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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> |
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<html> |
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<head> |
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<title>Selection syntax for OOPSE utility programs</title> |
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</head> |
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<body style="background-color: white;"> |
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<basefont size="3"> |
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<div align="center"> |
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<p><font size="+2"><b>Selection syntax for OOPSE utility programs</b></font><span |
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style="font-weight: bold;"></span><br> |
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</p> |
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<h2 align="left"><a name="introduction" id="introduction"> Introduction |
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</a></h2> |
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<p style="text-align: left;">The OOPSE utility programs compute |
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properties from the <span |
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style="font-family: monospace; font-weight: bold;">dump</span><span |
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style="font-weight: bold;"> |
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</span>files that are generated during a molecular dynamics |
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simulation. |
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These programs are:<br> |
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</p> |
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<ul style="text-align: left;"> |
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<li><span style="font-family: monospace; font-weight: bold;">Dump2XYZ</span><span |
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style="font-weight: bold;"> </span>- Converts an OOPSE dump file into |
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a file suitable |
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for viewing in a molecular dynamics viewer like <a |
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href="http://www.jmol.org">Jmol</a><br> |
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</li> |
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<li><span style="font-family: monospace; font-weight: bold;">StaticProps</span><span |
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style="font-weight: bold;"> </span>- Computes static properties like |
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the pair distribution function, <span style="font-style: italic;">g(r)</span>.<br> |
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</li> |
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<li><span style="font-family: monospace; font-weight: bold;">DynamicProps</span><span |
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style="font-weight: bold;"> </span>- Computes time correlation |
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functions like the |
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velocity autocorrelation function, <span style="font-style: italic;"><<span |
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style="font-weight: bold;">v</span>(t)<span style="font-weight: bold;">v</span>(0)></span>, |
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or the mean square displacement <span style="font-style: italic;"><|<span |
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style="font-weight: bold;">r</span>(t) - <span |
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style="font-weight: bold;">r</span>(0)|<sup>2</sup>>.</span></li> |
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</ul> |
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<div style="text-align: left;">These programs often need to operate on |
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a subset of the data contained within a dump file. For example, |
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if you want only the <span style="font-style: italic;">oxygen-oxygen</span> |
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pair distribution from a water simulation, or if you want to make a |
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movie including only the water molecules within a 6 angstrom radius of |
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lipid head groups, you need a way to specify your selection to these |
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utility programs. OOPSE has a selection syntax which allows |
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you to specify the selection in a compact form in order to generate |
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only the data you want. For example a common use of the |
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StaticProps command would be:<br> |
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<br> |
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<div style="margin-left: 80px;"><span |
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style="font-family: monospace; font-weight: bold;">StaticProps -i |
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tp4.dump --gofr --sele1="select O*" --sele2="select O*"</span><br> |
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</div> |
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<br> |
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This command computes the oxygen-oxygen pair distribution function, <span |
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style="font-style: italic;">g<sub>OO</sub>(r)</span>, from a file |
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named <span style="font-family: monospace;">tp4.dump</span>. In |
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order to understand this selection syntax and to make full use of the |
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selection capabilities of the analysis programs, it is necessary to |
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understand a few of the core concepts that are used to perform |
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simulations.<br> |
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<h2><a name="Concepts"></a>Concepts</h2> |
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OOPSE manipulates both traditional atoms as well as some objects that <span |
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style="font-style: italic;">behave like atoms</span>. These |
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objects can be rigid collections of atoms or atoms which have |
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orientational degrees of freedom. Here is a diagram of the class |
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heirarchy:<br> |
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<span style="font-style: italic;"></span></div> |
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<p align="center"><img src="classoopse_1_1StuntDouble.png" height="136" |
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width="292"><br> |
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</p> |
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<ul style="text-align: left;"> |
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<li>A <span style="font-family: monospace; font-weight: bold;">StuntDouble</span> |
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is <span style="font-style: italic;">any</span> object that can be |
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manipulated by the integrators and minimizers.</li> |
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<li>An <span style="font-family: monospace; font-weight: bold;">Atom</span> |
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is a fundamental point-particle that can be moved around during a |
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simulation.</li> |
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<li>A <span style="font-family: monospace; font-weight: bold;">DirectionalAtom</span> |
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is an atom which has <span style="font-style: italic;">orientational</span> |
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as well as translational degrees of freedom.</li> |
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<li>A <span style="font-family: monospace; font-weight: bold;">RigidBody</span> |
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is a collection of <span |
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style="font-family: monospace; font-weight: bold;">Atom</span>s or <span |
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style="font-family: monospace; font-weight: bold;">DirectionalAtom</span>s |
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which behaves as a <span style="font-style: italic;">single unit.</span></li> |
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</ul> |
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<p align="left"> Every Molecule, Atom and DirectionalAtom in OOPSE |
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have their own names which are specified in the <span |
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style="font-family: monospace; font-weight: bold;">.md</span> file. In |
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contrast, RigidBodies are denoted by their membership and index inside |
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a particular molecule: <span style="font-family: monospace;">[MoleculeName]_RB_[index]</span> |
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(the contents inside |
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the brackets depend on the specifics of the simulation). The names of |
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rigid bodies are generated automatically. For |
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example, the name of the first rigid body in a DMPC molecule is |
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DMPC_RB_0.<br> |
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</p> |
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</div> |
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<h2><a name="select"></a>Syntax of the Select Command</h2> |
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The most general form of the select command is: <b>select <i>expression</i> |
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</b> |
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<p>This expression represents an arbitrary set of StuntDoubles (Atoms |
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or |
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RigidBodies) in OOPSE. Expressions are composed of either name |
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expressions, index expression, predefined sets, user-defined |
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expression, |
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comparison operators, within expressions, or logical combinations of |
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the above expression types. Expression can be combined using |
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parentheses |
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and the Boolean operators</p> |
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<p><b><a name="logic"></a> Logical expression. </b> </p> |
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<p>The logical operators allow complex queries to be constructed out of |
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simpler ones using the standard boolean connectives <b>and, or, not</b>. |
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Parentheses can be used to alter the precedence of the operators. |
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</p> |
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<ul> |
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<table bgcolor="#ffffff" border="1" cellpadding="5" width="441"> |
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<tbody> |
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<tr bgcolor="#ffccff"> |
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<td width="174"> |
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<div align="left">logical operator </div> |
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</td> |
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<td width="241"> |
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<div align="left">equivalent operator</div> |
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</td> |
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</tr> |
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<tr bgcolor="#ffccff"> |
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<td> |
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<div align="left">and</div> |
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</td> |
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<td> |
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<div align="left">"&", "&&" </div> |
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</td> |
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</tr> |
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<tr bgcolor="#ffccff"> |
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<td> |
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<div align="left">or</div> |
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</td> |
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<td> |
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<div align="left">"|", "||", "," </div> |
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</td> |
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</tr> |
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<tr bgcolor="#ffccff"> |
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<td> |
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<div align="left">not</div> |
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</td> |
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<td> |
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<div align="left">"!"</div> |
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</td> |
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</tr> |
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</tbody> |
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</table> |
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<p> </p> |
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</ul> |
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<p><a name="name"><b> Name expression. |
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</b></a> </p> |
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<ul> |
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<table bgcolor="#ffffcc" border="1" bordercolor="#6b7683" width="886"> |
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<tbody> |
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<tr> |
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<td colspan="2"> |
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<div align="center">expression</div> |
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</td> |
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<td width="434"> |
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<div align="center">description</div> |
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</td> |
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</tr> |
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<tr> |
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<td rowspan="3" width="183">expression without "." </td> |
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<td width="247"> |
