git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3996 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
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This directory contains utility scripts for using VMD to visualize and analyze
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LAMMPS trajectories (hopefully in the future this will turn into a plugin or
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proper library). Below are short descriptions and examples on how to use
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them. Additional information on VMD as well as additional scripts can be found
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at: http://www.ks.uiuc.edu/Research/vmd/
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and: http://www.theochem.rub.de/go/cpmd-vmd.html
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The scripts are maintained by Axel Kohlmeyer <akohlmey@cmm.chem.upenn.edu>;
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please contact him through the LAMMPS mailing list in case of problems.
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-------------------------
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0. Installation.
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The scripts below define new tcl procedures for use with the tcl script
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interpreter embedded into VMD. To activate them, you can load them by using
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the "source" command. However it is more convenient to have VMD load them
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automatically on demand. To do this, you need to modify your .vmdrc (or
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vmd.rc) file (see the VMD User's Guide for details) and add the and adapted
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version of the following code.
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# add local (auto-loaded) scripts to the interpreter search path
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set auto_path [concat $env(HOME)/lammps/tools/lmp2vmd $auto_path]
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With this change the "source" command lines below are no longer needed. If
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you add new files or procedures to this directory, you have to run the
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mkindex script to update the tclIndex file.
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-------------------------
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1. lmpbonds2vmd.tcl - translate bonding information from a LAMMPS data
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file into VMD.
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1a. Background.
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With VMD one typically reads bonding information from a topology file and
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then reads a trajectory with the coordinate information on top of that. The
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most common use is the combination of a (CHARMM or X-PLOR style) PSF file
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and a DCD file (the latter can be produced by LAMMPS directly). If the
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bonding information is not available, VMD uses a heuristic guess which
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works reasonably well with biological systems, but can be particularly
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cumbersome in coarse grained MD or similar model systems. The
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lmpbonds2vmd.tcl script provides an option to transfer bonding information
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from a LAMMPS data file into VMD.
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1b. Usage.
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The script defines a new procedure "lmpbondsfromdata". To activate it type
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at the VMD command prompt:
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source lmpbonds2vmd.tcl
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To then build a PSF file for use in subsequent visualizations you can load
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one just frame of a native LAMMPS trajectory (not binary, not custom!), for
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example perusing the output from the micelle example.
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mol new dump.micelle type lammpstrj waitfor all
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lmpbondsfromdata [molinfo top] data.micelle
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Now you should only see the bonds that actually have bonded interactions.
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To avoid having to run the script all the time you can save the bonding
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information in an (incomplete) PSF file.
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animate write psf micelle.psf
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In the future you can now load this PSF file first and then the LAMMPS dump
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file(s) (or a more compact and faster loading DCD or XTC file) with:
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vmd micelle.psf -lammpstrj dump.micelle
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1c. Problems.
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The LAMMPS data file format is quite flexible and thus not always easy to
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parse independently from context. As a consequence, the lmpbondsfromdata
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parser may be confused by your specific setup.
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1d. History.
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First version. 2007, Axel Kohlmeyer <akohlmey@cmm.chem.upenn.edu>
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Added a sanity check 03/2008, Axel Kohlmeyer <akohlmey@cmm.chem.upenn.edu>
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-------------------------
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2. lmpresid2vmd.tcl - translate residue information from a LAMMPS data file
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into VMD.
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2a. Background.
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LAMMPS dump files contain information about the (numerical) atom type, but
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not a molecule or residue id as it is typically used in PSF or PDB files
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to define subunits of a system. Adding this information can be very helpful
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for analysis and post-processing of LAMMPS data in VMD.
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2b. Usage.
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The script defines a new procedure "lmpresidfromdata". To activate it type
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at the VMD command prompt:
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source lmpresid2vmd.tcl
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To then add the residue information to a PSF file, see the steps for from
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item 1 from above and then type into the VMD console.
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lmpresidfromdata [molinfo top] data.micelle
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To avoid having to run the script all the time you can save the residue
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information in an (incomplete) PSF file.
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animate write psf micelle2.psf
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In the future you can now load this PSF file first and then the LAMMPS dump
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file(s) (or a more compact and faster loading DCD or XTC file) with:
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vmd micelle2.psf -lammpstrj dump.micelle
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You can use the residue information to join bonds split across the periodic
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boundaries with:
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pbc join residue -all
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and then enjoy a nice visualization of the micelle example with VMD. :)
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2c. Problems.
