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  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_densorder</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 4.6<br>
  13 Sat 19 Jan 2013</B></td></tr></TABLE>
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  15 <H3>Description</H3>
  16 <p>
  17 A small program to reduce a two-phase density distribution
  18 along an axis, computed over a MD trajectory
  19 to 2D surfaces fluctuating in time, by a fit to
  20 a functional profile for interfacial densities
  21 A time-averaged spatial representation of the
  22 interfaces can be output with the option -tavg
  23 <P>
  24 <H3>Files</H3>
  25 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  26 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
  27 <TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">   topol.tpr</a></tt> </TD><TD> Input </TD><TD> Run input file: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
  28 <TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">    traj.xtc</a></tt> </TD><TD> Input </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
  29 <TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html">   index.ndx</a></tt> </TD><TD> Input </TD><TD> Index file </TD></TR>
  30 <TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="dat.html">Density4D.dat</a></tt> </TD><TD> Output, Opt. </TD><TD> Generic data file </TD></TR>
  31 <TR><TD ALIGN=RIGHT> <b><tt>-or</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="out.html">   hello.out</a></tt> </TD><TD> Output, Opt., Mult. </TD><TD> Generic output file </TD></TR>
  32 <TR><TD ALIGN=RIGHT> <b><tt>-og</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html">interface.xpm</a></tt> </TD><TD> Output, Opt., Mult. </TD><TD> X PixMap compatible matrix file </TD></TR>
  33 <TR><TD ALIGN=RIGHT> <b><tt>-Spect</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="out.html">intfspect.out</a></tt> </TD><TD> Output, Opt., Mult. </TD><TD> Generic output file </TD></TR>
  34 </TABLE>
  35 <P>
  36 <H3>Other options</H3>
  37 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
  38 <TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
  39 <TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Print help info and quit </TD></TD>
  40 <TR><TD ALIGN=RIGHT> <b><tt>-[no]version</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Print version info and quit </TD></TD>
  41 <TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
  42 <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>
  43 <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>
  44 <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>
  45 <TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> View output <tt>.<a href="xvg.html">xvg</a></tt>, <tt>.<a href="xpm.html">xpm</a></tt>, <tt>.<a href="eps.html">eps</a></tt> and <tt>.<a href="pdb.html">pdb</a></tt> files </TD></TD>
  46 <TR><TD ALIGN=RIGHT> <b><tt>-[no]1d</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no    </tt> </TD><TD> Pseudo-1d interface geometry </TD></TD>
  47 <TR><TD ALIGN=RIGHT> <b><tt>-bw</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.2   </tt> </TD><TD> Binwidth of density distribution tangential to interface </TD></TD>
  48 <TR><TD ALIGN=RIGHT> <b><tt>-bwn</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.05  </tt> </TD><TD> Binwidth of density distribution normal to interface </TD></TD>
  49 <TR><TD ALIGN=RIGHT> <b><tt>-order</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Order of Gaussian filter, order 0 equates to NO filtering </TD></TD>
  50 <TR><TD ALIGN=RIGHT> <b><tt>-axis</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt>Z</tt> </TD><TD> Axis Direction - X, Y or Z </TD></TD>
  51 <TR><TD ALIGN=RIGHT> <b><tt>-method</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>bisect</tt> </TD><TD> Interface location method: <tt>bisect</tt> or <tt>functional</tt> </TD></TD>
  52 <TR><TD ALIGN=RIGHT> <b><tt>-d1</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0     </tt> </TD><TD> Bulk density phase 1 (at small z) </TD></TD>
  53 <TR><TD ALIGN=RIGHT> <b><tt>-d2</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1000  </tt> </TD><TD> Bulk density phase 2 (at large z) </TD></TD>
  54 <TR><TD ALIGN=RIGHT> <b><tt>-tblock</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>100</tt> </TD><TD> Number of frames in one time-block average </TD></TD>
  55 <TR><TD ALIGN=RIGHT> <b><tt>-nlevel</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>100</tt> </TD><TD> Number of Height levels in 2D - XPixMaps </TD></TD>
  56 </TABLE>
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