Syntax error by extra/bond/per/atom in read_data command

Dear lammps users,

I have the same problem of
http://lammps.sandia.gov/threads/msg71104.html

I’m trying to combine two data files by using read_data command.
When I run without extra/bond/per/atom keyword, I get the following error message.

Subsequent read data induced too many bonds per atom (…/read_data.cpp:1222)

When I changed the syntax with the keyword, extra/bond/per/atom, and I get
“Ilegal read_data” error.

Previously, a solution using moltemplate was introduced.
Could somebody let me know the way to directly solve this problem by using right lammps syntax?

The follows are the lines in my input file.

read_data water.dat group solvent extra/atom/types 5 extra/bond/types 10 extra/angle/types 10 extra/bond/per/atom

read_data extra.dat add append group extra

Many Thanks
Mook

Dear lammps users,

I have the same problem of
http://lammps.sandia.gov/threads/msg71104.html

I'm trying to combine two data files by using read_data command.
When I run without extra/bond/per/atom keyword, I get the following error
message.

Subsequent read data induced too many bonds per atom
(../read_data.cpp:1222)

When I changed the syntax with the keyword, extra/bond/per/atom, and I get
"Ilegal read_data" error.

​there is no number following extra/bond/per/atom, hence the error.​

Previously, a solution using moltemplate was introduced.
Could somebody let me know the way to directly solve this problem by using
right lammps syntax?

​compare your input very carefully to the read_data documentation.

axel.​

As following the read_data document, no number is required for the keyword (leave space). In addition, when I input some numbers following extra/bond/per/atom, I get the same error “Ilegal read_data” error.

Could you give me other tips?

Thanks,
Mook

As following the read_data document, no number is required for the keyword
(leave space).

​that is incorrect. the documentation clearly says, that an argument has to
follow the keyword.
...and "leave space for this many XXX" means that, e.g. N more ​bonds

​if i change the read_data command in the peptide example to:

​read_data data.peptide group solvent extra/atom/types 5 extra/bond/types
10 extra/angle/types 10 extra/bond/per/atom 10

​there is no syntax error for the read_data command (it will fail on "run",
because i didn't set any parameters for the extra atom, bond or angle
types).
this is with LAMMPS 1 Sep 2017:


LAMMPS (1 Sep 2017)
Reading data file ...
  orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  2004 atoms
  reading velocities ...
  2004 velocities
  scanning bonds ...
  13 = max bonds/atom
  scanning angles ...
  6 = max angles/atom
  scanning dihedrals ...
  14 = max dihedrals/atom
  scanning impropers ...
  1 = max impropers/atom
  reading bonds ...
  1365 bonds
  reading angles ...
  786 angles
  reading dihedrals ...
  207 dihedrals
  reading impropers ...
  12 impropers
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj: 0 0 0
  special bond factors coul: 0 0 0
  4 = max # of 1-2 neighbors
  7 = max # of 1-3 neighbors
  14 = max # of 1-4 neighbors
  18 = max # of special neighbors
Finding SHAKE clusters ...
  19 = # of size 2 clusters
  6 = # of size 3 clusters
  3 = # of size 4 clusters
  640 = # of frozen angles
84 atoms in group peptide
PPPM initialization ...
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
  G vector (1/distance) = 0.268725
  grid = 15 15 15
  stencil order = 5
  estimated absolute RMS force accuracy = 0.0228209
  estimated relative force accuracy = 6.87243e-05
  using double precision FFTs
  3d grid and FFT values/proc = 10648 3375

In addition, when I input some numbers following extra/bond/per/atom, I
get the same error "Ilegal read_data" error.

​are you using an up-to-date LAMMPS version?​

Could you give me other tips?

​what i suggested is correct. see above.

axel.​