The scripts below  define new tcl procedures for  use  with the tcl  script
interpreter embedded into VMD. To activate them, you can load them by using
the "source" command. However  it is more convenient  to have VMD load them
automatically  on demand. To  do this, you need to  modify  your .vmdrc (or
vmd.rc) file (see the VMD User's Guide for details) and add the and adapted
version of the following code.

  # add local (auto-loaded) scripts to the interpreter search path
  set auto_path [concat $env(HOME)/lammps/tools/lmp2vmd $auto_path]

With this change the "source" command lines below are no longer needed.  If
you add new  files or procedures   to this directory, you  have  to run the
mkindex script to update the tclIndex file.

With  VMD one typically reads bonding  information from a topology file and
then reads a trajectory with the coordinate information on top of that. The
most common use is the  combination of a (CHARMM  or X-PLOR style) PSF file
and  a DCD file  (the latter can be  produced by LAMMPS  directly).  If the
bonding information is not   available, VMD uses   a heuristic guess  which
works  reasonably  well with  biological  systems, but  can be particularly
cumbersome     in  coarse grained  MD   or    similar model  systems.   The
lmpbonds2vmd.tcl script provides an option  to transfer bonding information
from a LAMMPS data file into VMD.

The script defines a new procedure "lmpbondsfromdata".  To activate it type
at the VMD command prompt:

  source lmpbonds2vmd.tcl

To then build a PSF file for use in subsequent  visualizations you can load
one just frame of a native LAMMPS trajectory (not binary, not custom!), for
example perusing the output from the micelle example.

  mol new dump.micelle type lammpstrj waitfor all
  lmpbondsfromdata [molinfo top] data.micelle

Now you should only see the bonds that actually have bonded interactions.

To  avoid having to run  the script all the time   you can save the bonding
information in an (incomplete) PSF file.

  animate write psf micelle.psf

In the future you can now load this PSF file first and then the LAMMPS dump
file(s) (or a more compact and faster loading DCD or XTC file) with:

  vmd micelle.psf -lammpstrj dump.micelle

The LAMMPS data file format  is quite flexible and thus  not always easy to
parse independently from context.  As a consequence,  the lmpbondsfromdata
parser may be confused by your specific setup.

First version. 2007, Axel Kohlmeyer <akohlmey@cmm.chem.upenn.edu>
Added a sanity check 03/2008, Axel Kohlmeyer <akohlmey@cmm.chem.upenn.edu>

LAMMPS dump files contain information about  the (numerical) atom type, but
not a molecule or residue id as it is typically  used in PSF or PDB files
to define subunits of a system. Adding this information can be very helpful
for analysis and post-processing of LAMMPS data in VMD.

The script defines a new  procedure "lmpresidfromdata". To activate it type
at the VMD command prompt:

  source lmpresid2vmd.tcl

To then add the residue information to a PSF file, see the steps for from
item 1 from above and then type into the VMD console.

  lmpresidfromdata [molinfo top] data.micelle

To  avoid having to run  the script all the time  you  can save the residue
information in an (incomplete) PSF file.

  animate write psf micelle2.psf

In the future you can now load this PSF file first and then the LAMMPS dump
file(s) (or a more compact and faster loading DCD or XTC file) with:

  vmd micelle2.psf -lammpstrj dump.micelle

You can use the residue information to join bonds split across the periodic
boundaries with:

  pbc join residue -all

and then enjoy a nice visualization of the micelle example with VMD. :)

The LAMMPS data file  format is quite flexible and  thus not always easy to
parse  independent from  context.  As a  consequence, the  lmpresidfromdata
parser may be confused by your specific setup.

First version. 2008, Axel Kohlmeyer <akohlmey@cmm.chem.upenn.edu>

LAMMPS dump files contain information about  the (numerical) atom type, but
not atom names like in PSF or PDB files. The names are used in VMD to guess
element, radius and (default) coloring. Adding this information can be very
helpful to set convenient defaults for visualization of LAMMPS data in VMD.

The script defines a new  procedure "lmptypetoname". To activate it type
at the VMD command prompt:

  source lmpname2vmd.tcl

To then add atom name information,  e.g., to a PSF  file, see the steps for
item 1 from above and then type into the VMD console.

  lmptypetoname [molinfo top] "SOL HDR TL1 TL2"

To avoid having to run the script all the time you can save the bonding
information in an (incomplete) PSF file.

  animate write psf micelle3.psf

In the future you can now load this PSF file first and then the LAMMPS dump
file(s) (or a more compact and faster loading DCD or XTC file) with:

  vmd micelle3.psf -lammpstrj dump.micelle

And you'll see that VMD will assign different colors to the atom types. You
cat get the previous coloring back by using the "Type" coloring scheme.

This script assumes the data  originates from a LAMMPS  dump file and  thus
the atoms types are numerical starting from 1. If  those have been modified
by some means, no name will be assigned.

First version. 2008, Axel Kohlmeyer <akohlmey@cmm.chem.upenn.edu>

The radii used for VDW and derived representations in VMD are guessed from 
the atom names. This script offers a convenient way to reset them (e.g. by
using the sigma parameters from matching LJ interactions).

The script defines a new  procedure "lmptypetoradius". To activate it type
at the VMD command prompt:

  source lmpradius2vmd.tcl

To then add atom radius information, see the steps for
item 1 from above and then type into the VMD console.

  lmptypetoradius [molinfo top] "1.00 1.00 0.75 0.50"

This script assumes the  data originates from  a LAMMPS dump file and  thus
the atoms types are numerical starting from 1. If  those have been modified
by some means, no name will be assigned. There is  currently no file format
that  exports the radius  information,  so  this script/command  has to  be
added, e.g., to "saved states" and other visualization scripts.

First version. 2008, Axel Kohlmeyer <akohlmey@cmm.chem.upenn.edu>