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<div align="left">select DMPC</div> |
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</td> |
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<td>select all StuntDoubles belonging to all DMPC molecules </td> |
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</tr> |
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<tr> |
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<td> |
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<div align="left">select C*</div> |
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</td> |
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<td>select all atoms which have atom types beginning with C<br> |
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</td> |
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</tr> |
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<tr> |
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<td> |
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<div align="left">select DMPC_RB_*</div> |
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</td> |
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<td>select all RigidBodies in DMPC molecules (only select |
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rigid-bodies, but not |
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include the atoms belong to them)</td> |
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</tr> |
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<tr> |
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<td rowspan="3">expression has one "." </td> |
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<td>select TIP3P.O_TIP3P</td> |
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<td>select the O_TIP3P Atoms belong to TIP3P molecules </td> |
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</tr> |
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<tr> |
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<td>select DMPC_RB_0.PO4</td> |
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<td>select the PO4 Atoms belonging to first RigidBody in each |
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DMPC molecule<br> |
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</td> |
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</tr> |
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<tr> |
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<td>select DMPC.20</td> |
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<td>select the 20th StuntDouble in each DMPC molecule<br> |
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</td> |
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</tr> |
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<tr> |
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<td>expression has two "."</td> |
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<td>select DMPC.DMPC_RB_?.*</td> |
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<td>select all Atoms belonging to all rigid-bodies within all |
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DMPC molecules</td> |
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</tr> |
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</tbody> |
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</table> |
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<p> </p> |
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</ul> |
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<p><a name="index" id="index"><b> Index expression </b></a></p> |
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<ul> |
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<table bgcolor="#ffffff" border="1" cellpadding="5" width="894"> |
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<tbody> |
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<tr bgcolor="#ffffcc"> |
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<td width="113">select 20 </td> |
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<td width="520">select all of the StuntDoubles belonging to |
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Molecule 20</td> |
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</tr> |
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<tr bgcolor="#ffffcc"> |
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<td>select 20 to 30 </td> |
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<td>select all of the StuntDoules belonging to molecules which |
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have global |
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indices between 20 (inclusive) and 30 (exclusive) </td> |
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</tr> |
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</tbody> |
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</table> |
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</ul> |
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<p> </p> |
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<p><a name="predefine" id="predefine"><b> Predefined sets </b></a></p> |
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<ul> |
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<table bgcolor="#ffffff" border="1" cellpadding="5" width="449"> |
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<tbody> |
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<tr bgcolor="#ffccff"> |
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<td width="91"> |
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<div align="left">keyword</div> |
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</td> |
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<td width="332"> |
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<div align="left">description</div> |
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</td> |
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</tr> |
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<tr bgcolor="#ffccff"> |
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<td> |
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<div align="left">all</div> |
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</td> |
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<td> |
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<div align="left">select all StuntDoubles</div> |
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</td> |
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</tr> |
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<tr bgcolor="#ffccff"> |
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<td> |
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<div align="left">none</div> |
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</td> |
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<td> |
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<div align="left">select none of the StuntDoubles </div> |
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</td> |
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</tr> |
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</tbody> |
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</table> |
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</ul> |
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<p> </p> |
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<p><a name="user" id="user"><b> User defined expressions</b></a></p> |
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<p> Users can define arbitrary terms to represent groups of |
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StuntDoubles, and then use the define terms in select |
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commands. The general form for the define command is: <strong>define <em>term |
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expression</em></strong></p> |
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<p> Once defined, the user can specify such terms in boolean |
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expressions </p> |
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<ul> |
