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[lammps-users] Shear Deformation: Monomers and Simulation Box Deforming Out of Sync
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[lammps-users] Shear Deformation: Monomers and Simulation Box Deforming Out of Sync

From: MASATO KOIZUMI <mkoizumi@...3709...>
Date: Fri, 15 Sep 2017 18:10:35 -0700

Dear LAMMPS Users,

Hello. This is Masato Koizumi, and I am an incoming student at UCLA. I am using LAMMPS to do my molecular simulations.

I modeled a simulation box containing polymer chains. Initially, the simulation box is a cube. I used fix deform command to apply shear such that the box will deform into a parallelepiped. I have outputted dump files so that I could view the shear deformation in OVITO.

When OVITO reads the dump files, I see the instantaneous shear deformation of my polymer matrix without any problems

I wanted to add bonds in between the modeled monomers, and since the dump files only provides the x, y and z coordinates of the monomers, I have converted the dump files into a data file following the format used in data files outputted by the write_data command. Therefore, the first portion of my converted data file looks like the following:

LAMMPS data file via dump file, version 10 Feb 2015, timestep = 200000
250000 atoms
1 atom types
263728 bonds
1 bond types
-3.2590800000000002e+01 4.5627099999999999e+01 xlo xhi
-3.2590800000000002e+01 3.2590800000000002e+01 ylo yhi
-3.2590800000000002e+01 3.2590800000000002e+01 zlo zhi
1.3036300000000001e+01 0.0000000000000000e+00 0.0000000000000000e+00 xy xz yz

However, when OVITO read my converted data file, the monomers and the simulation box geometry is out of sync like the following:

Inline image 1

The simulation box is now deforming differently compared to how it was reading the original dump files. I did not change the xy, xz and yz values but when I converted the dump files into a data file without changing the simulation box parameters and the timesteps, the simulation box is deforming differently.

I would greatly appreciate if anyone could provide me with any hints or advices in resolving this problem. Thank you.


Masato Koizumi