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1 + <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
2   <html>
3   <head>
4 < <title>Select Commands in OOPSE</title>
4 >  <title>Selection syntax for OOPSE utility programs</title>
5   </head>
6 <
7 < <body bgcolor=white>
8 < <basefont size=3>
9 <
10 < <div align=center>
11 < <font size="+2"><b>Select Commands in </b></font><b><font size="+2">OOPSE</font></b><br>
6 > <body style="background-color: white;">
7 > <basefont size="3">
8 > <div align="center">
9 > <p><font size="+2"><b>Selection syntax for OOPSE utility programs</b></font><span
10 > style="font-weight: bold;"></span><br>
11 > </p>
12 > <h2 align="left"><a name="introduction" id="introduction"> Introduction
13 > </a></h2>
14 > <p style="text-align: left;">The OOPSE utility programs compute
15 > properties from the <span
16 > style="font-family: monospace; font-weight: bold;">dump</span><span
17 > style="font-weight: bold;">
18 > </span>files that are generated during a molecular dynamics
19 > simulation.&nbsp;
20 > These programs are:<br>
21 > </p>
22 > <ul style="text-align: left;">
23 >  <li><span style="font-family: monospace; font-weight: bold;">Dump2XYZ</span><span
24 > style="font-weight: bold;"> </span>- Converts an OOPSE dump file into
25 > a file suitable
26 > for viewing in a molecular dynamics viewer like <a
27 > href="http://www.jmol.org">Jmol</a><br>
28 >  </li>
29 >  <li><span style="font-family: monospace; font-weight: bold;">StaticProps</span><span
30 > style="font-weight: bold;"> </span>- Computes static properties like
31 > the pair distribution function, <span style="font-style: italic;">g(r)</span>.<br>
32 >  </li>
33 >  <li><span style="font-family: monospace; font-weight: bold;">DynamicProps</span><span
34 > style="font-weight: bold;"> </span>- Computes time correlation
35 > functions like the
36 > velocity autocorrelation function, <span style="font-style: italic;">&lt;<span
37 > style="font-weight: bold;">v</span>(t)<span style="font-weight: bold;">v</span>(0)&gt;</span>,
38 > or the mean square displacement <span style="font-style: italic;">&lt;|<span
39 > style="font-weight: bold;">r</span>(t) - <span
40 > style="font-weight: bold;">r</span>(0)|<sup>2</sup>&gt;.</span></li>
41 > </ul>
42 > <div style="text-align: left;">These programs often need to operate on
43 > a subset of the data contained within a dump file.&nbsp; For example,
44 > if you want only the <span style="font-style: italic;">oxygen-oxygen</span>
45 > pair distribution from a water simulation, or if you want to make a
46 > movie including only the water molecules within a 6 angstrom radius of
47 > lipid head groups, you need a way to specify your selection to these
48 > utility programs.&nbsp;&nbsp; OOPSE has a selection syntax which allows
49 > you to specify the selection in a compact form in order to generate
50 > only the data you want.&nbsp; For example a common use of the
51 > StaticProps command would be:<br>
52 > <br>
53 > <div style="margin-left: 80px;"><span
54 > style="font-family: monospace; font-weight: bold;">StaticProps -i
55 > tp4.dump --gofr --sele1="select O*" --sele2="select O*"</span><br>
56   </div>
57 < <a name="syntax" id="syntax">
58 < <h2>
59 < Syntax of the select command
60 < </h2>
61 < </a>
62 <
63 < The most general form of the select command is: <b>select <i>expression</i>
57 > <br>
58 > This command computes the oxygen-oxygen pair distribution function, <span
59 > style="font-style: italic;">g<sub>OO</sub>(r)</span>, from a file
60 > named <span style="font-family: monospace;">tp4.dump</span>.&nbsp; In
61 > order to understand this selection syntax and to make full use of the
62 > selection capabilities of the analysis programs, it is necessary to
63 > understand a few of the core concepts that are used to perform
64 > simulations.<br>
65 > <h2><a name="Concepts"></a>Concepts</h2>
66 > OOPSE manipulates both traditional atoms as well as some objects that <span
67 > style="font-style: italic;">behave like atoms</span>.&nbsp; These
68 > objects can be rigid collections of atoms or atoms which have
69 > orientational degrees of freedom.&nbsp; Here is a diagram of the class
70 > heirarchy:<br>
71 > <span style="font-style: italic;"></span></div>
72 > <p align="center"><img src="classoopse_1_1StuntDouble.png" height="136"
73 > width="292"><br>
74 > </p>
75 > <ul style="text-align: left;">
76 >  <li>A <span style="font-family: monospace; font-weight: bold;">StuntDouble</span>