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<table bgcolor="#ffffff" border="1" cellpadding="5" width="659"> |
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<tbody> |
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<tr bgcolor="#ffffcc"> |
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<td> |
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<p>define SSDWATER SSD or SSD1 or SSDRF</p> |
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<p>select SSDWATER </p> |
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</td> |
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</tr> |
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</tbody> |
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</table> |
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</ul> |
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<p><a name="comparison" id="comparison"> <b>Comparison expression.</b></a></p> |
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<p>StuntDoubles can be selected by using comparision operators on |
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their properties. The general form for the comparison command is: a |
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property name, followed by a comparision operator and then a number.</p> |
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<ul> |
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<table bgcolor="#ffffff" border="1" cellpadding="5" width="668"> |
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<tbody> |
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<tr bgcolor="#ffccff"> |
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<td width="305"> |
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<div align="left">property</div> |
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</td> |
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<td width="331"> |
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<div align="left">mass, dipole, charge </div> |
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</td> |
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</tr> |
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<tr bgcolor="#ffccff"> |
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<td> |
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<div align="left">comparision operator</div> |
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</td> |
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<td> |
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<div align="left">">", "<", "=", ">=", "<=", "!=" </div> |
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</td> |
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</tr> |
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</tbody> |
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</table> |
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</ul> |
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<ul> |
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<table bgcolor="#ffffff" border="1" cellpadding="5" width="672"> |
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<tbody> |
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<tr bgcolor="#ffffcc"> |
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<td width="302">select mass > 16.0 and charge < -2 </td> |
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<td width="338">select StuntDoubles which have mass greater |
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than |
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16.0 and charges less than -2 </td> |
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</tr> |
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</tbody> |
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</table> |
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</ul> |
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<p> </p> |
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<p><b> <a name="within"></a> Within expression.</b> |
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</p> |
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<p> The "within" selection allows the user to select all StuntDoubles |
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within the specified |
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distance (in Angstroms) from a selection, including the selected atom |
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itself. The |
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general form for within selection is: <b>select within(<i>distance, |
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expression</i>) </b> |
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</p> |
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<ul> |
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<table bgcolor="#ffffff" border="1" cellpadding="5" width="681"> |
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<tbody> |
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<tr bgcolor="#ffffcc"> |
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<td width="306">select within(2.5, PO4 or NC4) </td> |
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<td width="343"> |
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<blockquote>select all StuntDoubles which are within 2.5 |
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angstroms of PO4 or NC4 atoms<br> |
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</blockquote> |
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</td> |
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</tr> |
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</tbody> |
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</table> |
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</ul> |
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<p> |
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</p> |
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<h2><a name="syntax" id="syntax"> Tools which use the selection command |
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</a></h2> |
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<p><b><a name="within"></a> Dump2XYZ</b> |
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</p> |
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<p>Dump2XYZ can transform an OOPSE dump file into a xyz file which |
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could be opened by other molecular viewers, such as Jmol and VMD. </p> |
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<ul> |
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<table bgcolor="#ffffff" border="1" cellpadding="5" width="890"> |
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<tbody> |
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<tr bgcolor="#6699ff"> |
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<td width="191"> |
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<blockquote> |
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<p>--selection</p> |
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</blockquote> |
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</td> |
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<td width="667">Specifying --selection="selection command" with |
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Dump2XYZ, user can select an arbitrary set of stuntdoubles to be |
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converted. </td> |
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</tr> |
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<tr bgcolor="#ccff99"> |
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<td> |
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<blockquote> |
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<p>--originsele</p> |
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</blockquote> |
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</td> |
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<td rowspan="2">In order to rotate the system, --originsele and |
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--refselec must be given to define the new coordinate set. A |
