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  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_dielectric</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
  12 </TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.5<br>
  13 Thu 26 Aug 2010</B></td></tr></TABLE>
  14 <HR>
  15 <H3>Description</H3>
  16 <p>
  17 dielectric calculates frequency dependent dielectric constants
  18 from the autocorrelation function of the total dipole moment in
  19 your simulation. This ACF can be generated by <a href="g_dipoles.html">g_dipoles</a>.
  20 For an estimate of the error you can run g_statistics on the
  21 ACF, and use the output thus generated for this program.
  22 The functional forms of the available functions are:<p>
  23 One parameter  : y = Exp[-a1 x],
  24 Two parameters : y = a2 Exp[-a1 x],
  25 Three parameters: y = a2 Exp[-a1 x] + (1 - a2) Exp[-a3 x].
  26 Start values for the fit procedure can be given on the command line.
  27 It is also possible to fix parameters at their start value, use -fix
  28 with the number of the parameter you want to fix.
  29 <p>
  30 Three output files are generated, the first contains the ACF,
  31 an exponential fit to it with 1, 2 or 3 parameters, and the
  32 numerical derivative of the combination data/fit.
  33 The second file contains the real and imaginary parts of the
  34 frequency-dependent dielectric constant, the last gives a plot
  35 known as the Cole-Cole plot, in which the imaginary
  36 component is plotted as a function of the real component.
  37 For a pure exponential relaxation (Debye relaxation) the latter
  38 plot should be one half of a circle.
  39 <P>
  40 <H3>Files</H3>
  41 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  42 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
  43 <TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> dipcorr.xvg</a></tt> </TD><TD> Input </TD><TD> xvgr/xmgr file </TD></TR>
  44 <TR><TD ALIGN=RIGHT> <b><tt>-d</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">   deriv.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  45 <TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">    epsw.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  46 <TR><TD ALIGN=RIGHT> <b><tt>-c</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">    cole.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
  47 </TABLE>
  48 <P>
  49 <H3>Other options</H3>
  50 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  51 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
  52 <TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Print help info and quit </TD></TD>
  53 <TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Print version info and quit </TD></TD>
  54 <TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
  55 <TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
  56 <TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
  57 <TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
  58 <TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
  59 <TR><TD ALIGN=RIGHT> <b><tt>-xvg</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>xmgrace</tt> </TD><TD> <a href="xvg.html">xvg</a> plot formatting: <tt>xmgrace</tt>, <tt>xmgr</tt> or <tt>none</tt> </TD></TD>
  60 <TR><TD ALIGN=RIGHT> <b><tt>-[no]fft</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> use fast fourier transform for correlation function </TD></TD>
  61 <TR><TD ALIGN=RIGHT> <b><tt>-[no]x1</tt></b> </TD><TD ALIGN=RIGHT> gmx_bool </TD><TD ALIGN=RIGHT> <tt>yes   </tt> </TD><TD> use first column as X axis rather than first data set </TD></TD>
  62 <TR><TD ALIGN=RIGHT> <b><tt>-eint</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>5     </tt> </TD><TD> Time were to end the integration of the data and start to use the fit </TD></TD>
  63 <TR><TD ALIGN=RIGHT> <b><tt>-bfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>5     </tt> </TD><TD> Begin time of fit </TD></TD>
  64 <TR><TD ALIGN=RIGHT> <b><tt>-efit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>500   </tt> </TD><TD> End time of fit </TD></TD>
  65 <TR><TD ALIGN=RIGHT> <b><tt>-tail</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>500   </tt> </TD><TD> Length of function including data and tail from fit </TD></TD>
  66 <TR><TD ALIGN=RIGHT> <b><tt>-A</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.5   </tt> </TD><TD> Start value for fit parameter A </TD></TD>
  67 <TR><TD ALIGN=RIGHT> <b><tt>-tau1</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>10    </tt> </TD><TD> Start value for fit parameter tau1 </TD></TD>
  68 <TR><TD ALIGN=RIGHT> <b><tt>-tau2</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1     </tt> </TD><TD> Start value for fit parameter tau2 </TD></TD>
  69 <TR><TD ALIGN=RIGHT> <b><tt>-eps0</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>80    </tt> </TD><TD> Epsilon 0 of your liquid </TD></TD>
  70 <TR><TD ALIGN=RIGHT> <b><tt>-epsRF</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>78.5  </tt> </TD><TD> Epsilon of the reaction field used in your simulation. A value of 0 means infinity. </TD></TD>
  71 <TR><TD ALIGN=RIGHT> <b><tt>-fix</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Fix parameters at their start values, A (2), tau1 (1), or tau2 (4) </TD></TD>
  72 <TR><TD ALIGN=RIGHT> <b><tt>-ffn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: <tt>none</tt>, <tt>exp</tt>, <tt>aexp</tt>, <tt>exp_exp</tt>, <tt>vac</tt>, <tt>exp5</tt>, <tt>exp7</tt> or <tt>exp9</tt> </TD></TD>
  73 <TR><TD ALIGN=RIGHT> <b><tt>-nsmooth</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>3</tt> </TD><TD> Number of points for smoothing </TD></TD>
  74 </TABLE>
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