77 > is <span style="font-style: italic;">any</span> object that can be
78 > manipulated by the integrators and minimizers.</li>
79 >  <li>An <span style="font-family: monospace; font-weight: bold;">Atom</span>
80 > is a fundamental point-particle that can be moved around during a
81 > simulation.</li>
82 >  <li>A <span style="font-family: monospace; font-weight: bold;">DirectionalAtom</span>
83 > is an atom which has <span style="font-style: italic;">orientational</span>
84 > as well as translational degrees of freedom.</li>
85 >  <li>A <span style="font-family: monospace; font-weight: bold;">RigidBody</span>
86 > is a collection of <span
87 > style="font-family: monospace; font-weight: bold;">Atom</span>s or <span
88 > style="font-family: monospace; font-weight: bold;">DirectionalAtom</span>s
89 > which behaves as a <span style="font-style: italic;">single unit.</span></li>
90 > </ul>
91 > <p align="left"> Every Molecule, Atom and DirectionalAtom in OOPSE
92 > have their own names which are specified in the <span
93 > style="font-family: monospace; font-weight: bold;">.md</span> file. In
94 > contrast, RigidBodies are denoted by their membership and index inside
95 > a particular molecule: <span style="font-family: monospace;">[MoleculeName]_RB_[index]</span>
96 > (the contents inside
97 > the brackets depend on the specifics of the simulation). The names of
98 > rigid bodies are generated automatically. For
99 > example, the name of the first rigid body in a DMPC molecule is
100 > DMPC_RB_0.<br>
101 > </p>
102 > </div>
103 > <h2><a name="select"></a>Syntax of the Select Command</h2>
104 > The most general form of the select command is: <b>select <i>expression</i>
105   </b>
106 < <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>
106 > <p>This expression represents an arbitrary set of StuntDoubles (Atoms
107 > or
108 > RigidBodies) in OOPSE. Expressions are composed of either name
109 > expressions, index expression, predefined sets, user-defined
110 > expression,
111 > comparison operators, within expressions, or logical combinations of
112 > the above expression types. Expression can be combined using
113 > parentheses
114 > and the Boolean operators</p>
115   <p><b><a name="logic"></a> Logical expression. </b> </p>
116 < <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.
116 > <p>The logical operators allow complex queries to be constructed out of
117 > simpler ones using the standard boolean connectives <b>and, or, not</b>.
118 > Parentheses can be used to alter the precedence of the operators.
119 > </p>
120   <ul>
121 <  <table width="441" border=1 cellpadding=5 bgcolor="#FFFFFF">
122 <    <tr bgcolor="#FFCCFF">
123 <      <td width="174"><div align="left">logical operator </div></td>
124 <      <td width="241"><div align="left">equivalent operator</div></td>
125 <    </tr>
126 <    <tr bgcolor="#FFCCFF">
127 <      <td><div align="left">and</div></td>
128 <      <td><div align="left">&quot;&amp;&quot;, &quot;&amp;&amp;&quot; </div></td>
129 <    </tr>
130 <    <tr bgcolor="#FFCCFF">
131 <      <td><div align="left">or</div></td>
132 <      <td><div align="left">&quot;|&quot;,&quot;||&quot;, &quot;,&quot; </div></td>
133 <    </tr>
134 <    <tr bgcolor="#FFCCFF">
135 <      <td><div align="left">not</div></td>
136 <      <td><div align="left">&quot;!&quot;</div></td>
137 <    </tr>
121 >  <table bgcolor="#ffffff" border="1" cellpadding="5" width="441">
122 >    <tbody>
123 >      <tr bgcolor="#ffccff">
124 >        <td width="174">
125 >        <div align="left">logical operator </div>
126 >        </td>
127 >        <td width="241">
128 >        <div align="left">equivalent operator</div>
129 >        </td>
130 >      </tr>
131 >      <tr bgcolor="#ffccff">
132 >        <td>
133 >        <div align="left">and</div>
134 >        </td>
135 >        <td>
136 >        <div align="left">"&amp;", "&amp;&amp;" </div>
137 >        </td>
138 >      </tr>
139 >      <tr bgcolor="#ffccff">
140 >        <td>
141 >        <div align="left">or</div>
142 >        </td>
143 >        <td>
144 >        <div align="left">"|", "||", "," </div>
145 >        </td>
146 >      </tr>
147 >      <tr bgcolor="#ffccff">
148 >        <td>
149 >        <div align="left">not</div>
150 >        </td>
151 >        <td>
152 >        <div align="left">"!"</div>
153 >        </td>
154 >      </tr>
155 >    </tbody>
156    </table>
157    <p>&nbsp;</p>
158   </ul>
159   <p><a name="name"><b> Name expression.
