Amorphous Polymer Generator

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Figure 1. Movie showing deformation of an amorphous polyethylene structure with 20 chains of 1000 monomers length. The strain rate is 1010 s-1 and the temperature is 100 K.

Contents

Abstract

This script generates an amorphous polymer input file for LAMMPS based on an FCC lattice with a self-avoiding random walk, as used by Tschopp et al[1][2].

Author(s): Mark A. Tschopp, Don K. Ward

Code

Download these files:

To run

  • Compile the C code.
    • `gcc -o mc_gen mc_gen.c -lm'
  • Run the executable.
    • `./mc_gen'
  • Check for the output LAMMPS file... Voila!

Note: For the large number of chains the SEED value may need to be changed.

Output

For example the output file should look like this:

# Model for PE

     10000     atoms
      9990     bonds
      9980     angles
      9970     dihedrals

         1     atom types
         1     bond types
         1     angle types
         1     dihedral types

    0.0000   80.0586 xlo xhi
    0.0000   80.0586 ylo yhi
    0.0000   80.0586 zlo zhi

Masses

         1          14.02

Atoms

         1         1         1    8.6550   61.6668    5.4094
         2         1         1    8.6550   60.5849    6.4912
         3         1         1    7.5731   59.5030    6.4912
         4         1         1    6.4912   60.5849    6.4912
         5         1         1    6.4912   61.6668    7.5731
         6         1         1    5.4094   62.7487    7.5731
         7         1         1    4.3275   62.7487    6.4912
         8         1         1    3.2456   62.7487    7.5731
         9         1         1    2.1637   61.6668    7.5731
        10         1         1    1.0819   61.6668    8.6550
...

Bonds 

         1         1         1         2
         2         1         2         3
         3         1         3         4
         4         1         4         5
         5         1         5         6
         6         1         6         7
         7         1         7         8
         8         1         8         9
         9         1         9        10
        10         1        10        11
...

Dihedrals 

         1         1         1         2         3         4
         2         1         2         3         4         5
         3         1         3         4         5         6
         4         1         4         5         6         7
         5         1         5         6         7         8
         6         1         6         7         8         9
         7         1         7         8         9        10
         8         1         8         9        10        11
         9         1         9        10        11        12
        10         1        10        11        12        13
...
      9965         1      9992      9993      9994      9995
      9966         1      9993      9994      9995      9996
      9967         1      9994      9995      9996      9997
      9968         1      9995      9996      9997      9998
      9969         1      9996      9997      9998      9999
      9970         1      9997      9998      9999     10000

Questions

Please contact me if you have any questions or comments.

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References

  1. 1.0 1.1 Hossain, D., Tschopp, M.A., Ward, D.K., Bouvard, J.L., Wang, P., Horstemeyer, M.F., "Molecular dynamics simulations of deformation mechanisms of amorphous polyethylene," Polymer, 51 (2010) 6071-6083.
  2. 2.0 2.1 Tschopp, M.A., Ward, D.K., Bouvard, J.L., Horstemeyer, M.F., "Atomic Scale Deformation Mechanisms of Amorphous Polyethylene under Tensile Loading," TMS 2011 Conference Proceedings.
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