local atomic number density

Dear all,

I want to visualise a structure with a contour map of local atomic number density (rho/rho_mean). What sort of compute or fix shall I use.

Also for visualizing localized Von mises strain near a crack simulation, what computes should I put in place.I have tried stress/atom but it does not give the desired visual. I am using AtomEye and Ovito for visualisation.

Thanks ,

regards,

Ashish

Dear all,
I want to visualise a structure with a contour map of local atomic number
density (rho/rho_mean). What sort of compute or fix shall I use.

have you checked the list​ of what is available?

http://lammps.sandia.gov/doc/Section_commands.html#cmd_5

Also for visualizing localized Von mises strain near a crack simulation,
what computes should I put in place.I have tried stress/atom but it does
not give the desired visual. I am using AtomEye and Ovito for visualisation.

​if you need a different stress formulation may have to implement it
yourself. virial stress is what LAMMPS computes directly. you may check
with the Atom-to-Continuum (USER-ATC) package ​if their approach is helpful
for your needs, but outside of that, it'll be a question of getting out a
text editor and starting to program.

axel.

You can use fix ave/spatial with 2d or 3d bins to get number density. Visualizing
it with a contour map is a task for a viz program, not LAMMPS.

Jon Zimmerman (CCd) may want to comment on alternate stress

calculations.

Steve

You do have all necessary stress tensor components to compute the Van
Mises stress yourself using an atom style variable (formula can be
found here for example
https://en.wikipedia.org/wiki/Von_Mises_yield_criterion)
Daniel

Hi Ashish,

Regarding visualizing stress, can you explain/elaborate what you mean by “it does not give the desired visual”? Does the field look incorrect, or is there just more oscillations/fluctuations than what you expected?

Jon Z.

Hi all,

Apologies for the late reply. The stress map that i get does not show any concentration near the crack, and as said by Jon the stresses are widely fluctuating all along the space. I did some study on this and found that per atom stress are different from continuum stress, and they have to be related in some way .I am still exploring the USER-ATC pacakage. About the von mises strain , there is something of that kind in Atom eye ,where some frame is considered as reference and strains are calculated, however i cant even do that correctly as well. May be as Axel says I will have to write my own code to visualize the stresses and strains.

Thanks for all the help

regrads

Ashish

Hello Ashish,

Regarding plotting of stresses, I recommend that you first just use LAMMPS’ native stress/atom compute and examine the stress field components within the material around the crack tip. Although there will be oscillations in the values, you should see the characteristic stress fields of a crack-tip. If you don’t, then your crack model is probably incorrect in some way. The USER-ATC package will have a somewhat different metric of stress, but it should appear similar to the one produced by the stress/atom compute (I.e. the virial method).

Regarding the von mises strain field, this is tricky as you do need to specify a “reference state” to quantify strain. This state ideally would be your system – whatever its geometry – without a crack-tip. USER-ATC can be used to specify a reference state that is different from any “initial state”, one that presumably does have a crack in it. For information about this, check out the “Eshelby” test in the examples/atc directory.

Jon Z.