	tim	2061	<tr bgcolor="#FFCCFF">
230	tim	2063
231	tim	2061	<td><div align="left">none</div></td>
232	tim	2063
233	tim	2061	<td><div align="left">select none of the stuntdoubles </div></td>
234	tim	2063
235	tim	2061	</tr>
236	tim	2063
237	tim	2061	</table>
238	tim	2063
239	tim	2061	</ul>
240	tim	2063
241	tim	2061	<p> </p>
242	tim	2063
243	tim	2061	<p><a name="user" id="user"><b> User define expression.</b></a></p>
244	tim	2063
245	tim	2061	<p> User can define arbitrary terms to represent groups of stuntdoubles, and then use the terms you have defined in select commands. The general form for the define command is: <strong>define <em>term expression</em></strong></p>
246	tim	2063
247	tim	2061	<p> Once defined, user can use such terms in boolean expressions </p>
248	tim	2063
249	tim	2061	<ul>
250	tim	2063
251	tim	2061	<table width="659" border=1 cellpadding=5 bgcolor="#FFFFFF">
252	tim	2063
253	tim	2061	<tr bgcolor="#FFFFCC">
254	tim	2063
255	tim	2061	<td><p>define SSDWATER SSD or SSD1 or SSDRF</p>
256	tim	2063
257	tim	2061	<p>select SSDWATER </p> <div align="left"></div></td>
258	tim	2063
259	tim	2061	</tr>
260	tim	2063
261	tim	2061	</table>
262	tim	2063
263	tim	2061	</ul>
264	tim	2063
265	tim	2061	<p><a name="comparison" id="comparison"> <b>Comparison expression.</b></a></p>
266	tim	2063
267	tim	2061	<p>Stuntdoubles can be distinguished using comparision operators on their properties. The general form for the comparison command is: a property name, followed by a comparision operator and then a number.</p>
268	tim	2063
269	tim	2061	<ul>
270	tim	2063
271	tim	2061	<table width="668" border=1 cellpadding=5 bgcolor="#FFFFFF">
272	tim	2063
273	tim	2061	<tr bgcolor="#FFCCFF">
274	tim	2063
275	tim	2061	<td width="305"><div align="left">property</div></td>
276	tim	2063
277	tim	2061	<td width="331"><div align="left">mass, dipole, charge </div></td>
278	tim	2063
279	tim	2061	</tr>
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282	tim	2063
283	tim	2061	<td><div align="left">comparision operator</div></td>
284	tim	2063
285	tim	2061	<td><div align="left">">", "<", "=", ">=", "<=", "!=" </div></td>
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290	tim	2063
291	tim	2061	</ul>
292	tim	2063
293	tim	2061	<ul>
294	tim	2063
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296	tim	2063
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298	tim	2063
299	tim	2061	<td width="302">select mass > 16.0 and charge < -2 </td>
300	tim	2063
301	tim	2061	<td width="338">select stuntdoubles which mass is great than 16.0 and charge is less than -2 </td>
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307	tim	2061	</ul>
308	tim	2063
309	tim	2061	<p> </p>
310	tim	2063
311	tim	2061	<p><b> <a name="within"></a> Within expression.</b>
312	tim	2063
313	tim	2061	<p> Within selection selects all stuntdoubles within the specified distance (in ?) from a selection, including the selection itself. The general form for within selection is: <b>select within(<i>distance, expression</i>) </b>
314	tim	2063
315	tim	2061	<ul>
316	tim	2063
317			<table width="681" border=1 cellpadding=5 bgcolor="#FFFFFF">
318
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320	tim	2063
321			<td width="306">select within(2.5, PO4 or NC4) </td>
322
323			<td width="343"><blockquote>select stunntdoules which are within 2.5 ? from either PO4 or NC4 </blockquote></td>
324
325	tim	2061	</tr>
326			</table>
327	tim	2063
328	tim	2061	</ul>
329	tim	2063
330	tim	2061	<p>
331	tim	2063
332			<h2><a name="syntax" id="syntax"> Tools using selection command </a></h2>
333			<p><b><a name="within"></a> Dump2XYZ</b>
334			<p>Dump2XYZ can transform an OOPSE dump file into a xyz file which could be opened by other molecular viewers, such as Jmol and VMD.
