Dear All,
I want to dump per atom stress after minimization.
Input script is:
...
compute myS all stress/atom pair bond angle
dump 1 all custom 5000 dump.${simname} id type x y z fx fy fz c_myS
minimize 1.0e-8 1.0e-8 5000 50000
but I got an error:
ERROR: Dump custom compute does not calculate per-atom vector
how is it possible considering that compute should calculate
"The tensor for each atom has 6 components and is stored as a 6-element vector",
from the dump command description:
"If c_ID is used as a attribute, then the local vector calculated by the compute is printed."
It must be some simple error, but I just don't see it.
Thank you in advance.
Regards,
Denis Davydov
You need c_myS[n], where N is which of the 6 components
you want. See the bottom of the doc page:
This compute calculates a per-atom array with 6 columns, which can be
accessed by indices 1-6 by any command that uses per-atom values from
a compute as input.
Steve
Dear Steve,
Thank you for you help. It works now.
I have a small question on visualization.
I use pizza.py, and run the following commands:
d = dump("dump.*")
v = vtk (d)
v.many()
when I read dump, i see
...
assigned columns: id type x y z fx fy fz c_myS[1] c_myS[2] c_myS[3] c_myS[4] c_myS[5] c_myS[6]
...
so it seems the info is there. But when I open
vtk file, there is nothing except "id", that is:
POINT_DATA 9660
SCALARS atom_type int 1
LOOKUP_TABLE default
I went through "dump" and "vtk" description in pyzza and
don't see any info how to control or check what is written to vtk.
Thank you in advance.
Kind regards,
Denis Davydov
If you're asking about the auxiliary columns in the dump file (myS[1], etc)
then the vtk tool isn't writing those to the vtk file. The vtk tool would
need to be extended to do that, similar to how the ensight tool in Pizza.py
can write auxiliary info. If you know the format of the VTK file for
that info, it probably isn't hard to do.
Steve