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
|
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<title>MMTK.ForceFields.ForceFieldTest — MMTK User Guide 2.7.7 documentation</title>
<link rel="stylesheet" href="../../../_static/default.css" type="text/css" />
<link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../../../',
VERSION: '2.7.7',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
};
</script>
<script type="text/javascript" src="../../../_static/jquery.js"></script>
<script type="text/javascript" src="../../../_static/underscore.js"></script>
<script type="text/javascript" src="../../../_static/doctools.js"></script>
<link rel="top" title="MMTK User Guide 2.7.7 documentation" href="../../../index.html" />
<link rel="up" title="Module code" href="../../index.html" />
</head>
<body>
<div class="related">
<h3>Navigation</h3>
<ul>
<li class="right" style="margin-right: 10px">
<a href="../../../genindex.html" title="General Index"
accesskey="I">index</a></li>
<li class="right" >
<a href="../../../py-modindex.html" title="Python Module Index"
>modules</a> |</li>
<li><a href="../../../index.html">MMTK User Guide 2.7.7 documentation</a> »</li>
<li><a href="../../index.html" accesskey="U">Module code</a> »</li>
</ul>
</div>
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
<div class="body">
<h1>Source code for MMTK.ForceFields.ForceFieldTest</h1><div class="highlight"><pre>
<span class="c"># This module implements test functions.</span>
<span class="c">#</span>
<span class="c"># Written by Konrad Hinsen</span>
<span class="c">#</span>
<span class="sd">"""</span>
<span class="sd">Force field consistency tests</span>
<span class="sd">"""</span>
<span class="n">__docformat__</span> <span class="o">=</span> <span class="s">'restructuredtext'</span>
<span class="kn">from</span> <span class="nn">MMTK</span> <span class="kn">import</span> <span class="n">Utility</span>
<span class="kn">from</span> <span class="nn">Scientific.Geometry</span> <span class="kn">import</span> <span class="n">Vector</span><span class="p">,</span> <span class="n">ex</span><span class="p">,</span> <span class="n">ey</span><span class="p">,</span> <span class="n">ez</span>
<span class="kn">from</span> <span class="nn">Scientific</span> <span class="kn">import</span> <span class="n">N</span>
<span class="kn">import</span> <span class="nn">itertools</span>
<span class="c">#</span>
<span class="c"># Check consistency of energies and gradients.</span>
<span class="c">#</span>
<div class="viewcode-block" id="gradientTest"><a class="viewcode-back" href="../../../modules.html#MMTK.ForceFields.ForceFieldTest.gradientTest">[docs]</a><span class="k">def</span> <span class="nf">gradientTest</span><span class="p">(</span><span class="n">universe</span><span class="p">,</span> <span class="n">atoms</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="n">delta</span> <span class="o">=</span> <span class="mf">0.0001</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Test gradients by comparing to numerical derivatives of the energy.</span>
<span class="sd"> :param universe: the universe on which the test is performed</span>
<span class="sd"> :type universe: :class:`~MMTK.Universe.Universe`</span>
<span class="sd"> :param atoms: the atoms of the universe for which the gradient</span>
<span class="sd"> is tested (default: all atoms)</span>
<span class="sd"> :type atoms: list</span>
<span class="sd"> :param delta: the step size used in calculating the numerical derivatives</span>
<span class="sd"> :type delta: float</span>
<span class="sd"> """</span>
<span class="n">e0</span><span class="p">,</span> <span class="n">grad</span> <span class="o">=</span> <span class="n">universe</span><span class="o">.</span><span class="n">energyAndGradients</span><span class="p">()</span>
<span class="k">print</span> <span class="s">'Energy: '</span><span class="p">,</span> <span class="n">e0</span>
<span class="k">if</span> <span class="n">atoms</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">atoms</span> <span class="o">=</span> <span class="n">universe</span><span class="o">.</span><span class="n">atomList</span><span class="p">()</span>
