Lammps ATC, create Non-orthogonal mesh, ERROR: can't match periodic nodes with tolerance 1.12991

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1

Dear all,
When i do a simple practice on ATC, using my own python script to create Non-orthogonal mesh, the problem occur.
Here is part of my in.* file, before using fix atc command, i create atoms with read_data Be84_B16.dat command and it’s a Hexagonal structure(30x30x30 suppercell contains 54000 atoms) :

# Create region for ATC
variable       tmp1        equal (${xhi_final}-${xlo_final})/30
variable       tmp2        equal (${yhi_final}-${ylo_final})/30
variable       tmp3        equal (${zhi_final}-${zlo_final})/30
variable       tmp4        equal ${xy_final}/30
variable       tmp5        equal ${xz_final}/30
variable       tmp6        equal ${yz_final}/30
region         BOx prism ${xlo_final} ${xhi_final} ${ylo_final} ${yhi_final} ${zlo_final} ${zhi_final} ${xy_final} ${xz_final} ${yz_final} units box 
lattice        custom 1.0 a1 ${tmp1} 0.0 0.0 a2 ${tmp4} ${tmp2} 0.0 &
                          a3 ${tmp5} ${tmp6} ${tmp3} basis 0.33333 0.666667 0.25 basis 0.666667 0.333333 0.75


#ID  group atc PhysicsType ParameterFile
fix            AtC all   atc field
#fix_modify     AtC mesh  create 15 15 15 BOx p p p
fix_modify      AtC atom_weight element
fix_modify     AtC mesh read data.mesh p p p 
fix_modify     AtC fields none
fix_modify     AtC fields add displacement
fix_modify     AtC fields add internal_energy stress cauchy_born_energy cauchy_born_stress
fix_modify     AtC gradients add displacement
fix_modify     AtC set reference_potential_energy 0.

And I got the error from log file:

Lattice spacing in x,y,z = 3.3897385 1.9570665 3.5698780
ATC: constructing shape function field estimate
 ATC: version 2.0
 ATC: peratom PE compute created with ID: 3
 ATC: read 2816 nodes
 ATC: read 2250 HEX8 elements
 ATC: condensed 256 periodic nodes in the 3 direction
 ATC: P12, ERROR: can't match periodic nodes with tolerance 1.12991
 ATC: P14, ERROR: can't match periodic nodes with tolerance 1.12991
 ATC: P1, ERROR: can't match periodic nodes with tolerance 1.12991

I would appreciate it if someone could help .I also upload my script and mesh file.
8HEX.py (3.9 KB)
data.mesh (182.8 KB)

2

There is too much information missing to be able to reproduce the error and perhaps have a guess at what could be a problem, but the error message you get is too specific that I suspect that nobody can help you unless you contact the ATC developers. Unfortunately, the ATC project has ended over 5 years ago and they all moved on to other projects, so you will need good luck to get some help, but that will also require that you provide better information to that person.

3

Dear akohlmey,
Thanks for your replay! I check my mesh again using python, and I make sure all the nodes in ‘data.mesh’ are right.
And i change the code in in.Be_FE from
fix_modify AtC mesh read data.mesh p p p
to
fix_modify AtC mesh read data.mesh f f f,
the prior error disappear, but gets another problem:

 ATC: WARNING: mesh is not aligned with the coordinate directions atom-to-element mapping will be expensive
 ATC: P0, ERROR: can't compute cauchy-born stress w/o cauchy born model

It seems that the ATC can accept the mesh i give, but couldn’t compute cauchy-born stress.
I would upload all the file so that you can reproduce the error. (the python script has a bug and i already fixed)
Be.tersoff (881 Bytes)
Be_30x30x30.dat (2.5 MB)
data.mesh (179.1 KB)
in.Be_FE (3.1 KB)
8HEX.py (4.3 KB)

By the way, I find an email address in examples/PACKAGES/atc/README, [email protected], could i use this to contact the ATC developers?

Many thanks!

4

I might konw the how the error “can’t compute cauchy-born stress w/o cauchy born model” occur.
I looked up the .cpp code of ATC, and i got useful info below,
image
if cauchyBornStress_ is false, then throw the error, so i checked in " ATC _Transfer .cpp" and found this,
image
If the matParamFile is not defined in in-file, the error would be thrown. And when i add the matParamFile, the error disapear. However, the description in lammps manual is

Note: Neither hardy nor field requires a parameter file