Possible issue in molecule command for 1-2, 3, 4 neighbors

Dear all,

I think there may be an issue involving the molecule command in the latest LAMMPS version.

When I use it to insert new molecules in the simulation box, 1-2,3,4 neighbors are not automatically calculated.

Defining the special neighbors list in the molecule file seems to solve the problem, though it is not very practical for complex molecular shapes.

Moreover, I have this issue only in the recent release from 14th May 2016 (compiled both for a single CPU on Cygwin and with MPI on Unix).

The previous release I used (June 2014) worked fine and the special neighbors list was calculated automatically.

Do you have any suggestions concerning this problem?

Thank you in advance,

Daniele Savio

From the molecule doc page:

If a Bonds section is specified then the Special Bond Counts and Special Bonds sections can also be used, if desired, to explicitly list the 1-2, 1-3, 1-4 neighbors within the molecule topology (see details below). This is optional since if these sections are not included, LAMMPS will auto-generate this information.

Which is likely a change between June 2014 and now.

So there should be special bonds defined for your molecules, whether you list them or not.

If there is a problem with this functionality, then please post as simple/small a problem

as possible, that illustrates the issue. Or post it to the Github LAMMPS site for bug tracking.


Dear Steve,

I was also expecting the Special Bond Counts and Special Bonds to be calculated automatically.

I have included a sample file, where I insert 10 n-decane molecules (United Atoms potential) into a box and let them move a bit at 300K.

There are two versions for the molecule, ‘decane.mol’ which includes the Special sections, and ‘decane_nospecial.mol’ which doesn’t. Which one is used can be specified in the middle of ‘lammps.in.equil’.

I guess both inputs should generate similar outputs in terms of energy if Specials are automatically calculated, but they clearly do not in my latest LAMMPS version.

For instance, I get a bond energy of +13000 kcal/mol if I do not define the specials, and -10 kcal/mol if I do.

The latter value seems reasonable, the first one definitely not.

Using my old LAMMPS versions, I also get the -10 kcal/mol value for ebond whether I define the Specials sections or not . There, the automatic calculation of specials seemed to work fine.

Best regards,


decane.mol (882 Bytes)

decane_nospecial.mol (642 Bytes)

lammps.in.equil (1.97 KB)