# Atomic strain

This modifier calculates he atomic-level strain tensors from two configurations of the simulated system. See [Mater. Trans. 48 (2007), 2923] for a description of how the per-particle deformation tensors are calculated by OVITO.

The input data set, to which the modifier is applied, is considered the current (or deformed) configuration of the system. The reference (or initial) configuration of the system is loaded from a separate input file by the modifier.

OVITO calculates the local deformation gradient tensor F for each particle from the relative displacements of the particle's nearest neighbors within the given cutoff radius. Note that the set of neighbors around the central particle is determined in the initial configuration. At least three non-coplanar neighbors are required to calculate F for a particle. Thus, the calculation will fail for isolated or undercoordinated particles. The modifier can select those invalid particles for diagnostic purposes.

After calculating the atomic deformation gradient tensor F, the Green-Langrangian strain tensor E=1/2(FTF-I) is derived from it. Finally, the modifier calculates and outputs the von Mises local shear invariant and the volumetric (hydrostatic) part of the strain tensor.

Use the "Reference: External data source" panel to pick the file containing the initial particle positions. Note that this reference file must contain the same set of particles as the input configuration seen by the modifier. That implies that you should not delete particles before applying the Atomic strain modifier. The modifier should usually be placed at the beginning of the processing pipeline.

To calculate the displacement vectors of individual particles, the modifier has to find corresponding particles in the two configurations of the system. If the particles have unique IDs assigned to them, the modifier will use this information to map particles from the reference configuration to the current configuration. If no particle IDs are available, the modifier assumes that particles have the same ordering in both configurations.

## Parameters

Cutoff radius

  Controls the range of neighbors that are taken into account to compute the deformation gradient tensor of a particle. This radius must be large enough to include at least three non-coplanar neighbors for every particle in the reference configuration. The larger the cutoff, the larger the volume over which the local deformation gradient tensor is averaged.

Eliminate homogeneous cell deformation

  This option lets the modifier first rescale the current simulation cell including all particle coordinates to match the cell shape in the reference configuration before calculating the deformation tensors. This effectively eliminates any macroscopic, homogeneous deformation of the simulation cell, and the calculated deformation tensors will reflect only the internal, microscopic displacements of particles.

Assume unwrapped coordinates

  This only affects the treatment of simulation cells with periodic boundary conditions. If activated, the particle coordinates in the reference and the current configuration are taken as is. If this option is not active, the minimum image convention is used to deal with particles that have crossed a periodic boundary.

Output deformation gradient tensors

  If activated, the modifier stores the nine components of the calculated per-particle deformation gradient tensors in an output property. Turn this off to save memory if you do not need the complete deformation gradient tensors.

Output strain tensors

  If activated, the modifier stores the six components of the calculated per-particle strain tensors in an output property. Turn this off to save memory if you do not need the complete strain tensor tensors.

Select invalid particles

  If activated, the modifier selects those particles for which it could not calculate the local deformation gradient and strain tensors (due to too few neighbors within the cutoff radius).