<span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">atoms</span><span class="p">:</span>
<span class="k">print</span> <span class="n">a</span>
<span class="k">print</span> <span class="n">grad</span><span class="p">[</span><span class="n">a</span><span class="p">]</span>
<span class="n">num_grad</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">v</span> <span class="ow">in</span> <span class="p">[</span><span class="n">ex</span><span class="p">,</span> <span class="n">ey</span><span class="p">,</span> <span class="n">ez</span><span class="p">]:</span>
<span class="n">x</span> <span class="o">=</span> <span class="n">a</span><span class="o">.</span><span class="n">position</span><span class="p">()</span>
<span class="n">a</span><span class="o">.</span><span class="n">setPosition</span><span class="p">(</span><span class="n">x</span><span class="o">+</span><span class="n">delta</span><span class="o">*</span><span class="n">v</span><span class="p">)</span>
<span class="n">eplus</span> <span class="o">=</span> <span class="n">universe</span><span class="o">.</span><span class="n">energy</span><span class="p">()</span>
<span class="n">a</span><span class="o">.</span><span class="n">setPosition</span><span class="p">(</span><span class="n">x</span><span class="o">-</span><span class="n">delta</span><span class="o">*</span><span class="n">v</span><span class="p">)</span>
<span class="n">eminus</span> <span class="o">=</span> <span class="n">universe</span><span class="o">.</span><span class="n">energy</span><span class="p">()</span>
<span class="n">a</span><span class="o">.</span><span class="n">setPosition</span><span class="p">(</span><span class="n">x</span><span class="p">)</span>
<span class="n">num_grad</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="mf">0.5</span><span class="o">*</span><span class="p">(</span><span class="n">eplus</span><span class="o">-</span><span class="n">eminus</span><span class="p">)</span><span class="o">/</span><span class="n">delta</span><span class="p">)</span>
<span class="k">print</span> <span class="n">Vector</span><span class="p">(</span><span class="n">num_grad</span><span class="p">)</span>
<span class="c">#</span>
<span class="c"># Check consistency of gradients and force constants.</span>
<span class="c">#</span></div>
<div class="viewcode-block" id="forceConstantTest"><a class="viewcode-back" href="../../../modules.html#MMTK.ForceFields.ForceFieldTest.forceConstantTest">[docs]</a><span class="k">def</span> <span class="nf">forceConstantTest</span><span class="p">(</span><span class="n">universe</span><span class="p">,</span> <span class="n">atoms</span> <span class="o">=</span> <span class="bp">None</span><span class="p">,</span> <span class="n">delta</span> <span class="o">=</span> <span class="mf">0.0001</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Test force constants by comparing to the numerical derivatives</span>
<span class="sd"> of the gradients.</span>
<span class="sd"> :param universe: the universe on which the test is performed</span>
<span class="sd"> :type universe: :class:`~MMTK.Universe.Universe`</span>
<span class="sd"> :param atoms: the atoms of the universe for which the gradient</span>
<span class="sd"> is tested (default: all atoms)</span>
<span class="sd"> :type atoms: list</span>
<span class="sd"> :param delta: the step size used in calculating the numerical derivatives</span>
<span class="sd"> :type delta: float</span>
<span class="sd"> """</span>
<span class="n">e0</span><span class="p">,</span> <span class="n">grad0</span><span class="p">,</span> <span class="n">fc</span> <span class="o">=</span> <span class="n">universe</span><span class="o">.</span><span class="n">energyGradientsAndForceConstants</span><span class="p">()</span>
<span class="k">if</span> <span class="n">atoms</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
<span class="n">atoms</span> <span class="o">=</span> <span class="n">universe</span><span class="o">.</span><span class="n">atomList</span><span class="p">()</span>
