This directory contains utility scripts for using VMD to visualize and

analyze LAMMPS trajectories (well, right now there is only two

scripts, but more are to come). Below are short descriptions and

examples on how to use them. Additional information on VMD as well as

additional scripts can be found at:

http://www.ks.uiuc.edu/Research/vmd/

The scripts here are maintained by Axel Kohlmeyer

<akohlmey@cmm.chem.upenn.edu>.

This directory contains utility scripts for using VMD to visualize and analyze

LAMMPS trajectories (hopefully in  the future this will  turn into a plugin or

proper  library).  Below are  short  descriptions and  examples  on how to use

them. Additional information on VMD as well as additional scripts can be found

at:   http://www.ks.uiuc.edu/Research/vmd/  

and:  http://www.theochem.rub.de/go/cpmd-vmd.html

The scripts are maintained by Axel Kohlmeyer <akohlmey@cmm.chem.upenn.edu>;

please contact him through the LAMMPS mailing list in case of problems.

-------------------------

0. Installation.

   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.

-------------------------

1a. Background.

   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. If the bonding information is not avaiable, VMD uses

   a heuristic guess, which does not always work, but can be particularly

   cumbersome in coarse grained MD or similar systems. The lmpbonds2vmd.tcl

   script provide an option to transfer bonding information from a LAMMPS data

   file into VMD.

1b. Usage 

   The script defines a new procedure "lmpbondsfromdata". To activate it

   type at the VMD command prompt:

   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.

1b. Usage.

   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 that can be used for subsequent

   visualizations you can load one frame of a native LAMMPS trajectory

   (not binary, not custom!), e.g. perusing the output from the

   micelle example.

   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 0 data.micelle

     lmpbondsfromdata [molinfo top] data.micelle

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

   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.

   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

   and now in the future you can load this psf file first and then 

   the dump file (or a more compact and faster loading .dcd or .xtc file).

   e.g., with:

   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

1c. Problems

   The data file format is quite flexible and thus not always easy to parse

   independent from context. As a consequence, the lmpbondsfromdata parser

   may be confused by your specific setup.

1c. Problems.

   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.

1d. History

   First version. 2007, axel kohlmeyer <akohlmey@cmm.chem.upenn.edu>

1d. History.

   First version. 2007, Axel Kohlmeyer <akohlmey@cmm.chem.upenn.edu>

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

-------------------------

2. lmpresid2vmd.tcl - translate residue information from a LAMMPS data

   file into VMD.

2. lmpresid2vmd.tcl - translate residue information from a LAMMPS data file 

   into VMD.

2a Background.  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 .pdf files to define subunits of a

   system. Adding this information can be very helpful for analysis

   and postprocessing of LAMMPS data in VMD.

2a. Background.  

   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.

2b Usage.

   The script defines a new procedure "lmpresidfromdata". To activate it

   type at the VMD command prompt:

2b. Usage.

   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

   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 0 data.micelle

     lmpresidfromdata [molinfo top] data.micelle

   to avoid having to run the script all the time you can save the bonding

   information in an (incomplete) .psf file.

   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

   and now in the future you can load this psf file first and then

   the dump file (or a more compact and faster loading .dcd or .xtc file).

   e.g., with:

   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

   now you can use the residue information to "join" the bonds split

   across the periodic boundaries with:

   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. :)

2c. Problems

   The 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.

2c. Problems.

   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.

2d. History.

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

-------------------------

3. lmpname2vmd.tcl - set atom names based on LAMMPS type in VMD.

3a. Background.  

   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.

3b. Usage.

   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.

3c. Problems.

   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.

3d. History.

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

-------------------------

4. lmpradius2vmd.tcl - set VdW radius based on LAMMPS type in VMD.

4a. Background.  

   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).

4b. Usage.

   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"

4c. Problems.

   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.

2d. History

   First version. 2008, axel kohlmeyer <akohlmey@cmm.chem.upenn.edu>

4d. History.

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

proc lmpbondsfromdata {mol filename} {

    if {"$mol" == "top"} {

        set mol [molinfo top]

    }

    # create an empty bondlist

    set na [molinfo $mol get numatoms]; # number of atoms

    set nb 0;                           # number of bonds

    # skip one line

    gets $fp line

    # read the bonds file

    # read the bonds data

    for {set i 0} {$i < $nb} {incr i} {

        gets $fp line

        # grep bond numbers from entry and adjust to VMD numbering style

        incr ba -1

        incr bb -1

        # sanity check

        if { ($ba > $na) || ($bb > $na) } {

            puts stderr "number of atoms in VMD molecule ($na) does not match data file"

            return -1

        }

        set bn [lindex $bl $ba]

        lappend bn $bb

        set bl [lreplace $bl $ba $ba $bn]

    set sel [atomselect $mol all]

    $sel setbonds $bl

    $sel delete

    return 0

}

# small script to assign atom names to type numbers in LAMMPS .

# (c) 2008 Axel Kohlmeyer <akohlmey@cmm.chem.upenn.edu>

proc lmptypetoname {mol names} {

    if {"$mol" == "top"} {

        set mol [molinfo top]

    }

    set t 0

    foreach n $names {

        incr t

        set sel [atomselect $mol "type $t"]

        $sel set name $n

        $sel delete

    }

    return 0

}

# small script to assign a radius by type number in VMD

# (c) 2008 Axel Kohlmeyer <akohlmey@cmm.chem.upenn.edu>

proc lmptypetoradius {mol rlist} {

    if {"$mol" == "top"} {

        set mol [molinfo top]

    }

    set t 0

    foreach r $rlist {

        incr t

        set sel [atomselect $mol "type $t"]

        $sel set radius $r

        $sel delete

    }

    return 0

}

proc lmpresidfromdata {mol filename} {

    if {"$mol" == "top"} {

        set mol [molinfo top]

    }

    # create an empty bondlist

    set na [molinfo $mol get numatoms]; # number of atoms of molecule

    set nb 0;                           # number of atoms in data file

    set bl {};                          # resid list

    set da 0;                           # number of atoms in data file

    set rl {};                          # resid list

    for {set i 0} {$i < $na} {incr i} {

        lappend bl 0

        lappend rl 0

    }

    # open lammps data file

    # read file line by line until we hit the Bonds keyword

    while {[gets $fp line] >= 0} {

        # pick number of bonds

        regexp {^\s*(\d+)\s+atoms} $line dummy nb

        # pick number of atoms

        regexp {^\s*(\d+)\s+atoms} $line dummy da

        if { [regexp {^\s*Atoms} $line] } {

            puts "atoms= $nb\n now reading Atoms section"

            # sanity check

            if {$na != $da} {

                puts stderr \

                    "number of atoms in VMD molecule ($na) does not match data file ($da)"

                return -1

            }

            puts "atoms= $da\nnow reading Atoms section"

            break

        }

    }

    # skip one line

    gets $fp line

    # read the Atoms data

    for {set i 0} {$i < $nb} {incr i} {

    for {set i 0} {$i < $da} {incr i} {

        gets $fp line

        # grep bond numbers from entry and adjust to VMD numbering style

        regexp {^\s*(\d+)\s+(\d+)\s+\d+.*} $line dummy ba bb

        incr ba -1

        lset bl $ba $bb

        lset rl $ba $bb

    }

    close $fp

    set sel [atomselect $mol all]

    $sel set resid $bl

    $sel set resid $rl

    $sel delete

}