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selection expression

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# 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 <p>Index expression is used to select stuntdobules by their global indices. </p>
182
183 <ul>
184
185 <table width="894" border=1 cellpadding=5 bgcolor="#FFFFFF"><tr bgcolor="#FFFFCC">
186
187 <td width="113">select 20 </td>
188
189 <td width="520">select stuntdoubles which global index is 20 </td>
190
191 </tr>
192
193 <tr bgcolor="#FFFFCC">
194
195 <td>select 20 to 30 </td>
196
197 <td>select stuntdoubles which global indices are between 20 (inclusive) and 30 (exclusive) </td>
198
199 </tr>
200
201 </table>
202
203 </ul>
204
205
206
207 <p>&nbsp; </p>
208
209 <p><a name="predefine" id="predefine"><b> Predefine set </b></a></p>
210
211 <ul>
212
213 <table width="449" border=1 cellpadding=5 bgcolor="#FFFFFF">
214
215 <tr bgcolor="#FFCCFF">
216
217 <td width="91"><div align="left">keyword</div></td>
218
219 <td width="332"><div align="left">description</div></td>
220
221 </tr>
222
223 <tr bgcolor="#FFCCFF">
224
225 <td><div align="left">all</div></td>
226
227 <td><div align="left">select all stuntdoubles</div></td>
228
229 </tr>
230
231 <tr bgcolor="#FFCCFF">
232
233 <td><div align="left">none</div></td>
234
235 <td><div align="left">select none of the stuntdoubles </div></td>
236
237 </tr>
238
239 <tr bgcolor="#FFCCFF">
240
241 <td><div align="left">rigidbody</div></td>
242
243 <td><div align="left">select all rigid-bodies</div></td>
244
245 </tr>
246
247 </table>
248
249 </ul>
250
251 <p>&nbsp;</p>
252
253 <p><a name="user" id="user"><b> User define expression.</b></a></p>
254
255 <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>
256
257 <p> Once defined, user can use such terms in boolean expressions </p>
258
259 <ul>
260
261 <table width="659" border=1 cellpadding=5 bgcolor="#FFFFFF">
262
263 <tr bgcolor="#FFFFCC">
264
265 <td><p>define SSDWATER SSD or SSD1 or SSDRF</p>
266
267 <p>select SSDWATER </p> <div align="left"></div></td>
268
269 </tr>
270
271 </table>
272
273 </ul>
274
275 <p><a name="comparison" id="comparison"> <b>Comparison expression.</b></a></p>
276
277 <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>
278
279 <ul>
280
281 <table width="668" border=1 cellpadding=5 bgcolor="#FFFFFF">
282
283 <tr bgcolor="#FFCCFF">
284
285 <td width="305"><div align="left">property</div></td>
286
287 <td width="331"><div align="left">mass, dipole, charge </div></td>
288
289 </tr>
290
291 <tr bgcolor="#FFCCFF">
292
293 <td><div align="left">comparision operator</div></td>
294
295 <td><div align="left">&quot;&gt;&quot;, &quot;&lt;&quot;, &quot;=&quot;, &quot;&gt;=&quot;, &quot;&lt;=&quot;, &quot;!=&quot; </div></td>
296
297 </tr>
298
299 </table>
300
301 </ul>
302
303 <ul>
304
305 <table width="672" border=1 cellpadding=5 bgcolor="#FFFFFF">
306
307 <tr bgcolor="#FFFFCC">
308
309 <td width="302">select mass &gt; 16.0 and charge &lt; -2 </td>
310
311 <td width="338">select stuntdoubles which mass is great than 16.0 and charge is less than -2 </td>
312
313 </tr>
314
315 </table>
316
317 </ul>
318
319 <p>&nbsp;</p>
320
321 <p><b> <a name="within"></a> Within expression.</b>
322
323 <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>
324
325 <ul>
326
327 <table width="681" border=1 cellpadding=5 bgcolor="#FFFFFF">
328
329 <tr bgcolor="#FFFFCC">
330
331 <td width="306">select within(2.5, PO4 or NC4) </td>
332
333 <td width="343"><blockquote>select stunntdoules which are within 2.5 ? from either PO4 or NC4 </blockquote></td>
334
335 </tr>
336 </table>
337
338 </ul>
339
340 <p>
341
342 <h2><a name="syntax" id="syntax"> Tools using selection command </a></h2>
343 <p><b><a name="within"></a> Dump2XYZ</b>
344 <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.
