Possible bug for Voronoi anlaysis after box is flipped upon shearing

Dear Steve,

There might be a bug for the voronoi analysis after the simulation box is flipped upon shearing. I noticed there is an early post for discussing the voronoi analysis of a triclinic box
http://lammps.sandia.gov/threads/msg60447.html

I used the latest version (14May16). It is no problem for the normal shearing with this version. However, when I do a severe shearing simulation that allows box flipping. I found after the flipping, only a part of the atoms have the values from the voronoi analysis, such as atomic volume, number of faces, but the rest are all zero. So it seems that there is still a bug in dealing with the triclinic box. I am trying to debug it but still not making it all right…

Best regards,

Suzhi

Dear Steve,

There might be a bug for the voronoi analysis after the simulation box is
flipped upon shearing. I noticed there is an early post for discussing the
voronoi analysis of a triclinic box
LAMMPS Molecular Dynamics Simulator

I used the latest version (14May16). It is no problem for the normal
shearing with this version. However, when I do a severe shearing simulation
that allows box flipping. I found after the flipping, only a part of the
atoms have the values from the voronoi analysis, such as atomic volume,
number of faces, but the rest are all zero. So it seems that there is still
a bug in dealing with the triclinic box. I am trying to debug it but still
not making it all right...

thanks for the report. i've filed it on our LAMMPS project issue
tracker on github as issue #77

can you please provide a simple input for as small a system as
possible, that can reproduce the problem.
that will make it much easier to check it out.

thanks,
   axel.

Dear Axel,

Thanks. My case is in a relatively large size. Here I tested a simple case in a small system (see below). The values from voronoi analysis have a large change after box flipping (after step 125 000). For example, the volume of Voronoi cell (c_1[1]) of some atoms can even go to be 76 A^3 from the original 12 A^3. Hopefully it will be helpful for your debugging.

test

units metal
boundary p p p
atom_style atomic
lattice fcc 3.639087
region box prism 0 50 0 20 0 2 0 0 0
create_box 1 box
create_atoms 1 box

pair_style eam/fs
pair_coeff * * ./CuZr_mm.eam.fs Cu
neighbor 1.0 bin
neigh_modify delay 0 every 10 check yes

thermo 1000
thermo_style custom step temp pxx pyy pzz pxy pxz pyz pe lx ly lz

variable T equal 10.0
velocity all create $T 4928459 rot yes dist gaussian
fix 1 all nvt temp $T $T 0.1
fix 2 all deform 100 xy erate 0.01 flip yes
compute 1 all voronoi/atom

shell mkdir Shear
dump 1 all cfg 1000 ./Shear/cfg.* mass type xs ys zs c_1[1] c_1[2]
dump_modify 1 element Cu
run 150000

all the best,

Suzhi

Dear Axel,

Thanks. My case is in a relatively large size. Here I tested a simple case
in a small system (see below). The values from voronoi analysis have a
large change after box flipping (after step 125 000). For example, the
volume of Voronoi cell (c_1[1]) of some atoms can even go to be 76 A^3 from
the original 12 A^3. Hopefully it will be helpful for your debugging.

thanks a lot. i've added it to the issue tracker.

axel.

finally got around to testing this, but cannot reproduce the described
behavior with the current version (18 Jun 2016). there have been a
couple of bugfixes to the compute voronoi package since the 14 May
2016 version, so i'll assume that the issue has been addressed by
those fixes.

axel.

Dear Axel,

Thanks for the feedback. I will track the versions to double-check my case.

all the best,

Suzhi