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[Jan Stránský <question702065@xxxxxxxxxxxxxxxxxxxxx>]

Question #702065 on Yade changed:
https://answers.launchpad.net/yade/+question/702065

    Status: Open => Answered

Jan Stránský proposed the following answer:
> when I set periodic boundaries, all the particles are found to club
together

You only set the simulation to be periodic with O.periodic=True
This sets the periodic cell size to its default value, (1,1,1).
You should adjust its size [3,5,6,] according to your needs (e.g. packing bounding box [4]):
###
size = aabbDim()
O.cell.setBox(size)
###

Also note that using periodicity for non-periodic packing may create
some artifacts on "seams" or "periodic boundaries" which in fact are not
(geometrically) periodic.

>> do not ask urgent questions on Saturday
> I'm sorry

no need to be sorry, just do not expect urgent answers :-)

>> Which examples?
> https://gitlab.com/yade-dev/trunk/blob/master/doc/sphinx/tutorial/06-periodic-triaxial-test.py

so consider also [2] as a tutorial for non-periodic triaxial tests

> Yade documentation 3rd edition

This is too broad, please select relevant sections, we may then point you e.g. to a section you missed or something like this.
Here e.g. [5,6].

>> Please provide full error message.
> This is the message: 'PeriTriaxController run on aperiodic simulation'

Please provide FULL error message, including error stack, which also
mention from which command it comes from etc.

>> Where / how did you get this understanding?
> ...

Yes, setting periodic boundaries together with packing creation is a natural process and therefore it is present in examples.
However, it is not limited to this scenario.

> .... to form a clump.

"Clump" has in Yade context a special meaning - rigid compound of
several particles. So let's call it maybe "cluster"?

> drive.google.com

please read [1], section "Please, no external links!"

Cheers
Jan

[3] https://yade-dem.org/doc/yade.wrapper.html#yade.wrapper.Cell.setBox
[4] https://yade-dem.org/doc/yade.utils.html#yade.utils.aabbDim
[5] https://gitlab.com/yade-dev/trunk/-/blob/master/examples/PeriodicBoundaries/periodic-simple.py
[6] https://gitlab.com/yade-dev/trunk/-/blob/master/examples/PeriodicBoundaries/periodic-compress.py

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