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The LAMMPS data file format is quite flexible and thus not always easy to
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parse independent from context. As a consequence, the lmpresidfromdata
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parser may be confused by your specific setup.
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2d. History.
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First version. 2008, Axel Kohlmeyer <akohlmey@cmm.chem.upenn.edu>
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-------------------------
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3. lmpname2vmd.tcl - set atom names based on LAMMPS type in VMD.
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3a. Background.
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LAMMPS dump files contain information about the (numerical) atom type, but
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not atom names like in PSF or PDB files. The names are used in VMD to guess
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element, radius and (default) coloring. Adding this information can be very
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helpful to set convenient defaults for visualization of LAMMPS data in VMD.
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3b. Usage.
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The script defines a new procedure "lmptypetoname". To activate it type
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at the VMD command prompt:
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source lmpname2vmd.tcl
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To then add atom name information, e.g., to a PSF file, see the steps for
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item 1 from above and then type into the VMD console.
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lmptypetoname [molinfo top] "SOL HDR TL1 TL2"
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To avoid having to run the script all the time you can save the bonding
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information in an (incomplete) PSF file.
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animate write psf micelle3.psf
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In the future you can now load this PSF file first and then the LAMMPS dump
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file(s) (or a more compact and faster loading DCD or XTC file) with:
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vmd micelle3.psf -lammpstrj dump.micelle
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And you'll see that VMD will assign different colors to the atom types. You
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cat get the previous coloring back by using the "Type" coloring scheme.
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3c. Problems.
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This script assumes the data originates from a LAMMPS dump file and thus
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the atoms types are numerical starting from 1. If those have been modified
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by some means, no name will be assigned.
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3d. History.
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First version. 2008, Axel Kohlmeyer <akohlmey@cmm.chem.upenn.edu>
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-------------------------
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4. lmpradius2vmd.tcl - set VdW radius based on LAMMPS type in VMD.
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4a. Background.
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The radii used for VDW and derived representations in VMD are guessed from
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the atom names. This script offers a convenient way to reset them (e.g. by
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using the sigma parameters from matching LJ interactions).
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4b. Usage.
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The script defines a new procedure "lmptypetoradius". To activate it type
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at the VMD command prompt:
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source lmpradius2vmd.tcl
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To then add atom radius information, see the steps for
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item 1 from above and then type into the VMD console.
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lmptypetoradius [molinfo top] "1.00 1.00 0.75 0.50"
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4c. Problems.
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This script assumes the data originates from a LAMMPS dump file and thus
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the atoms types are numerical starting from 1. If those have been modified
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by some means, no name will be assigned. There is currently no file format
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that exports the radius information, so this script/command has to be
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added, e.g., to "saved states" and other visualization scripts.
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4d. History.
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First version. 2008, Axel Kohlmeyer <akohlmey@cmm.chem.upenn.edu>
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@ -1,67 +0,0 @@
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# small script to extract bonding info from a lammps data file
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# so that VMD will display the correct bonds for CG-MD.
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# (c) 2007 Axel Kohlmeyer <akohlmey@cmm.chem.upenn.edu>
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proc lmpbondsfromdata {mol filename} {
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if {"$mol" == "top"} {
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set mol [molinfo top]
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}
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# create an empty bondlist
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set na [molinfo $mol get numatoms]; # number of atoms
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set nb 0; # number of bonds
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set bl {}; # bond list
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for {set i 0} {$i < $na} {incr i} {
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lappend bl {}
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}
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# open lammps data file
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if {[catch {open $filename r} fp]} {
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puts stderr "could not open file $filename"
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return -1
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}
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# read file line by line until we hit the Bonds keyword
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while {[gets $fp line] >= 0} {
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# pick number of bonds
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regexp {^\s*(\d+)\s+bonds} $line dummy nb
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if { [regexp {^\s*Bonds} $line] } {
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puts "nbonds= $nb\nnow reading Bonds section"
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break
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}
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}
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# skip one line
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gets $fp line
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# read the bonds data
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for {set i 0} {$i < $nb} {incr i} {
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gets $fp line
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# grep bond numbers from entry and adjust to VMD numbering style
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regexp {^\s*\d+\s+\d+\s+(\d+)\s+(\d+)} $line dummy ba bb
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incr ba -1
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incr bb -1
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# sanity check
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if { ($ba > $na) || ($bb > $na) } {
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puts stderr "number of atoms in VMD molecule ($na) does not match data file"
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return -1
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}
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set bn [lindex $bl $ba]
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lappend bn $bb
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set bl [lreplace $bl $ba $ba $bn]
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set bn [lindex $bl $bb]
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lappend bn $ba
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set bl [lreplace $bl $bb $bb $bn]
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}
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close $fp
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set sel [atomselect $mol all]
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$sel setbonds $bl
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$sel delete
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return 0
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}
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@ -1,18 +0,0 @@
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# small script to assign atom names to type numbers in LAMMPS .
