LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Mailing List Archives
[lammps-users] reading initial configuration and simulation box boundaries
[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

[lammps-users] reading initial configuration and simulation box boundaries


From: Carol Baruffi <baruffi.carolina@...24...>
Date: Mon, 4 Sep 2017 13:13:24 +0200

Hello LAMMPS users,
I have a question about reading input files.

Context: crystallin materials, simulation of twins in Titanium

I have a configuration, result of a previous simulation, which I would like to use as an input file for another simulation. This configuration respects periodicity, I check this with the visualization tool OVITO i.e. using the common neigh. analysis and looking at the energy per atom ( I check there were no strange energy excess at the boundary).

What I did is writing a small program to create an input file for LAMMPS from the dump file of the previous simulation. In ths input file number of atoms, box limits of my triclinic simulation box and atom typology + coordinates are specified.

I run the new simulation using this file as input and what I noticed is that from the really begin of the simulation the box limits change and I loose periodicity in the direction X and Y. This is strange, because I am pretty sure that periodicity is respected in the initial configuration so I dont't understand how it can be lost so quickly. The lost of periodicity can be seen using OVITO and looking at the energy per atom, all the atoms at the boundary have not the good energy value ...

Find attached the dump fie with the initial configuration (macle), the input file for the new run (Ti_macle) I wrote and the LAMMPS script (macle.inp).

Thank You for Your help in advance, I wish a good Monday !

Carolina

ps. a naive question ... using FIX NVT should imply no change in the box volume but possible change in the box limits, am I right ? But I think that if periodic boundary conditions in the 3 dimensions are used the system is forced also to not change its shape.

2017-09-04 13:02 GMT+02:00 Carol Baruffi <baruffi.carolina@...24...>:
Hello LAMMPS users,
I have a question about reading input files.

Context: crystallin materials, simulation of twins in Titanium

I have a configuration, result of a previous simulation, which I would like to use as an input file for another simulation. This configuration respects periodicity, I check this with the visualization tool OVITO i.e. using the common neigh. analysis and looking at the energy per atom ( I check there were no strange energy excess at the boundary).

What I did is writing a small program to create an input file for LAMMPS from the dump file of the previous simulation. In ths input file number of atoms, box limits of my triclinic simulation box and atom typology + coordinates are specified.

I run the new simulation using this file as input and what I noticed is that from the really begin of the simulation the box limits change and I loose periodicity in the direction X and Y. This is strange, because I am pretty sure that periodicity is respected in the initial configuration so I dont't understand how it can be lost so quickly. The lost of periodicity can be seen using OVITO and looking at the energy per atom, all the atoms at the boundary have not the good energy value ...

Find attached the dump fie with the initial configuration (fie macle), the input file for the new run I wrote and the LAMMPS script (in the zip file).

Thank You for Your help in advance, I wish a good Monday !

Carolina

ps. a naive question ... using FIX NVT should imply no change in the box volume but possible change in the box limits, am I right ? But I think that if periodic boundary conditions in the 3 dimensions are used the system is forced also to not change its shape.

Attachment: macle.inp
Description: chemical/gamess-input

Attachment: Ti_macle
Description: Binary data

Attachment: macle
Description: Binary data