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Re: [lammps-users] Syntax error by extra/bond/per/atom in read_data command
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Re: [lammps-users] Syntax error by extra/bond/per/atom in read_data command


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Wed, 13 Sep 2017 21:41:04 -0400



On Wed, Sep 13, 2017 at 7:49 PM, Hyungmook Kang <hmkang@...633...> wrote:
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.​


 

Thanks,
Mook


--
Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.