CNA not identifying the lattice structure

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1

This is my input for LAMMPS for tungsten thermalisation with EPH:

units metal
atom_style atomic
boundary p p p
atom_modify map yes
lattice bcc 3.165
region full_box block -15 15 -15 15 -15 15
region inner_material block -13 13 -13 13 -13 13
create_box 1 full_box
create_atoms 1 region full_box
group full_box region full_box
group inner_box region inner_material
group thermoboundary subtract full_box inner_box
fix integrate all nve
fix reset all dt/reset 10 1e-05 0.001 0.028664999 units box
pair_style eam/fs
pair_coeff * * eam.W.W.in_lammps_Ackland W
compute ke all ke/atom
compute pe all pe/atom
compute cna all cna/atom 3.820155
compute coord all coord/atom cutoff 2.952945
velocity all create 600.0 1 loop geom mom yes rot yes
thermo 100
thermo_style custom step dt time temp etotal ke pe
run 1000
unfix integrate
fix eph all eph 1 7 4 1.0 1.92e-07 0.1086 300.0 1 1 1 egrid0 100 egrid/egrid W_F1.beta W
thermo 100
thermo_style custom step dt time temp etotal ke pe f_eph[1] f_eph[2]
dump dump all custom 1000 simulation.xyz id element x y z c_pe c_ke c_cna c_coord f_eph[1] f_eph[2]
dump_modify dump element 74
run 1000

I get this message:

WARNING: Compute cna/atom cutoff may be too large to find ghost atom neighbors (../compute_cna_atom.cpp:80)

The CNA only returns 5 (unknow lattice structure) and the coordination number is 0. That’s for all atoms at all time.

If I apply the same script to iron (no EPH available yet), then it works as expected. If the ouput is processed with OVITO, it works in both cases.

The CNA cutoff is taken from LAMMPS docs and the coordination number cutoff from this article supplementary material.

These are the first lines of the W potential:

MNB tungsten potential
An empirical potential for simulating vacancy clusters in tungsten. D.R. Mason, D. Nguyen-Manh and C.S. Becquart
J. Phys.: Condens. Matter 29 (2017) 505501 https://doi.org/10.1088/1361-648X/aa9776
1 W
 10000      0.0010001000100010 10000      0.0004403440344034      4.4029999999999996
    74    183.8400000000000034      3.1652000000000000   BCC
      0.0000000000000000

And this is for iron

#Fe Mendelev from Carolina Björkas Modified to MDCASK with ZBL from P. Olsson
#From version sent by Carolina
#From MDCASK to LAMMPS (Dec. 2015)
1 Fe
 5000	0.0392	5000	0.00106013508	5.30067539
1 55.84500122070312500000 2.8664999 BCC
   0.0000000000000000
2

After more tests, I think the issue is with the EPH plugin. This is now with Ni:

units metal
atom_style atomic
boundary p p p
atom_modify map yes
lattice fcc 3.5365
region full_box block -15 15 -15 15 -15 15
region inner_material block -13 13 -13 13 -13 13
create_box 1 full_box
create_atoms 1 region full_box
group full_box region full_box
group inner_box region inner_material
group thermoboundary subtract full_box inner_box
fix integrate all nve
fix reset all dt/reset 10 1e-05 0.001 0.028664999 units box
pair_style eam/fs
pair_coeff * * eam.Ni.Ni.in_lammps Ni
compute ke all ke/atom
compute pe all pe/atom
compute cna all cna/atom 3.0187
compute coord all coord/atom cutoff 3.0187
velocity all create 600.0 1 loop geom mom yes rot yes
thermo 100
thermo_style custom step dt time temp etotal ke pe
dump dump all custom 1000 simulation.xyz id element x y z c_pe c_ke c_cna c_coord# f_eph[1] f_eph[2]
dump_modify dump element 28

run 1000
unfix integrate
fix eph all eph 1 7 4 1.0 3.5e-6 0.1248 300.0 3 3 3 NULL 1000 egrid/egrid Ni_PRB2019_High_Rho.beta Ni
#thermo 100
#thermo_style custom step dt time temp etotal ke pe f_eph[1] f_eph[2]
run 1000

The first snapshot in the dump is CNA/coordination right, the second is not. And there is no warning about ghosts atoms as with W.

3

Hi @acgc99,

This plugin is not part of the LAMMPS distribution as far as I can tell. If the issue stems out from it, you should contact the maintainers of the package directly. Removing any mention of the lib in your script returns BCC from cna/atom just fine.

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