|From:||"Wood, Mitchell" <mitwood@...3...>|
|Date:||Mon, 18 Sep 2017 15:44:29 +0000|
Thanks for your mail. I can think of a few different ways to resolve this. Since this is essentially a visualization problem and not a simulation problem I am going to keep my answers to thing done in OVITO rather than LAMMPS.
First thing to try is to go back and use your dump files with just coordinate information and add the 'Create Bonds' modification within OVITO and supply it with some cutoff radius to draw bonds. Make sure OVITO knows your cell is periodic by checking the
boxes under Input -> Simulation Cell. This way bonds will be created through the periodic boundaries without any trouble. Also, the header in your data files only has one bond type, so if you want OVITO to only create bonds to a subset of atoms, use the '_expression_
Select' command before the 'Create Bonds'. Order of operations in OVITO is bottom to top if you are using the graphical interface.
If you really like the data files with bond information in them, you can adjust the simulation cell boundaries within OVITO in Input -> Simulation Cell. The LAMMPS tilt factors go in the upper triangle of the 3x3 matrix that OVITO supplies.
From the picture you sent, and description of the problem, I would also suggest looking at your fix deform command to make sure you aren't adjusting the length of x in addition to the tilt angles in the x and y planes.
Hope that helps, if you continue to see strange results please provide us with the LAMMPS input file that generates this data.
Sandia National Labs - 1444 Multiscale Science
From: Steve Plimpton <sjplimp@...24...>
Sent: Monday, September 18, 2017 8:54 AM
To: MASATO KOIZUMI; Wood, Mitchell
Cc: LAMMPS Users Mailing List
Subject: [EXTERNAL] Re: [lammps-users] Shear Deformation: Monomers and Simulation Box Deforming Out of Sync
Mitch can likely answer (CCd).Steve
On Fri, Sep 15, 2017 at 7:10 PM, MASATO KOIZUMI <mkoizumi@...5197...09...> wrote: