I run the attached input script in lammps and write the bonds with the
following command in a second file
compute C2 all property/local natom1 natom2 ntype1 ntype2
and over the time the bonds are breaking and the amount of bonds
increase. I visualized the damage computed by the lammps Peridynamic
package in picture1.png and reconstruct his value from the computed
bonds with the described command picture2.png. The result differs and my
question is how to access the neighbor information for an atom/particle?
Why does this list differ from the computed damage?
Not clear what you are asking. The “n” fields you are outputting
by compute property/local and dump local are “neighbors” in the
non-bond lists used by the PD pair styles. They represent PD
particles that are currently close to an atom (bonded or not).
They are different
from the PD bonds that may exist (or have been previously broken)
at any point in time.
Not sure what info you are wanting to use to create a “correct”
image, or what you mean by “computed damage”.
I wanted to get all active bonds between PD particles at the time step I dumped the file.
I like to track the bonds over all time and extract fragments or crack patterns of this information and visualize it.
So I want all active bonds at time 0 and then a subset of them excluding the broken or non-active bonds.
The damage inside the PD module the the ratio of broken bonds to initial bonds. This scalar value is visualized in the first image.
In the second I reconstructed this information of the dumped file with the bonds to verify if I got the correct neighbor information. Ok, this explains the difference of the two images.
Is it possible to produce this information with lammps? A history of the bonds between PD particles excluding the close atoms without a bond?
I think with this supported information it is more understandable what I want to do. I run the simulation again with the patom property and the pictures look better.
In picture 1 i visualize the scalar value of the compute all damage/atom and this is equation (3.10) in the following document
. Now I use the bonds in the second dump file to reconstruct this values, because I need the bonds for some post-processing of the simulation. But this pictures do not look identical. MY question is how to get the same bond information as used in the computation of the damage. Regards Patrick
