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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, 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>
|
| 319 |
|
|
<tr bgcolor="#ffffcc">
|
| 320 |
|
|
<td width="302">select mass > 16.0 and charge < -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> </p>
|
| 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 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>
|
| 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. 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>
|
| 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> </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>
|
