Hello everyone I am running NEB calculation for diffusion of Si atom in 64 atoms supercell. I am facing error with number of replicas “ERROR: Cannot use NEB with a single replica”. I am using neb command with style “final” as ‘neb 0.0 0.1 1000 1000 100 final sic.final’.
It’s mentioned in documentation, “For each atom that appears in the file, the new coordinates are assigned to that atom in the final replica. Each intermediate replica also assigns a new position to that atom in an interpolated manner”
according to this, lammps should generate intermediate replica it self according to the coordinates of diffused atom in file.final . my question is,
why lammps is not generating more than 1 replica in the present case ?
how can we control number of replicas for this style, as it’s not given in the documentation ?
only ambiguity from my side could be while specifying the dimensions of ‘region’ command as I didn’t understand meanings of simulation ‘box’ units, so I followed the example NEB in lammps database.
the my in put is given below
-----input—
units metal
dimension 3
boundary p p p
atom_style atomic
variable u uloop 20
#initial data
read_data sic.si.vac.initial
#potential
pair_style tersoff
pair_coeff * * /usr/local/Cellar/lammps/20220623/share/lammps/potentials/SiC.tersoff Si C
#initial minimization to relax whole supercell
minimize 1.0e-6 1.0e-4 1000 10000
timestep 0.003
#define groups
region surround block 10 18 17 20 22 28 units box
#group of NEB atoms
group nebatoms region surround
group nebatoms id 40
group nonneb subtract all nebatoms
#apply nudging among replica, fix 1,fix 2,fix3 . specify as many as u want
fix 1 nebatoms neb 1.0 parallel ideal
thermo 100
#save dump
dump 1 nebatoms atom 10 dump.neb.$u
dump 2 nonneb atom 10 dump.nonneb.$u
#run NEB for 2000 steps or to force tolerance
min_style quickmin
neb 0.0 0.1 1000 1000 100 final sic.final
----sic.final-----
1
40 2 3.28467 5.47445 5.47445
------sic.si.vac.initial—
64 atoms
2 atom types
0.0 8.75912 xlo xhi
0.0 8.75912 ylo yhi
0.0 8.75912 zlo zhi
Masses
1 28.0855 # Si
2 12.0107 # C
Atoms # atomic
1 1 1.09489 1.09489 3.28467
2 1 1.09489 1.09489 7.66423
3 1 1.09489 5.47445 3.28467
4 1 1.09489 5.47445 7.66423
5 1 5.47445 1.09489 3.28467
6 1 5.47445 1.09489 7.66423
7 1 5.47445 5.47445 3.28467
8 1 5.47445 5.47445 7.66423
9 1 1.09489 3.28467 1.09489
10 1 1.09489 3.28467 5.47445
11 1 1.09489 7.66423 1.09489
12 1 1.09489 7.66423 5.47445
13 1 5.47445 3.28467 1.09489
14 1 5.47445 3.28467 5.47445
15 1 5.47445 7.66423 1.09489
16 1 5.47445 7.66423 5.47445
17 1 3.28467 1.09489 1.09489
18 1 3.28467 1.09489 5.47445
19 1 3.28467 5.47445 1.09489
20 1 3.28467 5.47445 5.47445
21 1 7.66423 1.09489 1.09489
22 1 7.66423 1.09489 5.47445
23 1 7.66423 5.47445 1.09489
24 1 7.66423 5.47445 5.47445
25 1 3.28467 3.28467 3.28467
26 1 3.28467 3.28467 7.66423
27 1 3.28467 7.66423 3.28467
28 1 3.28467 7.66423 7.66423
29 1 7.66423 3.28467 3.28467
30 1 7.66423 3.28467 7.66423
31 1 7.66423 7.66423 3.28467
32 1 7.66423 7.66423 7.66423
33 2 0.0 0.0 0.0
34 2 0.0 0.0 4.37956
35 2 0.0 4.37956 0.0
36 2 0.0 4.37956 4.37956
37 2 4.37956 0.0 0.0
38 2 4.37956 0.0 4.37956
39 2 4.37956 4.37956 0.0
40 2 4.37956 4.37956 4.37956
41 2 0.0 2.18978 2.18978
42 2 0.0 2.18978 6.56934
43 2 0.0 6.56934 2.18978
44 2 0.0 6.56934 6.56934
45 2 4.37956 2.18978 2.18978
46 2 4.37956 2.18978 6.56934
47 2 4.37956 6.56934 2.18978
48 2 4.37956 6.56934 6.56934
49 2 2.18978 0.0 2.18978
50 2 2.18978 0.0 6.56934
51 2 2.18978 4.37956 2.18978
52 2 2.18978 4.37956 6.56934
53 2 6.56934 0.0 2.18978
54 2 6.56934 0.0 6.56934
55 2 6.56934 4.37956 2.18978
56 2 6.56934 4.37956 6.56934
57 2 2.18978 2.18978 0.0
58 2 2.18978 2.18978 4.37956
59 2 2.18978 6.56934 0.0
60 2 2.18978 6.56934 4.37956
61 2 6.56934 2.18978 0.0
62 2 6.56934 2.18978 4.37956
63 2 6.56934 6.56934 0.0
64 2 6.56934 6.56934 4.37956