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stuntdouble with a dipole, which direction is always (0, 0, 1) in body |
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frame, is specified by --originsele. The new x-z plane is defined by |
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the direction of dipole and the StuntDouble is specified by --refsele. </td> |
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</tr> |
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<tr bgcolor="#ccff99"> |
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<td> |
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<blockquote> |
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<p>--refsele</p> |
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</blockquote> |
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</td> |
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</tr> |
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</tbody> |
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</table> |
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</ul> |
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<p> |
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</p> |
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<p><b><a name="within"></a> StaticProps<br> |
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</b></p> |
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StaticProps can compute properties which are averaged over the |
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configurations that are contained within a dump file. The |
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most common example of a static property that can be computed is the |
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pair distribution function between atoms of type A and other atoms of |
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type B, <span style="font-style: italic;">g<sub>AB</sub>(r)</span>. |
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StaticProps can also be used to compute the density distributions of |
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other molecules in a reference frame <span style="font-style: italic;">fixed |
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to the body-fixed reference frame</span> of a selected atom or rigid |
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body.<b><br> |
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</b> |
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<p> </p> |
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<p align="center"><img src="definition.jpg" height="540" width="720"></p> |
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<p align="left">There are five seperate radial distribution functions |
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availiable in OOPSE. Since every radial distrbution function invlove |
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the calculation between a pair, --sele1 and --sele2 must be given. |
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</p> |
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<ul> |
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<table bgcolor="#ffffff" border="1" cellpadding="5" width="890"> |
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<tbody> |
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<tr bgcolor="#ccffcc"> |
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<td width="191"> |
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<blockquote> |
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<p>option</p> |
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</blockquote> |
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</td> |
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<td width="667"> |
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<blockquote> |
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<div align="center">description</div> |
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</blockquote> |
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</td> |
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</tr> |
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<tr bgcolor="#ccffcc"> |
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<td> |
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<blockquote> |
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<p>--gofr</p> |
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</blockquote> |
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</td> |
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<td>Computes the pair distribution function.</td> |
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</tr> |
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<tr bgcolor="#ccffcc"> |
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<td> |
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<blockquote> |
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<p>--r_theta</p> |
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</blockquote> |
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</td> |
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<td>Computes the angle-dependent pair distribution function. |
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The |
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angle is defined by the intermolecular vector r and z-axis of |
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DirectionalAtom A.<br> |
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</td> |
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</tr> |
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<tr bgcolor="#ccffcc"> |
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<td> |
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<blockquote> |
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<p>--r_omega</p> |
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</blockquote> |
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</td> |
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<td>Computes an angle-dependent pair distribution function. The |
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angle is defined by the z-axes of the two DirectionalAtoms A and B.<br> |
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</td> |
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</tr> |
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<tr bgcolor="#ccffcc"> |
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<td> |
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<blockquote> |
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<p>--theta_omega</p> |
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</blockquote> |
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</td> |
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<td>Calculate the pair distribution of the two angles.</td> |
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</tr> |
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<tr bgcolor="#ccffcc"> |
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<td> |
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<blockquote> |
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<p>--gxyz</p> |
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</blockquote> |
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</td> |
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<td>Calculate the density distribution of particles |
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of type B in the body frame of particle A. Therefore, --originsele and |
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--refsele must be given to define A's internal coordinate set. </td> |
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</tr> |
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</tbody> |
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</table> |
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</ul> |
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<p> </p> |
