Incorrect argument when using quip in lammps

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1

When carrying out the trhermal conductivity calculation of Ge2Sb2Te5, the ERROR: Number of arguments 5 is not correct, it should be 7 (…/pair_quip.cpp:243) appeared in out.log. The full statement of the document is as follows:

The start time is: 2024-02-26 15:51:12
My job ID is: 21415
The total cores is: 32
The hosts is:
comput2:32
srun: Job 21415 step creation temporarily disabled, retrying
srun: Step created for job 21415
LAMMPS (2 Aug 2023 - Update 2)
Reading data file …
orthogonal box = (-0.61555147 -1.066216 -0.99997528) to (58.479649 50.111784 178.99112)
2 by 2 by 8 MPI processor grid
reading atoms …
17280 atoms
Finding 1-2 1-3 1-4 neighbors …
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.002 seconds
read_data CPU = 0.078 seconds
ERROR: Number of arguments 5 is not correct, it should be 7 (…/pair_quip.cpp:243)
Last command: pair_coeff * * gp_merged_2bdmbd.xml “Potential xml_label=GAP_2017_5_7_60_20_48_12_148” 3
srun: Job step aborted: Waiting up to 32 seconds for job step to finish.
slurmstepd: error: *** STEP 21415.1 ON comput2 CANCELLED AT 2024-02-26T15:52:08 ***

We are wondering if there is any thing wrong with the atom type N, or there is problem in in file and data file. Thanks a lot if anyone can figure out the problem.

2

Looking at the source file of pair_quip.cpp, the error is triggered by int n = atom->ntypes. It seems that 3 atom types are expected, while only 1 is actually present in your system.

1 Like
3

Thank you very much for your reply, I’m still a fresher on the LAMMPS, would you like to point out further problems in the data file (Sorry I can only paste some of the text after as new users can’t upload documents):

LAMMPS data file. msi2lmp v3.9.10 / 10 Mar 2023 / CGCMM for C:\Users\caoning\Desktop\fuhe/333

17280 atoms
0 bonds
0 angles
0 dihedrals
0 impropers

3 atom types

-0.615551471    58.479648529 xlo xhi
-1.066215975    50.111784025 ylo yhi
-0.999975278   178.991124722 zlo zhi

Masses

1 72.5900 # ge
2 121.750 # sb
3 127.600 # te

Atoms # full

  1      1   1  0.000000     0.000000000     0.000000000     5.980238634   0   0   0 # ge
  2      1   1  0.000000     3.693453004     2.132416002     5.980238634   0   0   0 # ge
  3      1   1  0.000000     0.000000000     0.000000000    12.018866366   0   0   0 # ge
  4      1   1  0.000000     3.693453004     2.132416002    12.018866366   0   0   0 # ge
  5      1   2  0.000000     4.924606467     0.000000000     2.027743171   0   0   0 # sb
  6      1   2  0.000000     1.231153464     2.132416002     2.027743171   0   0   0 # sb
  7      1   2  0.000000     2.462299540     0.000000000    15.971361829   0   0   0 # sb
  8      1   2  0.000000     6.155752544     2.132416002    15.971361829   0   0   0 # sb
  9      1   3  0.000000     0.000000000     0.000000000     0.000000000   0   0   0 # te
 10      1   3  0.000000     3.693453004     2.132416002     0.000000000   0   0   0 # te
 11      1   3  0.000000     4.924606467     0.000000000    14.221236853   0   0   0 # te
 12      1   3  0.000000     1.231153464     2.132416002    14.221236853   0   0   0 # te
 13      1   3  0.000000     2.462299540     0.000000000     3.777868147   0   0   0 # te
 14      1   3  0.000000     6.155752544     2.132416002     3.777868147   0   0   0 # te
 15      1   3  0.000000     4.924606467     0.000000000     7.398442115   0   0   0 # te
 16      1   3  0.000000     1.231153464     2.132416002     7.398442115   0   0   0 # te
 17      1   3  0.000000     2.462299540     0.000000000    10.600662885   0   0   0 # te
 18      1   3  0.000000     6.155752544     2.132416002    10.600662885   0   0   0 # te
4

The logic is the other way around. There are three atom types, but only one of them is mapped in the pair_coeff command line, thus two arguments are missing.

Also, the mapping “3” makes no sense for a system containing Ge, Sb, and Te since 3 represents the element Li. I suspect this is a confusion due to misreading the documentation. Atomic number is not the number of atom types, but the number of an element in the periodic table.

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5

Thanks a lot ! The confusion of atom type N has been completely solved, and the command line is running correctly now.