ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/OOPSE-3.0/doc/SelectionExpression.html
Revision: 2102
Committed: Thu Mar 10 16:14:07 2005 UTC (19 years, 3 months ago) by tim
Content type: text/html
File size: 11874 byte(s)
Log Message: 
minor change

File Contents

# Content
1 <html>
2
3 <head>
4
5 <title>Select Commands in OOPSE</title>
6
7 </head>
8
9
10
11 <body bgcolor=white>
12
13 <basefont size=3>
14
15
16
17 <div align=center>
18
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">&nbsp;</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 </div>
30
31 <a name="syntax" id="syntax">
32
33 <h2>
34
35 Syntax of the select command
36
37 </h2>
38
39 </a>
40
41
42
43 The most general form of the select command is: <b>select <i>expression</i>
44
45 </b>
46
47 <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
49 <p><b><a name="logic"></a> Logical expression. </b> </p>
50
51 <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
53 <ul>
54
55 <table width="441" border=1 cellpadding=5 bgcolor="#FFFFFF">
56
57 <tr bgcolor="#FFCCFF">
58
59 <td width="174"><div align="left">logical operator </div></td>
60
61 <td width="241"><div align="left">equivalent operator</div></td>
62
63 </tr>
64
65 <tr bgcolor="#FFCCFF">
66
67 <td><div align="left">and</div></td>
68
69 <td><div align="left">&quot;&amp;&quot;, &quot;&amp;&amp;&quot; </div></td>
70
71 </tr>
72
73 <tr bgcolor="#FFCCFF">
74
75 <td><div align="left">or</div></td>
76
77 <td><div align="left">&quot;|&quot;, &quot;||&quot;, &quot;,&quot; </div></td>
78
79 </tr>
80
81 <tr bgcolor="#FFCCFF">
82
83 <td><div align="left">not</div></td>
84
85 <td><div align="left">&quot;!&quot;</div></td>
86
87 </tr>
88
89 </table>
90
91 <p>&nbsp;</p>
92
93 </ul>
94
95 <p><a name="name"><b> Name expression.
96
97 </b></a> </p>
98
99 <ul>
100
101 <table width="886" border="1" bordercolor="#6B7683" bgcolor="#FFFFCC">
102
103 <tr>
104
105 <td colspan="2"><div align="center">expression</div></td>
106
107 <td width="434"><div align="center">description</div></td>
108
109 </tr>
110
111 <tr>
112
113 <td width="183" rowspan="3">expression without &quot;.&quot; </td>
114
115 <td width="247"><div align="left">select DMPC</div></td>
116
117 <td>select all stuntdoubles belong to DMPC molecule </td>
118
119 </tr>
120
121 <tr>
122
123 <td><div align="left">select C*</div></td>
124
125 <td>select all carbon atoms </td>
126
127 </tr>
128
129 <tr>
130
131 <td><div align="left">select DMPC_RB_*</div></td>
132
133 <td>select all rigid-bodies (only select rigid-bodies, not include the atoms belong to them)</td>
134
135 </tr>
136
137 <tr>
138
139 <td rowspan="3">expression has one &quot;.&quot; </td>
140
141 <td>select TIP3P.O_TIP3P</td>
142
143 <td>select stuntdoubles belong to molecule </td>
144
145 </tr>
146
147 <tr>
148
149 <td>select DMPC_RB_0.PO4</td>
150
151 <td>select atoms belong to rigid-bodies</td>
152
153 </tr>
154
155 <tr>
156
157 <td>select DMPC.20</td>
158
159 <td>select stuntdoubles by their internal indices inside the molecules </td>
160
161 </tr>
162
163 <tr>
164
165 <td>expression has two &quot;.&quot;</td>
166
167 <td>select DMPC.DMPC_RB_?.*</td>
168
169 <td>select all atoms belong to rigid-bodies within DMPC molecule</td>
170
171 </tr>
172
173 </table>
174
175 <p>&nbsp;</p>
176
177 </ul>
178
179 <p><a name="index" id="index"><b> Index expression </b></a></p>
180
181 <ul>
182
