回转半径和扩散-建模

采用OPLS-UA模型使用moltemplate建立十六烷的模型。lt文件如下

ch2group.lt内容如下

import "oplsaa.lt"    

import "loplsaa.lt"                     

# Then define "CH2":

CH2 inherits OPLSAA {

  # atom-id mol-id atom-type charge  x    y  z

  write("Data Atoms") {

    $atom:c $mol:... @atom:13  0.0  0.000000     0.000000      0.000000

  }

} # CH2

CH2.move(0,0.4431163,0)

ch3group.lt内容如下

import "oplsaa.lt"    

import "loplsaa.lt"   

# Then define "CH3":

CH3 inherits OPLSAA {

  # atom-id  mol-id atom-type  charge   x             y                z

  write("Data Atoms") {

    $atom:c $mol:... @atom:10    0.0  0.000000     0.000000      0.000000

  }

} # CH3

CH3.move(0,0.4431163,0)

alkane16.lt内容如下

import "ch2group.lt"  # load the definition of the "CH2" object

import "ch3group.lt"  # load the definition of the "CH3" object

Alkane16 inherits OPLSAA {

  create_var {$mol}

  monomers = new CH2 [16].move(1.54,0,0)

  delete monomers[0]

  delete monomers[15]

  monomers[0] = new CH3

  monomers[15] = new CH3

  monomers[15].move(23.1,0,0)   

  write('Data Bond List') {

    $bond:b1  $atom:monomers[0]/c $atom:monomers[1]/c

    $bond:b2  $atom:monomers[1]/c $atom:monomers[2]/c

    $bond:b3  $atom:monomers[2]/c $atom:monomers[3]/c

    $bond:b4  $atom:monomers[3]/c $atom:monomers[4]/c

    $bond:b5  $atom:monomers[4]/c $atom:monomers[5]/c

    $bond:b6  $atom:monomers[5]/c $atom:monomers[6]/c

    $bond:b7  $atom:monomers[6]/c $atom:monomers[7]/c

    $bond:b8  $atom:monomers[7]/c $atom:monomers[8]/c

    $bond:b9   $atom:monomers[8]/c $atom:monomers[9]/c

    $bond:b10  $atom:monomers[9]/c $atom:monomers[10]/c

    $bond:b11  $atom:monomers[10]/c $atom:monomers[11]/c

    $bond:b12  $atom:monomers[11]/c $atom:monomers[12]/c

    $bond:b13  $atom:monomers[12]/c $atom:monomers[13]/c

    $bond:b14  $atom:monomers[13]/c $atom:monomers[14]/c

    $bond:b15  $atom:monomers[14]/c $atom:monomers[15]/c

  }

}

system.lt内容如下

import "alkane16.lt"  # Defines the "Alkane50" molecule

# Specify the size of the world the polymer lives in:

write_once("Data Boundary") {

   0.0  120.0  xlo xhi

   0.0  120.0  ylo yhi

   0.0  120.0  zlo zhi

}

 polymers = new Alkane16 [24].move(0, 0, 5.0)

                         [24].move(0, 5.0, 0)

                         [4].move(30.0, 0, 0)

在生成data文件后要使用cleanup_moltemplate.sh命令简化一下data文件

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