160   </b></a> </p>
161   <ul>
162 < <table width="886" border="1" bordercolor="#6B7683" bgcolor="#FFFFCC">
163 <  <tr>
164 <    <td colspan="2"><div align="center">expression</div></td>
165 <    <td width="434"><div align="center">description</div></td>
166 <  </tr>
167 <  <tr>
168 <    <td width="183" rowspan="3">expression without &quot;.&quot; </td>
169 <    <td width="247"><div align="left">select DMPC</div></td>
170 <    <td>select all stuntdoubles belong to DMPC molecule </td>
171 <  </tr>
172 <  <tr>
173 <    <td><div align="left">select C*</div></td>
174 <    <td>select all carbon atoms </td>
175 <  </tr>
176 <  <tr>
177 <    <td><div align="left">select DMPC_RB_*</div></td>
178 <    <td>select all rigid-bodies (only select rigid-bodies, not include the atoms belong to them)</td>
179 <  </tr>
180 <  <tr>
181 <    <td rowspan="3">expression has one &quot;.&quot; </td>
182 <    <td>select TIP3P.O_TIP3P</td>
183 <    <td>select stuntdoubles belong to molecule </td>
184 <  </tr>
185 <  <tr>
186 <    <td>select DMPC_RB_0.PO4</td>
187 <    <td>select atoms belong to rigid-bodies</td>
188 <  </tr>
189 <  <tr>
190 <    <td>select DMPC.20</td>
191 <    <td>select stuntdoubles by their internal indices inside the molecules </td>
192 <  </tr>
193 <  <tr>
194 <    <td>expression has two &quot;.&quot;</td>
195 <    <td>select DMPC.DMPC_RB_?.*</td>
196 <    <td>select all atoms belong to rigid-bodies within DMPC molecule</td>
197 <  </tr>
198 < </table>
199 < <p>&nbsp;</p>
162 >  <table bgcolor="#ffffcc" border="1" bordercolor="#6b7683" width="886">
163 >    <tbody>
164 >      <tr>
165 >        <td colspan="2">
166 >        <div align="center">expression</div>
167 >        </td>
168 >        <td width="434">
169 >        <div align="center">description</div>
170 >        </td>
171 >      </tr>
172 >      <tr>
173 >        <td rowspan="3" width="183">expression without "." </td>
174 >        <td width="247">
175 >        <div align="left">select DMPC</div>
176 >        </td>
177 >        <td>select all StuntDoubles belonging to all DMPC molecules </td>
178 >      </tr>
179 >      <tr>
180 >        <td>
181 >        <div align="left">select C*</div>
182 >        </td>
183 >        <td>select all atoms which have atom types beginning with C<br>
184 >        </td>
185 >      </tr>
186 >      <tr>
187 >        <td>
188 >        <div align="left">select DMPC_RB_*</div>
189 >        </td>
190 >        <td>select all RigidBodies in DMPC molecules (only select
191 > rigid-bodies, but not
192 > include the atoms belong to them)</td>
193 >      </tr>
194 >      <tr>
195 >        <td rowspan="3">expression has one "." </td>
196 >        <td>select TIP3P.O_TIP3P</td>
197 >        <td>select the O_TIP3P Atoms belong to TIP3P molecules </td>
198 >      </tr>
199 >      <tr>
200 >        <td>select DMPC_RB_0.PO4</td>
201 >        <td>select the PO4 Atoms belonging to first RigidBody in each
202 > DMPC molecule<br>
203 >        </td>
204 >      </tr>
205 >      <tr>
206 >        <td>select DMPC.20</td>
207 >        <td>select the 20th StuntDouble in each DMPC molecule<br>
208 >        </td>
209 >      </tr>
210 >      <tr>
211 >        <td>expression has two "."</td>
212 >        <td>select DMPC.DMPC_RB_?.*</td>
213 >        <td>select all Atoms belonging to all rigid-bodies within all
214 > DMPC molecules</td>
215 >      </tr>
216 >    </tbody>
217 >  </table>
218 >  <p>&nbsp;</p>
219   </ul>
