/usr/share/doc/python-scientific/Reference/Scientific.Physics.Potential-module.html is in python-scientific-doc 2.8-2build1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 | <?xml version="1.0" encoding="ascii"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
<head>
<title>Scientific.Physics.Potential</title>
<link rel="stylesheet" href="epydoc.css" type="text/css" />
<script type="text/javascript" src="epydoc.js"></script>
</head>
<body bgcolor="white" text="black" link="blue" vlink="#204080"
alink="#204080">
<!-- ==================== NAVIGATION BAR ==================== -->
<table class="navbar" border="0" width="100%" cellpadding="0"
bgcolor="#a0c0ff" cellspacing="0">
<tr valign="middle">
<!-- Home link -->
<th> <a
href="Scientific-module.html">Home</a> </th>
<!-- Tree link -->
<th> <a
href="module-tree.html">Trees</a> </th>
<!-- Index link -->
<th> <a
href="identifier-index.html">Indices</a> </th>
<!-- Help link -->
<th> <a
href="help.html">Help</a> </th>
<!-- Project homepage -->
<th class="navbar" align="right" width="100%">
<table border="0" cellpadding="0" cellspacing="0">
<tr><th class="navbar" align="center"
><a class="navbar" target="_top" href="http://dirac.cnrs-orleans.fr/ScientificPython/">Scientific Python</a></th>
</tr></table></th>
</tr>
</table>
<table width="100%" cellpadding="0" cellspacing="0">
<tr valign="top">
<td width="100%">
<span class="breadcrumbs">
<a href="Scientific-module.html">Package Scientific</a> ::
<a href="Scientific.Physics-module.html">Package Physics</a> ::
Module Potential
</span>
</td>
<td>
<table cellpadding="0" cellspacing="0">
<!-- hide/show private -->
<tr><td align="right"><span class="options"
>[<a href="frames.html" target="_top">frames</a
>] | <a href="Scientific.Physics.Potential-module.html"
target="_top">no frames</a>]</span></td></tr>
</table>
</td>
</tr>
</table>
<!-- ==================== MODULE DESCRIPTION ==================== -->
<h1 class="epydoc">Module Potential</h1><p class="nomargin-top"></p>
<p>Potential energy functions with automatic gradient evaluation</p>
<p>This module offers two strategies for automagically calculating the
gradients (and optionally force constants) of a potential energy function
(or any other function of vectors, for that matter). The more convenient
strategy is to create an object of the class PotentialWithGradients. It
takes a regular Python function object defining the potential energy and
is itself a callable object returning the energy and its gradients with
respect to all arguments that are vectors.</p>
<p>Example:</p>
<pre class="literalblock">
>>>def _harmonic(k,r1,r2):
>>> dr = r2-r1
>>> return k*dr*dr
>>>harmonic = PotentialWithGradients(_harmonic)
>>>energy, gradients = harmonic(1., Vector(0,3,1), Vector(1,2,0))
>>>print energy, gradients
</pre>
<p>prints:</p>
<pre class="literalblock">
>>>3.0
>>>[Vector(-2.0,2.0,2.0), Vector(2.0,-2.0,-2.0)]
</pre>
<p>The disadvantage of this procedure is that if one of the arguments is
a vector parameter, rather than a position, an unnecessary gradient will
be calculated. A more flexible method is to insert calls to two function
from this module into the definition of the energy function. The first,
DerivVectors(), is called to indicate which vectors correspond to
gradients, and the second, EnergyGradients(), extracts energy and
gradients from the result of the calculation. The above example is
therefore equivalent to:</p>
<pre class="literalblock">
>>>def harmonic(k, r1, r2):
>>> r1, r2 = DerivVectors(r1, r2)
>>> dr = r2-r1
>>> e = k*dr*dr
>>> return EnergyGradients(e,2)
</pre>
<p>To include the force constant matrix, the above example has to be
modified as follows:</p>
<pre class="literalblock">
>>>def _harmonic(k,r1,r2):
>>> dr = r2-r1
>>> return k*dr*dr
>>>harmonic = PotentialWithGradientsAndForceConstants(_harmonic)
>>>energy, gradients, force_constants = harmonic(1.,Vector(0,3,1),Vector(1,2,0))
>>>print energy
>>>print gradients
>>>print force_constants
</pre>
<p>The force constants are returned as a nested list representing a
matrix. This can easily be converted to an array for further processing
if the numerical extensions to Python are available.</p>
<!-- ==================== CLASSES ==================== -->
<a name="section-Classes"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td align="left" colspan="2" class="table-header">
<span class="table-header">Classes</span></td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Scientific.Physics.Potential.PotentialWithGradients-class.html" class="summary-name">PotentialWithGradients</a>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Scientific.Physics.Potential.PotentialWithGradientsAndForceConstants-class.html" class="summary-name">PotentialWithGradientsAndForceConstants</a>
</td>
</tr>
</table>
<!-- ==================== FUNCTIONS ==================== -->
<a name="section-Functions"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td align="left" colspan="2" class="table-header">
<span class="table-header">Functions</span></td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="DerivVectors"></a><span class="summary-sig-name">DerivVectors</span>(<span class="summary-sig-arg">*args</span>)</span></td>
<td align="right" valign="top">
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="EnergyGradients"></a><span class="summary-sig-name">EnergyGradients</span>(<span class="summary-sig-arg">e</span>,
<span class="summary-sig-arg">n</span>)</span></td>
<td align="right" valign="top">
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="EnergyGradientsForceConstants"></a><span class="summary-sig-name">EnergyGradientsForceConstants</span>(<span class="summary-sig-arg">e</span>,
<span class="summary-sig-arg">n</span>)</span></td>
<td align="right" valign="top">
</td>
</tr>
</table>
</td>
</tr>
</table>
<!-- ==================== NAVIGATION BAR ==================== -->
<table class="navbar" border="0" width="100%" cellpadding="0"
bgcolor="#a0c0ff" cellspacing="0">
<tr valign="middle">
<!-- Home link -->
<th> <a
href="Scientific-module.html">Home</a> </th>
<!-- Tree link -->
<th> <a
href="module-tree.html">Trees</a> </th>
<!-- Index link -->
<th> <a
href="identifier-index.html">Indices</a> </th>
<!-- Help link -->
<th> <a
href="help.html">Help</a> </th>
<!-- Project homepage -->
<th class="navbar" align="right" width="100%">
<table border="0" cellpadding="0" cellspacing="0">
<tr><th class="navbar" align="center"
><a class="navbar" target="_top" href="http://dirac.cnrs-orleans.fr/ScientificPython/">Scientific Python</a></th>
</tr></table></th>
</tr>
</table>
<table border="0" cellpadding="0" cellspacing="0" width="100%%">
<tr>
<td align="left" class="footer">
Generated by Epydoc 3.0 on Tue Oct 28 14:16:00 2008
</td>
<td align="right" class="footer">
<a target="mainFrame" href="http://epydoc.sourceforge.net"
>http://epydoc.sourceforge.net</a>
</td>
</tr>
</table>
<script type="text/javascript">
<!--
// Private objects are initially displayed (because if
// javascript is turned off then we want them to be
// visible); but by default, we want to hide them. So hide
// them unless we have a cookie that says to show them.
checkCookie();
// -->
</script>
</body>
</html>
|