Question #691584 on Yade changed:
https://answers.launchpad.net/yade/+question/691584

    Status: Open => Answered

Jan Stránský proposed the following answer:
Hello,

> O.cell [1] 
> hSize [2] 
> "Base cell vectors (columns of the matrix)" [2].
> O.cell [1] 
>  hSize [3]
> components of velocity gradient [4]
> trsf is deformation gradient [5]
> stress here is matrix form of Cauchy stress tensor [6].

This is the standard approach on this forum to "cite" references summarized at 
the end of the message (or at the end of a previous message in the thread)
Full links in the text looks messy and also this way you can easily reference 
one link at multiple places (like O.cell here)

> Does "hsize" mean the size of cell?

no, see [2] :-), where it states that hSize is "Base cell vectors
(columns of the matrix)". I.e. vectors of the edges of the cell.

> Does "diagonal terms" mean the size of cell?

In case of diagonal matrix, the diagonal terms represent size. In
general case not.

> O.cell.velGrad=Matrix3(0,0,.1, 0,0,0, 0,0,0)
> Here, how to determine it shears in xz?
> Why is it in the xz plane rather than in other planes?

because the only non-zero term is at index (0,2), corresponding to xz
(0=x,2=z) shear component, which is shear in xz plane.

> Why is it shearing rather than rotating?

just because it is..
see e.g. [7], section "2D Transformations" (or google "2x2 matrix mapping scale 
skew rotation"). It is for 2D, which easier to understand and does not differ 
from 3D much.
velGrad is "roughly" (in "small strain sense") time derivative of deformation 
gradient (see [4] for full definition and relation).

cheers
Jan

[7] https://www.cs.brandeis.edu/~cs155/Lecture_06.pdf

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