183 <table width="894" border=1 cellpadding=5 bgcolor="#FFFFFF"><tr bgcolor="#FFFFCC">
184
185 <td width="113">select 20 </td>
186
187 <td width="520">select all of the stuntdoubles of molecule 20</td>
188
189 </tr>
190
191 <tr bgcolor="#FFFFCC">
192
193 <td>select 20 to 30 </td>
194
195 <td>select all of the stuntdoubles of molecules which global indices are between 20 (inclusive) and 30 (exclusive) </td>
196
197 </tr>
198
199 </table>
200
201 </ul>
202
203
204
205 <p>&nbsp; </p>
206
207 <p><a name="predefine" id="predefine"><b> Predefine set </b></a></p>
208
209 <ul>
210
211 <table width="449" border=1 cellpadding=5 bgcolor="#FFFFFF">
212
213 <tr bgcolor="#FFCCFF">
214
215 <td width="91"><div align="left">keyword</div></td>
216
217 <td width="332"><div align="left">description</div></td>
218
219 </tr>
220
221 <tr bgcolor="#FFCCFF">
222
223 <td><div align="left">all</div></td>
224
225 <td><div align="left">select all stuntdoubles</div></td>
226
227 </tr>
228
229 <tr bgcolor="#FFCCFF">
230
231 <td><div align="left">none</div></td>
232
233 <td><div align="left">select none of the stuntdoubles </div></td>
234
235 </tr>
236
237 </table>
238
239 </ul>
240
241 <p>&nbsp;</p>
242
243 <p><a name="user" id="user"><b> User define expression.</b></a></p>
244
245 <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
247 <p> Once defined, user can use such terms in boolean expressions </p>
248
249 <ul>
250
251 <table width="659" border=1 cellpadding=5 bgcolor="#FFFFFF">
252
253 <tr bgcolor="#FFFFCC">
254
255 <td><p>define SSDWATER SSD or SSD1 or SSDRF</p>
256
257 <p>select SSDWATER </p> <div align="left"></div></td>
258
259 </tr>
260
261 </table>
262
263 </ul>
264
265 <p><a name="comparison" id="comparison"> <b>Comparison expression.</b></a></p>
266
267 <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
269 <ul>
270
271 <table width="668" border=1 cellpadding=5 bgcolor="#FFFFFF">
272
273 <tr bgcolor="#FFCCFF">
274
275 <td width="305"><div align="left">property</div></td>
276
277 <td width="331"><div align="left">mass, dipole, charge </div></td>
278
279 </tr>
280
281 <tr bgcolor="#FFCCFF">
282
283 <td><div align="left">comparision operator</div></td>
284
285 <td><div align="left">&quot;&gt;&quot;, &quot;&lt;&quot;, &quot;=&quot;, &quot;&gt;=&quot;, &quot;&lt;=&quot;, &quot;!=&quot; </div></td>
286
287 </tr>
288
289 </table>
290
291 </ul>
292
293 <ul>
294
295 <table width="672" border=1 cellpadding=5 bgcolor="#FFFFFF">
296
297 <tr bgcolor="#FFFFCC">
298
299 <td width="302">select mass &gt; 16.0 and charge &lt; -2 </td>
300
301 <td width="338">select stuntdoubles which mass is great than 16.0 and charge is less than -2 </td>
302
303 </tr>
304
305 </table>
306
307 </ul>
308
309 <p>&nbsp;</p>
310
311 <p><b> <a name="within"></a> Within expression.</b>
312
313 <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
315 <ul>
316
317 <table width="681" border=1 cellpadding=5 bgcolor="#FFFFFF">
318
319 <tr bgcolor="#FFFFCC">
320
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 </tr>
326 </table>
327
328 </ul>
329
330 <p>
331
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=&quot;selection command&quot; 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 <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 </tr>
401 </table>
402 </ul>
403 <p>&nbsp; </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>
428 </body>
429
430 </html>
431

Properties

Name Value
svn:executable *