220   <p><a name="index" id="index"><b> Index expression </b></a></p>
87 – <p>Index expression is used to select stuntdobules by their global indices. </p>
221   <ul>
222 < <table width="894" border=1 cellpadding=5 bgcolor="#FFFFFF"><tr bgcolor="#FFFFCC">
223 <  <td width="113">select 20 </td>
224 <    <td width="520">select stuntdoubles which global index is 20 </td>
225 < </tr>
226 <  <tr bgcolor="#FFFFCC">
227 <    <td>select 20 to 30      </td>
228 <    <td>select stuntdoubles which global indices are between 20 (inclusive) and 30 (exclusive) </td>
229 <  </tr>
230 < </table>
222 >  <table bgcolor="#ffffff" border="1" cellpadding="5" width="894">
223 >    <tbody>
224 >      <tr bgcolor="#ffffcc">
225 >        <td width="113">select 20 </td>
226 >        <td width="520">select all of the StuntDoubles belonging to
227 > Molecule 20</td>
228 >      </tr>
229 >      <tr bgcolor="#ffffcc">
230 >        <td>select 20 to 30 </td>
231 >        <td>select all of the StuntDoules belonging to molecules which
232 > have global
233 > indices between 20 (inclusive) and 30 (exclusive) </td>
234 >      </tr>
235 >    </tbody>
236 >  </table>
237   </ul>
99 –
238   <p>&nbsp; </p>
239 < <p><a name="predefine" id="predefine"><b> Predefine set </b></a></p>
239 > <p><a name="predefine" id="predefine"><b> Predefined sets </b></a></p>
240   <ul>
241 <  <table width="449" border=1 cellpadding=5 bgcolor="#FFFFFF">
242 <    <tr bgcolor="#FFCCFF">
243 <      <td width="91"><div align="left">keyword</div></td>
244 <      <td width="332"><div align="left">description</div></td>
245 <    </tr>
246 <    <tr bgcolor="#FFCCFF">
247 <      <td><div align="left">all</div></td>
248 <      <td><div align="left">select all stuntdoubles</div></td>
249 <    </tr>
250 <    <tr bgcolor="#FFCCFF">
251 <      <td><div align="left">none</div></td>
252 <      <td><div align="left">select none of the stuntdoubles </div></td>
253 <    </tr>
254 <    <tr bgcolor="#FFCCFF">
255 <      <td><div align="left">rigidbody</div></td>
256 <      <td><div align="left">select all rigid-bodies</div></td>
257 <    </tr>
241 >  <table bgcolor="#ffffff" border="1" cellpadding="5" width="449">
242 >    <tbody>
243 >      <tr bgcolor="#ffccff">
244 >        <td width="91">
245 >        <div align="left">keyword</div>
246 >        </td>
247 >        <td width="332">
248 >        <div align="left">description</div>
249 >        </td>
250 >      </tr>
251 >      <tr bgcolor="#ffccff">
252 >        <td>
253 >        <div align="left">all</div>
254 >        </td>
255 >        <td>
256 >        <div align="left">select all StuntDoubles</div>
257 >        </td>
258 >      </tr>
259 >      <tr bgcolor="#ffccff">
260 >        <td>
261 >        <div align="left">none</div>
262 >        </td>
263 >        <td>
264 >        <div align="left">select none of the StuntDoubles </div>
265 >        </td>
266 >      </tr>
267 >    </tbody>
268    </table>
269   </ul>
270   <p>&nbsp;</p>
271 < <p><a name="user" id="user"><b> User define expression.</b></a></p>
272 < <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>
273 < <p> Once defined, user can use such terms in boolean expressions </p>
271 > <p><a name="user" id="user"><b> User defined expressions</b></a></p>
272 > <p> Users can define arbitrary terms to represent groups of
273 > StuntDoubles, and then use the define terms in select
274 > commands. The general form for the define command is: <strong>define <em>term
