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xianggui7895

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[资源] 【原创】VMD如何显示晶胞格子

VMD是一款非常强大的分子动力学后处理软件，而在使用中有个问题经常困扰新手，如何在周期性模型上加上晶胞格子使其看起来更“漂亮”一点呢？VMD默认是不画晶格的

但作为一个强大的软件，能实现这个功能是肯定的，现在就有两种方法可以在VMD软件中画出晶格，试试吧：

（1）VMD内置的pbctool工具箱，可直接在vmd控制台或者Tk控制台（Main menu->Extensions->Tk Console）中输入以下命令：

pbc set [list a b c alpha beta gamma]
pbc box -on

其中，a、b、c、alpha、beta、gamma是各个晶胞参数，如下图所示：

还可以设置box的线型、线宽和颜色，分别通过以下命令：

pbc box -style lines|dashed|

pbc box -width 2

pbc box -color red

更多选项可查阅：http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/

（2）tcl脚本：vmd_draw_unitcell。将下面内容保存在名为vmd_draw_unitcell.tcl的文件，放在vmd安装目录下（如：C:\Program Files\University of Illinois\VMD）

# vmd extension procedure:
# provide a 'draw unitcell' command
#
# $Id: vmd_draw_unitcell.tcl,v 1.2 2005/01/11 13:05:12 akohlmey Exp $
# Time-stamp:
#
# Copyright (c) 2003-2005 by

# add a unitcell graphic to a molecule via a draw subcommand.
#
# options:
# cell (vmd|auto|[list ]), default: "vmd"
#       "vmd" will use the internal values,
#       "auto" will build an orthogonal unitcell from the result of
#          'measure minmax' plus 1 angstrom added in each direction.
#       else a list of a,b,c,alpha,beta,gamma will be assumed.
# origin ([list ]|auto), default: {0.0 0.0 0.0}, "auto" with 'cell auto'
# style: (lines|dashed|rod) default: line
# width: default: 1.0
# resolution:       default: 8
#

proc vmd_draw_unitcell {molid args} {

# parse arguments
foreach {flag arg} $args {
      switch $flag {
         cell    { set cell    "$arg" }
         origin    { set origin    "$arg" }
         style    { set style    "$arg" }
         width    { set width    "$arg" }
         resolution { set resolution "$arg" }
         default { puts "unknown option: $flag"; return }
      }
}

if [info exists cell] {
      if {![info exists origin] && $cell == "auto"} { set origin auto }
} else {
      set cell vmd
}

if ![info exists origin]    { set origin    {0.0 0.0 0.0} }
if ![info exists style]    { set style    lines       }
if ![info exists width]    { set width    1          }
if ![info exists resolution] { set resolution 8          }
# FIXME: add some checks on the arguments here.

# handle auto keywords
if {$cell == "auto" || $origin == "auto" } {
      set sel [atomselect $molid {all}]
      set minmax [measure minmax $sel]
      $sel delete
      unset sel

      if {$origin == "auto" } {set origin [vecsub [lindex $minmax 0] {1 1 1}]}
      if {$cell == "auto"} {
         set cell [vecadd [vecsub [lindex $minmax 1] [lindex $minmax 0]] {2 2 2}]
         lappend cell 90.0 90.0 90.0
      }
}

if {$cell == "vmd" } {set cell [molinfo $molid get {a b c alpha beta gamma}]}
global M_PI
set sa [expr sin([lindex $cell 3]/180.0*$M_PI)]
set ca [expr cos([lindex $cell 3]/180.0*$M_PI)]
set cb [expr cos([lindex $cell 4]/180.0*$M_PI)]
set cg [expr cos([lindex $cell 5]/180.0*$M_PI)]
set sg [expr sin([lindex $cell 5]/180.0*$M_PI)]

# set up cell vectors according to the VMD unitcell conventions.
# the a-vector is collinear with the x-axis and
# the b-vector is in the xy-plane.
set a [vecscale [lindex $cell 0] {1 0 0}]
set b [vecscale [lindex $cell 1] "$ca $sa 0"]
set c [vecscale [lindex $cell 2] "$cb [expr ($ca - $cb*$cg)/$sg] [expr sqrt((1.0 + 2.0*$ca*$cb*$cg - $ca*$ca - $cb*$cb - $cg*$cg)/(1.0 - $cg*$cg))]"]

# set up cell vertices
set vert(0) $origin
set vert(1) [vecadd $origin $a]
set vert(2) [vecadd $origin $b]
set vert(3) [vecadd $origin $a $b]
set vert(4) [vecadd $origin $c]
set vert(5) [vecadd $origin $a $c]
set vert(6) [vecadd $origin $b $c]
set vert(7) [vecadd $origin $a $b $c]
unset sa ca cb cg sg

set gid ""
switch $style {
      rod {
         # set size and radius of spheres and cylinders
         set srad [expr $width * 0.003 * [veclength [vecadd $a $b $c]]]
         set crad [expr 0.99 * $srad]

         # draw spheres into the vertices ...
         for {set i 0} {$i < 8} {incr i} {
            lappend gid [graphics $molid sphere $vert($i) radius $srad resolution $resolution]
         }
         # ... and connect them with cylinders
         foreach {i j} {0 1 0 2 0 4 1 5 2 3 4 6 1 3 2 6 4 5 7 3 7 5 7 6} {
            lappend gid [graphics $molid cylinder $vert($i) $vert($j) radius $crad resolution $resolution]
         }
      }

      lines {
         set width [expr int($width + 0.5)]
         foreach {i j} {0 1 0 2 0 4 1 5 2 3 4 6 1 3 2 6 4 5 7 3 7 5 7 6} {
            lappend gid [graphics $molid line $vert($i) $vert($j) width $width style solid]
         }
      }

      dashed {
         set width [expr int($width + 0.5)]
         foreach {i j} {0 1 0 2 0 4 1 5 2 3 4 6 1 3 2 6 4 5 7 3 7 5 7 6} {
            lappend gid [graphics $molid line $vert($i) $vert($j) width $width style dashed]
         }
      }
      default { puts "unknown unitcell style: $style" ; return }
}
# return list of graphics indices so that they can be saved and deleted later.
return $gid
}

############################################################
# Local Variables:
# mode: tcl
# time-stamp-format: "%u %02d.%02m.%y %02H:%02M:%02S %s"
# End:
############################################################

用记事本打开vmd安装目录下的vmd.rc文件，在最后添加一行：

source C:\\Program\ Files\ (x86)\\University\ of\ Illinois\\VMD\\vmd_draw_unitcell.tcl

然后在vmd控制台或这tk控制台即可输入一下命令显示晶胞格子：

draw unitcell cell [list a b c alpha beta gamma]

注意：a b c alpha beta gamma需要全部注明。

详细说明请看下面一段英文表述：

# cell (vmd|auto|[list ]), default: "vmd"
#       "vmd" will use the internal values,
#       "auto" will build an orthogonal unitcell from the result of
#          'measure minmax' plus 1 angstrom added in each direction.
#       else a list of a,b,c,alpha,beta,gamma will be assumed.
# origin ([list ]|auto), default: {0.0 0.0 0.0}, "auto" with 'cell auto'
# style: (lines|dashed|rod) default: line
# width: default: 1.0
# resolution:       default: 8

[ Last edited by xianggui7895 on 2010-12-13 at 21:57 ]

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