<span class="k">for</span> <span class="n">a1</span><span class="p">,</span> <span class="n">a2</span> <span class="ow">in</span> <span class="n">itertools</span><span class="o">.</span><span class="n">chain</span><span class="p">(</span><span class="n">itertools</span><span class="o">.</span><span class="n">izip</span><span class="p">(</span><span class="n">atoms</span><span class="p">,</span> <span class="n">atoms</span><span class="p">),</span>
<span class="n">Utility</span><span class="o">.</span><span class="n">pairs</span><span class="p">(</span><span class="n">atoms</span><span class="p">)):</span>
<span class="k">print</span> <span class="n">a1</span><span class="p">,</span> <span class="n">a2</span>
<span class="k">print</span> <span class="n">fc</span><span class="p">[</span><span class="n">a1</span><span class="p">,</span> <span class="n">a2</span><span class="p">]</span>
<span class="n">num_fc</span> <span class="o">=</span> <span class="p">[]</span>
<span class="k">for</span> <span class="n">v</span> <span class="ow">in</span> <span class="p">[</span><span class="n">ex</span><span class="p">,</span> <span class="n">ey</span><span class="p">,</span> <span class="n">ez</span><span class="p">]:</span>
<span class="n">x</span> <span class="o">=</span> <span class="n">a1</span><span class="o">.</span><span class="n">position</span><span class="p">()</span>
<span class="n">a1</span><span class="o">.</span><span class="n">setPosition</span><span class="p">(</span><span class="n">x</span><span class="o">+</span><span class="n">delta</span><span class="o">*</span><span class="n">v</span><span class="p">)</span>
<span class="n">e_plus</span><span class="p">,</span> <span class="n">grad_plus</span> <span class="o">=</span> <span class="n">universe</span><span class="o">.</span><span class="n">energyAndGradients</span><span class="p">()</span>
<span class="n">a1</span><span class="o">.</span><span class="n">setPosition</span><span class="p">(</span><span class="n">x</span><span class="o">-</span><span class="n">delta</span><span class="o">*</span><span class="n">v</span><span class="p">)</span>
<span class="n">e_minus</span><span class="p">,</span> <span class="n">grad_minus</span> <span class="o">=</span> <span class="n">universe</span><span class="o">.</span><span class="n">energyAndGradients</span><span class="p">()</span>
<span class="n">a1</span><span class="o">.</span><span class="n">setPosition</span><span class="p">(</span><span class="n">x</span><span class="p">)</span>
<span class="n">num_fc</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="mf">0.5</span><span class="o">*</span><span class="p">(</span><span class="n">grad_plus</span><span class="p">[</span><span class="n">a2</span><span class="p">]</span><span class="o">-</span><span class="n">grad_minus</span><span class="p">[</span><span class="n">a2</span><span class="p">])</span><span class="o">/</span><span class="n">delta</span><span class="p">)</span>
<span class="k">print</span> <span class="n">N</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="k">lambda</span> <span class="n">a</span><span class="p">:</span> <span class="n">a</span><span class="o">.</span><span class="n">array</span><span class="p">,</span> <span class="n">num_fc</span><span class="p">))</span>
<span class="c">#</span>
<span class="c"># Check consistency of gradients and virial</span>
<span class="c">#</span></div>
<div class="viewcode-block" id="virialTest"><a class="viewcode-back" href="../../../modules.html#MMTK.ForceFields.ForceFieldTest.virialTest">[docs]</a><span class="k">def</span> <span class="nf">virialTest</span><span class="p">(</span><span class="n">universe</span><span class="p">):</span>
<span class="sd">"""</span>
<span class="sd"> Test the virial by comparing to an explicit computation from</span>
<span class="sd"> positions and gradients.</span>
<span class="sd"> :param universe: the universe on which the test is performed</span>
<span class="sd"> :type universe: :class:`~MMTK.Universe.Universe`</span>
<span class="sd"> """</span>
<span class="n">ev</span> <span class="o">=</span> <span class="n">universe</span><span class="o">.</span><span class="n">energyEvaluator</span><span class="p">()</span>
<span class="n">e</span><span class="p">,</span> <span class="n">grad</span> <span class="o">=</span> <span class="n">ev</span><span class="p">(</span><span class="n">gradients</span> <span class="o">=</span> <span class="bp">True</span><span class="p">)</span>