275 > expression</em></strong></p>
276 > <p> Once defined, the user can specify such terms in boolean
277 > expressions </p>
278   <ul>
279 <  <table width="659" border=1 cellpadding=5 bgcolor="#FFFFFF">
280 <    <tr bgcolor="#FFFFCC">
281 <      <td><p>define SSDWATER SSD or SSD1 or SSDRF</p>
282 <      <p>select SSDWATER  </p>      <div align="left"></div></td>
283 <    </tr>
279 >  <table bgcolor="#ffffff" border="1" cellpadding="5" width="659">
280 >    <tbody>
281 >      <tr bgcolor="#ffffcc">
282 >        <td>
283 >        <p>define SSDWATER SSD or SSD1 or SSDRF</p>
284 >        <p>select SSDWATER </p>
285 >        </td>
286 >      </tr>
287 >    </tbody>
288    </table>
289   </ul>
290   <p><a name="comparison" id="comparison"> <b>Comparison expression.</b></a></p>
291 < <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>
291 > <p>StuntDoubles can be selected by using comparision operators on
292 > their properties. The general form for the comparison command is: a
293 > property name, followed by a comparision operator and then a number.</p>
294   <ul>
295 <  <table width="668" border=1 cellpadding=5 bgcolor="#FFFFFF">
296 <    <tr bgcolor="#FFCCFF">
297 <      <td width="305"><div align="left">property</div></td>
298 <      <td width="331"><div align="left">mass, dipole, charge </div></td>
299 <    </tr>
300 <    <tr bgcolor="#FFCCFF">
301 <      <td><div align="left">comparision operator</div></td>
302 <      <td><div align="left">&quot;&gt;&quot;, &quot;&lt;&quot;, &quot;=&quot;, &quot;&gt;=&quot;, &quot;&lt;=&quot;, &quot;!=&quot; </div></td>
303 <    </tr>
295 >  <table bgcolor="#ffffff" border="1" cellpadding="5" width="668">
296 >    <tbody>
297 >      <tr bgcolor="#ffccff">
298 >        <td width="305">
299 >        <div align="left">property</div>
300 >        </td>
301 >        <td width="331">
302 >        <div align="left">mass, charge </div>
303 >        </td>
304 >      </tr>
305 >      <tr bgcolor="#ffccff">
306 >        <td>
307 >        <div align="left">comparision operator</div>
308 >        </td>
309 >        <td>
310 >        <div align="left">"&gt;", "&lt;", "=", "&gt;=", "&lt;=", "!=" </div>
311 >        </td>
312 >      </tr>
313 >    </tbody>
314    </table>
315   </ul>
316   <ul>
317 <  <table width="672" border=1 cellpadding=5 bgcolor="#FFFFFF">
318 <    <tr bgcolor="#FFFFCC">
319 <      <td width="302">select mass &gt; 16.0 and charge &lt; -2 </td>
320 <      <td width="338">select stuntdoubles which mass is great than 16.0 and charge is less than -2 </td>
321 <    </tr>
317 >  <table bgcolor="#ffffff" border="1" cellpadding="5" width="672">
318 >    <tbody>
319 >      <tr bgcolor="#ffffcc">
320 >        <td width="302">select mass &gt; 16.0 and charge &lt; -2 </td>
321 >        <td width="338">select StuntDoubles which have mass greater
322 > than
323 > 16.0 and charges less than -2 </td>
324 >      </tr>
325 >    </tbody>
326    </table>
327   </ul>
328   <p>&nbsp;</p>
329 < <p><b> <a name="within"></a>    Within expression.</b>
330 < <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>
329 > <p><b> <a name="within"></a> Within expression.</b>
330 > </p>
331 > <p> The "within" selection allows the user to select all StuntDoubles
332 > within the specified
333 > distance (in Angstroms) from a selection, including the selected atom
334 > itself. The
335 > general form for within selection is: <b>select within(<i>distance,
