forked from lijiext/lammps
144 lines
5.6 KiB
HTML
144 lines
5.6 KiB
HTML
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<HTML>
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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</CENTER>
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<HR>
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<H3>fix imd command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>fix ID group-ID imd trate port keyword values ...
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</PRE>
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<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
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<LI>imd = style name of this fix command
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<LI>port = port number on which the fix listens for an IMD client
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<LI>keyword = <I>unwrap</I> or <I>fscale</I> or <I>trate</I>
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<PRE> <I>unwrap</I> arg = <I>on</I> or <I>off</I>
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off = coordinates are wrapped back into the principal unit cell (default)
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on = "unwrapped" coordinates using the image flags used
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<I>fscale</I> arg = factor
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factor = floating point number to scale IMD forces (default: 1.0)
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<I>trate</I> arg = transmission rate of coordinate data sets (default: 1)
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</PRE>
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>fix vmd all imd 5678
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fix comm all imd 8888 trate 5 unwrap on fscale 10.0
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>This fix implements the "Interactive MD" (IMD) protocol which allows
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to connect an IMD client, for example the VMD visualization program,
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to a running LAMMPS simulation and monitor the progress of the simulation
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and interactively apply forces to selected atoms.
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</P>
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<P>Upon initialization of the fix, it will open a communication port
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on the node with MPI task 0 and wait for an incoming connection.
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As soon as an IMD client is connected, the simulation will continue
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and the fix will send the current coordinates of the fix's group
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to the IMD client at every trate MD step. When using r-RESPA, trate
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applies to the steps of the outmost RESPA level.
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During a run with an active IMD connection also the IMD client can
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request to apply forces to selected atoms of the fix group.
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</P>
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<P>The port number selected must be an available network port number.
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On many machines, port numbers < 1024 are reserved for accounts with
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system manager privilege and specific applications. If multiple imd
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fixes would be active at the same time, each needs to use a different
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port number.
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</P>
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<P>The <I>trate</I> keyword allows to select how often the coordinate data
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is sent to the IMD client. It can also be changed on request of
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the IMD client through an IMD protocol message.
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The <I>unwrap</I> keyword allows to send "unwrapped" coordinates to
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the IMD client that undo the wrapping back of coordinates into
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the principle unit cell, as done by default in LAMMPS.
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The <I>fscale</I> keyword allows to apply a scaling factor to forces
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transmitted by the IMD client. The IMD protocols stipulates that
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forces are transferred in kcal/mol/angstrom under the assumption
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that coordinates are given in angstrom. For LAMMPS runs with
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different units or as a measure to tweak the forces generated
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by the manipulation of the IMD client, this option allows to
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make adjustments.
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</P>
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<P>To connect VMD to a waiting LAMMPS simulation on the same
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machine with fix imd enabled, one needs to start VMD and load
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a coordinate or topology file that matches the fix group.
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When the VMD command prompts appears, one types the command line:
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</P>
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<PRE>imd connect localhost 5678
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</PRE>
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<P>This assumes that <I>fix imd</I> was started with 5678 as a port
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number for the IMD protocol.
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</P>
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<P>The steps to do interactive manipulation of a running simulation
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in VMD are the following:
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</P>
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<P>In the Mouse menu of the VMD Main window, select "Mouse -> Force -> Atom".
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You may alternately select "Residue", or "Fragment" to apply forces to
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whole residues or fragments. Your mouse can now be used to apply forces
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to your simulation. Click on an atom, residue, or fragment and drag to
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apply a force. Click quickly without moving the mouse to turn the force
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off. You can also use a variety of 3D position trackers to apply forces
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to your simulation. Trackers with force-feedback such as the Sensable
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PHANTOM allow you to feel the forces you are applying to your molecules,
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as if they were real objects. See the <A HREF = "http://www.ks.uiuc.edu/Research/vmd/imd/">VMD IMD Homepage</A> for
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more details.
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</P>
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<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
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</P>
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<P>The fix does not write any information to restart files.
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</P>
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<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant
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to this fix.
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</P>
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<P>If IMD control messages are received, a line of text describing
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the message and its effect will be printed to the screen, if
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screen output is active.
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</P>
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<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
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the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
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minimization</A>.
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</P>
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<P><B>Restrictions:</B>
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</P>
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<P>This source code for this fix includes code developed by the
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Theoretical and Computational Biophysics Group in the Beckman
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Institute for Advanced Science and Technology at the University of
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Illinois at Urbana-Champaign.
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</P>
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<P>This fix is part of the "user-imd" package. It is only enabled if
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LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
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LAMMPS</A> section for more info.
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</P>
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<P>When used in combination with VMD, a topology or coordinate file
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has to be loaded, which matches in number and ordering of atoms
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the group the fix is applied to. The fix internally sorts atom
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IDs by ascending integer value; in VMD (and thus the IMD protocol)
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those will be assigned 0-based consecutive index numbers.
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</P>
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<P>When using multiple active IMD connections at the same time,
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each needs to use a different port number.
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</P>
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<P><B>Related commands:</B> none
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</P>
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<P><B>Default:</B> none
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</P>
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<HR>
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</HTML>
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