relaxation, stress and remapping.

dear Lammps developers/users,

I am not quite sure I understand what is happening as a response to the imposed deformation:

1) I deform a single swollen polymer chain with the following command:
fix 1 all deform 1 x scale 10.0 y volume z volume remap x units box

after the deformation step, I simply let the chain relax in the new, elongated box.

however, when I record the stress components during relaxation, I expect y and z to respond to the squeeze, because essentially, I was squeezing in y and z direction: the polymer never touches x boundaries and the box is periodic in y and z, and so x is free to adjust. What I see is a stress response from x, in which the chain elongates, and both y and z components are zero...

When I turn remapping off, I simply get fluctuations of stress, even though the chain is deforming and adopting a new configuration as the box elongates.

I am sure I am missing something, but what I want is to squeeze in y and z, not stretch in x...

Any input is very appreciated.

With best wishes,
Anna

stress.png

Have you monitored the box lengths during
the run with fix deform in place to be sure

the box shape is what you want it to be?

If so, then you can tell if you are squeezing

in y/z and stretching in x.

Steve

Dear Steve,

Thanks, I have indeed monitored the box lengths and it seems to be doing the right thing, stretching in x as y and z are squeezed. The polymer is also deforming (squeezing, not stretching if I am not using remap x), but the stress is just fluctuating around zero for all components if there is no remapping… I have also tried higher deformation, but there is no difference- just fluctuations around zero…

Thank you for your response in advanced.

With best wishes,
Anna

Dear Steve and Lammps users/developers,

I have now tried the following set-up (for reduced units):

1) fix langevin+fix nve to achieve the target temperature
2) npt for squeezing deformation:
fix 1 all npt temp 1 1 1 x 0 0 1 drag 2
fix 2 all deform 1 y scale 0.33 z scale 0.33 remap x units box
3) fix langevin+fix nve for relaxation

Now I have several quaestions:

1) I am not quite sure what the Tdamp parameter should be, and what exactly is meant by drag, and why this falls in a certain range of values: is there literature about this?

2) essentially, I am following the idea of Tschopp et al.: https://icme.hpc.msstate.edu/mediawiki/index.php/Atomistic_Deformation_of_Amorphous_Polyethylene#cite_note-one-0
I struggle to understand "zero-pressure condition for two lateral simulation faces" and "decoupling the boundary in the loading direction from the NTP equations of motion" in the following context:

"The amorphous PE system was then deformed under a uniaxial tensile strain applied at a constant strain rate with a zero-pressure condition for the two lateral simulation cell faces. This deformation condition was implemented in LAMMPS by decoupling the boundary in the loading direction from the NPT equations of motion."

Thank you a lot in advanced!

With best wishes,
Anna

Comments below.

Steve

Dear Steve and Lammps users/developers,

I have now tried the following set-up (for reduced units):

1) fix langevin+fix nve to achieve the target temperature
2) npt for squeezing deformation:
fix 1 all npt temp 1 1 1 x 0 0 1 drag 2
fix 2 all deform 1 y scale 0.33 z scale 0.33 remap x units box
3) fix langevin+fix nve for relaxation

Now I have several quaestions:

1) I am not quite sure what the Tdamp parameter should be, and what exactly
is meant by drag, and why this falls in a certain range of values: is there
literature about this?

2) essentially, I am following the idea of Tschopp et al.:
https://icme.hpc.msstate.edu/mediawiki/index.php/Atomistic_Deformation_of_Amorphous_Polyethylene#cite_note-one-0
I struggle to understand "zero-pressure condition for two lateral simulation
faces" and "decoupling the boundary in the loading direction from the NTP
equations of motion" in the following context:

"The amorphous PE system was then deformed under a uniaxial tensile strain
applied at a constant strain rate with a zero-pressure condition for the two
lateral simulation cell faces. This deformation condition was implemented in
LAMMPS by decoupling the boundary in the loading direction from the NPT
equations of motion."

This means if the uniaxial strain is applied along the x direction,
then the x boundary is not allowed to relax. On the other hand, y and
z boundaries are allowed to relax to zero pressures using fix npt.

It would mean something like the following:

fix 1 all npt temp temp1 temp2 tdamp y 0 0 pdamp z 0 0 pdamp
fix 2 all deform N x arg keyword

Ray

Dear Ray and Steve,

Thanks for your contributions! Ray- but pressure is a scalar, so are we talking about a decoupled stress tensor in x direction in case of uniaxial strain? And also, going back to npt equations, how does this change them? What about the tdamp parameter- how does it enter the equations? Thanks again, and apologies for numerous questions that come from the lack of experience! :slight_smile:

With best wishes,
Anna

Anna,

These MD questions can be answered by reading more references in the
Literature. I suggest you start with the ones listed at the end of
the fix npt doc page.

Ray