Dear LAMMPS users,

I am modeling a polymeric system. I have two separate questions:

1- I am going to stretch the plymer to obtain its Young’s modulus. In addition, I need to run my system under periodic boundary conditions. I was wondering if it is possible to use periodic boundary conditions and stretch the system using displace_atoms command at the same time. As I read in the manual the only way to change the size of the system under periodic boundary conditions is using change in pressure or using deform command.

2- when you run a system containing bonds like polymers under periodic conditions if an atom crosses one side of the boundary it practically re-enters from the other side even if it is bonded to another atom which is steel in its original place. It is practically means that there is huge distance between the two atoms which are bonded together. As long as you run your system under periodic boundary it does not seem to be a problem. However, if after a while you want to continue the modelling using other types of boundaries like shrink you get the error “bond atom %%% %%% missing”. IS there anyway to solve this problem or we simply should not run the polymeric system under periodic boundary conditions.

Any help would be highly appreciated.

Bests,

Kourosh

Comments below.

Steve

Dear LAMMPS users,

I am modeling a polymeric system. I have two separate questions:

1- I am going to stretch the plymer to obtain its Young's modulus. In

addition, I need to run my system under periodic boundary conditions. I was

wondering if it is possible to use periodic boundary conditions and stretch

the system using displace_atoms command at the same time. As I read in the

manual the only way to change the size of the system under periodic boundary

conditions is using change in pressure or using deform command.

I think you want fix deform. It stretches both the simulation box and

displaces the atoms.

2- when you run a system containing bonds like polymers under periodic

conditions if an atom crosses one side of the boundary it practically

re-enters from the other side even if it is bonded to another atom which is

steel in its original place. It is practically means that there is huge

distance between the two atoms which are bonded together. As long as you run

your system under periodic boundary it does not seem to be a problem.

However, if after a while you want to continue the modelling using other

types of boundaries like shrink you get the error "bond atom %%% %%%

missing". IS there anyway to solve this problem or we simply should not run

the polymeric system under periodic boundary conditions.

That error means you probably pulled too far and things blew up. Bonds

can't be stretched indefinitely w/out huge energy excursions.

If you don't use periodic boundary conditions, you have to put some

kind of wall at the boundaries to prevent atoms from exiting the box,

otherwise they will be lost.

Best,

Laurent

Dear Kourosh,

You mentioned that you are trying to get the Young's modulus of a

crosslinked epoxy network. If I were to do this simulation, I will use

periodic boundary conditions and fix deform. I will first equilibrate

my system using NPT. From this, I will then proceed to use NVT

simulaiton with a thermostat and dump the pressure variables

Pxx,Pyy, Pzz of my zero 0 strain configuration using dump or thermo

command.

I will then stretch one dimension by a small amount (e.g. along x) X

and decrease the other dimensions by sqrt(X) such that volume is

conserved using fix deform.The network will be uniaxially deformed by

changing the initial box size L along the strain direction to XL and

L/sqrt(X) along the other dimensions. I will do the stretching step

by step such that Ln = L(X+n*dX) with dX being small. I need to

equilibrate in between steps and gather Pxx, Pyy and Pzz data. From

these data set I can get the uniaxial stress, which is sigma_x which

is equal to 3/2Pxx - 1/2(Pxx+Pyy+Pzz).

At small strain, the shear modulus should be related to the equation

sigma_x = G *(X^2 - X^-1) where X is Ln/L. At high strain, this does

not hold true (you will see non linear effects).

Young's modulus E should be equal to 2G(1+v) where v is the Poisson's ratio.

Jan-Michael

Dear Kourosh,

you mentioned that you are trying to get the Young's modulus of a

crosslinked epoxy network. If I were to do this simulation, I will use

periodic boundary conditions and fix deform. I will first equilibrate

my system using NPT. From this, I will then proceed to use NVT

simulaiton with a thermostat and dump the pressure variables

Pxx,Pyy, Pzz of my zero 0 strain configuration using dump or thermo

command.

I will then stretch one dimension by a small amount (e.g. along x) X

and decrease the other dimensions by sqrt(X) such that volume is

conserved.The network will be uniaxially deformed by changing the

initial box size L along the strain direction to XL and L/sqrt(X)

along the other dimensions. I will do the stretching step by step

such that Ln = L(X+n*dX) with dX being small. I need to equilibrate in

between steps and gather Pxx, Pyy and Pzz data. From these data set I

can get the uniaxial stress, which is sigma_x which is equal to 3/2Pxx

- 1/2(Pxx+Pyy+Pzz).

At small strain, the shear modulus should be related to the equation

sigma_x = G *(X^2 - X^-1) where X is Ln/Lo. At high strain, this does

not hold true (you will see non linear effects).

Young's modulus E should be