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<p><b><a name="within"></a> DynamicProps<br> |
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<span style="font-weight: bold;"><br> |
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</span></b>DynamicProps computes time correlation functions from the |
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configurations stored in a dump file. Typical examples of time |
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correlation functions are the mean square displacement and the velocity |
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autocorrelation functions. <b><span style="font-weight: bold;"><br> |
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</span> </b></p> |
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<ul> |
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<table bgcolor="#ffffff" border="1" cellpadding="5" width="890"> |
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<tbody> |
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<tr bgcolor="#ccffcc"> |
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<td width="191"> |
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<p align="center">option</p> |
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</td> |
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<td width="667"> |
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<blockquote> |
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<div align="center">description</div> |
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</blockquote> |
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</td> |
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</tr> |
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<tr bgcolor="#ccffcc"> |
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<td> |
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<p align="center">--rcorr</p> |
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</td> |
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<td>mean square displacement </td> |
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</tr> |
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<tr bgcolor="#ccffcc"> |
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<td> |
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<p align="center">--vcorr</p> |
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</td> |
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<td>velocity autocorrelation function</td> |
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</tr> |
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<tr bgcolor="#ccffcc"> |
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<td> |
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<p align="center">--dcorr</p> |
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</td> |
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<td>dipole correlation function </td> |
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</tr> |
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</tbody> |
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</table> |
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</ul> |
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<p> |
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</p> |
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</body> |
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</html> |
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> |
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<html> |
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<head> |
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<title>Selection syntax for OOPSE utility programs</title> |
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</head> |
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<body style="background-color: white;"> |
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<basefont size="3"> |
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<div align="center"> |
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<p><font size="+2"><b>Selection syntax for OOPSE utility programs</b></font><span |
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style="font-weight: bold;"></span><br> |
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</p> |
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<h2 align="left"><a name="introduction" id="introduction"> Introduction |
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</a></h2> |
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<p style="text-align: left;">The OOPSE utility programs compute |
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> |
properties from the <span |
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style="font-family: monospace; font-weight: bold;">dump</span><span |
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style="font-weight: bold;"> |
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</span>files that are generated during a molecular dynamics |
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simulation. |
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These programs are:<br> |
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</p> |
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<ul style="text-align: left;"> |
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<li><span style="font-family: monospace; font-weight: bold;">Dump2XYZ</span><span |
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style="font-weight: bold;"> </span>- Converts an OOPSE dump file into |
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a file suitable |
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for viewing in a molecular dynamics viewer like <a |
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href="http://www.jmol.org">Jmol</a><br> |
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</li> |
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<li><span style="font-family: monospace; font-weight: bold;">StaticProps</span><span |
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style="font-weight: bold;"> </span>- Computes static properties like |
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the pair distribution function, <span style="font-style: italic;">g(r)</span>.<br> |
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</li> |
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<li><span style="font-family: monospace; font-weight: bold;">DynamicProps</span><span |
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style="font-weight: bold;"> </span>- Computes time correlation |
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> |
functions like the |
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> |
velocity autocorrelation function, <span style="font-style: italic;"><<span |
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> |
style="font-weight: bold;">v</span>(t)<span style="font-weight: bold;">v</span>(0)></span>, |
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> |
or the mean square displacement <span style="font-style: italic;"><|<span |
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> |
style="font-weight: bold;">r</span>(t) - <span |
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> |
style="font-weight: bold;">r</span>(0)|<sup>2</sup>>.</span></li> |
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> |
</ul> |
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> |
<div style="text-align: left;">These programs often need to operate on |
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> |
a subset of the data contained within a dump file. For example, |
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> |
if you want only the <span style="font-style: italic;">oxygen-oxygen</span> |
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> |
pair distribution from a water simulation, or if you want to make a |
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> |
movie including only the water molecules within a 6 angstrom radius of |
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> |
lipid head groups, you need a way to specify your selection to these |
