File: fix_efield.html

package info (click to toggle)
liggghts 3.8.0%2Brepack1-7
  • links: PTS, VCS
  • area: main
  • in suites: bullseye
  • size: 27,240 kB
  • sloc: cpp: 151,239; javascript: 9,132; sh: 910; python: 676; makefile: 459; ansic: 411
file content (372 lines) | stat: -rw-r--r-- 14,313 bytes parent folder | download | duplicates (5)
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
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372


<!DOCTYPE html>
<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
<head>
  <meta charset="utf-8">
  
  <meta name="viewport" content="width=device-width, initial-scale=1.0">
  
  <title>fix efield command &mdash; LIGGGHTS v3.X documentation</title>
  

  
  
  
  

  

  
  
    

  

  
  
    <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
  

  

  
    <link rel="top" title="LIGGGHTS v3.X documentation" href="index.html"/> 

  
  <script src="_static/js/modernizr.min.js"></script>

</head>

<body class="wy-body-for-nav" role="document">

   
  <div class="wy-grid-for-nav">

    
    <nav data-toggle="wy-nav-shift" class="wy-nav-side">
      <div class="wy-side-scroll">
        <div class="wy-side-nav-search">
          

          
            <a href="Manual.html" class="icon icon-home"> LIGGGHTS
          

          
          </a>

          
            
            
              <div class="version">
                v3.X
              </div>
            
          

          
<div role="search">
  <form id="rtd-search-form" class="wy-form" action="search.html" method="get">
    <input type="text" name="q" placeholder="Search docs" />
    <input type="hidden" name="check_keywords" value="yes" />
    <input type="hidden" name="area" value="default" />
  </form>
</div>

          
        </div>

        <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
          
            
            
              
            
            
              <ul>
<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_input_script.html">3. Input Script</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">4. Commands</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_gran_models.html">5. Contact models</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_mesh_modules.html">6. Mesh modules</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">7. Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">8. How-to discussions</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">9. Modifying &amp; extending LIGGGHTS(R)-PUBLIC</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_python.html">10. Python interface to LIGGGHTS(R)-PUBLIC</a></li>
<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">11. Errors</a></li>
</ul>

            
          
        </div>
      </div>
    </nav>

    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">

      
      <nav class="wy-nav-top" role="navigation" aria-label="top navigation">
        
          <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
          <a href="Manual.html">LIGGGHTS</a>
        
      </nav>


      
      <div class="wy-nav-content">
        <div class="rst-content">
          















<div role="navigation" aria-label="breadcrumbs navigation">

  <ul class="wy-breadcrumbs">
    
      <li><a href="Manual.html">Docs</a> &raquo;</li>
        
      <li>fix efield command</li>
    
    
      <li class="wy-breadcrumbs-aside">
        
            
            <a href="_sources/fix_efield.txt" rel="nofollow"> View page source</a>
          
          <a href="http://www.cfdem.com"> Website</a>
          
            <a href="Section_commands.html#comm" rel="nofollow"> Commands</a>
            
          
        
      </li>
    
  </ul>

  
  <hr/>
  
</div>
          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
           <div itemprop="articleBody">
            
