This post provides the approach to extract the plastic strain in MD simulation. We can compute the atom displacement as the trajectory from the MD simulation, but the strain is the concept in continuum mechanics, it is really hard to compute the tensor in a discrete system. Recently, some tools provide this function based on a theory that accounting the effects of the neighbor atoms. While considering the relative displacement with the neighbor atom and using the weight function, the deformation gradient tensor can be calculated. Therefore, the strain tensor is obtained. Plastic strain can be expressed as,

$$\boldsymbol{\varepsilon}^p = \boldsymbol{\varepsilon} – \boldsymbol{\varepsilon}^e $$

so two strain tensor should be generated in the simulation data: total strain tensor $\boldsymbol{\varepsilon}$ and the elastic strain tensor $\boldsymbol{\varepsilon}^e$. Obviously, LAMMPS data file does not provide such information. Here I use the OVITO to get this data.

OVITO provide two modifiers, the first one is the “Atomic strain” and the second one is the “Elastic strain calculation”. Both of them provide the deformation gradient tensor and the strain tensor data. But I found there are some bugs for strain tensor output in OVITO, so I use the deformation gradient tensor data and computing the strain tensor with a Python script.