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> |
utility programs. OOPSE has a selection syntax which allows |
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you to specify the selection in a compact form in order to generate |
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> |
only the data you want. For example a common use of the |
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StaticProps command would be:<br> |
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> |
<br> |
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<div style="margin-left: 80px;"><span |
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style="font-family: monospace; font-weight: bold;">StaticProps -i |
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tp4.dump --gofr --sele1="select O*" --sele2="select O*"</span><br> |
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</div> |
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<br> |
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This command computes the oxygen-oxygen pair distribution function, <span |
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style="font-style: italic;">g<sub>OO</sub>(r)</span>, from a file |
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> |
named <span style="font-family: monospace;">tp4.dump</span>. In |
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> |
order to understand this selection syntax and to make full use of the |
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> |
selection capabilities of the analysis programs, it is necessary to |
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understand a few of the core concepts that are used to perform |
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> |
simulations.<br> |
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> |
<h2><a name="Concepts"></a>Concepts</h2> |
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OOPSE manipulates both traditional atoms as well as some objects that <span |
67 |
> |
style="font-style: italic;">behave like atoms</span>. These |
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> |
objects can be rigid collections of atoms or atoms which have |
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> |
orientational degrees of freedom. Here is a diagram of the class |
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> |
heirarchy:<br> |
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<span style="font-style: italic;"></span></div> |
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<p align="center"><img src="classoopse_1_1StuntDouble.png" height="136" |
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> |
width="292"><br> |
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> |
</p> |
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> |
<ul style="text-align: left;"> |
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> |
<li>A <span style="font-family: monospace; font-weight: bold;">StuntDouble</span> |
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> |
is <span style="font-style: italic;">any</span> object that can be |
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> |
manipulated by the integrators and minimizers.</li> |
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> |
<li>An <span style="font-family: monospace; font-weight: bold;">Atom</span> |
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> |
is a fundamental point-particle that can be moved around during a |
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> |
simulation.</li> |
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> |
<li>A <span style="font-family: monospace; font-weight: bold;">DirectionalAtom</span> |
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> |
is an atom which has <span style="font-style: italic;">orientational</span> |
84 |
> |
as well as translational degrees of freedom.</li> |
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> |
<li>A <span style="font-family: monospace; font-weight: bold;">RigidBody</span> |
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> |
is a collection of <span |
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> |
style="font-family: monospace; font-weight: bold;">Atom</span>s or <span |
88 |
> |
style="font-family: monospace; font-weight: bold;">DirectionalAtom</span>s |
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> |
which behaves as a <span style="font-style: italic;">single unit.</span></li> |
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> |
</ul> |
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> |
<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> |
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> |
(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> |
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> |
</p> |
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> |
</div> |
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> |
<h2><a name="select"></a>Syntax of the Select Command</h2> |
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> |
The most general form of the select command is: <b>select <i>expression</i> |
105 |
> |
</b> |
106 |
> |
<p>This expression represents an arbitrary set of StuntDoubles (Atoms |
107 |
> |
or |
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> |
RigidBodies) in OOPSE. Expressions are composed of either name |
109 |
> |
expressions, index expression, predefined sets, user-defined |
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> |
expression, |
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> |
comparison operators, within expressions, or logical combinations of |
112 |
> |
the above expression types. Expression can be combined using |
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> |
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 |
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> |
simpler ones using the standard boolean connectives <b>and, or, not</b>. |
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> |
Parentheses can be used to alter the precedence of the operators. |
119 |
> |
</p> |
120 |
> |
<ul> |
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> |
<table bgcolor="#ffffff" border="1" cellpadding="5" width="441"> |
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> |
<tbody> |
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> |
<tr bgcolor="#ffccff"> |
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> |
<td width="174"> |
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<div align="left">logical operator </div> |
126 |
> |
</td> |
127 |
> |
<td width="241"> |
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> |
<div align="left">equivalent operator</div> |
129 |
> |
</td> |
130 |
> |
</tr> |
131 |
> |
<tr bgcolor="#ffccff"> |
132 |
> |
<td> |
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> |
<div align="left">and</div> |
134 |
> |
</td> |
135 |
> |
<td> |
136 |
> |
<div align="left">"&", "&&" </div> |
137 |
> |
</td> |
138 |
> |
</tr> |
139 |
> |
<tr bgcolor="#ffccff"> |
140 |
> |
<td> |
141 |
> |
<div align="left">or</div> |
142 |
> |
</td> |
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> |
<td> |
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> |
<div align="left">"|", "||", "," </div> |
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> |
</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> </p> |
158 |
> |
</ul> |
159 |
> |
<p><a name="name"><b> Name expression. |
160 |
> |
</b></a> </p> |
161 |
> |
<ul> |
162 |
> |
<table bgcolor="#ffffcc" border="1" bordercolor="#6b7683" width="886"> |
163 |
> |
<tbody> |
164 |
> |
<tr> |
165 |
> |
<td colspan="2"> |
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> |
<div align="center">expression</div> |
167 |
> |
</td> |
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> |
<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> </p> |
219 |
> |
</ul> |
220 |
> |
<p><a name="index" id="index"><b> Index expression </b></a></p> |
221 |
> |
<ul> |
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> |
238 |
> |
<p> </p> |
239 |
> |