335			<ul>
336			<table width="890" border=1 cellpadding=5 bgcolor="#FFFFFF">
337			<tr bgcolor="#6699FF">
338			<td width="191"><blockquote>
339			<p>--selection</p>
340			</blockquote></td>
341			<td width="667">Specifying --selection="selection command" with Dump2XYZ, user can select an arbitrary set of stuntdoubles to be converted. </td>
342			</tr>
343			<tr bgcolor="#CCFF99">
344			<td><blockquote>
345			<p>--originsele</p>
346			</blockquote></td>
347			<td rowspan="2">In order to rotate the system, --originsele and --refselec must be given to define the new coordinate set. A stuntdouble with a dipole, which direction is always (0, 0, 1) in body frame, is specified by --originsele. The new x-z plane is defined by the direction of dipole and the stuntdouble specified by --refsele. </td>
348			</tr>
349			<tr bgcolor="#CCFF99">
350			<td><blockquote>
351			<p>--refsele</p>
352			</blockquote></td>
353			</tr>
354			</table>
355			</ul>
356			<p>
357			<p><b><a name="within"></a> StaticProps</b>
358			<p>
359			<p align="center"><img src="definition.jpg" width="720" height="540">
360			<p align="left">There are five seperate radial distribution functions availiable in OOPSE. Since every radial distrbution function invlove the calculation between a pair, --sele1 and --sele2 must be given.
361			<ul>
362			<table width="890" border=1 cellpadding=5 bgcolor="#FFFFFF">
363			<tr bgcolor="#CCFFCC">
364			<td width="191"><blockquote>
365			<p>option</p>
366			</blockquote></td>
367			<td width="667"><blockquote>
368			<div align="center">description</div>
369			</blockquote></td>
370			</tr>
371			<tr bgcolor="#CCFFCC">
372			<td><blockquote>
373			<p>--gofr</p>
374			</blockquote></td>
375			<td>normal pair distribution function.</td>
376			</tr>
377			<tr bgcolor="#CCFFCC">
378			<td><blockquote>
379			<p>--r_theta</p>
380			</blockquote></td>
381			<td>Calculate angle dependent pair distribution function. The angle is defined by r and A's dipole moment. </td>
382			</tr>
383			<tr bgcolor="#CCFFCC">
384			<td><blockquote>
385			<p>--r_omega</p>
386			</blockquote></td>
387			<td>Calculate angle dependent pair distribution function. The angle is defined by A's dipole moment and B's dipole moment . </td>
388			</tr>
389			<tr bgcolor="#CCFFCC">
390			<td><blockquote>
391			<p>--theta_omega</p>
392			</blockquote></td>
393			<td>Calculate the two dimension distribution of two angles.</td>
394			</tr>
395			<tr bgcolor="#CCFFCC">
396			<td><blockquote>
397			<p>--gxyz</p>
398			</blockquote></td>
399	tim	2102	<td>Calculate the three dimension distribution of the particle B in the body frame of particle A. Therefore, --originsele and --refsele must be given to define A's internal coordinate set. </td>
400	tim	2063	</tr>
401			</table>
402			</ul>
403			<p>  </p>
404			<p><b><a name="within"></a> DynamicProps </b>
405			<ul>
406			<table width="890" border=1 cellpadding=5 bgcolor="#FFFFFF">
407			<tr bgcolor="#CCFFCC">
408			<td width="191"> <p align="center">option</p></td>
409			<td width="667"><blockquote>
410			<div align="center">description</div>
411			</blockquote></td>
412			</tr>
413			<tr bgcolor="#CCFFCC">
414			<td> <p align="center">--rcorr</p></td>
415			<td>mean square displacement </td>
416			</tr>
417			<tr bgcolor="#CCFFCC">
418			<td> <p align="center">--vcorr</p></td>
419			<td>velocity correlation function</td>
420			</tr>
421			<tr bgcolor="#CCFFCC">
422			<td> <p align="center">--dcorr</p></td>
423			<td>dipole correlation function </td>
424			</tr>
425			</table>
426			</ul>
427			<p>
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