Perhaps, I found a bug about compute property/atom nbonds keywords

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1

Hello Lammps community:
When using stable lammps version (30 Oct 2014),i found that the compute property/atom nbonds keywords can’t compute the correct connected bond number of an atom.
The example is the “CH3OH” dreiding file in the standard example folder.
I added some test command to dump all the atom type and its connected bond number.

     #################for test##############
     compute 1 all property/atom type nbonds
     dump 4a all custom 1 dump.test1.* c_1[1] c_1[2]
     run 0
     variable new_O atom "c_1[1]==4&&c_1[2]==2"
     group newbond_O variable new_O
     variable newO_nu equal count(newbond_O)
     print "************${newO_nu} O atom have been founded!"

The dump file is as follow

ITEM: TIMESTEP
0
ITEM: NUMBER OF ATOMS
384
ITEM: BOX BOUNDS pp pp pp
0 19.9969
0 19.1282
0 19.4697
ITEM: ATOMS c_1[1] c_1[2]
3 4
1 0
3 4
4 1 # atom “O” which the correct nbonds is 2
1 0 # atom “H” which the nbonds should be 1!
1 0
1 0
2 0
1 0

The atom “C” (type 3)has the correct nbonds of 4, but “O”,”H” both get a wrong number!
The data file and in file are attached!
Thanks!

Kang Jingtian

data.dreiding (75.6 KB)

dump.test1.0 (2 KB)

in.dreiding (2.25 KB)

2

If you have newton bond on (which is the default)
than an I-J bond is only stored with either I or J.
So I’m guessing the total # of bonds you are tallying
will be 1/2 what you expect. The compute property/atom
doc page should be more clear about this.

Steve

3

hello,steve
would you please explain more clearly why atom C get the “full” bond num 4 rather than half of it,and why H got zero.
where to alter the default newton bond?
i just aim at getting the bond num of a certain atom on topology ，is the nbonds suitable for the task?if not, how to achieve these goals ?
thanks
kang jingtian

4

Steve meant “the TOTAL # of bonds you are tallying will be 1/2 what you expect.”, not each of the atoms has half of the number of bonds. This is due to the default setting of “newton on” so that information of I-J pair is only stored on either I or J, not on both I and J.

To change this, use “newton off”. See http://lammps.sandia.gov/doc/newton.html for more info.

Ray

5

Many thanks to both ray and steve. Altering the newton command really settled my problem.

Now compute property/atom nbonds can give what i want! :slight_smile:

Kang Jingtian