345 <ul>
346 <table width="890" border=1 cellpadding=5 bgcolor="#FFFFFF">
347 <tr bgcolor="#6699FF">
348 <td width="191"><blockquote>
349 <p>--selection</p>
350 </blockquote></td>
351 <td width="667">Specifying --selection=&quot;selection command&quot; with Dump2XYZ, user can select an arbitrary set of stuntdoubles to be converted. </td>
352 </tr>
353 <tr bgcolor="#CCFF99">
354 <td><blockquote>
355 <p>--originsele</p>
356 </blockquote></td>
357 <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>
358 </tr>
359 <tr bgcolor="#CCFF99">
360 <td><blockquote>
361 <p>--refsele</p>
362 </blockquote></td>
363 </tr>
364 </table>
365 </ul>
366 <p>
367 <p><b><a name="within"></a> StaticProps</b>
368 <p>
369 <p align="center"><img src="definition.jpg" width="720" height="540">
370 <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.
371 <ul>
372 <table width="890" border=1 cellpadding=5 bgcolor="#FFFFFF">
373 <tr bgcolor="#CCFFCC">
374 <td width="191"><blockquote>
375 <p>option</p>
376 </blockquote></td>
377 <td width="667"><blockquote>
378 <div align="center">description</div>
379 </blockquote></td>
380 </tr>
381 <tr bgcolor="#CCFFCC">
382 <td><blockquote>
383 <p>--gofr</p>
384 </blockquote></td>
385 <td>normal pair distribution function.</td>
386 </tr>
387 <tr bgcolor="#CCFFCC">
388 <td><blockquote>
389 <p>--r_theta</p>
390 </blockquote></td>
391 <td>Calculate angle dependent pair distribution function. The angle is defined by r and A's dipole moment. </td>
392 </tr>
393 <tr bgcolor="#CCFFCC">
394 <td><blockquote>
395 <p>--r_omega</p>
396 </blockquote></td>
397 <td>Calculate angle dependent pair distribution function. The angle is defined by A's dipole moment and B's dipole moment . </td>
398 </tr>
399 <tr bgcolor="#CCFFCC">
400 <td><blockquote>
401 <p>--theta_omega</p>
402 </blockquote></td>
403 <td>Calculate the two dimension distribution of two angles.</td>
404 </tr>
405 <tr bgcolor="#CCFFCC">
406 <td><blockquote>
407 <p>--gxyz</p>
408 </blockquote></td>
409 <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 the A's internal coordinate set. </td>
410 </tr>
411 </table>
412 </ul>
413 <p>&nbsp; </p>
414 <p><b><a name="within"></a> DynamicProps </b>
415 <ul>
416 <table width="890" border=1 cellpadding=5 bgcolor="#FFFFFF">
417 <tr bgcolor="#CCFFCC">
418 <td width="191"> <p align="center">option</p></td>
419 <td width="667"><blockquote>
420 <div align="center">description</div>
421 </blockquote></td>
422 </tr>
423 <tr bgcolor="#CCFFCC">
424 <td> <p align="center">--rcorr</p></td>
425 <td>mean square displacement </td>
426 </tr>
427 <tr bgcolor="#CCFFCC">
428 <td> <p align="center">--vcorr</p></td>
429 <td>velocity correlation function</td>
430 </tr>
431 <tr bgcolor="#CCFFCC">
432 <td> <p align="center">--dcorr</p></td>
433 <td>dipole correlation function </td>
434 </tr>
435 </table>
436 </ul>
437 <p>
438 </body>
439
440 </html>
441

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