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,
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.
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.
decane.mol (882 Bytes)
decane_nospecial.mol (642 Bytes)
lammps.in.equil (1.97 KB)