Error-read_data

LAMMPS LAMMPS Mailing List Mirror
1

Dear LAMMPS Developers,

I use the following read_data file to build a supercell. I’ve checked the structure via Atomeye and it does look ok. but when I use read_data in LAMMPS (with and without box tilt), I get the error : Did not assign all atoms correctly.

Can you please tell me what the mistake is?

Best regards,

54 atoms
2 atom types

0.00000000 9.21900000 xlo xhi
0.00000000 7.98388820 ylo yhi
0.00000000 15.14400000 zlo zhi
-4.60950000 0.00000000 0.00000000 xy xz yz

Atoms

1 1 0.00000000 0.00000000 0.00000000
2 2 1.53650000 0.88709869 2.52400000
3 1 3.07300000 0.00000000 0.00000000
4 2 4.60950000 0.88709869 2.52400000
5 1 6.14600000 0.00000000 0.00000000
6 2 7.68250000 0.88709869 2.52400000
7 1 10.75550000 2.66129607 0.00000000
8 2 3.07300000 3.54839475 2.52400000
9 1 4.60950000 2.66129607 0.00000000
10 2 6.14600000 3.54839475 2.52400000
11 1 7.68250000 2.66129607 0.00000000
12 2 9.21900000 3.54839475 2.52400000
13 1 12.29200000 5.32259213 0.00000000
14 2 4.60950000 6.20969082 2.52400000
15 1 6.14600000 5.32259213 0.00000000
16 2 7.68250000 6.20969082 2.52400000
17 1 9.21900000 5.32259213 0.00000000
18 2 10.75550000 6.20969082 2.52400000
19 1 0.00000000 0.00000000 5.04800000
20 2 1.53650000 0.88709869 7.57200000
21 1 3.07300000 0.00000000 5.04800000
22 2 4.60950000 0.88709869 7.57200000
23 1 6.14600000 0.00000000 5.04800000
24 2 7.68250000 0.88709869 7.57200000
25 1 10.75550000 2.66129607 5.04800000
26 2 3.07300000 3.54839475 7.57200000
27 1 4.60950000 2.66129607 5.04800000
28 2 6.14600000 3.54839475 7.57200000
29 1 7.68250000 2.66129607 5.04800000
30 2 9.21900000 3.54839475 7.57200000
31 1 12.29200000 5.32259213 5.04800000
32 2 4.60950000 6.20969082 7.57200000
33 1 6.14600000 5.32259213 5.04800000
34 2 7.68250000 6.20969082 7.57200000
35 1 9.21900000 5.32259213 5.04800000
36 2 10.75550000 6.20969082 7.57200000
37 1 0.00000000 0.00000000 10.09600000
38 2 1.53650000 0.88709869 12.62000000
39 1 3.07300000 0.00000000 10.09600000
40 2 4.60950000 0.88709869 12.62000000
41 1 6.14600000 0.00000000 10.09600000
42 2 7.68250000 0.88709869 12.62000000
43 1 10.75550000 2.66129607 10.09600000
44 2 3.07300000 3.54839475 12.62000000
45 1 4.60950000 2.66129607 10.09600000
46 2 6.14600000 3.54839475 12.62000000
47 1 7.68250000 2.66129607 10.09600000
48 2 9.21900000 3.54839475 12.62000000
49 1 12.29200000 5.32259213 10.09600000
50 2 4.60950000 6.20969082 12.62000000
51 1 6.14600000 5.32259213 10.09600000
52 2 7.68250000 6.20969082 12.62000000
53 1 9.21900000 5.32259213 10.09600000
54 2 10.75550000 6.20969082 12.62000000

2

Dear LAMMPS Developers,

I use the following read_data file to build a supercell. I've checked the
structure via Atomeye and it does look ok. but when I use read_data in
LAMMPS (with and without box tilt), I get the error : Did not assign all
atoms correctly.
Can you please tell me what the mistake is?

have you noticed the following paragraph in the read_data documentation?

IMPORTANT NOTE: If the system is non-periodic (in a dimension), then
all atoms in the data file must have coordinates (in that dimension)
that are "greater than or equal to" the lo value and "less than or
equal to" the hi value. If the non-periodic dimension is of style
"fixed" (see the boundary command), then the atom coords must be
strictly "less than" the hi value, due to the way LAMMPS assign atoms
to processors. Note that you should not make the lo/hi values
radically smaller/larger than the extent of the atoms. For example, if
your atoms extend from 0 to 50, you should not specify the box bounds
as -10000 and 10000. This is because LAMMPS uses the specified box
size to layout the 3d grid of processors. A huge (mostly empty) box
will be sub-optimal for performance when using "fixed" boundary
conditions (see the boundary command). When using "shrink-wrap"
boundary conditions (see the boundary command), a huge (mostly empty)
box may cause a parallel simulation to lose atoms when LAMMPS
shrink-wraps the box around the atoms. The read_data command will
generate an error in this case.