fix imd command

Syntax

fix ID group-ID imd trate port keyword values ...

• ID, group-ID are documented in fix command

• imd = style name of this fix command

• port = port number on which the fix listens for an IMD client

• keyword = unwrap or fscale or trate

unwrap arg = on or off
off = coordinates are wrapped back into the principal unit cell (default)
on = "unwrapped" coordinates using the image flags used
fscale arg = factor
factor = floating point number to scale IMD forces (default: 1.0)
trate arg = transmission rate of coordinate data sets (default: 1)
nowait arg = on or off
off = LAMMPS waits to be connected to an IMD client before continuing (default)
on = LAMMPS listens for an IMD client, but continues with the run


Examples

fix vmd all imd 5678
fix comm all imd 8888 trate 5 unwrap on fscale 10.0


Description

This fix implements the “Interactive MD” (IMD) protocol which allows realtime visualization and manipulation of MD simulations through the IMD protocol, as initially implemented in VMD and NAMD. Specifically it allows LAMMPS to connect an IMD client, for example the VMD visualization program, so that it can monitor the progress of the simulation and interactively apply forces to selected atoms.

If LAMMPS is compiled with the pre-processor flag -DLAMMPS_ASYNC_IMD then fix imd will use POSIX threads to spawn a IMD communication thread on MPI rank 0 in order to offload data reading and writing from the main execution thread and potentially lower the inferred latencies for slow communication links. This feature has only been tested under linux.

There are example scripts for using this package with LAMMPS in examples/USER/imd. Additional examples and a driver for use with the Novint Falcon game controller as haptic device can be found at: http://sites.google.com/site/akohlmey/software/vrpn-icms.

The source code for this fix includes code developed by the Theoretical and Computational Biophysics Group in the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign. We thank them for providing a software interface that allows codes like LAMMPS to hook to VMD.

Upon initialization of the fix, it will open a communication port on the node with MPI task 0 and wait for an incoming connection. As soon as an IMD client is connected, the simulation will continue and the fix will send the current coordinates of the fix’s group to the IMD client at every trate MD step. When using r-RESPA, trate applies to the steps of the outmost RESPA level. During a run with an active IMD connection also the IMD client can request to apply forces to selected atoms of the fix group.

The port number selected must be an available network port number. On many machines, port numbers < 1024 are reserved for accounts with system manager privilege and specific applications. If multiple imd fixes would be active at the same time, each needs to use a different port number.

The nowait keyword controls the behavior of the fix when no IMD client is connected. With the default setting of off, LAMMPS will wait until a connection is made before continuing with the execution. Setting nowait to on will have the LAMMPS code be ready to connect to a client, but continue with the simulation. This can for example be used to monitor the progress of an ongoing calculation without the need to be permanently connected or having to download a trajectory file.

The trate keyword allows to select how often the coordinate data is sent to the IMD client. It can also be changed on request of the IMD client through an IMD protocol message. The unwrap keyword allows to send “unwrapped” coordinates to the IMD client that undo the wrapping back of coordinates into the principle unit cell, as done by default in LAMMPS. The fscale keyword allows to apply a scaling factor to forces transmitted by the IMD client. The IMD protocols stipulates that forces are transferred in kcal/mol/angstrom under the assumption that coordinates are given in angstrom. For LAMMPS runs with different units or as a measure to tweak the forces generated by the manipulation of the IMD client, this option allows to make adjustments.

To connect VMD to a listening LAMMPS simulation on the same machine with fix imd enabled, one needs to start VMD and load a coordinate or topology file that matches the fix group. When the VMD command prompts appears, one types the command line:

imd connect localhost 5678


This assumes that fix imd was started with 5678 as a port number for the IMD protocol.

The steps to do interactive manipulation of a running simulation in VMD are the following:

In the Mouse menu of the VMD Main window, select “Mouse -> Force -> Atom”. You may alternately select “Residue”, or “Fragment” to apply forces to whole residues or fragments. Your mouse can now be used to apply forces to your simulation. Click on an atom, residue, or fragment and drag to apply a force. Click quickly without moving the mouse to turn the force off. You can also use a variety of 3D position trackers to apply forces to your simulation. Game controllers or haptic devices with force-feedback such as the Novint Falcon or Sensable PHANTOM allow you to feel the resistance due to inertia or interactions with neighbors that the atoms experience you are trying to move, as if they were real objects. See the VMD IMD Homepage and the VRPN-ICMS Homepage for more details.

If IMD control messages are received, a line of text describing the message and its effect will be printed to the LAMMPS output screen, if screen output is active.

Restart, fix_modify, output, run start/stop, minimize info:

No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix. No global scalar or vector or per-atom quantities are stored by this fix for access by various output commands. No parameter of this fix can be used with the start/stop keywords of the run command. This fix is not invoked during energy minimization.

Restrictions

This fix is part of the USER-MISC package. It is only enabled if LAMMPS was built with that package. See the Build package doc page for more info.

When used in combination with VMD, a topology or coordinate file has to be loaded, which matches (in number and ordering of atoms) the group the fix is applied to. The fix internally sorts atom IDs by ascending integer value; in VMD (and thus the IMD protocol) those will be assigned 0-based consecutive index numbers.

When using multiple active IMD connections at the same time, each needs to use a different port number.

Related commands: none

Default: none