336 > expression</i>) </b>
337 > </p>
338   <ul>
339 <  <table width="890" border=1 cellpadding=5 bgcolor="#FFFFFF">
340 <    <tr bgcolor="#FFFFCC">
341 <      <td width="431">select within(2.5, PO4 or NC4) </td>
342 <      <td width="427"><blockquote>select stunntdoules which are within 2.5 ? from either PO4 or NC4 </blockquote></td>
343 <    </tr>
339 >  <table bgcolor="#ffffff" border="1" cellpadding="5" width="681">
340 >    <tbody>
341 >      <tr bgcolor="#ffffcc">
342 >        <td width="306">select within(2.5, PO4 or NC4) </td>
343 >        <td width="343">
344 >        <blockquote>select all StuntDoubles which are within 2.5
345 > angstroms of PO4 or NC4 atoms<br>
346 >        </blockquote>
347 >        </td>
348 >      </tr>
349 >    </tbody>
350    </table>
351   </ul>
352   <p>
353 < <p><p>    
353 > </p>
354 > <h2><a name="syntax" id="syntax"> Tools which use the selection command
355 > </a></h2>
356 > <p><b><a name="within"></a> Dump2XYZ</b>
357 > </p>
358 > <p>Dump2XYZ can transform an OOPSE dump file into a xyz file which
359 > could be opened by other molecular viewers, such as Jmol and VMD. </p>
360 > <ul>
361 >  <table bgcolor="#ffffff" border="1" cellpadding="5" width="890">
362 >    <tbody>
363 >      <tr bgcolor="#6699ff">
364 >        <td width="191">
365 >        <blockquote>
366 >          <p>--selection</p>
367 >        </blockquote>
368 >        </td>
369 >        <td width="667">Specifying --selection="selection command" with
370 > Dump2XYZ, user can select an arbitrary set of stuntdoubles to be
371 > converted. </td>
372 >      </tr>
373 >      <tr bgcolor="#ccff99">
374 >        <td>
375 >        <blockquote>
376 >          <p>--originsele</p>
377 >        </blockquote>
378 >        </td>
379 >        <td rowspan="2">In order to rotate the system, --originsele and
380 > --refselec must be given to define the new coordinate set. A
381 > stuntdouble with a dipole, which direction is always (0, 0, 1) in body
382 > frame, is specified by --originsele. The new x-z plane is defined by
383 > the direction of dipole and the StuntDouble is specified by --refsele. </td>
384 >      </tr>
385 >      <tr bgcolor="#ccff99">
386 >        <td>
387 >        <blockquote>
388 >          <p>--refsele</p>
389 >        </blockquote>
390 >        </td>
391 >      </tr>
392 >    </tbody>
393 >  </table>
394 > </ul>
395 > <p>
396 > </p>
397 > <p><b><a name="within"></a> StaticProps<br>
398 > </b></p>
399 > StaticProps can compute properties which are averaged over the
400 > configurations that are contained within a dump file.&nbsp;&nbsp; The
401 > most common example of a static property that can be computed is the
402 > pair distribution function between atoms of type A and other atoms of
403 > type B, <span style="font-style: italic;">g<sub>AB</sub>(r)</span>.&nbsp;
404 > StaticProps can also be used to compute the density distributions of
405 > other molecules in a reference frame <span style="font-style: italic;">fixed
406 > to the body-fixed reference frame</span> of a selected atom or rigid
407 > body.<b><br>
408 > </b>
409 > <p> </p>
410 > <p align="center"><img src="definition.jpg" height="540" width="720"></p>
411 > <p align="left">There are five seperate radial distribution functions
412 > availiable in OOPSE. Since every radial distrbution function invlove
413 > the calculation between a pair, --sele1 and --sele2 must be given.
