sampledoc

Replicate a P3HT for an MD runΒΆ

In this example a we use the replicate_data.py script to read in the structure from a LAMMPS input file and replicate the structure in space in two ways.

The first method is the default and chooses a random point within the box dimensions specified in the LAMMPS input file and places a copied structure at that point after randomly rotating the structure along 2 axes. Then the distance between the added particles of the copied structure and all the particles in the system is calculated to be sure structures are not overlapping each other.

Run:

replicate_data.py --mol_n 10
--in_data mols/thiophene_R_hexane_/acc1_thiophene_R_hexane__n5.data
--out_data  mols/thiophene_R_hexane_/acc1_thiophene_R_hexane__n5x10.data
--out_xyz mols/thiophene_R_hexane_/acc1_thiophene_R_hexane__n5x10.xyz

this creates the files:

mols/thiophene_R_hexane_/acc1_thiophene_R_hexane__n5x10.data
mols/thiophene_R_hexane_/acc1_thiophene_R_hexane__n5x10.xyz

The new LAMMPS input file with 10 molecules randomly placed and randomly oriented.

The second method is to place the molecular structures on a grid.

Run:

replicate_data.py --mol_n 10 --grid
--in_data mols/thiophene_R_hexane_/acc1_thiophene_R_hexane__n5.data
--out_data mols/thiophene_R_hexane_/acc1_thiophene_R_hexane__n5x10_g.data
--out_xyz mols/thiophene_R_hexane_/acc1_thiophene_R_hexane__n5x10_g.xyz

this creates the files:

mols/thiophene_R_hexane_/acc1_thiophene_R_hexane__n5x10_g.data
mols/thiophene_R_hexane_/acc1_thiophene_R_hexane__n5x10_g.xyz

The new LAMMPS input file with 10 molecules placed on grid in the box defined by the original LAMMPS input file. The grid method has the advantage on not need to calculate the inter-particle distances, so it is much faster.

Note

This entire example can be executed by running:

replicateP3HT.sh

in tools/examples. Needed files and scripts are

  • replicate_data.py

This example requires output from previous examples