<span class="n">virial</span> <span class="o">=</span> <span class="n">ev</span><span class="o">.</span><span class="n">lastVirial</span><span class="p">()</span>
<span class="n">conf</span> <span class="o">=</span> <span class="n">universe</span><span class="o">.</span><span class="n">configuration</span><span class="p">()</span>
<span class="k">print</span> <span class="n">virial</span><span class="p">,</span> <span class="o">-</span><span class="p">(</span><span class="n">conf</span><span class="o">*</span><span class="n">grad</span><span class="p">)</span><span class="o">.</span><span class="n">sumOverParticles</span><span class="p">()</span>
</div>
<span class="k">if</span> <span class="n">__name__</span> <span class="o">==</span> <span class="s">'__main__'</span><span class="p">:</span>
<span class="kn">from</span> <span class="nn">MMTK</span> <span class="kn">import</span> <span class="o">*</span>
<span class="kn">from</span> <span class="nn">MMTK.ForceFields</span> <span class="kn">import</span> <span class="n">Amber94ForceField</span>
<span class="n">delta</span> <span class="o">=</span> <span class="mf">0.001</span>
<span class="n">world</span> <span class="o">=</span> <span class="n">InfiniteUniverse</span><span class="p">(</span><span class="n">Amber94ForceField</span><span class="p">())</span>
<span class="n">m</span> <span class="o">=</span> <span class="n">Molecule</span><span class="p">(</span><span class="s">'water'</span><span class="p">)</span>
<span class="n">m</span><span class="o">.</span><span class="n">O</span><span class="o">.</span><span class="n">translateBy</span><span class="p">(</span><span class="n">Vector</span><span class="p">(</span><span class="mf">0.</span><span class="p">,</span><span class="mf">0.</span><span class="p">,</span><span class="mf">0.01</span><span class="p">))</span>
<span class="n">m</span><span class="o">.</span><span class="n">H1</span><span class="o">.</span><span class="n">translateBy</span><span class="p">(</span><span class="n">Vector</span><span class="p">(</span><span class="mf">0.01</span><span class="p">,</span><span class="mf">0.</span><span class="p">,</span><span class="mf">0.</span><span class="p">))</span>
<span class="n">atoms</span> <span class="o">=</span> <span class="bp">None</span>
<span class="n">world</span><span class="o">.</span><span class="n">addObject</span><span class="p">(</span><span class="n">m</span><span class="p">)</span>
<span class="n">gradientTest</span><span class="p">(</span><span class="n">world</span><span class="p">,</span> <span class="n">atoms</span><span class="p">,</span> <span class="n">delta</span><span class="p">)</span>
<span class="n">forceConstantTest</span><span class="p">(</span><span class="n">world</span><span class="p">,</span> <span class="n">atoms</span><span class="p">,</span> <span class="n">delta</span><span class="p">)</span>
<span class="n">virialTest</span><span class="p">(</span><span class="n">world</span><span class="p">)</span>
</pre></div>
</div>
</div>
</div>
<div class="sphinxsidebar">
<div class="sphinxsidebarwrapper">
<div id="searchbox" style="display: none">
<h3>Quick search</h3>
<form class="search" action="../../../search.html" method="get">
<input type="text" name="q" />
<input type="submit" value="Go" />
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
<p class="searchtip" style="font-size: 90%">
Enter search terms or a module, class or function name.
</p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
</div>
<div class="clearer"></div>
</div>
<div class="related">
<h3>Navigation</h3>
<ul>
<li class="right" style="margin-right: 10px">
<a href="../../../genindex.html" title="General Index"
>index</a></li>
<li class="right" >
<a href="../../../py-modindex.html" title="Python Module Index"
>modules</a> |</li>
<li><a href="../../../index.html">MMTK User Guide 2.7.7 documentation</a> »</li>
<li><a href="../../index.html" >Module code</a> »</li>
</ul>
</div>
<div class="footer">
© Copyright 2010, Konrad Hinsen.
Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.1.3.
</div>
</body>
</html>
|
