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Re: [lammps-users] What interactions are computed for pairwise energy?
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Re: [lammps-users] What interactions are computed for pairwise energy?


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Sat, 26 May 2018 22:24:08 -0400



On Sat, May 26, 2018 at 10:18 PM, Wujie Wang <wwj@...212...> wrote:
Thanks Axel 

I did a “brutal force” check by coding and find out that bond, angle and dihedral energies are excluded from pair energy. (LAMMPS does not have an easy method of outputting neighbor list I believe). With this understanding, my problem is solved.

​your believe is not correct. you can output the non-bonded neighbors through compute pair/local and dump local.

axel.​


 

Thank you for your comment!
On May 25, 2018, at 8:18 PM, Axel Kohlmeyer <akohlmey@...24...> wrote:



On Fri, May 25, 2018 at 8:06 PM, Wujie Wang <wwj@...212...> wrote:
Hey lammps users 

I am trying to figure out what goes into the neighbor list. 

In my toy system, I have 10 atoms of the same type. The pairwise potential is defined in the following manner: 

neighbor 0.4 bin
neigh_modify every 10 one 10000
bond_style      harmonic
bond_coeff 1 350 1.53
pair_style lj/cut 10.5
pair_coeff 1 1 0.112 4.01 10.5

In theory, there are should be 45 interactions in the pairwise potential energy, is that right?

​most likely not. there is crucial information missing:
- size of the simulation cell and choice of boundary conditions
- list of bonds and special_bonds settings​

​please note, that LAMMPS does not apply minimum image conventions, but creates "ghost atoms", which are real periodic copies.​
 
However, I am getting gigantic energy when try to compute this energy by “hand", but the Lammps output only gives really small energy like the following. 

Step PotEng KinEng E_bond E_pair Temp 
       0    3280.8242    134.13645    3280.8521 -0.027946372         5000 
      50    76.787747    233.18891    77.089967  -0.30221985    8692.2273 
     100    22.287439     27.21953    23.011246  -0.72380721    1014.6209 
     150    6.4999038    12.623158    7.3654589  -0.86555507     470.5342 

If you just look at the distance, the bond distance is around 1.53, the characteristic distance LJ is 4.01, so the pairwise energy between bonded atom should be big, which explains the huge energy I have been getting by “hand”.

So does this have something to do the neighbor function? But neighbor only adds a “skin” distance to the pair cutoff and should not affect the total energy of atoms that are close to each other. 

I think I generally lack of a understanding of Lammps mechanics. I would be really helpful if someone can point out what is wrong.

​you should read the LAMMPS paper and then the relevant sections of the manual. you seem to be making too many (and mostly incorrect) assumptions.

axel.​

 

Thank you!



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--
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.




--
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.