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# (c) 2008 Axel Kohlmeyer <akohlmey@cmm.chem.upenn.edu>
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proc lmptypetoname {mol names} {
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if {"$mol" == "top"} {
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set mol [molinfo top]
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}
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set t 0
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foreach n $names {
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incr t
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set sel [atomselect $mol "type $t"]
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$sel set name $n
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$sel delete
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}
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return 0
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}
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@ -1,18 +0,0 @@
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# small script to assign a radius by type number in VMD
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# (c) 2008 Axel Kohlmeyer <akohlmey@cmm.chem.upenn.edu>
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proc lmptypetoradius {mol rlist} {
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if {"$mol" == "top"} {
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set mol [molinfo top]
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}
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set t 0
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foreach r $rlist {
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incr t
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set sel [atomselect $mol "type $t"]
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$sel set radius $r
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$sel delete
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}
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return 0
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}
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@ -1,58 +0,0 @@
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# small script to extract residue info from a lammps data file
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# (c) 2008 Axel Kohlmeyer <akohlmey@cmm.chem.upenn.edu>
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proc lmpresidfromdata {mol filename} {
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if {"$mol" == "top"} {
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set mol [molinfo top]
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}
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# create an empty bondlist
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set na [molinfo $mol get numatoms]; # number of atoms of molecule
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set da 0; # number of atoms in data file
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set rl {}; # resid list
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for {set i 0} {$i < $na} {incr i} {
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lappend rl 0
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}
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# open lammps data file
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if {[catch {open $filename r} fp]} {
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puts stderr "could not open file $filename"
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return -1
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}
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# read file line by line until we hit the Bonds keyword
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while {[gets $fp line] >= 0} {
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# pick number of atoms
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regexp {^\s*(\d+)\s+atoms} $line dummy da
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if { [regexp {^\s*Atoms} $line] } {
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# sanity check
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if {$na != $da} {
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puts stderr \
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"number of atoms in VMD molecule ($na) does not match data file ($da)"
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return -1
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}
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puts "atoms= $da\nnow reading Atoms section"
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break
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}
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}
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# skip one line
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gets $fp line
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# read the Atoms data
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for {set i 0} {$i < $da} {incr i} {
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gets $fp line
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# grep bond numbers from entry and adjust to VMD numbering style
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regexp {^\s*(\d+)\s+(\d+)\s+\d+.*} $line dummy ba bb
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incr ba -1
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lset rl $ba $bb
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}
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close $fp
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set sel [atomselect $mol all]
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$sel set resid $rl
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$sel delete
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}
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@ -1,13 +0,0 @@
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#!/usr/bin/tclsh
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# recreate the tcl index file for on demand loading.
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#
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# Copyright (c) 2003 by <Axel.Kohlmeyer@theochem.ruhr-uni-bochum.de>
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#
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auto_mkindex . *.tcl
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############################################################
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# Local Variables:
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# mode: tcl
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# time-stamp-format: "%u %02d.%02m.%y %02H:%02M:%02S %s"
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# End:
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############################################################
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@ -1,12 +0,0 @@
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# Tcl autoload index file, version 2.0
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# This file is generated by the "auto_mkindex" command
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# and sourced to set up indexing information for one or
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# more commands. Typically each line is a command that
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# sets an element in the auto_index array, where the
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# element name is the name of a command and the value is
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# a script that loads the command.
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set auto_index(lmptypetoname) [list source [file join $dir lmpname2vmd.tcl]]
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set auto_index(lmpresidfromdata) [list source [file join $dir lmpresid2vmd.tcl]]
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set auto_index(lmpbondsfromdata) [list source [file join $dir lmpbonds2vmd.tcl]]
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set auto_index(lmptypetoradius) [list source [file join $dir lmpradius2vmd.tcl]]
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Reference in New Issue
Block a user