View source for LAMMPS Polymer Datafile

back to [[Deformation_of_Amorphous_Polyethylene|Atomistic Deformation of Amorphous Polyethylene]]

Here is an example datafile for a polyethylene system with 10 chains of 1000 monomers each.  Download this file and add this to the directory with the [[LAMMPS_Input_Deck_for_Atomistic_Deformation_of_Amorphous_Polyethylene|LAMMPS input script]].

* [[Media:PE_nc10_cl1000.dat|PE_nc10_cl1000.dat]]

Within the file there are several sections.  The first section describes the number of atoms, bonds, angles, and dihedrals so that LAMMPS can initialize the arrays and so LAMMPS knows how many values to read in.  Also, this sets the number of different atom/bond/angle/dihedral types, the periodic box bounds, and the corresponding masses for the atomtypes.  Last, the coordinates of the united atoms for polyethylene are given along with the atom ID, chain number, and atom type in the first, second, and third columns, respectively. 

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# 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

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After the united atom coordinates, the bond list, angle list, and dihedral list data is listed.  For instance, the first entry in the bond has an ID (1), a bond type (1), and the bond is between 2 atoms, atom ID 1 and atom ID 2, and so forth for all 9990 bonds in this system.

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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
...

Angles 

         1         1         1         2         3
         2         1         2         3         4
         3         1         3         4         5
         4         1         4         5         6
         5         1         5         6         7
         6         1         6         7         8
         7         1         7         8         9
         8         1         8         9        10
         9         1         9        10        11
        10         1        10        11        12
...

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
...

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[[Category: Polymers]]
[[Category: LAMMPS]]
[[Category: Input Deck]]