414 > </p>
415 > <ul>
416 >  <table bgcolor="#ffffff" border="1" cellpadding="5" width="890">
417 >    <tbody>
418 >      <tr bgcolor="#ccffcc">
419 >        <td width="191">
420 >        <blockquote>
421 >          <p>option</p>
422 >        </blockquote>
423 >        </td>
424 >        <td width="667">
425 >        <blockquote>
426 >          <div align="center">description</div>
427 >        </blockquote>
428 >        </td>
429 >      </tr>
430 >      <tr bgcolor="#ccffcc">
431 >        <td>
432 >        <blockquote>
433 >          <p>--gofr</p>
434 >        </blockquote>
435 >        </td>
436 >        <td>Computes the pair distribution function.</td>
437 >      </tr>
438 >      <tr bgcolor="#ccffcc">
439 >        <td>
440 >        <blockquote>
441 >          <p>--r_theta</p>
442 >        </blockquote>
443 >        </td>
444 >        <td>Computes the angle-dependent pair distribution function.
445 > The
446 > angle is defined by the intermolecular vector r and z-axis of
447 > DirectionalAtom A.<br>
448 >        </td>
449 >      </tr>
450 >      <tr bgcolor="#ccffcc">
451 >        <td>
452 >        <blockquote>
453 >          <p>--r_omega</p>
454 >        </blockquote>
455 >        </td>
456 >        <td>Computes an angle-dependent pair distribution function. The
457 > angle is defined by the z-axes of the two DirectionalAtoms A and B.<br>
458 >        </td>
459 >      </tr>
460 >      <tr bgcolor="#ccffcc">
461 >        <td>
462 >        <blockquote>
463 >          <p>--theta_omega</p>
464 >        </blockquote>
465 >        </td>
466 >        <td>Calculate the pair distribution of the two angles.</td>
467 >      </tr>
468 >      <tr bgcolor="#ccffcc">
469 >        <td>
470 >        <blockquote>
471 >          <p>--gxyz</p>
472 >        </blockquote>
473 >        </td>
474 >        <td>Calculate the density distribution of particles
475 > of type B in the body frame of particle A. Therefore, --originsele and
476 > --refsele must be given to define A's internal coordinate set. </td>
477 >      </tr>
478 >    </tbody>
479 >  </table>
480 > </ul>
481 > <p>&nbsp; </p>
482 > <p><b><a name="within"></a> DynamicProps<br>
483 > <span style="font-weight: bold;"><br>
484 > </span></b>DynamicProps computes time correlation functions from the
485 > configurations stored in a dump file.&nbsp; Typical examples of time
486 > correlation functions are the mean square displacement and the velocity
487 > autocorrelation functions. <b><span style="font-weight: bold;"><br>
488 > </span> </b></p>
489 > <ul>
490 >  <table bgcolor="#ffffff" border="1" cellpadding="5" width="890">
491 >    <tbody>
492 >      <tr bgcolor="#ccffcc">
493 >        <td width="191">
494 >        <p align="center">option</p>
495 >        </td>
496 >        <td width="667">
497 >        <blockquote>
498 >          <div align="center">description</div>
499 >        </blockquote>
500 >        </td>
501 >      </tr>
502 >      <tr bgcolor="#ccffcc">
503 >        <td>
504 >        <p align="center">--rcorr</p>
505 >        </td>
506 >        <td>mean square displacement </td>
507 >      </tr>
508 >      <tr bgcolor="#ccffcc">
509 >        <td>
510 >        <p align="center">--vcorr</p>
511 >        </td>
512 >        <td>velocity autocorrelation function</td>
513 >      </tr>
514 >      <tr bgcolor="#ccffcc">
515 >        <td>
516 >        <p align="center">--dcorr</p>
517 >        </td>
518 >        <td>dipole correlation function </td>
519 >      </tr>
520 >    </tbody>
521 >  </table>
522 > </ul>
523 > <p>
524 > </p>
525   </body>
526   </html>

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