<p><a name="predefine" id="predefine"><b> Predefined sets </b></a></p> |
240 |
> |
<ul> |
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> |
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> |
<div align="left">select none of the StuntDoubles </div> |
265 |
> |
</td> |
266 |
> |
</tr> |
267 |
> |
</tbody> |
268 |
> |
</table> |
269 |
> |
</ul> |
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> |
<p> </p> |
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> |
<p><a name="user" id="user"><b> User defined expressions</b></a></p> |
272 |
> |
<p> Users can define arbitrary terms to represent groups of |
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> |
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> |
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> |
<table bgcolor="#ffffff" border="1" cellpadding="5" width="659"> |
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<tbody> |
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<tr bgcolor="#ffffcc"> |
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> |
<td> |
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> |
<p>define SSDWATER SSD or SSD1 or SSDRF</p> |
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> |
<p>select SSDWATER </p> |
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> |
</td> |
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> |
</tr> |
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> |
</tbody> |
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> |
</table> |
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> |
</ul> |
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<p><a name="comparison" id="comparison"> <b>Comparison expression.</b></a></p> |
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<p>StuntDoubles can be selected by using comparision operators on |
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> |
their properties. The general form for the comparison command is: a |
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> |
property name, followed by a comparision operator and then a number.</p> |
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> |
<ul> |
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> |
<table bgcolor="#ffffff" border="1" cellpadding="5" width="668"> |
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> |
<tbody> |
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> |
<tr bgcolor="#ffccff"> |
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> |
<td width="305"> |
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> |
<div align="left">property</div> |
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> |
</td> |
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> |
<td width="331"> |
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> |
<div align="left">mass, charge </div> |
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> |
</td> |
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> |
</tr> |
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> |
<tr bgcolor="#ffccff"> |
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> |
<td> |
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> |
<div align="left">comparision operator</div> |
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> |
</td> |
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> |
<td> |
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> |
<div align="left">">", "<", "=", ">=", "<=", "!=" </div> |
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> |
</td> |
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> |
</tr> |
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> |
</tbody> |
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> |
</table> |
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> |
</ul> |
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> |
<ul> |
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> |
<table bgcolor="#ffffff" border="1" cellpadding="5" width="672"> |
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> |
<tbody> |
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> |
<tr bgcolor="#ffffcc"> |
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> |
<td width="302">select mass > 16.0 and charge < -2 </td> |
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> |
<td width="338">select StuntDoubles which have mass greater |
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> |
than |
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> |
16.0 and charges less than -2 </td> |
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> |
</tr> |
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> |
</tbody> |
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> |
</table> |
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> |
</ul> |
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> |
<p> </p> |
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> |
<p><b> <a name="within"></a> Within expression.</b> |
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> |
</p> |
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> |
<p> The "within" selection allows the user to select all StuntDoubles |
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> |
within the specified |
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> |
distance (in Angstroms) from a selection, including the selected atom |
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> |
itself. The |
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> |
general form for within selection is: <b>select within(<i>distance, |
336 |
> |
expression</i>) </b> |
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> |
</p> |
338 |
> |
<ul> |
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> |
<table bgcolor="#ffffff" border="1" cellpadding="5" width="681"> |
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> |
<tbody> |
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> |
<tr bgcolor="#ffffcc"> |
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> |
<td width="306">select within(2.5, PO4 or NC4) </td> |
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> |
<td width="343"> |
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> |
<blockquote>select all StuntDoubles which are within 2.5 |
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> |
angstroms of PO4 or NC4 atoms<br> |
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> |
</blockquote> |
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> |
</td> |
348 |
> |
</tr> |
349 |
> |
</tbody> |
350 |
> |
</table> |
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> |
</ul> |
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> |
<p> |
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> |
</p> |
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> |
<h2><a name="syntax" id="syntax"> Tools which use the selection command |
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> |
</a></h2> |
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> |
<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> |
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> |
<tr bgcolor="#6699ff"> |
364 |
> |
<td width="191"> |
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> |
<blockquote> |
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> |
<p>--selection</p> |
367 |
> |
</blockquote> |
368 |
> |
</td> |
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> |
<td width="667">Specifying --selection="selection command" with |
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> |
Dump2XYZ, user can select an arbitrary set of stuntdoubles to be |
371 |
> |
converted. </td> |
372 |
> |
</tr> |
373 |
> |
<tr bgcolor="#ccff99"> |
374 |
> |
<td> |
375 |
> |
<blockquote> |
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> |
<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. 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>. |
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> |
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> |
<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> </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. 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> |