  <div class="section" id="fix-efield-command">
<span id="index-0"></span><h1>fix efield command<a class="headerlink" href="#fix-efield-command" title="Permalink to this headline">¶</a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
<div class="highlight-python"><div class="highlight"><pre>fix ID group-ID efield ex ey ez keyword value ...
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><em>fix</em></a> command</li>
<li>efield = style name of this fix command</li>
<li>ex,ey,ez = E-field component values (electric field units)</li>
<li>any of ex,ey,ez can be a variable (see below)</li>
<li>zero or more keyword/value pairs may be appended to args</li>
<li>keyword = <em>region</em> or <em>energy</em></li>
</ul>
<pre class="literal-block">
<em>region</em> value = region-ID
  region-ID = ID of region atoms must be in to have added force
<em>energy</em> value = v_name
  v_name = variable with name that calculates the potential energy of each atom in the added E-field
</pre>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
<div class="highlight-python"><div class="highlight"><pre>fix kick external-field efield 1.0 0.0 0.0
fix kick external-field efield 0.0 0.0 v_oscillate
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
<p>Add a force F = qE to each charged atom in the group due to an
external electric field being applied to the system.  If the system
contains point-dipoles, also add a torque on the dipoles due to the
external electric field.</p>
<p>For charges, any of the 3 quantities defining the E-field components
can be specified as an equal-style or atom-style
<a class="reference internal" href="variable.html"><em>variable</em></a>, namely <em>ex</em>, <em>ey</em>, <em>ez</em>.  If the value is a
variable, it should be specified as v_name, where name is the variable
name.  In this case, the variable will be evaluated each timestep, and
its value used to determine the E-field component.</p>
<p>For point-dipoles, equal-style variables can be used, but atom-style
variables are not currently supported, since they imply a spatial
gradient in the electric field which means additional terms with
gradients of the field are required for the force and torque on
dipoles.</p>
<p>Equal-style variables can specify formulas with various mathematical
functions, and include <a class="reference internal" href="thermo_style.html"><em>thermo_style</em></a> command
keywords for the simulation box parameters and timestep and elapsed
time.  Thus it is easy to specify a time-dependent E-field.</p>
<p>Atom-style variables can specify the same formulas as equal-style
variables but can also include per-atom values, such as atom
coordinates.  Thus it is easy to specify a spatially-dependent E-field
with optional time-dependence as well.</p>
<p>If the <em>region</em> keyword is used, the atom must also be in the
specified geometric <a class="reference internal" href="region.html"><em>region</em></a> in order to have force added
to it.</p>
<hr class="docutils" />
<p>Adding a force or torque to atoms implies a change in their potential
energy as they move or rotate due to the applied E-field.</p>
<p>For dynamics via the &#8220;run&#8221; command, this energy can be optionally
added to the system&#8217;s potential energy for thermodynamic output (see
below).  For energy minimization via the &#8220;minimize&#8221; command, this
energy must be added to the system&#8217;s potential energy to formulate a
self-consistent minimization problem (see below).</p>
<p>The <em>energy</em> keyword is not allowed if the added field is a constant
vector (ex,ey,ez), with all components defined as numeric constants
and not as variables.  This is because LIGGGHTS(R)-PUBLIC can compute the energy
for each charged particle directly as E = -x dot qE = -q (x*ex + y*ey
+ z*ez), so that -Grad(E) = F.  Similarly for point-dipole particles
the energy can be computed as E = -mu dot E = -(mux*ex + muy*ey +
muz*ez).</p>
<p>The <em>energy</em> keyword is optional if the added force is defined with
one or more variables, and if you are performing dynamics via the
<a class="reference internal" href="run.html"><em>run</em></a> command.  If the keyword is not used, LIGGGHTS(R)-PUBLIC will set
the energy to 0.0, which is typically fine for dynamics.</p>
<p>The <em>energy</em> keyword is required if the added force is defined with
one or more variables, and you are performing energy minimization via
the &#8220;minimize&#8221; command for charged particles.  It is not required for
point-dipoles, but a warning is issued since the minimizer in LIGGGHTS(R)-PUBLIC
does not rotate dipoles, so you should not expect to be able to
minimize the orientation of dipoles in an applied electric field.</p>
<p>The <em>energy</em> keyword specifies the name of an atom-style
<a class="reference internal" href="variable.html"><em>variable</em></a> which is used to compute the energy of each
atom as function of its position.  Like variables used for <em>ex</em>, <em>ey</em>,
<em>ez</em>, the energy variable is specified as v_name, where name is the
variable name.</p>
<p>Note that when the <em>energy</em> keyword is used during an energy
minimization, you must insure that the formula defined for the
atom-style <a class="reference internal" href="variable.html"><em>variable</em></a> is consistent with the force
variable formulas, i.e. that -Grad(E) = F.  For example, if the force
due to the electric field were a spring-like F = kx, then the energy
formula should be E = -0.5kx^2.  If you don&#8217;t do this correctly, the
minimization will not converge properly.</p>
</div>
<hr class="docutils" />
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info<a class="headerlink" href="#restart-fix-modify-output-run-start-stop-minimize-info" title="Permalink to this headline">¶</a></h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>.</p>
<p>The <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> <em>energy</em> option is supported by this
fix to add the potential &#8220;energy&#8221; inferred by the added force due to
the electric field to the system&#8217;s potential energy as part of
<a class="reference internal" href="thermo_style.html"><em>thermodynamic output</em></a>.  This is a fictitious
quantity but is needed so that the <code class="xref doc docutils literal"><span class="pre">minimize</span></code> command
can include the forces added by this fix in a consistent manner.
I.e. there is a decrease in potential energy when atoms move in the
direction of the added force due to the electric field.</p>
<p>This fix computes a global scalar and a global 3-vector of forces,
which can be accessed by various <span class="xref std std-ref">output commands</span>.  The scalar is the potential
energy discussed above.  The vector is the total force added to the
group of atoms.  The scalar and vector values calculated by this fix
are &#8220;extensive&#8221;.</p>
<p>No parameter of this fix can be used with the <em>start/stop</em> keywords of
the <a class="reference internal" href="run.html"><em>run</em></a> command.</p>
<p>The forces due to this fix are imposed during an energy minimization,
invoked by the <code class="xref doc docutils literal"><span class="pre">minimize</span></code> command.  You should not
specify force components with a variable that has time-dependence for
use with a minimizer, since the minimizer increments the timestep as
the iteration count during the minimization.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">If you want the fictitious potential energy associated
with the added forces to be included in the total potential energy of
the system (the quantity being minimized), you MUST enable the
<a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> <em>energy</em> option for this fix.</p>
</div>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
<blockquote>
<div>none</div></blockquote>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
<p><a class="reference internal" href="fix_addforce.html"><em>fix addforce</em></a></p>
<p><strong>Default:</strong> none</p>
</div>
</div>


           </div>
           <div class="articleComments">
            
           </div>
          </div>
          <footer>
  

  <hr/>

  <div role="contentinfo">
    <p>
        &copy; Copyright 2016, DCS Computing GmbH, JKU Linz and Sandia Corporation.

    </p>
  </div>
  Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>. 

</footer>

        </div>
      </div>

    </section>

  </div>
  


  

    <script type="text/javascript">
        var DOCUMENTATION_OPTIONS = {
            URL_ROOT:'./',
            VERSION:'v3.X',
            LANGUAGE:'None',
            COLLAPSE_INDEX:false,
            FILE_SUFFIX:'.html',
            HAS_SOURCE:  true,
            SOURCELINK_SUFFIX: ''
        };
    </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>

  

  
  
    <script type="text/javascript" src="_static/js/theme.js"></script>
  

  
  
  <script type="text/javascript">
      jQuery(function () {
          SphinxRtdTheme.StickyNav.enable();
      });
  </script>
   

</body>
</html>